Translation initiation landscape profiling reveals hidden open reading frames required for the pathogenesis of tomato yellow leaf curl Thailand virus

Plant viruses with densely packed genomes employ non-canonical translational strategies to increase the coding capacity for virus function. However, the diverse translational strategies used make it challenging to define the full set of viral genes. Here, using tomato yellow leaf curl Thailand virus (TYLCTHV, genus Begomovirus) as a model system, we identified genes beyond the annotated gene sets by experimentally profiling in vivo translation initiation sites (TISs). We found the prevalent unanticipated AUG TISs, and their usages occurred via alternative transcriptional and/or translational start sites and were associated with flanking mRNA sequences. Specifically, two downstream in-frame TISs were identified in the viral gene AV2. These TISs were conserved in the begomovirus lineage and led to translation of different protein isoforms localized to cytoplasmic puncta and at the cell periphery, respectively. In addition, we found translational evidence of an unexplored gene, BV2. BV2 was conserved among TYLCTHV isolates and localized to the endoplasmic reticulum and plasmodesmata. Mutations of AV2 isoforms and BV2 significantly attenuated disease symptoms. In conclusion, our study pinpointing in vivo TISs untangles the coding complexity of a plant viral genome and, more importantly, illustrates the biological significance of the hidden open reading frames encoding viral factors for pathogenicity.
Ming-Jung Liu

Ching-Wen Chiu, Ya-Ru Li, Cheng-Yuan Lin, Hsin-Hung Yeh and Ming-Jung Liu (2022) Translation initiation landscape profiling reveals hidden open reading frames required for the pathogenesis of tomato yellow leaf curl Thailand virus Plant Cell, https://doi.org/10.1093/plcell/koac019