title: Pausing and termination by bacteriophage T7 RNA polymerase.
abstract: Two types of sites are known to cause pausing and/or termination by bacteriophage T7 RNA polymerase (RNAP). Termination at class I sites (typified by the signal found in the late region of T7 DNA, TPhi) involves the formation of a stable stem-loop structure in the nascent RNA ahead of the point of termination, and results in termination near runs of U. Class II sites, typified by a signal first identified in the cloned human preproparathyroid hormone (PTH) gene, generate no evident structure in the RNA but contain a conserved sequence ahead of the point of termination, and also contain runs of U. Termination at class I and class II sites may involve non-equivalent mechanisms, as mutants of T7 RNA polymerase have been identified that fail to recognize class II sites yet continue to recognize class I sites. In this work, we have analyzed pausing and termination at several class II sites, and variants of them. We conclude that the 7 bp sequence ATCTGTT (5' to 3' in the non-template strand) causes transcribing T7 or T3 RNA polymerase to pause. Termination 6 to 8 bp past this sequence is favored by the presence of runs of U, perhaps because they destabilize an RNA:DNA hybrid. The effects of T7 lysozyme on pausing and termination are consistent with the idea that termination involves a reversion of the polymerase from the elongation to the initiation conformation, and that lysozyme inhibits the return to the elongation conformation. A kinetic model of pausing and termination is presented that provides a consistent interpretation of our results.
authors.affiliation: Morse Institute for Molecular Genetics, Health Science Center at Brooklyn, State University of New York, 450 Clarkson Avenue, Brooklyn, Box 44, NY 11203-2098, USA.
authors.forename: D L
authors.initials: DL
authors.lastname: Lyakhov
authors.forename: B
authors.initials: B
authors.lastname: He
authors.forename: X
authors.initials: X
authors.lastname: Zhang
authors.forename: F W
authors.initials: FW
authors.lastname: Studier
authors.forename: J J
authors.initials: JJ
authors.lastname: Dunn
authors.forename: W T
authors.initials: WT
authors.lastname: McAllister
mesh_terms: D017123:Bacteriophage T7 / Q000201:enzymology* / Q000235:genetics; D001483:Base Sequence; D017124:Conserved Sequence; D004279:DNA, Viral / Q000235:genetics; D012321:DNA-Directed RNA Polymerases / Q000378:metabolism*; D007700:Kinetics; D008969:Molecular Sequence Data; D009238:N-Acetylmuramoyl-L-alanine Amidase / Q000378:metabolism; D010957:Plasmids; D013728:Terminator Regions, Genetic; D014764:Viral Proteins
chemical_list: D004279:DNA, Viral; D014764:Viral Proteins; C062210:bacteriophage T7 RNA polymerase; D012321:DNA-Directed RNA Polymerases; D009238:N-Acetylmuramoyl-L-alanine Amidase