November 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, Ma et al. investigate METTL16’s role in promoting efficient translation and alternative splicing during spermatogenesis. Brischigliaro et al. explore how TACO1 prevents ribosomal stalling on polyproline sequences during mitochondrial protein synthesis. Roiuk et al. examine an alternative mechanism of translation initiation via eIF3d under cellular stress when eIF4E is inhibited.
N6-methyladenosine writer METTL16-mediated alternative splicing and translation control are essential for murine spermatogenesis
Genome Biology, 2024
Ma, Q., Gui, Y., Ma, X., Zhang, B., Xiong, W., Yang, S., Cao, C., Mo, S., Shu, G., Ye, J., Liu, K., Wang, X., Gui, Y., Wang, F. and Yuan, S.
The study investigates the role of methyltransferase-like protein 16 (METTL16), an N6-methyladenosine (m⁶A) methyltransferase, in murine spermatogenesis. METTL16 deficiency leads to defective spermatogonial differentiation and meiosis initiation. Ribosome profiling (Ribo-seq) data reveals that METTL16 is crucial for the efficient translation of genes involved in the transition from mitosis to meiosis during spermatogenesis. Loss of METTL16 significantly impacts the translation efficiency of key meiotic genes in the testes. RNA sequencing (RNA-seq) shows widespread changes in gene expression, with many meiosis-related transcripts being downregulated upon METTL16 depletion.
Additionally, m⁶A-seq data reveal that METTL16 knockout alters m⁶A modifications of a small subset of genes, although it does not significantly alter global m⁶A levels. Among the downregulated genes, those involved in the regulation of the G1/S transition of the mitotic cell cycle were particularly enriched. The study concludes that METTL16-mediated m⁶A methylation is critical for proper germ cell differentiation and the success of spermatogenesis. Interestingly, METTL16 was also found to modulate the alternative splicing of the meiosis-related genes Stag3 and Ddb2.
These findings shed light on the role of m⁶A modifications in RNA processing and translation during key developmental stages, highlighting METTL16’s crucial involvement in alternative splicing and gene expression regulation in reproductive biology.
The human mitochondrial translation factor TACO1 alleviates mitoribosome stalling at polyproline stretches
Nucleic Acids Research, 2024
Brischigliaro, M., Krüger, A., Moran, J.C., Antonicka, H., Ahn, A., Shoubridge, E.A., Rorbach, J. and Barrientos, A.
This paper investigates the role of TACO1, a mitochondrial translation factor, in preventing ribosomal stalling during the synthesis of mitochondrial proteins, particularly those with polyproline stretches. Proteins such as COX1 and COX3, essential components of the cytochrome c oxidase complex (Complex IV of the electron transport chain), contain proline-rich sequences, which can cause ribosome stalling during translation elongation.
Mitoribosome profiling (mitoribo-seq) was performed on wild type and TACO1-knockout HEK293T cells, revealing 13 instances of stalling in knockout cells that were absent in the wild type. These stalls occurred predominantly, though not exclusively, at polyproline sequences, and could be rescued by the reintroduction of TACO1. Three of the stalls occurred in COX1, and two in COX3. TACO1 interacts with the large ribosomal subunit bL27m to stabilize the peptidyl-transferase centre, enhancing the efficiency of elongation and allowing for the smooth synthesis of polyproline-containing proteins. Loss of TACO1 leads to premature translation termination at certain polyproline motifs, impairing mitochondrial function due to COX deficiency.
These findings not only clarify the molecular role of TACO1 as the mitochondrial counterpart of prokaryotic translation elongation factor P (EF-P) and the eukaryotic eIF5A, but also highlight its potential implications for understanding diseases like Leigh syndrome, which is linked to defects in mitochondrial protein synthesis.
eIF4E-independent translation is largely eIF3d-dependent
Nature Communications, 2024
Roiuk, M., Neff, M. and Teleman, A.A.
Under conditions of cellular stress, such as hypoxia or nutrient deprivation, the mTORC1 pathway is inactivated, leading to the suppression of eIF4E-dependent translation. This paper explores an alternative mechanism of translation initiation that does not rely on traditional eIF4E-dependent translation initiation.
Using ribosome profiling (Ribo-seq), the authors identified a subset of mRNAs that are still efficiently translated even when eIF4E is blocked through the overexpression of a constitutively active eIF4E-binding protein (4E-BP). Polysome profiling further supported these findings, revealing that certain mRNAs, shown to be actively translated upon eIF4E inhibition in the ribosome profiling data, remain in the heavy polysome fraction or shift into even heavier fractions upon 4E-BP overexpression, despite a significant reduction in global polysomes. Notably, negative regulators of growth and cell cycle were enriched in the up-regulated mRNAs.
Interestingly, translation initiation on these upregulated mRNAs, which typically rely on eIF4E, remained cap-dependent. The authors propose a model in which, upon eIF4E inhibition, certain mRNAs recruit the pre-initiation complex through eIF3d binding to the 5′ UTR, followed by cap binding by eIF3d.
This study highlights a novel cap-binding function of eIF3d, which is particularly relevant in the context of cells exposed to stress, offering a potential alternative mechanism of translation regulation that could have implications for understanding stress responses in cancer and other diseases.