Skip to main content
Journal of Bacteriology logoLink to Journal of Bacteriology
. 1997 May;179(9):2976–2986. doi: 10.1128/jb.179.9.2976-2986.1997

Characterization of pURB500 from the archaeon Methanococcus maripaludis and construction of a shuttle vector.

D L Tumbula 1, T L Bowen 1, W B Whitman 1
PMCID: PMC179063  PMID: 9139917

Abstract

The complete sequence of the 8,285-bp plasmid pURB500 from Methanococcus maripaludis C5 was determined. Sequence analysis identified 18 open reading frames as well as two regions of potential iterons and complex secondary structures. The shuttle vector, pDLT44, for M. maripaludis JJ was constructed from the entire pURB500 plasmid and pMEB.2, an Escherichia coli vector containing a methanococcal puromycin-resistance marker (P. Gernhardt, O. Possot, M. Foglino, L. Sibold, and A. Klein, Mol. Gen. Genet. 221:273-279, 1990). By using polyethylene glycol transformation, M. maripaludis JJ was transformed at a frequency of 3.3 x 10(7) transformants per microg of pDLT44. The shuttle vector was stable in E. coli under ampicillin selection but was maintained at a lower copy number than pMEB.2. Based on the inability of various restriction fragments of pURB500 to support maintenance in M. maripaludis JJ, multiple regions of pURB500 were required. pDLT44 did not replicate in Methanococcus voltae.

Full Text

The Full Text of this article is available as a PDF (533.0 KB).

