Structure and comparative analysis of the genes encoding component C of methyl coenzyme M reductase in the extremely thermophilic archaebacterium Methanothermus fervidus (original) (raw)

Abstract

A 6-kilobase-pair (kbp) region of the genome of the extremely thermophilic arachaebacterium Methanothermus fervidus which encodes the alpha, beta, and gamma subunit polypeptides of component C of methyl coenzyme M reductase was cloned and sequenced. Genes encoding the beta (mcrB) and gamma (mcrG) subunits were separated by two open reading frames (designated mcrC and mcrD) which encode unknown gene products. The M. fervidus genes were preceded by ribosome-binding sites, separated by short A + T-rich intergenic regions, contained unexpectedly few NNC codons, and exhibited inflexible codon usage at some locations. Sites of transcription initiation and termination flanking the mcrBDCGA cluster of genes in M. fervidus were identified. The sequences of the genes, the encoded polypeptides, and transcription regulatory signals in M. fervidus were compared with the functionally equivalent sequences from two mesophilic methanogens (Methanococcus vannielii and Methanosarcina barkeri) and from a moderate thermophile (Methanobacterium thermoautotrophicum Marburg). The amino acid sequences of the polypeptides encoded by the mcrBCGA genes in the two thermophiles were approximately 80% identical, whereas all other pairs of these gene products contained between 50 and 60% identical amino acid residues. The mcrD gene products have diverged more than the products of the other mcr genes. Identification of highly conserved regions within mcrA and mcrB suggested oligonucleotide sequences which might be developed as hybridization probes which could be used for identifying and quantifying all methanogens.

