Chapter 6 : Transcription: Mechanism and Regulation

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The biochemical machinery involved in the processes of DNA replication, transcription, and translation shows a striking similarity and phylogenetic relationship to the equivalent machinery in eucarya. In particular, RNA polymerase (RNAP) and the basal transcriptional machinery of archaea share many properties with the eucaryal RNA polymerase II (RNAP II) transcription apparatus. Regulators of archaeal transcription repress initiation by preventing TFB/TBP access to the TATA-box region or RNAP recruitment to the transcription start site. The DNA-binding site of LrpA overlaps the RNAP-binding site, and DNA-bound LrpA inhibits transcription by blocking RNA polymerase recruitment. NrpR controls the transcription of the operon by binding cooperatively to two tandem operator sequences, OR and OR, located downstream of the transcription start site. The stronger and promoter proximal NrpR-binding site (OR) can mediate repression of nif transcription during growth on ammonia. Heat shock-induced upregulation of some TFB genes from haloarchaea and of TFB2 from have been reported. In cell-free transcription reactions, the addition of the substrate (maltodextrins) of this transporter system causes TrmB to dissociate from the promoter and relieves inhibition of RNA synthesis. The lack of genetic systems in many archaea hampers analysis of transcriptional regulation in vivo. The striking similarity of the archaeal and eucaryal genetic machinery is described in this chapter.

Citation: Thomm M. 2007. Transcription: Mechanism and Regulation, p 139-157. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch6
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Figure 1

Initiation of transcription in archaea. The first step of promoter recognition is binding of TBP to the archaeal TATA box. This complex is stabilized by the association of TFB. Bound TFB interacts with the purinerich BRE sequence 5ʹ of the TATA box. This complex recruits the RNA polymerase that binds to the DNA region downstream of the TATA box and covers the transcription start site and the DNA downstream region to position +18.

Citation: Thomm M. 2007. Transcription: Mechanism and Regulation, p 139-157. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch6
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Figure 2

Domain structure of TFB. The major structural features of TFB and their interactions with other components of the transcriptional machinery.

Citation: Thomm M. 2007. Transcription: Mechanism and Regulation, p 139-157. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch6
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Figure 3

Subunit structure of RNAPs from the three domains of life. The largest subunit in the and in the is split into two subunits, A1 and A2, in the In methanogens, subunit B is also split into two polypeptides, Bʹ and Bʹ. Different parts of bacterial subunit are encoded by the genes for the archaeal subunits D and L. Subunits E1, F, H, N, and P are only shared between the and The pattern shown is based on separation of subunits by polyacrylamide gel electrophoresis under denaturing conditions. The numbers in the subunits of the eucaryal RNAP A (I), B (II), and C (III) indicate the molecular mass.

Citation: Thomm M. 2007. Transcription: Mechanism and Regulation, p 139-157. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch6
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Figure 4

(.) Structural similarity of RNAP (A) and yeast RNAPII (B). Comparison of interactions of an archaeal RNAP inferred from Far-Western analysis with interactions of yeast RNAPII observed in the crystal structure of the enzyme. The width of the lines connecting subunits is a measure of the intensity of the interaction. Modified from ( ) with additional data from ( ).

Citation: Thomm M. 2007. Transcription: Mechanism and Regulation, p 139-157. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch6
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Figure 5

Mechanism of transcription by an archaeal RNAP. (A) TFE facilitates binding of the TFB zinc ribbon domain to the core domain of RNAP. (B) After open complex formation, the B finger of TFB stabilizes the template strand in the active center of RNAP. TFE provides additional stability to this complex by closing the clamp of RNAP. (C) After synthesis of a transcript longer than 10 nucleotides, RNAP reaches the elongation committed state. RNAP moves synchronously with RNA synthesis from this point.

Citation: Thomm M. 2007. Transcription: Mechanism and Regulation, p 139-157. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch6
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Figure 6

The two major transitions in archaeal transcription initiation. (A) In the preinitiation complex and during synthesis of the first five nucleotides, RNAP is in close contact with transcription factors and the transcription bubble extends from position — 7 to +5. (B) After synthesis of 6/7 nucleotides, the upstream edge of RNAP loses contact with transcription factors but the downstream edge is unchanged. (C) At position +10/+11, promoter clearance occurs and RNAP moves continuously to enable RNA synthesis.

