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

Journal of Bacteriology

Volumn 179, Issue 9, 1997, Pages 2976-2986

  Tumbula, Debra L ^a   Bowen, Timothy L ^a,b   Whitman, William B ^a  

^a UNIVERSITY OF GEORGIA   (United States)

^b NEW ENGLAND BIOLABS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMPICILLIN; MACROGOL;

ARTICLE; BACTERIUM TRANSFORMATION; ESCHERICHIA COLI; METHANOBACTERIUM; NONHUMAN; OPEN READING FRAME; PLASMID; PRIORITY JOURNAL; PROTEIN SECONDARY STRUCTURE; RESTRICTION FRAGMENT; SHUTTLE VECTOR;

EID: 0030903165     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/jb.179.9.2976-2986.1997     Document Type: Article

References (62)

1. Aagaard, C., I. Leviev, R. N. Aravalli, P. Forterre, D. Prieur, and R. A. Garrett. 1996. General vectors for archaeal hyperthermophiles: strategies based on a mobile intron and a plasmid. FEMS Microbiol. Rev. 18:93-104.
2. Akhmanova, A. S., V. K. Kagramanova, and A. S. Mankin. 1993. Heterogeneity of small plasmids from halophilic archaea. J. Bacteriol. 175:1081-1086.
3. Argyle, J. L., D. L. Tumbula, and J. A. Leigh. 1996. Neomycin resistance as a selectable marker in Methanococcus maripaludis. Appl. Environ. Microbiol. 62:4233-4237.
4. Bairoch, A., and P. Bucher. 1994. PROSITE: recent developments. Nucleic Acids Res. 22:3583-3589.
5. Berghöfer, Y., K. Agha-Amiri, and A. Klein. 1994. Selenium is involved in the negative regulation of the expression of selenium-free [NiFe] hydrogenases in Methanococcus valtae. Mol. Gen. Genet. 242:369-373.
6. Blank, C. E., P. S. Kessler, and J. A. Leigh. 1995. Genetics in methanogens: transposon insertion mutagenesis of a Methanococcus maripaludis nifH gene. J. Bacteriol. 177:5773-5777.
7. Bokranz, M., A. Klein, and L. Meile. 1990. Complete nucleotide sequence of plasmid pME2001 of Methanobacterium thermoautotrophicum (Marburg). Nucleic Acids Res. 18:363.
8. Bramhill, D., and A. Kornberg. 1988. A model for initiation at origins of DNA replication. Cell 54:915-918.
9. Brassard, S., H. Paquet, and P. H. Roy. 1995. A transposon-like sequence adjacent to the AccI restriction-modification operon. Gene 157:69-72.
10. Brown, J. W., C. J. Daniels, and J. N. Reeve. 1989. Gene structure, organization, and expression in archaebacteria. Crit. Rev. Microbiol. 16:287-338.
11. 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. Overheek, W. F. Kirkness, K. B. Weinstock, J. M. Merrick, A. Glodek, J. L. Scott, N. S. M. Geoghagen, J. F. Weidman, J. L. Fuhrmann, D. Nguyen, T. R. Utterback, J. M. Kelley, 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. M. Fraser, H. O. Smith, C. R. Woesc, and J. G. Venter. 1996. Complete genome sequence of the methanogenic archaeon. Methanococcus jannaschii. Science 273:1058-1073.
12. Charbonnier, F., and P. Forterre. 1994. Comparison of plasmid DNA topology among mesophilic and thermophilic eubacteria and archaebacteria. J. Bacteriol. 176:1251-1259.
13. Charlebois, R. L., W. L. Lam, S. W. Cline. and W. F. Doolittle. 1987. Characterization of pHV2 from Halobacterium volcanii and its use in demonstrating transformation of an archaebacterium. Proc. Natl. Acad. Sci. USA 84:8530-8534.
14. DasSarma, S. 1995. Natural plasmids and plasmid vectors of halophiles, p. 241-250. In F. T. Robb, K. R. Sowers. S. DasSarma. A. R. Place. H. J. Schreier, and E. M. Fleischmann (ed.). Archaea: a laboratory manual. Cold Spring Harbor Press. Cold Spring Harbor. N. Y.
15. Dillard, J. P., and J. Yother. 1991. Analysis of Streptococcus pneumoniae sequences cloned into Escherichia coli: effect of promoter strength and transcription terminators. J. Bacteriol. 173:5105-5109.
16. Erauso, G., S. Marsin, N. Benbouzid-Rollet, M.-F. Baucher, T. Barbeyron, Y. Zivanovic, D. Prieur, and P. Forterre. 1996. Sequence of plasmid pGT5 from the archaeon Pyrococcus abyssi: evidence for rolling-circle replication in a hyperthermophile. J. Bacteriol. 178:3232-3237.
17. Gardner, W. L., J.-P. Yu, and W. B. Whitman. Unpublished data
18. Gernhardt, P., O. Possot, M. Foglino, L. Sibold, and A. Klein. 1990. Construction of an integration vector for use in the archaebacterium Methanococcus voltae and expression of a eubacterial resistance gene. Mol. Gen. Genet. 221:273-279.
