Contribution of transcriptomics to systems-level understanding of methanogenic archaea

Archaea

Volumn 2013, Issue , 2013, Pages

  Browne, Patrick D ^a   Cadillo Quiroz, Hinsby ^a,b  

^a ARIZONA STATE UNIVERSITY   (United States)

^b ARIZONA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARCHAEA; BACTERIA (MICROORGANISMS);

METHANE; TRANSCRIPTOME;

ARCHAEON; GENE EXPRESSION REGULATION; GENETICS; HIGH THROUGHPUT SEQUENCING; METABOLISM; METHODOLOGY; REVIEW; SYSTEMS BIOLOGY;

ARCHAEA; GENE EXPRESSION REGULATION, ARCHAEAL; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; METHANE; SYSTEMS BIOLOGY; TRANSCRIPTOME;

MLCS; MLOWN;

EID: 84875446965     PISSN: 14723646     EISSN: None     Source Type: Journal    
DOI: 10.1155/2013/586369     Document Type: Review

References (68)

1. 2O, and NO). Microbiological Reviews 1996 60 4 609 640 2-s2.0-0029845048 (Pubitemid 26415670)
2. Ferry J. G., Fundamentals of methanogenic pathways that are key to the biomethanation of complex biomass. Current Opinion in Biotechnology 2011 22 3 351 357 2-s2.0-79957972499 10.1016/j.copbio.2011.04.011
3. Liu Y., Whitman W. B., Metabolic, phylogenetic, and ecological diversity of the Methanogenic archaea. Annals of the New York Academy of Sciences 2008 1125 171 189 2-s2.0-41349083576 10.1196/annals.1419.019 (Pubitemid 351451164)
4. Thauer R. K., Kaster A. K., Seedorf H., Buckel W., Hedderich R., Methanogenic archaea: ecologically relevant differences in energy conservation. Nature Reviews Microbiology 2008 6 8 579 591 2-s2.0-47549119041 10.1038/nrmicro1931
5. Sakai S., Imachi H., Hanada S., Ohashi A., Harada H., Kamagata Y., 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. International Journal of Systematic and Evolutionary Microbiology 2008 58 4 929 936 2-s2.0-47249105592 10.1099/ijs.0.65571-0
6. Paul K., Nonoh J. O., Mikulski L., Brune A., 'Methanoplasmatales,' thermoplasmatales -related archaea in termite guts and other environments, are the seventh order of methanogens. Applied and Environmental Microbiology 2012 78 23 8245 8253 10.1128/AEM.02193-12
7. Sowers K. R., Schmidt T. M., Schaechter M., Methanogenesisin topics. Ecological and Environmental Microbiology 2011 Academic Press 149 173
8. Culley D. E., Kovacik W. P., Brockman F. J., Zhang W., Optimization of RNA isolation from the archaebacterium Methanosarcina barkeri and validation for oligonucleotide microarray analysis. Journal of Microbiological Methods 2006 67 1 36 43 2-s2.0-33747764232 10.1016/j.mimet.2006.02.014 (Pubitemid 44279100)
9. Hovey R., Lentes S., Ehrenreich A., Salmon K., Saba K., Gottschalk G., Gunsalus R. P., Deppenmeier U., DNA microarray analysis of Methanosarcina mazei Gö1 reveals adaptation to different methanogenic substrates. Molecular Genetics and Genomics 2005 273 3 225 239 2-s2.0-20044381310 10.1007/s00438-005- 1126-9 (Pubitemid 40768510)
10. Li L., Li Q., Rohlin L., Kim U., Salmon K., Rejtar T., Gunsalus R. P., Karger B. L., Ferry J. G., Quantitative proteomic and microarray analysis of the archaeon Methanosarcina acetivorans grown with acetate versus methanol. Journal of Proteome Research 2007 6 2 759 771 2-s2.0-33847369414 10.1021/pr060383l (Pubitemid 46340179)
11. Opulencia R. B., Bose A., Metcalf W. W., Physiology and posttranscriptional regulation of methanol:coenzyme M methyltransferase isozymes in Methanosarcina acetivorans C2A. Journal of Bacteriology 2009 191 22 6928 6935 2-s2.0-70350468862 10.1128/JB.00947-09
12. Reichlen M. J., Vepachedu V. R., Murakami K. S., Ferry J. G., MreA functions in the global regulation of methanogenic pathways in Methanosarcina acetivorans. mBio 2012 3 4 e00189 e00112
