U.S. patent application number 12/565533 was filed with the patent office on 2010-06-24 for coryneform bacteria which produce chemical compounds i.
This patent application is currently assigned to EVONIK DEGUSSA GMBH. Invention is credited to BRIGITTE BATHE, CAROLINE KREUTZER, BETTINA MOCKEL, GEORG THIERBACH.
Application Number | 20100159523 12/565533 |
Document ID | / |
Family ID | 32849572 |
Filed Date | 2010-06-24 |
United States Patent
Application |
20100159523 |
Kind Code |
A1 |
BATHE; BRIGITTE ; et
al. |
June 24, 2010 |
Coryneform Bacteria Which Produce Chemical Compounds I
Abstract
The invention relates to coryneform bacteria which have, in
addition to at least one copy, present at the natural site (locus),
of an open reading frame (ORF), gene or allele which codes for the
synthesis of a protein or an RNA, in each case a second, optionally
third or fourth copy of this open reading frame (ORF), gene or
allele at in each case a second, optionally third or fourth site in
a form integrated into the chromosome and processes for the
preparation of chemical compounds by fermentation of these
bacteria.
Inventors: |
BATHE; BRIGITTE;
(SATZKOTTAN, DE) ; KREUTZER; CAROLINE; (MELLE,
DE) ; MOCKEL; BETTINA; (DUSSELDORF, DE) ;
THIERBACH; GEORG; (BIELEFELD, DE) |
Correspondence
Address: |
PILLSBURY WINTHROP SHAW PITTMAN, LLP
P.O. BOX 10500
MCLEAN
VA
22102
US
|
Assignee: |
EVONIK DEGUSSA GMBH
ESSEN
DE
|
Family ID: |
32849572 |
Appl. No.: |
12/565533 |
Filed: |
September 23, 2009 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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11612208 |
Dec 18, 2006 |
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12565533 |
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10358405 |
Feb 5, 2003 |
7160711 |
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11612208 |
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PCT/EP02/08464 |
Jul 30, 2002 |
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10358405 |
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60309878 |
Aug 6, 2001 |
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Current U.S.
Class: |
435/87 ; 435/106;
435/107; 435/108; 435/109; 435/110; 435/113; 435/114; 435/115;
435/116; 435/252.1; 435/320.1; 435/476; 435/89 |
Current CPC
Class: |
C12P 13/08 20130101;
C12N 15/52 20130101; C12R 1/15 20130101 |
Class at
Publication: |
435/87 ; 435/89;
435/106; 435/107; 435/108; 435/109; 435/110; 435/113; 435/114;
435/115; 435/116; 435/476; 435/252.1; 435/320.1 |
International
Class: |
C12P 19/38 20060101
C12P019/38; C12P 19/30 20060101 C12P019/30; C12P 13/04 20060101
C12P013/04; C12P 13/24 20060101 C12P013/24; C12P 13/22 20060101
C12P013/22; C12P 13/20 20060101 C12P013/20; C12P 13/14 20060101
C12P013/14; C12P 13/12 20060101 C12P013/12; C12P 13/10 20060101
C12P013/10; C12P 13/08 20060101 C12P013/08; C12P 13/06 20060101
C12P013/06; C12N 15/74 20060101 C12N015/74; C12N 1/20 20060101
C12N001/20; C12N 15/63 20060101 C12N015/63 |
Claims
1. Coryneform bacteria which produce chemical compounds, wherein
these have, in addition to at least one copy, present at the
natural site (locus), of an open reading frame (ORF), gene or
allele which codes for the synthesis of a protein or an RNA, a
second, optionally third or fourth copy of the open reading frame
(ORF), gene or allele in question at a second, optionally third or
fourth site in a form integrated into the chromosome, no nucleotide
sequence which is capable of/enables episomal replication, or
transposition in microorganisms and no nucleotide sequence(s) which
impart(s) resistance to antibiotics being present at the second,
optionally third or fourth site, and the second, optionally third
or fourth site not relating to open reading frames (ORF), genes or
alleles which are essential for the growth of the bacteria and the
production of the desired compound.
2. Coryneform bacteria according to claim 1 which produce chemical
compounds, wherein the corynefo/m bacteria belong to the genus
Corynebacterium.
3. Coryneform bacteria of the genus Corynebacterium according to
claim 2 which produce chemical compounds, wherein these belong to
the species Corynebacterium glutamicum.
4. Coryneform bacteria according to claim 1 which produce chemical
compounds, wherein the chemical compound is a compound chosen from
the group consisting of L-amino acids, vitamins, nucleosides and
nucleotides.
5. Coryneform bacteria according to claim 1 which produce chemical
compounds, wherein the chemical compound is one or more L-amino
acids chosen from the group consisting of L-aspartic acid,
L-asparagine, L-threonine, L-serine, L-glutamic acid, L-glutamine,
glycine, L-alanine, L-cysteine, L-valine, L-methionine,
L-isoleucine, L-leucine, L-tyrosine, L-phenylalanine, L-histidine,
L-lysine, L-tryptophan, L-proline and L-arginine.
6. Coryneform bacteria according to claims 1 and 4 which produce
chemical compounds, wherein the L-amino acid is L-lysine, and these
bacteria have, in addition to at least one copy of an open reading
frame (ORF), gene or allele of lysine production present at the
natural site (locus), in each case a second, optionally third or
fourth copy of the open reading frame (ORF), gene or allele of
lysine production in question at in each case a second, optionally
third or fourth site in a form integrated into the chromosome.
7. Coryneform bacteria according to claim 6 which produce L-lysine,
wherein the coryneform bacteria belong to the genus
Corynebacterium.
8. Coryneform bacteria of the genus Corynebacterium according to
claim 7 which produce L-lysine, wherein these belong to the species
Corynebacterium glutamicum.
9. Coryneform bacteria according to claim 6 which produce L-lysine,
wherein the open reading frame (ORF), gene or allele of lysine
production is one or more open reading frame(s), one or more
gene(s) or allele(s) chosen from the group consisting of accBC,
accDA, cstA, cysD, cysE, cysH, cysK, cysN, cysQ, dapA, dapB, dapC,
dapD, dapE, dapF, ddh, dps, eno, gap, gap2, gdh, gnd, lysC,
lysC.sup.FBR, lysE, msiK, opcA, oxyR, ppc, ppc.sup.FBR, pgk, pknA,
pknB, pknD, pknG, ppsA, ptsH, ptsI, ptsM, pyc, pyc P458S, sigC,
sigD, sigE, sigH, sigh, tal, thyA, tkt, tpi, zwa1, zwf and zwf
A213T.
10. Coryneform bacteria according to claim 6 which produce
L-lysine, wherein the open reading frame, gene or allele of lysine
production is one or more gene(s) or allele(s) chosen from the
group consisting of dapA, ddh, lysC.sup.FBR and pyc P458S.
11. Coryneform bacteria according to claim 6 which produce
L-lysine, wherein the open reading frame, gene or allele of lysine
production is a lysC.sup.FBR allele which codes for a feed back
resistant form of aspartate kinase.
12. Coryneform bacteria according to claim 11 which produce
L-lysine, wherein the feed back resistant fonts of aspartate kinase
coded by the lysC.sup.FBR allele contains an amino acid sequence
according to SEQ ID NO:2, SEQ ID NO:2 containing one or more amino
acid replacements chosen from the group consisting of A279T, A279V,
S301F, T308I, S301Y, G345D, R320G, T311I and S381F.
13. Coryneform bacteria according to claim 11 which produce
L-lysine, wherein the feed back resistant form of aspartate kinase
coded by the lysC.sup.FBR allele includes an amino acid sequence
according to SEQ ID NO:4.
14. Coryneform bacteria according to claim 11 which produce
L-lysine, wherein the coding region of the lysC.sup.FBR allele
includes the nucleotide sequence of SEQ ID NO:3.
15. Coryneform bacteria according to claim 6 which produce
L-lysine, wherein the particular second, optionally third or fourth
site is a gene chosen from the group consisting of aecD, ccpA1,
ccpA2, citA, citB, citE, fda, gluA, gluB, gluC, gluD, luxR, luxS,
lysR1, lysR2, lysR3, menE, mqo, pck, pgi and poxB.
16. Coryneform bacteria according to claim 6 which produce
L-lysine, wherein the particular second, optionally third or fourth
site is a site chosen from the group consisting of intergenic
regions of the chromosome, prophages contained in the chromosome
and defective phages contained in the chromosome.
17. Coryneform bacteria according to claim 15 which produce
L-lysine, wherein the particular second, optionally third or fourth
site is the aecD gene site.
18. Coryneform bacteria according to claim 15 which produce
L-lysine, wherein the particular second, optionally third or fourth
site is the gluB gene site.
19. Coryneform bacteria according to claim 15 which produce
L-lysine, wherein the particular second, optionally third or fourth
site is the pck gene site.
20. Process for the preparation of chemical compounds by
fermentation of coryneform bacteria, in which the following steps
are carried out: a) fermentation of coryneform bacteria, which a1)
which have, in addition to at least one copy, present at the
natural site (locus), of an open reading frame (ORF), gene or
allele which codes for the synthesis of a protein or an RNA, a
second, optionally third or fourth copy of this open reading frame
(ORF), gene or allele at a second, optionally third or fourth site
in a form integrated into the chromosome, no nucleotide sequence
which is capable of/enables episomal replication or transposition
in microorganisms and no nucleotide sequence(s) which impart(s)
resistance to antibiotics being present at the second, optionally
third or fourth site, and the second, optionally third or fourth
site not relating to open reading frames (ORF), genes or alleles
which are essential for the growth of the bacteria and the
production of the desired compound, and a2) in which the
intracellular activity of the corresponding protein is increased,
in particular the nucleotide sequence which codes for this protein
is over-expressed, b) concentration of the chemical compound(s) in
the fermentation broth and/or in the cells of the bacteria, c)
isolation of the chemical compound(s), optionally d) with
constituents from the fermentation broth and/or the biomass to the
extent of >(greater than) 0 to 100 wt. %.
21. Process according to claim 20, wherein the coryneform bacteria
belong to the genus Corynebacterium.
22. Process according to claim 20, wherein the coryneform bacteria
of the genus Corynebacterium belong to the species Corynebacterium
glutamicum.
23. Process according to claim 20, wherein the chemical compound is
a compound chosen from the group consisting of L-amino acids,
vitamins, nucleosides and nucleotides.
24. Process according to claim 20, wherein the chemical compound is
one or more L-amino acids chosen from the group consisting of
L-aspartic acid, L-asparagine, L-threonine, L-serine, L-glutamic
acid, L-glutamine, glycine, L-alanine, L-cysteine, L-valine,
L-methionine, L-isoleucine, L-leucine, L-tyrosine, L-phenylalanine,
L-histidine, L-lysine, L-tryptophan, L-proline and L-arginine.
25. Process according to claim 24, wherein the chemical compound is
L-lysine.
26. Process for the preparation of L-lysine, which comprises the
following steps: a) fermentation of coryneform bacteria which have,
in addition to at least one copy of an open reading frame (ORF),
gene or allele of lysine production present at the natural site
(locus), in each case a second, optionally third or fourth copy of
the open reading frame (ORF), gene or allele of lysine production
in question at in each case a second, optionally third or fourth
site in a form integrated into the chromosome under conditions
which allow expression of the said open reading frames (ORF), genes
or alleles mentioned.
27. Process for the preparation of L-lysine according to claim 26,
wherein the open reading frame (ORF), gene or allele of lysine
production is an open reading frame, a gene or allele chosen from
the group consisting of accBC, accDA, cstA, cysD, cysE, cysH, cysK,
cysN, cysQ, dapA, dapB, dapC, dapD, dapE, dapF, ddh, dps, eno, gap,
gap2, gdh, gnd, lysC, lysC.sup.FBR, lysE, msiK, opcA, oxyR, ppc,
ppc.sup.FBR, pgk, pknA, pknB, pknD, pknG, ppsA, ptsH, ptsI, ptsM,
pyc, pyc P458S, sigC, sigD, sigE, sigH, sigM, tal, thyA, tkt, tpi,
zwa1, zwf and zwf A213T.
28. Process for the preparation of L-lysine according to claim 26,
wherein the open reading frame (ORF), gene or allele of lysine
production is a gene or allele chosen from the group consisting of
dapA, ddh, lysC.sup.FBR and pyc P458S.
29. Process for the preparation of L-lysine according to claim 26,
wherein the open reading frame (ORF), gene or allele of lysine
production is a lysC.sup.FBR allele which codes for a feed back
resistant form of aspartate kinase.
30. Process for the preparation of L-lysine according to claim 29,
wherein the feed back resistant form of aspartate kinase coded by
the lysC.sup.FBR allele contains an amino acid sequence according
to SEQ ID NO:2, SEQ ID NO:2 containing one or more amino acid
replacements chosen from the group consisting of A279T, A279V,
S301F, T308I, S301Y, G345D, R320G, T311I and S381F.
31. Process for the preparation of L-lysine according to claim 29,
wherein the feed back resistant form of aspartate kinase coded by
the lysC.sup.FBR allele includes an amino acid sequence according
to SEQ ID NO:4.
32. Process for the preparation of L-lysine according to claim 29,
wherein the coding region of the lysC.sup.FBR allele includes the
nucleotide sequence of SEQ ID NO:3.
33. Process for the preparation of L-lysine according to claim 26,
wherein the particular second, optionally third or fourth site is a
site chosen from the group consisting of aecD, ccpA1, ccpA2, citA,
citB, citE, fda, gluA, gluB, gluC, gluD, luxR, luxS, lysR1, lysR2,
lysR3, menE, mqo, pck, pgi and poxB.
34. Process for the preparation of L-lysine according to claim 26,
wherein the second, optionally third or fourth site is the aecD
gene site.
35. Process for the preparation of L-lysine according to claim 26,
wherein the second, optionally third or fourth site is the gluB
gene site.
36. Process for the preparation of L-lysine according to claim 26,
wherein the second, optionally third or fourth site is the pck gene
site.
37. Process for the production of coryneform bacteria which produce
one or more chemical compounds, which comprises a) isolating the
nucleotide sequence of at least one desired ORF, gene or allele
which codes for a protein or an RNA, optionally including the
expression and/or regulation signals, preferably from coryneform
bacteria, b) providing the 5' and the 3' end of the ORF, gene or
allele with nucleotide sequences of the target site, c) preferably
incorporating the nucleotide sequence of the desired ORF, gene or
allele provided with nucleotide sequences of the target site into a
vector which does not replicate or replicates to only a limited
extent in coryneform bacteria, d) transferring the nucleotide
sequences according to b) or c) into coryneform bacteria, and e)
isolating coryneform bacteria in which the nucleotide sequence(s)
according to a) is incorporated at the target site, no nucleotide
sequence(s) which is(are) capable of/enable(s) episomal replication
or transposition in microorganisms, and no nucleotide sequence(s)
which impart(s) resistance to antibiotics remaining at the target
site.
38. Plasmid pK18mobsacBglu1.sub.--1 shown in FIG. 1 and deposited
in the form of a pure culture of the strain E. coli
DH5.alpha.mcr/pK18mobsacBglu1.sub.--1 (=DH5alpha
mcr/pK18mobsacBglu1.sub.--1) under number DSM14243.
39. Plasmid pK18mobsacBaecD1.sub.--1 shown in FIG. 2 and deposited
in the form of a pure culture of the strain E. coli
DH5.alpha.mcr/pK18mobsacBaecD1.sub.--1
(=DH5alphamcr/pK18mobsacBaecD1.sub.--1) under number DSM15040.
40. Corynebacterium glutamicum strain DSM12866glu::lysC deposited
in the form of a pure culture under number DSM15039.
41. Coryneform bacteria according to claim 1, wherein the second,
optionally third or fourth site is a site chosen from the group
consisting of intergenic regions of the chromosome, prophages
contained in the chromosome and defective phages contained in the
chromosome.
42. Coryneform bacteria according to claim 41, wherein the
intergenic region is selected from table 12.
43. Coryneform bacteria according to claim 41, wherein the
prophages contained in the chromosome and defective phages
contained in the chromosome are selected from table 13.
44. Process according to claim 20, wherein said second, third or
fourth site is selected from the group consisting of intergenic
regions of the chromosome, prophages contained in the chromosome
and defective phages contained in the chromosome.
45. Process according to claim 44, wherein the intergenic regions
are selected from table 12.
46. Process according to claim 44, wherein the prophages contained
in the chromosome and defective phages contained in the chromosome
are selected from table 13.
47. Process according to claim 37, wherein said nucleotide sequence
site is selected from the group consisting of intergenic regions of
the chromosome, prophagbes contained in the chromosome and
defective phages contained in the chromosome.
48. Process according to claim 47, wherein the intergenic regions
are selected from table 12.
Description
[0001] This is a continuation-in-part application of International
Patent Appl. No. PCT/EP02/08464 filed on Jul. 30, 2002 which claims
priority to U.S. Prov. Appl. No. 60/309,878, filed Aug. 6,
2001.
BACKGROUND
[0002] Chemical compounds, which means, in particular, L-amino
acids, vitamins, nucleosides and nucleotides and D-amino acids, are
used in human medicine, in the pharmaceuticals industry, in
cosmetics, in the foodstuffs industry and in animal nutrition.
[0003] Numerous of these compounds are prepared by fermentation
from strains of coryneform bacteria, in particular Corynebacterium
glutamicum. Because of their great importance, work is constantly
being undertaken to improve the preparation processes. Improvements
to the process can relate to fermentation measures, such as, for
example, stirring and supply of oxygen, or the composition of the
nutrient media, such as, for example, the sugar concentration
during the fermentation, or the working un to the product form by,
for example, ion exchange chromatography, or the intrinsic output
properties of the microorganism itself.
[0004] Methods of mutagenesis, selection and mutant selection are
used to improve the output properties of these microorganisms.
Strains which are resistant to antimetabolites or are auxotrophic
for metabolites of regulatory importance and which produce the
particular compounds are obtained in this manner.
[0005] Methods of the recombinant DNA technique have also been
employed for some years for improving the strain of Corynebacterium
strains, by amplifying individual biosynthesis genes and
investigating the effect on production.
[0006] A common method comprises amplification of certain
biosynthesis genes in the particular microorganism by means of
episomally replicating plasmids. This procedure has the
disadvantage that during the fermentation, which in industrial
processes is in general associated with numerous generations, the
plasmids are lost spontaneously (segregational instability).
[0007] Another method comprises duplicating certain biosynthesis
genes by means of plasmids which do not replicate in the particular
microorganism. In this method, the plasmid, including the cloned
biosynthesis gene, is integrated into the chromosomal biosynthesis
gene of the microorganism (Reinscheid et al., Applied and
Environmental Microbiology 60(1), 126-132 (1994); Jetten et al.,
Applied Microbiology and Biotechnology 43(1):76-82 (1995)). A
disadvantage of this method is that the nucleotide sequences of the
plasmid and of the antibiotic resistance gene necessary for the
selection remain in the microorganism. This is a disadvantage, for
example, for the disposal and utilization of the biomass. Moreover,
the expert expects such strains to be unstable as a result of
disintegration by "Campbell type cross over" in a corresponding
number of generations such as are usual in industrial
fermentations.
OBJECT OF THE INVENTION
[0008] The inventors had the object of providing new measures for
improved fermentative preparation chemical compounds using
coryneform bacteria.
SUMMARY OF THE INVENTION
[0009] Coryneform bacteria which produce chemical compounds,
characterised in that these have, in addition to at least one copy,
present at the natural site (locus), of an open reading frame
(ORF), gene or allele which codes for the synthesis of a protein or
an RNA, a second, optionally third or fourth copy of the open
reading frame (ORF), gene or allele in question at a second,
optionally third or fourth site in a form integrated into the
chromosome, no nucleotide sequence which is capable of/enables
episomal replication or transposition in microorganisms and no
nucleotide sequence(s) which impart(s) resistance to antibiotics
being present at the second, optionally third or fourth site, and
the second, optionally third or fourth site not relating to open
reading frames (ORF), genes or alleles which are essential for the
growth of the bacteria and the production of the desired
compound.
[0010] The invention also provides processes for the preparation of
one or more chemical compounds, in which the following steps are
carried out: [0011] a) fermentation of coryneform bacteria, [0012]
a1) which have, in addition to at least one copy, present at the
natural site (locus), of an open reading frame (ORF), gene or
allele which codes for the synthesis of a protein or an RNA, a
second, optionally third or fourth copy of this open reading frame
(ORF), gene or allele at a second, optionally third or fourth site
in a form integrated into the chromosome, no nucleotide sequence
which is capable of/enables episomal replication or transposition
in microorganisms and no nucleotide sequence(s) which impart(s)
resistance to antibiotics being present at the second, optionally
third or fourth site, and the second, optionally third or fourth
site not relating to open reading frames (ORF), genes or alleles
which are essential for the growth of the bacteria and the
production of the desired compound, and [0013] a2) in which the
intracellular activity of the corresponding protein is increased,
in particular the nucleotide sequence which codes for this protein
is over-expressed, [0014] b) concentration of the chemical
compound(s) in the fermentation broth and/or in the cells of the
bacteria, [0015] c) isolation of the chemical compound(s),
optionally [0016] d) with constituents from the fermentation broth
and/or the biomass to the extent of >(greater than) 0 to 100 wt.
%.
[0017] The invention also provides processes for the preparation of
one or more chemical compounds, which comprise the following steps:
[0018] a) fermentation of coryneform bacteria, in particular of the
genus Corynebacterium, which have, in addition to the copy of an
open reading frame (ORF), gene or allele present at the natural
site (locus), in each case a second, optionally third or fourth
copy of the open reading frame (ORF), gene or allele in question at
in each case a second, optionally third or fourth site in
integrated form, no nucleotide sequence which is capable of/enables
episomal replication in microorganisms, no nucleotide sequence
which is capable of/enables transposition and no nucleotide
sequence which imparts resistance to antibiotics being present at
the particular second, optionally third or fourth site, under
conditions which allow expression of the said open reading frames
(ORF), genes or alleles [0019] b) concentration of the chemical
compound(s) in the fermentation broth and/or in the cells of the
bacteria, [0020] c) isolation of the chemical compound(s),
optionally [0021] d) with constituents from the fermentation broth
and/or the biomass to the extent of >(greater than) 0 to
100%.
DETAILED DESCRIPTION OF THE INVENTION
[0022] Chemical compounds are to be understood, in particular, as
meaning amino acids, vitamins, nucleosides and nucleotides. The
biosynthesis pathways of these compounds are known and are
available in the prior art.
[0023] Amino acids mean, preferably, L-amino acids, in particular
the proteinogenic L-amino acids, chosen from the group consisting
of L-aspartic acid, L-asparagine, L-threonine, L-serine, L-glutamic
acid, L-glutamine, glycine, L-alanine, L-cysteine, L-valine,
L-methionine, L-isoleucine, L-leucine, L-tyrosine, L-phenylalanine,
L-histidine, L-lysine, L-tryptophan, L-proline and L-arginine and
salts thereof, in particular L-lysine, L-methionine and
L-threonine. L-Lysine is very particularly preferred.
[0024] Proteinogenic amino acids are understood as meaning the
amino acids which occur in natural proteins, that is to say in
proteins of microorganisms, plants, animals and humans.
[0025] Vitamins mean, in particular, vitamin B1 (thiamine), vitamin
B2 (riboflavin), vitamin B5 (pantothenic acid), vitamin B6
(pyridoxines), vitamin B12 (cyanocobalamin), nicotinic
acid/nicotinamide, vitamin M (folic acid) and vitamin E
(tocopherol) and salts thereof, pantothenic acid being
preferred.
[0026] Nucleosides and nucleotides mean, inter alia,
S-adenosyl-methionine, inosine-5'-monophosphoric acid and
guanosine-5'-monophosphoric acid and salts thereof.
[0027] The coryneform bacteria are, in particular, those of the
genus Corynebacterium. Of the genus Corynebacterium, the species
Corynebacterium glutamicum, Corynebacterium ammoniagenes and
Corynebacterium thermoaminogenes are preferred. Information on the
taxonomic classification of strains of this group of bacteria is to
be found, inter alia, in Kampfer and Kroppenstedt (Canadian Journal
of Microbiology 42, 989-1005 (1996)) and in U.S. Pat. No.
5,250,434.
[0028] Suitable strains of the species Corynebacterium glutamicum
(C. glutamicum) are, in particular, the known wild-type strains
[0029] Corynebacterium glutamicum ATCC13032 [0030] Corynebacterium
acetoglutamicum ATCC15806 [0031] Corynebacterium acetoacidophilum
ATCC13870 [0032] Corynebacterium lilium ATCC15990 [0033]
Corynebacterium melassecola ATCC17965 [0034] Corynebacterium
herculis ATCC13868 [0035] Arthrobacter sp. ATCC243 [0036]
Brevibacterium chang-fua ATCC14017 [0037] Brevibacterium flavum
ATCC14067 [0038] Brevibacterium lactofermentum ATCC13869 [0039]
Brevibacterium divaricatum ATCC14020 [0040] Brevibacterium taipei
ATCC13744 and [0041] Microbacterium ammoniaphilum ATCC21645 and
mutants or strains, such as are known from the prior art, produced
therefrom which produce chemical compounds.
[0042] Suitable strains of the species Corynebacterium ammoniagenes
(C. ammoniagenes) are, in particular, the known wild-type strains
[0043] Brevibacterium ammoniagenes ATCC6871 [0044] Brevibacterium
ammoniagenes ATCC15137 and [0045] Corynebacterium sp. ATCC21084 and
mutants or strains, such as are known from the prior art, produced
therefrom which produce chemical compounds.
[0046] Suitable strains of the species Corynebacterium
thermoaminogenes (C. thermoaminogenes) are, in particular, the
known wild-type strains [0047] Corynebacterium thermoaminogenes
FERM BP-1539 [0048] Corynebacterium thermoaminogenes FERM BP-1540
[0049] Corynebacterium thermoaminogenes FERM BP-1541 and [0050]
Corynebacterium thermoaminogenes FERM BP-1542 and mutants or
strains, such as are known from the prior art, produced therefrom
which produce chemical compounds.
[0051] Strains with the designation "ATCC" can be obtained from the
American Type Culture Collection (Manassas, Va., USA). Strains with
the designation "FERM" can be obtained from the National Institute
of Advanced Industrial Science and Technology (AIST Tsukuba Central
6, 1-1-1 Higashi, Tsukuba Ibaraki, Japan). The strains of
Corynebacterium thermoaminogenes mentioned (FERM BP-1539, FERM
BP-1540, FERM BP-1541 and FERM BP-1542) are described in U.S. Pat.
No. 5,250,434.
[0052] Open reading frame (ORF) describes a section of a nucleotide
sequence which codes or can code for a protein or polypeptide or
ribonucleic acid to which no function can be assigned according to
the prior art.
[0053] After assignment of a function to the nucleotide sequence
section in question, it is in general referred to as a gene.
[0054] Alleles are in general understood as meaning alternative
forms of a given gene. The forms are distinguished by differences
in the nucleotide sequence.
[0055] In the context of the present invention, endogenous, that is
to say species-characteristic, open reading frames, genes or
alleles are preferably used. These are understood as meaning the
open reading frames, genes or alleles or nucleotide sequences
thereof present in the population of a species, such as, for
example, Corynebacterium glutamicum.
[0056] "A copy of an open reading frame (ORF), a gene or allele
present at the natural site (locus)" in the context of this
invention is understood as meaning the position or situation of the
ORF or gene or allele in relation to the adjacent ORFs or genes or
alleles such as exists in the corresponding wild-type or
corresponding parent organism or starting organism.
[0057] Thus, for example, the natural site of the lysC gene or of
an lysC.sup.FBR which codes for a "feed back" resistant aspartate
kinase from Corynebacterium glutamicum is the lysC site or lysC
locus or lysC gene site with the directly adjacent genes or open
reading frames orfX and leuA on one flank and the asd gene on the
other flank.
[0058] "Feed back" resistant aspartate kinase is understood as
meaning aspartate kinases which, compared with the wild-type form,
have a lower sensitivity to inhibition by mixtures of lysine and
threonine or mixtures of AEC (aminoethylcysteine) and threonine or
lysine by itself or AEC by itself. Strains which produce L-lysine
typically contain such "feed back" resistant or desensitized
aspartate kinases.
[0059] The nucleotide sequence of the chromosome of Corynebacterium
glutamicum is known and can be found in Patent Application
EP-A-1108790 and Access Number (Accession No.) AX114121 of the
nucleotide sequence databank of the European Molecular Biologies
Laboratories (EMBL, Heidelberg, Germany and Cambridge, UK). The
nucleotide sequences of orfX, the leuA gene and the asd gene have
the Access Numbers AX120364 (orfX), AX123517 (leuA) and AX123519
(asd).
[0060] Other datenbanks e.g. the National Center for Biotechnology
Information (NCBI) of the National Library of Medicin (Bethesda,
Md., USA) may be also be used.
[0061] Further databanks, such as, for example, that of the
National Center for Biotechnology Information (NCBI, Bethesda, Md.,
USA) or that of the Swiss Institute of Bioinformatics (Swissprot,
Geneva, Switzerland) or that of the Protein Information Resource
Database (PIR, Washington, D.C., USA) can also be used.
