May 21st

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, Tsukamoto et al. investigate the regulatory mechanisms governing glutamine homeostasis under conditions of amino acid starvation, while Shiraishi et al. delve into the specifics of translation in the realm of cardiac muscle tissue. Finally, Wang et al. look into the role of a specific tRNA modification in the proliferation and resistance of osteosarcoma.

GCN2 kinase‐mediated upregulation of ubiquitin C maintains intracellular glutamine level and tRNAGln (CUG) charging under amino acid starvation

FEBS Letters, 2023
Tsukamoto, Y., Nakamura, Y., Hirata, M., Okuzaki, D., Sakate, R. and Kimura, T

The charging of tRNAs relates to their conjugation to free amino acids. Amino acid starvation can lead to an increase in the fraction of uncharged tRNAs, which is detected by the protein GCN2. Activated GCN2 is an important stimulator of the integrated stress response (ISR), halting general translation through phosphorylation of eIF2α, while at the same time initiating mechanisms for increased amino acid synthesis and uptake. Here, the researchers aim to investigate the relationship between amino acid starvation, tRNA charging, and such rescue mechanisms further.

Interestingly, while most tRNA charging ratios remain unchanged following amino acid starvation, tRNAGln(CUG) was strongly effected, having a significantly reduced charging ratio compared to others. The authors showed that observed changes in tRNAGln(CUG) were linked to the ISR and glutamine levels. Translational arrest partial rescued such a response, while inhibition of autophagy once again exacerbated it. Ribosome profiling revealed that GCN2 promotes the translation of ubiquitin C, under conditions of amino acid starvation. Under the same conditions, upon knockdown of this gene, the charging ratio of tRNAGln(CUG) was significantly reduced. Given glutamine itself is a known stimulator of protein synthesis, this paper adds an additional layer of information to the literature surrounding such regulatory mechanisms.

RPL3L-containing ribosomes determine translation elongation dynamics required for cardiac function

Nature Communications, 2023
Shiraishi, C., Matsumoto, A., Ichihara, K., Yamamoto, T., Yokoyama, T., Mizoo, T., Hatano, A., Matsumoto, M., Tanaka, Y., Matsuura-Suzuki, E. and Iwasaki, S et al.

Functional ribosome heterogeneity is a concept that has been gaining increasing traction in recent years. RPL3L, a paralog of the RPL3 protein, is specific to the heart and skeletal muscle tissue in terms of its expression. The highly conserved RPL3 is the ribosomal protein most closely located to the peptidyl transferase centre (PTC). It contains a number of domains, including the NH2-terminal extension, the W finger, and the basic thumb, which are important components in terms of the PTC. In this study, the authors generate RPL3L-deficient mice, to investigate the impact of RPL3L loss on translation elongation dynamics in cardiac tissue.

Given the known cardiac-specific expression of this paralog, authors noted impaired cardiac contractility in these mice. Interestingly, ablation of RPL3L led to upregulation of RPL3 mRNA, possibly as a compensatory mechanism. Ribosome profiling demonstrated no change in translational efficiency for any genes. It did, however, reveal increased occupancy at proline and alanine codons in the A-site. Gene ontology analysis revealed that genes for which such occupancy was pronounced had an enrichment of terms related to cardiac muscle contraction and ATP synthesis, functions key to such tissue. Disome-seq analysis revealed increased ribosome collisions in cardiac tissue lacking RPL3L. Finally, mass spectroscopy data suggested that downregulation of genes involved in cardiac muscle contraction (rather than ATP synthesis) is responsible for the phenotypic changes observed.

METTL1/WDR4-mediated tRNA m7G modification and mRNA translation control promote oncogenesis and doxorubicin resistance

Oncogene, 2023
Wang, Z., Yu, P., Zou, Y., Ma, J., Han, H., Wei, W., Yang, C., Zheng, S., Guo, S., Wang, J. and Liu, L.

METTL1 and WDR4 are members of the methyltransferase complex which catalyses the m7G tRNA modification, found in the 45-47 positions of the variable loop. Such a modification is essential in helping to stabilise tRNA. METTL1 is often specifically overexpressed in osteosarcoma, as a result of chromosomal rearrangement and amplification. Interestingly, the m7G modification is also known to function in embryonic stem cell renewal and differentiation, properties often acquired in cancers. Here, the authors seek to explore these connections further, with a particular focus on oncogenesis and drug resistance.

Knockdown of METTL1 in two osteosarcoma cell lines was demonstrated to significantly reduce cell migration and invasion, suggestive of its involvement in metastasis. Depletion of WDR4, a protein which prevents the degradation of METT1, in these cells displays a similar phenotype. Overexpression of these proteins enhances proliferation. METTL1 knockdown also reduced overall global translation, via a loss of m7G methylation, but preferentially targets those transcripts with an enrichment of m7G methylation-associated codons. Polysome profiling and GO analysis demonstrates a clustering of genes within the cell adhesion and extracellular matrix functionalities. Interestingly, knockdown of METTL1 and doxorubicin treatment work synergistically to reduce oncogenic cell growth, suggesting this gene may contribute to drug resistance.

Oscar Ting

Oscar Ting

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