CoV and NMD

(pmid: 30297408 2018) Nonsense-mediated decay (NMD) is a eukaryotic RNA surveillance pathway that detects mRNAs harboring aberrant features and targets them for degradation.

CoV mRNAs are of cytoplasmic origin, the presence of several NMD-inducing features (including multiple ORFs with internal termination codons that create a long 3′untranslated region).

CoV mRNAs are recognized by the NMD pathway as a substrate, resulting in their degradation.

CoV replication induced the inhibition of the NMD pathway, and N protein had an NMD inhibitory function that protected viral mRNAs from rapid decay.

the NMD pathway interferes with optimal viral replication by degrading viral mRNAs early in infection, before sufficient accumulation of N protein.

Our study presents clear evidence for the biological importance of the NMD pathway in controlling the stability of mRNAs and the efficiency of replication of a cytoplasmic RNA virus.

The role of NMD as a cell-intrinsic antiviral defense mechanism against cytoplasmic RNA viruses harboring genomes with recognizable NMD-activating features has gained traction as a novel research area (13, 16, 17). However, our understanding of the interplay between NMD and cytoplasmic RNA viruses is still in its infancy, as only a limited number of studies have addressed this area of research (13, 16, 17).

CoV mRNA

(pmid: 30297408 2018) CoV mRNAs have a common 3′end,constituting a 3′-coterminal nested-set structure; the 5′end of allCoV mRNAs carry a common∼70-nt leader sequence.

most of the CoV mRNAs, except for the smallest subgenomic mRNA, have multiple ORFs. Because only the 5′-most ORF in viral mRNAs is, in principle, used for translation, most of the CoV mRNAs have a long 3′untranslated region (UTR); in the case of genomic RNA, the length of the 3′UTR is∼10 kb (SI Appendix,Fig.S1). Although steady progress hasbeen made in understanding CoV gene expression strategies, there are still considerable gaps in our knowledge about the CoV–host interactions involved in the regulation of viral mRNA stability and viral gene expression.

N and NMD

(pmid: 30297408 2018) N protein as an NMD inhibitor.

virus-induced inhibition of the NMD pathway is important for the protection of viral mRNAs from rapid decay, thereby facilitating efficient virus replication.

The study represents a direct demonstration of the recognition and targeting of mRNAs of a cytoplasmic RNA virus by the NMD pathway, highlighting the biological importance of the virus-induced inhibition of the NMD pathway for efficient virus replication.

N protects transfected viral RNA - no direct link of N to NMD - could also inhibit other pathways

it is unclear whether other NMD factors that play a critical role in the NMD of mammalian mRNAs are also required for NMD-mediated turnover of CoV mRNAs.

besides N also other proteins may protect the RNA

It has been shown that in CoV reverse genetics systems, the addition of transcripts encoding N protein to in vitro-synthesized full-length CoV transcripts for electroporation enhances the recovery of infectious viruses (48–51).

cellular interactome of the CoV infectiousbronchitis virus N protein (52) and that of the arterivirus por-cine reproductive and respiratory syndrome virus N protein(53) suggested an interaction of these N proteins with UPF1.

-> screen for factors.