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Tamayo-Ordóñez YDJ, Rosas-García NM, Tamayo-Ordoñez FA, Ayil-Gutiérrez BA, Bello-López JM, Sosa-Santillán GDJ, Acosta-Cruz E, Anguebes-Franseschi F, Damas-Damas S, Domínguez-May AV, Córdova-Quiroz AV, Tamayo-Ordóñez MC. Genomic Evolution Strategy in SARS-CoV-2 Lineage B: Coevolution of Cis Elements. Curr Issues Mol Biol 2024; 46:5744-5776. [PMID: 38921015 PMCID: PMC11203041 DOI: 10.3390/cimb46060344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 05/14/2024] [Accepted: 05/26/2024] [Indexed: 06/27/2024] Open
Abstract
In the SARS-CoV-2 lineage, RNA elements essential for its viral life cycle, including genome replication and gene expression, have been identified. Still, the precise structures and functions of these RNA regions in coronaviruses remain poorly understood. This lack of knowledge points out the need for further research to better understand these crucial aspects of viral biology and, in time, prepare for future outbreaks. In this research, the in silico analysis of the cis RNA structures that act in the alpha-, beta-, gamma-, and deltacoronavirus genera has provided a detailed view of the presence and adaptation of the structures of these elements in coronaviruses. The results emphasize the importance of these cis elements in viral biology and their variability between different viral variants. Some coronavirus variants in some groups, depending on the cis element (stem-loop1 and -2; pseudoknot stem-loop1 and -2, and s2m), exhibited functional adaptation. Additionally, the conformation flexibility of the s2m element in the SARS variants was determined, suggesting a coevolution of this element in this viral group. The variability in secondary structures suggests genomic adaptations that may be related to replication processes, genetic regulation, as well as the specific pathogenicity of each variant. The results suggest that RNA structures in coronaviruses can adapt and evolve toward different viral variants, which has important implications for viral adaptation, pathogenicity, and future therapeutic strategies.
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Affiliation(s)
- Yahaira de J. Tamayo-Ordóñez
- Laboratorio de Biotecnología Ambiental del Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa 88710, Tamps, Mexico;
| | - Ninfa M. Rosas-García
- Laboratorio de Biotecnología Ambiental del Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa 88710, Tamps, Mexico;
| | - Francisco A. Tamayo-Ordoñez
- Facultad de Química, Universidad Autónoma del Carmen, Calle 56 N. 4, Av. Concordia Col. Benito Juárez, Ciudad del Carmen 24180, Campeche, Mexico; (F.A.T.-O.); (F.A.-F.); (S.D.-D.); (A.V.C.-Q.)
| | - Benjamín A. Ayil-Gutiérrez
- CONAHCYT—Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Biotecnología Vegetal, Reynosa 88710, Tamps, Mexico;
| | - Juan M. Bello-López
- División de Investigación, Hospital Juárez de México, Ciudad de México 07760, Mexico;
| | - Gerardo de J. Sosa-Santillán
- Laboratorio de Microbiología y Biosíntesis, Departamento de Biotecnología, Facultad de Ciencias Químicas, Universidad Autónoma de Coahuila, Saltillo 25280, Coahuila, Mexico;
| | - Erika Acosta-Cruz
- Laboratorio de Microbiología Molecular, Departamento de Biotecnología, Facultad de Ciencias Químicas, Universidad Autónoma de Coahuila, Saltillo 25280, Coahuila, Mexico;
| | - Francisco Anguebes-Franseschi
- Facultad de Química, Universidad Autónoma del Carmen, Calle 56 N. 4, Av. Concordia Col. Benito Juárez, Ciudad del Carmen 24180, Campeche, Mexico; (F.A.T.-O.); (F.A.-F.); (S.D.-D.); (A.V.C.-Q.)
| | - Siprian Damas-Damas
- Facultad de Química, Universidad Autónoma del Carmen, Calle 56 N. 4, Av. Concordia Col. Benito Juárez, Ciudad del Carmen 24180, Campeche, Mexico; (F.A.T.-O.); (F.A.-F.); (S.D.-D.); (A.V.C.-Q.)
| | - Angel V. Domínguez-May
- TecNM, Instituto Tecnológico Superior del Sur del Estado de Yucatán, Road Muna-Felipe Carrillo Puerto, Stretch Oxkutzcab-Akil Km 41+400, Oxkutzcab 97880, Yucatán, Mexico;
| | - Atl Victor Córdova-Quiroz
- Facultad de Química, Universidad Autónoma del Carmen, Calle 56 N. 4, Av. Concordia Col. Benito Juárez, Ciudad del Carmen 24180, Campeche, Mexico; (F.A.T.-O.); (F.A.-F.); (S.D.-D.); (A.V.C.-Q.)
| | - María Concepción Tamayo-Ordóñez
- Laboratorio de Ingeniería Genética, Departamento de Biotecnología, Facultad de Ciencias Químicas, Universidad Autónoma de Coahuila, Saltillo 25280, Coahuila, Mexico
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2
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Jain I, Kolesnik M, Kuznedelov K, Minakhin L, Morozova N, Shiriaeva A, Kirillov A, Medvedeva S, Livenskyi A, Kazieva L, Makarova KS, Koonin EV, Borukhov S, Severinov K, Semenova E. tRNA anticodon cleavage by target-activated CRISPR-Cas13a effector. SCIENCE ADVANCES 2024; 10:eadl0164. [PMID: 38657076 PMCID: PMC11042736 DOI: 10.1126/sciadv.adl0164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 03/20/2024] [Indexed: 04/26/2024]
Abstract
Type VI CRISPR-Cas systems are among the few CRISPR varieties that target exclusively RNA. The CRISPR RNA-guided, sequence-specific binding of target RNAs, such as phage transcripts, activates the type VI effector, Cas13. Once activated, Cas13 causes collateral RNA cleavage, which induces bacterial cell dormancy, thus protecting the host population from the phage spread. We show here that the principal form of collateral RNA degradation elicited by Leptotrichia shahii Cas13a expressed in Escherichia coli cells is the cleavage of anticodons in a subset of transfer RNAs (tRNAs) with uridine-rich anticodons. This tRNA cleavage is accompanied by inhibition of protein synthesis, thus providing defense from the phages. In addition, Cas13a-mediated tRNA cleavage indirectly activates the RNases of bacterial toxin-antitoxin modules cleaving messenger RNA, which could provide a backup defense. The mechanism of Cas13a-induced antiphage defense resembles that of bacterial anticodon nucleases, which is compatible with the hypothesis that type VI effectors evolved from an abortive infection module encompassing an anticodon nuclease.
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Affiliation(s)
- Ishita Jain
- Waksman Institute for Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Matvey Kolesnik
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Konstantin Kuznedelov
- Waksman Institute for Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Leonid Minakhin
- Waksman Institute for Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Natalia Morozova
- Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, Russia
| | - Anna Shiriaeva
- Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, Russia
- Saint Petersburg State University, Saint Petersburg, Russia
| | - Alexandr Kirillov
- Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, Russia
| | - Sofia Medvedeva
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Alexei Livenskyi
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | | | - Kira S. Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health; Bethesda, MD, USA
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health; Bethesda, MD, USA
| | - Sergei Borukhov
- Department of Cell Biology and Neuroscience, Rowan University School of Osteopathic Medicine at Stratford; Stratford, NJ, USA
| | - Konstantin Severinov
- Waksman Institute for Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Moscow, Russia
| | - Ekaterina Semenova
- Waksman Institute for Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
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3
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Vinogradov AA, Zhang Y, Hamada K, Kobayashi S, Ogata K, Sengoku T, Goto Y, Suga H. A Compact Reprogrammed Genetic Code for De Novo Discovery of Proteolytically Stable Thiopeptides. J Am Chem Soc 2024; 146:8058-8070. [PMID: 38491946 PMCID: PMC10979747 DOI: 10.1021/jacs.3c12037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 02/25/2024] [Accepted: 02/27/2024] [Indexed: 03/18/2024]
Abstract
Thiopeptides make up a group of structurally complex peptidic natural products holding promise in bioengineering applications. The previously established thiopeptide/mRNA display platform enables de novo discovery of natural product-like thiopeptides with designed bioactivities. However, in contrast to natural thiopeptides, the discovered structures are composed predominantly of proteinogenic amino acids, which results in low metabolic stability in many cases. Here, we redevelop the platform and demonstrate that the utilization of compact reprogrammed genetic codes in mRNA display libraries can lead to the discovery of thiopeptides predominantly composed of nonproteinogenic structural elements. We demonstrate the feasibility of our designs by conducting affinity selections against Traf2- and NCK-interacting kinase (TNIK). The experiment identified a series of thiopeptides with high affinity to the target protein (the best KD = 2.1 nM) and kinase inhibitory activity (the best IC50 = 0.15 μM). The discovered compounds, which bore as many as 15 nonproteinogenic amino acids in an 18-residue macrocycle, demonstrated high metabolic stability in human serum with a half-life of up to 99 h. An X-ray cocrystal structure of TNIK in complex with a discovered thiopeptide revealed how nonproteinogenic building blocks facilitate the target engagement and orchestrate the folding of the thiopeptide into a noncanonical conformation. Altogether, the established platform takes a step toward the discovery of thiopeptides with high metabolic stability for early drug discovery applications.
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Affiliation(s)
- Alexander A. Vinogradov
- Department
of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yue Zhang
- Department
of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Keisuke Hamada
- Department
of Biochemistry, Graduate School of Medicine, Yokohama City University, Kanazawa-ku, Yokohama 236-0004, Japan
| | - Shunsuke Kobayashi
- Department
of Biochemistry, Graduate School of Medicine, Yokohama City University, Kanazawa-ku, Yokohama 236-0004, Japan
| | - Kazuhiro Ogata
- Department
of Biochemistry, Graduate School of Medicine, Yokohama City University, Kanazawa-ku, Yokohama 236-0004, Japan
| | - Toru Sengoku
- Department
of Biochemistry, Graduate School of Medicine, Yokohama City University, Kanazawa-ku, Yokohama 236-0004, Japan
| | - Yuki Goto
- Department
of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroaki Suga
- Department
of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
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4
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Flügel T, Schacherl M, Unbehaun A, Schroeer B, Dabrowski M, Bürger J, Mielke T, Sprink T, Diebolder CA, Guillén Schlippe YV, Spahn CMT. Transient disome complex formation in native polysomes during ongoing protein synthesis captured by cryo-EM. Nat Commun 2024; 15:1756. [PMID: 38409277 PMCID: PMC10897467 DOI: 10.1038/s41467-024-46092-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 02/13/2024] [Indexed: 02/28/2024] Open
Abstract
Structural studies of translating ribosomes traditionally rely on in vitro assembly and stalling of ribosomes in defined states. To comprehensively visualize bacterial translation, we reactivated ex vivo-derived E. coli polysomes in the PURE in vitro translation system and analyzed the actively elongating polysomes by cryo-EM. We find that 31% of 70S ribosomes assemble into disome complexes that represent eight distinct functional states including decoding and termination intermediates, and a pre-nucleophilic attack state. The functional diversity of disome complexes together with RNase digest experiments suggests that paused disome complexes transiently form during ongoing elongation. Structural analysis revealed five disome interfaces between leading and queueing ribosomes that undergo rearrangements as the leading ribosome traverses through the elongation cycle. Our findings reveal at the molecular level how bL9's CTD obstructs the factor binding site of queueing ribosomes to thwart harmful collisions and illustrate how translation dynamics reshape inter-ribosomal contacts.
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Affiliation(s)
- Timo Flügel
- Charité - Univesitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Berlin, Germany
| | - Magdalena Schacherl
- Charité - Univesitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Berlin, Germany
| | - Anett Unbehaun
- Charité - Univesitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Berlin, Germany
| | - Birgit Schroeer
- Charité - Univesitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Berlin, Germany
| | - Marylena Dabrowski
- Charité - Univesitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Berlin, Germany
| | - Jörg Bürger
- Charité - Univesitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Berlin, Germany
- Max Planck Institute for Molecular Genetics, Microscopy and Cryo-Electron Microscopy Service Group, Berlin, Germany
| | - Thorsten Mielke
- Max Planck Institute for Molecular Genetics, Microscopy and Cryo-Electron Microscopy Service Group, Berlin, Germany
| | - Thiemo Sprink
- Core Facility for Cryo-Electron Microscopy, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Technology Platform Cryo-EM, Berlin, Germany
| | - Christoph A Diebolder
- Core Facility for Cryo-Electron Microscopy, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Technology Platform Cryo-EM, Berlin, Germany
| | - Yollete V Guillén Schlippe
- Charité - Univesitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Berlin, Germany.
| | - Christian M T Spahn
- Charité - Univesitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Berlin, Germany.