[0062] "In each case a second, optionally third or fourth site" is
understood as meaning a site which differs from the "natural site".
It is also called a "target site" or "target sequence" in the
following. It can also be called an "integration site" or
"transformation site". This second, optionally third or fourth
site, or the nucleotide sequence present at the corresponding
sites, is preferably in the chromosome and is in general not
essential for growth and for production of the desired chemical
compounds.
[0063] To produce the coryneform bacteria according to the
invention, the nucleotide sequence of the desired ORF, gene or
allele, optionally including expression and/or regulation signals,
is isolated and provided with nucleotide sequences of the target
site at the ends, these are then transferred into the desired
coryneform bacterium, preferably with the aid of vectors which do
not replicate or replicate to only a limited extent in coryneform
bacteria, and those bacteria in which the desired ORF, gene or
allele is incorporated at the target site are isolated, no
nucleotide sequence which is capable of/enables episomal
replication in microorganisms, no nucleotide sequence which is
capable of/enables transposition and no nucleotide sequence which
imparts resistance to antibiotics remaining at the target site.
[0064] The invention accordingly also provides a process for the
production of coryneform bacteria which produce one or more
chemical compounds, which comprises [0065] a) isolating the
nucleotide sequence of at least one desired ORF, gene or allele,
optionally including the expression and/or regulation signals,
[0066] b) providing the 5' and the 3' end of the ORF, gene or
allele with nucleotide sequences of the target site, [0067] c)
preferably incorporating the nucleotide sequence of the desired
ORF, gene or allele provided with nucleotide sequences of the
target site into a vector which does not replicate or replicates to
only a limited extent in coryneform bacteria, [0068] d)
transferring the nucleotide sequence according to b) or c) into
coryneform bacteria, and [0069] e) isolating coryneform bacteria in
which the nucleotide sequence according to a) is incorporated at
the target site, no nucleotide sequence which is capable of/enables
episomal replication in microorganisms, no nucleotide sequence
which is capable of/enables transposition and no nucleotide
sequence which imparts resistance to antibiotics remaining at the
target site.
[0070] Preferably, also, no residues of sequences of the vectors
used or species-foreign DNA, such as, for example, restriction
cleavage sites, remain at the target site. A maximum of 24,
preferably a maximum of 12, particularly preferably a maximum of 6
nucleotides of such DNA upstream or downstream of the ORF, gene or
allele incorporated optionally remain at the target site.
[0071] By the measures according to the invention, the productivity
of the coryneform bacteria or of the fermentative processes for the
preparation of chemical compounds is improved in respect of one or
more of the features chosen from the group consisting of
concentration (chemical compound formed, based on the unit volume),
yield (chemical compound formed, based on the source of carbon
consumed) and product formation rate (chemical compound formed,
based on the time) by at least 0.5-1.0% or at least 1.0 to 1.5% or
at least 1.5-2.0%.
[0072] Instructions on conventional genetic engineering methods,
such as, for example, isolation of chromosomal DNA, plasmid DNA,
handling of restriction enzymes etc., are found in Sambrook et al.
(Molecular Cloning--A Laboratory Manual (1989) Cold Spring Harbor
Laboratory Press). Instructions on transformation and conjugation
in coryneform bacteria are found, inter alia, in Thierbach et al.
(Applied Microbiology and Biotechnology 29, 356-362 (1988)), in
Schafer et al. (Journal of Bacteriology 172, 1663-1666 (1990) and
Gene 145, 69-73 (1994)) and in Schwarzer and Mahler (Bio/Technology
9, 84-87 (1991)).
[0073] Vectors which replicate to only a limited extent are
understood as meaning plasmid vectors which, as a function of the
conditions under which the host or carrier is cultured, replicate
or do not replicate. Thus, a temperature-sensitive plasmid for
coryneform bacteria which can replicate only at temperatures below
31.degree. C. has been described by Nakamura et al. (U.S. Pat. No.
6,303,383).
[0074] The invention furthermore provides coryneform bacteria, in
particular of the genus Corynebacterium, which produce L-lysine,
characterized in that these have, in addition to at least one of
the copy of an open reading frame (ORF), gene or allele of lysine
production present at the natural site (locus), in each case a
second, optionally third or fourth copy of the open reading frame
(ORF), gene or allele in question at in each case a second,
optionally third or fourth site in integrated form, no nucleotide
sequence which is capable of/enables episomal replication in
microorganisms, no nucleotide sequence which is capable of/enables
transposition and no nucleotide sequence which imparts resistance
to antibiotics being present at the particular second, optionally
third or fourth site.
[0075] The invention also furthermore provides a process for the
preparation of L-lysine, which comprises the following steps:
[0076] a) fermentation of coryneform bacteria, in particular
Corynebacterium glutamicum, characterized in that these have, in
addition to at least one of the copy of an open reading frame
(ORF), gene or allele of lysine production present at the natural
site (locus), in each case a second, optionally third or fourth
copy of the open reading frame (ORF), gene or allele in question at
in each case a second, optionally third or fourth site in
integrated form, no nucleotide sequence which is capable of/enables
episomal replication in microorganisms, no nucleotide sequence
which is capable of/enables transposition and no nucleotide
sequence which imparts resistance to antibiotics being present at
the particular second, optionally third or fourth site, under
conditions which allow expression of the said open reading frames
(ORF), genes or alleles, [0077] b) concentration of the L-lysine in
the fermentation broth, [0078] c) isolation of the L-lysine from
the fermentation broth, optionally [0079] d) with constituents from
the fermentation broth and/or the biomass to the extent of
>(greater than) 0 to 100%.
[0080] A "copy of an open reading frame (ORF), gene or allele of
lysine production" is to be understood as meaning all the,
preferably endogenous, open reading frames, genes or alleles of
which enhancement/over-expression can have the effect of improving
lysine production. Enhancement is understood as meaning an increase
in the intracellular concentration or activity of the particular
gene product, protein or enzyme.
[0081] These include, inter alia, the following open reading
frames, genes or alleles: accBC, accDA, cstA, cysD, cysE, cysH,
cysK, cysN, cysQ, dapA, dapB, dapC, dapD, dapE, dapF, ddh, dps,
eno, gap, gap2, gdh, gnd, lysC, lysC.sup.FBR, lysE, msiK, opcA,
oxyR, ppc, ppc.sup.FBR, pgk, pknA, pknB, pknD, pknG, ppsA, ptsH,
ptsI, ptsM, pyc, pyc P458S, sigC, sigD, sigE, sigH, sigM, tal,
thyA, tkt, tpi, zwa1, zwf and zwf A213T. These are summarized and
explained in Table 1.
[0082] These include, in particular, the lysC.sup.FBR alleles which
code for a "feed back" resistant aspartate kinase. Various
lysC.sup.FBR alleles are summarized and explained in Table 2.
[0083] The following lysC.sup.FBR alleles are preferred: lysC A279T
(replacement of alanine at position 279 of the aspartate kinase
protein coded, according to SEQ ID NO: 2, by threonine), lysC A279V
(replacement of alanine at position 279 of the aspartate kinase
protein coded, according to SEQ ID NO: 2, by valine), lysC S301F
(replacement of serine at position 301 of the aspartate kinase
protein coded, according to SEQ ID NO: 2, by phenylalanine), lysC
T308I (replacement of threonine at position 308 of the aspartate
kinase protein coded, according to SEQ ID NO: 2, by isoleucine),
lysC S301Y (replacement of serine at position 308 of the aspartate
kinase protein coded, according to SEQ ID NO: 2, by tyrosine), lysC
G345D (replacement of glycine at position 345 of the aspartate
kinase protein coded, according to SEQ ID NO: 2, by aspartic acid),
lysC R320G (replacement of arginine at position 320 of the
aspartate kinase protein coded, according to SEQ ID NO: 2, by
glycine), lysC T311I (replacement of threonine at position 311 of
the aspartate kinase protein coded, according to SEQ ID NO: 2, by
isoleucine), lysC S381F (replacement of serine at position 381 of
the aspartate kinase protein coded, according to SEQ ID NO: 2, by
phenylalanine).
[0084] The lysC.sup.FBR allele lysC T311I (replacement of threonine
at position 311 of the aspartate kinase protein coded, according to
SEQ ID NO: 2, by isoleucine), the nucleotide sequence of which is
shown as SEQ ID NO:3, is particularly preferred; the amino acid
sequence of the aspartate kinase protein coded is shown as SEQ ID
NO:4.
[0085] The second, optionally third or fourth copy of the open
reading frame (ORF), gene or allele of lysine production in
question can be integrated at in each case a second, optionally
third or fourth site. The following open reading frames, genes or
nucleotide sequences, inter alia, can be used for this: aecD,
ccpA1, ccpA2, citA, citB, citE, fda, gluA, gluB, gluC, gluD, luxR,
luxS, lysR1, lysR2, lysR3, menE, mqo, pck, pgi, poxB and zwa2, in
particular the genes aecD, gluA, gluB, gluC, gluD and pck. These
are summarized and explained in Table 3.
[0086] The sites mentioned include, of course, not only the coding
regions of the open reading frames or genes mentioned, but also the
regions or nucleotide sequences lying upstream which are
responsible for expression and regulation, such as, for example,
ribosome binding sites, promoters, binding sites for regulatory
proteins, binding sites for regulatory ribonucleic acids and
attenuators. These regions in general lie in a range of 1-800,
1-600, 1-400, 1-200, 1-100 or 1-50 nucleotides upstream of the
coding region. In the same way, regions lying downstream, such as,
for example, transcription terminators, are also included. These
regions in general lie in a range of 1-400, 1-200, 1-100, 1-50 or
1-25 nucleotides downstream of the coding region.
[0087] Intergenic regions in the chromosome, that is to say
nucleotide sequences without a coding function, can furthermore be
used. Finally, prophages or defective phages contained in the
chromosome can be used for this.
[0088] A prophage is understood as meaning a bacteriophage, in
particular the genome thereof, where this is replicated together
with the genome of the host and the formation of infectious
particles does not take place. A defective phage is understood as
meaning a prophage, in particular the genome thereof, which, as a
result of various mutations, has lost the ability to form so-called
infectious particles. Defective phages are also called cryptic.
Prophages and defective phages are often present in integrated form
in the chromosome of their host. Further details exist in the prior
art, for example in the textbook by Edward A. Birge (Bacterial and
Bacteriophage Genetics, 3.sup.rd ed., Springer-Verlag, New York,
USA, 1994) or in the textbook by S. Klaus et al. (Bakterienviren,
Gustav Fischer Verlag, Jena, Germany, 1992).
[0089] Examples of regions of the Corynebacterium glutamicum
chromosome representing intergenic regions, prophages, defective
phages or phage components are shown in tables 12 and 13. The
positions of the DNA regions refer to the genome map of
Corynebacterium glutamicum ATCC 13032 as presented in EP-A-1108790
or in the databank of the European Molecular Biologies Laboratories
(EMBL, Heidelberg, Germany and Cambridge, UK).
TABLE-US-00001 TABLE 1 Open reading frames, genes and alleles of
lysine production Access Name Description of the coded enzyme or
protein Reference Number accBC Acyl-CoA Carboxylase Jager et al.
U35023 EC 6.3.4.14 Archives of (acyl-CoA carboxylase) Microbiology
(1996) 166: 76-82 EP1108790; AX123524 WO0100805 AX066441 accDA
Acetyl-CoA Carboxylase EP1055725 EC 6.4.1.2 EP1108790 AX121013
(acetyl-CoA carboxylase) WO0100805 AX066443 cstA Carbon Starvation
Protein A EP1108790 AX120811 (carbon starvation protein A)
WO0100804 AX066109 cysD Sulfate Adenylyltransferase EP1108790
AX123177 sub-unit II EC 2.7.7.4 (sulfate adenylyltransferase small
chain) cysE Serine Acetyltransferase EP1108790 AX122902 EC 2.3.1.30
WO0100843 AX063961 (serine acetyltransferase) cysH 3'-Phosphoadenyl
Sulfate Reductase EP1108790 AX123178 EC 1.8.99.4 WO0100842 AX066001
(3'-phosphoadenosine 5'- phosphosulfate reductase) cysK Cysteine
Synthase EP1108790 AX122901 EC 4.2.99.8 WO0100843 AX063963
(cysteine synthase) cysN Sulfate Adenylyltransferase sub- EP1108790
AX123176 unit I AX127152 EC 2.7.7.4 (sulfate adenylyltransferase)
cysQ Transport Protein CysQ EP1108790 AX127145 (transporter cysQ)
WO0100805 AX066423 dapA Dihydrodipicolinate Synthase Bonnassie et
X53993 EC 4.2.1.52 al. Nucleic (dihydrodipicolinate synthase) Acids
Research 18: 6421 (1990) Pisabarro et Z21502 al., Journal of
Bacteriology 175: 2743-2749 (1993) EP1108790 WO0100805 EP0435132
EP1067192 AX123560 EP1067193 AX063773 dapB Dihydrodipicolinate
Reductase EP1108790 AX127149 EC 1.3.1.26 WO0100843 AX063753
(dihydrodipicolinate reductase) EP1067192 AX137723 EP1067193
AX137602 Pisabarro et X67737 al., Journal of Z21502 Bacteriology
175: 2743-2749 (1993) JP1998215883 E16749 JP1997322774 E14520
JP1997070291 E12773 JP1995075578 E08900 dapC N-Succinyl
Aminoketopimelate EP1108790 AX127146 Transaminase WO0100843
AX064219 EC 2.6.1.17 EP1136559 (N-succinyl diaminopimelate
transaminase) dapD Tetrahydrodipicolinate Succinylase EP1108790
AX127146 EC 2.3.1.117 WO0100843 AX063757 (tetrahydrodipicolinate
Wehrmann et al. AJ004934 succinylase) Journal of Bacteriology 180:
3159-3165 (1998) dapE N-Succinyl Diaminopimelate EP1108790 AX127146
Desuccinylase WO0100843 AX063749 EC 3.5.1.18 Wehrmann et al. X81379
(N-succinyl diaminopimelate Microbiology desuccinylase) 140:
3349-3356 (1994) dapF Diaminopimelate Epimerase EP1108790 AX127149
EC 5.1.1.7 WO0100843 AX063719 (diaminopimelate epimerase) EP1085094
AX137620 ddh Diaminopimelate Dehydrogenase EP1108790 AX127152 EC
1.4.1.16 WO0100843 AX063759 (diaminopimelate dehydrogenase) Ishino
et al., Y00151 Nucleic Acids Research 15: 3917-3917 (1987)
JP1997322774 E14511 JP1993284970 E05776 Kim et al., D87976 Journal
of Microbiology and Biotechnology 5: 250-256(1995) dps DNA
Protection Protein EP1108790 AX127153 (protection during starvation
protein) eno Enolase EP1108790 AX127146 EC 4.2.1.11 WO0100844
AX064945 (enolase) EP1090998 AX136862 Hermann et al.,
Electrophoresis 19: 3217-3221 (1998) gap Glyceraldehyde 3-Phosphate
EP1108790 AX127148 Dehydrogenase WO0100844 AX064941 EC 1.2.1.12
Eikmanns et X59403 (glyceraldehyde 3-phosphate al., Journal of
dehydrogenase) Bacteriology 174: 6076-6086 (1992) gap2
Glyceraldehyde 3-Phosphate EP1108790 AX127146 Dehydrogenase
WO0100844 AX064939 EC 1.2.1.12 (glyceraldehyde 3-phosphate
dehydrogenase 2) gdh Glutamate Dehydrogenase EP1108790 AX127150 EC
1.4.1.4 WO0100844 AX063811 (glutamate dehydrogenase) Boermann et
X59404 al., Molecular Microbiology 6: 317-326 (1992). Guyonvarch et
X72855 al., NCBI gnd 6-Phosphogluconate Dehydrogenase EP1108790
AX127147 EC 1.1.1.44 AX121689 (6-phosphogluconate dehydrogenase)
WO0100844 AX065125 lysC Aspartate Kinase EP1108790 AX120365 EC
2.7.2.4 WO0100844 AX063743 (aspartate kinase) Kalinowski et X57226
al., Molecular Microbiology 5: 1197-204 (1991) lysC.sup.FBR
Aspartate Kinase feedback resistant see Table 2 (fbr) EC 2.7.2.4
(aspartate kinase fbr) lysE Lysine Exporter EP1108790 AX123539
(lysine exporter protein) WO0100843 AX123539 Vrlji et al., X96471
Molecular Microbiology 22: 815-826 (1996) msiK Sugar Importer
EP1108790 AX120892 (multiple sugar import protein) opcA Glucose
6-phosphate Dehydrogenase WO0104325 AX076272 (subunit of glucose
6-phosphate dehydrogenase) oxyR Transcription Regulator EP1108790
AX122198 (transcriptional regulator) AX127149 ppc.sup.FBR
Phosphoenol Pyruvate Carboxylase EP0723011 feedback resistant
WO0100852 EC 4.1.1.31 (phosphoenol pyruvate carboxylase feedback
resistant) ppc Phosphoenol Pyruvate Carboxylase EP1108790 AX127148
EC 4.1.1.31 AX123554 (phosphoenol pyruvate carboxylase) O'Reagan et
M25819 al., Gene 77(2): 237-251 (1989) pgk Phosphoglycerate Kinase
EP1108790 AX121838 EC 2.7.2.3 AX127148 (phosphoglycerate kinase)
WO0100844 AX064943 Eikmanns, X59403 Journal of Bacteriology 174:
6076-6086 (1992) pknA Protein Kinase A EP1108790 AX120131 (protein
kinase A) AX120085 pknB Protein Kinase B EP1108790 AX120130
(protein kinase B) AX120085 pknD Protein Kinase D EP1108790
AX127150 (protein kinase D) AX122469 AX122468 pknG Protein Kinase G
EP1108790 AX127152 (protein kinase G) AX123109 ppsA Phosphoenol
Pyruvate Synthase EP1108790 AX127144 EC 2.7.9.2 AX120700
(phosphoenol pyruvate synthase) AX122469 ptsH Phosphotransferase
System Protein H EP1108790 AX122210 EC 2.7.1.69 AX127149
(phosphotransferase system WO0100844 AX069154 component H) ptsI
Phosphotransferase System Enzyme I EP1108790 AX122206 EC 2.7.3.9
AX127149 (phosphotransferase system enzyme I) ptsM Glukose-specific
Phosphotransferase Lee et al., L18874 System Enzyme II FEMS EC
2.7.1.69 Microbiology (glucose phosphotransferase system Letters
119 enzyme II) (1-2): 137-145 (1994) pyc Pyruvate Carboxylase
WO9918228 A97276 EC 6.4.1.1 Peters-Wendisch Y09548 (pyruvate
carboxylase) et al., Microbiology 144: 915-927 (1998) pyc Pyruvate
Carboxylase EP1108790 P458S EC 6.4.1.1 (pyruvate carboxylase) amino
acid exchange P458S sigC Sigma Factor C EP1108790 AX120368 EC
2.7.7.6 AX120085 (extracytoplasmic function alternative sigma
factor C) sigD RNA Polymerase Sigma Factor D EP1108790 AX120753 EC
2.7.7.6 AX127144 (RNA polymerase sigma factor) sigE Sigma Factor E
EP1108790 AX127146 EC 2.7.7.6 AX121325 (extracytoplasmic function
alternative sigma factor E) sigH Sigma Factor H EP1108790 AX127145
EC 2.7.7.6 AX120939 (sigma factor SigH) sigM Sigma Factor M
EP1108790 AX123500 EC 2.7.7.6 AX127145 (sigma factor SigM) tal
Transaldolase WO0104325 AX076272 EC 2.2.1.2 (transaldolase) thyA
Thymidylate Synthase EP1108790 AX121026 EC 2.1.1.45 AX127145
(thymidylate synthase) tkt Transketolase Ikeda et al., AB023377 EC
2.2.1.1 NCBI (transketolase) tpi Triose Phosphate Isomerase
Eikmanns, X59403 EC 5.3.1.1 Journal of (triose phosphate isomerase)
Bacteriology 174: 6076-6086 (1992) zwa1 Cell Growth Factor 1
EP1111062 AX133781 (growth factor 1) zwf Glucose 6-phosphate
1-Dehydrogenase EP1108790 AX127148 EC 1.1.1.49 AX121827
(glucose 6-phosphate 1- WO0104325 AX076272 dehydrogenase) zwf
Glucose 6-phosphate 1-Dehydrogenase EP1108790 A213T EC 1.1.1.49
(glucose 6-phosphate 1- dehydrogenase) amino acid exchange
A213T
TABLE-US-00002 TABLE 2 lysC.sup.FBR alleles which code for feed
back resistant aspartate kinases Name of the Further Access allele
information Reference Number lysC.sup.FBR-E05108 JP 1993184366-A
E05108 (sequence 1) lysC.sup.FBR-E06825 lysC A279T JP 1994062866-A
E06825 (sequence 1) lysC.sup.FBR-E06826 lysC A279T JP 1994062866-A
E06826 (sequence 2) lysC.sup.FBR-E06827 JP 1994062866-A E06827
(sequence 3) lysC.sup.FBR-E08177 JP 1994261766-A E08177 (sequence
1) lysC.sup.FBR-E08178 lysC A279T JP 1994261766-A E08178 (sequence
2) lysC.sup.FBR-E08179 lysC A279V JP 1994261766-A E08179 (sequence
3) lysC.sup.FBR-E08180 lysC S301F JP 1994261766-A E08180 (sequence
4) lysC.sup.FBR-E08181 lysC T308I JP 1994261766-A E08181 (sequence
5) lysC.sup.FBR-E08182 JP 1994261766-A E08182 (sequence 6)
lysC.sup.FBR-E12770 JP 1997070291-A E12770 (sequence 13)
lysC.sup.FBR-E14514 JP 1997322774-A E14514 (sequence 9)
lysC.sup.FBR-E16352 JP 1998165180-A E16352 (sequence 3)
lysC.sup.FBR-E16745 JP 1998215883-A E16745 (sequence 3)
lysC.sup.FBR-E16746 JP 1998215883-A E16746 (sequence 4)
lysC.sup.FBR-I74588 U.S. Pat. No. 5,688,671-A I74588 (sequence 1)
lysC.sup.FBR-I74589 lysC A279T U.S. Pat. No. 5,688,671-A I74589
(sequence 2) lysC.sup.FBR-I74590 U.S. Pat. No. 5,688,671-A I74590
(sequence 7) lysC.sup.FBR-I74591 lyaC A279T U.S. Pat. No.
5,688,671-A I74591 (sequence 8) lysC.sup.FBR-I74592 U.S. Pat. No.
5,688,671-A I74592 (sequence 9) lysC.sup.FBR-I74593 lysC A279T U.S.
Pat. No. 5,688,671-A I74593 (sequence 10) lysC.sup.FBR-I74594 U.S.
Pat. No. 5,688,671-A I74594 (sequence 11) lysC.sup.FBR-I74595 lysC
A279T U.S. Pat. No. 5,688,671-A I74595 (sequence 12)
lysC.sup.FBR-I74596 U.S. Pat. No. 5,688,671-A I74596 (sequence 13)
lysC.sup.FBR-I74597 lysC A279T U.S. Pat. No. 5,688,671-A I74597
(sequence 14) lysC.sup.FBR-X57226 lysC S301Y EP0387527 X57226
Kalinowski et al., Molecular and General Genetics 224: 317-324
(1990) lysC.sup.FBR-L16848 lysC G345D Follettie and L16848 Sinskey
NCBI Nucleotide Database (1990) lysC.sup.FBR-L27125 lysC R320G
Jetten et al., L27125 lysC G345D Applied Microbiology Biotechnology
43: 76-82 (1995) lysC.sup.FBR lysC T311I WO0063388 (sequence 17)
lysC.sup.FBR lysC S301F U.S. Pat. No. 3,732,144 lysC.sup.FBR lysC
S381F lysC.sup.FBR JP6261766 (sequence 1) lysC.sup.FBR lysC A279T
JP6261766 (sequence 2) lysC.sup.FBR lysC A279V JP6261766 (sequence
3) lysC.sup.FBR lysC S301F JP6261766 (sequence 4) lysC.sup.FBR lysC
T308I JP6261766 (sequence 5)
TABLE-US-00003 TABLE 3 Target sites for integration of open reading
frames, genes and alleles of lysine production Description of the
coded Gene name enzyme or protein Reference Access Number aecD beta
C--S Lyase Rossol et al., Journal M89931 EC 2.6.1.1 of Bacteriology
(beta C--S lyase) 174(9): 2968-77 (1992) ccpA1 Catabolite Control
WO0100844 AX065267 Protein EP1108790 AX127147 (catabolite control
protein A1) ccpA2 Catabolite Control WO0100844 AX065267 Protein
EP1108790 AX121594 (catabolite control protein A2) citA Sensor
Kinase CitA EP1108790 AX120161 (sensor kinase CitA) citB
Transcription Regulator EP1108790 AX120163 CitB (transcription
regulator CitB) citE Citrate Lyase WO0100844 AX065421 EC 4.1.3.6
EP1108790 AX127146 (citrate lyase) fda Fructose Bisphosphate von
der Osten et al., X17313 Aldolase Molecular Microbiology EC
4.1.2.13 3(11): 1625-37 (1989) (fructose 1,6- bisphosphate
aldolase) gluA Glutamate Transport ATP- Kronemeyer et al., X81191
binding Protein Journal of Bacteriology (glutamate transport
177(5): 1152-8 (1995) ATP-binding protein) gluB Glutamate-binding
Kronemeyer et al., X81191 Protein Journal of Bacteriology
(glutamate-binding 177(5): 1152-8 (1995) protein) gluC Glutamate
Transport Kronemeyer et al., X81191 Permease Journal of
Bacteriology (glutamate transport 177(5): 1152-8 (1995) system
permease) gluD Glutamate Transport Kronemeyer et al., X81191
Permease Journal of Bacteriology (glutamate transport 177(5):
1152-8 (1995) system permease) luxR Transcription Regulator
WO0100842 AX065953 LuxR EP1108790 AX123320 (transcription regulator
LuxR) luxS Histidine Kinase LuxS EP1108790 AX123323 (histidine
kinase LuxS) AX127145 lysR1 Transcription Regulator EP1108790
AX064673 LysR1 AX127144 (transcription regulator LysR1) lysR2
Transcription Activator EP1108790 AX123312 LysR2 (transcription
regulator LysR2) lysR3 Transcription Regulator WO0100842 AX065957
LysR3 EP1108790 AX127150 (transcription regulator LysR3) menE
O-Succinylbenzoic Acid WO0100843 AX064599 CoA Ligase EP1108790
AX064193 EC 6.2.1.26 AX127144 (O-succinylbenzoate CoA ligase) mqo
Malate-Quinone Molenaar et al., Eur. AJ224946 Oxidoreductase
Journal of Biochemistry (malate-quinone- 1; 254(2): 395-403 (1998)
oxidoreductase) pck Phosphoenol Pyruvate WO0100844 AJ269506
Carboxykinase AX065053 (phosphoenol pyruvate carboxykinase) pgi
Glucose 6-phosphate EP1087015 AX136015 Isomerase EP1108790 AX127146
EC 5.3.1.9 (glucose 6-phosphate isomerase) poxB Pyruvate Oxidase
WO0100844 AX064959 EC 1.2.3.3 EP1096013 AX137665 (pyruvate oxidase)
zwa2 Cell Growth Factor 2 EP1106693 AX113822 (growth factor 2)
EP1108790 AX127146
[0090] The invention accordingly also provides a process for the
production of coryneform bacteria which produce L-lysine, which
comprises [0091] a) isolating the nucleotide sequence of at least
one desired ORF, gene or allele of lysine production, optionally
including the expression and/or regulation signals, [0092] b)
providing the 5' and the 3' end of the ORF, gene or allele of
lysine production with nucleotide sequences of the target site,
[0093] c) preferably incorporating the nucleotide sequence of the
desired ORF, gene or allele provided with nucleotide sequences of
the target site into a vector which does not replicate or
replicates to only a limited extent in coryneform bacteria, [0094]
d) transferring the nucleotide sequence according to b) or c) into
coryneform bacteria, and [0095] e) isolating coryneform bacteria in
which the nucleotide sequence according to a) is incorporated at
the target site, no nucleotide sequence which is capable of/enables
episomal replication in microorganisms, no nucleotide sequence
which is capable of/enables transposition and no nucleotide
sequence which imparts resistance to antibiotics remaining at the
target site.
[0096] The invention furthermore provides coryneform bacteria, in
particular of the genus Corynebacterium, which produce L-methionine
and/or L-threonine, characterized in that these have, in addition
to at least one of the copy of an open reading frame (ORF), gene or
allele of methionine production or threonine production present at
the natural site (locus), in each case a second, optionally third
or fourth copy of the open reading frame (ORF), gene or allele in
question at in each case a second, optionally third or fourth site
in integrated form, no nucleotide sequence which is capable
of/enables episomal replication in microorganisms, no nucleotide
sequence which is capable of/enables transposition and no
nucleotide sequence which imparts resistance to antibiotics being
present at the particular second, optionally third or fourth
site.
