Title of Invention

METHOD FOR PRODUCING CYTOSINE NUCLEOSIDE COMPOUNDS

Abstract A method for producing a cytosine nucleoside compound by reacting a compound of formula (I) wherein X is carbon or nitrogen, Y is hydrogen, a halogen or a C1-4 alkyl with a sugar phosphate in the presence of an enzyme capable of catalysing their reaction, wherein the enzyme has the activity of cytosine nucleoside phosphorylase, and has the amino acid sequence shown in SEQ ID NO:4 or is a variant having an amino acid sequence obtainable by substituting a different amino acid or acids for at least one amino acid selected from the amino acids corresponding to No. 10, No.16, No. 42, No. 54, No. 67, No. 74, No. 104, No. 135, No. 157, No. 167, No. 168, No. 178, No. 179, No. 183, No. 199, No. 204, No. 210, No. 228 and No. 233 on the amino acid sequence of SEQ ID NO.: 4.
Full Text METHOD FOR PRODUCING CYTOSINE NUCLEOSIDE COMPOUNDS
BACKGROUND OF THE INVENTION
Field of the Invention
The present invention relates to a method for producing
cytosine nucleoside compounds, which are useful as starting
material for synthesis of compounds, such as those for medical
use. More specifically, the invention relates to a method
for producing cytosine nucleoside compounds from
pentose-1-phosphate and cytosine or a cytosine derivative,
by using an enzyme with cytosine-nucleoside phosphorylase
activity, microbial cells with the enzyme activity, an enzyme
preparation from the microbial cells or the culture thereof,
or the like.
Description of the related art
Nucleoside phosphorylases generally refer to enzymes
which phosphorolyze the N-glycoside bond of a nucleoside in
the presence of phosphoric acid, and in the case where
ribonucleoside is used, catalyze a reaction represented by
the following equation:
ribonucleoside + phosphoric acid (or a salt thereof)
—> base for nucleic acid + ribose-1-phosphate.
Those enzymes, roughly divided into purine-nucleoside
phosphorylases and pyrimidine-nucleoside phosphorylases,
are distributed in a wide variety of living organisms, such
as tissues including those of mammals, birds or fish, yeast
or bacteria. These enzyme reactions are reversible, and

synthesis of different nucleosides thus utilizing the reverse
rections has been known. For example, there are known methods
for production of thymidine (Japanese Patent Laid-Open No.
01-104190) , 2 ' -deoxyadenosine (Japanese Patent Laid-Open No.
11-137290) or 2' -deoxyguanosine (Japanese Patent Laid-Open
No. 11-137290), respectively, from
2'-deoxyribose-1-phosphate and a base for nucleic acid
(thymine, adenine or guanine). Thus, production of a
nucleoside using a phosphorylase can be produced
regio-specif ically and stereospecif ically in a mild condition,
and many nucleoside compounds are studied for synthesis.
Japanese Patent Laid-Open No. 1-60396 describes a process
for production of deoxycytidine by the reaction of
deoxyribose-1-phosphate with cytosine using bacterial cells
themselves as catalyst. Though the process of the application
uses bacterial cells per se as reaction catalyst, it is
uncertain whether cytosine-nucleoside phosphorylase itself
may exist therein. There is a possibility such that
deoxycytidine accumulated in the bacterial cells may have
leached out of the cells during the reaction, or that nucleoside
deoxyribosyltransf erase within the cells may have transferred
cytosine added as substrate to the base of deoxynucleoside
within the cells, resulting in detection of deoxycytidine.
The inventors sent for the seven bacterial strains that have
been deposited for the examples of the application, and tested
the production of deoxycytidine from deoxyribose-1-phosphate
and cytosine according to the examples. As a result,
deoxycytidine could not be detected in the solution of the

reaction using any one of the strains, indicating that enzyme
activity corresponding to cytosine-nucleoside phosphorylase
was not present in the strains themselves.
On the other hand, Japanese Patent Laid-Open No. 3-127986
describes a novel nucleoside phosphorylase acting on both
purine and pyrimidine bases, where the pyrimidine base is
deoxyuridine, deoxycytidine or deoxythymidine, but no
substrate specificity of the enzyme is disclosed in the
specification. Further, the application has already been
withdrawn and therefore the enzyme activity cannot be
characterized any more. The inventors of the application,
however, purified a nucleoside phosphorylase from the strain
of the same designation as that disclosed in the application,
and reported the characteristics thereof in Applied and
Environmental Microbiology, Vol. 56, pp. 3830-3834 (1990).
The article states that the above enzyme has no activity to
cytosine, cytidine or deoxycytidine.
Apart from the enzyme described above, it is not known
that cytosine or any derivative thereof may be a substrate
for either purine nucleoside phosphorylase or pyrimidine
nucleoside phosphorylase. For example, thymidine
nucleoside phosphorylase, one of pyrimidine nucleoside
phosphorylases , derived from Salmonera typhimurium described
in Method. Enzymology, Vol. 51, pp. 437-442 (1978) has no
activity to deoxycytidine. In addition, it is reported in
J. Biol. Chem. , Vol. 248, No. 6, pp. 2040-2043 (1973) that
purine nucleoside phosphorylase derived from Salmonera

typhimurium has no activity to pyrimidine nucleoside, such
as uridine, cytidine, deoxyuridine or deoxycytidine.
When these publications are totally considered, an enzyme
corresponding to cytosine nucleoside phosphorylase related
to the present invention may have been existent, but none
of those preceding publications could confirm it and actually
obtain the enzyme.
SUMMARY OF THE INVENTION
Production of a nucleoside compound using nucleoside
phosphorylase enables the nucleoside to be synthesized both
regiospecifically and stereospecifically under mild
conditions, thereby prompting synthetic studies of various
nucleoside compounds. However, no isolated and purified
nucleoside phosphorylase has ever been reported that is able
to synthesize a cytosine nucleoside compound from cytosine
or a derivative thereof and sugar phosphate as substrate.
Also, the inventors have found that if bacterial cells
per se are used, or if an enzyme preparation for use, prepared
from bacterial cells and/or culture broth thereof, has the
remainder of cytosine or cytidine deaminase activity, which
is generally present in the cells, both cytosine or the
derivative thereof as substrate and the cytosine nucleoside
compound as product may be deaminated, thereby making
efficient accumulation of the cytosine nucleoside compound
difficult.
One object of the present invention is thus to provide
the amino acid sequence of a nucleoside phosphorylase capable

of synthesizing a cytosine nucleoside compound. Another
object of the present invention is to provide a recombinant
plasmid containing the corresponding gene, a transformant
carrying the recombinant plasmid, a method for producing the
enzyme using the transformed bacterial strain and a method
for producing a cytosine nucleoside compound using the
transformed bacterial strain. Another object of the present
invention is to provide a method for reducing cytosine or
cytidine deaminase activity, while keeping the activity of
the nucleoside phosphorylase, or to provide a method for
efficiently producing a cytosine nucleoside compound by using
a bacterial strain having expressed cytosine nucleoside
phosphorylase in another bacterial strain devoid of both
deaminase.
Another object of the present invention is to provide
a method for reducing the activity of an enzyme capable of
dephosphorylating sugar phosphate as starting material, or
to provide a method for efficiently producing a cytosine
nucleoside compound by using a bacterial strain having
expressed cytosine nucleoside phosphorylase in another
bacterial strain devoid of the enzyme.
In the production of a cytosine nucleoside compound,
especially for preparing a pharmaceutical product, mixing
even a minute amount of a byproduct therein may cause a serious
problem. In the purification step, separation of the
byproduct nucleoside from the cytosine nucleoside compound
may impose a heavy burden on the step as well as decrease
the recovery of the compound, which will be a serious problem

in case of commercial production. In the case where the
compound is to be used for such a purpose, it is required
to eliminate cytosine or cytidine deaminase activity from
the enzyme preparation as completely as possible.
The inventors addressed themselves to solving these
subjects, resulting in the unexpected finding that a purine
nucleoside phosphorylase, which in itself should catalyze
a reaction involving purine base as substrate, is able to
catalyze a reaction for producing a cytosine nucleoside
compound from cytosine or a derivative thereof, which is a
sort of pyrimidine base, and pentose-1-phosphate.
The presence of the purine nucleoside phosphorylase that
the inventors found also indicates the presence of cytosine
nucleoside phosphorylase.
However, the reaction of cytosine or a derivative thereof
with pentose-1-phosphate in the presence of the bacterium
having this enzyme activity was found to produce almost
exclusively the deaminated products of cytosine or the
derivative thereof and the cytosine nucleoside compound, thus
failing in efficient accumulation of the cytosine nucleoside
compound of interest. Intensive work revealed that formation
of the deaminated products was due to the action of deaminases ,
and that the cytosine and cytidine deaminases could be
deactivated by placing the bacterial cells in an organic
solvent with or without stirring under still stand, or by
heating them, and also that deactivation of cytosine
nucleoside phosphorylase to be maintained could be controlled