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5
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Liu J, Nagy N, Ayala-Torres C, Aguilar-Alonso F, Morais-Esteves F, Xu S, Masucci MG. Remodeling of the ribosomal quality control and integrated stress response by viral ubiquitin deconjugases. Nat Commun 2023; 14:8315. [PMID: 38097648 PMCID: PMC10721647 DOI: 10.1038/s41467-023-43946-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 11/23/2023] [Indexed: 12/17/2023] Open
Abstract
The strategies adopted by viruses to reprogram the translation and protein quality control machinery and promote infection are poorly understood. Here, we report that the viral ubiquitin deconjugase (vDUB)-encoded in the large tegument protein of Epstein-Barr virus (EBV BPLF1)-regulates the ribosomal quality control (RQC) and integrated stress responses (ISR). The vDUB participates in protein complexes that include the RQC ubiquitin ligases ZNF598 and LTN1. Upon ribosomal stalling, the vDUB counteracts the ubiquitination of the 40 S particle and inhibits the degradation of translation-stalled polypeptides by the proteasome. Impairment of the RQC correlates with the readthrough of stall-inducing mRNAs and with activation of a GCN2-dependent ISR that redirects translation towards upstream open reading frames (uORFs)- and internal ribosome entry sites (IRES)-containing transcripts. Physiological levels of active BPLF1 promote the translation of the EBV Nuclear Antigen (EBNA)1 mRNA in productively infected cells and enhance the release of progeny virus, pointing to a pivotal role of the vDUB in the translation reprogramming that enables efficient virus production.
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Affiliation(s)
- Jiangnan Liu
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Noemi Nagy
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Carlos Ayala-Torres
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Francisco Aguilar-Alonso
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
- Unidad de Desarrollo e Investigación en Bioterapéuticos (UDIBI), Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Francisco Morais-Esteves
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Shanshan Xu
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Maria G Masucci
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.
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Vila-Sanjurjo A, Mallo N, Atkins JF, Elson JL, Smith PM. Our current understanding of the toxicity of altered mito-ribosomal fidelity during mitochondrial protein synthesis: What can it tell us about human disease? Front Physiol 2023; 14:1082953. [PMID: 37457031 PMCID: PMC10349377 DOI: 10.3389/fphys.2023.1082953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 02/28/2023] [Indexed: 07/18/2023] Open
Abstract
Altered mito-ribosomal fidelity is an important and insufficiently understood causative agent of mitochondrial dysfunction. Its pathogenic effects are particularly well-known in the case of mitochondrially induced deafness, due to the existence of the, so called, ototoxic variants at positions 847C (m.1494C) and 908A (m.1555A) of 12S mitochondrial (mt-) rRNA. It was shown long ago that the deleterious effects of these variants could remain dormant until an external stimulus triggered their pathogenicity. Yet, the link from the fidelity defect at the mito-ribosomal level to its phenotypic manifestation remained obscure. Recent work with fidelity-impaired mito-ribosomes, carrying error-prone and hyper-accurate mutations in mito-ribosomal proteins, have started to reveal the complexities of the phenotypic manifestation of mito-ribosomal fidelity defects, leading to a new understanding of mtDNA disease. While much needs to be done to arrive to a clear picture of how defects at the level of mito-ribosomal translation eventually result in the complex patterns of disease observed in patients, the current evidence indicates that altered mito-ribosome function, even at very low levels, may become highly pathogenic. The aims of this review are three-fold. First, we compare the molecular details associated with mito-ribosomal fidelity to those of general ribosomal fidelity. Second, we gather information on the cellular and organismal phenotypes associated with defective translational fidelity in order to provide the necessary grounds for an understanding of the phenotypic manifestation of defective mito-ribosomal fidelity. Finally, the results of recent experiments directly tackling mito-ribosomal fidelity are reviewed and future paths of investigation are discussed.
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Affiliation(s)
- Antón Vila-Sanjurjo
- Grupo GIBE, Departamento de Bioloxía e Centro de Investigacións Científicas Avanzadas (CICA), Universidade da Coruña (UDC), A Coruña, Spain
| | - Natalia Mallo
- Grupo GIBE, Departamento de Bioloxía e Centro de Investigacións Científicas Avanzadas (CICA), Universidade da Coruña (UDC), A Coruña, Spain
| | - John F Atkins
- Schools of Biochemistry and Microbiology, University College Cork, Cork, Ireland
| | - Joanna L Elson
- The Bioscience Institute, Newcastle University, Newcastle uponTyne, United Kingdom
- Human Metabolomics, North-West University, Potchefstroom, South Africa
| | - Paul M Smith
- Department of Paediatrics, Raigmore Hospital, Inverness, Scotland, United Kingdom
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7
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Proteostasis Deregulation in Neurodegeneration and Its Link with Stress Granules: Focus on the Scaffold and Ribosomal Protein RACK1. Cells 2022; 11:cells11162590. [PMID: 36010666 PMCID: PMC9406587 DOI: 10.3390/cells11162590] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 08/09/2022] [Accepted: 08/17/2022] [Indexed: 12/12/2022] Open
Abstract
The role of protein misfolding, deposition, and clearance has been the dominant topic in the last decades of investigation in the field of neurodegeneration. The impairment of protein synthesis, along with RNA metabolism and RNA granules, however, are significantly emerging as novel potential targets for the comprehension of the molecular events leading to neuronal deficits. Indeed, defects in ribosome activity, ribosome stalling, and PQC—all ribosome-related processes required for proteostasis regulation—can contribute to triggering stress conditions and promoting the formation of stress granules (SGs) that could evolve in the formation of pathological granules, usually occurring during neurodegenerating effects. In this review, the interplay between proteostasis, mRNA metabolism, and SGs has been explored in a neurodegenerative context with a focus on Alzheimer’s disease (AD), although some defects in these same mechanisms can also be found in frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS), which are discussed here. Finally, we highlight the role of the receptor for activated C kinase 1 (RACK1) in these pathologies and note that, besides its well characterized function as a scaffold protein, it has an important role in translation and can associate to stress granules (SGs) determining cell fate in response to diverse stress stimuli.
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8
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Jain A, Gupta AK. Modeling transport of extended interacting objects with drop-off phenomenon. PLoS One 2022; 17:e0267858. [PMID: 35499998 PMCID: PMC9060384 DOI: 10.1371/journal.pone.0267858] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 04/17/2022] [Indexed: 11/19/2022] Open
Abstract
We study a deterministic framework for important cellular transport phenomena involving a large number of interacting molecules called the excluded flow of extended interacting objects with drop-off effect (EFEIOD). This model incorporates many realistic features of biological transport process including the length of biological “particles” and the fact that they can detach along the biological ‘tracks’. The flow between the consecutive sites is unidirectional and is described by a “soft” simple exclusion principle and by repelling or attracting forces between neighboring particles. We show that the model admits a unique steady-state. Furthermore, if the parameters are periodic with common period T, then the steady-state profile converge to a unique periodic solution of period T. Simulations of the EFEIOD demonstrate several non-trivial effects of the interactions on the system steady-state profile. For example, detachment rates may help in increasing the steady-state flow by alleviating traffic jams that can exist due to several reasons like bottleneck rate or interactive forces between the particles. We also analyze the special case of our model, when there are no forces exerted by neighboring particles, and called it as the ribosome flow model of extended objects with drop-off effect (RFMEOD), and study the sensitivity of its steady-state to variations in the parameters.
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Affiliation(s)
- Aditi Jain
- Department of Mathematics, Indian Institute of Technology Ropar, Rupnagar, Punjab, India
| | - Arvind Kumar Gupta
- Department of Mathematics, Indian Institute of Technology Ropar, Rupnagar, Punjab, India
- * E-mail:
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9
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Galluccio M, Console L, Pochini L, Scalise M, Giangregorio N, Indiveri C. Strategies for Successful Over-Expression of Human Membrane Transport Systems Using Bacterial Hosts: Future Perspectives. Int J Mol Sci 2022; 23:ijms23073823. [PMID: 35409183 PMCID: PMC8998559 DOI: 10.3390/ijms23073823] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 03/28/2022] [Accepted: 03/28/2022] [Indexed: 02/06/2023] Open
Abstract
Ten percent of human genes encode for membrane transport systems, which are key components in maintaining cell homeostasis. They are involved in the transport of nutrients, catabolites, vitamins, and ions, allowing the absorption and distribution of these compounds to the various body regions. In addition, roughly 60% of FDA-approved drugs interact with membrane proteins, among which are transporters, often responsible for pharmacokinetics and side effects. Defects of membrane transport systems can cause diseases; however, knowledge of the structure/function relationships of transporters is still limited. Among the expression of hosts that produce human membrane transport systems, E. coli is one of the most favorable for its low cultivation costs, fast growth, handiness, and extensive knowledge of its genetics and molecular mechanisms. However, the expression in E. coli of human membrane proteins is often toxic due to the hydrophobicity of these proteins and the diversity in structure with respect to their bacterial counterparts. Moreover, differences in codon usage between humans and bacteria hamper translation. This review summarizes the many strategies exploited to achieve the expression of human transport systems in bacteria, providing a guide to help people who want to deal with this topic.
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Affiliation(s)
- Michele Galluccio
- Unit of Biochemistry and Molecular Biotechnology, Department of Biology, Ecology and Earth Sciences (DiBEST), University of Calabria, Via P. Bucci 4c, Arcavacata di Rende, 87036 Cosenza, Italy; (M.G.); (L.C.); (L.P.); (M.S.)
| | - Lara Console
- Unit of Biochemistry and Molecular Biotechnology, Department of Biology, Ecology and Earth Sciences (DiBEST), University of Calabria, Via P. Bucci 4c, Arcavacata di Rende, 87036 Cosenza, Italy; (M.G.); (L.C.); (L.P.); (M.S.)
| | - Lorena Pochini
- Unit of Biochemistry and Molecular Biotechnology, Department of Biology, Ecology and Earth Sciences (DiBEST), University of Calabria, Via P. Bucci 4c, Arcavacata di Rende, 87036 Cosenza, Italy; (M.G.); (L.C.); (L.P.); (M.S.)
| | - Mariafrancesca Scalise
- Unit of Biochemistry and Molecular Biotechnology, Department of Biology, Ecology and Earth Sciences (DiBEST), University of Calabria, Via P. Bucci 4c, Arcavacata di Rende, 87036 Cosenza, Italy; (M.G.); (L.C.); (L.P.); (M.S.)
| | - Nicola Giangregorio
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnology (IBIOM), National Research Council (CNR), Via Amendola 165/A, 70126 Bari, Italy;
| | - Cesare Indiveri
- Unit of Biochemistry and Molecular Biotechnology, Department of Biology, Ecology and Earth Sciences (DiBEST), University of Calabria, Via P. Bucci 4c, Arcavacata di Rende, 87036 Cosenza, Italy; (M.G.); (L.C.); (L.P.); (M.S.)
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnology (IBIOM), National Research Council (CNR), Via Amendola 165/A, 70126 Bari, Italy;
- Correspondence:
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10
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Abstract
Acetogens synthesize acetyl-CoA via the CO2-fixing Wood-Ljungdahl pathway. Despite their ecological and biotechnological importance, their translational regulation of carbon and energy metabolisms remains unclear. Here, we report how carbon and energy metabolisms in the model acetogen Acetobacterium woodii are translationally controlled under different growth conditions. Data integration of genome-scale transcriptomic and translatomic analyses revealed that the acetogenesis genes, including those of the Wood-Ljungdahl pathway and energy metabolism, showed changes in translational efficiency under autotrophic growth conditions. In particular, genes encoding the Wood-Ljungdahl pathway are translated at similar levels to achieve efficient acetogenesis activity under autotrophic growth conditions, whereas genes encoding the carbonyl branch present increased translation levels in comparison to those for the methyl branch under heterotrophic growth conditions. The translation efficiency of genes in the pathways is differentially regulated by 5′ untranslated regions and ribosome-binding sequences under different growth conditions. Our findings provide potential strategies to optimize the metabolism of syngas-fermenting acetogenic bacteria for better productivity. IMPORTANCE Acetogens are capable of reducing CO2 to multicarbon compounds (e.g., ethanol or 2,3-butanediol) via the Wood-Ljungdahl pathway. Given that protein synthesis in bacteria is highly energy consuming, acetogens living at the thermodynamic limit of life are inevitably under translation control. Here, we dissect the translational regulation of carbon and energy metabolisms in the model acetogen Acetobacterium woodii under heterotrophic and autotrophic growth conditions. The latter may be experienced when acetogen is used as a cell factory that synthesizes products from CO2 during the gas fermentation process. We found that the methyl and carbonyl branches of the Wood-Ljungdahl pathway are activated at similar translation levels during autotrophic growth. Translation is mainly regulated by the 5′-untranslated-region structure and ribosome-binding-site sequence. This work reveals novel translational regulation for coping with autotrophic growth conditions and provides the systematic data set, including the transcriptome, translatome, and promoter/5′-untranslated-region bioparts.
