1
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Schuntermann DB, Jaskolowski M, Reynolds NM, Vargas-Rodriguez O. The central role of transfer RNAs in mistranslation. J Biol Chem 2024:107679. [PMID: 39154912 DOI: 10.1016/j.jbc.2024.107679] [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: 04/25/2024] [Revised: 07/22/2024] [Accepted: 07/23/2024] [Indexed: 08/20/2024] Open
Abstract
Transfer RNAs (tRNA) are essential small non-coding RNAs that enable the translation of genomic information into proteins in all life forms. The principal function of tRNAs is to bring amino acid building blocks to the ribosomes for protein synthesis. In the ribosome, tRNAs interact with messenger RNA (mRNA) to mediate the incorporation of amino acids into a growing polypeptide chain following the rules of the genetic code. Accurate interpretation of the genetic code requires tRNAs to carry amino acids matching their anticodon identity and decode the correct codon on mRNAs. Errors in these steps cause the translation of codons with the wrong amino acids (mistranslation), compromising the accurate flow of information from DNA to proteins. Accumulation of mutant proteins due to mistranslation jeopardizes proteostasis and cellular viability. However, the concept of mistranslation is evolving, with increasing evidence indicating that mistranslation can be used as a mechanism for survival and acclimatization to environmental conditions. In this review, we discuss the central role of tRNAs in modulating translational fidelity through their dynamic and complex interplay with translation factors. We summarize recent discoveries of mistranslating tRNAs and describe the underlying molecular mechanisms and the specific conditions and environments that enable and promote mistranslation.
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Affiliation(s)
- Dominik B Schuntermann
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Otto-Stern-Weg 5 HPK H10, 8093 Zurich, Switzerland
| | - Mateusz Jaskolowski
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Otto-Stern-Weg 5 HPK H10, 8093 Zurich, Switzerland
| | - Noah M Reynolds
- School of Integrated Sciences, Sustainability, and Public Health, University of Illinois Springfield, Springfield, Illinois, USA
| | - Oscar Vargas-Rodriguez
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, 263 Farmington Avenue, Farmington, Connecticut 06030-3305, USA.
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2
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Li ZH, Zhou XL. Eukaryotic AlaX provides multiple checkpoints for quality and quantity of aminoacyl-tRNAs in translation. Nucleic Acids Res 2024; 52:7825-7842. [PMID: 38869066 PMCID: PMC11260482 DOI: 10.1093/nar/gkae486] [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: 01/30/2024] [Accepted: 05/27/2024] [Indexed: 06/14/2024] Open
Abstract
Translational fidelity relies critically on correct aminoacyl-tRNA supply. The trans-editing factor AlaX predominantly hydrolyzes Ser-tRNAAla, functioning as a third sieve of alanyl-tRNA synthetase (AlaRS). Despite extensive studies in bacteria and archaea, the mechanism of trans-editing in mammals remains largely unknown. Here, we show that human AlaX (hAlaX), which is exclusively distributed in the cytoplasm, is an active trans-editing factor with strict Ser-specificity. In vitro, both hAlaX and yeast AlaX (ScAlaX) were capable of hydrolyzing nearly all Ser-mischarged cytoplasmic and mitochondrial tRNAs; and robustly edited cognate Ser-charged cytoplasmic and mitochondrial tRNASers. In vivo or cell-based studies revealed that loss of ScAlaX or hAlaX readily induced Ala- and Thr-to-Ser misincorporation. Overexpression of hAlaX impeded the decoding efficiency of consecutive Ser codons, implying its regulatory role in Ser codon decoding. Remarkably, yeast cells with ScAlaX deletion responded differently to translation inhibitor treatment, with a gain in geneticin resistance, but sensitivity to cycloheximide, both of which were rescued by editing-capable ScAlaX, alanyl- or threonyl-tRNA synthetase. Altogether, our results demonstrated the previously undescribed editing peculiarities of eukaryotic AlaXs, which provide multiple checkpoints to maintain the speed and fidelity of genetic decoding.
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Affiliation(s)
- Zi-Han Li
- Key Laboratory of RNA Innovation, Science and Engineering, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
| | - Xiao-Long Zhou
- Key Laboratory of RNA Innovation, Science and Engineering, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
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3
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Cruz E, Vargas-Rodriguez O. The role of tRNA identity elements in aminoacyl-tRNA editing. Front Microbiol 2024; 15:1437528. [PMID: 39101037 PMCID: PMC11295145 DOI: 10.3389/fmicb.2024.1437528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Accepted: 06/18/2024] [Indexed: 08/06/2024] Open
Abstract
The rules of the genetic code are implemented by the unique features that define the amino acid identity of each transfer RNA (tRNA). These features, known as "identity elements," mark tRNAs for recognition by aminoacyl-tRNA synthetases (ARSs), the enzymes responsible for ligating amino acids to tRNAs. While tRNA identity elements enable stringent substrate selectivity of ARSs, these enzymes are prone to errors during amino acid selection, leading to the synthesis of incorrect aminoacyl-tRNAs that jeopardize the fidelity of protein synthesis. Many error-prone ARSs have evolved specialized domains that hydrolyze incorrectly synthesized aminoacyl-tRNAs. These domains, known as editing domains, also exist as free-standing enzymes and, together with ARSs, safeguard protein synthesis fidelity. Here, we discuss how the same identity elements that define tRNA aminoacylation play an integral role in aminoacyl-tRNA editing, synergistically ensuring the correct translation of genetic information into proteins. Moreover, we review the distinct strategies of tRNA selection used by editing enzymes and ARSs to avoid undesired hydrolysis of correctly aminoacylated tRNAs.
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Affiliation(s)
| | - Oscar Vargas-Rodriguez
- Department of Molecular Biology and Biophysics, University of Connecticut School of Medicine, Farmington, CT, United States
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4
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Ward C, Beharry A, Tennakoon R, Rozik P, Wilhelm SDP, Heinemann IU, O’Donoghue P. Mechanisms and Delivery of tRNA Therapeutics. Chem Rev 2024; 124:7976-8008. [PMID: 38801719 PMCID: PMC11212642 DOI: 10.1021/acs.chemrev.4c00142] [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: 02/19/2024] [Revised: 04/11/2024] [Accepted: 04/26/2024] [Indexed: 05/29/2024]
Abstract
Transfer ribonucleic acid (tRNA) therapeutics will provide personalized and mutation specific medicines to treat human genetic diseases for which no cures currently exist. The tRNAs are a family of adaptor molecules that interpret the nucleic acid sequences in our genes into the amino acid sequences of proteins that dictate cell function. Humans encode more than 600 tRNA genes. Interestingly, even healthy individuals contain some mutant tRNAs that make mistakes. Missense suppressor tRNAs insert the wrong amino acid in proteins, and nonsense suppressor tRNAs read through premature stop signals to generate full length proteins. Mutations that underlie many human diseases, including neurodegenerative diseases, cancers, and diverse rare genetic disorders, result from missense or nonsense mutations. Thus, specific tRNA variants can be strategically deployed as therapeutic agents to correct genetic defects. We review the mechanisms of tRNA therapeutic activity, the nature of the therapeutic window for nonsense and missense suppression as well as wild-type tRNA supplementation. We discuss the challenges and promises of delivering tRNAs as synthetic RNAs or as gene therapies. Together, tRNA medicines will provide novel treatments for common and rare genetic diseases in humans.
