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Virus-induced codon-specific reprogramming to favor viral RNA translation

ABSTRACT: How viruses, such as the emerging mosquito-borne Chikungunya virus (CHIKV), express their genomes at high levels despite an enrichment in suboptimal codons remains a puzzling question. By integrating subcellular fractionation and transcriptome-wide analyses of translation in CHIKV-infected human cells, we demonstrate an unanticipated virus-induced reprogramming of the host translation machinery to favor translation of viral RNA over cellular genes featuring optimal codon usage. This reprogramming was specifically apparent at the endoplasmic reticulum (ER), the preferred translation compartment of CHIKV RNA, and it is mediated by the wobble uridine 34 tRNA modification enzyme KIAA1456 whose expression is enhanced upon viral infection. Since KIAA1456 itself is encoded by a CHIKV-like codon usage, infection triggers a positive feed-back loop that ensures efficient virus protein production. Our findings demonstrate an unprecedented interplay of viruses with the host tRNA epitranscriptome to favor viral protein expression.

ORGANISM(S): Homo sapiens

PROVIDER: GSE143390 | GEO | 2022/06/17

REPOSITORIES: GEO

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Project description:West Nile virus (WNV) and Chikungunya virus (CHIKV) are arboviruses that are constantly (re)-emerging and expanding their territory. Both viruses often cause a mild form of disease, but severe forms of the disease can consist of neurological symptoms, most often observed in young children and the elderly, which are poorly understood. To elucidate the mechanisms responsible for end-stage WNV and CHIKV neuroinvasive disease and pathogenesis, we used transcriptomics to compare the effector pathways in the brain during the early and late stage of disease in young mice. Mice were infected with WNV strain NY99 (accession AF196835.2, obtained from the Health Protection Agency, Porton Down, UK; P5 on Vero E6 cells) or CHIKV strain S27, accession AF369024). Nine-day old female C57/BL6 mice were inoculated intraperitoneally with either 10^5 TCID50/100 µL of WNV-NY99 (n=6) or 10^6.5 TCID50/100 µL of CHIKV-S27 (n=6), or mock-infected. Mice were sacrificed 2, 3 or 5 days post-innoculation depending on the virus. For transcriptomic analysis, cerebellum was separated from the brain and the right hemisphere was gently washed once in ice-cold PBS and stored in RNAlater® (Thermo Fisher Scientific, Bleiswijk, The Netherlands) until further processing. Total RNA was isolated from the brain samples using Trizol Reagentand the RNEasy Mini kit. RNA (200 ng) was labeled using the MessageAmp Premier RNA Amplification kit (Applied Biosystems) and hybridized to Affymetrix GeneChip® Mouse 4302 Arrays. Image analysis was performed using GeneChip Operating Software. Microarray Suite version 5.0 software (Affymetrix) was used to generate .dat and .cel files for each experiment. Using this approach, we find evidence for a strong inflammatory response was found in mice infected with WNV and CHIKV. The transcriptomics profile measured in mice with WNV and CHIKV neuroinvasive disease in our study showed strong overlap with the mRNA profile described in the literature for other viral neuroinvasive diseases.

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Virus-induced codon-specific reprogramming to favor viral RNA translation

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