Transcription in the Archaea: Basal factors, regulation, and stress-gene expression

Critical Reviews in Biochemistry and Molecular Biology

Volumn 37, Issue 6, 2002, Pages 537-599

  Hickey, Anthony J ^a,b   Conway De Macario, Everly ^a,b   Macario, Alberto J L ^a,b  

^a WADSWORTH CENTER   (United States)

^b STATE UNIVERSITY OF NEW YORK   (United States)

Author keywords

Conformational changes; DNA binding; hsp70(dnaK) locus; Methanosarcina mazeii; Promoter; Regulatory factors; Stress genes; TBP; TFB; TFE; Transcription initiation

Indexed keywords

CHAPERONE; HEAT SHOCK PROTEIN 70; TRANSCRIPTION FACTOR;

ARCHAEBACTERIUM; BACTERIAL GENE; CONFORMATIONAL TRANSITION; DNA BINDING; DNA DETERMINATION; GENE EXPRESSION REGULATION; GENE LOCUS; METHANOSARCINA; MICROBIAL DIVERSITY; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; PROMOTER REGION; REGULATORY MECHANISM; REVIEW; TRANSCRIPTION INITIATION; TRANSCRIPTION REGULATION;

ARCHAEA; GENE EXPRESSION REGULATION, ARCHAEAL; HSP70 HEAT-SHOCK PROTEINS; TRANSCRIPTION, GENETIC;

ARCHAEA; BACTERIA (MICROORGANISMS); METHANOSARCINA; METHANOSARCINA MAZEI; PROKARYOTA;

EID: 0036946522     PISSN: 10409238     EISSN: None     Source Type: Journal    
DOI: 10.1080/10409230290771555     Document Type: Review

References (160)

