Archaeal intrinsic transcription termination in vivo

Journal of Bacteriology

Volumn 191, Issue 22, 2009, Pages 7102-7108

  Santangelo, Thomas J ^a   Cubonová, L'Ubomíra ^a   Skinner, Katherine M ^a   Reeve, John N ^a  

^a OHIO STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

SPACER DNA;

ARTICLE; CONTROLLED STUDY; DNA SEQUENCE; GENE AMPLIFICATION; IN VITRO STUDY; IN VIVO STUDY; INVERTED REPEAT; NONHUMAN; PLASMID; PRIORITY JOURNAL; REPORTER GENE; TATA BOX; THERMOCOCCUS; THERMOCOCCUS KODAKARENSIS; TRANSCRIPTION TERMINATION;

ARCHAEA; ARCHAEAL PROTEINS; GENE EXPRESSION REGULATION, ARCHAEAL; PROMOTER REGIONS, GENETIC; TERMINATOR REGIONS, GENETIC; TRANSCRIPTION, GENETIC;

ARCHAEA; BACTERIA (MICROORGANISMS); THERMOCOCCUS KODAKARENSIS;

EID: 70350459843     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/JB.00982-09     Document Type: Article

References (51)

1. Artsimovitch, I., and R. Landick. 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. (Pubitemid 28469311)
2. Artsimovitch, I., and R. Landick. 2000. Pausing by bacterial RNA polymerase is mediated by mechanistically distinct classes of signals. Proc. Natl. Acad. Sci. USA 97:7090-7095.
3. Bartlett, M. S. 2005. Determinants of transcription initiation by archaeal RNA polymerase. Curr. Opin. Microbiol. 8:677-684.
4. Braglia, P., R. Percudani, and G. Dieci. 2005. Sequence context effects on oligo(dT) termination signal recognition by Saccharomyces cerevisiae RNA polymerase III. J. Biol. Chem. 280:19551-19562.
5. Cavicchioli, R. (ed.). 2007. Archaea. Molecular and cellular biology. ASM Press, Washington, DC.
6. Core, L. J., and J. T. Lis. 2008. Transcription regulation through promoter-proximal pausing of RNA polymerase II. Science 319:1791-1792.
7. Datta, K., and P. H. von Hippel. 2008. Direct spectroscopic study of reconstituted transcription complexes reveals that intrinsic termination is driven primarily by thermodynamic destabilization of the nucleic acid framework. J. Biol. Chem. 283:3537-3549.
8. El Hage, A., M. Koper, J. Kufel, and D. Tollervey. 2008. Efficient termination of transcription by RNA polymerase I requires the 5′ exonuclease Rat1 in yeast. Genes Dev. 22:1069-1081. (Pubitemid 351544244)
9. Epshtein, V., C. J. Cardinale, A. E. Ruckenstein, S. Borukhov, and E. Nudler. 2007. An allosteric path to transcription termination. Mol. Cell 28:991-1001.
10. French, S. L., T. J. Santangelo, A. L. Beyer, and J. N. Reeve. 2007. Transcription and translation are coupled in Archaea. Mol. Biol. Evol. 24:893-895.
11. Fukui, T., H. Atomi, T. Kanai, R. Matsumi, S. Fujiwara, and T. Imanaka. 2005. Complete genome sequence of the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 and comparison with Pyrococcus genomes. Genome Res. 15:352-363. (Pubitemid 40467776)
12. Garrett, R. A., and H.-P. Klenk. 2007. Archaea. Evolution, physiology, and molecular biology. Blackwell Publishing, Oxford, United Kingdom.
13. Geiduschek, E. P., and M. Ouhammouch. 2005. Archaeal transcription and its regulators. Mol. Microbiol. 56:1397-1407.
14. Gilmour, D. S., and R. Fan. 2008. Derailing the locomotive: transcription termination. J. Biol. Chem. 283:661-664.
15. 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. 281:30581-30592.
