Genome-wide analysis of the L-methionine biosynthetic pathway in Corynebacterium glutamicum by targeted gene deletion and homologous complementation

Journal of Biotechnology

Volumn 104, Issue 1-3, 2003, Pages 213-228

  Ruckert C ^a   Puhler A ^a   Kalinowski, J ^a  

^a BIELEFELD UNIVERSITY   (Germany)

Author keywords

Corynebacterium glutamicum; Genome analysis; met genes; Methionine biosynthesis

Indexed keywords

AMINO ACIDS; BACTERIA; BIOSYNTHESIS; CATALYSIS;

GENE DELETION;

GENETIC ENGINEERING;

5 METHYLTETRAHYDROFOLIC ACID; AMINO ACID; HOMOCYSTEINE; HOMOSERINE; HOMOSERINE ACETYLTRANSFERASE; METHIONINE;

AMINO ACID SEQUENCE; AMINO ACID SYNTHESIS; ARTICLE; BACTERIAL GENE; BIOSYNTHESIS; CATALYSIS; CORYNEBACTERIUM GLUTAMICUM; GENE DELETION; GENE TARGETING; GENETIC COMPLEMENTATION; GENOME ANALYSIS; GRAM POSITIVE BACTERIUM; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PRIORITY JOURNAL; SOIL MICROFLORA;

BACTERIA (MICROORGANISMS); CORYNEBACTERIUM; CORYNEBACTERIUM GLUTAMICUM; POSIBACTERIA;

EID: 0041387671     PISSN: 01681656     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0168-1656(03)00158-5     Document Type: Article

References (49)

