Title of Invention

NEISSERIA MENNINGITIDIS ANTIGENS

Abstract The invention provides proteins from Naisseria maningitidas (strains A and B), including amino acid sequences, the corresponding nucleotide sequences, expression data and serological data. The proteins are useful antigens for vaccines, immunogenic compositions, and/or diagnostics.
Full Text NEISSER1A MENINGITIDIS ANTIGENS
This invention relates to antigens from the bacterium Neisseria meningitidis.
BACKGROUND
Neisseria meningitidis is a non-motile, gram negative diplococcus human pathogen. It colonises
the pharynx, causing meningitis and, occasionally, septicaemia in the absence of meningitis. It is
closely related to N.gonorrhoeae, although one feature that clearly differentiates meningococcus
from gonococcus is the presence of a polysaccharide capsule that is present in all pathogenic
meningococci.
N.meningitidis causes both endemic and epidemic disease. In the United States the attack rate is
0.6-1 per 100,000 persons per year, and it can be much greater during outbreaks (see Lieberman
et al. (1996) Safety and Immunogenicity of a Serogroups A/C Neisseria meningitidis
Oligosaccharide-Protein Conjugate Vaccine in Young Children. JAMA 275(19):1499-1503;
Schuchat et al (1997) Bacterial Meningitis in the United Stater in 1995. N Engl JMed 337(14):970-
976). In developing countries, endemic disease rates are much higher and during epidemics
incidence rates can reach 500 cases per 100,000 persons per year. Mortality is extremely high, at
10-20% in the United States, and much higher in developing countries. Following the introduction
of the conjugate vaccine against Haemophilia injluenzae, N. meningitidis is the major cause of
bacterial meningitis at all ages in the United States (Schuchat et al (1997) supra).
Based on the organism's capsular polysaccharide, 12 serogroups of N. memngitidis have been
identified. Group A is the pathogen most often implicated in epidemic disease in sub-Saharan
Africa. Serogroups B and C are responsible for the vast majority of cases in the United States and
in most developed countries. Serogroups W135 and Y are responsible for the rest of the cases in
the United States and developed countries. The meningococcal vaccine currently in use is a
tetravalent polysaccharide vaccine composed of serogroups A, C, Y and W135. Although
efficacious in adolescents and adults, it induces a poor immune response and short duration of
protection, and cannot be used in infants [eg. Morbidity and Mortality weekly report, Vol.46, No.
R R 5(1997) This is because polysaccharides are T-cell independent antigens that induce a weak

vaccination against H.influenzae, conjugate vaccines against serogroups A and C have been
developed and are at the final stage of clinical testing (Zollinger WD "New and Improved Vaccines
Against Meningococcal Disease" in: New Generation Vaccines, supra, pp. 469-488; Lieberman et
al (1996) supra; Costantino et al (1992) Development and phase I clinical testing of a conjugate
vaccine against meningococcus A and C. Vaccine 10:691-698).
Meningococcus B remains a problem, however. This serotype currently is responsible for
approximately 50% of total meningitis in the United States, Europe, and South America. The
polysaccharide approach cannot be used because the menB capsular polysaccharide is a polymer
of α(2-8)-linked N-acetyl neuraminic acid that is also present in mammalian tissue. This results in
tolerance to the antigen; indeed, if an immune response were elicited, it would be anti-self, and
therefore undesirable. In order to avoid induction of autoimmunity and to induce a protective
immune response, the capsular polysaccharide has, for instance, been chemically modified
substituting the N-acetyl groups, with N-propionyl groups, leaving the specific antigenicity
unaltered (Romero & Outschoorn (1994) Current status of Meningococcal group B vaccine
candidates: capsular or non-capsular? Clin Microbiol Rev 7(4):559-575).
Alternative approaches to menB vaccines have used complex mixtures of outer membrane proteins
(OMPs), containing either the OMPs alone, or OMPs enriched in porins, or deleted of the class 4
OMPs that are believed to induce antibodies that block bactericidal activity. This approach
produces vaccines that are not well characterized. They are able to protect against the homologous
strain, but are not effective at large where there are many antigenic variants of the outer membrane
proteins. To overcome the antigenic variability, multivalent vaccines containing up to nine different
porins have been constructed (eg. Poolman JT (1992) Development of a meningococcal vaccine.
Infect. Agents Dis. 4:13-28). Additional proteins to be used in outer membrane vaccines have been
the opa and ope proteins, but none of these approaches have been able to overcome the antigenic
variability (eg. Ala' Aldeen & Borriello (1996) The meningococcal transferrin-binding proteins 1
and 2 are both surface exposed and generate bactericidal antibodies capable of killing homologous
and heterologous strains. Vaccine 14(l):49-53).
A certain amount of sequence data is available for meningococcal and gonococcal genes and
proteins (eg. EP-A-0467714, WO96/29412), but this is by no means complete. The provision of
further sequences could provide an opportunity to identify secreted or surface-exposed proteins that

are presumed targets for the immune system and which are not antigenically variable. For instance,
some of the identified proteins could be components of efficacious vaccines against meningococcus
B. some could be components of vaccines against all meningococcal serotypes, and others could
be components of vaccines against all pathogenic Neisseriae.
THE INVENTION
The invention provides proteins comprising the N.meningitidis amino acid sequences disclosed in
the examples.
It also provides proteins comprising sequences homologous (ie. having sequence identity) to the
N.meningitidis amino acid sequences disclosed in the examples. Depending on the particular
sequence, the degree of sequence identity is preferably greater than 50% (eg. 60%, 70%, 80%, 90%,
95%, 99% or more). These homologous proteins include mutants and allelic variants of the
-sequences disclosed in the examples. Typically, 50% identity or more between two proteins is
considered to be an indication of functional equivalence. Identity between the proteins is preferably
determined by the Smith-Waterman homology search algorithm as implemented in the MPSRCH
program (Oxford Molecular), using an affine gap search with parameters gap open penalty= 12 and
gap extension penalty-1.
The invention further provides proteins comprising fragments of the N.meningitidis aniino acid
sequences disclosed in the examples. The fragments should comprise at least n consecutive amino
acids from the sequences and, depending on the particular sequence, n is 7 or more (eg. 8,10,12,
14,16,18,20 or more). Preferably the fragments comprise an epitope from the sequence.
The proteins of the invention can, of course, be prepared by various means (eg. recombinant
expression, purification from cell culture, chemical synthesis etc.) and in various forms (eg. native,
fusions etc.). They are preferably prepared in substantially pure form (ie. substantially free from
other N.meningitidis or host cell proteins)
According to a further aspect, the invention provides antibodies winch bind to these proteins. These
may be polyclonal or monoclonal and may be produced by any suitable means.

According to a further aspect, the invention provides nucleic acid comprising the N.meningitidis
nucleotide sequences disclosed in the examples. In addition, the invention provides nucleic acid
comprising sequences homologous (ie. having sequence identity) to the N.meningitidis nucleotide
sequences disclosed in the examples.
Furthermore, the invention provides nucleic acid which can hybridise to the N.meningitidis nucleic
acid disclosed in the examples, preferably under "high stringency" conditions (eg. 65°C in a
0.1xSSC, 0.5% SDS solution).
Nucleic acid comprising fragments of these sequences are also provided. These should comprise
at least n consecutive nucleotides from the N.meningitidis sequences and, depending on the
particular sequence, n is 10 or more {eg 12, 14, 15, 18, 20,25, 30, 35,40 or more).
According to a further aspect, the invention provides nucleic acid encoding the proteins and protein
fragments of the invention.
It should also be appreciated that the invention provides nucleic acid comprising sequences
complementary to those described above (eg. for antisense or probing purposes).
Nucleic acid according to the invention can, of course, be prepared in many ways (eg. by chemical
synthesis, from genomic or cDNA libraries, from the organism itself etc.) and can take various
forms (eg. single: stranded, double stranded, vectors, probes etc.).
In addition, the term "nucleic acid" includes DNA and RNA, and also their analogues, such as
those containing modified backbones, and also peptide nucleic acids (PNA) etc.
According to a further aspect, the invention provides vectors comprising nucleotide sequences of
the invention (eg. expression vectors) and host cells transformed with such vectors.
According to a further aspect, the invention provides compositions comprising protein, antibody,
and/or nucleic acid according to the invention. These compositions may be suitable as vaccines,
for instance, or as diagnostic reagents, or as immunogenic compositions.

The invention also provides nucleic acid, protein, or antibody according to the invention for use
as medicaments (eg. as vaccines) or as diagnostic reagents. It also provides the use of nucleic acid,
protein, or antibody according to the invention in the manufacture of: (i) a medicament for treating
or preventing infection due to Neisserial bacteria; (ii) a diagnostic reagent for detecting the
presence of Neisserial bacteria or of antibodies raised against Neisserial bacteria; and/or (iii) a
reagent which can raise antibodies against Neisserial bacteria. Said Neisserial bacteria may be any
species or strain (such as N.gonorrhoeae) but are preferably N.meningitidis, especially strain A,
strain B or strain C.
The invention also provides a method of treating a patient, comprising administering to the patient
a therapeutically effective amount of nucleic acid, protein, and/or antibody according to the
invention.
According to further aspects, the invention provides various processes.
A process for producing proteins of the invention is provided, comprising the step of culturing a
host: cell according to the invention under conditions which induce protein expression.
A process for producing protein or nucleic acid of the invention is provided, wherein the protein
or nucleic acid is synthesised in part or in whole using chemical means.
A process for detecting polynucleotides of the invention is provided, comprising the steps of: (a)
contacting a nucleic probe according to the invention with a biological sample under hybridizing
conditions to form duplexes; and (b) detecting said duplexes.
A process for detecting proteins of the invention is provided, comprising the steps of: (a) contacting
an antibody according to the invention with a biological sample under conditions suitable for the
formation of an antibody-antigen complexes; and (b) detecting said complexes.
Unlike the sequences disclosed in PCT/IB98/01665, the sequences disclosed in the present
application are believed not to have any significant homologs in N.gonorrhoeae. Accordingly, the
sequences of the present invention also find use in the preparation of reagents for distinguishing
between N.meningitidis and N.gonorrhoeae

A summary of standard techniques and procedures which may be employed in order to perform the
invention (eg. to utilise the disclosed sequences for vaccination or diagnostic purposes) follows.
This summary is not a limitation on the invention but, rather, gives examples that may be used, but
are not required
General
The practice of the present invention will employ, unless otherwise indicated, conventional
techniques of molecular biology, microbiology, recombinant DNA, and immunology, which are
within the skill of the art. Such techniques are explained fully in the literature eg. Sambrook
Molecular Cloning; A Laboratory Manual, Second Edition (1989); DNA Cloning, Volumes I and
ii (D.N Glover ed. 1985); Oligonucleotide Synthesis (MJ. Gait ed, 1984); Nucleic Acid
Hybridization (B.D. Hames & SJ. Higgins eds. 1984); Transcription and Translation (B.D. Hames
& S. J. Higgins eds. 1984); Animal Cell Culture (R.I. Freshney ed. 1986); Immobilized Cells and
Enzymes (IRL Press, 1986); B. Perbal, A Practical Guide to Molecular Cloning (1984); the
Methods in Enzymology series (Academic Press, Inc.), especially volumes 154 & 155; Gene
Transfer Vectors for Mammalian Cells (J.H. Miller and M.P. Calos eds. 1987, Cold Spring Harbor
Laboratory); Mayer and Walker, eds. (1987), Immunochemical Methods in Cell and Molecular
Biology (Academic Press, London); Scopes, (1987) Protein Purification: Principles and Practice,
Second Edition (Springer-Verlag, N.Y.), and Handbook of Experimental Immunology, Volumes
I-IV (DM. Weir and C. C. Blackwell eds 1986).
Standard abbreviations for nucleotides and amino acids are used in this specification.
All publications, patents, and patent applications cited herein are incorporated in full by reference.
In particular, the contents of UK patent applications 9800760.2, 9819015.0 and 9822143.5 are
incorporated herein.
Definitions
A composition containing X is "substantially free of Y when at least 85% by weight of the total
X+Y in the composition is X. Preferably, X comprises at least about 90% by weight of the total of
X+Y in the composition, more preferably at least about 95% or even 99% by weight.

The term "comprising'" means "including" as well as "consisting" eg. a composition "comprising"
X may consist exclusively of X or may include something additional to X, such as X+Y.
The term "heterologous" refers to two biological components that are not found together in nature.
The components may be host cells, genes, or regulatory regions, such as promoters. Although the
heterologous components are not found together in nature, they can function together, as when a
promoter heterologous to a gene is operably linked to the gene. Another example is where a
Neisserial sequence is heterologous to a mouse host cell. A further examples would be two epitopes
from the same or different proteins which have been assembled in a single protein in an
arrangement not found in nature.
An "origin of replication" is a polynucleotide sequence that initiates and regulates replication of
polynucleotides, such as an expression vector. The origin of replication behaves as an autonomous
unit of polynucleotide replication within a cell, capable of replication under its own control. An
origin of replication may be needed for a vector to replicate in a particular host cell. With certain
origins of replication, an expression vector can be reproduced at a high copy number in the
presence of the appropriate proteins within the cell. Examples of origins are the autonomously
replicating sequences, which are effective in yeast; and the viral T-antigen, effective in COS-7
cells.
A "mutant" sequence is defined as DNA, RNA or amino acid sequence differing from but having
sequence identity with the native or disclosed sequence. Depending on the particular sequence, the
degree of sequence identity between the native or disclosed sequence and the mutant sequence is
preferably greater than 50% (eg. 60%, 70%, 80%, 90%, 95%, 99% or more, calculated using the
Smith-Waterman algorithm as described above). As used herein, an "allelic variant" of a nucleic
acid molecule, or region, for which nucleic acid sequence is provided herein is a nucleic acid
molecule, ox region, that occurs essentially at the same locus in the genome of another or second
isolate, and that, due to natural variation caused by, for example, mutation or recombination, has
a similar but not identical nucleic acid sequence. A coding region allelic variant typically encodes
a protein having similar activity to that Of the protein encoded by the gene to which it is being
compared. An allelic variant can also comprise an alteration in the 5' or 3' untranslaied regions of
the gene, such as in regulatory control regions (eg. see US patent 5,753,235).

Expression systems
The Neisserial nucleotide sequences can be expressed in a variety of different expression systems;
for example those used with mammalian cells, baculoviruses, plants, bacteria, and yeast.
i. Mammalian Systems
Mammalian expression systems are known in the art. A mammalian promoter is any DNA
sequence capable of binding mammalian RNA polymerase and initiating the downstream (3*)
transcription of a coding sequence {eg. structural gene) into mRNA. A promoter will have a
transcription initiating region, which is usually placed proximal to the 5' end of the coding
sequence, and a TATA box, usually located 25-30 base pairs (bp) upstream of the transcription
initiation site. The TATA box is thought to direct RNA polymerase II to begin RNA synthesis at
the correct site. A mammalian promoter will also contain an upstream promoter element, usually
located within 100 to 200 bp upstream of the TATA box. An upstream promoter element
determines the rate at which transcription is initiated and can act in either orientation [Sambrook
et al. (1989) "Expression of Cloned Genes in Mammalian Cells." In Molecular Cloning: A
Laboratory Manual, 2nd ed].
Mammalian viral genes are often highly expressed and have a broad host range; therefore sequences
encoding mammalian viral genes provide particularly useful promoter sequences. Examples include
the SV40 early promoter, mouse mammary tumor virus LTR promoter, adenovirus major late
promoter (Ad Ml,P), and herpes simplex virus promoter. In addition, sequences derived from non-
viral genes, such as the murine metallotheionein gene, also provide useful promoter sequences.
Expression may be either constitutive or regulated (inducible), depending on the promoter can be
induced with glucocorticoid in hormone-responsive cells.
The presence of an enhancer element (enhancer), combined with the promoter elements described
above, will usually increase expression levels. An enhancer is a regulatory DNA sequence that can
stimulate transcription up to 1000-fold when linked to homologous or heterologous promoters, with
synthesis beginning at the normal RNA start site. Enhancers are also active when they are placed
upstream or downstream from the transcription initiation site, in either normal or flipped orien-
tation, or at a distance of more than 1000 nucleotides from the promoter [Maniatis et al. (1987)
Science 236:1237; Alberts et al. (1989) Molecular Biology of the Cell, 2nd ed.]. Enhancer elements
derived from viruses may be particularly useful, because they usually have a broader host range.

Examples include the SV40 early gene enhancer [Dijkema et al (1985) EMBO J. 4:761] and the
enhancer/promoters derived from the long terminal repeat (LTR) of the Rous Sarcoma Virus
[Gorman et al. (1982b) Proc. Nad. Acad. Sci. 79:6777] and from human cytomegalovirus fBoshart
et al. (1985) Cell 41:521]. Additionally, some enhancers are regulatable and become active only
in the presence of an inducer, such as a hormone or metal ion [Sassone-Corsi and Borelli (1986)
Trends Genet. 2:215; Maniatis et al. (1987) Science 236:1237].
A DNA molecule may be expressed intracellularly in mammalian cells. A promoter sequence may be
directly linked with the DNA molecule, in which case the first amino acid at the N-terminus of the
recombinant protein will always be a methionine, which is encoded by the ATG start codon. If desired,
the N-terminus may be cleaved from the protein by in vitro incubation with cyanogen bromide.
Alternatively, foreign proteins can also be secreted from the cell into the growth media by creating
chirneric DNA molecules that encode a fusion protein comprised of a leader sequence fragment that
provides for secretion of the foreign protein in mammalian cells. Preferably, there are processing
sites encoded between the leader fragment and the foreign gene that can be cleaved either in vivo
or in vitro. The leader sequence fragment usually encodes a signal peptide comprised of
hydrophobic amino acids which direct the secretion of the protein from the cell. The adenovirus
triparite leader is an example of a leader sequence that provides for secretion of a foreign protein
in mammalian cells.
Usually, transcription termination and polyadenylation sequences recognized by mammalian cells
are regulatory regions located 3' to the translation stop codon and thus, together with the promoter
elements, flank the coding sequence. The 3' terminus of the mature mRNA is formed by site-
specific post-transcriptional cleavage and polyadenylation [Bimstiel et al. (1985) Cell 41:349;
Proudfoot and Whitelaw (1988) Termination and 3' end processing of eukaryotic RNA. In
Tratiscription and splicing (ed. BD. Hames and D.M. Glover); Proudfoot (1989) Trends Biochem.
Sci. 14:105). These sequences direct the transcription of an mRNA which can be translated into the
polypeptide encoded by the DNA. Examples of transcription terminater/polyadenylation signals
include those derived from SV40 [Sambrook et al (1989) "Expression of cloned genes in cultured
mammalian cells." In Molecular Cloning: A Laboratory Manual].

