July 30th
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, Qanmber et al. look at the role of translation in cotton fibre development, Meng et al. look at RMC-6272 – a selective mTORC1 inhibitor – and its role in the PI3K-mTOR pathway and breast cancer therapy. Finally, Nagao et al. look at pep-tRNA drop-off using a variety of techniques such as ribosome profiling and pep-tRNA profiling.
Transcriptional and translational landscape fine-tune genome annotation and explores translation control in cotton
Journal of Advanced Research, 2023
Qanmber, G., You, Q., Yang, Z., Fang, L., Zhang, Z., Chai, M., Gao, B., Li, F. and Yang, Z
The lack of annotation for intergenic regions in whole genome sequencing and pan-genomics poses a challenge to improving crops. Despite progress in research, the influence of post-transcriptional regulation on fibre development and the analysis of translational profiles during various stages of fibre growth in cotton (G. hirsutum) has not been investigated.
Ribosome profiling was utilised to examine the cotton translatome. Reference-guided de novo transcriptome assembly for normal and short fibre cotton plants revealed additional transcripts that were absent from the previous genome annotation. The authors identified ribosomal P-site distribution at a characteristic three-nucleotide periodicity and a dominant ribosome footprint spanning 27 nucleotides. 1,589 small open reading frames (sORFs) were detected, consisting of 1,376 upstream ORFs (uORFs) and 213 downstream ORFs (dORFs). Additionally, 552 long non-coding RNAs (lncRNAs) with potential coding functions were discovered, which enhanced the annotation of the cotton genome. These findings play a role in refining our understanding of the cotton genome.
Despite diverging millions of years ago, similarities were found in the translatome of Arabidopsis, tomato, and cotton plants. Novel translational events involving sORFs, lncRNAs, and translational regulatory mechanisms were found to be conserved across species.
These findings highlight the similarities in translational processes and mechanisms among different plant species, including cotton, and provide insights into the regulation of gene expression at the translational level. More importantly, this provides valuable insights into cotton genomics and the extensive mechanisms involved in the translational control of cotton fibre development.
A bi-steric mTORC1-selective inhibitor overcomes drug resistance in breast cancer
Oncogene, 2023
Meng, D., Zhao, X., Yang, Y.C., Navickas, A., Helland, C., Goodarzi, H., Singh, M., and Bandyopadhyay, S.
The PI3K-mTOR pathway plays a crucial role in breast cancer development, including the resistance to various targeted treatments. The mTOR kinase consists of two different complexes, mTORC1 and mTORC2. However, our understanding of which complex is necessary for the survival of cancerous cells has been limited due to the lack of tools that can selectively and completely impair each subcomplex.
To address this limitation, the authors utilised a compound called RMC-6272, which is a bi-steric molecule that specifically targets the active site of mTOR, exhibiting more than 25-fold selectivity for mTORC1 over mTORC2 substrates. When mTORC1 is completely suppressed by RMC-6272, it induces apoptosis in ER+/HER2− breast cancer cell lines, particularly those with mutations in PIK3CA or PTEN. This effect is achieved by inhibiting a rapamycin-resistant mTORC1 substrate known as 4EBP1 and reducing the levels of the pro-survival protein MCL1.
In order to investigate the broader effects of the inhibition of mTORC1, the authors conducted ribosome profiling experiments to compare mRNA translation following treatment with everolimus and RMC-6272. Their findings revealed a significant decrease in the translational efficiency of 395 transcripts in MCF-7 cells treated with RMC-6272 compared to everolimus treatment. Pathway analysis indicated that RMC-6272 treatment led to more substantial reductions in ribosomal genes and MYC target genes compared to everolimus treatment. Therefore, the potent and selective inhibition of mTORC1 is likely to result in decreased protein synthesis and attenuation of oncogenic MYC signaling. Additionally, RMC-6272 decreases the translation of components of the CDK4/6 pathway. The authors did not observe changes in MCL1 translation, however.
Future investigation is needed to confirm whether there is a shift in the global mRNA translation in the CDK4/6 inhibitor resistant cells upon RMC-6272 treatment. In addition, it would be of interest to identify potential clinical biomarkers to predict the response to RMC-6272 (or other bi-steric mTORC1-selective inhibitor) treatment.
Quality control of protein synthesis in the early elongation stage
Nature Communications, 2023
Nagao, A., Nakanishi, Y., Yamaguchi, Y., Mishina, Y., Karoji, M., Toya, T., Fujita, T., Iwasaki, S., Miyauchi, K., Sakaguchi, Y. and Suzuki, T.
During the initial stage of bacterial translation, peptidyl-tRNAs frequently detach from the ribosome in the absence of a termination codon, a phenomenon known as “pep-tRNA drop-off.” These detached peptidyl-tRNAs are then recycled by peptidyl-tRNA hydrolase. In this study, a highly sensitive method using mass spectrometry was established to profile pep-tRNAs, leading to the successful detection of numerous nascent peptides originating from pep-tRNAs accumulated in Escherichia coli. The authors found that pep-tRNA drop-off is an active mechanism employed by the ribosome to reject miscoded pep-tRNAs during early elongation. This process significantly contributes to the quality control of protein synthesis after peptide bond formation.
To explore the role of ribosome recycling factor (RRF) in dissociating peptidyl-tRNAs and recycling ribosomes during early elongation in bacterial translation, the authors generated a temperature-sensitive mutant of RRF called frrts71. Subsequently, ribosome profiling was performed on this mutant strain to examine potential changes in ribosome occupancy near the mRNA initiation sites. The ribosome profiling data showed that in the frrts71 mutant cells, ribosomes accumulated near the beginning of translation when RRF was inactivated, indicating that RRF plays an active role in dissociating peptidyl-tRNAs and recycling ribosomes during the early elongation stage. This finding was further supported by additional analysis of ribosome-profiling data from E. coli cells with rapidly depleted RRF. The results showed a clear accumulation of ribosome-protected mRNA fragments at the translation initiation sites, which increased over time during RRF depletion, consistent with the previous observation.
Overall, this study shows a novel mechanism of quality control in protein synthesis during the early stage of translation elongation and that peptidyl-tRNA dissociation from the ribosome plays a crucial role in this mechanism.