The genome of Rhodobacter sphaeroides strain 2.4.1 encodes functional cobinamide salvaging systems of archaeal and bacterial origins

Molecular Microbiology

Volumn 70, Issue 4, 2008, Pages 824-836

  Gray, Michael J ^a   Tavares, Norbert K ^a   Escalante Semerena, Jorge C ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSYLCOBINAMIDE; ADENOSYLCOBINAMIDE AMINOHYDROLASE; ADENOSYLCOBINAMIDE GUANOSINE DIPHOSPHATE; ADENOSYLCOBINAMIDE PHOSPHATE; ADENOSYLCOBIRIC ACID; ADENOSYLCOBYRIC ACID; BACTERIAL ENZYME; COBINAMIDE; COBINAMIDE B SYNTHETASE; GUANYLYLTRANSFERASE; HYDROLASE; UNCLASSIFIED DRUG;

ARCHAEBACTERIUM; ARTICLE; BACTERIAL GENOME; BACTERIAL METABOLISM; BIOASSAY; CBIZ GENE; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; NONHUMAN; PRIORITY JOURNAL; RHODOBACTER SPHAEROIDES; ULTRAVIOLET SPECTROSCOPY;

ALLELES; AMIDOHYDROLASES; ARCHAEA; ARCHAEAL PROTEINS; BACTERIAL PROTEINS; COBAMIDES; GENES, ARCHAEAL; GENES, BACTERIAL; GENETIC COMPLEMENTATION TEST; GENOME, BACTERIAL; PHYLOGENY; PLASMIDS; RHODOBACTER SPHAEROIDES; SALMONELLA TYPHIMURIUM;

ARCHAEA; BACTERIA (MICROORGANISMS); RHODOBACTER SPHAEROIDES; RHODOBACTER SPHAEROIDES 2.4.1; SALMONELLA ENTERICA;

EID: 54249145198     PISSN: 0950382X     EISSN: 13652958     Source Type: Journal    
DOI: 10.1111/j.1365-2958.2008.06437.x     Document Type: Article

References (58)

