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Ramos-Lorente SE, Berzal-Herranz B, Romero-López C, Berzal-Herranz A. Recruitment of the 40S ribosomal subunit by the West Nile virus 3' UTR promotes the cross-talk between the viral genomic ends for translation regulation. Virus Res 2024; 343:199340. [PMID: 38387694 PMCID: PMC10907855 DOI: 10.1016/j.virusres.2024.199340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/19/2024] [Accepted: 02/20/2024] [Indexed: 02/24/2024]
Abstract
Flaviviral RNA genomes are composed of discrete RNA structural units arranged in an ordered fashion and grouped into complex folded domains that regulate essential viral functions, e.g. replication and translation. This is achieved by adjusting the overall structure of the RNA genome via the establishment of inter- and intramolecular interactions. Translation regulation is likely the main process controlling flaviviral gene expression. Although the genomic 3' UTR is a key player in this regulation, little is known about the molecular mechanisms underlying this role. The present work provides evidence for the specific recruitment of the 40S ribosomal subunit by the 3' UTR of the West Nile virus RNA genome, showing that the joint action of both genomic ends contributes the positioning of the 40S subunit at the 5' end. The combination of structural mapping techniques revealed specific conformational requirements at the 3' UTR for 40S binding, involving the highly conserved SL-III, 5'DB, 3'DB and 3'SL elements, all involved in the translation regulation. These results point to the 40S subunit as a bridge to ensure cross-talk between both genomic ends during viral translation and support a link between 40S recruitment by the 3' UTR and translation control.
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Affiliation(s)
- Sara Esther Ramos-Lorente
- Instituto de Parasitología y Biomedicina "López-Neyra" (IPBLN), CSIC, Av. del Conocimiento 17, 18016 Armilla Granada, Spain
| | - Beatriz Berzal-Herranz
- Instituto de Parasitología y Biomedicina "López-Neyra" (IPBLN), CSIC, Av. del Conocimiento 17, 18016 Armilla Granada, Spain
| | - Cristina Romero-López
- Instituto de Parasitología y Biomedicina "López-Neyra" (IPBLN), CSIC, Av. del Conocimiento 17, 18016 Armilla Granada, Spain.
| | - Alfredo Berzal-Herranz
- Instituto de Parasitología y Biomedicina "López-Neyra" (IPBLN), CSIC, Av. del Conocimiento 17, 18016 Armilla Granada, Spain.
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Landry-Voyer AM, Mir Hassani Z, Avino M, Bachand F. Ribosomal Protein uS5 and Friends: Protein-Protein Interactions Involved in Ribosome Assembly and Beyond. Biomolecules 2023; 13:biom13050853. [PMID: 37238722 DOI: 10.3390/biom13050853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 05/15/2023] [Accepted: 05/16/2023] [Indexed: 05/28/2023] Open
Abstract
Ribosomal proteins are fundamental components of the ribosomes in all living cells. The ribosomal protein uS5 (Rps2) is a stable component of the small ribosomal subunit within all three domains of life. In addition to its interactions with proximal ribosomal proteins and rRNA inside the ribosome, uS5 has a surprisingly complex network of evolutionarily conserved non-ribosome-associated proteins. In this review, we focus on a set of four conserved uS5-associated proteins: the protein arginine methyltransferase 3 (PRMT3), the programmed cell death 2 (PDCD2) and its PDCD2-like (PDCD2L) paralog, and the zinc finger protein, ZNF277. We discuss recent work that presents PDCD2 and homologs as a dedicated uS5 chaperone and PDCD2L as a potential adaptor protein for the nuclear export of pre-40S subunits. Although the functional significance of the PRMT3-uS5 and ZNF277-uS5 interactions remain elusive, we reflect on the potential roles of uS5 arginine methylation by PRMT3 and on data indicating that ZNF277 and PRMT3 compete for uS5 binding. Together, these discussions highlight the complex and conserved regulatory network responsible for monitoring the availability and the folding of uS5 for the formation of 40S ribosomal subunits and/or the role of uS5 in potential extra-ribosomal functions.