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Affiliation(s)
- Cian Ward
- Department of Biochemistry, Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Aruun Beharry
- Department of Biochemistry, Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Rasangi Tennakoon
- Department of Biochemistry, Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Peter Rozik
- Department of Biochemistry, Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Sarah D. P. Wilhelm
- Department of Biochemistry, Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Ilka U. Heinemann
- Department of Biochemistry, Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Patrick O’Donoghue
- Department of Biochemistry, Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
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5
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Pranjic M, Spät P, Semanjski Curkovic M, Macek B, Gruic-Sovulj I, Mocibob M. Resilience and proteome response of Escherichia coli to high levels of isoleucine mistranslation. Int J Biol Macromol 2024; 262:130068. [PMID: 38340920 DOI: 10.1016/j.ijbiomac.2024.130068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 01/12/2024] [Accepted: 02/07/2024] [Indexed: 02/12/2024]
Abstract
Accurate pairing of amino acids and tRNAs is a prerequisite for faithful translation of genetic information during protein biosynthesis. Here we present the effects of proteome-wide mistranslation of isoleucine (Ile) by canonical valine (Val) or non-proteinogenic norvaline (Nva) in a genetically engineered Escherichia coli strain with an editing-defective isoleucyl-tRNA synthetase (IleRS). Editing-defective IleRS efficiently mischarges both Val and Nva to tRNAIle and impairs the translational accuracy of Ile decoding. When mistranslation was induced by the addition of Val or Nva to the growth medium, an Ile-to-Val or Ile-to-Nva substitution of up to 20 % was measured by high-resolution mass spectrometry. This mistranslation level impaired bacterial growth, promoted the SOS response and filamentation during stationary phase, caused global proteome dysregulation and upregulation of the cellular apparatus for maintaining proteostasis, including the major chaperones (GroES/EL, DnaK/DnaJ/GrpE and HtpG), the disaggregase ClpB and the proteases (Lon, HslV/HslU, ClpA, ClpS). The most important consequence of mistranslation appears to be non-specific protein aggregation, which is effectively counteracted by the disaggregase ClpB. Our data show that E. coli can sustain high isoleucine mistranslation levels and remain viable despite excessive protein aggregation and severely impaired translational fidelity. However, we show that inaccurate translation lowers bacterial resilience to heat stress and decreases bacterial survival at elevated temperatures.
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Affiliation(s)
- Marija Pranjic
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10 000 Zagreb, Croatia
| | - Philipp Spät
- Interfaculty Institute of Cell Biology, University of Tuebingen, Auf der Morgenstelle 15, 72076 Tuebingen, Germany
| | - Maja Semanjski Curkovic
- Interfaculty Institute of Cell Biology, University of Tuebingen, Auf der Morgenstelle 15, 72076 Tuebingen, Germany
| | - Boris Macek
- Interfaculty Institute of Cell Biology, University of Tuebingen, Auf der Morgenstelle 15, 72076 Tuebingen, Germany
| | - Ita Gruic-Sovulj
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10 000 Zagreb, Croatia.
| | - Marko Mocibob
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10 000 Zagreb, Croatia.
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6
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Bily TMI, Heinemann IU, O'Donoghue P. Missense suppressor tRNA therapeutics correct disease-causing alleles by misreading the genetic code. Mol Ther 2024; 32:273-274. [PMID: 38219738 PMCID: PMC10861964 DOI: 10.1016/j.ymthe.2024.01.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 01/02/2024] [Accepted: 01/02/2024] [Indexed: 01/16/2024] Open
Affiliation(s)
- Teija M I Bily
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Ilka U Heinemann
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Patrick O'Donoghue
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada; Department of Chemistry, The University of Western Ontario, London, ON N6A 5C1, Canada.
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7
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Gupta S, Jani J, Vijayasurya, Mochi J, Tabasum S, Sabarwal A, Pappachan A. Aminoacyl-tRNA synthetase - a molecular multitasker. FASEB J 2023; 37:e23219. [PMID: 37776328 DOI: 10.1096/fj.202202024rr] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 08/31/2023] [Accepted: 09/12/2023] [Indexed: 10/02/2023]
Abstract
Aminoacyl-tRNA synthetases (AaRSs) are valuable "housekeeping" enzymes that ensure the accurate transmission of genetic information in living cells, where they aminoacylated tRNA molecules with their cognate amino acid and provide substrates for protein biosynthesis. In addition to their translational or canonical function, they contribute to nontranslational/moonlighting functions, which are mediated by the presence of other domains on the proteins. This was supported by several reports which claim that AaRS has a significant role in gene transcription, apoptosis, translation, and RNA splicing regulation. Noncanonical/ nontranslational functions of AaRSs also include their roles in regulating angiogenesis, inflammation, cancer, and other major physio-pathological processes. Multiple AaRSs are also associated with a broad range of physiological and pathological processes; a few even serve as cytokines. Therefore, the multifunctional nature of AaRSs suggests their potential as viable therapeutic targets as well. Here, our discussion will encompass a range of noncanonical functions attributed to Aminoacyl-tRNA Synthetases (AaRSs), highlighting their links with a diverse array of human diseases.
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Affiliation(s)
- Swadha Gupta
- School of Life Sciences, Central University of Gujarat, Gandhinagar, India
| | - Jaykumar Jani
- School of Life Sciences, Central University of Gujarat, Gandhinagar, India
| | - Vijayasurya
- School of Life Sciences, Central University of Gujarat, Gandhinagar, India
| | - Jigneshkumar Mochi
- School of Life Sciences, Central University of Gujarat, Gandhinagar, India
| | - Saba Tabasum
- Dana Farber Cancer Institute, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Akash Sabarwal
- Harvard Medical School, Boston, Massachusetts, USA
- Boston Children's Hospital, Boston, Massachusetts, USA
| | - Anju Pappachan
- School of Life Sciences, Central University of Gujarat, Gandhinagar, India
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8
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Schuntermann DB, Fischer JT, Bile J, Gaier SA, Shelley BA, Awawdeh A, Jahn M, Hoffman KS, Westhof E, Söll D, Clarke CR, Vargas-Rodriguez O. Mistranslation of the genetic code by a new family of bacterial transfer RNAs. J Biol Chem 2023; 299:104852. [PMID: 37224963 PMCID: PMC10404621 DOI: 10.1016/j.jbc.2023.104852] [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: 04/05/2023] [Revised: 05/16/2023] [Accepted: 05/18/2023] [Indexed: 05/26/2023] Open
Abstract
The correct coupling of amino acids with transfer RNAs (tRNAs) is vital for translating genetic information into functional proteins. Errors during this process lead to mistranslation, where a codon is translated using the wrong amino acid. While unregulated and prolonged mistranslation is often toxic, growing evidence suggests that organisms, from bacteria to humans, can induce and use mistranslation as a mechanism to overcome unfavorable environmental conditions. Most known cases of mistranslation are caused by translation factors with poor substrate specificity or when substrate discrimination is sensitive to molecular changes such as mutations or posttranslational modifications. Here we report two novel families of tRNAs, encoded by bacteria from the Streptomyces and Kitasatospora genera, that adopted dual identities by integrating the anticodons AUU (for Asn) or AGU (for Thr) into the structure of a distinct proline tRNA. These tRNAs are typically encoded next to a full-length or truncated version of a distinct isoform of bacterial-type prolyl-tRNA synthetase. Using two protein reporters, we showed that these tRNAs translate asparagine and threonine codons with proline. Moreover, when expressed in Escherichia coli, the tRNAs cause varying growth defects due to global Asn-to-Pro and Thr-to-Pro mutations. Yet, proteome-wide substitutions of Asn with Pro induced by tRNA expression increased cell tolerance to the antibiotic carbenicillin, indicating that Pro mistranslation can be beneficial under certain conditions. Collectively, our results significantly expand the catalog of organisms known to possess dedicated mistranslation machinery and support the concept that mistranslation is a mechanism for cellular resiliency against environmental stress.
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Affiliation(s)
- Dominik B Schuntermann
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA; Department of Microbiology, Technical University of Braunschweig, Braunschweig, Germany
| | - Jonathan T Fischer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Jonmatthew Bile
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Sarah A Gaier
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Brett A Shelley
- Genetic Improvement for Fruits and Vegetables Lab, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, Maryland, USA
| | - Aya Awawdeh
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Martina Jahn
- Department of Microbiology, Technical University of Braunschweig, Braunschweig, Germany
| | | | - Eric Westhof
- Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg, France
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA; Department of Chemistry, Yale University, New Haven, Connecticut, USA.
| | - Christopher R Clarke
- Genetic Improvement for Fruits and Vegetables Lab, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, Maryland, USA
| | - Oscar Vargas-Rodriguez
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA.
