Title of Invention

NOVEL SESQUITERPENE SYNTHASES AND METHOD

Abstract The present invention relates to novel terpene synthases. The terpene synthases are capable of synthesising mono-, bi- and/or tri-cyclic sesquiterpenes having a C2-C7 or a C3-C7 bond, starting from an acyclic pyrophosphate terpene precursor, far-nesyl- pyrophosphate. Accordingly, for the first time, sesquiterpene synthases catalysing the cyclisation to the santalene and berg-amotene carbon skeleton are disclosed. The present invention further relates to nucleic acid sequences encoding the sesquiterpene synthases and to methods for making terpenoids.
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Novel Sesquiterpene Synthases and Methods of Their Use
Technical Field
The present invention relates to novel terpene synthases. The invention further
relates to nucleic acids encoding terpene synthases, to methods for preparing variant
terpene synthases, and to host-organisms expressing the polypeptides of the invention.
The present invention further comprises methods for making a terpene synthase and
methods for making terpenoids.
Technical Background and Problems to be Solved
Terpenoids or terpenes represent a family of natural products found in most
organisms (bacteria, fungi, animal, plants). Terpenoids are made up of five carbon units
called isoprcne units. They can be classified by the number of isoprene units present in
their structure: monoterpenes (C10), sesquiterpenes (C15), diterpenes (C20), triterpenes
(C30), tetraterpenes (C40) and polyterpenes (Cn, n≥45). The plant kingdom contains the
highest diversity of monoterpenes and sesquiterpenes.
The monoterpenes and sesquiterpenes are the most structurally diverse
isoprenoids. They are usually volatile compounds and are mostly found in plants were
they play a role in defense against pathogens and herbivores attacks, in pollinator
attraction and in plant-plant communication.
Some plants, known as aromatic plants or essential-oil-plants, accumulate large
amounts of monoterpenes and sesquiterpenes in their leaves, roots or stems. Classical
examples of such plants are members from the plant families Lamiaceae, Rutaceae,
Solanaceae, and Poaceae, for example.
Monoterpene and sesquiterpene accumulating plants have been of interest for
thousands of years because of their flavor and fragrance properties and their cosmetic,
medicinal and anti-microbial effects. The terpenes accumulated in the plants can be
extracted by different means such as steam distillation that produces the so-called
essential oil containing the concentrated terpenes. Such natural plant extracts are
important components for the flavor and perfumery industry.
Many sesquiterpene compounds are used in perfumery. For example, Vetivcr oil,
extracted from the roots of Vetiver zizonoides, is known to contain a number of odorant
sesquiterpenes, amongst which α-vetivone, β-vetivone and zizanoic acid, are the most
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characteristic. Vetiver zizanoides is currently cultivated in Reunion, the Philippines,
Comoro Islands, Japan, West Africa and South America.
Generally, the price and availability of plant natural extracts such as Vetiver oil is
dependent on the abundance, the oil yield and the geographical origin of the plants. In
some years, the availability of commercially available natural extracts decreases, going
hand in hand with a worsening of their quality. Under these circumstances, the use of
these ingredients in high quality perfumery products is no longer possible.
Therefore, it would be an advantage to provide a source of sesquiterpenes, which
is less subjected to fluctuations in availability and quality. Chemical synthesis would
seem to be an evident option for the preparation of sesquiterpenes, however, these
compounds generally have a highly complex structure and so far no economic synthetic
process for the preparation of sesquiterpenes has been developed.
It is therefore an objective of the present invention to provide ways of producing a
high quality of sesquiterpenes in an economic and reliable way.
The biosynthesis of terpenes in plants has been extensively studied and is not
further detailed in here, but reference is made to Dewick P, Nat. Prod. Rep., 2002, 19,
181 -222, which reviews the state of the art of terpene biosynthetic pathways.
The sesquiterpene synthases convert FPP to the different sesquiterpene skeletons.
Over 300 sesquiterpene hydrocarbons and 3000 sesquiterpenoids have been identified
(Joulain, D., and Konig, W.A. The Atlas of Spectral Data of Sesquiterpene Hydrocarbons,
EB Verlag, Hamburg, 1998; Connolly, J.D., Hill R.A. Dictionary of Terpenoids, Vol 1,
Chapman and Hall (publisher), 1991), and many new structures are identified each year.
There is virtually an infinity of sesquiterpene synthases present in the plant kingdom, all
using the same substrate but having different product profiles.
A cDNA encoding a trans-a-bisabolene synthase has been reported by Bohlmann,
J, Crock, J., Jetter, R., and Croteau R. (1998) Terpenoid-based defenses in conifers:
cDNA cloning, characterization, and functional expression of wound-inducible (E)-a-
bisabolene synthase from grand fir (Abies grandis). Proc. Natl. Acad. Sci. USA 95, 6756-
6761. However, this enzyme catalyses one cyclation step and produces almost exclusively
the bisabolene sesquiterpene.
Kollner T et al (2004) The plant cell 16(5), 1115-1131, disclose a number of
putative terpene synthase genes isolated from Zea mays, most of which did not encode
functional enzymes. DNA sequences of functional synthases, Tps4-B73 and Tps5-1
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delprim are available under accession number AY518310 and AY518313. Bergamotene
was only a minor product produced by the encoded enzymes, representing maximally
2.6wt.% of the total sesquiterpenes produced.
Despite extensive chemical studies of terpene cyclisation, the isolation of the
enzymes is difficult, particularly in plants, due to their low abundance, often transient
expression patterns, and complexity of purifying them from the mixtures of resins and
phenolic compounds in tissues where they are expressed.
In view of the above, the objective of the present invention is to provide new
terpene synthases. Another objective is to isolate terpene synthases from the plant
Vetiveria zxzanoides. It is an objective of the present invention to provide terpene syntascs
capable of synthetizing terpenes for the synthesis of which so far no enzyme has been
reported.
In particular, it is an objective to provide enzymes capable of synthesising
substantial amounts of sesquiterpenes having a santalene or bergamotene carbon skeleton.
There is no report of the genetic basis underlying a santalene synthase, and bergamotane
is synthcsised only in trace amounts by known terpene synthases.
In the same line, it is an objective to provide methods for making terpenoids in an
economic way, as indicated above. Accordingly, the present invention has the objective to
produce sesquiterpenes while having little waste, a more energy and resource efficient
process and while reducing dependency on fossil fuels. It is a further objective to provide
enzymes capable of synthesizing terpenoids, which arc useful as perfumery and/or aroma
ingredients.
Summary of the Invention
Remarkably, the present inventors cloned cDNAs encoding novel sesquiterpenes
in roots of Vetiver zitanoides. Surprisingly, the novel sesquiterpene synthases were
capable of synthetising sesquiterpenes, which have so far not been isolated from Vetiver,
such as cyclocopacamphene, (+)-epi-β-santalene, trans-α-bergamotene, cis-a-
bergamotene, β-bisabolene, and/or trans-y-bisabolene. Therefore, the present invention
provides the first cloned sesquiterpene synthases able to catalyse the cyclisation of FPP to
the bisabolyl cation and subsequent cyclization to the bergamotane and santalane
skeleton. For the first time, a terpene cyclase capable of synthesizing substantial amounts
of bi-cyclic derivatives of the bisabolyl cation is reported.
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Accordingly, the present invention provides, in a first aspect, An isolated nucleic acid
selected from:
(a) a nucleic acid comprising a nucleotide sequence having at least 82.4% identity
with SEQ ID NO: 2;
(b) a nucleic acid comprising a nucleotide sequence encoding a polypeptide having at
least 76.8% sequence identity with SEQ ID NO: 5;
(c) a nucleic acid comprising a nucleotide sequence that hybridises to the nucleotide
sequence SEQ ID NO: 2 under moderate stringency conditions;
(d) a nucleic acid comprising a nucleotide sequence encoding a polypeptide capable
of synthesising a bi-cyclic and/or tri-cyclic sesquiterpene comprising a C3-C7 bond;
and/or,
(e) a nucleic acid comprising a nucleotide sequence encoding a polypeptide capable
of synthesising at least one bergamotene and, optionally, other sesquiterpenes,
characterized in that begamotenes constitute at least 10 wt.% of the total of sesquiterpene
products syntnesised by the polypeptide;
wherein the polypeptide encoded by any of the said nucleic acids of (a)-(e) has
terpene synthase activity.
In a further aspect, the present invention provides an isolated nucleic acid selected from:
(a) a nucleic acid comprising a nucleotide sequence having at least 59% sequence
identity with SEQ ID NO: 1;
(b) a nucleic acid comprising a nucleotide sequence encoding a polypeptide having at
least 50% of amino acid sequence identity with SEQ ID NO: 4;
(c) a nucleic acid that hybridises to SEQ ID NO: 1 under moderate stringency
conditions;
(d) a nucleic acid comprising a nucleotide sequence encoding a polypeptide capable
of synthesising cyclocopacamphene;
wherein the polypeptide encoded by said nucleic acid has terpene synthase activity.
In a further aspect, the present invention provides an isolated polypeptide selected
from:
(a) a polypeptide comprising an amino acid sequence having at least 76.8% of amino
acid sequence identity with SEQ ID NO: 5;
(b) a polypeptide capable of synthesising a bi-cyclic and/or tri-cyclic sesquiterpene
comprising a C3-C7 bond;
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(c) a polypeptide capable of synthesising at least one bergamotene and, optionally,
other sesquiterpenes, characterized in that begamotenes constitute at least 10 wt.% of the
total of sesquiterpene products synthesised by the polypeptide.
In a still further aspect, the present invention provides a polypeptide selected
from:
(a) a polypeptide comprising an amino acid sequence having at least 76.8% of amino
acid sequence identity with SEQ ID NO: 5;
(b) a polypeptide capable of synthesising a bi-cyclic and/or tri-cyclic sesquiterpene
comprising a C3-C7 bond;
(c) a polypeptide capable of synthesising at least one bergamotene and, optionally,
other sesquiterpenes, characterized in that begamotenes constitute at least 5 wt.% of the
total of sesquiterpene products synthesised by the polypeptide.
The present invention further relates to methods for preparing a variant
polypeptide having terpene synthase activity, as set out in the claims and the detailed
description.
In further aspects, the present invention provides vectors and host organisms or
cells comprising any of the nucleic acids of the invention.
In a still further aspects, the present invention provides different methods of
making a terpene synthase, and, in addition, methods of making terpenoids, for example
sesquiterpenes, as set out in the claims and the detailed description.
In the figures,
Figure 1 shows the structure of sesquiterpene compounds synthetized by the
terpene synthascs of the present invention, sesquiterpene compounds isolated from
Vetiver oil and other sesquiterpene compounds discussed in the text, in particular (1) cis-
alpha-bergamotcnc, (2) trans-alpha-bergamotene, (3) epi-beta-santalene, (4) beta-
bisabolene, (5) trans-gamma-bisabolene, (6) cyclosativene and (7) cyclocopacamphene.
Sesquiterpene compounds previously reported from Vetiver oil arc (8) zizanoic acid, (9)
alpha-vetivone, (10) beta-vetivone, (11) isobisabolene, (12) beta-bisabolol, (13)
dehydrocurcumene, (14) (Z)-trans-alpha-bergamotol, (15) (Z)-(+)-epi-beta-santalol.
Figure 2 shows the alignment of amino acid sequences deduced form the
fragments of cDNAs encoding for sesquiterpene synthases obtained by RT-PCR (SEQ ID
NO: 8-14).
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Figure 3 shows a comparison of the full length amino acid sequences SEQ ID
NO: 4, SEQ ID NO: 5, and SEQ ID NO: 6 of the present invention. Identical amino acids
are shown against a black background, amino acids having similar ionic charge are shown
against a grey background, and unrelated amino acids are shown against a white
background.
Figure 4 shows in part A) a gas chromatogram (GC) of sesquiterpenes obtained
from an enzymatic assay in which FFP was exposed to a polypeptide having an amino
acid sequence substantially as set out in SEQ ID NO: 4. In part B), Figure 4 shows a mass
spectre (MS) of the major peak (10.81) of part A), which is compared to the
corresponding spectre of standard cyclosativene, thus indicating the nature of the
sesquiterpene obtained in the enzymatic assay.
Figure 5 shows a GC of sesquiterpenes obtained from an enzymatic assay in
which FFP was exposed to a polypeptide having an amino acid sequence substantially as
set out in SEQ ID NO: 5. This recombinant protein produced a mixture of at least seven
different sesquiterpene hydrocarbons, from which 5, indicated as numbers 1-5, have
been identified by GC-MS (sec Figure 1 for the name of the compounds).
Figure 6 shows the putative biosynthetic mechanism of the synthesis of
sesquiterpenes catalysed by the polypeptides of the present invention, which reaction
starts from FPP (16) and passes by the intermediate bisabolyl-cation (17). In particular,
the reaction catalysed from polypeptides having an amino acid sequence substantially as
set out in SEQ ID NO: 5 and variants thereof. Figure 6 further shows the chemical
