ArticleNature microbiology2022
A bacterial pan-genome makes gene essentiality strain-dependent and evolvable.
Article in Nature microbiology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 83 papers.
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83 citing papers in PubMed.
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- Host adaptation drives genome evolution and virulence diversification in a bacterial zoonotic pathogen.bioRxiv : the preprint server for biology · 2026Article
- Mobile Genetic Elements as Key Drivers of Bacterial Evolution and Adaptation in Agroecosystems.Microbial ecology · 2026Review
- Gene loss and compensatory evolution as a source of metabolic preadaptations.Molecular biology and evolution · 2026Article
- Translation Inhibiting Antibiotics Induce an asRNA Regulating Purine Metabolism inbioRxiv : the preprint server for biology · 2026Article
- Integrated analysis of transposon insertion sequencing and pangenome reveals core and lineage-specific essential genes inMicrobial genomics · 2026Article
- Defining thebioRxiv : the preprint server for biology · 2026Article
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- Genomic perplexity and the evolution of context-dependent function.Molecular biology and evolution · 2026Article
- Septic Shock Caused by Coinfection of Shewanella algae Bloodstream Infection and Epstein-Barr Virus: Clinical Characteristics and Genomic Analysis.MicrobiologyOpen · 2026Article
- Gempipe: a tool for drafting, curating, and analyzing pan and multi-strain genome-scale metabolic models.mSystems · 2026Article
- PanForest: predicting genes in genomes using random forests.Bioinformatics (Oxford, England) · 2026Article
- Systematic analysis of the type VII secretion system inFrontiers in microbiology · 2026Article
- Suppressor analysis inFrontiers in microbiology · 2026Article
- tsAMP: a strain-level antimicrobial peptide identification framework based on large language models and pathogen genomic variation.Frontiers in microbiology · 2026Article
23 more citing papers are in PubMed but not listed here.
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Abstract
Many bacterial species are represented by a pan-genome, whose genetic repertoire far outstrips that of any single bacterial genome. Here we investigate how a bacterial pan-genome might influence gene essentiality and whether essential genes that are initially critical for the survival of an organism can evolve to become non-essential. By using Transposon insertion sequencing (Tn-seq), whole-genome sequencing and RNA-seq on a set of 36 clinical Streptococcus pneumoniae strains representative of >68% of the species' pan-genome, we identify a species-wide 'essentialome' that can be subdivided into universal, core strain-specific and accessory essential genes. By employing 'forced-evolution experiments', we show that specific genetic changes allow bacteria to bypass essentiality. Moreover, by untangling several genetic mechanisms, we show that gene essentiality can be highly influenced by and/or be dependent on: (1) the composition of the accessory genome, (2) the accumulation of toxic intermediates, (3) functional redundancy, (4) efficient recycling of critical metabolites and (5) pathway rewiring. While this functional characterization underscores the evolvability potential of many essential genes, we also show that genes with differential essentiality remain important antimicrobial drug target candidates, as their inactivation almost always has a severe fitness cost in vivo.
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