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9
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Kalotay E, Klugmann M, Housley GD, Fröhlich D. Dominant aminoacyl-tRNA synthetase disorders: lessons learned from in vivo disease models. Front Neurosci 2023; 17:1182845. [PMID: 37274211 PMCID: PMC10234151 DOI: 10.3389/fnins.2023.1182845] [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: 03/09/2023] [Accepted: 04/05/2023] [Indexed: 06/06/2023] Open
Abstract
Aminoacyl-tRNA synthetases (ARSs) play an essential role in protein synthesis, being responsible for ligating tRNA molecules to their corresponding amino acids in a reaction known as 'tRNA aminoacylation'. Separate ARSs carry out the aminoacylation reaction in the cytosol and in mitochondria, and mutations in almost all ARS genes cause pathophysiology most evident in the nervous system. Dominant mutations in multiple cytosolic ARSs have been linked to forms of peripheral neuropathy including Charcot-Marie-Tooth disease, distal hereditary motor neuropathy, and spinal muscular atrophy. This review provides an overview of approaches that have been employed to model each of these diseases in vivo, followed by a discussion of the existing animal models of dominant ARS disorders and key mechanistic insights that they have provided. In summary, ARS disease models have demonstrated that loss of canonical ARS function alone cannot fully account for the observed disease phenotypes, and that pathogenic ARS variants cause developmental defects within the peripheral nervous system, despite a typically later onset of disease in humans. In addition, aberrant interactions between mutant ARSs and other proteins have been shown to contribute to the disease phenotypes. These findings provide a strong foundation for future research into this group of diseases, providing methodological guidance for studies on ARS disorders that currently lack in vivo models, as well as identifying candidate therapeutic targets.
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Affiliation(s)
- Elizabeth Kalotay
- Translational Neuroscience Facility and Department of Physiology, School of Biomedical Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Matthias Klugmann
- Translational Neuroscience Facility and Department of Physiology, School of Biomedical Sciences, University of New South Wales, Sydney, NSW, Australia
- Research Beyond Borders, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Gary D. Housley
- Translational Neuroscience Facility and Department of Physiology, School of Biomedical Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Dominik Fröhlich
- Translational Neuroscience Facility and Department of Physiology, School of Biomedical Sciences, University of New South Wales, Sydney, NSW, Australia
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10
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Hauth F, Funck D, Hartig JS. A standalone editing protein deacylates mischarged canavanyl-tRNAArg to prevent canavanine incorporation into proteins. Nucleic Acids Res 2023; 51:2001-2010. [PMID: 36626933 PMCID: PMC10018355 DOI: 10.1093/nar/gkac1197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 11/16/2022] [Accepted: 12/06/2022] [Indexed: 01/12/2023] Open
Abstract
Error-free translation of the genetic code into proteins is vitally important for all organisms. Therefore, it is crucial that the correct amino acids are loaded onto their corresponding tRNAs. This process is highly challenging when aminoacyl-tRNA-synthetases encounter structural analogues to the native substrate like the arginine antimetabolite canavanine. To circumvent deleterious incorporation due to tRNA mischarging, editing mechanisms have evolved. However, only for half of the tRNA synthetases, editing activity is known and only few specific standalone editing proteins have been described. Understanding the diverse mechanisms resulting in error-free protein synthesis is of great importance. Here, we report the discovery of a protein that is upregulated upon canavanine stimulation in bacteria that live associated with canavanine-producing plants. We demonstrate that it acts as standalone editing protein specifically deacylating canavanylated tRNAArg. We therefore propose canavanyl-tRNAArgdeacylase (CtdA) as systematic name. Knockout strains show severe growth defects in canavanine-containing media and incorporate high amounts of canavanine into the proteome. CtdA is frequently found under control of guanidine riboswitches, revealing a functional connection of canavanine and guanidine metabolisms. Our results are the first to show editing activity towards mischarged tRNAArg and add to the puzzle of how faithful translation is ensured in nature.
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Affiliation(s)
- Franziskus Hauth
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
- Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Dietmar Funck
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Jörg S Hartig
- To whom correspondence should be addressed. Tel: +49 7531 88 4575;
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11
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Romero Romero ML, Landerer C, Poehls J, Toth‐Petroczy A. Phenotypic mutations contribute to protein diversity and shape protein evolution. Protein Sci 2022; 31:e4397. [PMID: 36040266 PMCID: PMC9375231 DOI: 10.1002/pro.4397] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 06/14/2022] [Accepted: 07/04/2022] [Indexed: 11/16/2022]
Abstract
Errors in DNA replication generate genetic mutations, while errors in transcription and translation lead to phenotypic mutations. Phenotypic mutations are orders of magnitude more frequent than genetic ones, yet they are less understood. Here, we review the types of phenotypic mutations, their quantifications, and their role in protein evolution and disease. The diversity generated by phenotypic mutation can facilitate adaptive evolution. Indeed, phenotypic mutations, such as ribosomal frameshift and stop codon readthrough, sometimes serve to regulate protein expression and function. Phenotypic mutations have often been linked to fitness decrease and diseases. Thus, understanding the protein heterogeneity and phenotypic diversity caused by phenotypic mutations will advance our understanding of protein evolution and have implications on human health and diseases.
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Affiliation(s)
- Maria Luisa Romero Romero
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
- Center for Systems Biology DresdenDresdenGermany
| | - Cedric Landerer
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
- Center for Systems Biology DresdenDresdenGermany
| | - Jonas Poehls
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
- Center for Systems Biology DresdenDresdenGermany
| | - Agnes Toth‐Petroczy
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
- Center for Systems Biology DresdenDresdenGermany
- Cluster of Excellence Physics of LifeTU DresdenDresdenGermany
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12
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Byun JK, Vu JA, He SL, Jang JC, Musier-Forsyth K. Plant-exclusive domain of trans-editing enzyme ProXp-ala confers dimerization and enhanced tRNA binding. J Biol Chem 2022; 298:102255. [PMID: 35835222 PMCID: PMC9425024 DOI: 10.1016/j.jbc.2022.102255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 07/06/2022] [Accepted: 07/08/2022] [Indexed: 11/26/2022] Open
Abstract
Faithful translation of the genetic code is critical for the viability of all living organisms. The trans-editing enzyme ProXp-ala prevents Pro to Ala mutations during translation by hydrolyzing misacylated Ala-tRNAPro that has been synthesized by prolyl-tRNA synthetase. Plant ProXp-ala sequences contain a conserved C-terminal domain (CTD) that is absent in other organisms; the origin, structure, and function of this extra domain are unknown. To characterize the plant-specific CTD, we performed bioinformatics and computational analyses that provided a model consistent with a conserved α-helical structure. We also expressed and purified wildtype Arabidopsis thaliana (At) ProXp-ala in Escherichia coli, as well as variants lacking the CTD or containing only the CTD. Circular dichroism spectroscopy confirmed a loss of α-helical signal intensity upon CTD truncation. Size-exclusion chromatography with multiangle laser-light scattering revealed that wildtype At ProXp-ala was primarily dimeric and CTD truncation abolished dimerization in vitro. Furthermore, bimolecular fluorescence complementation assays in At protoplasts support a role for the CTD in homodimerization in vivo. The deacylation rate of Ala-tRNAPro by At ProXp-ala was also significantly reduced in the absence of the CTD, and kinetic assays indicated that the reduction in activity is primarily due to a tRNA binding defect. Overall, these results broaden our understanding of eukaryotic translational fidelity in the plant kingdom. Our study reveals that the plant-specific CTD plays a significant role in substrate binding and canonical editing function. Through its ability to facilitate protein-protein interactions, we propose the CTD may also provide expanded functional potential for trans-editing enzymes in plants.
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Affiliation(s)
- Jun-Kyu Byun
- Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA; Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - John A Vu
- Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA; Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Siou-Luan He
- Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA; Department of Horticulture and Crop Science and Center for Applied Plant Sciences, The Ohio State University, Columbus, Ohio, USA
| | - Jyan-Chyun Jang
- Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA; Department of Horticulture and Crop Science and Center for Applied Plant Sciences, The Ohio State University, Columbus, Ohio, USA.
| | - Karin Musier-Forsyth
- Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA; Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA.
