ArticleJournal of bacteriology2013
Genomic reconstruction of the transcriptional regulatory network in Bacillus subtilis.
Article in Journal of bacteriology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers, 1 of them a synthesis that pooled it.
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Who cites it
40 citing papers in PubMed, 1 synthesis or guideline pooled it, 58 citations in OpenAlex.
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- Cecal Metabolomic Fingerprint of Unscathed Rats: Does It Reflect the Good Response to a Provocative Decompression?Frontiers in physiology · 2022Article
- Transcriptional Regulation of Plant Biomass Degradation and Carbohydrate Utilization Genes in the Extreme ThermophilemSystems · 2021Article
- Antitumor efficacy of a neoantigen cancer vaccine delivered by electroporation is influenced by microbiota composition.Oncoimmunology · 2021Article
- Article
- Machine learning uncovers independently regulated modules in the Bacillus subtilis transcriptome.Nature communications · 2020Article
- Genome-scale exploration of transcriptional regulation in the nisin Z producer Lactococcus lactis subsp. lactis IO-1.Scientific reports · 2020Article
- Two MarR-Type Repressors Balance Precursor Uptake and Glycine Betaine Synthesis inFrontiers in microbiology · 2020Article
- Determination of the Gene Regulatory Network of a Genome-Reduced Bacterium Highlights Alternative Regulation Independent of Transcription Factors.Cell systems · 2019Article
- Adaptation to Adversity: the Intermingling of Stress Tolerance and Pathogenesis in Enterococci.Microbiology and molecular biology reviews : MMBR · 2019Review
- Microbial life cycles link global modularity in regulation to mosaic evolution.Nature ecology & evolution · 2019Article
- Artificial Selection for Pathogenicity Mutations inInfection and immunity · 2019Article
- Comparative Genomics Reveals the Regulatory Complexity of Bifidobacterial Arabinose and Arabino-Oligosaccharide Utilization.Frontiers in microbiology · 2018Article
- Molecular and Physiological Logics of the Pyruvate-Induced Response of a Novel Transporter inmBio · 2017Article
- A novel bifunctional transcriptional regulator of riboflavin metabolism in Archaea.Nucleic acids research · 2017Article
- Article
Corrections and comments
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Authors and funding
6 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The adaptation of microorganisms to their environment is controlled by complex transcriptional regulatory networks (TRNs), which are still only partially understood even for model species. Genome scale annotation of regulatory features of genes and TRN reconstruction are challenging tasks of microbial genomics. We used the knowledge-driven comparative-genomics approach implemented in the RegPredict Web server to infer TRN in the model Gram-positive bacterium Bacillus subtilis and 10 related Bacillales species. For transcription factor (TF) regulons, we combined the available information from the DBTBS database and the literature with bioinformatics tools, allowing inference of TF binding sites (TFBSs), comparative analysis of the genomic context of predicted TFBSs, functional assignment of target genes, and effector prediction. For RNA regulons, we used known RNA regulatory motifs collected in the Rfam database to scan genomes and analyze the genomic context of new RNA sites. The inferred TRN in B. subtilis comprises regulons for 129 TFs and 24 regulatory RNA families. First, we analyzed 66 TF regulons with previously known TFBSs in B. subtilis and projected them to other Bacillales genomes, resulting in refinement of TFBS motifs and identification of novel regulon members. Second, we inferred motifs and described regulons for 28 experimentally studied TFs with previously unknown TFBSs. Third, we discovered novel motifs and reconstructed regulons for 36 previously uncharacterized TFs. The inferred collection of regulons is available in the RegPrecise database (http://regprecise.lbl.gov/) and can be used in genetic experiments, metabolic modeling, and evolutionary analysis.
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Registered trials
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