Functional analysis of the three TATA binding protein homologs in Methanosarcina acetivorans

Journal of Bacteriology

Volumn 192, Issue 6, 2010, Pages 1511-1517

  Reichlen, Matthew J ^a   Murakami, Katsuhiko S ^a   Ferry, James G ^a  

^a PENNSYLVANIA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACETIC ACID; TATA BINDING PROTEIN; TATA BINDING PROTEIN 1; TATA BINDING PROTEIN 2; TATA BINDING PROTEIN 3; TETRACYCLINE; UNCLASSIFIED DRUG;

ARTICLE; BACTERIAL GROWTH; BACTERIUM CULTURE; CELL GROWTH; CONTROLLED STUDY; DELETION MUTANT; DNA MICROARRAY; GENE CONTROL; GENE DELETION; GENE EXPRESSION; GENE MUTATION; GENETIC CONSERVATION; GENETIC STRAIN; GENETIC TRANSCRIPTION; GENOME; GROWTH CURVE; GROWTH RATE; METHANOSARCINA; METHANOSARCINA ACETIVORANS; METHYLOTROPHIC BACTERIUM; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FUNCTION; SEQUENCE HOMOLOGY; WILD TYPE;

ARCHAEAL PROTEINS; GENE DELETION; GENE EXPRESSION REGULATION, ARCHAEAL; GENOME, ARCHAEAL; METHANOSARCINA; TATA-BOX BINDING PROTEIN;

ARCHAEA; METHANOSARCINA; METHANOSARCINA ACETIVORANS;

EID: 77949361379     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/JB.01165-09     Document Type: Article

References (42)

