Diversity-generating retroelements (DGRs) are a family of

retroelements Retrotransposons (also called Class I transposable elements or transposons via RNA intermediates) are a type of genetic component that copy and paste themselves into different genomic locations (transposon) by converting RNA back into DNA through ...

that were first found in '' Bordetella phage (BPP-1)'', and since been found in bacteria (e.g.''

Treponema denticola ''Treponema denticola'' is a Gram-negative, obligate anaerobic, motile and highly proteolytic spirochete bacterium. It is one of four species of oral spirochetes to be reliably cultured, the others being ''Treponema pectinovorum, Treponema socra ...

'' ''and

Legionella pneumophila ''Legionella pneumophila'' is a thin, aerobic, pleomorphic, flagellated, non-spore-forming, Gram-negative bacterium of the genus ''Legionella''. ''L. pneumophila'' is the primary human pathogenic bacterium in this group and is the causative age ...

''),

Archaea Archaea ( ; singular archaeon ) is a domain of single-celled organisms. These microorganisms lack cell nuclei and are therefore prokaryotes. Archaea were initially classified as bacteria, receiving the name archaebacteria (in the Archaebac ...

, Archaean viruses (e.g. ANMV-1), temperate

phage A bacteriophage (), also known informally as a ''phage'' (), is a duplodnaviria virus that infects and replicates within bacteria and archaea. The term was derived from "bacteria" and the Greek φαγεῖν ('), meaning "to devour". Bacterio ...

s (e.g. Hankyphage and CrAss-like phage), and lytic phages. DGRs benefit their host by mutating particular regions of specific target proteins, for instance, phage tail fiber in BPP-1, lipoprotein in legionella ''pneumophila'' ( the pathogen behind Legionnaires disease), and TvpA in ''Treponema denticola (oral-associated periopathogen)'.'' An error-prone

reverse transcriptase A reverse transcriptase (RT) is an enzyme used to generate complementary DNA (cDNA) from an RNA template, a process termed reverse transcription. Reverse transcriptases are used by viruses such as HIV and hepatitis B to replicate their genomes, ...

is responsible for generating these

hypervariable region A hypervariable region (HVR) is a location within nuclear DNA or the D-loop of mitochondrial DNA in which base pairs of nucleotides repeat (in the case of nuclear DNA) or have substitutions (in the case of mitochondrial DNA). Changes or repeats in ...

s in target proteins (Mutagenic retrohoming). In mutagenic retrohoming, a mutagenized cDNA (containing substantial A to N mutations) is reverse transcribed from a template region (TR), and is replaced with a segment similar to the template region called variable region (VR). Accessory variability determinant (Avd) protein is another component of DGRs, and its complex formation with the error-prone RT is of importance to mutagenic rehoming. DGRs are beneficial to the evolution and survival of their host. A large fraction of

Faecalibacterium prausnitzii ''Faecalibacterium'' is a genus of bacteria. Its sole known species, ''Faecalibacterium prausnitzii'' is gram-positive, mesophilic, rod-shaped, anaerobic and is one of the most abundant and important commensal bacteria of the human gut microbiot ...

phages contain DGRs that are believed to have a role in phage adaptability to the digestive system, as patients with inflammatory bowel disease (IBD), have more phages, but less F.prausnitzii in their stool samples compared to healthy individuals, suggesting that these phages activate during the illness, and that they may trigger F.prausnitzii depletion. Several tools have been implemented to identify DGRs, such as DiGReF, DGRscan, MetaCSST, and myDGR

References

{{Organisms et al. Mobile genetic elements Molecular biology

See also

References