1. Albright, S.R. and Tjian, R. 2000. TAFs revisited: more data reveal new twists and confirm old ideas. Gene 242, 1-13.
2. Aravind, L. and Koonin, E.V. 1999. DNA-binding proteins and evolution of transcription regulation in the archaea. Nucl. Acids Res. 27, 4658-4670.
3. Baliga, N.S. and DasSarma, S. 2000. Saturation mutagenesis of the haloarchaeal bop gene promoter: identification of DNA supercoiling sensitivity sites in the absence of TFB recognition element and UAS enhancer activity. Mol. Microbiol. 36, 1175-1183.
4. Barns, S.M. Delwiche, C.F., Palmer, J.D., and Pace, N.R. 1996. Perspectives on archaeal diversity, thermophily, and monophyly from environmental rRNA sequences. Proc. Natl. Acad. Sci. USA 93, 9188-9193.
5. Bauer, A., Chauvet, S., Huber, O., Usseglio, F., Rothbacher, U., Aragnol, D., Kemler, R., and Pradel, J. 2000. Pontin52 and reptin52 function as antagonistic regulators of beta-catenin signalling activity. EMBO J. 19, 6121-6130.
6. Bauer, A., Huber, O., and Kemler, R. 1998. Pontin52, an interaction partner of beta-catenin, binds to the TATA box binding protein. Proc. Natl. Acad. Sci. USA 95, 14787-14792.
7. Bell, S.D., Botting, C.H., Wardleworth, B.N., Jackson, S.P., and White, M.F. 2002. The interaction of Alba, a conserved archaeal chromatin remodeling protein, with Sir2 and its regulation by acetylation. Science 296, 148-151.
8. Bell, S.D., Brinkman, A.B., van der Oost, J., and Jackson, S.P. 2001. The archaeal TFIIE alpha homologue facilitates transcription initiation by enhancing TATA-box recognition. EMBO Reports 21, 133-138.
9. Bell, S.D., Cairns, S.S., Robson, R.L., and Jackson, S.P. 1999a. Transcriptional regulation of an archaeal operon in vivo and in vitro. Mol. Cell 4, 971-982.
10. Bell, S.D. and Jackson, S.P. 2000a. The role of transcription factor B in transcription initiation and promoter clearance in the archaeon Sulfolobus acidocaldarius. J. Biol. Chem. 275, 12934-12940.
11. Bell, S.D. and Jackson, S.P. 2000b. Mechanism of autoregulation by an archaeal transcriptional repressor. J. Biol. Chem. 275, 31624-31629.
12. Bell, S.D., Jaxel, C., Nadal, M., Kosa, P.F., and Jackson, S.P. 1998. Temperature, template topology and factor requirements for archaeal transcription. Proc. Natl. Acad. Sci. USA 95, 15218-15222.
13. Bell, S.D., Kosa, P.L., Sigler, P.B., and Jackson, S.P. 1999b. Orientation of the transcription preinitiation complex in archaea. Proc. Natl. Acad. Sci. USA 96, 13662-13667.
14. Berg, J.M. 1990. Zinc fingers and other metal-binding domains. J. Biol. Chem. 265, 6513-6516.
15. Bergqvist, S., O'Brien, R., and Ladbury, J.E. 2001. Site specific cation binding mediates TATA binding protien-DNA interaction from a hyperthermophilic archaeon. Biochemistry 40, 2419-2425.
16. Bergqvist, S., Williams M.A., O'Brien R., and Ladbury J.E. 2002. Reversal of halophilicity in a protein-DNA interaction by limited mutation strategy. Structure 10, 629-637.
17. Best, A.A. and Olsen, G.J. 2001. Similar subunit architecture of archaeal and eukaryal RNA polymerases. FEMS Microbiol. Lett. 195, 85-90.
18. Blaszczak, A., Georgopoulos, C., and Liberek, K. 1999. On the mechanism of FtsH-dependent degradation of the sigma-32 transcriptional regulator of Escherichia coli and the role of the DnaK chaperone machine. Mol. Microbiol. 31, 157-166.
19. Boyd, J., Oza. M.N., and Murphy, J.R. 1990. Molecular cloning and DNA sequence analysis of diphtheria tox iron-dependent regulatory elements (dtxH) from Corynebacterium diphtheriae. Proc. Natl. Acad. Sci. USA 87, 5968-5972.
20. Brown, J.W., Daniels, C.J., and Reeve, J.R. 1989. Gene structure, organization, and expression in archaeabacteria. CRC Crit. Rev. Microbiol. 16, 287-338.
21. Bult, C.J., White, O., Olsen, G.J., Zhou, L., Fleischmann, R.D., Sutton, G.G., Blake, J.A., Fitzgerald, L.M., Clayton, R.A., Gocayne, J.D., Kerlavage, A.R., Dougherty, B.A., Tomb, J.-F., Adams, M.D., Reich, C.I., Overbeek, R., Kirkness, E.F., Weinstock, K.G., Merrick, J.M., Glodek, A., Scott, J.L., Geoghagen, N.S.M., Weidman, J.F., Fuhrmann, J.L., Nguyen, D., Utterback, T.R., Kelley, J.M., Peterson, J.D., Sadow, P.W., Hanna, M.C., Cotton, M.D., Roberts K.M., Hurst M.A., Kaine, B.P., Borodovsky, M., Klenk, H.-P., Fraser, C.M., Smith, H.O., Woese, C.R., and Venter, J.C. 1996. Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. Science 273, 1058-1073.
22. II60 of Drosophila. Genes Dev. 11, 3020-3031.
23. Bustard, K. and Gupta, R.S. 1997. The sequences of heat shock protein 40 (DnaJ) homologs provide evidence for a close evolutionary relationship between the Deinococcus-Thermus group and cyanobacteria. J. Mol. Evol. 45, 193-205.
24. 3His) zinc ribbon, a ubiquitous motif in archaeal and eucaryal transcription. Prot. Sci. 9, 1743-1752.
25. Clarens, M., Macario, A.J.L., and Conway de Macario, E. 1995. The archaea dnak-dnaJ gene cluster: organization and expression in the methanogen Methanosarcina mazei. J. Mol. Biol. 250, 191-201.
26. Cohen-Kupiec, R., Blank, C., and Leigh, J.A. 1997. Transcriptional regulation in archaea: in vitro demonstration of a respressor binding site in a methanogen. Proc. Natl. Acad. Sci. USA 94, 1316-1320.