1. Baliga, N. S., Y. A. Goo, W. V. Ng, L. Hood, C. J. Daniels, and S. DasSarma . 2000. Is gene expression in Halobacterium NRC-1 regulated by multiple TBP and TFB transcription factors? Mol. Microbiol. 36:1184-1185.
2. Bartlett, M. S., M. Thomm, and E. P. Geiduschek .2004. Topography of the euryarchaeal transcription initiation complex. J. Biol. Chem. 279:5894-5903.
3. Baumann, P., S. A. Qureshi, and S. P. Jackson .1995. Transcription: new insights from studies on Archaea. Trends Genet. 11:279-283.
4. Bell, S. D., and S. P. Jackson .1998. Transcription and translation in Archaea: a mosaic of eukaryal and bacterial features. Trends Microbiol. 6:222-228.
5. Bell, S. D., C. P. Magill, and S. P. Jackson .2001. Basal and regulated transcription in Archaea. Biochem. Soc. Trans. 29:392-395.
6. Boccazzi, P., J. K. Zhang, and W. W. Metcalf .2000. 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. 182:2611-2618.
7. Bolstad, B. M., R. A. Irizarry, M. Astrand, and T. P. Speed .2003. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19:185-193.
8. Coker, J. A., P. Dassarma, J. Kumar, J. A. Muller, and S. Dassarma .2007. Transcriptional profiling of the model archaeon Halobacterium sp. NRC-1: responses to changes in salinity and temperature. Saline Syst. 3:6.
9. Coker, J. A., and S. DasSarma .2007. Genetic and transcriptomic analysis of transcription factor genes in the model halophilic archaeon: coordinate action of TbpD and TfbA. BMC Genet. 8:61.
10. Deppenmeier, U., A. Johann, T. Hartsch, R. Merkl, R. A. Schmitz, R. Martinez-Arias, A. Henne, A. Wiezer, S. Baumer, C. Jacobi, H. Bruggemann, T. Lienard, A. Christmann, M. Bomeke, S. Steckel, A. Bhattacharyya, A. Lykidis, R. Overbeek, H. P. Klenk, R. P. Gunsalus, H. J. Fritz, and G. Gottschalk. 2002. The genome of Methanosarcina mazei: evidence for lateral gene transfer between bacteria and archaea. J. Mol. Microbiol. Biotechnol. 4:453-461.
11. Ding, Y. H., S. P. Zhang, J. F. Tomb, and J. G. Ferry .2002. Genomic and proteomic analyses reveal multiple homologs of genes encoding enzymes of the methanol:coenzyme M methyltransferase system that are differentially expressed in methanol- and acetate-grown Methanosarcina thermophila. FEMS Microbiol. Lett. 215:127-132.
12. Facciotti, M. T., D. J. Reiss, M. Pan, A. Kaur, M. Vuthoori, R. Bonneau, P. Shannon, A. Srivastava, S. M. Donohoe, L. E. Hood, and N. S. Baliga .2007. General transcription factor specified global gene regulation in archaea. Proc. Natl. Acad. Sci. U. S. A. 104:4630-4635.
13. Ferry, J. G. (ed.) .1993. Methanogenesis: ecology, physiology, biochemistry and genetics, vol. I. Chapman and Hall, New York, NY.
14. Ferry, J. G., and K. A. Kastead .2007. Methanogenesis, p. 288-314. In R. Cavicchioli (ed.), Archaea: molecular and cellular biology. ASM Press, Washington, DC.
15. Galagan, J. E., C. Nusbaum, A. Roy, M. G. Endrizzi, P. Macdonald, W. FitzHugh, S. Calvo, R. Engels, S. Smirnov, D. Atnoor, A. Brown, N. Allen, J. Naylor, N. Stange-Thomann, K. DeArellano, R. Johnson, L. Linton, P. McEwan, K. McKernan, J. Talamas, A. Tirrell, W. Ye, A. Zimmer, R. D. Barber, I. Cann, D. E. Graham, D. A. Grahame, A. M. Guss, R. Hedderich, C. Ingram-Smith, H. C. Kuettner, J. A. Krzycki, J. A. Leigh, W. Li, J. Liu, B. Mukhopadhyay, J. N. Reeve, K. Smith, T. A. Springer, L. A. Umayam, O. White, R. H. White, E. Conway de Macario, J. G. Ferry, K. F. Jarrell, H. Jing, A. J. Macario, I. Paulsen, M. Pritchett, K. R. Sowers, R. V. Swanson, S. H. Zinder, E. Lander, W. W. Metcalf, and B. Birren .2002. The genome of M. acetivorans reveals extensive metabolic and physiological diversity. Genome Res. 12:532-542.
16. Geiduschek, E. P., and M. Ouhammouch .2005. Archaeal transcription and its regulators. Mol. Microbiol. 56:1397-1407.
17. Goo, Y. A., E. C. Yi, N. S. Baliga, W. A. Tao, M. Pan, R. Aebersold, D. R. Goodlett, L. Hood, and W. V. Ng .2003. Proteomic analysis of an extreme halophilic archaeon, Halobacterium sp. NRC-1. Mol. Cell Proteomics 2:506-524.
18. Guss, A. M., M. Rother, J. K. Zhang, G. Kulkarni, and W. W. Metcalf .2008. New methods for tightly regulated gene expression and highly efficient chromosomal integration of cloned genes for Methanosarcina species. Archaea 2:193-203.
19. Hirtreiter, A. M., G. Calloni, F. Forner, B. Scheibe, M. Puype, J. Vandekerckhove, M. Mann, F. U. Hartl, and M. Hayer-Hartl .2009. Differential substrate specificity of group I and group II chaperonins in the archaeon Methanosarcina mazei. Mol. Microbiol. 74:1152-1168.