Usually, the above described components, comprising a promoter, polyadenylation signal, and
transcription termination sequence are put together into expression constructs. Enhancers, introns
with functional splice donor and acceptor sites, and leader sequences may also be included in an
expression construct, if desired. Expression constructs are often maintained in a replicon, such as
an extrachromosomal element {eg. plasmids) capable of stable maintenance in a host, such as
mammalian cells or bacteria. Mammalian replication systems include those derived from animal
viruses, which require trans-acting factors to replicate. For example, plasmids containing the
replication systems of papovaviruses, such as SV40 [Gluzman (1981) Cell 25:175] or
poly omavirus, replicate to extremely high copy number in the presence of the appropriate viral T
antigen. Additional examples of mammalian replicons include those derived from bovine
papillomavirus and Epstein-Barr virus. Additionally, the replicon may have two replicaton systems,
thus allowing it to be maintained, for example, in mammalian cells for expression and in a
prokaryotic host for cloning and amplification. Examples of such mammalian-bacteria shuttle
vectors include pMT2 {Kaufman et al. (1989) Mol. Cell Biol. 9:946] and pHEBO [Shimizu et al.
(1986) Mol. Cell. Biol. 6:1074].
The transformation procedure used depends upon the host to be transformed. Methods for
introduction of heterologous polynucleotides into mammalian cells are known in the art and include
dextran-mediated transfection, calcium phosphate precipitation, polybrene mediated transfection,
protoplast fusion, electroporation, encapsulation of the polynucleotide(s) in liposomes, and direct
microinjection of the DNA into nuclei.
Mammalian cell lines available as hosts for expression are known in the art and include many
immortalized cell lines available from the American Type Culture Collection (ATCC), including
but not limited to, Chinese hamster ovary (CHO) cells, HeLa cells, baby hamster kidney (BHK)
cells, monkey kidney cells (COS), human hepatocellular carcinoma cells (eg. Hep G2), and a
number of other cell lines.
ii. Baculovirus Systems
The polynucleotide encoding the protein can also be inserted into a suitable insect expression vector,
and is operably linked to the control elements within that vector. Vector construction employs
techniques which are known in the art. Generally, the components of the expression system include
a transfer vector, usually a bacterial plasmid, which contains both a fragment of the baculovirus

genome, and a convenient restriction site for insertion of the heterologous gene or genes to be
expressed; a wild type baculovirus with a sequence homologous to the baculovirus-specific fragment
in the transfer vector (this allows for the homologous recombination of the heterologous gene in to
the baculovirus genome); and appropriate insect host cells and growth media.
After inserting the DNA sequence encoding the protein into the transfer vector, the vector and the
wild type viral genome are transfected into an insect host cell where the vector and viral genome
are allowed to recombine. The packaged recombinant virus is expressed and recombinant plaques
are identified and purified. Materials and methods for baculovirus/insect cell expression systems
are commercially available in kit form from, inter alia, Invitrogen, San Diego CA ("MaxBac" kit).
These techniques are generally known to those skilled in the art and fully described in Summers
and Smith, Texas Agricultural Experiment Station Bulletin No. 1555 (1987) (hereinafter "Summers
and Smith").
Prior to inserting the DNA sequence encoding the protein into the baculovirus genome, the above
described components, comprising a promoter, leader (if desired), coding sequence of interest, and
transcription termination sequence, are usually assembled into an intermediate transplacement
construct (transfer vector). This construct may contain a single gene and operably linked regulatory
elements; multiple genes, each with its owned set of operably linked regulatory elements; or multiple
genes, regulated by the same set of regulatory elements. Intermediate transplacement constructs are
often maintained in a replicon, such as an extrachromosomal element (eg. plasmids) capable of stable
maintenance in a host, such as a bacterium. The replicon will have a replication system, thus allowing
it to be maintained in a suitable host for cloning and amplification.
Currently, the most commonly used transfer vector for introducing foreign genes into AcNPV is
pAc373. Many other vectors, known to those of skill in the art, have also been designed. These
include, for example, pVL985 (which alters the polyhedrin start codon from ATG to ATT, and
which introduces a BamHI cloning site 32 basepairs downstream from the ATT; see Luckow and
Summers, Virology (1989) 77:31.
The plasmid usually also contains the polyhedrin polyadenylation signal (Miller et al. (1988) Ann.
Rev. Microbiol, 42:177) and a prokaryotic ampicillin-resistance (amp) gene and origin of
replication for selection and propagation in E. coli.

Baculovirus transfer vectors usually contain a baculovirus promoter. A baculovirus promoter is any
DNA sequence capable of binding a baculovirus RNA polymerase and initiating the downstream
(5" to 3') transcription of a coding sequence (eg. structural gene) into mRNA. A promoter will have
a transcription initiation region which is usually placed proximal to the 5' end of the coding
sequence. This transcription initiation region usually includes an RNA polymerase binding site and
a transcription initiation site. A baculovirus transfer vector may also have a second domain called
an enhancer, which, if present, is usually distal to the structural gene. Expression may be either
regulated or constitutive.
Structural genes, abundantly transcribed at late times in a viral infection cycle, provide particularly
useful promoter sequences. Examples include sequences derived from the gene encoding the viral
polyhedron protein, Friesen et al., (1986) "The Regulation of Baculovirus Gene Expression," in:
The Molecular Biology of Baculoviruses (ed. Walter Doerfler); EPO Publ. Nos. 127 839 and 155
476; and the gene encoding the plO protein, Vlak et al.; (1988), J. Gen: Virol 69:765.
DNA encoding suitable signal sequences can be derived from genes for secreted insect or
baculovirus proteins, such as the baculovirus polyhedrin gene (Carbonell et al. (1988) Gene,
75:409). Alternatively, since the signals for mammalian cell posttranslational modifications (such
as signal peptide cleavage, proteolytic cleavage, and phosphorylation) appear to be recognized by
insect cells, and the signals required for secretion and nuclear accumulation also appear to be
conserved between the invertebrate cells and vertebrate cells, leaders of non-insect origin, such as
those derived from genes encoding human a-interferon, Maeda et al., (1985), Nature 315:592;
human gastrin-releasing peptide, Lebacq-Verheyden et al., (1988), Molec. Cell. Biol 5:3129;
human IL-2, Smith et al., (1985) Proc. Natl Acad. Sci USA, 52:8404; mouse IL-3, (Miyajima et
al., (1987) Gene 55:273; and human glucocerebrosidase, Martin et al. (1988) DNA, 7:99, can also
be used to provide for secretion in insects.
A recombmant polypeptide or polyprotein may be expressed intracellularly or, if it is expressed
with the proper regulatory sequences, it can be secreted. Good intracellular expression of nonfused
foreign proteins usually requires heterologous genes that ideally have a short leader sequence
containing suitable translation initiation signals preceding an ATG start signal. If desired,
methionine at the N-terminus may be cleaved from the mature protein by in vitro incubation with
cyanogen bromide.

Alternatively, recombinant polyproteins or proteins which are not naturally secreted can be secreted
from the insect cell by creating chimeric DNA molecules that encode a fusion protein comprised
of a leader sequence fragment that provides for secretion of the foreign protein in insects. The
leader sequence fragment usually encodes a signal peptide comprised of hydrophobic amino acids
which direct the translocation of the protein into the endoplasmic reticulum.
After insertion of the DNA sequence and/or the gene encoding the expression product precursor
of the protein, an insect cell host is co-transformed with the heterologous DNA of the transfer
vector and the genomic DNA of wild type baculovirus ~ usually by co-transfection. The promoter
and transcription termination sequence of the construct will usually comprise a 2-5kb section of the
baculovirus genome. Methods for introducing heterologous DNA into the desired site in the
baculovirus virus are known in the art. (See Summers and Smith supra; Ju et al. (1987); Smith et
al., Mol Cell. Biol. (1983) 5:2156; and Luckow and Summers (1989)). For example, the insertion
can be into a gene such as the polyhedrin gene, by homologous double crossover recombination;
insertion can also be into a restriction enzyme site engineered into the desired baculovirus gene.
Miller et al., (1989), Bioessays 4:91.The DNA sequence, when cloned in place of the polyhedrin
gene in the expression vector, is flanked both 5' and 3' by polyhedrin-specific sequences and is
positioned downstream of the polyhedrin promoter.
The newly formed baculovirus expression vector is subsequently packaged into an infectious
recombinant baculovirus. Homologous recombination occurs at low frequency (between about 1 %
and about 5%); thus, the majority of the virus produced after cotransfection is still wild-type virus.
Therefore, a method is necessary to identify recombinant viruses. An advantage of the expression
system is a visual screen allowing recombinant viruses to be distinguished. The polyhedrin protein,
which is produced by the native virus, is produced at very high levels in the nuclei of infected cells
at late times after viral infection. Accumulated polyhedrin protein forms occlusion bodies that also
contain embedded particles. These occlusion bodies, up to 15 μm in size, are highly refractile,
giving them a bright shiny appearance that is readily visualized under the light microscope. Cells
infected with recombinant viruses lack occlusion bodies. To distinguish recombinant virus from
wild-type virus, the transfection supernatant is plaqued onto a monolayer of insect cells by
techniques known to those skilled in the art. Namely, the plaques are screened under the light
microscope for the presence (indicative of wild-type virus) or absence (indicative of recombinant

virus) of occlusion bodies. "Current Protocols in Microbiology" Vol. 2 (Ausubel et al. eds) at 16.8
(Supp. 10, 1990); Summers and Smith, supra; Miller et al. (1989).
Recombinant baculovirus expression vectors have been developed for infection into several insect
cells. For example, recombinant baculoviruses have been developed for, inter alia: Aedes aegypti
Autographa californica, Bombyx mori, Drosophila melanogaster, Spodoptera frugiperda, and
Trichoplusia ni (WO 89/046699; Carbonell et al., (1985) J. Virol. J 527:718; Smith et al., (1983) Mol. Cell. Biol 5:2156; and see generally, Fraser, et al. (1989) In
Vitro Cell. Dev. Biol. 25:225).
Cells and cell culture media are commercially available for both direct and fusion expression of
heterologous polypeptides in a baculovirus/expression system; cell culture technology is generally
known to those skilled in the art. See, eg. Summers and Smith supra.
The modified insect cells may then be grown in an appropriate nutrient medium, which allows for
stable maintenance of the plasmid(s) present in the modified insect host Where the expression product
gene is under inducible control, the host may be grown to high density, and expression induced.
Alternatively, where expression is constitutive, the product will be continuously expressed into the
medium and the nutrient medium must be continuously circulated, while removing the product of
interest and augmenting depleted nutrients. The product may be purified by such techniques as
chromatography., eg. HPLC, affinity chromatography, ion exchange chromatography, etc.;
electrophoresis; density gradient centrifugation; solvent extraction, or the like. As appropriate, the
product may be further purified, as required, so as to remove substantially any insect proteins which
are also secreted in the medium or result from lysis of insect cells, so as to provide a product which
is at least substantially free of host debris, eg. proteins, lipids and polysaccharidcs.
In order to obtain protein expression, recombinant host cells derived from the transformants are
incubated under conditions which allow expression of the recombinant protein encoding sequence.
These conditions will vary, dependent upon the host cell selected. However, the conditions are
readily ascertainable to those of ordinary skill in the art, based upon what is known in the art.
iii. Plant Systems
There are many plant cell culture and whole plant genetic expression systems known in the art.
Exemplary plant cellular genetic expression systems include those described in patents, such as:

US 5,693,506; US 5,659,122; and US 5,608,143. Additional examples of genetic expression in
plant cell culture has been described by Zenk, Phytochemistry 30:3861-3863 (1991). Descriptions
of plant protein signal peptides may be found in addition to the references described above in
Vaulcombe et al., Mol. Gen. Genet. 209:33-40 (1987); Chandler et al., Plant Molecular Biology
3:407-418 (1984); Rogers, J. Biol. Chem. 260:3731-3738 (1985); Rothstein et al., Gene 55:353-356
(1987); Whittier et al., Nucleic Acids Research 15:2515-2535 (1987); Wirsel et al., Molecular
Microbiology 3:3-14 (1989); Yu et al., Gene 122:247-253 (1992). A description of the regulation
of plant gene expression by the phytohormone, gibberellic acid and secreted enzymes induced by
gibberellic acid can be found in R.L. Jones and J. MacMillin, Gibberellins: in: Advanced Plant
Physiology,. Malcolm B. Wilkins, ed., 1984 Pitman Publishing Limited, London, pp. 21-52.
References that describe other metabolically-regulaled genes: Sheen, Plant Cell, 2:1027-
1038(1990); Maas et al., EMBOJ. 9:3447-3452 (1990); Benkel and Hickey, Proc. Natl. Acad. Sci.
84:1337-1339(1987)
Typically, using techniques known in the art, a desired polynucleotide sequence is inserted into an
expression cassette comprising genetic regulatory elements designed for operation in plants. The
expression cassette is inserted into a desired expression vector with companion sequences upstream
and downstream from the expression cassette suitable for expression in a plant host. The
companion sequences will be of plasmid or viral origin and provide necessary characteristics to the
vector to permit the vectors to move DNA from an original cloning host, such as bacteria, to the
desired plant host. The basic bacterial/plant vector construct will preferably provide a broad host
range prokaryote replication origin; a prokaryote selectable marker; and, for Agrobacterium
transformations, T DNA sequences for Agrobacterium-mediated transfer to plant chromosomes.
Where the heterologous gene is not readily amenable to detection, the construct will preferably also
have a selectable marker gene suitable for determining if a plant cell has been transformed. A
general review of suitable markers, for example for the members of the grass family, is found in
Wilmink and Dons, 1993, Plant Mol. Biol. Reptr, 11 (2):I65-185.
Sequences suitable for permitting integration of the heterologous sequence into the plant genome
are also recommended. These might include transposon sequences and the like for homologous
recombination as well as Ti sequences which permit random insertion of a heterologous expression
cassette into a plant genome. Suitable prokaryote selectable markers include resistance toward

antibiotics such as ampicillin or tetracycline. Other DNA sequences encoding additional functions
may also be present in the vector, as is known in the art.
The nucleic acid molecules of the subject invention may be included into an expression cassette
for expression of the protein(s) of interest. Usually, there will be only one expression cassette,
although two or more are feasible. The recombinant expression cassette will contain in addition
to the heterologous protein encoding sequence the following elements, a promoter region, plant 5'
untranslated sequences, initiation codon depending upon whether or not the structural gene comes
equipped with one, and a transcription and translation termination sequence. Unique restriction
enzyme sites at the 5' and 3' ends of the cassette allow for easy insertion into a pre-existing vector.
A heterologous coding sequence may be for any protein relating to the present invention. The
sequence encoding the protein of interest will encode a signal peptide which allows processing and
translocation of the protein, as appropriate, and will usually lack any sequence which might result
in the binding of the desired protein of the invention to a membrane. Since, for the most part, the
transcriptional initiation region will be for a gene which is expressed and translocated during
germination, by employing the signal peptide which provides for translocation, one may also
provide for translocation of the protein of interest. In this way, the protein(s) of interest will be
translocated from the cells in which they are expressed and may be efficiently harvested. Typically
secretion in seeds are across the aleurone or scutellar epithelium layer into the endosperm of the
seed. While it is not required that the protein be secreted from the cells in which the protein is
produced, this facilitates the isolation and purification of the recombinant protein.
Since the ultimate expression of the desired gene product will be in a eucaryotic cell it is desirable
to determine whether any portion of the cloned gene contains sequences which will be processed
out as introns by the host's splicosome machinery. If so, site-directed mutagenesis of the "intron"
region may be conducted to prevent losing a portion of the genetic message as a false intron code,
Reed and Maniatis, Cell 41:95-105,1985.
The vector can be microinjected directly into plant cells by use of micropipettes to mechanically
transfer the recombinant DNA. Crossway, Mol. Gen. Genet, 202:179-185, 1985. The genetic
material may also be transferred into the plant cell by using polyethylene glycol, Krens, et al.,
Nature, 296, 72-74, 1982. Another method of introduction of nucleic acid segments is high

velocity ballistic penetration by small particles with the nucleic acid either within the matrix of
small beads or particles, or on the surface, Klein, et ah. Nature, 327, 70-73, 1987 and Knudsen and
Muller, 1991, Planta, 185:330-336 teaching particle bombardment of barley endosperm to create
transgenic barley. Yet another method of introduction would be fusion of protoplasts with other
entities, either minicells, cells, lysosomes or other fusible lipid-surfaced bodies, Fraley, et al., Proc
Nad. Acad. Sci. USA,79, 1859-1863, 1982.
The vector may also be introduced into the plant cells by electroporation. (Fromm et al., Proc. Natl
Acad Sci. USA 82:5824, 1985). In this technique, plant protoplasts are electroporated in the
presence of plasmids containing the gene construct. Electrical impulses of high field strength
reversibly permeabilize biomembranes allowing the introduction of the plasmids. Electroporated
plant protoplasts reform the cell wall, divide, and form plant callus.
All plants from which protoplasts can be isolated and cultured to give whole regenerated plants can
be transformed by the present invention so that whole plants are recovered which contain the
transferred gene. It is known that practically all plants can be regenerated from cultured cells or
tissues, including but .not limited to all major species of sugarcane, sugar beet, cotton, fruit and
other trees, legumes and vegetables. Some suitable plants include, for example, species from the
genera Fragaria, Lotus, Medicago, Onobrychis, Trifolium, Trigonella, Vigna, Citrus, Linum,
Geranium, Manihot, Daucus, Arabidopsis, Brassica, Raphanus, Sinapis, Atropa, Capsicum,
Datura, Hyoscyamus, Lycopersion, Nicotiana, Solarium, Petunia, Digitalis, Mqjorana, Cichorium,
Helianthus, Lactuca, Bromus, Asparagus, Antirrhinum, Hererocallis, Nemesia, Pelargonium,
Panicum, Pennisetum, Ranunculus, Senecio, Salpiglossis, Cucumis, Browaalia, Glycine, Lolium,
Zea, Triticum, Sorghum, and Datura.
Means for regeneration vary from species to species of plants, but generally a suspension of
transformed protoplasts containing copies of the heterologous gene is first provided. Callus tissue
is formed and shoots may be induced from callus and subsequently rooted. Alternatively, embryo
formation can be induced from the protoplast suspension. These embryos germinate as natural
embryos to form plants. The culture media will generally contain various amino acids and
hormones, such as auxin and cytokinins. It is also advantageous to add glutamic acid and proline
to the medium, especially for such species as corn and alfalfa. Shoots and roots normally develop
simultaneously. Efficient regeneration will depend on the medium, on the genotype, and on the

history of the culture. If these three variables are controlled, then regeneration is fully reproducible
and repeatable.
In some plaint cell culture systems, the desired protein of the invention may be excreted or
alternatively, the protein may be extracted from the whole plant. Where the desired protein of the
invention is secreted into the medium, it may be collected. Alternatively, the embryos and
embryoless-half seeds or other plant tissue may be mechanically disrupted to release any secreted
protein between cells and tissues. The mixture may be suspended in a buffer solution to retrieve
soluble proteins. Conventional protein isolation and purification methods will be then used to
purify the recombinant protein. Parameters of time, temperature pH, oxygen, and volumes will be
adjusted through routine methods to optimize expression and recovery of heterologous protein.
iv. Bacterial Systems
Bacterial expression techniques are known in the art. A bacterial promoter is any DNA sequence
capable of binding bacterial RNA polymerase and initiating the downstream (3') transcription of
a coding sequence (eg. structural gene) into mRNA. A promoter will have a transcription initiation
region which is usually placed proximal to the 5' end of the coding sequence. This transcription
initiation region usually includes an RNA polymerase binding she and a transcription initiation site.
A bacterial promoter may also have a second domain called an operator, that may overlap an
adjacent RNA polymerase binding site at which RNA synthesis begins. The operator permits
negative regulated (inducible) transcription, as a gene repressor protein may bind the operator and
thereby inhibit transcription of a specific gene. Constitutive expression may occur in the absence
of negative regulatory elements, such as the operator. In addition, positive regulation may be
achieved by a gene activator protein binding sequence, which, if present is usually proximal (51)
to the RNA polymerase binding sequence. An example of a gene activator protein is the catabolite
activator protein (CAP), which helps intiate transcription of the lac operon in Escherichia coli (E.
coli) [Raibaud et al. (1984) Annu. Rev. Genet. 18:113]. Regulated expression may therefore be
either positive or negative, thereby either enhancing or reducing transcription.
Sequences encoding metabolic pathway enzymes provide particularly useful promoter sequences.
Examples include promoter sequences derived from sugar metabolizing enzymes, such as galactose,
lactose (lac) [Chang et al. (1977) Nature 198:1056], and maltose. Additional examples include
promoter sequences derived from biosynthetic enzymes such as tryptophan (trp) [Goeddel et al.