structures of the precursor (FPP) and the sesquiterpene products.
Abbreviations Used
bp base paire
DNA dcoxyribonucleic acid
cDNA complementary DNA
DTT dithiothrcitol
FPP Farnesyl-pyrophosphate
NPP Nerolidol-pyrophosphate
IPTG isopropyl-D-thiogalacto-pyranoside
PCR polymerase chain reaction
RT-PCR reverse transcription - polymerase chain reaction
3'-/5'-RACE 3' and 5' rapid amplification of cDNA ends
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RNA ribonucleic acid
mRNA messenger ribonucleic acid
nt nucleotide
RNase ribonuclease
SDS-PAGE SDS-polyacrylamid gel electrophoresis
Detailed Description of the Preferred Embodiments
The present invention provides isolated nucleic acids encoding novel
sesquiterpene synthases capable of synthesising mono-, bi- and/or tricyclic
sesquiterpenes. Bicyclic or tricyclic sesquiterpenes comprising a C3-C7 bond are defined
as sesquiterpenes having a santalene carbon skeleton, while those comprising a C2-C7
bond are defined as sesquiterpenes of the bergamotene skeleton.
A "terpene" is an hydrocarbon based on an isoprene unit (C5H8), which may be
acyclic or cyclic. "Terpenes" include but are not limited to cyclosativene,
cyclocopacamphene, cyclocopacamphenol epimers, cyclocopacamphenal epimers,
cyclocopacamphenic acid epimers, cis-α-bergamotene, trans-α-bergamotene, (+)-epi-
β-santalene, β-bisabolene, and trans-γ-bisabolene.
"Terpenes" and "Terpenoids", as used herein include terpenes and terpene
derivatives, including compounds that have undergone one or more steps of
functionalisation such as hydroxylations, isomerizations, oxido-reductions, dimethylation
or acylation. As used herein, a "sesquiterpene" is a terpene based on a C15 structure and
includes sesquiterpenes and sesquiterpene derivatives, including compounds that have
undergone one or more steps of functionalization.
As used herein, a "derivative" is any compound obtained from a known or
hypothetical compound and containing essential elements of the parent substance.
As used herein, a "terpene synthase" is any enzyme that catalyses the synthesis of
a terpene. A "sesquiterpene synthase" is an enzyme that catalyses the synthesis of a
sesquiterpene.
Sequence identity, as used in the term "identity" or "identical" can be readily
calculated by standard alignment algorithms. Preferably, for assessing sequence identity
of the sequences of the present invention with another sequence, for example from the
prior art, CLUSTAL W. is used, as disclosed in J. D. Thompson , D. J. Higgins, T. J.
Gibson (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence
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alignment through sequence weighting, position-specific gap penalties and weight matrix
choice. Nucleic Acids Res 22(22), 4673-4680. The standard parameters are selected for
assessing sequence identity. The sequence comparison may be performed on-line, at
http://www.ebi.ac.uk/clustalw/, or, alternatively, suitable software can be down-loaded.
For example, the BioEdit software available from
http://www.mbio.ncsu.edu/BioEdit/bioedit.html.
In an aspect, the present invention provides isolated nucleic acids hybridising to
any of the nucleic acids of the invention, such as those detailed under SEQ ID NO: 1, 2 or
3 under low stringency conditions. Preferably, the defined conditions are moderate
stringency conditions, more preferably they are high stringency conditions.
Surprisingly, the sequence at the N-term end of SEQ ID NO 6 differs from other
known terpene synthase sequences in that it contains an unusual motif PAAAASSQQQQ
(SEQ ID NO 7) that does not resemble to any known signal sequence. The present
invention is also directed to this particular sequence, and to any nucleotide sequence
encoding this motif, such as the one of SEQ ID NO 3.
In a particular embodiment, the invention relates to certain isolated nucleotide
sequences including those that are substantially free from contaminating endogenous
material. The terms "nucleic acid" or "nucleic acid molecule" include
deoxyribomicleotide or ribonucleotide polymers in either single-or double-stranded form
(DNA and/or RNA). A "nucleotide sequence" also refers to a polynucleotide molecule or
oligonucleolide molecule in the form of a separate fragment or as a component of a larger
nucleic acid.
In an embodiment, the present invention provides a nucleic acid selected from:
(a) any nucleic acid selected from the group consisting of SEQ ID NO: 1, 2 and 3, (b) any
nucleic acid selected from the group consisting of the nucleic acids encoding any of the
polypeptides substantially as set out in SEQ ID NO: 4, 5, and 6, (c) a nucleic acid that
hybridises to the nucleic acid of (a) or (b) under low stringency conditions, wherein the
polypeptide encoded by said nucleic acid has sesquiterpene synthase activity.
In an embodiment, the nucleic acid comprises a nucleotide sequence, which is at
least 59%, preferably at least 60%, more preferably at least 65% and most preferably at
least 70% identical to SEQ ID NO: 1. For example, the nucleic acid sequence of the
invention is at least 75%, 80%, 85%, 90%, 95% or 98% identical to SEQ ID NO: 1.
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In an embodiment, the nucleic acid comprises a nucleotide sequence, which is at
least 82.4%, preferably at least 85%, more preferably at least 90%, and most preferably at
least 95% identical to SEQ ID NO: 2. For example, the nucleic acid sequence of the
invention is at least 95%, 97%, or 98% identical to SEQ ID NO: 2.
In an embodiment, the nucleic acid comprises a nucleotide sequence, which is at
least 49%, preferably at least 50%, more preferably at least 55% and most preferably at
least 60% identical to SEQ ID NO: 3. For example, the nucleic acid sequence of the
invention is at least 65%, 70%, 75%, 80%, 85%, 90%, 95% or 98% identical to SEQ ID
NO: 3.
Preferably, the nucleic acid of step (c) hybridises under moderate, more preferably
under high stringency conditions to the nucleic acids of (a) or (b) above, but preferably to
the sequence SEQ ID NO 1, 2, or 3. For example, the nucleic acid of (c) hybridised to
SEQ ID NO 1. According to another example, it hybridised to SEQ ID NO 3 under the
above-mentioned conditions.
Preferably, the nucleic acids of the invention hybridise with the nucleic acid of
SEQ ID NO: 1 and do not hybridise with a nucleic acid encoding a putative scsquitcrpenc
synthase found in Oryza sativa under accession number AP003911.
According to an embodiment, the nucleic acids of the invention hybridises with
the nucleic acid of SEQ ID NO: 2 and do not hybridise with nucleic acids selected from
those having accession numbers AY518310 or AY518313 encoding sesquiterpene
synthases in Zea mays. Preferably, the nucleic acid of the present invention does further
not hybridise with any of the nucleic acid sequences selected from those having accession
numbers AY518311, AY518312, and AY518314. These latter sequence are not reported
to encode an active sesquiterpene synthase.
Preferably, the nucleic acids of the invention hybridise with the nucleic acid of
SEQ ID NO: 3 and do not hybridise with a nucleic acid encoding a putative sesquiterpene
synthase found in Zea mays, having accession number AAG37841.
Preferably, the isolated nucleic acid, which specifically hybridise with the nucleic
acid of SEQ ID NO: 3 under stringent conditions do not hybridise at the stringent
conditions with a nucleic acids present in Zea mays, putatively encoding terpene
synthases having accession number AF296122.
Preferably, the nucleic acid sequence according to the invention comprises SEQ
ID NO 1, 2 and/or 3. More preferably, it essentially consists of SEQ ID NO 1, 2 and/or 3.
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In another embodiment, the nucleic acid comprises a contiguous fragment of at
least 20, 100, 200, 300,400, 500, or 750 nucleotides of SEQ ID NO 1, 2 and/or 3.
Preferably, the nucleic acid of the invention hybridises to the fragments having the
above length under low, moderate or high stringency conditions.
Preferably, the nucleic acid of the invention comprises the fragment from about nt
900 to nt 1647, 1641 and 1791 of SEQ ID NO:1, 2, and/or 3, respectively. These
fragments include the active sites of the polypepu'des of the invention.
Preferably, a nucleic acid and/or polypeptide of the invention is isolated from
Vetiver (Vetiveria zizanoides). In an embodiment, the nucleic acid is isolated from
Vetiver roots.
As used herein, the term "hybridization or hybridizes under certain conditions" are
defined as disclosed below. The conditions may be such that sequences, which are at least
about 70%, such as at least about 80%, and such as at least about 85-90% identical,
remain bound to each other.
Appropriate hybridization conditions can be selected by those skilled in the art
with minimal experimentation as exemplified in Ausubcl et al. (1995), Current Protocols
in Molecular Biology, John Wiley & Sons, sections 2, 4, and 6. Additionally, stringency
conditions are described in Sambrook et al. (1989), chapters 7, 9, and 11.
As used herein, defined conditions of "low stringency" are as follows. Filters
containing DNA are pretreated for 6 h at 40°C. in a solution containing 35% formamide,
5x SSC, 50 mM Tris-HCl (pH 7,5), 5 mM EDTA, 0.1% PVP, 0.1% Ficoll, 1% BSA, and
500 μg/ml denatured salmon sperm DNA. Hybridizations are carried out in the same
solution with the following modifications: 0.02% PVP, 0.02% Ficoll, 0.2% BSA,
100μg/ml salmon sperm DNA, 10% (wt/vol) dextran sulfate, and 5-20x106 32P-labclcd
probe is used.
Filters are incubated in hybridization mixture for 18-20 h at 40°C, and then
washed for 1.5 h at 55°C in a solution containing 2x SSC, 25 mM Tris-HCl (pH 7.4),
5 mM EDTA, and 0.1% SDS. The wash solution is replaced with fresh solution and
incubated an additional 1.5 h at 60°C. Filters are blotted dry and exposed for
autoradiography.
As used herein, defined conditions of "moderate" stringency are different from
those of "low" stringency conditions in that filters containing DNA are pretreated for 7 h
at 50°C (moderate) and 8 hours at 65°C (high) in the corresponding solution given above.
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Hybridizations are carried out in the same solution as for "low stringency" but for 30 h at
50°C, respectively and then washed for 1.5 h at 55°C (moderate) in the washing solution
detailed above. The wash solution is replaced with fresh solution and incubated an
additional 1.5 h at 60°C.
Conditions for "high" stringency: prehybridization for 8h at 65°C in solution as
above, but with 6xSSC, a nM EDTA, 0.02%PVP, 0.02% Ficoll, 0.02%BSA and
500ng/ml denatures salmon sperm DNA instead. Filters are hybridized for 48 h at 65°C in
the prehybridization mixture containing 100 μg/ml denatured salmon sperm DNA and
5-20x106 cpm of 32P-labeled probe. Washing of filters is done at 37°C for 1 h in a
solution containing 2x SSC, 0.01% PVP, 0.01% Ficoll, and 0,01% BSA. This is followed
by a wash in 0.1xSSC at 50°C for 45 min. Other conditions of low, moderate, and high
stringency well known in the art (e.g., as employed for cross-species hybridizations) may
be used if the above conditions arc inappropriate.
The present invention also encompasses "variant nucleotide sequences", obtained
by mutations in of any of SEQ ID NO 1, 2, and 3, for example. Mutations may be any
kind of mutations of the sequences of the present invention, such as point mutations,
deletion mutations, insertion mutations and/or frame shift mutations. Variant nucleotide
sequences may be prepared in order to adapt a sequence to a specific expression system.
For example, bacterial expression systems are known to more efficiently express
polypeptides if amino acids are encoded with a preferred codon. Due to the degeneracy of
the genetic code, wherein more than one codon can encode the same arnino acid, multiple
DNA sequences can code for the same polypcptidc, which are encompassed by the
nucleic acids or nucleotide sequences of the present invention.
In addition, the present invention also encompasses variant nucleotide sequences
encoding polypeptides which are substantially different from the amino acid sequences
reported herein, but which are obtained by modifying, e.g. by mutagenesis, or otherwise
taking use of the present nucleotide sequences.
Preferably, the polypeptide of the invention is capable of synthesising mono-and
bi-cyclic sesquiterpenes. Preferably, it is capable of synthesising bi-or tricyclic
sesquiterpenes. Most preferably, it is capable of synthesising mono-, bi-, and tricyclic
sesquiterpenes.
Preferably, the isolated polypeptide of the present invention is capable of forming
a bisabolyl cation from FPP and capable of further creating a bond between the C3 and the
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C7 carbon atom of FPP to produce a bi-cyclic or tricyclic sesquiterpene comprising a C3-
C7 bond.
Similarly, the polypeptide of the present invention is capable of forming a
bisabolyl cation from FPP and capable of further creating a bond between the C2 and the
C7 carbon atom of FPP to produce a bi-cyclic or tricyclic sesquiterpene comprising a C2-
C7 bond.
The term 'capable of synthesising" a compound, such as a specific sesquiterpene,
and the terms "terpene synthase activity", preferably "sesquiterpene synthase activity",
refers to polypeptidesof the present invention, as well as nucleic acids encoding these
polypeptides, which are capable of synthesizing a terpene, preferably a sesquiterpene and
most preferably the sesquiterpene compounds mentioned herein from at least one starting
compound, which preferably is an acyclic pyrophosphate terpene precursor. Preferably,
the capacity of synthesising is determined with the enzyme essay detailed in Example 5.
If a specific product is detected by this assay, the "capacity of synthesising", or "synthase
activity" it is given for the product. Preferably, the acyclic terpene precursor is FPP,
which is given in formula (I) below with standard numeration of the carbon skeleton of
sesquiterpenes. OPP refers to pyrophosphate.

