Studying gene regulation in methanogenic archaea

Methods in Enzymology

Volumn 494, Issue , 2011, Pages 91-110

  Rother, Michael ^a   Sattler, Christian ^a   Stock, Tilmann ^a  

^a GOETHE UNIVERSITY   (Germany)

Author keywords

Methane; Methanogen; Mutagenesis; qRT PCR; Regulation; Transposon; uidA; Glucuronidase

Indexed keywords

TRANSPOSASE;

ARCHAEBACTERIUM; ARTICLE; BACTERIUM CULTURE; BACTERIUM MUTANT; BACTERIUM TRANSFORMATION; DNA SYNTHESIS; GENE CONTROL; GENE EXPRESSION; GENETIC MANIPULATION; METHANOCOCCUS MARIPALUDIS; METHANOGEN; METHANOSARCINA ACETIVORANS; NONHUMAN; PLASMID; PRIORITY JOURNAL; REPORTER GENE; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; TRANSPOSON;

ARCHAEA; METHANOCOCCUS; METHANOCOCCUS MARIPALUDIS; METHANOSARCINA; METHANOSARCINA ACETIVORANS;

EID: 79952605449     PISSN: 00766879     EISSN: None     Source Type: Book Series    
DOI: 10.1016/B978-0-12-385112-3.00005-6     Document Type: Chapter

References (81)