27. Cohen-Kupiec, R., Marx, C.J., and Leigh, J.A. 1999. Function and regulation of glnA in the methanogenic archaeon Methanococcus maripaludis. J. Bacteriol. 181, 256-261.
28. Conway de Macario, E., Clarens, M., and Macario, A.J.L. 1995. Archaeal grpE: transcription in two different morphologic stages of Methanosarcina mazei and comparison with dnaK and dnaJ. J. Bacteriol. 177, 544-550.
29. Conway de Macario, E., Dugan, C.B., and Macario, A.J.L. 1994. Identification of a grpE heat-shock homolog in the archaeon Methanosarcina mazei. J. Mol. Biol. 240, 95-101.
30. Conway de Macario, E., Guerrini, M., Dugan, C.B., and Macario, A.J.L. 1996. Integration of foreign DNA in an intergenic region of the archaeon Methanosarcina mazei without effect on transcription of adjacent genes. J. Mol. Biol. 262, 12-20.
31. Conway de Macario, E. and Macario, A.J.L. 1995. Transcription of the archaeal trkA homolog in Methanosarcina mazei S-6. J. Bacteriol. 177, 6077-6082.
32. Cramer, P., Buchnesll, D.A., Fu., J., Gnatt, A.L. Maier-Davis, B., Thompson, N.E., Burgess, R.E., Edwards, A.M., David., P. R., and Kronberg, R.D. 2000. Architecture of RNA polymerase II and implications for the transcription mechanism. Science 288, 640-649.
33. Dahlke, I. and Thomm, M. 2002. A Pyrococcus homolog of the leucine-responsive regulatory protein, LprA, inhibits transcription by abrogating RNA polymerase recruitment. Nucl. Acids Res. 30, 701-710.
34. Darcy, T.J., Hausner, W., Awery, D.E., Edwards, A.M., Thomm, M., and Reeve, J.N. 1999. Methanobacterium thermoautotrophicum RNA polymerase and transcription in vitro. J. Bacteriol. 181, 4424-4429.
35. De Biase, A., Macario, A.J.L., and Conway de Macario, E. 2002. Effect of heat stress on promoter binding by transcription factors in the cytosol of the archaeon Methanosarina mazeii. Gene 282, 189-197.
36. DeDecker, B.S., O'Brien R., Fleming, P.J., Geiger, J.H., Jackson, S.P., and Sigler, P.B. 1996. The crystal structure of a hyperthermophilic archaeal TATA-box binding protein. J. Mol. Biol. 264, 1072-1084.
37. Deppenmeier, U., Johann, A., Hartsch, T., Merkl, R., Schmitz, R.A., Martinez-Arias, R., Henne, A., Wiezer, A., Baumer, S., Jacobi, C., Brueggemann, H., Lienard, T., Christmann, A., Boemeke, M., Steckel, S., Bhattacharyya, A., Lykidis, A., Overbeek, R., Klenk, H-P., Gunsalus, R.P., Fritz, H-J., and Gottschalk, G. 2002. The genome of Methanosarcina mazei: Evidence for lateral gene transfer between bacteria and archaea. J. Mol. Microbiol. Biotechnol. 4, 453-461.
38. Evans, R., Fairley, J.A., and Roberts, S.G.G. 2001. Activator-mediated disruption of sequence-specific DNA contacts by the general transcription factor TFIIB. Genes Dev. 15, 2945-2949.
39. Fernandes, M., O'Brien, T., and Lis, J.T. 1994. Structure and regulation of heat shock gene promoters. In: The Biology of Heat Shock Proteins and Molecular Chaperones, R.I. Morimoto, A. Tissieres and C. Georgopoulos, Eds. Cold Spring Harbor Laboratory Press, Plainview, NY, pp. 375-393.
40. Fitz-Gibbon, S.T., Ladner, H., Kim, U.-J., Stetter, K.O., Simon, M.I., and Miller, J.H. 2002. Genome sequence of the hyperthermophilic crenarchaeon Pyrobaculum aerophilum. Proc. Natl. Acad. Sci. USA 99, 984-989.
41. Galagan, J.E., Nusbaum, C., Roy, A., Endrizzi, M.G., Macdonald, P., FitzHugh, W., Calvo, C., Engels, R., Smimov, S., Atnoor, D., Brown, A., Allen, N., Naylor, J., Stange-Thomann, N., DeArellano, K., Johnson, R., Linton, L., McEwan, P., McKernan, K., Talamas, J., Tirrell, A., Ye, W., Zimmer, A., Barber, R.D., Cann, I., Graham, D.E., Grahame, D.A., Guss, A., Hedderich, R., Ingram-Smith, C., Kuettner, H.D., Krzycki, J.A., Leigh, J.A., Li, W., Liu, J., Mukhopadhyay, B., Reeve, J.N., Smith, K., Springer, T., Umayam, L.A., White, O., White, R.H., Conway de Macario, E., Ferry, J.G., Jarrell, K.F., Jing, H., Macario, A.J.L., Paulsen, I., Pritchett, M., Sowers, K.R., Swanson, R.V., Zinder, S.H., Lander, E., Metcalf, W.W., and Birren, B. 2002. The genome of Methanosarcina acetivorans reveals extensive metabolic and physiological diversity. Genome Res. 12, 532-542.
42. Gautier, T., Berges, T., Tollervey, D., and Hurt, E. 1997. Nucleolar KKE/D repeat proteins Nop56p and Nop58p interact with Nop1p and are required for ribosome biogenesis. Mol. Cell Biol. 17, 7088-7098.
43. Gelfand, M.S., Koonin, E.V., and Mironov, A.A. 2000. Prediction of transcription regulatory sites in archaea by a comparative genomic approach. Nucl. Acids Res. 28, 695-705.
44. Georgopoulos, C., Liberek, K., Zylicz, M., and Ang, D. 1994. Properties of the heat shock proteins of Escherichia coli and the autoregulation of the heat shock response. In: The Biology of Heat Shock Proteins and Molecular Chaperones, R.I. Morimoto, A. Tissiéres, and C. Georgopoulos, Eds. Cold Spring Harbor Laboratory Press, Plainview, NY, pp. 209-249.
45. Gohl, H. P., Groendahl, B., and Thomm, M. 1995. Promoter recognition in archaea is mediated by transcription factors: identification of transcription factor aTFB from Methanococcus thermolithotrophicus as archaeal TATA-binding protein. Nucl. Acids Res. 23, 3837-3841.
46. Gregor, D. and Pfeifer, F. 2001. Use of a halobacterial bgaH reporter gene to analyze the regulation of gene expression in halophillic archaea. Microbiology 147, 1745-1754.