Citation: Thomm M. 2007. Transcription: Mechanism and Regulation, p 139-157. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch6
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Figure 7

Interaction of a heat shock regulator (Phr) with heat shock promoters. Phr binds specifically to a conserved palindromic sequence of archaeal heat shock promoters overlapping the transcription start site. When bound to the DNA, Phr blocks RNAP recruitment. The factors modulating the DNA-binding properties of Phr are unknown.

Citation: Thomm M. 2007. Transcription: Mechanism and Regulation, p 139-157. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch6
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Figure 8

The archaeal regulator TrmB responds to different ligands when bound at different promoters. In the absence of any ligands, TrmB binds to its operator sequences at the maltose and maltodextrin promoter. At the promoter, TrmB binding is influenced by maltose as inducer, but not by maltodextrins. At the promoter maltose has no effect on TrmB binding but maltodextrins lower its affinity for the operator. The TrmB-binding sites differ substantially at both promoters, and the TrmB-binding site overlaps the transcription start site at the promoter, and the BRE/TATA box sequence at the promoter. The smaller triangle represents maltose, and the larger triangle, maltodextrins. The TATA box is indicated; the DNA-binding sequence of TrmB is represented by a shaded box and shown on both promoters, and the binding sequence is shown below TrmB. The transcription start site is indicated by +1. The binding site of TrmB contains a palindrome at the promoter and is represented by two horizontal arrows. Only one half of it is conserved in the promoter.

Citation: Thomm M. 2007. Transcription: Mechanism and Regulation, p 139-157. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch6
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Figure 9

The ROMA approach. Fragmented genomic DNA is transcribed in a cell-free transcription system in the presence and absence of a regulator. Each DNA fragment harbors on average one promoter. Some promoters are unaffected (no regulation) by a given regulator, some are upregulated (by activators), and some are downregulated (by repressors). The in vitro RNA is converted to labeled cDNA and hybridized with a whole-genome microarray. By comparison of the hybridization patterns of RNAs synthesized in the presence and absence of a regulator the genes modulated by the regulatory protein can be identified.

