Caenorhabditis elegans ADAR editing and the ERI-6/7/MOV10 RNAi pathway silence endogenous viral elements and LTR retrotransposons

Abstract

18Endogenous retroviruses and LTR retrotransposons are mobile genetic elements that 19 are closely related to retroviruses. Desilenced endogenous retroviruses are associated 20 with human autoimmune disorders and neurodegenerative diseases. C. elegans and 21 related Caenorhabdites contain LTR retrotransposons and, as described here, 22 numerous integrated viral genes including viral envelope genes that are part of LTR 23 retrotransposons. We found that both LTR retrotransposons and endogenous viral 24 elements are silenced by ADARs (adenosine deaminases acting on double-stranded 25 RNA (dsRNA)) together with the endogenous RNAi factor ERI-6/7, a homolog of Mov10 26 helicase, a retrotransposon and retrovirus restriction factor in human. siRNAs 27 Transposons can have profound effects on cellular function such as disruption of gene 53 function by transposon insertion, cell death as a consequence of transposon-induced 54 double stranded breaks, and genomic rearrangements caused by homologous 55 recombination between repeat elements. Retrotransposons and endogenous 56 retroviruses may affect cellular function through overexpression of toxic proteins or the 57 activity of retroviral proteins on endogenous sequences. Palindromic repeat elements 58 such as those formed by adjacent but inverted insertion of vertebrate Alu elements 59 into genes can cause the accumulation of dsRNA. 60 Many RNA viruses replicate via a dsRNA intermediate, which is detected to 61 trigger an interferon-based antiviral response in mammals and an RNA interference 62 response in invertebrates. To avoid an anti-viral response to endogenous palindromic 63 dsRNAs when in fact there is no viral infection, ADARs edit adenosines to inosines in 64 endogenous dsRNA destabilizing the RNA duplex and thus preventing recognition by 65

Induction of RNA interference byC. elegansmitochondrial dysfunction via the DRH-1/RIG-I homologue RNA helicase and the EOL-1/RNA decapping enzyme

“…The RNAi pathway drives gene silencing of mRNAs that have signatures of being foreign. For example, many of the enhanced RNAi mutants mediate the silencing of integrated viruses in the C. elegans genome that are recently acquired (Fischer and Ruvkun, 2020). These viral genes are recognized as foreign by their small number of introns, for example, and by poor splice sites (Newman et al, 2018).…”

“…The enhanced RNAi of hsp-6(mg585) most resembled the eri-6/7 RNA helicase and ergo-1 Argonaute enhanced RNAi phenotypes, associated with desilencing of recently acquired viral genes and induction of viral immunity, without nuclear NRDE-3 or somatic P granule expression Fischer et al, 2013;Fischer and Ruvkun, 2020). In mammalian cells, the RNA helicase MDA5 mediates an interferon antiviral immune response that is strongly enhanced by a mitochondrial RNA degradation mutation that enhances production of mitochondrial dsRNAs (Dhir et al, 2018).…”

“…In mammalian cells, the RNA helicase MDA5 mediates an interferon antiviral immune response that is strongly enhanced by a mitochondrial RNA degradation mutation that enhances production of mitochondrial dsRNAs (Dhir et al, 2018). Intriguingly, mutations in the C. elegans homologue of MDA5, drh-1 suppress the synthetic lethality of enhanced RNAi and dsRNA editing double mutants (Fischer and Ruvkun, 2020;Reich et al, 2018). C. elegans DRH-1 contains three domains, including conserved helicase domain and C-terminal domain (CTD) ( Figure 1F), and an Nterminal domain (NTD) that is only conserved in nematodes (Supplemental Figure 1).…”

“…The eol-1 RNA decapping gene was also strongly induced in virally infected and mitochondrial mutant C. elegans ( Supplemental Table S1). We selected eol-1 for detailed analysis because a. it is conserved from yeast to mammals ( Figure 2B), b. eol-1 expression is induced by multiple mitochondrial mutations as well as in a eri-6; adr-1/2 enhanced RNAi mutant that desilences endogenous retroviruses and retrotransposons (Fischer and Ruvkun, 2020;Senchuk et al, 2018), c. the induction of eol-1 by Orsay virus infection is dependent on drh-1 (Sowa et al, 2020), and d. the human orthologue of EOL-1, DXO represses hepatitis C virus replication (Amador-Canizares et al, 2018). C. elegans eol-1 was initially identified as a mutant that enhanced olfactory learning after Pseudomonas aeruginosa infection (Shen et al, 2014).…”

“…But the Argonaute and RdRp gene families are expanded in C. elegans compared to most animals, and surprisingly, loss of function mutations in some of those genes cause an increase in the response to siRNAs: mutations in the RdRp RRF-3, the specialized Argonaute ERGO-1, the RNA helicase ERI-6/7, or the exoribonuclease ERI-1 enhance silencing by siRNAs (Fischer et al, 2008;Kennedy et al, 2004). Many of these enhanced RNAi mutations desilence retroviral elements in the C. elegans genome so that antiviral response pathways are triggered to in turn induce the expression of RNAi-based antiviral defense (Fischer and Ruvkun, 2020).…”