1. R. Allmansberger, S. Knaub, and A. Klein Conserved elements in the transcription initiation regions preceding highly expressed structural genes of methanogenic archaebacteria Nucleic Acids Res. 16 1988 7419 7436
2. K.L. Anderson, E.E. Apolinario, S.R. MacAuley, and K.R. Sowers A 5′ leader sequence regulates expression of methanosarcinal CO dehydrogenase/acetyl coenzyme A synthase J. Bacteriol. 191 2009 7123 7128
3. E.E. Apolinario, K.M. Jackson, and K.R. Sowers Development of a plasmid-mediated reporter system for in vivo monitoring of gene expression in the archaeon Methanosarcina acetivorans Appl. Environ. Microbiol. 71 2005 4914 4918 (Pubitemid 41129557)
4. M.K. Ashby Distribution, structure and diversity of "bacterial" genes encoding two-component proteins in the Euryarchaeota Archaea 2 2006 11 30 (Pubitemid 44377984)
5. F.M. Ausubel, R. Brent, R.E. Kingston, D.D. Moore, J.G. Seidmann, J.A. Smith, and K. Struhl Current Protocols in Molecular Biology 1997 John Wiley & sons, Inc. New York
6. A. Bellack, H. Huber, R. Rachel, G. Wanner, and R. Wirth Methanocaldococcus villosus sp. nov., a heavily flagellated archaeon adhering to surfaces and forming cell-cell contacts Int. J. Syst. Evol. Microbiol. 2010 10.1099/ijs.1090.023663-023660
7. S. Beneke, H. Bestgen, and A. Klein 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. B.A. Bensing, B.J. Meyer, and G.M. Dunny Sensitive detection of bacterial transcription initiation sites and differentiation from RNA processing sites in the pheromone-induced plasmid transfer system of Enterococcus faecalis Proc. Natl. Acad. Sci. USA 93 1996 7794 7799 (Pubitemid 26277117)
9. G. Bertani Studies on lysogenesis. I. The mode of phage liberation by lysogenic Escherichia coli J. Bacteriol. 62 1951 293 300
10. C.E. Blank, P.S. Kessler, and J.A. Leigh Genetics in methanogens: Transposon insertion mutagenesis of a Methanococcus maripaludis nifH gene J. Bacteriol. 177 1995 5773 5777
11. P. Boccazzi, J.K. Zhang, and W.W. Metcalf Generation of dominant selectable markers for resistance to pseudomonic acid by cloning and mutagenesis of the ileS gene from the archaeon Methanosarcina barkeri Fusaro J. Bacteriol. 182 2000 2611 2618 (Pubitemid 30212923)
12. A. Bose, and W.W. Metcalf Distinct regulators control the expression of methanol methyltransferase isozymes in Methanosarcina acetivorans C2A Mol. Microbiol. 67 2008 649 661
13. T.L. Bowen, J.A. Ladapo, and W.B. Whitman Selection for auxotrophic mutants of Methanococcus K.R. Sowers, H.J. Schreier, Methanogens, Vol. 2 1995 Cold Spring Harbor Laboratory Press Plainview, NY 405 407
14. M.M. Bradford A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding Anal. Biochem. 72 1976 248 254
15. O. Breas, C. Guillou, F. Reniero, and E. Wada The global methane cycle: Isotopes and mixing ratios, sources and sinks Isot. Environ. Health Stud. 37 2001 257 379 (Pubitemid 34961565)
16. R. Cohen-Kupiec, C. Blank, and J.A. Leigh 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)
17. D.S. Cram, B.A. Sherf, R.T. Libby, R.J. Mattaliano, K.L. Ramachandran, and J.N. Reeve 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. USA 84 1987 3992 3996
18. L. Cubonova, K. Sandman, E.A. Karr, A.J. Cochran, and J.N. Reeve Spontaneous trpY mutants and mutational analysis of the TrpY archaeal transcription regulator J. Bacteriol. 189 2007 4338 4342 (Pubitemid 46847386)
19. U. Deppenmeier Different structure and expression of the operons encoding the membrane-bound hydrogenases from Methanosarcina mazei G1 Arch. Microbiol. 164 1995 370 376
20. U. Deppenmeier, A. Johann, T. Hartsch, R. Merkl, R.A. Schmitz, R. Martinez-Arias, A. Henne, A. Wiezer, S. Bumer, C. Jacobi, H. Brggemann, and T. Lienard The genome of Methanosarcina mazei: Evidence for lateral gene transfer between bacteria and archaea J. Mol. Microbiol. Biotechnol. 4 2002 453 461 (Pubitemid 34784706)
