March 17th, 2024
Recent Publications Harnessing the Power of Translatomics.
Every week we provide a digest of a small number of recent interesting papers in the field of translatomics.
In this week’s Sunday papers, Dopkins et al. (2024) perform the first large-scale analysis of HERV translation in healthy tissues using publicly available ribosomal profiling datasets. Fedry et al. (2023) use cryoelectron tomography to observe translation machinery in mammalian cells under persistent collision stress. Lastly, Aviner et al. (2023) employ subcellular proteomics, ribosome profiling analyses, and reporter assays to identify alterations in protein synthesis dynamics induced by SARS-CoV-2 infection.
Ribosomal profiling of human endogenous retroviruses in healthy tissues
BMC Genomics, 2024
Dopkins, N., Singh, B., Michael, S., Zhang, P., Marston, J.L., Fei, T., Singh, M., Feschotte, C., Collins, N., Bendall, M.L. and Nixon, D.F.
Human endogenous retroviruses (HERVs) are remnants of ancient retroviral infections that integrated into the germline, persisting within the human genome. Over time, mutations or deletions accumulate in these retroviruses, rendering them unable to produce infectious particles, thus becoming “endogenous.” Endogenization is a complex, transgenerational process demonstrated by active events in Koala species. Various factors drive endogenization, including xenotropic restriction, mutations, host-antiviral responses, and recombination events. HERVs constitute about 8% of the human genetic material and have significantly impacted the genome. While mostly inactive, some HERVs show activity in somatic and developing cells. They have been coopted for various molecular tasks in reproduction, immune responses, and cell type-specific transcription. Our understanding of HERVs primarily focuses on their genomic and transcriptomic functions, with limited knowledge about their protein encoding capabilities.
This study represents the first large-scale analysis of HERV translation in healthy tissues using publicly available ribosomal profiling datasets. By utilizing ‘hervQuant’, the expression of over 3000 annotated HERV proviruses were quantified across various healthy tissues and cell types which enabled mapping sequencing fragments to full-length proviruses. This method provides an assessment of potential translation HERV proviruses under normal conditions. This study reveals that HERVs contribute to 0.1–0.4% of all mapped ribosome fragments in tissue-specific patterns. Although it’s not clear to what extent the mappings are an artifact or representative of genuine translation, the findings reinforce the notion that HERVs are actively translated across healthy tissues, adding sequences of retroviral origin to the human proteome.
Visualization of translation reorganization upon persistent ribosome collision stress in mammalian cells
Molecular Cell, 2024
Fedry, J., Silva, J., Vanevic, M., Fronik, S., Mechulam, Y., Schmitt, E., des Georges, A., Faller, W.J. and Förster, F.
The stalling of ribosomes during the elongation stage may occur due to various factors like damaged or incorrectly processed mRNA, lack of amino acids, or rare codons. These events can cause collisions with trailing ribosomes. Cells have evolved mechanisms to detect and address these issues, with ribosome collisions being a major sentinel for abnormal translation. The recognition of stalling triggers quality control mechanisms, signaling pathways, and a reduction in translation activity. In this study, cryoelectron tomography is used to observe translation machinery in mammalian cells under persistent collision stress. Using image classification approaches they identified nine 80S ribosome states, seven of which are previously well established.
The additional 2 states consisted of tRNAs absent from the E-site but present further out in a position referred as the Z-site. This Z-site state becomes more frequent with treatments inducing collision stress. The study also shows that polysomes are compressed, with a significant portion of ribosomes in helical polysomes or collided disomes, some interacting with the stress effector GCN1. The collision interface extends beyond the in vitro-characterized 40S and includes the L1 stalk and eEF2, possibly inhibiting translocation. Accumulation of unresolved tRNA-bound ribosomes and aberrant configurations suggests potential bottlenecks in collision responses. This work offers insights into how cells globally respond to persistent collisions and a basis for quantitatively analyzing translation dynamics in vivo.
SARS-CoV-2 Nsp1 cooperates with initiation factors EIF1 and 1A to selectively enhance translation of viral RNA
PLoS Pathogens, 2024
Host-directed antivirals show promise against various viruses, including SARS-CoV-2, but their development requires a deeper understanding of virus-host interactions. Particularly intriguing are interactions that selectively boost viral protein synthesis, involving RNA-binding proteins, translation factors, and molecular chaperones. In this study, the authors employ subcellular proteomics, ribosome profiling analyses, and reporter assays to identify alterations in protein synthesis dynamics induced by SARS-CoV-2 (CoV2) infection. They isolated translating ribosomes from CoV2-infected and control cells and used mass spectrometry to analyze their interacting partners. They identified several biosynthetic factors specifically enriched on polysomes translating CoV2, including translation initiation factors EIF1 and 1A.
These factors regulate translation start site selection, collaborate with viral non-structural protein 1 (Nsp1) to enhance translation of viral genomic RNA, and are exploited by CoV2 to control viral protein synthesis timing and quantity. Targeting EIF1A via siRNA reduces infection with minimal host toxicity. Moreover, depletion of EIF1/1A leads to an increase in ribosomes initiating translation from a conserved upstream CUG start codon present in all genomic and subgenomic viral RNAs. Consequently, there is enhanced translation of an upstream open reading frame (uORF1) and reduced translation of the main ORF, resulting in a shift in the balance of viral proteins and a decrease in infection severity. Substituting the upstream CUG with AUG significantly hampers translation of the main ORF, regardless of the presence of Nsp1, EIF1, or EIF1A. Although the exact nature of EIF1/1A and Nsp1 interactions is unclear, this interplay suggests a novel avenue for antiviral therapy.