Citation: Thomm M. 2007. Transcription: Mechanism and Regulation, p 139-157. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch6
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1. Aravind, L., and, E. V. Koonin. 1999. DNA-binding proteins and evolution of transcription regulation in the archaea. Nucleic Acids Res. 27: 46584670.
2. Armache, K. J.,, H. Kettenberger, and, P. Cramer. 2003. Architecture of initiation-competent 12-subunit RNA polymerase II. Proc. Natl. Acad. Sci. USA 100: 69646968.
3. Baliga, N. S., and, S. DasSarma. 1999. Saturation mutagenesis of the TATA box upstream activator sequence in the halo-archael bop gene promoter. J. Bacteriol. 181: 25132518.
4. Baliga, N. S., and, S. DasSarma 2000. Saturation mutagenesis of the haloarchaeal bop gene promoter: identification of DNA supersoiling sensitivity sites and absence of TFB recognition element and UAS enhancer activity. Mol. Microbiol. 36: 11751183.
5. 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. 35: 11841185.
6. Baliga, N. S.,, S. P. Kennedy,, W. V. Ng,, L. Hood, and, S. DasSarma. 2001. Genomic and genetic dissection of an archaeal regulon. Proc. Natl. Acad. Sci. USA 98: 25212525.
7. Bartlett, M. S.,, M. Thomm, and, E. P. Geiduschek. 2000. The orientation of DNA in an archaeal transcription initiation complex. Nat. Struct. Biol. 7: 782785.
8. Bartlett, M. S.,, M. Thomm, and, E. P. Geiduschek. 2004. Topography of the euryarchaeal transcription initiation complex. J. Biol. Chem. 279: 58945903.
9. Bell, S. D.,, A. B. Brinkman,, J. van der Oost, and, S. P. Jackson. 2001. The archaeal TFIIEalpha homologue facilitates transcription initiation by enhancing TATA-box recognition. EMBO Rep. 2: 133138.
10. Bell, S. D.,, C. H. Botting,, B. N. Wardleworth,, S.P. Jackson, and, M. F. White. 2002. The interaction of Alba, a conserved archaeal chromatin protein, with Sir2 and its regulation by acetylation. Science 296: 148151.
11. Bell, S. D.,, S. S. Cairns,, R.L. Robson, and, S. P. Jackson. 1999. Transcriptional regulation of an archaeal operon in vivo and in vitro. Mol. Cell 4: 971982.
12. Bell. S. D., and, S. P. Jackson. 1998. Transcription and translation in Archaea: a mosaic of eukaryal and bacterial features. Trends Microbiol. 6: 222228.
13. Bell, S. D., and, S. P. Jackson. 2000. Charting a course through RNA polymerase. Nature Struct. Biol. 7: 703705.
14. Bell, S. D., and, S. P. Jackson. 2000. The role of transcription factor B in transcription initiation and promoter clearance in the archaeon Sulfolobus acidocaldarius. J. Biol. Chem. 275: 1293412940.
15. Bell, S. D., and, S. P. Jackson. 2000. Mechanism of autoregulation by an archaeal transcriptional repressor. J. Biol. Chem. 275: 3162431629.
16. Bell, S. D.,, C. Jaxel,, M. Nadal,, P. F. Kosa, and, S. P. Jackson. 1998. Temperature, template topology, and factor requirements of archaeal transcription. Proc. Natl. Acad. Sci. USA 95: 1521815222.
17. Bell, S. D.,, P. L. Kosa,, P. D. Sigler, and, S. P. Jackson. 1999. Orientation of the transcription preinitiation complex in archaea. Proc. Natl. Acad. Sci. USA 96: 1366213667.
18. Brinkman, A. B.,, S. D. Bell,, R. J. Lebbink,, W. M. de Vos, and, J. van der Oost. 2002. The Sulfolobus solfataricus Lrp-like protein LysM regulates lysine biosynthesis in response to lysine availability. J. Biol. Chem. 277: 2953729549.
19. Brinkman, A. B.,, I. Dahlke,, J. E. Tuininga,, T. Lammers,, V. Dumay, and, E. de Heus. 2000. An Lrp-like transcriptional regulator from the archaeon Pyrococcus furiosus is negatively autoregulated. J. Biol. Chem. 275: 3816038169.
20. Brinkman, A. B.,, T. J. Ettema,, W. M. de Vos, and, J. van der Oost. 2003. The Lrp family of transcriptional regulators. Mol. Microbiol. 48: 287294
