The impact of genetic diversity on gene essentiality within the Escherichia coli species
- 1 March 2021
- journal article
- research article
- Published by Springer Science and Business Media LLC in Nature Microbiology
- Vol. 6 (3), 301-+
- https://doi.org/10.1038/s41564-020-00839-y
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 similar to 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.This publication has 86 references indexed in Scilit:
- Genome-Wide Detection of Fitness Genes in Uropathogenic Escherichia coli during Systemic InfectionPLoS Pathogens, 2013
- Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas systemNucleic Acids Research, 2013
- Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene ExpressionCell, 2013
- Fast gapped-read alignment with Bowtie 2Nature Methods, 2012
- Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic miceProceedings of the National Academy of Sciences of the United States of America, 2011
- Phenotypic Landscape of a Bacterial CellCell, 2011
- Deletion of the RluD pseudouridine synthase promotes SsrA peptide tagging of ribosomal protein S7Molecular Microbiology, 2010
- The Sequence Alignment/Map format and SAMtoolsBioinformatics, 2009
- Multicopy Suppression Underpins Metabolic EvolvabilityMolecular Biology and Evolution, 2007
- Construction of Escherichia coli K‐12 in‐frame, single‐gene knockout mutants: the Keio collectionMolecular Systems Biology, 2006