Insights into the genome of the enteric bacterium Escherichia blattae: Cobalamin (B12) biosynthesis, B12-dependent reactions, and inactivation of the gene region encoding B12-dependent glycerol dehydratase by a new mu-like prophage

Journal of Molecular Microbiology and Biotechnology

Volumn 8, Issue 3, 2005, Pages 150-168

  Andres, Sönke ^a   Wiezer, Arnim ^a   Bendfeldt, Hanna ^a   Waschkowitz, Tanja ^a   Toeche Mittler, Caroline ^a   Daniel, Rolf ^a  

^a UNIVERSITY OF GÖTTINGEN   (Germany)

Author keywords

Bacteriophage Mu; Cobalamin (B12); dha regulon; Escherichia blattae; Glycerol dehydratase

Indexed keywords

1,3 PROPANEDIOL; BACTERIAL ENZYME; CYANOCOBALAMIN; DIHYDROXYACETONE; GLYCEROL; HYDROLYASE; PHOSPHOTRANSFERASE;

ARTICLE; BACTERIAL GENOME; BACTERIAL STRAIN; BIOSYNTHESIS; COENZYME; CONTROLLED STUDY; CORRELATION ANALYSIS; ESCHERICHIA; ESCHERICHIA BLATTAE; FERMENTATION; GENE INACTIVATION; GENE INSERTION; INTESTINE FLORA; NONHUMAN; NUCLEOTIDE SEQUENCE; PROPHAGE; REGULON; SEQUENCE ANALYSIS; UNINDEXED SEQUENCE;

AMINO ACID SEQUENCE; BACTERIOPHAGE MU; BASE SEQUENCE; ESCHERICHIA; GENOME, BACTERIAL; HYDRO-LYASES; MOLECULAR SEQUENCE DATA; PHYLOGENY; PROPHAGES; REGULON; VITAMIN B 12;

ENTERIC BACTERIA; ENTEROBACTERIA PHAGE MU; ESCHERICHIA BLATTAE; SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM;

EID: 23944489078     PISSN: 14641801     EISSN: None     Source Type: Journal    
DOI: 10.1159/000085788     Document Type: Article

References (60)

