Direct observation of abortive initiation and promoter escape within single immobilized transcription complexes

Biophysical Journal

Volumn 90, Issue 4, 2006, Pages 1419-1431

  Margeat, Emmanuel ^a,c   Kapanidis, Achillefs N ^a,d   Tinnefeld, Philip ^a,e   Wang, You ^a   Mukhopadhyay, Jayanta ^b   Ebright, Richard H ^b   Weiss, Shimon ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b RUTGERS UNIVERSITY   (United States)

^c CENTRE DE BIOCHIMIE STRUCTURALE   (France)

^d UNIVERSITY OF OXFORD   (United Kingdom)

^e BIELEFELD UNIVERSITY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; FLUORESCENT DYE; RIBONUCLEOSIDE DERIVATIVE; RIBONUCLEOSIDE TRIPHOSPHATE; RNA POLYMERASE; UNCLASSIFIED DRUG; DNA DIRECTED RNA POLYMERASE;

ARTICLE; CONCENTRATION (PARAMETERS); CONSENSUS; FLUORESCENCE MICROSCOPY; FLUORESCENCE RESONANCE ENERGY TRANSFER; GENETIC TRANSCRIPTION; IMMOBILIZATION; METHODOLOGY; POPULATION DISTRIBUTION; PROMOTER REGION; TRANSCRIPTION INITIATION; GENETICS; METABOLISM; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYSIOLOGY; REGULATORY SEQUENCE; TRANSCRIPTION INITIATION SITE;

BASE SEQUENCE; DNA; DNA-DIRECTED RNA POLYMERASES; FLUORESCENCE RESONANCE ENERGY TRANSFER; MOLECULAR SEQUENCE DATA; PROMOTER REGIONS (GENETICS); REGULATORY SEQUENCES, NUCLEIC ACID; TRANSCRIPTION INITIATION SITE; TRANSCRIPTION, GENETIC;

EID: 33645765585     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.105.069252     Document Type: Article

References (39)