(1980) Nuc. Acids Res. 5:4057; Yelverton et al. (1981) Nucl. Acids Res. 9:731; US
patent 4,738,921; EP-A-0036776 and EP-A-0121775]. The g-laotamase (bid) promoter system
[Weissmann (1981) "The cloning of interferon and other mistakes." In Interferon 3 (ed. I. Gresser)],
bacteriophage lambda PL [Shimatake et al. (1981) Nature 292:128] and T5 [US patent 4,689,406]
promoter systems also provide useful promoter sequences.
In addition, synthetic promoters which do not occur in nature also function as bacterial promoters.
For example, transcription activation sequences of one bacterial or bacteriophage promoter may
be joined with the operon sequences of another bacterial or bacteriophage promoter, creating a
synthetic hybrid promoter [US patent 4,551,433]. For example, the tac promoter is a hybrid trp-lac
promoter comprised of both trp promoter and lac operon sequences that is regulated by the lac
repressor [Amann et al. (1983) Gene 25:167; de Boer et al. (1983) Proc. Natl. Acad. Sci. 80:21).
Furthermore, a bacterial promoter can include naturally occurring promoters of non-bacterial origin
that have the ability to bind bacterial RNA polyrrierase and initiate transcription. A naturally
occurring promoter of non-bacterial origin can also be coupled with a compatible RNA polymerase
to produce high levels of expression of some genes in prokaryotes. The bacteriophage T7 RNA
polymerase/promoter system is an example of a coupled promoter system [Studier et al. (1986) J.
Mol. Biol. J89:113; Tabor et al. (1985) Proc Natl. Acad Sci. 52:1074]. In addition, a hybrid
promoter can also be comprised of a bacteriophage promoter and an E. coli operator region (EPO-
A-0 267 851).
In addition to a functioning promoter sequence, an efficient ribosome binding site is also useful for
the expression of foreign genes in prokaryotes. In E. coli, the ribosome binding site is called the
Shine-Dalgarno (SD) sequence and includes an initiation codon (ATG) and a sequence 3-9
nucleotides in length located 3-11 nucleotides upstream of the initiation codon [Shine et al. (1975)
Nature 254:34]. The SD sequence is thought to promote binding of mRNA to the ribosome by the
pairing of bases between the SD sequence and the 3' and of E. coli 16S rRNA [Steitz et al. (1979)
"Genetic signals and nucleotide sequences in messenger RNA." In Biological Regulation and
Development: Gene Expression (ed. R.F. Goldberger)]. To express eukaryotic genes and
prokaryotic genes with weak ribosome-binding site [Sambrook et al. (1989) "Expression of cloned
genes in Escherichia coli." In Molecular Cloning: A Laboratory Manual].

A DNA molecule may be expressed intracellularly. A promoter sequence may be directly linked
with the DNA molecule, in which case the first amino acid at the N-terminus will always be a
methionine, which is encoded by the ATG start codon. If desired, methionine at the N-terminus
may be cleaved from the protein by in vitro incubation with cyanogen bromide or by either in vivo
on in vitro incubation with a bacterial methionine N-terminal peptidase (EPO-A-0 219 237).
Fusion proteins provide an alternative to direct expression. Usually, a DNA sequence encoding the
N-terminal portion of an endogenous bacterial protein, or other stable protein, is fused to the 5' end
of heterologous coding sequences. Upon expression, this construct will provide a fusion of the two
amino acid sequences. For example, the bacteriophage lambda cell gene can be linked at the 5'
terminus of a foreign gene and expressed in bacteria. The resulting fusion protein preferably retains
a site for a processing enzyme (factor Xa) to cleave the bacteriophage protein from the foreign gene
[Nagai et al. (1984) Nature 309:810]. Fusion proteins can also be made with sequences from the
iacZ [Jia et al (1987) Gene 60:197], trpE [Allen et al. (1987) J. Biotechnol. 5:93; Makoff et al.
(1989) J. Gen. Microbiol. 135:11], and Chey [EP-A-0 324 647] genes. The DNA sequence at the
junction of the two amino acid sequences may or may not encode a cleavable site. Another example
is a ubiquitin fusion protein. Such a fusion protein is made with the ubiquitin region that preferably
retains a site for a processing enzyme (eg. ubiquitin specific processing-protease) to cleave the
ubiquitin from the foreign protein. Through this method, native foreign protein can be isolated
[Miller et al. (1989) Bio/Technology 7:698].
Alternatively, foreign proteins can also be secreted from the cell by creating chimeric DNA molecules
that encode a fusion protein comprised of a signal peptide sequence fragment mat provides for secretion
of the foreign protein in bacteria [US patent 4,336,336]. The signal sequence fragment usually encodes
a signal peptide comprised of hydrophobic amino acids which direct the secretion of the protein from the
cell. The protein is either secreted into the growth media (gram-positive bacteria) or into the periplasmic
space, located between the inner and outer membrane of the cell (gram-negative bacteria). Preferably
there are processing sites, which can be cleaved either in vivo or in vitro encoded between the signal
peptide fragment and the foreign gene.
DNA encoding suitable signal sequences can be derived from genes for secreted bacterial proteins,
such as the E. coli outer membrane protein gene (ompA) [Masui et al. (1983), in: Experimental
Manipulation of Gene Expression; Ghrayeb et al. (1984) EMBO J. 3:2437] and the E. coli alkaline

phosphatase signal sequence (phoA) [Oka et al. (1985) Proc. Nad. Acad. Sci. 82:7212]. As an
additional example, the signal sequence of the alpha-amylase gene from various Bacillus strains
can be used to secrete heterologous proteins from B. subtilis [Palva et al. (1982) Proc. Natl. Acad.
Sci. USA 79:5582; EP-A-0 244 042].
Usually, transcription termination sequences recognized by bacteria are regulatory regions located
3' to the translation stop codon, and thus together with the promoter flank the coding sequence.
These sequences direct the transcription of an mRNA which can be translated into the polypeptide
encoded by the DNA. Transcription termination sequences frequently include DNA sequences of
about SO nucleotides capable of forming stem loop structures that aid in terminating transcription.
Examples include transcription termination sequences derived from genes with strong promoters,
such as the trp gene in E. coli as well as other biosynthetic genes.
Usually, the above described components, comprising a promoter, signal sequence (if desired),
coding sequence of interest, and transcription termination sequence, are put together into expression
constructs. Expression constructs are often maintained in a replicon, such as an extrachromosomal
element (eg. plasmids) capable of stable maintenance in a host, such as bacteria. The replicon will
have a replication system, thus allowing it to be maintained in a prokaryotic host either for
expression or for cloning and amplification. In addition, a replicon may be either a high or low
copy number plasmid. A high copy number plasmid will generally have a copy number ranging
from about 5 to about 200, and usually about 10 to about 150. A host containing a high copy
number plasmid will preferably contain at least about 10, and more preferably at least about 20
plasmids. Either a high or low copy number vector may be selected, depending upon the effect of
the vector and the foreign protein on the host.
Alternatively, the expression constructs can be integrated into the bacterial genome with an
integrating vector. Integrating vectors usually contain at least one sequence homologous to the
bacterial chromosome that allows the vector to integrate. Integrations appear to result from
recombinations between homologous DNA in the vector and the bacterial chromosome. For
example, integrating vectors constructed with DNA from various Bacillus strains integrate into the
Bacillus chromosome (EP-A- 0 127 328). Integrating vectors may also be comprised of
bacteriophage or transposon sequences.

Usually, extrachromosomal and integrating expression constructs may contain selectable markers
to allow for the selection of bacterial strains that have been transformed. Selectable markers can
be expressed in the bacterial host and may include genes which render bacteria resistant to drugs
such as ampicillin, chloramphenicol, erythromycin, kanamycin (neomycin), and tetracycline
[Davies et al. (1978) Annu. Rev.,, Microbiol. 32:469). Selectable markers may also include
biosynthetic genes, such as those in the histidine, tryptophan, and leucine biosynthetic pathways.
Alternatively, some of the above described components can be put together in transformation
vectors. Transformation vectors are usually comprised of a selectable market that is either
maintained in a replicon or developed into an integrating vector, as described above.
Expression and transformation vectors, either extra-chromosomal repiicons or integrating vectors,
have been developed for transformation into many bacteria. For example, expression vectors have
been developed for, inter alia, the following bacteria: Bacillus subtilis [Palva et al. (1982) Proc.
Natl Acad. Sci. USA 79:5582; EP-A-0 036 259 and EP-A-0 063 953; WO 84/04541], Escherichia
coli [Shimatake et al. (1981) Nature 292:128; Amann et al. (1985) Gene 40:183; Studier et al.
(1986) J. Mol. Biol. 189:113; EP-A-0 036 776.EP-A-0 136 829 and EP-A-0 136 907],
Streptococcus cremoris [Powell et al. (1988) Appl. Environ. Microbiol. 54:655]; Streptococcus
lividans [Powell et al. (1988) Appl. Environ. Microbiol. 54:655], Streptomyces lividans [US patent
4,745,056].
Methods of introducing exogenous DNA into bacterial hosts are well-known in the art, and usually
include either the transformation of bacteria treated with CaCl2 or other agents, such as divalent
cations and DMSO. DNA can also be introduced into bacterial cells by electroporation.
Transformation procedures usually vary with the bacterial species to be transformed. See eg.
[Masson et al. (1989) FEMS Microbiol Lett. 60:273; Palva et al (1982) Proc. Natl. Acad Sci. USA
79:5582r EP-A-0 036 259 and EP-A-0 063 953; WO 84/04541, Bacillus], (Miller et al. (1988)
Proc. Natl. Acad Sci. 55:856; Wang el al. (1990) J. Bacteriol 172:949, Campylobacter], [Cohen
et al (1973) Proc. Natl. Acad. Sci. 69:2110; Dower et al. (1988) Nucleic Acids Res. 16:6121;
Kushner (1978) "An improved method for transformation of Escherichia coli with ColE1-derived
plasmids. In Genetic Engineering: Proceedings of the International Symposium on Genetic
Engineering (eds. H.W. Boyer and S. Nicosia); Mandel et al. (1970) J. Mol. Biol. 53:159; Taketo
(1988) Biochim. Biophys. Acta 949:318; Escherichia], [Chassy et al (1987) FEMS Microbiol. Lett.

44:173 Lactobacillus]; [Fiedler et al. (1988)Anal. Biochem 770:38, Pseudomonas]; [Augustin et
al. (1990) FEMS Microbiol. Lett. 66:203, Staphyiococcus], [Barany et al. (1980) J. Bacteriol
144:69%; Harlander (1987) "Transformation of Streptococcus lactis by electroporation, in:
Streptococal Genetics (ed. J. Ferretti and R. Curtiss III); Perry et al. (1981) Infect, lmmun
32:1295; Powell et al. (1988)Appl. Environ. Microbiol. 54:655; Somkuti et al. (1987) Proc. 4th
Evr. Cong. Biotechnology 7:412, Streptococcus].
v. Yeast Expression
Yeast expression systems are also known to one of ordinary skill in the art. A yeast promoter is any
DNA sequence capable of binding yeast RNA polymerase and initiating the downstream (3')
transcription of a coding sequence (eg. structural gene) into mRNA. A promoter will have a
transcription initiation region which is usually placed proximal to the 5' end of the coding sequence.
This transcription initiation region usually includes an RNA polymerase binding site (the "TATA
Box") and a transcription initiation site. A yeast promoter may also have a second domain called
an upstream activator sequence (UAS), which, if present, is usually distal to the structural gene.
The UAS permits regulated (inducible) expression. Constitutive expression occurs in the absence
of a UAS. Regulated expression may be either positive or negative, thereby either enhancing or
reducing transcription.
Yeast is a fermenting organism with an active metabolic pathway, therefore sequences encoding
enzymes in the metabolic pathway provide particularly useful promoter sequences. Examples
include alcohol dehydrogenase (ADH) (EP-A-0 284 044), enolase, glucokinase, glucoses-
phosphate isomerase, glyceraldehyde-3-phosphate-dehydrogenase (GAP or GAPDH), hexokinase,
phosphofructokinase, 3-phosphoglycente mutase, and pyruvate kinase (PyK) (EPO-A-0 329 203).
The yeast PHO5 gene, encoding acid phosphatase, also provides useful promoter sequences
[Myanohara et al (1983) Proc. Natl Acad. Sci. USA 80:1].
In addition, synthetic promoters which do not occur in nature also function as yeast promoters. For
example, UAS sequences of one yeast promoter may be joined with the transcription activation
region of another yeast promoter, creating a synthetic hybrid promoter. Examples of such hybrid
promoters include the ADH regulatory sequence linked to the GAP transcription activation region
(US Patent Nos. 4,876,197 and 4,880,734). Other examples of hybrid promoters include promoters
which consist of the regulatory sequences of either the ADH2, GAL4, GAL JO, OR PHO5 genes,

combined with the transcriptional activation region of a glycolytic enzyme gene such as GAP or
PyK (EP-A-0 164 556). Farthermore, a yeast promoter can include naturally occurring promoters
of non-yeast origin that have the ability to bind yeast RNA polymerase and initiate transcription.
Examples of such promoters include, inter alia, [Cohen et al. (1980) Proc. Natl. Acad. Sci. USA
77:1078; Henikoff et al. (1981) Nature 283:835; Hollenberg et al. (1981) Curr. Topics Microbiol.
Immunol 96:119; Hollenberg et al. (1979) "The Expression of Bacterial Antibiotic Resistance
Genes in the Yeast Saccharomyces cerevisiae," in: Plasmids of Medical, Environmental and
Commercial Importance (eds. K.N. Timmis and A. Puhler); Mercerau-Puigalon et al. (1980) Gene
/7:163; Panthier et al. (1980) Curr. Genet. 2:109;].
A DNA molecule may be expressed intracellularly in yeast. A promoter sequence may be directly
Jinked with the DNA molecule, in which case the first amino acid at the N-terminus of the
recombinant protein will always be a methionine, which is encoded by the ATG start codon. If
desired, methionine at the N-terminus may be cleaved from the protein by in vitro incubation with
cyanogen bromide.
Fusion proteins provide an alternative for yeast expression systems, as well as in mammalian,
baculovirus, and bacterial expression systems. Usually, a DNA sequence encoding the N-terminal
portion of an endogenous yeast protein, or other stable protein, is fused to the 5' end of
heterologous coding sequences. Upon expression, this construct will provide a fusion of the two
amino acid sequences. For example, the yeast or human superoxide dismutase (SOD) gene, can be
linked at the 5' terminus of a foreign gene and expressed in yeast. The DNA sequence at the
junction of the two amino acid sequences may or may not encode a cieavabk site. See eg. EP-A-0
196 056. Another example is a ubiquitin fusion protein. Such a fusion protein is made with the
ubiquitin region that preferably retains a site for a processing enzyme (eg. ubiquitin-specific
processing protease) to cleave the ubiquitin from the foreign protein. Through this method,
therefore, native foreign protein can be isolated (eg. WO88/024066).
Alternatively, foreign proteins can also be secreted from the cell into the growth media by creating
chimeric DNA molecules that encode a fusion protein comprised of a leader sequence fragment that
provide for secretion in yeast of the foreign protein. Preferably, there are processing sites encoded
between the leader fragment and the foreign gene that can be cleaved either in vivo or in vitro. The

leader sequence fragment usually encodes a signal peptide comprised of hydrophobic amino acids
which direct the secretion of the protein from the cell.
DNA encoding suitable signal sequences can be derived from genes for secreted yeast proteins,
such as the yeast invertase gene (EP-A-0 012 873; JPO. 62,096,086) and the A-factor gene (US
patent 4,588,684). Alternatively, leaders of non-yeast origin, such as an interferon leader, exist that
also provide for secretion in yeast (EP-A-0 060 057).
A preferred class of secretion leaders are those that employ a fragment of the yeast alpha-factor
gene, which contains both a "pxe" signal sequence, and a "pro" region. The types of alpha-factor
fragments that can be employed include the full-length pre-pro alpha factor leader (about 83 amino
acid residues) as well as truncated alpha-factor leaders (usually about 25 to about 50 amino acid
residues) (US Patents 4,546,083 and 4,870,008; EP-A-0 324 274). Additional leaders employing
an alpha-factor leader fragment that provides for secretion include hybrid alpha-factor leaders made
with a presequence of a first yeast, but a pro-region from a second yeast alphafactor. (eg. see WO
89/02463.)
Usually, transcription termination sequences recognized by yeast are regulatory regions located 3'
to the translation stop codon, and thus together with the promoter flank the coding sequence. These
sequences direct the transcription of an mRNA which can be translated into the polypeptide
encoded by the DNA. Examples of transcription terminator sequence and other yeast-recognized
termination sequences, such as those coding for glycolytic enzymes.
Usually, the above described components, comprising a promoter, leader (if desired), coding
sequence of interest, and transcription termination sequence, are put together into expression
constructs. Expression constructs are often maintained in a replicon, such as an extrachromosomal
element (eg. plasmids) capable of stable maintenance in a host, such as yeast or bacteria. The
replicon may have two replication systems, thus allowing it to be maintained, for example, in yeast
for expression and in a prokaryotic host for cloning and amplification. Examples of such yeast-
bacteria shuttle vectors include YEp24 [Botstein et al. (1979) Gene 8:17-24}, pCl/1 [Brake et al.
(1984) Proc. Natl. Acad. Sci USA 87:4642-4646], and YRpl7 [Stinchcomb et al (1982) J. Mol.
Biol. 158:157]. In addition, a replicon may be either a high or low copy number plasmid. A high
copy number piasmid will generally have a copy number ranging from about 5 to about 200, and

usually about 10 to about 150. A host containing a high copy number plasmid will preferably have
at least about 10, and more preferably at least about 20. Enter a high or low copy number vector
may be selected, depending upon the effect of the vector and the foreign protein on the host. See
eg. Brake et al, supra.
Alternatively, the expression constructs can be integrated into the yeast genome with an integrating
vector. Integrating vectors usually contain at least one sequence homologous to a yeast
chromosome that allows the vector to integrate, and preferably contain two homologous sequences
flanking the expression construct. Integrations appear to result from recombinations between
homologous DNA in the vector and the yeast chromosome [Orr-Weaver et al. (1983) Methods in
Enzymol. 707:228-245}. An integrating vector may be directed to a specific locus in yeast by
selecting the appropriate homologous sequence for inclusion in the vector. See Orr-Weaver et al,
supra. One or more expression construct may integrate, possibly affecting levels of recombinant
protein produced [Rine et al. (1983) Proc. Nat!. Acad. Sci. USA 80:6750]. The chromosomal
sequences included in the vector can occur either as a single segment in the vector, which results
in the integration of the entire vector, or two segments homologous to adjacent segments in the
chromosome and flanking the expression construct in the vector, which can result in the stable
integration of only the expression construct.
Usually, extrachromosomal and integrating expression constructs may contain selectable markers
to allow for the selection of yeast strains that have been transformed. Selectable markers may
include biosynthetic genes that can be expressed in the yeast host, such as ADE2, HIS4, LEU2,
TRP1, and ALG7, and the G418 resistance gene, which confer resistance in yeast cells to
tunicamycin and G418, respectively. In addition, a suitable selectable marker may also provide
yeast with the ability to grow in the presence of toxic compounds, such as metal. For example, the
presence of CUP1 allows yeast to grow in the presence of copper ions [Butt et al. (1987) Kiicrobiol,
Rev. 51-351].
Alternatively, some of the above described components can be put together into transformation
vectors. Transformation vectors are usually comprised of a selectable marker that is either
maintained in a replicon or developed into an integrating vector, as described above.

