Rast between the fortunes of the two systems could be due to the toxicity of certain Cas proteins that would be unleashed in eukaryotes because of operon disruption. In eukaryotes, numerous inactivated Argonautes are recruited for regulatory roles, primarily in conjunction with miRNA, and the same can be expected to occur in prokaryotes although experimental data are currently lacking. The CRISPR-Cas system also assumed non-defense, regulatory functions in various bacteria even as these remain understudied as well [127]. The use of RNA or DNA guides for targeting unique areas of the genome (or transcriptome) is the most general possible strategy to achieve the goals of defense, attack and regulation. Apart from the two defense systems discussed above, each of which also had been repeatedly recruited for regulatory functions, there are several other molecular machineries involved in natural genome engineering and regulation. A striking case in point is the system of DNA elimination during ciliate macronucleus development that relies on the so called scanRNAs and leads to the removal of varying fraction of the genome (up to more the 90 ) in different ciliates [19, 128]. Many of the PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/28499442 removed sequences originate from (largely inactive) transposable elements, and therefore, these mechanisms, in a sense, represent a distinct form of anti-parasite defense [129]. Although not studied in comparable detail, it appears most likely the DNA diminution that occurs during the developments of certain animals, e.g. Crustacea, employs analogous mechanisms [130]. A widespread regulatory system that functions on the RNA-guide principle is the prokaryotic small RNA regulation [131]. Bacterial and archaeal genomes encode from tens to hundreds small regulatory that in bacteria function mostly as complexes with the RNA chaperone Hfq [132]. This regulatory network is completely unrelated to either the Argonaute machinery or CRISPR-Cas. The existence of yet other RNA-guided pathways is indicated by the growing evidence of the major role of endogenous antisense RNA in the regulation of gene expression in eukaryotes [133, 134]. The universality of the central principle of RNA/DNAguided defense and regulation strongly suggests that systems functioning on this principle evolved on multipleoccasions in all forms of life. Even if the most common of these systems are already known, identification of new ones through combination of comparative genomics and experimentation is a major research challenge.Reviewers’ commentsReviewer 1: Mikhail Gelfand, Research and Training Center on Bioinformatics, A.A. Kharkevich Institute for Pedalitin permethyl ether web Information Transmission Problems, Russian Academy of SciencesThis is a dual-purpose manuscript. Mainly it consists of a precise and complete, as of today, review of prokaryotic systems of nucleic acid (NA)-based immunity and prokaryotic origins of eukaryotic systems. However, I suspect that the real reason for writing this text has been the hypothesis explaining why adaptive NA-based CRISPRCas immunity has not been inherited by eukaryotes, unlike RNA-interference mechanisms. Author’s response: I appreciate the positive assessment and to a large degree concur with the reviewer regarding the incentive behind this manuscript. I would not go so far as to say that this is the “real” reason but, indeed, the main idea was to trace the dramatically different fates of different eukaryotic defense systems in eukaryotes, and in particular, to understand as bes.