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Affiliation(s)
- Anne-Marie Landry-Voyer
- Dept of Biochemistry & Functional Genomics, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | - Zabih Mir Hassani
- Dept of Biochemistry & Functional Genomics, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | - Mariano Avino
- Dept of Biochemistry & Functional Genomics, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | - François Bachand
- Dept of Biochemistry & Functional Genomics, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
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Eukaryotic Ribosomal Protein S5 of the 40S Subunit: Structure and Function. Int J Mol Sci 2023; 24:ijms24043386. [PMID: 36834797 PMCID: PMC9958902 DOI: 10.3390/ijms24043386] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 02/01/2023] [Accepted: 02/06/2023] [Indexed: 02/10/2023] Open
Abstract
The ribosomal protein RPS5 is one of the prime proteins to combine with RNA and belongs to the conserved ribosomal protein family. It plays a substantial role in the process of translation and also has some non-ribosome functions. Despite the enormous studies on the relationship between the structure and function of prokaryotic RPS7, the structure and molecular details of the mechanism of eukaryotic RPS5 remain largely unexplored. This article focuses on the structure of RPS5 and its role in cells and diseases, especially the binding to 18S rRNA. The role of RPS5 in translation initiation and its potential use as targets for liver disease and cancer are discussed.
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Notopoulou S, Gkekas I, Petrakis S. Omics Analyses in a Neural Stem Cell Model of Familial Parkinson's Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1423:149-160. [PMID: 37525039 DOI: 10.1007/978-3-031-31978-5_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Parkinson's disease (PD) is the second most common neurodegenerative disorder, affecting millions of people worldwide. Despite considerable efforts, the underlying pathological mechanisms remain elusive, and yet, no treatment has been developed to efficiently reverse or modify disease progression. Thus, new experimental models are required to provide insights into the pathology of PD. Small-molecule neural precursor cells (smNPCs) are ideal for the study of neurodegenerative disorders due to their neural identity and stem cell properties. Cytoplasmic aggregates of α-synuclein (αSyn) are considered a hallmark of PD and a point mutation in the gene encoding p.A53T is responsible for a familial PD form with earlier and robust symptom onset. In order to study the cellular pathology of PD, we genetically modified smNPCs to inducibly overexpress EYFP-SNCA A53T. This cellular model was biochemically characterized, while dysregulated biological pathways and key regulators of PD pathology were identified by computational analyses. Our study indicates three novel genes, UBA52, PIP5K1A, and RPS2, which may mediate PD cellular pathology.
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Affiliation(s)
| | - Ioannis Gkekas
- Institute of Applied Biosciences, CERTH, Thessaloniki, Greece
| | - Spyros Petrakis
- Institute of Applied Biosciences, CERTH, Thessaloniki, Greece
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Biziaev N, Sokolova E, Yanvarev DV, Toropygin IY, Shuvalov A, Egorova T, Alkalaeva E. Recognition of 3' nucleotide context and stop codon readthrough are determined during mRNA translation elongation. J Biol Chem 2022; 298:102133. [PMID: 35700825 PMCID: PMC9272376 DOI: 10.1016/j.jbc.2022.102133] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 06/06/2022] [Accepted: 06/08/2022] [Indexed: 11/16/2022] Open
Abstract
The nucleotide context surrounding stop codons significantly affects the efficiency of translation termination. In eukaryotes, various 3′ contexts that are unfavorable for translation termination have been described; however, the exact molecular mechanism that mediates their effects remains unknown. In this study, we used a reconstituted mammalian translation system to examine the efficiency of stop codons in different contexts, including several previously described weak 3′ stop codon contexts. We developed an approach to estimate the level of stop codon readthrough in the absence of eukaryotic release factors (eRFs). In this system, the stop codon is recognized by the suppressor or near-cognate tRNAs. We observed that in the absence of eRFs, readthrough occurs in a 3′ nucleotide context-dependent manner, and the main factors determining readthrough efficiency were the type of stop codon and the sequence of the 3′ nucleotides. Moreover, the efficiency of translation termination in weak 3′ contexts was almost equal to that in the tested standard context. Therefore, the ability of eRFs to recognize stop codons and induce peptide release is not affected by mRNA context. We propose that ribosomes or other participants of the elongation cycle can independently recognize certain contexts and increase the readthrough of stop codons. Thus, the efficiency of translation termination is regulated by the 3′ nucleotide context following the stop codon and depends on the concentrations of eRFs and suppressor/near-cognate tRNAs.
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Affiliation(s)
- Nikita Biziaev
- Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, 119991 Moscow, Russia.
| | - Elizaveta Sokolova
- Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, 119991 Moscow, Russia.
| | - Dmitry V Yanvarev
- Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, 119991 Moscow, Russia.
| | - Ilya Yu Toropygin
- Orekhovich Research Institute of Biomedical Chemistry, Moscow, 119992, Russia.
| | - Alexey Shuvalov
- Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, 119991 Moscow, Russia; Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia.
| | - Tatiana Egorova
- Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, 119991 Moscow, Russia; Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; Pirogov Russian National Research Medical University, Moscow, 117997, Russia.
| | - Elena Alkalaeva
- Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, 119991 Moscow, Russia; Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia.
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