21. Brown, J.,, M. Thomm,, G. Beckler,, G. Frey,, K. O. Stetter, and, J. N. Reeve. 1988. Archaebacterial RNA polymerase binding site and transcription of the hisA gene of Methanococcus vannielii. Nucleic Acids Res. 16: 135164.
22. Bushnell, D. A.,, K. D. Westover,, R. E. Davis, and, R. D. Kornberg. 2004. Structural basis of transcription: an RNA polymerase II-TFIIB cocrystal at 4.5 Ångströms. Science 303: 983988.
23. Cao, M.,, P. A. Kobel,, M. M. Morshedi,, M. F. Wu,, C. Paddon, and, J. D. Heimann. 2002. Defining the Bacillus subtilis sigma (W) regulon: a comparative analysis of promoter consensus search, run-off transcription/macroarray analysis (ROMA), and transcriptional profiling approaches. J. Mol. Biol. 316: 443457.
24. Chen, H. T., and, S. Hahn. 2003. Binding of TFIIB to RNA polymerase II: mapping the binding site for the TFIIB zinc ribbon domain within the preinitiation complex. Mol. Cell 12: 437447.
25. Chen, H. T., and, S. Hahn. 2004. Mapping the location of TFIIB within the RNA polymerase II transcription preinitiation complex: a model for the structure of the PIC. Mol. Cell. 119: 169180.
26. Cramer, P.,, D. A. Bushnell,, J. Fu,, A. L. Gnatt,, B. Maier-Davis,, N. E. Thompson,, R. R. Burgess,, A. M. Edwards,, P. R. David, and, R. D. Kornberg. 2000. Architecture of RNA polymerase II and implications for the transcription mechanism. Science 288: 640649.
27. Cramer, P.,, D. A. Bushnell, and, R. D. Kornberg. 2001. Structural basis of transcription: RNA polymerase II at 2.8 Å resolution. Science 292: 18631876
28. Dahlke, I., and, M. Thomm. 2002. A Pyrococcus homologue of the Leucine-responsive regulatory protein, LrpA, inhibits transcription by abrogating RNA polymerase recruitment. Nucleic Acids Res. 30: 701710.
29. Danner, S., and, J. Soppa. 1996. Characterization of the distal promoter element of halobacteria in vivo using saturation mutagenesis and selection. Mol. Microbiol. 19: 12651276.
30. DeDecker, B.,, R. OʹBrien,, P. J. Fleming,, J. H. Geiger,, S. Jackson, and, P. B. Sigler. 1996. The crystal structure of a hyper-thermophilic archaeal TATA-box binding protein. J. Mol. Biol. 264: 10721084.
31. Eloranta, J. J.,, A. Kato,, M. Teng, and, R. O. Weinzierl. 1998. In vitro assembly of an archaeal D-L-N RNA polymerase sub-unit complex reveals a eukaryote-like structural arrangement. Nucleic Acids Res. 26: 55625567.
32. Florentino, G.,, R. Cannio,, M. Rossi, and, S. Bartolucci. 2003. Transcriptional regulation of the gene encoding an alcohol dehydrogenase in the archaeon Sulfolobus solfataricus involves multiple factors and control elements. J. Bacteriol. 185: 39263934.
33. Frey, G.,, M. Thomm,, B. Brüdigam,, H. Gohl, and, W. Hausner. 1990. An archaebacterial cell-free transcription system. The expression of tRNA genes from Methanococcus vannielii is mediated by a transcription factor. Nucleic Acids Res. 18: 13611367.
34. Geiduschek, E. P., and, M. Ouhammouch. 2005. Archaeal transcription and its regulators. Mol. Microbiol. 56: 13971407.
35. Geiduschek, E. P., and, G. P. Tocchini-Valentini. 1988. Transcription by RNA polymerase III. Annu. Rev. Biochem. 57: 873914.
36. Gelfand, M. S.,, E. V. Koonin, and, A. A. Mironov. 2000. Prediction of transcription regulatory sites in Archaea by a comparative genomic approach. Nucleic Acids Res. 28: 695705.
37. Goede, B.,, S. Naji,, O. von Kampen,, K. Ilg, and, M. Thomm. 2006. Protein-protein interactions in the archaeal transcriptional machinery: binding studies of isolated RNA polymerase subunits and transcription factors. J. Biol. Chem. 281: 3058130592.