Expression and transformation vectors, either extrachromosomal replicons or integrating vectors,
have been developed for transformation into many yeasts. For example, expression vectors have
been developed for, inter alia, the following yeasts:Candida albicans [Kurtz, et al. (1986) Mol.
Cell. Biol. 6:142], Candida maltosa [Kunze, et al. (1985) J. Basic Microbiol 25:141]. Hansenula
polymorpha [Gleeson, et al. (1986) J. Gen. Microbiol. J32:3459; Roggenkamp et al. (1986) Mol.
Gen. Genet. 202:302], Kluyveromyces fragilis [Das, et al. (1984) J. Bacteriol. 158:1165],
Kluyveromyces lactis [De Louvencourt et al. (1983) J. Bacteriol. 154:131; Van den Berg el al.
(1990) Bio/Technology 5:135], Pichia guillerimondii [Kunze et al. (1985) J. Basic Microbiol.
25:141], Pichia pastoris [Cregg, et al. (1985) Mol. Cell Biol. 5:3316; US Patent Nos. 4,837,148
and 4,929,555], Saccharomyces cerevisiae [Hinnen et al. (1978) Proc. Natl. Acad. Sci. USA
75:1929; Ito et al. (1983) J. Bacteriol. 755:163], Schizosaccharomyces pombe [Beach and Nurse
(1981)Nature 300:106], and Yarrowia lipolytica [Davidow, et al. (1985) Curr. Genet. 70:380471
Gaillardin, et al. (1985) Curr. Genet. 10:49].
Methods of introducing exogenous DNA into yeast hosts are well-known in the art, and usually
include either the transformation of spheroplasts or of intact yeast cells treated with alkali cations.
Transformation procedures usually vary with the yeast species to be transformed. See eg. [Kurtz
et al. (1986) Mol. Cell Biol. 6:142; Kunze et al. (1985) J. Basic Microbiol 25:141; Candida];
[Gleeson et al (1986) J. Gen. Microbiol. 132:3459; Roggenkamp et al. (1986) Mol. Gen. Genet.
202:302; Hansenula]; [Das et al. (1984) J. Bacteriol. 158:1165; De Louvencourt et al. (1983) J.
Bacteriol 154:1165; Van den Berg et al. (1990) Bio/Technology 5:135; Kluyveromyces]; [Cregg
et al. (1985) Mol. Cell. Biol. 5:3376; Kunze et al. (1985) J. Basic Microbiol. 25:141; US Patent
Nos. 4,837,148 and 4,929,555; Pichia]; [Hinnen et al. (1978) Proc. Natl. Acad Sci. USA 75;1929;
Ito et al. (1983) J. Bacteriol 153:163 Saccharomyces]; [Beach and Nurse (1981) Nature 300:706;
Schizosaccharomyces]; [Davidow et al. (1985) Curr. Genet. 10:39; Gaillardin et al. (1985) Curr.
Genet. 10:49; Yarrowia].
Antibodies
As used herein, the term "antibody" refers to a polypeptide or group of polypeptides composed of
at least one antibody combining site. An "antibody combining site" is the three-dimensional
binding space with an internal surface shape and charge distribution complementary to the features
of an epitope of an antigen, which allows a binding of the antibody with the antigen. "Antibody"

includes, for example, vertebrate antibodies, hybrid antibodies, chimeric antibodies, humanised
antibodies, altered antibodies, univalent antibodies, Fab proteins, and single domain antibodies.
Antibodies against the proteins of the invention are useful for affinity chromatography,
immunoassays, and distinguishing/identifying Neisserial proteins.
Antibodies to the proteins of the invention, both polyclonal and monoclonal, may be prepared by
conventional methods. In general, the protein is first used to immunize a suitable animal, preferably
a mouse, rat, rabbit or goat. Rabbits and goats are preferred for the preparation of polyclonal sera
due to the volume of serum obtainable, and the availability of labeled anti-rabbit and anti-goat
antibodies. Immunization is generally performed by mixing or emulsifying the protein in saline,
preferably in an adjuvant such as Freund's complete adjuvant, and injecting the mixture or
emulsion parenterally (generally subcutaneously or intramuscularly). A dose of 50-200 μg/injection
is typically sufficient. Immunization is generally boosted 2-6 weeks later with one or more
injections of the protein in saline, preferably using Freund's incomplete adjuvant. One may
alternatively generate antibodies by in vitro immunization using methods known in the art, which
for the purposes of this invention is considered equivalent to in vivo immunization. Polyclonal
antisera is obtained by bleeding the immunized animal into a glass or plastic container, incubating
the blood at 25°C for one hour, followed by incubating at 4°C for 2-18 hours. The serum is
recovered by centrifugation (eg. 1,000g for 10 minutes). About 20-50 ml per bleed may be obtained
from rabbits.
Monoclonal antibodies are prepared using the standard method of Kohler & Milstein [Nature
(1975) 256:495-96], or a modification thereof. Typically, a mouse or rat is immunized as described
above. However, rather man bleeding the animal to extract serum, the spleen (and optionally
several large lymph nodes) is removed and dissociated into single cells. If desired, the spleen cells
may be screened (after removal of nonspecifically adherent cells) by applying a cell suspension to
a plate or well coated with the protein antigen. B-cells expressing membrane-bound
unmunoglobulin specific for the antigen bind to the plate, and are not rinsed away with the rest of
the suspension. Resulting B-cells, or all dissociated spleen cells, are then induced to fuse with
myeloma cells to form hybridomas, and are cultured in a selective medium (eg. hypoxanthine,
aminopterin, thymidine medium, "HAT"). The resulting hybridomas are plated by limiting dilution,
and are assayed for the production of antibodies which bind specifically to the immunizing antigen

(and which do not bind to unrelated antigens). The selected MAb-secreting hybridomas are then
cultured either in vitro (eg. in tissue culture bottles or hollow fiber reactors), or in vivo (as ascites
in mice).
If desired, the antibodies (whether polyclonal or monoclonal) may be labeled using conventional
techniques. Suitable labels include fluorophores, chromophores, radioactive atoms (particularly 32P
and I), electron-dense reagents, enzymes, and ligands having specific binding partners. Enzymes
are typically detected by their activity. For example, horseradish peroxidase is usually detected by its
ability to convert 3,3',5,5'-tetramethylbenzidine (TMB) to a blue pigment, quantifiable with a
spectrophotometer. "Specific binding partner" refers to a protein capable of binding a ligand molecule
with high specificity, as for example in the case of an antigen and a monoclonal antibody specific
therefor. Other specific binding partners include biotin and avidin or streptavidin, IgG and protein A,
and the numerous receptor-ligand couples known in the art. It should be understood that the above
description is not meant to categorize the various labels into distinct classes, as the same label may
serve in several different modes. For example, I25I may serve as a radioactive label or as an
electron-dense reagent HRP may serve as enzyme or as antigen for a MAb. Further, one may combine
various labels for desired effect. For example, MAbs and avidin also require labels in the practice of
this invention: thus, one might label a MAb with biotin, and detect its presence with avidin labeled
with 125I, or with an anti-biotin MAb labeled with HRP. Other permutations and possibilities will be
readily apparent to those of ordinary skill in the art, and are considered as equivalents within the scope
of the instant invention.
Pharmaceutical Compositions
Pharmaceutical compositions can comprise either polypeptides, antibodies, or nucleic acid of the
invention. The pharmaceutical compositions will comprise a therapeutically effective amount of
either polypeptides, antibodies, or polynucleotides of the claimed invention.
The term "tberapeutically effective amount" as used herein refers to an amount of a therapeutic
agent to treat, ameliorate, or prevent a desired disease or condition, or to exhibit a detectable
therapeutic or preventative effect. The effect can be detected by, for example, chemical markers or
antigen levels. Therapeutic effects also include reduction in physical symptoms, such as decreased
body temperature. The precise effective amount for a subject will depend upon the subject's size
and health, the nature and extent of the condition, and the therapeutics or combination of

therapeutics selected for administration. Thus, it is not useful to specify an exact effective amount
in advance. However, the effective amount for a given situation can be determined by routine
experimentation and is within the judgement of the clinician.
For purposes of the present invention, an effective dose will be from about 0.01 mg/ kg to 50 mg/kg
or 0.05 mg/kg to about 10 mg/kg of the DNA constructs in the individual to which it is administered.
A pharmaceutical composition can also contain a pharmaceutically acceptable carrier. The term
"pharmaceutically acceptable carrier" refers to a carrier for administration of a therapeutic agent, such
as antibodies or a polypeptide, genes, and other therapeutic agents. The term refers to any
pharmaceutical carrier that does not itself induce the production of antibodies harmful to the
individual receiving the composition, and which may be administered without undue toxicity. Suitable
carriers may be large, slowly metabolized macromolecules such as proteins, polysaccharides,
polylactic acids, polyglycolic acids, polymeric amino acids, amino acid copolymers, and inactive virus
particles. Such carriers are well known to those of ordinary skill in the art.
Pharmaceutically acceptable salts can be used therein, for example, mineral acid salts such as
hydrochlorides, hydrobromides, phosphates, sulfates, and the like; and the salts of organic acids
such as acetates, propionates, malonates, benzoates, and the like. A thorough discussion of
pharrnaceutically acceptable excipients is available in Remington's Pharmaceutical Sciences (Mack
Pub. Co., NJ. 1991).
Pharmaceutically acceptable carriers in therapeutic compositions may contain liquids such as water,
saline, glycerol and ethanol. Additionally, auxiliary substances, such as wetting or emulsifying agents,
pH buffering substances, and the like, may be present in such vehicles. Typically, the therapeutic
compositions are prepared as injectables, either as liquid solutions or suspensions; solid forms suitable
for solution in, or suspension in, liquid vehicles prior to injection may also be prepared. Liposomes
are included within the definition of a pharmaceutically acceptable carrier.
Delivery Methods
Once formulated, the compositions of the invention can be administered directly to the subject. The
subjects to be treated can be animals; in particular, human subjects can be treated.

Direct delivery of the compositions will generally be accomplished by injection, either
subcutaneously, intraperitoneally, intravenously or intramuscularly or delivered to the interstitial
space of a tissue. The compositions can also be administered into a lesion. Other modes of
administration include oral and pulmonary administration, suppositories, and transdermal or
transcutaneous applications (eg. see WO98/20734), needles, and gene guns or hyposprays. Dosage
treatment may be a single dose schedule or a multiple dose schedule.
Vaccines
Vaccines according to the invention may either be prophylactic (ie. to prevent infection) or
therapeutic (ie. to treat disease after infection).
Such vaccines comprise immunising antigen(s), immunogen(s), polypeptide(s), protein(s) or nucleic acid,
usually in combination with "pharmaceutically acceptable carriers," which include any carrier that does
not itself induce the production of antibodies harmful to the individual receiving the composition.
Suitable carriers are typically large, slowly metabolized macromolecules such as proteins,
poiysaccharides, polylactic acids, polygiycolic acids, polymeric amino acids, amino acid copolymers,
Jipid aggregates (such as oil droplets or liposomes), and inactive virus particles. Such carriers are well
known to those of ordinary skill in the art. Additionally, these carriers may function as
immunostimulating agents ("adjuvants"). Furthermore, the antigen or immunogen may be conjugated to
a bacterial toxoid, such as a toxoid from diphtheria, tetanus, cholera, H. pylori, etc. pathogens.
Preferred adjuvants to enhance effectiveness of the composition include, but are not limited to: (1)
aluminum salts (alum), such as aluminum hydroxide, aluminum phosphate, aluminum sulfate, etc;
(2) oil-in-water emulsion formulations (with or without other specific immunostimulating agents
such as muramyl peptides (see below) or bacterial cell wall components), such as for example (a)
MF59™ (WO 90/14837; Chapter 10 in Vaccine design: the subunit and adjuvant approach, eds.
Powell & Newman, Plenum Press 1995), containing 5% Squalene, 0.5% Tween 80, and 0.5% Span
85 (optionally containing various amounts of MTP-PE (see below), although not required)
formulated into submicron particles using a microfluidizer such as Model 110Y microfluidizer
(Microfluidics, Newton, MA), (b) SAF, containing 10% Squalane, 0.4% Tween 80,5% pluronic-
blocked polymer L121, and thr-MDP (see below) either microfluidized into a submicron emulsion
or vortexed to generate a larger partkie size emulsion, and (c) Ribi™ adjuvant system (RAS), (Ribi
Immunochem, Hamilton, MT) containing 2% Squalene, 0.2% Tween 80, and one or more bacterial

cell wall components from the group consisting of monophosphorylipid A (MPL), trehalose
dimycolate (TDM), and cell wall skeleton (CWS), preferably MPL + CWS (Detox™); (3) saponin
adjuvants, such as Stimulon™ (Cambridge Bioscience, Worcester, MA) may be used or particles
generated therefrom such as ISCOMs (immunostimulating complexes); (4) Complete Freund's
Adjuvant (CFA) and Incomplete Freund's Adjuvant (IFA); (5) cytokines, such as interleukins (eg.
IL-1, IL-2, IL-4, IL-5, IL-6, IL-7, IL-12, etc.), interferons (eg. gamma interferon), macrophage
colony stimulating factor (M-CSF), tumor necrosis factor (TNF), etc; and (6) other substances that
act as immunostimulating agents to enhance the effectiveness of the composition. Alum and
MF59™ are preferred.
As mentioned above, muramyl peptides include, but are not limited to, N-acetyl-muramyl-L-
threonyl-D-isoglutamine (thr-MDP), N-acetyl-normuramyl-L-alanyl-D-isoglutamine (nor-MDP),
N-acetylmuramyl-L-alanyl-D-isoglutaminyl-L-alanine-2-(r-2'-dipalmitoyl-5n-glycero-3-
hydroxyphosphoryloxy)-ethylamine (MTP-PE), etc.
The immunogenic compositions (eg. the immunising antigen/immunogen/polypeptide/protein/
nucleic acid, pharmaceutically acceptable carrier, and adjuvant) typically will contain diluents, such
as water, saline, glycerol, ethanol, etc. Additionally, auxiliary substances, such as wetting or
emulsifying agents, pH buffering substances, and the like, may be present in such vehicles.
Typically, the immunogenic compositions are prepared as injectables, either as liquid solutions or
suspensions; solid forms suitable for solution in, or suspension in, liquid vehicles prior to injection
may also be prepared. The preparation also may be emulsified or encapsulated in liposomes for
enhanced adjuvant effect, as discussed above under pharmaceutically acceptable carriers.
Immunogenic compositions used as vaccines comprise an immunologically effective amount of the
antigenic or immunogenic polypeptides, as well as any other of the above-mentioned components,
as needed, By "immunologically effective amount", it is meant that the administration of mat
amount to an individual, either in a single dose or as part of a series, is effective for treatment or
prevention. This amount varies depending upon the health and physical condition of the individual
to be treated, the taxonomic group of individual to be treated (eg. nonhuman primate, primate, etc.),
the capacity of the individual's immune system to synthesize antibodies, the degree of protection
desired, the formulation of the vaccine, the treating doctor's assessment of the medical situation,

and other relevant factors. It is expected that the amount will fall in a relatively broad range that
can be determined through routine trials.
The immunogenic compositions are conventionally administered parenterally, eg. by injection,
either subcutaneously, intramuscularly, or transdermally/transcutaneously (eg. WO98/20734).
Additional formulations suitable for other modes of administration include oral and pulmonary
formulations, suppositories, and transdermal applications. Dosage treatment may be a single dose
schedule or a multiple dose schedule. The vaccine may be administered in conjunction with other
immunoregulatory agents.
As an alternative to protein-based vaccines, DNA vaccination may be employed [eg. Robinson &
Torres (1997) Seminars in Immunology 9:271-283; Donnelly et al. (1997) Annu Rev Immunol
15:617-648; see later herein].
Gene Delivery Vehicles
Gene therapy vehicles for delivery of constructs including a coding sequence of a therapeutic of
the invention, to be delivered to the mammal for expression in the mammal, can be administered
either locally or systemically. These constructs can utilize viral or non-viral vector approaches in
in vivo or ex vivo modality. Expression of such coding sequence can be induced vising endogenous
mammalian or heterologous promoters. Expression of the coding sequence in vivo can be either
constitutive or regulated.
The invention includes gene delivery vehicles capable of expressing the contemplated nucleic acid
sequences. The gene delivery vehicle is preferably a viral vector and, more preferably, a retroviral,
adenoviral, adeno-associated viral (AAV), herpes viral, or alphavirus vector. The viral vector can
also be an astrovirus, coronavirus, orthomyxovirus, papovavirus, paramyxovirus, parvovirus,
picomavirus, poxvirus, or togavinis viial vector. See generally, Jolly (1994) Cancer Gene Therapy
1:51-64; Kimura (1994) Human Gene Therapy 5:845-852; Connelly (1995) Human Gene Therapy
6:185-193; and Kaplitt (1994) Nature Genetics 6:148-153.
Retroviral vectors are well known in the art and we contemplate that any retroviral gene therapy vector
is employable in the invention, including B, C and D type retroviruses, xenotropic retroviruses (for
example,NZB-X1,NZB-X2 and NZB9-1 (see O'Neill (1985) J. Virol. 53:160)polytropic retrovinises

eg. MCF and MCF-MLV (see Kelly (1983) J. Virol. 45:291), spumaviruses and lentiviruses. See RNA
Tumor Viruses, Second Edition, Cold Spring Harbor Laboratory, 1985.
Portions of the retroviral gene therapy vector may be derived from different retroviruses. For
example, retrovector LTRs may be derived from a Murine Sarcoma Virus, a tRNA binding site
from a Rous Sarcoma Virus, a packaging signal from a Murine Leukemia Virus, and an origin of
second strand synthesis from an Avian Leukosis Virus.
These recombinant retroviral vectors may be used to generate transduction competent retroviral
vector particles by introducing them into appropriate packaging cell lines (see US patent
5,591,624). Retrovirus vectors can be constructed for site-specific integration into host cell DNA
by incorporation of a chimeric integrase enzyme into the retroviral particle (see WO96/37626). It
is preferable that the recombinant viral vector is a replication defective recombinant virus.
Packaging cell lines suitable for use with the above-described retrovirus vectors are well known
in the art, are readily prepared (see WO95/30763 and WO92/05266), and can be used to create
producer cell lines (also termed vector cell lines or "VCLs") for the production of recombinant
vector particles. Preferably, the packaging cell lines are made from human parent cells (eg. HT1080
cells) or mink parent cell lines, which eliminates inactivation in human serum.
Preferred retroviruses for the construction of retroviral gene therapy vectors include Avian
Leukosis Virus, Bovine Leukemia, Virus, Murine Leukemia Virus, Mink-Cell Focus-Inducing
Virus, Murine Sarcoma Virus, Reticuloendotheliosis Virus and Rous Sarcoma Virus. Particularly
preferred Murine Leukemia Viruses include 4070A and 1S04A (Hartley and Rowe (1976) J Virol
19:19-25), Abelson (ATCC No. VR-999), Friend (ATCC No. VR-245), Graffi, Gross (ATCC Nol
VR-590), Kirsten, Harvey Sarcoma Virus and Rauscher (ATCC No. VR-998) and Moloney Murine
Leukemia Virus (ATCC No. VR-190). Such retroviruses may be obtained from depositories or
collections such as the American Type Culture Collection ("ATCC") in Rockville, Maryland or
isolated from known sources using commonly available techniques.
Exemplary known retroviral gene therapy vectors employable in this invention include those
described in patent applications GB2200651, EP0415731, EP0345242, EP0334301, WO89/02468;
WO89/05349, WO89/09271, WO90/02806, WO90/07936, WO94/03622, WO93/25698,

