bims-micpro 2023-12-24 papers

Int J Mol Sci. 2023 Dec 05. pii: 17149. [Epub ahead of print]24(24):

The Roles of eIF4G2 in Leaky Scanning and Reinitiation on the Human Dual-Coding POLG mRNA.

Ekaterina D Shestakova, Roman S Tumbinsky, Dmitri E Andreev, Fedor N Rozov, Ivan N Shatsky, Ilya M Terenin.

Upstream open reading frames (uORFs) are a frequent feature of eukaryotic mRNAs. Upstream ORFs govern main ORF translation in a variety of ways, but, in a nutshell, they either filter out scanning ribosomes or allow downstream translation initiation via leaky scanning or reinitiation. Previous reports concurred that eIF4G2, a long-known but insufficiently studied eIF4G1 homologue, can rescue the downstream translation, but disagreed on whether it is leaky scanning or reinitiation that eIF4G2 promotes. Here, we investigated a unique human mRNA that encodes two highly conserved proteins (POLGARF with unknown function and POLG, the catalytic subunit of the mitochondrial DNA polymerase) in overlapping reading frames downstream of a regulatory uORF. We show that the uORF renders the translation of both POLGARF and POLG mRNAs reliant on eIF4G2. Mechanistically, eIF4G2 enhances both leaky scanning and reinitiation, and it appears that ribosomes can acquire eIF4G2 during the early steps of reinitiation. This emphasizes the role of eIF4G2 as a multifunctional scanning guardian that replaces eIF4G1 to facilitate ribosome movement but not ribosome attachment to an mRNA.

Keywords: 40S; AUG selection; MYCBP2; PHD2; cap-dependent translation; mitochondrial disfunction; non-AUG translation; polyglutamine; ribosome collision; translation reinitiation

DOI: https://doi.org/10.3390/ijms242417149

Blood Adv. 2023 Dec 21. pii: bloodadvances.2023011120. [Epub ahead of print]

Identification of novel canonical and cryptic HCMV-specific T-cell epitopes for HLA-A*03 and HLA-B*15 via peptide-PRISM.

Alice Felicitas Rein, Chris David Lauruschkat, Ihsan Muchsin, Carolin Köchel, Sabine Tischer-Zimmermann, Liane Bauersfeld, Annika Nelde, Maren Lübke, Bhupesh Kumar Prusty, Andreas Schlosser, Anne Halenius, Britta Eiz-Vesper, Lars Dölken, Götz Ulrich Grigoleit, Hermann Einsele, Florian Erhard, Sabrina Kraus.

Human cytomegalovirus (HCMV) reactivation poses a substantial risk to transplant patients. Effective risk stratification and vaccine development is hampered by a lack of HCMV-derived immunogenic peptides in patients with common HLA-A*03:01 and HLA-B*15:01 haplotypes. This study aimed to discover novel HCMV immunogenic peptides for these haplotypes by combining Ribo-seq and mass spectrometry with state-of-the-art computational tools, Peptide-PRISM and PRICE. Furthermore, employing machine learning, an algorithm was developed to predict immunogenicity based on translational activity, binding affinity and peptide localization within small open reading frames to identify the most promising peptides for in vitro validation. Immunogenicity of these peptides was subsequently tested by analyzing peptide-specific T-cell responses of HCMV-seropositive and -seronegative healthy donors as well as transplant patients. This resulted in the direct identification of three canonical and one cryptic HLA-A*03-restricted immunogenic peptides as well as five canonical and one cryptic HLA-B*15-restricted immunogenic peptide, with a specific IFNγ+/CD8+ T-cell response of ≥ 0.02%. High T-cell responses were detected against two HLA A*03-restricted and three HLA-B*15-restricted canonical peptides with frequencies of up to 8.77% IFNγ+/CD8+ T cells in patients post alloSCT. Therefore, our comprehensive strategy establishes a framework for efficient identification of novel immunogenic peptides from both existing and novel Ribo-seq datasets.

DOI: https://doi.org/10.1182/bloodadvances.2023011120

Life Sci Alliance. 2024 Mar;pii: e202302338. [Epub ahead of print]7(3):

Loss-of-function cancer-linked mutations in the EIF4G2 non-canonical translation initiation factor.

Sara Meril, Marcela Bahlsen, Miriam Eisenstein, Alon Savidor, Yishai Levin, Shani Bialik, Shmuel Pietrokovski, Adi Kimchi.

Tumor cells often exploit the protein translation machinery, resulting in enhanced protein expression essential for tumor growth. Since canonical translation initiation is often suppressed because of cell stress in the tumor microenvironment, non-canonical translation initiation mechanisms become particularly important for shaping the tumor proteome. EIF4G2 is a non-canonical translation initiation factor that mediates internal ribosome entry site (IRES)- and uORF-dependent initiation mechanisms, which can be used to modulate protein expression in cancer. Here, we explored the contribution of EIF4G2 to cancer by screening the COSMIC database for EIF4G2 somatic mutations in cancer patients. Functional examination of missense mutations revealed deleterious effects on EIF4G2 protein-protein interactions and, importantly, on its ability to mediate non-canonical translation initiation. Specifically, one mutation, R178Q, led to reductions in protein expression and near-complete loss of function. Two other mutations within the MIF4G domain specifically affected EIF4G2's ability to mediate IRES-dependent translation initiation but not that of target mRNAs with uORFs. These results shed light on both the structure-function of EIF4G2 and its potential tumor suppressor effects.

DOI: https://doi.org/10.26508/lsa.202302338