July 23rd
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 see a fascinating novel finding, in that Zhang, F et al. report the first multicellular eukaryotic example of an anticodon nuclease, activated in response to poxvirus infection. Meanwhile, Zhang, H et al. potentially uncover a novel cap-independent form of translation initiation in VEGFA, a prominent angiogenesis factor in a range of cancers. Finally, Breznak et al. delve into the details of the impact of RNA modifications on the process of oogenesis.
Human SAMD9 is a poxvirus-activatable anticodon nuclease inhibiting codon-specific protein synthesis
Science Advances, 2023
Zhang, F., Ji, Q., Chaturvedi, J., Morales, M., Mao, Y., Meng, X., Dong, L., Deng, J., Qian, S.B. and Xiang, Y.
Anticodon nucleases (ACNases) are proteins typically found in bacteria, used to deplete specific tRNAs through cleavage of the anticodon stem loop, thus acting as a defence against viral infection or competitors. While the stress response in eukaryotes can result in some tRNA degradation, tRNA pools are not substantially affected. Instead, interferon-associated innate responses predominate, and in the case of poxviruses, SAMD9/9L are some of the most strongly expressed restriction factors that block its replication. They also have anti-proliferative and protein synthesis dampening properties. A previous screen identified SAMD9, along with WDR6 and FTSJ1, as factors contributing to host viral response, although the links between them remained unclear. Here, the authors sought to investigate the role of SAMD9 in this response further.
The identification of the tRNA modifying activity of FTSJ1 and WDR6 as the key factor in viral restriction led to a focus in this area. tRNAPhe is one of the predominant targets for FTSJ1, and subsequent knockdown studies found that FTSJ1-induced modification is required for tRNAPhe degradation, and that this degradation also required SAMD9. Other tRNAs tested did not demonstrate any changes in degradation under the same conditions. Ribosome profiling later revealed significant Phe codon pausing when SAMD9 was activated by poxvirus infection. Such pausing was later linked to a ribotoxic stress response, inducing eIF2α phosphorylation and ATF3 activation, leading to an overall translational reduction, as well as a halt to viral replication. Overexpression of tRNAPhe reversed such a phenotype.
N6-methyladenosine promotes translation of VEGFA to accelerate angiogenesis in lung cancer
Cancer Research, 2023
Zhang, H., Zhou, J., Li, J., Wang, Z., Chen, Z., Lv, Z., Ge, L., Xie, G., Deng, G., Rui, Y. and Wang, H.
Novel angiogenesis is a critical factor in cancer development. VEGFA is among the most well known angiogenic factors, and displays particularly complex translational regulation. It displays two hypothesised internal ribosome entry sites (IRES), as well as a highly conserved uORF. Furthermore, it can produce functional protein products from non-AUG initiation events. N6-methyladenosine (m6A), on the other hand, is the most common mRNA modification in eukaryotes, and is controlled through “writers” (e.g. METTL3), “erasers” (e.g. ALKBH5), and “readers” (e.g. YTHDF1). Such a modification, depending where on the transcript it is present, can influence different aspects of translational efficiency, including initiation, elongation, and ribosome recycling. Here, the authors aim to investigate the role of such m6A modifications in angiogenesis, and VEGFA specifically.
They find that METTL3 is positively associated with angiogenesis and cancer progression. More detailed analysis revealed VEGFA to be the main target of METTL3 with regard to angiogenesis, with other angiogenic proteins unaffected by METTL3 knockdown. METTL3 increased VEGFA levels via more efficient translation of its mRNA. More specifically, it methylates an adenosine residue located within the putative IRES-A of VEGFA. Intriguingly, this site was also located within a highly conserved uORF in this region. Through mutational analysis, they were able to determine that methylation at this site can suppress uORF translation, while promoting internal, cap-independent translation initiation of the VEGFA protein as a whole. This initiation was later shown to be reliant on the m6A reader YTHDC2, as well as eIF4GI.
H/ACA snRNP–dependent ribosome biogenesis regulates translation of polyglutamine proteins
Science Advances, 2023
Breznak, S.M., Peng, Y., Deng, L., Kotb, N.M., Flamholz, Z., Rapisarda, I.T., Martin, E.T., LaBarge, K.A., Fabris, D., Gavis, E.R. and Rangan, P.
Ribosome biogenesis and regulation is crucial for proper stem cell terminal differentiation, particularly so during the process of oogenesis. In Drosophilia, this begins with germline stem cells giving rise to cystoblasts, which in turn divide to form 2-, 4, 8-, and 16-cell cysts, with one of these 16 finally forming the oocyte. The H/ACA small nuclear ribonucleoprotein complex, meanwhile, is responsible for the modification of rRNA, depositing pseudouridine at specific sites, and is crucial for proper ribosome biogenesis. Here, the authors investigate the role of posttranscriptional modifications on RNA during oogenesis, and determine intriguing links between this pseudouridine-depositing complex and polyglutamine repeat motifs.
First, they ran RNAi screens against a number of RNA modifying genes in Drosophilia germlines, uncovering a number which gave rise to either loss germline or defects therein. Among these genes, there was a particular enrichment for genes that were a part of the H/ACA snRNP complex. Loss of this complex led to an accumulation of 8-cell cysts, with a distinct lack of developmental progression onwards. Polysome profiling also revealed that it was responsible for the translation of certain differentiation factors, such as Rbfox1 and Bru1. Intriguingly, further motif analysis on this polysome profiling data revealed an enrichment of the repeating CAG motif (coding for polyglutamine tracts) in the CDS of downregulated genes. Ribosome profiling analysis revealed that CAG repeat regions display increased ribosome density, and associates such CAG repeat-containing genes to sensitivity to reduced ribosome biogenesis during oogenesis.
