ArticleBMC genomics2015
Lifespan of restriction-modification systems critically affects avoidance of their recognition sites in host genomes.
Article in BMC genomics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed, 29 citations in OpenAlex.
- Biology of host-dependent restriction-modification in prokaryotes.EcoSal Plus · 2025Review
- Methylome evolution suggests lineage-dependent selection in the gastric pathogen Helicobacter pylori.Communications biology · 2023Article
- Base-excision restriction enzymes: expanding the world of epigenetic immune systems.DNA research : an international journal for rapid publication of reports on genes and genomes · 2023Article
- Article
- Role of DNA modifications in Mycoplasma gallisepticum.PloS one · 2022Article
- First Comparative Analysis ofFrontiers in microbiology · 2021Article
- Evolutionary Ecology and Interplay of Prokaryotic Innate and Adaptive Immune Systems.Current biology : CB · 2020Review
- Evolutionary selection against short nucleotide sequences in viruses and their related hosts.DNA research : an international journal for rapid publication of reports on genes and genomes · 2020Article
- Single-molecule sequencing detection of N6-methyladenine in microbial reference materials.Nature communications · 2019Article
- Avoidance of recognition sites of restriction-modification systems is a widespread but not universal anti-restriction strategy of prokaryotic viruses.BMC genomics · 2018Article
- Methylomic and phenotypic analysis of the ModH5 phasevarion of Helicobacter pylori.Scientific reports · 2017Article
- Evolutionary Genomics of Defense Systems in Archaea and Bacteria.Annual review of microbiology · 2017Review
- The third restriction-modification system from Thermus aquaticus YT-1: solving the riddle of two TaqII specificities.Nucleic acids research · 2017Article
- Restriction glycosylases: involvement of endonuclease activities in the restriction process.Nucleic acids research · 2017Article
- On avoided words, absent words, and their application to biological sequence analysis.Algorithms for molecular biology : AMB · 2017Article
- Evolutionary Ecology of Prokaryotic Immune Mechanisms.Microbiology and molecular biology reviews : MMBR · 2016Review
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundAvoidance of palindromic recognition sites of Type II restriction-modification (R-M) systems was shown for many R-M systems in dozens of prokaryotic genomes. However the phenomenon has not been investigated systematically for all presently available genomes and annotated R-M systems. We have studied all known recognition sites in thousands of prokaryotic genomes and found factors that influence their avoidance.
resultsOnly Type II R-M systems consisting of independently acting endonuclease and methyltransferase (called 'orthodox' here) cause avoidance of their sites, both palindromic and asymmetric, in corresponding prokaryotic genomes; the avoidance takes place for ~ 50 % of 1774 studied cases. It is known that prokaryotes can acquire and lose R-M systems. Thus it is possible to talk about the lifespan of an R-M system in a genome. We have shown that the recognition site avoidance correlates with the lifespan of R-M systems. The sites of orthodox R-M systems that are encoded in host genomes for a long time are avoided more often (up to 100 % in certain cohorts) than the sites of recently acquired ones. We also found cases of site avoidance in absence of the corresponding R-M systems in the genome. An analysis of closely related bacteria shows that such avoidance can be a trace of lost R-M systems. Sites of Type I, IIС/G, IIM, III, and IV R-M systems are not avoided in vast majority of cases.
conclusionsThe avoidance of orthodox Type II R-M system recognition sites in prokaryotic genomes is a widespread phenomenon. Presence of an R-M system without an underrepresentation of its site may indicate that the R-M system was acquired recently. At the same time, a significant underrepresentation of a site may be a sign of presence of the corresponding R-M system in this organism or in its ancestors for a long time. The drastic difference between site avoidance for orthodox Type II R-M systems and R-M systems of other types can be explained by a higher rate of specificity changes or a less self-toxicity of the latter.
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