ABSTRACT Plant umbraviruses (UVs) encode, in embedded open reading frames, an unstructured movement protein (MP) (ORF3) required for vascular long-distance movement and a structured 30K-type MP (ORF4) for cell-to-cell movement. UVs do not encode capsid proteins and require helper viruses for vector acquisition. Umbra-like viruses (ULVs) comprise two groups whose RNA-dependent RNA polymerases share significant similarity with UVs and whose non-replicase ORFs, if any, are either single, embedded, or separate. Group 2 ULVs, which lack encoded MPs, use a host-encoded MP and do not require a helper virus, presumably due to encoding a capsid-like protein. Group 1 ULVs are more closely related to UVs and have been identified in Ageratum, Arborvitae, Paspalum paspaloides , switchgrass, and grapevine. Structural and phylogenetic analyses of Group 1 ULVs suggest that ULVs evolved from UVs following the loss of ORF3, duplication of 30K MP ORF 4, recombination to remove an intergenic region, and evolution of the paralog ORF4s to encode a capsid-like protein and a protein of unknown function. Neither duplicated ORF in Group 1 grapevine GULV4 was required for systemic infection of Nicotiana benthamiana . Structural comparisons of 17 UV and 8 Group 1 ULV frameshifting sites revealed strong conservation, including two previously unknown hairpins and pseudoknots that were absent in Group 2 ULVs. Group 1 ULVs also contain I-shaped structure (ISS) 3ʹ cap-independent translation enhancers with novel conformations not found in UVs or Group 2 ULVs. These and other findings comprise a baseline of knowledge that will inform further experimental examination of these unique viruses. IMPORTANCE The key defining feature of plant viruses is their encoding of movement proteins (MPs), with most from a superfamily of MPs known as 30K. It has been proposed that 30K MPs evolved from capsid proteins, as both contain similar “jelly roll” domains. Umbraviruses encode two MPs in overlapping ORFs, with ORF4 encoding a 30K-type MP. Umbraviruses and umbra-like viruses (ULVs) have related replication proteins (ORFs 1 and 2) but differ in their non-replication ORFs. Recently, Group 2 ULVs were found to encode a capsid-like protein and no MPs, relying instead on host proteins for movement. Current investigation of the sequences and structures of Group 1 ULVs, which contain one or two ORFs of unknown function, revealed that ULVs likely evolved from umbraviruses following duplication of the 30K MP ORF and neofunctionalizations to a jelly roll-containing capsid-like protein and a second non-MP, suggesting that capsid proteins can also evolve from MPs.
Simon et al. (Thu,) studied this question.