WO93/25234, WO93/11230, WO93/10218, WO91/02805, WO91/02825, WO95/07994, US
5,219,740, US 4,405,712, US 4,861,719, US 4,980,289, US 4,777,127, US 5,591,624. See also Vile
(1993) Cancer Res 53:3860-3864; Vile (1993) Cancer Res 53:962-967; Ram (1993) Cancer Res
53 (1993) 83-88; Takamiya (1992) J Neurosci Res 33:493-503; Baba (1993) J Neurosurg
79:729-735; Mann (1983) Cell 33:153; Cane (1984) Proc Natl Acad Sci 81:6349; and Miller (1990)
Human Gene Therapy 1.
Human adenoviral gene therapy vectors are also known in the art and employable in this invention.
See, for example, Berkner (1988) Biotechniques 6:616 and Rosenfeld (1991) Science 252:431, and
WO93/07283, WO93/06223, and WO93/07282. Exemplary known adenoviral gene therapy vectors
employable in this invention include those described in the above referenced documents and in
WO94/12649, WO93/03769, WO93/19191, WO94/28938, WO95/11984, WO95/00655,
WO95/27071, WO95/29993, WO95/34671, WO96/05320, WO94/08026, WO94/11506,
WO93/06223, WO94/24299, WO95/14102, WO95/24297, WO95/02697, WO94/28152,
WO94/24299, WO95/09241, WO95/25807, WO95/05835, WO94/18922 and WO95/09654.
Alternatively, administration of DNA linked to killed adenovirus as described in Curiel (1992)
Hum. Gene Ther. 3:147-154 may be employed. The gene delivery vehicles of the invention also
include adenovirus associated virus (AAV) vectors. Leading and preferred examples of such
vectors for use in this invention are the AAV-2 based vectors disclosed in Srivastava,
WO93/09239. Most preferred AAV vectors comprise the two AAV inverted terminal repeats in
which the native D-sequences are modified by substitution of nucleotides, such that at least 5 native
nucleotides and up to 18 native nucleotides, preferably at least 10 native nucleotides up to 18 native
nucleotides, most preferably 10 native nucleotides are retained and the remaining nucleotides of
the D-sequence are deleted or replaced with non-native nucleotides. The native D-sequences of the
AAV inverted terminal repeats are sequences of 20 consecutive nucleotides in each AAV inverted
terminal repeat (ie. there is one sequence at each end) which are not involved in HP formation. The
non-native replacement nucleotide may be any nucleotide other than the nucleotide found in the
native D-sequence in the same position Oilier employable exemplary AAV vectors are pWP-19,
pWN-1, both of which are disclosed in Nahreini (1993) Gene 124:257-262. Another example of
such an AAV vector is psub201 (see Samdski (1987) J. Virol. 61:3096). Another exemplary AAV
vector is the Double-D ITR vector. Construction of the Double-D ITR vector is disclosed in US
Patent 5,478,745. Still other vectors are those disclosed in Carter US Patent 4,797,368 and

Muzyczka US Patent 5,139,941, Chartejee US Patent 5,474,935, and Kotin WO94/288157. Yet a
further example of an AAV vector employable in this invention is SSV9AFABTKneo, which
contains the AFP enhancer and albumin promoter and directs expression predominantly in the liver.
Its structure and construction are disclosed in Su (1996) Human Gene Therapy 7:463-470.
Additional AAV gene therapy vectors are described in US 5,354,678, US 5,173,414, US 5,139,941,
and US 5,252,479.
The gene therapy vectors of the invention also include herpes vectors. Leading and preferred
examples are herpes simplex virus vectors containing a sequence encoding a thymidine kinase
polypeptide such as those disclosed in US 5,288,641 and EP0176170 (Roizman). Additional
exemplary herpes simplex virus vectors include HFEM/ICP6-LacZ disclosed in WO95/04139
(Wistar Institute), pHSVlac described in Geller (1988) Science 241:1667-1669 and in WO90/09441
and WO92/07945, HSV Us3::pgC-lacZ described in Fink (1992) Human Gene Therapy 3:11-19
and HSV 7134, 2 RH 105 and GAL4 described in EP 0453242 (Breakefield), and those deposited
with the ATCC as accession numbers ATCC VR-977 and ATCC VR-26Q.
Also contemplated are alpha virus gene therapy vectors that can be employed in this invention.
Preferred alpha virus vectors are Sindbis viruses vectors. Togaviruses, Semliki Forest virus (ATCC
VR-67; ATCC VR-1247), Middleberg virus (ATCC VR-370), Ross River virus (ATCC VR-373;
ATCC VR-1246), Venezuelan equine encephalitis virus (ATCC VR923; ATCC VR-1250; ATCC
VR-1249; ATCC VR-532), and those described in US patents 5,091,309, 5,217,879, and
WO92/10578. More particularly, those alpha vims vectors described in US Serial No. 08/405,627,
filed March 15,1995,WO94/21792, WO92/10578, WO95/07994, US 5,091,309 and US 5,217,879
are employable. Such alpha viruses may be obtained from depositories or collections such as the
ATCC in Rockville, Maryland or isolated from known sources using commonly available
techniques. Preferably, alphavirus vectors with reduced cytotoxicity are used (see USSN
08/679640).
DNA vector systems such as eukaryotic layered expression systems are also useful for expressing
the nucleic acids of the invention. See WO95/07994 for a detailed description of eukaryotic layered
expression systems. Preferably, the eukaryotic layered expression systems of the invention are
derived from alphavirus vectors and most preferably from Sindbis viral vectors.

Other viral vectors suitable for use in the present invention include those derived from poliovirus. for
example ATCC VR-58 and those described in Evans, Nature 339 (1989) 385 and Sabin (1973) J. Biol.
Standardization 1:115; rhinovirus, for example ATCC VR-1110 and those described in Arnold (1990)
J Cell Biochem L401; pox viruses such as canary pox virus or vaccinia virus, for example ATCC
VR-111 and ATCC VR-2010 and those described in Fisher-Hoch (1989) Proc Natl Acad Sci 86:317;
Flexner (1989) Ann NY Acad Sci 569:86, Flexner (1990) Vaccine 8:17; in US 4,603,112 and US
4,769,330 and WO89/01973; SV40 virus, for example ATCC VR-305 and those described in
Mulligan (1979) Nature 277:108 and Madzak (1992) J Gen Virol 73:1533; influenza virus, for
example ATCC VR-797 and recombinant influenza viruses made employing reverse genetics
techniques as described in US 5,166,057 and in Enami (1990) Proc Natl Acad Sci 87:3802-3805;
Enami & Palese (1991) J Virol 65:2711-2713 and Luytjes (1989) Cell 59:110, (see also McMichael
(1983) NEJ Med 309:13, and Yap (1978) Nature 273:238 and Nature (1979) 277:108); human
immunodeficiency virus as described in EP-0386882 and in Buchschacher (1992) J. Virol. 66:2731;
measles virus, for example ATCC VR-67 and VR-1247 and those described in EP-0440219; Aura
virus, for example ATCC VR-368; Bebaru virus, for example ATCC VR-600 and ATCC VR-1240;
Cabassou virus, for example ATCC VR-922; Chikungunya virus, for example ATCC VR-64 and
ATCC VR-1241; Fort Morgan Virus, for example ATCC VR-924; Getah virus, for example ATCC
VR-369 and ATCC VR-1243; Kyzylagach virus, for example ATCC VR-927; Mayaro virus, for
example ATCC VR-66; Mucambo virus, for example ATCC VR-580 and ATCC VR-1244; Ndumu
virus, for example ATCC VR-371; Pixuna virus, for example ATCC VR-372 and ATCC VR-1245;
Tonate virus, for example ATCC VR-925; Triniti virus, for example ATCC VR-469; Una virus, for
example ATCC VR-374; Whataroa virus, for example ATCC VR-926; Y-62-33 virus, for example
ATCC VR-375; O'Nyong virus, Eastern encephalitis virus, for example ATCC VR-65 and ATCC
VR-1242; Western encephalitis virus, for example ATCC VR-70, ATCC VR-1251, ATCC VR-622
and ATCC VR-1252; and coronavirus, for example ATCC VR-740 and those described in Hamre
(1966) Proc Soc Exp Biol Med 121:190.
Delivery of the compositions of mis invention into cells is not limited to the above mentioned viral
vectors. Other delivery methods and media may be employed such as, for example, nucleic acid
expression vectors, polycationic condensed DNA linked or unlinked to killed adenovirus alone, for
example see US Serial No. 08/366,787, filed December 30,1994 and Curiel (1992) Hum Gene Ther
3:147-154 ligand linked DNA, for example see Wu (1989) J Biol Chem 264:16985-16987,
eucaryotic cell delivery vehicles cells, for example see US Serial No.08/240,030, filed May 9,

1994, and US Serial No. 08/404,796, deposition of photopolymerized hydrogel materials,
hand-held gene transfer particle gun, as described in US Patent 5,149,655, ionizing radiation as
described in US5,206,152 and in WO92/11033, nucleic charge neutralization or fusion with cell
membranes. Additional approaches are described in Philip (1994) Mol Cell Biol 14:2411-2418 and
in Woffendin (1994) Proc Natl Acad Sci 91:581-1585.
Particle mediated gene transfer may be employed, for example see US Serial No. 60/023,867.
Briefly, the sequence can be inserted into conventional vectors that contain conventional control
sequences for high level expression, and then incubated with synthetic gene transfer molecules such
as polymeric DNA-binding cations like polylysine, protamine, and albumin, linked to cell targeting
ligands such as asialoorosomucoid, as described in Wu & Wu (1987) J. Biol. Chem.
262:4429-4432, insulin as described in Hucked (1990) Biochem Pharmacol 40:253-263, galactose
as described in Plank (1992) Bioconjugate Chem 3:533-539, lactose or transferrin.
Naked DNA may also be employed. Exemplary naked DNA introduction methods are described in
WO 90/11092 and US 5,580,859. Uptake efficiency may be improved using biodegradable latex
beads. DNA coated latex beads are efficiently transported into cells after endocytosis initiation by the
beads. The method may be improved further by treatment of the beads to increase hydrophobicity and
thereby facilitate disruption of the endosome and release of the DNA into the cytoplasm.
Liposomes that can act as gene delivery vehicles are described in US 5,422,120, WO95/13796,
WO94/23697, WO91/14445 and EP-524,968. As described in USSN. 60/023,867, on non-viral
delivery, the nucleic acid sequences encoding a polypeptide can be inserted into conventional
vectors that contain conventional control sequences for high level expression, and then be incubated
with synthetic gene transfer molecules such as polymeric DNA-binding cations like polylysine,
protamine, and albumin, linked to cell targeting ligands such as asialoorosomucoid, insulin,
galactose, lactose, or transferrin. Other delivery systems include the use of liposomes to encapsulate
DNA comprising the gene under the control of a variety of tissue-specific or ubiquitously-active
promoters. Further non-viral delivery suitable for use includes mechanical delivery systems such
as the approach described in Woflfendin et al (1994) Proc. Natl. Acad. Sci. USA
91 (24): 11581 -11585. Moreover, the coding sequence and the product of expression of such can be
delivered through deposition of photopolymerized hydrogel materials. Other conventional methods
for gene delivery that can be used for delivery of the coding sequence include, for example, use of

hand-held gene transfer particle gun, as described in US 5,149,655; use of ionizing radiation for
activating transferred gene, as described in US 5,206,152 and WO92/11033
Exemplary liposome and polycationic gene delivery vehicles are those described in US 5,422,120
and 4,762,915; in WO 95/13796; WO94/23697; and WO91/14445; in EP-0524968; and in Stryer,
Biochemistry, pages 236-240 (1975) W.H. Freeman, San Francisco; Szoka (1980) Biochem
Biophys Ada 600:1; Bayer (1979) Biochem Biophys Ada 550:464; Rivnay (1987) Meth Enzymol
149:119; Wang (1987) Proc Natl Acad Sci 84:7851; Plant (1989) Anal Biochem 176:420.
A polynucleotide composition can comprises therapeutically effective amount of a gene therapy
vehicle, as the term is defined above. For purposes of the present invention, an effective dose will
be from about 0.01 mg/ kg to 50 mg/kg or 0.05 mg/kg to about 10 mg/kg of the DNA constructs
in the individual to which it is administered.
Delivery Methods
Once formulated, the polynucleotide compositions of the invention can be administered (1) directly
to the subject; (2) delivered ex vivo, to cells derived from the subject; or (3) in vitro for expression
of recombinant proteins. The subjects to be treated can be mammals or birds. Also, human subjects
can be treated.
Direct delivery of the compositions will generally be accomplished by injection, either
subcutaneous ly, intraperitoneally, intravenously or intramuscularly or delivered to the interstitial
space of a tissue. The compositions can also be administered into a lesion. Other modes of
administration include oral and pulmonary administration, suppositories, and transdermal or
transcutaneous applications (eg. see WO98/20734), needles, and gene guns or hyposprays. Dosage
treatment may be a single dose schedule or a multiple dose schedule.
Methods for the ex vivo delivery and reimplantation of transformed cells into a subject are known
in the art and described in eg. WO93/14778. Examples of cells useful in ex vivo applications
include, for example, stem cells, particularly hematopoetic, lymph cells, macrophages, dendritic
cells, or tumor cells.

Generally, delivery of nucleic acids for both ex vivo and in vitro applications can be accomplished
by the following procedures, for example, dextran-mediated transfection, calcium phosphate
precipitation, polybrene mediated transfection, protoplast fusion, electroporation, encapsulation of
the polynucleotide(s) in liposomes, and direct microinjection of the DNA into nuclei, all well
known in the art.
Polynucleotide and polypeptide pharmaceutical compositions
In addition to the pharmaceutically acceptable carriers and salts described above, the following
additional agents can be used with polynucleotide and/or polypeptide compositions.
A.Polvpeptides
One example are polypeptides which include, without limitation: asioloorosomucoid (ASOR);
transferrin; asialoglycoproteins; antibodies; antibody fragments; ferritin; interleukins; interferons,
granulocyte, macrophage colony stimulating factor (GM-CSF), granulocyte colony stimulating
factor (G-CSF), macrophage colony stimulating factor (M-CSF), stem cell factor and
erythropoietin. Viral antigens, such as envelope proteins, can also be used. Also, proteins from
other invasive organisms, such as the 17 amino acid pepude from the circumsporozoite protein of
plasmodium falciparum known as RII.
B. Hormones. Vitamins, etc.
Other groups that can be included are, for example: hormones, steroids, androgens, estrogens,
thyroid hormone, or vitamins, folic acid.
C.Polyalkylenes Polysaccharides. etc.
Also, polyalkylene glycol can be included with the desired polynucleotides/polypeptides. In a
preferred embodiment, the polyalkylene glycol is polyethlylene glycol. In addition, mono-, di-, or
polysaccharides can be included. In a preferred embodiment of this aspect, the polysaccharide is
dextran or DEAE-dextran. Also, chitosan and poly(lactide-co-glycolide)
D.Lipids. and Liposomes
The desired polynucleotide/polypeptide can also be encapsulated in lipids or packaged in liposomes
prior to delivery to the subject or to cells derived therefrom.

