Plant RNA viruses encode essential viral proteins that depend on the host translation machinery for their expression. However, genomic RNAs of most plant RNA viruses lack the classical characteristics of eukaryotic cellular mRNAs, such as mono-cistron, 5′ cap structure, and 3′ polyadenylation. To adapt and utilize the eukaryotic translation machinery, plant RNA viruses have evolved a variety of translation strategies such as cap-independent translation, translation recoding on initiation and termination sites, and post-translation processes. This review focuses on advances in cap-independent translation and translation recoding in plant viruses.

Polyadenylation influences many aspects of mRNA as well as viral RNA. variable polyadenylation at the 3' end have been reported in RNA viruses. It is interesting to identify the characteristic and potential role of 3' polyadenylation of Wheat yellow mosaic virus (WYMV), which has been reported to contain two genomic RNAs with 3' poly(A) tails and caused severe disease on wheat in East Asia region. 3' RACE was used to identify sequences of the 3′ end in WYMV RNAs from naturally infected wheat by WYMV. In vitro translation assay was performed to analyze effect of UTRs of WYMV with or without 3’polyadenylation on translation. In vitro replication mediated by WYMV NIb protein were performed to evaluate effect of variable polyadenylation on replication. Variable polyadenylation in WYMV RNAs was identified via 3′ RACE. WYMV RNAs in naturally infected wheat in China simultaneously present with regions of long, short, or no adenylation at the 3' ends. The effects of variable polyadenylation on translation and replication of WYMV RNAs were evaluated. 5’UTR and 3’UTR of WYMV RNA1 or RNA2 synergistically enhanced the translation of the firefly luciferase (Fluc) gene in in vitro WGE system, whereas additional adenylates had an oppositive effect on this enhancement on translation mediated by UTRs of WYMV. Additional adenylates remarkably inhibited the synthesis of complementary strand from viral genome RNA during the in vitro replication mediated by WYMV NIb protein. 3' end of WYMV RNAs present variable polyadenylation even no polyadenylation. 3' polyadenylation have opposite effect on translation mediated by UTRs of WYMV RNA1 or RNA2. 3' polyadenylation have negative effect on minus-strand synthesis of WYMV RNA in vitro. Variable polyadenylation of WYMV RNAs may provide sufficient selection on the template for translation and replication.

Some debilitating mutations in RNA viruses are repairable; however, the triggering factors of mutation repair remain largely unknown. In this study, multiple triggering factors of mutation repair are identified based on genetic damage to the TLS in CMV. TLS mutations in different RNAs distinctively impact viral pathogenicity and present different types of mutation repair. RNA2 relative reduction level or RNA3 sequence change resulting from TLS mutation is correlated with a high rate of mutation repair, and the TLS mutation of RNA1 fails to be repaired at the high inoculum dose. However, the TLS mutation of RNA1 can be repaired at a low dose of inoculation, particularly around the dilution end-point or in the mixed inoculation with RNA2 having a pre-termination mutation of the 2b gene, an RNAi suppressor. Taken together, TLS mutations resulting in quality or quantity defects of the viral genome or TLS mutations at low doses around the dilution end-point are likely to be repaired. Different levels of TLS mutation repair necessarily require cell-to-cell movement, therefore implying its obligated effect on the evolution of low-fitness viruses and providing a new insight into Muller’s ratchet. This study provides important information on virus evolution and the application of mild viral vaccines.

Wheat yellow mosaic virus (WYMV), a member of the genus Bymovirus, causes substantial losses in wheat production in East Asia, including China and Japan. Although genomic RNA replication is an important process in the viral life cycle, the independent regulation of WYMV RNA replication by its 3ʹ and 5ʹ untranslated regions (UTRs) remains unclear. In this study, we sought to analyze the core structural features of the 3ʹ UTR in the regulation of the replication of WYMV RNA1 in vitro, locate the viral RNA sites to which the NIb protein binds, and determine the regulatory effects of the VPg, P3, and 14 K proteins on NIb RNA-dependent RNA polymerase (RdRp) activity. We found that the NIb protein in WYMV RNA1 only specifically recognized its 3ʹ UTR as the core enzyme for replication. Moreover, the 14 K and P3 proteins were established to synergistically enhanc the in vitro RdRp activity of the NIb protein, whereas the VPg protein was found to play an inhibitory role. Based on RNA structure probing and mutational analysis, we identified ⁷⁶²⁴UU and ⁷⁵⁷¹UU as putative sites for interaction with the NIb protein and demonstrated that replication is dependent on their coexistence. In addition, hairpins 2 and 5 of the 3' UTR were found to be essential for NIb protein replication. Collectively, the findings of our in vitro analysis of the replication regulatory elements of WYMV RNA1 3ʹ UTR, provide a basis for in vivo studies on the regulation of WYMV replication and the identification of potential targets for the prevention and control of WYMV-caused crop diseases.