Genetic systems for hydrogenotrophic methanogens

Methods in Enzymology

Volumn 494, Issue , 2011, Pages 43-73

  Felipe Sarmiento, B ^a   Leigh, John A ^b   Whitman, William B ^a  

^a UNIVERSITY OF GEORGIA   (United States)

^b UNIVERSITY OF WASHINGTON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BETA GLUCURONIDASE; MACROGOL; MESYLIC ACID ETHYL ESTER;

ANAEROBIC BACTERIUM; ARTICLE; AUXOTROPHIC MUTANT; BACTERIAL GENETICS; BACTERIAL GENOME; BACTERIAL GROWTH; BACTERIUM TRANSFORMATION; CULTURE MEDIUM; ELECTROPORATION; ENZYME ASSAY; GENETIC MARKER; METHANOGEN; METHANOGENESIS; NONHUMAN; NUCLEOTIDE SEQUENCE; PLASMID; PRIORITY JOURNAL; PROTOPLAST; SHUTTLE VECTOR; SITE DIRECTED MUTAGENESIS; TRANSPOSON;

METHANOCOCCI; METHANOCOCCUS MARIPALUDIS;

EID: 79952601439     PISSN: 00766879     EISSN: None     Source Type: Book Series    
DOI: 10.1016/B978-0-12-385112-3.00003-2     Document Type: Chapter

References (56)