Preferably, the isolated polypeptide is capable of synthesising at least one
sesquiterpene, more preferably at least one sesquiterpene having a santalenc or
bergamotene carbon skeleton. In a preferred embodiment, the polypeptide is capable of
forming a bisabolyl cation from FPP, and capable of further creating a bond between the
C3 or C2 and the C7 carbon atom of FPP to produce one or several bi-cyclic and/or
tricyclic sesquiterpenes.
The term "bond" refers to a single covalent bond.
The present invention relates to nucleic acids encoding a polypeptide, as well as to
the polypeptide itself, capable of synthesising at least one bi-cyclic and/or tri-cyclic
sesquiterpene comprising a C3-C7 bond. Preferably, the sesquiterpenes comprising a C3-
C7 bond constitute at least 5 wt.% of the sesquiterpene products synthesised by the
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polypeptide. More preferably, at least 10 wt%, even more preferably at least 15 wt%, and
most preferably at least 20 wt% of the sesquiterpenes produced by the polypeptide are
constituted by sesquiterpenes having a C3-C7 bond. The quantitative sesquiterpene
product distribution of a sesquiterpene synthase, for the purpose of the present invention,
is preferably determined by employing the procedure detailed in Example 5 (enzyme
assay, extraction of products and GC).
Accordingly, the present invention relates to isolated polypeptides capable of
forming compounds having a C3-C7 bond of the formula (II) and/or (III) below

in which R1, R2, R3, R4 are, independently of each other, a linear or branched alkyl or
alkylene group from C1 to C20, and whereby R1 and R2 and/or R3 and R4 may form a
double bond instead of two individual single bonds.
Preferably, R1, R2, R3, R4 are, independently of each other, a linear or branched
alkyl or alkylene group from C1 to C15, more preferably from C1 to C10, most preferably,
from C1 to C8.
In particular, the polypeptides of the present invention are capable of forming
compounds of the formula (IV), (V) and/or (VI) below

in which R1, R2, R3, R4 are defined as above.
Preferably, in formula (IV) and/or (VI), either R1 or R2 is a C1-C5 alkyl and the
other is a C2-C8 alkylene. In addition R3 in formula (VI) preferably is a C1-C5, more
preferably a C1-C3 alkyl. Preferably, in formula (V), R3 and R4 are defined as R1 and R2 in
formula (IV) above.
The present invention relates to nucleic acids encoding a polypeptide, and to the
polypeptide it-selves, capable of forming at least one sesquiterpene having a C2-C7 bond.
According to a preferred embodiment, sesquiterpenes comprising a C2-C7 bond
constitutes at least 5 wt.% of the sesquiterpene products synthesised by the polypeptide.
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More preferably, at least 10 wt%, even more preferably at least 15 wt%, and most
preferably at least 20 wt% of the sesquiterpenes produced by the polypeptide are
constituted by the sesquiterpene having a C2-C7 bond. Preferably, the sesquiterpene is
bergamotene and/or one of its isomers, preferably stereoisomers.
According to an embodiment, the present invention relates to isolated
polypeptides capable of forming compounds having a C2-C7 bond according to the
formula (VII) and/or (VIII) below