Lspid encapsulation is generally accomplished using liposomes which are able to stably bind or
entrap and retain nucleic acid. The ratio of condensed polynucleotide to lipid preparation can van'
but will generally be around 1:1 (mg DNA:micromoles lipid), or more of lipid. For a review of the
use of liposomes as carriers for delivery of nucleic acids, see, Hug and Sleight (1991) Biochim.
Biophys. Acta. 1097:1-17; Straubinger( 1983) Meth. Enzymol. 101:512-527.
Liposomal preparations for use in the present invention include cationic (positively charged),
anionic (negatively charged) and neutral preparations. Cationic liposomes have been shown to
mediate intracellular delivery of plasmid DNA (Feigner (1987) Proc. Natl. Acad. Sci. USA
84:7413-7416); mRNA (Malone (1989) Proc. Natl. Acad Sci. USA 86:6077-6081); and purified
transcription factors (Debs (1990) J. Biol. Chem. 265:10189-10192), in functional form.
Cationic liposomes are readily available. For example, N[l-2,3-dioleyloxy)propyl]-N,N,N-triethylammnionium
(DOTMA) liposomes are available under the trademark Lipofectin, from GIBCO BRL, Grand
Island, NY. (See, also, Feigner supra). Other commercially available liposomes include
transfectace (DDAB/DOPE) and DOTAP/DOPE (Boerhinger). Other cationic liposomes can be
prepared from readily available materials using techniques well known in the art. See, eg. Szoka
(1978) Proc Natl. Acad Sci. USA 75:4194-4198; WO90/11092 for a description of the synthesis
of DOTAP (l,2-bis(oleoyloxy)-3 Similarly, anionic and neutral liposomes are readily available, such as from Avanti Polar Lipids
(Birmingham, AL), or can be easily prepared using readily available materials Such materials include
phosphatidyl choline, cholesterol, phosphatidy] ethanolamine, diokoylphosphatidyl choline (DOPC),
dioleoylphosphatidyl glycerol (DOPG), dioleoylphoshatidyl ethanolamuie (DOPE), among others.
These materials can also be mixed with the DOTMA and DOTAP starting materials in appropriate
ratios. Methods for making liposomes using these materials are well known in the art.
The liposomes can comprise multilammelar vesicles (MLVs), small unilamellar vesicles (SUVs),
or large unilamellar vesicles (LUVs). The various liposome-nuclcic acid complexes are prepared
using methods known in the art. See eg. Straubinger (1983) Meth. Immunol. 101:512-527; Szoka
(1978) Proc. Natl. Acad. Sci. USA 75:4194-4198; Papahadjopoulos (1975) Biochm. Biophys. Acta
394:483; Wilson (1979) Cell 17:77); Deamer & Bangham (1976) Biochim. Biophys. Acta 443:629;
Ostro (1977) Biochem. Biophys. Res. Commun. 76:836; Fraley (1979) Proc. Natl. Acad. Sci. USA

76:3348); Enoch & Strittmatter (1979) Proc. Nad. Acad. Sci. USA 76:145; Fraley (1980) J. Biol.
Chem. (1980) 255:10431; Szoka & Papahadjopoulos (1978) Proc. Nail. Acad. Sci USA 75:145:
and Schaefer-Ridder (1982) Science 215:166.
E. Lipoproteins
In addition, lipoproteins can be included with the polynucleotide/polypeptide to be delivered.
Examples of lipoproteins to be utilized include: chylomicrons, HDL, DDL, LDL, and VLDL. Mutants,
fragments, or fusions of these proteins can also be used. Also, modifications of naturally occurring
lipoproteins can be used, such as acetylated LDL. These lipoproteins can target the delivery of
polynucleotides to cells expressing lipoprotein receptors. Preferably, if lipoproteins are including with
the polynucleotide to be delivered, no other targeting ligand is included in the composition.
Naturally occurring lipoproteins comprise a lipid and a protein portion. The protein portion are
known as apoproteins. At the present, apoproteins A, B, C, D, and E have been isolated and
identified. At least two of these contain several proteins, designated by Roman numerals, AI, All,
AIV; CI, CO, CIII.
A lipoprotein can comprise more than one apoprotein. For example, naturally occurring
chylomicrons comprises of A, B, C, and E, over time these lipoproteins lose A and acquire C and
E apoproteins. VLDL comprises A, B, C, and E apoproteins, LDL comprises apoprotein B; and
HDL comprises apoproteins A, C, and £.
The amino acid of these apoproteins are known and are described in, for example, Breslow (1985)
Annu Rev. Biochem 54:699; Law (1986) Adv. Exp Med. Biol. 151:162; Chen (1986) J Biol Chem
261:12918; Kane (1980) Proc Natl Acad Sci USA 77:2465; and Utermann (1984) Hum Genet 65:232.
Lipoproteins contain a variety of lipids including, triglycerides, cholesterol (free and esters), and
phosphoHpids. The composition of the lipids varies in naturally occurring lipoproteins. For
example, chylomicrons comprise mainly triglycerides. A more detailed description of the lipid
content of naturally occurring lipoproteins can be found, for example, in Meih. Enzymol. 128
(1986). The composition of the lipids are chosen to aid in conformation of the apoprotein for
receptor binding activity. The composition of lipids can also be chosen to facilitate hydrophobic
interaction and association with the polynucleotide binding molecule.

Naturally occurring lipoproteins can be isolated from serum by ultracentrifugation, for instance.
Such methods are described in Meth. Enzymol. (supra); Pitas (1980) J. Biochem. 255:5454-5460
and Mahey (1979) J Clin. Invest 64:743-750. Lipoproteins can also be produced by in vitro or
recombinant methods by expression of the apoprotein genes in a desired host cell. See, for example,
Atkinson (1986) Annu Rev Biophys Chem 15:403 and Radding (1958) Biochim Biophys Acta 30:
443. Lipoproteins can also be purchased from commercial suppliers, such as Biomedical
Techniologies, Inc., Stoughton, Massachusetts, USA. Further description of lipoproteins can be
found in Zuckermann et al. PCT/US97/14465.
F.Polvcationic Agents
Polycationic agents can be included, with or without lipoprotein, in a composition with the desired
polynucleotide/polypeptide to be delivered.
Polycationic agents, typically, exhibit a net positive charge at physiological relevant pH and are
capable of neutralizing the electrical charge of nucleic acids to facilitate delivery to a desired
location. These agents have both in vitro, ex vivo, and in vivo applications. Polycationic agents can
be used to deliver nucleic acids to a living subject either intramuscularly, subcutaneously, etc.
The following are examples of useful polypeptides as polycationic agents: polylysinc, polyarginine,
polyomithine, and protamine. Other examples include histones, protamines, human serum albumin,
DNA binding proteins, non-histone chromosomal proteins, coat proteins from DNA viruses, such
as (X174, transcriptional factors also contain domains that bind DNA and therefore may be useful
as nucleic aid condensing agents. Briefly, transcriptional factors such as C/CEBP, c-jun, c-fos,
AP-1, AP-2, AP-3, CPF, Prot-1, Sp-1, Oct-1, Oct-2, CREP, and TFIID contain basic domains that
bind DNA sequences.
Organic polycationic agents include: spermine, spermidine, and purtrescine.
The dimensions and of the physical properties of a polycationic agent can be extrapolated from the
list above, to construct other polypeptide polycationic agents or to produce synthetic polycationic
agents.

Synthetic polycationic agents which are useful include, for example, DEAE-dextran, polybrene.
Lipofectin™, and lipofectAMINE™ are monomers that form polycationic complexes when
combined with polynucleotides/polypeptides.
Immunodiognostic Assays
Neisserial antigens of the invention can be used in immunoassays to detect antibody levels (or,
conversely, anti-Neisserial antibodies can be used to detect antigen levels). Immunoassays based
on well defined, recombinant antigens can be developed to replace invasive diagnostics methods.
Antibodies to Neisserial proteins within biological samples, including for example, blood or serum
samples, can be detected. Design of the immunoassays is subject to a great deal of variation, and
a variety of these are known in the art. Protocols for the immunoassay may be based, for example,
upon competition, or direct reaction, or sandwich type assays. Protocols may also, for example, use
solid supports, or may be by immunoprecipitation. Most assays involve the use of labeled antibody
or polypeptide; the labels may be, for example, fluorescent, chemiluminescent, radioactive, or dye
molecules. Assays which amplify the signals from the probe are also known; examples of which
are assays which utilize biotin and avidin, and enzyme-labeled and mediated immunoassays, such
as ELISA assays.
Kits suitable for immunodiagnosis and containing the appropriate labeled reagents are constructed
by packaging the appropriate materials, including the compositions of the invention, in suitable
containers, along with the remaining reagents and materials (for example, suitable buffers, salt
solutions, etc.) required for the conduct of the assay, as well as suitable set of assay instructions.
Nucleic Acid Hybridisation
"Hybridization" refers to the association of two nucleic acid sequences to one another by hydrogen
bonding. Typically, one sequence will be fixed to a solid support and the other will be free in solution.
Then, the two sequences will be placed in contact with one another under conditions that favor
hydrogen bonding. Factors that affect this bonding include: the type and volume of solvent; reaction
temperature; time of hybridization; agitation; agents to block the non-specific attachment of the liquid
phase sequence to the solid support (Denhardfs reagent or BLOTTO); concentration of the sequences;
use of compounds to increase the rate of association of sequences (dextran sulfate or polyethylene
glycol); and the stringency of the washing conditions following hybridization. See Sambrook et al.
[supra] Volume 2, chapter 9, pages 9.47 to 9.57.

"Stringency" refers to conditions in a hybridization reaction that favor association of very similar
sequences over sequences that differ. For example, the combination of temperature and salt
concentration should be chosen that is approximately 120 to 200°C below the calculated Tm of the
hybrid under study. The temperature and salt conditions can often be determined empirically in
preJiminary experiments in which samples of genomic DNA immobilized on filters are hybridized
to the sequence of interest and then washed under conditions of different stringencies. See
Sambrook et al. at page 9.50.
Variables to consider when performing, for example, a Southern blot are (1) the complexity of the
DNA being blotted and (2) the homology between the probe and the sequences being detected. The
total amount of the fragment(s) to be studied can vary a magnitude of 10, from 0.1 to 1 μg for a
plasmid or phage digest to 10-9 to 10-8 g for a single copy gene in a highly complex eukaryotic
genome. For lower complexity polynucleotides, substantially shorter blotting, hybridization, and
exposure times, a smaller amount of starting polynucleotides, and lower specific activity of probes
can be used. For example, a single-copy yeast gene can be detected with an exposure time of only
1 hour starting with 1 ug of yeast DNA, blotting for two hours, and hybridizing for 4-8 hours with
a probe of 103 cpm/ug. For a single-copy mammalian gene a conservative approach would start
with 10 ug of DNA, blot overnight, and hybridize overnight in the presence of 10% dextran sulfate
using a probe of greater than 108 cpm/ug, resulting in an exposure time of—24 hours.
Several factors can affect the melting temperature (Tm) of a DNA-DNA hybrid between the probe
and the fragment of interest, and consequently, the appropriate conditions for hybridization and
washing. In many cases the probe is not 100% homologous to the fragment. Other commonly
encountered variables include the length and total G+C content of the hybridizing sequences and
the ionic strength and formamide content of the hybridization buffer. The effects of all of these
factors can be approximated by a single equation:
Tm= 81 + 16.6(log10Ci) + 0.4[%(G + C)]-0.6(%formamide) - 600/n-1.5(%mismatch).
where Ci is the salt concentration (monovalent ions) and n is the length of the hybrid in base pairs
(slightly modified from Meinkoth & Wahl (1984) Anal Biochem. 138:267-284).

In designing a hybridization experiment, some factors affecting nucleic acid hybridization can be
conveniently altered. The temperature of the hybridization and washes and the salt concentration
during the washes are the simplest to adjust. As the temperature of the hybridization increases (ie.
stringency), it becomes less likely for hybridization to occur between strands that are
nonhomologous, and as a result, background decreases. If the radiolabeled probe is not completely
homologous with the immobilized fragment (as is frequently the case in gene family and
interspecies hybridization experiments), the hybridization temperature must be reduced, and
background will increase. The temperature of the washes affects the intensity of the hybridizing
band and the degree of background in a similar manner. The stringency of the washes is also
increased with decreasing salt concentrations.
In general, convenient hybridization temperatures in the presence of 50% formamide are 42°C for
a probe with is 95% to 100% homologous to the target fragment, 37°C for 90% to 95% homology,
and 32°C for 85% to 90% homology. For lower homologies, formamide content should be lowered
and temperature adjusted accordingly, using the equation above. If the homology between the probe
and the target fragment are not known, the simplest approach is to start with both hybridization and
wash conditions which are nonstringent If non-specific bands or high background are observed
after autoradiography, the filter can be washed at high stringency and reexposed. If the time
required for exposure makes this approach impractical, several hybridization and/or washing
stringencies should be tested in parallel.
Nucleic Acid Probe Assays
Methods such as PCR, branched DNA probe assays, or blotting techniques utilizing nucleic acid
probes according to the invention can determine the presence of cDNA or mRNA. A probe is said
to "hybridize" with a sequence of the invention if it can form a duplex or double stranded complex,
which is stable enough to be detected.
The nucleic acid probes will hybridize to the Neisserial nucleotide sequences of the invention
(including both sense and antisense stnmds). Though many different nucleotide sequences will
encode the amino acid sequence, the native Neisserial sequence is preferred because it is the actual
sequence present in cells. mRNA represents a coding sequence and so a probe should be
complementary to the coding sequence; single-stranded cDNA is complementary to mRNA, and
so a cDNA probe should be complementary to the non-coding sequence.

The probe sequence need not be identical to the Neisserial sequence (or its complement) — some
variation in the sequence and length can lead to increased assay sensitivity if the nucleic acid probe
can form a duplex with target nucleotides, which can be detected. Also, the nucleic acid probe can
include additional nucleotides to stabilize the formed duplex. Additional Neisserial sequence may
also be helpful as a label to detect the formed duplex. For example, a non-complementary
nucleotide sequence may be attached to the 5' end of the probe, with the remainder of the probe
sequence being complementary to a Neisserial sequence. Alternatively, non-complementary bases
or longer sequences can be interspersed into the probe, provided that the probe sequence has
sufficient complementarity with the a Neisserial sequence in order to hybridize therewith and
thereby form a duplex which can be detected.
The exact length and sequence of the probe will depend on the hybridization conditions, such as
temperature, salt condition and the like. For example, for diagnostic applications, depending on the
complexity of the analyte sequence, the nucleic acid probe typically contains at least 10-20
nucleotides, preferably 15-25, and more preferably at least 30 nucleotides, although it may be
shorter than this. Short primers generally require cooler temperatures to form sufficiently stable
hybrid complexes with the template.
Probes may be produced by synthetic procedures, such as the triester method of Matteucci et al.
[J. Am. Chem. Soc. (1981) 103:3185], or according to Urdea et al. [Proc. Natl. Acad. Sci. USA
(1983) 80: 7461], or using commercially available automated oligonucleotide synthesizers.
The chemical nature of the probe can be selected according to preference. For certain applications,
DNA or RNA are appropriate. For other applications, modifications may be incorporated eg.
backbone modifications, such as phosphorothioates or rnethylphosphonates, can be used to increase
in vivo half-life, alter RNA affinity, increase nuclease resistance etc. [eg. see Agrawal & Iyer
(1995) Curr Opin Biotechnol 6:12-19; Agrawal (1996) TIBTECH 14376-387]; analogues such as
peptide nucleic acids may also be used [eg. see Corey (1997) TIBTECH 15:224-229; Buchardt et
al. (1993) TIBTECH 11:384-386J.
Alternatively, the polymerase chain reaction (PCR) is another well-known means for detecting
small amounts of target nucleic acids. The assay is described in: Mullis et al. [Meth. Enzymol.
(1987) 155: 335-350]; US patents 4,683,195 and 4,683,202. Two "primer" nucleotides hybridize

with the target nucleic acids and are used to prime the reaction. The primers can comprise sequence
that does noi hybridize to the sequence of the amplification target (or its complement) to aid with
duplex stability or, for example, to incorporate a convenient restriction site. Typically, such
sequence will flank the desired Neisserial sequence.
A thermostable polymerase creates copies of target nucleic acids from the primers using the
original target nucleic acids as a template. After a threshold amount of target nucleic acids are
generated by the polymerase, they can be detected by more traditional methods, such as Southern
blots. When using the Southern blot method, the labelled probe will hybridize to the Neisserial
sequence (or its complement).
Also, mRNA or cDNA can be detected by traditional blotting techniques described in Sambrook
et al [supra]. mRNA, or cDNA generated from mRNA using a polymerase enzyme, can be purified
and separated using gel electrophoresis. The nucleic acids on the gel are then blotted onto a solid
support, such as nitrocellulose. The solid support is exposed to a labelled probe and then washed
to remove any unhybridized probe. Next, the duplexes containing the labeled probe are detected.
Typically, the probe is labelled with a radioactive moiety.
BRIEF DESCRIPTION OF THE ACCOMPANYING DRAWINGS
Figures 1-7 show biochemical data and sequence analysis pertaining to Examples 1, 2, 3, 7, 13,
16 and 19, respectively, with ORFs 40,38,44, 52,114,41 and 124.. Ml and M2 are molecular
weight markers. Arrows indicate the position of the main recombinant product or, in Western blots,
the position of the main N.meningitidis immunoreactive band. TP indicates N.meningitidis total
protein extract; OMV indicates N.meningitidis outer membrane vesicle preparation. In bactericidal
assay results: a diamond (♦) shows preimmune data; a triangle (A) shows GST control data; a
circle (•) shows data with recombinant N.meningitidis protein. Computer analyses show a
hydrophilicity plot (upper), an antigenic index plot (middle), and an AMPHI analysis (lower). The
AMPHI program has been used to predict T-cell epitopes [Gao et al (1989) J. Immunol. 143:3007;
Roberts et al. (1996) AIDS Res Hum Rctrovir 12:593; Quakyi et al. (1992) Scand J Immunol
suppl.l 1:9) and is available in the Protean package of DNASTAR, Inc. (1228 South Park Street,
Madison, Wisconsin 53715 USA).

EXAMPLES
The examples describe nucleic acid sequences which have been identified in N.meningitidis. along
with their putative translation products. Not all of the nucleic acid sequences are complete ie. they
encode less than the full-length wild-type protein It is believed at present that none of the DNA
sequences described herein have significant homologs in N.gonorrhoeae.
The examples are generally in the following format:
• a nucleotide sequence which has been identified in N.meningitidis (strain B)
• the putative translation product of this sequence
• a computer analysis of the translation product based on database comparisons
• a corresponding gene and protein sequence identified in N.meningitidis (strain A)
• a description of the characteristics of the proteins which indicates that they might be
suitably antigenic
• results of biochemical analysis (expression, purification, ELISA.FACS etc.)
The examples typically include details of sequence homology between species and strains. Proteins
that are similar in sequence are generally similar in both structure and function, and the homology
often indicates a common evolutionary origin. Comparison with sequences of proteins of known
function is widely used as a guide for the assignment of putative protein function to a new sequence
and has proved particularly useful in whole-genome analyses.
Sequence comparisons were performed at NCBI (http://www.ncbi.nlm.nih.gov) using the
algorithms BLAST, BLAST2, BLASTn, BLASTp, tBLASTn, BLASTx, & tBLASTx [eg. see also
Altschul et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database
search programs. Nucleic Acids Research 23:2289-3402]. Searches were performed against the
following databases; non-redundant GenBank+EMBL+DDB J+PDB sequences and non-redundant
GenBank CDS translations+PDB+SwissProt+SPupdate+PIR sequences
Dots within nucleotide sequences (eg. position 288 in Example 12) represent nuckotides which
have been arbitrarily introduced in order to maintain a reading frame. In the same way. double-
underlined nucleotides were removed. Lower case letters (eg. position 589 in Example 12)
represent ambiguities which arose during alignment of independent sequencing reactions (some of

the nucleotide sequences in the examples are derived from combining the results of two or more
experiments).
Nucleotide sequences were scanned in all six reading frames to predict the presence of hydrophobic
domains using an algorithm based on the statistical studies of Esposti et al. [Critical evaluation of
the hydropathy of membrane proteins (1990) Eur J Biochem 190:207-219]. These domains
represent potential transmembrane regions or hydrophobic leader sequences.
Open reading frames were predicted from fragmented nucleotide sequences using the program
ORFFINDER (NCBI).
Underlined amino acid sequences indicate possible transmembrane domains or leader sequences
in the ORFs, as predicted by the PSORT algorithm (http://www.psort.nibb.ac.jp). Functional
domains were also predicted using the MOTIFS program (GCG Wisconsin & PROSITE).
Various tests can be used to assess the in vivo immunogenicity of the proteins identified in the
examples. For example, the proteins can be expressed recombinantly and used to screen patient sera
by immunoblot. A positive reaction between the protein and patient serum indicates that the patient
has previously mounted an immune response to the protein in question ie. the protein is an
immunogen. This method can also be used to identify immunodominant proteins.
The recombinant protein can also be conveniently used to prepare antibodies eg. in a mouse. These
can be used for direct confirmation that a protein is located on the cell-surface. Labelled antibody
(eg. fluorescent labelling for FACS) can be incubated with intact bacteria and the presence of label
on the bacterial surface confirms the location of the protein.
In particular, the following methods (A) to (S) were used to express, purify and biochemically
characterise the proteins of the invention:
A) Chromosomal DNA preparation
N.meningitidis strain 2996 was grown to exponential phase in 100ml of GC medium, harvested by
centrifugation, and resuspended in 5ml buffer (20% Sucrose, 50mM Tris-HCl, 50mM EDTA, pH8).
After 10 minutes incubation on ice, the bacteria were lysed by adding 10ml lysis solution (50mM
NaCl, 1% Na-Sarkosyl, 50μg/ml Proteinase K), and the suspension was incubated at 37°C for 2

hours. Two phenol extractions (equilibrated to pH 8) and one ChCl3/isoamylalcohol (24:1)
extraction were performed. DNA was precipitated by addition of 0.3M sodium acetate and 2
volumes ethanol, and was collected by centrifugation. The pellet was washed once with 70%
ethanol and redissolved in 4ml buffer (lOmM Tris-HCl, lmM EDTA, pH 8). The DNA
concentration was measured by reading the OD at 260 nm.
B) Oligonucleotide design
Synthetic oligonucleotide primers were designed on the basis of the coding sequence of each ORF,
using (a) the meningococcus B sequence when available, or (b) the gonococcus/meningococcus A
sequence, adapted to the codon preference usage of meningococcus as necessary. Any predicted
signal peptides were omitted, by deducing the 5'-end amplification primer sequence immediately
downstream from the predicted leader sequence.
The 5' primers included two restriction enzyme recognition sites (Bam Hi-Ndel, BamHI-Nhel, or
EcoRI-NheI, depending on the gene's own restriction pattern); the 3' primers included a Xhorestriction site. This procedure was established in order to direct the cloning of each amplification
product (corresponding to each ORF) into two different expression systems: pGEX-KG (using
cither BamHI-XhoI or EcoRI-XhoI), and pET21b+ (using either NdeI-XhoI or NheI-XhoI).

