References for Prokaryotic Transcription Cycle

Biochemistry/MCB 568 -- Fall 2007
John W. Little--University of Arizona

Bioc/MCB568 Home Page

 

Note: Most of the links given here are to PubMed pages; from University computers, there should be a link near the top of the page to the article itself. If there is no link, you can usually get there from the Science Library Biochem Journals link. Some links here are to the articles themselves; these can be accessed only from University computers.

Reviews:

Busby, S. and Ebright, R.H. Cell 79:743-746 (1994). "Promoter structure, promoter recognition, and transcription activation in prokaryotes".

deHaseth, P.L., Zupancic, M.L. and Record, M.T. J. Bacteriol. 180:3019-3025 (1998). "RNA polymerase-promoter interactions: the comings and goings of RNA polymerase".

Von Hippel, P. H. Science 281: 660-665 (1998). "Transcription - An integrated model of the transcription complex in elongation, termination, and editing".

Landick, R. Cell 105: 567-570 (2001). "RNA polymerase clamps down."

Darst, S. Curr Opin Struct Biol 2:155-62 (2001). "Bacterial RNA polymerase."

Grieve, S.J. and von Hippel, P.H. Nature Reviews--Molecular and Cellular Biology 6:221-232 (2005). "Thinking quantitatively about transcriptional regulation." Mostly discusses mechanisms of transcription, rather than regulation.

Papers:

Structure of RNA polymerase

Zhang, G.Y., Campbell, E.A., Minakhin, L., Richter, C., Severinov, K., and Darst, S.A. Cell 98, 811-824 (1999). "Crystal structure of Thermus aquaticus core RNA polymerase at 3.3 Å resolution."

Gnatt, A. L., Cramer, P., Fu, J. H., Bushnell, D. A., and Kornberg, R. D. Science 292: 1876-1882 (2001). "Structural basis of transcription: An RNA polymerase II elongation complex at 3.3 Å resolution."

Murakami KS, Masuda S, Darst SA. Science 296: 1280-1284 (2002). "Structural basis of transcription initiation: RNA polymerase holoenzyme at 4 Å resolution."

Murakami KS, Masuda S, Campbell EA, Muzzin O, and Darst SA. Science 296:1285-1290 (2002). "Structural basis of transcription initiation: an RNA polymerase holoenzyme-DNA complex."

Vassylyev, D. G., Vassylyeva, M. N., Zhang, J. et al. Nature 448: 163-168 (2007). Structural basis for substrate loading in bacterial RNA polymerase.

Vassylyev, D. G., Vassylyeva, M. N., Perederina, A., Tahirov, T. H., and Artsimovitch, I. Nature 448: 157-162 (2007). Structural basis for transcription elongation by bacterial RNA polymerase.

Open Complex Formation: Analysis of Binding and Isomerization Steps by tau plots:

McClure, PNAS 77:5634-5638 (1980). "Rate-limiting steps in RNA chain initiation". Describes the method. This method is also described on the class Web site at "Methods/tau plots"

Hawley and McClure, PNAS 77:6381-5 (1980). "In vitro comparison of initiation properties of bacteriophage l wild-type P_R and x3 mutant promoters".

Shih and Gussin, PNAS 80:496-500 (1983). "Mutations affecting two different steps in transcription initiation at the phage l P_RM promoter".

Open Complex Formation--Characterization by KMnO₄ Treatment

Sasse-Dwight S and Gralla JD, J. Biol. Chem. 264:8074-8081 (1989). "KMn0₄ as a probe for lac promoter DNA melting and mechanism in vivo."

Open Complex Formation--Role of sigma⁷⁰

Young, Gruber and Gross, Science 303:1382-1384 (2004). "Minimal machinery of RNA polymerase holoenzyme sufficient for promoter melting." See also commentary on pp. 56--describes several hypotheses for melting and how these experiments support one of the models.

Effects of transcription on DNA supercoiling

Liu and Wang, PNAS 84:7024-7027 (1987). "Supercoiling of the DNA template during transcription".

Wu et al., Cell 53:433-440 (1988). "Transcription generates positively and negatively supercoiled domains in the template".

Transition from initiation to elongation

Roberts, J. W. Science 314: 1097-1098 (2006). "RNA polymerase, a scrunching machine." Minireview of the following two papers.

Kapanidis, A. N., Margeat, E., Ho, S. O. et al. Science 314: 1144-1147 (2006). "Initial transcription by RNA polymerase proceeds through a DNA-scrunching mechanism."

