Nucleic Acids Research, 1981, Vol. 9, No. 3 563-577
© 1981
MOLECULAR BIOLOGY |
Rho-independent termination: dyad symmetry in DNA causes RNA polymerase to pause during transcription in vitro
Department of Molecular Biophysics and Biochemistry, Yale University 333 Cedar Street, New Haven, CT 06510, USA
Received November 17, 1980. Termination of transcription by RNA polymerase at rho-independent sites appears to depend primarily upon two structural features, a region of GC-rich dyad symmetry in the DNA preceding the stop point and a stretch of uridines at the 3' end of the transcript. The possibility that the former might be responsible for slowing elongation prompted us to perform a kinetic analysis of transcription across the leader and terminator regions of the E. coli tryptophan (trp) operon. Regions where the elongation rate is dramatically slowed or stopped are identifiable because they generate discrete transcript bands on a gel. Species derived from pause sites, unlike those resulting from termination sites, are transient and detectable only within the first two minutes of transcription, since polymerase eventually resumes elongation. At two mutant trp attenuator sites (trp a135 and trp a1419), where termination is incomplete or absent in vitro, a substantial pause is nevertheless observed. Likewise, a significant pause occurs at trp t, the termination site at the end of the operon. Our experiments also reveal a major pause site at about position 90 in the trp leader sequence, just past a region of dyad symmetry. The RNA hairpin corresponding to this site is U-rich, and pausing is strongly enhanced by incorporation of BrUTP. In contrast, this analog does not affect pausing at the attenuator or terminator sites with hairpins that are GC-rich. These results strongly support the hypothesis that pausing of the polymerase is an obligatory prelude to rho-independent termination. Moreover, the termination event evidently results from consecutive but discrete responses to separate structural features of these sites.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  T. D. Witchell, S. A. J. Coutts, D. M. Bulach, and B. Adler Differential Expression of the Bhmp39 Major Outer Membrane Proteins of Brachyspira hyodysenteriae. Infect. Immun., June 1, 2006; 74(6): 3271 - 3276. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 N. Wang, S.-E. Lu, Q. Yang, S.-H. Sze, and D. C. Gross Identification of the syr-syp Box in the Promoter Regions of Genes Dedicated to Syringomycin and Syringopeptin Production by Pseudomonas syringae pv. syringae B301D J. Bacteriol., January 1, 2006; 188(1): 160 - 168. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 T. Yano, C. Sanders, J. Catalano, and F. Daldal sacB-5-Fluoroorotic Acid-pyrE-Based Bidirectional Selection for Integration of Unmarked Alleles into the Chromosome of Rhodobacter capsulatus Appl. Envir. Microbiol., June 1, 2005; 71(6): 3014 - 3024. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. Unniraman, R. Prakash, and V. Nagaraja Conserved economics of transcription termination in eubacteria Nucleic Acids Res., February 1, 2002; 30(3): 675 - 684. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. Unniraman, R. Prakash, and V. Nagaraja Alternate Paradigm for Intrinsic Transcription Termination in Eubacteria J. Biol. Chem., November 2, 2001; 276(45): 41850 - 41855. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. A. Lesnik, R. Sampath, H. B. Levene, T. J. Henderson, J. A. McNeil, and D. J. Ecker Prediction of rho-independent transcriptional terminators in Escherichia coli Nucleic Acids Res., September 1, 2001; 29(17): 3583 - 3594. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 T. Pan, I. Artsimovitch, X.-w. Fang, R. Landick, and T. R. Sosnick Folding of a large ribozyme during transcription and the effect of the elongation factor NusA PNAS, August 17, 1999; 96(17): 9545 - 9550. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. McDowell, J. Roberts, D. Jin, and C Gross Determination of intrinsic transcription termination efficiency by RNA polymerase elongation rate Science, November 4, 1994; 266(5186): 822 - 825. [Abstract] [PDF]
|
|
|
|
 |
|
 R Landick, J Stewart, and D N Lee Amino acid changes in conserved regions of the beta-subunit of Escherichia coli RNA polymerase alter transcription pausing and termination. Genes & Dev., September 1, 1990; 4(9): 1623 - 1636. [Abstract] [PDF]
|
|