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Mohler K, Moen JM, Rogulina S, Rinehart J. System-wide optimization of an orthogonal translation system with enhanced biological tolerance. Mol Syst Biol 2023; 19:e10591. [PMID: 37477096 PMCID: PMC10407733 DOI: 10.15252/msb.202110591] [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: 07/20/2021] [Revised: 07/05/2023] [Accepted: 07/05/2023] [Indexed: 07/22/2023] Open
Abstract
Over the past two decades, synthetic biological systems have revolutionized the study of cellular physiology. The ability to site-specifically incorporate biologically relevant non-standard amino acids using orthogonal translation systems (OTSs) has proven particularly useful, providing unparalleled access to cellular mechanisms modulated by post-translational modifications, such as protein phosphorylation. However, despite significant advances in OTS design and function, the systems-level biology of OTS development and utilization remains underexplored. In this study, we employ a phosphoserine OTS (pSerOTS) as a model to systematically investigate global interactions between OTS components and the cellular environment, aiming to improve OTS performance. Based on this analysis, we design OTS variants to enhance orthogonality by minimizing host process interactions and reducing stress response activation. Our findings advance understanding of system-wide OTS:host interactions, enabling informed design practices that circumvent deleterious interactions with host physiology while improving OTS performance and stability. Furthermore, our study emphasizes the importance of establishing a pipeline for systematically profiling OTS:host interactions to enhance orthogonality and mitigate mechanisms underlying OTS-mediated host toxicity.
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Affiliation(s)
- Kyle Mohler
- Department of Cellular & Molecular PhysiologyYale School of MedicineNew HavenCTUSA
- Systems Biology InstituteYale UniversityNew HavenCTUSA
| | - Jack M Moen
- Quantitative Biosciences Institute (QBI)University of California, San FranciscoSan FranciscoCAUSA
- 2QBI Coronavirus Research Group (QCRG)San FranciscoCAUSA
- Department of Cellular and Molecular PharmacologyUniversity of California, San FranciscoSan FranciscoCAUSA
| | - Svetlana Rogulina
- Department of Cellular & Molecular PhysiologyYale School of MedicineNew HavenCTUSA
- Systems Biology InstituteYale UniversityNew HavenCTUSA
| | - Jesse Rinehart
- Department of Cellular & Molecular PhysiologyYale School of MedicineNew HavenCTUSA
- Systems Biology InstituteYale UniversityNew HavenCTUSA
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2
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Gogoi J, Bhatnagar A, Ann KJ, Pottabathini S, Singh R, Mazeed M, Kuncha SK, Kruparani SP, Sankaranarayanan R. Switching a conflicted bacterial DTD-tRNA code is essential for the emergence of mitochondria. SCIENCE ADVANCES 2022; 8:eabj7307. [PMID: 35020439 PMCID: PMC8754408 DOI: 10.1126/sciadv.abj7307] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 11/17/2021] [Indexed: 06/09/2023]
Abstract
Mitochondria emerged through an endosymbiotic event involving a proteobacterium and an archaeal host. However, the process of optimization of cellular processes required for the successful evolution and survival of mitochondria, which integrates components from two evolutionarily distinct ancestors as well as novel eukaryotic elements, is not well understood. We identify two key switches in the translational machinery—one in the discriminator recognition code of a chiral proofreader DTD [d-aminoacyl–transfer RNA (tRNA) deacylase] and the other in mitochondrial tRNAGly—that enable the compatibility between disparate elements essential for survival. Notably, the mito-tRNAGly discriminator element is the only one to switch from pyrimidine to purine during the bacteria-to-mitochondria transition. We capture this code transition in the Jakobida, an early diverging eukaryotic clade bearing the most bacterial-like mito-genome, wherein both discriminator elements are present. This study underscores the need to explore the fundamental integration strategies critical for mitochondrial and eukaryotic evolution.
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Affiliation(s)
- Jotin Gogoi
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana 500007, India
| | - Akshay Bhatnagar
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana 500007, India
| | - Kezia. J. Ann
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana 500007, India
| | | | - Raghvendra Singh
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana 500007, India
| | - Mohd Mazeed
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana 500007, India
| | - Santosh Kumar Kuncha
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana 500007, India
| | - Shobha P. Kruparani
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana 500007, India
| | - Rajan Sankaranarayanan
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana 500007, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR–CCMB Campus, Uppal Road, Hyderabad 500007, India
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3
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Pernod K, Schaeffer L, Chicher J, Hok E, Rick C, Geslain R, Eriani G, Westhof E, Ryckelynck M, Martin F. The nature of the purine at position 34 in tRNAs of 4-codon boxes is correlated with nucleotides at positions 32 and 38 to maintain decoding fidelity. Nucleic Acids Res 2020; 48:6170-6183. [PMID: 32266934 PMCID: PMC7293025 DOI: 10.1093/nar/gkaa221] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 03/19/2020] [Accepted: 03/25/2020] [Indexed: 12/29/2022] Open
Abstract
Translation fidelity relies essentially on the ability of ribosomes to accurately recognize triplet interactions between codons on mRNAs and anticodons of tRNAs. To determine the codon-anticodon pairs that are efficiently accepted by the eukaryotic ribosome, we took advantage of the IRES from the intergenic region (IGR) of the Cricket Paralysis Virus. It contains an essential pseudoknot PKI that structurally and functionally mimics a codon-anticodon helix. We screened the entire set of 4096 possible combinations using ultrahigh-throughput screenings combining coupled transcription/translation and droplet-based microfluidics. Only 97 combinations are efficiently accepted and accommodated for translocation and further elongation: 38 combinations involve cognate recognition with Watson-Crick pairs and 59 involve near-cognate recognition pairs with at least one mismatch. More than half of the near-cognate combinations (36/59) contain a G at the first position of the anticodon (numbered 34 of tRNA). G34-containing tRNAs decoding 4-codon boxes are almost absent from eukaryotic genomes in contrast to bacterial genomes. We reconstructed these missing tRNAs and could demonstrate that these tRNAs are toxic to cells due to their miscoding capacity in eukaryotic translation systems. We also show that the nature of the purine at position 34 is correlated with the nucleotides present at 32 and 38.