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11
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Marucci G, Zullino I, Bertuccini L, Camerini S, Cecchetti S, Pietrantoni A, Casella M, Vatta P, Greenwood AD, Fiorillo A, Lalle M. Re-Discovery of Giardiavirus: Genomic and Functional Analysis of Viruses from Giardia duodenalis Isolates. Biomedicines 2021; 9:654. [PMID: 34201207 PMCID: PMC8230311 DOI: 10.3390/biomedicines9060654] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 06/01/2021] [Accepted: 06/02/2021] [Indexed: 12/29/2022] Open
Abstract
Giardiasis, caused by the protozoan parasite Giardia duodenalis, is an intestinal diarrheal disease affecting almost one billion people worldwide. A small endosymbiotic dsRNA viruses, G. lamblia virus (GLV), genus Giardiavirus, family Totiviridae, might inhabit human and animal isolates of G. duodenalis. Three GLV genomes have been sequenced so far, and only one was intensively studied; moreover, a positive correlation between GLV and parasite virulence is yet to be proved. To understand the biological significance of GLV infection in Giardia, the characterization of several GLV strains from naturally infected G. duodenalis isolates is necessary. Here we report high-throughput sequencing of four GLVs strains, from Giardia isolates of human and animal origin. We also report on a new, unclassified viral sequence (designed GdRV-2), unrelated to Giardiavirus, encoding and expressing for a single large protein with an RdRp domain homologous to Totiviridae and Botybirnaviridae. The result of our sequencing and proteomic analyses challenge the current knowledge on GLV and strongly suggest that viral capsid protein translation unusually starts with a proline and that translation of the RNA-dependent RNA polymerase (RdRp) occurs via a +1/-2 ribosomal frameshift mechanism. Nucleotide polymorphism, confirmed by mass-spectrometry analysis, was also observed among and between GLV strains. Phylogenetic analysis indicated the occurrence of at least two GLV subtypes which display different phenotypes and transmissibility in experimental infections of a GLV naïve Giardia isolate.
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Affiliation(s)
- Gianluca Marucci
- Unit of Foodborne and Neglected Parasitic Disease, Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (G.M.); (I.Z.); (P.V.)
| | - Ilaria Zullino
- Unit of Foodborne and Neglected Parasitic Disease, Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (G.M.); (I.Z.); (P.V.)
| | - Lucia Bertuccini
- Core Facilities, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (L.B.); (S.C.); (S.C.); (A.P.); (M.C.)
| | - Serena Camerini
- Core Facilities, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (L.B.); (S.C.); (S.C.); (A.P.); (M.C.)
| | - Serena Cecchetti
- Core Facilities, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (L.B.); (S.C.); (S.C.); (A.P.); (M.C.)
| | - Agostina Pietrantoni
- Core Facilities, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (L.B.); (S.C.); (S.C.); (A.P.); (M.C.)
| | - Marialuisa Casella
- Core Facilities, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (L.B.); (S.C.); (S.C.); (A.P.); (M.C.)
| | - Paolo Vatta
- Unit of Foodborne and Neglected Parasitic Disease, Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (G.M.); (I.Z.); (P.V.)
| | - Alex D. Greenwood
- Leibniz Institute for Zoo and Wildlife Research, 10315 Berlin, Germany;
- Department of Veterinary Medicine, Freie Universität Berlin, 14195 Berlin, Germany
| | - Annarita Fiorillo
- Department of Biochemical Science “A. Rossi-Fanelli”, Sapienza University, 00185 Rome, Italy;
| | - Marco Lalle
- Unit of Foodborne and Neglected Parasitic Disease, Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (G.M.); (I.Z.); (P.V.)
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12
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Matsumoto S, Sugimoto N. New Insights into the Functions of Nucleic Acids Controlled by Cellular Microenvironments. Top Curr Chem (Cham) 2021; 379:17. [PMID: 33782792 DOI: 10.1007/s41061-021-00329-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 03/11/2021] [Indexed: 12/11/2022]
Abstract
The right-handed double-helical B-form structure (B-form duplex) has been widely recognized as the canonical structure of nucleic acids since it was first proposed by James Watson and Francis Crick in 1953. This B-form duplex model has a monochronic and static structure and codes genetic information within a sequence. Interestingly, DNA and RNA can form various non-canonical structures, such as hairpin loops, left-handed helices, triplexes, tetraplexes of G-quadruplex and i-motif, and branched junctions, in addition to the canonical structure. The formation of non-canonical structures depends not only on sequence but also on the surrounding environment. Importantly, these non-canonical structures may exhibit a wide variety of biological roles by changing their structures and stabilities in response to the surrounding environments, which undergo vast changes at specific locations and at specific times in cells. Here, we review recent progress regarding the interesting behaviors and functions of nucleic acids controlled by molecularly crowded cellular conditions. New insights gained from recent studies suggest that nucleic acids not only code genetic information in sequences but also have unknown functions regarding their structures and stabilities through drastic structural changes in cellular environments.
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Affiliation(s)
- Saki Matsumoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-Minamimachi, Kobe, 650-0047, Japan
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-Minamimachi, Kobe, 650-0047, Japan. .,Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-Minamimachi, Kobe, 650-0047, Japan.
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13
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Tian T, Li S, Lang P, Zhao D, Zeng J. Full-length ribosome density prediction by a multi-input and multi-output model. PLoS Comput Biol 2021; 17:e1008842. [PMID: 33770074 PMCID: PMC8026034 DOI: 10.1371/journal.pcbi.1008842] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 04/07/2021] [Accepted: 03/01/2021] [Indexed: 11/29/2022] Open
Abstract
Translation elongation is regulated by a series of complicated mechanisms in both prokaryotes and eukaryotes. Although recent advance in ribosome profiling techniques has enabled one to capture the genome-wide ribosome footprints along transcripts at codon resolution, the regulatory codes of elongation dynamics are still not fully understood. Most of the existing computational approaches for modeling translation elongation from ribosome profiling data mainly focus on local contextual patterns, while ignoring the continuity of the elongation process and relations between ribosome densities of remote codons. Modeling the translation elongation process in full-length coding sequence (CDS) level has not been studied to the best of our knowledge. In this paper, we developed a deep learning based approach with a multi-input and multi-output framework, named RiboMIMO, for modeling the ribosome density distributions of full-length mRNA CDS regions. Through considering the underlying correlations in translation efficiency among neighboring and remote codons and extracting hidden features from the input full-length coding sequence, RiboMIMO can greatly outperform the state-of-the-art baseline approaches and accurately predict the ribosome density distributions along the whole mRNA CDS regions. In addition, RiboMIMO explores the contributions of individual input codons to the predictions of output ribosome densities, which thus can help reveal important biological factors influencing the translation elongation process. The analyses, based on our interpretable metric named codon impact score, not only identified several patterns consistent with the previously-published literatures, but also for the first time (to the best of our knowledge) revealed that the codons located at a long distance from the ribosomal A site may also have an association on the translation elongation rate. This finding of long-range impact on translation elongation velocity may shed new light on the regulatory mechanisms of protein synthesis. Overall, these results indicated that RiboMIMO can provide a useful tool for studying the regulation of translation elongation in the range of full-length CDS. Translation elongation is a process in which amino acids are linked into proteins by ribosomes in cells. Translation elongation rates along the mRNAs are not constant, and are regulated by a series of mechanisms, such as codon rarity and mRNA stability. In this study, we modeled the translation elongation process at a full-length coding sequence level and developed a deep learning based approach to predict the translation elongation rates from mRNA sequences, through extracting the regulatory codes of elongation rates from the contextual sequences. The analyses, based on our interpretable metric named codon impact score, for the first time (to the best of our knowledge), revealed that in addition to the neighboring codons of the ribosomal A sites, the remote codons may also have an important impact on the translation elongation rates. This new finding may stimulate additional experiments and shed light on the regulatory mechanisms of protein synthesis.
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Affiliation(s)
- Tingzhong Tian
- Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China
| | - Shuya Li
- Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China
| | - Peng Lang
- Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China
| | - Dan Zhao
- Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China
- * E-mail: (DZ); (JZ)
| | - Jianyang Zeng
- Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China
- MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China
- * E-mail: (DZ); (JZ)
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14
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De Santis M, Hahn J, Dubnau D. ComEB protein is dispensable for the transformation but must be translated for the optimal synthesis of comEC. Mol Microbiol 2021; 116:71-79. [PMID: 33527432 DOI: 10.1111/mmi.14690] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/26/2021] [Accepted: 01/27/2021] [Indexed: 01/05/2023]
Abstract
We show that the ComEB protein is not required for transformation in Bacillus subtilis, despite its expression from within the comE operon under competence control, nor is it required for the correct polar localization of ComGA. We show further that the synthesis of the putative channel protein ComEC is translationally coupled to the upstream comEB open reading frame, so that the translation of comEB and a suboptimal ribosomal-binding site embedded in its sequence are needed for proper comEC expression. Translational coupling appears to be a common mechanism in three major competence operons for the adjustment of protein amounts independent of transcriptional control, probably ensuring the correct stoichiometries for assembly of the transformation machinery. comEB and comFC, respectively, encode cytidine deaminase and a protein resembling type 1 phosphoribosyl transferases and we speculate that nucleotide scavenging proteins are produced under competence control for efficient reutilization of the products of degradation of the non-transforming strand during DNA uptake.
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Affiliation(s)
- Micaela De Santis
- Public Health Research Institute Center, New Jersey Medical School, Rutgers University, Newark, NJ, USA
| | - Jeanette Hahn
- Public Health Research Institute Center, New Jersey Medical School, Rutgers University, Newark, NJ, USA
| | - David Dubnau
- Public Health Research Institute Center, New Jersey Medical School, Rutgers University, Newark, NJ, USA
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15
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Van Aalst E, Yekefallah M, Mehta AK, Eason I, Wylie B. Codon Harmonization of a Kir3.1-KirBac1.3 Chimera for Structural Study Optimization. Biomolecules 2020; 10:biom10030430. [PMID: 32164257 PMCID: PMC7175280 DOI: 10.3390/biom10030430] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 02/27/2020] [Accepted: 03/06/2020] [Indexed: 02/06/2023] Open
Abstract
The expression of functional, folded, and isotopically enriched membrane proteins is an enduring bottleneck for nuclear magnetic resonance (NMR) studies. Indeed, historically, protein yield optimization has been insufficient to allow NMR analysis of many complex Eukaryotic membrane proteins. However, recent work has found that manipulation of plasmid codons improves the odds of successful NMR-friendly protein production. In the last decade, numerous studies showed that matching codon usage patterns in recombinant gene sequences to those in the native sequence is positively correlated with increased protein yield. This phenomenon, dubbed codon harmonization, may be a powerful tool in optimizing recombinant expression of difficult-to-produce membrane proteins for structural studies. Here, we apply this technique to an inward rectifier K+ Channel (Kir) 3.1-KirBac1.3 chimera. Kir3.1 falls within the G protein-coupled inward rectifier K+ (GIRK) channel family, thus NMR studies may inform on the nuances of GIRK gating action in the presence and absence of its G Protein, lipid, and small molecule ligands. In our hands, harmonized plasmids increase protein yield nearly two-fold compared to the traditional ‘fully codon optimized’ construct. We then employ a fluorescence-based functional assay and solid-state NMR correlation spectroscopy to show the final protein product is folded and functional.
