title: NusA-dependent transcription termination prevents misregulation of global gene expression.
abstract: Intrinsic transcription terminators consist of an RNA hairpin followed by a U-rich tract, and these signals can trigger termination without the involvement of additional factors. Although NusA is known to stimulate intrinsic termination in vitro, the in vivo targets and global impact of NusA are not known because it is essential for viability. Using genome-wide 3' end-mapping on an engineered Bacillus subtilis NusA depletion strain, we show that weak suboptimal terminators are the principle NusA substrates. Moreover, a subclass of weak non-canonical terminators was identified that completely depend on NusA for effective termination. NusA-dependent terminators tend to have weak hairpins and/or distal U-tract interruptions, supporting a model in which NusA is directly involved in the termination mechanism. Depletion of NusA altered global gene expression directly and indirectly via readthrough of suboptimal terminators. Readthrough of NusA-dependent terminators caused misregulation of genes involved in essential cellular functions, especially DNA replication and metabolism. We further show that nusA is autoregulated by a transcription attenuation mechanism that does not rely on antiterminator structures. Instead, NusA-stimulated termination in its 5' UTR dictates the extent of transcription into the operon, thereby ensuring tight control of cellular NusA levels.
authors: Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.|Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.
authors: Smarajit
authors: S
authors: Mondal
authors: Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.|Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.
authors: Alexander V
authors: AV
authors: Yakhnin
authors: Bioinformatics Consulting Center, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.
authors: Aswathy
authors: A
authors: Sebastian
authors: Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.|Bioinformatics Consulting Center, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.
authors: Istvan
authors: I
authors: Albert
authors: Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.|Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.
authors: Paul
authors: P
authors: Babitzke
mesh_terms: D001412:Bacillus subtilis / Q000235:genetics*; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism*; D015964:Gene Expression Regulation, Bacterial; D005798:Genes, Bacterial; D012329:RNA, Bacterial / Q000235:genetics / Q000378:metabolism; D013379:Substrate Specificity; D061806:Transcription Termination, Genetic
chemical_list: D001426:Bacterial Proteins; D012329:RNA, Bacterial