1. Record, M. T. Jr., W. Reznikoff, M. Craig, K. McQuade, and P. Schlax. 1996. Escherichia coli and Salmonella. F. C. Neidhart, editor. ASM Press, Washington, DC.
2. deHaseth, P. L., M. L. Zupancic, and M. T. Record, Jr. 1998. RNA polymerase-promoter interactions: the comings and goings of RNA polymerase. J. Bacteriol. 180:3019-3025.
3. Hsu, L. M. 2002. Promoter clearance and escape in prokaryotes. Biochim. Biophys. Acta. 1577:191-207.
4. Murakami, K. S., and S. A. Darst. 2003. Bacterial RNA polymerases: the wholo story. Curr. Opin. Struct. Biol. 13:31-39.
5. Young, B. A., T. M. Gruber, and C. A. Gross. 2002. Views of transcription initiation. Cell. 109:417-420.
6. Lilley, D. M., and T. J. Wilson. 2000. Fluorescence resonance energy transfer as a structural tool for nucleic acids. Curr. Opin. Chem. Biol. 4:507-517.
7. Kapanidis, A. N., E. Margeat, T. Laurence, S. Doose, S. O. Ho, J. Mukhopadhyay, E. Kortkhonjia, R. Ebright, and S. Weiss. 2005. Retention of transcription initiation factor σ70 in transcription elongation complexes: single molecule analysis. Mol. Cell. 20:347-356.
8. Mukhopadhyay, J., V. Mekler, E. Kortkhonjia, A. N. Kapanidis, Y. W. Ebright, and R. H. Ebright. 2003. Fluorescence resonance energy transfer (FRET) in analysis of transcription-complex structure and function. Methods Enzymol. 371:144-159.
9. Mukhopadhyay, J., A. N. Kapanidis, V. Mekler, E. Kortkhonjia, Y. W. Ebright, and R. H. Ebright. 2001. Translocation of sigma(70) with RNA polymerase during transcription: fluorescence resonance energy transfer assay for movement relative to DNA. Cell. 106:453-463.
10. Nickels, B. E., J. Mukhopadhyay, S. J. Garrity, R. H. Ebright, and A. Hochschild. 2004. The sigma(70) subunit of RNA polymerase mediates a promoter-proximal pause at the lac promoter. Nat. Struct. Mol. Biol. 11:544-550.
11. Travers, A. A., and R. R. Burgess. 1969. Cyclic re-use of the RNA polymerase sigma factor. Nature. 222:537-540.
12. Hansen, U. M., and W. R. McClure. 1980. Role of the sigma subunit of Escherichia coli RNA polymerase in initiation. II. Release of sigma from ternary complexes. J. Biol. Chem. 255:9564-9570.
13. Straney, D. C., and D. M. Crothers. 1985. Intermediates in transcription initiation from the E. coli lac UV5 promoter. Cell. 43:449-459.
14. Krummel, B., and M. J. Chamberlin. 1989. RNA chain initiation by Escherichia coli RNA polymerase. Structural transitions of the enzyme in early ternary complexes. Biochemistry. 28:7829-7842.
15. Metzger, W., P. Schickor, T. Meier, W. Werel, and H. Heumann. 1993. Nucleation of RNA chain formation by Escherichia coli DNA-dependent RNA polymerase. J. Mol. Biol. 232:35-49.
16. Kapanidis, A. N., T. A. Laurence, N. K. Lee, E. Margeat, X. Kong, and S. Weiss. 2005. Alternating-laser excitation of single molecules. Acc. Chem. Res. 37:523-533.
17. Kapanidis, A., N.-K. Lee, T. Laurence, S. Doose, E. Margeat, and S. Weiss. 2004. Fluorescence-aided molecule sorting. Analysis of structure and interactions by alternating laser excitation of single molecules. Proc. Natl. Acad. Sci. USA. 101:8936-8941.
18. Yildiz, A., J. N. Forkey, S. A. McKinney, T. Ha, Y. E. Goldman, and P. R. Selvin. 2003. Myosin V walks hand-over-hand: single fluorophore imaging with 1.5-nm localization. Science. 300:2061-2065.
19. Kinosita, K., H. Itoh, S. Ishiwata, K. Hirano, T. Nishizaka, and T. Hayakawa. 1991. Dual-view microscopy with a single camera: real-time imaging of molecular orientations and calcium. J. Cell Biol. 115:67-73.
20. Lee, N. K., A. N. Kapanidis, Y. Wang, X. Michalet, J. Mukhopadhyay, R. H. Ebright, and S. Weiss. 2005. Accurate FRET measurements within single diffusing biomolecules using alternating-laser excitation. Biophys. J. 88:2939-2943.
21. Mekler, V., E. Kortkhonjia, J. Mukhopadhyay, J. Knight, A. Revyakin, A. N. Kapanidis, W. Niu, Y. W. Ebright, R. Levy, and R. H. Ebright. 2002. Structural organization of bacterial RNA polymerase holoenzyme and the RNA polymerase-promoter open complex. Cell. 108:599-614.
22. Clegg, R. M. 1992. Fluorescence resonance energy transfer and nucleic acids. Methods Enzymol. 211:353-388.
23. Ha, T., I. Rasnik, W. Cheng, H. P. Babcock, G. H. Gauss, T. M. Lohman, and S. Chu. 2002. Initiation and re-initiation of DNA unwinding by the Escherichia coli Rep helicase. Nature. 419:638-641.
24. Zhuang, X., L. E. Bartley, H. P. Babcock, R. Russell, T. Ha, D. Herschlag, and S. Chu. 2000. A single-molecule study of RNA catalysis and folding. Science. 288:2048-2051.
25. Axelrod, D. 2001. Total internal reflection fluorescence microscopy in cell biology. Traffic. 2:764-774.
26. Wu, P., and L. Brand. 1992. Orientation factor in steady-state and time-resolved resonance energy transfer measurements. Biochemistry. 31:7939-7947.
27. Ha, T., A. Y. Ting, J. Liang, A. A. Deniz, D. S. Chemla, P. G. Schultz, and S. Weiss. 1999. Temporal fluctuations of fluorescence resonance energy transfer between two dyes conjugated to a single protein. Chem. Phys. 247:107-118.
28. Rhoades, E., M. Cohen, B. Schuler, and G. Haran. 2004. Two-state folding observed in individual protein molecules. J. Am. Chem. Soc. 126:14686-14687.
29. Blanchard, S. C., R. L. Gonzalez, H. D. Kim, S. Chu, and J. D. Puglisi. 2004. tRNA selection and kinetic proofreading in translation. Nat. Struct. Mol. Biol. 11:1008-1014.
30. 70 subunit of RNA polymerase induces lacUV5 promoter-proximal pausing of transcription. Nat. Struct. Mol. Biol. 11:551-557.
31. Mooney, R. A., and R. Landick. 2003. Tethering sigma70 to RNA polymerase reveals high in vivo activity of sigma factors and sigma 70-dependent pausing at promoter-distal locations. Genes Dev. 17:2839-2851.
32. Gill, S. C., S. E. Weitzel, and P. H. von Hippel. 1991. Escherichia coli sigma 70 and NusA proteins. I. Binding interactions with core RNA polymerase in solution and within the transcription complex. J. Mol. Biol. 220:307-324.
33. Carpousis, A. J., and J. D. Gralla. 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.
34. Carpousis, A. J., and J. D. Gralla. 1980. Cycling of ribonucleic acid polymerase to produce oligonucleotides during initiation in vitro at the lac UV5 promoter. Biochemistry. 19:3245-3253.
35. Ha, T. 2001. Single-molecule fluorescence resonance energy transfer. Methods. 25:78-86.
36. Heilemann, M., E. Margeat, R. Kasper, M. Sauer, and P. Tinnefeld. 2005. Carbocyanine dyes as efficient reversible single-molecule optical switch. J. Am. Chem. Soc. 127:3801-3806.
37. Bates, M., T. R. Blosser, and X. Zhuang. 2005. Short-range spectroscopic ruler based on a single-molecule optical switch. Phys. Rev. Lett. 94:108101.
38. Brieba, L. G., and R. Sousa. 2001. T7 promoter release mediated by DNA scrunching. EMBO J. 20:6826-6835.
39. Jia, Y., and S. S. Patel. 1997. Kinetic mechanism of transcription initiation by bacteriophage T7 RNA polymerase. Biochemistry. 36:4223-4232.