ArticlePLoS computational biology2005
Prediction of transcriptional terminators in Bacillus subtilis and related species.
Article in PLoS computational biology, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 115 papers.
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115 citing papers in PubMed, 190 citations in OpenAlex.
- Conserved 3' stem-loop structures enable comprehensive analysis of bacterial transcription termination in metagenomes.Microbiome · 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
- Characterization of Hairpin Loops and Cruciforms Across 118,019 Genomes Spanning the Tree of Life.Genome biology and evolution · 2026Article
- Synthetic Biology of Plants and Microbes for Agriculture, Environment, and Future Applications.Chemical reviews · 2026Review
- Canonical transcription termination mechanisms explain a minority of operons in cyanobacteria.bioRxiv : the preprint server for biology · 2025Article
- Promoter-proximal transcription-translation coupling controls early transcription in Escherichia coli.Nucleic acids research · 2025Article
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- Comprehensive mapping of transcription terminator Rho utilization (Rut) sites across the Bacillus subtilis genome.Nucleic acids research · 2025Article
- pTripleTREP - A vector for tightly controlled expression and purification of virulence factors in Staphylococcus aureus.Microbial cell factories · 2025Article
- Unconventional mRNA processing and degradation pathways for the polycistronic yrzI (spyTA) mRNA in Bacillus subtilis.FEBS letters · 2025Article
- BacTermFinder: a comprehensive and general bacterial terminator finder using a CNN ensemble.NAR genomics and bioinformatics · 2025Article
- Embedding a ribonuclease in the spore crust couples gene expression to spore development in Bacillus subtilis.Nucleic acids research · 2025Article
- Characterization of novel double-reporter strains ofMicrobiology spectrum · 2024Article
- Single-mode termination of phage transcriptions, disclosing bacterial adaptation for facilitated reinitiations.Nucleic acids research · 2024Article
- Utilizing RNA-seq Data to Infer Bacterial Transcription Termination Sites and Validate Predictions.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Extraordinary long-stem confers resistance of intrinsic terminators to processive antitermination.Nucleic acids research · 2023Article
- Design of artificial small regulatorySynthetic and systems biotechnology · 2023Article
- Minimization and optimization of α-amylase terminator for heterologous protein production in Bacillus licheniformis.Bioresources and bioprocessing · 2022Article
- Inverse folding based pre-training for the reliable identification of intrinsic transcription terminators.PLoS computational biology · 2022Article
55 more citing papers are in PubMed but not listed here.
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4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In prokaryotes, genes belonging to the same operon are transcribed in a single mRNA molecule. Transcription starts as the RNA polymerase binds to the promoter and continues until it reaches a transcriptional terminator. Some terminators rely on the presence of the Rho protein, whereas others function independently of Rho. Such Rho-independent terminators consist of an inverted repeat followed by a stretch of thymine residues, allowing us to predict their presence directly from the DNA sequence. Unlike in Escherichia coli, the Rho protein is dispensable in Bacillus subtilis, suggesting a limited role for Rho-dependent termination in this organism and possibly in other Firmicutes. We analyzed 463 experimentally known terminating sequences in B. subtilis and found a decision rule to distinguish Rho-independent transcriptional terminators from non-terminating sequences. The decision rule allowed us to find the boundaries of operons in B. subtilis with a sensitivity and specificity of about 94%. Using the same decision rule, we found an average sensitivity of 94% for 57 bacteria belonging to the Firmicutes phylum, and a considerably lower sensitivity for other bacteria. Our analysis shows that Rho-independent termination is dominant for Firmicutes in general, and that the properties of the transcriptional terminators are conserved. Terminator prediction can be used to reliably predict the operon structure in these organisms, even in the absence of experimentally known operons. Genome-wide predictions of Rho-independent terminators for the 57 Firmicutes are available in the Supporting Information section.
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