Bacterial variations on the methionine salvage pathway

BMC Microbiology

Volumn 4, Issue , 2004, Pages 1-17

  Sekowska, Agnieszka ^a,b,f   Dénervaud, Valérie ^c   Ashida, Hiroki ^d   Michoud, Karine ^e   Haas, Dieter ^c   Yokota, Akiho ^d   Danchin, Antoine ^a,b  

^a HKU PASTEUR RESEARCH CENTRE   (Hong Kong)

^b INSTITUT PASTEUR   (France)

^c UNIVERSITY OF LAUSANNE   (Switzerland)

^d NARA INSTITUTE OF SCIENCE AND TECHNOLOGY   (Japan)

^e SWISS INSTITUTE OF BIOINFORMATICS   (Switzerland)

^f SYMPATHOS Laboratory   (France)

Author keywords

[No Author keywords available]

Indexed keywords

1,2 DIHYDROXY 3 KETO 5 METHYLTHIOPENTENE; 5' METHYLTHIOADENOSINE PHOSPHORYLASE; ALKENE; AMINOTRANSFERASE; BUTYRIC ACID DERIVATIVE; CARBON MONOXIDE; ENOLASE; HISTIDINOLPHOSPHATE; HYDROLYASE; ISOMERASE; KETOMETHYLTHIOBUTYRATE; METHIONINE; METHYLTHIORIBOSE 1 PHOSPHATE ISOMERASE; METHYLTHIORIBULOSE 1 PHOSPHATE DEHYDRATASE; NUCLEOSIDE PHOSPHORYLASE; OXYGEN; PHOSPHATASE; PHOSPHATE; UNCLASSIFIED DRUG; 2 METHYLTHIOADENOSINE; 2-METHYLTHIOADENOSINE; 5'-METHYLTHIOADENOSINE PHOSPHORYLASE; ADENOSINE; DRUG DERIVATIVE; NUCLEOSIDE; PURINE NUCLEOSIDE PHOSPHORYLASE; RIBULOSEBISPHOSPHATE CARBOXYLASE;

AMINO ACID METABOLISM; ARTICLE; BACILLUS SUBTILIS; BACTERIUM; ENZYME MECHANISM; ENZYME SPECIFICITY; ENZYME SYNTHESIS; GENE SEQUENCE; GENOME ANALYSIS; KLEBSIELLA PNEUMONIAE; LEPTOSPIRA INTERROGANS; NONHUMAN; PROTEIN FAMILY; PSEUDOMONAS AERUGINOSA; STRAIN DIFFERENCE; THERMOANAEROBACTER TENGCOGENSIS; THERMOPHILIC BACTERIUM; TRANSAMINATION; XYLELLA FASTIDIOSA; HYDROLYSIS; METABOLISM; PHOSPHORYLATION;

ARCHAEA; BACILLUS SUBTILIS; BACTERIA (MICROORGANISMS); EUKARYOTA; FIRMICUTES; KLEBSIELLA; KLEBSIELLA PNEUMONIAE; LEPTOSPIRA; LEPTOSPIRA INTERROGANS; PSEUDOMONAS; PSEUDOMONAS AERUGINOSA; THERMOANAEROBACTER; THERMOANAEROBACTER TENGCONGENSIS; XYLELLA FASTIDIOSA;

ADENOSINE; BACILLUS SUBTILIS; HYDROLYSIS; KLEBSIELLA PNEUMONIAE; METHIONINE; OXYGEN; PHOSPHOPYRUVATE HYDRATASE; PHOSPHORYLATION; PSEUDOMONAS AERUGINOSA; PURINE-NUCLEOSIDE PHOSPHORYLASE; RIBULOSE-BISPHOSPHATE CARBOXYLASE; THIONUCLEOSIDES;

EID: 2642542612     PISSN: 14712180     EISSN: 14712180     Source Type: Journal    
DOI: 10.1186/1471-2180-4-9     Document Type: Article

References (54)

