ArticlePloS one2012
Genomic arrangement of regulons in bacterial genomes.
Article in PloS one, 2012. 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, 24 citations in OpenAlex.
- Insights into genetic determinants of volatile fatty acid catabolism inApplied and environmental microbiology · 2025Article
- RNA polymerase sliding on DNA can couple the transcription of nearby bacterial operons.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- RNA polymerase sliding on DNA can couple the transcription of nearby bacterial operons.bioRxiv : the preprint server for biology · 2023Article
- The Spatial Organization of Bacterial Transcriptional Regulatory Networks.Microorganisms · 2022Article
- The High Mutational Sensitivity of ccdA Antitoxin Is Linked to Codon Optimality.Molecular biology and evolution · 2022Article
- New insights into the activation of Radiation Desiccation Response regulon inJournal of biosciences · 2021Article
- Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655.Nucleic acids research · 2018Article
- Article
- Spatial features for Escherichia coli genome organization.BMC genomics · 2015Article
- Unprecedented high-resolution view of bacterial operon architecture revealed by RNA sequencing.mBio · 2014Article
- Acetobixan, an inhibitor of cellulose synthesis identified by microbial bioprospecting.PloS one · 2014Article
- Computational analyses of transcriptomic data reveal the dynamic organization of the Escherichia coli chromosome under different conditions.Nucleic acids research · 2013Article
- High-throughput screen of essential gene modules in Mycobacterium tuberculosis: a bibliometric approach.BMC infectious diseases · 2013Article
- Global genomic arrangement of bacterial genes is closely tied with the total transcriptional efficiency.Genomics, proteomics & bioinformatics · 2013Article
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Regulons, as groups of transcriptionally co-regulated operons, are the basic units of cellular response systems in bacterial cells. While the concept has been long and widely used in bacterial studies since it was first proposed in 1964, very little is known about how its component operons are arranged in a bacterial genome. We present a computational study to elucidate of the organizational principles of regulons in a bacterial genome, based on the experimentally validated regulons of E. coli and B. subtilis. Our results indicate that (1) genomic locations of transcriptional factors (TFs) are under stronger evolutionary constraints than those of the operons they regulate so changing a TF's genomic location will have larger impact to the bacterium than changing the genomic position of any of its target operons; (2) operons of regulons are generally not uniformly distributed in the genome but tend to form a few closely located clusters, which generally consist of genes working in the same metabolic pathways; and (3) the global arrangement of the component operons of all the regulons in a genome tends to minimize a simple scoring function, indicating that the global arrangement of regulons follows simple organizational principles.
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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.