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13
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Rozik P, Szabla R, Lant JT, Kiri R, Wright DE, Junop M, O'Donoghue P. A novel fluorescent reporter sensitive to serine mis-incorporation. RNA Biol 2022; 19:221-233. [PMID: 35167412 PMCID: PMC8855846 DOI: 10.1080/15476286.2021.2015173] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
High-fidelity translation was considered a requirement for living cells. The frozen accident theory suggested that any deviation from the standard genetic code should result in the production of so much mis-made and non-functional proteins that cells cannot remain viable. Studies in bacterial, yeast, and mammalian cells show that significant levels of mistranslation (1–10% per codon) can be tolerated or even beneficial under conditions of oxidative stress. Single tRNA mutants, which occur naturally in the human population, can lead to amino acid mis-incorporation at a codon or set of codons. The rate or level of mistranslation can be difficult or impossible to measure in live cells. We developed a novel red fluorescent protein reporter that is sensitive to serine (Ser) mis-incorporation at proline (Pro) codons. The mCherry Ser151Pro mutant is efficiently produced in Escherichia coli but non-fluorescent. We demonstrated in cells and with purified mCherry protein that the fluorescence of mCherry Ser151Pro is rescued by two different tRNASer gene variants that were mutated to contain the Pro (UGG) anticodon. Ser mis-incorporation was confirmed by mass spectrometry. Remarkably, E. coli tolerated mistranslation rates of ~10% per codon with negligible reduction in growth rate. Conformational sampling simulations revealed that the Ser151Pro mutant leads to significant changes in the conformational freedom of the chromophore precursor, which is indicative of a defect in chromophore maturation. Together our data suggest that the mCherry Ser151 mutants may be used to report Ser mis-incorporation at multiple other codons, further expanding the ability to measure mistranslation in living cells.
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Affiliation(s)
- Peter Rozik
- Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada
| | - Robert Szabla
- Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada
| | - Jeremy T Lant
- Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada
| | - Rashmi Kiri
- Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada
| | - David E Wright
- Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada
| | - Murray Junop
- Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada
| | - Patrick O'Donoghue
- Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada.,Department of Chemistry, The University of Western Ontario, London, Ontario, Canada
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14
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Han NC, Kavoor A, Ibba M. Characterizing the amino acid activation center of the naturally editing-deficient aminoacyl-tRNA synthetase PheRS in Mycoplasma mobile. FEBS Lett 2022; 596:947-957. [PMID: 35038769 DOI: 10.1002/1873-3468.14287] [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: 07/05/2021] [Revised: 01/06/2022] [Accepted: 01/09/2022] [Indexed: 11/09/2022]
Abstract
To ensure correct amino acids are incorporated during protein synthesis, aminoacyl-tRNA synthetases (aaRSs) employ proofreading mechanisms collectively referred to as editing. Although editing is important for viability, editing-deficient aaRSs have been identified in host-dependent organisms. In Mycoplasma mobile, editing-deficient PheRS and LeuRS have been identified. We characterized the amino acid activation site of MmPheRS and identified a previously unknown hyperaccurate mutation, L287F. Additionally, we report that m-Tyr, an oxidation byproduct of Phe which is toxic to editing-deficient cells, is poorly discriminated by MmPheRS activation and is not subjected to editing. Furthermore, expressing MmPheRS and the hyperaccurate variants renders Escherichia coli susceptible to m-Tyr stress, indicating that active site discrimination is insufficient in tolerating excess m-Tyr.
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Affiliation(s)
- Nien-Ching Han
- Department of Microbiology, The Ohio State University, Columbus, OH, 43220, USA
| | - Arundhati Kavoor
- Molecular, Cellular and Developmental Biology Program, The Ohio State University, Columbus, OH, 43220, USA
| | - Michael Ibba
- Department of Microbiology, The Ohio State University, Columbus, OH, 43220, USA.,Molecular, Cellular and Developmental Biology Program, The Ohio State University, Columbus, OH, 43220, USA.,Schmid College of Science and Technology, Chapman university, Orange, CA, 92866, USA
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15
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Berg MD, Isaacson JR, Cozma E, Genereaux J, Lajoie P, Villén J, Brandl CJ. Regulating Expression of Mistranslating tRNAs by Readthrough RNA Polymerase II Transcription. ACS Synth Biol 2021; 10:3177-3189. [PMID: 34726901 PMCID: PMC8765249 DOI: 10.1021/acssynbio.1c00461] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
![]()
Transfer RNA (tRNA)
variants that alter the genetic code increase
protein diversity and have many applications in synthetic biology.
Since the tRNA variants can cause a loss of proteostasis, regulating
their expression is necessary to achieve high levels of novel protein.
Mechanisms to positively regulate transcription with exogenous activator
proteins like those often used to regulate RNA polymerase II (RNAP
II)-transcribed genes are not applicable to tRNAs as their expression
by RNA polymerase III requires elements internal to the tRNA. Here,
we show that tRNA expression is repressed by overlapping transcription
from an adjacent RNAP II promoter. Regulating the expression of the
RNAP II promoter allows inverse regulation of the tRNA. Placing either
Gal4- or TetR–VP16-activated promoters downstream of a mistranslating
tRNASer variant that misincorporates serine at proline
codons in Saccharomyces cerevisiae allows
mistranslation at a level not otherwise possible because of the toxicity
of the unregulated tRNA. Using this inducible tRNA system, we explore
the proteotoxic effects of mistranslation on yeast cells. High levels
of mistranslation cause cells to arrest in the G1 phase. These cells
are impermeable to propidium iodide, yet growth is not restored upon
repressing tRNA expression. High levels of mistranslation increase
cell size and alter cell morphology. This regulatable tRNA expression
system can be applied to study how native tRNAs and tRNA variants
affect the proteome and other biological processes. Variations of
this inducible tRNA system should be applicable to other eukaryotic
cell types.
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Affiliation(s)
- Matthew D. Berg
- Department of Biochemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
| | - Joshua R. Isaacson
- Department of Biology, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Ecaterina Cozma
- Department of Biochemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Julie Genereaux
- Department of Biochemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Patrick Lajoie
- Department of Anatomy and Cell Biology, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Judit Villén
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
| | - Christopher J. Brandl
- Department of Biochemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
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16
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Sullivan JR, Lupien A, Kalthoff E, Hamela C, Taylor L, Munro KA, Schmeing TM, Kremer L, Behr MA. Efficacy of epetraborole against Mycobacterium abscessus is increased with norvaline. PLoS Pathog 2021; 17:e1009965. [PMID: 34637487 PMCID: PMC8535176 DOI: 10.1371/journal.ppat.1009965] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 10/22/2021] [Accepted: 09/23/2021] [Indexed: 12/16/2022] Open
Abstract
Mycobacterium abscessus is the most common rapidly growing non-tuberculous mycobacteria to cause pulmonary disease in patients with impaired lung function such as cystic fibrosis. M. abscessus displays high intrinsic resistance to common antibiotics and inducible resistance to macrolides like clarithromycin. As such, M. abscessus is clinically resistant to the entire regimen of front-line M. tuberculosis drugs, and treatment with antibiotics that do inhibit M. abscessus in the lab results in cure rates of 50% or less. Here, we identified epetraborole (EPT) from the MMV pandemic response box as an inhibitor against the essential protein leucyl-tRNA synthetase (LeuRS) in M. abscessus. EPT protected zebrafish from lethal M. abscessus infection and did not induce self-resistance nor against clarithromycin. Contrary to most antimycobacterials, the whole-cell activity of EPT was greater against M. abscessus than M. tuberculosis, but crystallographic and equilibrium binding data showed that EPT binds LeuRSMabs and LeuRSMtb with similar residues and dissociation constants. Since EPT-resistant M. abscessus mutants lost LeuRS editing activity, these mutants became susceptible to misaminoacylation with leucine mimics like the non-proteinogenic amino acid norvaline. Proteomic analysis revealed that when M. abscessus LeuRS mutants were fed norvaline, leucine residues in proteins were replaced by norvaline, inducing the unfolded protein response with temporal changes in expression of GroEL chaperonins and Clp proteases. This supports our in vitro data that supplementation of media with norvaline reduced the emergence of EPT mutants in both M. abscessus and M. tuberculosis. Furthermore, the combination of EPT and norvaline had improved in vivo efficacy compared to EPT in a murine model of M. abscessus infection. Our results emphasize the effectiveness of EPT against the clinically relevant cystic fibrosis pathogen M. abscessus, and these findings also suggest norvaline adjunct therapy with EPT could be beneficial for M. abscessus and other mycobacterial infections like tuberculosis. Current antimycobacterial drugs are inadequate to handle the increasing number of non-tuberculous mycobacteria infections that eclipse tuberculosis infections in many developed countries. Of particular importance for cystic fibrosis patients, Mycobacterium abscessus is notoriously difficult to treat where patients spend extended time on antibiotics with cure rates comparable to extreme drug resistant M. tuberculosis. Here, we identified epetraborole (EPT) with in vitro and in vivo activities against M. abscessus. We showed that EPT targets the editing domain of the leucyl-tRNA synthetase (LeuRS) and that escape mutants lost LeuRS editing activity, making these mutants susceptible to misaminoacylation with leucine mimics. Most importantly, combination therapy of EPT and norvaline limited the rate of EPT resistance in both M. abscessus and M. tuberculosis, and this was the first study to demonstrate improved in vivo efficacy of EPT and norvaline compared to EPT in a murine model of M. abscessus pulmonary infection. The demonstration of norvaline adjunct therapy with EPT for M. abscessus infections is promising for cystic fibrosis patients and could translate to other mycobacterial infections, such as tuberculosis.
