December 29th, 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, Gottlieb et al. identify a novel factor contributing to translational control of immune related genes in response to T cell activation, while Lefèvre et al. identify functional uORFs within the Zika virus 5’ UTR, critical to viral replication. Finally, Shen et al. draw a link from the little studied eIF6 and the development of rheumatoid arthritis.
AMBRA1 controls the translation of immune-specific genes in T lymphocytes
PNAS, 2024
Gottlieb, S., Shang, W., Ye, D., Kubo, S., Jiang, P.D., Shafer, S., Xu, L., Zheng, L., Park, A.Y., Song, J. and Chan, W.
T cell activation involves extensive reprogramming of gene expression and metabolic processes, prioritising translational control for rapid protein synthesis. Activation of the T cell receptor can lead to downstream activation of mTORC1, promoting translation initiation. Investigators were interested in the role of FAS-regulated cell death in T lymphocytes, an important process in maintaining homeostasis. A CRISPR screen for regulators of this process in these cells identified AMBRA1, a gene typically associated with autophagy and cell cycle control. Here, the authors investigate this gene further.
Further experimentation demonstrated that AMBRA knock-out reduces FAS surface expression. Both FAS mRNA levels, as well as FAS protein degradation, were unaffected by AMBRA1 knock-out. FAS translation, however, was impacted. Interestingly, AMBRA1 itself also seems to be translationally regulated, with increased expression at a translational level following TCR induction. mTOR inhibitors reduced its expression, and a TOP-like motif was identified in its 5’ UTR. Proximity-dependent mass spectrometry revealed that much of AMBRA1’s interacting partners fell within the category of ribosomal proteins.
Zika viruses encode 5′ upstream open reading frames affecting infection of human brain cells
Nature Communications, 2024
Lefèvre, C., Cook, G.M., Dinan, A.M., Torii, S., Stewart, H., Gibbons, G., Nicholson, A.S., Echavarría-Consuegra, L., Meredith, L.W., Lulla, V. and McGovern, N.
Zika virus (ZIKV) is a mosquito-borne Flavivirus, and includes two main strains – African (Dak84) and Asian/American (PE243). Symptoms are typically mild, although in certain cases it can lead to severe neurological defects, such as Guillain-Barre syndrome, and congenital Zika syndrome in infants, causing microcephaly and developmental delays. ZIKV is a single-stranded RNA virus with a long open reading frame (ORF), resulting in the translation of a polyprotein. Here, however, the authors investigate genetic variations between strains, uncovering novel uORFs in the 5’ UTR of these viruses.
Utilising ribosome profiling of both the PE243 and Dak84 strains, they find that both harbour novel uORFs. Interestingly, PE243 contains two uORFs (uORF1 and uORF2) in different frames, both overlapping the main ORF, while in Dak84, both uORFs are fused into a single uORF that overlaps with the main ORF. uORF1 of the PE243 strain and the single uORF od the Dak84 strain are both initiated by a CUG start site. Luciferase assays revealed that initiation at these uORFs impacts the translation of the main coding region. Furthermore, the encoded product of both uORF1 and the African uORF displayed binding affinity for intermediate filaments, particularly with vimentin, leading to its collapse. ZIKV is known to use these collapsed cytoskeletal cages as sites of viral factories, and knockout of these uORFs leads to reduced formation of these factories, resulting in reduced viral replication. In vitro infectivity assays in neural cultures demonstrated that knockout of either uORF1 or the African uORF reduce viral infection. Although the uORFs are translated in mosquito cells, the authors do not see a measurable effect on transmission by the mosquito vector in vivo.
Eukaryotic translation initiation factor 6-mediated ribosome biogenesis promotes synovial aggression and inflammation by increasing the translation of SP1 in rheumatoid arthritis
International Immunopharmacology, 2024
Shen, C., Peng, C., Zhang, S., Li, R., Liu, S., Kuang, Y., Su, F., Liu, Y., Liang, L., Xiao, Y. and Xu, H.
Rheumatoid arthritis (RA) is an autoimmune disorder marked by aggressive synovial tissue, leading to joint damage. Current treatments are often insufficient, highlighting the need for novel therapeutic targets. Fibroblast-like synoviocytes (FLSs) play a central role in RA progression through abnormal inflammatory behaviour, excessive migration, and resistance to apoptosis. Ribosome biogenesis, a critical cellular process, is often dysregulated in autoimmune diseases. The translation initiation factor eIF6, known for its role in ribosome assembly and linked to cell proliferation, was as significantly upregulated in FLSs from RA patients compared to controls. Here, the authors aim to further investigate the role eIF6 in RA.
In knockdown assays of eIF6 in FLSs, chemotaxis migration was significantly reduced, going hand-in-hand with decreased F-actin intensity and lamellipodia formation. Furthermore, lower levels of inflammatory markers IL-6, IL-8 CCL-2, and MMP-9 were observed. By comparing eIF6-high and eIF6-low groups, researchers identified SP1 as an additional factor influencing gene expression, and knockdown of SP1 resulted in similar phenotypes to eIF6 knockdown. They further demonstrate that eIF6 knockdown reduced SP1 translation, linking these two phenotypes together. However, the authors do not demonstrate if eIF6 specifically targets SP1, or simply is caught in the generalised impact of the knockdown of eIF6 on translation, as this factor was further shown to downregulate rRNA processing, which would have much wider translational implications. They do, however, demonstrate beneficial impacts of eIF6 knockdown in in vivo rodent models of RA, reinforcing the evidence of eIF6 as a therapeutic target in this disease.