ArticleInternational journal of molecular sciences2014
Identification of diversity-generating retroelements in human microbiomes.
Article in International journal of molecular sciences, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- A genomic atlas of the human gut virome elucidates genetic factors shaping host interactions.bioRxiv : the preprint server for biology · 2025Article
- Article
- Identification of diversity-generating retroelements in host-associated and environmental genomes: prevalence, diversity, and roles.BMC genomics · 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
- Optimization and evaluation of viral metagenomic amplification and sequencing procedures toward a genome-level resolution of the human fecal DNA virome.Journal of advanced research · 2023Article
- Candida expansion in the gut of lung cancer patients associates with an ecological signature that supports growth under dysbiotic conditions.Nature communications · 2023Article
- Identification and classification of reverse transcriptases in bacterial genomes and metagenomes.Nucleic acids research · 2022Article
- Review
- Prokaryotic reverse transcriptases: from retroelements to specialized defense systems.FEMS microbiology reviews · 2021Review
- Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome.Nature microbiology · 2021Article
- Ecology and molecular targets of hypermutation in the global microbiome.Nature communications · 2021Article
- NovelMicroorganisms · 2021Article
- Thousands of previously unknown phages discovered in whole-community human gut metagenomes.Microbiome · 2021Article
- Determinants of adenine-mutagenesis in diversity-generating retroelements.Nucleic acids research · 2021Article
- Review
- Article
- 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
Corrections and comments
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Authors and funding
1 author.
Funding
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Abstract
Diversity-generating retroelements (DGRs) are a unique family of retroelements that confer selective advantages to their hosts by accelerating the evolution of target genes through a specialized, error-prone, reverse transcription process. First identified in a Bordetella phage (BPP-1), which mediates the phage tropism specificity by generating variability in an involved gene, DGRs were predicted to be present in a larger collection of viral and bacterial species. A minimal DGR system is comprised of a reverse transcriptase (RTase) gene, a template sequence (TR) and a variable region (VR) within a target gene. We developed a computational tool, DGRscan, to allow either de novo identification (based on the prediction of potential template-variable region pairs) or similarity-based searches of DGR systems using known template sequences as the reference. The application of DGRscan to the human microbiome project (HMP) datasets resulted in the identification of 271 non-redundant DGR systems, doubling the size of the collection of known DGR systems. We further identified a large number of putative target genes (651, which share no more than 90% sequence identity at the amino acid level) that are potentially under diversification by the DGR systems. Our study provides the first survey of the DGR systems in the human microbiome, showing that the DGR systems are frequently found in human-associated bacterial communities, although they are of low incidence in individual genomes. Our study also provides functional clues for a large number of genes (reverse transcriptases and target genes) that were previously annotated as proteins of unknown functions or nonspecific functions.
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