Paralogous metabolism: S-alkyl-cysteine degradation in Bacillus subtilis

Environmental Microbiology

Volumn 16, Issue 1, 2014, Pages 101-117

  Chan, Che Man ^a   Danchin, Antoine ^b   Marlière, Philippe ^c   Sekowska, Agnieszka ^b  

^a UNIVERSITY OF HONG KONG   (Hong Kong)

^b AMAbiotics SAS   (France)

^c CENTRE NATIONAL DE SÉQUENÇAGE   (France)

Author keywords

[No Author keywords available]

Indexed keywords

BACILLUS SUBTILIS; BACTERIA (MICROORGANISMS);

BACTERIAL PROTEIN; CYSTEINE; DRUG DERIVATIVE; MECYSTEINE; METHIONINE; SULFUR;

ARTICLE; BACILLUS SUBTILIS; ENZYMOLOGY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; OPERON;

BACILLUS SUBTILIS; BACTERIAL PROTEINS; CYSTEINE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, BACTERIAL; METABOLIC NETWORKS AND PATHWAYS; METHIONINE; OPERON; SULFUR;

EID: 84891631824     PISSN: 14622912     EISSN: 14622920     Source Type: Journal    
DOI: 10.1111/1462-2920.12210     Document Type: Article

References (60)

