Different RNA Elements Control Viral Protein Synthesis in Polerovirus Isolates Evolved in Separate Geographical Regions

Abstract

Most plant viruses lack the 5′-cap and 3′-poly(A) structures, which are common in their host mRNAs, and are crucial for translation initiation. Thus, alternative translation initiation mechanisms were identified for viral mRNAs, one of these being controlled by an RNA element in their 3′-ends that is able to enhance mRNA cap-independent translation (3′-CITE). The 3′-CITEs are modular and transferable RNA elements. In the case of poleroviruses, the mechanism of translation initiation of their RNAs in the host cell is still unclear; thus, it was studied for one of its members, cucurbit aphid-borne yellows virus (CABYV). We determined that efficient CABYV RNA translation requires the presence of a 3′-CITE in its 3′-UTR. We showed that this 3′-CITE requires the presence of the 5′-UTR in cis for its eIF4E-independent activity. Efficient virus multiplication depended on 3′-CITE activity. In CABYV isolates belonging to the three phylogenetic groups identified so far, the 3′-CITEs differ, and recombination prediction analyses suggest that these 3′-CITEs have been acquired through recombination with an unknown donor. Since these isolates have evolved in different geographical regions, this may suggest that their respective 3′-CITEs are possibly better adapted to each region. We propose that translation of other polerovirus genomes may also be 3′-CITE-dependent.

Advances in Understanding the Mechanism of Cap-Independent Cucurbit Aphid-Borne Yellows Virus Protein Synthesis

“…To study the 5 ′ -UTR requirements of the CABYV CITEs, the firefly luciferase reporter gene was flanked with the genomic 5 ′ -and/or 3 ′ -UTRs of a Spanish isolate (Sq_04_1.9), representing the Mediterranean group and including the CMTE in its 3 ′ -UTR, or with the 5 ′ -and/or 3 ′ -UTRs from the Xinjiang isolate, representing the Asian group and including the CXTE in its 3 ′ -UTR [35]. Figure 1A shows the proposed secondary structures of both 3 ′ -CITES as obtained after chemical structure probing in Miras [35].…”

“…To study the 5 ′ -UTR requirements of the CABYV CITEs, the firefly luciferase reporter gene was flanked with the genomic 5 ′ -and/or 3 ′ -UTRs of a Spanish isolate (Sq_04_1.9), representing the Mediterranean group and including the CMTE in its 3 ′ -UTR, or with the 5 ′ -and/or 3 ′ -UTRs from the Xinjiang isolate, representing the Asian group and including the CXTE in its 3 ′ -UTR [35]. Figure 1A shows the proposed secondary structures of both 3 ′ -CITES as obtained after chemical structure probing in Miras [35]. Luciferase activities, corresponding to the in vivo cap-independent translation efficiencies, were measured after the expression of each RNA in melon protoplasts and represented relative to the activity obtained with the wild-type construct 5 ′ -UTR-luc-3 ′ -UTR of CABYV-Med (100%) (Figure 1B).…”

“…Cucurbit aphid-borne yellows virus (CABYV), a member of the polerovirus genus recently assigned to the Solemoviridae family [31], has a positive-sense RNA genome that lacks a 5 ′ -cap and a 3 ′ -poly(A)-tail [32,33]. Recently, different functional 3 ′ -CITEs in the genomic 3 ′ -UTRs of CABYV isolates belonging to different phylogenetic groups [34], the CXTE for the Asian, and the CMTE for the Mediterranean groups were identified [35]. The 3 ′ -UTR sequences of Mediterranean isolates are nearly identical, and the 3 ′ -UTR sequences of Asian isolates are also highly conserved.…”

“…However, the first half of the 3 ′ -UTRs, where the 3 ′ -CITEs were identified, are quite different between both groups. These two 3 ′ -CITEs, differing in sequence and structure and possibly acquired by recombination, evolved in different geographical regions, which may suggest that their respective 3 ′ -CITEs are possibly better adapted to each region [35]. Notably, the translation of other polerovirus genomes was also proposed to be 3 ′ -CITE-dependent.…”

“…The host factors required for the activity of the newly identified CABYV 3 ′ -CITEs CXTE and CMTE are still unknown. Both are functional in melon plants silenced for eIF4E; thus, their activity must be eIF4Eindependent [5,35]. In this manuscript, the molecular mechanisms of cap-independent translation initiation controlled by the CABYV 3 ′ -CITEs CXTE and CMTE were studied, resulting in the identification of several host proteins that may be involved in their capindependent translation activities.…”