47. Gribaldo, S., Lumia, V., Creti, R., Conway de Macario, E., Sanangelantoni A., and Cammarano, P. 1999. Discontinuous occurrence of the hsp70(dnaK) gene among archaea and sequence features of HSP70 suggest a novel outlook on phylogenies inferred from this protein. J. Bacteriol. 181, 434 443.
48. Gupta, R.S. 1998. Protein phylogenies and signature sequences: a reappraisal of evolutionary relationships among archaebacteria, eubacteria, and eukaryotes. Micrbiol. Mol. Biol. Rev. 62, 1435-1491.
49. Gupta, R.S. and Singh, B. 1992. Cloning of the HSP70 gene from Halobacterium marimortui: relatedness of archaebacterial HSP70 to its eubacterial homologs and a model of the evolution of the HSP70 gene. J. Bacteriol. 174, 4594-4605.
50. Gupta, R.S. and Singh, B. 1994. Phylogenetic analysis of 70kD heat shock protein sequences suggests a chimeric origin for the eucaryotic cell nucleus. Curr. Biol. 4, 1104-1114.
51. Guzikevich-Guerstein, G. and Shakked Z. 1996. A novel form of the DNA double helix imposed on the TATA box by the TATA binding protein. Nature Struct. Biol. 3, 32-37.
52. Hampsey, M. 1998. Molecular genetics of the RNA polymerase II general transcription machinery. Microbiol. Mol. Biol. Rev. 62, 465-503.
53. Hanzelka, B.L, Darcy, T.J., and Reeve, J.N. 2001. TFE, an archaeal transcription factor in Methanobacterium thermoautotrophicum related to eucaryal transcription factor TFIIE alpha. J. Bacteriol. 183, 1813-1816.
54. Hausner, W. and Thomm, M. 1993. Purification and characterization of a general transcription factor, aTFB, from the archaeon Methanococcus thermolithotrophicus. J. Biol. Chem. 268, 24047-24052.
55. Hausner, W., Wettach, J., Hethke, C., and Thomm, M. 1996. Two transcription factors related with the eucaryal transcription factors TATA-binding protein and transcription factor IIB direct promoter recognition by an archaeal RNA polymerase. J. Biol. Chem. 271, 30144-30148.
56. Hethke, C., Bergerat, A., Hausner, W., Foterre, P., and Thomm, M. 1999. Cell-free transcription at 95°: thermostability of transcriptional components and DNA topology requirements of Pyrococcus transcription. Genetics 152, 1325-1333.
57. Hickey, A.J., Macario, A.J.L, and Conway de Macario, E. 2000. Identification of genes in the genome of the archaeon Methanosarcina mazeii that code for homologs of nuclear eukcaryotic molecules involved in RNA processing. Gene 253, 77-58.
58. Hochheimer, A., Hedderich, R., and Thauer, R. 1998. The formylmethanofuran dehydrogenase iosenzymes in Methanobacterium wolfei and Methanobacterium thermoautotrophicum. Induction of molybdenum isoenzyme by molybdate and constitutive synthesis of tungsten isoenzyme. Arch. Microbiol. 170, 389-393.
59. Hochheimer, A., Hedderich, R., and Thauer, R. 1999. The DNA binding protein Tfx from Methanobacterium thermoautotrophicum: structure, DNA binding properties and transcription regulation. Mol. Microbiol. 31, 641-650.
60. Hofman-Bang, J., Lange, M., Conway de Macario, E., Macario, A.J.L, and Ahring, B.K. 1999. The genes encoding for the hsp70(dnaK) molecular chaperone machine occur in the moderate thermophillic archaeon Methanosarcina thermophila TM-1. Gene 238, 387-395.
61. Huffman, J.L. and Brennan, R.G. 2002. Prokaryotic transcription regulators: more than just the helix-turn-helix motif. Curr. Opin. Struct. Biol. 12, 98-106.
62. Ikura, T. Ogryzko, V.V., Grigoriev, M., Groisman, R., Wang, J., Horikoshii, M., Scully, R., Qin, J., and Nakatani, Y. 2000. Involvement of te TIP60 histone acetylase comples in DNA repair and apoptosis. Cell 102, 463-473.
63. Inostroza, J., Flores, O., and Reinberg, D. 1991. Factors involved in specific transcription by mammalian RNA polymerase II: purification and functional analysis of general transcription factor IIE. J. Biol. Chem. 266, 9304-9308.
64. Jackson-Fisher, A.J., Chitikila, C., Mitra, M., and Pugh, B.F. 1999. A role for TBP dimerization in preventing unregulated gene expression. Mol. Cell 3, 717-727.
65. Kadonaga J.T. 1998. Eukaryotic transcription: an interlaced network of transcription factors and chromatin-modifying machines. Cell 92, 307-313.
66. Kaine, B.P., Mehr, I. J., and Woese, C.R. 1994. The sequence, and its evolutionary implications, of a Thermococcus celer protein associated with transcription. Proc. Natl. Acad. Sci. USA 91, 3854-3856.
67. Kanemaki, M. Kurokawa, Y., Matsu-ura, T., Makino, Y., Masani, A., Okazaki, K., Morishita, T., and Tamura, T. 1999. TIP49b, a new RuvB-like DNA helicase, is included in a complex together with another RuvB-like DNA helicase, TIP49a. J. Biol. Chem. 274, 22437-22444.
68. Kanemaki, M., Makino, Y., Yoshida, T., Kishimoto, T., Koga, A., Yamamoto, K., Yamamoto, M., Moncollin, V., Egly, J.-M., Muramatsu, M., and Tamura, T. 1997. Molecular cloning of a rat 49-kDa TBP-interacting protein (TIP49) that is highly homologous to the bacterial RuvB. Biochem. Biophys. Res. Comm. 235, 64-68.