1. Sekowska A, Kung HF, Danchin A: Sulfur metabolism in Escherichia coli and related bacteria: facts and fiction. J Mol Microbiol Biotechnol 2000, 2:145-177.
2. Rando RR: Chemical biology of protein isoprenylation/methylation. Biochim Biophys Acta 1996, 1300:5-16.
3. Takemura M, Kitanaka N, Kitanaka J: Signal transduction by histamine in the cerebellum and its modulation by N-methyltransferase. Cerebellum 2003, 2:39-43.
4. Turner BM: Memorable transcription. Nat Cell Biol 2003, 5:390-393.
5. Nakahigashi K, Kubo N, Narita S, Shimaoka T, Goto S, Oshima T, Mori H, Maeda M, Wada C, Inokuchi H: HemK, a class of protein methyl transferase with similarity to DNA methyl transferases, methylates polypeptide chain release factors, and hemK knockout induces defects in translational termination. Proc Natl Acad Sci U S A 2002, 99:1473-1478.
6. Deppenmeier U: The unique biochemistry of methanogenesis. Prog Nucleic Acid Res Mol Biol 2002, 71:223-283.
7. Winans SC, Bassler BL: Mob psychology. J Bacteriol 2002, 184:873-883.
8. Ashida H, Saito Y, Kojima C, Kobayashi K, Ogasawara N, Yokota A: A functional link between RuBisCO-like protein of Bacillus and photosynthetic RuBisCO. Science 2003, 302:286-290.
9. Zappia V, Oliva A, Cacciapuoti G, Galletti P, Mignucci G, Carteni-Farina M: Substrate specificity of 5′-methylthioadenosine phosphorylase from human prostate. Biochem J 1978, 175:1043-1050.
10. Riscoe MK, Ferro AJ, Fitchen JH: Analogs of 5-methylthioribose, a novel class of antiprotozoal agents. Antimicrob Agents Chemother 1988, 32:1904-1906.
11. Tower PA, Alexander DB, Johnson LL, Riscoe MK: Regulation of methylthioribose kinase by methionine in Klebsiella pneumoniae. J Gen Microbiol 1993, 139 (Pt 5):1027-1031.
12. Schroeder HR, Barnes CJ, Bohinski RC, Mallette MF: Biological production of 5-methylthioribose. Can J Microbiol 1973, 19:1347-1354.
13. Savarese TM, Cannistra AJ, Parks R. E., Jr., Secrist J. A., 3rd, Shortnacy AT, Montgomery JA: 5′-deoxy-5′-methylthioadenosine phosphorylase - IV. Biological activity of 2-fluoroadenine-substituted 5′-deoxy-5′-methylthioadenosine analogs. Biochem Pharmacol 1987, 36:1881-1893.
14. Foglino M, Borne F, Bally M, Ball G, Patte JC: A direct sulfhydrylation pathway is used for methionine biosynthesis in Pseudomonas aeruginosa. Microbiology 1995, 141:431-439.
15. Bao Q, Tian Y, Li W, Xu Z, Xuan Z, Hu S, Dong W, Yang J, Chen Y, Xue Y, Xu Y, Lai X, Huang L, Dong X, Ma Y, Ling L, Tan H, Chen R, Wang J, Yu J, Yang H: A complete sequence of the T. tengcongensis genome. Genome Res 2002, 12:689-700.
16. Walker RD, Duerre JA: S-adenosylhomocysteine metabolism in various species. Can J Biochem 1975, 53:312-319.
17. Winzer K, Hardie KR, Burgess N, Doherty N, Kirke D, Holden MT, Linforth R, Cornell KA, Taylor AJ, Hill PJ, Williams P: LuxS: its role in central metabolism and the in vitro synthesis of 4-hydroxy-5-methyl-3(2H)-furanone. Microbiology 2002, 148:909-922.
18. Lee JE, Cornell KA, Riscoe MK, Howell PL: Structure of E. coli 5′-methylthioadenosine/S-adenosylhomocysteine nucleosidase reveals similarity to the purine nucleoside phosphorylases. Structure (Camb) 2001, 9:941-953.
19. Sekowska A, Danchin A: Identification of yrrU as the methylthioadenosine nucleosidase gene in Bacillus subtilis. DNA Res 1999, 6:255-264.
20. Grundy FJ, Henkin TM: The S box regulon: a new global transcription termination control system for methionine and cysteine biosynthesis genes in gram-positive bacteria. Mol Microbiol 1998, 30:737-749.
21. Winkler WC, Nahvi A, Sudarsan N, Barrick JE, Breaker RR: An mRNA structure that controls gene expression by binding S-adenosylmethionine. Nat Struct Biol 2003, 10:701-707.