16. Grundy, F. J., and T. M. Henkin. 2006. From ribosome to riboswitch: control of gene expression in bacteria by RNA structural rearrangements. Crit. Rev. Biochem. Mol. Biol. 41:329-338.
17. Gusarov, I., and E. Nudler. 1999. The mechanism of intrinsic transcription termination. Mol. Cell 3:495-504.
18. Henkin, T. M. 2008. Riboswitch RNAs: using RNA to sense cellular metabolism. Genes Dev. 22:3383-3390.
19. Hirata, A., B. J. Klein, and K. S. Murakami. 2008. The X-ray crystal structure of RNA polymerase from Archaea. Nature 451:851-854. (Pubitemid 351253162)
20. Kashlev, M., and N. Komissarova. 2002. Transcription termination: primary intermediates and secondary adducts. J. Biol. Chem. 277:14501-14508.
21. Kawauchi, J., H. Mischo, P. Braglia, A. Rondon, and N. J. Proudfoot. 2008. Budding yeast RNA polymerases I and II employ parallel mechanisms of transcriptional termination. Genes Dev. 22:1082-1092. (Pubitemid 351544245)
22. Koide, T., D. J. Reiss, J. C. Bare, W. L. Pang, M. T. Facciotti, A. K. Schmid, M. Pan, B. Marzolf, P. T. Van, F. Y. Lo, A. Pratap, E. W. Deutsch, A. Peterson, D. Martin, and N. S. Baliga. 2009. Prevalence of transcription promoters within archaeal operons and coding sequences. Mol. Syst. Biol. 5:285.
23. Komissarova, N., J. Becker, S. Solter, M. Kireeva, and M. Kashlev. 2002. Shortening of RNA:DNA hybrid in the elongation complex of RNA polymerase is a prerequisite for transcription termination. Mol. Cell 10:1151-1162. (Pubitemid 35453832)
24. Korkhin, Y., U. M. Unligil, O. Littlefield, P. J. Nelson, D. I. Stuart, P. B. Sigler, S. D. Bell, and N. G. Abrescia. 2009. Evolution of complex RNA polymerases: the complete archaeal RNA polymerase structure. PLoS Biol. 7:e102.
25. Kusser, A. G., M. G. Bertero, S. Naji, T. Becker, M. Thomm, R. Beckmann, and P. Cramer. 2008. Structure of an archaeal RNA polymerase. J. Mol. Biol. 376:303-307.
26. Landrieux, E., N. Alic, C. Ducrot, J. Acker, M. Riva, and C. Carles. 2006. A subcomplex of RNA polymerase III subunits involved in transcription termination and reinitiation. EMBO J. 25:118-128. (Pubitemid 43077301)
27. Merino, E., and C. Yanofsky. 2005. Transcription attenuation: a highly conserved regulatory strategy used by bacteria. Trends Genet. 21:260-264. (Pubitemid 40558929)
28. Mooney, R. A., I. Artsimovitch, and R. Landick. 1998. Information processing by RNA polymerase: recognition of regulatory signals during RNA chain elongation. J. Bacteriol. 180:3265-3275.
29. Naji, S., M. G. Bertero, P. Spitalny, P. Cramer, and M. Thomm. 2008. Structure-function analysis of the RNA polymerase cleft loops elucidates initial transcription, DNA unwinding and RNA displacement. Nucleic Acids Res. 36:676-687. (Pubitemid 351250457)
30. Nudler, E., and M. E. Gottesman. 2002. Transcription termination and anti-termination in E. coli. Genes Cells 7:755-768.
31. Pihl, T. D., S. Sharma, and J. N. Reeve. 1994. Growth phase-dependent transcription of the genes that encode the two methyl coenzyme M reductase isoenzymes and N5-methyltetrahydromethanopterin:coenzyme M methyltransferase in Methanobacterium thermoautotrophicum ΔH. J. Bacteriol. 176:6384-6391.
32. Reynolds, R., R. M. Bermúdez-Cruz, and M. J. Chamberlin. 1992. Parameters affecting transcription termination by Escherichia coli RNA polymerase. I. Analysis of 13 rho-independent terminators. J. Mol. Biol. 224:31-51.