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Affiliation(s)
- Jaryd R. Sullivan
- Department of Microbiology & Immunology, McGill University, Montréal, Canada
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montréal, Canada
- McGill International TB Centre, Montréal, Canada
| | - Andréanne Lupien
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montréal, Canada
- McGill International TB Centre, Montréal, Canada
| | - Elias Kalthoff
- Department of Biochemistry, McGill University, Montréal, Canada
- Centre de Recherche en Biologie Structural, McGill University, Montréal, Canada
| | - Claire Hamela
- Centre National de la Recherche Scientifique UMR 9004, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, Montpellier, France
| | - Lorne Taylor
- Clinical Proteomics Platform, Research Institute of the McGill University Health Centre, Montréal, Canada
| | - Kim A. Munro
- Department of Biochemistry, McGill University, Montréal, Canada
- Centre de Recherche en Biologie Structural, McGill University, Montréal, Canada
| | - T. Martin Schmeing
- Department of Biochemistry, McGill University, Montréal, Canada
- Centre de Recherche en Biologie Structural, McGill University, Montréal, Canada
| | - Laurent Kremer
- Centre National de la Recherche Scientifique UMR 9004, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, Montpellier, France
- INSERM, IRIM, Montpellier, France
| | - Marcel A. Behr
- Department of Microbiology & Immunology, McGill University, Montréal, Canada
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montréal, Canada
- McGill International TB Centre, Montréal, Canada
- Department of Medicine, McGill University Health Centre, Montréal, Canada
- * E-mail:
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17
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Ra D, Sa B, Sl B, Js M, Sj M, DA D, Ew S, O K, Eb B, Ad C, Vx T, Gg G, Pa C, Dc M, Wg B. Is Exposure to BMAA a Risk Factor for Neurodegenerative Diseases? A Response to a Critical Review of the BMAA Hypothesis. Neurotox Res 2021; 39:81-106. [PMID: 33547590 PMCID: PMC7904546 DOI: 10.1007/s12640-020-00302-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 10/19/2020] [Accepted: 10/20/2020] [Indexed: 12/15/2022]
Abstract
In a literature survey, Chernoff et al. (2017) dismissed the hypothesis that chronic exposure to β-N-methylamino-L-alanine (BMAA) may be a risk factor for progressive neurodegenerative disease. They question the growing scientific literature that suggests the following: (1) BMAA exposure causes ALS/PDC among the indigenous Chamorro people of Guam; (2) Guamanian ALS/PDC shares clinical and neuropathological features with Alzheimer's disease, Parkinson's disease, and ALS; (3) one possible mechanism for protein misfolds is misincorporation of BMAA into proteins as a substitute for L-serine; and (4) chronic exposure to BMAA through diet or environmental exposures to cyanobacterial blooms can cause neurodegenerative disease. We here identify multiple errors in their critique including the following: (1) their review selectively cites the published literature; (2) the authors reported favorably on HILIC methods of BMAA detection while the literature shows significant matrix effects and peak coelution in HILIC that may prevent detection and quantification of BMAA in cyanobacteria; (3) the authors build alternative arguments to the BMAA hypothesis, rather than explain the published literature which, to date, has been unable to refute the BMAA hypothesis; and (4) the authors erroneously attribute methods to incorrect studies, indicative of a failure to carefully consider all relevant publications. The lack of attention to BMAA research begins with the review's title which incorrectly refers to BMAA as a "non-essential" amino acid. Research regarding chronic exposure to BMAA as a cause of human neurodegenerative diseases is emerging and requires additional resources, validation, and research. Here, we propose strategies for improvement in the execution and reporting of analytical methods and the need for additional and well-executed inter-lab comparisons for BMAA quantitation. We emphasize the need for optimization and validation of analytical methods to ensure that they are fit-for-purpose. Although there remain gaps in the literature, an increasingly large body of data from multiple independent labs using orthogonal methods provides increasing evidence that chronic exposure to BMAA may be a risk factor for neurological illness.
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Affiliation(s)
- Dunlop Ra
- Brain Chemistry Labs, Institute for Ethnomedicine, Jackson, WY, USA.
| | - Banack Sa
- Brain Chemistry Labs, Institute for Ethnomedicine, Jackson, WY, USA
| | - Bishop Sl
- Lewis Research Group, Faculty of Science, University of Calgary, Alberta, Canada
| | - Metcalf Js
- Brain Chemistry Labs, Institute for Ethnomedicine, Jackson, WY, USA
| | - Murch Sj
- Department of Chemistry, University of British Columbia, Kelowna, BC, Canada
| | - Davis DA
- Department of Neurology, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Stommel Ew
- Department of Neurology, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
| | - Karlsson O
- Department of Environmental Science, Stockholm University, Stockholm, Sweden
| | - Brittebo Eb
- Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | | | - Tan Vx
- Department of Biological Sciences, Macquarie University Centre for Motor Neuron Disease Research, Macquarie University, Ryde, Australia
| | - Guillemin Gg
- Department of Biological Sciences, Macquarie University Centre for Motor Neuron Disease Research, Macquarie University, Ryde, Australia
| | - Cox Pa
- Brain Chemistry Labs, Institute for Ethnomedicine, Jackson, WY, USA
| | - Mash Dc
- Nova Southeastern University, Fort Lauderdale, FL, USA
| | - Bradley Wg
- Department of Neurology, Miller School of Medicine, University of Miami, Miami, FL, USA
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18
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Vargas-Rodriguez O, Bakhtina M, McGowan D, Abid J, Goto Y, Suga H, Musier-Forsyth K. Human trans-editing enzyme displays tRNA acceptor-stem specificity and relaxed amino acid selectivity. J Biol Chem 2020; 295:16180-16190. [PMID: 33051185 PMCID: PMC7705315 DOI: 10.1074/jbc.ra120.015981] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/06/2020] [Indexed: 01/20/2023] Open
Abstract
Accurate translation of genetic information into proteins is vital for cell sustainability. ProXp-ala prevents proteome-wide Pro-to-Ala mutations by hydrolyzing misacylated Ala-tRNAPro, which is synthesized by prolyl-tRNA synthetase. Bacterial ProXp-ala was previously shown to combine a size-based exclusion mechanism with conformational and chemical selection for the recognition of the alanyl moiety, whereas tRNAPro is selected via recognition of tRNA acceptor-stem elements G72 and A73. The identity of these critical bases changed during evolution with eukaryotic cytosolic tRNAPro possessing a cytosine at the corresponding positions. The mechanism by which eukaryotic ProXp-ala adapted to these changes remains unknown. In this work, recognition of the aminoacyl moiety and tRNA acceptor stem by human (Homo sapiens, or Hs) ProXp-ala was examined. Enzymatic assays revealed that Hs ProXp-ala requires C72 and C73 in the context of Hs cytosolic tRNAPro for efficient deacylation of mischarged Ala-tRNAPro The strong dependence on these bases prevents cross-species deacylation of bacterial Ala-tRNAPro or of Hs mitochondrial Ala-tRNAPro by the human enzyme. Similar to the bacterial enzyme, Hs ProXp-ala showed strong tRNA acceptor-stem recognition but differed in its amino acid specificity profile relative to bacterial ProXp-ala. Changes at conserved residues in both the Hs and bacterial ProXp-ala substrate-binding pockets modulated this specificity. These results illustrate how the mechanism of substrate selection diverged during the evolution of the ProXp-ala family, providing the first example of a trans-editing domain whose specificity evolved to adapt to changes in its tRNA substrate.