1. Akroyd, J., and Symonds, N. 1986. Localization of the gam gene of bacteriophage Mu and characterization of the gene product. Gene 49:273-282.
2. Andersson, L.O., Borg, H., and Mikaelsson, M. 1972. Molecular weight estimation of proteins by electrophoresis in polyacrylamide gel of graded porosity. FEBS Lett 20:199-202.
3. Ausubel, F.M., Brent, R., Kingston, R.E., Moore, D.D., Seidman, J.G., Smith, J.A., and Struhl, K. 1987. Current Protocols in Molecular Biology. New York, Wiley, USA.
4. 12 synthesis and propanediol degradation. J Bacteriol 174:2253-2266.
5. Bobik, T.A., Xu, Y., Jeter, R.M., Otto, K.E., and Roth, J.R. 1997. Propanediol utilization genes (pdu) of Salmonella typhimurium: Three genes for the propanediol dehydratase. J Bacteriol 179:6633-6639.
6. Bradford, M.M. 1976. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem 72:248-254.
7. Burgess, N.R., McDermott, S.N., and Whiting, J. 1973. Aerobic bacteria occurring in the hind-gut of the cockroach, Blatta orientalis. J Hyg 71:1-7.
8. Casjens, S. 2003. Prophages and bacterial genomics: What have we learned so far? Mol Microbiol 49:277-300.
9. Chen, P., Andersson, D.I., and Roth, J.R. 1994. The control region of the cob/pdu regulon in Salmonella typhimurium. J Bacteriol 176:5474-5482.
10. Daniel, R., and Gottschalk, G. 1992. Growth temperature-dependent activity of glycerol dehydratase in Escherichia coli expressing the Citrobacter freundii dha regulon. FEMS Microbiol Lett 100:281-286.
11. 12-dependent glycerol and diol dehydratases and organization of the encoding genes. FEMS Microbiol Rev 22:553-566.
12. Daniel, R., Boenigk, R., and Gottschalk, G. 1995a. Purification of the 1,3-propanediol dehydrogenase from Citrobacter freundii and cloning, sequencing and overexpression of the corresponding gene in Escherichia coli. J Bacteriol 177:2151-2156.
13. Daniel, R., Stuertz, K., and Gottschalk, G. 1995b. Biochemical and molecular characterization of the oxidative branch of glycerol utilization by Citrobacter freundii. J Bacteriol 177:4392-4401.
14. Devereux, J., Haeberli, P., and Smithies, O. 1984. A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res 12:387-395.
15. Drummond, J.T., and Matthews, R.G. 1993. Cobalamin-dependent and cobalamin-independent methionine synthases in Escherichia coli: Two solutions to the same chemical problem. Adv Exp Med Biol 338:687-692.
16. Forage, R.G., and Foster, M.A. 1979. Resolution of the coenzyme B-12-dependent dehydratases of Klebsiella sp. and Citrobacter freundii. Biochim Biophys Acta 569:249-258.
17. Giphart-Gassler, M., Plasterk, R.H.A., and van de Putte, P. 1982. G inversion in bacteriophage Mu: A novel way of gene splicing. Nature 297:339-342.
18. Grundy, F.J., and Howe, M.M. 1984. Morphogenetic structures present in lysates of amber mutants of bacteriophage Mu. Virology 143:485-504.
19. Gutknecht, R., Beutler, R., Garcia-Alles, L.F., Baumann, U., and Erni, B. 2001. The dihydroxyacetone kinase of Escherichia coli utilizes a phosphoprotein instead of ATP as phosphoryl donor. EMBO J 20:2480-2486.
20. Haller, T., Buckel, T., Rétéy, J., and Gerlt, J.A. 2000. Discovering new enzymes and metabolic pathways: Conversion of succinate to propionate by Escherichia coli. Biochemistry 39:4622-4629.
21. Heidelberg, J.F., Paulsen, I.T., Nelson, K.E., Gaidos, E.J., Nelson, W.C., Read, T.D., Eisen, J.A., Seshadri, R., Ward, N., Methe, B., Clayton, R.A., Meyer, T., Tsapin, A., Scott, J., Beanan, M., Brinkac, L., Daugherty, S., De-Boy, R.T., Dodson, R.J., Durkin, A.S., Haft, D.H., Kolonay, J.F., Madupu, R., Peterson, J.D., Umayam, L.A., White, O., Wolf, A.M., Vamathevan, J., Weidman, J., Impraim, M., Lee, K., Berry, K., Lee, C., Mueller, J., Khouri, H., Gill, J., Utterback, T.R., McDonald, L.A., Feldblyum, T.V., Smith, H.O., Venter, J.C., Nealson, K.H., and Fraser, C.M. 2002. Genome sequence of the dissimilatory metal ion-reducing bacterium Shewanella oneidensis. Nat. Biotechnol 20:1118-1123.
22. Howe, M.M., and Bade, E.G. 1995. Molecular biology of the bacteriophage Mu. Science 190:624-632.
23. 12) de novo under anaerobic growth condition. J Bacteriol 159:206-216.
24. Johnson, E.A., Burke, S.K., Forage, R.G., and Lin, E.C.C. 1984. Purification and properties of dihydroxyacetone kinase from Klebsiella pneumoniae. J Bacteriol 160:55-60.
25. Kahmann, R., Seiler, A., Wulczyn, F.G., and Pfaff, E. 1985. The mom gene of bacteriophage Mu: a unique regulatory scheme to control a lethal function. Gene 39:61-70.
26. Kamp, D., Kahmann, R., Zipser, D., Broker, T.R., and Chow, L.T. 1978. Inversion of the G DNA segment of phage Mu controls phage infectivity. Nature 271:577-580.
27. 12 production by Citrobacter freundii or Klebsiella pneumoniae during tempeh fermentation and proof of enterotoxin absence by PCR. Appl Environ Microbiol 60:1495-1499.
28. 12-dependent glycerol and diol dehydratases from metagenomic DNA libraries derived from enrichment cultures. Appl Environ Microbiol 69:3048-3060.