69. Kawarabayasi, Y., Hino, Y., Horikawa, H., Yamazaki, S., Haikawa, Y., Jin-no, K., Takahashi, M., Sekine, M., Baba, S., Ankai, A., Kosugi, H., Hosoyama, A., Fukui, S., Nagai, Y., Nishijima, K., Nakazawa, H., Takamiya, M., Masuda, S., Funahashi, T., Tanaka, T., Kudoh, Y., Yamazaki, J., Kushida, N., Oguchi, A., Aoki, K., Kubota, K., Nakamura, Y., Nomura, N., Sako, Y., and Kikuchi, H. 1999. Complete genome sequence of an aerobic hyperthermophilic crenarchaeon, Aeropyrum pernix K1. DNA Res. 6, 83-101.
70. Kawarabayasi, Y., Hino, Y., Horikawa, H., Jin-no, K., Takahashi, M., Sekine, M., Baba, S., Ankai, A., Kosugi, H., Hosoyama, A., Fukui, S., Nagai, Y., Nishijima, K., Otsuka, R., Nakazawa, H., Takamiya, M., Kato, Y., Yoshizawa, T., Tanaka, T., Kudoh, Y., Yamazaki, J., Kushida, N., Oguchi, A., Aoki, K., Masuda, S., Yanagii, M., Nishimura, M., Yamagishi, A., Oshima, T., and Kikuchi, H. 2001. Complete genome sequence of an aerobic thermoacidophilic crenarchaeon, Sulfolobus tokodaii strain7. DNA Res. 8, 123-140.
71. Kawarabayasi, Y., Sawada, M., Horikawa, H., Haikawa, Y., Hino, Y., Yamamoto, S., Sekine, M., Baba S.-I., Kosugi H., Hosoyama A., Nagai, Y., Sakai, M., Ogu, K., Otsuka, R., Nakazawa, H., Takamiya, M., Ohfuku, Y., Funahashi, T., Tanaka, T., Kudoh, Y., Yamazaki, J., Kushida, N., Oguchi, A., Aoki, K.-I., Yoshizawa, T., Nakamu,Y., Robb, F.T., Horikoshi, K., Masuchi, Y., Shizuya, H., and Kikuchi H. 1998. Complete sequence and gene organization of the genome of a hyper-thermophilic archaebacterium, Pyrococcus horikoshii OT3. DNA Res. 5, 55-76.
72. Kawashima, T., Amano, N., Koike, H., Makino, S., Higuchi, S., Kawashima-Ohya, Y., Watanabe, K., Yamazaki, M., Kanehori, K., Kawamoto, T., Nunoshiba, T., Yamamoto, Y., Aramaki, H., Makino, K., and Suzuki, M. 2000. Archaeal adaptation to higher temperatures revealed by genomic sequence of Thermoplasma volcanium. Proc. Natl. Acad. Sci. USA 97, 14257-14262.
73. Kim, J.L., Nikolov, B.B., and Burley, S.K. 1993a. Co-crystal structure of TBP recognizing the minor groove of a TATA element. Nature 365, 520-527.
74. Kim, Y., Geiger, J.H., Hahn, S., and Sigler, P.B. 1993b. Crystal structure of a yeast TBP/TATA-box complex. Nature 365, 512-520.
75. King, T.H., Decatur, W.A., Bertrand, E., Maxwell, E.S., and Fournier, M.J. 2001. A well-connected and conserved nucleoplasmic helicase is required for production of box C/D/ and H/ACA snoRNAs and localization of snoRNP proteins. Mol. Cell Biol. 21, 7731-7746.
76. Klenk, H.-P., Clayton, R.A., Tomb, J-F., White, O., Nelson, K.E., Ketchum, K.A., Dodson, R.J., Gwinn, M., Hickey, E.K., Peterson, J.D., Richardson D.L., Kerlavage A.R., Graham D.E., Kyrpides, N.C., Fleischmann, R.D., Quackenbush, J., Lee, N.H., Sutton G.G, Gill, S. Kirkness, E.F., Dougherty, B.A. McKenney, K. Adams, M.D., Loftus, B. Peterson, S. Reich, C.I., McNeil, L.K., Badger, J.H., Glodek, A. Zhou, L., Overbeek, R. Gocayne, J.D., Weidman, J.F., McDonald, L., Utterbach, T., Cotton, M.D., Spriggs, T., Artiach, P. Kaine, B.P., Sykes, S.M., Sadow, P.W., D'andrea, K.P., Bowman, C., Fujii, C., Garland, S.A., Mason, T.M., Olsen, G.J., Fraser, C.M., Smith H.O. Woese, C.R., and Venter, J.C. 1997. The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus. Nature 390, 364-370.
77. Kletzin, A. 1992. Molecular characterization of the sor gene, which encodes the sulfur oxygenase/reductase of the thermoacidophilic Archaeum Desulfurolobus ambivalens. J. Bacteriol. 174, 5854-5859.
78. Kosa, P.F., Ghosh, G., DeDecker, B.S., and Sigler, P.B. 1997. The 2.1-Angstrom crystal structure of an archaeal preinitiation complex: TATA-box-binding protein/transcription factor (II)B core/TATA-box. Proc. Natl. Acad. Sci. USA 94, 6042-6047.
79. Kuldell, N.H. and Buratowski, S. 1997. Genetic analysis of the large subunit of yeast transcription factor IIE reveals two regions with distinct function. Mol. Cell Biol. 17, 5288-5298.
80. Krueger, K., Hermann, T., Armbruster, V., and Pfeifer, F. 1998. The transcriptional activator GvpE for the Halobacterial gas vesicle genes resembles a basic region leucine-zipper regulatory protein. J. Mol. Biol. 279, 761-771.
81. Kuo, Y.P., Thompson, D.K., St. Jean, A., Charlebois, R.L., and Daniels, C.J. 1997. Characterization of two heat shock genes from Haloferax volcanii: a model system of regulation in the archaea. J. Bacteriol. 179, 6318-6324.
82. Lagrange, T., Kapanidis, A.N., Tang, H., Reinberg, D., and Ebright, R.H. 1998. New core promoter dement in RNA polymerase II-dependent transcription: sequence-specific DNA binding by transcription factor IIB. Genes Dev. 12, 34-44.
83. Langer, D., Hain, J., Thuriaux, P., and Zillig, W. 1995. Transcription in archaea: similarity to that in eucarya. Proc. Natl. Acad. Sci. USA 92, 5768-5772.
84. Langer, D. and Zillig, W. 1993. Putative tfIIs gene of Sulfolobus acidocaldarius encoding an archaeal transcription elongation factor is situated directly downstream of the gene for a small subunit of DNA-dependant RNA polymerase. Nucl. Acids Res. 21, 2251.
85. Lee, T.I. and Young, R.A. 2000. Transcription of eucaryotic protein-coding genes. Annu. Rev. Genet. 34, 77-137.
86. Lemon, B. and Tjian, R. 2000. Orchestrated response: a symphony of transcription factors for gene control. Genes Dev. 14, 2551-2569.
87. Littlefield, O., Korkhin, Y., and Sigler, P.B. 1999. The structural basis for the oriented assembly of a TBP/TFB/promoter complex. Proc. Natl. Acad. Sci. USA 96, 13668-13673.
