title: Nascent RNA length dictates opposing effects of NusA on antitermination.
abstract: The NusA protein is a universally conserved bacterial transcription elongation factor that binds RNA polymerase (RNAP). When functioning independently, NusA enhances intrinsic termination. Paradoxically, NusA stimulates the function of the N and Q antiterminator proteins of bacteriophage λ. The mechanistic basis for NusA's functional plasticity is poorly understood. Here we uncover an effect of nascent RNA length on the ability of NusA to collaborate with Q. Ordinarily, Q engages RNAP during early elongation when it is paused at a specific site just downstream of the phage late-gene promoter. NusA facilitates this engagement process and both proteins remain associated with the transcription elongation complex (TEC) as it escapes the pause and transcribes the late genes. We show that the λ-related phage 82 Q protein (82Q) can also engage RNAP that is paused at a promoter-distal position and thus contains a nascent RNA longer than that associated with the natively positioned TEC. However, the effect of NusA in this context is antagonistic rather than stimulatory. Moreover, cleaving the long RNA associated with the promoter-distal TEC restores NusA's stimulatory effect. Our findings reveal a critical role for nascent RNA in modulating NusA's effect on 82Q-mediated antitermination, with implications for understanding NusA's functional plasticity.
authors.affiliation: Department of Microbiology and Immunobiology, Boston, MA 02115, USA.
authors.forename: Christopher D
authors.initials: CD
authors.lastname: Wells
authors.affiliation: Department of Microbiology and Immunobiology, Boston, MA 02115, USA Department of Biology, Emmanuel College, Boston, MA 02115, USA.
authors.forename: Padraig
authors.initials: P
authors.lastname: Deighan
authors.affiliation: Department of Microbiology and Immunobiology, Boston, MA 02115, USA.
authors.forename: MacKenzie
authors.initials: M
authors.lastname: Brigham
authors.affiliation: Department of Microbiology and Immunobiology, Boston, MA 02115, USA ahochschild@hms.harvard.edu.
authors.forename: Ann
authors.initials: A
authors.lastname: Hochschild
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry / Q000378:metabolism*; D001667:Binding, Competitive; D008954:Models, Biological; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D012313:RNA / Q000235:genetics* / Q000378:metabolism*; D061806:Transcription Termination, Genetic; D035602:Transcriptional Elongation Factors / Q000737:chemistry / Q000378:metabolism*; D054334:Viral Regulatory and Accessory Proteins / Q000737:chemistry / Q000378:metabolism
chemical_list: D001426:Bacterial Proteins; D035602:Transcriptional Elongation Factors; D054334:Viral Regulatory and Accessory Proteins; D012313:RNA