Revyakin, A., Liu, C., Ebright, R. H., and Strick, T. R. Science 314: 1139-1143 (2006). "Abortive initiation and productive initiation by RNA polymerase involve DNA scrunching."

Elongation

Kainz, M. and Roberts, J. Science 255:838-841 (1992). "Structure of transcription elongation complexes in vivo."

Kashlev, M., Nudler, E., Severinov, K. et al. Methods Enzymol. 274: 326-334 (1996). "Histidine-tagged RNA polymerase of Escherichia coli and transcription in solid phase". One of the tools that has made a lot of the recent progress possible.

Komissarova, N. and Kashlev, M. PNAS 94: 1755-1760 (1997). "Transcriptional arrest: Escherichia coli RNA polymerase translocates backward, leaving the 3' end of the RNA intact and extruded".

Komissarova, N. and Kashlev, M. PNAS 95: 14699-14704 (1998). "Functional topography of nascent RNA in elongation intermediates of RNA polymerase".

Sidorenkov, I., Komissarova, N., and Kashlev, M. Mol.Cell. 2: 55-64 (1998). "Crucial role of the RNA:DNA hybrid in the processivity of transcription".

Nudler, E., Mustaev, A., Lukhtanov, E., and Goldfarb, A. Cell 89: 33-41 (1997). "The RNA-DNA hybrid maintains the register of transcription by preventing backtracking of RNA polymerase".

Yarnell, W. S. and Roberts, J. W. Science 284: 611-615 (1999). "Mechanism of intrinsic transcription termination and antitermination".

See also structure papers (Vassylyev et al, 2 papers) above.

Sigma release after initiation

Mukhopadhyay, J., Kapanidis, A. N., Mekler, V. et al. Cell 106: 453-463 (2001). Translocation of s⁷⁰ with RNA polymerase during transcription: Fluorescence resonance energy transfer assay for movement relative to DNA.

Bar-Nahum, G. and Nudler, E. Cell 106: 443-451 (2001). Isolation and characterization of s⁷⁰ -retaining transcription elongation complexes from Escherichia coli.

Mooney,R.A., Darst,S.A., and Landick,R. Molecular Cell 20, 335-345 (2005). "Sigma and RNA Polymerase: An on-Again, off-Again relationship?" A minireview of the following two papers.

Raffaelle,M., Kanin,E.I., Vogt,J., Burgess,R.R., and Ansari,A.Z. Molecular Cell 20: 357-366 (2005). "Holoenzyme switching and stochastic release of sigma factors from RNA polymerase in vivo."

Kapanidis,A.N., et al. Molecular Cell 20, 347-356 (2005). "Retention of transcription initiation factor sigma⁷⁰ in transcription elongation: Single-molecule analysis.

RNAP proofreading

Cramer, P. Science 313: 447-448 (2006). "Self-correcting messages." Minireview of the next paper.

Zenkin, N., Yuzenkova, Y., and Severinov, K. Science 313: 518-520 (2006). "Transcript-assisted transcriptional proofreading".

Pausing

Shankar, S., Hatoum, A., and Roberts, J. W. Mol.Cell 27: 914-927 (2007). A transcription antiterminator constructs a NusA-dependent shield to the emerging transcript.

Toulokhonov, I., Zhang, J., Palangat, M., and Landick, R. Mol.Cell. 27: 406-419 (2007). A central role of the RNA polymerase trigger loop in active-site rearrangement during transcriptional pausing.

Termination

Komissarova, N., Becker, J., Solter, S., Kireeva, M. and Kashlev, M. Molecular Cell 10:1151-1162 (2002). "Shortening of RNA-DNA hybrid in the elongation complex of RNA polymerase is a prerequisite for transcription termination."

Single-molecule studies

Yin, H., Wang, M. D., Svoboda, K. et al. Science 270: 1653-1657 (1995). "Transcription against an applied force".

Wang, M. D., Schnitzer, M. J., Yin, H. et al. Science 282: 902-907 (1998). "Force and velocity measured for single molecules of RNA polymerase". 

Dalal, R.V., Larson, M.H., Neuman, K.C., Gelles, J., Landick, R., and Block, S.M. Mol. Cell. 23: 231-239 (2006). "Pulling on the nascent RNA during transcription does not alter kinetics of elongation or ubiquitous pausing."

Herbert, K.M., La, P.A., Wong, B.J., Mooney, R.A., Neuman, K.C., Landick, R., and Block, S.M. Cell 125: 1083-1094 (2006). "Sequence-resolved detection of pausing by single RNA polymerase molecules."