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Int. J. Mol. Sci. 2014, 15(8), 14234-14246; doi:10.3390/ijms150814234

Identification of Diversity-Generating Retroelements in Human Microbiomes

Division of Computer Science, School of Informatics and Computing, Indiana University, Bloomington, IN 47405, USA
Received: 21 June 2014 / Revised: 2 August 2014 / Accepted: 6 August 2014 / Published: 15 August 2014
(This article belongs to the Special Issue Metagenomics: a Powerful Lens Viewing the Microbial World)
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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. View Full-Text
Keywords: DGR; human microbiome; DGRscan; reverse transcriptase (RTase); template region (TR); variable region (VR) DGR; human microbiome; DGRscan; reverse transcriptase (RTase); template region (TR); variable region (VR)
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This is an open access article distributed under the Creative Commons Attribution License (CC BY 3.0).

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Ye, Y. Identification of Diversity-Generating Retroelements in Human Microbiomes. Int. J. Mol. Sci. 2014, 15, 14234-14246.

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