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González-García JS. A model for ribosome translocation based on the alternated displacement of its subunits. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2023:10.1007/s00249-023-01662-z. [PMID: 37291414 DOI: 10.1007/s00249-023-01662-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 05/03/2023] [Accepted: 05/21/2023] [Indexed: 06/10/2023]
Abstract
A meaningful dilemma in ribosome translocation arising from experimental facts is that, although the ribosome-mRNA interaction force always has a significant magnitude, the ribosome still moves to the next codon on the mRNA. How does the ribosome move to the next codon in the sequence while holding the mRNA tightly? The hypothesis proposed here is that ribosome subunits alternate the grip of the ribosome on the mRNA, freeing the other subunit of such interaction for a while, thus allowing its motion to the following codon. Based on this assumption, a single-loop cycle of ribosome configurations involving the relative position of its subunits is elaborated. When its dynamic is modeled as a Markov network, it gives expressions for the average ribosome translocation speed and stall force as functions of the equilibrium constants among the proposed ribosome configurations. The calculations have a reasonable agreement with experimental results, and the succession of molecular events considered here is consistent with current biomolecular concepts of the ribosome translocation process. Thus, the alternative displacements hypothesis developed in the present work suggests a feasible explanation of ribosome translocation.
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Affiliation(s)
- José S González-García
- Seminario de Bifurcaciones y Singularidades, Departamento de Matemáticas, Universidad Autónoma Metropolitana-Iztapalapa, Av. San Rafael Atlixco 186 Col. Vicentina, 09340, Iztapalapa, Ciudad de México, México.
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Zhang D, Zhu L, Wang F, Li P, Wang Y, Gao Y. Molecular mechanisms of eukaryotic translation fidelity and their associations with diseases. Int J Biol Macromol 2023; 242:124680. [PMID: 37141965 DOI: 10.1016/j.ijbiomac.2023.124680] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 04/27/2023] [Indexed: 05/06/2023]
Abstract
Converting genetic information into functional proteins is a complex, multi-step process, with each step being tightly regulated to ensure the accuracy of translation, which is critical to cellular health. In recent years, advances in modern biotechnology, especially the development of cryo-electron microscopy and single-molecule techniques, have enabled a clearer understanding of the mechanisms of protein translation fidelity. Although there are many studies on the regulation of protein translation in prokaryotes, and the basic elements of translation are highly conserved in prokaryotes and eukaryotes, there are still great differences in the specific regulatory mechanisms. This review describes how eukaryotic ribosomes and translation factors regulate protein translation and ensure translation accuracy. However, a certain frequency of translation errors does occur in translation, so we describe diseases that arise when the rate of translation errors reaches or exceeds a threshold of cellular tolerance.
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Affiliation(s)
- Dejiu Zhang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Lei Zhu
- College of Basic Medical, Qingdao Binhai University, Qingdao, China
| | - Fei Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Peifeng Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Yin Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China.
| | - Yanyan Gao
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China.
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Nätt D, Kugelberg U, Casas E, Nedstrand E, Zalavary S, Henriksson P, Nijm C, Jäderquist J, Sandborg J, Flinke E, Ramesh R, Örkenby L, Appelkvist F, Lingg T, Guzzi N, Bellodi C, Löf M, Vavouri T, Öst A. Human sperm displays rapid responses to diet. PLoS Biol 2019; 17:e3000559. [PMID: 31877125 PMCID: PMC6932762 DOI: 10.1371/journal.pbio.3000559] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 11/18/2019] [Indexed: 11/25/2022] Open
Abstract
The global rise in obesity and steady decline in sperm quality are two alarming trends that have emerged during recent decades. In parallel, evidence from model organisms shows that paternal diet can affect offspring metabolic health in a process involving sperm tRNA-derived small RNA (tsRNA). Here, we report that human sperm are acutely sensitive to nutrient flux, both in terms of sperm motility and changes in sperm tsRNA. Over the course of a 2-week diet intervention, in which we first introduced a healthy diet followed by a diet rich in sugar, sperm motility increased and stabilized at high levels. Small RNA-seq on repeatedly sampled sperm from the same individuals revealed that tsRNAs were up-regulated by eating a high-sugar diet for just 1 week. Unsupervised clustering identified two independent pathways for the biogenesis of these tsRNAs: one involving a novel class of fragments with specific cleavage in the T-loop of mature nuclear tRNAs and the other exclusively involving mitochondrial tsRNAs. Mitochondrial involvement was further supported by a similar up-regulation of mitochondrial rRNA-derived small RNA (rsRNA). Notably, the changes in sugar-sensitive tsRNA were positively associated with simultaneous changes in sperm motility and negatively associated with obesity in an independent clinical cohort. This rapid response to a dietary intervention on tsRNA in human sperm is attuned with the paternal intergenerational metabolic responses found in model organisms. More importantly, our findings suggest shared diet-sensitive mechanisms between sperm motility and the biogenesis of tsRNA, which provide novel insights about the interplay between nutrition and male reproductive health.