1. Alaminos M., Ramos J.L. The methionine biosynthetic pathway from homoserine in Pseudomonas putida involves the metW, metX, metZ, metH and metE gene products. Arch. Microbiol. 176:(1-2):2001;151-154.
2. Altschul S.F., Madden T.L., Schäffer A.A., Zhang J., Zhang Z., Miller W., Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:(17):1997;3389-3402.
3. Amador E., Castro J.M., Correia A., Martín J.F. Structure and organization of the rrnD operon of 'Brevibacterium lactofermentum': analysis of the 16S rRNA gene. Microbiology. 145:(4):1999;915-924.
4. Archer J.A.C., Solow-Cordero D.E., Sinskey A.J. A C-terminal deletion in Corynebacterium glutamicum homoserine dehydrogenase abolishes allosteric inhibition by L-threonine. Gene. 107:1991;53-59.
5. Bairoch, A., Apweiler, R. The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res. 28 (1) (2000) 45-48. Available from: http://us.expasy.org/sprot .
6. Benson, D.A, Karsch-Mizrachi, T., David J., Lipman, D.J., Ostell, J., Rapp, B.A., Wheeler, D.L. GenBank. Nucleic Acids Res. 28 (1) (2000) 15-18. Available from: http://www.ncbi.nlm,nih.gov/Genbank/index.html .
7. Bentley S.D., Chater K.F., Cerdeno-Tarraga A.M., Challis G.L., Thomson N.R., James K.D., Harris D.E., Quail M.A., Kieser H., Harper D., Bateman A., Brown S., Chandra G., Chen C.W., Collins M., Cronin A., Fraser A., Goble A., Hidalgo J., Hornsby T., Howarth S., Huang C.H., Kieser T., Larke L., Murphy L., Oliver K., O'Neil S., Rabbinowitsch E., Rajandream M.A., Rutherford K., Rutter S., Seeger K., Saunders D., Sharp S., Squares R., Squares S., Taylor K., Warren T., Wietzorrek A., Woodward J., Barrell B.C., Parkhill J., Hopwood D.A. Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2). Nature. 417:(6885):2002;141-147.
8. Bourhy R., Martel A., Margarita D., Saint-Girons I., Belfaiza J. Homoserine O-acetyltransferase, involved in the Leptospira meyeri methionine biosynthetic pathway, is not feedback inhibited. J. Bacteriol. 179:(13):1997;4396-4398.
9. Claes W.A., Pühler A., Kalinowski J. Identification of two prpDBC gene clusters in Corynebacterium glutamicum and their involvement in propionate degradation via the 2-methylcitrate cycle. J. Bacteriol. 184:(10):2002;2728-2739.
10. Cole S.T., Brosch R., Parkhill J., Garnier T., Churcher C., Harris D., Gordon S.V., Eiglmeier K., Gas S., Barry C.E. III, Tekaia F., Badcock K., Basham D., Brown D., Chillingworth T., Connor R., Davies R., Devlin K., Feltwell T., Gentles S., Hamlin N., Holroyd S., Hornsby T., Jagels K., Krogh A., McLean J., Moule S., Murphy L., Oliver K., Osborne J., Quail M.A., Rajandream M.-A., Rogers J., Rutter S., Seeger K., Skelton J., Squares R., Squares S.E.S.J., Taylor K., Whitehead S., Barrell B.G. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature. 393:(6685):1998;537-544.
11. Cole S.T., Eiglmcier K., Parkhill J., James K.D., Thomson N.R., Wheeler P.R., Honore N., Ganier T., Churcher C., Harris D., Mungall K., Basham D., Brown D., Chillingworth T., Connor R., Davies R.M., Devlin K., Duthoy S., Feltwell T., Fraser A., Hamlin N., Holroyd S., Hornsby T., Jagels K., Lacroix J.C., Maclean J., Moule S., Murphy L., Oliver K., Quail M.A., Rajandream M.-A., Rutherford K., Rutter S., Seeger K., Simon S., Simmonds M., Skelton J., Squares R., Squares S., Stevens K., Taylor K., Whitehead S., Woodward J.R., Barrell B.G. Massive gene decay in the leprosy bacillus. Nature. 409:2001;1007-1011.
12. 12. J. Bacteriol. 60:1950;17-28.
13. Dusch N., Pühler A., Kalinowski J. Expression of the Corynebacterium glutamicum panD gene encoding L-aspartate-α-decarboxylase leads to pantothenate overproduction in Escherichia coli. Appl. Environ. Microbiol. 65:(4):1999;1530-1539.
14. Grant S.G.N., Jesse J., Bloom F.R., Hanahan D. Differential plasmid rescue from transgenic mouse DNAs into Escherichia coli methylation-restriction mutants. Proc. Natl. Acad. Sci. 87:1990;4645-4649.
15. Greene R.C. Biosynthesis of methionine. Neidhardt F.C., Curtis R. III, Ingraham J.L., Lin E.C.C., Low K.B., Magasanik B., Reznikoff W.S., Riley M., Schaechter M., Umbargcr H.E. second ed Escherichia coli and Salmonella: Cellular and Molecular Biology. 1:1996;542-560 ASM Press, Washington DC.
16. Hermann T., Pfefferle W., Baumann C., Busker E., Schaffer S., Bott M., Sahm H., Dusch N., Kalinowski J., Pühler A., Bendt A.K., Krämer R., Burkovski A. Proteome analysis of Corynebacterium glutamicum. Electrophoresis. 22:2001;1712-1723.
17. Horton R.M., Hunt H.D., Ho S.N., Pullen J.K., Pease L.R. Engineering hybrid genes without the use of restriction enzymes: gene splicing by overlap extension. Gene. 77:(1):1989;61-68.
18. Hwang B.-J., Kim Y., Kim H.-B., Hwang H.-J., Kim J.-H., Lee H.-S. Analysis of Corynebacterium glutamicum methionine biosynthetic pathway. Mol. Cells. 9:(3):1999;300-308.
19. Hwang B.-J., Yeom H.-J., Kim Y., Lee H.-S. Corynebacterium glutamicum utilizes both transsulfuration and direct sulfhydrylation pathways for methionine biosynthesis. J. Bacteriol. 184:(5):2002;1277-1286.
20. Jensen R.A., Gu W. Evolutionary recruitment of biochemically specialized subdivisions of family I within the protein superfamily of aminotransferases. J. Bacteriol. 178:(8):1996;2161-2171.
21. Kalinowski J., Bathe B., Bartels D., Bischoff N., Bott M., Burkovski A., Dusch N., Eggeling L., Eikmanns B.J., Gaigalat L., Goesmann A., Hartmann M., Huthmacher K., Krämer R., Linke B., McHardy A.C., Meyer F., Möckel B., Pfefferle W., Pühler A., Rey D.A., Rückert C., Rupp O., Sahm H., Wendisch V.F., Wiegräbe I., Tauch A. The complete Corynebacterium glutamicum ATCC 13032 genome sequence and its impact on the production of L-aspartate derived amino acids and vitamins. J. Biotechnol. 104:(1-3):2003;5-25.