[0097] The invention also furthermore provides a process for the
preparation of L-methionine and/or L-threonine, which comprises the
following steps: [0098] a) fermentation of coryneform bacteria, in
particular Corynebacterium glutamicum, characterized in that these
have, in addition to at least one of the copy of an open reading
frame (ORF), gene or allele of methionine production or threonine
production present at the natural site (locus), in each case a
second, optionally third or fourth copy of the open reading frame
(ORF), gene or allele in question at in each case a second,
optionally third or fourth site in integrated form, no nucleotide
sequence which is capable of/enables episomal replication in
microorganisms, no nucleotide sequence which is capable of/enables
transposition and no nucleotide sequence which imparts resistance
to antibiotics being present at the particular second, optionally
third or fourth site, [0099] under conditions which allow
expression of the said open reading frames (ORF), genes or alleles,
[0100] b) concentration of the L-methionine and/or L-threonine in
the fermentation broth, [0101] c) isolation of the L-methionine
and/or L-threonine from the fermentation broth, optionally [0102]
d) with constituents from the fermentation broth and/or the biomass
to the extent of >(greater than) 0 to 100%.
[0103] A "copy of an open reading frame (ORF), gene or allele of
methionine production" is to be understood as meaning all the,
preferably endogenous, open reading frames, genes or alleles of
which enhancement/over-expression can have the effect of improving
methionine production.
[0104] These include, inter alia, the following open reading
frames, genes or alleles: accBC, accDA, aecD, cstA, cysD, cysE,
cysH, cysK, cysN, cysQ, dps, eno, fda, gap, gap2, gdh, gnd, glyA,
horn, hom.sup.FBR, lysC, lysC.sup.FBR, metA, metB, metE, metH,
metY, msiK, opcA, oxyR, ppc, ppc.sup.FBR, pgk, pknA, pknB, pknD,
pknG, ppsA, ptsH, ptsI, ptsM, pyc, pyc P458S, sigC, sigD, sigE,
sigH, sigM, tal, thyA, tkt, tpi, zwa1, zwf and zwf A213T. These are
summarized and explained in Table 4. These include, in particular,
the lysC.sup.FBR alleles which code for a "feed back" resistant
aspartate kinase (see Table 2) and the hom.sup.FBR alleles which
code for a "feed back" resistant homoserine dehydrogenase.
[0105] The second, optionally third or fourth copy of the open
reading frame (ORF), gene or allele of methionine production in
question can be integrated at in each case a second, optionally
third or fourth site. The following open reading frames, genes or
nucleotide sequences, inter alia, can be used for this: brnE, brnF,
brnQ, ccpA1, ccpA2, citA, citB, citE, ddh, gluA, gluB, gluC, gluD,
luxR, luxS, lysR1, lysR2, lysR3, menE, metD, metK, pck, pgi, poxB
and zwa2. These are summarized and explained in Table 5.
[0106] The sites mentioned include, of course, not only the coding
regions of the open reading frames or genes mentioned, but also the
regions or nucleotide sequences lying upstream which are
responsible for expression and regulation, such as, for example,
ribosome binding sites, promoters, binding sites for regulatory
proteins, binding sites for regulatory ribonucleic acids and
attenuators. These regions in general lie in a range of 1-800,
1-600, 1-400, 1-200, 1-100 or 1-50 nucleotides upstream of the
coding region. In the same way, regions lying downstream, such as,
for example, transcription terminators, are also included. These
regions in general lie in a range of 1-400, 1-200, 1-100, 1-50 or
1-25 nucleotides downstream of the coding region.
[0107] Intergenic regions in the chromosome, that is to say
nucleotide sequences without a coding function, can furthermore be
used. Finally, prophages or defective phages contained in the
chromosome can be used for this.
[0108] Examples of regions of the Corynebacterium glutamicum
chromosome representing intergenic regions, prophages, defective
phages or phage components are shown in tables 12 and 13. The
positions of the DNA regions refer to the genome map of
Corynebacterium glutamicum ATCC 13032 as presented in EP-A-1108790
or in the databank of the European Molecular Biologies Laboratories
(EMBL, Heidelberg, Ge/many and Cambridge, UK).
TABLE-US-00004 TABLE 4 Open reading frames, genes and alleles of
methionine production Description of the coded enzyme or Access
Name protein Reference Number AccBC Acyl-CoA Carboxylase Jager et
al. U35023 EC 6.3.4.14 Archives of (acyl-CoA carboxylase)
Microbiology (1996) 166: 76-82 EP1108790; AX123524 WO0100805
AX066441 AccDA Acetyl-CoA Carboxylase EP1055725 EC 6.4.1.2
EP1108790 AX121013 (acetyl-CoA carboxylase) WO0100805 AX066443 AecD
Cystathionine beta-Lyase Rossol et al., M89931 EC 4.4.1.8 Journal
of (cystathionine beta-lyase) Bacteriology 174: 2968-2977 (1992)
CstA Carbon Starvation Protein A EP1108790 AX120811 (carbon
starvation protein A) WO0100804 AX066109 CysD Sulfate
Adenylyltransferase EP1108790 AX123177 sub-unit II EC 2.7.7.4
(sulfate adenylyltransferase small chain) CysE Serine
Acetyltransferase EP1108790 AX122902 EC 2.3.1.30 WO0100843 AX063961
(serine acetyltransferase) CysH 3'-Phosphoadenyl Sulfate Reductase
EP1108790 AX123178 EC 1.8.99.4 WO0100842 AX066001
(3'-phosphoadenosine 5'- phosphosulfate reductase) CysK Cysteine
Synthase EP1108790 AX122901 EC 4.2.99.8 WO0100843 AX063963
(cysteine synthase) CysN Sulfate Adenylyltransferase sub- EP1108790
AK123176 unit I AX127152 EC 2.7.7.4 (sulfate adenylyltransferase)
CysQ Transport protein CysQ EP1108790 AX127145 (transporter cysQ)
WO0100805 AX066423 Dps DNA Protection Protein EP1108790 AX127153
(protection during starvation protein) Eno Enolase EP1108790
AX127146 EC 4.2.1.11 WO0100844 AX064945 (enolase) EP1090998
AX136862 Hermann et al., Electrophoresis 19: 3217-3221 (1998) Fda
Fructose Bisphosphate Aldolase van der Osten et X17313 EC 4.1.2.13
al., Molecular (fructose bisphosphate aldolase) Microbiology 3:
1625-1637 (1989) Gap Glyceraldehyde 3-Phosphate EP1108790 AX127148
Dehydrogenase WO0100844 AX064941 EC 1.2.1.12 Eikmanns et al.,
X59403 (glyceraldehyde 3-phosphate Journal of dehydrogenase)
Bacteriology 174: 6076-6086 (1992) gap2 Glyceraldehyde 3-Phosphate
EP1108790 AX127146 Dehydrogenase WO0100844 AX064939 EC 1.2.1.12
(glyceraldehyde 3-phosphate dehydrogenase 2) Gdh Glutamate
Dehydrogenase EP1108790 AX127150 EC 1.4.1.4 WO0100844 AX063811
(glutamate dehydrogenase) Boermann et al., X59404 Molecular
Microbiology 6: 317-326 (1992); Guyonvarch et X72855 al., NCBI GlyA
Glycine/Serine EP1108790 AX127146 Hydroxymethyltransferase AX121194
EC 2.1.2.1 (glycine/serine hydroxymethyltransferase) Gnd
6-Phosphogluconate Dehydrogenase EP1108790 AX127147 EC 1.1.1.44
AX121689 (6-phosphogluconate dehydrogenase) WO0100844 AX065125 Hom
Homoserine Dehydrogenase Peoples et al., Y00546 EC 1.1.1.3
Molecular (homoserine dehydrogenase) Microbiology 2: 63-72 (1988)
hom.sup.FBR Homoserine Dehydrogenase feedback Reinscheid et
resistant (fbr) al., Journal of EC 1.1.1.3 Bacteriology (homoserine
dehydrogenase fbr) 173: 3228-30 (1991) LysC Aspartate Kinase
EP1108790 AX120365 EC 2.7.2.4 WO0100844 AX063743 (aspartate kinase)
Kalinowski et X57226 al., Molecular Microbiology 5: 1197-204 (1991)
lysC.sup.FBR Aspartate Kinase feedback resistant see Table 2 (fbr)
EC 2.7.2.4 (aspartate kinase fbr) MetA Homoserine Acetyltransferase
Park et al., AF052652 EC 2.3.1.31 Molecular Cells (homoserine
acetyltransferase) 8: 286-94 (1998) MetB Cystathionine
.gamma.-Lyase Hwang et al., AF126953 EC 4.4.1.1 Molecular Cells
(cystathionine gamma-synthase) 9: 300-308 (1999) MetE Homocysteine
Methyltransferase EP1108790 AX127146 EC 2.1.1.14 AX121345
(homocysteine methyltransferase) MetH Homocysteine
Methyltransferase EP1108790 AX127148 (Vitamin B12-dependent)
AX121747 EC 2.1.1.14 (homocysteine methyltransferase) MetY
Acetylhomoserine Sulfhydrolase EP1108790 AX120810 (acetylhomoserine
sulfhydrolase) AX127145 MsiK Sugar Importer EP1108790 AX120892
(multiple sugar import protein) OpcA Glucose 6-phosphate
Dehydrogenase WO0104325 AX076272 (subunit of glucose 6-phosphate
dehydrogenase) OxyR Transcription Regulator EP1108790 AX122198
(transcriptional regulator) AX127149 ppc.sup.FBR Phosphoenol
Pyruvate Carboxylase EP0723011 feedback resistent WO0100852 EC
4.1.1.31 (phosphoenol pyruvate carboxylase feedback resistant) Ppc
Phosphoenol Pyruvate Carboxylase EP1108790 AX127148 EC 4.1.1.31
AX123554 (phosphoenol pyruvate carboxylase) O'Reagan et al., M25819
Gene 77(2): 237-251 (1989) Pgk Phosphoglycerate Kinase EP1108790
AX121838 EC 2.7.2.3 AX127148 (phosphoglycerate kinase) WO0100844
AX064943 Eikmanns, X59403 Journal of Bacteriology 174: 6076-6086
(1992) PknA Protein Kinase A EP1108790 AX120131 (protein kinase A)
AX120085 PknB Protein Kinase B EP1108790 AX120130 (protein kinase
B) AX120085 PknD Protein Kinase D EP1108790 AX127150 (protein
Kinase D) AX122469 AX122468 PknG Protein Kinase G EP1108790
AX127152 (protein kinase G) AX123109 PpsA Phosphoenol Pyruvate
Synthase EP1108790 AX127144 EC 2.7.9.2 AX120700 (phosphoenol
pyruvate synthase) AX122469 PtsH Phosphotransferase System Protein
H EP1108790 AX122210 EC 2.7.1.69 AX127149 (phosphotransferase
system WO0100844 AX069154 component H) PtsI Phosphotransferase
System Enzyme I EP1108790 AX122206 EC 2.7.3.9 AX127149
(phosphotransferase system enzyme I) PtsM Glucose-specific
Phosphotransferase Lee et al., FEMS L18874 System Enzyme II
Microbiology EC 2.7.1.69 Letters 119 (glucose phosphotransferase
system (1-2): 137-145 enzyme II) (1994) Pyc Pyruvate Carboxylase
WO9918228 A97276 EC 6.4.1.1 Peters-Wendisch Y09548 (pyruvate
carboxylase) et al., Microbiology 144: 915-927 (1998) Pyc Pyruvate
Carboxylase EP1108790 P458s EC 6.4.1.1 (pyruvate carboxylase) amino
acid exchange P458S SigC Sigma Factor C EP1108790 AX120368 EC
2.7.7.6 AX120085 (extracytoplasmic function alternative sigma
factor C) SigD RNA Polymerase Sigma Factor D EP1108790 AX120753 EC
2.7.7.6 AX127144 (RNA polymerase sigma factor) SigE Sigma Factor E
EP1108790 AX127146 EC 2.7.7.6 AX121325 (extracytoplasmic function
alternative sigma factor E) SigH Sigma Factor H EP1108790 AX127145
EC 2.7.7.6 AX120939 (sigma factor SigH) SigM Sigma Factor M
EP1108790 AX123500 EC 2.7.7.6 AX127153 (sigma factor SigM) Tal
Transaldolase WO0104325 AX076272 EC 2.2.1.2 (transaldolase) ThyA
Thymidylate Synthase EP1108790 AX121026 EC 2.1.1.45 AX127145
(thymidylate synthase) Tkt Transketolase Ikeda et al., AB023377 EC
2.2.1.1 NCBI (transktolase) Tpi Triose Phosphate Isomerase
Eikmanns, X59403 EC 5.3.1.1 Journal of (triose phosphate isomerase)
Bacteriology 174: 6076-6086 (1992) zwa1 Cell Growth Factor 1
EP1111062 AX133781 (growth factor 1) Zwf Glucose 6-phosphate
1-Dehydrogenase EP1108790 AX127148 EC 1.1.1.49 AX121827 (glucose
6-phosphate 1- WO0104325 AX076272 dehydrogenase) Zwf Glucose
6-phosphate 1-Dehydrogenase EP1108790 A213T EC 1.1.1.49 (glucose
6-phosphate 1- dehydrogenase) amino acid exchange A213T
TABLE-US-00005 TABLE 5 Target sites for integration of open reading
frames, genes and alleles of methionine production Gene Description
of the Access name coded enzyme or protein Reference Number BrnE
Transporter of EP1096010 AX137709 branched-chain amino AX137714
acids (branched-chain amino acid transporter) BrnF Transporter of
EP1096010 AX137709 branched-chain amino AX137714 acids
(branched-chain amino acid transporter) BrnQ Carrier protein of
Tauch et al., Archives M89931 branched-chain amino of Microbiology
AX066841 acids 169(4): 303-12 (1998) AX127150 (branched-chain amino
WO0100805 acid transport system EP1108790 carrier protein) ccpA1
Catabolite Control WO0100844 AX065267 Protein EP1108790 AX127147
(catabolite control protein A1) ccpA2 Catabolite Control WO0100844
AX065267 Protein EP1108790 AX121594 (catabolite control protein A2)
citA Sensor Kinase CitA EP1108790 AX120161 (sensor kinase CitA)
citB Transcription Regulator EP1108790 AX120163 CitB (transcription
regulator CitB) citE Citrate Lyase WO0100844 AX065421 EC 4.1.3.6
EP1108790 AX127146 (citrate lyase) ddh Diaminopimelate Ishino et
al., Nucleic S07384 Dehydrogenase Acids Research 15: AX127152 EC
1.4.1.16 3917 (1987) (diaminopimelate EP1108790 dehydrogenase) gluA
Glutamate Transport Kronemeyer et al., X81191 ATP-binding Protein
Journal of (glutamate transport Bacteriology ATP-binding protein)
177(5): 1152-8 (1995) gluB Glutamate-binding Kronemeyer et al.,
X81191 Protein Journal of (glutamate-binding Bacteriology protein)
177(5): 1152-8 (1995) gluC Glutamate Transport Kronemeyer et al.,
X81191 Permease Journal of (glutamate transport Bacteriology system
permease) 177(5): 1152-8 (1995) gluD Glutamate Transport Kronemeyer
et al., X81191 Permease Journal of (glutamate transport
Bacteriology system permease) 177(5): 1152-8 (1995) luxR
Transcription Regulator WO0100842 AX065953 LuxR EP1108790 AX123320
(transcription regulator LuxR) luxS Histidine Kinase LuxS EP1108790
AX123323 (histidine kinase LuxS) AX127145 lysR1 Transcription
Regulator EP1108790 AX064673 LysR1 AX127144 (transcription
regulator LysR1) lysR2 Transcription Activator EP1108790 AX123312
LysR2 (transcription regulator LysR2) lysR3 Transcription Regulator
WO0100842 AX065957 LysR3 EP1108790 AX127150 (transcription
regulator LysR3) menE O-Succinylbenzoic Acid WO0100843 AX064599 CoA
Ligase EP1108790 AX064193 EC 6.2.1.26 AX127144 (O-succinylbenzoate
CoA ligase) metD Transcription Regulator EP1108790 AX123327 MetD
AX127153 (transcription regulator MetD) metK Methionine Adenosyl
WO0100843 AX063959 Transferase EP1108790 AX127148 EC 2.5.1.6
(S-adenosylmethionine synthetase) pck Phosphoenol Pyruvate
WO0100844 AJ269506 Carboxykinase AX065053 (phosphoenol pyruvate
carboxykinase) pgi Glucose 6-Phosphate EP1087015 AX136015 Isomerase
EP1108790 AX127146 EC 5.3.1.9 (glucose-6-phosphate isomerase) poxB
Pyruvate Oxidase WO0100844 AX064959 EC 1.2.3.3 EP1096013 AX137665
(pyruvate oxidase) zwa2 Cell Growth Factor 2 EP1106693 AX113822
(growth factor 2) EP1108790 AX127146
[0109] A "copy of an open reading frame (ORF), gene or allele of
threonine production" is to be understood as meaning all the open
reading frames, genes or alleles of which
enhancement/over-expression can have the effect of improving
threonine production.
[0110] These include, inter alia, the following open reading
frames, genes or alleles: accBC, accDA, cstA, cysD, cysE, cysH,
cysI, cysN, cysQ, dps, eno, fda, gap, gap2, gdh, gnd, horn,
hom.sup.FBR, lysC, lysC.sup.FBR, msiK, opcA, oxyR, ppc,
ppc.sup.FBR, pgk, pknA, pknB, pknD, pknG, ppsA, ptsH, ptsI, ptsM,
pyc, pyc P458S, sigC, sigD, sigE, sigH, sigM, tal, thyA, tkt, tpi,
thrB, thrC, thrE, zwa1, zwf and zwf A213T. These are summarized and
explained in Table 6. These include, in particular, the
lysC.sup.FBR alleles which code for a "feed back" resistant
aspartate kinase (See Table 2) and the hom.sup.FBR alleles which
code for a "feed back" resistant homoserine dehydrogenase.
[0111] The second, optionally third or fourth copy of the open
reading frame (ORF), gene or allele of threonine production in
question can be integrated at in each case a second, optionally
third or fourth site. The following open reading frames, genes or
nucleotide sequences, inter alia, can be used for this: ccpA1,
ccpA2, citA, citB, citE, ddh, gluA, gluB, gluC, gluD, glyA, ilvA,
ilvBN, ilvC, ilvD, luxR, luxS, lysR1, lysR2, lysR3, mdh, menE,
metA, metD, pck, poxB, sigB and zwa2. These are summarized and
explained in Table 7.
[0112] The sites mentioned include, of course, not only the coding
regions of the open reading frames or genes mentioned, but also the
regions or nucleotide sequences lying upstream which are
responsible for expression and regulation, such as, for example,
ribosome binding sites, promoters, binding sites for regulatory
proteins, binding sites for regulatory ribonucleic acids and
attenuators. These regions in general lie in a range of 1-800,
1-600, 1-400, 1-200, 1-100 or 1-50 nucleotides upstream of the
coding region. In, the same way, regions lying downstream, such as,
for example, transcription terminators, are also included. These
regions in general lie in a range of 1-400, 1-200, 1-100, 1-50 or
1-25 nucleotides downstream of the coding region.
[0113] Intergenic regions in the chromosome, that is to say
nucleotide sequences without a coding function, can furthermore be
used. Finally, prophages or defective phages contained in the
chromosome can be used for this.
[0114] Examples of regions of the Corynebacterium glutamicum
chromosome representing intergenic regions, prophages, defective
phages or phage components are shown in tables 12 and 13. The
positions of the DNA regions refer to the genome map of
Corynebacterium glutamicum ATCC 13032 as presented in EP-A-1108790
or in the databank of the European Molecular Biologies Laboratories
(EMBL, Heidelberg, Germany and Cambridge, UK).
TABLE-US-00006 TABLE 6 Open reading frames, genes and alleles of
threonine production Description of the coded enzyme or Access Name
protein Reference Number accBC Acyl-CoA Carboxylase Jager et al.
U35023 EC 6.3.4.14 Archives of (acyl-CoA carboxylase) Microbiology
166: 76-82 (1996) EP1108790 AX123524 WO0100805 AX066441 accDA
Acetyl-CoA Carboxylase EP1055725 EC 6.4.1.2 EP1108790 AX121013
(acetyl-CoA carboxylase) WO0100805 AX066443 cstA Carbon Starvation
Protein A EP1108790 AX120811 (carbon starvation protein A)
WO0100804 AX066109 cysD Sulfate Adenylyltransferase EP1108790
AX123177 sub-unit II EC 2.7.7.4 (sulfate adenylyltransferase small
chain) cysE Serine Acetyltransferase EP1108790 AX122902 EC 2.3.1.30
WO0100843 AX063961 (serine acetyltransferase) cysH 3'-Phosphoadenyl
Sulfate Reductase EP1108790 AX123178 EC 1.8.99.4 WO0100842 AX066001
(3'-phosphoadenosine 5'- phosphosulfate reductase) cysK Cysteine
Synthase EP1108790 AX122901 EC 4.2.99.8 WO0100843 AX063963
(cysteine synthase) cysN Sulfate Adenylyltransferase sub- EP1108790
AX123176 unit I AX127152 EC 2.7.7.4 (sulfate adenylyltransferase)
cysQ Transport protein CysQ EP1108790 AX127145 (transporter cysQ)
WO0100805 AX066423 dps DNA Protection Protein EP1108790 AX127153
(protection during starvation protein) eno Enolase EP1108790
AX127146 EC 4.2.1.11 WO0100844 AX064945 (enolase) EP1090998
AX136862 Hermann et al., Electrophoresis 19: 3217-3221 (1998) fda
Fructose Bisphosphate Aldolase van der Osten et X17313 EC 4.1.2.13
al., Molecular (fructose bisphosphate aldolase) Microbiology 3:
1625-1637 (1989) gap Glyceraldehyde 3-Phosphate EP1108790 AX127148
Dehydrogenase WO0100844 AX064941 EC 1.2.1.12 Eikmanns et al.,
X59403 (glyceraldehyde 3-phosphate Journal of dehydrogenase)
Bacteriology 174: 6076-6086 (1992) gap2 Glyceraldehyde 3-Phosphate
EP1108790 AX127146 Dehydrogenase WO0100844 AX064939 EC 1.2.1.12
(glyceraldehyde 3-phosphate dehydrogenase 2) gdh Glutamate
Dehydrogenase EP1108790 AX127150 EC 1.4.1.4 WO0100844 AX063811
(glutamate dehydrogenase) Boermann et al., X59404 Molecular
Microbiology 6: 317-326 (1992); Guyonvarch et X72855 al., NCBI gnd
6-Phosphogluconate Dehydrogenase EP1108790 AX127147 EC 1.1.1.44
AX121689 (6-phosphogluconate dehydrogenase) WO0100844 AX065125 hom
Homoserine Dehydrogenase Peoples et al., Y00546 EC 1.1.1.3
Molecular (homoserine dehydrogenase) Microbiology 2: 63-72 (1988)
hom.sup.FBR Homoserine Dehydrogenase feedback Reinscheid et
resistant (fbr) al., Journal of EC 1.1.1.3 Bacteriology (homoserine
dehydrogenase fbr) 173: 3228-30 (1991) lysC Aspartate Kinase
EP1108790 AX120365 EC 2.7.2.4 WO0100844 AX063743 (aspartate kinase)
Kalinowaki et X57226 al., Molecular Microbiology 5: 1197-204 (1991)
lysC.sup.FBR Aspartate Kinase feedback resistent see Table 2 (fbr)
EC 2.7.2.4 (aspartate kinase fbr) msiK Sugar Importer EP1108790
AX120892 (multiple sugar import protein) opcA Glucose 6-Phosphate
Dehydrogenase WO0104325 AX076272 (subunit of glucose 6-phosphate
dehydrogenase) oxyR Transcription Regulator EP1108790 AX122198
(transcriptional regulator) AX127149 ppc.sup.FBR Phosphoenol
Pyruvate Carboxylase EP0723011 feedback resistent WO0100852 EC
4.1.1.31 (phosphoenol pyruvate carboxylase feedback resistant) ppc
Phosphoenol Pyruvate Carboxylase EP1108790 AX127148 EC 4.1.1.31
AX123554 (phosphoenol pyruvate carboxylase) O'Reagan et al., M25819
Gene 77(2): 237-251 (1989) pgk Phosphoglycerate Kinase EP1108790
AX121838 EC 2.7.2.3 AX127148 (phosphoglycerate kinase) WO0100844
AX064943 Eikmanns, X59403 Journal of Bacteriology 174: 6076-6086
(1992) pknA Protein Kinase A EP1108790 AX120131 (protein kinase A)
AX120085 pknB Protein Kinase B EP1108790 AX120130 (protein kinase
B) AX120085 pknD Protein Kinase D EP1108790 AX127150 (protein
kinase D) AX122469 AX122468 pknG Protein Kinase G EP1108790
AX127152 (protein kinase G) AX123109 ppsA Phosphoenol Pyruvate
Synthase EP1108790 AX127144 EC 2.7.9.2 AX120700 (phosphoenol
pyruvate synthase) AX122469 ptsH Phosphotransferase System Protein
H EP1108790 AX122210 EC 2.7.1.69 AX127149 (phosphotransferase
system WO0100844 AX069154 component H) ptsI Phosphotransferase
System Enzyme I EP1108790 AX122206 EC 2.7.3.9 AX127149
(phosphotransferase system enzyme I) ptsM Glukose-specific
Phosphotransferase Lee et al., FEMS L18874 System Enzyme II
Microbiology EC 2.7.1.69 Letters 119 (glucose
phosphotransferase-system (1-2): 137-145 enzyme II) (1994) pyc
Pyruvate Carboxylase WO9918228 A97276 EC 6.4.1.1 Peters-Wendisch
Y09548 (pyruvate carboxylase) et al., Microbiology 144: 915-927
(1998) pyc Pyruvate Carboxylase EP1108790 P458S EC 6.4.1.1
(pyruvate carboxylase) amino acid exchange P458S sigC Sigma Factor
C EP1108790 AX120368 EC 2.7.7.6 AX120085 (extracytoplasmic function
alternative sigma factor C) sigD RNA Polymerase Sigma Factor D
EP1108790 AX120753 EC 2.7.7.6 AX127144 (RNA polymerase sigma
factor) sigE Sigma Factor E EP1108790 AX127146 EC 2.7.7.6 AX121325
(extracytoplasmic function alternative sigma factor B) sigH Sigma
Factor H EP1108790 AX127145 EC 2.7.7.6 AX120939 (sigma factor SigH)
sigM Sigma Factor M EP1108790 AX123500 EC 2.7.7.6 AX127153 (sigma
factor SigM) tal Transaldolase WO0104325 AX076272 EC 2.2.1.2
(transaldolase) thrB Homoserine Kinase Peoples et al., Y00546 EC
2.7.1.39 Molecular (homoserine kinase) Microbiology 2: 63-72 (1988)
thrC Threonine Synthase Han et al., X56037 EC 4.2.99.2 Molecular
(threonine synthase) Microbiology 4: 1693-1702 (1990) thrE
Threonine Exporter EP1085091 AX137526 (threonine export carrier)
thyA Thymidylate Synthase EP1108790 AX121026 EC 2.1.1.45 AX127145
(thymidylate synthase) tkt Transketolase Ikeda et al., AB023377 EC
2.2.1.1 NCBI (transketolase) tpi Triose phosphate Isomerase
Eikmanns, X59403 EC 5.3.1.1 Journal of (triose phosphate isomerase)
Bacteriology 174: 6076-6086 (1992) zwal Cell Growth Factor 1
EP1111062 AX133781 (growth factor 1) zwf Glucose 6-Phosphate
1-Dehydrogenase EP1108790 AX127148 EC 1.1.1.49 AX121827 (glucose
6-phosphate 1- WO0104325 AX076272 dehydrogenase) zwf Glucose
6-Phosphate 1-Dehydrogenase EP1108790 A213T EC 1.1.1.49 (glucose
6-phosphate 1- dehydrogenase) amino acid exchange A213T
TABLE-US-00007 TABLE 7 Target sites for integration of open reading
frames, genes and alleles of threonine production Gene Description
of the coded Access name enzyme or protein Reference Number ccpA1
Catabolite Control WO0100844 AX065267 Protein EP1108790 AX127147
(catabolite control protein A1) ccpA2 Catabolite Control WO0100844
AX065267 Protein EP1108790 AX121594 (catabolite control protein A2)
citA Sensor Kinase CitA EP1108790 AX120161 (sensor kinase CitA)
citB Transcription Regulator EP1108790 AX120163 CitB (transcription
regulator CitB) citE Citrate Lyase WO0100844 AX065421 EC 4.1.3.6
EP1108790 AX127146 (citrate lyase) ddh Diaminopimelate Ishino et
al., Nucleic S07384 Dehydrogenase Acids Research 15: AX127152 EC
1.4.1.16 3917 (1987) (diaminopimelate EP1108790 dehydrogenase) gluA
Glutamate Transport Kronemeyer et al., X81191 ATP-binding Protein
Journal of (glutamate transport Bacteriology ATP-binding protein)
177(5): 1152-8 (1995) gluB Glutamate-binding Kronemeyer et al.,
X81191 Protein Journal of (glutamate-binding Bacteriology protein)
177(5): 1152-8 (1995) gluC Glutamate Transport Kronemeyer et al.,
X81191 Permease Journal of (glutamate transport Bacteriology system
permease) 177(5): 1152-8 (1995) gluD Glutamate Transport Kronemeyer
et al., X81191 Permease Journal of (glutamate transport
Bacteriology system permease) 177(5): 1152-8 (1995) glyA Glycine
WO0100843 AX063861 Hydroxymethyl- AF327063 transferase EC 2.1.2.1
(glycine hydroxymethyl- transferase) ilvA Threonine Dehydratase
Mockel et al., Journal A47044 EC 4.2.1.16 of Bacteriology 174
L01508 (threonine dehydratase) (24), 8065-8072 AX127150 (1992)
EP1108790 ilvBN Acetolactate Synthase Keilhauer et al., L09232 EC
4.1.3.18 Journal of AX127147 (acetolactate synthase) Bacteriology
175(17): 5595-603 (1993) EP1108790 ilvC Reductoisomerase Keilhauer
et al., C48648 EC 1.1.1.86 Journal of AX127147 (ketol-acid
Bacteriology reductoisomerase) 175(17): 5595-603 (1993) EP1108790
ilvD Dihydroxy-acid EP1006189 AX136925 Dehydratase EC 4.2.1.9
(dihydroxy-acid dehydratase) luxR Transcription Regulator WO0100842
AX065953 LuxR EP1108790 AX123320 (transcription regulator LuxR)
luxS Histidine Kinase LuxS EP1108790 AX123323 (histidine kinase
LuxS) AX127153 lysR1 Transcription Regulator EP1108790 AX064673
LysR1 AX127144 (transcription regulator LysR1) lysR2 Transcription
Activator EP1108790 AX123312 LysR2 (transcription regulator LysR2)
lysR3 Transcription Regulator WO0100842 AX065957 LysR3 EP1108790
AX127150 (transcription regulator LysR3) mdh Malate Dehydrogenase
WO0100844 AX064895 EC 1.1.1.37 (malate dehydrogenase) menE
O-Succinylbenzoic Acid WO0100843 AX064599 CoA Ligase EP1108790
AX064193 EC 6.2.1.26 AX127144 (O-succinylbenzoate CoA ligase) metA
Homoserine O- Park et al., Molecular AX063895 Acetyltransferase
Cells 30; 8(3): 286-94 AX127145 EC 2.3.1.31 (1998) (homoserine O-
WO0100843 acetyltransferase) EP1108790 metD Transcription Regulator
EP1108790 AX123327 MetD AX127153 (transcription regulator MetD) pck
Phosphoenol Pyruvate WO0100844 AJ269506 Carboxykinase AX065053
(phosphoenol pyruvate carboxykinase) poxB Pyruvate Oxidase
WO0100844 AX064959 EC 1.2.3.3 EP1096013 AX137665 (pyruvate oxidase)
sigB RNA Polymerase EP1108790 AX127149 Transcription Factor (RNA
polymerase transcription factor) zwa2 Cell Growth Factor 2
EP1106693 AX113822 (growth factor 2) EP1108790 AX127146
[0115] The invention accordingly also provides a process for the
production of coryneform bacteria which produce L-methionine and/or
L-threonine, which comprises [0116] a) isolating the nucleotide
sequence of at least one desired ORF, gene or allele of methionine
production or threonine production, optionally including the
expression and/or regulation signals, [0117] b) providing the 5'
and the 3' end of the ORF, gene or allele with nucleotide sequences
of the target site, [0118] c) preferably incorporating the
nucleotide sequence of the desired ORF, gene or allele provided
with nucleotide sequences of the target site into a vector which
does not replicate or replicates to only a limited extent in
coryneform bacteria, [0119] d) transferring the nucleotide sequence
according to b) or c) into coryneform bacteria, and [0120] e)
isolating coryneform bacteria in which the nucleotide sequence
according to a) is incorporated at the target site, no nucleotide
sequence which is capable of/enables episomal replication in
microorganisms, no nucleotide sequence which is capable of/enables
transposition and no nucleotide sequence which imparts resistance
to antibiotics remaining at the target site.