As well as containing the restriction enzyme recognition sequences, the primers included
nucleotides which hybridised to the sequence to be amplified. The number of hybridizing
nucleoudes depended on the melting temperature of the whole primer, and was determined for each
primer using the formulae:

The average melting temperature of the selected oligos were 65-70°C for the whole oligo and
50-55°C for the hybridising region alone.

Table 1 shows the forward and reverse primers used for each amplification. Oligos were
synthesized by a Perkin Elmer 394 DNA/RNA Synthesizer, eluted from the columns in 2ml
NH4OH, and deprotected by 5 hours incubation at 56°C. The oligos were precipitated by addition
of 0.3M Na-Acetate and 2 volumes ethanol. The samples were then centrifuged and the pellets
resuspended in either 100μl or lml of water. OD260 was determined using a Perkin Elmer Lambda
Bio spectrophotometer and the concentration was determined and adjusted to 2-10pmol/μl.
C) Amplification
The standard PCR protocol was as follows: 50-200ng of genomic DNA were used as a template
in the presence of 20-40μM of each oligo, 400-800uM dNTPs solution, 1x PCR buffer (including
1.5mM MgCl2), 2.5 units TaqI DNA polymerase (using Perkin-Elmer AmpliTaQ, GIBCO
Platinum, Pwo DNA polymerase, or Tahara Shuzo Taq polymerase).
In some cases, PCR was optimised by the addition of 10μl DMSO or 50μl 2M betaine.
After a hot start (adding the polymerase during a preliminary 3 minute incubation of the whole mix
at 95°C), each sample underwent a double-step amplification: the first 5 cycles were performed
using as the hybridization temperature the one of the oligos excluding the restriction enzymes tail,
followed by 30 cycles performed according to the hybridization temperature of the whole length
oligos. The cycles were followed by a final 10 minute extension step at 72°C.



The amplifications were performed using either a 9600 or a 2400 Perkin Elmer GeneAmp PCR
System. To check the results, 1/10 of the amplification volume was loaded onto a 1-1.5% agarose
gel and the size of each amplified fragment compared with a DNA molecular weight marker.
The amplified DNA was either loaded directly on a 1 % agarose gel or first precipitated with ethanol
and resuspended in a suitable volume to be loaded on a 1% agarose gel. The DNA fragment
corresponding to the right size band was then eluted and purified from gel, using the Qiagen Gel
Extraction Kit, following the instructions of the manufacturer. The final volume of the DNA
fragment was 30μl or 50μl of either water or 10mM Tris, pH 8.5.
D) Digestion of PCR fragments
The purified DNA corresponding to the amplified fragment was split into 2 aliquots and double-
digested with:
- NdeI/XhoI or NheI/XhoI for cloning into pET-21 b+ and further expression of the protein
as a C-terminus His-tag fusion
- BamHI/XhoI or EcoRI/XhoI for cloning into pGEX-KG and further expression of the
protein as N-terminus GST fusion.
- EcoRI/PstI, EcoRI/Sall, Sall/PstI for cloning into pGex-His and further expression of
the protein as N-terminus His-tag fusion
Each purified DNA fragment was incubated (37°C for 3 hours to overnight) with 20 units of each
restriction enzyme (New England Biolabs) in a either 30 or 40μl final volume in the presence of
the appropriate buffer. The digestion product was then purified using the QlAquick PCR
purification kit, following the manufacturer's instructions, and eluted in a final volume of 30 or
50μl of cither water or 10mM Tris-HCl, pH 8.5. The final DNA concentration was determined by
1% agarose gel electrophoresis in the presence of titrated molecular weight marker.
E) Digestion of the cloning vector* (pET22B, pGEX-KG, pTRC-His A, and pGex-His)
10μg plasmid was double-digested with SO units of each restriction enzyme in 200μl reaction
volume in the presence of appropriate buffer by overnight incubation at 37°C. After loading the

whole digestion on a 1% agarose gel, the band corresponding to the digested vector was purified
from the gel using the Qiagen QIAquick Gel Extraction Kit and the DNA was eluted in 50μl of
10mM Tris-HCl, pH 8.5. The DNA concentration was evaluated by measuring OD260 of the sample,
and adjusted to 50μg/μl. 1 μl of plasmid was used for each cloning procedure.
The vector pGEX-His is a modified pGEX-2T vector carrying a region encoding six histidine
residues upstream to the thrombin cleavage site and containing the multiple cloning site of the
vector pTRC99 (Pharmacia).
F) Cloning
The fragments corresponding to each ORF, previously digested and purified, were ligated in both pET22b
and pGEX-KG. In a final volume of 20μl, a molar ratio of 3:1 fragment/vector was ligated using 0.5μ1
of NEB T4 DNA ligase (400 units/μl), in the presence of the buffer supplied by the manufacturer.
The reaction was incubated at room temperature for 3 hours. In some experiments, ligation was
performed using the Boehringer "Rapid Ligation Kit", following the manufacturer's instructions.
In order to introduce the recombinant plasmid in a suitable strain, 100μl E. coli DH5 competent
cells were incubated with the ligase reaction solution for 40 minutes on ice, then at 37°C for 3
minutes, then, after adding 800μl LB broth, again at 37°C for 20 minutes. The cells were then
centrifuged at maximum speed in an Eppendorf microfuge and resuspended in approximately 200μl
of the supernatant The suspension was then plated on LB ampicillin (100mg/ml).
The screening of the recombinant clones was performed by growing 5 randomly-chosen colonies
overnight at 37°C in either 2ml (pGEX or pTC clones) or 5ml (pET clones) LB broth + 100μg/ml
ampicillin. The cells were then pelletted and the DNA extracted using the Qiagen QIAprep Spin
Mmiprep Kit, following the manufacturer's instructions, to a final volume of 30μl 5μl of each
individual mmiprep (approximately 1g) were digested with either NdeIVXhol or BamHUXhol and
the whole digestion loaded onto a 1 -1.5% agarose gel (depending on the expected insert size), in
parallel with the molecular weight marker (1Kb DNA Ladder, GIBCO). The screening of the
positive clones was made on the base of the correct insert size.

G) Expression
Each ORF cloned into the expression vector was transformed into the strain suitable for expression
of the recombinant protein product, 1μl of each construct was used to transform 30ul of E. coli
BL21 (pGEX vector), Exoli TOP 10 (pTRC vector) or E.coli BL21-DE3 (pET vector), as described
above. In the case of the pGEX-His vector, the same E.coli strain (W3110) was used for initial
cloning and expression. Single recombinant colonies were inoculated into 2ml LB+Amp
(100μg/ml), incubated at 37°C overnight, then diluted 1:30 in 20ml of LB+Amp (100μg/ml) in
100ml flasks, making sure that the OD600 ranged between 0.1 and 0.15. The flasks were incubated
at 30°C into gyratory water bath shakers until OD indicated exponential growth suitable for
induction of expression (0.4-0.8 OD for pET and pTRC vectors; 0.8-1 OD for pGEX and pGEX-
His vectors). For the pET, pTRC and pGEX-His vectors, the protein expression was induced by
addition of 1mM IPTG, whereas in the case of pGEX system the final concentration of IPTG was
0.2mM. After 3 hours incubation at 30°C, the final concentration of the sample was checked by
OD. In order to check expression, 1ml of each sample was removed, centrifuged in a microfuge,
the pellet resuspended in PBS, and analysed by 12% SDS-PAGE with Coomassie Blue staining.
The whole sample was centrifuged at 6000g and the pellet resuspended in PBS for further use.
H) GST-fusion proteins large-scale purification.
A single colony was grown overnight at 37°C on LB+Amp agar plate. The bacteria were inoculated
into 20ml of LB+Amp liquid culture in a water bath shaker and grown overnight. Bacteria were
diluted 1:30 into 600ml of fresh medium and allowed to grow at the optimal temperature (20-37°C)
to OD550 0.8-1. Protein expression was induced with 0.2mM IPTG followed by three hours
incubation. The culture was centrifuged at 8000rpm at 4°C. The supernatant was discarded and the
bacterial pellet was resuspended in 7.5ml cold PBS. The cells were disrupted by sonication on ice
for 30 sec at 40W using a Branson sonifier B-15, frozen and thawed twice and centrifuged again.
The supernatant was collected and mixed with 150μl Glutanone-Sepharose 4B resin (Pharmacia)
(previously washed with PBS) and incubated at room temperature for 30 minutes. The sample was
centrifuged at 700g for 5 minutes at 4oC The resin was washed twice with 10ml cold PBS for 10
minutes, resuspended in lml cold PBS, and loaded on a disposable column. The resin was washed
twice with 2ml cold PBS until the flow-through reached OD280, of 0.02-0.06. The GST-fusion
protein was eluted by addition of 700μl cold Glutathione elution buffer (10mM reduced


glutathione, 50mM Tris-HCi) and fractions collected until the OD28() was 0.1. 21 μl of each fraction
were loaded on a 12% SDS gel using either Biorad SDS-PAGE Molecular weight standard broad
range (Ml) (200, 116.25, 97.4, 66.2, 45, 31, 21.5, 14.4, 6.5 kDa) or Amersham Rainbow Marker
(M2) (220, 66, 46, 30, 21.5, 14.3 kDa) as standards. As the MW of GST is 26kDa, this value must
be added to the MW of each GST-fusion protein.
I) His-fusion solubility analysis
To analyse the solubility of the His-fusion expression products, pellets of 3ml cultures were
resuspended in buffer M1 [500ul PBS pH 7.2]. 25μl lysozyme (lOmg/ml) was added and the
bacteria were incubated for 15 min at 4°C. The pellets were sonicated for 30 sec at 40W using a
Branson sonifier B-15, frozen and thawed twice and then separated again into pellet and
supernatant by a centrifugation step. The supernatant was collected and the pellet was resuspended
in buffer M2 [8M urea, 0.5M NaCl, 20mM imidazole and 0.1M NaH3 PO4] and incubated for 3 to
4 hours at 4°C. After centrifugation, the supernatant was collected and the pellet was resuspended
in buffer M3 [6M guanidinium-HCl, 0.5M NaCl, 20mM imidazole and 0.1M NaH2PO4] overnight
at 4°C. The supernatants from all steps were analysed by SDS-PAGE.
J) His-fusion large-scale purification.
A single colony was grown overnight at 37°C on a LB + Amp agar plate. The bacteria were
inoculated into 20ml of LB+Amp liquid culture and incubated overnight in a water baft shaker.
Bacteria were diluted 1:30 into 600ml fresh medium and allowed to grow at the optimal
temperature (20-37°C) to OD550 0.6-0.8. Protein expression was induced by addition of 1mM IPTG
and the culture further incubated for three hours. The culture was centrifuged at 8000rpm at 4°C,
the supernatant was discarded and the bacterial pellet was resuspended in 7.5ml of either (i) cold
buffer A (300mM NaCl, 50mM phosphate buffer, 10mM imidazole, pH 8) for soluble proteins or
(ii) buffer B (urea 8M, 10mM Tris-HCl, 100mM phosphate buffer, pH 8.8) for insoluble proteins.
The cells were disrupted by sonication on ice for 30 sec at 40W using a Branson sonifier B-15,
frozen and thawed two times and centrifuged again.

For insoluble proteins, the supernatant was stored at -20°C, while the pellets were resuspended in 2ml
buffer C (6M guanidine hydrochloride, 10mM phosphate buffer, 10mM Tris-HCl, pH 7.5) and
treated in a homogenizer for 10 cycles. The product was centrifuged at 13000rpm for 40 minutes.
Supematants were collected and mixed with 150μl Ni2+-resin (Pharmacia) (previously washed with
either buffer A or buffer B, as appropriate) and incubated at room temperature with gentle agitation
for 30 minutes. The sample was centrifuged at 700g for 5 minutes at 4°C. The resin was washed
twice with 10ml buffer A or B for 10 minutes, resuspended in 1ml buffer A or B and loaded on a
disposable column. The resin was washed at either (i) 4°C with 2ml cold buffer A or (ii) room
temperature with 2ml buffer B, until the flow-through reached OD280 of 0.02-0.06.
The resin was washed with either (i) 2ml cold 20mM imidazole buffer (300mM NaCl, 50mM
phosphate buffer, 20mM imidazole, pH 8) or (ii) buffer D (urea 8M, lOmM Tris-HCI, lOOmM
phosphate buffer, pH 6.3) until the flow-through reached the O.D210 of 0.02-0.06. The His-fusion
protein was eluted by addition of 700μl of either (i) cold elution buffer A (300mM NaCl, 50mM
phosphate buffer, 250mM imidazole, pH 8) or (ii) elution buffer B (urea 8M, lOmM Tris-HCl,
lOOmM phosphate buffer, pH 4.5) and fractions collected until the O.D280 was 0.1. 21μl of each
fraction were loaded on a 12% SDS gel.
K) His-fusion proteins renaturation
10% glyceroi was added to the denatured proteins. The proteins were then diluted to 20ug/ml using
dialysis buffer 1(10% giyceroi, O.SM arginine, 50mM phosphate buffer, SmM reduced glutathione,
0.5mM oxidised glutathione, 2M urea, pH 8.8) and dialysed against the same buffer at 4°C for 12-
14 hours. The protein was further dialysed against dialysis buffer II (10% giyceroi, O.SM arginine,
50mM phosphate buffer, SmM reduced glutathione, 0.5mM oxidised glutathione, pH 8.8) for 12-14
hours at 4°C. Protein concentration was evaluated using the formula:
Protein (mg/ml) = (1.55 x OD280) - (0.76 x OD280)
L) His-fusion large-teak purification
500ml of bacterial cultures were induced and the fusion proteins were obtained soluble in buffer
M1, M2 or M3 using the procedure described above. The crude extract of the bacteria was loaded

onto a Ni-NTA superflow column (Qiagen) equilibrated with buffer Ml, M2 or M3 depending on
the solubilization buffer of the fusion proteins. Unbound material was eluted by washing the
column with the same buffer. The specific protein was eluted with the corresponding buffer
containing 500mM imidazole and dialysed against the corresponding buffer without imidazole.
After each run the columns were sanitized by washing with at least two column volumes of 0.5 M
sodium hydroxide and reequilibrated before the next use.
M) Mice immunisations
20ug of each purified protein were used to immunise mice intraperitoneally. In the case of ORF 44,
CD1 mice were immunised with Al(OH)3 as adjuvant on days 1,21 and 42, and immune response
was monitored in samples taken on day 56. For ORF 40, CD1 mice were immunised using
Freund's adjuvant, rather than Al(OH)3, and the same immunisation protocol was used, except that
the immune response was measured on day 42, rather than 56. Similarly, for ORF 38, CD1 mice
were immunised with Freund's adjuvant, but the immune response was measured on day 49.
N) ELISA assay (sera analysis)
The acapsulated MenB M7 strain was plated on chocolate agar plates and incubated overnight at
37°C. Bacterial colonies were collected from the agar plates using a sterile dracon swab and
inoculated into 7ml of Mueller-Hinton Broth (Difco) containing 0.25% Glucose. Bacterial growth
was monitored every 30 minutes by following OD620. The bacteria were let to grow until the OD
reached the value of 0.3-0.4. The culture was centrifuged for 10 minutes at 10000rpm. The
supernatant was discarded and bacteria were washed once with PBS, resuspended in PBS
containing 0.025% formaldehyde, and incubated for 2 hours at room temperature and then
overnight at 4°C with stirring. 100μl bacterial cells were added to each well of a 96 well Greiner
plate and incubated overnight at 4°C. The wells were then washed three times with PBT washing
buffer (0.1% Tween-20 in PBS). 200μl of saturation buffer (2.7% Polyvinylpyrrolidone 10 in
water) was added to each well and the plates incubated for 2 hours at 37°C. Wells were washed
three times with PBT. 200ul of diluted sera (Dilution buffer 1% BSA, 0.1% Tween-20,0.1% NaN3
in PBS) were added to each well and the plates incubated for 90 minutes at 37°C. Wells were
washed three times with PBT. 100μl of HRP-conjugated rabbit anti-mouse (Dako) serum diluted
1:2000 in dilution buffer were added to each well and the plates were incubated for 90 minutes at

