ArticleBMC genomics2018
Avoidance of recognition sites of restriction-modification systems is a widespread but not universal anti-restriction strategy of prokaryotic viruses.
Article in BMC genomics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
35 citing papers in PubMed, 46 citations in OpenAlex.
- Characteristics of an NDM-1-producing Klebsiella pneumoniae strain belonging to ST105.Antonie van Leeuwenhoek · 2026Article
- The leading region of many plasmids is adapted for translational efficiency.Nucleic acids research · 2026Article
- Auxin (Indole-3-acetic acid) modulation of quorum sensing enhances phage susceptibility in Klebsiella pneumoniae.European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology · 2026Article
- Unraveling the Coevolutionary Dynamics of Phage and Bacterial Protein Warfare Occurring in the Drains of Beef-Processing Plants.Microorganisms · 2026Article
- Immunity: defense against infections essential for all living organisms.Frontiers in immunology · 2026Review
- Biology of host-dependent restriction-modification in prokaryotes.EcoSal Plus · 2025Review
- Bacterial restriction-modification systems: mechanisms of defense against phage infection.Biophysics reports · 2025Article
- The early injected genomic region determines sensitivity to Type I restriction-modification defence against Autographiviridae phages.Nucleic acids research · 2025Article
- Advances in Diversity, Evolutionary Dynamics and Biotechnological Potential of Restriction-Modification Systems.Microorganisms · 2025Review
- Re-Emergence of Bacteriophages and Their Products as Antibacterial Agents: An Overview.International journal of molecular sciences · 2025Review
- First whole genome report ofCurrent research in microbial sciences · 2025Article
- Challenges and opportunities of phage therapy forApplied and environmental microbiology · 2024Review
- An enterococcal phage protein inhibits type IV restriction enzymes involved in antiphage defense.Nature communications · 2024Article
- An enterococcal phage protein broadly inhibits type IV restriction enzymes involved in antiphage defense.bioRxiv : the preprint server for biology · 2024Article
- RecA-dependent or independent recombination of plasmid DNA generates a conflict with the host EcoKI immunity by launching restriction alleviation.Nucleic acids research · 2024Article
- Inhibitors of bacterial immune systems: discovery, mechanisms and applications.Nature reviews. Genetics · 2024Review
- Recovering high-quality bacterial genomes from cross-contaminated cultures: a case study of marine Vibrio campbellii.BMC genomics · 2024Article
- Improving phage therapy by evasion of phage resistance mechanisms.JAC-antimicrobial resistance · 2024Review
- Diversity ofMicrobiology spectrum · 2024Article
- Regulation of anti-phage defense mechanisms by using cinnamaldehyde as a quorum sensing inhibitor.Frontiers in microbiology · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
Abstract
backgroundRestriction-modification (R-M) systems protect bacteria and archaea from attacks by bacteriophages and archaeal viruses. An R-M system specifically recognizes short sites in foreign DNA and cleaves it, while such sites in the host DNA are protected by methylation. Prokaryotic viruses have developed a number of strategies to overcome this host defense. The simplest anti-restriction strategy is the elimination of recognition sites in the viral genome: no sites, no DNA cleavage. Even a decrease of the number of recognition sites can help a virus to overcome this type of host defense. Recognition site avoidance has been a known anti-restriction strategy of prokaryotic viruses for decades. However, recognition site avoidance has not been systematically studied with the currently available sequence data. We analyzed the complete genomes of almost 4000 prokaryotic viruses with known host species and more than 17,000 restriction endonucleases with known specificities in terms of recognition site avoidance.
resultsWe observed considerable limitations of recognition site avoidance as an anti-restriction strategy. Namely, the avoidance of recognition sites is specific for dsDNA and ssDNA prokaryotic viruses. Avoidance is much more pronounced in the genomes of non-temperate bacteriophages than in the genomes of temperate ones. Avoidance is not observed for the sites of Type I and Type IIG systems and is very rarely observed for the sites of Type III systems. The vast majority of avoidance cases concern recognition sites of orthodox Type II restriction-modification systems. Even under these constraints, complete or almost complete elimination of sites is observed for approximately one-tenth of viral genomes and a significant under-representation for approximately one-fourth of them.
conclusionsAvoidance of recognition sites of restriction-modification systems is a widespread but not universal anti-restriction strategy of prokaryotic viruses.
Indexed as
Identifiers
What OpenQuestion holds
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.