[0121] The invention furthermore provides coryneform bacteria, in
particular of the genus Corynebacterium, which produce L-valine,
wherein these have, in addition to at least one of the copy of an
open reading frame (ORF), gene or allele of valine production
present at the natural site (locus), in each case a second,
optionally third or fourth copy of the open reading frame (ORF),
gene or allele in question at in each case a second, optionally
third or fourth site in integrated form, no nucleotide sequence
which is capable of/enables episomal replication in microorganisms,
no nucleotide sequence which is capable of/enables transposition
and no nucleotide sequence which imparts resistance to antibiotics
being present at the particular second, optionally third or fourth
site.
[0122] The invention also furthermore provides a process for the
preparation of L-valine, which comprises the following steps:
[0123] a) fermentation of coryneform bacteria, in particular
Corynebacterium glutamicum, characterized in that these have, in
addition to at least one of the copy of an open reading frame
(ORF), gene or allele of valine production present at the natural
site (locus), in each case a second, optionally third or fourth
copy of the open reading frame (ORF), gene or allele in question at
in each case a second, optionally third or fourth site in
integrated form, no nucleotide sequence which is capable of/enables
episomal replication in microorganisms, no nucleotide sequence
which is capable of/enables transposition and no nucleotide
sequence which imparts resistance to antibiotics being present at
the particular second, optionally third or fourth site, [0124]
under conditions which allow expression of the said open reading
frames (ORF), genes or alleles, [0125] b) concentration of the
L-valine in the fermentation broth, [0126] c) isolation of the
L-valine from the fermentation broth, optionally [0127] d) with
constituents from the fermentation broth and/or the biomass to the
extent of >(greater than) 0 to 100%.
[0128] A "copy of an open reading frame (ORF), gene or allele of
valine production" is to be understood as meaning all the open
reading frames, genes or alleles of which
enhancement/over-expression can have the effect of improving valine
production.
[0129] These include, inter alia, the following open reading
frames, genes or alleles: brnE, brnF, brnEF, cstA, cysD, dps, eno,
fda, gap, gap2, gdh, ilvB, ilvN, ilvBN, ilvC, ilvD, ilvE msiK, pgk,
ptsH, ptsl, ptsM, sigC, sigD, sigE, sigH, sigM, tpi, zwa1. These
are summarized and explained in Table 8. These include in
particular the ilvBN alleles which code for a valine-resistant
acetolactate synthase.
[0130] The second, optionally third or fourth copy of the open
reading frame (ORF), gene or allele of valine production in
question can be integrated at in each case a second, optionally
third or fourth site. The following open reading frames, genes or
nucleotide sequences, inter alia, can be used for this: aecD,
ccpA1, ccpA2, citA, citB, citE, ddh, gluA, gluB, gluC, gluD, glyA,
ilvA, luxR, lysR1, lysR2, lysR3, panB, panC, poxB and zwa2. These
are summarized and explained in Table 9.
[0131] The sites mentioned include, of course, not only the coding
regions of the open reading frames or genes mentioned, but also the
regions or nucleotide sequences lying upstream which are
responsible for expression and regulation, such as, for example,
ribosome binding sites, promoters, binding sites for regulatory
proteins, binding sites for regulatory ribonucleic acids and
attenuators. These regions in general lie in a range of 1-800,
1-600, 1-400, 1-200, 1-100 or 1-50 nucleotides upstream of the
coding region. In the same way, regions lying downstream, such as,
for example, transcription terminators, are also included. These
regions in general lie in a range of 1-400, 1-200, 1-100, 1-50 or
1-25 nucleotides downstream of the coding region.
[0132] Intergenic regions in the chromosome, that is to say
nucleotide sequences without a coding function, can furthermore be
used. Finally, prophages or defective phages contained in the
chromosome can be used for this.
[0133] Examples of regions of the Corynebacterium glutamicum
chromosome representing intergenic regions, prophages, defective
phages or phage components are shown in tables 12 and 13. The
positions of the DNA regions refer to the genome map of
Corynebacterium glutamicum ATCC 13032 as presented in EP-A-1108790
or in the databank of the European Molecular Biologies Laboratories
(EMBL, Heidelberg, Germany and Cambridge, UK).
TABLE-US-00008 TABLE 8 Open reading frames, genes and alleles of
valine production Description of the coded enzyme or Access Name
protein Reference Number brnEF Export of branched-chain amino
EP1096010 acids (branched chain amino acid export) Kennerknecht et
AF454053 al., NCBI cstA Carbon Starvation Protein A EP1108790
AX120811 (carbon starvation protein A) WO0100804 AX066109 dps DNA
Protection Protein EP1108790 AX127153 (protection during starvation
protein) eno Enolase EP1108790 AX127146 EC 4.2.1.11 WO0100844
AX064945 (enolase) EP1090998 AX136862 Hermann et al.,
Electrophoresis 19: 3217-3221 (1998) fda Fructose Bisphosphate
Aldolase van der Osten et X17313 EC 4.1.2.13 al., Molecular
(fructose bisphosphate aldolase) Microbiology 3: 1625-1637 (1989)
gap Glyceraldehyde 3-Phosphate EP1108790 AX127148 Dehydrogenase
WO0100844 AX064941 EC 1.2.1.12 Eikmanns et al., X59403
(glyceraldehyde 3-phosphate Journal of dehydrogenase) Bacteriology
174: 6076-6086 (1992) gap2 Glyceraldehyde 3-Phosphate EP1108790
AX127146 Dehydrogenase WO0100844 AX064939 EC 1.2.1.12
(glyceraldehyde 3-phosphate dehydrogenase 2) gdh Glutamate
Dehydrogenase EP1108790 AX127150 EC 1.4.1.4 WO0100844 AX063811
(glutamate dehydrogenase) Boermann et al., X59404 Molecular
Microbiology 6: 317-326 (1992); Guyonvarch et X72855 al., NCBI
ilvBN Acetolactate Synthase Keilhauer et L09232 EC 4.1.3.18 al.,
Journal of (acetolactate synthase) Bacteriology 175(17): 5595-603
(1993) EP1108790 AX127147 ilvC Isomeroreductase Keilhauer et C48648
EC 1.1.1.86 al., Journal of AX127147 (acetohydroxy acid
Bacteriology isomeroreductase) 175(17): 5595-603 (1993) EP1108790
ilvD Dihydroxy-acid Dehydratase EP1006189 AX136925 EC 4.2.1.9
(dihydroxy acid dehydratase) ilvE Transaminase B EP1108790 AX127150
EC 2.6.1.42 AX122498 (transaminase B) msiK Sugar Importer EP1108790
AX120892 (multiple sugar import protein) pgk Phosphoglycerate
Kinase EP1108790 AX121838 EC 2.7.2.3 AX127148 (phosphoglycerate
kinase) WO0100844 AX064943 Eikmanns, X59403 Journal of Bacteriology
174: 6076-6086 (1992) ptsH Phosphotransferase System Protein H
EP1108790 AX122210 EC 2.7.1.69 AX127149 (phosphotransferase system
WO0100844 AX069154 component H) ptsI Phosphotransferase System
Enzyme I EP1108790 AX122206 EC 2.7.3.9 AX127149 (phosphotransferase
system enzyme I) ptsM Glucose-specific Phosphotransferase Lee et
al., FEMS L18874 System Enzyme II Microbiology EC 2.7.1.69 Letters
119 (glucose phosphotransferase-system (1-2): 137-145 enzyme II)
(1994) sigC Sigma Factor C EP1108790 AX120368 EC 2.7.7.6 AX120085
(extracytoplasmic function alternative sigma factor C) sigD RNA
Polymerase Sigma Factor D EP1108790 AX120753 EC 2.7.7.6 AX127144
(RNA polymerase sigma factor) sigE Sigma Factor E EP1108790
AX127146 EC 2.7.7.6 AX121325 (extracytoplasmic function alternative
sigma factor E) sigH Sigma Factor H EP1108790 AX127145 EC 2.7.7.6
AX120939 (sigma factor SigH) sigM Sigma Factor M EP1108790 AX123500
EC 2.7.7.6 AX127153 (sigma factor SigM) tpi Triose Phosphate
Isomerase Eikmanns, X59403 EC 5.3.1.1 Journal of (triose phosphate
isomerase) Bacteriology 174: 6076-6086 (1992) zwal Cell Growth
Factor 1 EP1111062 AX133781 (growth factor 1)
TABLE-US-00009 TABLE 9 Target sites for integration of open reading
frames, genes and alleles of valine production Description Gene of
the coded Access name enzyme or protein Reference Number aecD beta
C-S Lyase Rossol et al., Journal M89931 EC 2.6.1.1 of Bacteriology
(beta C-S lyase) 174(9): 2968-77 (1992) ccpA1 Catabolite Control
WO0100844 AX065267 Protein EP1108790 AX127147 (catabolite control
protein A1) ccpA2 Catabolite Control WO0100844 AX065267 Protein
EP1108790 AX121594 (catabolite control protein A2) citA Sensor
Kinase CitA EP1108790 AX120161 (sensor kinase CitA) citB
Transcription EP1108790 AX120163 Regulator CitB (transcription
regulator CitB) citE Citrate Lyase WO0100844 AX065421 EC 4.1.3.6
EP1108790 AX127146 (citrate lyase) ddh Diaminopimelate Ishino et
al., Nucleic S07384 Dehydrogenase Acids Research 15: 3917 AX127152
EC 1.4.1.16 (1987) (diaminopimelate EP1108790 dehydrogenase) gluA
Glutamate Transport Kronemeyer et al., X81191 ATP-binding Protein
Journal of Bacteriology (glutamate transport 177(5): 1152-8 (1995)
ATP-binding protein) gluB Glutamate-binding Kronemeyer et al.,
X81191 Protein Journal of Bacteriology (glutamate-binding 177(5):
1152-8 (1995) protein) gluC Glutamate Transport Kronemeyer et al.,
X81191 Permease Journal of Bacteriology (glutamate transport
177(5): 1152-8 (1995) system permease) gluD Glutamate Transport
Kronemeyer et al., X81191 Permease Journal of Bacteriology
(glutamate transport 177(5): 1152-8 (1995) system permease) glyA
Glycine WO0100843 AX063861 Hydroxymethyl- AF327063 transferase EC
2.1.2.1 (glycine hydroxymethyl- transferase) ilvA Threonine
Dehydratase Mockel et al., Journal A47044 EC 4.2.1.16 of
Bacteriology 174 L01508 (threonine (24), 8065-8072 (1992) AX127150
dehydratase) EP1108790 luxR Transcription WO0100842 AX065953
Regulator LuxR EP1108790 AX123320 (transcription regulator LuxR)
lysR1 Transcription EP1108790 AX064673 Regulator LysR1 AX127144
(transcription regulator LysR1) lysR2 Transcription EP1108790
AX123312 Activator LysR2 (transcription regulator LysR2) lysR3
Transcription WO0100842 AX065957 Regulator LysR3 EP1108790 AX127150
(transcription regulator LysR3) panB Ketopantoate US6177264 X96580
Hydroxymethyl- transferase EC 2.1.2.11 (ketopantoate hydroxymethyl-
transferase) panC pantothenate US6177264 X96580 Synthetase EC
6.3.2.1 (pantothenate synthetase) poxB Pyruvate Oxidase WO0100844
AX064959 EC 1.2.3.3 EP1096013 AX137665 (pyruvate oxidase) zwa2 Cell
Growth Factor 2 EP1106693 AX113822 (growth factor 2) EP1108790
AX127146
[0134] The invention accordingly also provides a process for the
production of coryneform bacteria which produce L-valine, which
comprises [0135] a) isolating the nucleotide sequence of at least
one desired ORF, gene or allele of valine production, optionally
including the expression and/or regulation signals, [0136] b)
providing the 5' and the 3' end of the ORF, gene or allele with
nucleotide sequences of the target site, [0137] c) preferably
incorporating the nucleotide sequence of the desired ORF, gene or
allele provided with nucleotide sequences of the target site into a
vector which does not replicate or replicates to only a limited
extent in coryneform bacteria, [0138] d) transferring the
nucleotide sequence according to b) or c) into coryneform bacteria,
and [0139] e) isolating coryneform bacteria in which the nucleotide
sequence according to a) is incorporated at the target site, no
nucleotide sequence which is capable of/enables episomal
replication in microorganisms, no nucleotide sequence which is
capable of/enables transposition and no nucleotide sequence which
imparts resistance to antibiotics remaining at the target site.
[0140] The invention also furthermore provides a process for the
preparation of L-tryptophane, which comprises the following steps:
[0141] a) fermentation of coryneform bacteria, in particular
Corynebacterium glutamicum, characterized in that these have, in
addition to at least one of the copy of an open reading frame
(ORF), gene or allele of tryptophane production present at the
natural site (locus), in each case a second, optionally third or
fourth copy of the open reading frame (ORF), gene or allele in
question at in each case a second, optionally third or fourth site
in integrated form, no nucleotide sequence which is capable
of/enables episomal replication in microorganisms, no nucleotide
sequence which is capable of/enables transposition and no
nucleotide sequence which imparts resistance to antibiotics being
present at the particular second, optionally third or fourth site,
[0142] under conditions which allow expression of the said open
reading frames (ORF), genes or alleles, [0143] b) concentration of
the tryptophane in the fermentation broth, [0144] c) isolation of
the tryptophane from the fermentation broth, optionally [0145] d)
with constituents from the fermentation broth and/or the biomass to
the extent of >(greater than) 0 to 100%.
[0146] A "copy of an open reading frame (ORF), gene or allele of
tryptophane production" is to be understood as meaning all the open
reading frames, genes or alleles of which
enhancement/over-expression can have the effect of improving
tryptophane production.
[0147] These include, inter alia, the following open reading
frames, genes or alleles: aroA, aroB, aroC, aroD, aroE, aroG, aroK,
cstA, eno, gap, gap2, gnd, ppsA, rpe, serA, serB, serC, tal, thyA,
tkt, tpi, trpA, trpB, trpC, trpD optionally comprising at least one
of the amino acid exchanges selected from the group consisting of
A215T (exchange of alanine at position 215 against threonine),
D138A (exchange of aspartic acid at position 138 against alanine),
S149F (exchange of serine at position 149 against phenylalanine)
and A162E (exchange of alanine at position 162 against glutamic
acid), trpE, trpE.sup.FBR e.g. the amino acid exchange S38R
(exchange of serine at position 38 against arginine), trpG, trpL
optionally comprising the mutation W14*, zwa1, zwf optionally
comprising the amino acid exchange A213T (exchange of alanine at
position 213 against threonine). These are summarized and explained
in Table 10. These include in particular the tryptophane operon
comprising trpE, trpG, trpD, trpC and trpA and optionally trpL.
Furthermore these include in particular a trpE.sup.FBR allele which
codes for a tryptophane-resistant anthranilate synthase.
[0148] The second, optionally third or fourth copy of the open
reading frame (ORF), gene or allele of tryptophane production in
question can be integrated at in each case a second, optionally
third or fourth site. The following open reading frames, genes or
nucleotide sequences, inter alia, can be used for this: ccpA1,
ccpA2, citA, citB, citE, cysE, gluA, gluB, gluC, gluD, glyA, luxR,
luxS, lysR1, lysR2, lysR3, menE, pgi, pheA, poxB and zwa2. These
are summarized and explained in Table 11.
[0149] The sites mentioned include, of course, not only the coding
regions of the open reading frames or genes mentioned, but also the
regions or nucleotide sequences lying upstream which are
responsible for expression and regulation, such as, for example,
ribosome binding sites, promoters, binding sites for regulatory
proteins, binding sites for regulatory ribonucleic acids and
attenuators. These regions in general lie in a range of 1-800,
1-600, 1-400, 1-200, 1-100 or 1-50 nucleotides upstream of the
coding region. In the same way, regions lying downstream, such as,
for example, transcription terminators, are also included. These
regions in general lie in a range of 1-400, 1-200, 1-100, 1-50 or
1-25 nucleotides downstream of the coding region.
[0150] Intergenic regions in the chromosome, that is to say
nucleotide sequences without a coding function, can furthermore be
used. Finally, prophages or defective phages contained in the
chromosome can be used for this.
[0151] Examples of regions of the Corynebacterium glutamicum
chromosome representing intergenic regions, prophages, defective
phages or phage components are shown in tables 12 and 13. The
positions of the DNA regions refer to the genome map of
Corynebacterium glutamicum ATCC 13032 as presented in EP-A-1108790
or in the databank of the European Molecular Biologies Laboratories
(EMBL, Heidelberg, Germany and Cambridge, UK).
TABLE-US-00010 TABLE 10 Open reading frames, genes and alleles of
tryptophane production Gene Description of the coded enzyme or
Access- name protein Reference Number aroA Enolpyruvylsahikimate
Phosphate O'Donohue et AF114233 Synthase al., NCBI EC 2.5.1.19
(enolpyruvylshikimate 3-phosphate synthase) aroB Dehydroquinate
Synthetase Burke et al., AF124600 EC 4.6.1.3 NCBI (dehydroquinate
synthetase) aroC Chorismate Synthase Burke et al., AF124600 EC
4.6.1.4 NCBI (chorismate synthase) aroD Dehydroquinate Dehydratase
Joy et al., AF124518 EC 4.2.1.10 NCBI (dehydroquinate dehydratase)
aroE Shikimate Dehydrogenase Joy et al., AF124518 EC 1.1.1.25 NCBI
(shikimate dehydrogenase) aroG Dehydro-3-Deoxyphosphoheptonate Chen
et al., L07603 Aldolase FEMS EC4.1.2.15 Microbioliology
(dehydro-3-deoxyphosphoheptonate Letters aldolase) 107: 223-230
(1993). aroK Shikimate Kinase Burke et al., AF124600 EC 2.7.1.71
NCBI (shikimate kinase) cstA Carbon Starvation Protein A EP1108790
AX120811 (carbon starvation protein A) WO0100804 AX066109 eno
Enolase EP1108790 AX127146 EC 4.2.1.11 WO0100844 AX064945 (enolase)
EP1090998 AX136862 Hermann et al., Electrophoresis 19: 3217-3221
(1998) gap Glyceraldehyde-3-Phosphate EP1108790 AX127148
Dehydrogenase WO0100844 AX064941 EC 1.2.1.12 Eikmanns et X59403
(glyceraldehyde-3-phosphate al., Journal of dehydrogenase)
Bacteriology 174: 6076-6086 (1992) gap2 Glyceraldehyde-3-Phosphate
EP1108790 AX127146 Dehydrogenase WO0100844 AX064939 EC 1.2.1.12
(glyceraldehyde-3-phosphate dehydrogenase 2) gnd 6-Phosphogluconate
Dehydrogenase EP1108790 AX127147 EC 1.1.1.44 AX121689
(6-phosphogluconate dehydrogenase) WO0100844 AX065125 ppsA
Phosphoenolpyruvate Synthetase EP1108790 AX127144 EC 2.7.9.2
AX120700 (phosphoenolpyruvate-synthase) rpe Ribulose-Phosphate
Epimerase EP1108790 AX127148 EC 5.1.3.1 AX121852
(ribulose-phosphate-epimerase) serA Phosphoglycerate Dehydrogenase
EP1108790 AX127147 EC1.1.1.95 AX121499
(phosphoglycerate-dehydrogenase) serB Phosphoserine Phosphatase
EP1108790 AX127144 EC 3.1.3.3 AX120551 (phosphoserine phosphatase)
serC Phosphoserine Aminotransferase EP1108790 AX127145 EC 2.6.1.52
AX121012 (phosphoserine aminotransferase) tal Transaldolase
WO0104325 AX076272 EC 2.2.1.2 (transaldolase) thyA Thymidylate
Synthase EP1108790 AX121026 EC 2.1.1.45 AX127145 (thymidylate
synthase) tkt Transketolase Ikeda et al., AB023377 EC 2.2.1.1 NCBI
(transketolase) tpi Triose-phosphate Isomerase Eikmanns, X59403 EC
5.3.1.1 Journal of (triose-phosphate isomerase) Bacteriology 174:
6076-6086 (1992) trpA Tryptophane Synthase (alpha Kette) Matsui et
al., X04960 EC 4.2.1.20 Nucleic Acids (tryptophan synthase (alpha
chain)) Research 14: 10113-10114 (1986) trpB Tryptophane Synthase
(beta Kette) Matsui et al., X04960 EC 4.2.1.20 Nucleic Acids
(tryptophan synthase (beta chain)) Research 14: 10113-10114 (1986)
trpC Phosphoribosylanthranilate Matsui et al., X04960 Isomerase
Nucleic Acids EC 5.3.1.24 Research (phosphoribosylanthranilate 14:
10113-10114 isomerase) (1986) trpD Anthranilate Matsui et al.,
X04960 Phosphoribosyltransferase Nucleic Acids EC 2.4.2.18 Research
(anthranilate 14: 10113-10114 phosphoribosyltransferase) (1986)
trpD Anthranilate O'Gara et al., A125T, Phosphoribosyltransferase
Applied and D138A, EC 2.4.2.18 Environmental S149F, anthranilate
Microbiology A162E (phosphoribosyltransferase) 61: 4477-4479 amino
acid exchanges A125T, D138A, (1995) S149F, A162E trpE Anthranilate
Synthase Komponente I Matsui et al., X04960 EC 4.1.3.27 Nucleic
Acids (anthranilate synthase component I) Research 14: 10113-10114
(1986) trpE Anthranilat Synthase Component I Matsui et al., fbr
feedback resistent Journal of EC 4.1.3.27 Bacteriology
(anthranilate synthase component I 169: 5330-5332 feedback
resistant) (1987) trpG Anthranilate Synthase Komponente II Matsui
et al, X04960 EC 4.1.3.24 Nucleic Acids (anthranilate synthase
component Research II) 14: 10113-10114 (1986) trpL Trp Operon
Leader Peptide Matsui et al., X04960 (trp operon leader peptide)
Nucleic Acids Research 14: 10113-10114 (1986) trpL Trp Operon
Leaderpeptid Herry et al., W14* (trp operon leader peptide Applied
and mutation W14*) Environmental Microbiology 59: 791-799 (1993)
zwal Cell Growth Factor 1 EP1111062 AX133781 (growth factor 1) zwf
Glucose-6-phosphat1-1-Dehydrogenase EP1108790 AX127148 EC 1.1.1.49
AX121827 (glucose-6-phosphate-1- WO0104325 AX076272 dehydrogenase)
zwf Glucose-6-phosphate-1-Dehydrogenase EP1108790 A213T EC 1.1.1.49
(glucose-6-phosphate-1- dehydrogenase) amino acid exchange
A213T
TABLE-US-00011 TABLE 11 Target sites for integration of open
reading frames, genes and alleles of tryptophane production Gene
Description of the coded Access name enzyme or protein Reference
Number ccpA1 Catabolite Control WO0100844 AX065267 Protein
EP1108790 AX127147 (catabolite control protein A1) ccpA2 Catabolite
Control WO0100844 AX065267 Protein EP1108790 AX121594 (catabolite
control protein A2) citA Sensor-Kinase CitA EP1108790 AX120161
(sensor kinase CitA) citB Transcription Regulator EP1108790
AX120163 CitB (transcription regulator CitB) citE Citrate-Lyase
WO0100844 AX065421 EC 4.1.3.6 EP1108790 AX127146 (citrate lyase)
cysE Serine O- EP1108790 AX122902 Acetyltransferase EC 2.3.1.30
(serine O- acetyltransferase) gluA Glutamate Transport ATP-
Kronemeyer et al., X81191 binding Protein Journal of (glutamate
transport ATP- Bacteriology binding protein) 177(5): 1152-8 (1995)
gluB Glutamate-binding Protein Kronemeyer et al., X81191 (glutamate
binding Journal of protein) Bacteriology 177(5): 1152-8 (1995) gluC
Glutamate Transport Kronemeyer et al., X81191 Permease Journal of
(glutamate transport Bacteriology system permease) 177(5): 1152-8
(1995) gluD Glutamate Transport Kronemeyer et al., X81191 Permease
Journal of (glutamate transport Bacteriology system permease)
177(5): 1152-8 (1995) glyA glycine JP1997028391 E12594
hydroxymethyltransferase EC 2.1.2.1 (glycine
hydroxymethyltransferase) luxR Transkription Regulator WO0100842
AX065953 LuxR EP1108790 AX123320 (transcription regulator LuxR)
luxS Histidine Kinase LuxS EP1108790 AX123323 (histidine kinase
LuxS) AX127153 lysR1 Transkription Regulator EP1108790 AX064673
LysR1 AX127144 (transcription regulator LysR1) lysR2 Transkription
Activator EP1108790 AX123312 LysR2 (transcription regulator LysR2)
lysR3 Transkription Regulator WO0100842 AX065957 LysR3 EP1108790
AX127150 (transcription regulator LysR3) menE O-Succinylbenzoic
acid- WO0100843 AX064599 CoA-Ligase EP1108790 AX064193 EC 6.2.1.26
AX127144 (O-succinylbenzoate-CoA ligase) pgi Glucose-6-Phosphate-
EP1087015 AX136015 Isomerase EP1108790 AX127146 EC 5.3.1.9
(glucose-6-phosphate isomerase) pheA Prephenate Dehydratase
Follettie et al., M13774 EC 4.2.1.51 Journal of (prephenate
dehydratase) Bacteriology 167: 695-702(1986) poxB pyruvate-Oxidase
WO0100844 AX064959 EC 1.2.3.3 EP1096013 AX137665 (pyruvate oxidase)
zwa2 Cell Growth Factor 2 EP1106693 AX113822 (growth factor 2)
EP1108790 AX127146
[0152] The invention accordingly also provides a process for the
production of coryneform bacteria which produce L-valine, which
comprises [0153] a) isolating the nucleotide sequence of at least
one desired ORF, gene or allele of valine production, optionally
including the expression and/or regulation signals, [0154] b)
providing the 5' and the 3' end of the ORF, gene or allele with
nucleotide sequences of the target site, [0155] c) preferably
incorporating the nucleotide sequence of the desired ORF, gene or
allele provided with nucleotide sequences of the target site into a
vector which does not replicate or replicates to only a limited
extent in coryneform bacteria, [0156] d) transferring the
nucleotide sequence according to b) or c) into coryneform bacteria,
and [0157] e) isolating coryneform bacteria in which the nucleotide
sequence according to a) is incorporated at the target site, no
nucleotide sequence which is capable of/enables episomal
replication in microorganisms, no nucleotide sequence which is
capable of/enables transposition and no nucleotide sequence which
imparts resistance to antibiotics remaining at the target site.
