Bacterial methionine biosynthesis

Microbiology (United Kingdom)

Volumn 160, Issue PART 8, 2014, Pages 1571-1584

  Ferla, Matteo P ^a   Patrick, Wayne M ^a  

^a UNIVERSITY OF OTAGO   (New Zealand)

Author keywords

[No Author keywords available]

Indexed keywords

CYSTEINE; HOMOSERINE; METHIONINE;

ACYLATION; AMINO ACID SYNTHESIS; BACTERIAL GENE; BACTERIAL PHENOMENA AND FUNCTIONS; BIOTECHNOLOGY; ESCHERICHIA COLI; GENETIC CODE; METHYLATION; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; PROTEIN METABOLISM; REVIEW; SIGNAL TRANSDUCTION; SULFATION;

EID: 84905245200     PISSN: 13500872     EISSN: 14652080     Source Type: Journal    
DOI: 10.1099/mic.0.077826-0     Document Type: Review

References (86)

1. Aitken, S. M.; Kirsch, J. F. (2005). The enzymology of cystathionine biosynthesis: strategies for the control of substrate and reaction specificity. Arch Biochem Biophys 433, 166-175.
2. Aitken, S. M., Kim, D. H.; Kirsch, J. F. (2003). Escherichia coli cystathionine c-synthase does not obey ping-pong kinetics. Novel continuous assays for the elimination and substitution reactions. Biochemistry 42, 11297-11306.
3. Aitken, S. M., Lodha, P. H.; Morneau, D. J. (2011). The enzymes of the transsulfuration pathways: active-site characterizations. Biochim Biophys Acta 1814, 1511-1517.
4. Alaminos, M.; Ramos, J. L. (2001). The methionine biosynthetic pathway from homoserine in Pseudomonas putida involves the metW, metX, metZ, metH and metE gene products. Arch Microbiol 176, 151-154.
5. Alexander, F. W., Sandmeier, E., Mehta, P. K.; Christen, P. (1994). Evolutionary relationships among pyridoxal-59-phosphate-dependent enzymes. Regio-specific a, b and c families. Eur J Biochem 219, 953-960.
6. Andersen, G. L., Beattie, G. A.; Lindow, S. E. (1998). Molecular characterization and sequence of a methionine biosynthetic locus from Pseudomonas syringae. J Bacteriol 180, 4497-4507.
7. Auger, S., Yuen, W. H., Danchin, A.; Martin-Verstraete, I. (2002). The metIC operon involved in methionine biosynthesis in Bacillus subtilis is controlled by transcription antitermination. Microbiology 148, 507-518.
8. Auger, S., Gomez, M. P., Danchin, A.; Martin-Verstraete, I. (2005). The PatB protein of Bacillus subtilis is a C-S-lyase. Biochimie 87, 231-238.
9. Bairoch, A. (2000). The ENZYME database in 2000. Nucleic Acids Res 28, 304-305.
10. Barra, L., Fontenelle, C., Ermel, G., Trautwetter, A., Walker, G. C.; Blanco, C. (2006). Interrelations between glycine betaine catabolism and methionine biosynthesis in Sinorhizobium meliloti strain 102F34. J Bacteriol 188, 7195-7204.
11. Bartlem, D., Lambein, I., Okamoto, T., Itaya, A., Uda, Y., Kijima, F., Tamaki, Y., Nambara, E.; Naito, S. (2000). Mutation in the threonine synthase gene results in an over-accumulation of soluble methionine in Arabidopsis. Plant Physiol 123, 101-110.
12. Bennett, B. D., Kimball, E. H., Gao, M., Osterhout, R., Van Dien, S. J.; Rabinowitz, J. D. (2009). Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli. Nat Chem Biol 5, 593-599.
13. Bigelow, D. J.; Squier, T. C. (2005). Redox modulation of cellular signaling and metabolism through reversible oxidation of methionine sensors in calcium regulatory proteins. Biochim Biophys Acta 1703, 121-134.
14. Blanco, J., Moore, R. A., Kabaleeswaran, V.; Viola, R. E. (2003). A structural basis for the mechanism of aspartate-b-semialdehyde dehydrogenase from Vibrio cholerae. Protein Sci 12, 27-33.
15. Bolten, C. J., Schröder, H., Dickschat, J.; Wittmann, C. (2010). Towards methionine overproduction in Corynebacterium glutami-cum-methanethiol and dimethyldisulfide as reduced sulfur sources. J Microbiol Biotechnol 20, 1196-1203.