Selected References

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

  1. Aagaard C., Leviev I., Aravalli R. N., Forterre P., Prieur D., Garrett R. A. General vectors for archaeal hyperthermophiles: strategies based on a mobile intron and a plasmid. FEMS Microbiol Rev. 1996 May;18(2-3):93–104. doi: 10.1111/j.1574-6976.1996.tb00229.x. [DOI] [PubMed] [Google Scholar]
  2. Akhmanova A. S., Kagramanova V. K., Mankin A. S. Heterogeneity of small plasmids from halophilic archaea. J Bacteriol. 1993 Feb;175(4):1081–1086. doi: 10.1128/jb.175.4.1081-1086.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Argyle J. L., Tumbula D. L., Leigh J. A. Neomycin resistance as a selectable marker in Methanococcus maripaludis. Appl Environ Microbiol. 1996 Nov;62(11):4233–4237. doi: 10.1128/aem.62.11.4233-4237.1996. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Bairoch A., Bucher P. PROSITE: recent developments. Nucleic Acids Res. 1994 Sep;22(17):3583–3589. [PMC free article] [PubMed] [Google Scholar]
  5. Berghöfer Y., Agha-Amiri K., Klein A. Selenium is involved in the negative regulation of the expression of selenium-free [NiFe] hydrogenases in Methanococcus voltae. Mol Gen Genet. 1994 Feb;242(4):369–373. doi: 10.1007/BF00281785. [DOI] [PubMed] [Google Scholar]
  6. Blank C. E., Kessler P. S., Leigh J. A. Genetics in methanogens: transposon insertion mutagenesis of a Methanococcus maripaludis nifH gene. J Bacteriol. 1995 Oct;177(20):5773–5777. doi: 10.1128/jb.177.20.5773-5777.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Bokranz M., Klein A., Meile L. Complete nucleotide sequence of plasmid pME2001 of Methanobacterium thermoautotrophicum (Marburg). Nucleic Acids Res. 1990 Jan 25;18(2):363–363. doi: 10.1093/nar/18.2.363. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Bramhill D., Kornberg A. A model for initiation at origins of DNA replication. Cell. 1988 Sep 23;54(7):915–918. doi: 10.1016/0092-8674(88)90102-x. [DOI] [PubMed] [Google Scholar]
  9. Brassard S., Paquet H., Roy P. H. A transposon-like sequence adjacent to the AccI restriction-modification operon. Gene. 1995 May 19;157(1-2):69–72. doi: 10.1016/0378-1119(94)00734-a. [DOI] [PubMed] [Google Scholar]
  10. Brown J. W., Daniels C. J., Reeve J. N. Gene structure, organization, and expression in archaebacteria. Crit Rev Microbiol. 1989;16(4):287–338. doi: 10.3109/10408418909105479. [DOI] [PubMed] [Google Scholar]
  11. Bult C. J., White O., Olsen G. J., Zhou L., Fleischmann R. D., Sutton G. G., Blake J. A., FitzGerald L. M., Clayton R. A., Gocayne J. D. Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. Science. 1996 Aug 23;273(5278):1058–1073. doi: 10.1126/science.273.5278.1058. [DOI] [PubMed] [Google Scholar]
  12. Charbonnier F., Forterre P. Comparison of plasmid DNA topology among mesophilic and thermophilic eubacteria and archaebacteria. J Bacteriol. 1994 Mar;176(5):1251–1259. doi: 10.1128/jb.176.5.1251-1259.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Charlebois R. L., Lam W. L., Cline S. W., Doolittle W. F. Characterization of pHV2 from Halobacterium volcanii and its use in demonstrating transformation of an archaebacterium. Proc Natl Acad Sci U S A. 1987 Dec;84(23):8530–8534. doi: 10.1073/pnas.84.23.8530. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Dillard J. P., Yother J. Analysis of Streptococcus pneumoniae sequences cloned into Escherichia coli: effect of promoter strength and transcription terminators. J Bacteriol. 1991 Aug;173(16):5105–5109. doi: 10.1128/jb.173.16.5105-5109.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Erauso G., Marsin S., Benbouzid-Rollet N., Baucher M. F., Barbeyron T., Zivanovic Y., Prieur D., Forterre P. Sequence of plasmid pGT5 from the archaeon Pyrococcus abyssi: evidence for rolling-circle replication in a hyperthermophile. J Bacteriol. 1996 Jun;178(11):3232–3237. doi: 10.1128/jb.178.11.3232-3237.1996. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Gernhardt P., Possot O., Foglino M., Sibold L., Klein A. Construction of an integration vector for use in the archaebacterium Methanococcus voltae and expression of a eubacterial resistance gene. Mol Gen Genet. 1990 Apr;221(2):273–279. doi: 10.1007/BF00261731. [DOI] [PubMed] [Google Scholar]
  17. Hackett N. R., Krebs M. P., DasSarma S., Goebel W., RajBhandary U. L., Khorana H. G. Nucleotide sequence of a high copy number plasmid from Halobacterium strain GRB. Nucleic Acids Res. 1990 Jun 11;18(11):3408–3408. doi: 10.1093/nar/18.11.3408. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Hall M. J., Hackett N. R. DNA sequence of a small plasmid from Halobacterium strain GN101. Nucleic Acids Res. 1989 Dec 25;17(24):10501–10501. doi: 10.1093/nar/17.24.10501. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Hayashi S., Wu H. C. Lipoproteins in bacteria. J Bioenerg Biomembr. 1990 Jun;22(3):451–471. doi: 10.1007/BF00763177. [DOI] [PubMed] [Google Scholar]
  20. Held P. G., Heintz N. H. Eukaryotic replication origins. Biochim Biophys Acta. 1992 Apr 6;1130(3):235–246. doi: 10.1016/0167-4781(92)90435-3. [DOI] [PubMed] [Google Scholar]
  21. Holmes M. L., Pfeifer F., Dyall-Smith M. L. Analysis of the halobacterial plasmid pHK2 minimal replicon. Gene. 1995 Feb 3;153(1):117–121. doi: 10.1016/0378-1119(94)00761-g. [DOI] [PubMed] [Google Scholar]
  22. Hopwood D. A. Genetic studies with bacterial protoplasts. Annu Rev Microbiol. 1981;35:237–272. doi: 10.1146/annurev.mi.35.100181.001321. [DOI] [PubMed] [Google Scholar]
  23. Ilyina T. V., Koonin E. V. Conserved sequence motifs in the initiator proteins for rolling circle DNA replication encoded by diverse replicons from eubacteria, eucaryotes and archaebacteria. Nucleic Acids Res. 1992 Jul 11;20(13):3279–3285. doi: 10.1093/nar/20.13.3279. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Jarrell K. F., Bayley D. P., Florian V., Klein A. Isolation and characterization of insertional mutations in flagellin genes in the archaeon Methanococcus voltae. Mol Microbiol. 1996 May;20(3):657–666. doi: 10.1046/j.1365-2958.1996.5371058.x. [DOI] [PubMed] [Google Scholar]