21. J.A. Dodsworth, and J.A. Leigh Regulation of nitrogenase by 2-oxoglutarate-reversible, direct binding of a PII-like nitrogen sensor protein to dinitrogenase Proc. Natl. Acad. Sci. USA 103 2006 9779 9784 (Pubitemid 43993574)
22. R.I. Eggen, R. van Kranenburg, A.J. Vriesema, A.C. Geerling, M.F. Verhagen, W.R. Hagen, and W.M. de Vos Carbon monoxide dehydrogenase from Methanosarcina frisia G1: Characterization of the enzyme and the regulated expression of two operon-like cdh gene clusters J. Biol. Chem. 271 1996 14256 14263
23. C. Ehlers, K. Veit, G. Gottschalk, and R.A. Schmitz Functional organization of a single nif cluster in the mesophilic archaeon Methanosarcina mazei strain G1 Archaea 1 2002 143 150 (Pubitemid 38871656)
24. M. Filutowicz, M.J. McEachern, and D.R. Helinski Positive and negative roles of an initiator protein at an origin of replication Proc. Natl. Acad. Sci. USA 83 1986 9645 9649 (Pubitemid 17010668)
25. J.E. Galagan, C. Nusbaum, A. Roy, M.G. Endrizzi, P. Macdonald, W. FitzHugh, S. Calvo, R. Engels, S. Smirnov, D. Atnoor, A. Brown, and N. Allen The genome of M. acetivorans reveals extensive metabolic and physiological diversity Genome Res. 12 2002 532 542 (Pubitemid 34308633)
26. 2 metabolism between closely related species Mol. Microbiol. 55 2005 1671 1680 (Pubitemid 40445205)
27. E.L. Hendrickson, A.K. Haydock, B.C. Moore, W.B. Whitman, and J.A. Leigh Functionally distinct genes regulated by hydrogen limitation and growth rate in methanogenic Archaea Proc. Natl. Acad. Sci. USA 104 2007 8930 8934 (Pubitemid 47175414)
28. E.L. Hendrickson, Y. Liu, G. Rosas-Sandoval, I. Porat, D. Sll, W.B. Whitman, and J.A. Leigh Global responses of Methanococcus maripaludis to specific nutrient limitations and growth rate J. Bacteriol. 190 2008 2198 2205 (Pubitemid 351355342)
29. R. Hovey, S. Lentes, A. Ehrenreich, K. Salmon, K. Saba, G. Gottschalk, R.P. Gunsalus, and U. Deppenmeier DNA microarray analysis of Methanosarcina mazei G1 reveals adaptation to different methanogenic substrates Mol. Genet. Genomics 273 2005 225 239 (Pubitemid 40768510)
30. D. Jger, C.M. Sharma, J. Thomsen, C. Ehlers, J. Vogel, and R.A. Schmitz Deep sequencing analysis of the Methanosarcina mazei G1 transcriptome in response to nitrogen availability Proc. Natl. Acad. Sci. USA 106 2009 21878 21882
31. M.K. Jain, and G.J. Zeikus Methods for isolation of auxotrophic mutants of Methanobacterium ivanovii and initial characterization of acetate auxotrophs Appl. Environ. Microbiol. 53 1987 1387 1390
32. W.J. Jones, M.J.B. Paynter, and R. Gupta Characterization of Methanococcus maripaludis sp. nov., a new methanogen isolated from salt marsh sediment Arch. Microbiol. 135 1983 91 97
33. P.J. Kennelly Sensing, signal transduction, and posttranslational modification R. Cavicchioli, ArchaeaMolecular and Cellular Biology 2007 ASM Press Washington, DC 224 259
34. D.J. Lampe, M.E. Churchill, and H.M. Robertson A purified mariner transposase is sufficient to mediate transposition in vitro EMBO J. 15 1996 5470 5479 (Pubitemid 26336228)
35. D.J. Lampe, B.J. Akerley, E.J. Rubin, J.J. Mekalanos, and H.M. Robertson Hyperactive transposase mutants of the Himar1 mariner transposon Proc. Natl. Acad. Sci. USA 96 1999 11428 11433 (Pubitemid 29487397)
36. 2 to methane in CO-grown Methanosarcina acetivorans revealed by proteomics Proc. Natl. Acad. Sci. USA 103 2006 17921 17926 (Pubitemid 44852261)
37. Q. Li, L. Li, T. Rejtar, D.J. Lessner, B.L. Karger, and J.G. Ferry Electron transport in the pathway of acetate conversion to methane in the marine archaeon Methanosarcina acetivorans J. Bacteriol. 188 2006 702 710 (Pubitemid 43100558)
38. 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)
39. T.J. Lie, G.E. Wood, and J.A. Leigh Regulation of nif expression in Methanococcus maripaludis: Roles of the euryarchaeal repressor NrpR, 2-oxoglutarate, and two operators J. Biol. Chem. 280 2005 5236 5241 (Pubitemid 40279995)
40. T.J. Lie, E.L. Hendrickson, U.M. Niess, B.C. Moore, A.K. Haydock, and J.A. Leigh Overlapping repressor binding sites regulate expression of the Methanococcus maripaludis glnK operon Mol. Microbiol. 75 2009 755 762
