Clustered genes encoding the methyltransferases of methanogenesis from monomethylamine

Journal of Bacteriology

Volumn 180, Issue 13, 1998, Pages 3432-3440

  Burke, Stephen A ^a   Lo, Sam L ^a   Krzycki, Joseph A ^a  

^a OHIO STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MESNA; METHYLAMINE; METHYLTRANSFERASE;

AMINO ACID SEQUENCE; ARTICLE; CODON; ENZYME ACTIVITY; ENZYME INDUCTION; GENE CLUSTER; METHANOGENESIS; METHANOSARCINA BARKERI; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PRIORITY JOURNAL; SEQUENCE ANALYSIS; TRANSLATION REGULATION;

METHANOSARCINA BARKERI;

EID: 0031799184     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/jb.180.13.3432-3440.1998     Document Type: Article

References (58)

1. Altschul, S. F., W. Gish, W. Miller, E. W. Myers, and D. J. Lipman. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403-410.
2. Bonne, D. R., W. B. Whitman, and P. Rouvière. 1993. Diversity and taxonomy of methanogens. p. 35-80. In James G. Ferry (ed.), Methanogenesis. Ecology, physiology, biochemistry, and genetics. Chapman & Hall, New York, N.Y.
3. Bult, C. J., O. White, G. J. Olsen, L. Zhou, R. D. Fleischmann, G. G. Sutton, J. A. Blake, L. M. Fitzgerald, R. A. Clayton, J. D. Gocayne, A. R. Kerlavage, B. A. Dougherty, J.-F. Tomb, M. D. Adams, C. I. Reich, R. Overbeek, E. F. Kirkness, K. G. Weinstock, J. M. Merrick, A. Glodeck, J. L. Scott, N. S. M. Georghagen, J. F. Weidman, J. L. Fuhrman, D. Nguyen, T. R. Utterback, J. M. Kelly, J. D. Peterson, P. W. Sadow, M. C. Hanna, M. D. Cotton, K. M. Roberts, M. A. Hurst, B. P. Kaine, M. Borodovsky, H.-P. Klenk, C. F. Fraser, H. O. Smith, C. R. Woese, and J. C. Venter. 1996. Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. Science 273:1058-1073.
4. Burgett, S. G., and P. R. Rosteck. 1994. Use of dimethylsulfoxide in fluorescent tag sequencing, p. 211-215. In M. D. Adams, C. Fields, and J. C. Venter (ed.), Automated DNA sequencing and analysis. Academic Press, San Diego, Calif.
5. Burke, S. A., and J. A. Krzycki. 1995. Involvement of the "A" isozyme of methyltransferase II and the 29-kilodalton corrinoid protein in methanogenesis from monomethylamine. J. Bacteriol. 177:4410-4416.
6. Burke, S. A., and J. A. Krzycki. 1997. Reconstitution of monomethylamine: coenzyme M methyl transfer with a corrinoid protein and two methyltransferases purified from Methanosarcina barkeri. J. Biol. Chem. 272:16570-16577.
7. Daas, P. J. H., K. A. A. Gerrits, J. T. Keltjens, C. van der Drift, and G. D. Vogels. 1993. Involvement of an activation protein in the methanol:2-mercaptoethanesulfonic acid methyltransferase reaction in Methanosarcina barkeri. J. Bacteriol. 175:1278-1283.
8. Daas, P. J. H., R. W. Wassenaar, P. Willemsen, R. J. Theunissen, J. T. Keltjens, C. van der Drift, and G. D. Vogels. 1996. Purification and properties of an enzyme involved in the ATP-dependent activation of the methanol: 2mercaptoethanesulfonic acid methyltransferase reaction in Methanosarcina barkeri. J. Biol. Chem. 271:22339-22345.
9. Daniels, L. 1994. Biochemistry of methanogenesis, p. 41-112. In M. Kates, D. J. Kushner, and A. T. Matheson (ed.), The biochemistry of archaea. Elsevier, New York, N.Y.
