Inhibition of a transcriptional pause by RNA anchoring to RNA polymerase.
We describe a mechanism by which nascent RNA inhibits transcriptional pausing. PutL RNA of bacteriophage HK022 suppresses transcription termination at downstream terminators and pausing within a nearby U-rich sequence. In vitro transcription and footprinting assays reveal that this pausing results from backtracking of RNA polymerase and that binding of nascent putL RNA to polymerase limits backtracking by restricting re-entry of the transcript into the RNA exit channel. The restriction is local and relaxes as the transcript elongates. Our results suggest that putL RNA binds to the surface of polymerase close to the RNA exit channel, a region that includes amino acid residues important for antitermination. Although binding is essential for antipausing and antitermination, these two activities of put differ: antipausing is limited to the immediate vicinity of the putL site, but antitermination is not. We propose that RNA anchoring to the elongation complex is a widespread mechanism of pause regulation.
Komissarova
Natalia
N
Section on Microbial Genetics, Laboratory of Molecular Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, 6 Center Drive, Bethesda, MD 20892-2785, USA.
Velikodvorskaya
Tatiana
T
Sen
Ranjan
R
King
Rodney A
RA
Banik-Maiti
Sarbani
S
Weisberg
Robert A
RA
D000818:Animals; D025523:Bacteriophage HK022 / Q000235:genetics / Q000378:metabolism; D001483:Base Sequence; D012321:DNA-Directed RNA Polymerases / Q000235:genetics / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000235:genetics / Q000378:metabolism; D005786:Gene Expression Regulation; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D016376:Oligonucleotides, Antisense / Q000235:genetics / Q000378:metabolism; D011487:Protein Conformation; D012313:RNA / Q000235:genetics / Q000378:metabolism*; D014158:Transcription, Genetic; D035602:Transcriptional Elongation Factors / Q000235:genetics / Q000378:metabolism; D014529:Uridine / Q000378:metabolism; D014764:Viral Proteins / Q000235:genetics / Q000378:metabolism*
D029968:Escherichia coli Proteins; C079667:GreB protein, E coli; D016376:Oligonucleotides, Antisense; D035602:Transcriptional Elongation Factors; D014764:Viral Proteins; D012313:RNA; D012321:DNA-Directed RNA Polymerases; D014529:Uridine
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