Email updates

Keep up to date with the latest news and content from BMC Genomics and BioMed Central.

Open Access Research article

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

Thomas Schillinger1, Mohamed Lisfi2, Jingyun Chi2, John Cullum2 and Nora Zingler13*

Author Affiliations

1 Department of Molecular Genetics, University of Kaiserslautern, Kaiserslautern, Germany

2 Department of Genetics, University of Kaiserslautern, Kaiserslautern, Germany

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

For all author emails, please log on.

BMC Genomics 2012, 13:430  doi:10.1186/1471-2164-13-430

Published: 28 August 2012

Abstract

Background

Diversity 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.

Results

Here 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.

Conclusions

DiGReF 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.

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