in which R5 and R6 are defined as R1 and R2 above. Preferably, R5 is a methyl and R6 is a
C2-C10 alkenyl, or vice versa.
Preferably, at least one alkenyl possibly present in one of the residues R1, R2, R3,
R1, R5 or R6 mentioned above is 4-methyl-3-pentenyl, while another residue linked to the
same carbon atom is methyl.
The polypeptides capable of synthesizing the compounds of formulae (II), (III),
(IV), (V), (VI), (VII) and/or (VIII) above preferably arc the polypeptides having the
amino acid sequence SEQ ID NO: 5, or polypeptide variants thereof.
Sesquiterpenes having a C3-C7 bond are santalcne and its stereoisomers, in
particular (+)-cpi-β-santalene, (-)-β-santalcnc, (+)-β-santalcnc (all three of which are bi-
cyclic), and (+)-α-santalene, and (-)-α-santalene (both of which are tri-cyclic), for
example.
Sesquiterpenes having a C2-C7 bond are bergamotene including its stereoisomers,
in particular, cis-α-bergamotene, trans-α-bergamotene, trans-β-bergamotene and cis-β-
bergamotene, for example.
Most preferably, the polypeptides of the present invention are capable of
synthesizing the compounds reproduced in the figures.
In a further aspect, the invention provides an isolated polypeptide capable of
synthesising santalene, bergamotene, and/or bisabolene.
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In a preferred embodiment, the invention provides an isolated polypeptide capable
of synthesising (+)-epi-β-santalene, trans-α-bergamotene, cis-α-bergamotene,
p-bisaboiene, and/or trans-γ-bisabolene.
Preferably, the polypeptide is capable of synthesizing any or all of (+)-epi-β-
santalene, trans-α-bergamotene, cis-α-bergamotene, P-bisabolene, and/or trans-γ-
bisabolenc. More preferably, the polypeptide is capable of synthesizing at least one of
them. Most preferably, the polypeptide is capable of synthetizing (+)-cpi-β-santalcnc,
trans-α-bergamotene and/or cis-α-bergamotene.
As used herein, the term "poly peptides" refers to a genus of polypeptide or peptide
fragments that encompass the amino acid sequences identified herein, as well as smaller
fragments.
A "polypeptide variant" as referred to herein means a polypeptide substantially
homologous to a native polypeptide, but which has an amino acid sequence different from
that encoded by any of the nucleic acid sequences of the invention because of one or more
detections, insertions or substitutions.
The polypeptide, and polypeptide variants of the present invention preferably have
terpene synthase activity. More preferably, they have sesquiterpene synthase activity.
Variants can comprise conservatively substituted sequences, meaning that a given
amino acid residue is replaced by a residue having similar physiochemical characteristics.
Examples of conservative substitutions include substitution of one aliphatic residue for
another, such as He, Val, Leu, or Ala for one another, or substitutions of one polar residue
for another, such as between Lys and Arg; Glu and Asp; or Gin and Asn. See Zubay,
Biochemistry, Addison-Wesley Pub. Co., (1983). The effects of such substitutions can be
calculated using substitution score matrices such a PAM-120, PAM-200, and PAM-250
as discussed in Altschul, (J. Mol. Biol. 219:555-65, 1991). Other such conservative
substitutions, for example, substitutions of entire regions having similar hydrophobicity
characteristics, are well known.
Naturally occurring peptide variants are also encompassed by the invention.
Examples of such variants are proteins that result from alternate mRNA splicing events or
from proteolytic cleavage of the polypeptides described herein. Variations attributable to
proteolysis include, for example, differences in the N- or C-termini upon expression in
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different types of host cells, due to proteolytic removal of one or more terminal amino
acids from the polypeptides encoded by the sequences of the invention.
Variants of the sesquiterpenes synthases of the invention may be used to attain
desired enhanced or reduced enzymatic activity, modified regiochemistry or
stereochemistry, or altered substrate utilization or product distribution. Furthermore,
variants may be prepared to have at least one modified property, for example an increased
affinity for the substrate, an improved specificity for the production of one or more
desired compounds, a different product distribution, a different enzymatic activity, an
increase of the velocity of the enzyme reaction, a higher activity or stability in a specific
environment (pH, temperature, solvent, etc), or an improved expression level in a desired
expression system. A variant or site direct mutant may be made by any method known in
the art. As stated above, the invention provides recombinant and non-recombinant,
isolated and purified polypeptides, such as from Vetiver plants. Variants and derivatives
of native polypeptides can be obtained by isolating naturally-occurring variants, or the
nucleotide sequence of variants, of other or same plant lines or species, or by artificially
programming mutations of nucleotide sequences coding for native terpenc synthases.
Alterations of the native amino acid sequence can be accomplished by any of a number of
conventional methods.
Polypeptide variants resulting from a fusion of additional peptide sequences at the
amino and carboxyl terminal ends of the polypeptides of the invention can be used to
enhance expression of the polypeptides, aid in the purification of the protein or improve
the enzymatic activity of the polypeptide in a desired environment or expression system.
Such additional peptide sequences may be signal peptides, for example. Accordingly, the
present invention encompasses variants of the polypeptides of the invention, such as those
obtained by fusion with other oligo-or polypeptides and/or polypeptides which arc linked
to signal peptides.
Therefore, in an embodiment, the present invention provides a method for
preparing a variant polypeptide having a desired terpene synthase activity, the method
comprising the steps of:
(a) selecting any of the nucleic acids from the group consisting of SEQ ID NO 1, 2 or 3,
or nucleic acids therewith related therewith comprising nucleotide sequences
described above;
(b) modifying the selected nucleic acid to obtain at least one mutant nucleic acid;
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(c) transforming host cells with the mutant nucleic acid sequence to express a
polypeptide encoded by the mutant nucleic acid sequence;
(d) screening the polypeptide for a functional polypeptide having at least one modified
property; and,
(e) optionally, if the polypeptide has no desired variant terpene synthase activity, repeat
the process steps (a) to (d) until a polypeptide with a desired variant terpene
synthase activity is obtained (= DNA shuffling).
The method for providing a variant polypeptide is suitable of screening and
functional polypeptides having a desirable property, such as activity parameter, from
polypeptides encoded by a pool of mutant nucleic acids. In step (a), any of the nucleic
acids of the present invention may be selected.
Thereafter, in step (b), a large number of mutant nucleic acid sequences may be
created, for example by random mutagenesis, site-specific mutagenesis, or DNA
shuffling. The detailed procedures of gene shuffling are found in Stemmer, W.P. (1994)
DNA shuffling by random fragmentation and reassembly: in vitro recombination for
molecular evolution. Proc Natl Acad Sci USA. 91(22): 10747-1075. In short, DNA
shuffling refers to a process of random recombination of known sequences in vitro,
involving at least two nucleic acids selected for recombination. For example mutations
can be introduced at particular loci by synthesizing oligonucleotides containing a mutant
sequence, flanked by restriction sites enabling ligation to fragments of the native
sequence. Following ligation, the resulting reconstructed sequence encodes an analog
having the desired amino acid insertion, substitution, or deletion. Alternatively,
oligonuclcotidc-dircctcd site-specific mutagenesis procedures can be employed to provide
an altered gene wherein predetermined codons can be altered by substitution, deletion or
insertion.
Accordingly, any of SEQ ID NO 1, 2 or 3 may be recombined with a different
sequence selected from any of SEQ ID NO 1, 2 or 3, and/or with other terpene synthase
encoding nucleic acids, for example isolated from an organism other than Vetiver
zizanoides. Thus, mutant nucleic acids may be obtained and separated, which may be
used for transforming a host cells according to standard procedures, for example such as
disclosed in the present examples.
In step (d), the polypeptide obtained in step (e) is screened for a modified
property, for example a desired modified enzymatic activity. Examples, for desired
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enzymatic activities for which an expressed polypeptide may be screened include
enhanced or reduced enzymatic activity, as measured by KM or Vmax value, for example,
modified regio-chemistry or stereochemistry, altered substrate utilization or product
distribution. The screening of enzymatic activity can be performed according to
procedures familiar to the skilled person and those disclosed in the present examples.
Step (e) provides for repetition of process steps (a)-(d), which may, preferably,
performed in parallel. Accordingly, by creating a significant number of mutant nucleic
acids, many host cells may be transformed with different mutant nucleic acids at the same
time, allowing for the subsequent screening of a elevated number of polypeptides. The
chances of obtaining a desired variant polypeptide may thus be increased at the discretion
of the skilled person.
In an embodiment, the present invention provides a method for preparing a nucleic
acid encoding a variant polypeptide having terpene synthase activity, the method
comprising the steps (a)-(e) disclosed above and further comprising the step of:
(f) if a polypeptide having desired variant terpene activity was identified,
acquiring the mutant nucleic acid obtained in step (c), which was used to transform host
cells to express the variant terpene synthase following staps (c) and (d).
Polypeptide variants also include polypeptides having a specific minimal sequence
identity with any of the polypeplides comprising the amino acid sequences according to
SEQ ID NO: 4, 5, and/or 6.
In an embodiment, the isolated polypeptide comprising an amino acid sequence
which has at least 50% of amino acid sequence identity with SEQ ID NO: 4 and which
has terpene synthase activity. Preferably, the isolated polypeptide comprises an amino
acid sequence, which has at least 55%, 60%, 65%, 70%, 75%, 80%, 90%, and most
preferably 95% of sequence identity with SEQ ID NO: 4.
In an embodiment, the isolated polypeptide comprising an amino acid sequence
which has at least 76.8% of amino acid sequence identity with SEQ ID NO: 5 and which
has terpene synthase activity. Preferably, the isolated polypeptide comprises an amino
acid sequence, which has at least 78%, 79%, 80%, 85%, 90%, 95% and most preferably
97% of sequence identity with SEQ ID NO: 5.
In an embodiment, the isolated polypeptide comprising an amino acid sequence
which has at least 49% of amino acid sequence identity with SEQ ID NO: 6 and which
has terpene synthase activity. Preferably, the isolated polypeptide comprises an amino
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acid sequence, which has al least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%,
95% and more preferably 97% of sequence identity with SEQ ID NO: 6.
Preferably, the polypeptide essentially consists of an amino acid sequence
according to SEQ ID NO: 4, 5 or 6.
In a further aspect, the invention provides a vector comprising the nucleic acid of
the invention.
A "vector" as used herein includes any recombinant vector including but not
limited to viral vectors, bacteriophages and plasmids. The skilled person is capable of
selecting a suitable vector according to the expression system. In one embodiment, the
expression vectors include a cDNA sequence encoding the polypeptide operably linked to
regulatory sequences such as transcriptional promoters, operators, or enhancers, mRNA
ribosomal binding sites, and appropriate sequences which control transcription and
translation initiation and termination for example. Nucleotide sequences are "operably
linked" when the regulatory sequence functionally relates to the cDNA sequence of the
invention.
The vectors of the present invention may be used in the methods for preparing a
genetically modified host organisms and/or cells, in host organisms and/or cells
harbouring the nucleic acids of the invention and in the methods for producing or making
terpene synthases, as is set out further below.
In an aspect, the present invention provides a method of making a terpene
synthase comprising, culturing a host organism and/or ceil modified to contain at least
one nucleic acid sequence under conditions conducive to the production of said terpene
synthasc, wherein said at least one nucleic acid is the nucleic acid according to the
invention.
For example, the method of producing a terpene synthase comprises the steps of
(a) selecting a host organism and/or cell which does not express the nucleic acids
according to the invention;
(b) transforming the organism to express the nucleic acid according to the invention;
(c) culturing the organism under conditions conducive to the production of the terpene
synthase encoded by said nucleic acid.
