
October 13th, 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, Yang et al. discovered how translatome remodelling happens in hepatocytes during fasting, Vieira de Souza et al. uncovers the reasons why many short ORFs that are found by Ribo-seq are not detectable with proteomics and Chen et al. unveils the translatomic adaptation of lychee to cold environment.
Remodelling of the translatome controls diet and its impact on tumorigenesis
Nature, 2024
Yang, H., Zingaro, V.A., Lincoff, J., Tom, H., Oikawa, S., Oses-Prieto, J.A., Edmondson, Q., Seiple, I., Shah, H., Kajimura, S. and Burlingame, A.L.
Fasting has been linked to numerous health benefits. However, the mechanisms by which fasting signals trigger changes in the proteome to establish metabolic programs remain unclear.
In this study, with the use of PolyRibo-seq, the authors demonstrated that during fasting, mice hepatocytes undergo selective translatome remodelling. 983 genes were shown to be translationally downregulated on fasting including mTOR translation targets. 615 transcripts were significantly translationally upregulated and gene enrichment analysis revealed the predominant function of regulated genes in lipid metabolism and ketone body production.
The reason for such translational rewiring can be explained by an increase of phosphorylation of eukaryotic translation initiation factor 4E (P-eIF4E) which is the major cap-binding protein. During fasting or with a ketogenic diet, P-eIF4E becomes a selective translation factor important for the translation of specific mRNAs in the liver that are critically required for ketogenesis. The results indicated that P-eIF4E controls these messenger RNAs via a specific pyrimidine-rich translational element located within their 5′UTRs.
Activity of eIF4E only kinase, MNK, was also increased on fasting. Transient inhibition of P-eIF4E in mice using a MNK inhibitor eFT508 resulted in a more than 50% reduction of ketogenesis. Researchers also demonstrated that fatty acids derived from adipocyte lipolysis can signal to activate the MNK–P-eIF4E axis in the liver during fasting and its downstream translational control of ketogenic transcripts. Overall, this work suggests that controlling ketone concentrations by modifying translational control may be beneficial for a diet intervention therapy for cancer and various conditions of excess blood ketone amounts.
Rp3: Ribosome profiling-assisted proteogenomics improves coverage and confidence during microprotein discovery
Nature Communications, 2024
Vieira de Souza, E., L. Bookout, A., Barnes, C.A., Miller, B., Machado, P., Basso, L.A., Bizarro, C.V. and Saghatelian, A.
Ribosome profiling (Ribo-Seq) is widely regarded as the gold standard for identifying novel small Open Reading Frames (smORFs) that encode microproteins. The key challenges of this method for detection of smORFs is the short nature of ribosome footprint reads leading to ambiguous mapping. Also, overlap between Ribo-seq predicted and proteomics predicted smORFs is usually small. To find whether such limitations could be resolved and how such a discordance in overlap can be explained, the authors developed Rp3, a workflow that integrates proteogenomics and Ribo-seq.
It turned out that their proteogenomics-based approach, Rp3, predicts a different set of smORFs in comparison to Ribo-seq-only based tools such as RibORF, Ribocode and PRICE. The vast majority of smORFs identified with Rp3 reside in genome regions that are predicted to be either non-coding or that are pseudogenes or retrotransposons. Ribo-seq based tools primarily identified upstream ORFs (uORFs). Rp3 tends to identify longer microproteins, and most smORFs identified by the Ribo-seq based methods tend to be shorter. The sequence composition also turned out to be different. Lysine is less common in Ribo-seq microproteins than Rp3 likely because trypsin cleaves after lysine and arginine residues. Proline, which is substantially enriched in Ribo-seq predicted microproteins, is known to confound the interpretation of fragmentation spectra. This could explain some of the difficulty in Ribo-seq predicted microprotein identification by mass spectrometry.
Overall, the authors demonstrated that the orthogonal approach of using both proteogenomics and Ribo-seq for identification of smORFs is necessary for a truly comprehensive microprotein identification analysis.
Unveiling the translational dynamics of lychee (Litchi chinesis Sonn.) in response to cold stress
BMC Genomics, 2024
Chen, M., Dai, S., Chen, D., Chen, H., Feng, N. and Zheng, D.
A study published in BMC Genomics explores the complex translational dynamics in lychee (Litchi chinensis Sonn.) under cold stress. This research offers groundbreaking insights into how lychee, a subtropical fruit crop, adapts at the molecular level to chilling temperatures, which typically pose a threat to its growth and survival. By comparing translatomic and transcriptomic data, the study uncovers a nuanced layer of gene expression regulation through selective translation. One of the key findings is the identification of ribosome stalling at specific codons— notably the AAU codon when it is in the ribosomes E site. This stalling mechanism is suggested to play a vital role in the plant’s adaptive response to cold, possibly by regulating the synthesis of proteins critical for stress tolerance.
Further analysis revealed that the translation efficiency of certain genes involved in stress and defence responses was distinctly altered under cold stress conditions. This indicates that lychee plants can selectively upregulate proteins necessary for resilience against cold, beyond the changes detectable at the mRNA level alone.
This study highlights the importance of translational control in plant stress responses. Understanding these mechanisms opens new avenues for enhancing cold tolerance in lychee and potentially other crops through biotechnological or breeding strategies aimed at optimizing translational responses to environmental stresses. This research not only broadens our understanding of the molecular responses of plants to abiotic stress but also underscores the potential of integrating ribosome profiling with RNA sequencing to uncover regulatory strategies that could lead to more robust agricultural systems.