efficiently by addition of phosphate or sugar phosphate into
the fluid to be processed.
It was now found possible, by means of the method
described above, to reduce specifically decomposition of the
substrate and/or the product with the activity of the
nucleoside phosphorylase maintained, and to produce the
cytosine nucleoside compound with little or no byproduct from
cytosine or the derivative thereof and the sugar phosphate,
by using the bacterial cells whose deaminase activity was
previously eliminated or decreased by the processing as
mentioned above. The finding is inventive.
The processing for eliminating or decreasing the
deaminase activity according to the present invention may
eliminate the decomposing activity almost completely, while
the activity of the cytosine nucleoside phosphorylase can
be maintained almost completely. Furthermore, it was also
found possible to efficiently produce a cytosine nucleoside
compound by expressing the phosphorylase in a bacterium devoid
of both enzyme activities of cytosine and cytidine deaminases .
The findings are inventive.
Also, the reaction yield was found to be lowered in the
presence of an enzyme capable of dephosphorylating the sugar
phosphate as starting material. The enzyme could be
selectively deactivated by addition of a polar solvent to
the disrupted cells of a bacterium having the enzyme activity.
The enzyme activity could be also removed through a
purification procedure for the cytosine nucleoside
phosphorylase, such as fractionation by salting out or

adsorption onto an ion-exchange resin carrier or the like.
It was found that these treatments enabled a cytosine
nucleoside compound to be produced efficiently. The finding
is inventive. Further, expression of the cytosine nucleoside
phosphorylase in a bacterium devoid of the dephosphorylating
enzyme was found to efficiently produce the cytosine
nucleoside compound. The findings are inventive.
The present invention provides a method for efficiently
producing a cytosine nucleoside compound using cytosine
nucleoside phosphorylase, which has never been attained.
The present invention is thus described as follows.
The method for producing a cytosine nucleoside compound
according to the present invention is characterized by
including a step wherein the cytosine nucleoside compound
is obtained in the reaction of a sugar phosphate with cytosine
or a derivative thereof in the presence of an enzyme with
the activity of cytosine nucleoside phosphorylase.
The enzyme includes an enzyme with the activity of purine
nucleoside phosphorylase, and thus an enzyme preparation
containing the activity of purine nucleoside phosphorylase
may be used appropriately in the method for producing the
cytosine nucleoside compound of the present invention. An
example of such enzyme with the activity of purine nucleoside
phosphorylase is an enzyme derived from Escherichia coli.
The cytosine derivative described above is represented
by formula (I) as follows:


wherein X denotes a carbon or nitrogen atom, and Y is a hydrogen
atom, a halogen atom or a lower alkyl group. Examples thereof
are azacytosine and 5-fluorocytosine.
The enzyme with the activity of cytosine nucleoside
phosphorylase as described above may be provided in the form
of bacterial cells having the enzyme, or enzyme preparations
including crude enzyme extract and purified enzyme
preparation which can be obtained from the cells or the culture
thereof into the reaction system.
The bacterial cells or enzyme preparation may be
preferably devoid of cytosine and cytidine deaminase
activities, or if they are present, so depleted as to be able
to produce the cytosine nucleoside compound by means of the
activity of cytosine nucleoside phosphorylase. As an example,
the bacterial cells or enzyme preparation with a higher
activity of cytosine nucleoside phosphorylase than cytosine
and cytidine deaminase activities are suitable for use.
An example of such bacterial cells or enzyme preparation
is one processed to reduce cytosine and cytidine deaminase
activities that it has.
The processed bacterial cells as described above, where
the deaminase activities have been lost or reduced, may be
obtained, as an example, by contacting the bacterial cells
having the activity of cytosine nucleoside phosphorylase with

an aqueous solution containing organic solvent in order to
reduce selectively cytosine and cytidine deaminase activities .
The organic solvent includes a polar solvent such as an alcohol.
The organic solvent may be at least one solvent selected from
the group including, for example, methyl alcohol, ethyl
alcohol, propyl alcohol, butyl alcohol, dioxane and acetone.
In addition, the concentration of the organic solvent
in water may be preferably 20% (v/v) or more when the organic
solvent eliminates or reduces the cytosine and cytidine
deaminase activities.
On the other hand, the processed bacterial cells, where
the deaminase activities have been lost or reduced, may also
be obtained by heating the bacterial cells having the activity
of cytosine nucleoside phosphorylase in an aqueous solution
at such a temperature as to reduce selectively cytosine and
cytidine deaminase activities. Heating may be conducted at
50°C or higher for 10 minutes to 40 hours.
In addition, when the bacterial cells are processed so
as to eliminate or reduce the deaminase activities, the
presence of pentose-1-phosphate allows the activity of
cytosine nucleoside phosphorylase to be maintained more
efficiently. The concentration of pentose-1-phosphate may
be preferably in the range from 1 mM to 100 mM.
BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1A shows an analytical chart of HPLC in the
Comparative Example 1, FIG. 1B shows an analytical chart of
HPLC of a reaction solution in the Comparative Example 1,

and FIG. 1C shows an analytical chart of HPLC of Example 6;
and
FIG. 2A shows an analytical chart of HPLC in the
Comparative Example 2, FIG. 2B shows an analytical chart of
HPLC of a reaction solution in the Comparative Example 2,
and FIG. 2C shows an analytical chart of HPLC of Example 5.
Fig. 3 shows the results in Example 8.
DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS
The term cytosine nucleoside phosphorylase refers to
an enzyme able to produce a cytosine nucleoside compound from
cytosine or a derivative thereof as substrate, and may be
derived from any of an animal, a plant or a microbe if the
requirement is satisfied. Generally, the enzyme termed
cytosine nucleoside phosphorylase is unknown in the art.
Therefore, this term is defined only in the present invention
as mentioned above. A suitable example of such cytosine
nucleoside phosphorylases is an enzyme conventionally known
as purine nucleoside phosphorylase which bacteria belonging
to genus Escherichia, such as Escherichia coli contain and
having also the activity of cytosine nucleoside phosphorylase.
As an embodiment, the DNA base sequence for the purine
nucleoside phosphorylase of Escherichia coli is illustrated
as SEQ ID NO: 3 and the amino acid sequence translated from
the base sequence as SEQ ID NO: 4. Recent progress in genetic
engineering has made it easier to modify an amino acid sequence
by means of deactivation, insertion or substitution for a
part of the base sequence. Such level of technology has

enabled the amino acid sequence to be modified through
modification of the part of the base sequence without affecting
the desired enzyme activity, that is to say, with the enzyme
activity maintained or even elevated, and the amino acid
sequence thus modified is also included by the cytosine
nucleoside phosphorylase according to the present invention.
For example, an amino acid sequence modified from the amino
acid sequence of SEQ ID NO: 4, wherein deletion, substitution
or addition has occurred for 2 to 3 amino acids without
affecting the enzyme activity of interest, and an amino acid
sequence coded by a base sequence modified from the base
sequence of SEQ ID NO: 3, where mutation such as deletion,
substitution or addition has occurred without affecting the
enzyme activity of interest, while the complementary sequence
can hybridize under stringent conditions, may be used in the
present invention.
If an enzyme has thus the activity of purine nucleoside
phosphorylase, the enzyme alone can produce both purine-type
and cytosine nucleoside compounds , thereby providing a great
advantage for commercial production of nucleosides.
The enzyme with the activity of cytosine nucleoside
phosphorylase used in the method of the present invention
may be provided in the form of bacterial cells having the
enzyme, or an enzyme preparation prepared from the cells or
the culture thereof into the reaction system. This enzyme
preparation includes the bacterial cells or the culture
thereof processed variously, enzyme extract, the enzyme
extract purified to some extent or as isolate and the like.