The present invention also provides a method of producing a terpene synthase, the
method comprising the steps of
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(a) selecting a host organism and/or cell which does express any of the nucleic acids
according to the invention;
(b) transforming the organism to express the nucleic acid according to any of Claims
1 -3or 12 in higher quantity;
(c) culturing the organism under conditions conducive to the production of the terpene
synthase encoded by said nucleic acid.
Accordingly, in a further aspect, the present invention provides a recombinant host
organism and/or cell transformed to harbour the nucleic acid of the invention. The host
organism may be a unicellular or a multi-cellular organism, but is non-human. The host
may be a cell of a multicellular organism, for example. Preferably, the host organism is a
bacterium, for example E. coli. Preferably, the host organism heterologously comprises a
nucleic acid of the invention.
Further preferred host organisms include fungi, preferably yeasts, most preferably
Sacharomyces cerevisiae. Suitable host organisms for expression of polypeptides of the
invention include higher eukaryotic cells, preferably plants. Preferably, the plant is a
species belonging to the family of the Solanaceae or Lamiaceac, more preferably the
genus of Nicotiana. For example, the suitable host cell is a plant cell.
In an aspect, the present invention provides a recombinant host organism or cell
expressing the polypeptide of the present invention. Preferably, the host organism is
transformed to express the polypeptide in a higher quantity than in the same organism not
so transformed.
The term "transformed" refers to the fact that the host was subjected to genetic
engineering to comprise one, two or more copies of any of the nucleic acids of the
invention.
Preferably, the term "transformed" relates to hosts heterologuously expressing
polypeptides of the invention and/or encoded by nucleic acids of the invention.
Accordingly, in an embodiment, the present invention provides a transformed
organism in which the polypeptide of the invention is expressed in a higher quantity than
in the same organism not so transformed.
There are several methods known in the art for the creation of transgenic,
recombinant host organisms or cells such as plants, yeasts, bacteria, or cell cultures of
higher eukaryotic organisms. For example, appropriate cloning and expression vectors for
use with bacterial, fungal, yeast, and mammalian cellular hosts are described, for
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example, in Pouwels et al., Cloning Vectors: A Laboratory Manual, Elsevier, New York,
(1985), and Sambrook et al. cited above.
Cloning and expression vectors for higher plants and/or plant cells in particular
are available to the skilled person, see for example Schardl et al (1987) Gene 61: 1-11.
Methods for transforming host-organisms, for example, producing transgenic
plants, modifying host organisms or cells to harbour transgenic nucleic acids, such as
those of the present invention, are familiar to the skilled person. For the creation of
transgenic plants, for example, current methods include: electroporation of plant
protoplasts, liposome-mediated transformation, agrobacterium-mediated transformation,
polyethylene-glycol-medialed transformation, particle bombardement, microinjection of
plant cells, and transformation using viruses.
In one embodiment, transformed DNA is integrated into a chromosome of a non-
human host organism and/or cell such that a stable recombinant systems results. Any
chromosomal integration method known in the art may be used in the practice of the
invention, including but not limited to, recombinase-mediated cassette exchange
(RMCE), viral site-specific chromosomal insertion, adenovirus, and pronuclear injection.
In a still further aspect, the present invention provides processes and/or methods
for making terpenoids.
Accordingly, the present invention provides a method of making at least one
terpenoid comprising:
(a) cuntacting at least one acyclic pyrophosphate lerpene precursor with, at least one
polypeptide of the invention or encoded by any of the nucleic acids of the invention,
and,
(b) optionally, isolating at least one terpenoid produced in step (a).
Furthermore, the present invention provides a method of making at least one
terpenoid comprising:
cultivating a non-human organism transformed to express or increasingly express
the polypeptide encoded by the nucleic acid of any of claims 1 - 3 or the polypeptide of
claim 4 under conditions conducive to the production of terpenoids, and,
optionally, isolating at least one terpenoid from the non-human organism.
According to a preferred embodiment, the method further comprises the step of:
transforming a non-human organism with a recombinant nucleic acid to express or
increasingly express the polypeptide encoded by the nucleic acid of any of claims 1-3 or
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the polypeptide of claim 4, before the step of cultivating said organism under conditions
conducive to the production of terpenoids.
Preferably, the at least one terpenoid is the terpenoid disclosed in the present
description. More preferably, the methods are suitable to make at least one cyclic terpene
according to formulae (I) to (VII).
The method of making at least one terpenoid comprises the step of contacting at
least one acyclic pyrophosphate terpene precursor with at least one polypeptide of the
invention. For example, polypeptides as obtained in the above methods for producing
terpene synthases may be used. Such polypeptides may be extracted from host organisms
expressing the nucleic acids of the invention according to standard protein or enzyme
extraction technologies. If the host organism is a unicellular organism or cell releasing the
polypeptide of the invention into the culture medium, the polypeptide may simply be
collected from the culture medium, for example by centrifugation, optionally followed by
washing steps and resuspension in suitable buffer solutions.
If the host organism is a plant or a unicellular organism or cell accumulating the
polypeptide of the invention within the cell, the polypeptide may be obtained by
disruption or lysis of the cells and extracting the polypeptide from the cell lysate.
The isolated polypeptide may then suspended in a buffer solution at optimal pH
and temperature. If adequate, salts, BSA and other kinds of enzymatic co-factors may be
added in order to optimise enzyme activity.
The terpene precursor may be added to polypeptide suspension or solution,
followed by incubation at optimal temperature, for example 30°C. After incubation, the
terpenoid compound may be isolated from the incubated solution by standard isolation
procedures, such as solvent extraction and distillation, preferably after removal of
polypeptides from the solution.
In a step of the process for making at least one terpenoid compound, the host
organism or cell is cultivated under conditions conducive to the production of terpenoids.
Accordingly, if the host is a transgenic plant, optimal growing conditions are provided,
such as optimal light, water and nutient conditions, for example. If the host is a
unicellular organism, conditions conducive to the production of the terpenoid may
comprise addition of suitable cofactors to the culture medium of the host. In addition, a
culture medium may be selected which proves to maximize terpenoid synthesis. External
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factors such as optimised pH and temperature are usually also conducive to terpenoid
production in a given expression system.
All the publications mentioned in this application are incorporated by reference to
disclose and describe the methods and/or materials in connection with which the
publications are cited.
The following examples are intended to illustrate the invention without limiting
the scope as a result.
Examples
Example 1
Vetiver roots material, isolation of mRNA and cDNA synthesis
Vetiveria zizanoides (Vetiver) plants were obtained from a plant nurseries ('La
Compagnie des Plantes Australes', Les Avirons, The Reunion Island, France). The plants
were cultivated in pots in a green house at the Lullier Agronomy research Station
(Switzerland) and were propagated vegetatively by dividing six months to one-year-old
clumps. In the greenhouse conditions, transplanted vetiver cuttings start sprouting after
one to three weeks and the roots volume is generally tripled or quadrupled after one-year
cultivation.
For harvesting of the roots, the plants were dug out from the pots and rinsed with
tap water. The sesquiterpene content of the roots was evaluated as follows: the roots were
cut in small pieces or crushed in liquid nitrogen using a mortar and pestle and extracted
with diethyl ether or pentane; after concentration, the extracts were analyzed by GC and
GC-MS. Plants obtained after transplantation of splits from a mother plant were harvested
at different growing stages: from plants with actively expending root system (4 to 6
months after transplantation) to plants with a well-developed dense root system (1 to 2
years after transplantation). Sesquiterpenes characteristic of vetiver oil were found in all
roots analysed and zizanoic acid was the major constituent.
For the cloning experiments, young plants, obtained approximately 6 month after
transplantation, were used. The roots were cut off from the leaves and frozen in liquid
nitrogen. They were first roughly chopped in liquid nitrogen using a Waring Blendor and
then grounded to a fine powder using a mortar and pestle. Total RNA were extracted
using the Concert™ Plant RNA Reagent from In vitro gen following the manufacturer's
instructions. The concentration of RNA was estimated from the OD at 260 nm and the
integrity of the RNA was evaluated on an agarose gel by verifying the integrity of the
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ribosomal RNA bands. The mRNA were purified from the total RNA by oligodT-
cellulose affinity chromatography using the FastTrack® 2.0 mRNA isolation Kit
(Invitrogen) following the manufacturer's instructions. The concentration of the mRNA
was estimated from the OD at 260 nm and an aliquot was deposited on an agarose gel to
verify the size distribution of the mRNA pool.
Adaptor ligated double stranded cDNA was prepared from the 1 μg of mRNA
using the Marathon™ cDNA Amplification Kit (Clontech) following the manufacturer's
protocol. An aliquot of the cDNA library was deposited on an agarose gel to evaluate the
quantity and size distribution.
Example 2
Isolation of fragments of cDNA encoding for sesquiterpene synthases from vetiver
roots
Fragments of cDNA encoding for sesquiterpene synthases were amplified using
degenerated primers specific for plant sesquiterpene synthases nucleotidic sequences.
Sesquiterpene-synthase-specific oligonucleotides have been previously designed
from an alignment of plant sesquiterpene synthases amino-acid sequences (WO
04/031376). Six primers (four forward and two reverse) were designed from three regions
conserved among the plant sesquiterpene synthases amino-acid sequences. They were
named TpsVFl, TpsVF2, TpsCFl, TpsCF2, TpsVR3 and TpsCR3 (WO 04/031376).
In addition, a set of oligonucleotides was designed for improved specificity towards
sesquiterpene synthases nucleotidic sequences of vetiver. Sequence comparison of
terpene synthases isolated from different plants has shown high sequence homologies in
relation to phylogeny. The sequence homology is high among terpene synthases from
taxonomically related species and is not related to functional specialization (enzymatic
activity). We thus decided to design new sesquiterpene synthases-specific primers based
on the alignment of the sequence of sesquiterpene synthases obtained from plant species
related to vetiver. Vetiver is a Gramineae plant (grass family) and belongs to the
Monocotyledons class (Liliopsida). The amino-acid sequences of sesquiterpene synthases
from monocotyledon plants (accession number AAC31570 from Elaeis oleifera (oil
palm), accession numbers BAC99549, BAC99543, AAR01759, BAD03024, NP_908798,
BAC20102, AAR87368 from Oryza sativa (Rice) and accession numbers AAG37841,
AAS88575, AAS88574, AAS88573, AAS88572, AAS88571 from Zea mays (corn)) were
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aligned using ClustalW [Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994)
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment
through sequence weighting, position specific gap penalties and weight matrix choice.
Nucleic Acids Res. 22, 4673-4680] and regions conserved across all sequences were
selected. From these regions, primers were design using the CODEHOP strategy [Rose
T.M., Schultz E.R., Henikoff J.G, Pietrokovski S. McCallum C.M and Nenikoff S. (1998)
Consensus-degenerated hybrid oligo-nucleotide primers for amplification of distantly
related sequences. Nucleic Acids Research 26(7), 1628-1635] implemented as a computer
program accessible over the World Wide Web
[http://blocks.fhcrc.org/blocks/make blocks.html and
http://blocks.fhcrc.org/blocks/codehop.html]. The parameters of the program were set so
as to design primers with a degenerated core of 11 to 13 bases, a maximum degeneracy
(number of different sequences specified by each primer) of 256 and an annealing
temperature around 60 °C. The codon usage of the monocotyledon plant Zea mays was
used. Using this approach, four forward primers and two reverse primers were designed
from five conserved regions (Table 1).