22. Sekowska A, Mulard L, Krogh S, Tse JK, Danchin A: MtnK, methylthioribose kinase, is a starvation-induced protein in Bacillus subtilis. BMC Microbiol 2001, 1:15.
23. Ku SY, Yip P, Cornell KA, Riscoe MK, Howell PL: Crystallization and preliminary X-ray analysis of 5′-methylthioribose kinase from Bacillus subtilis and Arabidopsis thaliana. Acta Crystallogr D Biol Crystallogr 2004, 60:116-119.
24. Yamashita S, Hosaka K: Choline kinase from yeast. Biochim Biophys Acta 1997, 1348:63-69.
25. Trackman PC, Abeles RH: Methionine synthesis from 5′ -S-Methylthioadenosine. Resolution of enzyme activities and identification of 1-phospho-5-S methylthioribulose. J Biol Chem 1983, 258:6717-6720.
26. Sekowska A, Danchin A: The methionine salvage pathway in Bacillus subtilis. BMC Microbiol 2002, 2:8.
27. Hanson TE, Tabita FR: A ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO)-like protein from Chlorobium tepidum that is involved with sulfur metabolism and the response to oxidative stress. Proc Natl Acad Sci U S A 2001, 98:4397-4402.
28. Myers RW, Abeles RH: Conversion of 5-S-methyl-5-thio-D-ribose to methionine in Klebsiella pneumoniae. Stable isotope incorporation studies of the terminal enzymatic reactions in the pathway. J Biol Chem 1990, 265:16913-16921.
29. Wray JW, Abeles RH: The methionine salvage pathway in Klebsiella pneumoniae and rat liver. Identification and characterization of two novel dioxygenases. J Biol Chem 1995, 270:3147-3153.
30. Pochapsky TC, Pochapsky SS, Ju T, Mo H, Al-Mjeni F, Maroney MJ: Modeling and experiment yields the structure of acireductone dioxygenase from Klebsiella pneumoniae. Nat Struct Biol 2002, 9:966-972.
31. Gelfand DH, Steinberg RA: Escherichia coli mutants deficient in the aspartate and aromatic amino acid aminotransferases. J Bacteriol 1977, 130:429-440.
32. Berger BJ, English S, Chan G, Knodel MH: Methionine regeneration and aminotransferases in Bacillus subtilis, Bacillus cereus, and Bacillus anthracis. J Bacteriol 2003, 185:2418-2431.
33. Sekowska A, Robin S, Daudin JJ, Henaut A, Danchin A: Extracting biological information from DNA arrays: an unexpected link between arginine and methionine metabolism in Bacillus subtilis. Genome Biol 2001, 2:RESEARCH0019.
34. Heilbronn J, Wilson J, Berger BJ: Tyrosine aminotransferase catalyzes the final step of methionine recycling in Klebsiella pneumoniae. J Bacteriol 1999, 181:1739-1747.
35. Nitschke P, Guerdoux-Jamet P, Chiapello H, Faroux G, Henaut C, Henaut A, Danchin A: Indigo: a World-Wide-Web review of genomes and gene functions. FEMS Microbiol Rev 1998, 22:207-227.
36. Marques MV, da Silva AM, Gomes SL: Genetic organization of plasmid pXF51 from the plant pathogen Xylella fastidiosa. Plasmid 2001, 45:184-199.
37. Ren SX, Fu G, Jiang XG, Zeng R, Miao YG, Xu H, Zhang YX, Xiong H, Lu G, Lu LF, Jiang HQ, Jia J, Tu YF, Jiang JX, Gu WY, Zhang YQ, Cai Z, Sheng HH, Yin HF, Zhang Y, Zhu GF, Wan M, Huang HL, Qian Z, Wang SY, Ma W, Yao ZJ, Shen Y, Qiang BQ, Xia QC, Guo XK, Danchin A, Saint Girons I, Somerville RL, Wen YM, Shi MH, Chen Z, Xu JG, Zhao GP: Unique physiological and pathogenic features of Leptospira interrogans revealed by whole-genome sequencing. Nature 2003, 422:888-893.
38. Rocha EP, Sekowska A, Danchin A: Sulphur islands in the Escherichia coli genome: markers of the cell's architecture? FEBS Lett 2000, 476:8-11.
39. Patthy L: Genome evolution and the evolution of exon-shufflinga - a review. Gene 1999, 238:103-114.
40. Gibbons SJ, Farrugia G: The role of carbon monoxide in the gastrointestinal tract. J Physiol 2004.
