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Report No.
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A Predicted CRISPR-mediated symbiosis between uncultivated archaea

Esser, S. P.*; Rahlff, J.*; Zhao, W.*; Predl, M.*; Plewka, J.*; Sures, K.*; Wimmer, F.*; Lee, J.*; Adam, P. S.*; McGonigle, J.*; Turzynski, V.*; Banas, I.*; Schwank, K.*; Krupovic, M.*; Bornemann, T. L. V.*; Figueroa-Gonzalez, P. A.*; Jarett, J.*; Rattei, T.*; Amano, Yuki   ; Blaby, I. K.*; Cheng, J.-F.*; Brazelton, W. J.*; Beisel, C. L.*; Woyke, T.*; Zhang, Y.*; Probst, A. J.*

CRISPR-Cas systems defend prokaryotic cells from viruses, plasmids, and other mobile genetic elements. Capitalizing on multi-omics approaches, we show here that the CRISPR-Cas systems of uncultivated archaea also play an integral role in mitigating potentially detrimental interactions with episymbionts. A comprehensive analysis of CRISPR-Cas-based infection histories revealed that uncultivated deep-subsurface archaeal primary-producers defend themselves from archaeal episymbionts of the DPANN superphylum of archaea, some of which are known to fuse their membranes with their host. We show that host cells counter these attacks by deploying one of two CRISPR-Cas systems (type I-B and type III-A) to target and disrupt essential genes in the episymbiont. However, genome-scale modeling of metabolic interactions between two deep subsurface host-symbiont systems revealed that host cells also benefit from the symbionts via metabolic complementation. We speculate that populations of these uncultivated archaeal episymbionts are currently transitioning from a parasitic lifestyle to one of mutualism, as must have occurred in countless mutualistic systems known today. By expanding our analysis to thousands of archaeal genomes, we conclude that CRISPR-Cas mediated resistance to archaeal episymbiosis evolved independently in various archaeal lineages and may be a wide-spread evolutionary phenomenon.

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