ArticleBMC bioinformatics2015
Phylogenomics and sequence-structure-function relationships in the GmrSD family of Type IV restriction enzymes.
Article in BMC bioinformatics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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33 citing papers in PubMed, 47 citations in OpenAlex.
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- The early injected genomic region determines sensitivity to Type I restriction-modification defence against Autographiviridae phages.Nucleic acids research · 2025Article
- Defence systems encoded by core genomic islands of seventh pandemicPhilosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Review
- Modified DNA substrate selectivity by GmrSD-family Type IV restriction enzyme BrxU.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Article
- Anti-restriction functions of injected phage proteins revealed by peeling back layers of bacterial immunity.Nature communications · 2025Article
- Metagenomic selections reveal diverse antiphage defenses in human and environmental microbiomes.Cell host & microbe · 2025Article
- West African-South American pandemic Vibrio cholerae encodes multiple distinct phage defence systems.Nature microbiology · 2025Article
- Unveiling the multifaceted domain polymorphism of the Menshen antiphage system.Nucleic acids research · 2025Article
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- Metagenomic selections reveal diverse antiphage defenses in human and environmental microbiomes.bioRxiv : the preprint server for biology · 2025Article
- Bacterial Shedu immune nucleases share a common enzymatic core regulated by diverse sensor domains.Molecular cell · 2025Article
- A chromosomal mutation is superior to a plasmid-encoded mutation for plasmid fitness cost compensation.PLoS biology · 2024Article
- AJournal of bacteriology · 2024Article
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- Compensatory evolution of chromosomes and plasmids counteracts the plasmid fitness cost.Ecology and evolution · 2024Article
- An enterococcal phage protein broadly inhibits type IV restriction enzymes involved in antiphage defense.bioRxiv : the preprint server for biology · 2024Article
- AbioRxiv : the preprint server for biology · 2024Article
- Mobile class A β-lactamase geneMicrobiology spectrum · 2024Article
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundGmrSD is a modification-dependent restriction endonuclease that specifically targets and cleaves glucosylated hydroxymethylcytosine (glc-HMC) modified DNA. It is encoded either as two separate single-domain GmrS and GmrD proteins or as a single protein carrying both domains. Previous studies suggested that GmrS acts as endonuclease and NTPase whereas GmrD binds DNA.
methodsIn this work we applied homology detection, sequence conservation analysis, fold recognition and homology modeling methods to study sequence-structure-function relationships in the GmrSD restriction endonucleases family. We also analyzed the phylogeny and genomic context of the family members.
resultsResults of our comparative genomics study show that GmrS exhibits similarity to proteins from the ParB/Srx fold which can have both NTPase and nuclease activity. In contrast to the previous studies though, we attribute the nuclease activity also to GmrD as we found it to contain the HNH endonuclease motif. We revealed residues potentially important for structure and function in both domains. Moreover, we found that GmrSD systems exist predominantly as a fused, double-domain form rather than as a heterodimer and that their homologs are often encoded in regions enriched in defense and gene mobility-related elements. Finally, phylogenetic reconstructions of GmrS and GmrD domains revealed that they coevolved and only few GmrSD systems appear to be assembled from distantly related GmrS and GmrD components.
conclusionsOur study provides insight into sequence-structure-function relationships in the yet poorly characterized family of Type IV restriction enzymes. Comparative genomics allowed to propose possible role of GmrD domain in the function of the GmrSD enzyme and possible active sites of both GmrS and GmrD domains. Presented results can guide further experimental characterization of these enzymes.
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