RNA-guided RNA silencing by an Asgard archaeal Argonaute

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 ‘CandidatusHarpocratesius repetitus’ that shares a common origin with eukaryotic PIWI proteins. HrAgo1 exhibits RNA-guided RNA cleavagein vitroand 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.

Prokaryotic Argonaute nuclease cooperates with co-encoded RNase to acquire guide RNAs and target invader DNA

“…Previous studies of representative proteins from various subclades of long-A pAgos demonstrated that most of them act as DNA-guided DNA nucleases (DNA > DNA pAgos) ( 12 , 15–19 , 30–32 ), with small groups of DNA-guided RNA nucleases (DNA > RNA pAgos, including PliAgo, PnyAgo and MbpAgo) ( 33 , 34 ) and the RNA-guided DNA nucleases from thermophilic bacteria mentioned above (RNA > DNA pAgos, including MpAgo and TmAgo) ( 22 ) (Figure 1B ). An RNA-guided pAgo that recognizes RNA targets (RNA > RNA pAgo) was discovered very recently in thermophilic Asgard archaea ( 35 ). While in vitro activities of these pAgos have been studied in much detail, their functional analysis in vivo has been limited to just a few proteins, all of which are DNA-guided DNA nucleases.…”