ArticlemBio2022
Bacterial Transcription Factors Bind to Coding Regions and Regulate Internal Cryptic Promoters.
Article in mBio, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 29 citations in OpenAlex.
- Blocked transcription-translation complexes are rescued by transcript release followed byJournal of bacteriology · 2026Article
- De novo promoters emerge more readily from random DNA than from genomic DNA.Science advances · 2026Article
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- Adaptive microevolution in CC17Frontiers in cellular and infection microbiology · 2026Article
- Molecular Cloning, Optimization of Expression and Functional Characterization of the Global Transcriptional Regulator MosR (Rv0348) of Mycobacterium tuberculosis.Applied biochemistry and biotechnology · 2025Article
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- A WYL domain transcription factor regulates Lactiplantibacillus plantarum intestinal colonization via perceiving c-di-GMP.Nature communications · 2025Article
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- ENcyclopedia of TRAnscription Factors in Bacteria and Archaea genomes (ENTRAF) version 2.0.Database : the journal of biological databases and curation · 2025Article
- AND Logic Based on Suppressor tRNAs Enables Stringent Control of Sliding Base Editors inACS synthetic biology · 2024Article
- HigA2 (Rv2021c) Is a Transcriptional Regulator with Multiple Regulatory Targets inMicroorganisms · 2024Article
- Regulatory role ofFrontiers in microbiology · 2024Article
- Roles of adenine methylation in the physiology of Lacticaseibacillus paracasei.Nature communications · 2023Article
- Article
Corrections and comments
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Authors and funding
7 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Transcription factors (TFs) regulate transcription by binding to the specific sequences at the promoter region. However, the mechanisms and functions of TFs binding within the coding sequences (CDS) remain largely elusive in prokaryotes. To this end, we collected 409 data sets for bacterial TFs, including 104 chromatin immunoprecipitation sequencing (ChIP-seq) assays and 305 data sets from the systematic evolution of ligands by exponential enrichment (SELEX) in seven model bacteria. Interestingly, these TFs displayed the same binding capabilities for both coding and intergenic regions. Subsequent biochemical and genetic experiments demonstrated that several TFs bound to the coding regions and regulated the transcription of the binding or adjacent genes. Strand-specific RNA sequencing revealed that these CDS-binding TFs regulated the activity of the cryptic promoters, resulting in the altered transcription of the corresponding antisense RNA. TF RhpR hindered the transcriptional elongation of a subgenic transcript within a CDS. A ChIP-seq and Ribo-seq coanalysis revealed that RhpR influenced the translational efficiency of binding genes. Taken together, the present study reveals three regulatory mechanisms of CDS-bound TFs within individual genes, operons, and antisense RNAs, which demonstrate the variability of the regulatory mechanisms of TFs and expand upon the complexity of bacterial transcriptomes.
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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.