38. Gohl, H. P.,, B. Gröndahl, and, M. Thomm. 1995. Promoter recognition in archaea is mediated by transcription factors: Identification of a TFB from Methanococcus thermolithotrophicus as archaeal TATA-binding protein. Nucleic Acids Res. 23: 38373841.
39. Grabowski, B., and, Z. Kelman. 2003. Archaeal DNA replication: Eukaryal proteins in a bacterial context. Annu. Rev. Microbiol. 57: 487516.
40. Gropp, F.,, W. D. Reiter,, A. Sentenac,, W. Zillig,, R. Schnabel,, M. Thomm, and, K. O. Stetter. 1986. Homologies of components of DNA-dependent RNA polymerases of Archaebacteria, Eukaryotes and Eubacteria. Syst. Appl. Microbiol. 7: 95101.
41. Hain, J.,, W. D. Reiter,, U. Hüdepohl, and, W. Zillig. 1992. Elements of an archaeal promoter defined by mutational analysis. Nucleic Acids Res. 20: 54235428.
42. Hanzelka, B. L.,, T. J. Darcy, and, J. N. Reeve. 2001. TFE, an archaeal transcription factor in Methanobacterium thermoautotrophicum related to eucaryal transcription factor TFI-IFalpha. J. Bacteriol. 183: 18131818.
43. Hausner, W.,, G. Frey, and, M. Thomm. 1991. Control regions of an archaeal gene. A TATA box and initiator element promote cell-free transcription of the RNAVa l gene of Methanococcus vannielii. J. Mol. Biol. 222: 495508.
44. Hausner, W.,, U. Lange, and, M. Musfeldt. 2000. Transcription factor S, a cleavage induction factor of the archaeal RNA polymerase. J. Biol. Chem. 275: 1239312399.
45. Hausner, W., and, M Thomm. 1993. Purification and characterization of a general transcription factor, aTFB from the archaeon Methanococcus thermolithotrophicus. J. Biol. Chem. 268: 2404724052
46. Hausner, W., and, M. Thomm. 1995. The translation product of the presumptive Thermococcus celer TATA-binding protein sequence is a transcription factor related in structure and function to Methanococcus Factor B. J. Biol. Chem. 270: 1764917651.
47. Hausner, W., and, M. Thomm. 2001. Events during initiation of archaeal transcription: Open complex formation and DNA-protein interactions. J. Bacteriol. 183: 30253031.
48. Hausner, W.,, J. Wettach,, C. Hethke, and, M. Thomm. 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: 3014430148.
49. Hofacker, A,, K. M. Schmitz,, A. Cichonczyk,, S. Sartorius-Neef, and, F. Pfeifer. 2004. GvpE- and GvpD-mediated transcription regulation of the p-gvp genes encoding gas vesicles in Halobacterium salinarum. Microbiology 150: 18291838.
50. Hüdepohl, U.,, W. D. Reiter, and, W. Zillig. 1990. In vitro transcription of two rRNA genes of the archaebacterium Sulfolobus sp. B 12 indicates a factor requirement for specific initiation. Proc. Natl. Acad. Sci. USA 87: 58515855.
51. Ishihama, A. 1981. Subunit assembly of E. coli RNA polymerase. Adv. Biophys. 14: 135.
52. Jafri, S.,, S. Chen, and, J. M. Calvo. 2002. ilvlH operon expression in Escherichia coli requires Lrp binding to two distinct regions of DNA. J. Bacteriol. 184: 52935300.
53. Koike, H.,, S. A. Ishijima,, L. Clowney, and, M. Suzuki. 2004. The archaeal feast/famine regulatory protein: Potential roles of its assembly forms for regulating transcription. Proc. Natl. Acad. Sci. USA 101: 28402845.
54. Kosa, P. F.,, G. Ghosh,, B. S. Deecker, and, P. B. Sigler. 1997. The 2.1-Å crystal structure of an archaeal preinitiation complex: TATA-box-binding protein/transcription factor (II) B core/TATA-box. Proc. Natl. Acad. Sci. USA 94: 60426047.
55. Krüger, K.,, T. Hermann,, V. Armbruster, and, F. Pfeifer. 1998. The transcriptional activator GvpE for the halobacterial gas vesicle genes resembles a basic region leucine-zipper regulatory protein. J. Mol. Biol. 279: 761771.
56. Kyrpides, N. C., and, C. A. Ouzounis. 1995. The eubacterial transcriptional activator Lrp is present in the archaeon Pyrococcus furiosus. Trends Biochem. Sci. 20: 140141.