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Affiliation(s)
- Evan Van Aalst
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79423, USA; (E.V.A.); (M.Y.); (I.E.)
| | - Maryam Yekefallah
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79423, USA; (E.V.A.); (M.Y.); (I.E.)
| | - Anil K. Mehta
- National High Magnetic Field Laboratory and McKnight Brain Institute, University of Florida, Box 10015, Gainesville, FL 32610, USA;
| | - Isaac Eason
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79423, USA; (E.V.A.); (M.Y.); (I.E.)
| | - Benjamin Wylie
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79423, USA; (E.V.A.); (M.Y.); (I.E.)
- Correspondence:
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16
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Planson AG, Sauveplane V, Dervyn E, Jules M. Bacterial growth physiology and RNA metabolism. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194502. [PMID: 32044462 DOI: 10.1016/j.bbagrm.2020.194502] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 01/17/2020] [Accepted: 02/06/2020] [Indexed: 12/31/2022]
Abstract
Bacteria are sophisticated systems with high capacity and flexibility to adapt to various environmental conditions. Each prokaryote however possesses a defined metabolic network, which sets its overall metabolic capacity, and therefore the maximal growth rate that can be reached. To achieve optimal growth, bacteria adopt various molecular strategies to optimally adjust gene expression and optimize resource allocation according to the nutrient availability. The resulting physiological changes are often accompanied by changes in the growth rate, and by global regulation of gene expression. The growth-rate-dependent variation of the abundances in the cellular machineries, together with condition-specific regulatory mechanisms, affect RNA metabolism and fate and pose a challenge for rational gene expression reengineering of synthetic circuits. This article is part of a Special Issue entitled: RNA and gene control in bacteria, edited by Dr. M. Guillier and F. Repoila.
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Affiliation(s)
- Anne-Gaëlle Planson
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France.
| | - Vincent Sauveplane
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France.
| | - Etienne Dervyn
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France.
| | - Matthieu Jules
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France.
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17
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Patel U, Gautam S, Chatterji D. Unraveling the Role of Silent Mutation in the ω-Subunit of Escherichia coli RNA Polymerase: Structure Transition Inhibits Transcription. ACS OMEGA 2019; 4:17714-17725. [PMID: 31681877 PMCID: PMC6822122 DOI: 10.1021/acsomega.9b02103] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 09/05/2019] [Indexed: 05/07/2023]
Abstract
The bacterial RNA polymerase is a multi-subunit enzyme complex composed of six subunits, α2ββ'σω. The function of this enzyme is to transcribe the DNA base sequence to the RNA intermediate, which is ultimately translated to protein. Though the contribution of each subunit in RNA synthesis has been clearly elucidated, the role of the smallest ω-subunit is still unclear despite several studies. Recently, a study on a dominant negative mutant of rpoZ has been reported in which the mutant was shown to render the RNA polymerase defective in transcription initiation (ω6, N60D) and gave an insight on the function of ω in RNA polymerase. Serendipitously, we also obtained a silent mutant, and the mutant was found to be lethal during the isolation of toxic mutants. The primary focus of this study is to understand the mechanistic details of this lethality. Isolated ω shows a predominantly unstructured circular dichroism profile and becomes α-helical in the enzyme complex. This structural transition is perhaps the reason for this lack of function. Subsequently, we generated several silent mutants of ω to investigate the role of codon bias and the effect of rare codons with respect to their position in rpoZ. Not all silent mutations affect the structure. RNA polymerase when reconstituted with structurally altered silent mutants of ω is transcriptionally inactive. The CodonPlus strain, which has surplus tRNA, was used to assess for the rescue of the phenotype in lethal silent mutants.
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Affiliation(s)
| | - Sudhanshu Gautam
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Dipankar Chatterji
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
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18
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Haronikova L, Olivares-Illana V, Wang L, Karakostis K, Chen S, Fåhraeus R. The p53 mRNA: an integral part of the cellular stress response. Nucleic Acids Res 2019; 47:3257-3271. [PMID: 30828720 PMCID: PMC6468297 DOI: 10.1093/nar/gkz124] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Revised: 02/12/2019] [Accepted: 02/21/2019] [Indexed: 12/16/2022] Open
Abstract
A large number of signalling pathways converge on p53 to induce different cellular stress responses that aim to promote cell cycle arrest and repair or, if the damage is too severe, to induce irreversible senescence or apoptosis. The differentiation of p53 activity towards specific cellular outcomes is tightly regulated via a hierarchical order of post-translational modifications and regulated protein-protein interactions. The mechanisms governing these processes provide a model for how cells optimize the genetic information for maximal diversity. The p53 mRNA also plays a role in this process and this review aims to illustrate how protein and RNA interactions throughout the p53 mRNA in response to different signalling pathways control RNA stability, translation efficiency or alternative initiation of translation. We also describe how a p53 mRNA platform shows riboswitch-like features and controls the rate of p53 synthesis, protein stability and modifications of the nascent p53 protein. A single cancer-derived synonymous mutation disrupts the folding of this platform and prevents p53 activation following DNA damage. The role of the p53 mRNA as a target for signalling pathways illustrates how mRNA sequences have co-evolved with the function of the encoded protein and sheds new light on the information hidden within mRNAs.
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Affiliation(s)
- Lucia Haronikova
- RECAMO, Masaryk Memorial Cancer Institute, Zluty kopec 7, 656 53 Brno, Czech Republic
| | - Vanesa Olivares-Illana
- Laboratorio de Interacciones Biomoleculares y cáncer. Instituto de Física Universidad Autónoma de San Luis Potosí, Manuel Nava 6, Zona universitaria, 78290 SLP, México
| | - Lixiao Wang
- Department of Medical Biosciences, Umeå University, 90185 Umeå, Sweden
| | | | - Sa Chen
- Department of Medical Biosciences, Umeå University, 90185 Umeå, Sweden
| | - Robin Fåhraeus
- RECAMO, Masaryk Memorial Cancer Institute, Zluty kopec 7, 656 53 Brno, Czech Republic.,Department of Medical Biosciences, Umeå University, 90185 Umeå, Sweden.,Inserm U1162, 27 rue Juliette Dodu, 75010 Paris, France.,ICCVS, University of Gdańsk, Science, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland
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19
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Golubev AA, Validov SZ, Usachev KS, Yusupov MM. Elongation Factor P: New Mechanisms of Function and an Evolutionary Diversity of Translation Regulation. Mol Biol 2019. [DOI: 10.1134/s0026893319040034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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20
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Poidevin L, Unal D, Belda-Palazón B, Ferrando A. Polyamines as Quality Control Metabolites Operating at the Post-Transcriptional Level. PLANTS 2019; 8:plants8040109. [PMID: 31022874 PMCID: PMC6524035 DOI: 10.3390/plants8040109] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 04/17/2019] [Accepted: 04/19/2019] [Indexed: 01/04/2023]
Abstract
Plant polyamines (PAs) have been assigned a large number of physiological functions with unknown molecular mechanisms in many cases. Among the most abundant and studied polyamines, two of them, namely spermidine (Spd) and thermospermine (Tspm), share some molecular functions related to quality control pathways for tightly regulated mRNAs at the level of translation. In this review, we focus on the roles of Tspm and Spd to facilitate the translation of mRNAs containing upstream ORFs (uORFs), premature stop codons, and ribosome stalling sequences that may block translation, thus preventing their degradation by quality control mechanisms such as the nonsense-mediated decay pathway and possible interactions with other mRNA quality surveillance pathways.
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Affiliation(s)
- Laetitia Poidevin
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València, 46022 Valencia, Spain.
| | - Dilek Unal
- Biotechnology Application and Research Center, and Department of Molecular Biology, Faculty of Science and Letter, Bilecik Seyh Edebali University, 11230 Bilecik, Turkey.
| | - Borja Belda-Palazón
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València, 46022 Valencia, Spain.
| | - Alejandro Ferrando
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València, 46022 Valencia, Spain.
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"CodonWizard" - An intuitive software tool with graphical user interface for customizable codon optimization in protein expression efforts. Protein Expr Purif 2019; 160:84-93. [PMID: 30953700 DOI: 10.1016/j.pep.2019.03.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 03/25/2019] [Accepted: 03/31/2019] [Indexed: 11/22/2022]
Abstract
Optimization of coding sequences to maximize protein expression yield is often outsourced to external service providers during commercial gene synthesis and thus unfortunately remains a black box for many researchers. The presented software program "CodonWizard" offers scientists a powerful but easy-to-use tool for customizable codon optimization: The intuitive graphical user interface empowers even scientists inexperienced in the art to straightforward design, modify, test and save complex codon optimization strategies and to publicly share successful otimization strategies among the scientific community. "Codon Wizard" provides highly flexible features for sequence analysis and completely customizable modification/optimization of codon usage of any given input sequence data (DNA/RNA/peptide) using freely combinable algorithms, allowing for implementation of contemporary, well-established optimization strategies as well as novel, proprietary ones alike. Contrary to comparable tools, "Codon Wizard" thus finally opens up ways for an empirical approach to codon optimization and may also >be used completely offline to protect resulting intellectual property. As a benchmark, the reliability, intuitiveness and utility of the application could be demonstrated by increasing the yield of recombinant TEV-protease expressed in E. coli by several orders of magnitude after codon optimization using "CodonWizard" - Permanently available for download on the web at http://schwalbe.org.chemie.uni-frankfurt.de/node/3324.
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22
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Doerr A, de Reus E, van Nies P, van der Haar M, Wei K, Kattan J, Wahl A, Danelon C. Modelling cell-free RNA and protein synthesis with minimal systems. Phys Biol 2019; 16:025001. [DOI: 10.1088/1478-3975/aaf33d] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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23
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Nieuwkoop T, Claassens NJ, van der Oost J. Improved protein production and codon optimization analyses in Escherichia coli by bicistronic design. Microb Biotechnol 2019; 12:173-179. [PMID: 30484964 PMCID: PMC6302717 DOI: 10.1111/1751-7915.13332] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 10/08/2018] [Accepted: 10/09/2018] [Indexed: 12/19/2022] Open
Abstract
Different codon optimization algorithms are available that aim at improving protein production by optimizing translation elongation. In these algorithms, it is generally not considered how the altered protein coding sequence will affect the secondary structure of the corresponding RNA transcript, particularly not the effect on the 5'-UTR structure and related ribosome binding site availability. This is a serious drawback, because the influence of codon usage on mRNA secondary structures, especially near the start of a gene, may strongly influence translation initiation. In this study, we aim to reduce the effect of codon usage on translation initiation by applying a bicistronic design (BCD) element. Protein production of several codon-optimized gene variants is tested in parallel for a BCD and a standard monocistronic design (MCD). We demonstrate that these distinct architectures can drastically change the relative performance of different codon optimization algorithms. We conclude that a BCD is indispensable in future studies that aim to reveal the impact of codon optimization and codon usage correlations. Furthermore, irrespective of the algorithm used, using a BCD does improve protein production compared with an MCD. The overall highest expression from BCDs for both GFP and RFP is at least twofold higher than the highest levels found for the MCDs, while for codon variants having very low expression from the MCD, even 10-fold to 100-fold increases in expression were achieved by the BCD. This shows the great potential of the BCD element for recombinant protein production.
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Affiliation(s)
- Thijs Nieuwkoop
- Laboratory of MicrobiologyWageningen University and ResearchStippeneng 46708 WEWageningenThe Netherlands
| | - Nico J. Claassens
- Laboratory of MicrobiologyWageningen University and ResearchStippeneng 46708 WEWageningenThe Netherlands
- Max Planck Institute of Molecular Plant PhysiologyAm Mühlenberg 114476Potsdam‐GolmGermany
| | - John van der Oost
- Laboratory of MicrobiologyWageningen University and ResearchStippeneng 46708 WEWageningenThe Netherlands
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Rogozin IB, Gertz EM, Baranov PV, Poliakov E, Schaffer AA. Genome-Wide Changes in Protein Translation Efficiency Are Associated with Autism. Genome Biol Evol 2018; 10:1902-1919. [PMID: 29986017 PMCID: PMC6086092 DOI: 10.1093/gbe/evy146] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/06/2018] [Indexed: 01/05/2023] Open
Abstract
We previously proposed that changes in the efficiency of protein translation are associated with autism spectrum disorders (ASDs). This hypothesis connects environmental factors and genetic factors because each can alter translation efficiency. For genetic factors, we previously tested our hypothesis using a small set of ASD-associated genes, a small set of ASD-associated variants, and a statistic to quantify by how much a single nucleotide variant (SNV) in a protein coding region changes translation speed. In this study, we confirm and extend our hypothesis using a published set of 1,800 autism quartets (parents, one affected child and one unaffected child) and genome-wide variants. Then, we extend the test statistic to combine translation efficiency with other possibly relevant variables: ribosome profiling data, presence/absence of CpG dinucleotides, and phylogenetic conservation. The inclusion of ribosome profiling abundances strengthens our results for male-male sibling pairs. The inclusion of CpG information strengthens our results for female-female pairs, giving an insight into the significant gender differences in autism incidence. By combining the single-variant test statistic for all variants in a gene, we obtain a single gene score to evaluate how well a gene distinguishes between affected and unaffected siblings. Using statistical methods, we compute gene sets that have some power to distinguish between affected and unaffected siblings by translation efficiency of gene variants. Pathway and enrichment analysis of those gene sets suggest the importance of Wnt signaling pathways, some other pathways related to cancer, ATP binding, and ATP-ase pathways in the etiology of ASDs.
