PMCCPMCCPMCC

Search tips
Search criteria 

Advanced

 
Logo of jbacterPermissionsJournals.ASM.orgJournalJB ArticleJournal InfoAuthorsReviewers
 
J Bacteriol. 2010 November; 192(21): 5850–5851.
Published online 2010 August 27. doi:  10.1128/JB.00844-10
PMCID: PMC2953689

Complete Genome Sequence of Methanothermobacter marburgensis, a Methanoarchaeon Model Organism[down-pointing small open triangle]

Abstract

The circular genome sequence of the chemolithoautotrophic euryarchaeon Methanothermobacter marburgensis, with 1,639,135 bp, was determined and compared with that of Methanothermobacter thermautotrophicus. The genomes of the two model methanogens differ substantially in protein coding sequences, in insertion sequence (IS)-like elements, and in clustered regularly interspaced short palindromic repeats (CRISPR) loci.

Methanothermobacter marburgensis (DSM 2133) (formerly Methanobacterium thermoautotrophicum strain Marburg), a member of the Methanobacteriales (2), was isolated in 1978 from anaerobic sewage sludge in Marburg, Germany (5). The hydrogenotrophic methanogen grows even faster (2 h versus 3 h doubling time) and to higher cell concentrations (3 g versus 1.5 g dry mass per liter) than Methanothermobacter thermautotrophicus (DSM 1053) (formerly Methanobacterium thermoautotrophicum strain ΔH) (20) (for other differences, see references 3 and 19). Both methanogens were used in the last 35 years for the elucidation of the enzymes and coenzymes involved in CO2 reduction to methane with H2 (4, 16-18). The genome sequence of M. thermautotrophicus was reported in 1997 (15); that of M. marburgensis is announced here.

The genome size of M. marburgensis is 1,639,135 bp (that of M. thermautotrophicus is 1,751,377 bp), the genome G+C content is 48.64% (49.54% for M. thermautotrophicus), and the part coding is 90.94% (91.02% for M. thermautotrophicus). Comparison of the sequences (13) revealed that the two genomes have 1,607 protein coding sequences (CDS) in common and 411 CDS not in common (145 CDS are found only in M. marburgensis and 266 CDS only in M. thermautotrophicus) and show a high degree of synteny. The CDS not in common could be traced back to gene splitting (15%), gene deletion (30%), gene duplication (30%), and lateral gene transfer (24%) events (percentages given are for M. marburgensis). Of the 1,607 CDS in common, approximately 40% show BLAST search expectation values of >10−100 at the protein level, reflecting large differences in sequence divergence. Almost 470 CDS encode conserved hypothetical proteins.

The genome of M. marburgensis harbors 15 insertion sequence (IS)-like elements, whereas there is no evidence for a classically organized IS-like element in M. thermautotrophicus. Consistently, a CDS for a transposase is found only in M. marburgensis.

In the genome of M. marburgensis there is only one clustered regularly interspaced short palindromic repeat (CRISPR) locus with 36 repeats and only one CRISPR-associated (cas) gene (csa3), indicating that the organism is not protected from invasion by phage and plasmid DNA (7, 8, 10, 12). By comparison, in the genome of M. thermautotrophicus there are three CRISPR loci with 124, 4, and 47 repeats and 18 cas genes that encode proteins involved in adaptation and interference (http://genoweb1.irisa.fr/Serveur-GPO/outils/repeatsAnalysis/CRISPR/). The spacer sequences from locus 2 match DNA sequences found in phage ΨM1 of M. marburgensis (6, 11) and ΨM100 of M. wolfei (9), which supports the observation that M. thermautotrophicus is not lysed by those two phages. Unfortunately, there is no DNA sequence available for phage ΦF1, which is able to lyse M. thermautotrophicus (14), to compare it with the spacer sequences of the CRISPR regions. In the plasmid pM2001 (= pMTBMA4) (4,439-bp circular multicopy plasmid found only in M. marburgensis) (1, 19), no sequence identities for CRISPR spacer sequences of M. thermautotrophicus were found (14).

Approximately 200 CDS were identified that are required for the synthesis of the enzymes, coenzymes, and prosthetic groups involved in CO2 reduction to methane and in the coupling of this process with energy conservation. Some of the genes have been found only recently; others, such as those for coenzyme F430 biosynthesis, still remain to be discovered.

Nucleotide sequence accession number.

The complete genome sequence of M. marburgensis was deposited in GenBank under accession numbers CP001710 (chromosome) and CP001711 (pMTBMA4).

Acknowledgments

This work was supported by the Max Planck Society, by the Fonds der Chemischen Industrie, and by a grant from the Niedersächsische Ministerium für Wissenschaft und Kultur.

Footnotes

[down-pointing small open triangle]Published ahead of print on 27 August 2010.