57. Kyrpides, N. C., and, C. A. Ouzounis. 1999. Transcription in archaea. Proc. Natl. Acad. Sci. USA 96: 854550.
58. Laksanalamai, P.,, D. L. Maeder, and, F. T. Robb. 2001. Regulation and mechanism of action of the small heat shock protein from the hyperthermophilic archaeon Pyrococcus fu-riosus. J. Bacteriol. 183: 51985202.
59. Laksanalamai, P.,, T. A. Whitehead, and, F. T. Robb. 2004. Minimal protein-folding systems in hyperthermophilic archaea. Nat. Rev. Microbiol. 2: 315324.
60. Lange, U., and, W. Hausner. 2004. Transcriptional fidelity and proofreading in Archaea and implications for the mechanism of TFS-induced RNA cleavage. Mol. Microbiol. 52: 11331143.
61. Langer, D.,, J. Hain,, P. Thuriaux, and, W. Zillig. 1995. Transcription in Archaea: Similarity to that in Eukarya. Proc. Natl. Acad. Sci. USA 92: 57685772.
62. Lee, S. J.,, A. Engelmann,, R. Horlacher,, Q. Qu,, G. Vierke,, C. Hebbeln,, M. Thomm, and, W. Boos. 2003. TrmB, a sugar-specific transcriptional regulator of the trehalose/maltose ABC transporter from the hyperthermophilic archaeon Thermococcus litoralis. J. Biol. Chem. 278: 983990.
63. Lee, S. J.,, C. Moulakakis,, W. Hausner,, S. M. Koning,, M. Thomm, and, W Boos. 2005. TrmB, a sugar sensing regulator of ABC transporter genes in Pyrococcus furiosus exhibits dual promoter specificity and is controlled by different inducers. Mol. Microbiol. 57: 17971807.
64. Leonard, P. M.,, S. H. J. Smits,, S. E. Sedelnikova,, A. B. Brinkman,, W. M. de Vos,, J. Van der Oost,, D. W. Rice, and, J. B. Rafferty. 2001. Crystal structure of the Lrp-like transcription regulator from the archaeon Pyrococcus furiosus. EMBO J. 20: 990997.
65. Lie, T. J., and, J. A. Leigh. 2003. A novel repressor of nif and ginA expression in the methanogenic archaeon Methanococcus maripaludis. Mol. Microbiol. 47: 235246.
66. Lie, T. J.,, G. E. Wood, and, J. A. Leigh. 2005. Regulation of nif expression in Methanococcus maripaludis. J. Biol. Chem. 200: 52365241.
67. Lim, J.,, T. Thomas, and, R. Cavicchioli. 2000. Low temperature regulated DEAD-box RNA helicase from the Antarctic archaeon, Methanococcoides burtonii. J. Mol. Biol. 297: 553567.
68. Macario, A. J. L., and, E. Conway de Macario. 2001. The molecular chaperone system and other anti-stress mechanisms in archaea. Front. Biosci. 6: 262283.
69. Magilli, C. P.,, S. P. Jackson, and, S. D. Bell. 2001. Identification of a conserved archaeal RNA polymerase subunit contacted by the basal transcription factor TFB. J. Biol. Chem. 276: 4669346696.
70. Marsh, T. L.,, C. I. Reich,, R. B. Whitelock, and, G. J. Olsen. 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: 41804184.
71. Martin, W., and, M. Müller. 1998. The hydrogen hypothesis for the first eukaryote. Nature 392: 3741.
72. Matsuda, T.,, M. Fujikawa,, S. Ezaki,, T. Imanaka,, M. Morikawa, and, S. Kanaya. 2001. Interaction of TIP26 from a hyperthermophilic archaeon with TFB/TBP/DNA ternary complex. Extremophiles 5: 177182.
73. Matsunaga, F.,, P. Forterre,, Y. Ishino, and, H. Myllykallio. 2001. In vivo interactions of archaeal Cdc6/Orc1 and minichromosome maintenance proteins with the replication origin. Proc. Natl. Acad. Sci. USA 98: 1115211157.
74. Meinhart, A.,, J. Blobel, and, P. Cramer. 2003. An extended winged helix domain in general transcription factor E/IIE alpha. J. Biol. Chem. 278: 4826748274.
75. Napoli, A.,, J. van der Oost,, C. W. Sensen,, R. L. Charlebois,, M. Rossi, and, M. Ciaramella. 1999. An Lrp-like protein of the hyperthermophilic archaeon Sulfolobus solfataricus which binds to its own promoter. J. Bacteriol. 181: 14741480.