29. Kofoid, E., Rappleye, C., Stojiljkovic, I., and Roth, J.R. 1999. The 17-gene ethanolamine (eut) operon of Salmonella typhimurium encodes five homologues of carboxysome shell proteins. J Bacteriol 181:5317-5329.
30. Krzycki, J., and Zeikus, J.G. 1980. Quantification of corrinoids in methanogenic bacteria. Curr Microbiol 3:243-245.
31. 12 synthesis among enteric bacteria: Evidence for loss and reacquisition of a multigene complex. Genetics 142:11-26.
32. 12-dependent glycerol dehydratase of Clostridium pasteurianum. FEMS Microbiol Lett 164:21-28.
33. 12. Appl Microbiol Biotechnol 58:275-285.
34. 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., and Wilson, R.K. 2001. Complete genome sequence of Salmonella enterica serovar Typhimurium LT2. Nature 413:852-856.
35. Morgan, G.J., Hatfull, G.F., Casjens, S., and Hendrix, R.W. 2002. Bacteriophage Mu genome sequence: Analysis and comparison with Mu-like prophages in Haemophilus, Neisseria and Deinococcus. J Mol Biol 317:337-359.
36. Nakamura, C.E., and Whited, G.M. 2003. Metabolic engineering for the microbial production of 1,3-propanediol. Curr Opin Biotechnol 14:454-459.
37. 12-Bedürfnis phototropher Schwefelbakterien. Arch Microbiol 55:245-256.
38. 12-dependent glycerol dehydratase and diol dehydratase. Eur J Biochem 245:398-401.
39. Rondon, M.R., and Escalante-Semerena, J.C. 1992. The poc locus is required for 1,2-propanediol-dependent transcription of the cobalamin biosynthetic (cob) and propanediol utilization (pdu) genes of Salmonella typhimurium. J Bacteriol 174:2267-2272.
40. Roth, J.R., Lawrence, J.G., and Bobik, T.A. 1996. Cobalamin (coenzyme 612): Synthesis and biological significance. Annu Rev Microbiol 50:137-181.
41. 12) biosynthetic genes of Salmonella typhimurium. J Bacteriol 175:3303-3316.
42. Salmon, K.A., Freedman, O., Ritchings, B.W., and DuBow, M.S. 2000. Characterization of the lysogenic repressor (c) gene of the Pseudomonas aeruginosa transposable bacteriophage D3112. Virology 272:85-97.
43. Scott, A., and Roessner, C.A. 2002. Biosynthesis of cobalamin (vitamin 612). Biochem Soc Trans 30:613-620.
44. 12-dependent glycerol dehydratase of Citrobacter freundii. Eur J Biochem 268:2369-2378.
45. 12-dependent glycerol dehydratase of Citrobacter freundii. J Bacteriol 178:5793-5796.
46. Shibata, N., Masuda, J., Tobimatsu, T., Toraya, T., Suto, K., Morimoto, Y., and Yasuoka, N. 1999. A new mode of 812 binding and the direct participation of a potassium ion in enzyme catalysis: X-ray structure of diol dehydratase. Structure Fold Des 7:997-1008.
47. Skraly, F.A., Lyte, B.L., and Cameron, D.C. 1998. Construction and characterization of a 1,3-propanediol operon. Appl Environ Microbiol 64:98-105.
48. Sprenger, G.A., Hammer, B.A., Johnson, E.A., and Lin, E.C.C. 1989. Anaerobic growth of Escherichia coli on glycerol by importing genes of the dha regulon from Klebsiella pneumoniae. J Gen Microbiol 135:1255-1262.
49. Sun J., van den Heuvel, J., Soucaille, P., Qu, Y., and Zeng, A.P. 2003. Comparative genomic analysis of dha regulon and related genes for anaerobic glycerol metabolism in bacteria. Biotechnol Prog 19:263-272.
50. Tech, M., and Merkl, R. 2003. YACOP: enhanced gene prediction obtained by a combination of existing methods. In Silico Biol 3:441-451.
51. Tobimatsu, T., Azuma, M., Matsubara, H., Takatori, H., Niida, T., Nishimoto, K., Satoh, H., Hayashi, R., and Toraya, T. 1996. Cloning, sequencing, and high level expression of the genes encoding adenosylcobalamin-dependent glycerol dehydrase of Klebsiella pneumoniae. J Biol Chem 271:22352-22357.
52. Tobimatsu, T., Hara, T., Sakaguchi, M., Kishimoto, Y., Wada, Y., Isoda, M., Sakai, T., and Toraya, T. 1995. Molecular cloning, sequencing, and expression of the genes encoding adenosylcobalamin-dependent diol dehydrase of Klebsiella oxytoca. J Biol Chem 270:7142-7148.
53. Tobimatsu, T., Sakai, T., Hashida, Y., Mizoguchi, N., Miyoshi, S., and Toraya, T. 1997. Heterologous expression, purification, and properties of diol dehydratase, an adenosylcobalamin-dependent enzyme of Klebsiella oxytoca. Arch Biochem Biophys 347:132-140.
54. 12-dependent diol dehydratase and glycerol dehydratase in selected genera of Enterobacteriaceae and Propionibacteriaceae. J Bacteriol 141:1439-1442.
55. Wang, P.W., Chu, L., and Guttman, D.S. 2004. Complete sequence and evolutionary genomic analysis of the Pseudomonas aeruginosa transposable bacteriophage D3112. J Bacteriol 186:400-410.
56. Wang, X., and Higgins, N.P. 1994. 'Mutprints' of the lac operon demonstrate physiological control over the randomness of in vivo transposition. Mol Microbiol 12:665-677.
57. 12). Nat Prod Rep 19:390-412.
58. 12-mediated repression of the Salmonella typhimurium metE gene. J Bacteriol 174:4833-4837.
59. Wulczyn, F.G., and Kahmann, R. 1991. Translational stimulation: RNA sequence and structure requirements for binding of Com protein. Cell 65:259-269.
60. 12-dependent glycerol dehydratase in complex with cobalamin and propane-1,2-diol. Eur J Biochem 269:4484-4494.