41. - ΔΔC T method Methods 25 2001 402 408 (Pubitemid 34164012)
42. D.G. Longstaff, S.K. Blight, L. Zhang, K.B. Green-Church, and J.A. Krzycki In vivo contextual requirements for UAG translation as pyrrolysine Mol. Microbiol. 63 2007 229 241 (Pubitemid 44968121)
43. D.L. Maeder, I. Anderson, T.S. Brettin, D.C. Bruce, P. Gilna, C.S. Han, A. Lapidus, W.W. Metcalf, E. Saunders, R. Tapia, and K.R. Sowers The Methanosarcina barkeri genome: Comparative analysis with Methanosarcina acetivorans and Methanosarcina mazei reveals extensive rearrangement within methanosarcinal genomes J. Bacteriol. 188 2006 7922 7931 (Pubitemid 44764528)
44. W.W. Metcalf, J.K. Zhang, X. Shi, and R.S. Wolfe Molecular, genetic, and biochemical characterization of the serC gene of Methanosarcina barkeri Fusaro J. Bacteriol. 178 1996 5797 5802 (Pubitemid 26327686)
45. W.W. Metcalf, J.K. Zhang, E. Apolinario, K.R. Sowers, and R.S. Wolfe 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
46. R.M. Morgan, T.D. Pihl, J. Nlling, and J.N. Reeve Hydrogen regulation of growth, growth yields, and methane gene transcription in Methanobacterium thermoautotrophicum DH J. Bacteriol. 179 1997 889 898 (Pubitemid 27051847)
47. M.G. Murray, and W.F. Thompson Rapid isolation of high molecular weight plant DNA Nucleic Acids Res. 8 1980 4321 4325
48. E. Oelgeschlger, and M. Rother In vivo role of three fused corrinoid/methyl transfer proteins in Methanosarcina acetivorans Mol. Microbiol. 72 2009 1260 1272
49. R.B. Opulencia, A. Bose, and W.W. Metcalf Physiology and posttranscriptional regulation of methanol:coenzyme M methyltransferase isozymes in Methanosarcina acetivorans C2A J. Bacteriol. 191 2009 6928 6935
50. M.W. Pfaffl A new mathematical model for relative quantification in real-time RT-PCR Nucleic Acids Res. 29 2001 e45
51. 5 -methyltetrahydromethanopterin:coenzyme M methyltransferase in Methanobacterium thermoautotrophicum DH J. Bacteriol. 176 1994 6384 6391 (Pubitemid 24313819)
52. 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
53. M.A. Pritchett, and W.W. Metcalf Genetic, physiological and biochemical characterization of multiple methanol methyltransferase isozymes in Methanosarcina acetivorans C2A Mol. Microbiol. 56 2005 1183 1194 (Pubitemid 40756003)
54. M.A. Pritchett, J.K. Zhang, and W.W. Metcalf 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)
55. L. Rohlin, and R.P. Gunsalus Carbon-dependent control of electron transfer and central carbon pathway genes for methane biosynthesis in the Archaean, Methanosarcina acetivorans strain C2A BMC Microbiol. 10 2010 62
56. M. Rother Methanogenesis K.N. Timmis, Handbook of Hydrocarbon and Lipid Microbiology, Vol. 1 2010 Springer Berlin, Heidelberg 483 499
57. M. Rother, I. Mathes, F. Lottspeich, and A. Bck Inactivation of the selB gene in Methanococcus maripaludis: Effect on synthesis of selenoproteins and their sulfur-containing homologs J. Bacteriol. 185 2003 107 114 (Pubitemid 36008827)
58. M. Rother, P. Boccazzi, A. Bose, M.A. Pritchett, and W.W. Metcalf Methanol-dependent gene expression demonstrates that methyl-CoM reductase is essential in Methanosarcina acetivorans C2A and allows isolation of mutants with defects in regulation of the methanol utilization pathway J. Bacteriol. 187 2005 5552 5559 (Pubitemid 41134289)
59. M. Rother, E. Oelgeschlger, and W.W. Metcalf Genetic and proteomic analyses of CO utilization by Methanosarcina acetivorans Arch. Microbiol. 188 2007 463 472 (Pubitemid 47583432)
60. J. Sambrook, E.F. Fritsch, and T. Maniatis Molecular Cloning: A Laboratory Manual 1989 Cold Spring Harbor Laboratory Press Plainview, NY
61. R. Saum, A. Mingote, H. Santos, and V. Mller Genetic analysis of the role of the ABC transporter Ota and Otb in glycine betaine transport in Methanosarcina mazei G1 Arch. Microbiol. 191 2009 291 301
