
Umbravirus-like Viruses
The first RNA viruses were likely transferred from organisms feeding on plants, thus requiring the use of host movement proteins (MPs) for transiting through plasmodesmata to establish systemic infection. Before the discovery of umbra-like viruses (ULVs), encoding of specialized MPs was accepted as a required feature of all modern plant viruses. Umbraviruses (family Tombusviridae) encode a 30K-type cell-to-cell MP and a long-distance MP for systemic infection, but rely on a helper virus for trans-encapsidation and plant-to-plant transmission. The recent discovery of two groups of novel viruses sharing umbravirus-like RNA-dependent RNA polymerases and 3ʹ-terminal structures, but which do not necessarily encode MPs is expanding our understanding of the minimum requirements for a modern plant RNA virus. ULV CY1 from citrus uses host protein PHLOEM PROTEIN 2 for systemic movement, and related ULVs encode a capsid protein thereby providing an explanation for the lack of helper viruses in many ULV infected plants.

Projects on the biology of ULVs:
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What are the binding sites for PP2 on CY1?
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What is the movement complex for CY1
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How does CY1 enhance secondary pathogen infections?
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Infectivity differences between Group 1 and Group 2 ULVs​
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Structure of CY2 virus-like particles​
Selected ULV publications:
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Jang, C., Needham, J.M., Johnson, P.Z., Gao, F., and Simon, A.E. 2025. Hairpin inserts in viral genomes are stable when they conform to the thermodynamic properties of viral RNA substructures. J. Virol. In press.
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Johnson, P.Z., Needham, J.M., Lim, N.K., and Simon, A.E. 2024. Direct nanopore RNA sequencing of umbra-like virus-infected plants reveals long non-coding RNAs, specific cleavage sites, D-RNAs, foldback RNAs, and temporal- and tissue-specific profiles. Nucleic Acids Res Genomics Bioinform 6 https://doi.org/10.1093/nargab/lqae104
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Ying, X., Bera, S., Liu, J., Toscano-Morales, R., Jang, C., Yang, S., Ho, J., and Simon, A.E. 2024. Umbravirus-like RNA viruses are capable of independent systemic plant infection in the absence of encoded movement proteins. PLoS Biol 22:e3002600. https://doi.org/10.1371/journal.pbio.3002600
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Simon, A.E., Quito-Avila, D.F., and Bera, S. 2024. Expanding the plant virome: umbra-like viruses use host proteins for movement. Annu Rev Virol doi: 10.1146/annurev-virology-111821-122718.
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