13. Krätzer C., Carini P., Hovey R., Deppenmeier U., Transcriptional profiling of methyltransferase genes during growth of Methanosarcina mazei on trimethylamine. Journal of Bacteriology 2009 191 16 5108 5115 2-s2.0-67749124076 10.1128/JB.00420-09
14. Smith M. R., Mah R. A., Growth and methanogenesis by Methanosarcina strain 227 on acetate and methanol. Applied and Environmental Microbiology 1978 36 6 870 879 2-s2.0-0018127547 (Pubitemid 9070708)
15. Costa K. C., Wong P. M., Wang T., Lie T. J., Dodsworth J. A., Swanson I., Burn J. A., Hackett M., Leigh J. A., Protein complexing in a methanogen suggests electron bifurcation and electron delivery from formate to heterodisulfide reductase. Proceedings of the National Academy of Sciences of the United States of America 2010 107 24 11050 11055 2-s2.0-77954636353 10.1073/pnas.1003653107
16. Rohlin L., Gunsalus R. P., Carbon-dependent control of electron transfer and central carbon pathway genes for methane biosynthesis in the Archaean, Methanosarcina acetivorans strain C2A. BMC Microbiology 2010 10, article 62 2-s2.0-77649295501 10.1186/1471-2180-10-62
17. Welte C., Kallnik V., Grapp M., Bender G., Ragsdale S., Deppenmeier U., Function of Ech hydrogenase in ferredoxin-dependent, membrane-bound electron transport in Methanosarcina mazei. Journal of Bacteriology 2010 192 3 674 678 2-s2.0-75149154830 10.1128/JB.01307-09
18. Ferry J. G., Lessner D. J., Methanogenesis in marine sediments. Annals of the New York Academy of Sciences 2008 1125 147 157 2-s2.0-41349089084 10.1196/annals.1419.007 (Pubitemid 351451153)
19. Veit K., Ehlers C., Ehrenreich A., Salmon K., Hovey R., Gunsalus R. P., Deppenmeier U., Schmitz R. A., Global transcriptional analysis of Methanosarcina mazei strain Gö1 under different nitrogen availabilities. Molecular Genetics and Genomics 2006 276 1 41 55 2-s2.0-33745394713 10.1007/s00438-006- 0117-9 (Pubitemid 43946093)
20. Habicht K. S., Gade M., Thamdrup B., Berg P., Canfield D. E., Calibration of sulfate levels in the Archean ocean. Science 2002 298 5602 2372 2374 2-s2.0-0037147193 10.1126/science.1078265 (Pubitemid 36014206)
21. 420 dehydrogenase in electron transport of Methanosarcina mazei. FEBS Journal 2011 278 8 1277 1287 2-s2.0-79953690203 10.1111/j.1742-4658.2011.08048. x
22. Buan N. R., Metcalf W. W., Methanogenesis by Methanosarcina acetivorans involves two structurally and functionally distinct classes of heterodisulfide reductase. Molecular Microbiology 2010 75 4 843 853 2-s2.0-76449096786 10.1111/j.1365-2958.2009.06990.x
23. Kato S., Kosaka T., Watanabe K., Comparative transcriptome analysis of responses of Methanothermobacter thermautotrophicus to different environmental stimuli. Environmental Microbiology 2008 10 4 893 905 2-s2.0-40949088993 10.1111/j.1462-2920.2007.01508.x (Pubitemid 351406087)
24. Hendrickson E. L., Liu Y., Rosas-Sandoval G., Porat I., Söll D., Whitman W. B., Leigh J. A., Global responses of Methanococcus maripaludis to specific nutrient limitations and growth rate. Journal of Bacteriology 2008 190 6 2198 2205 2-s2.0-40449095396 10.1128/JB.01805-07 (Pubitemid 351355342)
25. Hendrickson E. L., Haydock A. K., Moore B. C., Whitman W. B., Leigh J. A., Functionally distinct genes regulated by hydrogen limitation and growth rate in Methanogenic archaea. Proceedings of the National Academy of Sciences of the United States of America 2007 104 21 8930 8934 2-s2.0-34547405862 10.1073/pnas.0701157104 (Pubitemid 47175414)
26. Xia Q., Wang T., Hendrickson E. L., Lie T. J., Hackett M., Leigh J. A., Quantitative proteomics of nutrient limitation in the hydrogenotrophic methanogen Methanococcus maripaludis. BMC Microbiology 2009 9, article 149 2-s2.0-68849088492 10.1186/1471-2180-9-149
27. 420 and production of hydrogen during methanogenesis. Journal of Bacteriology 2008 190 14 4818 4821 2-s2.0-47249144402 10.1128/JB.00255-08 (Pubitemid 351991049)