The bacterial cells or enzyme preparation may be one
commercially available or prepared utilizing any of various
methods. The preparation with the enzyme activity may be
selected from, for example, a commercially available enzyme,
bacterial cells with the enzyme activity and a preparation
by cell treatment or an immobilized form thereof. Examples
of the cell treatment preparation include acetone-dried cells
and disrupted cells, cell debris, prepared by means of any
treatment, such as mechanical disruption, ultrasonic
disruption, freezing and thawing, pressurization and
depressurization, osmotic shock, self-lysation, cell wall
disintegration or surfactant treatment, and also a purified
enzyme obtained by precipitation with ammonium sulfate or
acetone, or by column chromatography, if necessary.
The bacterium with the activity of cytosine nucleoside
phosphorylase is not limited in particular, if it expresses
cytosine nucleoside phosphorylase able to produce a cytosine
nucleoside compound from cytosine or a derivative thereof
as substrate. Such a bacterium may be selected from, for
example, common bacteria expressing nucleoside phosphorylase.
Suitable examples of such bacteria producing nucleoside
phosphorylase are bacteria belonging to genus Escherichia,
such as Escherichia coli. Recent progress in molecular
biology and genetic engineering has made it possible and then
easier to obtain the gene for the purine nucleoside
phosphorylase from the bacterial strain via analysis of the
molecular biological properties and amino acid sequence of
the enzyme, then construct a recombinant plasmid where the

gene and a regulator region for expressing it have been inserted,
and then create a recombinant bacterium where the protein
has been expressed, through transfer of the plasmid into any
host bacterium. Considering such level of technology, a
recombinant bacterium created by incorporation of the gene
for the nucleoside phosphorylase into any host bacterium is
also included in the bacterium expressing the activity of
nucleoside phosphorylase according to the present invention.
The regulatory region necessary for the gene expression
described herein includes a promoter sequence (including a
operator sequence to control transcription), a
ribosome-binding sequence (a SD sequence), and a
transcription termination sequence. Examples of the
promoter sequence may be a trp promoter that is a tryptophan
operon derived from E. coli, a lac promoter as lactose operon,
a PL or PR promoter derived from λ phage, a gluconate synthase
promoter (gnt) derived from Bacillus subtilis, an alkaline
protease promoter (apr), a neutral protease promoter (npr)
and an a-amylase promoter (amy). Sequences specifically
designed and modified, such as a tac promoter may also be
used. Examples of the ribosome-binding sequence may be such
sequences derived from E. coli or B. subtilis, but are not
limited in particular provided that they function within a
desirable host such as E. coli or B. subtilis. As an example,
a consensus sequence where a sequence of 4 or more consecutive
bases is complementary to the 3'-terminal region of a 16 S
ribosomal RNA may be prepared in DNA synthesis, and then used
for the purpose. The transcription termination sequence is

not essential, but, if necessary, ones independent of the
p factor, such as a lipoprotein terminator and a trp operon
terminator can be used. These regulatory regions on the
recombinant plasmid are preferably arranged in the order of
the promoter sequence, the ribosome-binding sequence, the
gene coding nucleoside phosphorylase and the transcription
termination sequence, from the 5'-terminal on the upstream
side.
Examples of the plasmid described herein that can be
used as vector may be pBR322, pUC18, Bluescript II SK (+),
pKK223-3 and pSClOl having a region in E. coli where it is
able to self-replicate, and pUB11O, pTZ4, pC194, ρ11, 1 and
105 having a region in B. subtilis where it is able to
self-replicate. In addition, examples of the plasmid that
is able to self-replicate in more than one bacterial strain
and may be used as vector are pHV14, TRp7, YEp7 and pBS7.
Any bacterial host described herein includes Escherichia
coli as typical example which will be described below in the
Examples, but is not limited to E. coli in particular and
also includes other microbial strains, such as bacteria
belonging to Genus Bacillus such as Bacillus subtilis, yeasts
and actinomycetes.
The cytosine nucleoside compound according to the present
invention refers to a compound where a sugar phosphate and
cytosine or a derivative thereof as base of nucleic acid are
bound together via a N-glycoside bond. Its typical examples
arecytidine, deoxycytidine, dideoxycytidine, azacytidine.

deoxyazacytidine, 5-fluorocytidine and
5-fluorodeoxycytidine, but not limited to these compounds.
The cytosine derivative according to the present
invention refers to a compound which has a cytosine structural .
moiety convertible to a cytosine nucleoside structure by the
action of cytosine nucleoside phosphorylase. Preferable
examples of the cytosine derivative are cytosine derivatives
represented by the general formula (I) described above. As
the lower alkyl group of Y in the general formula (I), an
alkyl group having 1 to 4 carbon atoms such as a methyl group,
an ethyl group, a propyl group, an isopropyl group, a n-butyl
group, a sec-butyl group and a tert-butyl group. Among the
cytosine derivatives, for example, azacytosine,
5-fluorocytosine and 5-methylcytosine are particularly
preferred.
The sugar phosphate according to the present invention
refers to a polyhydroxyaldehyde, a polyhydroxyketone or a
derivative thereof whose position 1 is esterified with
phosphoric acid. Typical examples thereof are preferably
ribose 1-phosphate, 2'-deoxyribose 1-phosphate, 2',3'-di
deoxyribose 1-phosphate, arabinose 1-phosphate and
dioxolane-type sugar phosphate.
The polyhydroxyaldehyde or polyhydroxyketone derived
from natural products includes an aldopentose such as
D-arabinose, L-arabinose, D-xylose, L-lyxose or D-ribose,
a ketopentose such as D-xylulose, L-xylulose or D-ribulose,
a deoxysugar such as D-2-deoxyribose orD-2, 3-dideoxyribose,
or the like, but is not limited to these.

These sugar phosphates can be prepared by the method
wherein they are produced by phosphorolysis of nucleoside
compounds with nucleoside phosphorylase (J. Biol. Chem. Vol.
184, 437, 1950), or also by methods of chemical synthesis
selective to the anomers.
Furthermore, the method of enzymatic synthesis for
deoxyribose 1-phosphate as described in WO 01/14566 may be
utilized. (The route for synthesis of deoxyribose 1-phosphate
according to the patent assigned to Roche Ltd. is also referred
to therein.)
The processing for reducing cytosine and cytidine
deaminase activities according to the present invention is
not limited in particular, provided that the deaminase
activities can be eliminated or reduced without deactivating
nucleoside phosphorylase, but a suitable processing is
exemplified by exposure of the bacterial cells, their culture
or the processed material thereof to an organic solvent, or
heat treatment of any one of the above.
The organic solvent according to the present invention
may be any solvent capable of eliminating cytosine and cytidine
deaminase activities. The organic solvent includes, but is
not limited to, a polar solvent, such as methyl alcohol, ethyl
alcohol, propyl alcohol, butyl alcohol, dioxane,
tetrahydrofuran, methyl ethyl ketone or acetone; an alcohol,
such as 1-hexanol, 2-methyl-1-pentanol, 4-methyl-2-pentanol,
2-ethyl-1-butanol, 1-heptanol, 2-heptanol, 3-heptanol,
1-octanol, 2-octanol or 1-nonanol; an ester, such as propyl
acetate, butyl acetate, isobutyl acetate, sec-butyl acetate.

pentyl acetate, isopentyl acetate, cyclohexyl acetate or
benzyl acetate; a hydrocarbon, such as pentane, hexane,
2-methylhexane, 2,2-dimethylbutane, 2,3-dimethylbutane,
cyclohexane, methylcyclohexane, heptane, cycloheptane,
octane, cyclooctane, isooctane, nonane, decane, dodecane,
petroleum ether, petroleum benzin, ligroin, industrial
gasoline, kerosene, benzene, toluene, xylene, ethylbenzene,
propylbenzene, cumene, mesitylene or naphthalene; a
halogenated hydrocarbon, such as dichloromethane, chloroform,
carbon tetrachloride, dichloroethane, chlorobenzene or
dichlorobenzene; a phenol, such as cresol or xylenol; aketone,
such as methyl isobutyl ketone or 2-hexanone; and an ether,
such as dipropyl ether, diisopropyl ether, diphenyl ether
and dibenzyl ether; and also a hydrocarbon, such as pentane,
hexane, heptane, octane, cyclopentane, cyclohexane,
cycloheptane, cycloctane, toluene or ethylbenzene. Among
other organic solvents used in the present invention are amide
compounds, such as N,N-dimethylformamide,
N,N-dimethylacetamide, N,N-dimethylbenzamide,
N-methyl-2-pyrrolidone, N-methylformamide,
N-ethylformamide, N-methylacetamide, formamide, acetamide
and benzamide, urea compounds, such as urea,
N,N'-dimethylurea, tetramethylurea and
N,N' -dimethylimidazolidinone, and sulf oxide compounds, such
as dimethyl sulfoxide, diethyl sulfoxide and diphenyl
sulfoxide.
The processing with the organic solvent for eliminating
or reducing deaminase activities according to the present