76. Nikolov, D. B.,, H. Chen,, E. D. Halay,, A. A. Usheva,, K. Hisa-take, and, D. K. Lee. 1995. Crystal structure of a TFIIB-TBP-TATA-element ternary complex. Nature 377: 119128.
77. Nocker, A.,, T. Hausherr,, S. Balsiger,, N.-P. Krstulovic,, H. Hennecke, and, F. Narberhaus.. 2001. A mRNA-based thermosensor controls expression of rhizobial heat shock genes. Nucleic Acids Res. 29: 48004807.
78. Ouhammouch, M.,, R. E. Dewhurst,, W. Hausner,, M. Thomm, and, E. P. Geiduschek. 2003. Activation of archaeal transcription by recruitment of the TATA-binding protein. Proc. Natl. Acad. Sci. USA 100: 50975102.
79. Ouhammouch, M., and, E. P. Geiduschek. 2001. A thermostable platform for transcriptional regulation: the DNA-binding properties of two Lrp homologs from the hyperthermophilic archaeon Methanococcus jannaschii. EMBO J. 20: 146156.
80. Ouhammouch, M.,, G. E. Langham,, W. Hausner,, A. J. Simpson,, N. M. A. El-Sayed, and, E. P. Geiduschek. 2005. Promoter architecture and response to a positive regulator of archaeal transcription. Mol. Microbiol. 56: 625637.
81. Ouhammouch, M.,, F. Werner,, R. O. Weinzierl, and, E. P. Geiduschek. 2004. A fully recombinant system for activator-dependent archaeal transcription. J. Biol. Chem. 279: 5171951721.
82. Ouzounis, C., and, C. Sander. 1992. TFIIB, an evolutionary link between the transcription machineries of archaebacteria and eukaryotes. Cell 71: 189190.
83. Palmer, J. R., and, C. J. Daniels. 1995. In vivo definition of an archaeal promoter. J. Bacteriol. 177: 18441849.
84. Pühler, G.,, H. Leffers,, F. Gropp,, P. Palm,, H. P. Klenk,, F. Lottspeich,, R. A. Garrett, and, W. Zillig. 1989. Archaebacterial DNA-dependent RNA polymerases testify to the evolution of the eukaryotic nuclear genome. Proc. Natl. Acad. Sci. USA 86: 45694573.
85. Qureshi, S. A.,, S. D. Bell, and, S. P. Jackson. 1997 Factor requirements for transcription in the archaeon Sulfolobus shibatae. EMBO J. 16: 29272936.
86. Reeve, J. N. 2003. Archaeal chromatin and transcription. Mol. Microbiol. 48: 587598.
87. Reiter, W. D.,, U. Hüdepohl, and, W. Zillig. 1990. Mutational analysis of an archaebacterial promoter: Essential role of a TATA box for transcription efficiency and start-site selection. Proc. Natl. Acad. Sci. USA 87: 95099513.
88. Reiter, W. D.,, P. Palm, and, W. Zillig. 1988. Analysis of transcription in the archaebacterium Sulfolobus indicates that archaebacterial promoters are homologous to eukaryotic pol II promoters. Nucleic Acids Res. 16: 1119.
89. Renfrow, M. B.,, N. Naryshkin,, L. M. Lewis,, H. T. Chen,, R. M. Ebright, and, R. A. Scott. 2004. Transcription factor B contacts promoter DNA near the transcription start site of the archaeal transcription initiation complex. J. Biol. Chem. 279: 28252831.
90. Richard, D. J.,, S. D. Bell, and, M. F. White. 2004. Physical and functional interaction of the archaeal single-stranded DNA-binding protein SSB with RNA polymerase. Nucleic Acids Res. 32: 10651074.
91. Rowlands, T.,, P. Baumann, and, S. P. Jackson. 1994. The TATA-binding protein: A general transcription factor in Eukaryotes and Archaebacteria. Science 264: 13261329.
92. Schnabel, R.,, M. Thomm,, R. Gerardy-Schahn,, W. Zillig,, K. O. Stetter, and, J. Huet. 1983. Structural homology between different archaebacterial DNA-dependent RNA polymerases analyzed by immunological comparison of their components. EMBO J. 2: 751755.
93. Schut, G. J.,, S. D. Brehm,, S. Datta, and, M. W. Adams. 2003. Whole-genome DNA microarray analysis of a hyperthermophile and an archaeon: Pyrococcus furiosus grown on carbohydrates or peptides. J. Bacteriol. 185: 39353947.
