ArticleNature microbiology2022
Comprehensive transcription terminator atlas for Bacillus subtilis.
Article in Nature microbiology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed, 37 citations in OpenAlex.
- An intrinsically disordered domain of transcription terminator Rho governs genome-wide Rho utilization (Rut) site selection in Mycobacterium tuberculosis.Nucleic acids research · 2026Article
- Expression of conjugation genes is controlled by a novel zipper-type transcriptional attenuation mechanism.Nucleic acids research · 2026Article
- Systems-level analysis predicts no autotrophy-linked protein-RNA interactions in Clostridium autoethanogenum.Nature communications · 2026Article
- Article
- Conserved 3' stem-loop structures enable comprehensive analysis of bacterial transcription termination in metagenomes.Microbiome · 2026Article
- Purine bias in bacterial genes is driven by runaway transcription.Nature microbiology · 2026Article
- Canonical transcription termination mechanisms explain a minority of operons in cyanobacteria.mSystems · 2026Article
- Design and discovery of 'tug-of-war' riboswitches.bioRxiv : the preprint server for biology · 2026Article
- TerminatorNet: comprehensive identification of intrinsic transcription terminators in bacteria.Bioinformatics (Oxford, England) · 2026Article
- Cell-free genomics reveals fundamental regulatory principles of the Mycobacterium tuberculosis transcription cycle.Molecular cell · 2026Article
- The FsrA-Mediated Iron-Sparing Response Regulates the Biosynthesis of the Epipeptide EPE in Bacillus subtilis.Molecular microbiology · 2026Article
- Article
- Canonical transcription termination mechanisms explain a minority of operons in cyanobacteria.bioRxiv : the preprint server for biology · 2025Article
- Optimization Strategy of Expression Vectors and Regulatory Elements for Enhanced Protein Production inInternational journal of molecular sciences · 2025Review
- Multi-omics analysis reveals the genetic basis for rapid COmSystems · 2025Article
- Rho-dependent transcription termination: mechanisms and roles in bacterial fitness and adaptation to environmental changes.RNA (New York, N.Y.) · 2025Review
- Comprehensive mapping of transcription terminator Rho utilization (Rut) sites across the Bacillus subtilis genome.Nucleic acids research · 2025Article
- Applying the brakes to transcription: regulation of gene expression by RNA polymerase pausing.Journal of bacteriology · 2025Review
- Characterization of bacterial intrinsic transcription terminators identified with TERMITe-a novel method for comprehensive analysis of Term-seq data.Nucleic acids research · 2025Article
- Hallmarks of DNA replication stress responses in Escherichia coli and Bacillus subtilis.FEMS microbiology reviews · 2025Review
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
The transcriptome-wide contributions of Rho-dependent and intrinsic (Rho-independent) transcription termination mechanisms in bacteria are unclear. By sequencing released transcripts in a wild-type strain and strains containing deficiencies in NusA, NusG and/or Rho (10 strains), we produced an atlas of terminators for the model Gram-positive bacterium Bacillus subtilis. We found that NusA and NusG stimulate 77% and 19% of all intrinsic terminators, respectively, and that both proteins participate in Rho-dependent termination. We also show that Rho stimulates termination at 10% of the intrinsic terminators in vivo. We recapitulated Rho-stimulated intrinsic termination at 5 terminators in vitro and found that Rho requires the KOW domain of NusG to stimulate this process at one of these terminators. Computational analyses of our atlas using RNAstructure, MEME suite and DiffLogo, combined with in vitro transcription experiments, revealed that Rho stimulates intrinsic terminators with weak hairpins and/or U-rich tracts by remodelling the RNA upstream of the intrinsic terminator to prevent the formation of RNA structures that could otherwise compete with the terminator hairpin. We also identified 56 putative examples of 'hybrid Rho-dependent termination', wherein classical Rho-dependent termination occurs after readthrough of a Rho-stimulated intrinsic terminator.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.