December 17th
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, Li et al, investigates the role of PCIF1 in mediating the methylation of m6Am in mRNA and explores its interplay with potential cofactors, particularly focusing on its pathological significance. McQuown et al, studied the protein folding mechanism mediated by Zpr1, an ATP-independent chaperone responsible for the biogenesis of eukaryotic translation elongation factor 1A (eEF1A). Zhou et al, demonstrated that DCAF13, highly expressed in lymphoid organs, is crucial for T cell survival and proliferation.
The CTBP2-PCIF1 complex regulates m6Am modification of mRNA in head and neck squamous cell carcinoma
Journal of Clinical Investigation, 2023
Li, K., Chen, J., Zhang, C., Cheng, M., Chen, S., Song, W., Yang, C., Ling, R., Chen, Z., Wang, X., Xiong, G., Ma, J., Zhu, Y., Yuan, Q., Liu, Q., Peng, L., Chen, Q., & Chen, D.
The study underscores the significance of dysregulated mRNA modifications and modifiers in tumor aggressiveness. Over 60% of RNA modifications are methylated, with various types characterized, including N6-methyladenosine (m6A), 5-methylcytosine (5mC), N6-methyl-2′-O-methyladenosine (m6Am), and N7-methylguanosine (m7G). M6Am plays a crucial role in tumorigenesis by affecting mRNA stability, decapping, and translation of key oncogenes and tumor suppressors. Phosphorylated RNA polymerase II CTD-interacting factor 1 (PCIF1) is identified as the sole known methyltransferase to catalyse m6Am marks, whereas fat mass- and obesity-associated protein (FTO) demethylates cap m6Am. While the involvement of m6A modification in cancer biology is widely understood, the impact of m6Am in tumor progression is still unfolding. The study investigates the role of PCIF1 in mediating the methylation of m6Am in mRNA and explores its interplay with potential cofactors, particularly focusing on its pathological significance.
Recent studies reveal that cap-adjacent m6Am on mRNA negatively regulates cap-dependent translation of methylated mRNAs. Ribosome sequencing in PCIF1-knockout SCC25 cells showed changes in ribosome footprints for transcripts, with 1,600 upregulated and 800 downregulated. Gene ontology analysis implicated transcription and RNA methylation. Notably, TET2, a tumor suppressor, emerged as the most upregulated gene among overlapping genes in Ribo-Seq and m6Am-Seq data. The m6Am-Seq data identified 2 m6Am sites in 5′-UTRs of TET2 in both PCIF1 and CTBP2 knockouts, suggesting TET2 as a downstream target in head and neck squamous cell carcinoma (HNSCC).
Overall, the study highlights the oncogenic function of the PCIF1-CTBP2 complex in the epitranscriptome, emphasizing the importance of m6Am modification in tumor progression.
A Zpr1 co-chaperone mediates folding of eukaryotic translation elongation factor 1A via a GTPase cycle
Molecular Cell, 2023
McQuown, A. J., Nelliat, A. R., Reif, D., Sabbarini, I. M., Membreno, B. S., Wu, C. C., & Denic, V.
The molecular chaperones, particularly Zinc-finger protein 1 (Zpr1), play a crucial role in protein folding and stress response. The study investigates the protein folding mechanism mediated by Zpr1, an ATP-independent chaperone responsible for the biogenesis of eukaryotic translation elongation factor 1A (eEF1A). While general protein folding is typically regulated by chaperones using ATP hydrolysis, the specific mechanisms governing Zpr1-mediated folding and its rapid recycling are not well understood.
Through yeast genetics, microscopy analysis, biochemical reconstitution, and structural modelling, the researchers find that the folding of eEF1A by Zpr1 requires GTP hydrolysis. Additionally, they identify the Altered inheritance of mitochondria 29 (Aim29) proteins as a Zpr1 co-chaperone that recognizes eEF1A in its GTP-bound state, prior to hydrolysis. This interaction with Aim29 reduces Zpr1, eEF1A GTPase activity, facilitating the exit of the client protein from the folding cycle. Ribo-seq analysis revealed that GCN4 mRNA translation was de-repressed in aim29Δ cells, a finding corroborated by a fluorescent reporter assay. The analysis also identified elevated levels of ribosomes with 21-nucleotide footprints, indicating open A sites, suggesting a global defect in eEF1A-mediated delivery of aminoacylated-tRNAs (aa-tRNA) during the elongation cycle in aim29Δ cells. In summary, aim29Δ cells exhibited phenotypic similarities with Zpr1-depleted cells, suggesting that both conditions may arise from a shared defect in eEF1A biogenesis.
The findings highlight a unique ATP-independent chaperone system that, despite lacking ATP hydrolysis, relies on client GTP hydrolysis to regulate the chaperone-client interaction, adding a novel layer of complexity to our understanding of protein folding processes. The study reveals unexpected parallels between eEF1A biogenesis and ATPase chaperone systems, shedding light on cellular protein folding mechanisms.
T cell proliferation requires ribosomal maturation in nucleolar condensates dependent on DCAF13
Journal of cell biology, 2023
Zhou, L., Wang, S., Hu, W., Liu, X., Xu, L., Tong, B., Zhang, T., Xue, Z., Guo, Y., Zhao, J., Lu, L., Fan, H., Qian, W., Chen, J., Chen, W., Wang, L.
This study focuses on the importance of rapid T cell proliferation for initiating adaptive immunity against pathogens. Upon encountering foreign antigens, initially dormant T cells undergo rapid activation and clonal expansion, necessitating accelerated ribosomal machinery to produce proteins. While previous studies have mainly focused on transcriptional and posttranslational regulation of T cell proliferation, this research emphasizes the significance of posttranscriptional processes, particularly protein translation, in governing T cell functionality. The nucleolus, a membrane-less subnuclear compartment, emerges as a key player in this process, with numerous proteins identified, including DCAF13. This study demonstrates that DCAF13, highly expressed in lymphoid organs, is crucial for T cell survival and proliferation.
Recent studies highlight the crucial role of ribosome biogenesis in sustaining T cell proliferation upon stimulation. In this context, researchers conducted polysome profiling analysis on ERT2 Cre+ Dcaf13fl/flT cells with or without tamoxifen treatment to investigate the influence of DCAF13 on stimulated T cell ribosome status, including ribosome composition and polysome formation during translation. The analysis revealed a notable decrease in the peak of the 40S small ribosomal subunit in DCAF13-depleted T cells, which consists of 18S rRNA and various ribosomal proteins. Interestingly, this 40S decrease was consistent between stimulated and naïve DCAF13-deleted T cells, indicating the presence of idle ribosomes in naïve T cells. This observation aligns with the notion that these ribosomes may handle short-term protein demands following rapid activation, as suggested by previous findings.
The findings highlight the emerging and increasingly attractive field of nucleolar regulation in T cell proliferation.