TABLE-US-00012 [0157] TABLE 12 Intergenic regions as target sites
for integration of open reading frames, genes and alleles Position
of Position of Access sequence sequence Reference number start end
EP1108790 AX120085 192176 194501 EP1108790 AX127145 235840 237311
EP1108790 AX127145 236096 237311 EP1108790 AX127148 322628 330877
EP1108790 AX127148 334045 336467 EP1108790 AX127148 289565 291841
EP1108790 AX127149 154823 161111 EP1108790 AX127149 190088 193497
EP1108790 AX127149 27398 28707 EP1108790 AX127149 61478 62944
EP1108790 AX127149 116234 117561 EP1108790 AX127149 140847 144605
EP1108790 AX127150 113274 114324 EP1108790 AX127152 244281
246403
TABLE-US-00013 TABLE 13 Target sites coding for phages or phage
components suitable for integration of open reading frames, genes
and alleles Position of Position Access sequence of Reference
number start Sequence end EP1108790 AX127149 50474 51049 EP1108790
AX127149 67886 68587 EP1108790 AX127151 72893 73480 EP1108790
AX127149 88231 89445 EP1108790 AX127148 139781 140155 EP1108790
AX127148 140546 141001 EP1108790 AX127149 194608 195294 EP1108790
AX127147 200185 200940 EP1108790 AX127147 208157 208450 EP1108790
AX127149 269616 269948 EP1108790 AX127148 336468 338324 EP1108790
AX127148 342235 342681 EP1108790 AX127148 343518 345356 EP1108790
AX127148 345872 346207
[0158] During work on the present invention, it was possible to
incorporate a second copy of an lysC.sup.FBR allele into the gluB
gene of Corynebacterium glutamicum such that no nucleotide sequence
which is capable of/enables episomal replication in microorganisms,
no nucleotide sequence which is capable of/enables transposition
and no nucleotide sequence which imparts resistance to antibiotics
remained at the gluB gene site. This strain, which is called
DSM13994glu::lysC, carries the lysC.sup.FBR allele lysC T311I at
its natural lysC site and a second copy of the lysC.sup.FBR allele
lysC T311I at a second site (target site), namely the gluB gene. A
plasmid with the aid of which the incorporation of the lysC.sup.FBR
allele into the gluB gene can be achieved is shown in FIG. 1. It
carries the name pK18mobsacBglu1.sub.--1.
[0159] During work on the present invention, it was furthermore
possible to incorporate a copy of an lysC.sup.FBR allele into the
target site of the gluB gene of Corynebacterium glutamicum such
that no nucleotide sequence which is capable of/enables episomal
replication in microorganisms, no nucleotide sequence which is
capable of/enables transposition and no nucleotide sequence which
imparts resistance to antibiotics remained at the gluB gene site.
This strain, which is called DSM12866glu::lysC, carries the
wild-type form of the lysC gene at its natural lysC site and a
second copy of the lysC gene in the form of the lysC.sup.FBR allele
lysC T311I at a second site (target site), namely the gluB gene. It
has been deposited under number DSM15039 at the Deutsche Sammlung
fur Mikroorganismen and Zellkulturen (German Collection of
Microorganisms and Cell Cultures). A plasmid with the aid of which
the incorporation of the lysC.sup.FBR allele into the gluB gene can
be achieved is shown in FIG. 1. It carries the name
pK18mobsacBglu1.sub.--1.
[0160] During work on the present invention, it was furthermore
possible to incorporate a copy of an lysC.sup.FBR allele into the
target site of the aecD gene of Corynebacterium glutamicum such
that no nucleotide sequence which is capable of/enables episomal
replication in microorganisms, no nucleotide sequence which is
capable of/enables transposition and no nucleotide sequence which
imparts resistance to antibiotics remained at the aecD gene site.
This strain, which is called DSM12866aecD::lysC, carries the
wild-type form of the lysC gene at its natural lysC site and a
second copy of the lysC gene in the form of the lysC.sup.FBR allele
lysC T311I at a second site (target site), namely the aecD gene. A
plasmid with the aid of which the incorporation of the lysC.sup.FBR
into the aecD gene can be achieved is shown in FIG. 2. It carries
the name pK18mobsacBaecD1.sub.--1.
[0161] During work on the present invention, it was furthermore
possible to incorporate a copy of an lysC.sup.FBR allele into the
target site of the pck gene of Corynebacterium glutamicum such that
no nucleotide sequence which is capable of/enables episomal
replication in microorganisms, no nucleotide sequence which is
capable of/enables transposition and no nucleotide sequence which
imparts resistance to antibiotics remained at the pck gene site.
This strain, which is called DSM12866 pck::lysC, carries the
wild-type form of the lysC gene at its natural lysC site and a
second copy of the lysC gene in the form of the lysC.sup.FBR allele
lysC T311I at a second site (target site), namely the pck gene. A
plasmid with the aid of which the incorporation into the pck gene
can be achieved is shown in FIG. 3. It carries the name
pK18mobsacBpck1.sub.--1.
[0162] During work on the present invention, it was furthermore
possible to incorporate a copy of the ddh gene into the target site
of the gluB gene of Corynebacterium glutamicum such that no
nucleotide sequence which is capable of/enables episomal
replication in microorganisms, no nucleotide sequence which is
capable of/enables transposition and no nucleotide sequence which
imparts resistance to antibiotics remained at the gluB gene site.
This strain, which is called DSM12866glu::ddh, carries a copy of
the ddh gene at its natural ddh site and a second copy of the ddh
gene at a second site (target site), namely the gluB gene. A
plasmid with the aid of which the incorporation of the ddh gene
into the gluB gene can be achieved is shown in FIG. 4. It carries
the name pK18mobsacBgluB2.sub.--1.
[0163] During work on the present invention, it was furthermore
possible to incorporate a copy of the dapA gene into the target
site of the aecD gene of Corynebacterium glutamicum such that no
nucleotide sequence which is capable of/enables episomal
replication in microorganisms, no nucleotide sequence which is
capable of/enables transposition and no nucleotide sequence which
imparts resistance to antibiotics remained at the aecD gene site.
This strain, which is called DSM12866aecD::dapA, carries a copy of
the dapA gene at its natural dapA site and a second copy of the
dapA gene at a second site (target site), namely the aecD gene. A
plasmid with the aid of which the incorporation of the dapA gene
into the aecD gene can be achieved is shown in FIG. 5. It carries
the name pK18mobsacBaecD2.sub.--1.
[0164] During work on the present invention, it was furthermore
possible to incorporate a copy of a pyc allele into the target site
of the pck gene of Corynebacterium glutamicum such that no
nucleotide sequence which is capable of/enables episomal
replication in microorganisms, no nucleotide sequence which is
capable of/enables transposition and no nucleotide sequence which
imparts resistance to antibiotics remained at the pck gene site.
This strain, which is called DSM12866 pck::pyc, carries a copy of
the wild-type form of the pyc gene at its natural pyc site and a
second copy of the pyc gene in the form of the pyc allele pyc P458S
at a second site (target site), namely the pck gene. A plasmid with
the aid of which the incorporation of the pyc allele into the pck
gene can be achieved is shown in FIG. 6. It carries the name
pK18mobsacBpck1.sub.--3.
[0165] The coryneform bacteria produced according to the invention
can be cultured continuously or discontinuously in the batch
process (batch culture) or in the fed batch (feed process) or
repeated fed batch process (repetitive feed process) for the
purpose of production of chemical compounds. A summary of known
culture methods is described in the textbook by Chmiel
(Bioprozesstechnik 1. Einfuhrung in die Bioverfahrenstechnik
(Gustav Fischer Verlag, Stuttgart, 1991)) or in the textbook by
Storhas (Bioreaktoren und periphere Einrichtungen (Vieweg Verlag,
Braunschweig/Wiesbaden, 1994)).
[0166] The culture medium to be used must meet the requirements of
the particular strains in a suitable manner. Descriptions of
culture media for various microorganisms are contained in the
handbook "Manual of Methods for General Bacteriology" of the
American Society for Bacteriology (Washington D.C., USA, 1981).
[0167] Sugars and carbohydrates, such as e.g. glucose, sucrose,
lactose, fructose, maltose, molasses, starch and cellulose, oils
and fats, such as e.g. soya oil, sunflower oil, groundnut oil and
coconut fat, fatty acids, such as e.g. palmitic acid, stearic acid
and linoleic acid, alcohols, such as e.g. glycerol and ethanol, and
organic acids, such as e.g. acetic acid or lactic acid, can be used
as the source of carbon. These substances can be used individually
or as a mixture.
[0168] Organic nitrogen-containing compounds, such as peptones,
yeast extract, meat extract, malt extract, corn steep liquor, soya
bean flour and urea, or inorganic compounds, such as ammonium
sulfate, ammonium chloride, ammonium phosphate, ammonium carbonate
and ammonium nitrate, can be used as the source of nitrogen. The
sources of nitrogen can be used individually or as a mixture.
[0169] Phosphoric acid, potassium dihydrogen phosphate or
dipotassium hydrogen phosphate or the corresponding
sodium-containing salts can be used as the source of phosphorus.
The culture medium must furthermore comprise salts of metals, such
as e.g. magnesium sulfate or iron sulfate, which are necessary for
growth. Finally, essential growth substances, such as amino acids
and vitamins, can be employed in addition to the above-mentioned
substances. Suitable precursors can moreover be added to the
culture medium. The starting substances mentioned can be added to
the culture in the form of a single batch, or can be fed in during
the culture in a suitable manner.
[0170] Basic compounds, such as sodium hydroxide, potassium
hydroxide, ammonia or aqueous ammonia, or acid compounds, such as
phosphoric acid or sulfuric acid, can be employed in a suitable
manner to control the pH of the culture. Antifoams, such as e.g.
fatty acid polyglycol esters, can be employed to control the
development of foam. Suitable substances having a selective action,
such as e.g. antibiotics, can be added to the medium to maintain
the stability of plasmids. To maintain aerobic conditions, oxygen
or oxygen-containing gas mixtures, such as e.g. air, are introduced
into the culture. The temperature of the culture is usually
20.degree. C. to 45.degree. C., and preferably 25.degree. C. to
40.degree. C. Culturing is continued until a maximum of the desired
chemical compound has formed. This target is usually reached within
10 hours to 160 hours.
[0171] It has been found that the coryneform bacteria according to
the invention, in particular the coryneform bacteria which produce
L-lysine, have an unexpectedly high stability. They were stable for
at least 10-20, 20-30, 30-40, 40-50, preferably at least 50-60,
60-70, 70-80 and 80-90 generations or cell division cycles.
[0172] The following microorganisms have been deposited:
[0173] The strain Corynebacterium glutamicum DSM12866glu::lysC was
deposited in the form of a pure culture on 5 Jun. 2002 under number
DSM15039 at the Deutsche Sammlung fur Mikroorganismen und
Zellkulturen (DSMZ=German Collection of Microorganisms and Cell
Cultures, Braunschweig, Germany) in accordance with the Budapest
Treaty.
[0174] The plasmid pK18mobsacBglu1.sub.--1 was deposited in the
form of a pure culture of the strain E. coli
DH5.alpha.mcr/pK18mobsacBglu1.sub.--1
(=DH5alphamcr/pK18mobsacBglu1.sub.--1) on 20 Apr. 2001 under number
DSM14243 at the Deutsche Sammlung fur Mikroorganismen und
Zellkulturen (DSMZ, Braunschweig, GeLmany) in accordance with the
Budapest Treaty.
[0175] The plasmid pK18mobsacBaecD1.sub.--1 was deposited in the
form of a pure culture of the strain E. coli
DH5.alpha.mcr/pK18mobsacBaecD1.sub.--1
(=DH5alphamcr/pK18mobsacBaecD1.sub.--1) on 5 Jun. 2002 under number
DSM15040 at the Deutsche Sammlung fur Mikroorganismen und
Zellkulturen (DSMZ, Braunschweig, Germany) in accordance with the
Budapest Treaty.
Example 1
Incorporation of a Second Copy of the lysC.sup.FBR Allele into the
Chromosome of the Strain DSM13994 and of the Strain DSM12866
[0176] The Corynebacterium glutamicum strain DSM13994 was produced
by multiple, non-directed mutagenesis, selection and mutant
selection from C. glutamicum ATCC13032. The strain is resistant to
the lysine analogue S-(2-aminoethyl)-L-cysteine and has a feed
back-resistant aspartate kinase which is insensitive to inhibition
by a mixture of lysine and threonine (in each case 25 mM). The
nucleotide sequence of the lysC.sup.FBR allele of this strain is
shown as SEQ ID NO:3. It is also called lysC T311I in the
following. The amino acid sequence of the aspartate kinase protein
coded is shown as SEQ ID NO:4. A pure culture of this strain was
deposited on 16 Jan. 2001 at the Deutsche Sammlung fur
Mikroorganismen und Zellkulturen (DSMZ=German Collection of
Microorganisms and Cell Cultures, Braunschweig, Germany) in
accordance with the Budapest Treaty.
[0177] The strain DSM12866 was produced from C. glutamicum
ATCC13032 by non-directed mutagenesis and selection of the mutants
with the best L-lysine accumulation. It is methionine-sensitive.
Growth on minimal medium comprising L-methionine can be
re-established by addition of threonine. This strain has the
wild-type form of the lysC gene shown as SEQ ID NO:1. The
corresponding amino acid sequence of the wild-type aspartate kinase
protein is shown as SEQ ID NO:2. A pure culture of this strain was
deposited on 10 Jun. 1999 at the Deutsche Sammlung fur
Mikroorganismen und Zellkulturen (DSMZ, Braunschweig, Germany) in
accordance with the Budapest Treaty.
1.1 Isolation and Sequencing of the DNA of the lysC Allele of
Strain DSM13994
[0178] From the strain DSM13994, chromosomal DNA is isolated by the
conventional methods (Eikmanns et al., Microbiology 140: 1817-1828
(1994)). With the aid of the polymerase chain reaction, a DNA
section which carries the lysC gene or allele is amplified. On the
basis of the sequence of the lysC gene known for C. glutamicum
(Kalinowski et al., Molecular Microbiology, 5 (5), 1197-1204
(1991); Accession Number X57226), the following primer
oligonucleotides were chosen for the PCR:
TABLE-US-00014 lysC1beg (SEQ ID No: 5): 5' TA(G GAT CC)T CCG GTG
TCT GAC CAC GGT G 3' lysC2end: (SEQ ID NO: 6): 5' AC(G GAT CC)G CTG
GGA AAT TGC GCT CTT CC 3'
[0179] The primers shown are synthesized by MWG Biotech and the PCR
reaction is carried out by the standard PCR method of Innis et al.
(PCR Protocols. A Guide to Methods and Applications, 1990, Academic
Press). The primers allow amplification of a DNA section of approx.
1.7 kb in length, which carries the lysC gene or allele. The
primers moreover contain the sequence for a cleavage site of the
restriction endonuclease BamHI, which is marked by parentheses in
the nucleotide sequence shown above.
[0180] The amplified DNA fragment of approx. 1.7 kb in length which
carries the lysC allele of the strain DSM13994 is identified by
electrophoresis in a 0.8% agarose gel, isolated from the gel and
purified by conventional methods (QIAquick Gel Extraction Kit,
Qiagen, Hilden).
[0181] Ligation of the fragment is then carried out by means of the
Topo TA Cloning Kit (Invitrogen, Leek, The Netherlands, Cat. Number
K4600-01) in the vector pCRII-TOPO. The ligation batch is
transformed in the E. coli strain TOP10 (Invitrogen, Leek, The
Netherlands). Selection of plasmid-carrying cells is made by
plating out the transformation batch on kanamycin (50
mg/l)-containing LB agar with X-Gal (5-bromo-4-chloro-3-indolyl
.beta.-D-galactopyranoside, 64 mg/l).
[0182] The plasmid obtained is checked by means of restriction
cleavage, after isolation of the DNA, and identified in agarose
gel. The resulting plasmid is called pCRIITOPOlysC.
[0183] The nucleotide sequence of the amplified DNA fragment or PCR
product is determined by the dideoxy chain termination method of
Sanger et al. (Proceedings of the National Academy of Sciences USA,
74:5463-5467 (1977)) using the "ABI Prism 377" sequencing apparatus
of PE Applied Biosystems (Weiterstadt, Germany). The sequence of
the coding region of the PCR product is shown in SEQ ID No:3. The
amino acid sequence of the associated aspartate kinase protein is
shown in SEQ ID NO:4.
[0184] The base thymine is found at position 932 of the nucleotide
sequence of the coding region of the lysC.sup.FBRallele of strain
DSM13994 (SEQ ID NO:3). The base cytosine is found at the
corresponding position of the wild-type gene (SEQ ID NO:1).
[0185] The amino acid isoleucine is found at position 311 of the
amino acid sequence of the aspartate kinase protein of strain
DSM13994 (SEQ ID No:4). The amino acid threonine is found at the
corresponding position of the wild-type protein (SEQ ID No:2).
[0186] The lysC allele, which contains the base thymine at position
932 of the coding region and accordingly codes for an aspartate
kinase protein which contains the amino acid isoleucine at position
311 of the amino acid sequence, is called the lysC.sup.FBR allele
or lysC T311I in the following.
[0187] The plasmid pCRIITOPOlysC, which carries the lysC.sub.FBR
allele lysC T311I, was deposited in the form of a pure culture of
the strain E. coli TOP 10/pCRIITOPOlysC under number DSM14242 on 20
Apr. 2001 at the Deutsche Sammlung fur Mikroorganismen and
Zellkulturen (DSMZ, Braunschweig, Germany) in accordance with the
Budapest Treaty.
1.2 Construction of the Replacement Vector
pK18mobsacBglu1.sub.--1
[0188] The Corynebacterium glutamicum strain ATCC13032 is used as
the donor for the chromosomal DNA. From the strain ATCC13032,
chromosomal DNA is isolated using the conventional methods
(Eikmanns et al., Microbiology 140: 1817-1828 (1994)). With the aid
of the polymerase chain reaction, a DNA fragment which carries the
gluB gene and surrounding regions is amplified. On the basis of the
sequence of the gluABCD gene cluster known for C. glutamicum
(Kronemeyer et al., Journal of Bacteriology, 177: 1152-1158 (1995))
(Accession Number X81191), the following primer oligonucleotides
are chosen for the PCR:
TABLE-US-00015 gluBgl1 (SEQ ID NO: 7): 5' TA(A GAT CT)G TGT TGG ACG
TCA TGG CAA G 3' gluBgl2 (SEQ ID NO: 8): 5' AC(A GAT CT)T GAA GCC
AAG TAC GGC CAA G 3'
[0189] The primers shown are synthesized by MWG Biotech and the PCR
reaction is carried out by the standard PCR method of Innis et al.
(PCR Protocols. A Guide to Methods and Applications, 1990, Academic
Press). The primers allow amplification of a DNA fragment of approx
1.7 kb in size, which carries the gluB gene and surrounding
regions. The surrounding regions are a sequence section approx.
0.33 kb in length upstream of the gluB gene, which represents the
3' end of the gluA gene, and a sequence section approx. 0.44 kb in
length downstream of the gluB gene, which represents the 5' end of
the gluC gene. The primers moreover contain the sequence for the
cleavage site of the restriction endonuclease BglII, which is
marked by parentheses in the nucleotide sequence shown above.
[0190] The amplified DNA fragment of approx. 1.7 kb in length which
carries the gluB gene and surrounding regions is identified by
means of electrophoresis in a 0.8% agarose gel and isolated from
the gel and purified by conventional methods (QIAquick Gel
Extraction Kit, Qiagen, Hilden).
[0191] Ligation of the fragment is then carried out by means of the
TOPO TA Cloning Kit (Invitrogen, Leek, The Netherlands, Cat. Number
K4600-01) in the vector pCRII-TOPO. The ligation batch is
transformed in the E. coli strain TOP10 (Invitrogen, Leek, The
Netherlands). Selection of plasmid-carrying cells is made by
plating out the transformation batch on kanamycin (50
mg/l)-containing LB agar with X-Gal (5-bromo-4-chloro-3-indolyl
.beta.-D-galactopyranoside, 64 mg/l).
[0192] The plasmid obtained is checked by means of restriction
cleavage, after isolation of the DNA, and identified in agarose
gel. The resulting plasmid is called pCRII-TOPOglu.
[0193] The plasmid pCRII-TOPOglu is cleaved with the restriction
enzyme BglII (Aersham-Pharmacia, Freiburg, Germany) and after
separation in an agarose gel (0.8%) with the aid of the QIAquick
Gel Extraction Kit (Qiagen, Hilden, Germany) the gluB fragment of
approx. 1.7 kb is isolated from the agarose gel and employed for
ligation with the mobilizable cloning vector pK18mobsacB described
by Schafer et al. (Gene 14: 69-73 (1994)). This is cleaved
beforehand with the restriction enzyme BamHI and dephosphorylated
with alkaline phosphatase (Alkaline Phosphatase, Boehringer
Mannheim), mixed with the gluB fragment of approx. 1.7 kb, and the
mixture is treated with T4 DNA Ligase (Amersham-Pharmacia,
Freiburg, Germany).
[0194] The E. coli strain DH5a (Grant et al.; Proceedings of the
National Academy of Sciences USA, 87 (1990) 4645-4649) is then
transformed with the ligation batch (Hanahan, In. DNA Cloning. A
Practical Approach. Vol. 1, ILR-Press, Cold Spring Harbor, N.Y.,
1989). Selection of plasmid-carrying cells is made by plating out
the transformation batch on LB agar (Sambrook et al., Molecular
Cloning: A Laboratory Manual. 2.sup.nd Ed., Cold Spring Harbor,
N.Y., 1989), which is supplemented with 50 mg/l kanamycin.
[0195] Plasmid DNA is isolated from a transformant with the aid of
the QIAprep Spin Miniprep Kit from Qiagen and checked by
restriction cleavage and subsequent agarose gel electrophoresis.
The plasmid is called pK18mobsacBglu1.
[0196] Plasmid DNA was isolated from the strain DSM14242 (see
Example 1.1), which carries the plasmid pCRIITOPOlysC, and cleaved
with the restriction enzyme BamHI (Amersham-Pharmacia, Freiburg,
Germany), and after separation in an agarose gel (0.8%) with the
aid of the QIAquick Gel Extraction Kit (Qiagen, Hilden, Germany)
the lysC.sup.FBR-containing DNA fragment of approx. 1.7 kb in
length was isolated from the agarose gel and employed for ligation
with the vector pK18mobsacBglu1 described above. This is cleaved
beforehand with the, restriction enzyme BamHI, dephosphorylated
with alkaline phosphatase (Alkaline Phosphatase, Boehringer
Mannheim, Germany), mixed with the lysC.sup.FBR fragment of approx.
1.7 kb and the mixture is treated with T4 DNA Ligase
(Amersham-Pharmacia, Freiburg, Germany).
[0197] The E. coli strain DH5.alpha.mcr (Life Technologies GmbH,
Karlsruhe, Germany) is then transformed with the ligation batch
(Hanahan, In: DNA Cloning. A Practical Approach. Vol. 1, ILR-Press,
Cold Spring Harbor, N.Y., 1989). Selection of plasmid-carrying
cells is made by plating out the transformation batch on LB agar
(Sambrook et al., Molecular Cloning: A Laboratory Manual. 2.sup.nd
Ed., Cold Spring Harbor, N.Y., 1989), which was supplemented with
50 mg/l kanamycin.
[0198] Plasmid DNA is isolated from a transformant with the aid of
the QIAprep Spin Miniprep Kit from Qiagen and checked by
restriction cleavage and subsequent agarose gel electrophoresis.
The plasmid is called pK18mobsacBglu1.sub.--1. A map of the plasmid
is shown in FIG. 1.
[0199] The plasmid pK18mobsacBglu1.sub.--1 was deposited in the
form of a pure culture of the strain E. coli
DH5.alpha.mcr/pK18mobsacBglu1.sub.--1
(=DH5alphamcr/pK18mobsacBglu1.sub.--1) under number DSM14243 on
20.04.2001 at the Deutsche Sammiung fur Mikroorganismen und
Zeilkulturen (DSMZ, Braunschweig, Germany) in accordance with the
Budapest Treaty.
1.3 Incorporation of a Second Copy of the lysC.sup.FBR allele lysC
T311I into the Chromosome (Target Site: gluB Gene) of the Strain
DSM13994 by Means of the Replacement Vector
pK18mobsacBglu1.sub.--1
[0200] The vector pK18mobsacBglu1.sub.--1 described in Example 1.2
is transferred by the protocol of Schafer et al. (Journal of
Microbiology 172: 1663-1666 (1990)) into the C. glutamicum strain
DSM13994 by conjugation. The vector cannot replicate independently
in DSM13994 and is retained in the cell only if it has integrated
into the chromosome. Selection of clones or transconjugants with
integrated pK18mobsacBglu1.sub.--1 is made by plating out the
conjugation batch on LB agar (Sambrook et al., Molecular Cloning: A
Laboratory Manual. 2.sup.nd Ed., Cold Spring Harbor, N.Y., 1989),
which is supplemented with 15 mg/l kanamycin and 50 mg/l nalidixic
acid. Kanamycin-resistant transconjugants are plated out on LB agar
plates with 25 mg/l kanamycin and incubated for 48 hours at
33.degree. C.
[0201] For selection of mutants in which excision of the plasmid
has taken place as a consequence of a second recombination event,
the clones are cultured for 20 hours in LB liquid medium and then
plated out on LB agar with 10% sucrose and incubated for 48
hours.
[0202] The plasmid pK18mobsacBglu1.sub.--1, like the starting
plasmid pK18mobsacB, contains, in addition to the kanamycin
resistance gene, a copy of the sacB gene which codes for levan
sucrase from Bacillus subtilis. The expression which can be induced
by sucrose leads to the formation of levan sucrase, which catalyses
the synthesis of the product levan, which is toxic to C.
glutamicum. Only those clones in which the integrated
pK18mobsacBglu1.sub.--1 has excised as the consequence of a second
recombination event therefore grow on LB agar. Depending on the
position of the second recombination event, after the excision the
second copy of the lysC.sup.FBR allele manifests itself in the
chromosome at the gluB locus, or the original gluB locus of the
host remains.
[0203] Approximately 40 to 50 colonies are tested for the phenotype
"growth in the presence of sucrose" and "non-growth in the presence
of kanamycin". Approximately 20 colonies which show the phenotype
"growth in the presence of sucrose" and "non-growth in the presence
of kanamycin" are investigated with the aid of the polymerase chain
reaction. A DNA fragment which carries the gluB gene and
surrounding regions is amplified here from the chromosomal DNA of
the colonies. The same primer oligonucleotides as are described in
Example 1.2 for the construction of the integration plasmid are
chosen for the PCR.
TABLE-US-00016 gluBgl1 (SEQ ID NO: 7): 5' TA(A GAT CT)G TGT TGG ACG
TCA TGG CAA G 3' gluBgl2 (SEQ ID NO: 8): 5' AC(A GAT CT)T GAA GCC
AAG TAC GGC CAA G 3'
[0204] The primers allow amplification of a DNA fragment approx.
1.7 kb in size in control clones with the original gluB locus. In
clones with a second copy of the lysC.sup.FBR allele in the
chromosome at the gluB locus, DNA fragments with a size of approx.
3.4 kb are amplified.
[0205] The amplified DNA fragments are identified by means of
electrophoresis in a 0.8% agarose gel.
[0206] A clone which, in addition to the copy present at the lysC
locus, has a second copy of the lysC.sup.FBR allele lysC T311I at
the gluB locus in the chromosome was identified in this manner.
This clone was called strain DSM13994glu::lysC.
1.4 Incorporation of a Second Copy of the lysC Gene in the Form of
the lysC.sup.FBR Allele lysC T311I into the Chromosome (Target
Site: gluB gene) of the Strain DSM12866 by Means of the Replacement
Vector pK18mobsacBglu1.sub.--1
[0207] As described in Example 1.3, the plasmid
pK18mobsacBglu1.sub.--1 is transferred into the C. glutamicum
strain DSM12866 by conjugation. A clone which, in addition to the
copy of the wild-type gene present at the lysC locus, has a second
copy of the lysC gene in the form of the lysC.sup.FBR allele lysC
T311I at the gluB locus in the chromosome was identified in the
manner described in 1.3. This clone was called strain
DSM12866glu::lysC.