1. Ausubel, F.A., Brent, R., Kingston, R.E., Moore, D.D., Seidman, J.G., Smith, J.A. Struhl, K. (1989) Current Protocols in Molecular Biology. New York : Greene Publishing Associates & Wiley Interscience.
2. Balch, W.E. Wolfe, R.S. (1976) New approach to the cultivation of methanogenic bacteria: 2-mercaptoethanesulfonic acid (HS-CoM)-dependent growth of Methanobacterium ruminantium in a pressureized atmosphere. Appl Environ Microbiol 32 : 781 791.
3. Barker, H.A., Smyth, R.D., Weissbach, H., Toohey, J.I., Ladd, J.N. Volcani, B.E. (1960) Isolation and properties of crystalline cobamide coenzymes containing benzimidazole or 5, 6-dimethylbenzimidazole. J Biol Chem 235 : 480 488.
4. Bentley, S.D., Chater, K.F., Cerdeno-Tarraga, A.M., Challis, G.L., Thomson, N.R., James, K.D., et al. (2002) Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2). Nature 417 : 141 147.
5. Berkowitz, D., Hushon, J.M., Whitfield, H.J., Jr, Roth, J. Ames, B.N. (1968) Procedure for identifying nonsense mutations. J Bacteriol 96 : 215 220.
6. Bertani, G. (1951) Studies on lysogenesis. I. The mode of phage liberation by lysogenic Escherichia coli. J Bacteriol 62 : 293 300.
7. Bertani, G. (2004) Lysogeny at mid-twentieth century: P1, P2, and other experimental systems. J Bacteriol 186 : 595 600.
8. 12: how the problem of its biosynthesis was solved. Angew Chem Int Ed Engl 34 : 383 411.
9. Blanche, F., Debussche, L., Famechon, A., Thibaut, D., Cameron, B. Crouzet, J. (1991) A bifunctional protein from Pseudomonas denitrificans carries cobinamide kinase and cobinamide phosphate guanylyltransferase activities. J Bacteriol 173 : 6052 6057.
10. Blanche, F., Thibaut, D., Couder, M. Muller, J.C. (1990) Identification and quantitation of corrinoid precursors of cobalamin from Pseudomonas denitrificans by high-performance liquid chromatography. Anal Biochem 189 : 24 29.
11. Borths, E.L., Poolman, B., Hvorup, R.N., Locher, K.P. Rees, D.C. (2005) In vitro functional characterization of BtuCD-F, the Escherichia coli ABC transporter for vitamin B12 uptake. Biochemistry 44 : 16301 16319.
12. Brindley, A.A., Raux, E., Leech, H.K., Schubert, H.L. Warren, M.J. (2003) A story of chelatase evolution: identification and characterization of a small 13-15-kDa 'ancestral' cobaltochelatase (CbiXS) in the archaea. J Biol Chem 278 : 22388 22395.
13. Brushaber, K.R., O'Toole, G.A. Escalante-Semerena, J.C. (1998) CobD, a novel enzyme with 1-threonine-O-3-phosphate decarboxylase activity, is responsible for the synthesis of (R)-1-amino-2-propanol O-2-phosphate, a proposed new intermediate in cobalamin biosynthesis in Salmonella typhimurium LT2. J Biol Chem 273 : 2684 2691.
14. Bult, C.J., White, O., Olsen, G.J., Zhou, L., Fleischmann, R.D., Sutton, G.G., et al. (1996) Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. Science 273 : 1058 1073.
15. Cherezov, V., Yamashita, E., Liu, W., Zhalnina, M., Cramer, W.A. Caffrey, M. (2006) In meso structure of the cobalamin transporter, BtuB, at 1.95 Å resolution. J Mol Biol 364 : 716 734.
16. Chowdhury, S., Thomas, M.G., Escalante-Semerena, J.C. Banerjee, R. (2001) The coenzyme B12 analog 5′-deoxyadenosylcobinamide-GDP supports catalysis by methylmalonyl-CoA mutase in the absence of trans-ligand co-ordination. J Biol Chem 276 : 1015 1019.
17. DeSantis, T.Z., Hugenholtz, P., Larsen, N., Rojas, M., Brodie, E.L., Keller, K., et al. (2006) Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 72 : 5069 5072.
18. Escalante-Semerena, J.C. (2007) Conversion of cobinamide into adenosylcobamide in bacteria and archaea. J Bacteriol 189 : 4555 4560.
19. Felsenstein, J. (2005) PHYLIP (Phylogeny Inference Package), Version 3.6. Distributed by the author. Seattle, WA : Department of Genome Sciences, University of Washington.
20. Finn, R.D., Mistry, J., Schuster-Bockler, B., Griffiths-Jones, S., Hollich, V., Lassmann, T., et al. (2006) Pfam: clans, web tools and services. Nucleic Acids Res 34 : D247 D251.