invention is not limited in particular, provided that cytosine
and cytidine deaminase activities can be eliminated or reduced
without deactivating nucleoside phosphorylase, but a suitable
processing is conducted under conditions where the bacterial
cells, their culture or the processed material thereof is
kept standstill or suspended at pH 4.0 to 10.0, preferably
pH 6.0 to 9.0, at the concentration of the organic solvent
in water not less than 10% by volume, preferably not less
than 20% by volume, more preferably not less than 30% by volume,
at a temperature not lower than 0°C, preferably ranging from
20°C, preferably 50°C, to 80°C, for 10 minutes or more,
preferably up to 40 hours, more preferably for 1 to 20 hours.
Further, addition of the sugar phosphate at not less
than 1 mM, preferably at not more than 100 mM, to the above
processed fluid can make the nucleoside phosphorylase more
stable.
Addition of the organic solvent into the reaction
solution may be also effective similarly.
Heat treatment according to the present invention is
not limited in particular, provided that cytosine and cytidine
deaminase activities can be eliminated or reduced without
deactivating nucleoside phosphorylase, but a suitable heat
treatment is conducted under conditions where the bacterial
cells, their culture or the processed material thereof is
kept standstill or suspended in an aqueous medium at pH 4.0
to 10.0, preferably pH 6.0 to 9 .0, at a temperature not lower
than 50°C, preferably ranging from 60 to 80°C, for 10 minutes
or more, more preferably for 30 minutes or more. Further,

addition of the sugar phosphate at not less than 1 mM,
preferably at 10 to 100 mM, to the above treated fluid can
make the nucleoside phosphorylase more stable.
As regards the bacterium without either cytosine or
cytidine deaminase activity, a cytidine-deaminase deficient
strain of a bacterium belonging to Bacillus genus may be used
because bacteria belonging to the genus generally have only
cytidine deaminase, but not cytosine deaminase. Such a strain
is, for example. Bacillus subtilis 1A479 available from
Bacillus Genetic Stock Center (BGCS) . Bacterial cells having
expressed the nucleoside phosphorylase in such a strain may
also be used herein.
The phosphatase deficient strain according to the present
invention is exemplified by E. coliK-12 DH5α devoid of alkaline
phosphatase. Bacterial cells having expressed the cytosine
nucleoside phosphorylase in such a strain may also be used
herein.
Heat treatment of such bacterial cells may deactivate
or decrease acid phosphatase, thereby attaining a higher yield
of the product. A suitable heat treatment is conducted under
conditions where the bacterial cells, their culture or the
processed material thereof is kept standstill or suspended
in an aqueous medium at pH 4.0 to 10.0, preferably pH 6.0
to 9 . 0 , at a temperature not lower than 50°C, preferably ranging
from 60 to 80°C, for 10 minutes or more, more preferably for
30 minutes or more.
The processing for reducing or removing an inhibitor
of the activity of cytosine nucleoside phosphorylase

according to the present invention is not limited in particular,
provided that the inhibitor can be removed or reduced, but
a suitable processing is typically to prepare a solution of
the enzyme through ultrasonic disruption of the bacterial
cells, and then to add a polar solvent to the enzyme solution
in order to precipitate the cytosine nucleoside phosphorylase,
or to add ammonium sulfate to the solution in order to salt
out and precipitate the enzyme, or to purify it with ion
exchange resin.
The reaction for synthesis of the cytosine nucleoside
compound according to the present invention is conducted using
the bacterial cells, their culture or the processed material
thereof, derived from the bacterium that expresses the
cytosine nucleoside phosphorylase capable of synthesizing
the cytosine nucleoside compound from cytosine or a derivative
thereof and the sugar phosphate as substrate, wherein the
bacterium-derived matter has lost or is devoid of activity
to decompose cytosine or the derivative thereof and the
cytosine nucleoside compound, and it may usually be conducted
under the conditions of pH 4 to 10 and a temperature ranging
from 10 to 80°C. Both concentrations of the sugar phosphate
and cytosine or the derivative thereof used in the reaction
may range preferably from 0.1 to 1000 mM, and the molar
concentration ratio of cytosine or the derivative thereof
to the sugar phosphate or its salt should be from 0.1 to 10,
preferably about 0.95 taking into account the conversion rate
of the reaction.

A metal salt which forms a poorly soluble phosphate salt
with phosphoric acid, or a carrier such as ion exchange resin
may be added in order to trap phosphoric acid formed in the
reaction medium and thereby elevate the reaction yield.
Separation of the cytosine nucleoside compound from the
reaction solution may be conducted taking advantage of the
solubility difference of the compound against the solvent
such as water, or using ion exchange or adsorbent resin.
A trace amount of cytosine remaining in the reaction
solution may be eliminated by converting it to uracil, using
a bacterium expressing cytosine deaminase which has been
processed to reduce or deactivate cytidine deaminase, or using
a bacterium created by expression of cytosine deaminase in
a bacterial strain devoid of cytidine deaminase.
The procedure of passing the reaction solution through
cationic ion exchange resin enables the cytosine nucleoside
compound to be separated and purified readily, because uracil
that has been formed from remaining cytosine and/or the uracil
nucleoside compound that has been formed via decomposition
of the cytosine nucleoside compound are not adsorbed by the
resin, though only the cytosine nucleoside compound is
adsorbed.
[Examples]
The present invention will be described in the Examples
below, but is not limited by these Examples.
Analytical Procedure:
[Analytical method]

Cytosine nucleoside compounds produced were all
quantified by means of high performance liquid chromatography.
The conditions of analysis are shown in the following.
Column: Develosil ODS-MG-5, 4.6 x 250 mm (Nomura Kagaku)
Column temperature; 40°C
Pumping flow rate; 1.0 ml/min
Detection; UV 254 nm
Eluate; 50 mM monopotassium phosphate : methanol = 8:1
(v/v)
Reference Example 1: (a reproducibility test with respect
to Japanese Patent Laid-Open No. 1-60396)
Synthesis of deoxycytidine was attempted according to
Example 1 described in Japanese Patent Laid-Open No. 1-60396 .
Thus, the 7 bacterial strains deposited, as shown in Table
1, were selected from the group of 24 strains described in
the Example 1 and then received. A 50 ml aliquot of a medium
(pH 7.0) containing yeast extract at 0.5 g/dl, peptone at
1.0 g/dl, meat extract at 1.0 g/dl and NaCl at 10.5 g/dl was
poured into a flask with shoulders of 500 ml by volume and
then sterilized. Each of the bacteria, shown in Table 1,
that was cultured preliminarily on a nutrient-broth agar
medium at 30°C for 16 hours, was seeded to the above medium
with a loop of the cells and shake cultured at 30°C for 16
hours. The cell mass was separated from the culture solution
by centrifugation, then washed with 0.05 M phosphate buffer
(pH 7.0) and then centrifuged to prepare the cleaned mass.
The above cleaned mass was added to a solution of 20
mM 2'-deoxyribose-1-phosphate and 20 mM cytosine in 100 ml

of 0.05 M tris buffer (pH 7.2) so as to make its concentration
at 5 g/dl, and then subjected to the reaction at 60°C for
24 hours. After the reaction solution was diluted and a
portion of the dilution was then analyzed by HPLC, it was
found that cytosine as substrate was decomposed to a nearly
100% loss, and that deoxycytidine was not detected.

Reference Example 2 : (PNP cloning and creation of a strain
expressing the cloned DNA, and preparation of the control
cells)
The genomic DNA from Escherichia coli was prepared as
follows:
Escherichia coli strain K-12/XL-10 (from Stratagene)
was seeded into 50 ml of LB medium and cultured at 37°C overnight,
and thereafter the cell mass was collected and then lyzated
with a lyzating solution containing lysozyme at 1 mg/ml. The
lyzating solution was treated with phenol and then the DNA
was precipitated with ethanol as usual. The resulting DNA
precipitate was wound around a glass stick for recovery and
then washed to use it for PCR.

