Interfamilial recombination between viruses led to acquisition of a novel translation‐enhancing RNA element that allows resistance breaking

Abstract

Summary Many plant viruses depend on functional RNA elements, called 3′-UTR cap-independent translation enhancers (3′-CITEs), for translation of their RNAs. In this manuscript we provide direct proof for the existing hypothesis that 3′-CITEs are modular and transferable by recombination in nature, and that this is associated with an advantage for the created virus. By characterizing a newly identified Melon necrotic spot virus (MNSV; Tombusviridae) isolate, which is able to overcome eukaryotic translation initiation factor 4E (eIF4E)-mediated resistance, we found that it contains a 55 nucleotide insertion in its 3′-UTR. We provide strong evidence that this insertion was acquired by interfamilial recombination with the 3′-UTR of an Asiatic Cucurbit aphid-borne yellows virus (CABYV; Luteoviridae). By constructing chimeric viruses, we showed that this recombined sequence is responsible for resistance breaking. Analysis of the translational efficiency of reporter constructs showed that this sequence functions as a novel 3′-CITE in both resistant and susceptible plants, being essential for translation control in resistant plants. In conclusion, we showed that a recombination event between two clearly identified viruses from different families led to the transfer of exactly the sequence corresponding to a functional RNA element, giving rise to a new isolate with the capacity to infect an otherwise non-susceptible host.

The 3′ Untranslated Region of Pea Enation Mosaic Virus Contains Two T-Shaped, Ribosome-Binding, Cap-Independent Translation Enhancers

“…Some possibilities for why a virus might have multiple 3=CITEs include the following: (i) redundancy to support a critical aspect of translation; (ii) ribosomes could be recycled from different translation termination sites; (iii) ribosomes could be recycled to different initiation sites, such as the sgRNA initiation site; and (iv) ability to overcome translation-based resistance in different hosts (29). Since mutations in the kl-TSS that disrupt the kissing-loop interaction are highly detrimental despite maintaining the potential kl-H/5H2 interaction, the answer is unlikely to be redundancy of a single function.…”

“…With the possible exception of the paired PTE/kl-TSS elements of PEMV and an isolate of Melon necrotic spot virus that acquired an additional 3=CITE by recombination (29), only single 3=CITEs have been discovered in 3= regions of plant viruses, leading to the general assumption that a single element is normally sufficient for all necessary translation enhancement. We now report that PEMV contains a second T-shaped structure downstream from the kl-TSS/PTE, located in the same position in the genome as the TCV TSS.…”

Differential use of 3’CITEs by the subgenomic RNA of Pea enation mosaic virus 2

“…While most viruses contain a single 3′CITE, one virulent isolate of Melon necrotic spot virus (MNSV-N) contains a second, previously unobserved 3′CITE that was acquired through interfamiliar recombination with a polerovirus and permits infection of otherwise resistant melon varieties (Miras et al , 2014). Another virus with multiple 3′CITEs is the umbravirus Pea enation mosaic virus 2 (PEMV2), which has three 3′CITEs in its unusually long (703 nt) 3′UTR (Gao et al , 2014).…”

Recruitment of the 40S Ribosome Subunit to the 3′-Untranslated Region (UTR) of a Viral mRNA, via the eIF4 Complex, Facilitates Cap-independent Translation

“…The tRNA-shaped 3Ј-CITE of turnip crinkle virus binds directly to ribosomal 60S subunits and 80S ribosomes, but its interactions with initiation factors are unknown (29). The factor requirements of the most recently discovered 3Ј-CITE (from the Xinjiang isolate of Cucurbit aphid-borne yellows virus) are also unknown (30).…”