This is quite a fascinating paper (h/t: @suryasaha). Here Koonin is connecting the evolutionary dots from bacterial immune system all the way to V(D)J.
For those who do not know, Eugene Koonin’s group predicted the existence of CRISPR-cas immune system in 2005 using bioinformatics methods [also check - Makarova, K. S. et al. A putative RNA-interference based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action. Biol. Direct 1, 7 (2006).]. That was a year before Barrangou published his experimental paper and five years before George Church decided to call himself the inventor and applied for patent.
Adaptive immune systems in prokaryotes and animals give rise to long-term memory through modification of specific genomic loci, such as by insertion of foreign (viral or plasmid) DNA fragments into clustered regularly interspaced short palindromic repeat (CRISPR) loci in prokaryotes and by V(D)J recombination of immunoglobulin genes in vertebrates. Strikingly, recombinases derived from unrelated mobile genetic elements have essential roles in both prokaryotic and vertebrate adaptive immune systems. Mobile elements, which are ubiquitous in cellular life forms, provide the only known, naturally evolved tools for genome engineering that are successfully adopted by both innate immune systems and genome-editing technologies. In this Opinion article, we present a general scenario for the origin of adaptive immunity from mobile elements and innate immune systems.