ArticlePLoS genetics2018
Genome-wide CRISPR-dCas9 screens in E. coli identify essential genes and phage host factors.
Article in PLoS genetics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 135 papers.
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Who cites it
135 citing papers in PubMed, 232 citations in OpenAlex.
- In vivo CRISPRi screens reveal Escherichia coli functional adaptations in the mouse gut.Nature microbiology · 2026Article
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- Phage host range: determinants, dynamics and applications.Nature reviews. Microbiology · 2026Review
- A programmableApplied and environmental microbiology · 2026Article
- Multiple prophage acquisition events over the course of an outbreak drive lysogenic conversion of capsular polysaccharides produced by carbapenem-resistantMicrobiology spectrum · 2026Article
- Deciphering the Implications ofPathogens (Basel, Switzerland) · 2026Review
- The ω subunit stabilizes transcribing RNA polymerase to balance processivity and collision resolution.bioRxiv : the preprint server for biology · 2026Article
- Gradient metapopulation microfluidic ecologies shape genetic and biofilm drivers of T4r phage resistance in E. coli.NPJ biofilms and microbiomes · 2026Article
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- A platform for CRISPRi-seq inmBio · 2026Article
- Orthogonal chemical genomics approaches reveal genomic targets for increasing anaerobic chemical tolerance inmSystems · 2026Article
- Regulatory time-kill sequencing maps antibiotic-specific transcriptional control ofFrontiers in microbiology · 2026Article
- Transcription-replication collisions trigger high-fidelity replication reset.Nucleic acids research · 2025Article
- Systematic genome-wide mapping of host determinants of bacteriophage infectivity.Cell systems · 2025Article
- Loss of essential outer membrane functions causes drug hypersensitization inbioRxiv : the preprint server for biology · 2025Article
- Exploring phage-host interactions inMicrobiology spectrum · 2025Article
- Analysis of essential genes inJournal of bacteriology · 2025Article
- CRISPRi-seq in Haemophilus influenzae reveals genome-wide and medium-specific growth determinants.PLoS pathogens · 2025Article
- Article
- CRISPR-based genetic tools for the study of host-microbe interactions.Infection and immunity · 2025Review
75 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
High-throughput genetic screens are powerful methods to identify genes linked to a given phenotype. The catalytic null mutant of the Cas9 RNA-guided nuclease (dCas9) can be conveniently used to silence genes of interest in a method also known as CRISPRi. Here, we report a genome-wide CRISPR-dCas9 screen using a starting pool of ~ 92,000 sgRNAs which target random positions in the chromosome of E. coli. To benchmark our method, we first investigate its utility to predict gene essentiality in the genome of E. coli during growth in rich medium. We could identify 79% of the genes previously reported as essential and demonstrate the non-essentiality of some genes annotated as essential. In addition, we took advantage of the intermediate repression levels obtained when targeting the template strand of genes to show that cells are very sensitive to the expression level of a limited set of essential genes. Our data can be visualized on CRISPRbrowser, a custom web interface available at crispr.pasteur.fr. We then apply the screen to discover E. coli genes required by phages λ, T4 and 186 to kill their host, highlighting the involvement of diverse host pathways in the infection process of the three tested phages. We also identify colanic acid capsule synthesis as a shared resistance mechanism to all three phages. Finally, using a plasmid packaging system and a transduction assay, we identify genes required for the formation of functional λ capsids, thus covering the entire phage cycle. This study demonstrates the usefulness and convenience of pooled genome-wide CRISPR-dCas9 screens in bacteria and paves the way for their broader use as a powerful tool in bacterial genomics.
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