Finally got around to publishing this, about three years late. First ribosome profiling of a tombusvirid. Kudos to Pulkit Kanodia for his meticulous, rigorous bench work and analysis! I think the ribosome profiling of the viral RNA is particularly interesting. journals.asm.org/doi/10.1128/...
journals.asm.org
Changes in the translational landscape during red clover necrotic mosaic virus infection | Journal of Virology
Positive-strand RNA viruses usurp the host’s translation machinery to synthesize viral proteins. Moreover, translation of host mRNAs is altered by virus infection, both as part of the host immune response and by the virus to inhibit host defenses. To assess all these changes globally, we used ribosome profiling of plants infected with a member of the large and ubiquitous Tombusviridae family. We identified key host genes and pathways that were differentially altered in translation efficiency, giving us an understanding of host responses not detectable by conventional RNA sequencing. Moreover, ribosome profiling revealed (i) the most accurate calculation of the efficiency of ribosomal frameshifting during infection for any plant virus, (ii) the extremely high level of translation of viral coat protein, and (iii) an unexpectedly strong ribosomal pause site in the movement protein gene. This work provides an understanding of a new dimension of gene expression control in plant-virus interactions.
