November 26th
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, Keller et al. performed chloroplast ribosome profiling to study the role of DEAP2 in PSII biogenesis and the potential effects on transcript accumulation and translation. Bhin et al. reveals the role of MYC in mTOR inhibitor resistance in breast cancer by analysing the genome-wide ribosome footprints. Gan et al. showed that NSP12 influences host mRNA translation by interfering with eEF1A factors. Ribosome profiling analysis showed several differentially translated genes in the NSP12-overexpressed condition.
Eukaryote-specific assembly factor DEAP2 mediates an early step of photosystem II assembly in Arabidopsis
Plant Physiology, 2023
Keller, J.-M., Frieboes, M. J., Jödecke, L., Kappel, S., Wulff, N., Rindfleisch, T., Sandoval-Ibanez, O., Gerlach, I., Thiele, W., Bock, R., Eirich, J., Finkemeier, I., Schünemann, D., Zoschke, R., Schöttler, M. A., & Armbruster, U.
Keller et al. (2023) delved into the intricate process of photosystem II (PSII) assembly, a fundamental component of photosynthesis in plants. The study focused on a unique eukaryotic assembly factor which the authors have named Decreased Electron Transport at PSII (DEAP2), and its role in the early assembly stages of PSII formation in Arabidopsis thaliana. DEAP2 was shown to be intimately involved in the assembly of PSII complexes, playing a pivotal role in the incorporation of essential PSII subunits in a similar fashion to Photosynthesis Affected Mutant 68 (PAM68), which is known to be involved in PSII assembly.
Using immunoblot analyses with DEAP2/PAM68 mutants, the authors found the levels of all PSII subunits were found to be decreased to around 40% in both mutants compared to WT. Ribosome profiling and RNA-seq also revealed many similarities with both mutants showing similar increases in gene expression for certain subunits (petB, petD) and decreases in others (rbcL). The translation efficiencies (TE) of subunits also had similar trends between both mutants, with significant decreases found in petA, psaA, psaB and atpB. The authors note that the gene expression and translation efficiency differences are mild in both mutants indicating that neither DEAP2 nor PAM68 are likely to have a primary function in the expression of chloroplast-encoded PSII subunits or any other chloroplast gene. They speculate that the common trends in both TE and gene expression could be explained by regulatory feedback loops that are engaged to counteract the negative effects of both mutants on PSII accumulation. Lastly the authors demonstrate that DEAP2 can at least partially compensate for the loss of PAM68 but not vice versa.
The study meticulously dissected the molecular interactions and functions of DEAP2 within the PSII assembly process. It revealed that DEAP2 interacts with key PSII assembly intermediates, aiding in their maturation and integration into the developing complex. This interaction was identified as an early and critical step in the intricate choreography of PSII assembly.
MYC is a clinically significant driver of mTOR inhibitor resistance in breast cancer
Journal of Experimental Medicine, 2023
Bhin, J., Yemelyanenko, J., Chao, X., Klarenbeek, S., Opdam, M., Malka, Y., Hoekman, L., Kruger, D., Bleijerveld, O., Brambillasca, C. S., Sprengers, J., Siteur, B., Annunziato, S., van Haren, M. J., Martin, N. I., van de Ven, M., Peters, D., Agami, R., Linn, S. C., Boven, E., Altelaar, M., Jonkers, J., Zingg, D., & Wessels, L. F. A.
Bhin et al. (2023) investigated a critical aspect of breast cancer biology and treatment resistance. The study focused on the role of the oncogene MYC in mediating resistance to mTOR inhibitors, a class of drugs that can suppress tumor growth and thus hold promise for breast cancer therapy. However, patients can develop a resistance to these inhibitors, limiting their efficacy. This study unveiled that MYC, a potent oncogenic protein frequently overexpressed in cancer, plays a pivotal role in this resistance mechanism.
As part of this study ribosome profiling and corresponding RNA-Seq was carried out on KEP1.23 cells, that were either treated with AZD8055 (an inhibitor of mTOR kinase activity) or overexpressing MYC. Results were then compared to treatment naïve KEP cells. The analysis identified that AZD8055 significantly suppressed the translation efficiency (TE) of ribosomal genes while MYC overexpression increased the TE of most of those same genes, counteracting the effects of mTOR inhibition. The authors note that MYC did not affect TEs of genes encoding translation machinery factors other than ribosomal proteins, which suggests that MYC overcomes mTORi-mediated translation inhibition by recovering the translation of ribosomal gene transcripts.
Motif enrichment analysis of genes which showed increased TE on MYC overexpression showed that their 5′-UTR regions were enriched for motifs of known RNA-binding proteins including LARP1, SRSF1, and ZCRH14. Larp1, Srsf1, and Zc3h14 transcripts were significantly upregulated in KEP cells overexpressing Myc. Taken together this implies that MYC induces transcriptional induction of RNA-binding proteins leading to increased translation of ribosomal proteins and ultimately mTORi resistance.
The authors conclude by stating that their findings suggest that MYC is an important mediator of the mTORi response and its status should be considered to select patients who may benefit from mTOR-targeted therapies.
RNA-dependent RNA polymerase of SARS-CoV-2 regulate host mRNA translation efficiency by hijacking eEF1A factors
Biochimica et Biophysica Acta (BBA)-Molecular Basis of Disease, 2023
Gan, H., Zhou, X., Lei, Q., Wu, L., Niu, J., & Zheng, Q.
Gan et al. (2023) delved into the molecular mechanisms employed by the SARS-CoV-2 virus to manipulate host cell processes. The study primarily focused on the viral RNA-dependent RNA polymerase (RdRp) and its interaction with eEF1A factors. RdRp (also known as NSP12) is a crucial viral enzyme that plays a central role in the replication of the virus’s RNA genome. This paper uncovers an additional function of RdRp in regulating host mRNA translation.
Ribosome profiling was performed in parallel with RNA-seq to investigate the effect of eEF1A-associated RdRp on the mRNA translational behaviour of HEK293T cells. When RdRp was overexpressed it was found that it significantly affected the translation efficiency of many host mRNAs (such as ISG15, NF-κB2, ILK and SERPINI2). Many of these genes are involved in pathways related to the upregulation of ubiquitin-dependent proteasomal process and the NIK/NF-κB signaling pathway, in addition to the negative regulation of type I interferon production.
The authors demonstrated that RdRp binds to eEF1A, an essential cellular protein involved in protein synthesis, and disrupts its normal function. This interference leads to a significant alteration in the translation efficiency of host mRNAs. By targeting eEF1A, RdRp influences the host cell’s translational machinery, potentially favoring the production of viral proteins over cellular ones. The authors conclude that these results provide new insight for us to evaluate the impact of the SARS-CoV2 virus on the host and our ability to study potential drug targets.