A polymerase III-like reinitiation mechanism is operating in regulation of histone expression in archaea

Molecular Microbiology

Volumn 67, Issue 5, 2008, Pages 958-970

  Spitalny, Patrizia ^a   Thomm, Michael ^a  

^a UNIVERSITY OF REGENSBURG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

DNA DIRECTED RNA POLYMERASE III; HISTONE;

ARCHAEBACTERIUM; ARTICLE; GENE; NONHUMAN; PRIORITY JOURNAL; PROTEIN EXPRESSION; PYROCOCCUS FURIOSUS;

ARCHAEA; ARCHAEAL PROTEINS; BASE SEQUENCE; DNA-DIRECTED RNA POLYMERASES; GENE EXPRESSION REGULATION, ARCHAEAL; HISTONES; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; PROMOTER REGIONS (GENETICS); PYROCOCCUS FURIOSUS; RNA POLYMERASE III; RNA, ARCHAEAL; SEQUENCE ALIGNMENT; TEMPERATURE; TERMINATOR REGIONS (GENETICS); TRANSCRIPTION INITIATION SITE; TRANSCRIPTION, GENETIC;

ARCHAEA; PYROCOCCUS FURIOSUS;

EID: 38849140302     PISSN: 0950382X     EISSN: 13652958     Source Type: Journal    
DOI: 10.1111/j.1365-2958.2007.06084.x     Document Type: Article

References (44)