16. Born, T. L.; Blanchard, J. S. (1999). Enzyme-catalyzed acylation of homoserine: mechanistic characterization of the Escherichia coli metA-encoded homoserine transsuccinylase. Biochemistry 38, 14416-14423.
17. Born, T. L., Franklin, M.; Blanchard, J. S. (2000). Enzyme-catalyzed acylation of homoserine: mechanistic characterization of the Haemophilus influenzae met2-encoded homoserine transacetylase. Biochemistry 39, 8556-8564.
18. Bryant, D.; Moulton, V. (2004). Neighbor-net: an agglomerative method for the construction of phylogenetic networks. Mol Biol Evol 21, 255-265.
19. Chassagnole, C., Raïs, B., Quentin, E., Fell, D. A.; Mazat, J. P. (2001). An integrated study of threonine-pathway enzyme kinetics in Escherichia coli. Biochem J 356, 415-423.
20. Chiang, P. K., Gordon, R. K., Tal, J., Zeng, G. C., Doctor, B. P., Pardhasaradhi, K.; McCann, P. P. (1996). S-Adenosylmethionine and methylation. FASEB J 10, 471-480.
21. Clausen, T., Huber, R., Laber, B., Pohlenz, H. D.; Messerschmidt, A. (1996). Crystal structure of the pyridoxal-59-phosphate dependent cystathionine b-lyase from Escherichia coli at 1.83 Å. J Mol Biol 262,202-224.
22. Duclos, B., Cortay, J. C., Bleicher, F., Ron, E. Z., Richaud, C., Saint Girons, I.; Cozzone, A. J. (1989). Nucleotide sequence of the metA gene encoding homoserine trans-succinylase in Escherichia coli. Nucleic Acids Res 17, 2856.
23. Edgar, R. C. (2004). MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32, 1792-1797.
24. Eliot, A. C.; Kirsch, J. F. (2004). Pyridoxal phosphate enzymes: mechanistic, structural, and evolutionary considerations. Annu Rev Biochem 73, 383-415.
25. Erb, T. J., Evans, B. S., Cho, K., Warlick, B. P., Sriram, J., Wood, B. M. K., Imker, H. J., Sweedler, J. V., Tabita, F. R.; Gerlt, J. A. (2012). A RubisCO-like protein links SAM metabolism with isoprenoid biosynthesis. Nat Chem Biol 8, 926-932.
26. Farsi, A., Lodha, P. H., Skanes, J. E., Los, H., Kalidindi, N.; Aitken, S. M. (2009). Interconversion of a pair of active-site residues in Escherichia coli cystathionine c-synthase, E. coli cystathionine b-lyase, and Saccharomyces cerevisiae cystathionine c-lyase and development of tools for the investigation of their mechanisms and reaction specificity. Biochem Cell Biol 87, 445-457.
27. Flavin, M.; Slaughter, C. (1967). Enzymatic synthesis of homo-cysteine or methionine directly from O-succinyl-homoserine. Biochim Biophys Acta 132, 400-405.
28. Foglino, M., Borne, F., Bally, M., Ball, G.; Patte, J. C. (1995). A direct sulfhydrylation pathway is used for methionine biosynthesis in Pseudomonas aeruginosa. Microbiology 141, 431-439.
29. Foster, J., Ganatra, M., Kamal, I., Ware, J., Makarova, K., Ivanova, N., Bhattacharyya, A., Kapatral, V., Kumar, S.; other authors (2005). The Wolbachia genome of Brugia malayi: endosymbiont evolution within a human pathogenic nematode. PLoS Biol 3, e121.
30. González, J. C., Peariso, K., Penner-Hahn, J. E.; Matthews, R. G. (1996). Cobalamin-independent methionine synthase from Escherichia coli: a zinc metalloenzyme. Biochemistry 35, 12228-12234.
31. Gophna, U., Bapteste, E., Doolittle, W. F., Biran, D.; Ron, E. Z. (2005). Evolutionary plasticity of methionine biosynthesis. Gene 355, 48-57.
32. Goudarzi, M.; Born, T. L. (2006). Purification and characterization of Thermotoga maritima homoserine transsuccinylase indicates it is a transacetylase. Extremophiles 10, 469-478.