28. Hansen E. E., Lozupone C. A., Rey F. E., Wu M., Guruge J. L., Narra A., Goodfellow J., Zaneveld J. R., McDonald D. T., Goodrich J. A., Heath A. C., Knight R., Gordon J. I., Pan-genome of the dominant human gut-associated archaeon, Methanobrevibacter smithii, studied in twins. Proceedings of the National Academy of Sciences of the United States of America 2011 108 1 4599 4606 2-s2.0-79952749405 10.1073/pnas.1000071108
29. Walker C. B., Redding-Johanson A. M., Baidoo E. E., Rajeev L., He Z., Hendrickson E. L., Joachimiak M. P., Stolyar S., Arkin A. P., Leigh J. A., Zhou J., Keasling J. D., Mukhopadhyay A., Stahl D. A., Functional responses of Methanogenic archaea to syntrophic growth. The ISME Journal 2012 6 11 2045 2055 10.1038/ismej.2012.60
30. Luo H. W., Zhang H., Suzuki T., Hattori S., Kamagata Y., Differential expression of methanogenesis genes of Methanothermobacter thermoautotrophicus (formerly Methanobacterium thermoautotrophicum) in pure culture and in cocultures with fatty acid-oxidizing syntrophs. Applied and Environmental Microbiology 2002 68 3 1173 1179 2-s2.0-0036197915 10.1128/AEM.68.3.1173-1179. 2002 (Pubitemid 34205355)
31. Zhang W., Culley D. E., Nie L., Brockman F. J., DNA microarray analysis of anaerobic Methanosarcina barkeri reveals responses to heat shock and air exposure. Journal of Industrial Microbiology and Biotechnology 2006 33 9 784 790 2-s2.0-33746317296 10.1007/s10295-006-0114-3 (Pubitemid 44106685)
32. Lie T. J., Hendrickson E. L., Niess U. M., Moore B. C., Haydock A. K., Leigh J. A., Overlapping repressor binding sites regulate expression of the Methanococcus maripaludis glnK1 operon. Molecular Microbiology 2010 75 3 755 762 2-s2.0-75149128080 10.1111/j.1365-2958.2009.07016.x
33. Campanaro S., Williams T. J., Burg D. W., De Francisci D., Treu L., Lauro F. M., Cavicchioli R., Temperature-dependent global gene expression in the Antarctic archaeon Methanococcoides burtonii. Environmental Microbiology 2011 13 8 2018 2038 10.1111/j.1462-2920.2010.02367.x
34. Williams T. J., Lauro F. M., Ertan H., Burg D. W., Poljak A., Raftery M. J., Cavicchioli R., Defining the response of a microorganism to temperatures that span its complete growth temperature range (- 2 ° C to 28 ° C) using multiplex quantitative proteomics. Environmental Microbiology 2011 13 8 2186 2203 10.1111/j.1462-2920.2011.02467.x
35. Pflüger K., Ehrenreich A., Salmon K., Gunsalus R. P., Deppenmeier U., Gottschalk G., Müller V., Identification of genes involved in salt adaptation in the archaeon Methanosarcina mazei Gö1 using genome-wide gene expression profiling. FEMS Microbiology Letters 2007 277 1 79 89 2-s2.0-35748985540 10.1111/j.1574-6968.2007.00941.x (Pubitemid 350045659)
36. Bräuer S. L., Cadillo-Quiroz H., Ward R. J., Yavitt J. B., Zinder S. H., Methanoregula boonei gen. nov., sp. nov., an acidiphilic methanogen isolated from an acidic peat bog. International Journal of Systematic and Evolutionary Microbiology 2011 61 1 45 52 2-s2.0-78651463463 10.1099/ijs.0.021782-0
37. Cadillo-Quiroz H., Yashiro E., Yavitt J. B., Zinder S. H., Characterization of the archaeal community in a minerotrophic fen and terminal restriction fragment length polymorphism-directed isolation of a novel hydrogenotrophic methanogen. Applied and Environmental Microbiology 2008 74 7 2059 2068 2-s2.0-42049084820 10.1128/AEM.02222-07 (Pubitemid 351522059)
38. Brioukhanov A. L., Netrusov A. I., Eggen R. I. L., The catalase and superoxide dismutase genes are transcriptionally up-regulated upon oxidative stress in the strictly anaerobic archaeon Methanosarcina barkeri. Microbiology 2006 152 6 1671 1677 2-s2.0-33745228417 10.1099/mic.0.28542-0