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Affiliation(s)
- Igor B Rogozin
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, Maryland
| | - E Michael Gertz
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, Maryland
| | - Pasha V Baranov
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Eugenia Poliakov
- National Eye Institute, NIH, Laboratory of Retinal Cell and Molecular Biology, Bethesda, Maryland
| | - Alejandro A Schaffer
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, Maryland
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25
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Paley EL, Perry G. Towards an Integrative Understanding of tRNA Aminoacylation-Diet-Host-Gut Microbiome Interactions in Neurodegeneration. Nutrients 2018; 10:nu10040410. [PMID: 29587458 PMCID: PMC5946195 DOI: 10.3390/nu10040410] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 03/19/2018] [Accepted: 03/22/2018] [Indexed: 02/07/2023] Open
Abstract
Transgenic mice used for Alzheimer’s disease (AD) preclinical experiments do not recapitulate the human disease. In our models, the dietary tryptophan metabolite tryptamine produced by human gut microbiome induces tryptophanyl-tRNA synthetase (TrpRS) deficiency with consequent neurodegeneration in cells and mice. Dietary supplements, antibiotics and certain drugs increase tryptamine content in vivo. TrpRS catalyzes tryptophan attachment to tRNAtrp at initial step of protein biosynthesis. Tryptamine that easily crosses the blood–brain barrier induces vasculopathies, neurodegeneration and cell death via TrpRS competitive inhibition. TrpRS inhibitor tryptophanol produced by gut microbiome also induces neurodegeneration. TrpRS inhibition by tryptamine and its metabolites preventing tryptophan incorporation into proteins lead to protein biosynthesis impairment. Tryptophan, a least amino acid in food and proteins that cannot be synthesized by humans competes with frequent amino acids for the transport from blood to brain. Tryptophan is a vulnerable amino acid, which can be easily lost to protein biosynthesis. Some proteins marking neurodegenerative pathology, such as tau lack tryptophan. TrpRS exists in cytoplasmic (WARS) and mitochondrial (WARS2) forms. Pathogenic gene variants of both forms cause TrpRS deficiency with consequent intellectual and motor disabilities in humans. The diminished tryptophan-dependent protein biosynthesis in AD patients is a proof of our model-based disease concept.
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Affiliation(s)
- Elena L Paley
- Expert Biomed, Inc., 11933 SW 271st TER Homestead, Miami Dade, FL 33032-3305, USA.
- Stop Alzheimers Corp., Miami Dade, FL 33032, USA.
- Nova Southeastern University, 3301 College Ave, Fort Lauderdale, FL 33314, USA.
| | - George Perry
- Stop Alzheimers Corp., Miami Dade, FL 33032, USA.
- University of Texas at San Antonio, 1 UTSA Circle, San Antonio, TX 78249, USA.
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26
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Analysis of Ribosome Stalling and Translation Elongation Dynamics by Deep Learning. Cell Syst 2017; 5:212-220.e6. [DOI: 10.1016/j.cels.2017.08.004] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 06/27/2017] [Accepted: 08/04/2017] [Indexed: 01/16/2023]
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27
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Bonnin P, Kern N, Young NT, Stansfield I, Romano MC. Novel mRNA-specific effects of ribosome drop-off on translation rate and polysome profile. PLoS Comput Biol 2017; 13:e1005555. [PMID: 28558053 PMCID: PMC5469512 DOI: 10.1371/journal.pcbi.1005555] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 06/13/2017] [Accepted: 05/08/2017] [Indexed: 11/19/2022] Open
Abstract
The well established phenomenon of ribosome drop-off plays crucial roles in translational accuracy and nutrient starvation responses during protein translation. When cells are under stress conditions, such as amino acid starvation or aminoacyl-tRNA depletion due to a high level of recombinant protein expression, ribosome drop-off can substantially affect the efficiency of protein expression. Here we introduce a mathematical model that describes the effects of ribosome drop-off on the ribosome density along the mRNA and on the concomitant protein synthesis rate. Our results show that ribosome premature termination may lead to non-intuitive ribosome density profiles, such as a ribosome density which increases from the 5' to the 3' end. Importantly, the model predicts that the effects of ribosome drop-off on the translation rate are mRNA-specific, and we quantify their resilience to drop-off, showing that the mRNAs which present ribosome queues are much less affected by ribosome drop-off than those which do not. Moreover, among those mRNAs that do not present ribosome queues, resilience to drop-off correlates positively with the elongation rate, so that sequences using fast codons are expected to be less affected by ribosome drop-off. This result is consistent with a genome-wide analysis of S. cerevisiae, which reveals that under favourable growth conditions mRNAs coding for proteins involved in the translation machinery, known to be highly codon biased and using preferentially fast codons, are highly resilient to ribosome drop-off. Moreover, in physiological conditions, the translation rate of mRNAs coding for regulatory, stress-related proteins, is less resilient to ribosome drop-off. This model therefore allows analysis of variations in the translational efficiency of individual mRNAs by accounting for the full range of known ribosome behaviours, as well as explaining mRNA-specific variations in ribosome density emerging from ribosome profiling studies.
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Affiliation(s)
- Pierre Bonnin
- Institute for Complex Systems and Mathematical Biology, Physics Department, University of Aberdeen, Aberdeen, UK
- Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen, UK
| | - Norbert Kern
- Université Montpellier 2, Laboratoire Charles Coulomb UMR 5221, Montpellier, France
| | - Neil T. Young
- Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen, UK
| | - Ian Stansfield
- Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen, UK
| | - M. Carmen Romano
- Institute for Complex Systems and Mathematical Biology, Physics Department, University of Aberdeen, Aberdeen, UK
- Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen, UK
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28
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Brender JR, Shultis D, Khattak NA, Zhang Y. An Evolution-Based Approach to De Novo Protein Design. Methods Mol Biol 2017; 1529:243-264. [PMID: 27914055 PMCID: PMC5667548 DOI: 10.1007/978-1-4939-6637-0_12] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
EvoDesign is a computational algorithm that allows the rapid creation of new protein sequences that are compatible with specific protein structures. As such, it can be used to optimize protein stability, to resculpt the protein surface to eliminate undesired protein-protein interactions, and to optimize protein-protein binding. A major distinguishing feature of EvoDesign in comparison to other protein design programs is the use of evolutionary information in the design process to guide the sequence search toward native-like sequences known to adopt structurally similar folds as the target. The observed frequencies of amino acids in specific positions in the structure in the form of structural profiles collected from proteins with similar folds and complexes with similar interfaces can implicitly capture many subtle effects that are essential for correct folding and protein-binding interactions. As a result of the inclusion of evolutionary information, the sequences designed by EvoDesign have native-like folding and binding properties not seen by other physics-based design methods. In this chapter, we describe how EvoDesign can be used to redesign proteins with a focus on the computational and experimental procedures that can be used to validate the designs.
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29
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Lavrov DV, Pett W. Animal Mitochondrial DNA as We Do Not Know It: mt-Genome Organization and Evolution in Nonbilaterian Lineages. Genome Biol Evol 2016; 8:2896-2913. [PMID: 27557826 PMCID: PMC5633667 DOI: 10.1093/gbe/evw195] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/06/2016] [Indexed: 12/11/2022] Open
Abstract
Animal mitochondrial DNA (mtDNA) is commonly described as a small, circular molecule that is conserved in size, gene content, and organization. Data collected in the last decade have challenged this view by revealing considerable diversity in animal mitochondrial genome organization. Much of this diversity has been found in nonbilaterian animals (phyla Cnidaria, Ctenophora, Placozoa, and Porifera), which, from a phylogenetic perspective, form the main branches of the animal tree along with Bilateria. Within these groups, mt-genomes are characterized by varying numbers of both linear and circular chromosomes, extra genes (e.g. atp9, polB, tatC), large variation in the number of encoded mitochondrial transfer RNAs (tRNAs) (0-25), at least seven different genetic codes, presence/absence of introns, tRNA and mRNA editing, fragmented ribosomal RNA genes, translational frameshifting, highly variable substitution rates, and a large range of genome sizes. This newly discovered diversity allows a better understanding of the evolutionary plasticity and conservation of animal mtDNA and provides insights into the molecular and evolutionary mechanisms shaping mitochondrial genomes.
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Affiliation(s)
- Dennis V Lavrov
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University
| | - Walker Pett
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University Laboratoire de Biométrie et Biologie Évolutive, Université Lyon 1, Villeurbanne, France
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30
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Zupanic A, Meplan C, Huguenin GVB, Hesketh JE, Shanley DP. Modeling and gene knockdown to assess the contribution of nonsense-mediated decay, premature termination, and selenocysteine insertion to the selenoprotein hierarchy. RNA (NEW YORK, N.Y.) 2016; 22:1076-1084. [PMID: 27208313 PMCID: PMC4911915 DOI: 10.1261/rna.055749.115] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 04/25/2016] [Indexed: 06/05/2023]
Abstract
The expression of selenoproteins, a specific group of proteins that incorporates selenocysteine, is hierarchically regulated by the availability of Se, with some, but not all selenoprotein mRNA transcripts decreasing in abundance with decreasing Se. Selenocysteine insertion into the peptide chain occurs during translation following recoding of an internal UGA stop codon. There is increasing evidence that this UGA recoding competes with premature translation termination, which is followed by nonsense-mediated decay (NMD) of the transcript. In this study, we tested the hypothesis that the susceptibility of different selenoprotein mRNAs to premature termination during translation and differential sensitivity of selenoprotein transcripts to NMD are major factors in the selenoprotein hierarchy. Selenoprotein transcript abundance was measured in Caco-2 cells using real-time PCR under different Se conditions and the data obtained fitted to mathematical models of selenoprotein translation. A calibrated model that included a combination of differential sensitivity of selenoprotein transcripts to NMD and different frequency of non-NMD related premature translation termination was able to fit all the measurements. The model predictions were tested using SiRNA to knock down expression of the crucial NMD factor UPF1 (up-frameshift protein 1) and selenoprotein mRNA expression. The calibrated model was able to predict the effect of UPF1 knockdown on gene expression for all tested selenoproteins, except SPS2 (selenophosphate synthetase), which itself is essential for selenoprotein synthesis. These results indicate an important role for NMD in the hierarchical regulation of selenoprotein mRNAs, with the exception of SPS2 whose expression is likely regulated by a different mechanism.