1. Tyr gene. EMBO J 4 : 2657 2664.
2. Artsimovitch, I. Landick, R. (1998) Interaction of a nascent RNA structure with RNA polymerase is required for hairpin-dependent transcriptional pausing but not for transcript release. Genes Dev 12 : 3110 3122.
3. Bell, S.D. Jackson, S.P. (2001) Mechanism and regulation of transcription in archaea. Curr Opin Microbiol 4 : 208 213.
4. Bell, S.D., Brinkman, A.B., van der Oost, J. Jackson, S.P. (2001) The archaeal TFIIEalpha homologue facilitates transcription initiation by enhancing TATA-box recognition. EMBO Rep 2 : 133 138.
5. Bogenhagen, D.F. Brown, D.D. (1981) Nucleotide sequences in Xenopus 5S DNA required for transcription termination. Cell 24 : 261 270.
6. Braglia, P., Rercudani, R. Dieci, G. (2005) Sequence context effects on oligo(dT) termination signal recognition by Saccharomyces cerevisiae RNA polymerase III. J Biol Chem 280 : 19551 19562.
7. Brown, J.D., Daniels, C. Reeve, J.N. (1989) Gene structure, organization and expression in archaebacteria. Crit Rev Microbiol 16 : 287 338.
8. Campbell, F.E. Setzer, D.R. (1992) Transcription termination by RNA polymerase III: uncoupling of polymerase release from termination signal recognition. Mol Cell Biol 12 : 2260 2272.
9. Chu, W.-M., Ballard, R.E. Schmid, C.W. (1997) Palindromic sequences preceding the terminator increase polymerase III template activity. Nucleic Acids Res 25 : 2077 2082.
10. Cozzarelli, N.R., Gerrard, S.P., Schlissel, M., Brown, D.D. Bogenhagen, D.F. (1983) Purified RNA polymerase III accurately and efficiently terminates transcription of 5S RNA genes. Cell 34 : 829 835.
11. Dieci, G. Sentenac, A. (1996) Facilitated recycling pathway for RNA polymerase III. Cell 84 : 245 252.
12. Dieci, G. Sentenac, A. (2003) Detours and shortcuts to transcription reinitiation. Trends Biochem Sci 28 : 202 209.
13. Ederth, J., Artisimovitch, I., Isaksson, L.A. Landick, R. (2002) The downstream DNA jaw of bacterial RNA polymerase facilitates both transcriptional initiation and pausing. J Biol Chem 277 : 37456 37463.
14. Fiala, G. Stetter, K.O. (1986) Pyrococcus furiosus sp. Nov represents a novel genus of marine heterotrophic archaebacteria growing optimally at 100°C. Arch Microbiol 145 : 56 61.
15. Geiduschek, E.P. Kassavetis, G.A. (1992) RNA polymerase III transcription complexes. In Transcription Regulation. McKnight, S.L. Yamamoti, K.R. (eds). Cold Spring Harbor, NY : Cold Spring Harbor Laboratory Press, pp. 247 280.
16. Geiduschek, E.P. Ouhammouch, M. (2005) Archaeal transcription and its regulators. Mol Microbiol 56 : 1397 1407.
17. Gelfand, M.S., Koonin, E.V. Mironov, A.A. (2000) Prediction of transcription regulatory sites in archaea by a comparative genomic approach. Nucleic Acids Res 28 : 695 705.
18. Grünberg, S., Bartlett, M.S., Naji, S. Thomm, M. (2007) Transcription factor E is a part of transcription elongation complexes. J Biol Chem 282 : 35482 35490. doi:10.1074/jbs.M707371200
19. Gunnery, S. Mathews, M.B. (1995) Functional mRNA can be generated by RNA polymerase III. Mol Cell Biol 15 : 3597 3607.
20. Gunnery, S., Ma, Y. Mathews, M.B. (1999) Termination sequence requirements vary among genes transcribed by RNA polymerase III. J Mol Biol 286 : 745 757.
21. Hamada, M., Sakulich, A.L., Boduru, S.B. Marain, R.J. (2000) Transcription termination by RNA polymerase III in fission yeast. J Biol Chem 275 : 29076 29081.
22. Hanzelka, B.L., Darcy, T.J. Reeve, J.N. (2001) TFE, an archaeal transcription factor in Methanobacterium thermoautotrophicum related to eucaryal transcription factor TFIIEalpha. J Bacteriol 183 : 1813 1818.
23. Hethke, C. (1997) Aufstellung und Charakterisierung eines zellfreien Transkriptionssystems für das hyperthermophile Archaebakterium Pyrococcus furiosus. PhD Thesis, University of Kiel, Kiel.
24. Hethke, C., Geerling, A.C.M., Hausner, W., de Vos, W. Thomm, M. (1996) A cell-free transcription system for the hyperthermophilic Archaeon Pyrococcus furiosus. Nucleic Acids Res 24 : 2369 2376.
25. Hethke, C., Bergerat, A., Hausner, W., Forterre, P. Thomm, M. (1999) Cell-free transcription at 95: thermostability of transcriptional components and DNA topology requirements of Pyrococcus transcription. Genetics 152 : 1325 1333.
26. Kassavetis, G.A., Riggs, D.L., Negri, R., Nguyen, L.H. Geiduschek, E.P. (1989) Transcription factor IIIB generates extended DNA interactions in RNA polymerase III transcription complexes on tRNA genes. Mol Cell Biol 9 : 2551 2566.
27. Lee, D.N., Phung, L., Stewart, J. Landick, R. (1990) Transcription pausing by Escherichia coli RNA polymerase is modulated by downstream DNA sequences. J Biol Chem 265 : 15145 15153.
28. Matsuzaki, H., Kassavetis, G.A. Geiduscheck, E.P. (1994) Analysis of RNA chain elongation and termination by Saccharomyces cerevisiae RNA polymerase III. J Mol Biol 235 : 1173 1192.
29. Naji, S., Grünberg, S. Thomm, M. (2007) The RPB7 orthologue E' is required for transcriptional activity of a reconstituted archaeal core enzyme at low temperatures and stimulates open complex formation. J Biol Chem 282 : 11047 11057.
30. Naryshkina, T., Kuznedelov, K. Severinov, K. (2006) The role of the largest RNA polymerase subunit lid element in preventing the formation of extended RNA-DNA hybrid. J Mol Biol 361 : 634 643.
31. Palangat, M., Hittinger, C.T. Landick, R. (2004) Downstream DNA selectively affects a paused conformation of human RNA polymerase II. J Mol Biol 341 : 429 442.
32. Reiter, W.D., Palm, P. Zillig, W. (1988) Transcription termination in the archaebacterium Sulfolobus: signal structures and linkage to transcription initiation. Nucleic Acids Res 16 : 12445 12459.
33. Reynolds, R. Chamberlin, M.J. (1992) Parameters affecting transcription termination by Escherichia coli RNA. J Mol Biol 224 : 53 63.
34. Santangelo, T.J. Reeve, J.N. (2006) Archaeal RNA polymerase is sensitive to intrinsic termination directed by transcribed and remote sequences. J Mol Biol 355 : 196 210.
35. Santangelo, T.J. Roberts, J.W. (2004) Forward translocation is the natural pathway of RNA release at an intrinsic terminator. Mol Cell 14 : 117 126.
36. Spitalny, P. Thomm, M. (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 : 30497 30505.
37. Thomm, M. (2007) Transcription: mechanism and regulation. In Archaea Molecular and Cellular Biology. Cavicchioli, R. (ed.). Washington, DC : American Society for Microbiology Press, Chapter 6, 139 157.
38. Thomm, M., Hausner, W. Hethke, C. (1994) Transcription factors and termination of transcription in Methanococcus. Syst Appl Microbiol 16 : 148 155.
39. Wang, D., Severinov, K. Landick, R. (1997) Preferential interaction of the his pause RNA hairpin with RNA polymerase β subunit residues 904-950 correlates with strong transcriptional pausing. Proc Natl Acad Sci USA 94 : 8433 8438.
40. Werner, F. Weinzierl, R.O. (2005) Direct modulation of RNA polymerase core functions by basal transcription fabors. Mol Cell Biol 25 : 8344 8355.
41. Wilson, K.S. von Hippel, P.H. (1995) Transcription termination at intrinsic terminators: the role of the RNA hairpin. Proc Natl Acad Sci USA 92 : 8793 8797.
42. Wolffe, A.P., Jordan, E. Brown, D.D. (1986) A bacteriophage RNA polymerase transcribes through a Xenopus 5S RNA gene transcription complex without disrupting it. Cell 44 : 381 389.
43. Yarnell, W.S. Roberts, J.W. (1999) Mechanism of intrinsic transcription termination and antitermination. Science 284 : 611 615.
44. Yin, H., Artsimovitch, I., Landick, R. Gelles, J. (1999) None-equilibrium mechanism of transcription termination from observations of single RNA polymerase molecules. Proc Natl Acad Sci USA 96 : 13124 13129.