1. Anagnostopoulos, C., and Spizizen, J. (1961) Requirements for transformation in Bacillus subtilis. J Bacteriol 81: 741-746.
2. Auger, S., Danchin, A., and Martin-Verstraete, I. (2002) Global expression profile of Bacillus subtilis grown in the presence of sulphate or methionine. J Bacteriol 184: 5179-5186.
3. Austin, A.T., and Ballare, C.L. (2010) Dual role of lignin in plant litter decomposition in terrestrial ecosystems. Proc Natl Acad Sci USA 107: 4618-4622.
4. Barbe, V., Cruveiller, S., Kunst, F., Lenoble, P., Meurice, G., Sekowska, A., etal. (2009) From a consortium sequence to a unified sequence: the Bacillus subtilis 168 reference genome a decade later. Microbiology 155: 1758-1775.
5. Belda, E., Sekowska, A., Le Fevre, F., Morgat, A., Mornico, D., Ouzounis, C., etal. (2013) An updated metabolic view of the Bacillus subtilis 168 genome. Microbiology 159: 757-770.
6. Bertani, G. (1951) Studies on lysogenesis. I. The mode of phage liberation by lysogenic Escherichia coli. J Bacteriol 62: 293-300.
7. Brockhurst, M.A., Colegrave, N., Hodgson, D.J., and Buckling, A. (2007) Niche occupation limits adaptive radiation in experimental microcosms. PLoS ONE 2: e193.
8. Burguiere, P., Fert, J., Guillouard, I., Auger, S., Danchin, A., and Martin-Verstraete, I. (2005) Regulation of the Bacillus subtilis ytmI operon, involved in sulphur metabolism. J Bacteriol 187: 6019-6030.
9. Clement-Ziza, M., Malabat, C., Weber, C., Moszer, I., Aittokallio, T., Letondal, C., and Rousseau, S. (2009) Genoscape: a Cytoscape plug-in to automate the retrieval and integration of gene expression data and molecular networks. Bioinformatics 25: 2617-2618.
10. Coppee, J.Y., Auger, S., Turlin, E., Sekowska, A., Le Caer, J.P., Labas, V., etal. (2001) Sulphur-limitation-regulated proteins in Bacillus subtilis: a two-dimensional gel electrophoresis study. Microbiology 147: 1631-1640.
11. Danchin, A. (2009) Cells need safety valves. Bioessays 31: 769-773.
12. Dartois, V., Debarbouille, M., Kunst, F., and Rapoport, G. (1998) Characterization of a novel member of the DegS-DegU regulon affected by salt stress in Bacillus subtilis. J Bacteriol 180: 1855-1861.
13. Dassler, T., Maier, T., Winterhalter, C., and Bock, A. (2000) Identification of a major facilitator protein from Escherichia coli involved in efflux of metabolites of the cysteine pathway. Mol Microbiol 36: 1101-1112.
14. Delmar, P., Robin, S., and Daudin, J.J. (2005) VarMixt: efficient variance modelling for the differential analysis of replicated gene expression data. Bioinformatics 21: 502-508.
15. Erwin, K.N., Nakano, S., and Zuber, P. (2005) Sulphate-dependent repression of genes that function in organosulfur metabolism in Bacillus subtilis requires Spx. J Bacteriol 187: 4042-4049.
16. Even, S., Burguiere, P., Auger, S., Soutourina, O., Danchin, A., and Martin-Verstraete, I. (2006) Global control of cysteine metabolism by CymR in Bacillus subtilis. J Bacteriol 188: 2184-2197.
17. Gingold, H., and Pilpel, Y. (2011) Determinants of translation efficiency and accuracy. Mol Syst Biol 7: 481.
18. Grundy, F.J., and Henkin, T.M. (1998) The S box regulon: a new global transcription termination control system for methionine and cysteine biosynthesis genes in gram-positive bacteria. Mol Microbiol 30: 737-749.
19. Guillouard, I., Auger, S., Hullo, M.F., Chetouani, F., Danchin, A., and Martin-Verstraete, I. (2002) Identification of Bacillus subtilis CysL, a regulator of the cysJI operon, which encodes sulphite reductase. J Bacteriol 184: 4681-4689.
20. Haas, M., Beyer, D., Gahlmann, R., and Freiberg, C. (2001) YkrB is the main peptide deformylase in Bacillus subtilis, a eubacterium containing two functional peptide deformylases. Microbiology 147: 1783-1791.
21. Helfrich, M., Entian, K.D., and Stein, T. (2007) Structure-function relationships of the lanthionine cyclase SpaC involved in biosynthesis of the Bacillus subtilis peptide antibiotic subtilin. Biochemistry 46: 3224-3233.
22. Higashitsuji, Y., Angerer, A., Berghaus, S., Hobl, B., and Mack, M. (2007) RibR, a possible regulator of the Bacillus subtilis riboflavin biosynthetic operon, in vivo interacts with the 5'-untranslated leader of rib mRNA. FEMS Microbiol Lett 274: 48-54.
