ArticleGenome research2007
Genes under positive selection in Escherichia coli.
Article in Genome research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 105 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
105 citing papers in PubMed, 166 citations in OpenAlex.
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- Genomic profiling of Nitrospira species reveals ecological success of comammox Nitrospira.Microbiome · 2022Article
- Purifying selection enduringly acts on the sequence evolution of highly expressed proteins in Escherichia coli.G3 (Bethesda, Md.) · 2022Article
- Shigella viruses Sf22 and KRT47 require outer membrane protein C for infection.Biochimica et biophysica acta. Biomembranes · 2022Article
- A genome-wide scan of wastewater E. coli for genes under positive selection: focusing on mechanisms of antibiotic resistance.Scientific reports · 2022Article
- Comparative Genomics Applied to Systematically Assess Pathogenicity Potential in Shiga Toxin-ProducingMicroorganisms · 2022Article
- Mosaic Evolution of Beta-Barrel-Porin-Encoding Genes inApplied and environmental microbiology · 2022Article
- Evolutionary Ecology of Natural ComammoxmSystems · 2022Article
- Comparative genomics and evolutionary analysis ofMicrobial genomics · 2022Article
- Mutational Pattern Induced by 5-Fluorouracil and Oxaliplatin in the Gut Microbiome.Frontiers in microbiology · 2022Article
- Evidence of episodic positive selection inPeerJ · 2022Article
- Diversification of OmpA and OmpF of Yersinia ruckeri is independent of the underlying species phylogeny and evidence of virulence-related selection.Scientific reports · 2021Article
- Characterization of the first vaginalPeerJ · 2021Article
- Insights into the Metabolism and Evolution of the GenusmSystems · 2020Article
- Standardized phylogenetic and molecular evolutionary analysis applied to species across the microbial tree of life.Scientific reports · 2020Article
45 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We used a comparative genomics approach to identify genes that are under positive selection in six strains of Escherichia coli and Shigella flexneri, including five strains that are human pathogens. We find that positive selection targets a wide range of different functions in the E. coli genome, including cell surface proteins such as beta barrel porins, presumably because of the involvement of these genes in evolutionary arms races with other bacteria, phages, and/or the host immune system. Structural mapping of positively selected sites on trans-membrane beta barrel porins reveals that the residues under positive selection occur almost exclusively in the extracellular region of the proteins that are enriched with sites known to be targets of phages, colicins, or the host immune system. More surprisingly, we also find a number of other categories of genes that show very strong evidence for positive selection, such as the enigmatic rhs elements and transposases. Based on structural evidence, we hypothesize that the selection acting on transposases is related to the genomic conflict between transposable elements and the host genome.
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Registered trials
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.