[0208] The Corynebacterium glutamicum strain according to the
invention which carries a second copy of an lysC.sup.FBR allele in
the gluB gene was deposited in the form of a pure culture of the
strain Corynebacterium glutamicum DSM12866glu::lysC on 5 Jun. 2002
under number DSM15039 at the Deutsche Sammlung fur Mikroorganismen
and Zellkulturen (DSMZ, Braunschweig, Germany) in accordance with
the Budapest Treaty.
1.5 Construction of the Replacement Vector
pK18mobsacBpck1.sub.--1
[0209] The Corynebacterium glutamicum strain ATCC13032 is used as
the donor for the chromosomal DNA. From the strain ATCC13032,
chromosomal DNA is isolated using the conventional methods
(Eikmanns et al., Microbiology 140: 1817-1828 (1994)). With the aid
of the polymerase chain reaction, a DNA fragment which carries the
pck gene and surrounding regions is amplified. On the basis of the
sequence of the pck gene known for C. glutamicum (EP1094111 and
Riedel et al., Journal of Molecular and Microbiological
Biotechnology 3:573-583 (2001)) (Accession Number AJ269506), the
following primer oligonucleotides are chosen for the PCR:
TABLE-US-00017 pck_beg (SEQ ID NO: 9): 5' TA(A GAT CT) G CCG GCA
TGA CTT CAG TTT 3' pck_end (SEQ ID NO: 10): 5' AC(A GAT CT) G GTG
GGA GCC TTT CTT GTT ATT 3'
[0210] The primers shown are synthesized by MWG Biotech and the PCR
reaction is carried out by the standard PCR method of Innis et al.
(PCR Protocols. A Guide to Methods and Applications, 1990, Academic
Press). The primers allow amplification of a DNA fragment of approx
2.9 kb in size, which carries the pck gene and adjacent regions.
The primers moreover contain the sequence for the cleavage site of
the restriction endonuclease BglII, which is marked by parentheses
in the nucleotide sequence shown above.
[0211] The amplified DNA fragment of approx. 2.9 kb in length which
carries the pck gene and surrounding regions is identified by means
of electrophoresis in a 0.8% agarose gel and isolated from the gel
and purified by conventional methods (QIAquick Gel Extraction Kit,
Qiagen, Hilden).
[0212] Ligation of the fragment is then carried out by means of the
TOPO TA Cloning Kit (Invitrogen, Leek, The Netherlands, Cat. Number
K4600-01) in the vector pCRII-TOPO. The ligation batch is
transformed in the E. coli strain TOP10 (Invitrogen, Leek, The
Netherlands). Selection of plasmid-carrying cells is made by
plating out the transformation batch on kanamycin (50
mg/l)-containing LB agar with X-Gal (64 mg/l).
[0213] The plasmid obtained is checked by means of restriction
cleavage, after isolation of the DNA, and identified in agarose
gel. The resulting plasmid is called pCRII-TOPOpck. The plasmid
pCRII-TOPOpck is cleaved with the restriction enzyme BglII
(Amersham-Pharmacia, Freiburg, Germany) and after separation in an
agarose gel (0.8%) with the aid of the QIAquick Gel Extraction Kit
(Qiagen, Hilden, Germany) the pck fragment of approx. 2.9 kb is
isolated from the agarose gel and employed for ligation with the
mobilizable cloning vector pK18mobsacB described by Schafer et al.
(Gene 14: 69-73 (1994)). This is cleaved beforehand with the
restriction enzyme BamHI and dephosphorylated with alkaline
phosphatase (Alkaline Phosphatase, Boehringer Mannheim), mixed with
the pck fragment of approx. 2.9 kb, and the mixture is treated with
T4 DNA Ligase (Amersham-Pharmacia, Freiburg, Germany).
[0214] The E. coli Strain DH5.alpha. (Grant et al.; Proceedings of
the National Academy of Sciences USA, 87 (1990) 4645-4649) is then
transformed with the ligation batch (Hanahan, In. DNA Cloning. A
Practical Approach. Vol. 1, ILR-Press, Cold Spring Harbor, N.Y.,
1989) Selection of plasmid-carrying cells is made by plating out
the transformation batch on LB agar (Sambrook et al., Molecular
Cloning: A Laboratory Manual. 2.sup.nd Ed., Cold Spring Harbor,
N.Y., 1989), which is supplemented with 50 mg/l kanamycin.
[0215] Plasmid DNA is isolated from a transformant with the aid of
the QIAprep Spin Miniprep Kit from Qiagen and checked by
restriction cleavage and subsequent agarose gel electrophoresis.
The plasmid is called pK18mobsacBpck1.
[0216] Plasmid DNA was isolated from the strain DSM14242 (see
Example 1.1), which carries the plasmid pCRIITOPOlysC, and cleaved
with the restriction enzyme BamHI (Amersham-Pharmacia, Freiburg,
Germany), and after separation in an agarose gel (0.8%) with the
aid of the QIAquick Gel Extraction Kit (Qiagen, Hilden, Germany)
the lysC.sup.FBR-containing DNA fragment approx. 1.7 kb long was
isolated from the agarose gel and employed for ligation with the
vector pK18mobsacBpck1 described above. This is cleaved beforehand
with the restriction enzyme BamHI, dephosphorylated with alkaline
phosphatase (Alkaline Phosphatase, Boehringer Mannheim, Germany),
mixed with the lysC.sup.FBR fragment of approx. 1.7 kb and the
mixture is treated with T4 DNA Ligase (Amersham-Pharmacia,
Freiburg, Germany).
[0217] The E. coli strain DH5.alpha.mcr (Life Technologies GmbH,
Karlsruhe, Germany) is then transformed with the ligation batch
(Hanahan, In: DNA Cloning. A Practical Approach. Vol. 1, ILR-Press,
Cold Spring Harbor, N.Y., 1989). Selection of plasmid-carrying
cells is made by plating out the transformation batch on LB agar
(Sambrook et al., Molecular Cloning: A Laboratory Manual. 2.sup.nd
Ed., Cold Spring Harbor, N.Y., 1989), which was supplemented with
50 mg/l kanamycin.
[0218] Plasmid DNA is isolated from a transformant with the aid of
the QIAprep Spin Miniprep Kit from Qiagen and checked by
restriction cleavage and subsequent agarose gel electrophoresis.
The plasmid is called pK18mobdsacBpck1.sub.--1. A map of the
plasmid is shown in FIG. 3.
1.6 Incorporation of a Second Copy of the lysC Gene in the Form of
the lysC.sup.FBR Allele lysC T311I into the Chromosome (Target
Site: pck Gene) of the Strain DSM12866 by Means of the Replacement
Vector pK18mobsacBpck1.sub.--1
[0219] As described in Example 1.3, the plasmid
pK18mobsacBpck1.sub.--1 described in Example 1.5 is transferred
into the C. glutamicum strain DSM12866 by conjugation. Selection is
made for targeted recombination events in the chromosome of C.
glutamicum DSM12866 as described in Example 1.3. Depending on the
position of the second recombination event, after the excision the
second copy of the lysC.sup.FBR allele manifests itself in the
chromosome at the pck locus, or the original pck locus of the host
remains.
[0220] Approximately 40 to 50 colonies are tested for the phenotype
"growth in the presence of sucrose" and "non-growth in the presence
of kanamycin". Approximately 20 colonies which show the phenotype
"growth in the presence of sucrose" and "non-growth in the presence
of kanamycin" are investigated with the aid of the polymerase chain
reaction. A DNA fragment which carries the pck gene and surrounding
regions is amplified here from the chromosomal DNA of the colonies.
The same primer oligonucleotides as are described in Example 1.5
for the construction of the integration plasmid are chosen for the
PCR.
TABLE-US-00018 pck_beg (SEQ ID NO: 9): 5' TA(A GAT CT) G CCG GCA
TGA CTT CAG TTT 3' pck_end (SEQ ID NO: 10): 5' AC(A GAT CT) G GTG
GGA GCC TTT CTT GTT ATT 3'
[0221] The primers allow amplification of a DNA fragment approx.
2.9 kb in size in control clones with the original pck locus. In
clones with a second copy of the lysC.sup.FBR in the chromosome at
the pck locus, DNA fragments with a size of approx. 4.6 kb are
amplified.
[0222] The amplified DNA fragments are identified by means of
electrophoresis in a 0.8% agarose gel.
[0223] A clone which, in addition to the copy of the wild-type gene
present at the lysC locus, has a second copy of the lysC gene in
the form of the lysC.sup.FBR allele lysC T311I at the pck locus in
the chromosome was identified in this manner. This clone was called
strain DSM12866 pck::lysC.
1.7 Construction of the Replacement Vector
pK18mobsacBaecD1.sub.--1
[0224] The Corynebacterium glutamicum strain ATCC13032 is used as
the donor for the chromosomal DNA. From the strain ATCC13032,
chromosomal DNA is isolated using the conventional methods
(Eikmanns et al., Microbiology 140: 1817-1828 (1994)). With the aid
of the polymerase chain reaction, a DNA fragment which carries the
aecD gene and surrounding regions is amplified. On the basis of the
sequence of the aecD gene known for C. glutamicum (Rossol et al.,
Journal of Bacteriology 174:2968-2977 (1992)) (Accession Number
M89931), the following primer oligonucleotides are chosen for the
PCR:
TABLE-US-00019 aecD_beg (SEQ ID NO: 11): 5' GAA CTT ACG CCA AGC TGT
TC 3' aecD_end (SEQ ID NO: 12): 5' AGC ACC ACA ATC AAC GTG AG
3'
[0225] The primers shown are synthesized by MWG Biotech and the PCR
reaction is carried out by the standard PCR method of Innis et al.
(PCR Protocols. A Guide to Methods and Applications, 1990, Academic
Press). The primers allow amplification of a DNA fragment of approx
2.1 kb in size, which carries the aecD gene and adjacent
regions.
[0226] The amplified DNA fragment of approx. 2.1 kb in length is
identified by means of electrophoresis in a 0.8% agarose gel and
isolated from the gel and purified by conventional methods
(QIAquick Gel Extraction Kit, Qiagen, Hilden).
[0227] The DNA fragment purified is cleaved with the restriction
enzyme BamHI and EcoRV (Amersham Pharmacia, Freiburg, Germany). The
ligation of the fragment in the vector pUC18 then takes place
(Norrander et al., Gene 26:101-106 (1983)). This is cleaved
beforehand with the restriction enzymes BglII and SmaI,
dephosphorylated, mixed with the aecD-carrying fragment of approx.
1.5 kb, and the mixture is treated with T4 DNA Ligase
(Amersham-Pharmacia, Freiburg, Germany). The ligation batch is
transformed in the E. coli strain TOP10 (Invitrogen, Leek, The
Netherlands). Selection of plasmid-carrying cells is made by
plating out the transformation batch on kanamycin (50
mg/l)-containing LB agar with X-Gal (64 mg/l).
[0228] The plasmid obtained is checked by means of restriction
cleavage, after isolation of the DNA, and identified in agarose
gel. The resulting plasmid is called pUC18aecD.
[0229] Plasmid DNA was isolated from the strain DSM14242 (see
Example 1.1) which carries the plasmid pCRIITOPOlysC and cleaved
with the restriction enzyme BamHI (Amersham-Pharmacia, Freiburg,
Germany) and then treated with Klenow polymerase. After separation
in an agarose gel (0.8%) with the aid of the QIAquick Gel
Extraction Kit (Qiagen, Hilden, Germany) the
lysC.sup.FBR-containing DNA fragment approx. 1.7 kb in length is
isolated from the agarose gel and employed for ligation with the
vector pUC18aecD described above. This is cleaved beforehand with
the restriction enzyme StuI, dephosphorylated with alkaline
phosphatase (Alkaline Phosphatase, Boehringer Mannheim, Germany),
mixed with the lysC.sup.FBR fragment of approx. 1.7 kb and the
mixture is treated with T4 DNA Ligase (Amersham-Pharmacia,
Freiburg, Germany).
[0230] The E. coli strain DH5.alpha.mcr (Life Technologies GmbH,
Karlsruhe, Germany) is then transformed with the ligation batch
(Hanahan, In: DNA Cloning. A Practical Approach. Vol. 1, ILR-Press,
Cold Spring Harbor, N.Y., 1989). Selection of plasmid-carrying
cells is made by plating out the transformation batch on LB agar
(Sambrook et al., Molecular Cloning: A Laboratory Manual. 2.sup.nd
Ed., Cold Spring Harbor, N.Y., 1989), which was supplemented with
50 mg/l kanamycin.
[0231] Plasmid DNA is isolated from a transformant with the aid of
the QIAprep Spin Miniprep Kit from Qiagen and checked by
restriction cleavage and subsequent agarose gel electrophoresis.
The plasmid is called pUC18aecD1.
[0232] The plasmid pUC18aecD1 is cleaved with the restriction
enzyme KpnI and then treated with Klenow polymerase. The plasmid is
then cleaved with the restriction enzyme SalI (Amersham-Pharmacia,
Freiburg, Germany) and after separation in an agarose gel (0.8%)
with the aid of the QIAquick Gel Extraction Kit (Qiagen, Hilden,
Germany) the fragment of approx. 3.2 kb which carries aecD and lysC
is isolated from the agarose gel and employed for ligation with the
mobilizable cloning vector pK18mobsacB described by Schafer et al.
(Gene 14: 69-73 (1994)). This is cleaved beforehand with the
restriction enzymes SmaI and SalI and dephosphorylated with
alkaline phosphatase (Alkaline Phosphatase, Boehringer Mannheim),
mixed with the fragment of approx. 3.2 kb which carries aecD and
lysC, and the mixture is treated with T4 DNA Ligase
(Amersham-Pharmacia, Freiburg, Germany).
[0233] The E. coli strain DH5.alpha. (Grant et al.; Proceedings of
the National Academy of Sciences USA, 87 (1990) 4645-4649) is then
transformed with the ligation batch (Hanahan, In. DNA Cloning. A
Practical Approach. Vol. 1, ILR-Press, Cold Spring Harbor, N.Y.,
1989). Selection of plasmid-carrying cells is made by plating out
the transfo/mation batch on LB agar (Sambrook et al., Molecular
Cloning: A Laboratory Manual. 2.sup.nd Ed., Cold Spring Harbor,
N.Y., 1989), which is supplemented with 50 mg/l kanamycin.
[0234] Plasmid DNA is isolated from a transformant with the aid of
the QIAprep Spin Miniprep Kit from Qiagen and checked by
restriction cleavage and subsequent agarose gel electrophoresis.
The plasmid is called pK18mobsacBaecD1.sub.--1. A map of the
plasmid is shown in FIG. 2.
[0235] The plasmid pK18mobsacBaecD1.sub.--1 was deposited in the
form of a pure culture of the strain E. coli
DH5.alpha.mcr/pK18mobsacBaecD1.sub.--1
(=DH5alphamcr/pK18mobsacBaecD1.sub.--1) on 5 Jun. 2002 under number
DSM15040 at the Deutsche Sammlung fur Mikroorganismen und
Zellkulturen (DSMZ, Braunschweig, Germany) in accordance with the
Budapest Treaty.
1.8 Incorporation of a Second Copy of the lysC Gene as the
lysC.sup.FBR Allele into the Chromosome (Target Site: aecD Gene) of
the Strain DSM12866 by Means of the Replacement Vector
pK18mobsacBaecD1.sub.--1
[0236] As described in Example 1.3, the plasmid
pK18mobsacBaecD1.sub.--1 described in Example 1.4 is transferred
into the C. glutamicum strain DSM12866 by conjugation. Selection is
made for targeted recombination events in the chromosome of C.
glutamicum DSM12866 as described in Example 1.3. Depending on the
position of the second recombination event, after the excision the
second copy of the lysC.sup.FBR allele manifests itself in the
chromosome at the aecD locus, or the original aecD locus of the
host remains.
[0237] Approximately 40 to 50 colonies are tested for the phenotype
"growth in the presence of sucrose" and "non-growth in the presence
of kanamycin". Approximately 20 colonies which show the phenotype
"growth in the presence of sucrose" and "non-growth in the presence
of kanamycin" are investigated with the aid of the polymerase chain
reaction. A DNA fragment which carries the aecD gene and
surrounding regions is amplified here from the chromosomal DNA of
the colonies. The same primer oligonucleotides as are described in
Example 1.7 for the construction of the integration plasmid are
chosen for the PCR.
TABLE-US-00020 aecD_beg (SEQ ID NO: 11): 5' GAA CTT ACG CCA AGC TGT
TC 3' aecD_end (SEQ ID NO: 12): 5' AGC ACC ACA ATC AAC GTG AG
3'
[0238] The primers allow amplification of a DNA fragment approx.
2.1 kb in size in control clones with the original aecD locus. In
clones with a second copy of the lysC.sup.FBR allele in the
chromosome at the aecD locus, DNA fragments with a size of approx.
3.8 kb are amplified.
[0239] The amplified DNA fragments are identified by means of
electrophoresis in a 0.8% agarose gel.
[0240] A clone which, in addition to the copy of the wild-type gene
present at the lysC locus, has a second copy of the lysC gene in
the form of the lysC.sup.FBR allele lysC T311I at the aecD locus in
the chromosome was identified in this manner. This clone was called
strain DSM12866aecD::lysC.
Example 2
Incorporation of a Second Copy of the ddh Gene into the Chromosome
(Target Site: gluB Gene) of the Strain DSM12866
[0241] 2.1 Construction of the Replacement Vector
pK18mobsacBglu2.sub.--1
[0242] The Corynebacterium glutamicum strain ATCC13032 is used as
the donor for the chromosomal DNA. From the strain ATCC13032,
chromosomal DNA is isolated using the conventional methods
(Eikmanns et al., Microbiology 140: 1817-1828 (1994)). With the aid
of the polymerase chain reaction, a DNA fragment which carries the
gluB gene and surrounding regions is amplified. On the basis of the
sequence of the gluABCD gene cluster known for C. glutamicum
(Kronemeyer et al., Journal of Bacteriology, 177: 1152-1158 (1995);
EP1108790) (Accession Number X81191 and AX127149), the following
primer oligonucleotides are chosen for the PCR:
TABLE-US-00021 gluA_beg (SEQ ID NO: 13): 5' CAC GGT TGC TCA TTG TAT
CC 3' gluD_end (SEQ ID NO: 14): 5' CGA GGC GAA TCA GAC TTC TT
3'
[0243] The primers shown are synthesized by MWG Biotech and the PCR
reaction is carried out by the standard PCR method of Innis et al.
(PCR Protocols. A Guide to Methods and Applications, 1990, Academic
Press). The primers allow amplification of a DNA fragment of approx
4.4 kb in size, which carries the gluB gene and surrounding
regions.
[0244] The amplified DNA fragment is identified by means of
electrophoresis in a 0.8% agarose gel and isolated from the gel and
purified by conventional methods (QIAquick Gel Extraction Kit,
Qiagen, Hilden).
[0245] Ligation of the fragment is then carried out by means of the
TOPO TA Cloning Kit (Invitrogen, Leek, The Netherlands, Cat. Number
K4600-01) in the vector pCRII-TOPO. The ligation batch is
transformed in the E. coli strain TOP10 (Invitrogen, Leek, The
Netherlands). Selection of plasmid-carrying cells is made by
plating out the transformation batch on kanamycin (50
mg/l)-containing LB agar with X-Gal (64 mg/l).
[0246] The plasmid obtained is checked by means of restriction
cleavage, after isolation of the DNA, and identified in agarose
gel. The resulting plasmid is called pCRII-TOPOglu2.
[0247] The plasmid pCRII-TOPOglu2 is cleaved with the restriction
enzymes EcoRI and SalI (Amersham-Pharmacia, Freiburg, Germany) and
after separation in an agarose gel (0.8%) with the aid of the
QIAquick Gel Extraction Kit (Qiagen, Hilden, Germany) the gluB
fragment of approx. 3.7 kb is isolated from the agarose gel and
employed for ligation with the mobilizable cloning vector
pK18mobsacB described by Schafer et al. (Gene 14, 69-73 (1994)).
This is cleaved beforehand with the restriction enzymes EcoRI and
SalI and dephosphorylated with alkaline phosphatase (Alkaline
Phosphatase, Boehringer Mannheim), mixed with the gluB fragment of
approx. 3.7 kb, and the mixture is treated with T4 DNA Ligase
(Amersham-Pharmacia, Freiburg, Germany).
[0248] The E. coli Strain DH5.alpha. (Grant et al.; Proceedings of
the National Academy of Sciences USA, 87 (1990) 4645-4649) is then
transformed with the ligation batch (Hanahan, In. DNA Cloning. A
Practical Approach. Vol. 1, ILR-Press, Cold Spring Harbor, N.Y.,
1989). Selection of plasmid-carrying cells is made by plating out
the transformation batch on LB agar (Sambrook et al., Molecular
Cloning: A Laboratory Manual. 2.sup.nd Ed., Cold Spring Harbor,
N.Y., 1989), which is supplemented with 50 mg/l kanamycin.
[0249] Plasmid DNA is isolated from a transformant with the aid of
the QIAprep Spin Miniprep Kit from Qiagen and checked by
restriction cleavage and subsequent agarose gel electrophoresis.
The plasmid is called pK18mobsacBglu2.
[0250] As described in Example 2.1, a DNA fragment which carries
the ddh gene and surrounding regions is also amplified with the aid
of the polymerase chain reaction. On the basis of the sequence of
the ddh gene cluster known for C. glutamicum (Ishino et al.,
Nucleic Acids Research 15, 3917 (1987)) (Accession Number Y00151),
the following primer oligonucleotides are chosen for the PCR:
TABLE-US-00022 ddh_beg (SEQ ID NO: 15): 5' CTG AAT CAA AGG CGG ACA
TG 3' ddh_end (SEQ ID NO: 16): 5' TCG AGC TAA ATT AGA CGT CG 3'
[0251] The primers shown are synthesized by MWG Biotech and the PCR
reaction is carried out by the standard PCR method of Innis et al.
(PCR Protocols. A Guide to Methods and Applications, 1990, Academic
Press). The primers allow amplification of a DNA fragment of approx
1.6 kb in size, which carries the ddh gene.
[0252] The amplified DNA fragment of approx. 1.6 kb in length,
which the ddh gene, is identified by means of electrophoresis in a
0.8% agarose gel and isolated from the gel and purified by
conventional methods (QIAquick Gel Extraction Kit, Qiagen,
Hilden).
[0253] After purification, the fragment carrying the ddh gene is
employed for ligation in the vector pK18mobsacBglu2 described. This
is partly cleaved beforehand with the restriction enzyme BamHI. By
treatment of the vector with a Klenow polymerase
(Amersham-Pharmacia, Freiburg, Germany), the overhangs of the
cleaved ends are completed to blunt ends, the vector is then mixed
with the DNA fragment of approx. 1.6 kb which carries the ddh gene
and the mixture is treated with T4 DNA ligase (Amersham-Pharmacia,
Freiburg, Germany). By using Vent Polymerase (New England Biolabs,
Frankfurt, Germany) for the PCR reaction, a ddh-carrying DNA
fragment which has blunt ends and is suitable for ligation in the
pretreated vector pK18mobsacBglu2 is generated.
[0254] The E. coli strain DH5.alpha.mcr (Life Technologies GmbH,
Karlsruhe, Germany) is then transformed with the ligation batch
(Hanahan, In: DNA Cloning. A Practical Approach. Vol. 1, ILR-Press,
Cold Spring Harbor, N.Y., 1989). Selection of plasmid-carrying
cells is made by plating out the transformation batch on LB agar
(Sambrook et al., Molecular Cloning: A Laboratory Manual. 2.sup.nd
Ed., Cold Spring Harbor, N.Y., 1989), which was supplemented with
50 mg/l kanamycin.
[0255] Plasmid DNA is isolated from a transformant with the aid of
the QIAprep Spin Miniprep Kit from Qiagen and checked by
restriction cleavage and subsequent agarose gel electrophoresis.
The plasmid is called pK18mobsacBglu2.sub.--1. A map of the plasmid
is shown in FIG. 4.
2.2 Incorporation of a Second Copy of the ddh Gene into the
Chromosome (Target Site: gluB Gene) of the Strain DSM12866 by Means
of the Replacement Vector pK18mobsacBglu2.sub.--1
[0256] As described in Example 1.3, the plasmid
pK18mobsacBglu2.sub.--1 described in Example 2.1 is transferred
into the C. glutamicum strain DSM12866 by conjugation. Selection is
made for targeted recombination events in the chromosome of C.
glutamicum DSM12866 as described in Example 1.3. Depending on the
position of the second recombination event, after the excision the
second copy of the ddh gene manifests itself in the chromosome at
the gluB locus, or the original gluB locus of the host remains.
[0257] Approximately 40 to 50 colonies are tested for the phenotype
"growth in the presence of sucrose" and "non-growth in the presence
of kanamycin". Approximately 20 colonies which show the phenotype
"growth in the presence of sucrose" and "non-growth in the presence
of kanamycin" are investigated with the aid of the polymerase chain
reaction. A DNA fragment which carries the glu region described is
amplified here from the chromosomal DNA of the colonies. The same
primer oligonucleotides as are described in Example 2.1 for the
construction of the replacement plasmid are chosen for the PCR.
TABLE-US-00023 gluA_beg (SEQ ID NO: 13): 5' CAC GGT TGC TCA TTG TAT
CC 3' gluD_end (SEQ ID NO: 14): 5' CGA GGC GAA TCA GAC TTC TT
3'
[0258] The primers allow amplification of a DNA fragment approx.
4.4 kb in size in control clones with the original glu locus. In
clones with a second copy of the ddh gene in the chromosome at the
gluB locus, DNA fragments with a size of approx. 6 kb are
amplified.
[0259] The amplified DNA fragments are identified by means of
electrophoresis in a 0.8% agarose gel.
[0260] A clone which, in addition to the copy present at the ddh
locus, has a second copy of the ddh gene at the gluB locus in the
chromosome was identified in this manner. This clone was called
strain DSM12866glu::ddh.
Example 3
Incorporation of a Second Copy of the dapA Gene into the Chromosome
(Target Site: aecD Gene) of the Strain DSM12866
[0261] 3.1 Construction of the Replacement Vector
pK18mobsacBaecD2.sub.--1
[0262] The Corynebacterium glutamicum strain ATCC13032 is used as
the donor for the chromosomal DNA. From the strain ATCC13032,
chromosomal DNA is isolated using the conventional methods
(Eikmanns et al., Microbiology 140: 1817-1828 (1994)). With the aid
of the polymerase chain reaction, a DNA fragment which carries the
aecD gene and surrounding regions is amplified. On the basis of the
sequence of the aecD gene known for C. glutamicum (Rossol et al.,
Journal of Bacteriology 174:2968-2977 (1992)) (Accession Number
M89931), the following primer oligonucleotides are chosen for the
PCR:
TABLE-US-00024 aecD_beg (SEQ ID NO: 11): 5' GAA CTT ACG CCA AGC TGT
TC 3' aecD_end (SEQ ID NO: 12): 5' AGC ACC ACA ATC AAC GTG AG
3'
[0263] The primers shown are synthesized by MWG Biotech and the PCR
reaction is carried out by the standard PCR method of Innis et al.
(PCR Protocols. A Guide to Methods and Applications, 1990, Academic
Press). The primers allow amplification of a DNA fragment of approx
2.1 kb in size, which carries the aecD gene and adjacent
regions.
[0264] The amplified DNA fragment of approx. 2.1 kb in length is
identified by means of electrophoresis in a 0.8% agarose gel and
isolated from the gel and purified by conventional methods
(QIAquick Gel Extraction Kit, Qiagen, Hilden).
[0265] The DNA fragment purified is cleaved with the restriction
enzyme BglII and EcoRV (Amersham Pharmacia, Freiburg, Germany). The
ligation of the fragment in the vector pUC18 then takes place
(Norrander et al., Gene 26:101-106 (1983)). This is cleaved
beforehand with the restriction enzymes BamHI and SmaI and
dephosphorylated, mixed with the aecD-carrying fragment of approx.
1.5 kb, and the mixture is treated with T4 DNA Ligase
(Amersham-Pharmacia, Freiburg, Germany). The ligation batch is
transformed in the E. coli strain TOP10 (Invitrogen, Leek, The
Netherlands). Selection of plasmid-carrying cells is made by
plating out the transformation batch on kanamycin (50
mg/l)-containing LB agar with X-Gal (64 mg/l).
[0266] The plasmid obtained is checked by means of restriction
cleavage, after isolation of the DNA, and identified in agarose
gel. The resulting plasmid is called pUC18aecD.
[0267] With the aid of the polymerase chain reaction, a further DNA
fragment which carries the dapA gene and surrounding regions is
amplified. On the basis of the sequence of the dapA gene known for
C. glutamicum (Bonassi et al., Nucleic Acids Research 18:6421
(1990)) (Accession Number X53993 and AX127149), the following
primer oligonucleotides are chosen for the PCR:
TABLE-US-00025 dapA_beg (SEQ ID NO: 17): 5' CGA GCC AGT GAA CAT GCA
GA 3' dapA_end (SEQ ID NO: 18): 5' CTT GAG CAC CTT GCG CAG CA
3'
[0268] The primers shown are synthesized by MWG Biotech and the PCR
reaction is carried out by the standard PCR method of Innis et al.