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Affiliation(s)
- Ketty Pernod
- Institut de Biologie Moléculaire et Cellulaire, 'Architecture et Réactivité de l'ARN' CNRS UPR9002, Université de Strasbourg, 2, allée Konrad Roentgen, F-67084 Strasbourg, France
| | - Laure Schaeffer
- Institut de Biologie Moléculaire et Cellulaire, 'Architecture et Réactivité de l'ARN' CNRS UPR9002, Université de Strasbourg, 2, allée Konrad Roentgen, F-67084 Strasbourg, France
| | - Johana Chicher
- Institut de Biologie Moléculaire et Cellulaire, Plateforme Protéomique Strasbourg - Esplanade, CNRS FRC1589, Université de Strasbourg, 2, allée Konrad Roentgen Descartes, F-67084 Strasbourg, France
| | - Eveline Hok
- Laboratory of tRNA Biology, Department of Biology, Rita Liddy Hollings Science Center, 58 Coming Street, Charleston, SC, USA
| | - Christian Rick
- Institut de Biologie Moléculaire et Cellulaire, 'Architecture et Réactivité de l'ARN' CNRS UPR9002, Université de Strasbourg, 2, allée Konrad Roentgen, F-67084 Strasbourg, France
| | - Renaud Geslain
- Laboratory of tRNA Biology, Department of Biology, Rita Liddy Hollings Science Center, 58 Coming Street, Charleston, SC, USA
| | - Gilbert Eriani
- Institut de Biologie Moléculaire et Cellulaire, 'Architecture et Réactivité de l'ARN' CNRS UPR9002, Université de Strasbourg, 2, allée Konrad Roentgen, F-67084 Strasbourg, France
| | - Eric Westhof
- Institut de Biologie Moléculaire et Cellulaire, 'Architecture et Réactivité de l'ARN' CNRS UPR9002, Université de Strasbourg, 2, allée Konrad Roentgen, F-67084 Strasbourg, France
| | - Michael Ryckelynck
- Institut de Biologie Moléculaire et Cellulaire, 'Architecture et Réactivité de l'ARN' CNRS UPR9002, Université de Strasbourg, 2, allée Konrad Roentgen, F-67084 Strasbourg, France
| | - Franck Martin
- Institut de Biologie Moléculaire et Cellulaire, 'Architecture et Réactivité de l'ARN' CNRS UPR9002, Université de Strasbourg, 2, allée Konrad Roentgen, F-67084 Strasbourg, France
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Kapur M, Ackerman SL. mRNA Translation Gone Awry: Translation Fidelity and Neurological Disease. Trends Genet 2018; 34:218-231. [PMID: 29352613 DOI: 10.1016/j.tig.2017.12.007] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 12/04/2017] [Accepted: 12/11/2017] [Indexed: 10/18/2022]
Abstract
Errors during mRNA translation can lead to a reduction in the levels of functional proteins and an increase in deleterious molecules. Advances in next-generation sequencing have led to the discovery of rare genetic disorders, many caused by mutations in genes encoding the mRNA translation machinery, as well as to a better understanding of translational dynamics through ribosome profiling. We discuss here multiple neurological disorders that are linked to errors in tRNA aminoacylation and ribosome decoding. We draw on studies from genetic models, including yeast and mice, to enhance our understanding of the translational defects observed in these diseases. Finally, we emphasize the importance of tRNA, their associated enzymes, and the inextricable link between accuracy and efficiency in the maintenance of translational fidelity.
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Affiliation(s)
- Mridu Kapur
- Howard Hughes Medical Institute, Department of Cellular and Molecular Medicine, Section of Neurobiology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Susan L Ackerman
- Howard Hughes Medical Institute, Department of Cellular and Molecular Medicine, Section of Neurobiology, University of California, San Diego, La Jolla, CA 92093, USA.