88. Lim, C.R. Kimata, Y., Ohdate, H., Kokubo, T., Kikuchi, N., Horigome, T., and Kohno, K. 2000. The Saccharomyces cerevisiae RuvB-like protein, Tih2p is required for cell cycle progression and RNA polymerase II-directed transcription. J. Biol. Chem. 275, 22409-22417.
89. Lopez-Garcia, P. and Forterre, P. 2000. DNA topology and the thermal stress response, a tale from mesophiles and hyperthermophiles. BioEssays 22, 738-746.
90. Macario, A.J.L. and Conway de Macario, E. 1997. Stress genes: an introductory overview. Stress 1, 123-134.
91. Macario, A.J.L. and Conway de Macario, E. 1999. The archaeal molecular chaperone machine: peculiarities and paradoxes. Genetics 152, 1277-1283.
92. Macario, A.J.L. and Conway de Macario, E. 2001. The molecular charperone system and other anti-stress mechanisms in archaea. Front. Biosci. 6, d262-283 http://www.bioscience.org/2001/v6/d/macario/fulltext.htm
93. Macario, A.J.L., Dugan, C.B., and Conway de Macario, E. 1991. A dnaK homolog in the archaebacterium Methanosarcina mazeii S6. Gene 108, 133-137.
94. Macario, A.J L., Lange, M., Ahring, B.K., and Conway de Macario, E. 1999. Stress genes and proteins in the Archaea. Microbiol. Mol. Biol. Rev. 63, 923-967.
95. Makino, Y., Kanemaki, M., Kurokawa, Y., Koji, T., and Tamura, T.A. 1999. A rat RuvB-like protein, TIP49a, is a germ cell-enriched novel DNA helicase. J. Biol. Chem. 274, 15329-15335.
96. Magill, C.P., Jackson, S.P., and Bell, S.D. 2001. Identification of a conserved archaeal RNA polymerase subunit contacted by the basal transcription factor TFB. J. Biol. Chem. 276, 46693-46696.
97. Marsh, T.L., Reich, C.I., Whitelock, R.B., and Olsen, G.J. 1994. Transcription factor IID in the archaea: sequences in the Thermococcus celer genome would encode a product closely related to the TATA-binding protein of eukaryotes. Proc. Natl. Acad. Sci. USA 91, 4180-4184.
98. Matsuda, T. Morikawa M., Haruki, M., Higashibata, H., Imanaka, T., and Kanaya, S. 1999. Isolation of TBP-interacting protein (TIP) from a hyperthermophilic archaeon that inhibits the binding of TBP to the TATA-DNA. FEBS Lett. 457, 38-42.
99. Matsuda, T., Fujikawa, M., Haruki, M., Tang, XF., Ezaki, S. Imanaka, T., Morikawa, M., and Kanaya, S. 2001. Interaction of TIP26 from a hyperthermophilic archaeon with TFB/TBP/DNA ternary complex. Extremophiles 5, 177-182.
100. Maxon, M.E., Goodrich, J.A., and Tjian, R. 1994. Transcription factor IIE binds preferentially to RNA polymerase IIa and recruits TFIIH: a model for promoter clearance. Genes Dev. 8, 515-524.
101. Maxon, M.E., Tjian, R. 1994. Transcriptional activity of transcription factor IIE is dependant on zinc binding. Proc. Natl. Acad. Sci. USA 91, 9529-9533.
102. Mayerhofer, L E., Macario, A.J.L., and Conway de Macario, E. 1992. Lamina, a novel multicellular form of Methanosarcina mazei S-6. J. Bacteriol. 174, 309-314.
103. Metcalf, W.W., Zhang, K.K., Apolinario, E., Sowers, K.R., and Wolfe, R.S. 1997. A genetic system for Archaea of the genus Methanosarcina: Liposome-mediated transformation and construction of shuttle vectors. Proc. Natl. Acad. Sci. USA 94, 2626-2631.
104. Miller, J., McLachlan, A.D., and Klug, A. 1985. Repetive zinc-binding domains in the protein transcription factor mA from Xenopus oocytes. EMBO J. 4, 1609-1614.
105. Missiakas, D., Raina, S., and Georgopoulos, C. 1996. Heat shock regulation. In: Regulation of Gene Expression in Escherichia coli, E.C.C. Lin and A.S. Lynch, Eds. Chapman & Hall, New York, NY; pp. 481-501.
106. Morimoto, R.I. 1998. Regulation of the heat shock transcriptional response: Cross talk between a family of heat shock factors, molecular chaperones, and negative regulators. Genes Dev. 12, 3788-3796.
107. Napoli, A., Van der Oost, J., Sensen, C.W., Charlebois, R.L., Rossi, M., and Ciaramella, M. 1999. An Lrp-like protein of the hyperthermophilic archaeon Sulfolobus solfactaricus which binds to its own promoter. J. Bacteriol. 181, 1474-1480.
108. Newman, E.B. and Lin, R. 1995. Leucine-responsive regulatory protein, a global regulator of gene expression in E. coli. Annu. Rev. Microbiol. 49, 747-775.
109. Newman, D.R., Kuhn, J.F., Shanab, G.M., and Maxwell E.S. 2000. Box C/D snoRNA-associated proteins: two pair of evolutionarily ancient proteins and possible links to replication and transcription. RNA 6, 861-879.
110. Nikolov, D.B., Chen, H., Halay, E.D., Hoffmann, A., Roeder, R.G., and Burley, S.K. 1996. Crystal structure of a human TATA box-binding protein/TATA element complex. Proc. Natl. Acad. Sci. USA. 93, 4862-4867.
111. Nikolov, D., Hu, S-H., Lin, J., Gasch, A., Hoffmann, A., Horikoshi, M., Chua., N-H., Roeder, R.G., and Burley, S.K. 1992. Crystal structure of TFIID TATA-box binding protein. Nature 360, 40-46.
112. Ng, W.V., Ciufo, S.A., Smith, T.M., Bumgarner, R.E., Baskin, D., Faust, J., Hall, B., Loretz, C., Seto, J., Slagel, J., Hood, L., and DasSarma, S. 1998. Snapshot of a large dynamic replicon in a halophilic archaeon: megaplasmid or minichromosome? Genome Res. 8, 1131-1141.