19. Hackett, N. R., M. P. Krebs, S. DasSarma, W. Goebel, U. L. RajBhandary, and H. G. Khorana. 1990. Nucleotide sequence of a high copy number plasmid from Halobacterium strain GRB. Nucleic Acids Res. 18:3408.
20. Hall, M. J., and N. R. Hackett. 1989. DNA sequence of a small plasmid from Halobacterium strain GN101. Nucleic Acids Res. 17:10501.
21. Hayashi, S., and H. C. Wu. 1990. Lipoproteins in bacteria. J. Bioenerg. Biomembr. 22:451-471.
22. Held, P. G., and N. H. Heintz. 1992. Eukaryotic replication origins. Biochim. Biophys. Acta 1130:235-246.
23. Holmes, M. L., F. Pfeifer, and M. L. Dyall-Smith. 1995. Analysis of the halobacterial plasmid pHK2 minimal replicon. Gene 153:117-121.
24. Hopwood, D. A. 1981. Genetic studies with bacterial protoplasts. Annu. Rev. Microbiol, 35:237-272.
25. Ilyina, T, V., and E. V. Koonin. 1992. Conserved sequence motifs in the initiator proteins for rolling circle DNA replication encoded by diverse replicons from eubacteria. eucaryotes and archaebacteria. Nucleic Acids Res. 20:3279-3285.
26. Jarrell, K. F., D. P. Bayley, V. Florian, and A. Klein. 1996. Isolation and characterization of insertional mutations in flagellin genes in the archaeon Methanococcus voltae. Mol. Microbiol. 20:657-666.
27. Jarrell, K. F., C. Julseth, B. Pearson, and J. Kuzio. 1987. Paucity of the Sau3AI recognition sequence (GATC) in the genome of Methanococcus voltae. Mol. Gen. Genet. 208:191-194.
28. Jones, W. J., M. J. B. Paynter, and R. Gupta. 1983. Characterization of Methanococcus maripaludis sp. nov., a new methanogen isolated from salt marsh sediment. Arch. Microbiol. 135:91-97.
29. Jones, W. J., W. B. Whitman, R. D. Fields, and R. S. Wolfe. 1983. Growth and plating efficiency of methanococci on agar media. Appl. Environ. Microbiol. 46:220-226.
30. Keeling, P. J., H.-P. Klenk, R. K. Singh, O. Feeley, C. Schleper, W. Zillig, W. F. Doolittle, and C. W. Sensen. 1996. Complete nucleotide sequence of the Sulfolobus islandicus multicopy plasmid pRN1. Plasmid 35:141-144.
31. Keswani, J., S. Orkand, U. Premachandran, L. Mandelco, M. J. Franklin, and W. B. Whitman. 1996. Phylogeny and taxonomy of mesophilic Methanococcus spp. and comparison of rRNA. DNA hybridization, and phenotypic methods. Int. J. Syst. Bacteriol. 46:727-735.
32. Koonin, E. V. 1992. Archaebacterial virus SSV1 encodes a putative DnaA-like protein. Nucleic Acids Res. 20:1143.
33. Kornacki, J. A., C.-H. Chang, and D. H. Figurski. 1993. kil-kor regulon of promiscuous plasmid RK2: structure, products, and regulation of two operons that constitute the kilE locus. J. Bacteriol. 175:5078-5090.
34. Kües, U., and U. Stahl. 1989. Replication of plasmids in gram-negative bacteria. Microbiol. Rev. 53:491-516.
35. Maniatis, T., E. F. Fritsch. and J. Sambrook. 1982. Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
36. Mattar, S., B. Scharf, S. B. H. Kent, K. Rodewald, D. Oesterhelt, and M. Engelhard. 1994. The primary structure of halocyanin, an archaeal blue copper protein, predicts a lipid anchor for membrane fixation. J. Biol. Chem. 269:14939-14945.
37. Meile. L., J. Madon, and T. Leisinger. 1988. Identification of a transcript and its promoter region on the archaebacterial plasmid pME2001. J. Bacteriol. 170:478-481.
38. Mojica, F. J. M., C. Ferrer, G. Juez, and F. Rodríguez-Valera. 1995. 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. 17:85-93.
39. Ng, W.-L., and S. DasSarma. 1993. Minimal replication origin of the 200-kilobase Halobacterium plasmid pNRC100. J. Bacteriol. 175:4584-4596.
40. Nölling, J., F. J. M. van Eaden, R. I. L. Eggen, and W. M. de Vos. 1992. Modular organization of related archaeal plasmids encoding different restriction-modification systems in Methanobacterium thermoformicicum. Nucleic Acids Res. 20:6501-6507.
41. Nordström, K, 1993. Plasmid replication and maintenance, p. 1-38. In K. G. Hardy (ed.), Plasmids: a practical approach. IRL Press. Oxford, England.
