Evolutionary Genomics of Defense Systems in Archaea and Bacteria

Abstract

Evolution of bacteria and archaea involves an incessant arms race against an enormous diversity of genetic parasites. Accordingly, a substantial fraction of the genes in most bacteria and archaea are dedicated to antiparasite defense. The functions of these defense systems follow several distinct strategies, including innate immunity; adaptive immunity; and dormancy induction, or programmed cell death. Recent comparative genomic studies taking advantage of the expanding database of microbial genomes and metagenomes, combined with direct experiments, resulted in the discovery of several previously unknown defense systems, including innate immunity centered on Argonaute proteins, bacteriophage exclusion, and new types of CRISPR-Cas systems of adaptive immunity. Some general principles of function and evolution of defense systems are starting to crystallize, in particular, extensive gain and loss of defense genes during the evolution of prokaryotes; formation of genomic defense islands; evolutionary connections between mobile genetic elements and defense, whereby genes of mobile elements are repeatedly recruited for defense functions; the partially selfish and addictive behavior of the defense systems; and coupling between immunity and dormancy induction/programmed cell death.

Characterization and repurposing of the endogenous Type I-F CRISPR-Cas system ofZymomonas mobilisfor genome engineering

“…In this study, we demonstrated that the enhancement of plasmid DNA transformation efficiencies through inactivating the Type IV DNA R-M system in Z. mobilis led to boosted genome engineering efficiencies of up to 100%, which are comparable to that with other endogenous Type I CRISPRbased prokaryotic engineering toolkits. R-M systems naturally occur in prokaryotes even more broadly than the CRISPR-Cas systems do, pointing towards a fact that both the adaptive CRISPR-Cas immune systems and the innate R-M systems may coexist in many bacteria and archaea (62). Thus, it may explain the perplexity that the diverse CRISPR-Cas systems broadly occur in prokaryotes in nature whereas the native CRISPR-based technologies are much lesser applied.…”

Towards physical principles of biological evolution

“…Once again, the outcome of such modeling studies represents patterning, a typical consequence of frustration in glass-like states (Figure 2). Apart from compartmentalization, host-parasite conflicts drive the evolution of versatile defense systems in the host and counter-defense systems in parasites, which is another prominent manifestation of biological complexity [76,[87][88][89].…”

Ecological memory preserves phage resistance mechanisms in bacteria

“…Survival of species in the presence of pathogens requires effective defense mechanisms, which exist in a wide range of biological systems [1][2][3][4]. Host-pathogen interactions are subject to the availability of susceptible hosts that sustain a viable pool of pathogens, while defense mechanisms are under evolutionary pressure to reduce or eliminate the ability of pathogens to proliferate.…”

“…In all instances, there is a metabolic cost associated with maintaining the resistance mechanisms [15][16][17], with the additional fitness costs due to self-targeting in RM systems [18] and CRISPR [19]. Yet, the diversity of phage-host systems in terms of routes of infection and modes of resistance points to strong evolutionary pressures favoring the emergence and maintenance of resistance [2,20,21].…”