113. Ng, W.V., Kennedy, S.P., Mahairas, G.G., Berquist, B., Pan, M., Shukla, H.D., Lasky, S.R., Baliga, N.S., Thorsson, V., Sbrogna, J., Swartzell, S., Weir, D., Hall, J., Dahl, T.A., Welti, R., Goo, Y.A., Leithauser, B., Keller, K., Cruz, R., Danson, M.J., Hough, D.W., Maddocks, D.G., Jablonski, P.E., Krebs, M.P., Angevine, C.M., Dale,H., Isenbarger, T.A., Peck, R.F., Pohlschroder, M., Spudich, J.L., Jung, K-H., Alam, M., Freitas, T., Hou, S., Daniels, C.J., Dennis, P.P., Omer, A.D., Ebhardt, H., Lowe, T.M., Liang, P., Riley, M., Hood, L., and DasSarma, S. 2000. Genome sequence of Halobacterium sp. NRC-1. Proc. Natl. Acad. Sci. USA 97, 12176-12181.
114. O'Brien, R., DeDecker, B., Fleming, K.G., Sigler, P.B., and Ladbury, J.E. 1998. The effects of salt on the TATA Binding Protein-DNA interaction from a hyperthemophilic archaeon. J. Mol. Biol. 279, 117-125.
115. Ogata, Y., Mizushisma, T., Kataoka, K., Kita, K. Miki, T., and Sekimizu, K. 1996. DnaK heat shock protein of Esherichia coli maintains the negative supercoiling of DNA against thermal stress. J. Biol. Chem. 271, 29407-29414.
116. Orphanides, G. and Reinberg, D. 2002. A unified theory of gene expression. Cell 108, 439-451.
117. Ouhammouch, M. and Geiduschek. E.P. 2001. A thermostable platform for transcriptional regulation: the DNA-binding properties of two Lrp homologs from the hyperthermophilic archaeon Methanococcus jannaschii. EMBO J. 20, 146-156.
118. Ouzounis, C. and Sander C. 1992. TFIIB, an evolutionary link between the transcription machineries of archaebacteria and eukaryotes. Cell 71, 189-190.
119. Pastor, N. and Weinstein, H. 1995. Electrostatic analysis of DNA binding properties in lysine to leucine mutants of TATA-box binding proteins. Prot. Eng. 8, 543-549.
120. Perler, F.B., Davis, E.O., Dean, G.E., Gimble, F.S., Jack, W.E., Neff, N., Noren, C.J., Thorner, J., and Belfort., M. 1994. Protein splicing elements: inteins and exteins - a definition of terms and recommended nomenclature. Nucl. Acids Res. 22, 1125-1127.
121. Pfeifer, F., Zotzel, J., Kurenbach, B., Röder, R., and Zimmermann, P. 2001. A p-loop motif and two basic regions in the regulatory protein GvpD are important for the repression of gas vesicle formation in the archaeon Haloferax mediterranei. Microbiology 147, 63-73.
122. Pugh, B.F. 2000. Control of gene expression through regulation of the TATA-binding protein. Gene 255, 1-14.
123. Puhler, G., Lottspiech, F., and Zillig, W. 1989. Organization and nucleotide sequence of the genes encoding the large subunits A, B and C of the DNA-dependent RNA polymerase of the archaebacterium Sulfolobus acidocaldarius. Nucl. Acids Res. 17, 4517-4534.
124. Qureshi, S.A., Bell, S.D., and Jackson, S.P. 1997. Factor requirements for transcription in the archaeon Sulfolobus shibatae. EMBO J. 16, 2927-2936.
125. Qureshi, S.A. and Jackson, S.P. 1998. Sequence-specific DNA binding by the S. shibatae TFIIB homolog, TFB, and its effect on promoter strength. Mol. Cell 1, 389-400.
126. Qureshi S.A., Khoo, B., Baumann, P., and Jackson, S.P. 1995. Molecular cloning of the transcription factor TFIIB homolog from Sulfolobus shibatae. Proc. Natl. Acad. Sci. USA 92, 6077-6081.
127. Rashid, N., Morikawa, M., and Imanaka, T. 1995. An abnormally acidic TATA-binding protein from a hyperthermophilic archaeon. Gene 166, 139-143.
128. Reiter, W-D., Hudelpohl, U., and Zillig, W. 1990. Mutational analysis of an archaebacterial promoter; essential role of a TATA box for transcription efficiency and start-site selection in vitro. Proc. Natl. Acad. Sci. USA 87, 9509-9513.
129. Roberts, S.G.S. and Greene, M.R. 1994. Activator-induced conformational change in general transcription factor TFIIB. Nature 371, 717-720.
130. Rowlands, T., Baumann, P., and Jackson, S.P. 1994. The TATA-binding protein: a general transcription factor in eukaryotes and archaebacteria. Science 264, 1326-1329.
131. Ruepp, A., Graml, W., Santos-Martinez, M-L., Koretke, K.K., Volker, C., Mewes, H.W. Frishman, D., Stocker, S., Lupas, A.N., and Baumeister, W. 2000. The genome sequence of the thermoacidophilic scavenger Thermoplasma acidophilum. Nature 407, 508-513.
132. Ruepp, A., Rockel, B., Gusche, I., Baumeister, W., and Lupas, A.N. 2001. The chaperones of the archaeon Thermoplasma acidophilum. J. Struct. Biol. 135, 126-138.
133. Sandman, K. and Reeve, J.N. 2000. Structure and functional relationships of archaeal and eukaryal histones and nucleosomes. Arch. Microbiol. 173, 165-169.
134. Scandurra, R., Consalvi, V., Chiaraluce, R., Politi, L., and Engel, P.C. 2000. Protein stability in extremophilic archaea. Front. Biosci. 5, d787-795 http://www.bioscience.org.v5/d/scan/fulltext.htm
135. Schmidt, J.E. and Ahring, B.K. 1995. Granular sludge formation in upflow anaerobic sludge blanket (UASB) reactors. Biotechnol. Bioeng. 49, 229-246.
136. She, Q., Singh, R.K., Confalonieri, F., Zivanovic, Y., Allard, G., Awayez, M.J., Chan-Weiher, C.C., Clausen, I.G., Curtis, B.A., De Moors, A., Erauso, G., Fletcher, C., Gordon, P.M.K, Heikampde Jong, I., Jeffries, A.C., Kozera, C.J., Medina, N., Peng, X., Thi-Ngoc, H.P., Redder, P., Schenk, M.E., Theriault. C., Tolstrup, N., Charlebois, R.L., Doolittle, W.F., Duguet, M., Gaasterland, T., Garrett, R.A., Ragan, M.A., Sensen, C.W., and Van der Oost, J. 2001. The complete genome of the crenarchaeon Sulfolobus solfataricus P2. Proc. Natl. Acad. Sci. USA 98, 7835-7840.
