Polerovirus genomic variation

Abstract

The polerovirus (family Solemoviridae, genus Polerovirus) genome consists of single, positive strand RNA organized in overlapping open reading frames (ORFs) that, in addition to others, code for protein 0 (P0, a gene silencing suppressor), a coat protein (CP, ORF3) and a read-through domain (ORF5) that is fused to the CP to form a CP-RT protein. The genus Polerovirus contains 26 virus species that infect a wide variety of plants from cereals to cucurbits, to peppers. Poleroviruses are transmitted by a wide range of aphid species in the genera Rhopalosiphum, Stiobion, Aphis, and Myzus. Aphid transmission is mediated both by the CP and the CP-RT. In viruses, mutational robustness and structural flexibility are necessary for maintaining functionality in genetically diverse sets of host plants and vectors. Under this scenario, within a virus genome, mutations preferentially accumulate in areas that are determinants of host adaptation or vector transmission. In this study, we profiled genomic variation in poleroviruses. Consistent with their multifunctional nature, single nucleotide variation and selection analyses showed that ORFs coding for P0 and the read-through domain within the CP-RT are the most variable and contain the highest frequency of sites under positive selection. An order/disorder analysis showed that protein P0 is not disordered. In contrast, proteins CP-RT and VPg contain areas of disorder. Disorder is a property of multifunctional proteins with multiple interaction partners. Results described here suggest that using contrasting mechanisms, P0, VPg and CP-RT mediate adaptation to host plants, to vectors, and are contributors to the broad host and vector range of poleroviruses. Profiling genetic variation across the polerovirus genome has practical applications in diagnostics, breeding for resistance, identification of susceptibility genes, and contributes to our understanding of virus interactions with their host, vectors, and environment.

Characterization of Cucurbit Aphid-Borne Yellows Virus (CABYV) from Passion Fruit in Brazil: Evidence of a Complex of Species within CABYV Isolates

“…Among all CABYV isolates analyzed, P0 was the most divergent protein ( Table S5 ), in agreement with LaTourrette et al [ 80 ], which identified this genome region as hypervariable with high nucleotide diversity. P0 of CABYV-PF-799 (89.5%), CABYV-PF-724-1 (88.7%), and CABYV-PF-723-3 (89.1%) showed amino acid identity <90% regarding the French CABYV-N isolate (sequence X76931).…”

Complex and simple translational readthrough signals in pea enation mosaic virus 1 and potato leafroll virus, respectively

“…The net result being that these viruses have evolved via divergent pathways to give rise to secondary structures of vastly contrasting complexity. Considering these extreme examples, and the predicted variability of PRTE/DRTE interactions [ 13 ], we anticipate the existence of a range of readthrough structures with different levels of complexity within the expansive and diverse polerovirus and luteovirus genera [ 49 ].…”

Assessment of the RNA Silencing Suppressor Activity of Protein P0 of Pepper Vein Yellows Virus 5: Uncovering Natural Variability, Relevant Motifs and Underlying Mechanism

“…In summary, in this work we have proven VSR activity of the P0 protein encoded by PeVYV-5, a pathogen closely related to other emerging poleroviruses threatening peppers in distinct parts of the world. High mutation and recombination rates seem to contribute to the rapid diversification of this group of viruses [ 19 , 24 , 50 ], which may lead to important shifts in molecular and biological properties, as illustrated by recent reports [ 50 ]. Hence, in order to develop control measures to prevent extensive damages, it seems essential both to deepen the knowledge and to track the occurrences of these infectious agents.…”

“…The activity as VSR of protein P0 was demonstrated for several viral species of these genera, though it could not be proven in other cases [ 18 ]. It should be noted in this context that the distinct P0 products share relatively low sequence similarity, with an average identity value of about 38 % [ 19 ]. Despite this, all of them seem to contain an F-box-like motif, of uncertain biological meaning, near the N-terminus, and several P0 proteins exhibit a conserved sequence, (K/R)IYGEDGX 3 FWR, at the C-terminus.…”