94. Shockley, K. R.,, D. E. Ward,, S. R. Chhabra,, S. B. Conners,, C. I. Montero, and, R. M. Kelly. 2003. Heat shock response by the hyperthermophilic archaeon Pyrococcus furiosus. Appl. Environ. Microbiol. 69: 23652371.
95. Soppa, J. 1999. Normalized nucleotide frequencies allow the definition of archaeal promoter elements for different archaeal groups and reveal base-specific TFB contacts upstream of the TATA box. Mol. Microbiol. 31: 15891601.
96. Soppa, J. 1999. Transcription initiation in Archaea: facts, factors and future aspects. Mol. Microbiol. 31: 12951305.
97. Spitalny, P., and, M. Thomm. 2003. Analysis of the open region and of DNA-protein contacts of archaeal RNA polymerase transcription complexes during transition from initiation to elongation. J. Biol. Chem. 278: 3049730505.
98. Thomm, M.,, W. Hausner, and, C. Hethke. 1994. Transcription factors and termination of transcription in Methanococcus. Syst. Appl. Microbiol. 16: 148155.
99. Thomm, M., and, G. Wich. 1988. An archaebacterial promoter element for stable RNA genes with homology to the TATA box of higher eukaryotes. Nucleic Acids Res. 16: 151163.
100. Thomm, M. 1996. Archaeal transcription factors and their role in transcription initiation. FEMS Microbiol. Rev. 18: 159171.
101. Thomson, D. K.,, J. R. Palmer, and, C. J. Daniels. 1999. Expression and heat-responsive regulation of a TFIB homologue from the archaeon Haloferax volcanii. Mol. Microbiol. 33: 10811092.
102. Torarinsson, E.,, H. P. Klenk, and, R. A. Garrett. 2005. Divergent transcriptional and translational signals in Archaea. Environ. Microbiol. 7: 4754.
103. Trakselis, M. A., and, S. D. Bell. 2004. The loader of the rings. Nature 429: 708709.
104. Vierke, G.,, A. Engelmann,, C. Hebbeln, and, M. Thomm. 2003. A novel archaeal transcriptional regulator of heat shock response. J. Biol. Chem. 278: 1826.
105. Werner, F.,, J. J. Eloranta, and, R. O. Weinzierl. 2000. Archaeal RNA polymerase subunits F and P are bona fide homologs of eukaryotic RPB4 and RPB12. Nucleic Acids Res. 28: 4299305.
106. Werner, F., and, R. O. Weinzierl. 2002. A recombinant RNA polymerase II-like enzyme capable of promoter-specific transcription. Mol. Cell 10: 635646.
107. Werner, F., and, R. O. Weinzierl. 2005. Direct modulation of RNA polymerase core functions by basal transcription factors. Mol. Cell. Biol. 25: 83448355.
108. Wettach, J.,, H. P. Gohl,, H. Tschochner, and, M. Thomm. 1995. Functional interaction of yeast and human TATA-binding proteins with an archaeal RNA polymerase and promoter. Proc. Natl. Acad. Sci. USA 92: 472476.
109. Wich, G.,, H. Hummel,, M. Jarsch,, U. Bär, and, A. Böck. 1986. Transcription signals for stable RNA genes in Methanococcus. Nucleic Acids Res. 14: 24472479.
110. Xie, Y., and, J. N. Reeve. 2004. Transcription by Methanothermobacter thermoautotrophicus RNA polymerase in vitro releases archaeal transcription factor B but not TATA-box binding protein from the template DNA. J. Bacteriol. 186: 63066310.
111. Xie, Y., and, J. N. Reeve. 2005. Regulation of tryptophan operon expression in the archaeon Methanothermobacter thermautotrophicus. J. Bacteriol. 187: 64196429.
112. Yanofsky, C. 2003. Using studies of tryptophan metabolism to answer basic biology questions. J. Biol. Chem. 278: 1085910878.
113. Zhu, W.,, Q. Zeng,, C. M. Colangelo,, M. Lewis,, M. F. Summers, and, R. A. Scott. 1996. The N-terminal domain of TFIIB from Pyrococcus furiosus forms a zinc ribbon. Nat. Struct. Biol. 3: 122124.
114. Zillig, W.,, K. O. Stetter,, R. Schnabel,, J. Madon, and, A. Gierl. 1982. Transcription in Archaebacteria. Zbl. Bakt. Hyg., I. Abt. Orig. C 3: 218227.

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