piRNA processing by a trimeric Schlafen-domain nuclease

Abstract

Transposable elements are genomic parasites that expand within and spread between genomes1. Piwi proteins control transposon activity, notably in the germline2,3. These proteins recognize their targets through small RNA co-factors named piRNAs, making piRNA biogenesis a key specificity-determining step in this crucial genome immunity system. While the processing of piRNA precursors is an essential step in this process, many molecular details of this process remain unknown. We identify a novel endoribonuclease, PUCH, that initiates piRNA processing in the nematode Caenorhabditis elegans. Genetic and biochemical studies show that PUCH, a trimer of Schlafen-like-domain proteins (SLFL proteins), executes 5-end piRNA precursor cleavage. PUCH-mediated processing strictly requires an m7G-Cap and a uracil at position three. We also demonstrate how PUCH interacts with PETISCO, a complex that binds piRNA precursors4, and that this interaction enhances piRNA production in vivo. The identification of PUCH completes the repertoire of C. elegans piRNA biogenesis factors and uncovers a novel type of RNA endonuclease formed by three SLFL proteins. Mammalian Schlafen (Slfn) genes have been associated with immunity responses5, exposing a thus far unknown molecular link between immune responses in mammals and deeply conserved RNA-based mechanisms that control transposable elements.

Recurrent Evolutionary Innovations in Rodent and PrimateSchlafenGenes

“…SLFNL1 has yet to be functionally characterized and shares only that RNase E domain with other SLFNs such as SLFN11. Recently, structurally similar SLFN-like proteins have been shown to help piRNA processing in C.elegans (Podvalnaya et al 2023). Thus, it is possible that orphan genes such as SLFNL1 might carry out ancestral functions in RNA biogenesis, perhaps related to retrotransposon control (Bartonicek et al 2022; Ding et al 2023; Podvalnaya et al 2023).…”

An extended Tudor domain within Vreteno interconnects Gtsf1L and Ago3 for piRNA biogenesis in Bombyx mori

“…However, more structural studies are needed to understand to which extent the hydrophobic pocket is conserved among other eTudor domains. Interestingly, we recently uncovered another, novel binding interface on an eTudor domain of the C. elegans protein TOFU‐6 (Podvalnaya et al , 2023). This implicates that eTudor domains are much more versatile in establishing multivalent interactions than previously anticipated.…”

An extended Tudor domain within Vreteno interconnects Gtsf1L and Ago3 for piRNA biogenesis inBombyx mori

“…However, more structural studies are needed to understand to which extent the hydrophobic pocket is conserved among other eTudor domains. Interestingly, we recently uncovered another, novel binding interface on an eTudor domain of the C.elegans protein TOFU-6 (Podvalnaya et al , 2023). This implicates that eTudor domains are much more versatile in establishing multivalent interactions than previously anticipated.…”