Structural basis of transcription-translation coupling. A two-way street: regulatory interplay between RNA polymerase and nascent RNA structure. Transcriptional pausing as a mediator of bacterial gene regulation. RNA polymerase pausing and nascent-RNA structure formation are linked through clamp-domain movement. Mg 2+ shifts ligand-mediated folding of a riboswitch from induced-fit to conformational selection. The flap domain is required for pause RNA hairpin inhibition of catalysis by RNA polymerase and can modulate intrinsic termination. Structural insights into riboswitch control of the biosynthesis of queuosine, a modified nucleotide found in the anticodon of tRNA. Transcription factors modulate RNA polymerase conformational equilibrium. Structural basis for transcript elongation control by NusG family universal regulators. Maintenance of RNA-DNA hybrid length in bacterial RNA polymerases.
RNA polymerase stalls in a post-translocated register and can hyper-translocate. Structural basis for transcription elongation by bacterial RNA polymerase. cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Structural basis of transcription-translation coupling and collision in bacteria. Structural basis of transcription arrest by coliphage HK022 Nun in an Escherichia coli RNA polymerase elongation complex. RNA polymerase accommodates a pause RNA hairpin by global conformational rearrangements that prolong pausing. A riboswitch selective for the queuosine precursor preQ1 contains an unusually small aptamer domain. Riboswitch regulation mechanisms: RNA, metabolites and regulatory proteins. Dual-targeting small-molecule inhibitors of the Staphylococcus aureus FMN riboswitch disrupt riboflavin homeostasis in an infectious setting. Riboswitch-mediated gene regulation: novel RNA architectures dictate gene expression responses. Ligand modulates cross-coupling between riboswitch folding and transcriptional pausing. Structural basis of transcription: RNA polymerase backtracking and its reactivation. Structural basis for NusA stabilized transcriptional pausing. Pausing by bacterial RNA polymerase is mediated by mechanistically distinct classes of signals. Mechanisms of transcriptional pausing in bacteria. A pause sequence enriched at translation start sites drives transcription dynamics in vivo. The mechanism of intrinsic transcription termination. Native elongating transcript sequencing reveals human transcriptional activity at nucleotide resolution. The transcriptional regulator RfaH stimulates RNA chain synthesis after recruitment to elongation complexes by the exposed nontemplate DNA strand. A translational riboswitch coordinates nascent transcription–translation coupling. A ratchet mechanism of transcription elongation and its control. Molecular evolution of multisubunit RNA polymerases: structural analysis. Our study reveals the tight coupling by which nascent RNA structures and their ligands can functionally regulate the macromolecular transcription machinery. Strikingly, on ligand binding, the riboswitch rotates around its helical axis, expanding the surrounding RNAP exit channel and repositioning the transcript for elongation. In the absence of preQ 1, the RNA transcript is in an unexpected hyper-translocated state, preventing downstream nucleotide incorporation. Here, we report single-particle cryo-electron microscopy reconstructions of que-PEC in ligand-free and ligand-bound states. Ligand binding to the riboswitch induces RNAP pause release and downstream transcription termination however, the mechanism by which riboswitch folding modulates pausing is unclear. A pause of RNAP during transcription of a preQ 1 riboswitch (termed que-PEC) is stabilized by a previously characterized template consensus sequence and the ligand-free conformation of the nascent RNA. Folding of nascent transcripts can be modulated by the RNA polymerase (RNAP) that carries out their transcription, and vice versa.
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