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For each primer in table 1 the nucleotide sequence is given and the corresponding
amino acid sequence in the alignment is shown. The degeneracies in the nucleotides
sequences are indicated using the IUPAC one letter code.
These primers were used in RT-PCR experiments with total RNA extracted from
vetiver roots.
In all experiments, the reverse transcriptions were performed at 60°C, using
vctivcr roots total RNA, an oligo(dT)2o primer and the Thermo script™ reverse
transcriptase (Invitrogen) as described by the manufacturer.
The PCR conditions were adapted for the two sets of primers. With the plant-
sesquiterpene-synthases-specific primers, the PCR were performed using the Platinum®
Taq DNA polymerase (Invitrogen). The different possible combinations of the forward
primers TpsVFl, TpsVF2, TpsCFl and TpsCF2 and the reverse primers TpsVR3,
TpsCR3 and dTadaptor primer (Table 2) were used for the first round PCR. The PCR mix
contained 5 μL 10X PCR reaction buffer (invitrogen), 1.5 mM MgCl2, 0.2 mM dNTPs,
200 nM forward primer, 200 nM reverse primer, 0.4 μL (2 units) Platinum® Taq DNA
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polymerase, 2 μL of cDNA from the reverse transcription described above and distilled
water to a final volume of 50 uL. The reactions were performed on a Eppendorf
Mastercycler Gradiant thermal cycler and the cycling conditions were as follows: 2 min at
95°C; 35 cycles of 45 sec at 94°C, 45 sec at 42°C, 2 min 30 sec at 72°C; and 10 min final
extension at 72°C. A second round of PCR was performed with the same conditions as for
the first round of PCR using as template 5 μL of the first PCR mixture and the same
primers or nested primers. The size of the PCR products were evaluated on a 1% agarose
gel. Among the several RT-PCR, two produced the expected fragments: TpsCFl+
dTadaptor in the first PCR followed by TpsCF2+TpsCR3 in the second PCR, and
TpsCF2+ dTadaptor in the first PCR followed by TpsCF2+TpsCR3 in the second PCR.
The bands were excised from the gel, purified using the QIAquick Gel Extraction Kit
(Qiagen) and cloned in the pCR®2.1-TOPO vector using the TOPO TA cloning Kit
(Invitrogen). Inserted cDNAs were then subject to DNA sequencing and the sequences
compared against the GenBank non-redundant protein database (NCBI) using the
BLASTX algorithm (Altschul, S.F., Gish, W., Miller, W., Myers, E.W., and Liprnan, D.J.
(1990) Basic local alignment search tool. J. Mol. Biol. 215, 403-410). The comparison
was performed on-line at http://www.ncbi.nlm.nih.gov/BLAST/. The sequence analysis
revealed homology with sesquiterpene synthases and comparison of the sequences
showed that we had four distinct fragments of cDNA with significant sequence
differences: CA711, CA717, CA782 and CA783 (Figure 2).
With the monocot-sesquiterpene-synthases-specific primers, The PCR steps were
performed using the Advantage 2 Polymerase Mix from Clontech. Each PCR mixture
contained 5 ΜL of Advantage 2 PCR Buffer, 200 μM dNTPs, 200 nM each
oligonucleotide primer, 2 μL of cDNA from the reverse transcription described above,
1μL of Advantage 2 Polymerase Mix and distilled water to a final volume of 50 μL. The
following conditions were used for the amplifications: 3 minutes of denaturation at 94°C;
15 cycles of 1 minutes denaturation at 94°C, 1 min of annealing at 65°C for the first cycle
and minus one degree for each following cycle, and 2 minutes extension at 72°C;
20 cycles of 1 minutes denaturation at 94°C, 1 min of annealing at 58°C and 2 minutes
extension at 72°C; and finally 10 minutes extension at 72°C. Different PCR were
performed with the possible combination of monocot-sesquiterpene-synthases-specific
forward and reverse primers. A second round of PCR was performed using as template
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28
5μL of the first PCR mixture, with the same conditions and same primers as described
above for the first round of PCR. The combination of forward and reverse primers
TpsmonocotF3 + TpsMonocotRl, TpsmonocotF3 + TpsMonocotR2, TpsmonocotF4 +
TpsMonocotRl and TpsmonocotF4 + TpsMonocotR2 produced amplicons with the
expected size. Sequence analysis and comparison showed that we had partial cDNA
encoding for three distinct and new sesquitcrpene synthases: CA725, CA731 and CA733
(Figure 2).
Example 3
Amplification of full-length cDNA encoding for sesquiterpene synthases by Rapid
Amplifcation of cDNA Ends (RACE)
Forward specific primers were designed from these new cDNA fragments (Table
2). 3'RACE was performed as follows. First, a reverse transcription was performed at
60°C using the oligo(dT)2o primer, 1.5 microg of total RNA and the Thcrmoscript™
reverse transcriptase, in the same condition as described above for the RT-PCR. A first
PCR was performed using the dTadaptor primer and a forward cDNA-pecific primer. The
PCR mixture contained 0.4 μM cDNA-specific primer, 0.4 μM of dTadaptor primer
(Table 2), 300 μM each dNTPs, 5 μL of 10X HotStartTaq® DNA polymerase buffer
(Qiagen), 2 μL of the cDNA, 0.5 μL of HotStartTaq® DNA polymerase in a final volume
of 50 μL. The cycling conditions were: 15 min at 95°C; 35 cycles of 45 sec at 94°C,
45sec at 48°C and 2 min 30 sec at 72°C; and 10 min at 72°C. A nested PCR was
performed using a PCR mixture with the same composition as above except for the
following modifications: a nested cDNA-specific primer and the adaptorP primer (Table
2) were used, 5 mL of the first PCR was used for the template, and the annealing
temperature was increased to 60°C. The amplification products were evaluated, sub-
cloned, and their sequence analyzed as described above. The 3'RACE succeeded for
CA717 and CA733 (Figure 3), but not for the other cDNAs. A 3'RACE experiment with
the Therrnoscript™ and the primers CA711_F1 and CA711_F2 (Table 2) and with an
annealing temperature of the nested PCR lowered at 48°C instead of 60°C, allowed the
non-specific amplification of the 3'end of a new sesquiterpene synthase cDNA, named
CA775.
Table 2: Primers used for 3'RACE and 5'RACE