37°C. Wells were washed three times with PBT buffer. 100μ1 of substrate buffer for HRP (25ml
of citrate buffer pH5, 10mg of O-phenildiamine and 10μl of H2O) were added to each well and the
plates were left at room temperature for 20 minutes. 100μl H2SO4 was added to each well and OD490
was followed. The EL1SA was considered positive when OD490 was 2.5 times the respective
pre-immune sera.
O) FACScan bacteria Binding Assay procedure.
The acapsulated MenB M7 strain was plated on chocolate agar plates and incubated overnight at
37°C. Bacterial colonies were collected from the agar plates using a sterile dracon swab and
inoculated into 4 tubes containing 8ml each Mueller-Hinton Broth (Difco) containing 0.25%
glucose. Bacterial growth was monitored every 30 minutes by following ODW0. The bacteria were
let to grow until the OD reached the value of 0.35-0.5. The culture was centrifuged for 10 minutes
at 4000rpm. The supernatant was discarded and the pellet was resuspended in blocking buffer (1%
BSA, 0.4% NaN3) and centrifuged for 5 minutes at 4000rpm. Cells were resuspended in blocking
buffer to reach OD620 of 0.07. 100μl bacterial cells were added to each well of a Costar 96 well
plate. lOOuJ of diluted (1:200) sera (in blocking buffer) were added to each well and plates
incubated for 2 hours at 4oC. Cells were centrifuged for 5 minutes at 4000rpm, the supernatant
aspirated and cells washed by addition of 200μl/well of blocking buffer in each well. 100μl of R-
Phicoerytrin conjugated F(ab)2 goat anti-mouse, diluted 1:100, was added to each well and plates
incubated for 1 hour at 4°C. Cells were spun down by centrifugation at 4000rpm for 5 minutes and
washed by addition of 200μl/well of blocking buffer. The supernatant was aspirated and cells
resuspended in 200μl/well of PBS, 025% formaldehyde. Samples were transferred to FACScan
tubes and read. The condition for FACScan setting were: FL1 on, FL2 and FL3 off; FSC-H
threshold:92; FSC PMT Voltage: E 02; SSC PMT: 474; Amp. Gains 7.1; FL-2 PMT: 539;
compensation values: 0.
P) OMV preparations
Bacteria were grown overnight on 5 GC plates, harvested with a loop and resuspended in 10ml 20mM
Tris-HCl. Heat inactivation was performed at 56°C for 30 minutes and the bacteria disrupted by
sonication for 10 minutes on ice (50% duty cycle, 50% output). Unbroken cells were removed by
centrifugation at 5000g for 10 minutes and the total cell envelope fraction recovered by centrifugation

at 50000g at 4°C for 75 minutes. To extract cytoplasmic membrane proteins from the crude outer
membranes, the whole fraction was resuspended in 2% sarkosyl (Sigma) and incubated at room
temperature for 20 minutes. The suspension was centrifuged at 10000g for 10 minutes to remove
aggregates, and the supernatant further ultracentrifuged at 50000g for 75 minutes to pellet the outer
membranes. The outer membranes were resuspended in 10mM Tris-HCl, pH8 and the protein
concentration measured by the Bio-Rad Protein assay, using BSA as a standard.
Q) Whole Extracts preparation
Bacteria were grown overnight on a GC plate, harvested with a loop and resuspended in 1ml of
20mM Tris-HCl. Heat inactivation was performed at 56°C for 30 minutes.
R) Western blotting
Purified proteins (500ng/lane), outer membrane vesicles (5μg) and total cell extracts (25μg) derived
from MenB strain 2996 were loaded on 15% SDS-PAGE and transferred to a nitrocellulose
membrane. The transfer was performed for 2 hours at 150mA at 4°C, in transferring buffer (0.3 %
Tris base, 1.44 % glycine, 20% methanol). The membrane was saturated by overnight incubation
at 4°C in saturation buffer (10% skimmed milk, 0.1 % Triton X100 in PBS). The membrane was
washed twice with washing buffer (3% skimmed milk, 0.1 % Triton X100 in PBS) and incubated
for 2 hours at 37°C with mice sera diluted 1:200 in washing buffer. The membrane was washed
twice and incubated for 90 minutes with a 1:2000 dilution of horseradish peroxidase labelled anti-
mouse Ig. The membrane was washed twice with 0.1% Triton X100 in PBS and developed with
the Opti-4CN Substrate Kit (Bio-Rad). The reaction was stopped by adding water.
S) Bactericidal assay
MC58 strain was grown overnight at 37°C on chocolate agar plates. 5-7 colonies were collected and
used to inoculate 7ml Muelier-Hinton broth. The suspension was incubated at 37°C on a nutator
and let to grow until OD620, was 0.5-0.8. The culture was aliquoted into sterile 1.5ml Eppendorf
tubes and centrifuged for 20 minutes at maximum speed in a microfuge. The pellet was washed
once in Gey's buffer (Gibco) and resuspended in the same buffer to an OD6M of 0.5, diluted
1:20000 in Gey's buffer and stored at 25°C.











results of expression of the GST-fusion in E.coli. Purified His-fusion protein was used to immunise
mice, whose sera were used for FACS analysis (Figure 1C), a bactericidal assay (Figure 1D), and
ELISA (positive result). These experiments confirm that ORF40-1 is a surface-exposed protein, and
that it is a useful immunogen.





ORF38-1 (32kDa) was cloned in pET and pGex vectors and expressed in Exoli, as described
above. The products of protein expression and purification were analyzed by SDS-PAGE. Figure
2A shows the results of affinity purification of the His-fusion protein, and Figure 2B shows the
results of expression of the GST-fusion in Exoli. Purified His-fusion protein was used to immunise
mice, whose sera were used for Western blot analysis (Figure 2C) and FACS analysis (Figure 2D).
These experiments confirm that ORF38-1 is a surface-exposed protein, and that it is a useful
immunogen.
Figure 2E shows plots of hydrophilicity, antigenic index, and AMPHI regions for ORF38-1.
Example 3
The following N.meningitidis DNA sequence was identified :



LecA 194 TTNAMDSANYRSQDIIVSAPNGQMLYKDCSF 224
Based on homology with the adhesin, it was predicted that this protein from N.meningitidis. and
its epitopes, could be useful antigens for vaccines or diagnostics.
ORF44-1 (11.2kDa) was cloned in pET and pGex vectors and expressed in E.coli, as described
above. The products of protein expression and purification were analyzed by SDS-PAGE. Figure
3 A shows the results of affinity purification of the His-fusion protein, and Figure 3B shows the
results of expression of the GST-fusion in E.coli. Purified His-fusion protein was used to immunise
mice, whose sera were used for ELISA, which gave positive results, and for a bactericidal assay
(Figure 3C). These experiments confirm that ORF44-1 is a surface-exposed protein, and that it is
a useful immunogen.
Figure 3D shows plots of hydrophilicity, antigenic index, and AMPHI regions for ORF44-1.








Computer analysis predicts two transmembrane domains and also indicates that ORF50 has no
significant amino acid homology with known proteins.
Based on the presence of a putative transmembrane domain, it is predicted that this protein from
N.meningitidis, and its epitopes, could be useful antigens for vaccines or diagnostics.











Computer analysis of this amino acid sequence predicts a prokaryotic membrane lipoprotein lipid
attachment site (underlined).
ORF52-1 (7kDa) was cloned in the pGex vectors and expressed in E.coli, as described above. The
products of protein expression and purification were analyzed by SDS-PAGE. Figure 4 A shows
the results of affinity purification of the GST-fusion. Figure 4B shows plots of hydrophilicity,
antigenic index, and AMPHI regions for ORF52-1.
Based on this analysis, it is predicted that this protein from N.meningitidis, and its epitopes, could
be useful antigens for vaccines or diagnostics.





Computer analysis of this amino acid sequence predicts a transmembrane region.
A corresponding ORF from strain A of N.meningitidis was also identified:










orf 112-1 LKLFGGICXGLLFHLAGRLFGFTSQL
Based on this analysis, it is predicted that this protein from N.meningitidis, and its epitopes. could
be useful antigens for vaccines or diagnostics.

















Amino acids 1-1423 of ORF114-1 were cloned in the pGex vector ami expressed in E.colit as
described above. GST-fusion expression was visible using SDS-PAGE, and Figure S shows plots
of hydrophilicity, antigenic index, and AMPHI regions for ORF114-1.
Based on these results, including the homology with the putative aeactcd protein of N.meningitidis
and on the presence of a transmembrane domain, it is predicted that this protein from
N.meningitidis, and its epitopes, could be useful antigens for vaccines or diagnostics.
Example 14
The following partial DNA sequence was identified in N.meningitidis












Amino acids 25-619 of ORF41-1 were amplified as described above. Figure 6 shows plots of
hydrophilichy, antigenic index, and AMPHI regions for ORF41-1.
Based on this analysis, it is predicted that this protein from N.meningitidis, and its epitopes, could
be useful antigens for vaccines or diagnostics.













ORF124-1 was amplified as described above. Figure 7 shows plots of hydrophilicity, antigenic
index, and AMPHI regions for ORF 124-1.
Based on this analysis, it is predicted that this protein from N meningitidis, and its epitopes, could
be useful antigens for vaccines or diagnostics.
It will be appreciated that the invention has been described by means of example only, and that
modifications may be made whilst remaining within the spirit and scope of the invention.





WE CLAIM
1. A protein comprising amino acid sequence SEQ ID NO: 2.
2. The protein of claim 1, comprising amino acid sequence SEQ ID NO: 4.

3. A protein comprising an amino acid sequence with 80% or greater sequence identity to SEQ
ID NO: 2, provided that said protein is not (i) a protein having amino acid sequence SEQ ID NO: 7,
or (ii) a fragment of SEQ ID NO: 7, wherein the fragment has 6 or more amino acids of SEQ ID NO:
7 and includes an antigenic determinant.
4. The protein of claim 3, comprising an amino acid sequence with 80% or greater sequence
identity to SEQ ID NO: 4.
5. The protein of claim 3, comprising an amino acid sequence with 90% or greater sequence
identity to SEQ ID NO: 2.
6. The protein of claim 4, comprising an amino acid sequence with 90% or greater sequence
identity to SEQ ID NO: 4.
7. The protein of claim 5, comprising an amino acid sequence with 95% or greater sequence
identity to SEQ ID NO: 2.
8. The protein of claim 6, comprising an amino acid sequence with 95% or greater sequence
identity to SEQ ID NO: 4.
9. The protein of claim 7, comprising an amino acid sequence with 99% or greater sequence
identity to SEQ ID NO: 2.
10. The protein of claim 8, comprising an amino acid sequence with 99% or greater sequence
identity to SEQ ID NO: 4.
11. The protein of claim 4, comprising amino acid sequence SEQ ID NO: 6.
12. A protein comprising a fragment of at least 20 consecutive amino acids of amino acid
sequence SEQ ID NO: 2, provided that said protein is not (i) a protein having amino acid sequence
SEQ ID NO: 7, or (ii) a fragment of SEQ ID NO: 7, wherein the fragment has 6 or more amino acids
of SEQ ID NO' 7 and includes an antigenic determinant.
13. The protein of claim 12, wherein said fragment comprises an epitope from SEQ ID NO: 1.
14. The protein of claim 12, comprising a fragment of at least 20 consecutive amino acids of
amino acid sequence SEQ ID NO: 4.
15. The protein of claim 14, wherein said fragment comprises an epitope from SEQ ID NO: 4.
116. The protein of any preceding claim, wherein the protein is a fusion protein.
17. The protein of claim 16, which is a fusion with GST.
18. A protein of claim 17, which is a fusion with six histidine residues.

19. A protein comprising (i) an amino acid sequence with 80% or greater sequence identity to
SEQ ID NO: 2 or (ii) a fragment of at least 20 consecutive amino acids of amino acid sequence SEQ
ID NO; 2, wherein the protein is a fusion protein including six histidine residues.
20. The protein of any preceding claim, which is prepared by recombinant expression.
2 1. The protein of any one of claims 1 to 19, which is prepared by purification from cell culture.
22. An antibody which binds to a protein according to any one of claims 3 to 18.
23. The antibody of claim 22, which is monoclonal.
24. The antibody of claim 22, which is polyclonal.
25. A nucleic acid molecule which encodes a protein according to any one of claims 1 to 20.
26. The nucleic acid molecule of claim 25, comprising a fragment of at least 10 consecutive
nucleotides from a nucleotide sequence selected from the group consisting of SEQ ID NOs: 1,3, & 5
27. The nucleic acid molecule of claim 26, comprising a fragment of at least 12 consecutive
riucieotides from said group.
18. The nucleic acid molecule of claim 26, comprising a fragment of at least 14 consecutive
nucleotides from said group.
29. The nucleic acid molecule of claim 26, comprising a fragment of at least 15 consecutive
nucleotides from said group.
30. The nucleic acid molecule of claim 26, comprising a fragment of at least 18 consecutive
nucleotides from said group.
31. The nucleic acid molecule of claim 26, comprising a fragment of at least 20 consecutive
nucleotides from said group.
32. The nucleic acid molecule of claim 26, comprising a fragment of at least 25 consecutive
nucleotides from said group.
33. The nucleic acid molecule of claim 26, comprising a fragment of at least 30 consecutive
nucleotides from said group.
34 The nucleic acid molecule of claim 26, comprising a fragment of at least 35 consecutive
nucleotides from said group.
35. The nucleic acid molecule of claim 26, comprising a fragment of at least 40 consecutive
nucleotides from said group.
36. The nucleic acid molecule of claim 35, comprising a nucleotide sequence selected from the
group consisting of SEQ ID NO:1 and SEQ ID NO:3.
37. The nucleic acid molecule of claim 36, comprising nucleotide sequence SEQ ID NO: 1,
38. A nucleic acid molecule comprising a nucleotide sequence complementary to a nucleic acid
molecule according to any one of claims 25 to 37.

39. A nucleic acid molecule comprising a nucleotide sequence having 80% or greater sequence
identity to a nucleic acid molecule according to any one of claims 25 to 37.
4D. A nucleic acid molecule which can hybridise to a nucleic acid molecule according to any one
of claims 25 to 37 under high stringency conditions.
41. The nucleic acid molecule of any one of claims 25 to 40, which is DNA.
42. A vector comprising the nucleic acid of any one of claims 25 to 41.
43. The vector of claim 42, which is an expression vector.
44. A bacterial expression vector encoding (i) a protein comprising an amino acid sequence with
80% or greater sequence identity to SEQ ID NO: 2 or (ii) a protein comprising a fragment of at least
20 consecutive amino acids of amino acid sequence SEQ ID NO: 2, wherein the vector includes a
Shine-Dalgamo sequence.
45. A host cell transformed with the vector of claim 42 or claim 43 or claim 44.
46. The host cell of claim 45, which is a bacterium, yeast, or mammalian cell,
47. The host cell of claim 46, which is a bacterium.
48. A bacterial host cell transformed with a vector encoding (i) a protein comprising an amino
acid sequence with 80% or greater sequence identity to SEQ ID NO: 2 or (ii) a protein comprising a
fragment of at least 20 consecutive amino acids of amino acid sequence SEQ ID NO: 2, provided
that the host cell is not a Salmonella.
19. The host cell of claim 47 or claim 48, where the vector includes a bacterial promoter.
20. The host cell of claim 49, wherein the bacterial promoter is from a metabolic pathway
enzyme.
51. The host cell of any one of claims 45 to 50, wherein the bacterium is an E.coli.
52. A composition comprising a protein, a nucleic acid molecule, or an antibody according to
any one of claims 1 to 41.
53. A composition according to claim 52 being a vaccine composition or a diagnostic
composition.
54. The composition of claim 52, which is a vaccine composition.
55. A composition according to claim 52, for use as a medicament.
56. The composition of any one of claims 52 to 54, including a pharmaceutically acceptable
carrier.
57 The composition of claim 56, wherein the carrier comprises a polysaccharide.
58 The composition of claim 56, wherein the carrier comprises saline.
59 The composition of claim 56, wherein the carrier comprises a pH buffering substance.

60. A composition comprising; (i) a protein comprising an amino acid sequence with 80% or
greater sequence identity to SEQ ID NO: 2, or a protein comprising a fragment of at least 20
consecutive amino acids of amino acid sequence SEQ ID NO: 2; and (ii) a pharmaceutically
acceptable carrier comprising saline, a polysaccharide, a polylactic acid, a polyglycolic acid, or a
pH buffering substance.
61. The composition of any one of claims 52 to 60, prepared as an injectable.
62. The composition of any one of claims 52 to 59, prepared as a solid form suitable for solution
n, or suspension in, a liquid vehicle prior to injection.
63. A composition comprising: (i) a protein comprising an amino acid sequence with 80% or
greater sequence identity to SEQ ID NO: 2, or a protein comprising a fragment of at least 20
consecutive amino acids of amino acid sequence SEQ ID NO: 2; and (ii) a pharmaceuticaily
acceptable carrier, wherein the composition is an injectable.
64. The composition of any one of claims 52 to 60, including an adjuvant.
65. . The composition of claim 64, wherein the adjuvant is selected from: an aluminum salt; an
oil-in-water emulsion; a saponin; or a cytokine.
66. The composition of claim 65, wherein the adjuvant is an aluminum hydroxide or an
aluminium phosphate salt.
67. A composition comprising: (i) a protein comprising an amino acid sequence with 80% or
greater sequence identity to SEQ ID NO: 2, or a protein comprising a fragment of at least 20
consecutive amino acids of amino acid sequence SEQ ID NO: 2; and (ii) an adjuvant selected from
aluminum hydroxide, aluminum phosphate, or aluminum sulfate.
68. The composition of any one of claims 52 to 55, including chitosan.
69. The composition of any one of claims 52 to 55, including poly(lactide-co-glycolide).
70. The use of the protein of any one of claims 1 to 20, in the manufacture of a medicament for
the treatment or prevention of infection due to Neisserial bacteria, particularly Neisseria
meningitidis.
71. The use of (i) a protein comprising an amino acid sequence with 80% or greater sequence
identity to SEQ ID NO: 2, or (ii) a protein comprising a fragment of at least 20 consecutive amino
acids of amino acid sequence SEQ ID NO: 2, in the manufacture of a medicament for the treatment
or prevention of infection due to Neisseria meningitidis serogroup B.
72. A process for producing the protein of any one of claims 1 to 20, comprising the step of
culturing a host cell of any one of claims 45 to 51 under conditions which induce protein expression.

The invention provides proteins from Naisseria maningitidas
(strains A and B), including amino acid sequences, the
corresponding nucleotide sequences, expression data and
serological data. The proteins are useful antigens for
vaccines, immunogenic compositions, and/or diagnostics.

Documents:

IN-PCT-2000-109-KOL-FORM 27.pdf

IN-PCT-2000-109-KOL-FORM-27.pdf

in-pct-2000-109-kol-granted-abstract.pdf

in-pct-2000-109-kol-granted-claims.pdf

in-pct-2000-109-kol-granted-correspondence.pdf

in-pct-2000-109-kol-granted-description (complete).pdf

in-pct-2000-109-kol-granted-drawings.pdf

in-pct-2000-109-kol-granted-examination report.pdf

in-pct-2000-109-kol-granted-form 1.pdf

in-pct-2000-109-kol-granted-form 18.pdf

in-pct-2000-109-kol-granted-form 2.pdf

in-pct-2000-109-kol-granted-form 26.pdf

in-pct-2000-109-kol-granted-form 3.pdf

in-pct-2000-109-kol-granted-form 5.pdf

in-pct-2000-109-kol-granted-reply to examination report.pdf

in-pct-2000-109-kol-granted-specification.pdf

in-pct-2000-109-kol-granted-translated copy of priority document.pdf


Patent Number 228098
Indian Patent Application Number IN/PCT/2000/109/KOL
PG Journal Number 05/2009
Publication Date 30-Jan-2009
Grant Date 28-Jan-2009
Date of Filing 26-Jun-2000
Name of Patentee CHIRON SPA
Applicant Address VIA FIORENTINA 1, I-53100 SIENA
Inventors:
# Inventor's Name Inventor's Address
1 MASIGNANI VEGA VIA PANTANETO 105 53100 SIENA
2 RAPPUOLI RINO VIA DELLE ROCCHE 1, VAGLIAGLI, 53019 CASTELNUOVO BERARDENGA (SI)
3 PIZZA MARIAGRAZIA STRADA DI MONTALBUCCIO, 160 53100 SIENA
4 SCARLATO VINCENZO VIA FIRENZE, 3/37 53134 COLLE VAL D'ELSA (SI)
5 GRANDI GUIDO 9° STRADA, 4, 20090 SEGRATE (MI)
PCT International Classification Number C12N 15/31
PCT International Application Number PCT/IB99/00103
PCT International Filing date 1999-01-14
PCT Conventions:
# PCT Application Number Date of Convention Priority Country
1 9822143.5 1998-10-09 U.K.
2 9800760.2 1998-01-14 U.K.
3 9819015.0 1998-09-01 U.K.