33. Hacham, Y., Gophna, U.; Amir, R. (2003). In vivo analysis of various substrates utilized by cystathionine c-synthase and O-acetylhomoserine sulfhydrylase in methionine biosynthesis. Mol Biol Evol 20, 1513-1520.
34. Hopwood, E. M., Ahmed, D.; Aitken, S. M. (2014). A role for glutamate-333 of Saccharomyces cerevisiae cystathionine c-lyase as a determinant of specificity. Biochim Biophys Acta 1844, 465-472.
35. Hullo, M. F., Auger, S., Soutourina, O., Barzu, O., Yvon, M., Danchin, A.; Martin-Verstraete, I. (2007). Conversion of methionine to cysteine in Bacillus subtilis and its regulation. J Bacteriol 189, 187-197.
36. Hunter, S., Jones, P., Mitchell, A., Apweiler, R., Attwood, T. K., Bateman, A., Bernard, T., Binns, D., Bork, P.; other authors (2012). InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Res 40 (D1), D306-D312.
37. Hwang, B. J., Kim, Y., Kim, H. B., Hwang, H. J., Kim, J. H.; Lee, H. S. (1999). Analysis of Corynebacterium glutamicum methionine biosyn-thetic pathway: isolation and analysis of metB encoding cystathionine c-synthase. Mol Cells 9, 300-308.
38. Hwang, B. J., Yeom, H. J., Kim, Y.; Lee, H. S. (2002). Corynebacterium glutamicum utilizes both transsulfuration and direct sulfhydrylation pathways for methionine biosynthesis. J Bacteriol 184, 1277-1286.
39. Hwang, B. J., Park, S. D., Kim, Y., Kim, P.; Lee, H. S. (2007). Biochemical analysis on the parallel pathways of methionine biosynthesis in Corynebacterium glutamicum. J Microbiol Biotechnol 17, 1010-1017.
40. Ivanova, N., Daum, C., Lang, E., Abt, B., Kopitz, M., Saunders, E., Lapidus, A., Lucas, S., Glavina Del Rio, T.; other authors (2010). Complete genome sequence of Haliangium ochraceum type strain (SMP-2). Stand Genomic Sci 2, 96-106.
41. Iwama, T., Hosokawa, H., Lin, W., Shimizu, H., Kawai, K.; Yamagata, S. (2004). Comparative characterization of the oah2 gene homologous to the oah1 of Thermus thermophilus HB8. Biosci Biotechnol Biochem 68, 1357-1361.
42. Kerr, D. S. (1971). O-Acetylhomoserine sulfhydrylase from Neurospora. Purification and consideration of its function in homocysteine and methionine synthesis. J Biol Chem 246, 95-102.
43. Kiene, R. P., Linn, L. J., González, J., Moran, M. A.; Bruton, J. A. (1999). Dimethylsulfoniopropionate and methanethiol are important precursors of methionine and protein-sulfur in marine bacterio-plankton. Appl Environ Microbiol 65, 4549-4558.
44. Koutmos, M., Datta, S., Pattridge, K. A., Smith, J. L.; Matthews, R. G. (2009). Insights into the reactivation of cobalamin-dependent methionine synthase. Proc Natl Acad Sci U S A 106, 18527-18532.
45. Krömer, J. O., Wittmann, C., Schröder, H.; Heinzle, E. (2006). Metabolic pathway analysis for rational design of L-methionine production by Escherichia coli and Corynebacterium glutamicum. Metab Eng 8, 353-369.
46. Kumar, D.; Gomes, J. (2005). Methionine production by fermentation. Biotechnol Adv 23, 41-61.
47. Lawrence, J. G.; Roth, J. R. (1996). Evolution of coenzyme B12 synthesis among enteric bacteria: evidence for loss and reacquisition of a multigene complex. Genetics 142, 11-24.
48. Lee, L. W., Ravel, J. M.; Shive, W. (1966). Multimetabolite control of a biosynthetic pathway by sequential metabolites. J Biol Chem 241, 5479-5480.
49. Ma, Y., Biava, H., Contestabile, R., Budisa, N.; di Salvo, M. L. (2014). Coupling bioorthogonal chemistries with artificial metabolism: intracellular biosynthesis of azidohomoalanine and its incorporation into recombinant proteins. Molecules 19, 1004-1022.
50. Manders, A. L., Jaworski, A. F., Ahmed, M.; Aitken, S. M. (2013). Exploration of structure-function relationships in Escherichia coli cystathionine c-synthase and cystathionine b-lyase via chimeric constructs and site-specific substitutions. Biochim Biophys Acta 1834, 1044-1053.
