Major radiations of enigmatic Bacteria and Archaea with large inventories of uncharacterized proteins are a striking feature of the Tree of Life The processes that led to functional diversity in these lineages, which may contribute to a host-dependent lifestyle, are poorly understood. Here, we show that diversity-generating retroelements (DGRs), which guide site-specific protein hypervariability, are prominent features of genomically reduced organisms from the bacterial candidate phyla radiation (CPR) and as yet uncultivated phyla belonging to the DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota and Nanohaloarchaea) archaeal superphylum. From reconstructed genomes we have defined monophyletic bacterial and archaeal DGR lineages that expand the known DGR range by 120% and reveal a history of horizontal retroelement transfer. Retroelement-guided diversification is further shown to be active in current CPR and DPANN populations, with an assortment of protein targets potentially involved in attachment, defence and regulation. Based on observations of DGR abundance, function and evolutionary history, we find that targeted protein diversification is a pronounced trait of CPR and DPANN phyla compared to other bacterial and archaeal phyla. This diversification mechanism may provide CPR and DPANN organisms with a versatile tool that could be used for adaptation to a dynamic, host-dependent existence.
Parasitic organisms depend upon evasive genetic strategies towards defense, including adaptive protein diversification. Although this phenomenon has not been widely examined in subsurface ecosystems, my recent assessment of subseafloor and subterranean archaeal genomes revealed a prodigious driver of protein evolution (Paul et al. 2015). Here, I propose to expand upon this discovery, leveraging the C-DEBI collaborative network, to examine the role of targeted protein diversification in shaping host-parasite interactions in subseafloor ecosystems. Importantly, I propose to investigate this mechanism in the following three stages: 1) directly probe methane seep sediments sampled from the Santa Monica Basin, using a novel screening assay for known genetic diversifiers; 2) conduct metagenomic sequencing and bioinformatic analysis for samples prioritized in the previous step; 3) in collaboration with current C-DEBI researchers, apply newly developed bioinformatic tools to screen for latent hypervariable proteins in existing subseafloor metagenomes. This research will directly address C-DEBI phase-II research themes 2 and 3 by investigating a targeted mechanism thought to drive protein evolution in subsurface microorganisms and their viruses. The collective efforts of this proposal will lead to a broad collaboration for the identification and annotation of proteins that have evolved through adaptive diversification in subseafloor microorganisms.