Direct tests of the energetic basis of abortive cycling in transcription

Biochemistry

Volumn 50, Issue 32, 2011, Pages 7015-7022

  Vahia, Ankit V ^a   Martin, Craig T ^a  

^a UNIVERSITY OF MASSACHUSETTS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA-TEMPLATE; DRIVING FORCES; MECHANISTIC MODELS; N-TERMINAL DOMAINS; RNA POLYMERASE; STABLE PROCESS; STERIC BULK; STRUCTURAL CHANGE; STRUCTURAL DATA;

DNA; RNA; STABILITY CRITERIA;

TRANSCRIPTION;

RNA POLYMERASE;

AMINO TERMINAL SEQUENCE; ARTICLE; BIOENERGY; DNA FLANKING REGION; DNA TEMPLATE; GENETIC TRANSCRIPTION; GENOMIC INSTABILITY; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; TRANSCRIPTION REGULATION; TRANSCRIPTION TERMINATION;

BASE SEQUENCE; DNA; DNA-DIRECTED RNA POLYMERASES; TRANSCRIPTION, GENETIC; VIRAL PROTEINS;

EID: 80051494401     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi200620q     Document Type: Article

References (31)

1. Carpousis, A. J. and Gralla, J. D. (1980) Cycling of ribonucleic acid polymerase to produce oligonucleotides during initiation in vitro at the lac UV5 promoter Biochemistry 19, 3245-3253
2. Carpousis, A. J. and Gralla, J. D. (1985) Interaction of RNA polymerase with lacUV5 promoter DNA during mRNA initiation and elongation. Footprinting, methylation, and rifampicin-sensitivity changes accompanying transcription initiation J. Mol. Biol. 183, 165-177 (Pubitemid 16083736)
3. Jin, D. J. and Turnbough, C. L., Jr. (1994) An Escherichia coli RNA polymerase defective in transcription due to its overproduction of abortive initiation products J. Mol. Biol. 236, 72-80 (Pubitemid 24148948)
4. Goldman, S. R., Ebright, R. H., and Nickels, B. E. (2009) Direct detection of abortive RNA transcripts in vivo Science 324, 927-928
5. Straney, D. C. and Crothers, D. M. (1987) A stressed intermediate in the formation of stably initiated RNA chains at the Escherichia coli lac UV5 promoter J. Mol. Biol. 193, 267-278 (Pubitemid 17025714)
6. Cheetham, G. M. and Steitz, T. A. (1999) Structure of a transcribing T7 RNA polymerase initiation complex Science 286, 2305-2309 (Pubitemid 30016883)
7. Durniak, K. J., Bailey, S., and Steitz, T. A. (2008) The structure of a transcribing T7 RNA polymerase in transition from initiation to elongation Science 322, 553-557
8. Tang, G. Q., Roy, R., Ha, T., and Patel, S. S. (2008) Transcription initiation in a single-subunit RNA polymerase proceeds through DNA scrunching and rotation of the N-terminal subdomains Mol. Cell 30, 567-577 (Pubitemid 351755060)
9. Kapanidis, A. N., Margeat, E., Ho, S. O., Kortkhonjia, E., Weiss, S., and Ebright, R. H. (2006) Initial transcription by RNA polymerase proceeds through a DNA-scrunching mechanism Science 314, 1144-1147 (Pubitemid 44789044)
10. Revyakin, A., Liu, C., Ebright, R. H., and Strick, T. R. (2006) Abortive initiation and productive initiation by RNA polymerase involve DNA scrunching Science 314, 1139-1143 (Pubitemid 44789043)
11. Cheetham, G. M., Jeruzalmi, D., and Steitz, T. A. (1998) Transcription regulation, initiation, and "DNA scrunching" by T7 RNA polymerase Cold Spring Harb. Symp. Quant. Biol. 63, 263-267 (Pubitemid 29282170)
12. Brieba, L. G. and Sousa, R. (2001) T7 promoter release mediated by DNA scrunching EMBO J. 20, 6826-6835 (Pubitemid 33134212)
13. Liu, C. and Martin, C. T. (2002) Promoter clearance by T7 RNA polymerase. Initial bubble collapse and transcript dissociation monitored by base analog fluorescence J. Biol. Chem. 277, 2725-2731 (Pubitemid 34953301)