WO 2006/134523 PCT/IB2006/051831
30
Based on the three half-full-length sequences obtained after the 3'RACE, we
designed specific reverse primers for use in 5'RACE. The 5'RACE System from
Invitrogen was used. For this procedure, three primers were used for each cDNA (one to
prime the reverse transcription, and two nested primers for the first and second PCR). The
reverse transcription part of the protocol was adapted for transcripts with high GC
content, as described by the manufacturer. The PCR was performed using the Platinum®
Taq DNA polymerase (Invitrogen). For the first PCR, the template was 5 μL of dC-tailed
cDNA, and a cDNA specific primer (Table 2) and the Abridged Anchor Primer
(Invitrogen) were used. The cycling conditions were: 2 min at 94°C; 35 cycles of 0.5 min
at 94°C, 0.5 min at 55°C and 2 min at 72°C; and 10 min at 72°C, For the second PCR, the
template was 5 μL of 100 fold diluted first PCR product, and a nested cDNA-specific
primer (table 2) and the Universal Amplification Primer (Invitrogen). The cycling
conditions for the second PCR were: 2 min at 94°C; 12 cycles of 0.5 min at 94°C, 0.5 min
at 68°C for the first cycle and minus 1 °C for each subsequent cycle, and 2 min at 72°C;
25 cycles of 0.5 min at 94°C, 0.5 min at 60°C and 2 min at 72°C; and 10 min at 72°C.
The amplification products were evaluated, sub-cloned, and their sequence analyzed as
described above.
The amplification of the 5'end succeeded for CA717 and CA733, and for these
two clones the full-length nucleotide sequence could be reconstituted (Vet 717: SEQ ID
NO 1; Vet 733: SEQ ID NO: 2).
For CA775, a first 5'RACE using the same approach allowed amplification of an
820 bp fragment. The analysis of the sequence showed a 60 bp overlap with the CA775
3'RACE product but revealed that the 5'RACE was not complete and that a portion of the
5'end was still missing. A new set of primers was designed based on the 5'PACE
sequence obtained (further close to the 5'-end) and the 5'RACE was repeated in the same
condition. These permitted to obtain an additional 100 bp but the translation initiation
codon was still missing.
A third set of primers was designed for use with the cDNA obtained with the
Marathon cDNA synthesis Eat (Clontech). The amplification was performed on an
Eppendorf Mastercycler Gradiant thermal cycler with the Advantage® 2 Polymerase Mix,
WO 2006/134523 PCT/IB2006/051831
31
as described by the manufacturer. This third 5'RACE provided a additional 100 bp
sequence that finally contained the start codon and thus provided the full length
nucleotide sequence (Vet 775, SEQ ID NO: 3).
Comparison of the aminoacid sequences deduced from the full-length
sesquiterpene synthase-encoding cDNAs (named Vet717, Vet733 and Vet775,
corresponding to SEQ ID NO: 4, 5 and 6, respectively) showed a relative low homology
(Figure 3) (identity ranging from 31 to 40 %). The closest mach found in the public
sequences databanks are putative sesquiterpenes sesquiterpene synthases sequences from
Oryza sativa (Rice) and Zea mays (corn). For Vet717 and Vet775, the closest sequences
are respectively 47 % and 50 % identical. Vet733 has relative high sequences homology
(76.8 % identity) with sequences of sesquiterpene synthases from Zea mays encoded by
the nucleotide sequences with accession number AY518310 to AY518314 (Kollner et al
(2004) The Plant cell 16(5), 1115-1131). The sequence at the N-term end of Vet755
differs from the two others and from other know sesquiterpene synthases: the N-terminal
end is extended by 50 amino-acids and contains an unusual motif PAAAASSQQQQ
(SEQ ID NO: 7). Such N-tcrminal additional sequence is unusual and docs not resemble
any known peptide signal sequence.
Example 4
Heterologous expression in bacteria of the sesquiterpene synthases from vetiver
The Vel717 full-length cDNA was amplified from the Marathon cDNA library
using the primers CA717_Nde and CA717_Kpn (Table 3) designed from the sequence
information obtained by RACE. PCR was performed using the Pfu polymerasc
(Promega), in a final volume of 50 μl containing 5μl of Pfu DNA polymerase 10X buffer,
200 ΜM each dNTP, 0.4 ΜM each forward and reverse primer, 2.9 units Pfu DNA
polymerase and 5 μl of 100-fold diluted cDNA (prepared as described above using the
Marathon™ cDNA Amplification Kit (Clontech)). The thermal cycling conditions were as
follows: 2 min at 95°C; 30 cycles of 30 sec at 95°C, 30 sec at 55°C and 4 min at 72°C;
and 10 min at 72°C. The PCR product, consisting of the full-length Vet717 cDNA
containg a Ndel site including the translation initiation codon and the Kpnl site
immediately after the stop codon, was purified on an agarose gel and eluted using the
QIAquick® Gel Extraction Kit (Qiagen). The PCR product was digested with Ndel and
WO 2006/134523 PCT/IB2006/051831
32
Kpnl and ligated into the pETDuet-1 plasmid (Novagen) digested with the same enzymes.
Sequencing of the insert showed no sequence difference with the RACE products.
Table 3: Primers used for construction of the expression plasmids
The plasmid was then transferred into E. coli BL21 (DE3) cells (Novagen). Single
colonies of transformed cells were used to inoculate 5 ml LB medium. After 5 to 6 hours
incubation at 37°C, the cultures were cooled to a 20°C and expression of the protein was
induced with 0.5 mM IPTG. After over-night incubation the cells were collected by
centrifugation, resuspended in 0.5 ml Extraction Buffer (50 mM MOPSO pH 7, 5 mM
WO 2006/134523 PCT/IB2006/051831
33
DTT, 10% glycerol) and sonicated 3 times 20 s. The cell debris were sediraented by
centrifugation 30 rain at 18,000g and the supernatant containing the soluble proteins was
recovered. Analysis by SDS-PAGE analysis revealed the production of a recombinant
protein with the expected molecular weight.
In the same way, the Vet733 cDNA was amplified from the Marathon cDNA
library using the primers 733_Nco and 733_Eco (Table 3) and ligated as a Ndel-EcoRl
fragment into the pETDuet-1 expression plasmid. The constructs were verified by
sequencing. The heterologous expression in BL2KDE3) using these plasmids provided a
recombinant protein clearly visible by SDS-PAGE.
For ligation of Vet775 into the pETDuet-1 expression plasmid, since the cDNA
already contained two Ndel and one Ncol restriction sites (respectively at position 603,
1483 and 1020), the amplification was performed in two stages, using the overlap
extension PCR strategy (Horton, R.M., Hunt, H.D., Do, S.N., Pullen, J.K. and Pease, L.R.
(1989) Engineering hybrid genes without the use of restriction enzymes: gene splicing by
overlap extension. Gene 77, 61-68), in order to introduce the Ncol and Ecorl sites at the
extremities and to remove the internal Ncol restriction site. Two separate PCR reactions
were first performed: one with primers Vet775_Nco (introducing a Ncol site immediately
before the start codon) and 775_mut_F2; the second with the primers 775_mut_R2 and
775_fus_Eco (introducing a EcoRI site immediately after the stop codon). The
775_mut_F2 and 775_mut_R2 primers are forward and reverse mutagenic primers with
32 nucleotides overlapping region and allowing the suppression of the Ncol recognition
site at position 1020 in the cDNA without modifying the protein sequence (change the
codon for Ala340 from GCC to GCA) (Table 3). The products from these two PCR were
purified, combined and used as template in a last PCR were the full-length mutated
Vct775 cDNA is amplified with the primers Vct775_Nco and 775_fus_Eco. The PCR
product was then ligated between the Ncol and EcoRI restriction sites of the pETDuet-1
plasmid.
In addition, to evaluate the effect of the unusual N-terminal sequence of Vet775
on the expression in E. coli and on the enzymatic activity, we made two constructs
consisting of removing portions of the N-terminal end of Vet775 and replacing them with
the equivalent portion derived from Vet717. Two modified cDNA were thus made,
Vet775_fusl and Vet775_fus2. In the first construct, the 68 first codons were removed
and replaced with the 24 N-terminal codons of Vet717. In the second construct, the 91
WO 2006/134523 PCT/EB2006/051831
34
first codons were removed and replaced with the 42 N-terminal codons of Vet717. These
construct were made by overlap extension PCR. For Vet775_fusl, a first PCR was
performed using the primers 775_fus_Nco and 775_fusl-r and as template the Vet717
cDNA in pETDuet-1. A second PCR was performed with the primers 775_fusl-f and
775_fus_Eco and as template the Marathon cDNA library. The primers 775_fusl-f and
775_fus 1-r contain an overlapping region of 29 nucleotides (Table 3). The PCR products
from the two amplifications were purified and used as template in another PCR using as
the primers 775_fus_Nco and 775_fus_Eco. The PCR product, consisting of the open
reading frame of Vet775 with the 204 5'-end bp replaced by the 72 5'-end bp of Vet717
and flanked by the Ncol and Ecorl restriction sites, was ligated in the pCR®2.1-TOPO
vector using the TOPO TA cloning Kit (In vitro gen). The inserts from three separated
clones were fully sequenced to ensure that there was no sequence variation. The plasmid
was then used as template for site directed mutagencsis by overlap extension PCR to
remove the two Ncol sites at position 72 and 888 in nucleotidic sequence. This last
modification was performed as described above by generating three overlapping
fragments using the mutagenic primers pairs 775_mut_Fl and 775_mut_Rl (change the
codon for Pro24 from CCA to CCT) (Table 3) and 775_mut_F2 and 775_mut_R2
(described above). The PCR product was finally ligated between the Ncol and EcoRl
restriction sites of the pETDuet-1 plasmid. The construction of the cDNA coding for the
Vet775_fus2 was made in the same way using the primers 775_fus2-f and 775_fus2-r
(Table 3) in the first PCR to produce a cDNA consisting of nucleotides 1-126 for Vet717
fused to the nucleotides 274 to 1521 fro Vct775.
All these PCR for the amplification of the full-length or modified Vet775 cDNA
were performed with the Pfu DNA poiymerasc as described above.
Heterologous expression in E. coli BL21(DE3) followed by SDS-PAGE analysis
showed the production of a recombinant protein for the Vet775_fusl and Vet775_fus2
constructs, but no recombinant protein was seen for the full-length non-modified Vet775.
Example 5
Characterization of the enzyme activities of the recombinant sesquiterpene
synthases
The recombinant proteins obtained were assayed for sesquitepene synthase
activity using FPP as substrate. The enzymatic assays were performed in Teflon sealed
WO 2006/134523 PCT/IB2006/051831
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glass tubes using 50 to 100 μl of crude E. coli protein extract, obtained following the
procedure given in Example 3 (following Table 3) in a final volume of 1 mL Extraction
Buffer supplemented with 15 mM MgCl2 and 100 to 250 uM purified FPP. The media
were overlaid with 1 ml pentane and the tubes incubated 12 to 18 hours at 30°C.
The sesquiterpenes produced were extracted twice with pentane and analyzed by
GC and GC/MS as described previously (WO 04/031376, Example 6).
Enzymes assays with protein extracts obtained from cultures of E. coli
transformed with the expression plasmids containing the Vet775 Full-length cDNA or the
two Vet775 fusion proteins, did not permit to detect any sesquiterpene synthase activity.
The reasons for this apparent inactivity remain undetermined.
The Vet717 recombinant protein (SEQ ID NO: 4) produced a major sesquiterpene
hydrocarbon and several minor products (Figure 4). The mass spectrum of the major
product matched the mass spectrum of cyclosativene ((6) in Figure 1) and the rentention
time of this major product lined up with the retention time of a cyclosativene standard, on
an apolar (SPB-1, Supelco) as well as on a polar column (InnoWax, Hewlett-packard).
Cyclosativene or derivatives thereof were never identified in vetiver oil. Among the many
sesquiterpenes identified, (he oxygenated cyclocopacamphane sesquiterpenes (Figure 1)
are the most structurally close to cyclosativene. Cyclocopacamphene (7) is the
stereoisomer of cyclosativene (Kido F et al (1969) Tetrahedron letters 37, 3169-3172)
and interestingly, oxygenated derivatives of cyclocopacamphene are present in relative
large quantities, up to 4%, in vetiver oil (Homa ct al (1970) Tetrahedron letters 3, 231-
234; Weyerstahl et al (2000) Flavour Frag. J. 15, 61-83; Weyerstahl et al (2000) Flavour
Frag. J. 15, 153-173; Weyerstahl et al (2000) Flavour Frag. J. 15, 395-412).
To distinguish the product of Vet717 from cyclosativene, I employed chiral GC
chromatography using a Megadex-5 (MEGA s.n.c, Legnano, Italy) capillary column (12
m, 0.25 mm, 0.25 |im) with the initial oven temperature set at 60°C for 2 min hold,
followed by a ramp of 5°C/min to 150°C and a second ramp of 20°C/min to 270°C. In
these conditions, cyclosativene had a retention time of 5.60 min and was clearly separated
from the Vet717 product that had a retention time of 5.75 min.
The Vet717 enzyme produces also several minor products which, based on the MS
spectra, could have related structures such as cubebane or copaane skeletons.
The Vet733 recombinant protein (SEQ ID NO: 5) does not produce a major
product but a mixture of at least 7 different sesquiterpene hydrocarbons (Figure 5). The
WO 2006/134523 PCT/IB2006/051831
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following compounds could be identified based on the MS spectra and comparison of the
rentention index with published data: (1) cis-alpha-bergamotene, (2) trans-alpha-
bergamotene, (3) epi-beta-santalene, (4) beta-bisabolene, and (5) trans-gama-bisabolene.
They were further confirmed by comparison to in house standards containing beta-
bisabolene, trans-gama-bisabolene, trans-alpha-bergamotene and cis-alpha-bergamotene.
The structure of epi-beta-santalene was confirmed by comparison to a GC-MS analysis of
opoponax extract.
The sesquiterpene hydrocarbons produced by Vet733, or derivatives of these
sesquiterpenes, have never been isolated from vetiver oil. It could be possible that Vet733
is expressed at low level in the roots of vetiver and that the sesquiterpenes produced by
this enzyme are present in the oil at a level to low to be detected. The alcohols derivatives
of some of the products of Vet733, (Z)-(+)-epi-beta-santalol and (Z)-alpha-trans-
bergamotol (Figure 1), have been described as being important contributors to the scent of
sandalwood oil (DE 3 205 320; Frater, G., Bajgrowicz, J.A, and Kraft, P. (1998)
Fragrance Chemistry. Tetrahedron 456, 7633-7703.). The odour of vetiver is very
complex and, among many others, the sandalwood-likc note has been described for this
oil. It could thus be possible that the sandalwood aspect could be related to the presence
of trace amounts of oxygenated derivatives of the Vet733 products.
Drawing of the mechanistic scheme for the formation of the sesquiterpenes
produced by Vet733 explains the relationship of the multiple products formed (Figure 6).
Each turnover cycle starts with the isomerization of FPP ((16) in Figure 6) to nerolydol-
pyrophosphate (NPP) (with rotation about the C2-C3 bond), followed by cyclization to the
bisabolyl cation (17). The cyclization can then go on via several mechanisms. The beta-
bisabolene and trans-gamma-bisbolene can be formed by deprotonation at C6 or C14
respectively. C2-C7 closure followed by deprotonation leads to cis- and trans-alpha-
bergamotenes. C3-C7 closure, followed by Wagner-Meerwein rearrangement and
deprotonation at C15 leads to epi-beta-santalene. The Vet733 sesquiterpene synthase is the
first cloned sesquiterpene synthase able to catalyse the cyclisation of FPP to the bisabolyl
cation and subsequent cyclization to the bergamotane and santalane skeleton.
WO 2006/134523 PCT/IB2006/051831
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Claims
1. An isolated nucleic acid selected from:
(a) a nucleic acid comprising a nucleotide sequence having at least 82.4% identity
5 with SEQ ID NO: 2;
(b) a nucleic acid comprising a nucleotide sequence encoding a polypeptide having at
least 76.8% sequence identity with SEQ ID NO: 5;
(c) a nucleic acid comprising a nucleotide sequence that hybridises to the nucleotide
sequence SEQ ID NO: 2 under moderate stringency conditions;
10 (d) a nucleic acid comprising a nucleotide sequence encoding a polypeptide capable
of synthesising at least one bi-cyclic and/or tri-cyclic sesquiterpene comprising a C3-C7
bond; and/or,
(e) a nucleic acid comprising a nucleotide sequence encoding a polypeptide capable
of synthesising at least one bergamotene and, optionally, other sesquiterpenes,
15 characterized in that begamotenes constitute at least 5 wt.% of the total of sesquiterpene
products synthcsiscd by the polypeptide;
wherein the polypeptide encoded by any of the said nucleic acids of (a)-(e) has terpene
synthase activity.
20 2. The isolated nucleic acid of claims 1, which hybridises with the nucleic acid of
SEQ ID NO: 2 and which does not hybridise with a nucleic acid sequence selected from
those having accession numbers AY518310 or AY518313 encoding sesquiterpene
synthases in Zea mays.
25 3. The isolated nucleic acid of claims 1 or 2, encoding a polypeptide capable of
synthesising one or more bi- or tricyclic sesquiterpenes selected from the group of
(+)-epi-β-santalene, trans-α-bergamotene, cis-α-bergamotene, β-bisabolene, trans-γ-
bisabolene and/or a combination of two or more of the aforementioned.
30 4. An isolated polypeptide selected from:
(a) a polypeptide comprising an amino acid sequence having at least 76.8% of amino
acid sequence identity with SEQ ID NO: 5;
WO 2006/134523 PCT/IB2006/051831
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(b) a polypeptide capable of synthesising a bi-cyclic and/or tri-cyclic sesquiterpene
comprising a C3-C7 bond;
(c) a polypeptide capable of synthesising at least one bergamotene and, optionally,
other sesquiterpenes, characterized in that begamotenes constitute at least 5 wt.% of the
5 total of sesquiterpene products synthesised by the polypeptide.
5. A recombinant host organism and/or cell transformed to harbour the nucleic acid
of any of Claims 1-3.
10 6. A method of making at least one terpenoid comprising:
(a) contacting at least one acyclic pyrophosphate terpene precursor with at least one
polypeptide according of claim 4 or encoded by the nucleic acid according to any of
claims 1-3, and,
(b) optionally, isolating at least one terpenoid produced in step (a).
15
7. A method of making at least one terpenoid comprising:
- cultivating a non-human organism transformed to express or increasingly express the
polypeptide encoded by the nucleic acid of any of claims 1 - 3 or the polypeptide of
claim 4 under conditions conducive to the production of terpenoids, and,
20 - optionally, isolating at least one terpenoid from the non-human organism.
8. The method of claim 7 comprising the step of:
transforming a non-human organism with a recombinant nucleic acid to express or
increasingly express the polypeptide encoded by the nucleic acid of any of claims 1-3
25 or the polypeptide of claim 4, before the step of cultivating said organism under
conditions conducive to the production of terpenoids.
9. A method of making a terpene synthase comprising, culturing a host organism or
cell modified to contain at least one nucleic acid sequence under conditions conducive to
30 the production of said terpene synthase, wherein said at least one nucleic acid is the
nucleic acid according to any of claims 1-3.
WO 2006/134523 PCT/IB2006/051831
39
10. A method for preparing a variant polypeptide having a desired terpene synthase
activity, the method comprising the steps of:
(a) selecting a nucleic acid comprising a nucleotide sequence having at least 82.4%
identity with SEQ ID NO 2;
5 (b) modifying the selected nucleic acid to obtain at least one mutant nucleic acid;
(c) transforming host cells with the mutant nucleic acid sequence to express a
polypeptide encoded by the mutant nucleic acid sequence;
(d) screening the polypeptide for a functional polypeptide having at least one
modified property; and,
10 (e) optionally, if the polypeptide has no desired variant terpene synthase activity,
repeat the process steps (a) to (d) until a polypeptide with a desired variant terpene
synthase activity is obtained.
11. A method for preparing a nucleic acid encoding a variant polypeptide having a
15 desired terpene synthase activity, the method comprising the steps of claim 10 and further
comprising the step of:
(f) if a polypeptide having desired variant terpene activity was identified, acquiring
the mutant nucleic acid obtained in step (c), which was used to transform host cells to
express the variant terpene synthase following steps (c) and (d).
20
12. An isolated nucleic acid selected from:
(a) a nucleic acid comprising a nucleotide sequence having at least 59% sequence
identity with SEQ ID NO: 1;
(b) a nucleic acid comprising a nucleotide sequence encoding a polypeptide having at
25 least 50% of amino acid sequence identity with SEQ ID NO: 4;
(c) a nucleic acid that hybridises to SEQ ID NO: 1 under moderate stringency
conditions;
(d) a nucleic acid comprising a nucleotide sequence encoding a polypeptide capable
of synthesising cyclocopacamphene;
30 wherein the polypeptide encoded by said nucleic acid has terpene synthase activity.
13. An isolated polypeptide selected from:
WO 2006/134523 PCT/IB2006/051831
40
(a) a polypeplide having at least 50% of amino acid sequence identity with SEQ ID
NO: 4;
(b) a polypeptide capable of synthesising cyclocopacamphene.
5 14. A recombinant host organism and/or cell transformed to harbour the nucleic acid
of claim 12 and/or transformed to express or increasingly express the polypeptide of
claim 13.

