ArticleNature microbiology2021
The impact of genetic diversity on gene essentiality within the Escherichia coli species.
Article in Nature microbiology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 81 papers.
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Who cites it
81 citing papers in PubMed, 138 citations in OpenAlex.
- Diverse Genetic Lineages Spreading Across Healthcare and Community Boundaries Underlie Extended-Spectrum Cephalosporin-Resistant Enterobacterales Colonization Burden in Botswana.The Journal of infectious diseases · 2026Article
- In vivo CRISPRi screens reveal Escherichia coli functional adaptations in the mouse gut.Nature microbiology · 2026Article
- Comparative essentialome analysis of sixMicrobial genomics · 2026Article
- Gene loss and compensatory evolution as a source of metabolic preadaptations.Molecular biology and evolution · 2026Article
- Comparative analysis of gene importance inmSystems · 2026Article
- Cross-Strain Transferability of CRISPRi Systems and Design Rules from Laboratory to ClinicalACS synthetic biology · 2026Article
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- Cross-strain transferability of CRISPRi systems and design rules from laboratory to clinicalbioRxiv : the preprint server for biology · 2026Article
- Genomic insight into the antibiotic-resistant determinants ofFrontiers in microbiology · 2026Article
- Rare metabolic gene essentiality is a determinant of microniche adaptation in Eschherichia coli.PLoS pathogens · 2025Article
- Basic reproduction number varies markedly between closely related pandemic Escherichia coli clones.Nature communications · 2025Article
- Dissecting pOXA-48 fitness effects in clinical Enterobacterales using plasmid-wide CRISPRi screens.Nature communications · 2025Article
- Genomic potential of crustose coralline algae-associated bacteria for the biosynthesis of novel antimicrobials.Microbial genomics · 2025Article
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- Protein-primed DNA homopolymer synthesis by an antiviral reverse transcriptase.bioRxiv : the preprint server for biology · 2025Article
- Genetic properties underlying transcriptional variability across different perturbations.Nature communications · 2025Article
- Transcriptomic and proteomic effects of gene deletion are not evolutionarily conserved.Genome research · 2025Article
- Chemical genomics informs antibiotic and essential gene function in Acinetobacter baumannii.PLoS genetics · 2025Article
- Transposon-sequencing across multiplemBio · 2025Article
- Article
21 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
- Erratum issued
Authors and funding
8 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Bacteria from the same species can differ widely in their gene content. In Escherichia coli, the set of genes shared by all strains, known as the core genome, represents about half the number of genes present in any strain. Although recent advances in bacterial genomics have unravelled genes required for fitness in various experimental conditions, most studies have focused on single model strains. As a result, the impact of the species' genetic diversity on core processes of the bacterial cell remains largely under-investigated. Here, we have developed a CRISPR interference platform for high-throughput gene repression that is compatible with most E. coli isolates and closely related species. We have applied it to assess the importance of ~3,400 nearly ubiquitous genes in three growth conditions in 18 representative E. coli strains spanning most common phylogroups and lifestyles of the species. Our screens revealed extensive variations in gene essentiality between strains and conditions. Investigation of the genetic determinants for these variations highlighted the importance of epistatic interactions with mobile genetic elements. In particular, we have shown how prophage-encoded defence systems against phage infection can trigger the essentiality of persistent genes that are usually non-essential. This study provides broad insights into the evolvability of gene essentiality and argues for the importance of studying various isolates from the same species under diverse conditions.
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