Skip to main content
PMC home page
Journal of Bacteriology logoLink to Journal of Bacteriology
. 1996 Nov;178(22):6599–6607. doi: 10.1128/jb.178.22.6599-6607.1996

Sequence and transcript analysis of a novel Methanosarcina barkeri methyltransferase II homolog and its associated corrinoid protein homologous to methionine synthase.

L Paul 1, J A Krzycki 1
PMCID: PMC178547  PMID: 8932317

Abstract

The sequence and transcript of the genes encoding a recently discovered coenzyme M methylase in Methanosarcina barkeri were analyzed. This 480-kDa protein is composed of two subunits in equimolar concentrations which bind one corrinoid cofactor per alphabeta dimer. The gene for the alphabeta polypeptide, mtsA, is upstream of that encoding the beta polypeptide, mtsB. The two genes are contiguous and overlap by several nucleotides. A 1.9-kb mRNA species which reacted with probes specific for either mtsA or mtsB was detected. Three possible methanogen consensus BoxA sequences as well as two sets of direct repeats were found upstream of mtsA. The 5' end of the mts transcript was 19 nucleotides upstream of the translational start site of mtsA and was positioned 25 bp from the center of the proximal BoxA sequence. The transcript was most abundant in cells grown to the late log phase on acetate but barely detectable in cells grown on methanol or trimethylamine. The amino acid sequence of MtsB was homologous to the cobalamin-binding fragment of methionine synthase from Escherichia coli and possessed the signature residues involved in binding the corrinoid, including a histidyl residue which ligates cobalt. The sequence of MtsA is homologous to the "A" and "M" isozymes of methylcobamide:coenzyme M methyltransferases (methyltransferase II), indicating that the alpha polypeptide is a new member of the methyltransferase II family of coenzyme M methylases. All three methyltransferase II homolog sequences could be aligned with the sequences of uroporphyrinogen decarboxylase from various sources. The implications of these homologies for the mechanism of corrinoid binding by proteins involved in methylotrophic methanogenesis are discussed.

