2012
DOI: 10.1186/1471-2164-13-430
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Analysis of a comprehensive dataset of diversity generating retroelements generated by the program DiGReF

Abstract: 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 bacterio… Show more

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Cited by 32 publications
(75 citation statements)
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“…DGRs can have either one or two target genes, and there is variation as well in the order and orientations of the RT, TR, avd, and target genes (62). Relevant to this article is the fact that even without experimental validation, DGRs can be identified bioinformatically in genomic sequences through the detection of the two repeat sequences, TR and VR (∼90% identity), which are adjacent to an RT gene, with the VR sequence bearing A-to-N differences relative to the TR sequence (71). This illustrates how a retroelement and its potential properties can be identified and/or classified based on sequence alone, a pertinent point when considering the many uncharacterized RT and RT-like sequences (below).…”
Section: Dgrs: Retroelements That Evolved a Useful Functionmentioning
confidence: 99%
“…DGRs can have either one or two target genes, and there is variation as well in the order and orientations of the RT, TR, avd, and target genes (62). Relevant to this article is the fact that even without experimental validation, DGRs can be identified bioinformatically in genomic sequences through the detection of the two repeat sequences, TR and VR (∼90% identity), which are adjacent to an RT gene, with the VR sequence bearing A-to-N differences relative to the TR sequence (71). This illustrates how a retroelement and its potential properties can be identified and/or classified based on sequence alone, a pertinent point when considering the many uncharacterized RT and RT-like sequences (below).…”
Section: Dgrs: Retroelements That Evolved a Useful Functionmentioning
confidence: 99%
“…Diversity-generating retroelements (DGRs) rely on reverse transcription to create diversity in DNA sequences that encode proteins involved in ligandreceptor interactions, mainly extracellular, cell wall, or membrane proteins. The main studied example is in the BPP-1 bacteriophage of Bordetella species, but DGR sequence patterns have been found in a wide range of bacterial prophages, plasmids, and chromosomes (178)(179)(180)(181)(182)(183)(184). DGRs are usually composed of two repeats of about 150 bp and two ORFs (Fig.…”
Section: Inteins Introns and Retroelementsmentioning
confidence: 99%
“…This discovery demonstrated that DGRs are common in the genomes of bacteriophages found in the lower gastrointestinal tract. Using a custom-made script called DiGReF, Schillinger et al conducted a large scale search of sequence databases and identified 155 DGRs in phage and bacteria, both Gram-positive and Gram-negative (13). DGRs are particularly abundant in certain phyla, with bacteroides (27.7%), firmicutes (31.0%) and proteobacteria (25.2%) containing the greatest numbers of unique elements.…”
Section: Dgrs Are Widespread In Bacterial and Phage Genomesmentioning
confidence: 99%
“…DGR RTs range from 260 to 527 amino acids, with an average length of ~380 residues (Figure 6B) (13). They have divergent sequences at their N- and C-termini, with a conserved central core that includes common structural motifs found in most other RTs.…”
Section: Dgr Rts and Adenine Mutagenesismentioning
confidence: 99%
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