ArticleBMC genomics2012
Analysis of a comprehensive dataset of diversity generating retroelements generated by the program DiGReF.
Article in BMC genomics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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24 citing papers in PubMed, 36 citations in OpenAlex.
- High-throughput analyses of a reconstituted diversity-generating retroelement identify intrinsic and extrinsic determinants of diversification.PLoS genetics · 2026Article
- Identification of diversity-generating retroelements in host-associated and environmental genomes: prevalence, diversity, and roles.BMC genomics · 2024Article
- Genome Analysis of Epsilon CrAss-like Phages.Viruses · 2024Article
- Targeted hypermutation of putative antigen sensors in multicellular bacteria.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Tentaclins-A Novel Family of Phage Receptor-Binding Proteins That Can Be Hypermutated by DGR Systems.International journal of molecular sciences · 2023Article
- Review
- Prokaryotic reverse transcriptases: from retroelements to specialized defense systems.FEMS microbiology reviews · 2021Review
- Review
- Article
- Discovery and characterization of the evolution, variation and functions of diversity-generating retroelements using thousands of genomes and metagenomes.BMC genomics · 2019Article
- MyDGR: a server for identification and characterization of diversity-generating retroelements.Nucleic acids research · 2019Article
- A diversity-generating retroelement encoded by a globally ubiquitous Bacteroides phage.Microbiome · 2018Article
- Diversity-generating retroelements: natural variation, classification and evolution inferred from a large-scale genomic survey.Nucleic acids research · 2018Article
- Retroelement-guided protein diversification abounds in vast lineages of Bacteria and Archaea.Nature microbiology · 2017Article
- Article
- Conservation of the C-type lectin fold for accommodating massive sequence variation in archaeal diversity-generating retroelements.BMC structural biology · 2016Article
- Genomic and Metagenomic Analysis of Diversity-Generating Retroelements Associated with Treponema denticola.Frontiers in microbiology · 2016Article
- Targeted diversity generation by intraterrestrial archaea and archaeal viruses.Nature communications · 2015Article
- Diversity-generating Retroelements in Phage and Bacterial Genomes.Microbiology spectrum · 2014Review
- Identification of diversity-generating retroelements in human microbiomes.International journal of molecular sciences · 2014Article
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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
backgroundDiversity Generating Retroelements (DGRs) are genetic cassettes that can introduce tremendous diversity into a short, defined region of the genome. They achieve hypermutation through replacement of the variable region with a strongly mutated cDNA copy generated by the element-encoded reverse transcriptase. In contrast to "selfish" retroelements such as group II introns and retrotransposons, DGRs impart an advantage to their host by increasing its adaptive potential. DGRs were discovered in a bacteriophage, but since then additional examples have been identified in some bacterial genomes.
resultsHere we present the program DiGReF that allowed us to comprehensively screen available databases for DGRs. We identified 155 DGRs which are found in all major classes of bacteria, though exhibiting sporadic distribution across species. Phylogenetic analysis and sequence comparison showed that DGRs move between genomes by associating with various mobile elements such as phages, transposons and plasmids. The DGR cassettes exhibit high flexibility in the arrangement of their components and easily acquire additional paralogous target genes. Surprisingly, the genomic data alone provide new insights into the molecular mechanism of DGRs. Most notably, our data suggest that the template RNA is transcribed separately from the rest of the element.
conclusionsDiGReF is a valuable tool to detect DGRs in genome data. Its output allows comprehensive analysis of various aspects of DGR biology, thus deepening our understanding of the role DGRs play in prokaryotic genome plasticity, from the global down to the molecular level.
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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.