51. McCutcheon, J. P.; Moran, N. A. (2012). Extreme genome reduction in symbiotic bacteria. Nat Rev Microbiol 10, 13-26.
52. Messerschmidt, A., Worbs, M., Steegborn, C., Wahl, M. C., Huber, R., Laber, B.; Clausen, T. (2003). Determinants of enzymatic specificity in the Cys-Met-metabolism PLP-dependent enzymes family: crystal structure of cystathionine c-lyase from yeast and intrafamiliar structure comparison. Biol Chem 384, 373-386.
53. Nakamori, S., Kobayashi, S., Nishimura, T.; Takagi, H. (1999). Mechanism of L-methionine overproduction by Escherichia coli: the replacement of Ser-54 by Asn in the MetJ protein causes the derepression of L-methionine biosynthetic enzymes. Appl Microbiol Biotechnol 52, 179-185.
54. Pasamontes, A.; Garcia-Vallve, S. (2006). Use of a multi-way method to analyze the amino acid composition of a conserved group of orthologous proteins in prokaryotes. BMC Bioinformatics 7, 257.
55. Patrick, W. M., Quandt, E. M., Swartzlander, D. B.; Matsumura, I. (2007). Multicopy suppression underpins metabolic evolvability. Mol Biol Evol 24, 2716-2722.
56. Picardeau, M., Bauby, H.; Saint Girons, I. (2003). Genetic evidence for the existence of two pathways for the biosynthesis of methionine in the Leptospira spp. FEMS Microbiol Lett 225, 257-262.
57. Punta, M., Coggill, P. C., Eberhardt, R. Y., Mistry, J., Tate, J., Boursnell, C., Pang, N., Forslund, K., Ceric, G.; other authors (2012). The Pfam protein families database. Nucleic Acids Res 40 (D1), D290-D301.
58. Rabeh, W. M.; Cook, P. F. (2004). Structure and mechanism of O-acetylserine sulfhydrylase. J Biol Chem 279, 26803-26806.
59. Ravanel, S., Gakière, B., Job, D.; Douce, R. (1998). The specific features of methionine biosynthesis and metabolism in plants. Proc Natl Acad Sci U S A 95, 7805-7812.
60. Rodionov, D. A., Vitreschak, A. G., Mironov, A. A.; Gelfand, M. S. (2004). Comparative genomics of the methionine metabolism in Gram-positive bacteria: a variety of regulatory systems. Nucleic Acids Res 32, 3340-3353.
61. Rotem, O., Biran, D.; Ron, E. Z. (2013). Methionine biosynthesis in Agrobacterium tumefaciens: study of the first enzyme. Res Microbiol 164, 12-16.
62. Rowbury, R. J. (1983). Methionine biosynthesis and its regulation. In Amino Acids: Biosynthesis and Genetic Regulation, pp. 191-211. Edited by K. M. Hermann; R. L. Somerville. Reading, MA: Addison-Wesley.
63. Rowbury, R. J.; Woods, D. D. (1961). Further studies on the repression of methionine synthesis in Escherichia coli. J Gen Microbiol 24, 129-144.
64. Rowbury, R. J.; Woods, D. D. (1964). O-Succinylhomoserine as an intermediate in the synthesis of cystathionine by Escherichia coli. J Gen Microbiol 36, 341-358.
65. Rückert, C., Pühler, A.; Kalinowski, J. (2003). Genome-wide analysis of the L-methionine biosynthetic pathway in Corynebacterium glutamicum by targeted gene deletion and homologous complementation. J Biotechnol 104, 213-228.
66. Saha, B., Mukherjee, S.; Das, A. K. (2009). Molecular characterization of Mycobacterium tuberculosis cystathionine gamma synthase-Apo- and holoforms. Int J Biol Macromol 44, 385-392.
67. Sayers, E. W., Barrett, T., Benson, D. A., Bryant, S. H., Canese, K., Chetvernin, V., Church, D. M., DiCuccio, M., Edgar, R.; other authors (2009). Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 37 (Database), D5-D15.
68. Seiflein, T. A.; Lawrence, J. G. (2006). Two transsulfurylation pathways in Klebsiella pneumoniae. J Bacteriol 188, 5762-5774.