137. Shen, X., Mizuguchi, G., Hamiche, A., and Wu, C. 2000. A chromatin remodeling complex formed involved in transcription and DNA processing. Nature 406, 541-544.
138. Shimkets, L.J. and Brun, Y.I. 2000. Prokaryotic development: Strategies to enhance survival. In: Prokaryotic Development, Y.I. Brun and L.J. Shimkets, Eds. American Society for Microbiology Press, Washington, DC, pp.1-7.
139. Skorko, R. 1984. Protein phosphorylation in the archaeabacterium Sulfolobus acidocaldarius. Eur. J. Biochem. 145, 617-622.
140. Slesarev, A.I., Mezhevaya, K.V., Makarova, K.S., Polushin, N.N., Shcherbinina, O.V., Shakhova, V.V., Belova, G.I., Aravind, L., Natale, D.A., Rogozin, I.B.,Tatusov, R.L., Wolf, Y.I., Stetter, K.O., Malykh, A.G., Koonin, E.V., and Kozyavkin, S.A. 2002. The complete genome of hyperthermophile Methanopyrus kandleri AV19 and monophyly of archaeal methanogens. Proc. Natl. Acad. Sci. USA 99, 4644-4649.
141. Smith, D.R., Doucette-Stamm, L.A., Deloughery, C., Lee, H., Dubois, J., Aldredge, T., Bashirzadeh, R., Blakely, D., Cook, R., Gilbert, K., Harrison, D., Hoang, L., Keagle, P., Lumm, W., Pothier, B., Qiu, D., Spadafora, R., Vicaire, R., Wang, Y., Wierzbowski, J., Gibson, R., Jiwani, N., Caruso, A., Bush, D., Safer, H, Patwell, D, Prabhakar, S., McDougall, S., Shimer, G., Goyal, A., Pietrokovski, S., Church, G.M., Daniels, C.J., Mao, J., Rice, P., Nölling, J., and Reeve, J.N. 1997. Complete genome
142. Soppa, J. 1999. Transcription initiation in archaea: facts, factors and future aspects. Mol. Microbiol. 31, 1295-1305.
143. Soerensen, A.H., Torsvik, V.L., Torsvik, T., Poulsen, L.K., and Ahring, B.K. 1997. Whole-cell hybridization of Methanosarcina cells with two new oligonucleotide probes. Appl. Environ. Microbiol. 63, 3043-3050.
144. Spencer, V.A. and Davie, J.R. 1999. Role of covalent modifications of histones in regulating gene expression. Gene 240, 1-12.
145. Takemaru, K., Li, F.Q., Ueda, H., and Hirose, S. 1997. Multiprotein bridging factor (MBF1) is an evolutionarily conserved transcriptional coactivator that connects a regulatory factor and TATA element-binding protein. Proc. Natl. Acad. Sci. USA 94, 7251-7256.
146. Takemaru, K., Harashima, S., Ueda, H., and Hirose, S. 1998. Yeast coactivator MBF1 mediates GCN4-dependent transcriptional activation. Mol. Cellul. Biol. 18, 4971-4976.
147. Thompson, D.K. and Daniels, C.J. 1998. Heat shock inducibility of an archaeal TATA-like promoter is controlled by adjacent sequence elements. Mol. Microbiol. 27, 541-551.
148. Thomsen, J., De Biase, A., Kaczanowski, S., Macario, A.J.L., Thomm, M., Zielenkiewicz, P., MacColl, R., and Conway de Macario, E. 2001. The basal transcription factors TBP and TFB from the mesophillic archaeaon Methanosarcina mazeii: structure and conformational changes upon interaction with stress-gene promoters. J. Mol. Biol. 309, 589-603.
149. Todone, F., Brick, P., Werner, F., Weinziert, R.O.J., and Onesti, S. 2001. Structure of an archaeal homolg of the eukaryotic RNA polymerase II RPB4/RPB7 complex. Mol. Cell 8, 1137-1143.
150. Um, M. and Manley, J.L. 2000. The Drosophila TATA binding protein contains a strong but masked activation domain. Gene Exp. 9, 123-132.
151. Werner, F., Eloranta, J.J., and Weinzierl, R.O.J. 2000. Archaeal RNA polymerase subunits F and P are bona fide homologs of eucaryotic RBP4 and RBP12. Nucl. Acids. Res. 28, 4299-4305.
152. Wang, Q. and Calvo, J.M. 1993. Lrp, a major regulatory protein in Escherichia coli, bends DNA and can organize the assembly of a higher-order nucleoprotein structure. EMBO J. 12, 2495-2501.
153. Woychik, N.A. and Hampsey, M. 2002. The RNA polymerase II machinery: structure illuminates function. Cell 108, 453-463.
154. Yao, R., Macario, A.J.L., and Conway de Macario, E. 1992. Immunochemical differences among Methanosarcina mazei S-6 morphologic forms. J. Bacteriol. 174, 4683-4688.
155. Yang, C-F., Kim, J., Molinari, E., and DasSarma, S. 1996. Genetic and topological analysis of the bop promoter of Halobacterium halobium: stimulation by DNA supercoiling and non-B-DNA structure. J. Bacteriol. 178, 840-845.
156. Yokomori, K., Verrijzer, C.P., and Tjian, R. 1998. An interplay between TATA box-binding protein and transcription factors IIE and IIA modulates DNA binding and transcription. Proc. Natl. Acad. Sci. USA 95, 6722-6727.
157. Zhang, J.L., White, A.K., Kuettner, H.C., Boccazzi, P., and Metcalf, W.W. 2002. Directed mutagenesis and plasmid-based complementation in the methanogenic archaeon Methanosarcina acetivorans C2A demonstrated by genetic analysis of proline biosynthesis. J. Bacteriol. 184, 1449-1454.
158. Zhu, W., Zeng, Q., Colangelo, C.M., Lewis, L. M., Summers, M.F., and Scott, R.A. 1996. The N-terminal domain of TFIIB from Pyrococcus furiosus forms a zinc ribbon. Nature Struct. Biol. 3, 122-124.
159. Zillig, W., Palm P., Langer, D., Klenk, H-P., Lanzendorfer, M., Hudepohl, U., and Hain, J. 1992. RNA-polymerases and transcription in archeabacteria. Biochem. Soc. Symp. 58, 79-88.
160. Zinder, S.H. 1993. Physiological ecology of methanogens. In: Methanogenesis, J.G. Ferry, Ed. Chapman & Hall, New York, NY; pp. 161-206.