As primer for PCR, oligonucleotides (entrusted to
Hokkaido System Science for synthesis) with the base sequences
shown by SEQ ID NOs: 1 and 2, respectively, were used, wherein
the base sequences were designed based on the base sequence
on the deoD gene (GenBank accession No. AE000508 (with the
coding region of BASE NOs. 11531 to 12250)) that codes a known
purine nucleoside phosphorylase native to E. coli. These
primers have the recognition sequences of restriction enzymes
EcoRI and HindIII, respectively, near 5'-terminal and
3'-terminal. The PCR was conducted by 30 cycles for the
reaction cycle consisting of denaturation at 96°C for 1 minute,
anealing at 55°C for 1 minute and extension reaction at 74°C
for 1 minute, using 0 .1 ml of PCR reaction solution containing
6 ng/μl of the above described genomic DNA from Escherichia
coli, which has been completely digested by the restriction
enzyme HindIII , and 3 μM of each primer.
The above reaction product and plasmid pUC18 (from Takara
Shuzo) were digested by EcoRI and HindIII, ligated with
Ligation Hi (from Toyobo) and then E. coli DH5α was transformed
using the resulting recombinant plasmid. The transformant
was cultured on a LB agar medium containing 50 μg/ml of
ampicillin (Am) and X-Gal
(5-bromo-4-chloro-3-indolyl-β-D-galactoside) to obtain the
transformant that has become Am resistant and formed white
colonies.
The plasmid extracted from the transformant thus obtained
and having the DNA fragment of interest inserted was named
pUC-PNP73. The base sequence of the DNA fragment inserted

in pUC-PNP73 was identified by the common method for
determining base sequences. The identified base sequence
is shown as SEQ ID NO: 3, while the amino acid sequence
translated from the base sequence is shown as SEQ ID NO: 4.
The present enzyme has subunits of molecular weight of
approximately 26,000 and its activity is known to be expressed
in the form of hexamer. The enzyme has the optimum temperature
of about 70°C and the optimum pH range of about 7.0 to 7.5.
The transformant thus obtained was named Escherichia coli
MT-10905.
Escherichia coli strain MT-10905 was shake cultured in
100 ml of LB medium containing 50 μg/ml of Am at 37°C overnight.
The culture was centrif uged at 13,000 rpm for 10 min. to obtain
the cell mass, which was then suspended in 20 ml of 100 mM
tris hydrochloride buffer (pH 8.0). The suspension was
centrifuged again at 13,000 rpm for 10 min. to obtain the
cell mass, which was then suspended in 2 ml of 100 mM tris
hydrochloride buffer (pH 8.0) and 10 mM
2' -deoxyribose-1-phosphate di(monocyclohexylammonium) salt
(produced by SIGMA), and frozen and stored at -20°C.
Escherichia coli DH5awas transf ormedusingplasmidpUC18
(from Takara Shuzo). This transformant strain was named
pUC18/DH5a. The strain pUC18/DH5a was shake cultured in 100
ml of LB medium containing 50 μg/ml of Am at 37°C overnight.
The culture was centrif uged at 13,000 rpm for 10 min. to obtain
the cell mass, which was then suspended in 20 ml of 100 mM
tris hydrochloride buffer (pH 8.0). The suspension was
centrifuged again at 13,000 rpm for 10 min. to obtain the

cell mass, which was then suspended in 2 ml of 100 mM tris
hydrochloride buffer (pH 8.0) and 10 mM
2' -deoxyribose-1-phosphate di(monocyclohexylammonium) salt
(produced by SIGMA), and frozen and stored at -20°C.
Comparative Example 1: (synthesis of deoxycytidine by

the PNP non recombinant E. coli)

A reaction solution with 1.0 ml by volume consisting
of 20 mM 2'-deoxyribose-1-phosphate
di(monocyclohexylammonium) salt (produced by SIGMA), 20 mM
cytosine (produced by Wako Pure Chemicals, guaranteed grade),
100 mM tris hydrochloride buffer (pH 8.0) and 0.1 ml of the
cell mass suspension of the strain pUC18/DH5α obtained in
Reference Example 2 was treated at 50°C for 20 hours . Another
solution of the same composition except the absence of the
substrates was heat treated similarly and then used as
comparative example. When the reaction solution was diluted
and then analyzed, deoxycytidine could not be detected. The
analysis chart from HPLC of the treated solution for the
comparative example is shown in FIG. 1A, and the corresponding
chart of the treated reaction solution in FIG. 1B.
Comparative Example 2: (synthesis of deoxycytidine by
the PNP non recombinant E. coli)
A reaction solution with 1.0 ml by volume consisting
of 20 mM 2'-deoxyribose-1-phosphate
di(monocyclohexylammonium) salt (produced by SIGMA), 20 mM
cytosine (produced by Wako Pure Chemicals, guaranteed grade),
100 mM tris hydrochloride buffer (pH 8.0) and 0.1 ml of the
cell mass suspension of the strain MT-10905 obtained in

Reference Example 2 was treated at 50°C for 20 hours. Another
solution of the same composition except the absence of the
substrates was heat treated similarly and then used as
comparative example. When the reaction solution was diluted
and then analyzed, 10 mM deoxyuridine and 3 mM uracil were
produced, but deoxycytidine could not be detected. The
analysis chart from HPLC of the treated solution for the
comparative example is shown in FIG. 2A, and the corresponding
chart of the treated reaction solution in FIG. 2B.
Example 1: (processing with organic solvent)
To the cell mass suspension of the strain MT-10905
obtained in Reference Example 2 was added a certain amount
of methanol so as to attain any one of the methanol
concentrations listed in Table 2, and then the suspension
was kept at 30°C for 1 hour. Cytidine deaminase will be
expressed as cdd hereafter. The activity of cdd was analyzed
after the cell mass suspension was added to 1.0 ml of the
reaction solution consisting of 100 mM tris hydrochloride
buffer (pH 8.0) and 20 mM cytidine, and then treated at 50°C
for 2 hours.
The cell mass suspension described above was kept at
30°C for 1 hour without addition of methanol, and then the
activity of cdd of the suspension was set at 100% of relative
value.
The activity of PNP was analyzed after the cell mass
suspension was added to 1.0 ml of the reaction solution
consisting of 20 mM 2'-deoxyribose-1-phosphate
di(monocyclohexylammonium) salt (produced by SIGMA) , 5 . 4 mM

adenine (produced by Wako Pure Chemicals, guaranteed grade)
and 100 mM tris hydrochloride buffer (pH 8.0) , and then treated
at 50°C for 15 minutes . The above reaction was conducted using
such an amount of the cell mass as to produce not more than
2 mM deoxyadenosine. The cell mass suspension described above
was kept at 30°C for 1 hour without addition of methanol,
and then the activity of PNP of the suspension was set at
100% of relative value. The results shown in Table 2 reveal
that the activity of PNP was reduced minimally, but the activity
of cdd was eliminated nearly completely.

Example 2: (processing with organic solvents)
To the cell mass suspension of the strain MT-10905
obtained in Reference Example 2 was added any one of the organic
solvents as shown in Table 3, and then the suspension was
kept at 30°C for 1 hour.
The results shown in Table 3 reveal that the activity
of PNP was reduced minimally, but the activity of cdd was
eliminated nearly completely.


Example 3: (heat treatment)
The cell mass suspension of the strain MT-10905 obtained
in Reference Example 2 was kept at 60°C. Cytosine deaminase
will be expressed as cod hereafter. The activity of cod was
analyzed after the cell mass suspension was added to 100 mM
tris hydrochloride buffer (pH 8.0) and 20 mM cytosine, and
then treated at 50°C for 2 hours. The cod activity of the
cell mass suspension that was not heat treated was set at
100% and the remaining activities were expressed with relative
values. The results shown in Table 4 reveal that the activity
of PNP was reduced minimally, but the activity of cod was
eliminated nearly completely.


Example 4: (heat treatment plus processing with organic
solvent)
The cell mass suspension heat treated for 20 hours in
Example 3 was processed with methanol in the same way as in
Example 1. The individual activities of the cell mass
suspension that was heat treated for 20 hours in Example 3
were set at 100% and the remaining activities were expressed
with relative values. The results shown in Table 5 reveal
that the activity of PNP was reduced minimally, but the
activities of both cod and cdd were eliminated nearly
completely.