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Affiliation(s)
- Anze Zupanic
- Centre for Integrated Systems Biology of Ageing and Nutrition, Newcastle University, Newcastle-upon-Tyne NE4 5PL, United Kingdom Eawag, Institute for Aquatic Science and Technology, 8600 Dübendorf, Switzerland
| | - Catherine Meplan
- Centre for Integrated Systems Biology of Ageing and Nutrition, Newcastle University, Newcastle-upon-Tyne NE4 5PL, United Kingdom Institute for Cell and Molecular Biosciences and Human Nutrition Research Centre, Newcastle University, Newcastle-upon-Tyne NE2 4HH, United Kingdom
| | - Grazielle V B Huguenin
- Institute for Cell and Molecular Biosciences and Human Nutrition Research Centre, Newcastle University, Newcastle-upon-Tyne NE2 4HH, United Kingdom Faculty of Medicine, Federal University of Rio de Janeiro, Rio de Janeiro, CEP: 21941-902, Brazil
| | - John E Hesketh
- Centre for Integrated Systems Biology of Ageing and Nutrition, Newcastle University, Newcastle-upon-Tyne NE4 5PL, United Kingdom Institute for Cell and Molecular Biosciences and Human Nutrition Research Centre, Newcastle University, Newcastle-upon-Tyne NE2 4HH, United Kingdom
| | - Daryl P Shanley
- Centre for Integrated Systems Biology of Ageing and Nutrition, Newcastle University, Newcastle-upon-Tyne NE4 5PL, United Kingdom Institute for Cell and Molecular Biosciences and Human Nutrition Research Centre, Newcastle University, Newcastle-upon-Tyne NE2 4HH, United Kingdom
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31
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Buhr F, Jha S, Thommen M, Mittelstaet J, Kutz F, Schwalbe H, Rodnina MV, Komar AA. Synonymous Codons Direct Cotranslational Folding toward Different Protein Conformations. Mol Cell 2016; 61:341-351. [PMID: 26849192 DOI: 10.1016/j.molcel.2016.01.008] [Citation(s) in RCA: 240] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Revised: 11/12/2015] [Accepted: 12/24/2015] [Indexed: 11/26/2022]
Abstract
In all genomes, most amino acids are encoded by more than one codon. Synonymous codons can modulate protein production and folding, but the mechanism connecting codon usage to protein homeostasis is not known. Here we show that synonymous codon variants in the gene encoding gamma-B crystallin, a mammalian eye-lens protein, modulate the rates of translation and cotranslational folding of protein domains monitored in real time by Förster resonance energy transfer and fluorescence-intensity changes. Gamma-B crystallins produced from mRNAs with changed codon bias have the same amino acid sequence but attain different conformations, as indicated by altered in vivo stability and in vitro protease resistance. 2D NMR spectroscopic data suggest that structural differences are associated with different cysteine oxidation states of the purified proteins, providing a link between translation, folding, and the structures of isolated proteins. Thus, synonymous codons provide a secondary code for protein folding in the cell.
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Affiliation(s)
- Florian Buhr
- Center for Biomolecular Magnetic Resonance, Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-Universität Frankfurt am Main, 60438 Frankfurt am Main, Germany
| | - Sujata Jha
- Center for Gene Regulation in Health and Disease and Department of Biological, Geological and Environmental Sciences, Cleveland State University, Cleveland, Ohio 44115, USA
| | - Michael Thommen
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Goettingen, Germany
| | - Joerg Mittelstaet
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Goettingen, Germany
| | - Felicitas Kutz
- Center for Biomolecular Magnetic Resonance, Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-Universität Frankfurt am Main, 60438 Frankfurt am Main, Germany
| | - Harald Schwalbe
- Center for Biomolecular Magnetic Resonance, Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-Universität Frankfurt am Main, 60438 Frankfurt am Main, Germany
| | - Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Goettingen, Germany
| | - Anton A Komar
- Center for Gene Regulation in Health and Disease and Department of Biological, Geological and Environmental Sciences, Cleveland State University, Cleveland, Ohio 44115, USA.,Department of Biochemistry and Center for RNA Molecular Biology, Case Western Reserve University, Cleveland, Ohio 44106, USA.,Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
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Amer AAA, Gurung JM, Costa TRD, Ruuth K, Zavialov AV, Forsberg Å, Francis MS. YopN and TyeA Hydrophobic Contacts Required for Regulating Ysc-Yop Type III Secretion Activity by Yersinia pseudotuberculosis. Front Cell Infect Microbiol 2016; 6:66. [PMID: 27446813 PMCID: PMC4914553 DOI: 10.3389/fcimb.2016.00066] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 06/03/2016] [Indexed: 11/29/2022] Open
Abstract
Yersinia bacteria target Yop effector toxins to the interior of host immune cells by the Ysc-Yop type III secretion system. A YopN-TyeA heterodimer is central to controlling Ysc-Yop targeting activity. A + 1 frameshift event in the 3-prime end of yopN can also produce a singular secreted YopN-TyeA polypeptide that retains some regulatory function even though the C-terminal coding sequence of this YopN differs greatly from wild type. Thus, this YopN C-terminal segment was analyzed for its role in type III secretion control. Bacteria producing YopN truncated after residue 278, or with altered sequence between residues 279 and 287, had lost type III secretion control and function. In contrast, YopN variants with manipulated sequence beyond residue 287 maintained full control and function. Scrutiny of the YopN-TyeA complex structure revealed that residue W279 functioned as a likely hydrophobic contact site with TyeA. Indeed, a YopNW279G mutant lost all ability to bind TyeA. The TyeA residue F8 was also critical for reciprocal YopN binding. Thus, we conclude that specific hydrophobic contacts between opposing YopN and TyeA termini establishes a complex needed for regulating Ysc-Yop activity.
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Affiliation(s)
- Ayad A A Amer
- Department of Molecular Biology, Umeå UniversityUmeå, Sweden; Umeå Centre for Microbial Research, Umeå UniversityUmeå, Sweden
| | - Jyoti M Gurung
- Department of Molecular Biology, Umeå UniversityUmeå, Sweden; Umeå Centre for Microbial Research, Umeå UniversityUmeå, Sweden
| | - Tiago R D Costa
- Department of Molecular Biology, Umeå UniversityUmeå, Sweden; Umeå Centre for Microbial Research, Umeå UniversityUmeå, Sweden
| | - Kristina Ruuth
- Department of Molecular Biology, Umeå UniversityUmeå, Sweden; Umeå Centre for Microbial Research, Umeå UniversityUmeå, Sweden
| | - Anton V Zavialov
- Department of Molecular Biology, Uppsala BioCenter, Swedish University of Agricultural SciencesUppsala, Sweden; Joint Biotechnology Laboratory, Department of Chemistry, University of TurkuTurku, Finland
| | - Åke Forsberg
- Department of Molecular Biology, Umeå UniversityUmeå, Sweden; Umeå Centre for Microbial Research, Umeå UniversityUmeå, Sweden; Laboratory for Molecular Infection Medicine Sweden, Umeå UniversityUmeå, Sweden
| | - Matthew S Francis
- Department of Molecular Biology, Umeå UniversityUmeå, Sweden; Umeå Centre for Microbial Research, Umeå UniversityUmeå, Sweden
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Mechanical insights into ribosomal progression overcoming RNA G-quadruplex from periodical translation suppression in cells. Sci Rep 2016; 6:22719. [PMID: 26948955 PMCID: PMC4780275 DOI: 10.1038/srep22719] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 02/18/2016] [Indexed: 01/10/2023] Open
Abstract
G-quadruplexes formed on DNA and RNA can be roadblocks to movement of polymerases and ribosome on template nucleotides. Although folding and unfolding processes of the G-quadruplexes are deliberately studied in vitro, how the mechanical and physical properties of the G-quadruplexes affect intracellular biological systems is still unclear. In this study, mRNAs with G-quadruplex forming sequences located either in the 5′ untranslated region (UTR) or in the open reading frame (ORF) were constructed to evaluate positional effects of the G-quadruplex on translation suppression in cells. Periodic fluctuation of translation suppression was observed at every three nucleotides within the ORF but not within the 5′ UTR. The results suggested that difference in motion of ribosome at the 5′ UTR and the ORF determined the ability of the G-quadruplex structure to act as a roadblock to translation in cells and provided mechanical insights into ribosomal progression to overcome the roadblock.
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Lian X, Guo J, Gu W, Cui Y, Zhong J, Jin J, He QY, Wang T, Zhang G. Genome-Wide and Experimental Resolution of Relative Translation Elongation Speed at Individual Gene Level in Human Cells. PLoS Genet 2016; 12:e1005901. [PMID: 26926465 PMCID: PMC4771717 DOI: 10.1371/journal.pgen.1005901] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 02/05/2016] [Indexed: 11/18/2022] Open
Abstract
In the process of translation, ribosomes first assemble on mRNAs (translation initiation) and then translate along the mRNA (elongation) to synthesize proteins. Elongation pausing is deemed highly relevant to co-translational folding of nascent peptides and the functionality of protein products, which positioned the evaluation of elongation speed as one of the central questions in the field of translational control. By integrating three types of RNA-seq methods, we experimentally and computationally resolved elongation speed, with our proposed elongation velocity index (EVI), a relative measure at individual gene level and under physiological condition in human cells. We successfully distinguished slow-translating genes from the background translatome. We demonstrated that low-EVI genes encoded more stable proteins. We further identified cell-specific slow-translating codons, which might serve as a causal factor of elongation deceleration. As an example for the biological relevance, we showed that the relatively slow-translating genes tended to be associated with the maintenance of malignant phenotypes per pathway analyses. In conclusion, EVI opens a new view to understand why human cells tend to avoid simultaneously speeding up translation initiation and decelerating elongation, and the possible cancer relevance of translating low-EVI genes to gain better protein quality. In protein synthesis, ribosome assembles to mRNA to initiate translation, followed by the process of elongation to read the codons along the mRNA molecule for polypeptide chain production. It is known that slowing down the elongation speed at certain regions of mRNA is critical for the correct folding of numerous proteins—the so-called “pause-to-fold”. However, it has been an open question to evaluate elongation speed under cellular physiological conditions in genome-wide scale. Here, we used three types of next-generation sequencing approaches to experimentally and computationally address this question. With a new relative measure of elongation velocity index (EVI), we successfully distinguished slow-translating genes. Their protein products are more stable than the background genes. We found that different cell types tended to have distinct slow-translating codons, which might be relevant to the cell/tissue specific tRNA composition. Such elongation deceleration is potentially disease-relevant: cancer cells tend to slow down numerous cancer-favorable genes, and vice versa. Furthermore, we justified that translation initiation and elongation are evolutionarily synergistic as no gene with both high initiation efficiency and low elongation speed was observed: that would cause a traffic jam of ribosomes that should be maximally avoided per evolution.
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Affiliation(s)
- Xinlei Lian
- Institute of Life and Health Engineering, Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Jinan University, Guangzhou, China
| | - Jiahui Guo
- Institute of Life and Health Engineering, Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Jinan University, Guangzhou, China
| | - Wei Gu
- Institute of Life and Health Engineering, Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Jinan University, Guangzhou, China
| | - Yizhi Cui
- Institute of Life and Health Engineering, Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Jinan University, Guangzhou, China
| | - Jiayong Zhong
- Institute of Life and Health Engineering, Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Jinan University, Guangzhou, China
| | - Jingjie Jin
- Institute of Life and Health Engineering, Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Jinan University, Guangzhou, China
| | - Qing-Yu He
- Institute of Life and Health Engineering, Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Jinan University, Guangzhou, China
- * E-mail: (GZ); (TW); (QYH)
| | - Tong Wang
- Institute of Life and Health Engineering, Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Jinan University, Guangzhou, China
- * E-mail: (GZ); (TW); (QYH)
| | - Gong Zhang
- Institute of Life and Health Engineering, Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Jinan University, Guangzhou, China
- * E-mail: (GZ); (TW); (QYH)
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35
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The Art of Gene Redesign and Recombinant Protein Production: Approaches and Perspectives. TOPICS IN MEDICINAL CHEMISTRY 2016. [DOI: 10.1007/7355_2016_2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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36
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Whisper mutations: cryptic messages within the genetic code. Oncogene 2015; 35:3753-9. [PMID: 26657150 DOI: 10.1038/onc.2015.454] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 10/28/2015] [Accepted: 10/28/2015] [Indexed: 01/17/2023]
Abstract
Recent years have seen a great expansion in our understandings of how silent mutations can drive a disease and that mRNAs are not only mere messengers between the genome and the encoded proteins but also encompass regulatory activities. This review focuses on how silent mutations within open reading frames can affect the functional properties of the encoded protein. We describe how mRNAs exert control of cell biological processes governed by the encoded proteins via translation kinetics, protein folding, mRNA stability, spatio-temporal protein expression and by direct interactions with cellular factors. These examples illustrate how additional levels of information lie within the coding sequences and that the degenerative genetic code is not redundant and have co-evolved with the encoded proteins. Hence, so called synonymous mutations are not always silent but 'whisper'.
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Mu X, Fu Y, Zhu Y, Wang X, Xuan Y, Shang H, Goff SP, Gao G. HIV-1 Exploits the Host Factor RuvB-like 2 to Balance Viral Protein Expression. Cell Host Microbe 2015. [PMID: 26211835 DOI: 10.1016/j.chom.2015.06.018] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The correct ratio of the HIV-1 structural protein Gag to the envelope protein (Env) is important for maximal virion infectivity. How the virus ensures the production of Gag and Env proteins in an appropriate ratio remains unknown. We report that HIV-1 exploits the host factor RuvB-like 2 (RVB2) to balance relative expression of Gag and Env for efficient production of infectious virions. RVB2 inhibits Gag expression by interacting with both the encoded Matrix (MA) domain of Gag protein and 5' UTR of the translating mRNA and promoting mRNA degradation in a translation-dependent manner. This inhibitory activity of RVB2 is antagonized by Env through competitive interaction with MA, allowing Gag synthesis to proceed when Env levels are adequate for virion assembly. In HIV-1-positive patients, RVB2 levels positively correlate with viral loads and disease progression status. These findings reveal a mechanism by which HIV-1 regulates its protein expression.