REFERENCES

1. Bokranz, M., A. Klein, and L. Meile. 1990. Complete nucleotide sequence of plasmid pME2001 of Methanobacterium thermoautotrophicum (Marburg). Nucleic Acids Res. 18:363. [PMC free article] [PubMed]
2. Boone, D. R., W. B. Whitman, and P. Rouvière. 1993. Diversity and taxonomy of methanogens, p. 35-80. In J. G. Ferry (ed.), Methanogenesis.Chapman & Hall, New York, NY.
3. Brandis, A., R. K. Thauer, and K. O. Stetter. 1981. Relatedness of strains DH and Marburg of Methanobacterium thermoautotrophicum. Zentralbl. Bakt. Hyg. I Abt. Orig. C 2:311-317.
4. Dimarco, A. A., T. A. Bobik, and R. S. Wolfe. 1990. Unusual coenzymes of methanogenesis. Annu. Rev. Biochem. 59:355-394. [PubMed]
5. Fuchs, G., E. Stupperich, and R. K. Thauer. 1978. Acetate assimilation and the synthesis of alanine, aspartate and glutamate in Methanobacterium thermoautotrophicum. Arch. Microbiol. 117:61-66. [PubMed]
6. Jordan, M., L. Meile, and T. Leisinger. 1989. Organization of Methanobacterium thermoautotrophicum bacteriophage psi M1 DNA. Mol. Gen. Genet. 220:161-164. [PubMed]
7. Karginov, F. V., and G. J. Hannon. 2010. The CRISPR system: small RNA-guided defense in bacteria and archaea. Mol. Cell 37:7-19. [PMC free article] [PubMed]
8. Lillestol, R. K., P. Redder, R. A. Garrett, and K. Brugger. 2006. A putative viral defence mechanism in archaeal cells. Archaea 2:59-72. [PMC free article] [PubMed]
9. Luo, Y., P. Pfister, T. Leisinger, and A. Wasserfallen. 2001. The genome of archaeal prophage psiM100 encodes the lytic enzyme responsible for autolysis of Methanothermobacter wolfeii. J. Bacteriol. 183:5788-5792. [PMC free article] [PubMed]
10. Marraffini, L. A., and E. J. Sontheimer. 2010. Self versus non-self discrimination during CRISPR RNA-directed immunity. Nature 463:568-571. [PMC free article] [PubMed]
11. Meile, L., U. Jenal, D. Studer, M. Jordan, and T. Leisinger. 1989. Characterization of psiM1, a virulent phage of Methanobacterium thermoautotrophicum Marburg. Arch. Microbiol. 152:105-110.
12. Mojica, F. J., C. Diez-Villasenor, J. Garcia-Martinez, and E. Soria. 2005. Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements. J. Mol. Evol. 60:174-182. [PubMed]
13. Needleman, S. B., and C. D. Wunsch. 1970. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 48:443-453. [PubMed]
14. Nölling, J., A. Groffen, and W. M. Devos. 1993. phiF1 and phiF3, 2 novel virulent, archaeal phages infecting different thermophilic strains of the genus Methanobacterium. J. Gen. Microbiol. 139:2511-2516.
15. 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. Qiu, 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. 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. [PMC free article] [PubMed]
16. Thauer, R. K. 1998. Biochemistry of methanogenesis: a tribute to Marjory Stephenson. Microbiology 144:2377-2406. [PubMed]
17. Thauer, R. K., A. K. Kaster, M. Goenrich, M. Schick, T. Hiromoto, and S. Shima. 2010. Hydrogenases from methanogenic archaea, nickel, a novel cofactor, and H2 storage. Annu. Rev. Biochem. 79:507-536. [PubMed]
18. Thauer, R. K., A. K. Kaster, H. Seedorf, W. Buckel, and R. Hedderich. 2008. Methanogenic archaea: ecologically relevant differences in energy conservation. Nat. Rev. Microbiol. 6:579-591. [PubMed]
19. Wasserfallen, A., J. Nölling, P. Pfister, J. Reeve, and E. Conway de Macario. 2000. Phylogenetic analysis of 18 thermophilic Methanobacterium isolates supports the proposals to create a new genus, Methanothermobacter gen. nov., and to reclassify several isolates in three species, Methanothermobacter thermautotrophicus comb. nov., Methanothermobacter wolfeii comb. nov., and Methanothermobacter marburgensis sp. nov. Int. J. Syst. Evol. Microbiol. 1:43-53. [PubMed]
20. Zeikus, J. G., and R. S. Wolfe. 1972. Methanobacterium thermoautotrophicus sp. n., an anaerobic, autotrophic, extreme thermophile. J. Bacteriol. 109:707-713. [PMC free article] [PubMed]

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