Full Text

The Full Text of this article is available as a PDF (486.5 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J. Basic local alignment search tool. J Mol Biol. 1990 Oct 5;215(3):403–410. doi: 10.1016/S0022-2836(05)80360-2. [DOI] [PubMed] [Google Scholar]
  2. Banerjee R. V., Johnston N. L., Sobeski J. K., Datta P., Matthews R. G. Cloning and sequence analysis of the Escherichia coli metH gene encoding cobalamin-dependent methionine synthase and isolation of a tryptic fragment containing the cobalamin-binding domain. J Biol Chem. 1989 Aug 15;264(23):13888–13895. [PubMed] [Google Scholar]
  3. Becher B., Müller V., Gottschalk G. N5-methyl-tetrahydromethanopterin:coenzyme M methyltransferase of Methanosarcina strain Gö1 is an Na(+)-translocating membrane protein. J Bacteriol. 1992 Dec;174(23):7656–7660. doi: 10.1128/jb.174.23.7656-7660.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Burke S. A., Krzycki J. A. Involvement of the "A" isozyme of methyltransferase II and the 29-kilodalton corrinoid protein in methanogenesis from monomethylamine. J Bacteriol. 1995 Aug;177(15):4410–4416. doi: 10.1128/jb.177.15.4410-4416.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Cao X. J., Krzycki J. A. Acetate-dependent methylation of two corrinoid proteins in extracts of Methanosarcina barkeri. J Bacteriol. 1991 Sep;173(17):5439–5448. doi: 10.1128/jb.173.17.5439-5448.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Drennan C. L., Huang S., Drummond J. T., Matthews R. G., Lidwig M. L. How a protein binds B12: A 3.0 A X-ray structure of B12-binding domains of methionine synthase. Science. 1994 Dec 9;266(5191):1669–1674. doi: 10.1126/science.7992050. [DOI] [PubMed] [Google Scholar]
  7. Ferguson D. J., Jr, Krzycki J. A., Grahame D. A. Specific roles of methylcobamide:coenzyme M methyltransferase isozymes in metabolism of methanol and methylamines in Methanosarcina barkeri. J Biol Chem. 1996 Mar 1;271(9):5189–5194. doi: 10.1074/jbc.271.9.5189. [DOI] [PubMed] [Google Scholar]
  8. Ferry J. G. Biochemistry of methanogenesis. Crit Rev Biochem Mol Biol. 1992;27(6):473–503. doi: 10.3109/10409239209082570. [DOI] [PubMed] [Google Scholar]
  9. Ferry J. G. Methane from acetate. J Bacteriol. 1992 Sep;174(17):5489–5495. doi: 10.1128/jb.174.17.5489-5495.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Garey J. R., Labbe-Bois R., Chelstowska A., Rytka J., Harrison L., Kushner J., Labbe P. Uroporphyrinogen decarboxylase in Saccharomyces cerevisiae. HEM12 gene sequence and evidence for two conserved glycines essential for enzymatic activity. Eur J Biochem. 1992 May 1;205(3):1011–1016. doi: 10.1111/j.1432-1033.1992.tb16868.x. [DOI] [PubMed] [Google Scholar]
  11. Grahame D. A. Catalysis of acetyl-CoA cleavage and tetrahydrosarcinapterin methylation by a carbon monoxide dehydrogenase-corrinoid enzyme complex. J Biol Chem. 1991 Nov 25;266(33):22227–22233. [PubMed] [Google Scholar]
  12. Grahame D. A. Different isozymes of methylcobalamin:2-mercaptoethanesulfonate methyltransferase predominate in methanol- versus acetate-grown Methanosarcina barkeri. J Biol Chem. 1989 Aug 5;264(22):12890–12894. [PubMed] [Google Scholar]
  13. Gärtner P., Weiss D. S., Harms U., Thauer R. K. N5-methyltetrahydromethanopterin:coenzyme M methyltransferase from Methanobacterium thermoautotrophicum. Catalytic mechanism and sodium ion dependence. Eur J Biochem. 1994 Dec 1;226(2):465–472. doi: 10.1111/j.1432-1033.1994.tb20071.x. [DOI] [PubMed] [Google Scholar]
  14. Hansson M., Hederstedt L. Cloning and characterization of the Bacillus subtilis hemEHY gene cluster, which encodes protoheme IX biosynthetic enzymes. J Bacteriol. 1992 Dec;174(24):8081–8093. doi: 10.1128/jb.174.24.8081-8093.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Harms U., Thauer R. K. Methylcobalamin: coenzyme M methyltransferase isoenzymes MtaA and MtbA from Methanosarcina barkeri. Cloning, sequencing and differential transcription of the encoding genes, and functional overexpression of the mtaA gene in Escherichia coli. Eur J Biochem. 1996 Feb 1;235(3):653–659. doi: 10.1111/j.1432-1033.1996.00653.x. [DOI] [PubMed] [Google Scholar]
  16. Harms U., Weiss D. S., Gärtner P., Linder D., Thauer R. K. The energy conserving N5-methyltetrahydromethanopterin:coenzyme M methyltransferase complex from Methanobacterium thermoautotrophicum is composed of eight different subunits. Eur J Biochem. 1995 Mar 15;228(3):640–648. doi: 10.1111/j.1432-1033.1995.0640m.x. [DOI] [PubMed] [Google Scholar]
  17. Hausner W., Frey G., Thomm M. Control regions of an archaeal gene. A TATA box and an initiator element promote cell-free transcription of the tRNA(Val) gene of Methanococcus vannielii. J Mol Biol. 1991 Dec 5;222(3):495–508. doi: 10.1016/0022-2836(91)90492-o. [DOI] [PubMed] [Google Scholar]