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Affiliation(s)
- Oscar Vargas-Rodriguez
- Department of Chemistry and Biochemistry and Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA
| | - Marina Bakhtina
- Department of Chemistry and Biochemistry and Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA
| | - Daniel McGowan
- Department of Chemistry and Biochemistry and Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA
| | - Jawad Abid
- Department of Chemistry and Biochemistry and Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA
| | - Yuki Goto
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Karin Musier-Forsyth
- Department of Chemistry and Biochemistry and Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA.
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19
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Chen H, Ercanbrack C, Wang T, Gan Q, Fan C. A Synthetic Reporter for Probing Mistranslation in Living Cells. Front Bioeng Biotechnol 2020; 8:623. [PMID: 32671035 PMCID: PMC7326783 DOI: 10.3389/fbioe.2020.00623] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 05/21/2020] [Indexed: 01/13/2023] Open
Abstract
Aminoacyl-tRNA synthetases (AARSs) play key roles in maintaining high fidelity of protein synthesis. They charge cognate tRNAs with corresponding amino acids and hydrolyze mischarged tRNAs by editing mechanisms. Impairment of AARS editing activities can reduce the accuracy of tRNA aminoacylation to produce mischarged tRNAs, which cause mistranslation and cell damages. To evaluate the mistranslation rate of threonine codons in living cells, in this study, we designed a quantitative reporter derived from the green fluorescent protein (GFP). The original GFP has multiple threonine codons which could affect the accuracy of measurement, so we generated a GFP variant containing only one threonine residue to specifically quantify mistranslation at the threonine codon. To validate, we applied this single-threonine GFP reporter to evaluate mistranslation at the threonine codon with mutations or modifications of threonine-tRNA synthetase and compared it with other methods of mistranslation evaluation, which showed that this reporter is reliable and facile to use.
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Affiliation(s)
- Hao Chen
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, United States
| | - Carson Ercanbrack
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR, United States
| | - Tony Wang
- Depratment of Biology, University of Arkansas, Fayetteville, AR, United States
| | - Qinglei Gan
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR, United States
| | - Chenguang Fan
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, United States.,Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR, United States
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20
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Weitzel CS, Li L, Zhang C, Eilts KK, Bretz NM, Gatten AL, Whitaker RJ, Martinis SA. Duplication of leucyl-tRNA synthetase in an archaeal extremophile may play a role in adaptation to variable environmental conditions. J Biol Chem 2020; 295:4563-4576. [PMID: 32102848 DOI: 10.1074/jbc.ra118.006481] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 02/25/2020] [Indexed: 12/23/2022] Open
Abstract
Aminoacyl-tRNA synthetases (aaRSs) are ancient enzymes that play a fundamental role in protein synthesis. They catalyze the esterification of specific amino acids to the 3'-end of their cognate tRNAs and therefore play a pivotal role in protein synthesis. Although previous studies suggest that aaRS-dependent errors in protein synthesis can be beneficial to some microbial species, evidence that reduced aaRS fidelity can be adaptive is limited. Using bioinformatics analyses, we identified two distinct leucyl-tRNA synthetase (LeuRS) genes within all genomes of the archaeal family Sulfolobaceae. Remarkably, one copy, designated LeuRS-I, had key amino acid substitutions within its editing domain that would be expected to disrupt hydrolytic editing of mischarged tRNALeu and to result in variation within the proteome of these extremophiles. We found that another copy, LeuRS-F, contains canonical active sites for aminoacylation and editing. Biochemical and genetic analyses of the paralogs within Sulfolobus islandicus supported the hypothesis that LeuRS-F, but not LeuRS-I, functions as an essential tRNA synthetase that accurately charges leucine to tRNALeu for protein translation. Although LeuRS-I was not essential, its expression clearly supported optimal S. islandicus growth. We conclude that LeuRS-I may have evolved to confer a selective advantage under the extreme and fluctuating environmental conditions characteristic of the volcanic hot springs in which these archaeal extremophiles reside.
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Affiliation(s)
| | - Li Li
- Department of Biochemistry, University of Illinois, Urbana, Illinois 61801.,Center for Biophysics and Quantitative Biology, University of Illinois, Urbana, Illinois 61801
| | - Changyi Zhang
- Department of Microbiology, University of Illinois, Urbana, Illinois 61801.,Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois 61801
| | - Kristen K Eilts
- Department of Chemistry, Illinois State University, Normal, Illinois 61761
| | - Nicholas M Bretz
- Department of Chemistry, Illinois State University, Normal, Illinois 61761
| | - Alex L Gatten
- Department of Biochemistry, University of Illinois, Urbana, Illinois 61801
| | - Rachel J Whitaker
- Department of Microbiology, University of Illinois, Urbana, Illinois 61801.,Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois 61801
| | - Susan A Martinis
- Department of Biochemistry, University of Illinois, Urbana, Illinois 61801.,Center for Biophysics and Quantitative Biology, University of Illinois, Urbana, Illinois 61801
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21
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Han NC, Bullwinkle TJ, Loeb KF, Faull KF, Mohler K, Rinehart J, Ibba M. The mechanism of β-N-methylamino-l-alanine inhibition of tRNA aminoacylation and its impact on misincorporation. J Biol Chem 2020. [DOI: 10.1016/s0021-9258(17)49898-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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22
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Han NC, Bullwinkle TJ, Loeb KF, Faull KF, Mohler K, Rinehart J, Ibba M. The mechanism of β- N-methylamino-l-alanine inhibition of tRNA aminoacylation and its impact on misincorporation. J Biol Chem 2019; 295:1402-1410. [PMID: 31862734 DOI: 10.1074/jbc.ra119.011714] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 12/10/2019] [Indexed: 11/06/2022] Open
Abstract
β-N-methylamino-l-alanine (BMAA) is a nonproteinogenic amino acid that has been associated with neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS) and Alzheimer's disease (AD). BMAA has been found in human protein extracts; however, the mechanism by which it enters the proteome is still unclear. It has been suggested that BMAA is misincorporated at serine codons during protein synthesis, but direct evidence of its cotranslational incorporation is currently lacking. Here, using LC-MS-purified BMAA and several biochemical assays, we sought to determine whether any aminoacyl-tRNA synthetase (aaRS) utilizes BMAA as a substrate for aminoacylation. Despite BMAA's previously predicted misincorporation at serine codons, following a screen for amino acid activation in ATP/PPi exchange assays, we observed that BMAA is not a substrate for human seryl-tRNA synthetase (SerRS). Instead, we observed that BMAA is a substrate for human alanyl-tRNA synthetase (AlaRS) and can form BMAA-tRNAAla by escaping from the intrinsic AlaRS proofreading activity. Furthermore, we found that BMAA inhibits both the cognate amino acid activation and the editing functions of AlaRS. Our results reveal that, in addition to being misincorporated during translation, BMAA may be able to disrupt the integrity of protein synthesis through multiple different mechanisms.
