Analysis of a comprehensive dataset of diversity generating retroelements generated by the program DiGReF

BMC Genomics

Research Article

John Cullum¹  Mohamed Lisfi¹  Jingyun Chi¹  Thomas Schillinger²  Nora Zingler³ 

[1] Department of Genetics, University of Kaiserslautern, Kaiserslautern, Germany;Department of Molecular Genetics, University of Kaiserslautern, Kaiserslautern, Germany;Department of Molecular Genetics, University of Kaiserslautern, Kaiserslautern, Germany;Department of Biology - Group of Molecular Genetics, University of Kaiserslautern, Paul-Ehrlich-Straße Building 24, Room 117, D-67663, Kaiserslautern, Germany;

关键词: DGR;    Diversity-generating retroelement;    Targeted mutagenesis;    Prokaryote evolution;    Horizontal gene transfer;    Reverse transcriptase;    DiGReF;   

DOI  :  10.1186/1471-2164-13-430

 received in 2012-05-16, accepted in 2012-08-18,  发布年份 2012

来源: Springer

【 摘 要 】

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.

【 授权许可】

Unknown   
© Schillinger et al.; licensee BioMed Central Ltd. 2012. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.