Summary: We report here evidence of the role that the isoform of the eukaryotic translation initiation factor 4G (eIF(iso)4G) plays in naturally occurring resistance in plant/virus interactions. A genetic and physical mapping approach was developed to isolate the Rymv1 locus controlling the high recessive resistance to Rice yellow mottle virus (RYMV) in the rice (Oryza sativa) variety Gigante. The locus was mapped to a 160‐kb interval containing a gene from the eIF(iso)4G family. The stable transformation of a resistant line with the cDNA of this gene, derived from a susceptible variety, resulted in the loss of resistance in transgenic plants. The allelic variability of this gene was analysed in three resistant and 17 susceptible varieties from different cultivated rice species or subspecies. Compared with susceptible varieties, resistant varieties present specific alleles, characterized by either amino acid substitutions or short amino‐acid deletions in the middle domain of the protein. The structure of this domain was modelled and showed that the substitutions were clustered on a small surface patch. This suggests that this domain may be involved in an interaction with the virus.

Hundreds of species of plant viruses, many of them economically important, are transmitted by noncirculative vector transmission (acquisition by attachment of virions to vector mouthparts and inoculation by subsequent release), but virus receptors within the vector remain elusive. Here we report evidence for the existence, precise location, and chemical nature of the first receptor for a noncirculative virus, cauliflower mosaic virus, in its insect vector. Electron microscopy revealed virus-like particles in a previously undescribed anatomical zone at the extreme tip of the aphid maxillary stylets. A novel in vitro interaction assay characterized binding of cauliflower mosaic virus protein P2 (which mediates virus–vector interaction) to dissected aphid stylets. A P2-GFP fusion exclusively labeled a tiny cuticular domain located in the bottom-bed of the common food/salivary duct. No binding to stylets of a non-vector species was observed, and a point mutation abolishing P2 transmission activity correlated with impaired stylet binding. The novel receptor appears to be a nonglycosylated protein deeply embedded in the chitin matrix. Insight into such insect receptor molecules will begin to open the major black box of this scientific field and might lead to new strategies to combat viral spread.

A novel dwarf and twisting syndrome first observed on rice in Nghe An Province, Vietnam, in 2009 has spread rapidly to the other 19 provinces of North and Central Vietnam. Infected rice plants showed stunting, darkening of leaves, twisting of leaf tips, and splitting of leaf margins. At a later stage, white waxy enations that eventually turned black were observed on the underside of leaf blades, leaf sheaths, and culms. The disease also infected maize after rice was harvested. Infected maize plants were stunted and dark green with small enations along the minor veins on the back of leaves. The disease agent has now been identified as Southern rice black-streaked dwarf virus (SRBSDV) recently reported from Southern China. Typical fijivirus viroplasms containing crystalline arrayed spherical virions approximately 70 to 75 nm in diameter were observed under the electron microscope in ultrathin sections of infected rice leaves. The virus was transmitted to rice and maize seedlings by the white-backed planthopper (Sogatella furcimera). A one-step reverse transcription-polymerase chain reaction (RT-PCR) protocol was used to confirm the presence of SRBSDV in 477 samples of rice or maize from 29 provinces among 5 agroecological regions in North and Central Vietnam. Rice black-streaked dwarf virus was not detected in these samples. Partial sequences of RNA segments 4 and 10 from several isolates showed very low genetic divergences between isolates from Vietnam and China, suggesting a common origin, and phylogenetic analysis confirmed the placement of SRBSDV as a distinct virus within subgroup 2 of the genus Fijivirus.

Fourteen isolates of Rice yellow mottle virus (RYMV) were selected as representative of the genetic variability of the virus in Africa from a total set of 320 isolates serologically typed or partially sequenced. The 14 isolates were fully sequenced and analyzed together with two previously reported sequences. RYMV had a genomic organization similar to that of Cocksfoot mottle sobemovirus . The average nucleotide diversity among the 16 isolates of RYMV was 7%, and the maximum diversity between any two isolates was 10%. A strong conservative selection was apparent on both synonymous and nonsynonymous substitutions, through the amino acid replacement pattern, on the genome size, and through the limited number of indel events. Furthermore, there was a lack of positive selection on single amino acid sites and no evidence of recombination events. RYMV diversity had a pronounced and characteristic geographic structure. The branching order of the clades correlated with the geographic origin of the isolates along an east-to-west transect across Africa, and there was a marked decrease in nucleotide diversity moving westward across the continent. The insertion-deletion polymorphism was related to virus phylogeny. There was a partial phylogenetic incongruence between the coat protein gene and the rest of the genome. Overall, our results support the hypothesis that RYMV originated in East Africa and then dispersed and differentiated gradually from the east to the west of the continent.

VPgs are viral proteins linked to the 5' end of some viral genomes. Interactions between several VPgs and eukaryotic translation initiation factors eIF4Es are critical for plant infection. However, VPgs are not restricted to phytoviruses, being also involved in genome replication and protein translation of several animal viruses. To date, structural data are still limited to small picornaviral VPgs. Recently three phytoviral VPgs were shown to be natively unfolded proteins. In this paper, we report the bacterial expression, purification and biochemical characterization of two phytoviral VPgs, namely the VPgs of Rice yellow mottle virus (RYMV, genus Sobemovirus) and Lettuce mosaic virus (LMV, genus Potyvirus). Using far-UV circular dichroism and size exclusion chromatography, we show that RYMV and LMV VPgs are predominantly or partly unstructured in solution, respectively. Using several disorder predictors, we show that both proteins are predicted to possess disordered regions. We next extend theses results to 14 VPgs representative of the viral diversity. Disordered regions were predicted in all VPg sequences whatever the genus and the family. Based on these results, we propose that intrinsic disorder is a common feature of VPgs. The functional role of intrinsic disorder is discussed in light of the biological roles of VPgs.

The adaptation of Rice yellow mottle virus (RYMV) to recessive resistance mediated by the rymv1-2 allele has been reported as a model to study the emergence and evolution of virulent variants. The resistance and virulence factors have been identified as eukaryotic translation initiation factor eIF(iso)4G1 and viral genome–linked protein (VPg), respectively, but the molecular mechanisms involved in their interaction are still unknown. In this study, we demonstrated a direct interaction between RYMV VPg and the central domain of rice eIF(iso)4G1 both in vitro, using recombinant proteins, and in vivo, using a yeast two-hybrid assay. Insertion of the E309K mutation in eIF(iso)4G1, conferring resistance in planta, strongly diminished the interaction with avirulent VPg. The efficiency of the major virulence mutations at restoring the interaction with the resistance protein was assessed. Our results explain the prevalence of virulence mutations fixed during experimental evolution studies and are consistent with the respective viral RNA accumulation levels of avirulent and virulent isolates. Our results also explain the origin of the residual multiplication of wild-type isolates in rymv1-2–resistant plants and the role of genetic context in the poor adaptability of the S2/S3 strain. Finally, the strategies of RYMV and members of family Potyviridae to overcome recessive resistance were compared.