June 9th, 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, Hofmann et al. investigate the role of ATF6 during the complexities of cardiac hypertrophy, while Zhang et al. uncover a novel translational mechanism by which the Epstein-Barr virus is able to evade detection. Finally, but perhaps most significantly, Henis et al. present evidence of a novel kinase of eEF2, with important implications for neurodevelopment disorders.

ATF6 protects against protein misfolding during cardiac hypertrophy

Journal of Molecular and Cellular Cardiology, 2024

Hofmann, C., Aghajani, M., Alcock, C.D., Blackwood, E.A., Sandmann, C., Herzog, N., Groß, J., Plate, L., Wiseman, R.L., Kaufman, R.J. and Katus, H.A.

Misfolded proteins are thought to impair cardiac function, and it has been demonstrated that these proteins accumulate during cardiac hypertrophy-associated heart failure. However, whether or not these misfolded proteins are present in the early stages of heart failure, or simply a product present in the later stages, is unknown. Such misfolded proteins are sensed by PERK, IRE1α, and ATF6, triggering the unfolded protein response (UPR). Here, general translation is suppressed via eIF2S1 phosphorylation, while ER chaperones and ER-associated degradation genes are upregulated. However, the precise mechanisms mediating the protective effects of ATF6 have not been well characterised. Here, the authors sought to investigate these mechanisms further.

RNA-Seq, ribosome profiling, and mass spectrometry analysis demonstrates that protein folding and ER stress response genes were among the most significantly enriched after TAC (transverse aortic constriction)-induced cardiac hypertrophy, with particular upregulation for the genes GRP94 (Hsp90b1), GRP78 (Hspa50), and PDIA6. Individual inhibition of PERK, IRE1α, and ATF6 (proteins partially responsible for increased cardiac hypertrophy) displayed no alteration in cardiomyocyte size, while inhibition of all three displayed significantly reduced size, suggesting compensatory effects in instances of individual inhibitions. However, when treated with phenylephrine, inducing growth, all 3 individually stunted growth, with ATF6 having the strongest effect. Further experimentation attributed this to ATF6’s transcriptional activity following pressure overload. Interestingly, in ATF6 knockout mice under non-growth conditions, there was a significant reduction in protein levels of genes involved in oxidation-reduction processes (specifically those involved in the respiratory complex I pathway), revealing additional baseline functions outside of cardiomyocyte growth in these cells.

Epstein-Barr virus suppresses N6-methyladenosine modification of TLR9 to promote immune evasion

Journal of Biological Chemistry2024

Zhang, X., Li, Z., Peng, Q., Liu, C., Wu, Y., Wen, Y., Zheng, R., Xu, C., Tian, J., Zheng, X. and Yan, Q.

Epstein-Barr virus (EBV) is a double-stranded DNA herpes virus, latently infecting approximately 95% of the world’s adult population. While harmless in most cases, it is well known for its ability to transform B cells, resulting in several types of lymphoma, including Burkitt’s and Hodgkin’s lymphoma. TLR9 itself is a toll-like receptor, with an ability to recognise a variety of DNA viruses, including EBV. However, EBV is also known to supress TLR9 during latency, in order to evade detection. Recent advances have also highlighted the role of the N6-methyladenosine (m6A) modification (the most common eukaryotic RNA modification) in regulating EBV activity. However, the exact mechanisms of such regulation remain unclear. Here, the authors sought to investigate these processes further.

MeRIP-seq assays were conducted post-EBV infection determined that the m6A levels of genes involved in transcriptional regulation were strongly repressed. It was noted that TLR9 was among those heavily repressed at both the m6A level, and later, the protein level, and that this was partially linked to the expression of Epstein-Barr nuclear antigen (EBNA1). Endogenous knockdown of METTL3, a known m6A “writer”, also demonstrated a negative impact on TLR9 levels, confirming its m6A-based regulation. It was later found that EBNA1 promoted METTL3 protein degradation (which was blocked by proteosome inhibitors), likely through upregulation of PRKN, a component of the E3 ubiquitin ligase complex. The study also revealed that YTHDF1 (an m6A “reader”) binds to TLR9 mRNA in an m6A dependent manner and promotes translation of TLR9. Curiously, the repression observed with knockdown of YTHDF1 was rescued by the mutation of one of TLR9 m6a sites present in the CDS region.

The autism susceptibility kinase, TAOK2, phosphorylates eEF2 and modulates translation

Science Advances, 2024

Henis, M., Rücker, T., Scharrenberg, R., Richter, M., Baltussen, L., Hong, S., Meka, D.P., Schwanke, B., Neelagandan, N., Daaboul, D. and Murtaza, N.


Protein kinases have been implicated in a range of translational processes, with well documented cases including the phosphorylation of eIF4E binding protein (promoting cap binding and initiation), as well as eIF2S1 (resulting in a generalised suppression of initiation). Another well known case is eEF2, which only has one known phosphorylation kinase, eEF2K, which typically results in slower elongation speeds. Interestingly, a number of translation-associated genes are known to be involved in neurodevelopmental disorders, such as FMRP in Fragile X syndrome. TAOK2 itself is a serine/threonine kinase, typically associated with organisation and apoptosis. However, recent whole genome sequencing of autism spectrum disorder patients and their families identified novel mutations located within the TAOK2 locus. Other preliminary protein-protein interaction studies identify it as being heavily associated with proteins involved in ribosomal regulation. Here, the authors sought to investigate this connection further.

Utilising immunoblotting analysis, they were able to determine that the TAOK2 protein is present among the polysome complexes acquired via sucrose gradients. Exploring further with polysome profiling, they find that knocking out TAOK2 results in a generalised increase in translation, demonstrating that TAOK2 itself acts as a negative regulator. Similar conclusions were obtained from puromycin assays in mouse cortical slices, as well as lymphoblastoid cell lines obtained from patients. A phosphoproteomics approach was utilised in order to identify substrates of TAOK2 activity, revealing eEF2 as a high confidence target. Indeed, in TAOK2-/- cells, immunoblots demonstrated reduced eEF2 phosphorylation, which was restored upon TAOK2 transfection. Together, this paper conclusively demonstrates a hitherto undescribed kinase acting upon eEF2, significantly influencing translation, with further implications for neurodevelopment disorders.

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