  18. Henikoff S., Henikoff J. G. Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci U S A. 1992 Nov 15;89(22):10915–10919. doi: 10.1073/pnas.89.22.10915. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Henikoff S. Unidirectional digestion with exonuclease III creates targeted breakpoints for DNA sequencing. Gene. 1984 Jun;28(3):351–359. doi: 10.1016/0378-1119(84)90153-7. [DOI] [PubMed] [Google Scholar]
  20. Hennigan A. N., Reeve J. N. mRNAs in the methanogenic archaeon Methanococcus vannielii: numbers, half-lives and processing. Mol Microbiol. 1994 Feb;11(4):655–670. doi: 10.1111/j.1365-2958.1994.tb00344.x. [DOI] [PubMed] [Google Scholar]
  21. Inoue H., Nojima H., Okayama H. High efficiency transformation of Escherichia coli with plasmids. Gene. 1990 Nov 30;96(1):23–28. doi: 10.1016/0378-1119(90)90336-p. [DOI] [PubMed] [Google Scholar]
  22. Kengen S. W., Daas P. J., Duits E. F., Keltjens J. T., van der Drift C., Vogels G. D. Isolation of a 5-hydroxybenzimidazolyl cobamide-containing enzyme involved in the methyltetrahydromethanopterin: coenzyme M methyltransferase reaction in Methanobacterium thermoautotrophicum. Biochim Biophys Acta. 1992 Feb 1;1118(3):249–260. doi: 10.1016/0167-4838(92)90282-i. [DOI] [PubMed] [Google Scholar]
  23. Kiel J. A., Ten Berge A. M., Venema G. Nucleotide sequence of the Synechococcus sp. PCC7942 hemE gene encoding the homologue of mammalian uroporphyrinogen decarboxylase. DNA Seq. 1992;2(6):415–418. doi: 10.3109/10425179209020822. [DOI] [PubMed] [Google Scholar]
  24. Kovalenko S. A., Tanaka M., Ozawa T. Simple methods for preparation of plasmid DNA yielding long and accurate sequence data. Nucleic Acids Res. 1994 Dec 25;22(25):5771–5772. doi: 10.1093/nar/22.25.5771. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Kremer J. D., Cao X., Krzycki J. Isolation of two novel corrinoid proteins from acetate-grown Methanosarcina barkeri. J Bacteriol. 1993 Aug;175(15):4824–4833. doi: 10.1128/jb.175.15.4824-4833.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Kremer J., Burchfield S., Frazier C., Krzycki J. Differential in vitro methylation and synthesis of the 480-kilodalton corrinoid protein in Methanosarcina barkeri grown on different substrates. J Bacteriol. 1994 Jan;176(1):253–255. doi: 10.1128/jb.176.1.253-255.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Kwon H. B., Park S. C., Peng H. P., Goodman H. M., Dewdney J., Shih M. C. Identification of a light-responsive region of the nuclear gene encoding the B subunit of chloroplast glyceraldehyde 3-phosphate dehydrogenase from Arabidopsis thaliana. Plant Physiol. 1994 May;105(1):357–367. doi: 10.1104/pp.105.1.357. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. LeClerc G. M., Grahame D. A. Methylcobamide:coenzyme M methyltransferase isozymes from Methanosarcina barkeri. Physicochemical characterization, cloning, sequence analysis, and heterologous gene expression. J Biol Chem. 1996 Aug 2;271(31):18725–18731. doi: 10.1074/jbc.271.31.18725. [DOI] [PubMed] [Google Scholar]
  29. Lu W. P., Becher B., Gottschalk G., Ragsdale S. W. Electron paramagnetic resonance spectroscopic and electrochemical characterization of the partially purified N5-methyltetrahydromethanopterin:coenzyme M methyltransferase from Methanosarcina mazei Gö1. J Bacteriol. 1995 May;177(9):2245–2250. doi: 10.1128/jb.177.9.2245-2250.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Marsh E. N., Holloway D. E. Cloning and sequencing of glutamate mutase component S from Clostridium tetanomorphum. Homologies with other cobalamin-dependent enzymes. FEBS Lett. 1992 Sep 28;310(2):167–170. doi: 10.1016/0014-5793(92)81321-c. [DOI] [PubMed] [Google Scholar]
  31. Mattern S. G., Brawner M. E., Westpheling J. Identification of a complex operator for galP1, the glucose-sensitive, galactose-dependent promoter of the Streptomyces galactose operon. J Bacteriol. 1993 Mar;175(5):1213–1220. doi: 10.1128/jb.175.5.1213-1220.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Maupin-Furlow J., Ferry J. G. Characterization of the cdhD and cdhE genes encoding subunits of the corrinoid/iron-sulfur enzyme of the CO dehydrogenase complex from Methanosarcina thermophila. J Bacteriol. 1996 Jan;178(2):340–346. doi: 10.1128/jb.178.2.340-346.1996. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Morris C. J., Reeve J. N. Conservation of structure in the human gene encoding argininosuccinate synthetase and the argG genes of the archaebacteria Methanosarcina barkeri MS and Methanococcus vannielii. J Bacteriol. 1988 Jul;170(7):3125–3130. doi: 10.1128/jb.170.7.3125-3130.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Nishimura K., Nakayashiki T., Inokuchi H. Cloning and sequencing of the hemE gene encoding uroporphyrinogen III decarboxylase (UPD) from Escherichia coli K-12. Gene. 1993 Oct 29;133(1):109–113. doi: 10.1016/0378-1119(93)90233-s. [DOI] [PubMed] [Google Scholar]