Example 5: (synthesis of deoxycytidine by the recombinant
bacterium expressing PNP and treated as in Example 4)
1.0 ml of the reaction solution consisting of 20 mM
2' -deoxyribose-1 -phosphate di(monocyclohexylammonium) salt
(produced by SIGMA), 20 mM cytosine (produced by Wako Pure
Chemicals, guaranteed grade), 100 mM tris hydrochloride
buffer (pH 8. 0) and 0.1 ml of the cell mass suspension processed
with 50% methanol in Example 4 was treated at 50°C for 20
hours. When the reaction solution was diluted and then

analyzed, 10 . 7 mM deoxycytidine, 0 . 2 mM deoxyuridine and 0 .1
mM uracil were produced. The reaction yield was then 53%.
The analysis chart from HPLC of the treated solution is shown
in FIG. 2C.
Example 6: (synthesis of deoxycytidine by Escherichia
coli treated as in Example 4)
1.0 ml of the reaction solution consisting of 20 mM
2' -deoxyribose-1-phosphate di(monocyclohexylammonium) salt
(produced by SIGMA) , 20 mM cytosine (produced by Wako Pure
Chemicals, guaranteed grade), 100 mM tris hydrochloride
buffer (pH 8.0) and 0.1 ml of the cell mass suspension of
pUC18/DH5α which was obtained in Reference Example 2 and
processed with 50% methanol as in Example 4, was treated at
50°C for 20 hours. When the reaction solution was diluted
and then analyzed, 0.14 mM deoxycytidine and 0.17 mM
deoxyuridine were produced. The reaction yield was then 0.7%.
The analysis chart from HPLC of the treated solution is shown
in FIG. 1C.
Example 7: (synthesis of cytidine by the recombinant
bacterium expressing PNP and treated as in Example 4)
1.0 ml of the reaction solution consisting of 20 mM
ribose-1-phosphate di(cyclohexylammonium) salt (produced by
SIGMA), 20 mM cytosine (produced by Wako Pure Chemicals,
guaranteed grade) , 100 mM tris hydrochloride buffer (pH 8.0)
and 0.1 ml of the cell mass suspension processed with 50%
methanol in Example 4 was treated at 50°C for 20 hours. When
the reaction solution was diluted and then analyzed, 5 mM

cytidine, 0.1 mM uridine and 0.1 mM uracil were produced.
The reaction yield was then 25%.
Example 8: (purification of PNP and synthesis of
deoxycytidine by the purified PNP)
The cell mass obtained in Example 4 was suspended in
10 ml of 10 mM tris hydrochloride buffer (pH 7 . 5) and disrupted
with an ultrasonic disrupter. The disrupted cell suspension
was then centrifuged to obtain a crude enzyme solution, which
was then added onto a column loaded with DEAE-Toyopearl (3cm
x 10cm: from Toso) that was equilibrated with 50 mM tris
hydrochloride buffer (pH 7.5) and then eluted with a linear
gradient of 50 mMNaCl to 500 mMNaCl to recover active fractions.
The eluate was saturated with 70% aqueous ammonium sulfate
to form precipitate, which was then dialyzed against 10 mM
tris hydrochloride buffer (pH 7.5). The dialyzed solution
was added onto a column loaded with hydroxyapatite (3 cm x
15 cm) that was equilibrated with 10 mM tris hydrochloride
buffer (pH 7.5) and then eluted with a gradient of 10 mM tris
hydrochloride buffer (pH 7.5) to 50 mM tris hydrochloride
buffer (pH 7.5) to recover active fractions. The enzyme
solution was saturated with 70% aqueous ammonium sulfate to
form and recover precipitate, which was then dissolved in
1 ml of 10 mM tris hydrochloride buffer (pH 7.5) and dialyzed
against 10 mM tris hydrochloride buffer (pH 7.5) to obtain
2 ml of purified PNP. The purified PNP thus obtained was
found to form a single band in electrophoresis using a
SDS-polyacrylamide system. The result is shown in FIG. 3.

1.0 ml of the reaction solution consisting of 20 mM
2' -deoxyribose-1-phosphate di(monocyclohexylammonium) salt
(produced by SIGMA), 20 mM cytosine (produced by Wako Pure
Chemicals, guaranteed grade), 100 mM tris hydrochloride
buffer (pH 8.0) and 0.1 ml of the purified PNP was treated
at 50°C for 20 hours. When the reaction solution was diluted
and then analyzed, 11.5 mM deoxycytidine was produced and
the reaction yield was then 57.5%.
Example 9: (synthesis of azacytidine by the recombinant
bacterium expressing PNP and treated as in Example 4)
1.0 ml of the reaction solution consisting of 20 mM
ribose-1-phosphate di(cyclohexylammonium) salt (produced by
SIGMA), 20 mM azacytosine (produced by SIGMA), 100 mM tris
hydrochloride buffer (pH 8.0) and 0.1 ml of the cell mass
suspension processed with 50% methanol in Example 4 was treated
at 50°C for 20 hours. When the reaction solution was diluted
and then analyzed, 3.2 mM azacytidine was produced. The
reaction yield was then 16%.
Example 10: (synthesis of fluorocytidine by the
recombinant bacterium expressing PNP and treated as in Example
4)
1.0 ml of the reaction solution consisting of 20 mM
ribose-1 -phosphate di(cyclohexylammonium) salt (produced by
SIGMA), 20 mM 5-fluorocytosine (produced by SIGMA), 100 mM
tris hydrochloride buffer (pH 8.0) and 0.1 ml of the cell
mass suspension processed with 50% methanol in Example 4 was
treated at 50°C for 20 hours. When the reaction solution was

diluted and then analyzed, 2.4 mM 5-fluorocytidine was
produced. The reaction yield was then 12%.
Example 11: (synthesis of methylcytidine by the
recombinant bacterium expressing PNP and treated as in Example
4)
1.0 ml of the reaction solution consisting of 20 mM
ribose-1 -phosphate di(cyclohexylammonium) salt (produced by
SIGMA), 20 mM 5-methylcytosine (produced by SIGMA), 100 mM
tris hydrochloride buffer (pH 8.0) and 0.1 ml of the cell
mass suspension processed with 50% methanol in Example 4 was
treated at 50°C for 20 hours. When the reaction solution was
diluted and then analyzed, 2.1 mM 5-methylcytidine was
produced. The reaction yield was then 10.5%.
Example 12: (synthesis of deoxycytidine by bacterial
mass devoid of degrading activity with PNP incorporated)
(1) Creation of Escherichia coli-Bacillus subtilis
shuttle vectors pPNP04 and pPNP05 for expressing E. coli PNP
in B. subtilis
The PCR using pUC-PNP73 as template and the synthetic
oligonucleotide primer of SEQ ID NOs: 5 and 6 allowed the
gene for purine nucleoside phosphorylase of Escherichia coli
to be amplified, resulting in production of 0 . 8 kb DNA fragment
A. Then, by the PCR which used pNP150 (FERMBP-425) described
in Japanese Patent Laid-Open No. 60-210986 as template and
the synthetic oligonucleotide primer of SEQ ID NOs: 7 and
8, the region including the transcription promoter and
translation regulating site derived from the neutral protease
of Bacillus amyloliquefaciens was amplified, resulting in

production of l.o kb DNA fragment B. Then, annealing was
carried out using overlapping regions of DNA fragments A and
B. The PCR using the resulting fragment as template and the
synthetic oligonucleotide primer of SEQ ID NOs: 6 and 7 allowed
approximately 1.8 kb DNA fragment C to be produced via
amplification. This DNA fragment C was digested by the
restriction enzymes EcoRI and HindIII to produce insert
fragments. Escherichia coli-Bacillus subtilis shuttle
vectors pRB373 and pRB374 were received from Bacillus Genetic
Stock Center (BGSC; OH) and then each digested by the
restriction enzymes EcoRI and Hindlll to prepare vector
fragments. The vector fragments were ligated in the presence
of an excessive amount of the above insert fragments to create
shuttle vectors pPNP04 and pPNP05 expressing the purine
nucleoside phosphorylase of E. coli.
(2) Entry of pPNP04 and pPNPOS into Bacillus subtilis,
and synthesis of deoxycytidine using the transformant
Bacillus subtilis strains 1A479 and 1A480, both devoid
of cytidine deaminase activity, were received from Bacillus
Genetic Stock Center (BGSC; OH).
Transformation with plasmids pPNP04 and pPNP05 obtained
in procedure (1) was conducted according to the protoplast
method by Chang (Chang. S. and Cohen, S. N.; Mol. Gen. Genet.
168, 111 (1978)) to obtain transformants 1A480 (pPNP04), 1A480
(pPNP05), 1A479 (pPNP04) and 1A479 (pPNP05).
Then, the strain 1A480 (pPNP04) was evaluated for
activity of deoxycytidine synthesis as follows:

The strain 1A480 (pPNP04) was cultured in 20 ml of the
L medium of two-fold concentration at 35°C for 17 hours. 1.5
ml of the culture was centrifuged to obtain the cell mass,
which was then frozen and stored at -20°C. 1.0 ml of a reaction
solution consisting of 24 mM 2'-deoxyribose-1-phosphate
di(monocyclohexylammonium) salt (produced by SIGMA), 20 mM
cytosine (produced by Wako Pure Chemicals , guaranteed grade)
and 100 mM tris hydrochloride buffer (pH 8.0) was added to
0.1 ml of the frozen cell mass and shaken at 50°C. The solution
was sampled 1. 5 hours and 18 hours after the start. The samples
were diluted with water by 20 fold and centrifuged to remove
the cell mass. The supernatants thereof were analyzed by
HPLC to reveal that accumulation of deoxycytidine was from
1.4 to 1.5 mM after 1.5 hours and from 6.4 to 7.0 mM after
18 hours, while no degradation of either the substrates or
the product was detected.
Analysis of deoxycytidine synthesis by the strains 1A480
(pPNP05). 1A479 (pPNP04) and 1A479 (pPNP05) revealed that
they were as effective as the strain 1A480 (pPNP04) for
deoxycytidine synthesis.
Example 13: (obtainment of enzymes substituted by an
amino acid but keeping cytosine nucleoside phosphorylase
activity)
Mutagenesis was introduced using the plasmid DNA of
pUC-PNP73 obtained in Reference Example 2 as template and
Quick Change Site-Directed Mutagenesis Kit from STRATAGENE,
which will be referred to simply as Kit hereafter. The

examples below basically followed the principle and procedure
of the Kit.
10 ml of a LB liquid medium was prepared in a 30-ml test
tube and then sterilized in an autoclave at 121°C for 20 minutes .
A certain amount of ampicillin was added to the medium so
as to set its final concentration at 100 μg/ml. The strain
MT-10905 obtained in Reference Example 2 was seeded by a loop
of the cell mass and then cultured at 37°C and 300 rpm for
about 20 hours. Then, 1 -ml aliquot s of the culture were poured
into any suitable centrifuge tubes to separate the cell mass
by centrifugation (at 15,000 rpm for 5 minutes) . After that,
the plasmid DNA of pUC-PNP73 was prepared from the cell mass
by the alkaline SDS extraction.
The PCR was carried out using the plasmid DNA of pUC-PNP73
as template, and the respective DNAs of SEQ ID NOs: 9 and
10, 11 and 12, 13 and 14, 15 and 16, 17 and 18, 19 and 20,
21 and 22, 23 and 24, 25 and 26, 27 and 28, 29 and 30, 31
and 32, 33 and 34, 35 and 36, 37 and 38, 39 and 40, 41 and
42, 43 and 44, and 45 and 46 as primers. The composition
of the PCR medium is shown in Table 6. The conditions of
amplification are shown in Table 7.
The restriction enzyme DpnI was added to the above PCR
medium by 4 units and maintained at 37°C for 1 hour. 1 μl
of the reaction medium was added to 100 μl of the competent
cells (from Toyobo) of E. coli K-12DH5α, and maintained in
ice for 30 minutes. Then, the cell suspension was immersed
in a thermostatic water bath at 42°C for 30 seconds. 0.9 ml
of the NZY+ medium, which is an accessory to the competent

cells, was added to the cell suspension and shaken at 37°C
for 1 hour.
The above culture was smeared onto LB agar medium where
a certain amount of ampicillin had been added so as to set
its final concentration at 100 μg/ml, and then maintained
at 37°C for 20 hours to form colonies.
Five clones were arbitrarily selected from the colonies,
seeded by a loop of each cell mass in 100ml of LB medium
containing 50 μg/ml of Am and shake cultured at 37°C overnight.
The culture was centrifuged at 13,000 rpm for 10 minutes to
obtain the cell mass, which was then suspended in 20 ml of
100 mM tris hydrochloride buffer (pH 8.0). The suspension
was centrifuged again at 13,000 rpm for 10 minutes to obtain
the cell mass, which was then suspended in 2 ml of 100 mM
tris hydrochloride buffer (pH 8.0) and 10 mM
2' -deoxyribose-1 -phosphate di(monocyclohexylammonium) salt
(produced by SIGMA) , processed as in Example 4 and subjected
to the reaction for deoxycytidine synthesis as in Example
5. Analysis of deoxycytidine by HPLC revealed that four of
the five clones produced deoxycytidine, thus holding the
activity of cytosine nucleoside phosphorylase.
The cell mass of each of the above four clones was separated
from 1 ml of the above culture remaining after analysis of
the activity of cytosine nucleoside phosphorylase. The
plasmid DNA of each of the four clones was prepared from the
cell mass by alkaline SDS extraction. The base sequences
of the DNA fragments were identified by the common method
for determining base sequences . Enzyme activity was measured




Reference Example 3: (Transformation of Escherichia coli
strain K-12 W3110)
Escherichia coli strain K-12 W3110 (ATCC27325) was
transformed with the plasmid pUC-PNP73 obtained in Reference
Example 2 according to the common procedure. The transf ormant
thus obtained was named MT-10948 . When the transf ormant was
cultured as in Reference Example 2, it was twice as active

as the corresponding transf ormant of Escherichia coli strain
K-12 DH5α.
Example 14: (removal of reaction inhibitors through
precipitation with polar solvent)
The cell mass of the strain MT-10948 cultured as in
Reference Example 2 was disrupted with an ultrasonic disrupter.
The same volume of acetone as the disruption fluid was added
to the fluid, which was then centrifuged to remove the
precipitate.
Then, a half volume of acetone compared to the above
was added to the above supernatant formed by centrifugation
and centrifuged to recover the precipitate.
The recovered precipitate was dried up in a vacuum dryer.
The dried precipitate was dissolved in 2 ml of 100 mM tris
hydrochloride buffer (pH 8.0) and 10 mM
2' -deoxyribose-1 -phosphate di(monocyclohexylammonium) salt
(produced by SIGMA) and then processed as in Example 4. A
2-ml solution of the enzyme fractionated with acetone was
added to water (105.3 g) together with cytosine (6.96 g),
2'-deoxyribose-1-phosphate diammonium salt (18.7 g) and
magnesium hydroxide (6.2 g), and the reaction took place at
50°C for 24 hours. The HPLC analysis after the reaction
demonstrated that 11.4 g (80%) of 2'-deoxycytidine was
produced. For comparison, a 2-ml fluid containing disrupted
cell mass before addition of acetone was similarly subjected
to the reaction. As a result, 8 . 5 g (60%) of 2 ' -deoxycytidine
was produced.

Example 15: (removal of reaction inhibitors through
precipitation with ammonium sulfate)
The cell mass of the strain MT-10948 cultured as in
Reference Example 2 was disrupted with an ultrasonic
disrupter.
Ground pieces of ammonium sulfate were slowly added to
the disruption fluid so as to attain 40% saturation finally.
The fluid was slowly agitated in ice for 1 hour and centrifuged
to remove the precipitate. Similarly, ground pieces of
ammonium sulfate were added to the supernatant formed by
centrifugation so as to attain 70% saturation finally. The
fluid was slowly agitated in ice for 1 hour and centrifuged
to obtain the precipitate. The precipitate was then dissolved
in 2 ml of 100 mM tris hydrochloride buffer (pH 8.0) and 10
mM 2'-deoxyribose-1-phosphate di(monocyclohexylammonium)
salt (produced by SIGMA) . The solution was processed as in
Example 4 and subjected to the reaction for deoxycytidine
synthesis as in Example 14. As a result, 11.0 g (80%) of
2'-deoxycytidine was produced.
Example 16: (removal of reaction inhibitors: purified
enzyme in Example 8)
A 2-ml solution of the enzyme obtained as in Example
8 was subjected to the reaction for deoxycytidine synthesis
as in Example 14 . As a result, 11. 0 g ( 80% ) of 2 ' -deoxycytidine
was produced.
Example 17: (the effect of a phoA deficient strain)
A 2-ml suspension of the cell mass obtained in Example
4 was subjected to the same reaction as in Example 14. As

a result, 11.0 g (80%) of 2'-deoxycytidine was produced. On
the other hand, when the strain MT-10948 was processed as
in Example 4, this strain was twice as high as the strain
MT-10905 for activity. However, when this strain was
subjected to the same reaction as in Example 14, only 8.5
g (60%) of 2'-deoxycytidine was produced.
Example 18
To the mixture of water (96.4 g) and 4 .8 g of cyclohexane,
were added 6.96 g (62.6 mmol) of cytosine, 18.7 g (75.4 mmol)
of 2'-deoxyribose-1-phosphate diammonium salt, 7.58 g (132
mmol) of magnesium hydroxide and the frozen cell mass (2.0
g) prepared in Reference Example 3. The reaction took place
at 45°C for 18 hours, controlling the solution at pH 8.8 with
acetic acid. The HPLC analysis after the reaction
demonstrated that 10.03 g (70.5 mol%/cytosine) of
2'-deoxycytidine was produced as object compound. At the
same time, 0.73 g (10.4 mol%/cytosine) of uracil and 1.80
g (12.6 mol%/cytosine) of 2'-deoxyuridine were produced as
byproduct, respectively.
Example 19
Synthesis of 2' -deoxycytidine was carried out under the
same conditions as in Example 18, except that the solvent
for processing the cell mass and/or the solvent added for
the reaction were different. The results are shown in Tables
9 and 10.


