Arenaviridae exoribonuclease presents genomic RNA edition capacity

Abstract

The Arenaviridae is a large family of viruses causing both acute and persistent infections and causing significant public health concerns in afflicted regions. A "trademark" of infection is the quick and efficient immuno-suppression mediated in part by a 3'-5' RNA exonuclease domain (ExoN) of the Nucleoprotein (NP). Mopeia virus, the eastern African counterpart of Lassa virus, carries such ExoN domain, but does not suppress the host innate immunity. We have recently reported the crystal structure of the Mopeia virus ExoN domain, which presents a conserved fold and active site. In the present study, we show that the ExoN activity rules out a direct link between ExoN activity and alteration of the host innate immunity. We found that the Arenavirus ExoN, however, is able to excise mis-incorporated bases present at the 3'-end of double stranded RNA.ExoN(-) arenaviruses cultured in cells dampened in innate immunity still replicated in spite of a significant reduction in the viral charge over several passages. The remaining ExoN(-) virus population showed an increased base substitution rate on a narrow nucleotide spectrum, linking the ExoN activity to genome editing. Since, the Arenavirus ExoN belongs to the same nuclease family as that of the nsp14 coronavirus ExoN ; which has been recently shown to promote viral RNA synthesis proofreading; we propose that Arenavirus ExoN is involved in a "limited RNA editing" mechanism mainly controlled by structural constraints and a low mutational/fitness ratio.

The Enzymatic Activity of the nsp14 Exoribonuclease Is Critical for Replication of MERS-CoV and SARS-CoV-2

“…Outside the order Nidovirales, arenaviruses are the only other RNA viruses known to employ an ExoN domain, which is part of the arenavirus nucleoprotein and has been implicated in fidelity control (31) and/or immune evasion, the latter by possibly degrading viral dsRNA (32,33). Based on results obtained with TGEV and MHV ExoN knockout mutants, also the CoV ExoN activity was suggested to counteract innate responses (34,35).…”

Brothers in Arms: Structure, Assembly and Function of Arenaviridae Nucleoprotein

“…The mechanism underlying dsRNA accumulation in JUNV and MACV infections is still unclear, as dsRNA is readily accumulated during JUNV and MACV infections or in JUNV minigenome replication studies. The ExoN activity of PICHV [41] and MACV have been determined in vitro and behave similarly to other OW ExoN [43]. The crystal structure study of the JUNV ExoN shows that the domain is conserved and similar to the ExoN of LCMV LASV, MOPV, TCRV [47][48][49][50].…”

“…of the catalytic motifs DEDDh to DEEDh (Figures 2 & S2), an observation that added to the topology and the in vitro activity conservation with the ExoN domaine of Coronaviridae Nsp14, suggesting a common origin of the Coronaviridae nsp14 and Arenaviridae NP ExoNs [43,45]. This domain has a canonical fold of the DEDDh family of 3′-5′ exoribonucleases, consisting of two β-sheets (with six mixed strands and two anti-parallel strands) and eight α-helices connected by a series of loops.…”

“…This assertion, however, needs to be carefully evaluated as PICV, LASV and LCMV with a mutant NP lacking the 3 -5 exonuclease activity had either not rescuable, impaired replication or a significant decrease in fitness during its replication [38,41,42]. Moreover, a recent in vitro study has shown a removing capability of mismatched nucleotide, which could be a first step in an editing process [43]. The ExoN belongs to the DEDDh family, that process their substrate through a two-metal ion catalytic mechanism [44], the two ions being coordinated by the residues of the motif.…”

“…The ExoN belongs to the DEDDh family, that process their substrate through a two-metal ion catalytic mechanism [44], the two ions being coordinated by the residues of the motif. A sequence analysis of the ExoN domain of Arenaviridae shows the evolution of the catalytic motifs DEDDh to DEEDh (Figure 2 and Figure S2), an observation that added to the topology and the in vitro activity conservation with the ExoN domaine of Coronaviridae Nsp14, suggesting a common origin of the Coronaviridae nsp14 and Arenaviridae NP ExoNs [43,45]. This domain has a canonical fold of the DEDDh family of 3 -5 exoribonucleases, consisting of two β-sheets (with six mixed strands and two anti-parallel strands) and eight α-helices connected by a series of loops.…”