  35. Orengo C. A., Jones D. T., Thornton J. M. Protein superfamilies and domain superfolds. Nature. 1994 Dec 15;372(6507):631–634. doi: 10.1038/372631a0. [DOI] [PubMed] [Google Scholar]
  36. Palmer J. R., Daniels C. J. In vivo definition of an archaeal promoter. J Bacteriol. 1995 Apr;177(7):1844–1849. doi: 10.1128/jb.177.7.1844-1849.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Pihl T. D., Sharma S., Reeve J. N. Growth phase-dependent transcription of the genes that encode the two methyl coenzyme M reductase isoenzymes and N5-methyltetrahydromethanopterin:coenzyme M methyltransferase in Methanobacterium thermoautotrophicum delta H. J Bacteriol. 1994 Oct;176(20):6384–6391. doi: 10.1128/jb.176.20.6384-6391.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Pol A., van der Drift C., Vogels G. D. Corrinoids from Methanosarcina barkeri: structure of the alpha-ligand. Biochem Biophys Res Commun. 1982 Sep 30;108(2):731–737. doi: 10.1016/0006-291x(82)90890-7. [DOI] [PubMed] [Google Scholar]
  39. Reeve J. N. Molecular biology of methanogens. Annu Rev Microbiol. 1992;46:165–191. doi: 10.1146/annurev.mi.46.100192.001121. [DOI] [PubMed] [Google Scholar]
  40. Rinker A. G., Jr, Evans D. R. Isolation of chromosomal DNA from a methanogenic archaebacteria using a French pressure cell press. Biotechniques. 1991 Nov;11(5):612–613. [PubMed] [Google Scholar]
  41. Singh-Wissmann K., Ferry J. G. Transcriptional regulation of the phosphotransacetylase-encoding and acetate kinase-encoding genes (pta and ack) from Methanosarcina thermophila. J Bacteriol. 1995 Apr;177(7):1699–1702. doi: 10.1128/jb.177.7.1699-1702.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. Smith T. F., Waterman M. S. Identification of common molecular subsequences. J Mol Biol. 1981 Mar 25;147(1):195–197. doi: 10.1016/0022-2836(81)90087-5. [DOI] [PubMed] [Google Scholar]
  43. Sonnhammer E. L., Kahn D. Modular arrangement of proteins as inferred from analysis of homology. Protein Sci. 1994 Mar;3(3):482–492. doi: 10.1002/pro.5560030314. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Stupperich E., Juza A., Hoppert M., Mayer F. Cloning, sequencing and immunological characterization of the corrinoid-containing subunit of the N5-methyltetrahydromethanopterin: coenzyme-M methyltransferase from Methanobacterium thermoautotrophicum. Eur J Biochem. 1993 Oct 1;217(1):115–121. doi: 10.1111/j.1432-1033.1993.tb18225.x. [DOI] [PubMed] [Google Scholar]
  45. Tallant T. C., Krzycki J. A. Coenzyme M methylase activity of the 480-kilodalton corrinoid protein from Methanosarcina barkeri. J Bacteriol. 1996 Mar;178(5):1295–1301. doi: 10.1128/jb.178.5.1295-1301.1996. [DOI] [PMC free article] [PubMed] [Google Scholar]
  46. Thompson J. D., Higgins D. G., Gibson T. J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994 Nov 11;22(22):4673–4680. doi: 10.1093/nar/22.22.4673. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. Weiss D. S., Gärtner P., Thauer R. K. The energetics and sodium-ion dependence of N5-methyltetrahydromethanopterin:coenzyme M methyltransferase studied with cob(I)alamin as methyl acceptor and methylcob(III)alamin as methyl donor. Eur J Biochem. 1994 Dec 15;226(3):799–809. doi: 10.1111/j.1432-1033.1994.00799.x. [DOI] [PubMed] [Google Scholar]
  48. Wolfe R. S. My kind of biology. Annu Rev Microbiol. 1991;45:1–35. doi: 10.1146/annurev.mi.45.100191.000245. [DOI] [PubMed] [Google Scholar]
  49. Yeliseev A., Gärtner P., Harms U., Linder D., Thauer R. K. Function of methylcobalamin: coenzyme M methyltransferase isoenzyme II in Methanosarcina barkeri. Arch Microbiol. 1993;159(6):530–536. doi: 10.1007/BF00249031. [DOI] [PubMed] [Google Scholar]
  50. van der Meijden P., Heythuysen H. J., Pouwels A., Houwen F., van der Drift C., Vogels G. D. Methyltransferases involved in methanol conversion by Methanosarcina barkeri. Arch Microbiol. 1983 Jun;134(3):238–242. doi: 10.1007/BF00407765. [DOI] [PubMed] [Google Scholar]
  51. van der Meijden P., te Brömmelstroet B. W., Poirot C. M., van der Drift C., Vogels G. D. Purification and properties of methanol:5-hydroxybenzimidazolylcobamide methyltransferase from Methanosarcina barkeri. J Bacteriol. 1984 Nov;160(2):629–635. doi: 10.1128/jb.160.2.629-635.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Journal of Bacteriology are provided here courtesy of American Society for Microbiology (ASM)

RESOURCES