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Affiliation(s)
- Daniel Nätt
- Linköping University, Department of Clinical and Experimental Medicine, Division of Neurobiology, Linkoping, Sweden
| | - Unn Kugelberg
- Linköping University, Department of Clinical and Experimental Medicine, Division of Neurobiology, Linkoping, Sweden
| | - Eduard Casas
- Josep Carreras Leukaemia Research Institute (IJC), Program for Predictive and Personalized Medicine of Cancer (PMPPC-IGTP), Barcelona, Spain
| | - Elizabeth Nedstrand
- Linköping University, Department of Clinical and Experimental Medicine, Division of Obstetrics and Gynecology, Linköping, Sweden
| | - Stefan Zalavary
- Linköping University, Department of Clinical and Experimental Medicine, Division of Obstetrics and Gynecology, Linköping, Sweden
| | - Pontus Henriksson
- Karolinska Institute, Department of Biosciences and Nutrition, Huddinge, Sweden
- Linköping University, Department of Medical and Health Sciences, Division of Community Medicine, Linköping, Sweden
| | - Carola Nijm
- Linköping University, Department of Clinical and Experimental Medicine, Division of Obstetrics and Gynecology, Linköping, Sweden
| | - Julia Jäderquist
- Linköping University, Department of Clinical and Experimental Medicine, Division of Obstetrics and Gynecology, Linköping, Sweden
| | - Johanna Sandborg
- Karolinska Institute, Department of Biosciences and Nutrition, Huddinge, Sweden
- Linköping University, Department of Medical and Health Sciences, Division of Community Medicine, Linköping, Sweden
| | - Eva Flinke
- Linköping University, Department of Medical and Health Sciences, Division of Community Medicine, Linköping, Sweden
| | - Rashmi Ramesh
- Linköping University, Department of Clinical and Experimental Medicine, Division of Neurobiology, Linkoping, Sweden
| | - Lovisa Örkenby
- Linköping University, Department of Clinical and Experimental Medicine, Division of Neurobiology, Linkoping, Sweden
| | - Filip Appelkvist
- Linköping University, Department of Clinical and Experimental Medicine, Division of Neurobiology, Linkoping, Sweden
| | - Thomas Lingg
- Linköping University, Department of Clinical and Experimental Medicine, Division of Neurobiology, Linkoping, Sweden
| | - Nicola Guzzi
- Lund University, Stem Cell Center, Department of Laboratory Medicine, Division of Molecular Hematology, Lund, Sweden
| | - Cristian Bellodi
- Lund University, Stem Cell Center, Department of Laboratory Medicine, Division of Molecular Hematology, Lund, Sweden
| | - Marie Löf
- Karolinska Institute, Department of Biosciences and Nutrition, Huddinge, Sweden
- Linköping University, Department of Medical and Health Sciences, Division of Community Medicine, Linköping, Sweden
| | - Tanya Vavouri
- Josep Carreras Leukaemia Research Institute (IJC), Program for Predictive and Personalized Medicine of Cancer (PMPPC-IGTP), Barcelona, Spain
| | - Anita Öst
- Linköping University, Department of Clinical and Experimental Medicine, Division of Neurobiology, Linkoping, Sweden
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