ArticleProceedings of the National Academy of Sciences of the United States of America2010
Genomic arrangement of bacterial operons is constrained by biological pathways encoded in the genome.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed, 61 citations in OpenAlex.
- 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
- Biology and applications of co-produced, synergistic antimicrobials from environmental bacteria.Nature microbiology · 2021Review
- Network analyses in microbiome based on high-throughput multi-omics data.Briefings in bioinformatics · 2021Review
- The Exploration of Novel Regulatory Relationships Drives Haloarchaeal Operon-Like Structural Dynamics over Short Evolutionary Distances.Microorganisms · 2020Article
- Physicochemical Foundations of Life that Direct Evolution: Chance and Natural Selection are not Evolutionary Driving Forces.Life (Basel, Switzerland) · 2020Article
- Transcription of Bacterial Chromatin.Journal of molecular biology · 2019Review
- Transcriptome and Comparative Genomics Analyses Reveal New Functional Insights on Key Determinants of Pathogenesis and Interbacterial Competition inApplied and environmental microbiology · 2019Article
- Single-Cell RNA Sequencing of Plant-Associated Bacterial Communities.Frontiers in microbiology · 2019Review
- Features of genomic organization in a nucleotide-resolution molecular model of the Escherichia coli chromosome.Nucleic acids research · 2017Article
- Assessment of genome annotation using gene function similarity within the gene neighborhood.BMC bioinformatics · 2017Article
- Supra-operonic clusters of functionally related genes (SOCs) are a source of horizontal gene co-transfers.Scientific reports · 2017Article
- Coevolution of the Organization and Structure of Prokaryotic Genomes.Cold Spring Harbor perspectives in biology · 2016Review
- Conserved Units of Co-Expression in Bacterial Genomes: An Evolutionary Insight into Transcriptional Regulation.PloS one · 2016Article
- Revisiting operons: an analysis of the landscape of transcriptional units in E. coli.BMC bioinformatics · 2015Article
- Spatial features for Escherichia coli genome organization.BMC genomics · 2015Article
- Analysis of genomic rearrangements, horizontal gene transfer and role of plasmids in the evolution of industrial important Thermus species.BMC genomics · 2014Article
- Characterization of a planctomycetal organelle: a novel bacterial microcompartment for the aerobic degradation of plant saccharides.Applied and environmental microbiology · 2014Article
- Article
- Computational analyses of transcriptomic data reveal the dynamic organization of the Escherichia coli chromosome under different conditions.Nucleic acids research · 2013Article
Corrections and comments
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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
It is generally known that bacterial genes working in the same biological pathways tend to group into operons, possibly to facilitate cotranscription and to provide stoichiometry. However, very little is understood about what may determine the global arrangement of bacterial genes in a genome beyond the operon level. Here we present evidence that the global arrangement of operons in a bacterial genome is largely influenced by the tendency that a bacterium keeps its operons encoding the same biological pathway in nearby genomic locations, and by the tendency to keep operons involved in multiple pathways in locations close to the other members of their participating pathways. We also observed that the activation frequencies of pathways also influence the genomic locations of their encoding operons, tending to have operons of the more frequently activated pathways more tightly clustered together. We have quantitatively assessed the influences on the global genomic arrangement of operons by different factors. We found that the current arrangements of operons in most of the bacterial genomes we studied tend to minimize the overall distance between consecutive operons of a same pathway across all pathways encoded in the genome.
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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.