33. Santangelo, T. J., L. Cubonová, 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.
34. Santangelo, T. J., L. Cubonová, R. Matsumi, H. Atomi, T. Imanaka, and J. N. Reeve. 2008. Polarity in archaeal operon transcription in Thermococcus kodakaraensis. J. Bacteriol. 190:2244-2248.
35. Santangelo, T. J., L. Cubonová, and J. N. Reeve. 2008. Shuttle vector expression in Thermococcus kodakaraensis: contributions of cis elements to protein synthesis in a hyperthermophilic archaeon. Appl. Environ. Microbiol. 74:3099-3104.
36. Santangelo, T. J., and J. N. Reeve. 2006. Archaeal RNA polymerase is sensitive to intrinsic termination directed by transcribed and remote sequences. J. Mol. Biol. 355:196-210.
37. Santangelo, T. J., and J. W. Roberts. 2004. Forward translocation is the natural pathway of RNA release at an intrinsic terminator. Mol. Cell 14:117-126.
38. Sato, T., T. Fukui, H. Atomi, and T. Imanaka. 2005. Improved and versatile transformation system allowing multiple genetic manipulations of the hyperthermophilic archaeon Thermococcus kodakaraensis. Appl. Environ. Microbiol. 71:3889-3899. (Pubitemid 40980560)
39. Sato, T., T. Fukui, H. Atomi, and T. Imanaka. 2003. Targeted gene disruption by homologous recombination in the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1. J. Bacteriol. 185:210-220.
40. 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. 278:30497-30505.
41. Spitalny, P., and M. Thomm. 2008. A polymerase III-like reinitiation mechanism is operating in regulation of histone expression in Archaea. Mol. Microbiol. 67:958-970. (Pubitemid 351207327)
42. Telesnitsky, A., and M. J. Chamberlin. 1989. Terminator-distal sequences determine the in vitro efficiency of the early terminators of bacteriophages T3 and T7. Biochemistry 28:5210-5218.
43. Thomm, M., W. Hausner, and C. Hethke. 1994. Transcription factors and termination of transcription in Methanococcus. Syst. Appl. Microbiol. 16:648-655.
44. Toulokhonov, I., I. Artsimovitch, and R. Landick. 2001. Allosteric control of RNA polymerase by a site that contacts nascent RNA hairpins. Science 292:730-733. (Pubitemid 32385544)
45. Unniraman, S., R. Prakash, and V. Nagaraja. 2002. Conserved economics of transcription termination in eubacteria. Nucleic Acids Res. 30:675-684. (Pubitemid 34679632)
46. Uptain, S. M., C. M. Kane, and M. J. Chamberlin. 1997. Basic mechanisms of transcript elongation and its regulation. Annu. Rev. Biochem. 66:117-172.
47. Washio, T., J. Sasayama, and M. Tomita. 1998. Analysis of complete genomes suggests that many prokaryotes do not rely on hairpin formation in transcription termination. Nucleic Acids Res. 26:5456-5463. (Pubitemid 28542748)
48. Werner, F. 2008. Structural evolution of multisubunit RNA polymerases. Trends Microbiol. 16:247-250.
49. West, S., N. J. Proudfoot, and M. J. Dye. 2008. Molecular dissection of mammalian RNA polymerase II transcriptional termination. Mol. Cell 29:600-610.
50. Yarnell, W. S., and J. W. Roberts. 1999. Mechanism of intrinsic transcription termination and antitermination. Science 284:611-615. (Pubitemid 29289580)
51. Zhou, Y., D. M. Navaroli, M. S. Enuameh, and C. T. Martin. 2007. Dissociation of halted T7 RNA polymerase elongation complexes proceeds via a forward-translocation mechanism. Proc. Natl. Acad. Sci. USA 104:10352-10357.