23. Hullo, M.F., Auger, S., Soutourina, O., Barzu, O., Yvon, M., Danchin, A., and Martin-Verstraete, I. (2007) Conversion of methionine to cysteine in Bacillus subtilis and its regulation. J Bacteriol 189: 187-197.
24. Kim, L., Mogk, A., and Schumann, W. (1996) A xylose-inducible Bacillus subtilis integration vector and its application. Gene 181: 71-76.
25. Kleibl, K. (2002) Molecular mechanisms of adaptive response to alkylating agents in Escherichia coli and some remarks on O(6)-methylguanine DNA-methyltransferase in other organisms. Mutat Res 512: 67-84.
26. Kobayashi, K., Ehrlich, S.D., Albertini, A., Amati, G., Andersen, K.K., Arnaud, M., etal. (2003) Essential Bacillus subtilis genes. Proc Natl Acad Sci USA 100: 4678-4683.
27. Kotera, M., McDonald, A.G., Boyce, S., and Tipton, K.F. (2008) Eliciting possible reaction equations and metabolic pathways involving orphan metabolites. J Chem Inf Model 48: 2335-2349.
28. Kunst, F., and Rapoport, G. (1995) Salt stress in an environmental signal affecting degradative enzyme synthesis in Bacillus subtilis. J Bacteriol 177: 2403-2407.
29. Lynch, A.S., Tyrrell, R., Smerdon, S.J., Briggs, G.S., and Wilkinson, A.J. (1994) Characterization of the CysB protein of Klebsiella aerogenes: direct evidence that N-acetylserine rather than O-acetylserine serves as the inducer of the cysteine regulon. Biochem J 299 (Pt 1): 129-136.
30. McCullum, E.O., Williams, B.A., Zhang, J., and Chaput, J.C. (2010) Random mutagenesis by error-prone PCR. Methods Mol Biol 634: 103-109.
31. de Marco, P., Moradas-Ferreira, P., Higgins, T.P., McDonald, I., Kenna, E.M., and Murrell, J.C. (1999) Molecular analysis of a novel methanesulphonic acid monooxygenase from the methylotroph Methylosulphonomonas methylovora. J Bacteriol 181: 2244-2251.
32. Matamoros, V., Puigagut, J., Garcia, J., and Bayona, J.M. (2007) Behavior of selected priority organic pollutants in horizontal subsurface flow constructed wetlands: a preliminary screening. Chemosphere 69: 1374-1380.
33. de Melo Pereira, G.V., Magalhaes, K.T., Lorenzetii, E.R., Souza, T.P., and Schwan, R.F. (2012) A multiphasic approach for the identification of endophytic bacterial in strawberry fruit and their potential for plant growth promotion. Microb Ecol 63: 405-417.
34. Miller, D.J., Ouellette, N., Evdokimova, E., Savchenko, A., Edwards, A., and Anderson, W.F. (2003) Crystal complexes of a predicted S-adenosylmethionine-dependent methyltransferase reveal a typical AdoMet binding domain and a substrate recognition domain. Protein Sci 12: 1432-1442.
35. Morita, R., Nakagawa, N., Kuramitsu, S., and Masui, R. (2008) An O6-methylguanine-DNA methyltransferase-like protein from Thermus thermophilus interacts with a nucleotide excision repair protein. J. Biochem 144: 267-277.
36. Murphy, E. (1985) Nucleotide sequence of a spectinomycin adenyltransferase AAD(9) determinant from Staphylococcus aureus and its relationship to AAD(3')(9). Mol Gen Genet 200: 33-39.
37. Mutch, D.M., Berger, A., Mansourian, R., Rytz, A., and Roberts, M.A. (2002) The limit fold change model: a practical approach for selecting differentially expressed genes from microarray data. BMC Bioinformatics 3: 17.
38. Nakano, S., Erwin, K.N., Ralle, M., and Zuber, P. (2005) Redox-sensitive transcriptional control by a thiol/disulphide switch in the global regulator, Spx. Mol Microbiol 55: 498-510.
39. Neely, J.G., Hartman, J.M., Forsen, J.W., Jr, and Wallace, M.S. (2003) Tutorials in clinical research: VII. Understanding comparative statistics (contrast) - part B: application of T-test, Mann-Whitney U, and chi-square. Laryngoscope 113: 1719-1725.
40. Oh, Y.K., Palsson, B.O., Park, S.M., Schilling, C.H., and Mahadevan, R. (2007) Genome-scale reconstruction of metabolic network in Bacillus subtilis based on high-throughput phenotyping and gene essentiality data. J Biol Chem 282: 28791-28799.