(PCR Protocols. A Guide to Methods and Applications, 1990, Academic
Press). The primers allow amplification of a DNA fragment of
approx. 1.4 kb in size, which carries the dapA gene and adjacent
regions.
[0269] The amplified DNA fragment of approx. 1.4 kb in length is
identified by means of electrophoresis in a 0.8% agarose gel and
isolated from the gel and purified by conventional methods
(QIAquick Gel Extraction Kit, Qiagen, Hilden).
[0270] After purification, the dapA-containing D fragment approx.
1.4 kb in length is employed for ligation with the vector pUC18aecD
described above. This is cleaved beforehand with the restriction
enzyme StuI, mixed with the DNA fragment of approx. 1.4 kb, and the
mixture is treated with T4 DNA Ligase (Amersham-Pharmacia,
Freiburg, Germany).
[0271] The E. coli strain DH5.alpha.mcr (Life Technologies GmbH,
Karlsruhe, Germany) is then transformed with the ligation batch
(Hanahan, In: DNA Cloning. A Practical Approach. Vol. 1, ILR-Press,
Cold Spring Harbor, N.Y., 1989). Selection of plasmid-carrying
cells is made by plating out the transformation batch on LB agar
(Sambrook et al., Molecular Cloning: A Laboratory Manual. 2.sup.nd
Ed., Cold Spring Harbor, N.Y., 1989), which was supplemented with
50 mg/l kanamycin.
[0272] Plasmid DNA is isolated from a transformant with the aid of
the QIAprep Spin Miniprep Kit from Qiagen and checked by
restriction cleavage and subsequent agarose gel electrophoresis.
The plasmid is called pUC18aecD2.
[0273] The plasmid pUC18aecD2 is cleaved with the restriction
enzyme Sail and partly with EcoRI (Amersham-Pharmacia, Freiburg,
Germany) and after separation in an agarose gel (0.8%) with the aid
of the QIAquick Gel Extraction Kit (Qiagen, Hilden, Germany) the
fragment of approx. 2.7 kb which carries aecD and dapA is isolated
from the agarose gel and employed for ligation with the mobilizable
cloning vector pK18mobsacB described by Schafer et al. (Gene 14:
69-73 (1994)). This is cleaved beforehand with the restriction
enzymes EcoRI and with SalI and dephosphorylated with alkaline
phosphatase (Alkaline Phosphatase, Boehringer Mannheim), mixed with
the fragment of approx. 2.7 kb which carries aecD and dapA, and the
mixture is treated with T4 DNA Ligase (Amersham-Pharmacia,
Freiburg, Germany).
[0274] The E. coli strain DH5.alpha. (Grant et al.; Proceedings of
the National Academy of Sciences USA, 87 (1990) 4645-4649) is then
transformed with the ligation batch (Hanahan, In. DNA Cloning. A
Practical Approach. Vol. 1, ILR-Press, Cold Spring Harbor, N.Y.,
1989). Selection of plasmid-carrying cells is made by plating out
the transformation batch on LB agar (Sambrook et al., Molecular
Cloning: A Laboratory Manual. 2.sup.nd Ed., Cold Spring Harbor,
N.Y., 1989), which is supplemented with 50 mg/l kanamycin.
[0275] Plasmid DNA is isolated from a transformant with the aid of
the QIAprep Spin Miniprep Kit from Qiagen and checked by
restriction cleavage and subsequent agarose gel electrophoresis.
The plasmid is called pK18mobsacBaecD2.sub.--1. A map of the
plasmid is shown in FIG. 5.
3.2 Incorporation of a Second Copy of the dapA Gene into the
Chromosome (Target Site: aecD Gene) of the Strain DSM12866 by Means
of the Replacement Vector pK18mobsacBaecD2.sub.--1
[0276] As described in Example 1.3, the plasmid pK18mobsacBaecD21
described in Example 3.1 is transferred into the C. glutamicum
strain DSM12866 by conjugation. Selection is made for targeted
recombination events in the chromosome of C. glutamicum DSM12866 as
described in Example 1.3.
[0277] Depending on the position of the second recombination event,
after the excision the second copy of the dapA gene manifests
itself in the chromosome at the aecD locus, or the original aecD
locus of the host remains.
[0278] Approximately 40 to 50 colonies are tested for the phenotype
"growth in the presence of sucrose" and "non-growth in the presence
of kanamycin". Approximately 20 colonies which show the phenotype
"growth in the presence of sucrose" and "non-growth in the presence
of kanamycin" are investigated with the aid of the polymerase chain
reaction. A DNA fragment which carries the aecD gene and
surrounding regions is amplified here from the chromosomal DNA of
the colonies. The same primer oligonucleotides as are described in
Example 3.1 for the construction of the integration plasmid are
chosen for the PCR.
TABLE-US-00026 aecD_beg (SEQ ID NO: 11): 5' GAA CTT ACG CCA AGC TGT
TC 3' aecD_end (SEQ ID NO: 12): 5' AGC ACC ACA ATC AAC GTG AG
3'
[0279] The primers allow amplification of a DNA fragment approx.
2.1 kb in size in control clones with the original aecD locus. In
clones with a second copy of the dapA gene in the chromosome at the
aecD locus, DNA fragments with a size of approx. 3.6 kb are
amplified.
[0280] The amplified DNA fragments are identified by means of
electrophoresis in a 0.8% agarose gel.
[0281] A clone which, in addition to the copy present at the dapA
locus, has a second copy of the dapA gene at the aecD locus in the
chromosome was identified in this manner. This clone was called
strain DSM12866aecD::dapA.
Example 4
Incorporation of a Second Copy of the pyc Gene in the Form of the
pyc Allele pycP458S into the Chromosome (Target Site: pck Gene) of
the Strain DSM12866
[0282] 4.1 Construction of the Replacement Vector
pK18mobsacBpck1.sub.--3
[0283] The replacement vector pK18mobsacBpck1 described in Example
1.5 is used as the base vector for insertion of the pyc allele.
[0284] As described in Example 2.1, a DNA fragment which carries
the pyc gene and surrounding regions is also amplified with the aid
of the polymerase chain reaction. On the basis of the sequence of
the pyc gene cluster known for C. glutamicum (Peters-Wendisch et
al., Journal of Microbiology 144: 915-927 (1998)) (Accession Number
Y09548), the following primer oligonucleotides are chosen for the
PCR:
TABLE-US-00027 pyc_beg (SEQ ID NO: 19): 5' TC(A CGC GT)C TTG AAG
TCG TGC AGG TCA G 3' pyc_end (SEQ ID NO: 20): 5' TC(A CGC GT)C GCC
TCC TCC ATG AGG AAG A 3'
[0285] The primers shown are synthesized by MWG Biotech and the PCR
reaction is carried out by the standard PCR method of Innis et al.
(PCR Protocols. A Guide to Methods and Applications, 1990, Academic
Press). The primers allow amplification of a DNA fragment of approx
3.6 kb in size, which carries the pyc gene. The primers moreover
contain the sequence for the cleavage site of the restriction
endonuclease MluI, which is marked by parentheses in the nucleotide
sequence shown above.
[0286] The amplified DNA fragment of approx. 3.6 kb in length,
which carries the pyc gene, is cleaved with the restriction
endonuclease MluI, identified by means of electrophoresis in a 0.8%
agarose gel and isolated from the gel and purified by conventional
methods (QIAquick Gel Extraction Kit, Qiagen, Hilden).
[0287] After purification, the fragment carrying the pyc gene is
employed for ligation in the vector pK18mobsacBpck1 described. This
is cleaved beforehand with the restriction enzyme BssHII,
dephosphorylated with alkaline phosphatase (Alkaline Phosphatase,
Boehringer Mannheim, Germany), mixed with the DNA fragment of
approx. 3.6 kb which carries the pyc gene, and the mixture is
treated with T4 DNA Ligase (Amersham-Pharmacia, Freiburg,
GeLwany).
[0288] The E. coli strain DH5.alpha.mcr (Life Technologies GmbH,
Karlsruhe, Germany) is then transformed with the ligation batch
(Hanahan, In: DNA Cloning. A Practical Approach. Vol. 1, ILR-Press,
Cold Spring Harbor, N.Y., 1989). Selection of plasmid-carrying
cells is made by plating out the transformation batch on LB agar
(Sambrook et al., Molecular Cloning: A Laboratory Manual. 2.sup.nd
Ed., Cold Spring Harbor, N.Y., 1989), which was supplemented with
50 mg/l kanamycin.
[0289] Plasmid DNA is isolated from a transformant with the aid of
the QIAprep Spin Miniprep Kit from Qiagen and checked by
restriction cleavage and subsequent agarose gel electrophoresis.
The plasmid is called pK18mobsacBpck1.sub.--2.
4.2 Construction of the pyc Allele pyc P458S by Means of
Site-Specific Mutagenesis of the Wild-Type pyc Gene
[0290] The site-directed mutagenesis is carried out with the
QuikChange Site-Directed Mutagenesis Kit (Stratagene, La Jolla,
USA). EP-A-1108790 describes a point mutation in the pyc gene for
C. glutamicum which allows improved L-lysine production. On the
basis of the point mutation in the nucleotide sequence of cytosine
to thymine in the pyc gene at position 1372, replacement in the
amino acid sequence derived therefrom of proline for serine at
position 458 results. The allele is called pyc P458S. To generate
the mutation described, the following primer oligonucleotides are
chosen for the linear amplification:
TABLE-US-00028 P458S-1 (SEQ ID NO: 21): 5' GGATTCATTGCCGATCAC (TCG)
CACCTCCTTCAGGCTCCA 3' P458S-2 (SEQ ID NO: 22): 5'
GTGGAGGAAGTCCGAGGT (CGA) GTGATCGGCAATGAATCC 3'
[0291] The primers shown are synthesized by MWG Biotech. The codon
for serine, which is to replace the proline at position 458, is
marked by parentheses in the nucleotide sequence shown above. The
plasmid pK18mobsacBpck1.sub.--2 described in Example 4.1 is
employed with the two primers, which are each complementary to a
strand of the plasmid, for linear amplification by means of Pfu
Turbo DNA polymerase. By this lengthening of the primers, a mutated
plasmid with broken circular strands is formed. The product of the
linear amplification is treated with DpnI-this endonuclease cleaves
the methylated and half-methylated template DNA specifically. The
newly synthesized broken, mutated vector DNA is transformed in the
E. coli strain XL1 Blue (Bullock, Fernandez and Short,
BioTechniques (5) 376-379 (1987)). After the transformation, the
XL1 Blue cells repair the breaks in the mutated plasmids. Selection
of the transformants was carried out on LB medium with kanamycin 50
mg/l. The plasmid obtained is checked by means of restriction
cleavage, after isolation of the DNA, and identified in agarose
gel. The DNA sequence of the mutated DNA fragment is checked by
sequencing. The sequence of the PCR product coincides with the
sequence described Ohnishi et al. (2002). The resulting plasmid is
called pK18mobsacBpck1.sub.--3. A map of the plasmid is shown in
FIG. 6.
4.3 Incorporation of a Second Copy of the pyc Gene in the Form of
the pyc Allele pycP458S into the Chromosome (Target Site pck Gene)
of the Strain DSM12866 by Means of the Replacement Vector
pk18mobsacBpck1.sub.--3
[0292] The plasmid pK18mobsacBpck1.sub.--3 described in Example 4.2
is transferred as described in Example 1.3 into the C. glutamicum
strain DSM12866 by conjugation. Selection is made for targeted
recombination events in the chromosome of C. glutamicum DSM12866 as
described in Example 1.3. Depending on the position of the second
recombination event, after the excision the second copy of the pyc
allele manifests itself in the chromosome at the pck locus, or the
original pck locus of the host remains.
[0293] Approximately 40 to 50 colonies are tested for the phenotype
"growth in the presence of sucrose" and "non-growth in the presence
of kanamycin". Approximately 20 colonies which show the phenotype
"growth in the presence of sucrose" and "non-growth in the presence
of kanamycin" are investigated with the aid of the polymerase chain
reaction. A DNA fragment which carries the pck gene and surrounding
regions is amplified here from the chromosomal DNA of the colonies.
The same primer oligonucleotides as are described in Example 1.5
for the construction of the replacement plasmid are chosen for the
PCR.
TABLE-US-00029 pck_beg (SEQ ID NO: 9): 5' TA(A GAT CT) G CCG GCA
TGA CTT CAG TTT 3' pck_end (SEQ ID NO: 10): 5' AC(A GAT CT) G GTG
GGA GCC TTT CTT GTT ATT 3'
[0294] The primers allow amplification of a DNA fragment approx.
2.9 kb in size in control clones with the original pck locus. In
clones with a second copy of the pyc allele in the chromosome at
the pck locus, DNA fragments with a size of approx. 6.5 kb are
amplified.
[0295] The amplified DNA fragments are identified by means of
electrophoresis in a 0.8% agarose gel.
[0296] A clone which, in addition to the copy of the wild-type gene
present at the pyc locus, has a second copy of the pyc gene in the
form of the pyc allele pycP458S at the pck locus in the chromosome
was identified in this manner. This clone was called strain
DSM12866 pck::pyc.
Example 5
Preparation of Lysine
[0297] The C. glutamicum strains DSM13994glu::lysC,
DSM12866glu::lysC, DSM12866 pck::lysC, DSM12866aecD::lysC,
DSM12866glu::ddh, DSM12866aecD::dapA and DSM12866 pck::pyc obtained
in Example 1, 2, 3 and 4 are cultured in a nutrient medium suitable
for the production of lysine and the lysine content in the culture
supernatant was determined.
[0298] For this, the cultures are first incubated on a brain-heart
agar plate (Merck, Darmstadt, Germany) for 24 hours at 33.degree.
C. Starting from this agar plate culture, a preculture is seeded
(10 ml medium in a 100 ml conical flask). The medium MM is used as
the medium for the preculture. The preculture is incubated for 24
hours at 33.degree. C. at 240 rpm on a shaking machine. A main
culture is seeded from this preculture such that the initial OD
(660 nm) of the main culture is 0.1 OD. The Medium MM is also used
for the main culture.
TABLE-US-00030 Medium MM CSL 5 g/l MOPS 20 g/l Glucose (autoclaved
separately) 50 g/l Salts: (NH.sub.4).sub.2SO.sub.4 25 g/l
KH.sub.2PO.sub.4 0.1 g/l MgSO.sub.4*7 H.sub.2O 1.0 g/l CaCl.sub.2*2
H.sub.2O 10 mg/l FeSO.sub.4*7 H.sub.2O 10 mg/l MnSO.sub.4*H.sub.2O
5.0 mg/l Biotin (sterile-filtered) 0.3 mg/l Thiamine * HCl
(sterile-filtered) 0.2 mg/l CaCO.sub.3 25 g/l
[0299] The CSL (corn steep liquor), MOPS (morpholinopropanesulfonic
acid) and the salt solution are brought to pH 7 with aqueous
ammonia and autoclaved. The sterile substrate and vitamin
solutions, as well as the CaCO.sub.3 autoclaved in the dry state,
are then added.
[0300] Culturing is carried out in a 10 ml volume in a 100 ml
conical flask with baffles. Culturing is carried out at 33.degree.
C. and 80% atmospheric humidity.
[0301] After 48 hours, the OD is determined at a measurement
wavelength of 660 nm with a Biomek 1000 (Beckmann Instruments GmbH,
Munich). The amount of lysine formed is determined with an amino
acid analyzer from Eppendorf-BioTronik (Hamburg, Germany) by ion
exchange chromatography and post-column derivation with ninhydrin
detection.
[0302] The result of the experiment is shown in Table 14.
TABLE-US-00031 TABLE 14 OD Lysine HCl Strain (660 nm) g/l DSM13994
12.0 19.1 DSM13994glu::lysC 9.9 20.0 DSM12866 12.5 14.9 DSM15039
11.4 16.2 DSM12866pck::lysC 12.6 16.5 DSM12866aecD::lysC 12.0 15.9
DSM12866glu::ddh 11.0 15.5 DSM12866aecD::dapA 11.1 16.2
DSM12866pck::pyc 10.9 16.9
Example 6
Integration of a Copy of the lysC_T311I Allele into the Intergenic
Area ncode1 of the Chromosome of the Strain DSM13992
[0303] 6.1 Construction of the Exchange Vector
pK18mobsacBnc1::lysC
[0304] The Corynebacterium glutamicum strain DSM13994 (see example
1) is used as a donor for the chromosomal DNA. Chromosomal DNA is
isolated from the strain DSM13994 with the customary methods
(Eikmanns et al., Microbiology 140: 1817-1828 (1994). With the help
of the polymerase chain reaction (PCR), a DNA fragment which
encompasses an intergenic area of the chromosome labelled as
"ncode1" (SEQ ID NO: 23) is amplified. This area lies within the
positions 27398 to 28707 of the sequence of the Corynebacterium
glutamicum genome, which is accessible under the access code
AX127149 (see table 12). Due to the known sequence of this area,
the following primer oligonucleotides are selected for the PCR:
TABLE-US-00032 Primer ncode_1 (SEQ ID NO: 24): 5' GA(A GAT CT)A AGC
TCT ATT GTC CCC TAC G 3' Primer ncode_2 (SEQ ID NO: 25): 5' GAT CCT
TTT AAA AGC CAG TAA CAA G 3' Primer ncode_3 (SEQ ID NO: 26): 5' CTT
GTT ACT GGC TTT TAA AAG GAT CCT ATT AAA GAA CAC TCC CCT AT 3'
Primer ncode_4 (SEQ ID NO: 27): 5' GA(A GAT CT)C GAC TCT GGC TAA
TTG CTA C 3'
[0305] The primers shown are synthesized by the company MWG Biotech
and the PCR reaction is carried out using the standard PCR method
of Innis et al. (PCR protocols. A guide to methods and
applications, 1990, Academic Press), in which first two products
are amplified with the primer combinations ncode.sub.--1 and
ncode.sub.--2 or ncode.sub.--3 and ncode.sub.--4, which then serve
as a template for the primer combination ncode.sub.--1 and
ncode.sub.--4 together in a second PCR. In this manner, the
selected primers enable the amplification of an approx. 1.2 kb
sized DNA fragment which bears an artificially created interface of
the restriction endonuclease BamHI in the center of the intergenic
area (emphasized by underlining, (SEQ ID NO: 28)). Furthermore, the
primers contain the sequence for the interface of the restriction
endonuclease BglII, which is marked with brackets in the nucleotide
series shown above.
[0306] The amplified DNA fragment of a length of approx. 1.2 kb
which bears the intergenic area ncode1 is identified by means of
electrophoresis in an 0.8% agarose gel and is isolated from the gel
and cleaned using the customary methods (QIAquick Gel Extraction
Kit, Qiagen, Hilden).
[0307] Next, the ligation of the fragment using the Topo TA Cloning
Kit (Invitrogen, Leek, Netherlands, Cat. Number K4600-01) into the
vector pCRII-TOPO takes place. The ligation culture is transformed
into the E. coli strain TOP10 (Invitrogen, Leek, Netherlands). The
selection of plasmid-bearing cells takes place through plating of
the transformation culture onto Kanamycin (50 mg/l)-containing LB
agar with X-Gal (64 mg/l).
[0308] Following isolation of the DNA, the plasmid thus obtained is
verified using restriction splitting and identified in the agarose
gel. The plasmid obtained is called pCRII-TOPOnc.
[0309] The plasmid pCRII-TOPOnc is cut with the restriction enzyme
BglII (Amersham-Pharmacia, Freiburg, Germany), and following
splitting in an agarose gel (0.8%), the approx. 1.2 kb fragment is
isolated out of the agarose gel with the aid of the Qiagenquick Gel
Extraction Kit (Qiagen, Hilden, Germany) and used for ligation with
the mobilizable cloning vector pK18mobsacB described in Schafer et
al. (Gene 14, 69-73 (1994)). This is first split with the
restriction enzyme BamHI and dephosphorylized with alkaline
phosphatase (Alkaline Phosphatase, Boehringer Mannheim), mixed with
the approx. 1.2 kb fragment and the culture is treated with T4-DNA
ligase (Amersham-Pharmacia, Freiburg, Germany).
[0310] Following this, the E. coli strain DH5.alpha. (Grant et al.;
Proceedings of the National Academy of Sciences USA, 87 (1990)
4645-4649) is transformed with the ligation culture (Hanahan, In.
DNA cloning. A practical approach. Vol. 1. ILR-Press, Cold Spring
Harbor, N.Y., 1989). The selection of the plasmid-bearing cells
takes place through plating of the transformation cultures onto LB
agar (Sambrock et al., Molecular Cloning: a laboratory manual.
2.sup.nd Ed. Cold Spring Harbor, N.Y., 1989) which is supplemented
with 25 mg/l Kanamycin.
[0311] Plasmid DNA is isolated from a transformant with the aid of
the QIAprep Spin Miniprep Kit from the company Qiagen and verified
using restriction splitting with the enzyme XbaI and following
agarose gel electrophoresis. The plasmid is called
pK18mobsacBnc.
[0312] The plasmid pCRIITOPOlysC described in example 1 is cut
using the restriction enzyme BamHI (Amersham-Pharmarcia, Freiburg,
Germany). Following splitting in an agarose gel (0.8%) with the aid
of the Qiagenquick Gel Extraction Kit (Qiagen, Hilden, Germany),
the approx. 1.7 kb long, lysC_T311I containing DNA fragment is
isolated out of the agarose gel and used for ligation with the
vector pK18mobsacBnc described above. This is first split with the
restriction enzyme BamHI, dephosphorylized with alkaline
phosphatase (Alkaline Phosphatase, Boehringer Mannheim, Germany),
mixed with the approx. 1.7 kb DNA fragment and the culture is
treated with T4-DNA ligase (Amersham-Pharmacia, Freiburg,
Germany).
[0313] Following this, the E. coli Strain DH5.alpha.mcr (Life
Technologies GmbH, Karlsruhe, Germany) is transformed using the
ligation culture (Hanahan, In. DNA cloning. A practical approach.
Vol. 1. ILR-Press, Cold Spring Harbor, N.Y., 1989). The selection
of the plasmid-bearing cells takes place through plating of the
transformation culture onto LB agar (Sambrock et al., Molecular
Cloning: a laboratory manual. 2.sup.nd Ed. Cold Spring Harbor,
N.Y., 1989), which was supplemented with 25 mg/l Kanamycin.
[0314] Plasmid DNA is isolated from a transformant with the aid of
the QIAprep Spin Miniprep Kit from the company Qiagen isolated and
verified through restriction splitting with the enzymes HindIII and
XbaI and following agarose gel electrophoresis. The plasmid is
called pK18mobsacBnc::lysC. A card of the plasmid is shown in FIG.
7.
6.2 Integration of a Second Copy of the lysC Gene in the Form of
the lysC.sup.FBRm Allele lysC T311I into the Chromosome (Target
Site: the Intergenic Area ncode1) of the Strain DSM13992, using the
Exchange Vector pK18mobsacBnc::lysC
[0315] The vector pK18mobsacBnc::lysC named in example 6.1 is
transferred into the C. glutamicum strain DSM13992 according to a
modified protocol of Schafer et al. (1990 Journal of Microbiology
172: 1663-1666).
[0316] The Corynebacterium glutamicum strain DSM13992 was
manufactured by repeated, undirected mutagenesis, selection and
mutant selection from C. glutamicum ATCC13032. The strain is
resistant to the antibiotic Streptomycin and phenotypically
resistant to the lysine analogon S-(2-Aminoethyl)-L-Cysteine.
However, the strain has a wild-type aspartate kinase which is
sensitive to inhibition by a mixture of lysine and therein (25 mM
each). A pure culture of this strain was filed on Jan. 16, 2001
with the Deutsche Sammlung fur Mikroorganismen und Zellkulturen
[=German Collection of Microorganisms and Cell Cultures](DSMZ,
Braunschweig, Germany) in accordance with the Budapest
Convention.
[0317] The vector pK18mobsacBnc::lysC cannot replicate
independently in DSM13992 and only remains in the cell if it has
integrated into the chromosome through recombination.
[0318] The selection of clones with integrated pK18mobsacBnc::lysC
takes place through plating of the conjugation culture onto LB agar
(Sambrook et al., Molecular Cloning: A Laboratory Manual. 2.sup.nd
Ed., Cold Spring Harbor, N.Y., 1989) which was supplemented with 15
mg/l Kanamycin and 50 mg/l nalidixin acid. Clones that have begun
to grow are plated onto LB agar plates with 25 mg/l Kanamycin and
incubated for 16 hours at 33.degree. C. To bring about the excision
of the plasmid through a second recombination event, the clones are
started with 10% sucrose after the 16-hour incubation in the LB
liquid medium. The plasmid pK18mobsacB contains a copy of the sacB
gene, which changes sucrose into levan, which in turn is toxic to
C. glutamicum.
[0319] Consequently, only clones in which the integrated
pK18mobsacBnc::lysC has excised again grow on LB agar with sucrose.
In dependency from the position of the second recombination event,
during excision, either the copy of the lysC with the surrounding
intergenic area ncode1 will excise together with the plasmid, or
only the intergenic area ncode1 will excise.
[0320] In order to prove that the copy of lysC has remained in the
intergenic area ncode1 of the chromosome, approximately 20 colonies
which show the phenotype "Growth in the Presence of Sucrose" and
"Non-Growth in the Presence of Kanamycin" according to the standard
PCR method of Innis et al. (PCR Protocols. A Guide to Methods and
Applications, 1990, Academic Press) are researched with the aid of
the polymerase chain reaction. In this, a DNA fragment from the
chromosomal colonies of the DNA which carries the lysC gene as well
as the surrounding areas is amplified. The following primer
oligonucleotides are selected for the PCR.
TABLE-US-00033 3371V (SEQ ID NO: 29): 5' TAT CAT GCG GTG AGC TGT GA
3' 3372N (SEQ ID NO: 30): 5' TAG GGG TGA TGT GCT ACT GT 3'
[0321] In control clones with the original ncode1 location, the
primers enable the amplification of an approx. 1.3 kb sized DNA
fragment. In clones with a copy of the lysC gene in the intergenic
area ncode1 of the chromosome, DNA fragments with a size of approx.
3.0 kb are amplified.
[0322] The amplified DNA fragments are identified using
electrophoresis in an 0.8% agarose gel.
[0323] In this manner, a clone was identified which in addition to
the copy existing in the lysC location, has a second copy of the
lysC.sup.FBR allele lysC T311I in the intergenic area ncode1 in the
chromosome. This clone was named as the strain
DSM13992nc::lysC.
BRIEF DESCRIPTION OF THE FIGURES
[0324] The base pair numbers stated are approximate values obtained
in the context of reproducibility of measurements.
[0325] FIG. 1: Map of the plasmid pK18mobsacBglu1.sub.--1.
[0326] The abbreviations and designations used have the following
meaning: [0327] KanR: Kanamycin resistance gene [0328] HindIII:
Cleavage site of the restriction enzyme HindIII [0329] BamHI:
Cleavage site of the restriction enzyme BamHI [0330] lysC:
lysC.sup.FBR allele, lysC T311I [0331] 'gluA: 3' terminal fragment
of the gluA gene [0332] gluB': 5' terminal fragment of the gluB
gene [0333] 'gluB: 3' terminal fragment of the gluB gene [0334]
gluC': 5' terminal fragment of the gluC gene [0335] sacB: sacB gene
[0336] RP4mob: mob region with the replication origin for the
transfer (oriT) [0337] oriV: Replication origin V
[0338] FIG. 2: Map of the plasmid pK18mobsacBaecD1.sub.--1.
[0339] The abbreviations and designations used have the following
meaning: [0340] KanR: Kanamycin resistance gene [0341] SalI:
Cleavage site of the restriction enzyme SalI [0342] lysC:
lysC.sup.FBR allele, lysC T311I [0343] aecD': 5' terminal fragment
of the aecD gene [0344] 'aecD: 3' terminal fragment of the aecD
gene [0345] sacB: sacB gene [0346] RP4mob: mob region with the
replication origin for the transfer (oriT) [0347] oriV: Replication
origin V
[0348] FIG. 3: Map of the plasmid pK18mobsacBpck1.sub.--1.
[0349] The abbreviations and designations used have the following
meaning: [0350] KanR: Kanamycin resistance gene [0351] BamHI:
Cleavage site of the restriction enzyme BamHI [0352] lysC:
lysC.sup.FBR allele, lysC T311I [0353] pck': 5' terminal fragment
of the pck gene [0354] 'pck: 3' terminal fragment of the pck gene
[0355] sacB: sacB gene [0356] RP4mob: mob region with the
replication origin for the transfer (oriT) [0357] oriV: Replication
origin V
[0358] FIG. 4: Map of the plasmid pK18mobsacBgluB2.sub.--1.
