1
|
Fokina AS, Karyagina AS, Rusinov IS, Moshensky DM, Spirin SA, Alexeevski AV. Evolution of Restriction–Modification Systems Consisting of One Restriction Endonuclease and Two DNA Methyltransferases. Biochemistry Moscow 2023; 88:253-261. [PMID: 37072330 DOI: 10.1134/s0006297923020086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
Some restriction-modification systems contain two DNA methyltransferases. In the present work, we have classified such systems according to the families of catalytic domains present in the restriction endonucleases and both DNA methyltransferases. Evolution of the restriction-modification systems containing an endonuclease with a NOV_C family domain and two DNA methyltransferases, both with DNA_methylase family domains, was investigated in detail. Phylogenetic tree of DNA methyltransferases from the systems of this class consists of two clades of the same size. Two DNA methyltransferases of each restriction-modification system of this class belong to the different clades. This indicates independent evolution of the two methyltransferases. We detected multiple cross-species horizontal transfers of the systems as a whole, as well as the cases of gene transfer between the systems.
Collapse
Affiliation(s)
- Anastasiya S Fokina
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Anna S Karyagina
- N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Healthcare of the Russian Federation, Moscow, 123098, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
- All-Russia Research Institute of Agricultural Biotechnology, Moscow, 127550, Russia
| | - Ivan S Rusinov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - Denis M Moshensky
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119234, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - Sergey A Spirin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia.
- National Research University Higher School of Economics, Moscow, 109028, Russia
- Federal State Institution "Scientific Research Institute for System Analysis of the Russian Academy of Sciences", Moscow, 117218, Russia
| | - Andrey V Alexeevski
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119234, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
- Federal State Institution "Scientific Research Institute for System Analysis of the Russian Academy of Sciences", Moscow, 117218, Russia
| |
Collapse
|
2
|
Rusinov IS, Ershova AS, Karyagina AS, Spirin SA, Alexeevski AV. Avoidance of recognition sites of restriction-modification systems is a widespread but not universal anti-restriction strategy of prokaryotic viruses. BMC Genomics 2018; 19:885. [PMID: 30526500 PMCID: PMC6286503 DOI: 10.1186/s12864-018-5324-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 11/28/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Restriction-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. RESULTS We 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. CONCLUSIONS Avoidance of recognition sites of restriction-modification systems is a widespread but not universal anti-restriction strategy of prokaryotic viruses.
Collapse
Affiliation(s)
- I S Rusinov
- Belozersky Institute of Physical and Chemical Biology, Lomonosov Moscow State University, 119992, Moscow, Russia
| | - A S Ershova
- Belozersky Institute of Physical and Chemical Biology, Lomonosov Moscow State University, 119992, Moscow, Russia.,Gamaleya National Research Center of Epidemiology and Microbiology of the Ministry of Health of the Russian Federation, 123098, Moscow, Russia.,All-Russia Research Institute of Agricultural Biotechnology, 127550, Moscow, Russia
| | - A S Karyagina
- Belozersky Institute of Physical and Chemical Biology, Lomonosov Moscow State University, 119992, Moscow, Russia.,Gamaleya National Research Center of Epidemiology and Microbiology of the Ministry of Health of the Russian Federation, 123098, Moscow, Russia.,All-Russia Research Institute of Agricultural Biotechnology, 127550, Moscow, Russia
| | - S A Spirin
- Belozersky Institute of Physical and Chemical Biology, Lomonosov Moscow State University, 119992, Moscow, Russia.,Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119991, Moscow, Russia.,National Research University Higher School of Economics, 101000, Moscow, Russia.,Institute of System Studies, 117281, Moscow, Russia
| | - A V Alexeevski
- Belozersky Institute of Physical and Chemical Biology, Lomonosov Moscow State University, 119992, Moscow, Russia. .,Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119991, Moscow, Russia. .,Institute of System Studies, 117281, Moscow, Russia.
| |
Collapse
|
3
|
Rusinov IS, Ershova AS, Karyagina AS, Spirin SA, Alexeevski AV. Comparison of Methods of Detection of Exceptional Sequences in Prokaryotic Genomes. Biochemistry (Mosc) 2018; 83:129-139. [PMID: 29618299 DOI: 10.1134/s0006297918020050] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Many proteins need recognition of specific DNA sequences for functioning. The number of recognition sites and their distribution along the DNA might be of biological importance. For example, the number of restriction sites is often reduced in prokaryotic and phage genomes to decrease the probability of DNA cleavage by restriction endonucleases. We call a sequence an exceptional one if its frequency in a genome significantly differs from one predicted by some mathematical model. An exceptional sequence could be either under- or over-represented, depending on its frequency in comparison with the predicted one. Exceptional sequences could be considered biologically meaningful, for example, as targets of DNA-binding proteins or as parts of abundant repetitive elements. Several methods to predict frequency of a short sequence in a genome, based on actual frequencies of certain its subsequences, are used. The most popular are methods based on Markov chain models. But any rigorous comparison of the methods has not previously been performed. We compared three methods for the prediction of short sequence frequencies: the maximum-order Markov chain model-based method, the method that uses geometric mean of extended Markovian estimates, and the method that utilizes frequencies of all subsequences including discontiguous ones. We applied them to restriction sites in complete genomes of 2500 prokaryotic species and demonstrated that the results depend greatly on the method used: lists of 5% of the most under-represented sites differed by up to 50%. The method designed by Burge and coauthors in 1992, which utilizes all subsequences of the sequence, showed a higher precision than the other two methods both on prokaryotic genomes and randomly generated sequences after computational imitation of selective pressure. We propose this method as the first choice for detection of exceptional sequences in prokaryotic genomes.
Collapse
Affiliation(s)
- I S Rusinov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
| | | | | | | | | |
Collapse
|
4
|
Ershova AS, Rusinov IS, Spirin SA, Karyagina AS, Alexeevski AV. Role of Restriction-Modification Systems in Prokaryotic Evolution and Ecology. Biochemistry (Mosc) 2016; 80:1373-86. [PMID: 26567582 DOI: 10.1134/s0006297915100193] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Restriction-modification (R-M) systems are able to methylate or cleave DNA depending on methylation status of their recognition site. It allows them to protect bacterial cells from invasion by foreign DNA. Comparative analysis of a large number of available bacterial genomes and methylomes clearly demonstrates that the role of R-M systems in bacteria is wider than only defense. R-M systems maintain heterogeneity of a bacterial population and are involved in adaptation of bacteria to change in their environmental conditions. R-M systems can be essential for host colonization by pathogenic bacteria. Phase variation and intragenomic recombinations are sources of the fast evolution of the specificity of R-M systems. This review focuses on the influence of R-M systems on evolution and ecology of prokaryotes.
Collapse
Affiliation(s)
- A S Ershova
- Belozerksy Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.
| | | | | | | | | |
Collapse
|