February 4th, 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, Fedorovskiy et al. explored how diverse small-molecule translation inhibitors impact SG formation during severe oxidative stress induced by sodium arsenite. Kim et al. employed tissue-optimized ribosome profiling and a severe-COVID-19 mouse model to establish the first temporal translation profiles of virus and host genes in SARS-CoV-2-infected lungs. And He et al. focused on investigating translational regulation in cervical cancer, which plays a critical role in the gene expression.
A Solitary Stalled 80S Ribosome Prevents mRNA Recruitment to Stress Granules
Biochemistry (Moscow), 2023
Fedorovskiy, A.G. et al.
Eukaryotic cells respond to stress by suppressing protein synthesis, forming stress granules (SGs) with 40S ribosomal subunits. SGs, triggered by mRNA with extended ribosome-free segments, were thought to consist of ribosome-free mRNA, but recent evidence suggests association with actively translated mRNAs. Extended ribosome-free mRNA regions are crucial for SG formation. Stress and translation inhibitors affect SG assembly. Recent findings challenge models, revealing that mRNAs with a solitary 80S ribosome resist SG incorporation, raising questions about the role of ribosome. In this study, the authors explored how diverse small-molecule translation inhibitors impact SG formation during severe oxidative stress induced by sodium arsenite.
To assess the impact of compounds on cellular translation, HeLa cells were treated with various inhibitors for 30 minutes, and polysome profiles were analyzed. Cycloheximide, emetine, and anisomycin stabilized polysomes, while puromycin, pactamycin, lactimidomycin, harringtonine, T-2 toxin, and torin-1 induced polysome disassembly. Pactamycin and torin-1 showed incomplete disassembly. Puromycin generated “empty” 80S ribosomes, whereas lactimidomycin, harringtonine, T-2 toxin, and pactamycin led to 80S ribosomes halted at mRNA start codons. These conditions allowed the identification of mRNA with extended ribosome-free regions, each carrying a solitary 80S ribosome thereby preventing SG formation. This challenges the belief that extended ribosome-free mRNA segments are sufficient for SG formation, suggesting that mRNA entry into SGs may involve specific contacts between RNA-binding proteins and inaccessible regions on 40S subunits associated with ribosomes.
Additionally, the data indicates that the presence of at least one 80S ribosome on mRNA hinders its recruitment into SGs, offering new insights and questioning prior assumptions about the mechanisms underlying SG formation.
SARS-CoV-2 infection engenders heterogeneous ribonucleoprotein interactions to impede translation elongation in the lungs
Experimental and Molecular Medicine, 2023
Kim, Junsoo, et al.
The unprecedented COVID-19 pandemic, caused by SARS-CoV-2, continues despite vaccinations, emphasizing the need for post-infection therapies. Understanding viral behaviors and host responses is crucial, prompting transcriptome studies on infected tissues. However, mRNA level changes don’t always correlate with protein changes. Ribosome profiling provides insights by capturing in vivo ribosome-RNA interactions. Previous studies focused on in vitro systems, limiting our understanding of in vivo translational regulation during SARS-CoV-2 pathogenesis. This study employed tissue-optimized ribosome profiling and a severe-COVID-19 mouse model to establish the first temporal translation profiles of virus and host genes in SARS-CoV-2-infected lungs.
The study employed Ribo-seq and RNA-seq data to investigate SARS-CoV-2 infection dynamics in mouse tissues. During early infection, there was a continuous viral expansion, but a majority of viral transcripts showed limited translation, contrasting in vitro observations. In the late phase, a minor portion of reads aligned to the viral genome, indicating effective restraint of SARS-CoV-2 in mouse tissue. The research identified translation regulation targets, revealing increased pseudoribosomal ribonucleoprotein (RNP) interactions hindering elongation and dysfunctional ribosomes. Ribosome stalling on codons within transmembrane domains and compromised translation of immunity- and metabolism-related genes underscored disrupted translation integrity as a critical factor in SARS-CoV-2 tissue pathogenesis, suggesting potential therapeutic avenues.
Notably, RNP complexes, ribosome heterogeneity, and translation elongation impediment were identified, uncovering novel molecular signatures contributing to tissue pathology post-SARS-CoV-2 infection. The study suggests that the disruption of RNP complexes associated with translation is a significant molecular event underlying SARS-CoV-2 pathology.
Survey of the translational dysregulation in cervical cancer initiation and progression with ribosome profiling
International Journal of Gynaecologic Cancer, 2023
Translational regulation plays a pivotal role in the intricate gene expression control program, significantly influencing the onset and advancement of cancer. In China, cervical cancer stands as the second most prevalent malignant tumor among females. Despite its prominence, there remains a scarcity of high-resolution, genome-wide insights into the landscape of RNA translation in cervical cancer. Therefore, this study focused on investigating translational regulation in cervical cancer, which plays a critical role in the gene expression program.
Ribosome profiling was conducted on 25 cervical cancer samples at various stages and 10 normal cervical tissues. The findings revealed significant differences in the transcriptome and translatome during cervical cancer initiation and progression. Notably, proteins related to cell cycle and cell-cell adhesion exhibited significant translational upregulation and downregulation in cervical cancer compared to normal tissue. The analysis of translatome data in conjunction with clinical features suggested that translational dysregulation leading to immune dysregulation may contribute to the progression of cervical cancer.
Overall, this study has established the first translatome of cervical cancer, providing a valuable data resource and novel insights into its initiation and progression.