21. Fonseca, M.V., Buan, N.R., Horswill, A.R., Rayment, I. Escalante-Semerena, J.C. (2002) The ATP: co(I) rrinoid adenosyltransferase (CobA) enzyme of Salmonella enterica requires the 2′-OH Group of ATP for function and yields inorganic triphosphate as its reaction byproduct. J Biol Chem 277 : 33127 33131.
22. Fonseca, M.V. Escalante-Semerena, J.C. (2000) Reduction of cob(III) alamin to cob(II) alamin in Salmonella enterica Serovar Typhimurium LT2. J Bacteriol 182 : 4304 4309.
23. Grabau, C. Roth, J.R. (1992) A Salmonella typhimurium cobalamin-deficient mutant blocked in 1-amino-2-propanol synthesis. J Bacteriol 174 : 2138 2144.
24. Guzman, L.M., Belin, D., Carson, M.J. Beckwith, J. (1995) Tight regulation, modulation, and high-level expression by vectors containing the arabinose PBAD promoter. J Bacteriol 177 : 4121 4130.
25. Harmsen, H.J., Van Kuijk, B.L., Plugge, C.M., Akkermans, A.D., De Vos, W.M. Stams, A.J. (1998) Syntrophobacter fumaroxidans sp. nov., a syntrophic propionate-degrading sulfate-reducing bacterium. Int J Syst Bacteriol 48 (Part 4 1383 1387.
26. Hvorup, R.N., Goetz, B.A., Niederer, M., Hollenstein, K., Perozo, E. Locher, K.P. (2007) Asymmetry in the structure of the ABC transporter binding protein complex BtuCD-BtuF. Science 317 : 1387 1390.
27. 12) de novo under anaerobic growth conditions. J Bacteriol 159 : 206 213.
28. Jones, W.J., Leigh, J.A., Mayer, F., Woese, C.R. Wolfe, R.S. (1983) Methanococcus jannaschii sp. nov., an extremely thermophilic methanogen from a submarine hydrothermal vent. Arch Microbiol 136 : 254 261.
29. Kandt, C., Xu, Z. Tieleman, D.P. (2006) Opening and closing motions in the periplasmic vitamin B12 binding protein BtuF. Biochemistry 45 : 13284 13292.
30. Karpowich, N.K., Huang, H.H., Smith, P.C. Hunt, J.F. (2003) Crystal structures of the BtuF periplasmic-binding protein for vitamin B12 suggest a functionally important reduction in protein mobility upon ligand binding. J Biol Chem 278 : 8429 8434.
31. Kube, M., Beck, A., Zinder, S.H., Kuhl, H., Reinhardt, R. Adrian, L. (2005) Genome sequence of the chlorinated compound-respiring bacterium Dehalococcoides species strain CBDB1. Nat Biotechnol 23 : 1269 1273.
32. Laemmli, U.K. (1970) Cleavage and structural proteins during the assembly of the head of bacteriophage T4. Nature 227 : 680 685.
33. Lengyel, P., Mazumder, R. Ochoa, S. (1960) Mammalian methylmalonyl isomerase and vitamin B (12) coenzymes. Proc Natl Acad Sci USA 46 : 1312 1318.
34. Li, L., Bannantine, J.P., Zhang, Q., Amonsin, A., May, B.J., Alt, D., et al. (2005) The complete genome sequence of Mycobacterium avium subspecies paratuberculosis. Proc Natl Acad Sci USA 102 : 12344 12349.
35. Mackenzie, C., Eraso, J.M., Choudhary, M., Roh, J.H., Zeng, X., Bruscella, P., et al. (2007) Postgenomic adventures with Rhodobacter sphaeroides. Annu Rev Microbiol 61 : 283 307.
36. Markowitz, V.M., Korzeniewski, F., Palaniappan, K., Szeto, E., Werner, G., Padki, A., et al. (2006) The integrated microbial genomes (IMG) system. Nucleic Acids Res 34 : D344 D348.
37. Nascimento, A.L., Verjovski-Almeida, S., Van Sluys, M.A., Monteiro-Vitorello, C.B., Camargo, L.E., Digiampietri, L.A., et al. (2004) Genome features of Leptospira interrogans serovar Copenhageni. Braz J Med Biol Res 37 : 459 477.
38. Nelson, K.E., Fleischmann, R.D., DeBoy, R.T., Paulsen, I.T., Fouts, D.E., Eisen, J.A., et al. (2003) Complete genome sequence of the oral pathogenic bacterium Porphyromonas gingivalis strain W83. J Bacteriol 185 : 5591 6601.
39. O'Toole, G.A. Escalante-Semerena, J.C. (1995) Purification and characterization of the bifunctional CobU enzyme of Salmonella typhimurium LT2. Evidence for a CobU-GMP intermediate. J Biol Chem 270 : 23560 23569.
40. Otte, M.M., Woodson, J.D. Escalante-Semerena, J.C. (2007) The thiamine kinase (YcfN) enzyme plays a minor but significant role in cobinamide salvaging in Salmonella enterica. J Bacteriol 189 : 7310 7315.