41. Boehning D, Snyder SH: Novel neural modulators. Annu Rev Neurosci 2003, 26:105-131.
42. Spizizen J: Transformation of biochemically deficient strains of Bacillus subtilis by deoxyribonucleate. Proc Natl Acad Sci USA 1958, 44:1072-1078.
43. Kobayashi K, Ehrlich SD, Albertini A, Amati G, Andersen KK, Arnaud M, Asai K, Ashikaga S, Aymerich S, Bessieres P, Boland F, Brignell SC, Bron S, Bunai K, Chapuis J, Christiansen LC, Danchin A, Debarbouille M, Dervyn E, Deuerling E, Devine K, Devine SK, Dreesen O, Errington J, Fillinger S, Foster SJ, Fujita Y, Galizzi A, Gardan R, Eschevins C, Fukushima T, Haga K, Harwood CR, Hecker M, Hosoya D, Hullo MF, Kakeshita H, Karamata D, Kasahara Y, Kawamura F, Koga K, Koski P, Kuwana R, Imamura D, Ishimaru M, Ishikawa S, Ishio I, Le Coq D, Masson A, Mauel C, Meima R, Mellado RP, Moir A, Moriya S, Nagakawa E, Nanamiya H, Nakai S, Nygaard P, Ogura M, Ohanan T, O'Reilly M, O'Rourke M, Pragai Z, Pooley HM, Rapoport G, Rawlins JP, Rivas LA, Rivolta C, Sadaie A, Sadaie Y, Sarvas M, Sato T, Saxild HH, Scanlan E, Schumann W, Seegers JF, Sekiguchi J, Sekowska A, Seror SJ, Simon M, Stragier P, Studer R, Takamatsu H, Tanaka T, Takeuchi M, Thomaides HB, Vagner V, van Dijl JM, Watabe K, Wipat A, Yamamoto H, Yamamoto M, Yamamoto Y, Yamane K, Yata K, Yoshida K, Yoshikawa H, Zuber U, Ogasawara N: Essential Bacillus subtilis genes. Proc Natl Acad Sci U S A 2003, 100:4678-4683.
44. Del Sal G, Manfioletti G, Schneider C: A one-tube plasmid DNA mini-preparation suitable for sequencing. Nucleic Acids Res 1988, 16:9878.
45. Gamper M, Ganter B, Polito MR, Haas D: RNA processing modulates the expression of the arcDABC operon in Pseudomonas aeruginosa. J Mol Biol 1992, 226:943-957.
46. Farinha MA, Kropinski AM: High efficiency electroporation of Pseudomonas aeruginosa using frozen cell suspensions. FEMS Microbiol Lett 1990, 58:221-225.
47. Sambrook J, Fritsch EG, Maniatis T: Molecular Cloning: a Laboratory Manual. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory; 1989.
48. Voisard C, Bull CT, Keel C, Laville J, Maurhofer M, Schnider U, Défago G, Haas D: Biocontrol of root diseases by Pseudomonas fluorescens CHA0: current concepts and experimental approaches. Molecular ecology of rhizosphere microorganisms Edited by: F O'Gara, DN Dowling and B Boesten. VCH Weinheim; 1994:67-89.
49. Haas D, Watson J, Krieg R, Leisinger T: Isolation of an Hfr donor of Pseudomonas aeruginosa PAO by insertion of the plasmid RP1 into the tryptophan synthase gene. Mol Gen Genet 1981, 182:240-244.
50. Schlenk F, Zydek-Cwick CR, Dainko JL: 5′-Methylthioadenosine and related compounds as precursors of S- adenosylmethionine in yeast. Biochimica et Biophysica Acta 1973, 320:357-362.
51. Marchler-Bauer A, Anderson JB, DeWeese-Scott C, Fedorova ND, Geer LY, He S, Hurwitz DI, Jackson JD, Jacobs AR, Lanczycki CJ, Liebert CA, Liu C, Madej T, Marchler GH, Mazumder R, Nikolskaya AN, Panchenko AR, Rao BS, Shoemaker BA, Simonyan V, Song JS, Thiessen PA, Vasudevan S, Wang Y, Yamashita RA, Yin JJ, Bryant SH: CDD: a curated Entrez database of conserved domain alignments. Nucleic Acids Res 2003, 31:383-387.
52. Gattiker A, Michoud K, Rivoire C, Auchincloss AH, Coudert E, Lima T, Kersey P, Pagni M, Sigrist CJ, Lachaize C, Veuthey AL, Gasteiger E, Bairoch A: Automated annotation of microbial proteomes in SWISS-PROT. Comput Biol Chem 2003, 27:49-58.
53. Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG, Thompson JD: Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res 2003, 31:3497-3500.
54. Dayhoff MO, Schwartz RM, Orcutt BC: Atlas of Protein Sequence and Structure. Volume 5. Washington DC, National Biochemical Research Foundation; 1978.