August 18th, 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, we bring a focus to the research of tRNA modifications. Starting off, Tresky et al. uncover the role of TRMT10A in translation initiation through its influence on methionine initiator tRNAs, while Sui et al. explore the impact of the m3C modification, with a focus on serine tRNAs. Finally, Zuo et al. delve into the function of TRMT6 and its putative involvement in HSCs maintenance.
TRMT10A dysfunction perturbs codon translation of initiator methionine and glutamine and impairs brain functions in mice
Nucleic Acid Research, 2024
Tresky, R., Miyamoto, Y., Nagayoshi, Y., Yabuki, Y., Araki, K., Takahashi, Y., Komohara, Y., Ge, H., Nishiguchi, K., Fukuda, T., Kaneko, H., Maeda, N., Matsuura, J., Iwasaki, S., Sakakida, K., Shioda, N., Wei, F., Tomizawa, K. and Chujo, T.
Phenotypically, tRNA modopathies are overrepresented in the brain compared to other organs in the body. The tRNA methyltransferase 10A (TRMT10A) protein is responsible for the m1G modification of cytoplasmic tRNA which is present at position 9 at up to 40% of all tRNAs. Homozygotic mutations in the TRMT10A gene have been associated with development conditions such as microcephaly, short stature, and intellectual disabilities. Previous research in cell models has associated TRMT10A knockout with reduced steady-state initiator methionine tRNA levels, as well as increased glutamine tRNA fragmentation. Here, the authors establish a knockout mouse model, aiming to investigate the wider impacts of TRMT10A at a molecular and physiological level.
Trmt10a-null mice exhibited lower body weight in comparison to controls, reflective of what is seen in human patients. Furthermore, in mouse brains, they confirmed a decrease in tRNAiMet and tRNAGln(CUG) steady state levels. Ribosome profiling revealed increased occupancy on the glutamine CAG codon, consistent with the reduction in tRNAGln(CUG) levels. There were also changes in translation efficiency of a number of genes, although there was no correlation between genes and CAG codon content. Interestingly, Trmt10a knockout led to increased Atf4 CDS expression, which is typically suppressed under normal conditions and activated under the integrated stress response via eIF2 subunit alpha (eIF2S1)phosphorylation. Here, however, eIF2S1 phosphorylation was not observed, and increased Atf4 expression was instead linked to reduced tRNAiMet abundance, resulting in similarly reduced tRNAiMet-eIF2α-GTP ternary complex formation. Yet, translation levels overall were slightly increased, possibly due to increased m6Am formation. Reduced spatial learning and hippocampal plasticity was likely linked to smaller postsynaptic densities seen in these mice. The increase in mRNA modifications like m6Am in TRMT10A null brains provides insights into the complex regulatory mechanisms of translation influenced by tRNA and mRNA modifications. This opens potential avenues for therapeutic interventions targeting these modifications in neurological diseases.
m3C32 tRNA modification controls serine codon-biased mRNA translation, cell cycle, and DNA-damage response
Nature Communications, 2024
Cui, J., Sendinc, E., Liu, Q., Kim, S., Fang, J.Y. and Gregory, R.I.
tRNA modifications are essential for accurate decoding of mRNAs, as well as the stability of the tRNAs themselves. N3-methylcytidine (m3C) is a tRNA modification typically found at position 32 of a subset of tRNAs (including tRNA-Ser), but also at position 47 and 20. Interestingly, there are 4 orthologs of the yeast genes known to catalyse the m3C modification (METTL2A, METTL2B, METTL6, and METTL8). However, what each of these methylators individually target is currently unclear, despite previous attempts through mass spectrometry and primer extension analyses. Here, the authors undertake a transcriptome-wide analysis utilising a novel sequencing technique, termed HAC-Seq (hydrazine-aniline cleavage sequencing), in combination with individual gene knockouts, in order to comprehensively explore their targets.
They uncover that METTL6 is principally responsible for the m3C32 modification of tRNA-Ser, whereas METTL2A/2B held more influence on tRNA-Arg and tRNA-Thr m3C32 modification. Combination knockout of METTL2A/2B/6 resulted in the elimination of m3C32 from most cytoplasmic tRNAs. METTL8, on the other hand, is primarily responsible for mitochondrial m3C32 modification, with no function related to cytoplasmic tRNAs. The conserved GxGxGx motif in METTL2A/2B/6 was found to be crucial for their m3C activity , as were the specific N193 and F214 residues in METTL2A. Ribosome profiling revealed 827 upregulated and 590 downregulated genes in METTL3A/2B/6 knockout cells. Threonine and arginine codons had decreased codon occupancy in these cells, while serine codons displayed increased occupancy, particularly at the AGU codon (decoded by tRNA-Ser-GCT). Downregulated genes also exhibited a significantly larger number of serine codons compared to upregulated genes, especially AGU codons. Gene ontology analysis revealed that there is an enrichment of genes involved in the cell cycle and DNA damage response in the observed downregulated genes, with knockout cells displaying an impaired G2/M transition. The study extends our understanding of the epitranscriptome and its impact on gene expression regulation, with potential implications for various biological processes and disease states.
tRNA m¹A modification regulate HSC maintenance and self-renewal via mTORC1 signaling
Nature Communications, 2024
Zuo, H., Wu, A., Wang, M., Hong, L. and Wang, H.
Ribosomal stalling occurs when the ribosome encounters sequences in mRNA that are difficult to translate, such as polyproline tracts. This stalling can impede protein synthesis and cell growth. This paper by Takada et al. explores the mechanisms by which Bacillus subtilis manages ribosomal stalling, a critical issue in protein synthesis.
The study highlights the roles of elongation factor P (EF-P) and the ATP-binding cassette F (ABCF) ATPases YfmR and YkpA/YbiT in resolving these stalls. EF-P is known to alleviate stalling at polyproline sequences, facilitating their translation. The researchers found that YfmR, an ABCF ATPase, works in concert with EF-P to further enhance the translation of these challenging sequences.
Through genetic and biochemical analyses, the study demonstrates that the simultaneous loss of both EF-P and YfmR leads to significant growth defects in B. subtilis. This defect is characterized by severe ribosomal stalling and reduced levels of actively translating ribosomes. Interestingly, overexpression of another translation factor can partly compensate for the loss, indicating a complex network of factors involved in maintaining translation efficiency.
Moreover, the research reveals that YfmR associates with actively translating ribosomes and is crucial for the proper function of the ribosome in the absence of EF-P. Depletion of YfmR from cells lacking EF-P leads to lethal outcomes, underscoring its essential role in translation under these conditions.
This study advances our understanding of the molecular mechanisms behind ribosomal stalling and highlights the importance of ABCF ATPases in bacterial translation, suggesting potential targets for antimicrobial development.