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Affiliation(s)
- Xin Mu
- CAS Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yajing Fu
- Key Laboratory of AIDS Immunology of National Health and Family Planning Commission, The First Affiliated Hospital, China Medical University, Shenyang 110001, China
| | - Yiping Zhu
- Department of Biochemistry and Molecular Biophysics, Department of Microbiology and Immunology, and Howard Hughes Medical Institute, Columbia University Medical Center, Columbia University, New York NY, 10032, USA
| | - Xinlu Wang
- CAS Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yifang Xuan
- CAS Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Hong Shang
- Key Laboratory of AIDS Immunology of National Health and Family Planning Commission, The First Affiliated Hospital, China Medical University, Shenyang 110001, China
| | - Stephen P Goff
- Department of Biochemistry and Molecular Biophysics, Department of Microbiology and Immunology, and Howard Hughes Medical Institute, Columbia University Medical Center, Columbia University, New York NY, 10032, USA
| | - Guangxia Gao
- CAS Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
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Hess AK, Saffert P, Liebeton K, Ignatova Z. Optimization of translation profiles enhances protein expression and solubility. PLoS One 2015; 10:e0127039. [PMID: 25965266 PMCID: PMC4428881 DOI: 10.1371/journal.pone.0127039] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 04/11/2015] [Indexed: 12/12/2022] Open
Abstract
mRNA is translated with a non-uniform speed that actively coordinates co-translational folding of protein domains. Using structure-based homology we identified the structural domains in epoxide hydrolases (EHs) and introduced slow-translating codons to delineate the translation of single domains. These changes in translation speed dramatically improved the solubility of two EHs of metagenomic origin in Escherichia coli. Conversely, the importance of transient attenuation for the folding, and consequently solubility, of EH was evidenced with a member of the EH family from Agrobacterium radiobacter, which partitions in the soluble fraction when expressed in E. coli. Synonymous substitutions of codons shaping the slow-transiting regions to fast-translating codons render this protein insoluble. Furthermore, we show that low protein yield can be enhanced by decreasing the free folding energy of the initial 5’-coding region, which can disrupt mRNA secondary structure and enhance ribosomal loading. This study provides direct experimental evidence that mRNA is not a mere messenger for translation of codons into amino acids but bears an additional layer of information for folding, solubility and expression level of the encoded protein. Furthermore, it provides a general frame on how to modulate and fine-tune gene expression of a target protein.
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Affiliation(s)
- Anne-Katrin Hess
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Paul Saffert
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | | | - Zoya Ignatova
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Biochemistry, Department of Chemistry and Biochemistry, University of Hamburg, Hamburg, Germany
- * E-mail: (ZI); (KL)
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Gorochowski TE, Ignatova Z, Bovenberg RAL, Roubos JA. Trade-offs between tRNA abundance and mRNA secondary structure support smoothing of translation elongation rate. Nucleic Acids Res 2015; 43:3022-32. [PMID: 25765653 PMCID: PMC4381083 DOI: 10.1093/nar/gkv199] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 02/26/2015] [Indexed: 01/28/2023] Open
Abstract
Translation of protein from mRNA is a complex multi-step process that occurs at a non-uniform rate. Variability in ribosome speed along an mRNA enables refinement of the proteome and plays a critical role in protein biogenesis. Detailed single protein studies have found both tRNA abundance and mRNA secondary structure as key modulators of translation elongation rate, but recent genome-wide ribosome profiling experiments have not observed significant influence of either on translation efficiency. Here we provide evidence that this results from an inherent trade-off between these factors. We find codons pairing to high-abundance tRNAs are preferentially used in regions of high secondary structure content, while codons read by significantly less abundant tRNAs are located in lowly structured regions. By considering long stretches of high and low mRNA secondary structure in Saccharomyces cerevisiae and Escherichia coli and comparing them to randomized-gene models and experimental expression data, we were able to distinguish clear selective pressures and increased protein expression for specific codon choices. The trade-off between secondary structure and tRNA-concentration based codon choice allows for compensation of their independent effects on translation, helping to smooth overall translational speed and reducing the chance of potentially detrimental points of excessively slow or fast ribosome movement.
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Affiliation(s)
| | - Zoya Ignatova
- Department of Biochemistry, Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam-Golm, Germany Biochemistry and Molecular Biology, Department of Chemistry, University of Hamburg, 20146 Hamburg, Germany
| | | | - Johannes A Roubos
- DSM Biotechnology Center, P.O. Box 1, 2600 MA Delft, The Netherlands
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40
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Viero G, Lunelli L, Passerini A, Bianchini P, Gilbert RJ, Bernabò P, Tebaldi T, Diaspro A, Pederzolli C, Quattrone A. Three distinct ribosome assemblies modulated by translation are the building blocks of polysomes. ACTA ACUST UNITED AC 2015; 208:581-96. [PMID: 25713412 PMCID: PMC4347638 DOI: 10.1083/jcb.201406040] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Translation is increasingly recognized as a central control layer of gene expression in eukaryotic cells. The overall organization of mRNA and ribosomes within polysomes, as well as the possible role of this organization in translation are poorly understood. Here we show that polysomes are primarily formed by three distinct classes of ribosome assemblies. We observe that these assemblies can be connected by naked RNA regions of the transcript. We show that the relative proportions of the three classes of ribosome assemblies reflect, and probably dictate, the level of translational activity. These results reveal the existence of recurrent supra-ribosomal building blocks forming polysomes and suggest the presence of unexplored translational controls embedded in the polysome structure.
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Affiliation(s)
- Gabriella Viero
- Institute of Biophysics, National Research Council (CNR) Unit at Trento, 38123 Povo, Italy Laboratory of Translational Genomics, Centre for Integrative Biology, University of Trento, 38123 Mattarello, Italy
| | - Lorenzo Lunelli
- Laboratory of Biomolecular Sequence and Structure Analysis for Health, Fondazione Bruno Kessler, 38123 Povo, Italy
| | - Andrea Passerini
- Department of Information Engineering and Computer Science, University of Trento, 38123 Povo, Italy
| | - Paolo Bianchini
- Nanophysics Department, Italian Institute of Technology, 16163 Genova, Italy
| | - Robert J Gilbert
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, England, UK
| | - Paola Bernabò
- Institute of Biophysics, National Research Council (CNR) Unit at Trento, 38123 Povo, Italy
| | - Toma Tebaldi
- Laboratory of Translational Genomics, Centre for Integrative Biology, University of Trento, 38123 Mattarello, Italy
| | - Alberto Diaspro
- Nanophysics Department, Italian Institute of Technology, 16163 Genova, Italy
| | - Cecilia Pederzolli
- Laboratory of Biomolecular Sequence and Structure Analysis for Health, Fondazione Bruno Kessler, 38123 Povo, Italy
| | - Alessandro Quattrone
- Laboratory of Translational Genomics, Centre for Integrative Biology, University of Trento, 38123 Mattarello, Italy
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41
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Ay A, Holland J, Sperlea A, Devakanmalai GS, Knierer S, Sangervasi S, Stevenson A, Ozbudak EM. Spatial gradients of protein-level time delays set the pace of the traveling segmentation clock waves. Development 2014; 141:4158-67. [PMID: 25336742 DOI: 10.1242/dev.111930] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The vertebrate segmentation clock is a gene expression oscillator controlling rhythmic segmentation of the vertebral column during embryonic development. The period of oscillations becomes longer as cells are displaced along the posterior to anterior axis, which results in traveling waves of clock gene expression sweeping in the unsegmented tissue. Although various hypotheses necessitating the inclusion of additional regulatory genes into the core clock network at different spatial locations have been proposed, the mechanism underlying traveling waves has remained elusive. Here, we combined molecular-level computational modeling and quantitative experimentation to solve this puzzle. Our model predicts the existence of an increasing gradient of gene expression time delays along the posterior to anterior direction to recapitulate spatiotemporal profiles of the traveling segmentation clock waves in different genetic backgrounds in zebrafish. We validated this prediction by measuring an increased time delay of oscillatory Her1 protein production along the unsegmented tissue. Our results refuted the need for spatial expansion of the core feedback loop to explain the occurrence of traveling waves. Spatial regulation of gene expression time delays is a novel way of creating dynamic patterns; this is the first report demonstrating such a control mechanism in any tissue and future investigations will explore the presence of analogous examples in other biological systems.
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Affiliation(s)
- Ahmet Ay
- Department of Mathematics, Colgate University, Hamilton, NY 13346, USA Department of Biology, Colgate University, Hamilton, NY 13346, USA
| | - Jack Holland
- Department of Computer Science, Colgate University, Hamilton, NY 13346, USA
| | - Adriana Sperlea
- Department of Computer Science, Colgate University, Hamilton, NY 13346, USA
| | | | - Stephan Knierer
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | | | - Angel Stevenson
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Ertuğrul M Ozbudak
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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42
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43
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Gould N, Hendy O, Papamichail D. Computational tools and algorithms for designing customized synthetic genes. Front Bioeng Biotechnol 2014; 2:41. [PMID: 25340050 PMCID: PMC4186344 DOI: 10.3389/fbioe.2014.00041] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 09/16/2014] [Indexed: 11/13/2022] Open
Abstract
Advances in DNA synthesis have enabled the construction of artificial genes, gene circuits, and genomes of bacterial scale. Freedom in de novo design of synthetic constructs provides significant power in studying the impact of mutations in sequence features, and verifying hypotheses on the functional information that is encoded in nucleic and amino acids. To aid this goal, a large number of software tools of variable sophistication have been implemented, enabling the design of synthetic genes for sequence optimization based on rationally defined properties. The first generation of tools dealt predominantly with singular objectives such as codon usage optimization and unique restriction site incorporation. Recent years have seen the emergence of sequence design tools that aim to evolve sequences toward combinations of objectives. The design of optimal protein-coding sequences adhering to multiple objectives is computationally hard, and most tools rely on heuristics to sample the vast sequence design space. In this review, we study some of the algorithmic issues behind gene optimization and the approaches that different tools have adopted to redesign genes and optimize desired coding features. We utilize test cases to demonstrate the efficiency of each approach, as well as identify their strengths and limitations.
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Affiliation(s)
- Nathan Gould
- Department of Computer Science, The College of New Jersey , Ewing, NJ , USA
| | - Oliver Hendy
- Department of Biology, The College of New Jersey , Ewing, NJ , USA
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44
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Zupanic A, Meplan C, Grellscheid SN, Mathers JC, Kirkwood TBL, Hesketh JE, Shanley DP. Detecting translational regulation by change point analysis of ribosome profiling data sets. RNA (NEW YORK, N.Y.) 2014; 20:1507-1518. [PMID: 25147239 PMCID: PMC4174433 DOI: 10.1261/rna.045286.114] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 06/25/2014] [Indexed: 06/03/2023]
Abstract
Ribo-Seq maps the location of translating ribosomes on mature mRNA transcripts. While during normal translation, ribosome density is constant along the length of the mRNA coding region, this can be altered in response to translational regulatory events. In the present study, we developed a method to detect translational regulation of individual mRNAs from their ribosome profiles, utilizing changes in ribosome density. We used mathematical modeling to show that changes in ribosome density should occur along the mRNA at the point of regulation. We analyzed a Ribo-Seq data set obtained for mouse embryonic stem cells and showed that normalization by corresponding RNA-Seq can be used to improve the Ribo-Seq quality by removing bias introduced by deep-sequencing and alignment artifacts. After normalization, we applied a change point algorithm to detect changes in ribosome density present in individual mRNA ribosome profiles. Additional sequence and gene isoform information obtained from the UCSC Genome Browser allowed us to further categorize the detected changes into different mechanisms of regulation. In particular, we detected several mRNAs with known post-transcriptional regulation, e.g., premature termination for selenoprotein mRNAs and translational control of Atf4, but also several more mRNAs with hitherto unknown translational regulation. Additionally, our approach proved useful for identification of new transcript isoforms.