Example 20: Synthesis of 2'-deoxycytidine
To 20 g of pure water were added 20 ml (total exchange
capacity 24 mmol) of strongly basic anionic exchange resin
(Levatit MP500 : exchange capacity 1.1 eq/L) and
2-deoxyribose-l-phosphate diammonium salt (4.96 g, 20 mmol),
and the mixture was stirred at room temperature for 30 minutes .
Then, enzyme solution (0 . 5 ml) , prepared according to Example
4, and cytosine (2.11 g, 19 mmol) were added to the mixture,
which was stirred at 50°C for 10 hours. Analysis of the
reaction mixture by HPLC revealed that 2 ' -deoxycytidine, the
desired product was produced in the yield of 80%.

Production of a nucleoside compound using a nucleoside
phosphorylase may be conducted both regiospecifically and
stereospecifically under mild conditions. It is thus hoped
that an industrial method of production will be established,
but it is not attained yet. The present invention provides
a method for producing a cytosine nucleoside compound from
pentose-1-phosphate and cytosine or a derivative thereof
using a nucleoside phosphorylase reactive to cytosine. The
invention also provides a method for specifically reducing
an activity to degrade the substrates or the product, resulting
in efficient production of the cytosine nucleoside compound.

WE CLAIM;
1. A method for producing a cytosine nucleoside compound by reacting
a compound of formula (I)

wherein X is carbon or nitrogen, Y is hydrogen, a halogen or a C1-4
alkyl with a sugar phosphate in the presence of an enzyme capable of
catalysing their reaction, wherein the enzyme has the activity of
cytosine nucleoside phosphorylase, and has the amino acid sequence
shown in SEQ ID NO:4 or is a variant having an amino acid sequence
obtainable by substituting a different amino acid or acids for at least
one amino acid selected from the amino acids corresponding to No.
10, No.16, No. 42, No. 54, No. 67, No. 74, No. 104, No. 135, No. 157, .
No. 167, No. 168, No. 178, No. 179, No. 183, No. 199, No. 204, No. 210,
No. 228 and No. 233 on the amino acid sequence of SEQ ID NO.: 4.
2. The method as claimed in claim 1, wherein said enzyme has the
activity of purine nucleoside phosphorylase.
3. The method as claimed in claim 1 or claim 2 wherein said sugar
phosphate is ribose-1-phosphate, 2-deoxyribose-1-phosphate, 2',3'-
dideoxyribose-1-phopsphate or dioxolane sugar phosphate.

4. The method as claimed in any one of claims 1 to 3, wherein said
enzyme is provided in the form of bacterial mass having the activity of
cytosine nudeoside phosphorylase or an enzyme preparation obtained
from the bacterial mass or the culture thereof, wherein the bacterial
mass or enzyme preparation has no, or reduced, activity of cytosine
deaminase and/ or cytidine deaminase.
5. The method as claimed in claim 4, wherein the enzyme is a said
variant, the bacteria of said bacterial mass being a transformed strain
carrying a recombinant plasmid containing a gene encoding the
variant enzyme.
6. A method as claimed in claim 5, wherein said enzyme is produced by
culturing said transformed strain and recovering the enzyme from the
cultured cells, the culture fluid or processed material thereof.
7. A method for producing a cytosine nucleoside compound by reacting
a compound of formula (I)

wherein X is carbon or nitrogen, Y is hydrogen, a halogen or a Cw
alkyl with a sugar phosphate in the presence of an enzyme capable of
catalysing their reaction, wherein the enzyme has the activity of
cytosine nucleoside phosphorylase, wherein said enzyme is provided
in the form of a bacterial mass containing purine nucleoside
phosphorylase or an enzyme preparation obtained from the bacterial

mass or culture thereof, wherein aid bacterial mass or enzyme
preparation has no, or reduced, activity of cytosine deaminase and/or
cytidine deaminase, and optionally has no, or reduced, activity of
phosphatase.
8. The method as claimed in claim 7, wherein the activity of cytosine
deaminase and/or the activity of cytidine deaminase of said bacterial
mass or said enzyme preparation are lost or reduced by processing for
activity reduction.
9. The method as claimed in claim 8, wherein said bacterial mass
subjected to said processing is obtained by contacting bacterial mass
having the activity of cytosine nucleoside phosphorylase with water
containing organic solvent to eliminate or reduce selectively the
activity of cytosine deaminase and the activity of cytidine deaminase.
10. The method as claimed in any one of claims 7 to 9, wherein a substance
inhibiting the activity of cytosine nucleoside phosphorylase is
removed from said bacterial mass or enzyme preparation thereof by
any one of means of:

a) obtaining cytosine nucleoside phosphorylase as precipitate from
said enzyme preparation by use of a polar solvent
b) obtaining cytosine nucleoside phosphorylase as precipitate from
said enzyme preparation by use of salting out, or
c) separating cytosine nucleoside phosphorylase from said enzyme
preparation by use of any suitable carrier such as resin.

A method for producing a cytosine nucleoside compound by reacting
a compound of formula (I)
wherein X is carbon or nitrogen, Y is hydrogen, a halogen or a C1-4
alkyl with a sugar phosphate in the presence of an enzyme capable of
catalysing their reaction, wherein the enzyme has the activity of
cytosine nucleoside phosphorylase, and has the amino acid sequence
shown in SEQ ID NO:4 or is a variant having an amino acid sequence
obtainable by substituting a different amino acid or acids for at least
one amino acid selected from the amino acids corresponding to No.
10, No.16, No. 42, No. 54, No. 67, No. 74, No. 104, No. 135, No. 157,
No. 167, No. 168, No. 178, No. 179, No. 183, No. 199, No. 204, No. 210,
No. 228 and No. 233 on the amino acid sequence of SEQ ID NO.: 4.

Documents:

242-CAL-2002-FORM-27.pdf

242-cal-2002-granted-abstract.pdf

242-cal-2002-granted-claims.pdf

242-cal-2002-granted-correspondence.pdf

242-cal-2002-granted-description (complete).pdf

242-cal-2002-granted-drawings.pdf

242-cal-2002-granted-examination report.pdf

242-cal-2002-granted-form 1.pdf

242-cal-2002-granted-form 18.pdf

242-cal-2002-granted-form 2.pdf

242-cal-2002-granted-form 3.pdf

242-cal-2002-granted-form 5.pdf

242-cal-2002-granted-gpa.pdf

242-cal-2002-granted-priority document.pdf

242-cal-2002-granted-reply to examination report.pdf

242-cal-2002-granted-sequence listing.pdf

242-cal-2002-granted-specification.pdf

242-cal-2002-granted-translated copy of priority document.pdf


Patent Number 230198
Indian Patent Application Number 242/CAL/2002
PG Journal Number 09/2009
Publication Date 27-Feb-2009
Grant Date 25-Feb-2009
Date of Filing 29-Apr-2002
Name of Patentee MITSUI CHEMICALS, INC.
Applicant Address 2-5, KASUMIGASEKI 3-CHOME, CHIYODA-KU, TOKYO
Inventors:
# Inventor's Name Inventor's Address
1 ARAKI TADASHI 1144, TOGO, MOBARA-SHI, CHIBA
2 IKEDA ICHIROU 1144, TOGO, MOBARA-SHI, CHIBA
3 MATOISHI KAOARI 1144, TOGO, MOBARA-SHI, CHIBA
4 ARE REIKO 1144, TOGO, MOBARA-SHI, CHIBA
5 OIKAWA TOSHIHIRO 1144, TOGO, MOBARA-SHI, CHIBA
6 MATSUBA YASUKO C/O. MITSUI CHEMICALS, INC. 30, ASAMUTACHO, OMUTA-SHI, FUKUOKA
7 ISHIBASHI HIROKI C/O. MITSUI CHEMICALS, INC. 30, ASAMUTACHO, OMUTA-SHI, FUKUOKA
8 NAGAHARA KIYOTERU C/O. MITSUI CHEMICALS, INC. 30, ASAMUTACHO, OMUTA-SHI, FUKUOKA
9 FUKUIRI YASUSHI C/O. MITSUI CHEMICALS, INC. 30, ASAMUTACHO, OMUTA-SHI, FUKUOKA
PCT International Classification Number C12N 15/54
PCT International Application Number N/A
PCT International Filing date
PCT Conventions:
# PCT Application Number Date of Convention Priority Country
1 2001-134352 2001-05-01 Japan