The present invention relates to novel terpene synthases. The terpene synthases are capable of synthesising mono-,
bi- and/or tri-cyclic sesquiterpenes having a C2-C7 or a C3-C7 bond, starting from an acyclic pyrophosphate terpene precursor, far-nesyl- pyrophosphate.
Accordingly, for the first time, sesquiterpene synthases catalysing the cyclisation to the santalene and berg-amotene
carbon skeleton are disclosed. The present invention further relates to nucleic acid sequences encoding the sesquiterpene
synthases and to methods for making terpenoids.

Documents:

04392-kolnp-2007-abstract.pdf

04392-kolnp-2007-claims.pdf

04392-kolnp-2007-correspondence others.pdf

04392-kolnp-2007-description complete.pdf

04392-kolnp-2007-drawings.pdf

04392-kolnp-2007-form 1.pdf

04392-kolnp-2007-form 3.pdf

04392-kolnp-2007-form 5.pdf

04392-kolnp-2007-gpa.pdf

04392-kolnp-2007-international publication.pdf

04392-kolnp-2007-international search report.pdf

04392-kolnp-2007-pct priority document notification.pdf

04392-kolnp-2007-pct request form.pdf

04392-kolnp-2007-sequence listing.pdf

4392-KOLNP-2007-(04-04-2014)-CORRESPONDENCE.pdf

4392-KOLNP-2007-(06-03-2014)-CLAIMS.pdf

4392-KOLNP-2007-(06-03-2014)-CORRESPONDENCE.pdf

4392-KOLNP-2007-(13-11-2013)-CLAIMS.pdf

4392-KOLNP-2007-(13-11-2013)-CORRESPONDENCE.pdf

4392-KOLNP-2007-(23-04-2013)-ABSTRACT.pdf

4392-KOLNP-2007-(23-04-2013)-CLAIMS.pdf

4392-KOLNP-2007-(23-04-2013)-CORRESPONDENCE.pdf

4392-KOLNP-2007-(23-04-2013)-DESCRIPTION (COMPLETE).pdf

4392-KOLNP-2007-(23-04-2013)-DRAWINGS.pdf

4392-KOLNP-2007-(23-04-2013)-FORM 1.pdf

4392-KOLNP-2007-(23-04-2013)-FORM 13.pdf

4392-KOLNP-2007-(23-04-2013)-FORM 2.pdf

4392-KOLNP-2007-(23-04-2013)-FORM 3.pdf

4392-KOLNP-2007-(23-04-2013)-FORM 5.pdf

4392-KOLNP-2007-(23-04-2013)-OTHERS.pdf

4392-KOLNP-2007-(23-04-2013)-PETITION UNDER RULE 137-1.1.pdf

4392-KOLNP-2007-(23-04-2013)-PETITION UNDER RULE 137.pdf

4392-KOLNP-2007-AMENDED PAGE 36 OF COMPLETE SPECIFICATION.pdf

4392-kolnp-2007-ASSIGNMENT-1.1.pdf

4392-KOLNP-2007-ASSIGNMENT.pdf

4392-kolnp-2007-CANCELLED PAGES.pdf

4392-KOLNP-2007-CORRESPONDENCE OTHERS 1.2.pdf

4392-KOLNP-2007-CORRESPONDENCE OTHERS-1.1.pdf

4392-kolnp-2007-CORRESPONDENCE.pdf

4392-kolnp-2007-EXAMINATION REPORT.pdf

4392-kolnp-2007-FORM 13.pdf

4392-kolnp-2007-FORM 18-1.1.pdf

4392-kolnp-2007-form 18.pdf

4392-KOLNP-2007-FORM 3-1.1.pdf

4392-kolnp-2007-GPA.pdf

4392-kolnp-2007-GRANTED-ABSTRACT.pdf

4392-kolnp-2007-GRANTED-CLAIMS.pdf

4392-kolnp-2007-GRANTED-DESCRIPTION (COMPLETE).pdf

4392-kolnp-2007-GRANTED-DRAWINGS.pdf

4392-kolnp-2007-GRANTED-FORM 1.pdf

4392-kolnp-2007-GRANTED-FORM 2.pdf

4392-kolnp-2007-GRANTED-FORM 3.pdf

4392-kolnp-2007-GRANTED-FORM 5.pdf

4392-kolnp-2007-GRANTED-SPECIFICATION-COMPLETE.pdf

4392-kolnp-2007-INTERNATIONAL PUBLICATION.pdf

4392-kolnp-2007-INTERNATIONAL SEARCH REPORT & OTHERS.pdf

4392-kolnp-2007-OTHERS.pdf

4392-kolnp-2007-PETITION UNDER RULE 137.pdf

4392-kolnp-2007-REPLY TO EXAMINATION REPORT.pdf


Patent Number 260322
Indian Patent Application Number 4392/KOLNP/2007
PG Journal Number 17/2014
Publication Date 25-Apr-2014
Grant Date 23-Apr-2014
Date of Filing 15-Nov-2007
Name of Patentee FIRMENICH SA
Applicant Address 1, ROUTE DES JEUNES, P.O. BOX 239, CH-1211 GENEVA 8
Inventors:
# Inventor's Name Inventor's Address
1 SCHALK MICHEL 195, ALLEE DES RESIDENCES DU SALEVE, 74160 COLLONGES-SOUS-SALEVE
PCT International Classification Number C12N 9/00, C12P 1/00
PCT International Application Number PCT/IB2006/051831
PCT International Filing date 2006-06-08
PCT Conventions:
# PCT Application Number Date of Convention Priority Country
1 05105381.7 2005-06-17 EUROPEAN UNION