41. Ohshiro, T., Ishii, Y., Matsubara, T., Ueda, K., Izumi, Y., Kino, K., and Kirimura, K. (2005) Dibenzothiophene desulphurizing enzymes from moderately thermophilic bacterium Bacillus subtilis WU-S2B: purification, characterization and overexpression. J Biosci Bioeng 100: 266-273.
42. Perego, M. (1993) Integrational vectors for genetic manipulation in Bacillus subtilis. In Bacillus Subtilis and Other Gram-Positive Bacteria. Sonenshein, A.L., Hoch, J.A., and Losick, R. (eds). Washington, DC, USA: American Society for Microbiology, pp. 615-624.
43. van der Ploeg, J.R., Cummings, N.J., Leisinger, T., and Connerton, I.F. (1998) Bacillus subtilis genes for the utilization of sulphur from aliphatic sulphonates. Microbiology 144 (Part 9): 2555-2561.
44. Rebeille, F., Jabrin, S., Bligny, R., Loizeau, K., Gambonnet, B., Van Wilder, V., etal. (2006) Methionine catabolism in Arabidopsis cells is initiated by a gamma-cleavage process and leads to S-methylcysteine and isoleucine syntheses. Proc Natl Acad Sci USA 103: 15687-15692.
45. Sambrook, J., Fritsch, E., and Maniatis, T. (1989) Molecular Cloning: A Laboratory Manual. Cold Spring Harbour, New York, USA: Cold Spring Harbour Laboratory Press.
46. Saunders, C., Schmidt, B., Morot, M., Thompson, L., and Guyer, M. (1984) Use of chromosomal integration in the establishment and expression of blaZ, a Staphylococcus aureus β-lactamase gene, in Bacillus subtilis. J Bacteriol 157: 718-726.
47. Sausen, P.J., and Elfarra, A.A. (1990) Cysteine conjugate S-oxidase. Characterization of a novel enzymatic activity in rat hepatic and renal microsomes. J Biol Chem 265: 6139-6145.
48. Sekowska, A., Kung, H.F., and Danchin, A. (2000) Sulphur metabolism in Escherichia coli and related bacteria: facts and fiction. J Mol Microbiol Biotechnol 2: 145-177.
49. Sekowska, A., Robin, S., Daudin, J.J., Henaut, A., and Danchin, A. (2001) Extracting biological information from DNA arrays: an unexpected link between arginine and methionine metabolism in Bacillus subtilis. Genome Biol 2: RESEARCH0019.
50. Sekowska, A., Denervaud, V., Ashida, H., Michoud, K., Haas, D., Yokota, A., and Danchin, A. (2004) Bacterial variations on the methionine salvage pathway. BMC Microbiol 4: 9.
51. Solovieva, I.M., Kreneva, R.A., Errais Lopes, L., and Perumov, D.A. (2005) The riboflavin kinase encoding gene ribR of Bacillus subtilis is a part of a 10kb operon, which is negatively regulated by the yrzC gene product. FEMS Microbiol Lett 243: 51-58.
52. Spizizen, J. (1958) Transformation of biochemically deficient strains of Bacillus subtilis by deoxyribonucleate. Proc Natl Acad Sci USA 44: 1072-1078.
53. Thomas, P., and Soly, T.A. (2009) Endophytic bacteria associated with growing shoot tips of banana (Musa sp.) cv. Grand Naine and the affinity of endophytes to the host. Microb Ecol 58: 952-964.
54. Van Buskirk, J.J., Kirsch, W.M., Kleyer, D.L., Barkley, R.M., and Koch, T.H. (1984) Aminomalonic acid: identification in Escherichia coli and atherosclerotic plaque. Proc Natl Acad Sci USA 81: 722-725.
55. Winkler, W.C., Nahvi, A., Sudarsan, N., Barrick, J.E., and Breaker, R.R. (2003) An mRNA structure that controls gene expression by binding S-adenosylmethionine. Nat Struct Biol 10: 701-707.
56. Yap, Y., Zhang, X., Ling, M.T., Wang, X., Wong, Y.C., and Danchin, A. (2004) Classification between normal and tumor tissues based on the pair-wise gene expression ratio. BMC Cancer 4: 72.
57. Yap, Y.L. (2006) Expression Profiling of Bacillus Subtilis Sulphur Responsive Genes. Hong Kong: The University of Hong Kong.
58. Yoshida, Y., Nakano, Y., Amano, A., Yoshimura, M., Fukamachi, H., Oho, T., and Koga, T. (2002) lcd from Streptococcus anginosus encodes a C-S lyase with alpha, beta-elimination activity that degrades L-cysteine. Microbiology 148: 3961-3970.
59. You, C., Lu, H., Sekowska, A., Fang, G., Wang, Y., Gilles, A.M., and Danchin, A. (2005) The two authentic methionine aminopeptidase genes are differentially expressed in Bacillus subtilis. BMC Microbiol 5: 57.
60. Zeng, J., and Davies, M.J. (2005) Evidence for the formation of adducts and S-(carboxymethyl)cysteine on reaction of alpha-dicarbonyl compounds with thiol groups on amino acids, peptides, and proteins. Chem Res Toxicol 18: 1232-1241.