ArticlePLoS biology2023
Systematic and scalable genome-wide essentiality mapping to identify nonessential genes in phages.
Article in PLoS biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 28 citations in OpenAlex.
- Systematic mapping of bacteriophage gene essentiality with HIDEN-SEQ.Nature microbiology · 2026Article
- Defining the essential genome of diverse phages with phage Tn-seq.Nature microbiology · 2026Article
- Genome-wide characterization of host factors involved in single-stranded RNA and DNA phage infection pathways.bioRxiv : the preprint server for biology · 2026Article
- Cross-order detection of bacteriophage transduction in microbial communities using RNA barcoding.Nature communications · 2026Article
- An efficient CRISPR-Cas12a tool for iterative genome editing, streamlined minimization, and payload engineering ofSynthetic and systems biotechnology · 2026Article
- Orthogonal chemical genomics approaches reveal genomic targets for increasing anaerobic chemical tolerance inmSystems · 2026Article
- Article
- CRISPR-based genetic tools for the study of host-microbe interactions.Infection and immunity · 2025Review
- Systematic, high-throughput characterization of bacteriophage gene essentiality on diverse hosts.Cell host & microbe · 2025Article
- The prototypic crAssphage is a linear phage-plasmid.Cell host & microbe · 2025Article
- Phage-based delivery of CRISPR-associated transposases for targeted bacterial editing.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Article
- CRISPRi-ART enables functional genomics of diverse bacteriophages using RNA-binding dCas13d.Nature microbiology · 2025Article
- Revealing the Potential of Solamargine for Anti Metastasis and Angiogenesis Inhibition in Nasopharyngeal Carcinoma.Journal of inflammation research · 2025Article
- Programming CRISPRi to control the lifecycle of bacteriophage T7.Frontiers in microbiology · 2025Article
- Sequence modeling and design from molecular to genome scale with Evo.Science (New York, N.Y.) · 2024Article
- A long-context language model for deciphering and generating bacteriophage genomes.Nature communications · 2024Article
- Analysis and culturing of the prototypic crAssphage reveals a phage-plasmid lifestyle.bioRxiv : the preprint server for biology · 2024Article
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Authors and funding
8 authors at 4 institutions in 1 country.
Funding
Abstract
Phages are one of the key ecological drivers of microbial community dynamics, function, and evolution. Despite their importance in bacterial ecology and evolutionary processes, phage genes are poorly characterized, hampering their usage in a variety of biotechnological applications. Methods to characterize such genes, even those critical to the phage life cycle, are labor intensive and are generally phage specific. Here, we develop a systematic gene essentiality mapping method scalable to new phage-host combinations that facilitate the identification of nonessential genes. As a proof of concept, we use an arrayed genome-wide CRISPR interference (CRISPRi) assay to map gene essentiality landscape in the canonical coliphages λ and P1. Results from a single panel of CRISPRi probes largely recapitulate the essential gene roster determined from decades of genetic analysis for lambda and provide new insights into essential and nonessential loci in P1. We present evidence of how CRISPRi polarity can lead to false positive gene essentiality assignments and recommend caution towards interpreting CRISPRi data on gene essentiality when applied to less studied phages. Finally, we show that we can engineer phages by inserting DNA barcodes into newly identified inessential regions, which will empower processes of identification, quantification, and tracking of phages in diverse applications.
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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.