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Affiliation(s)
- Nien-Ching Han
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43220
| | - Tammy J Bullwinkle
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43220
| | - Kaeli F Loeb
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43220
| | - Kym F Faull
- Pasarow Mass Spectrometry Laboratory, Jane and Terry Semel Institute for Neuroscience and Human Behavior, Department of Psychiatry & Biobehavioral Sciences, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, California 90024-1759
| | - Kyle Mohler
- Department of Cellular and Molecular Physiology, Yale University, New Haven, Connecticut 06520.,Systems Biology Institute, Yale University, New Haven, Connecticut 06520
| | - Jesse Rinehart
- Department of Cellular and Molecular Physiology, Yale University, New Haven, Connecticut 06520.,Systems Biology Institute, Yale University, New Haven, Connecticut 06520
| | - Michael Ibba
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43220
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23
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Chen L, Tanimoto A, So BR, Bakhtina M, Magliery TJ, Wysocki VH, Musier-Forsyth K. Stoichiometry of triple-sieve tRNA editing complex ensures fidelity of aminoacyl-tRNA formation. Nucleic Acids Res 2019; 47:929-940. [PMID: 30418624 PMCID: PMC6344894 DOI: 10.1093/nar/gky1153] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 10/30/2018] [Indexed: 11/13/2022] Open
Abstract
Aminoacyl-tRNA synthetases catalyze the attachment of cognate amino acids onto tRNAs. To avoid mistranslation, editing mechanisms evolved to maintain tRNA aminoacylation fidelity. For instance, while rejecting the majority of non-cognate amino acids via discrimination in the synthetic active site, prolyl-tRNA synthetase (ProRS) misactivates and mischarges Ala and Cys, which are similar in size to cognate Pro. Ala-tRNAPro is specifically hydrolyzed by the editing domain of ProRS in cis, while YbaK, a free-standing editing domain, clears Cys-tRNAPro in trans. ProXp-ala is another editing domain that clears Ala-tRNAPro in trans. YbaK does not appear to possess tRNA specificity, readily deacylating Cys-tRNACysin vitro. We hypothesize that YbaK binds to ProRS to gain specificity for Cys-tRNAPro and avoid deacylation of Cys-tRNACys in the cell. Here, in vivo evidence for ProRS-YbaK interaction was obtained using a split-green fluorescent protein assay. Analytical ultracentrifugation and native mass spectrometry were used to investigate binary and ternary complex formation between ProRS, YbaK, and tRNAPro. Our combined results support the hypothesis that the specificity of YbaK toward Cys-tRNAPro is determined by the formation of a three-component complex with ProRS and tRNAPro and establish the stoichiometry of a 'triple-sieve' editing complex for the first time.
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Affiliation(s)
- Lin Chen
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA.,Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Akiko Tanimoto
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Byung Ran So
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Marina Bakhtina
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA.,Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Thomas J Magliery
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA.,Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Karin Musier-Forsyth
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA.,Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
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24
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Melnikov SV, van den Elzen A, Stevens DL, Thoreen CC, Söll D. Loss of protein synthesis quality control in host-restricted organisms. Proc Natl Acad Sci U S A 2018; 115:E11505-E11512. [PMID: 30455292 PMCID: PMC6298100 DOI: 10.1073/pnas.1815992115] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Intracellular organisms, such as obligate parasites and endosymbionts, typically possess small genomes due to continuous genome decay caused by an environment with alleviated natural selection. Previously, a few species with highly reduced genomes, including the intracellular pathogens Mycoplasma and Microsporidia, have been shown to carry degenerated editing domains in aminoacyl-tRNA synthetases. These defects in the protein synthesis machinery cause inaccurate translation of the genetic code, resulting in significant statistical errors in protein sequences that are thought to help parasites to escape immune response of a host. In this study we analyzed 10,423 complete bacterial genomes to assess conservation of the editing domains in tRNA synthetases, including LeuRS, IleRS, ValRS, ThrRS, AlaRS, and PheRS. We found that, while the editing domains remain intact in free-living species, they are degenerated in the overwhelming majority of host-restricted bacteria. Our work illustrates that massive genome erosion triggered by an intracellular lifestyle eradicates one of the most fundamental components of a living cell: the system responsible for proofreading of amino acid selection for protein synthesis. This finding suggests that inaccurate translation of the genetic code might be a general phenomenon among intercellular organisms with reduced genomes.
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Affiliation(s)
- Sergey V Melnikov
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511
| | - Antonia van den Elzen
- Department of Cellular and Molecular Physiology, Yale University, New Haven, CT 06520
| | - David L Stevens
- Department of Chemistry, Yale University, New Haven, CT 06511
| | - Carson C Thoreen
- Department of Cellular and Molecular Physiology, Yale University, New Haven, CT 06520
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511;
- Department of Chemistry, Yale University, New Haven, CT 06511
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25
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Zimmerman SM, Kon Y, Hauke AC, Ruiz BY, Fields S, Phizicky EM. Conditional accumulation of toxic tRNAs to cause amino acid misincorporation. Nucleic Acids Res 2018; 46:7831-7843. [PMID: 30007351 PMCID: PMC6125640 DOI: 10.1093/nar/gky623] [Citation(s) in RCA: 22] [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: 05/18/2018] [Revised: 06/22/2018] [Accepted: 07/01/2018] [Indexed: 12/16/2022] Open
Abstract
To develop a system for conditional amino acid misincorporation, we engineered tRNAs in the yeast Saccharomyces cerevisiae to be substrates of the rapid tRNA decay (RTD) pathway, such that they accumulate when RTD is turned off. We used this system to test the effects on growth of a library of tRNASer variants with all possible anticodons, and show that many are lethal when RTD is inhibited and the tRNA accumulates. Using mass spectrometry, we measured serine misincorporation in yeast containing each of six tRNA variants, and for five of them identified hundreds of peptides with serine substitutions at the targeted amino acid sites. Unexpectedly, we found that there is not a simple correlation between toxicity and the level of serine misincorporation; in particular, high levels of serine misincorporation can occur at cysteine residues without obvious growth defects. We also showed that toxic tRNAs can be used as a tool to identify sequence variants that reduce tRNA function. Finally, we generalized this method to another tRNA species, and generated conditionally toxic tRNATyr variants in a similar manner. This method should facilitate the study of tRNA biology and provide a tool to probe the effects of amino acid misincorporation on cellular physiology.
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Affiliation(s)
| | - Yoshiko Kon
- Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester School of Medicine, Rochester, NY 14642, USA
| | - Alayna C Hauke
- Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester School of Medicine, Rochester, NY 14642, USA
| | - Bianca Y Ruiz
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Stanley Fields
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Eric M Phizicky
- Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester School of Medicine, Rochester, NY 14642, USA
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26
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Chakraborty S, Ganguli S, Chowdhury A, Ibba M, Banerjee R. Reversible inactivation of yeast mitochondrial phenylalanyl-tRNA synthetase under oxidative stress. Biochim Biophys Acta Gen Subj 2018; 1862:1801-1809. [DOI: 10.1016/j.bbagen.2018.04.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 04/18/2018] [Accepted: 04/27/2018] [Indexed: 12/28/2022]
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27
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Vo MN, Terrey M, Lee JW, Roy B, Moresco JJ, Sun L, Fu H, Liu Q, Weber TG, Yates JR, Fredrick K, Schimmel P, Ackerman SL. ANKRD16 prevents neuron loss caused by an editing-defective tRNA synthetase. Nature 2018; 557:510-515. [PMID: 29769718 PMCID: PMC5973781 DOI: 10.1038/s41586-018-0137-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Accepted: 04/09/2018] [Indexed: 11/29/2022]
Abstract
Editing domains of aminoacyl tRNA synthetases correct tRNA charging errors to maintain translational fidelity. A mutation in the editing domain of alanyl tRNA synthetase (AlaRS) in Aars sti mutant mice results in an increase in the production of serine-mischarged tRNAAla and the degeneration of cerebellar Purkinje cells. Here, using positional cloning, we identified Ankrd16, a gene that acts epistatically with the Aars sti mutation to attenuate neurodegeneration. ANKRD16, a vertebrate-specific protein that contains ankyrin repeats, binds directly to the catalytic domain of AlaRS. Serine that is misactivated by AlaRS is captured by the lysine side chains of ANKRD16, which prevents the charging of serine adenylates to tRNAAla and precludes serine misincorporation in nascent peptides. The deletion of Ankrd16 in the brains of Aarssti/sti mice causes widespread protein aggregation and neuron loss. These results identify an amino-acid-accepting co-regulator of tRNA synthetase editing as a new layer of the machinery that is essential to the prevention of severe pathologies that arise from defects in editing.