10. Dawson, R. M. C., D. C. Elliot, W. H. Elliot, and K. M. Jones. 1986. Data for biochemical research, p. 24-25. Oxford University Press, New York, N.Y.
11. De Mot, R., I. Nagy, G. Schoofs, and J. Vanderleyden. 1994. Sequence of a Rhodococcus gene cluster encoding the subunits of ethanolamine ammonialyase and an APC-like permease. Can. J. Microbiol. 40:403-407.
12. Drennan, C. L., S. Huang, J. T. Drummond, R. G. Matthews, and M. L. Ludwig. 1994. How a protein binds B12: a 3.0 Å X-ray structure of B12-binding domains of methionine synthase. Science 266:1669-1674.
13. Fabiny, J. M., A. Jayakumar, A. C. Chinault, and E. M. Barnes, Jr. 1991. Ammonium transport in Escherichia coli: localization and nucleotide sequence of the amtA gene. J. Gen. Microbiol. 137:983-989.
14. Farabaugh, P. J. 1996. Programmed translational frameshifting. Microbiol. Rev. 60:103-134.
15. Feinberg, A. P., and B. Vogelstein. 1983. A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity. Anal. Biochem. 132:6.
16. Feinberg, A. P., and B. Vogelstein. 1984. Addendum: a technique for radiolabeling DNA restriction endonuclease fragments to high specific activity. Anal. Biochem. 137:266.
17. Ferguson, D. J., Jr., and J. A. Krzycki. 1997. Reconstitution of trimethylamine-dependent coenzyme M methylation with the trimethylamine corrinoid protein and the isozymes of methyltransferase II from Methanosarcina barkeri. J. Bacteriol. 179:846-852.
18. Ferguson, D. J., and J. A. Krzycki. Unpublished data.
19. Ferguson, D. J., J. A. Krzycki, and D. A. Grahame. 1996. Specific roles of methylcobamide:coenzyme M methyltransferase isozymes in metabolism of methanol and methylamines in Methanosarcina barkeri. J. Biol. Chem. 271: 5189-5194.
20. Fox, T. D. 1987. Natural variation in the genetic code. Annu. Rev. Genet. 21:67-91.
21. Gonnet, G. H. 1994. New algorithms for the computation of evolutionary phylogenetic trees. In S. Suhai (ed.), Computational methods in genome research. Plenum Press, New York, N.Y.
22. Grahame, D. A. 1989. Different isozymes of methylcobalamin:2-mercaptoethanesulfonate methyltransferase predominate in methanol-versus acetate-grown Methanosarcina barkeri. J. Biol. Chem. 264:12890-12894.
23. Harms, U., and R. K. Thauer. 1996. Methylcobalamin:coenzyme M methyltransferase isoenzymes MtaA and MtbA from Methanosarcina barkeri. Eur. J. Biochem. 235:653-659.
24. Henikoff, S., and J. G. Henikoff. 1992. Amino acid substitution matrices from protein blocks. Proc. Natl. Acad. Sci. USA 89:10915-10919.
25. Hennigan, A. N., and J. N. Reeve. 1994. mRNAs in the methanogenic archaeon Methanococcus vannielii: numbers, half-lives, and processing. Mol. Microbiol. 11:655-670.
26. Hofmann, R., and W. Stoffel. 1993. TMbase-a database of membrane-spanning protein segments. Biol. Chem. Hoppe-Seyler 347:166.
27. Klenk, H.-P., R. A. Clayton, J.-F. Tomb, O. White, K. E. Nelson, K. A. Ketchum, R. J. Dodson, M. Gwinn, E. K. Hickey, J. D. Peterson, D. L. Richardson, A. R. Kerlavage, D. E. Graham, N. C. Kyrpides, R. D. Fleischmann, J. Quackenbush, N. H. Lee, G. G. Sutton, S. Gill, E. F. Kirkness, B. A. Dougherty, K. McKenny, M. D. Adams, B. Loftus, S. Peterson, C. I. Reich, L. K. McNeil, J. H. Badger, A. Glodek, L. Zhou, R. Overbeek, J. D. Gocayne, J. F. Weidman, L. McDonald, T. Utterback, M. D. Cotton, T. Spriggs, P. Artiach, B. P. Kaine, S. M. Sykes, P. W. Sadow, K. P. D'Andrea, C. Bowman, C. Fujii, S. A. Garland, T. M. Mason, G. J. Olsen, C. M. Fraser, H. O. Smith, C. R. Woese, and J. C. Venter. 1997. The complete genome sequence of the hyperthermophilic, sulfate-reducing archaeon Archaeoglobus fulgidus. Nature 390:364-370.
