RNA-guided RNA silencing by an Asgard archaeal Argonaute

Bastiaanssen, C.; Ugarte, P. B.; Kim, K.; Feng, Y.; Finocchio, G.; Anzelon, T. A.; Kostlbacher, S.; Tamarit, D. C.; Ettema, T. J. G.; Jinek, M.; MacRae, I. J.; Joo, C.; Swarts, D. C.; Wu, F.

doi:10.1101/2023.12.14.571608

bioRxiv · 10.1101/2023.12.14.571608

RNA-guided RNA silencing by an Asgard archaeal Argonaute

Bastiaanssen, C.·Ugarte, P. B.·Kim, K.·Feng, Y.·Finocchio, G.·Anzelon, T. A.·Kostlbacher, S.·Tamarit, D. C.·Ettema, T. J. G.·Jinek, M.·MacRae, I. J.·Joo, C.·Swarts, D. C.·Wu, F.

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Abstract

Eukaryotic Argonaute proteins achieve gene repression and defense against viruses and transposons by RNA-guided RNA silencing. By contrast, known prokaryotic Argonautes adopt single-stranded DNA as guides and/or targets, leaving the evolutionary origin of RNA-guided RNA silencing elusive. Here, we show an evolutionary expansion of Asgard archaeal Argonautes (asAgos), including the discovery of HrAgo1 from the Lokiarchaeon Candidatus Harpocratesius repetitus that shares a common origin with eukaryotic PIWI proteins. HrAgo1 exhibits RNA-guided RNA cleavage in vitro and RNA silencing in human cells. The cryo-EM structure of HrAgo1 combined with quantitative single-molecule experiments reveals that HrAgo1 possesses hybrid structural features and target binding modes bridging those of the eukaryotic AGO and PIWI clades. Finally, genomic evidence suggests that eukaryotic Dicer-like processing of double-stranded RNA likely emerged as a mechanism of generating guide RNA for asAgos prior to eukaryogenesis. Our study provides new insights into the evolutionary origin and plasticity of Argonaute-based RNA silencing.

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Bastiaanssen, C., Ugarte, P. B., Kim, K., Feng, Y., Finocchio, G., Anzelon, T. A., Kostlbacher, S., Tamarit, D. C., Ettema, T. J. G., Jinek, M., MacRae, I. J., Joo, C., Swarts, D. C., Wu, F.. 2023-12-15. RNA-guided RNA silencing by an Asgard archaeal Argonaute. https://doi.org/10.1101/2023.12.14.571608

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