[0359] The abbreviations and designations used have the following
meaning: [0360] KanR. Kanamycin resistance gene [0361] SalI
Cleavage site of the restriction enzyme SalI [0362] EcoRI Cleavage
site of the restriction enzyme EcoRI [0363] BamHI: Cleavage site of
the restriction enzyme BamHI [0364] ddh: ddh gene [0365] gluA gluA
gene [0366] gluB': 5' terminal fragment of the gluB gene [0367]
'gluB: 3' terminal fragment of the gluB gene [0368] gluC gluC gene
[0369] gluD': 5' terminal fragment of the gluD gene [0370] sacB:
sacB gene [0371] RP4mob: mob region with the replication origin for
the transfer (oriT) [0372] oriV: Replication origin V
[0373] FIG. 5: Map of the plasmid pK18mobsacBaecD2.sub.--1.
[0374] The abbreviations and designations used have the following
meaning: [0375] KanR: Kanamycin resistance gene [0376] EcoRI
Cleavage site of the restriction enzyme EcoRI [0377] SalI: Cleavage
site of the restriction enzyme SalI [0378] dapA: dapA gene [0379]
aecD': 5' terminal fragment of the aecD gene [0380] 'aecD: 3'
terminal fragment of the aecD gene [0381] sacB: sacB gene [0382]
RP4mob: mob region with the replication origin for the transfer
(oriT) [0383] oriV: Replication origin V
[0384] FIG. 6: Map of the plasmid pK18mobsacBpck1.sub.--3.
[0385] The abbreviations and designations used have the following
meaning: [0386] KanR: Kanamycin resistance gene [0387] pyc: pyc
allele, pyc P458S [0388] pck': 5' terminal fragment of the pck gene
[0389] 'pck: 3' terminal fragment of the pck gene [0390] sacB: sacB
gene [0391] RP4mob: mob region with the replication origin for the
transfer (oriT) [0392] oriV: Replication origin V
[0393] FIG. 7: Map of the plasmid pK18mobsacBnc::lysC
[0394] The abbreviations and designations used have the following
meaning: [0395] KanR: Kanamycin resistance gene [0396] BamHI:
Cleavage site of the restriction enzyme BamHI [0397] HindIII
Cleavage site of the restriction enzyme HindIII [0398] XbaI
Cleavage site of the restriction enzyme XbaI [0399] lysC:
lysC.sup.FBR allele, lysC T311I [0400] sacB: sacB gene [0401]
RP4mob: mob region with the replication origin for the transfer
(oriT) [0402] oriV: Replication origin V
Sequence CWU 1
1
3011263DNACorynebacterium glutamicumCDS(1)..(1263)lysC wild-type
gene 1gtg gcc ctg gtc gta cag aaa tat ggc ggt tcc tcg ctt gag agt
gcg 48Met Ala Leu Val Val Gln Lys Tyr Gly Gly Ser Ser Leu Glu Ser
Ala1 5 10 15gaa cgc att aga aac gtc gct gaa cgg atc gtt gcc acc aag
aag gct 96Glu Arg Ile Arg Asn Val Ala Glu Arg Ile Val Ala Thr Lys
Lys Ala 20 25 30gga aat gat gtc gtg gtt gtc tgc tcc gca atg gga gac
acc acg gat 144Gly Asn Asp Val Val Val Val Cys Ser Ala Met Gly Asp
Thr Thr Asp 35 40 45gaa ctt cta gaa ctt gca gcg gca gtg aat ccc gtt
ccg cca gct cgt 192Glu Leu Leu Glu Leu Ala Ala Ala Val Asn Pro Val
Pro Pro Ala Arg 50 55 60gaa atg gat atg ctc ctg act gct ggt gag cgt
att tct aac gct ctc 240Glu Met Asp Met Leu Leu Thr Ala Gly Glu Arg
Ile Ser Asn Ala Leu65 70 75 80gtc gcc atg gct att gag tcc ctt ggc
gca gaa gcc caa tct ttc acg 288Val Ala Met Ala Ile Glu Ser Leu Gly
Ala Glu Ala Gln Ser Phe Thr 85 90 95ggc tct cag gct ggt gtg ctc acc
acc gag cgc cac gga aac gca cgc 336Gly Ser Gln Ala Gly Val Leu Thr
Thr Glu Arg His Gly Asn Ala Arg 100 105 110att gtt gat gtc act cca
ggt cgt gtg cgt gaa gca ctc gat gag ggc 384Ile Val Asp Val Thr Pro
Gly Arg Val Arg Glu Ala Leu Asp Glu Gly 115 120 125aag atc tgc att
gtt gct ggt ttc cag ggt gtt aat aaa gaa acc cgc 432Lys Ile Cys Ile
Val Ala Gly Phe Gln Gly Val Asn Lys Glu Thr Arg 130 135 140gat gtc
acc acg ttg ggt cgt ggt ggt tct gac acc act gca gtt gcg 480Asp Val
Thr Thr Leu Gly Arg Gly Gly Ser Asp Thr Thr Ala Val Ala145 150 155
160ttg gca gct gct ttg aac gct gat gtg tgt gag att tac tcg gac gtt
528Leu Ala Ala Ala Leu Asn Ala Asp Val Cys Glu Ile Tyr Ser Asp Val
165 170 175gac ggt gtg tat acc gct gac ccg cgc atc gtt cct aat gca
cag aag 576Asp Gly Val Tyr Thr Ala Asp Pro Arg Ile Val Pro Asn Ala
Gln Lys 180 185 190ctg gaa aag ctc agc ttc gaa gaa atg ctg gaa ctt
gct gct gtt ggc 624Leu Glu Lys Leu Ser Phe Glu Glu Met Leu Glu Leu
Ala Ala Val Gly 195 200 205tcc aag att ttg gtg ctg cgc agt gtt gaa
tac gct cgt gca ttc aat 672Ser Lys Ile Leu Val Leu Arg Ser Val Glu
Tyr Ala Arg Ala Phe Asn 210 215 220gtg cca ctt cgc gta cgc tcg tct
tat agt aat gat ccc ggc act ttg 720Val Pro Leu Arg Val Arg Ser Ser
Tyr Ser Asn Asp Pro Gly Thr Leu225 230 235 240att gcc ggc tct atg
gag gat att cct gtg gaa gaa gca gtc ctt acc 768Ile Ala Gly Ser Met
Glu Asp Ile Pro Val Glu Glu Ala Val Leu Thr 245 250 255ggt gtc gca
acc gac aag tcc gaa gcc aaa gta acc gtt ctg ggt att 816Gly Val Ala
Thr Asp Lys Ser Glu Ala Lys Val Thr Val Leu Gly Ile 260 265 270tcc
gat aag cca ggc gag gct gcg aag gtt ttc cgt gcg ttg gct gat 864Ser
Asp Lys Pro Gly Glu Ala Ala Lys Val Phe Arg Ala Leu Ala Asp 275 280
285gca gaa atc aac att gac atg gtt ctg cag aac gtc tct tct gta gaa
912Ala Glu Ile Asn Ile Asp Met Val Leu Gln Asn Val Ser Ser Val Glu
290 295 300gac ggc acc acc gac atc acc ttc acc tgc cct cgt tcc gac
ggc cgc 960Asp Gly Thr Thr Asp Ile Thr Phe Thr Cys Pro Arg Ser Asp
Gly Arg305 310 315 320cgc gcg atg gag atc ttg aag aag ctt cag gtt
cag ggc aac tgg acc 1008Arg Ala Met Glu Ile Leu Lys Lys Leu Gln Val
Gln Gly Asn Trp Thr 325 330 335aat gtg ctt tac gac gac cag gtc ggc
aaa gtc tcc ctc gtg ggt gct 1056Asn Val Leu Tyr Asp Asp Gln Val Gly
Lys Val Ser Leu Val Gly Ala 340 345 350ggc atg aag tct cac cca ggt
gtt acc gca gag ttc atg gaa gct ctg 1104Gly Met Lys Ser His Pro Gly
Val Thr Ala Glu Phe Met Glu Ala Leu 355 360 365cgc gat gtc aac gtg
aac atc gaa ttg att tcc acc tct gag att cgt 1152Arg Asp Val Asn Val
Asn Ile Glu Leu Ile Ser Thr Ser Glu Ile Arg 370 375 380att tcc gtg
ctg atc cgt gaa gat gat ctg gat gct gct gca cgt gca 1200Ile Ser Val
Leu Ile Arg Glu Asp Asp Leu Asp Ala Ala Ala Arg Ala385 390 395
400ttg cat gag cag ttc cag ctg ggc ggc gaa gac gaa gcc gtc gtt tat
1248Leu His Glu Gln Phe Gln Leu Gly Gly Glu Asp Glu Ala Val Val Tyr
405 410 415gca ggc acc gga cgc 1263Ala Gly Thr Gly Arg
4202421PRTCorynebacterium glutamicum 2Met Ala Leu Val Val Gln Lys
Tyr Gly Gly Ser Ser Leu Glu Ser Ala1 5 10 15Glu Arg Ile Arg Asn Val
Ala Glu Arg Ile Val Ala Thr Lys Lys Ala 20 25 30Gly Asn Asp Val Val
Val Val Cys Ser Ala Met Gly Asp Thr Thr Asp 35 40 45Glu Leu Leu Glu
Leu Ala Ala Ala Val Asn Pro Val Pro Pro Ala Arg 50 55 60Glu Met Asp
Met Leu Leu Thr Ala Gly Glu Arg Ile Ser Asn Ala Leu65 70 75 80Val
Ala Met Ala Ile Glu Ser Leu Gly Ala Glu Ala Gln Ser Phe Thr 85 90
95Gly Ser Gln Ala Gly Val Leu Thr Thr Glu Arg His Gly Asn Ala Arg
100 105 110Ile Val Asp Val Thr Pro Gly Arg Val Arg Glu Ala Leu Asp
Glu Gly 115 120 125Lys Ile Cys Ile Val Ala Gly Phe Gln Gly Val Asn
Lys Glu Thr Arg 130 135 140Asp Val Thr Thr Leu Gly Arg Gly Gly Ser
Asp Thr Thr Ala Val Ala145 150 155 160Leu Ala Ala Ala Leu Asn Ala
Asp Val Cys Glu Ile Tyr Ser Asp Val 165 170 175Asp Gly Val Tyr Thr
Ala Asp Pro Arg Ile Val Pro Asn Ala Gln Lys 180 185 190Leu Glu Lys
Leu Ser Phe Glu Glu Met Leu Glu Leu Ala Ala Val Gly 195 200 205Ser
Lys Ile Leu Val Leu Arg Ser Val Glu Tyr Ala Arg Ala Phe Asn 210 215
220Val Pro Leu Arg Val Arg Ser Ser Tyr Ser Asn Asp Pro Gly Thr
Leu225 230 235 240Ile Ala Gly Ser Met Glu Asp Ile Pro Val Glu Glu
Ala Val Leu Thr 245 250 255Gly Val Ala Thr Asp Lys Ser Glu Ala Lys
Val Thr Val Leu Gly Ile 260 265 270Ser Asp Lys Pro Gly Glu Ala Ala
Lys Val Phe Arg Ala Leu Ala Asp 275 280 285Ala Glu Ile Asn Ile Asp
Met Val Leu Gln Asn Val Ser Ser Val Glu 290 295 300Asp Gly Thr Thr
Asp Ile Thr Phe Thr Cys Pro Arg Ser Asp Gly Arg305 310 315 320Arg
Ala Met Glu Ile Leu Lys Lys Leu Gln Val Gln Gly Asn Trp Thr 325 330
335Asn Val Leu Tyr Asp Asp Gln Val Gly Lys Val Ser Leu Val Gly Ala
340 345 350Gly Met Lys Ser His Pro Gly Val Thr Ala Glu Phe Met Glu
Ala Leu 355 360 365Arg Asp Val Asn Val Asn Ile Glu Leu Ile Ser Thr
Ser Glu Ile Arg 370 375 380Ile Ser Val Leu Ile Arg Glu Asp Asp Leu
Asp Ala Ala Ala Arg Ala385 390 395 400Leu His Glu Gln Phe Gln Leu
Gly Gly Glu Asp Glu Ala Val Val Tyr 405 410 415Ala Gly Thr Gly Arg
42031263DNACorynebacterium glutamicumCDS(1)..(1263)lysC-fbr allele
lysC T311I 3gtg gcc ctg gtc gta cag aaa tat ggc ggt tcc tcg ctt gag
agt gcg 48Met Ala Leu Val Val Gln Lys Tyr Gly Gly Ser Ser Leu Glu
Ser Ala1 5 10 15gaa cgc att aga aac gtc gct gaa cgg atc gtt gcc acc
aag aag gct 96Glu Arg Ile Arg Asn Val Ala Glu Arg Ile Val Ala Thr
Lys Lys Ala 20 25 30gga aat gat gtc gtg gtt gtc tgc tcc gca atg gga
gac acc acg gat 144Gly Asn Asp Val Val Val Val Cys Ser Ala Met Gly
Asp Thr Thr Asp 35 40 45gaa ctt cta gaa ctt gca gcg gca gtg aat ccc
gtt ccg cca gct cgt 192Glu Leu Leu Glu Leu Ala Ala Ala Val Asn Pro
Val Pro Pro Ala Arg 50 55 60gaa atg gat atg ctc ctg act gct ggt gag
cgt att tct aac gct ctc 240Glu Met Asp Met Leu Leu Thr Ala Gly Glu
Arg Ile Ser Asn Ala Leu65 70 75 80gtc gcc atg gct att gag tcc ctt
ggc gca gaa gcc caa tct ttc acg 288Val Ala Met Ala Ile Glu Ser Leu
Gly Ala Glu Ala Gln Ser Phe Thr 85 90 95ggc tct cag gct ggt gtg ctc
acc acc gag cgc cac gga aac gca cgc 336Gly Ser Gln Ala Gly Val Leu
Thr Thr Glu Arg His Gly Asn Ala Arg 100 105 110att gtt gat gtc act
cca ggt cgt gtg cgt gaa gca ctc gat gag ggc 384Ile Val Asp Val Thr
Pro Gly Arg Val Arg Glu Ala Leu Asp Glu Gly 115 120 125aag atc tgc
att gtt gct ggt ttc cag ggt gtt aat aaa gaa acc cgc 432Lys Ile Cys
Ile Val Ala Gly Phe Gln Gly Val Asn Lys Glu Thr Arg 130 135 140gat
gtc acc acg ttg ggt cgt ggt ggt tct gac acc act gca gtt gcg 480Asp
Val Thr Thr Leu Gly Arg Gly Gly Ser Asp Thr Thr Ala Val Ala145 150
155 160ttg gca gct gct ttg aac gct gat gtg tgt gag att tac tcg gac
gtt 528Leu Ala Ala Ala Leu Asn Ala Asp Val Cys Glu Ile Tyr Ser Asp
Val 165 170 175gac ggt gtg tat acc gct gac ccg cgc atc gtt cct aat
gca cag aag 576Asp Gly Val Tyr Thr Ala Asp Pro Arg Ile Val Pro Asn
Ala Gln Lys 180 185 190ctg gaa aag ctc agc ttc gaa gaa atg ctg gaa
ctt gct gct gtt ggc 624Leu Glu Lys Leu Ser Phe Glu Glu Met Leu Glu
Leu Ala Ala Val Gly 195 200 205tcc aag att ttg gtg ctg cgc agt gtt
gaa tac gct cgt gca ttc aat 672Ser Lys Ile Leu Val Leu Arg Ser Val
Glu Tyr Ala Arg Ala Phe Asn 210 215 220gtg cca ctt cgc gta cgc tcg
tct tat agt aat gat ccc ggc act ttg 720Val Pro Leu Arg Val Arg Ser
Ser Tyr Ser Asn Asp Pro Gly Thr Leu225 230 235 240att gcc ggc tct
atg gag gat att cct gtg gaa gaa gca gtc ctt acc 768Ile Ala Gly Ser
Met Glu Asp Ile Pro Val Glu Glu Ala Val Leu Thr 245 250 255ggt gtc
gca acc gac aag tcc gaa gcc aaa gta acc gtt ctg ggt att 816Gly Val
Ala Thr Asp Lys Ser Glu Ala Lys Val Thr Val Leu Gly Ile 260 265
270tcc gat aag cca ggc gag gct gcg aag gtt ttc cgt gcg ttg gct gat
864Ser Asp Lys Pro Gly Glu Ala Ala Lys Val Phe Arg Ala Leu Ala Asp
275 280 285gca gaa atc aac att gac atg gtt ctg cag aac gtc tct tct
gta gaa 912Ala Glu Ile Asn Ile Asp Met Val Leu Gln Asn Val Ser Ser
Val Glu 290 295 300gac ggc acc acc gac atc atc ttc acc tgc cct cgt
tcc gac ggc cgc 960Asp Gly Thr Thr Asp Ile Ile Phe Thr Cys Pro Arg
Ser Asp Gly Arg305 310 315 320cgc gcg atg gag atc ttg aag aag ctt
cag gtt cag ggc aac tgg acc 1008Arg Ala Met Glu Ile Leu Lys Lys Leu
Gln Val Gln Gly Asn Trp Thr 325 330 335aat gtg ctt tac gac gac cag
gtc ggc aaa gtc tcc ctc gtg ggt gct 1056Asn Val Leu Tyr Asp Asp Gln
Val Gly Lys Val Ser Leu Val Gly Ala 340 345 350ggc atg aag tct cac
cca ggt gtt acc gca gag ttc atg gaa gct ctg 1104Gly Met Lys Ser His
Pro Gly Val Thr Ala Glu Phe Met Glu Ala Leu 355 360 365cgc gat gtc
aac gtg aac atc gaa ttg att tcc acc tct gag att cgt 1152Arg Asp Val
Asn Val Asn Ile Glu Leu Ile Ser Thr Ser Glu Ile Arg 370 375 380att
tcc gtg ctg atc cgt gaa gat gat ctg gat gct gct gca cgt gca 1200Ile
Ser Val Leu Ile Arg Glu Asp Asp Leu Asp Ala Ala Ala Arg Ala385 390
395 400ttg cat gag cag ttc cag ctg ggc ggc gaa gac gaa gcc gtc gtt
tat 1248Leu His Glu Gln Phe Gln Leu Gly Gly Glu Asp Glu Ala Val Val
Tyr 405 410 415gca ggc acc gga cgc 1263Ala Gly Thr Gly Arg
4204421PRTCorynebacterium glutamicum 4Met Ala Leu Val Val Gln Lys
Tyr Gly Gly Ser Ser Leu Glu Ser Ala1 5 10 15Glu Arg Ile Arg Asn Val
Ala Glu Arg Ile Val Ala Thr Lys Lys Ala 20 25 30Gly Asn Asp Val Val
Val Val Cys Ser Ala Met Gly Asp Thr Thr Asp 35 40 45Glu Leu Leu Glu
Leu Ala Ala Ala Val Asn Pro Val Pro Pro Ala Arg 50 55 60Glu Met Asp
Met Leu Leu Thr Ala Gly Glu Arg Ile Ser Asn Ala Leu65 70 75 80Val
Ala Met Ala Ile Glu Ser Leu Gly Ala Glu Ala Gln Ser Phe Thr 85 90
95Gly Ser Gln Ala Gly Val Leu Thr Thr Glu Arg His Gly Asn Ala Arg
100 105 110Ile Val Asp Val Thr Pro Gly Arg Val Arg Glu Ala Leu Asp
Glu Gly 115 120 125Lys Ile Cys Ile Val Ala Gly Phe Gln Gly Val Asn
Lys Glu Thr Arg 130 135 140Asp Val Thr Thr Leu Gly Arg Gly Gly Ser
Asp Thr Thr Ala Val Ala145 150 155 160Leu Ala Ala Ala Leu Asn Ala
Asp Val Cys Glu Ile Tyr Ser Asp Val 165 170 175Asp Gly Val Tyr Thr
Ala Asp Pro Arg Ile Val Pro Asn Ala Gln Lys 180 185 190Leu Glu Lys
Leu Ser Phe Glu Glu Met Leu Glu Leu Ala Ala Val Gly 195 200 205Ser
Lys Ile Leu Val Leu Arg Ser Val Glu Tyr Ala Arg Ala Phe Asn 210 215
220Val Pro Leu Arg Val Arg Ser Ser Tyr Ser Asn Asp Pro Gly Thr
Leu225 230 235 240Ile Ala Gly Ser Met Glu Asp Ile Pro Val Glu Glu
Ala Val Leu Thr 245 250 255Gly Val Ala Thr Asp Lys Ser Glu Ala Lys
Val Thr Val Leu Gly Ile 260 265 270Ser Asp Lys Pro Gly Glu Ala Ala
Lys Val Phe Arg Ala Leu Ala Asp 275 280 285Ala Glu Ile Asn Ile Asp
Met Val Leu Gln Asn Val Ser Ser Val Glu 290 295 300Asp Gly Thr Thr
Asp Ile Ile Phe Thr Cys Pro Arg Ser Asp Gly Arg305 310 315 320Arg
Ala Met Glu Ile Leu Lys Lys Leu Gln Val Gln Gly Asn Trp Thr 325 330
335Asn Val Leu Tyr Asp Asp Gln Val Gly Lys Val Ser Leu Val Gly Ala
340 345 350Gly Met Lys Ser His Pro Gly Val Thr Ala Glu Phe Met Glu
Ala Leu 355 360 365Arg Asp Val Asn Val Asn Ile Glu Leu Ile Ser Thr
Ser Glu Ile Arg 370 375 380Ile Ser Val Leu Ile Arg Glu Asp Asp Leu
Asp Ala Ala Ala Arg Ala385 390 395 400Leu His Glu Gln Phe Gln Leu
Gly Gly Glu Asp Glu Ala Val Val Tyr 405 410 415Ala Gly Thr Gly Arg
420528DNAArtificial sequencemisc_feature(1)..(28)Primer lysC1beg
5taggatcctc cggtgtctga ccacggtg 28629DNAArtificial
sequencemisc_feature(1)..(29)Primer lysC2end 6acggatccgc tgggaaattg
cgctcttcc 29728DNAArtificial sequencemisc_feature(1)..(28)Primer
gluBgl1 7taagatctgt gttggacgtc atggcaag 28828DNAArtificial
sequencemisc_feature(1)..(28)Primer gluBgl2 8acagatcttg aagccaagta
cggccaag 28927DNAArtificial sequencemisc_feature(1)..(27)Primer
pck_beg 9taagatctgc cggcatgact tcagttt 271030DNAArtificial
sequencemisc_feature(1)..(30)Primer pck_end 10acagatctgg tgggagcctt
tcttgttatt 301120DNACorynebacterium
glutamicummisc_feature(1)..(20)Primer aecD_beg 11gaacttacgc
caagctgttc 201220DNACorynebacterium
glutamicummisc_feature(1)..(20)Primer aecD_end 12agcaccacaa
tcaacgtgag 201320DNACorynebacterium
glutamicummisc_feature(1)..(20)Primer gluA_beg 13cacggttgct
cattgtatcc 201420DNACorynebacterium
glutamicummisc_feature(1)..(20)Primer gluD_end 14cgaggcgaat
cagacttctt 201520DNACorynebacterium
glutamicummisc_feature(1)..(20)Primer ddh_beg 15ctgaatcaaa
ggcggacatg 201620DNACorynebacterium
glutamicummisc_feature(1)..(20)Primer ddh_end 16tcgagctaaa
ttagacgtcg
201720DNACorynebacterium glutamicummisc_feature(1)..(20)Primer
dapA_beg 17cgagccagtg aacatgcaga 201820DNACorynebacterium
glutamicummisc_feature(1)..(20)Primer dapA_end 18cttgagcacc
ttgcgcagca 201928DNAArtificial sequencemisc_feature(1)..(28)Primer
pyc_beg 19tcacgcgtct tgaagtcgtg caggtcag 282028DNAArtificial
sequencemisc_feature(1)..(28)Primer pyc_end 20tcacgcgtcg cctcctccat
gaggaaga 282139DNACorynebacterium
glutamicummisc_feature(1)..(39)Primer P458S-1 21ggattcattg
ccgatcactc gcacctcctt caggctcca 392239DNACorynebacterium
glutamicummisc_feature(1)..(39)Primer P458S-2 22gtggaggaag
tccgaggtcg agtgatcggc aatgaatcc 39231310DNACorynebacterium
glutamicummisc_feature(1)..(1310)Intergenic region ncode1
23aagctctatt gtcccctacg tgctcgtttc tggcctttta gtaagcacca ggaataagcg
60ccgatgaaga cacaatcata ccgacaatta atcgtgccga tatgagctct taaaagacag
120cataaaacga gtttttcaaa agcctattaa gtgtcaatta cgacgtgcat
taatagatac 180tcaatcacct taaattgttg acacactcca ctaaaacagg
tctattaaaa gacaattgaa 240ttacgcccta gtagtacttg tttcaggcca
ccacttagaa ggcttttaag tatccactat 300gtatcaatta tctagaacct
ttagtgactt tgaaacggca gtactctatt ggctcttaat 360ggtcaattac
ataacaatta tattgagcct ttgaaacaac tcactctgct gcatattaaa
420aggtcgatta actaacgatt gaattgatcc ttaaaaagcc tttatctatc
gcattatgaa 480taaatattta atcgaccttt aatagtgacc taaaagcctt
ttaaaagcca acgcattcag 540tgacttttaa aaggctatta agtgtcaatt
gaattgcctt gttactggct tttaaaaggc 600tattaaagaa cactccccta
ttgtctttta atcgtcactt aatcgacctc taaaaggtaa 660ctaattgact
cttgagtgac acatatttaa ttgaccttta agtaacgatt ataaggcaat
720taatgtgacc aaataaagac acgtaactga ctaatcttta tctgactatt
acaaggcttt 780aaaagagcac ttatgtgtcg attaagtgtc tacgcaataa
ctgtgcttta agaggcttta 840aaaactacaa ttgaatcgac cactaatcgt
tacttaaatg actattaaca aaagtcactt 900ttagagcacc gcaaaagcct
tttaatggtc acgcaataag cctttaagta acaattaaat 960aagtggcttt
aaaatcacta ctgcagcacg attgaaaggt aattagcggt cgattaagtg
1020tcaattaatt aatagtgatt caaaatctca ttaaagcgca attcaattga
cagctaataa 1080gcccttaagt aacaaatact ttatccgtac tttaagggca
cgctaaaagc cttttaatcg 1140acatctaatt gtcataacgc ttcgatgcgc
ccatgggaat acacttagcg gtcgattaaa 1200tggatactaa gtagcaatta
gccagagtcg cgtgacagag ttgtggcgca cagtagcaca 1260tcacccctac
ccccgtgcat ctcttaatta gcactaaaac aacatttatc 13102428DNAArtificial
SequencePrimer 24gaagatctaa gctctattgt cccctacg 282525DNAArtificial
SequencePrimer 25gatcctttta aaagccagta acaag 252647DNAArtificial
SequencePrimer 26cttgttactg gcttttaaaa ggatcctatt aaagaacact
cccctat 472728DNAArtificial SequencePrimer 27gaagatctcg actctggcta
attgctac 28281249DNAArtificial SequencePCR-Produkt 28gaagatctaa
gctctattgt cccctacgtg ctcgtttctg gccttttagt aagcaccagg 60aataagcgcc
gatgaagaca caatcatacc gacaattaat cgtgccgata tgagctctta
120aaagacagca taaaacgagt ttttcaaaag cctattaagt gtcaattacg
acgtgcatta 180atagatactc aatcacctta aattgttgac acactccact
aaaacaggtc tattaaaaga 240caattgaatt acgccctagt agtacttgtt
tcaggccacc acttagaagg cttttaagta 300tccactatgt atcaattatc
tagaaccttt agtgactttg aaacggcagt actctattgg 360ctcttaatgg
tcaattacat aacaattata ttgagccttt gaaacaactc actctgctgc
420atattaaaag gtcgattaac taacgattga attgatcctt aaaaagcctt
tatctatcgc 480attatgaata aatatttaat cgacctttaa tagtgaccta
aaagcctttt aaaagccaac 540gcattcagtg acttttaaaa ggctattaag
tgtcaattga attgccttgt tactggcttt 600taaaaggatc ctattaaaga
acactcccct attgtctttt aatcgtcact taatcgacct 660ctaaaaggta
actaattgac tcttgagtga cacatattta attgaccttt aagtaacgat
720tataaggcaa ttaatgtgac caaataaaga cacgtaactg actaatcttt
atctgactat 780tacaaggctt taaaagagca cttatgtgtc gattaagtgt
ctacgcaata actgtgcttt 840aagaggcttt aaaaactaca attgaatcga
ccactaatcg ttacttaaat gactattaac 900aaaagtcact tttagagcac
cgcaaaagcc ttttaatggt cacgcaataa gcctttaagt 960aacaattaaa
taagtggctt taaaatcact actgcagcac gattgaaagg taattagcgg
1020tcgattaagt gtcaattaat taatagtgat tcaaaatctc attaaagcgc
aattcaattg 1080acagctaata agcccttaag taacaaatac tttatccgta
ctttaagggc acgctaaaag 1140ccttttaatc gacatctaat tgtcataacg
cttcgatgcg cccatgggaa tacacttagc 1200ggtcgattaa atggatacta
agtagcaatt agccagagtc gagatctag 12492920DNAArtificial
SequencePrimer 29tatcatgcgg tgagctgtga 203020DNAArtificial
SequencePrimer 30taggggtgat gtgctactgt 20
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