28. Kremer, J. D., X. Cao, and J. Krzycki. 1993. Isolation of two novel corrinoid proteins from acetate-grown Methanosarcina barkeri. J. Bacteriol. 175:4824-4833.
29. Kyte, J., and R. F. Doolittle. 1982. A simple method for displaying the hydrophobic character of a protein. J. Mol. Biol. 157:7217-7221.
30. Leclerc, G. M., and D. A. Grahame. 1996. Methylcobamide:coenzyme M methyltransferase isozymes from Methanosarcina barkeri: physicochemical characterization, cloning, sequence analysis, and heterologous gene expression. J. Biol. Chem. 271:18725-18731.
31. 12-dependent enzymes. Annu. Rev. Biochem. 66:269-313.
32. Marshall, B., and S. B. Levy. 1980. Prevalence of amber suppressor-containing coliforms in the natural environment. Nature 286:524-525.
33. Maupin-Furlow, J. A., and J. G. Ferry. 1996. Analysis of the CO dehydrogenase/acetyl-coenzyme A sythase operon of Methanosarcina thermophila. J. Bacteriol. 178:6849-6856.
34. Nakamura, Y., T. Gojobori, and T. Ikemura. 1997. Codon usage tabulated from the international DNA sequence databases. Nucleic Acids Res. 25:244-245.
35. Nölling, J., and J. N. Reeve. 1997. Growth- and substrate-dependent transcription of the formate dehydrogenase (fdhCAB) operon in Methanobacterium thermoformicicum Z-245. J. Bacteriol. 179:899-908.
36. Palmer, J. R., and C. J. Daniels. 1995. In vivo definition of an archael promoter. J. Bacteriol. 177:1844-1849.
37. Parker, J. 1985. Errors and alternatives in reading the universal genetic code. Microbiol. Rev. 53:273-298.
38. Paul, L., and J. A. Krzycki. 1996. Sequence and transcript analysis of a novel Methanosarcina barkeri methyltransferase II homolog and its associated corrinoid protein homologous to methionine synthase. J. Bacteriol. 178:6599-6607.
39. Reeve, J. N. 1992. Molecular biology of methanogens. Annu. Rev. Microbiol. 46:165-191.
40. Reizer, J., K. Finley, K. Kakuda, C. L. MacLeod, A. Reizer, and M. H. Saier, Jr. 1993. Mammalian integral membrane receptors are homologous to facilitators and antiporters of yeast, fungi, and eubacteria. Protein Sci. 2:20-30.
41. Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning: a laboratory manual, p. 1626. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
42. Sanger, F., S. Nicklen, and A. R. Coulson. 1977. DNA sequencing with chain-terminating inhibitors. Proc. Natl. Acad. Sci. USA 74:5463-5467.
43. Sauer, K., U. Harms, and R. K. Thauer. 1997. Methanol:coenzyme M methyltransferase from Methanosarcina barkeri. Purification, properties and encoding genes of the corrinoid protein MT1. Eur. J. Biochem. 243:670-677.
44. Siewe, R. M., B. Weil, A. Burkovski, B. J. Eikmanns, M. Eikmanns, and R. Kramer. 1996. Functional and genetic characterization of the (methyl)ammonium uptake carrier of Corynebacterium glutamicum. J. Biol. Chem. 271:5398-5403.