  25. Jones W. J., Whitman W. B., Fields R. D., Wolfe R. S. Growth and plating efficiency of methanococci on agar media. Appl Environ Microbiol. 1983 Jul;46(1):220–226. doi: 10.1128/aem.46.1.220-226.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Keeling P. J., Klenk H. P., Singh R. K., Feeley O., Schleper C., Zillig W., Doolittle W. F., Sensen C. W. Complete nucleotide sequence of the Sulfolobus islandicus multicopy plasmid pRN1. Plasmid. 1996 Mar;35(2):141–144. doi: 10.1006/plas.1996.0016. [DOI] [PubMed] [Google Scholar]
  27. Keswani J., Orkand S., Premachandran U., Mandelco L., Franklin M. J., Whitman W. B. Phylogeny and taxonomy of mesophilic Methanococcus spp. and comparison of rRNA, DNA hybridization, and phenotypic methods. Int J Syst Bacteriol. 1996 Jul;46(3):727–735. doi: 10.1099/00207713-46-3-727. [DOI] [PubMed] [Google Scholar]
  28. Koonin E. V. Archaebacterial virus SSV1 encodes a putative DnaA-like protein. Nucleic Acids Res. 1992 Mar 11;20(5):1143–1143. doi: 10.1093/nar/20.5.1143. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Kornacki J. A., Chang C. H., Figurski D. H. kil-kor regulon of promiscuous plasmid RK2: structure, products, and regulation of two operons that constitute the kilE locus. J Bacteriol. 1993 Aug;175(16):5078–5090. doi: 10.1128/jb.175.16.5078-5090.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Kües U., Stahl U. Replication of plasmids in gram-negative bacteria. Microbiol Rev. 1989 Dec;53(4):491–516. doi: 10.1128/mr.53.4.491-516.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Mattar S., Scharf B., Kent S. B., Rodewald K., Oesterhelt D., Engelhard M. The primary structure of halocyanin, an archaeal blue copper protein, predicts a lipid anchor for membrane fixation. J Biol Chem. 1994 May 27;269(21):14939–14945. [PubMed] [Google Scholar]
  32. Meile L., Madon J., Leisinger T. Identification of a transcript and its promoter region on the archaebacterial plasmid pME2001. J Bacteriol. 1988 Jan;170(1):478–481. doi: 10.1128/jb.170.1.478-481.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Mojica F. J., Ferrer C., Juez G., Rodríguez-Valera F. Long stretches of short tandem repeats are present in the largest replicons of the Archaea Haloferax mediterranei and Haloferax volcanii and could be involved in replicon partitioning. Mol Microbiol. 1995 Jul;17(1):85–93. doi: 10.1111/j.1365-2958.1995.mmi_17010085.x. [DOI] [PubMed] [Google Scholar]
  34. Ng W. L., DasSarma S. Minimal replication origin of the 200-kilobase Halobacterium plasmid pNRC100. J Bacteriol. 1993 Aug;175(15):4584–4596. doi: 10.1128/jb.175.15.4584-4596.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Nölling J., van Eeden F. J., Eggen R. I., de Vos W. M. Modular organization of related Archaeal plasmids encoding different restriction-modification systems in Methanobacterium thermoformicicum. Nucleic Acids Res. 1992 Dec 25;20(24):6501–6507. doi: 10.1093/nar/20.24.6501. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Patel G. B., Choquet C. G., Nash J. H., Sprott G. D. Formation and Regeneration of Methanococcus voltae Protoplasts. Appl Environ Microbiol. 1993 Jan;59(1):27–33. doi: 10.1128/aem.59.1.27-33.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Patel G. B., Nash J. H., Agnew B. J., Sprott G. D. Natural and Electroporation-Mediated Transformation of Methanococcus voltae Protoplasts. Appl Environ Microbiol. 1994 Mar;60(3):903–907. doi: 10.1128/aem.60.3.903-907.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Pfeifer F., Ghahraman P. Plasmid pHH1 of Halobacterium salinarium: characterization of the replicon region, the gas vesicle gene cluster and insertion elements. Mol Gen Genet. 1993 Apr;238(1-2):193–200. doi: 10.1007/BF00279547. [DOI] [PubMed] [Google Scholar]
  39. STADTMAN T. C., BARKER H. A. Studies on the methane fermentation. X. A new formate-decomposing bacterium, Methanococcus vannielii. J Bacteriol. 1951 Sep;62(3):269–280. doi: 10.1128/jb.62.3.269-280.1951. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Sandbeck K. A., Leigh J. A. Recovery of an integration shuttle vector from tandem repeats in Methanococcus maripaludis. Appl Environ Microbiol. 1991 Sep;57(9):2762–2763. doi: 10.1128/aem.57.9.2762-2763.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Sioud M., Baldacci G., Forterre P., de Recondo A. M. Novobiocin induces accumulation of a single strand of plasmid pGRB-1 in the archaebacterium Halobacterium GRB. Nucleic Acids Res. 1988 Aug 25;16(16):7833–7842. doi: 10.1093/nar/16.16.7833. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. 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]
  43. Whitman W. B., Sohn S., Kuk S., Xing R. Role of Amino Acids and Vitamins in Nutrition of Mesophilic Methanococcus spp. Appl Environ Microbiol. 1987 Oct;53(10):2373–2378. doi: 10.1128/aem.53.10.2373-2378.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Wood A. G., Whitman W. B., Konisky J. A newly-isolated marine methanogen harbors a small cryptic plasmid. Arch Microbiol. 1985 Aug;142(3):259–261. doi: 10.1007/BF00693400. [DOI] [PubMed] [Google Scholar]
  45. Xing R. Y., Whitman W. B. Characterization of enzymes of the branched-chain amino acid biosynthetic pathway in Methanococcus spp. J Bacteriol. 1991 Mar;173(6):2086–2092. doi: 10.1128/jb.173.6.2086-2092.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  46. Yu J. P., Ladapo J., Whitman W. B. Pathway of glycogen metabolism in Methanococcus maripaludis. J Bacteriol. 1994 Jan;176(2):325–332. doi: 10.1128/jb.176.2.325-332.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]

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

RESOURCES