39. Scholten J. C. M., Culley D. E., Nie L., Munn K. J., Chow L., Brockman F. J., Zhang W., Development and assessment of whole-genome oligonucleotide microarrays to analyze an anaerobic microbial community and its responses to oxidative stress. Biochemical and Biophysical Research Communications 2007 358 2 571 577 2-s2.0-34248583559 10.1016/j.bbrc.2007.04.160 (Pubitemid 46755742)
40. De Bok F. A. M., Luijten M. L. G. C., Stams A. J. M., Biochemical evidence for formate transfer in syntrophic propionate-oxidizing cocultures of Syntrophobacter fumaroxidans and Methanospirillum hungatei. Applied and Environmental Microbiology 2002 68 9 4247 4252 2-s2.0-0036731743 10.1128/AEM.68.9.4247-4252.2002 (Pubitemid 34988102)
41. Worm P., Stams A. J. M., Cheng X., Plugge C. M., Growth- and substrate-dependent transcription of formate dehydrogenase and hydrogenase coding genes in Syntrophobacter fumaroxidans and Methanospirillum hungatei. Microbiology 2011 157 1 280 289 2-s2.0-78650720286 10.1099/mic.0.043927-0
42. 2 assimilation in the archaeon Methanococcus maripaludis. Journal of Bacteriology 2006 188 4 1373 1380 2-s2.0-32444451427 10.1128/JB.188.4.1373-1380.2006 (Pubitemid 43228669)
43. Enoki M., Shinzato N., Sato H., Nakamura K., Kamagata Y., Comparative proteomic analysis of Methanothermobacter themautotrophicus ΔH in pure culture and in co-culture with a butyrate-oxidizing bacterium. PloS ONE 2011 6 8 e24309
44. Shimoyama T., Kato S., Ishii S., Watanabe K., Flagellum mediates symbiosis. Science 2009 323 5921 1574 2-s2.0-62849109612 10.1126/science.1170086
45. Samuel B. S., Hansen E. E., Manchester J. K., Coutinho P. M., Henrissat B., Fulton R., Latreille P., Kim K., Wilson R. K., Gordon J. I., Genomic and metabolic adaptations of Methanobrevibacter smithii to the human gut. Proceedings of the National Academy of Sciences of the United States of America 2007 104 25 10643 10648 2-s2.0-34447296622 10.1073/pnas.0704189104 (Pubitemid 47185718)
46. Freitag T. E., Prosser J. I., Correlation of methane production and functional gene transcriptional activity in a peat soil. Applied and Environmental Microbiology 2009 75 21 6679 6687 2-s2.0-70350475884 10.1128/AEM.01021-09
47. Freitag T. E., Toet S., Ineson P., Prosser J. I., Links between methane flux and transcriptional activities of methanogens and methane oxidizers in a blanket peat bog. FEMS Microbiology Ecology 2010 73 1 157 165 2-s2.0-77953179577 10.1111/j.1574-6941.2010.00871.x
48. Wirth R., Kovács E., Maráti G., Bagi Z., Rákhely G., Kovács K. L., Characterization of a biogas-producing microbial community by short-read next generation DNA sequencing. Biotechnology for Biofuels 2012 5, article 41 10.1186/1754-6834-5-41
49. Lange C., Zaigler A., Hammelmann M., Twellmeyer J., Raddatz G., Schuster S. C., Oesterhelt D., Soppa J., Genome-wide analysis of growth phase-dependent translational and transcriptional regulation in halophilic archaea. BMC Genomics 2007 8, article 415 2-s2.0-38149126389 10.1186/1471-2164-8-415
50. Xia Q., Hendrickson E. L., Zhang Y., Wang T., Taub F., Moore B. C., Porat I., Whitman W. B., Hackett M., Leigh J. A., Quantitative proteomics of the archaeon Methanococcus maripaludis validated by microarray analysis and real time PCR. Molecular and Cellular Proteomics 2006 5 5 868 881 2-s2.0-33646927488 10.1074/mcp.M500369-MCP200 (Pubitemid 43792796)
51. Huang T., Wan S., Xu Z., Zheng Y., Feng K.-Y., Li H.-P., Kong X., Cai Y.-D., Analysis and prediction of translation rate based on sequence and functional features of the mRNA. PLoS ONE 2011 6 1 e16036 10.1371/journal.pone. 0016036
52. Dressaire C., Laurent B., Loubière P., Besse P., Cocaign-Bousquet M., Linear covariance models to examine the determinants of protein levels in Lactococcus lactis. Molecular BioSystems 2010 6 7 1255 1264 2-s2.0-77953577608 10.1039/c001702g
