F pAgo have remained obscure. However, comparative analysis of the genomic neighborhoods of the pAgo

F pAgo have remained obscure. However, comparative analysis of the genomic neighborhoods of the pAgo genes has strongly suggested a role in defense [44]. Indeed, many of the pAgo genes are embedded in `defense islands’, the regions of bacterial and archaeal genomes that are significantly enriched for genes involved in various defense functions. Furthermore, even more tellingly, genes encoding pAgo variants withinactivated PIWI domains are often adjacent to genes encoding other nucleases, leading to the obvious hypothesis that PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/28993237 these enzymatically inactive pAgos ensure the recognition of targets that are then cleaved by the associated active nucleases. The hypothesis on the defense function of pAgo has been experimentally tested, with striking results, although the scope of the experiments remains limited. The ability to cleave target nucleic acids in vitro has been demonstrated for pAgos from the bacteria Aquifex aeolicus [42] and Thermus thermophilus [45], and the archaea Methanocaldococcus jannaschii [46] and Pyrococcus furiosus [47]. Notably, all three catalytically active pAgos employ ssDNA guides but differ in their ability to cleave RNA or DNA. In contrast, no nuclease activity has been demonstrated for the RNA-binding pAgo of the bacterium Rhodobacter sphaeroides that has been predicted to be inactive due to mutations in the catalytic center of the PIWI domain [48]. The defense functions have been demonstrated for the pAgo from R. spheroides [48] and T. thermophilus [49]. The T. thermophilus Ago restricts plasmid replication by cleaving the plasmid DNA using plasmid-derived small ssDNA guides. The mechanism of the guide generation is not understood in detail but it has been shown that the catalytic residues of the PIWI domain are required [49]. Accordingly, it appears likely that pAgo first shreds the plasmid DNA in a guide- (and presumably, sequence) independent manner and then becomes a target-specific nuclease after acquiring the guides. What determines the self/non-self discrimination at the first stage, remains get BMS-5 unclear. For the R. spheroides pAgo, association with short RNAs that represent much of the bacterial transcriptome has been demonstrated [48]. In addition, this Ago is associated with ssDNA molecules complementary to the small RNAs, and this DNA population is enriched in “foreign” sequences, those from plasmids as well as mobile elements integrated into the bacterial chromosome. Apparently, in R. sphaeroides, pAgo samples degradation products of the bacterial transcriptome and then, via yet unknown mechanisms, preferentially generates complementary DNAs for foreign sequences that are used to repress the expression of the cognate elements. Whether or not the function of this catalytically inactive pAgo requires other nucleases, remains to be determined. Nevertheless, the presence of pAgo within evolutionarily conserved operons with genes for nucleases and helicases [20, 44] implies complex organization of the prokaryotic Ago-centered defense systems that remains to be investigated. Such experiments should clarify the mechanisms employed by the prokaryotic pAgo-centered defense systems to generate the guide RNA and DNA molecules and discriminate the genomes of parasites from those of the hosts.Koonin Biology Direct (2017) 12:Page 4 ofUnlike the prokaryotic counterparts, the eukaryotic Ago-centered molecular machinery that is involved in RNAi has been studied in great detail. The diversity of the eukaryotic Ago family is.