20. Hovey, R., S. Lentes, A. Ehrenreich, K. Salmon, K. Saba, G. Gottschalk, R. P. Gunsalus, and U. Deppenmeier .2005. DNA microarray analysis of Methanosarcina mazei Go1 reveals adaptation to different methanogenic substrates. Mol. Genet Genomics 273:225-239.
21. Irizarry, R. A., B. M. Bolstad, F. Collin, L. M. Cope, B. Hobbs, and T. P. Speed .2003. Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res. 31:e15.
22. Irizarry, R. A., B. Hobbs, F. Collin, Y. D. Beazer-Barclay, K. J. Antonellis, U. Scherf, and T. P. Speed .2003. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4:249-264.
23. King, G. M., M. J. Klug, and D. R. Lovley .1983. Metabolism of acetate, methanol, and methylated amines in intertidal sediments of Lowes Cove, Maine. Appl. Environ. Microbiol. 45:1848-1853.
24. Klunker, D., B. Haas, A. Hirtreiter, L. Figueiredo, D. J. Naylor, G. Pfeifer, V. Muller, U. Deppenmeier, G. Gottschalk, F. U. Hartl, and M. Hayer-Hartl. 2003. Coexistence of group I and group II chaperonins in the archaeon Methanosarcina mazei. J. Biol. Chem. 278:33256-33267.
25. Kyrpides, N. C., and C. A. Ouzounis .1999. Transcription in archaea. Proc. Natl. Acad. Sci. U. S. A. 96:8545-8550.
26. 2 to methane in CO-grown Methanosarcina acetivorans revealed by proteomics. Proc. Natl. Acad. Sci. U. S. A. 103:17921-17926.
27. Li, L., Q. Li, L. Rohlin, U. Kim, K. Salmon, T. Rejtar, R. P. Gunsalus, B. L. Karger, and J. G. Ferry .2007. Quantitative proteomic and microarray analysis of the archaeon Methanosarcina acetivorans grown with acetate versus methanol. J. Proteome Res. 6:759-771.
28. Li, Q., L. Li, T. Rejtar, B. L. Karger, and J. G. Ferry .2005. Proteome of Methanosarcina acetivorans. Part I. An expanded view of the biology of the cell. J. Proteome Res. 4:112-128.
29. Li, Q., L. Li, T. Rejtar, B. L. Karger, and J. G. Ferry .2005. Proteome of Methanosarcina acetivorans. Part II. Comparison of protein levels in acetate-and methanol-grown cells. J. Proteome Res. 4:129-135.
30. Li, Q., L. Li, T. Rejtar, D. J. Lessner, B. L. Karger, and J. G. Ferry .2006. Electron transport in the pathway of acetate conversion to methane in the marine archaeon Methanosarcina acetivorans. J. Bacteriol. 188:702-710.
31. Lu, Q., J. Han, L. Zhou, J. A. Coker, P. DasSarma, S. DasSarma, and H. Xiang .2008. Dissection of the regulatory mechanism of a heat-shock responsive promoter in Haloarchaea: a new paradigm for general transcription factor directed archaeal gene regulation. Nucleic Acids Res. 36:3031-3042.
32. Metcalf, W. W., J. K. Zhang, E. Apolinario, K. R. Sowers, and R. S. Wolfe. 1997. A genetic system for Archaea of the genus Methanosarcina: liposomemediated transformation and construction of shuttle vectors. Proc. Natl. Acad. Sci. U. S. A. 94:2626-2631.
33. Micorescu, M., S. Grunberg, A. Franke, P. Cramer, M. Thomm, and M. Bartlett .2008. Archaeal transcription: function of an alternative transcription factor B from Pyrococcus furiosus. J. Bacteriol. 190:157-167.
34. Oremland, R. S., and S. Polcin .1982. Methanogenesis and sulfate reduction: competitive and noncompetitive substrates in estuarine sediments. Appl. Environ. Microbiol. 44:1270-1276.
35. Paytubi, S., and M. F. White .2009. The crenarchaeal DNA damage-inducible transcription factor B paralogue TFB3 is a general activator of transcription. Mol. Microbiol. 72:1487-1499.
36. Santangelo, T. J., L. Cubonova, C. L. James, and J. N. Reeve .2007. TFB1 or TFB2 is sufficient for Thermococcus kodakaraensis viability and for basal transcription in vitro. J. Mol. Biol. 367:344-357.
37. Schönheit, P., J. K. Kristjansson, and R. K. Thauer .1982. Kinetic mechanism for the ability of sulfate reducers to out-compete methanogens for acetate. Arch. Microbiol. 132:285.
38. Sørensen, J., D. Christensen, and B. B. Jørgensen .1981. Volatile fatty acids and hydrogen as substrates for sulfate-reducing bacteria in anaerobic marine sediment. Appl. Environ. Microbiol. 42:5-11.
39. Sowers, K. R., S. F. Baron, and J. G. Ferry .1984. Methanosarcina acetivorans sp. nov., an acetotrophic methane-producing bacterium isolated from marine sediments. Appl. Environ. Microbiol. 47:971-978.
40. Sowers, K. R., J. E. Boone, and R. P. Gunsalus .1993. Disaggregation of Methanosarcina spp. and growth as single cells at elevated osmolarity. Appl. Environ. Microbiol. 59:3832-3839.
41. Sowers, K. R., and J. G. Ferry .2002. Methanogenesis in the marine environment, p. 1913-1923. In G. Bitton (ed.), The encyclopedia of environmental microbiology. John Wiley & Sons, Inc., New York, NY.
42. Thomm, M. 2007. Transcription: mechanism and regulation, p. 139-157. In R. Cavicchioli (ed.), Archaea: molecular and cellular biology. ASM Press, Washington, DC.