14. Cheetham, G. M., Jeruzalmi, D., and Steitz, T. A. (1999) Structural basis for initiation of transcription from an RNA polymerase- promoter complex Nature 399, 80-83
15. Turingan, R. S., Theis, K., and Martin, C. T. (2007) Twisted or shifted? Fluorescence measurements of late intermediates in transcription initiation by T7 RNA polymerase Biochemistry 46, 6165-6168 (Pubitemid 46842860)
16. Gong, P., Esposito, E. A., and Martin, C. T. (2004) Initial bubble collapse plays a key role in the transition to elongation in T7 RNA polymerase J. Biol. Chem. 279, 44277-44285 (Pubitemid 39430831)
17. Zhou, Y. and Martin, C. T. (2006) Observed instability of T7 RNA polymerase elongation complexes can be dominated by collision-induced "bumping J. Biol. Chem. 281, 24441-24448 (Pubitemid 44274217)
18. Martin, C. T., Muller, D. K., and Coleman, J. E. (1988) Processivity in early stages of transcription by T7 RNA polymerase Biochemistry 27, 3966-3974
19. Újvári, A. and Martin, C. T. (1997) Identification of a minimal binding element within the T7 RNA polymerase promoter J. Mol. Biol. 273, 775-781 (Pubitemid 27493717)
20. Kuzmine, I. and Martin, C. T. (2001) Pre-steady-state Kinetics of Initiation of Transcription by T7 RNA Polymerase: A New Kinetic Model J. Mol. Biol. 305, 559-566 (Pubitemid 33032861)
21. Martin, C. T., Esposito, E. A., Theis, K., and Gong, P. (2005) Structure and Function in Promoter Escape by T7 RNA Polymerase Prog. Nucleic Acid Res. Mol. Biol. 80, 323-347 (Pubitemid 43574892)
22. Weston, B. F., Kuzmine, I., and Martin, C. T. (1997) Positioning of the start site in the initiation of transcription by bacteriophage T7 RNA polymerase J. Mol. Biol. 272, 21-30 (Pubitemid 27395534)
23. Kuzmine, I., Gottlieb, P. A., and Martin, C. T. (2003) Binding of the priming nucleotide in the initiation of transcription by t7 RNA polymerase J. Biol. Chem. 278, 2819-2823 (Pubitemid 36801184)
24. Jiang, M., Rong, M., Martin, C., and McAllister, W. T. (2001) Interrupting the template strand of the T7 promoter facilitates translocation of the DNA during initiation, reducing transcript slippage and the release of abortive products J. Mol. Biol. 310, 509-522 (Pubitemid 32692565)
25. Margeat, E., Kapanidis, A. N., Tinnefeld, P., Wang, Y., Mukhopadhyay, J., Ebright, R. H., and Weiss, S. (2006) Direct observation of abortive initiation and promoter escape within single immobilized transcription complexes Biophys. J. 90, 1419-1431
26. Ikeda, R. A. and Richardson, C. C. (1986) Interactions of the RNA polymerase of bacteriophage T7 with its promoter during binding and initiation of transcription Proc. Natl. Acad. Sci. U. S. A. 83, 3614-3618 (Pubitemid 16062335)
27. Guillerez, J., Lopez, P. J., Proux, F., Launay, H., and Dreyfus, M. (2005) A mutation in T7 RNA polymerase that facilitates promoter clearance Proc. Natl. Acad. Sci. U. S. A. 102, 5958-5963 (Pubitemid 40594237)
28. Tang, G. Q., Roy, R., Bandwar, R. P., Ha, T., and Patel, S. S. (2009) Real-time observation of the transition from transcription initiation to elongation of the RNA polymerase Proc. Natl. Acad. Sci. U. S. A. 106, 22175-22180
29. Liu, X. and Martin, C. T. (2009) Transcription elongation complex stability: the topological lock J. Biol. Chem. 284, 36262-36270
30. von Hippel, P. H. (1998) An integrated model of the transcription complex in elongation, termination, and editing Science 281, 660-665 (Pubitemid 28387269)
31. von Hippel, P. H. and Yager, T. D. (1991) Transcript elongation and termination are competitive kinetic processes Proc. Natl. Acad. Sci. U. S. A. 88, 2307-2311 (Pubitemid 21916405)