November 5th
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, Ngoennet, S. et al. investigated how altering the expression of Elongation factor G impacts various aspects of cellular function, particularly translation processes and stress responses. Shi, T. et al identified responsive microproteins during vesicular stomatitis virus (VSV) infection, both from coding and noncoding RNAs, using transcriptomic profiling and Ribo-seq. Xue, M. et al uncovered a novel connection between impaired translation and tissue homeostasis by investigating the role of Paip1 in development of Drosophila.
Active role of the protein translation machinery in protecting against stress tolerance in Synechococcus elongatus PCC7942
Archives of Biochemistry and Biophysics, 2023
Ngoennet, S., Sirisattha, S., Kusolkumbot, P., Hibino, T., Kageyama, H., & Waditee-Sirisattha, R.
Elongation factor G (EF-G) is a pivotal participant in protein synthesis, orchestrating the movement of tRNA and mRNA during translation and contributing to ribosome recycling. The influence of EF-G, conserved across all domains of life extends to processes beyond translation, including stress responses. Although studies that focus on the role of EF-G in Cyanobacteria and limited, research in Synechocystis sp. PCC6803 and Synechococcus elongatus PCC7942 have shown role of EF-G in oxidative stress and antibiotic responses. In fact, S. elongatus PCC7942 has two EF-G encoding genes, S0885 and S2082. This study seeks to understand how altering the expression of these EF-G genes impacts various aspects of cellular function, particularly translation processes and stress responses.
In this study, S. elongatus PCC7942 with modified S0885 expression was used to probe EF-G function. To assess translation efficiency, the researchers conducted polysome profiling on various cyanobacterial strains, including those with overexpressed EF-G (OX-S0885) and Elongation factor P (OX-S2565) genes. Fraction analysis revealed that fractions enriched in 16S rRNA represented the small 30S ribosomal subunit, while those with predominantly 23S rRNA indicated the large 50S ribosomal subunit. Fractions containing both 16S and 23S rRNA confirmed the presence of 70S monosomes, and the polysome fractions provided insight into the distribution of 70S ribosomes. Importantly, variations in the polysome-to-monosome (P/M) ratios were observed among the strains. The empty vector strain had the lowest P/M ratio, while OX-S2565 and OX-S0885 strains displayed higher values.
These findings suggest that alterations in cellular machinery during translation elongation result in enhanced active translation in the overexpressing strains compared to the empty vector strain, shedding light on the role of EF-G in this process. These findings deepen our understanding of EF-G and its potential applications in synthetic biology and stress response mechanisms.
MAVI1, an endoplasmic reticulum–localized microprotein, suppresses antiviral innate immune response by targeting MAVS on mitochondrion
Science Advances, 2023
Shi, T.-T., Huang, Y., Li, Y., Dai, X.-L., He, Y.-H., Ding, J.-C., Ran, T., Shi, Y., Yuan, Q., Li, W.-J., & Liu, W.
Innate immunity is the initial defence against microbial pathogens, using pattern recognition receptors (PRRs) like Toll-like receptors (TLRs) and retinoic acid-inducible gene I (RIG-I)-like receptors (RLRs) to detect viral RNA/DNA. RLRs such as RIG-I and MDA5 identify cytosolic RNA and activate downstream signalling via MAVS (microprotein in antiviral immunity) leading to type I interferon production and an antiviral response. Recent advances in genomics have revealed more human genes than initially thought, including noncoding RNAs encoding short peptides or proteins called microproteins. The role of these microproteins, particularly membrane-localized ones, in RLR-MAVS-mediated antiviral immunity is an unexplored area of research. In this study, researchers systematically identified responsive microproteins during vesicular stomatitis virus (VSV) infection, both from coding and noncoding RNAs, using transcriptomic profiling and Ribo-seq.
Using transcriptomic analysis in HEK293 cells, coupled with Ribo-seq, the authors uncovered the potential responsiveness of over 800 microproteins, originating from both coding and noncoding genes to VSV viral infection. They discovered a microprotein called MAVI1, containing a signal peptide and a transmembrane domain, localized on the endoplasmic reticulum (ER) membrane.
MAVI1 was found to attenuate RLR-mediated type I IFN signalling and antiviral immune responses by directly interacting with the mitochondrial MAVS protein. Knocking out MAVI1 in mice enhanced innate immune responses against RNA viruses, improving mouse survival. Furthermore, a peptide inhibitor targeting the MAVI1-MAVS interaction activated the type I IFN signaling pathway, effectively defending against viral infections. In summary, this study identifies a microprotein, MAVI1, as a crucial regulator of innate immune responses against viral infections, shedding light on the role of microproteins in antiviral immunity and suggesting potential therapeutic avenues for treating viral infections.
Loss of Paip1 causes translation reduction and induces apoptotic cell death through ISR activation and Xrp1
Cell Death Discovery, 2023
Xue, M., Cong, F., Zheng, W., Xu, R., Liu, X., Bao, H., Sung, Y. Y., Xi, Y., He, F., Ma, J., Yang, X., & Ge, W.
The regulation of protein translation initiation plays a critical role in cell growth and survival. This study focuses on PAIP1, poly (A)-binding protein interacting protein 1, which functions to stimulate translation initiation through its interaction with eIF3G and eIF4A. It is also found to be overexpressed in some human cancers. Despite knowledge of biochemical roles of PAIP1, its functions in animal development and tissue regulation remain poorly understood. The authors used a Drosophila homolog of PAIP1 to investigate role of Paip1 in animal development.
To investigate the gene-specific functions of Paip1, mRNAs associated with monosome or polysome fractions were separated and subjected to deep sequencing (Polysome-Seq). The analysis revealed 1190 genes with increased translation efficiency (Polysome/monosome) and 852 genes with decreased translation efficiency in Paip1 mutants compared to the control. Gene ontology (GO) analysis showed that genes with reduced translation were related to ribosomal components, while those with enhanced translation were associated with organelles, transferase complexes, and cytoskeletal structures. These findings indicate that Paip1 plays a crucial role in promoting translation in Drosophila, affecting the translation efficiency of specific genes related to ribosomal components and organelles. The study further demonstrates that Paip1 depletion induces proteotoxic stress and activates the integrated stress response (ISR) pathway. Additionally, the research finds that the loss of Paip1 increases the translation of the transcription factor gene Xrp1 through its 5’UTR.
In conclusion, the data suggest that the loss of Drosophila Paip1 reduces translation and triggers apoptotic cell death through ISR activation and Xrp1 induction. This research uncovers a novel connection between impaired translation and tissue homeostasis, highlighting the roles of ISR activation and Xrp1 in promoting cell death.