69. Serra, A. L., Mariscotti, J. F., Barra, J. L., Lucchesi, G. I., Domenech, C. E.; Lisa, A. T. (2002). Glycine betaine transmethylase mutant of Pseudomonas aeruginosa. J Bacteriol 184, 4301-4303.
70. Sletten, E. M.; Bertozzi, C. R. (2009). Bioorthogonal chemistry: fishing for selectivity in a sea of functionality. Angew Chem Int Ed Engl 48, 6974-6998.
71. Smacchi, E.; Gobbetti, M. (1998). Purification and characterization of cystathionine c-lyase from Lactobacillus fermentum DT41. FEMS Microbiol Lett 166, 197-202.
72. Stover, C. K., Pham, X. Q., Erwin, A. L., Mizoguchi, S. D., Warrener, P., Hickey, M. J., Brinkman, F. S., Hufnagle, W. O., Kowalik, D. J.; other authors (2000). Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic pathogen. Nature 406, 959-964.
73. Sun, J., Steindler, L., Thrash, J. C., Halsey, K. H., Smith, D. P., Carter, A. E., Landry, Z. C.; Giovannoni, S. J. (2011). One carbon metabolism in SAR11 pelagic marine bacteria. PLoS ONE 6, e23973.
74. Talavera, G.; Castresana, J. (2007). Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol 56, 564-577.
75. Tanioka, Y., Yabuta, Y., Yamaji, R., Shigeoka, S., Nakano, Y., Watanabe, F.; Inui, H. (2009). Occurrence of pseudovitamin B12 and its possible function as the cofactor of cobalamin-dependent methionine synthase in a cyanobacterium Synechocystis sp. PCC6803. J Nutr Sci Vitaminol (Tokyo) 55, 518-521.
76. Tanioka, Y., Miyamoto, E., Yabuta, Y., Ohnishi, K., Fujita, T., Yamaji, R., Misono, H., Shigeoka, S., Nakano, Y.; other authors (2010). Methyladeninylcobamide functions as the cofactor of methionine synthase in a Cyanobacterium, Spirulina platensis NIES-39. FEBS Lett 584, 3223-3226.
77. Tatusov, R. L., Fedorova, N. D., Jackson, J. D., Jacobs, A. R., Kiryutin, B., Koonin, E. V., Krylov, D. M., Mazumder, R., Mekhedov, S. L.; other authors (2003). The COG database: an updated version includes eukaryotes. BMC Bioinformatics 4, 41.
78. Tran, T. H., Krishnamoorthy, K., Begley, T. P.; Ealick, S. E. (2011). A novel mechanism of sulfur transfer catalyzed by O-acetylhomoserine sulfhydrylase in the methionine-biosynthetic pathway of Wolinella succinogenes. Acta Crystallogr D Biol Crystallogr 67, 831-838.
79. Usuda, Y.; Kurahashi, O. (2005). Effects of deregulation of methionine biosynthesis on methionine excretion in Escherichia coli. Appl Environ Microbiol 71, 3228-3234.
80. Valley, C. C., Cembran, A., Perlmutter, J. D., Lewis, A. K., Labello, N. P., Gao, J.; Sachs, J. N. (2012). The methionine-aromatic motif plays a unique role in stabilizing protein structure. J Biol Chem 287, 34979-34991.
81. Vermeij, P.; Kertesz, M. A. (1999). Pathways of assimilative sulfur metabolism in Pseudomonas putida. J Bacteriol 181, 5833-5837.
82. Whitfield, C. D., Steers, E. J. Jr; Weissbach, H. (1970). Purification and properties of 5-methyltetrahydropteroyltriglutamate-homocys-teine transmethylase. J Biol Chem 245, 390-401.
83. Yamagata, S. (1971). Homocysteine synthesis in yeast. Partial purification and properties of O-acetylhomoserine sulfhydrylase. J Biochem 70, 1035-1045.
84. Zdych, E., Peist, R., Reidl, J.; Boos, W. (1995). MalY of Escherichia coli is an enzyme with the activity of a b C-S lyase (cystathionase). J Bacteriol 177, 5035-5039.
85. Ziegler, K., Yusupov, M., Bishop, B.; Born, T. L. (2007). Substrate analysis of homoserine acyltransferase from Bacillus cereus. Biochem Biophys Res Commun 361, 510-515.
86. Zubieta, C., Arkus, K. A., Cahoon, R. E.; Jez, J. M. (2008). A single amino acid change is responsible for evolution of acyltransferase specificity in bacterial methionine biosynthesis. J Biol Chem 283, 7561-7567.