1. K. Agha-Amiri, and A. Klein Nucleotide sequence of a gene encoding a histone-like protein in the archaeon Methanococcus voltae Nucleic Acids Res. 21 1993 1491 (Pubitemid 23154385)
2. I. Anderson, M. Sieprawska-Lupa, E. Goltsman, A. Lapidus, A. Copeland, T.G. Del Rio, H. Tice, E. Dalin, K. Barry, S. Pitluck, L. Hauser, and M. Land Complete genome sequence of Methanocorpusculum labreanum type strain Z Stand. Genomic Sci. 1 2009 197 203
3. I. Anderson, L.E. Ulrich, B. Lupa, D. Susanti, I. Porat, S.D. Hooper, A. Lykidis, M. Sieprawska-Lupa, L. Dharmarajan, E. Goltsman, A. Lapidus, and E. Saunders Genomic characterization of methanomicrobiales reveals three classes of methanogens PLoS One 4 2009 e5797
4. J.L. Argyle, D.L. Tumbula, and J.A. Leigh Neomycin resistance as a selectable marker in Methanococcus maripaludis Appl. Environ. Microbiol. 62 1995 4233 4237 (Pubitemid 26371535)
5. W.E. Balch, and R.S. Wolfe New approach to the cultivation of methanogenic bacteria: 2-mercaptoethanesulfonic acid (HS-CoM)-dependent growth of Methanobacterium ruminantium in a pressurized atmosphere Appl. Environ. Microbiol. 32 1976 781 791 (Pubitemid 8008043)
6. G.S. Beckler Chloramphenicol acetyltransferase should not provide methanogens with resistance to chloramphenicol Appl. Environ. Microbiol. 47 1984 868 869 (Pubitemid 14147351)
7. S. Beneke Use of the Escherichia coli uidA gene as a reporter in Methanococcus voltae for the analysis of the regulatory function of the intergenic region between the operons encoding selenium-free hydrogenases Mol. Gen. Genet. 248 1995 225 228
8. G. Bertani, and L. Baresi Genetic transformation in the methanogen Methanococcus voltae PS J. Bacteriol. 169 1987 2730 2738 (Pubitemid 17104340)
9. C.E. Blank Genetics in methanogens: Transposon insertion mutagenesis of a Methanococcus maripaludis nifH gene J. Bacteriol. 177 1995 5773 5777
10. A. Bck, and O. Kandler Antibiotic sensitivity of archaebacteria The Bacteria, Vol. 8 1985 Academic Press New York 525 544
11. M. Bokranz Complete nucleotide sequence of plasmid pME2001 of Methanobacterium thermoautotrophicum (Marburg) Nucleic Acids Res. 18 1990 363 (Pubitemid 20053324)
12. T.L. Bowen, and W.B. Whitman Incorporation of exogenous purines and pyrimidines by Methanococcus voltae and isolation of analog-resistant mutants Appl. Environ. Microbiol. 53 1987 1822 1826
13. C.J. Bult, 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, and B.A. Dougherty Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii Science 273 1996 1058 1073 (Pubitemid 26278157)
14. R. Cohen-Kupiec Transcriptional regulation in Archaea: In vivo demonstration of a repressor binding site in a methanogen Proc. Natl. Acad. Sci. USA 94 1997 1316 1320 (Pubitemid 27087848)
15. C. Erkel, M. Kube, R. Reinhardt, and W. Liesack Genome of rice cluster I archaeaThe key methane producers in the rice rhizosphere Science 313 2006 370 372 (Pubitemid 44480965)
16. W.F. Fricke, H. Seedorf, A. Henne, M. Kruer, H. Liesegang, R. Hedderich, G. Gottschalk, and R.K. Thauer The genome sequence of Methanosphaera stadtmanae reveals why this human intestinal archaeon is restricted to methanol and H2 for methane formation and ATP synthesis J. Bacteriol. 188 2006 642 658 (Pubitemid 43100552)
17. W.L. Gardner, and W.B. Whitman Expression vectors for Methanococcus maripaludis: Overexpression of acetohydroxyacid synthase and beta-galactosidase Genetics 152 1999 1439 1447 (Pubitemid 29370327)
18. P. Gernhardt Construction of an integration vector for use in the archaebacterium Methanococcus voltae and expression of a eubacterial resistance gene Mol. Gen. Genet. 221 1990 273 279 (Pubitemid 20141642)
19. R. Hedderich, and W.B. Whitman Physiology and biochemistry of the methane-producing archaea The Prokaryotes, Vol. 2 2006 Springer-Verlag New York 1050 1079
20. E.L. Hendrickson, R. Kaul, Y. Zhou, D. Bovee, P. Chapman, J. Chung, E. Conway de Macario, J.A. Dodsworth, W. Gillett, D.E. Graham, M. Hackett, and A.K. Haydock Complete genome sequence of the genetically tractable hydrogenotrophic methanogen Methanococcus maripaludis J. Bacteriol. 186 2004 6956 6969 (Pubitemid 39332135)
21. H. Hippe Maintenance of methanogenic bacteria Maintenance of Microorganisms: A Manual of Laboratory Methods 1984 Academic Press London 69 81
22. R.E. Hungate The anaerobic mesophilic cellulolytic bacteria Bacteriol. Rev. 14 1950 1 49
23. M.K. Jain, and J.G. Zeikus Methods for isolation of auxotrophic mutants of Methanobacterium ivanovii and initial characterization of acetate auxotrophs Appl. Environ. Microbiol. 53 1987 1387 1390
24. W.J. Jones Growth and plating efficiency of methanococci on agar media Appl. Environ. Microbiol. 46 1983 220 226 (Pubitemid 13045863)
25. S.F. Koval, and K.F. Jarrell Ultrastructure and biochemistry of the cell wall of Methanococcus voltae J. Bacteriol. 169 1987 1298 1306 (Pubitemid 17043402)
26. J. Ladapo, and W.B. Whitman Method for isolation of auxotrophs in the methanogenic archaebacteria: Role of the acetyl-CoA pathway of autotrophic CO2 fixation in Methanococcus maripaludis Proc. Natl. Acad. Sci. USA 87 1990 5598 5602
27. T.J. Lie, and J.A. Leigh Regulatory response of Methanococcus maripaludis to alanine, an intermediate nitrogen source J. Bacteriol. 184 2002 5301 5306 (Pubitemid 35024375)
28. T.J. Lie, and J.A. Leigh Genetic screen for regulatory mutations in Methanococcus maripaludis and its use in identification of induction-deficient mutants of the euryarchaeal repressor NrpR Appl. Environ. Microbiol. 73 2007 6595 6600 (Pubitemid 47623719)