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Affiliation(s)
- Anze Zupanic
- Centre for Integrated Systems Biology of Ageing and Nutrition, Institute for Ageing and Health, Newcastle University, Newcastle-upon-Tyne, NE4 5PL, United Kingdom Department of Environmental Toxicology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
| | - Catherine Meplan
- Institute for Cell and Molecular Biosciences and Human Nutrition Research Centre, Newcastle University, Newcastle-upon-Tyne, NE2 4HH, United Kingdom
| | - Sushma N Grellscheid
- School of Biological and Biomedical Sciences, Durham University, Durham DH1 3LE, United Kingdom
| | - John C Mathers
- Centre for Integrated Systems Biology of Ageing and Nutrition, Institute for Ageing and Health, Newcastle University, Newcastle-upon-Tyne, NE4 5PL, United Kingdom
| | - Tom B L Kirkwood
- Centre for Integrated Systems Biology of Ageing and Nutrition, Institute for Ageing and Health, Newcastle University, Newcastle-upon-Tyne, NE4 5PL, United Kingdom
| | - John E Hesketh
- Institute for Cell and Molecular Biosciences and Human Nutrition Research Centre, Newcastle University, Newcastle-upon-Tyne, NE2 4HH, United Kingdom
| | - Daryl P Shanley
- Centre for Integrated Systems Biology of Ageing and Nutrition, Institute for Ageing and Health, Newcastle University, Newcastle-upon-Tyne, NE4 5PL, United Kingdom
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45
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Johnston CD, Bannantine JP, Govender R, Endersen L, Pletzer D, Weingart H, Coffey A, O'Mahony J, Sleator RD. Enhanced expression of codon optimized Mycobacterium avium subsp. paratuberculosis antigens in Lactobacillus salivarius. Front Cell Infect Microbiol 2014; 4:120. [PMID: 25237653 PMCID: PMC4154528 DOI: 10.3389/fcimb.2014.00120] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Accepted: 08/15/2014] [Indexed: 01/03/2023] Open
Abstract
It is well documented that open reading frames containing high GC content show poor expression in A+T rich hosts. Specifically, G+C-rich codon usage is a limiting factor in heterologous expression of Mycobacterium avium subsp. paratuberculosis (MAP) proteins using Lactobacillus salivarius. However, re-engineering opening reading frames through synonymous substitutions can offset codon bias and greatly enhance MAP protein production in this host. In this report, we demonstrate that codon-usage manipulation of MAP2121c can enhance the heterologous expression of the major membrane protein (MMP), analogous to the form in which it is produced natively by MAP bacilli. When heterologously over-expressed, antigenic determinants were preserved in synthetic MMP proteins as shown by monoclonal antibody mediated ELISA. Moreover, MMP is a membrane protein in MAP, which is also targeted to the cellular surface of recombinant L. salivarius at levels comparable to MAP. Additionally, we previously engineered MAP3733c (encoding MptD) and show herein that MptD displays the tendency to associate with the cytoplasmic membrane boundary under confocal microscopy and the intracellularly accumulated protein selectively adheres to the MptD-specific bacteriophage fMptD. This work demonstrates there is potential for L. salivarius as a viable antigen delivery vehicle for MAP, which may provide an effective mucosal vaccine against Johne's disease.
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Affiliation(s)
| | - John P Bannantine
- United States Department of Agriculture - Agricultural Research Service, National Animal Disease Center Ames, IA, USA
| | - Rodney Govender
- Biological Sciences Department, Cork Institute of Technology Cork, Ireland
| | - Lorraine Endersen
- Biological Sciences Department, Cork Institute of Technology Cork, Ireland
| | - Daniel Pletzer
- School of Engineering and Science, Jacobs University Bremen Bremen, Germany
| | - Helge Weingart
- School of Engineering and Science, Jacobs University Bremen Bremen, Germany
| | - Aidan Coffey
- Biological Sciences Department, Cork Institute of Technology Cork, Ireland
| | - Jim O'Mahony
- Biological Sciences Department, Cork Institute of Technology Cork, Ireland
| | - Roy D Sleator
- Biological Sciences Department, Cork Institute of Technology Cork, Ireland
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46
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Hersch SJ, Elgamal S, Katz A, Ibba M, Navarre WW. Translation initiation rate determines the impact of ribosome stalling on bacterial protein synthesis. J Biol Chem 2014; 289:28160-71. [PMID: 25148683 DOI: 10.1074/jbc.m114.593277] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Ribosome stalling during translation can be caused by a number of characterized mechanisms. However, the impact of elongation stalls on protein levels is variable, and the reasons for this are often unclear. To investigate this relationship, we examined the bacterial translation elongation factor P (EF-P), which plays a critical role in rescuing ribosomes stalled at specific amino acid sequences including polyproline motifs. In previous proteomic analyses of both Salmonella and Escherichia coli efp mutants, it was evident that not all proteins containing a polyproline motif were dependent on EF-P for efficient expression in vivo. The α- and β-subunits of ATP synthase, AtpA and AtpD, are translated from the same mRNA transcript, and both contain a PPG motif; however, proteomic analysis revealed that AtpD levels are strongly dependent on EF-P, whereas AtpA levels are independent of EF-P. Using these model proteins, we systematically determined that EF-P dependence is strongly influenced by elements in the 5'-untranslated region of the mRNA. By mutating either the Shine-Dalgarno sequence or the start codon, we find that EF-P dependence correlates directly with the rate of translation initiation where strongly expressed proteins show the greatest dependence on EF-P. Our findings demonstrate that polyproline-induced stalls exert a net effect on protein levels only if they limit translation significantly more than initiation. This model can be generalized to explain why sequences that induce pauses in translation elongation to, for example, facilitate folding do not necessarily exact a penalty on the overall production of the protein.
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Affiliation(s)
- Steven J Hersch
- From the Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada and
| | - Sara Elgamal
- the Department of Microbiology, Ohio State University, Columbus, Ohio 43210
| | - Assaf Katz
- the Department of Microbiology, Ohio State University, Columbus, Ohio 43210
| | - Michael Ibba
- the Department of Microbiology, Ohio State University, Columbus, Ohio 43210
| | - William Wiley Navarre
- From the Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada and
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Ishimura R, Nagy G, Dotu I, Zhou H, Yang XL, Schimmel P, Senju S, Nishimura Y, Chuang JH, Ackerman SL. RNA function. Ribosome stalling induced by mutation of a CNS-specific tRNA causes neurodegeneration. Science 2014; 345:455-9. [PMID: 25061210 DOI: 10.1126/science.1249749] [Citation(s) in RCA: 310] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
In higher eukaryotes, transfer RNAs (tRNAs) with the same anticodon are encoded by multiple nuclear genes, and little is known about how mutations in these genes affect translation and cellular homeostasis. Similarly, the surveillance systems that respond to such defects in higher eukaryotes are not clear. Here, we discover that loss of GTPBP2, a novel binding partner of the ribosome recycling protein Pelota, in mice with a mutation in a tRNA gene that is specifically expressed in the central nervous system causes ribosome stalling and widespread neurodegeneration. Our results not only define GTPBP2 as a ribosome rescue factor but also unmask the disease potential of mutations in nuclear-encoded tRNA genes.
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Affiliation(s)
- Ryuta Ishimura
- Howard Hughes Medical Institute and The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Gabor Nagy
- Howard Hughes Medical Institute and The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Ivan Dotu
- The Jackson Laboratory for Genomic Medicine, 263 Farmington Avenue, Farmington, CT 06030, USA
| | - Huihao Zhou
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Xiang-Lei Yang
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Paul Schimmel
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Satoru Senju
- Department of Immunogenetics, Graduate School of Medical Sciences, Kumamoto University, Honjo 1-1-1, Chuo-ku, Kumamoto 860-8556, Japan
| | - Yasuharu Nishimura
- Department of Immunogenetics, Graduate School of Medical Sciences, Kumamoto University, Honjo 1-1-1, Chuo-ku, Kumamoto 860-8556, Japan
| | - Jeffrey H Chuang
- The Jackson Laboratory for Genomic Medicine, 263 Farmington Avenue, Farmington, CT 06030, USA
| | - Susan L Ackerman
- Howard Hughes Medical Institute and The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA.
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48
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Poliakov E, Koonin EV, Rogozin IB. Impairment of translation in neurons as a putative causative factor for autism. Biol Direct 2014; 9:16. [PMID: 25011470 PMCID: PMC4099083 DOI: 10.1186/1745-6150-9-16] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 07/01/2014] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND A dramatic increase in the prevalence of autism and Autistic Spectrum Disorders (ASD) has been observed over the last two decades in USA, Europe and Asia. Given the accumulating data on the possible role of translation in the etiology of ASD, we analyzed potential effects of rare synonymous substitutions associated with ASD on mRNA stability, splicing enhancers and silencers, and codon usage. PRESENTATION OF THE HYPOTHESIS We hypothesize that subtle impairment of translation, resulting in dosage imbalance of neuron-specific proteins, contributes to the etiology of ASD synergistically with environmental neurotoxins. TESTING THE HYPOTHESIS A statistically significant shift from optimal to suboptimal codons caused by rare synonymous substitutions associated with ASD was detected whereas no effect on other analyzed characteristics of transcripts was identified. This result suggests that the impact of rare codons on the translation of genes involved in neuron development, even if slight in magnitude, could contribute to the pathogenesis of ASD in the presence of an aggressive chemical background. This hypothesis could be tested by further analysis of ASD-associated mutations, direct biochemical characterization of their effects, and assessment of in vivo effects on animal models. IMPLICATIONS OF THE HYPOTHESIS It seems likely that the synergistic action of environmental hazards with genetic variations that in themselves have limited or no deleterious effects but are potentiated by the environmental factors is a general principle that underlies the alarming increase in the ASD prevalence. REVIEWERS This article was reviewed by Andrey Rzhetsky, Neil R. Smalheiser, and Shamil R. Sunyaev.
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Affiliation(s)
- Eugenia Poliakov
- Laboratory of Retinal Cell & Molecular Biology, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Igor B Rogozin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
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49
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Ribosome profiling reveals sequence-independent post-initiation pausing as a signature of translation. Cell Res 2014; 24:842-51. [PMID: 24903108 DOI: 10.1038/cr.2014.74] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Revised: 03/30/2014] [Accepted: 04/24/2014] [Indexed: 02/07/2023] Open
Abstract
The journey of a newly synthesized polypeptide starts in the peptidyltransferase center of the ribosome, from where it traverses the exit tunnel. The interior of the ribosome exit tunnel is neither straight nor smooth. How the ribosome dynamics in vivo is influenced by the exit tunnel is poorly understood. Genome-wide ribosome profiling in mammalian cells reveals elevated ribosome density at the start codon and surprisingly the downstream 5th codon position as well. We found that the highly focused ribosomal pausing shortly after initiation is attributed to the geometry of the exit tunnel, as deletion of the loop region from ribosome protein L4 diminishes translational pausing at the 5th codon position. Unexpectedly, the ribosome variant undergoes translational abandonment shortly after initiation, suggesting that there exists an obligatory step between initiation and elongation commitment. We propose that the post-initiation pausing of ribosomes represents an inherent signature of the translation machinery to ensure productive translation.
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50
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Rosano GL, Ceccarelli EA. Recombinant protein expression in Escherichia coli: advances and challenges. Front Microbiol 2014; 5:172. [PMID: 24860555 PMCID: PMC4029002 DOI: 10.3389/fmicb.2014.00172] [Citation(s) in RCA: 1285] [Impact Index Per Article: 128.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 03/29/2014] [Indexed: 12/28/2022] Open
Abstract
Escherichia coli is one of the organisms of choice for the production of recombinant proteins. Its use as a cell factory is well-established and it has become the most popular expression platform. For this reason, there are many molecular tools and protocols at hand for the high-level production of heterologous proteins, such as a vast catalog of expression plasmids, a great number of engineered strains and many cultivation strategies. We review the different approaches for the synthesis of recombinant proteins in E. coli and discuss recent progress in this ever-growing field.
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Affiliation(s)
- Germán L Rosano
- Instituto de Biología Molecular y Celular de Rosario, Consejo Nacional de Investigaciones Científicas y Técnicas Rosario, Argentina ; Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario Rosario, Argentina
| | - Eduardo A Ceccarelli
- Instituto de Biología Molecular y Celular de Rosario, Consejo Nacional de Investigaciones Científicas y Técnicas Rosario, Argentina ; Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario Rosario, Argentina
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