53. Güell M., Yus E., Lluch-Senar M., Serrano L., Bacterial transcriptomics: what is beyond the RNA horiz-ome? Nature Reviews Microbiology 2011 9 9 658 669 10.1038/nrmicro2620
54. Marguerat S., Wilhelm B. T., Bähler J., Next-generation sequencing: applications beyond genomes. Biochemical Society Transactions 2008 36 5 1091 1096 10.1042/BST0361091
55. Wurtzel O., Sapra R., Chen F., Zhu Y., Simmons B. A., Sorek R., A single-base resolution map of an archaeal transcriptome. Genome Research 2010 20 1 133 141 2-s2.0-74949137952 10.1101/gr.100396.109
56. Sonnleitner E., Abdou L., Haas D., Small RNA as global regulator of carbon catabolite repression in Pseudomonas aeruginosa. Proceedings of the National Academy of Sciences of the United States of America 2009 106 51 21866 21871 2-s2.0-76049120271 10.1073/pnas.pnas.0910308106
57. Jäger D., Sharma C. M., Thomsen J., Ehlers C., Vogel J., Schmitz R. A., Deep sequencing analysis of the Methanosarcina mazei Gö 1 transcriptome in response to nitrogen availability. Proceedings of the National Academy of Sciences of the United States of America 2009 106 51 21878 21882 2-s2.0-76049099044 10.1073/pnas.0909051106
58. Ehlers C., Jäger D., Schmitz R. A., Establishing a markerless genetic exchange system for Methanosarcina mazei strain Gö1 for constructing chromosomal mutants of small RNA genes. Archaea 2011 2011 7 439608 10.1155/2011/439608
59. Jäger D., Pernitzsch S. R., Richter A. S., Backofen R., Sharma C. M., Schmitz R. A., An archaeal sRNA targeting cis -and trans -encoded mRNAs via two distinct domains. Nucleic Acids Research 2012 40 21 10964 10979 10.1093/nar/gks847
60. Londei P., Evolution of translational initiation: new insights from the archaea. FEMS Microbiology Reviews 2005 29 2 185 200 2-s2.0-15944390620 10.1016/j.femsre.2004.10.002 (Pubitemid 40432467)
61. Anderson K. L., Apolinario E. E., MacAuley S. R., Sowers K. R., A 5′ leader sequence regulates expression of methanosarcinal CO dehydrogenase/acetyl coenzyme A synthase. Journal of Bacteriology 2009 191 22 7123 7128 2-s2.0-70350455894 10.1128/JB.00731-09
62. Bose A., Metcalf W. W., Distinct regulators control the expression of methanol methyltransferase isozymes in Methanosarcina acetivorans C2A. Molecular Microbiology 2008 67 3 649 661 2-s2.0-37749010878 10.1111/j.1365-2958.2007. 06075.x
63. Torarinsson E., Klenk H. P., Garrett R. A., Divergent transcriptional and translational signals in Archaea. Environmental Microbiology 2005 7 1 47 54 2-s2.0-12544256546 10.1111/j.1462-2920.2004.00674.x
64. Brenneis M., Hering O., Lange C., Soppa J., Experimental characterization of Cis-acting elements important for translation and transcription in halophilic archaea. PLoS Genetics 2007 3 12 e229 2-s2.0-44449107516 10.1371/journal.pgen.0030229
65. Benelli D., Maone E., Londei P., Two different mechanisms for ribosome/mRNA interaction in archaeal translation initiation. Molecular Microbiology 2003 50 2 635 643 2-s2.0-0142093592 10.1046/j.1365-2958.2003.03721. x (Pubitemid 37297140)
66. O'Donnell S. M., Janssen G. R., Leaderless mRNAs bind 70S ribosomes more strongly than 30S ribosomal subunits in Escherichia coli. Journal of Bacteriology 2002 184 23 6730 6733 2-s2.0-0036889040 10.1128/JB.184.23.6730- 6733.2002 (Pubitemid 35332579)
67. Portnoy V., Schuster G., RNA polyadenylation and degradation in different Archaea; roles of the exosome and RNase R. Nucleic Acids Research 2006 34 20 5923 5931 2-s2.0-33845606715 10.1093/nar/gkl763 (Pubitemid 44941171)
68. Brenneis M., Soppa J., Regulation of translation in haloarchaea: 5′-and 3′-UTRs are essential and have to functionally interact in vivo. PLoS ONE 2009 4 2 2-s2.0-61849130109 10.1371/journal.pone.0004484 e4484