62. S. Schopf, G. Wanner, R. Rachel, and R. Wirth An archaeal bi-species biofilm formed by Pyrococcus furiosus and Methanopyrus kandleri Arch. Microbiol. 190 2008 371 377
63. K.R. Sowers, S.F. Baron, and J.G. Ferry Methanosarcina acetivorans sp. nov., an acetotrophic methane-producing bacterium isolated from marine sediments Appl. Environ. Microbiol. 47 1984 971 978
64. K.R. Sowers, J.E. Boone, and R.P. Gunsalus Disaggregation of Methanosarcina spp. and growth as single cells at elevated osmolarity Appl. Environ. Microbiol. 59 1993 3832 3839 (Pubitemid 23327589)
65. K.R. Sowers, T.T. Thai, and R.P. Gunsalus Transcriptional regulation of the carbon monoxide dehydrogenase gene (cdhA) in Methanosarcina thermophila J. Biol. Chem. 268 1993 23172 32178
66. R. Spanheimer, and V. Mller The molecular basis of salt adaptation in Methanosarcina mazei G1 Arch. Microbiol. 190 2008 271 279
67. T. Stock, and M. Rother Selenoproteins in Archaea and Gram-positive bacteria Biochim. Biophys. Acta 1790 2009 1520 1532
68. J. Sun, and A. Klein A LysR-type regulator is involved in the negative regulation of genes encoding selenium-free hydrogenases in the archaeon Methanococcus voltae Mol. Microbiol. 52 2004 563 571 (Pubitemid 38520723)
69. S. Tabor, and C.C. Richardson A bacteriophage T7 RNA polymerase/promoter system for controlled exclusive expression of specific genes Proc. Natl. Acad. Sci. USA 82 1985 1074 1078 (Pubitemid 15100497)
70. R.K. Thauer, A.K. Kaster, H. Seedorf, W. Buckel, and R. Hedderich Methanogenic archaea: Ecologically relevant differences in energy conservation Nat. Rev. Microbiol. 6 2008 579 591
71. M. Thomm, B.A. Sherf, and J.N. Reeve RNA polymerase-binding and transcription initiation sites upstream of the methyl reductase operon of Methanococcus vannielii J. Bacteriol. 170 1988 1958 1961
72. D.L. Tumbula, T.L. Bowen, and W.B. Whitman Transformation of Methanococcus maripaludis and identification of a PstI-like restriction system FEMS Microbiol. Lett. 121 1994 309 314
73. K. Veit, C. Ehlers, and R.A. Schmitz Effects of nitrogen and carbon sources on transcription of soluble methyltransferases in Methanosarcina mazei strain G1 J. Bacteriol. 187 2005 6147 6154 (Pubitemid 41262811)
74. K. Veit, C. Ehlers, A. Ehrenreich, K. Salmon, R. Hovey, R.P. Gunsalus, U. Deppenmeier, and R.A. Schmitz Global transcriptional analysis of Methanosarcina mazei strain G1 under different nitrogen availabilities Mol. Genet. Genomics 276 2006 41 55 (Pubitemid 43946093)
75. A.D. Walters, and J.P. Chong Methanococcus maripaludis: An archaeon with multiple functional MCM proteins? Biochem. Soc. Trans. 37 2009 1 6
76. W.B. Whitman, J. Shieh, S. Sohn, D.S. Caras, and U. Premachandran Isolation and characterisation of 22 mesophilic methanococci Syst. Appl. Microbiol. 7 1986 235 240
77. W.B. Whitman, D.L. Tumbula, J.P. Yu, and W. Kim Development of genetic approaches for the methane-producing archaebacterium Methanococcus maripaludis Biofactors 6 1997 37 46 (Pubitemid 27287122)
78. G.E. Wood, A.K. Haydock, and J.A. Leigh Function and regulation of the formate dehydrogenase genes of the methanogenic archaeon Methanococcus maripaludis J. Bacteriol. 185 2003 2548 2554 (Pubitemid 36417979)
79. Q. Xia, E.L. Hendrickson, Y. Zhang, T. Wang, F. Taub, B.C. Moore, I. Porat, W.B. Whitman, M. Hackett, and J.A. Leigh Quantitative proteomics of the archaeon Methanococcus maripaludis validated by microarray analysis and real time PCR Mol. Cell. Proteomics 5 2006 868 881 (Pubitemid 43792796)
80. Y.-L. Yang, J.A. Ladapo, and W.B. Whitman Mutagenesis of Methanococcus spp. with ethylmethanesulfonate K.R. Sowers, H.J. Schreier, Methanogens, Vol. 2 1995 Cold Spring Harbor Laboratory Press Plainview, NY 403 404
81. J.K. Zhang, M.A. Pritchett, D.J. Lampe, H.M. Robertson, and W.W. Metcalf In vivo transposon mutagenesis of the methanogenic archaeon Methanosarcina acetivorans C2A using a modified version of the insect mariner-family transposable element Himar1 Proc. Natl. Acad. Sci. USA 97 2000 9665 9670 (Pubitemid 30650833)