title: The bacteriophage lambda Q antiterminator protein contacts the beta-flap domain of RNA polymerase.
abstract: The multisubunit RNA polymerase (RNAP) in bacteria consists of a catalytically active core enzyme (alpha(2)beta beta'omega) complexed with a sigma factor that is required for promoter-specific transcription initiation. During early elongation the stability of interactions between sigma and core decreases, in part because of the nascent RNA-mediated destabilization of an interaction between region 4 of sigma and the flap domain of the beta-subunit (beta-flap). The nascent RNA-mediated destabilization of the sigma region 4/beta-flap interaction is required for the bacteriophage lambda Q antiterminator protein (lambdaQ) to engage the RNAP holoenzyme. Here, we provide an explanation for this requirement by showing that lambdaQ establishes direct contact with the beta-flap during the engagement process, thus competing with sigma(70) region 4 for access to the beta-flap. We also show that lambdaQ's affinity for the beta-flap is calibrated to ensure that lambdaQ activity is restricted to the lambda late promoter P(R'). Specifically, we find that strengthening the lambdaQ/beta-flap interaction allows lambdaQ to bypass the requirement for specific cis-acting sequence elements, a lambdaQ-DNA binding site and a RNAP pause-inducing element, that normally ensure lambdaQ is recruited exclusively to transcription complexes associated with P(R'). Our findings demonstrate that the beta-flap can serve as a direct target for regulators of elongation.
authors.affiliation: Department of Microbiology and Molecular Genetics, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA.
authors.forename: Padraig
authors.initials: P
authors.lastname: Deighan
authors.forename: Cristina Montero
authors.initials: CM
authors.lastname: Diez
authors.forename: Mark
authors.initials: M
authors.lastname: Leibman
authors.forename: Ann
authors.initials: A
authors.lastname: Hochschild
authors.forename: Bryce E
authors.initials: BE
authors.lastname: Nickels
mesh_terms: D019943:Amino Acid Substitution; D001665:Binding Sites; D012321:DNA-Directed RNA Polymerases / Q000737:chemistry* / Q000378:metabolism*; D008954:Models, Biological; D008957:Models, Genetic; D017434:Protein Structure, Tertiary; D012329:RNA, Bacterial / Q000378:metabolism; D014158:Transcription, Genetic; D014764:Viral Proteins / Q000737:chemistry* / Q000378:metabolism*
chemical_list: C066119:Q protein, Bacteriophage lambda; D012329:RNA, Bacterial; D014764:Viral Proteins; D012321:DNA-Directed RNA Polymerases