41. Raleigh, E.A., Lech, K., and Brent, R. (1989) Selected topics from classical bacterial genetics. In Current Protocols in Molecular Biology, Vol. 1. Ausubel, F.A., Brent, R., Kingston, R.E., Moore, D.D., Seidman, J.G., Smith, J.A. Struhl, K. (eds). New York : Wiley Interscience, p. 1.4.
42. Renz, P. (1999) Biosynthesis of the 5,6-dimethy-lbenzimidazole moiety of cobalamin and of other bases found in natural corrinoids. In Chemistry and Biochemistry of B12. Banerjee, R. (ed.). New York : John Wiley & Sons, pp. 557 575.
43. 12). J Bacteriol 188 : 7331 7334.
44. Sasse, J. (1991) Detection of proteins. In Current Protocols in Molecular Biology, Vol. 1. Ausubel, F.A., Brent, R., Kingston, R.E., Moore, D.D., Seidman, J.G., Smith, J.A. Struhl, K. (eds). New York : Wiley Interscience, pp. 10.16.11 10. 16.18.
45. Seshadri, R., Adrian, L., Fouts, D.E., Eisen, J.A., Phillippy, A.M., Methe, B.A., et al. (2005) Genome sequence of the PCE-dechlorinating bacterium Dehalococcoides ethenogenes. Science 307 : 105 108.
46. Song, S., Ahn, J.K., Lee, G.H. Park, Y.G. (2007) An epidemic of chronic pseudophakic endophthalmitis due to Ochrobacterium anthropi: clinical findings and managements of nine consecutive cases. Ocul Immunol Inflamm 15 : 429 437.
47. Takami, H., Nakasone, K., Takaki, Y., Maeno, G., Sasaki, R., Masui, N., et al. (2000) Complete genome sequence of the alkaliphilic bacterium Bacillus halodurans and genomic sequence comparison with Bacillus subtilis. Nucleic Acids Res 28 : 4317 4331.
48. Takami, H., Takaki, Y., Chee, G.J., Nishi, S., Shimamura, S., Suzuki, H., et al. (2004) Thermoadaptation trait revealed by the genome sequence of thermophilic Geobacillus kaustophilus. Nucleic Acids Res 32 : 6292 6303.
49. Thomas, M.G. Escalante-Semerena, J.C. (2000) Identification of an alternative nucleoside triphosphate: 5′-deoxyadenosylcobinamide phosphate nucleotidyltransferase in Methanobacterium thermoautotrophicumΔH. J Bacteriol 182 : 4227 4233.
50. Thomas, M.G., Thompson, T.B., Rayment, I. Escalante-Semerena, J.C. (2000) Analysis of the adenosylcobinamide kinase/adenosylcobinamide phosphate guanylyltransferase (CobU) enzyme of Salmonella typhimurium LT2. Identification of residue H46 as the site of guanylylation. J Biol Chem 275 : 27376 27386.
51. Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F. Higgins, D.G. (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25 : 4876 4882.
52. Woodcock, D.M., Crowther, P.J., Doherty, J., Jefferson, S., De Cruz, E., Noyer-Weidner, M., et al. (1989) Quantitative evaluation of Escherichia coli host strains for tolerance to cytosine methylation in plasmid and phage recombinants. Nucleic Acids Res 17 : 3469 3478.
53. Woodson, J.D. Escalante-Semerena, J.C. (2004) CbiZ, an amidohydrolase enzyme required for salvaging the coenzyme B12 precursor cobinamide in archaea. Proc Natl Acad Sci USA 101 : 3591 3596.
54. Woodson, J.D. Escalante-Semerena, J.C. (2006) The cbiS gene of the archaeon Methanopyrus kandleri AV19 encodes a bifunctional enzyme with adenosylcobinamide amidohydrolase and alpha-ribazole-phosphate phosphatase activities. J Bacteriol 188 : 4227 4235.
55. Woodson, J.D., Peck, R.F., Krebs, M.P. Escalante-Semerena, J.C. (2003a) The cobY gene of the archaeon Halobacterium sp. strain NRC-1 is required for de novo cobamide synthesis. J Bacteriol 185 : 311 316.
56. Woodson, J.D., Zayas, C.L. Escalante-Semerena, J.C. (2003b) A new pathway for salvaging the coenzyme B12 precursor cobinamide in archaea requires cobinamide-phosphate synthase (CbiB) enzyme activity. J Bacteriol 185 : 7193 7201.
57. Zayas, C.L., Woodson, J.D. Escalante-Semerena, J.C. (2006) The cobZ gene of Methanosarcina mazei Gö1 encodes the nonorthologous replacement of the α-ribazole-5′-phosphate phosphatase (CobC) enzyme of Salmonella enterica. J Bacteriol 188 : 2740 2743.
58. Zuo, Y., Xing, D., Regan, J.M. Logan, B.E. (2008) Isolation of the exoelectrogenic bacterium Ochrobactrum anthropi YZ-1 by using a U-tube microbial fuel cell. Appl Environ Microbiol 74 : 3130 3137.