ArticleNucleic acids research2002
Improving the predictive value of the competence transcription factor (ComK) binding site in Bacillus subtilis using a genomic approach.
Article in Nucleic acids research, 2002. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 84 papers.
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84 citing papers in PubMed, 161 citations in OpenAlex.
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- Improving gene set enrichment analysis (GSEA) by using regulation directionality.Microbiology spectrum · 2024Article
- The bacterial replication origin BUS promotes nucleobase capture.Nature communications · 2023Article
- Induction of the CtsR regulon improves Xylanase production in Bacillus subtilis.Microbial cell factories · 2023Article
- SirA inhibits the essential DnaA:DnaD interaction to block helicase recruitment during Bacillus subtilis sporulation.Nucleic acids research · 2023Article
- The DNA replication initiation protein DnaD recognises a specific strand of the Bacillus subtilis chromosome origin.Nucleic acids research · 2023Article
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- Repurposing drugs with specific activity against L-form bacteria.Frontiers in microbiology · 2023Article
- Chromosome remodelling by SMC/Condensin inProceedings of the National Academy of Sciences of the United States of America · 2022Article
- Low membrane fluidity triggers lipid phase separation and protein segregation in living bacteria.The EMBO journal · 2022Article
- Elements in the LftR Repressor Operator Interface Contributing to Regulation of Aurantimycin Resistance in Listeria monocytogenes.Journal of bacteriology · 2021Article
- Influence of the ABC Transporter YtrBCDEF ofFrontiers in microbiology · 2021Article
- A novel Rap-Phr system in Bacillus velezensis NAU-B3 regulates surfactin production and sporulation via interaction with ComA.Applied microbiology and biotechnology · 2020Article
- Cell morphology maintenance in Bacillus subtilis through balanced peptidoglycan synthesis and hydrolysis.Scientific reports · 2020Article
- Analyses of competent and non-competent subpopulations of Bacillus subtilis reveal yhfW, yhxC and ncRNAs as novel players in competence.Environmental microbiology · 2020Article
24 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Generally, the presence of a consensus sequence in the promoter of a gene is taken as indication for regulation by the transcription factor that binds to this sequence. In light of the recent developments in genome research, we were interested to what extent this supposition is valid. We examined the relationship between the presence of a binding site for ComK, the competence transcription factor of Bacillus subtilis, and actual transcriptional activation by ComK. Bacillus subtilis contains 1062 putative ComK-binding sites (K-boxes) in its genome. We employed DNA macroarrays to identify ComK-activated genes, and found that the presence of a K-box is an unreliable predictor for regulation. Only approximately 8% of the genes containing a K-box in the putative promoter region are regulated by ComK. The predictive value of a K-box could be improved by taking into consideration the degree of deviation from the K-box consensus sequence, the presence of extra ComK-binding motifs and the positions of RNA polymerase-binding sites. Finally, many of the ComK-activated genes show no apparent function related to the competence process. Based on our findings, we propose that the ComK-dependent activation of several genes might serve no biological purpose and can be considered 'evolutionary noise'.
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