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Mohler K, Mann R, Bullwinkle TJ, Hopkins K, Hwang L, Reynolds NM, Gassaway B, Aerni HR, Rinehart J, Polymenis M, Faull K, Ibba M. Editing of misaminoacylated tRNA controls the sensitivity of amino acid stress responses in Saccharomyces cerevisiae. Nucleic Acids Res 2017; 45:3985-3996. [PMID: 28168297 PMCID: PMC5397148 DOI: 10.1093/nar/gkx077] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 01/26/2017] [Indexed: 12/11/2022] Open
Abstract
Amino acid starvation activates the protein kinase Gcn2p, leading to changes in gene expression and translation. Gcn2p is activated by deacylated tRNA, which accumulates when tRNA aminoacylation is limited by lack of substrates or inhibition of synthesis. Pairing of amino acids and deacylated tRNAs is catalyzed by aminoacyl-tRNA synthetases, which use quality control pathways to maintain substrate specificity. Phenylalanyl-tRNA synthetase (PheRS) maintains specificity via an editing pathway that targets non-cognate Tyr-tRNAPhe. While the primary role of aaRS editing is to prevent misaminoacylation, we demonstrate editing of misaminoacylated tRNA is also required for detection of amino acid starvation by Gcn2p. Ablation of PheRS editing caused accumulation of Tyr-tRNAPhe (5%), but not deacylated tRNAPhe during amino acid starvation, limiting Gcn2p kinase activity and suppressing Gcn4p-dependent gene expression. While the PheRS-editing ablated strain grew 50% slower and displayed a 27-fold increase in the rate of mistranslation of Phe codons as Tyr compared to wild type, the increase in mistranslation was insufficient to activate an unfolded protein stress response. These findings show that during amino acid starvation a primary role of aaRS quality control is to help the cell mount an effective stress response, independent of the role of editing in maintaining translational accuracy.
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Affiliation(s)
- Kyle Mohler
- Department of Microbiology, The Ohio State University, 318 West 12th Avenue, Columbus, OH 43210, USA.,Center for RNA Biology, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA
| | - Rebecca Mann
- Department of Microbiology, The Ohio State University, 318 West 12th Avenue, Columbus, OH 43210, USA
| | - Tammy J Bullwinkle
- Department of Microbiology, The Ohio State University, 318 West 12th Avenue, Columbus, OH 43210, USA
| | - Kyle Hopkins
- Department of Microbiology, The Ohio State University, 318 West 12th Avenue, Columbus, OH 43210, USA
| | - Lin Hwang
- Pasarow Mass Spectrometry Laboratory, Semel Institute of Neuroscience and Human Behavior, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine at UCLA, 760 Westwood Plaza, Los Angeles, CA 90024, USA
| | - Noah M Reynolds
- Department of Microbiology, The Ohio State University, 318 West 12th Avenue, Columbus, OH 43210, USA
| | - Brandon Gassaway
- Department of Cellular & Molecular Physiology, Yale University School of Medicine, New Haven, CT 06520, USA.,Systems Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Hans-Rudolf Aerni
- Department of Cellular & Molecular Physiology, Yale University School of Medicine, New Haven, CT 06520, USA.,Systems Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Jesse Rinehart
- Department of Cellular & Molecular Physiology, Yale University School of Medicine, New Haven, CT 06520, USA.,Systems Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Michael Polymenis
- Biochemistry and Biophysics, Texas A&M University, Rm 333, 2128 TAMU, College Station, TX 77843, USA
| | - Kym Faull
- Pasarow Mass Spectrometry Laboratory, Semel Institute of Neuroscience and Human Behavior, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine at UCLA, 760 Westwood Plaza, Los Angeles, CA 90024, USA
| | - Michael Ibba
- Department of Microbiology, The Ohio State University, 318 West 12th Avenue, Columbus, OH 43210, USA.,Center for RNA Biology, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA
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6
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Translational fidelity and mistranslation in the cellular response to stress. Nat Microbiol 2017; 2:17117. [PMID: 28836574 DOI: 10.1038/nmicrobiol.2017.117] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 06/20/2017] [Indexed: 11/08/2022]
Abstract
Faithful translation of mRNA into the corresponding polypeptide is a complex multistep process, requiring accurate amino acid selection, transfer RNA (tRNA) charging and mRNA decoding on the ribosome. Key players in this process are aminoacyl-tRNA synthetases (aaRSs), which not only catalyse the attachment of cognate amino acids to their respective tRNAs, but also selectively hydrolyse incorrectly activated non-cognate amino acids and/or misaminoacylated tRNAs. This aaRS proofreading provides quality control checkpoints that exclude non-cognate amino acids during translation, and in so doing helps to prevent the formation of an aberrant proteome. However, despite the intrinsic need for high accuracy during translation, and the widespread evolutionary conservation of aaRS proofreading pathways, requirements for translation quality control vary depending on cellular physiology and changes in growth conditions, and translation errors are not always detrimental. Recent work has demonstrated that mistranslation can also be beneficial to cells, and some organisms have selected for a higher degree of mistranslation than others. The aims of this Review Article are to summarize the known mechanisms of protein translational fidelity and explore the diversity and impact of mistranslation events as a potentially beneficial response to environmental and cellular stress.
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