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  1. Balch W. E., Fox G. E., Magrum L. J., Woese C. R., Wolfe R. S. Methanogens: reevaluation of a unique biological group. Microbiol Rev. 1979 Jun;43(2):260–296. doi: 10.1128/mr.43.2.260-296.1979. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Bertani G., Baresi L. Genetic transformation in the methanogen Methanococcus voltae PS. J Bacteriol. 1987 Jun;169(6):2730–2738. doi: 10.1128/jb.169.6.2730-2738.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Bokranz M., Bäumner G., Allmansberger R., Ankel-Fuchs D., Klein A. Cloning and characterization of the methyl coenzyme M reductase genes from Methanobacterium thermoautotrophicum. J Bacteriol. 1988 Feb;170(2):568–577. doi: 10.1128/jb.170.2.568-577.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Bokranz M., Klein A. Nucleotide sequence of the methyl coenzyme M reductase gene cluster from Methanosarcina barkeri. Nucleic Acids Res. 1987 May 26;15(10):4350–4351. doi: 10.1093/nar/15.10.4350. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Cram D. S., Sherf B. A., Libby R. T., Mattaliano R. J., Ramachandran K. L., Reeve J. N. Structure and expression of the genes, mcrBDCGA, which encode the subunits of component C of methyl coenzyme M reductase in Methanococcus vannielii. Proc Natl Acad Sci U S A. 1987 Jun;84(12):3992–3996. doi: 10.1073/pnas.84.12.3992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Ellefson W. L., Wolfe R. S. Component C of the methylreductase system of Methanobacterium. J Biol Chem. 1981 May 10;256(9):4259–4262. [PubMed] [Google Scholar]
  7. Fabry S., Hensel R. Primary structure of glyceraldehyde-3-phosphate dehydrogenase deduced from the nucleotide sequence of the thermophilic archaebacterium Methanothermus fervidus. Gene. 1988 Apr 29;64(2):189–197. doi: 10.1016/0378-1119(88)90334-4. [DOI] [PubMed] [Google Scholar]
  8. Hamilton P. T., Reeve J. N. Structure of genes and an insertion element in the methane producing archaebacterium Methanobrevibacter smithii. Mol Gen Genet. 1985;200(1):47–59. doi: 10.1007/BF00383311. [DOI] [PubMed] [Google Scholar]
  9. Jones W. J., Nagle D. P., Jr, Whitman W. B. Methanogens and the diversity of archaebacteria. Microbiol Rev. 1987 Mar;51(1):135–177. doi: 10.1128/mr.51.1.135-177.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Kjems J., Leffers H., Garrett R. A., Wich G., Leinfelder W., Böck A. Gene organization, transcription signals and processing of the single ribosomal RNA operon of the archaebacterium Thermoproteus tenax. Nucleic Acids Res. 1987 Jun 25;15(12):4821–4835. doi: 10.1093/nar/15.12.4821. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Maxam A. M., Gilbert W. Sequencing end-labeled DNA with base-specific chemical cleavages. Methods Enzymol. 1980;65(1):499–560. doi: 10.1016/s0076-6879(80)65059-9. [DOI] [PubMed] [Google Scholar]
  12. Mayer F., Rohde M., Salzmann M., Jussofie A., Gottschalk G. The methanoreductosome: a high-molecular-weight enzyme complex in the methanogenic bacterium strain Gö1 that contains components of the methylreductase system. J Bacteriol. 1988 Apr;170(4):1438–1444. doi: 10.1128/jb.170.4.1438-1444.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Müller B., Allmansberger R., Klein A. Termination of a transcription unit comprising highly expressed genes in the archaebacterium Methanococcus voltae. Nucleic Acids Res. 1985 Sep 25;13(18):6439–6445. doi: 10.1093/nar/13.18.6439. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Reiter W. D., Palm P., Zillig W. Analysis of transcription in the archaebacterium Sulfolobus indicates that archaebacterial promoters are homologous to eukaryotic pol II promoters. Nucleic Acids Res. 1988 Jan 11;16(1):1–19. doi: 10.1093/nar/16.1.1. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Reiter W. D., Palm P., Zillig W. Transcription termination in the archaebacterium Sulfolobus: signal structures and linkage to transcription initiation. Nucleic Acids Res. 1988 Mar 25;16(6):2445–2459. doi: 10.1093/nar/16.6.2445. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Sanger F., Nicklen S., Coulson A. R. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463–5467. doi: 10.1073/pnas.74.12.5463. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Thomas L. K., Dix D. B., Thompson R. C. Codon choice and gene expression: synonymous codons differ in their ability to direct aminoacylated-transfer RNA binding to ribosomes in vitro. Proc Natl Acad Sci U S A. 1988 Jun;85(12):4242–4246. doi: 10.1073/pnas.85.12.4242. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Thomm M., Sherf B. A., Reeve J. N. RNA polymerase-binding and transcription initiation sites upstream of the methyl reductase operon of Methanococcus vannielii. J Bacteriol. 1988 Apr;170(4):1958–1961. doi: 10.1128/jb.170.4.1958-1961.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Thomm M., Stetter K. O. Transcription in methanogens. Evidence for specific in vitro transcription of the purified DNA-dependent RNA polymerase of Methanococcus thermolithotrophicus. Eur J Biochem. 1985 Jun 3;149(2):345–351. doi: 10.1111/j.1432-1033.1985.tb08932.x. [DOI] [PubMed] [Google Scholar]
  20. Thomm M., Wich G. An archaebacterial promoter element for stable RNA genes with homology to the TATA box of higher eukaryotes. Nucleic Acids Res. 1988 Jan 11;16(1):151–163. doi: 10.1093/nar/16.1.151. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Vieira J., Messing J. The pUC plasmids, an M13mp7-derived system for insertion mutagenesis and sequencing with synthetic universal primers. Gene. 1982 Oct;19(3):259–268. doi: 10.1016/0378-1119(82)90015-4. [DOI] [PubMed] [Google Scholar]
  22. Wackett L. P., Hartwieg E. A., King J. A., Orme-Johnson W. H., Walsh C. T. Electron microscopy of nickel-containing methanogenic enzymes: methyl reductase and F420-reducing hydrogenase. J Bacteriol. 1987 Feb;169(2):718–727. doi: 10.1128/jb.169.2.718-727.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Weil C. F., Beckler G. S., Reeve J. N. Structure and organization of the hisA gene of the thermophilic archaebacterium Methanococcus thermolithotrophicus. J Bacteriol. 1987 Oct;169(10):4857–4860. doi: 10.1128/jb.169.10.4857-4860.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Wich G., Hummel H., Jarsch M., Bär U., Böck A. Transcription signals for stable RNA genes in Methanococcus. Nucleic Acids Res. 1986 Mar 25;14(6):2459–2479. doi: 10.1093/nar/14.6.2459. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Woese C. R., Olsen G. J. Archaebacterial phylogeny: perspectives on the urkingdoms. Syst Appl Microbiol. 1986;7:161–177. doi: 10.1016/s0723-2020(86)80001-7. [DOI] [PubMed] [Google Scholar]
  26. Worrell V. E., Nagle D. P., Jr, McCarthy D., Eisenbraun A. Genetic transformation system in the archaebacterium Methanobacterium thermoautotrophicum Marburg. J Bacteriol. 1988 Feb;170(2):653–656. doi: 10.1128/jb.170.2.653-656.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Zillig W., Palm P., Reiter W. D., Gropp F., Pühler G., Klenk H. P. Comparative evaluation of gene expression in archaebacteria. Eur J Biochem. 1988 May 2;173(3):473–482. doi: 10.1111/j.1432-1033.1988.tb14023.x. [DOI] [PubMed] [Google Scholar]