45. Smith, D. R., L. A. Doucette-Stamm, C. Deloughery, H. Lee, J. Dubois, T. Aldredge, R. Bashirzadeh, D. Blakely, R. Cook, K. Gilbert, D. Harrison, L. Hoang, P. Keagle, W. Lumm, B. Pothier, D. Qui, R. Spadafora, R. Vicaire, Y. Wang, J. Wierzbowski, R. Gibson, N. Jiwani, A. Caruso, D. Bush, H. Safer, D. Patwell, S. Prabhakar, S. McDougall, G. Shimer, A. Goyal, S. Pietrokovski, G. M. Church, C. J. Daniels, J.-I. Mao, P. Rice, J. Nölling, and J. N. Reeve. 1997. Complete genome sequence of Methanobacterium thermoautotrophicum ΔH: functional analysis and comparative genomics. J. Bacteriol. 179:7135-7155.
46. Sowers, K. R., T. T. Thai, and R. P. Gunsalus. 1993. Transcriptional regulation of the carbon monoxide dehydrogenase gene (cdhA) in Methanosarcina thermophila. J. Biol. Chem. 268:23172-23178.
47. Tallant, T., and J. Krzycki. 1996. Coenzyme M methylase activity of the 480-kilodalton corrinoid protein from Methanosarcina barkeri. J. Bacteriol. 178:1295-1301.
48. Tallant, T. C., and J. A. Krzycki. 1997. Methylthiol:coenzyme M methyltransferase from Methanosarcina barkeri, an enzyme of methanogenesis from dimethylsulfide and methylmercaptopropionate. J. Bacteriol. 179:6902-6911.
49. Thompson, J. D., D. G. Higgins, and T. J. Gibson. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
50. van der Meijden, P., H. J. Heythuysen, A. Pouwels, F. Houwne, C. van der Drift, and G. D. Vogels. 1983. Methyltransferases involved in methanol conversion by Methanosarcina barkeri. Arch. Microbiol. 134:238-242.
51. van der Meijden, P., B. W. te Brömmelstroet, C. M. Poirot, C. van der Drift, and G. D. Vogels. 1984. Purification and properties of methanol:5-hydroxybenzimidazolylcobamide methyltransferase from Methanosarcina barkeri. J. Bacteriol. 160:629-635.
52. Wassenaar, R. W., P. J. H. Daas, W. J. Geerts, J. T. Keltjans, and C. van der Drift. 1996. Involvement of methyltransferase-activating protein and methyltransferase 2 isozyme II in methylamine:coenzyme M methyltransferase reactions in Methanosarcina barkeri Fusaro. J. Bacteriol. 178:6937-6944.
53. Weiss, R. B. 1991. Ribosomal frameshifting, jumping, and readthrough. Curr. Opin. Cell Biol. 3:1051-1055.
54. Woese, C. R. 1990. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc. Natl. Acad. Sci. USA 87:4576-4579.
55. Yeliseev, A., P. Gaertner, U. Harms, D. Linder, and R. K. Thauer. 1993. Function of methylcobalamin:coenzyme M methyltransferase isoenzyme II in Methanosarcina barkeri. Arch. Microbiol. 159:530-536.
56. Zillig, W., P. Palm, H.-P. Klenk, D. Langer, U. Hudepohl, J. Hain, M. Landendorfer, and I. Holz. 1993. Transcription in the archaea, p. 367-391. In M. Kates, D. J. Kushner, and A. T. Matheson (ed.), The biochemistry of archaea (Archaeabacteria). Elsevier Science Publishing, New York, N.Y.
57. Zionini, F., A. Birkmann, W. Leinfelder, and A. Bock. 1987. Cotranslational insertion of selenocysteine into formate dehydrogenase from Escherichia coli directed by a UAG codon. Proc. Natl. Acad. Sci. USA 84:3156-3160.
58. Zionini, F., A. Birkmann, T. C. Stadtman, and A. Bock. 1986 Nucleotide sequence and expression of the selenocysteine-containing polypeptide of formate dehydrogenase (formate-hydrogen-lyase-linked) from Escherichia coli. Proc. Natl. Acad. Sci. USA 83:4650-4654.