ArticleNucleic acids research2012
Movement of DNA sequence recognition domains between non-orthologous proteins.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers, 1 of them a synthesis that pooled it.
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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.
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Who cites it
22 citing papers in PubMed, 1 synthesis or guideline pooled it, 34 citations in OpenAlex.
- Pooled it
- Expanding the landscape of BREX diversity: uncovering multi-layered functional frameworks and identification of novel BREX-related defense systems.Nucleic acids research · 2026Article
- Towards molecular evolutionary epigenomics with an expanded nucleotide code involving methylated bases.DNA research : an international journal for rapid publication of reports on genes and genomes · 2025Article
- Methylome evolution suggests lineage-dependent selection in the gastric pathogen Helicobacter pylori.Communications biology · 2023Article
- Selective and non-selective bottlenecks as drivers of the evolution of hypermutable bacterial loci.Molecular microbiology · 2020Review
- The bacterial epigenome.Nature reviews. Microbiology · 2020Review
- Networking and Specificity-Changing DNA Methyltransferases inFrontiers in microbiology · 2020Article
- Evolution of a novel chimeric maltotriose transporter in Saccharomyces eubayanus from parent proteins unable to perform this function.PLoS genetics · 2019Article
- Kinetic and catalytic properties of M.HpyAXVII, a phase-variable DNA methyltransferase fromThe Journal of biological chemistry · 2019Article
- A survey of Type III restriction-modification systems reveals numerous, novel epigenetic regulators controlling phase-variable regulons; phasevarions.Nucleic acids research · 2018Article
- Methylomic and phenotypic analysis of the ModH5 phasevarion of Helicobacter pylori.Scientific reports · 2017Article
- Epigenetic regulation of development and pathogenesis in fungal plant pathogens.Molecular plant pathology · 2017Review
- Rpn (YhgA-Like) Proteins of Escherichia coli K-12 and Their Contribution to RecA-Independent Horizontal Transfer.Journal of bacteriology · 2017Article
- Restriction-Modification Systems as Mobile Genetic Elements in the Evolution of an Intracellular Symbiont.Molecular biology and evolution · 2016Article
- Distribution of the type III DNA methyltransferases modA, modB and modD among Neisseria meningitidis genotypes: implications for gene regulation and virulence.Scientific reports · 2016Article
- The Capricious Nature of Bacterial Pathogens: Phasevarions and Vaccine Development.Frontiers in immunology · 2016Review
- Lifespan of restriction-modification systems critically affects avoidance of their recognition sites in host genomes.BMC genomics · 2015Article
- Article
- Methylome diversification through changes in DNA methyltransferase sequence specificity.PLoS genetics · 2014Article
- To be or not to be: regulation of restriction-modification systems and other toxin-antitoxin systems.Nucleic acids research · 2014Review
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Comparisons of proteins show that they evolve through the movement of domains. However, in many cases, the underlying mechanisms remain unclear. Here, we observed the movements of DNA recognition domains between non-orthologous proteins within a prokaryote genome. Restriction-modification (RM) systems, consisting of a sequence-specific DNA methyltransferase and a restriction enzyme, contribute to maintenance/evolution of genomes/epigenomes. RM systems limit horizontal gene transfer but are themselves mobile. We compared Type III RM systems in Helicobacter pylori genomes and found that target recognition domain (TRD) sequences are mobile, moving between different orthologous groups that occupy unique chromosomal locations. Sequence comparisons suggested that a likely underlying mechanism is movement through homologous recombination of similar DNA sequences that encode amino acid sequence motifs that are conserved among Type III DNA methyltransferases. Consistent with this movement, incongruence was observed between the phylogenetic trees of TRD regions and other regions in proteins. Horizontal acquisition of diverse TRD sequences was suggested by detection of homologs in other Helicobacter species and distantly related bacterial species. One of these RM systems in H. pylori was inactivated by insertion of another RM system that likely transferred from an oral bacterium. TRD movement represents a novel route for diversification of DNA-interacting proteins.
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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.