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Identification of Diversity-Generating Retroelements in Human Microbiomes

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 mediat...

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Autor principal: Ye, Yuzhen
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4159848/
https://www.ncbi.nlm.nih.gov/pubmed/25196521
http://dx.doi.org/10.3390/ijms150814234
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author Ye, Yuzhen
author_facet Ye, Yuzhen
author_sort Ye, Yuzhen
collection PubMed
description 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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spelling pubmed-41598482014-09-18 Identification of Diversity-Generating Retroelements in Human Microbiomes Ye, Yuzhen Int J Mol Sci Article 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. MDPI 2014-08-15 /pmc/articles/PMC4159848/ /pubmed/25196521 http://dx.doi.org/10.3390/ijms150814234 Text en © 2014 by the authors; licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution license (http://creativecommons.org/licenses/by/3.0/).
spellingShingle Article
Ye, Yuzhen
Identification of Diversity-Generating Retroelements in Human Microbiomes
title Identification of Diversity-Generating Retroelements in Human Microbiomes
title_full Identification of Diversity-Generating Retroelements in Human Microbiomes
title_fullStr Identification of Diversity-Generating Retroelements in Human Microbiomes
title_full_unstemmed Identification of Diversity-Generating Retroelements in Human Microbiomes
title_short Identification of Diversity-Generating Retroelements in Human Microbiomes
title_sort identification of diversity-generating retroelements in human microbiomes
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4159848/
https://www.ncbi.nlm.nih.gov/pubmed/25196521
http://dx.doi.org/10.3390/ijms150814234
work_keys_str_mv AT yeyuzhen identificationofdiversitygeneratingretroelementsinhumanmicrobiomes