ArticlePLoS genetics2011
Target site recognition by a diversity-generating retroelement.
Article in PLoS genetics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
What it found
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Who cites it
21 citing papers in PubMed, 33 citations in OpenAlex.
- Diversity-generating retroelements for programmable targeted hypermutagenesis.Nature biotechnology · 2026Article
- High-throughput analyses of a reconstituted diversity-generating retroelement identify intrinsic and extrinsic determinants of diversification.PLoS genetics · 2026Article
- High-throughput approaches to understand and engineer bacteriophages.Trends in biochemical sciences · 2023Review
- Review
- Prokaryotic reverse transcriptases: from retroelements to specialized defense systems.FEMS microbiology reviews · 2021Review
- Ecology and molecular targets of hypermutation in the global microbiome.Nature communications · 2021Article
- Review
- Role of diversity-generating retroelements for regulatory pathway tuning in cyanobacteria.BMC genomics · 2020Article
- MyDGR: a server for identification and characterization of diversity-generating retroelements.Nucleic acids research · 2019Article
- Diversity-generating retroelements: natural variation, classification and evolution inferred from a large-scale genomic survey.Nucleic acids research · 2018Article
- DGR mutagenic transposition occurs via hypermutagenic reverse transcription primed by nicked template RNA.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Retroelement-guided protein diversification abounds in vast lineages of Bacteria and Archaea.Nature microbiology · 2017Article
- Conservation of the C-type lectin fold for accommodating massive sequence variation in archaeal diversity-generating retroelements.BMC structural biology · 2016Article
- Diversity-generating Retroelements in Phage and Bacterial Genomes.Microbiology spectrum · 2014Review
- Identification of diversity-generating retroelements in human microbiomes.International journal of molecular sciences · 2014Article
- Bacterial genome instability.Microbiology and molecular biology reviews : MMBR · 2014Review
- Surface display of a massively variable lipoprotein by a Legionella diversity-generating retroelement.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Structure of the essential diversity-generating retroelement protein bAvd and its functionally important interaction with reverse transcriptase.Structure (London, England : 1993) · 2013Article
- Protein engineering with biosynthesized libraries from Bordetella bronchiseptica bacteriophage.PloS one · 2013Article
- Analysis of a comprehensive dataset of diversity generating retroelements generated by the program DiGReF.BMC genomics · 2012Article
Corrections and comments
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Authors and funding
8 authors at 2 institutions in 1 country.
Funding
Abstract
Diversity-generating retroelements (DGRs) are in vivo sequence diversification machines that are widely distributed in bacterial, phage, and plasmid genomes. They function to introduce vast amounts of targeted diversity into protein-encoding DNA sequences via mutagenic homing. Adenine residues are converted to random nucleotides in a retrotransposition process from a donor template repeat (TR) to a recipient variable repeat (VR). Using the Bordetella bacteriophage BPP-1 element as a prototype, we have characterized requirements for DGR target site function. Although sequences upstream of VR are dispensable, a 24 bp sequence immediately downstream of VR, which contains short inverted repeats, is required for efficient retrohoming. The inverted repeats form a hairpin or cruciform structure and mutational analysis demonstrated that, while the structure of the stem is important, its sequence can vary. In contrast, the loop has a sequence-dependent function. Structure-specific nuclease digestion confirmed the existence of a DNA hairpin/cruciform, and marker coconversion assays demonstrated that it influences the efficiency, but not the site of cDNA integration. Comparisons with other phage DGRs suggested that similar structures are a conserved feature of target sequences. Using a kanamycin resistance determinant as a reporter, we found that transplantation of the IMH and hairpin/cruciform-forming region was sufficient to target the DGR diversification machinery to a heterologous gene. In addition to furthering our understanding of DGR retrohoming, our results suggest that DGRs may provide unique tools for directed protein evolution via in vivo DNA diversification.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.