29. W. Lin, and W.B. Whitman The importance of porE and porF in the anabolic pyruvate oxidoreductase of Methanococcus maripaludis Arch. Microbiol. 181 2004 68 73 (Pubitemid 38161238)
30. Y. Liu Taxonomy of methanogens Handbook of Hydrocarbon and Lipid Microbiology, Vol. 1 2010 Sprimger-Verlag Berlin Heidelberg, New York 550 558
31. Y. Liu, and W.B. Whitman Metabolic, phylogenetic and ecological diversity of the methanogenic archaea Incredible Anaerobes 2008 New York Academy of Sciences New York 171 189 (Pubitemid 351451164)
32. Y. Liu Methanococci use the diaminopimelate aminotransferase (DapL) pathway for lysine biosynthesis J. Bacteriol. 192 2010 3304 3310
33. W.W. Metcalf A genetic system for Archaea of the genus Methanosarcina: Liposome-mediated transformation and construction of shuttle vectors Proc. Natl. Acad. Sci. USA 94 1997 2626 2631
34. P.A. Micheletti Isolation of a coenzyme M-auxotrophic mutant and transformation by electroporation in Methanococcus voltae J. Bacteriol. 173 1991 3414 3418
35. J.H. Miller Experiments in molecular genetics 1972 Cold Spring Harbor Laboratory Cold Spring Harbor, New York
36. T.L. Miller Methanobrevibacter Bergey's Manual of Systematic Bacteriology, Vol. 3 1989 Williams & Wilkins Baltimore 2178 2183
37. B.C. Moore, and J.A. Leigh Markerless mutagenesis in Methanococcus maripaludis demonstrates roles for alanine dehydrogenase, alanine racemase, and alanine permease J. Bacteriol. 187 2005 972 979 (Pubitemid 40189771)
38. J. Nolling Modular organization of related Archaeal plasmids encoding different restriction-modification systems in Methanobacterium thermoformicicum Nucleic Acids Res. 20 1992 6501 6507 (Pubitemid 23052668)
39. G.B. Patel Formation and regeneration of Methanococcus voltae protoplasts Appl. Environ. Microbiol. 59 1993 27 33 (Pubitemid 23028363)
40. G.B. Patel Natural and electroporation-mediated transformation of Methanococcus voltae protoplasts Appl. Environ. Microbiol. 60 1994 903 907 (Pubitemid 24077979)
41. I. Porat, and W.B. Whitman Tryptophan auxotrophs were obtained by random transposon insertions in the Methanococcus maripaludis tryptophan operon FEMS Microbiol. Lett. 297 2009 250 254
42. O. Possot Analysis of drug resistance in the archaebacterium Methanococcus voltae with respect to potential use in genetic engineering Appl. Environ. Microbiol. 54 1988 734 740
43. M.A. Pritchett Development of a markerless genetic exchange method for Methanosarcina acetivorans C2A and its use in construction of new genetic tools for methanogenic archaea Appl. Environ. Microbiol. 70 2004 1425 1433 (Pubitemid 38365122)
44. S. Sakai Methanocella paludicola gen. nov., sp. nov., a methane-producing archaeon, the first isolate of the lineage 'Rice Cluster I', and proposal of the new archaeal order Methanocellales ord. nov Int. J. Syst. Evol. Microbiol. 58 2008 929 936
45. B.S. Samuel, E.E. Hansen, J.K. Manchester, P.M. Coutinho, B. Henrissat, R. Fulton, P. Latreille, K. Kim, R.K. Wilson, and J.I. Gordon Genomic and metabolic adaptations of Methanobrevibacter smithii to the human gut Proc. Natl. Acad. Sci. USA 104 2007 10643 10648 (Pubitemid 47185718)
46. A.I. Slesarev, K.V. Mezhevaya, K.S. Makarova, N.N. Polushin, O.V. Shcherbinina, V.V. Shakhova, G.I. Belova, L. Aravind, D.A. Natale, I.B. Rogozin, R.L. Tatusov, and Y.I. Wolf The complete genome of hyperthermophile Methanopyrus kandleri AV19 and monophyly of archaeal methanogens Proc. Natl. Acad. Sci. USA 99 2002 4644 4649 (Pubitemid 34286038)
47. D.R. Smith, L.A. Doucette-Stamm, C. Deloughery, H. Lee, J. Dubois, T. Aldredge, R. Bashirzadeh, D. Blakely, R. Cook, K. Gilbert, D. Harrison, and L. Hoang Complete genome sequence of Methanobacterium thermoautotrophicum deltaH: Functional analysis and comparative genomics J. Bacteriol. 179 1997 7135 7155 (Pubitemid 27492501)
48. C. Stathopoulos Cysteinyl-tRNA synthetase is not essential for viability of the archaeon Methanococcus maripaludis Proc. Natl. Acad. Sci. USA 98 2001 14292 14297 (Pubitemid 33121385)
49. R. Stettler, P. Pfister, and T. Leisinger Characterization of a plasmid carried by Methanobacterium thermoautotrophicum ZH3, a methanogens closely related to Methanobacterium thermoautotrophicum Marburg Syst. Appl. Microbiol. 17 1994 484 491
50. N.A. Thomas Insertional inactivation of the flaH gene in the archaeon Methanococcus voltae results in non-flagellated cells Mol. Genet. Genomics 265 2001 596 603 (Pubitemid 32763312)
51. D.L. Tumbula, and W.B. Whitman Genetics of Methanococcus: Possibilities for functional genomics in Archaea Mol. Microbiol. 33 1999 1 7 (Pubitemid 29304183)
52. D.L. Tumbula, R.A. Makula, and W.B. Whitman Transformation of Methanococcus maripaludis and identification of a PstI-like restriction system FEMS Microbiol. Lett. 121 1994 309 314
53. D.L. Tumbula Characterization of pURB500 from the archaeon Methanococcus maripaludis and construction of a shuttle vector J. Bacteriol. 179 1997 2976 2986 (Pubitemid 27194448)
54. R.L. Uffen, and R.S. Wolfe Anaerobic growth of purple nonsulfur bacteria under dark conditions J. Bacteriol. 104 1970 462 472
55. W.G. Weisberg, and R.S. Tanner Aminoglycoside sensitivity of archaebacteria FEMS Microbiol. Lett. 14 1982 307 310 (Pubitemid 12033590)
56. W.B. Whitman Isolation and characterization of 22 mesophilic methanococci Syst. Appl. Microbiol. 7 1986 235 240