42. Palmer, J. R., and J. N. Reeve. 1993. Structure and function of methanogen genes, p. 497-534. In M. Kates, D. J. Kushner, and A. T. Matheson (ed.), The biochemistry of archaea (archaebacteria). Elsevier, Amsterdam, The Netherlands.
43. Patel, G. B., C. G. Choquet, J. H. E. Nash, and G. D. Sprott. 1993. Formation and regeneration of Methanococcus voltae protoplasts. Appl. Environ. Microbiol. 59:27-33.
44. Patel, G. B., J. H. E. Nash, B. J. Agnew, and G. D. Sprott. 1994. Natural and electroporation-mediated transformation of Methanococcus voltae protoplasts. Appl. Environ. Microbiol. 60:903-907.
45. Pfeifer, F., and P. Ghahraman. 1993. Plasmid pHH1 of Halobacterium salinarium: characterization ot the replicon region, (he gas vesicle gene cluster and insertion elements. Mol. Gen. Genet. 238:193-200.
46. Sandbeck, K. A., and J. A. Leigh. 1991. Recovery of an integration shuttle vector from tandem repeats in Methanococcus maripaludis. Appl. Environ. Microbiol. 57:2762-2763.
47. Sioud, M., G. Baldacci, P. Forterre, and A.-M. de Recondo. 1988. Novobiocin induces accumulation of a single strand of plasmid pGRB-1 in the archaebacterium Halobacterium GRB. Nucleic Acids Res. 16:7833-7842.
48. Stadtman, T. C., and H. A. Barker. 1951. Studies on the methane fermentation: a new formate-decomposing bacterium, Methanococcus vannielii. J. Bacteriol. 62:269-280.
49. Stettler, R., P. Pfister, and T. Leisinger. 1994. Characterization of a plasmid carried by Methanobacterium thermoautotrophicum ZH3, a methanogen closely related to Methanobacterium thermoautotrophicum Marburg. Syst. Appl. Microbiol. 17:484-491.
50. Tumbula, D. L., T. L. Bowen, W. J. Jones, and W. B. Whitman. 1995. Growth of methanogens on solidified media, p. 49-55. In F. T. Robb, K. R. Sowers, S. DasSarma, A. R. Place, H. J. Schreier, and E. M. Fleischmann (ed.), Archaea: a laboratory manual. Cold Spring Harbor Press, Cold Spring Harbor, N.Y.
51. Tumbula, D. L., R. A. Makula, and W. B. Whitman. 1994. Transformation of Methanococcus maripaludis and identification of a PstI-like restriction system. FEMS Microbiol. Lett. 121:309-314.
52. Valentine, C. R. I., and C. I. Kado. 1989. Molecular genetics of IncW plasmids, p. 125-163. In C. M. Thomas (ed.), Promiscuous plasmids of gram-negative bacteria. Academic Press, London, England.
53. Vieira, J., and J. Messing. 1982. The pUC plasmids, an M13mp7-derived system for insertion mutagenesis and sequencing with synthetic universal primers. Gene 19:259-268.
54. Ward, J. M., P. H. Smith, and D. R. Boone. 1989. Emended description of strain PS (= OGC 70 = ATCC 33273 = DSM 1537), the type strain of Methanococcus voltae. Int. J. Syst. Bacteriol. 39:493-494.
55. Whitman, W. B. 1989. Methanococcales, p. 2185-2190. In J. T. Staley, M. P. Bryant, and N. Pfennig (ed.), Bergey's manual of systematic bacteriology. Williams & Wilkins, Baltimore, Md.
56. Whitman, W. B., T. L. Bowen, and D. R. Boone. 1991. The methanogenic bacteria, p. 719-767. In A. Balows. H. G. Trüper, M. Dworkin, W. Harder, and K. H. Schleifer (ed.). The prokaryotes, 2nd ed. Springer-Verlag, New York, N.Y.
57. Whitman, W. B., J. Shieh, S. Sohn, D. S. Caras, and U. Premachandran. 1986. Isolation and characterization of 22 mesophilic methanococci. Syst. Appl. Microbiol. 7:235-240.
58. Whitman, W. B., S. Sohn, S. Kuk, and R. Xing. 1987. Role of amino acids and vitamins in nutrition of mesophilic Methanococcus spp. Appl. Environ. Microbiol. 53:2373-2378.
59. Wood, A. G., W. B. Whitman, and J. Konisky. 1985. A newly-isolated marine methanogen harbors a small cryptic plasmid. Arch. Microbiol. 142:259-261.
60. Xing, R. Y., and W. B. Whitman. 1991. Characterization of enzymes of the branched-chain amino acid biosynthetic pathway in Methanococcus spp. J. Bacteriol. 173:2086-2092.
61. Yu, J.-P., J. Ladapo, and W. B. Whitman. 1994. Pathway of glycogen metabolism in Methanococcus maripaludis. J. Bacteriol. 176:325-332.
62. Zillig, W., P. Palm, H.-P. Klenk, D. Langer, U. Hüdepohl, J. Hain, M. Lanzendörfer, and I. Holz. 1993. Transcription in archaea, p. 367-391. In M. Kates, D. J. Kushner, and A. T. Matheson (ed.), The Biochemistry of archaea (archaebacteria). Elsevier, Amsterdam, The Netherlands.