22. Kanehisa M., Goto S., Kawashima S., Nakaya A. The KEGG databases at GenomeNet. Nucleic Acids Res. 30:(1):2002;42-46.
23. Kase H., Nakayama K. Production of O-acetyl-L-homoserine by methionine analog-resistant mutants and regulation of homoserine-O-transacetylase in Corynebacterium glutamicum. Agr. Biol. Chem. 38:(10):1974;2021-2030.
24. Kase H., Nakayama K. The regulation of L-methionine synthesis and the properties of cystathionine-γ-synthase and β-cystathionase in Corynebacterium glutamicum. Agr. Biol. Chem. 38:(11):1974;2235-2242.
25. Kase H., Nakayama K. Methionine biosynthesis by analog-resistant mutants of Corynebacterium glutamicum. Agr. Biol. Chem. 39:1975;153-158.
26. Kerjan P., Cherest H., Surdin-Kerjan Y. Nucleotide sequence of the Saccharomyces cerevisiae MET25 gene. Nucleic Acids Res. 14:(20):1994;7861-7871.
27. Kim J.W., Kim H.J., Kim Y., Lee M.S., Lee H.-S. Properties of the Corynebacterium glutamicum metC gene encoding cystathionine β-lyase. Mol. Cells. 11:(2):2001;220-225.
28. Kinoshita S., Udaka S., Shimono M. Amino acid fermentation. I. Production of L-glutamic acid by various microorganisms. Appl. Microbiol. 3:1957;193-205.
29. Laemmli U.K. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature. 227:1970;680-685.
30. Langin T., Faugeron G., Goyon C., Nicolas A., Rossignol J.-L. The MET2 gene of Saccharomyces cerevisiae: molecular cloning and nucleotide sequence. Gene. 49:1986;283-293.
31. Leuchtenberger W. Amino acids - technical production and use. Rehm H.J., Reed G., Pühler A., Stadler P. second ed Biotechnology. 6:1996;466-502 VCH, Weinheim.
32. Levonen A.-L., Lapatto R., Sakscla M., Raivio K.O. Human cystathionine γ-lyase: developmental and in vitro expression of two isoforms. Biochem. J. 347:(1):2000;89-94.
33. McClelland M., Sanderson K.E., Spieth J., Clifton S.W., Latreille P., Courtney L., Porwollik S., Ali J., Dante M., Du F., Hou S., Layman D., Leonard S., Nguyen C., Scott K., Holmes A., Grewal N., Mulvaney E., Ryan E., Sun H., Florea L., Miller W., Stoneking T., Nhan M., Waterston R., Wilson R.K. Complete genome sequence of Salmonella enterica serovar Typhimurium LT2. Nature. 413:2001;852-856.
34. Ono B.-I., Tanaka K., Naito K., Heike C., Shinoda S., Yamamoto S., Ohmori S., Oshima T., Toh-e A. Cloning and characterization of the CYS3 (CYII) gene of Saccharomyces cerevisiae. J. Bacteriol. 174:(10):1992;3339-3347.
35. Park S.-D., Lee J.-Y., Kim Y., Kim J.-H., Lee H.-S. Isolation and analysis of metA, a methionine biosynthetic gene encoding homoserine acetyltransferase in C. glutamicum. Mol. Cells. 8:(3):1998;286-294.
36. Perkins D.N., Pappin D.J.C., Creasy D.M., Cottrell J.S. Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis. 20:(18):1999;3551-3567.
37. Peters-Wendisch P.G., Schiel B., Wendisch V.F., Katsoulidis E., Möckel B., Sahm H., Eikmanns B.J. Pyruvate carboxylase is a major bottleneck for glutamate and lysine production by Corynebacterium glutamicum. J. Mol. Microbiol. Biotechnol. 3:(2):2001;295-300.
38. Rey D.A., Pühler A., Kalinowski J. The putative transcriptional repressor McbR, member of the TetR-family, is involved in the regulation of the metabolic network directing the synthesis of sulfur containing amino acids in Corynebacterium glutamicum. J. Biotechnol. 103:(1):2003;51-65.
39. Rossol I., Pühler A. The Corynebacterium glutamicum aecD gene encodes a C-S lyase with a α,β-elimination activity that degrades aminoethylcysteine. J. Bacteriol. 174:(9):1992;2968-2977.
40. Sahm H., Eggeling L., de Graaf A.A. Pathway analysis and metabolic engineering in Corynebacterium glutamicum. Biol. Chem. 381:2000;899-910.
41. Sambrook J., Fritsch E., Manialis T. Molecular Cloning. A Laboratory Manual. second ed:1989;Cold Spring Harbour Laboratory Press.
42. Schäfer A., Tauch A., Jäger W., Kalinowski J., Thierbach G., Pühler A. Small mobilizable multi-purpose cloning vectors derived from the Escherichia coli plasmids pK18 and pK19: selection of defined deletions in the chromosome of Corynebacterium glutamicum. Gene. 145:1994;69-73.
43. Schwarzer A., Pühler A. Manipulation of Corynebacterium glutamicum by gene disruption and replacement. Biotechnology. 9:1991;1195-1204.
44. Tauch A., Homann I., Mormann S., Rüberg S., Billault A., Bathe B., Brand S., Brockmann-Gretza O., Rückert C., Schischka N., Wrenger C., Hoheisel J., Möckel B., Huthmacher K., Pfefferle W., Pühler A., Kalinowski J. Strategy to sequence the genome of Corynebacterium glutamicum ATCC 13032: use of a cosmid and a bacterial artificial chromosome library. J. Biotechnol. 95:(1):2002;25-38.
45. Tauch A., Kirchner O., Löffler B., Götker S., Pühler A., Kalinowski J. Efficient electrotransformation of Corynebacterium diphtheriae with a minireplicon derived from the Corynebacterium glutamicum plasmid pGA1. Curr. Microbiol. 45:(5):2002;362-367.
46. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., Higgins D.G. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25:(24):1997;4876-4882.
47. Wada M., Awano N., Haisa K., Takagi H., Nakamori S. Purification, characterization and identification of cysteine desulfhydrase of Corynebacterium glutamicum and its relationship to cysteine production. FEMS Microbiol. Lett. 217:(1):2002;103-107.
48. Wolf H., Pühler A., Neumann E. Electrotransformation of intact and osmotically sensitive cells of Corynebacterium glutamicum. Appl. Microbiol. Biotechnol. 30:1989;282-289.
49. Zdych E., Peist R., Reidl J., Boos W. MalY of Escherichia coli is an enzyme with the activity of a βC-S lyase (cystathionase). J. Bacteriol. 177:(17):1995;5035-5039.