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Affiliation(s)
- My-Nuong Vo
- The Skaggs Institute for Chemical Biology, Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA, USA
| | - Markus Terrey
- Howard Hughes Medical Institute, Department of Cellular and Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Section of Neurobiology, University of California San Diego, La Jolla, CA, USA
- Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, ME, USA
- The Jackson Laboratory, Bar Harbor, ME, USA
| | - Jeong Woong Lee
- The Jackson Laboratory, Bar Harbor, ME, USA
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Bappaditya Roy
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - James J Moresco
- Department of Chemical Physiology, Scripps Research Institute, La Jolla, CA, USA
- Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Litao Sun
- The Skaggs Institute for Chemical Biology, Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA, USA
| | - Hongjun Fu
- The Jackson Laboratory, Bar Harbor, ME, USA
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY, USA
| | - Qi Liu
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH, USA
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH, USA
- Sharklet Technologies, Aurora, CO, USA
| | | | - John R Yates
- Department of Chemical Physiology, Scripps Research Institute, La Jolla, CA, USA
| | - Kurt Fredrick
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Paul Schimmel
- The Skaggs Institute for Chemical Biology, Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA, USA.
- The Scripps Research Institute, Jupiter, FL, USA.
| | - Susan L Ackerman
- Howard Hughes Medical Institute, Department of Cellular and Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, CA, USA.
- Section of Neurobiology, University of California San Diego, La Jolla, CA, USA.
- Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, ME, USA.
- The Jackson Laboratory, Bar Harbor, ME, USA.
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28
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Schmitt MA, Biddle W, Fisk JD. Mapping the Plasticity of the Escherichia coli Genetic Code with Orthogonal Pair-Directed Sense Codon Reassignment. Biochemistry 2018; 57:2762-2774. [PMID: 29668270 DOI: 10.1021/acs.biochem.8b00177] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The relative quantitative importance of the factors that determine the fidelity of translation is largely unknown, which makes predicting the extent to which the degeneracy of the genetic code can be broken challenging. Our strategy of using orthogonal tRNA/aminoacyl tRNA synthetase pairs to precisely direct the incorporation of a single amino acid in response to individual sense and nonsense codons provides a suite of related data with which to examine the plasticity of the code. Each directed sense codon reassignment measurement is an in vivo competition experiment between the introduced orthogonal translation machinery and the natural machinery in Escherichia coli. This report discusses 20 new, related genetic codes, in which a targeted E. coli wobble codon is reassigned to tyrosine utilizing the orthogonal tyrosine tRNA/aminoacyl tRNA synthetase pair from Methanocaldococcus jannaschii. One at a time, reassignment of each targeted sense codon to tyrosine is quantified in cells by measuring the fluorescence of GFP variants in which the essential tyrosine residue is encoded by a non-tyrosine codon. Significantly, every wobble codon analyzed may be partially reassigned with efficiencies ranging from 0.8 to 41%. The accumulation of the suite of data enables a qualitative dissection of the relative importance of the factors affecting the fidelity of translation. While some correlation was observed between sense codon reassignment and either competing endogenous tRNA abundance or changes in aminoacylation efficiency of the altered orthogonal system, no single factor appears to predominately drive translational fidelity. Evaluation of relative cellular fitness in each of the 20 quantitatively characterized proteome-wide tyrosine substitution systems suggests that at a systems level, E. coli is robust to missense mutations.
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Affiliation(s)
- Margaret A Schmitt
- Department of Chemical and Biological Engineering , Colorado State University , Fort Collins , Colorado 80523 , United States
| | - Wil Biddle
- Department of Chemistry , Colorado State University , Fort Collins , Colorado 80523 , United States
| | - John D Fisk
- Department of Chemical and Biological Engineering , Colorado State University , Fort Collins , Colorado 80523 , United States.,Department of Chemistry , Colorado State University , Fort Collins , Colorado 80523 , United States.,School of Biomedical Engineering , Colorado State University , Fort Collins , Colorado 80523 , United States
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29
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Lant JT, Berg MD, Sze DHW, Hoffman KS, Akinpelu IC, Turk MA, Heinemann IU, Duennwald ML, Brandl CJ, O'Donoghue P. Visualizing tRNA-dependent mistranslation in human cells. RNA Biol 2017; 15:567-575. [PMID: 28933646 DOI: 10.1080/15476286.2017.1379645] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
High-fidelity translation and a strictly accurate proteome were originally assumed as essential to life and cellular viability. Yet recent studies in bacteria and eukaryotic model organisms suggest that proteome-wide mistranslation can provide selective advantages and is tolerated in the cell at higher levels than previously thought (one error in 6.9 × 10-4 in yeast) with a limited impact on phenotype. Previously, we selected a tRNAPro containing a single mutation that induces mistranslation with alanine at proline codons in yeast. Yeast tolerate the mistranslation by inducing a heat-shock response and through the action of the proteasome. Here we found a homologous human tRNAPro (G3:U70) mutant that is not aminoacylated with proline, but is an efficient alanine acceptor. In live human cells, we visualized mistranslation using a green fluorescent protein reporter that fluoresces in response to mistranslation at proline codons. In agreement with measurements in yeast, quantitation based on the GFP reporter suggested a mistranslation rate of up to 2-5% in HEK 293 cells. Our findings suggest a stress-dependent phenomenon where mistranslation levels increased during nutrient starvation. Human cells did not mount a detectable heat-shock response and tolerated this level of mistranslation without apparent impact on cell viability. Because humans encode ∼600 tRNA genes and the natural population has greater tRNA sequence diversity than previously appreciated, our data also demonstrate a cell-based screen with the potential to elucidate mutations in tRNAs that may contribute to or alleviate disease.
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Affiliation(s)
- Jeremy T Lant
- a Department of Biochemistry , The University of Western Ontario , London , ON , Canada
| | - Matthew D Berg
- a Department of Biochemistry , The University of Western Ontario , London , ON , Canada
| | - Daniel H W Sze
- a Department of Biochemistry , The University of Western Ontario , London , ON , Canada
| | - Kyle S Hoffman
- a Department of Biochemistry , The University of Western Ontario , London , ON , Canada
| | | | - Matthew A Turk
- a Department of Biochemistry , The University of Western Ontario , London , ON , Canada
| | - Ilka U Heinemann
- a Department of Biochemistry , The University of Western Ontario , London , ON , Canada
| | - Martin L Duennwald
- b Department of Pathology , The University of Western Ontario , London , ON , Canada
| | - Christopher J Brandl
- a Department of Biochemistry , The University of Western Ontario , London , ON , Canada
| | - Patrick O'Donoghue
- a Department of Biochemistry , The University of Western Ontario , London , ON , Canada.,c Department of Chemistry , The University of Western Ontario , London , ON , Canada
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30
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Bacusmo JM, Kuzmishin AB, Cantara WA, Goto Y, Suga H, Musier-Forsyth K. Quality control by trans-editing factor prevents global mistranslation of non-protein amino acid α-aminobutyrate. RNA Biol 2017; 15:576-585. [PMID: 28737471 DOI: 10.1080/15476286.2017.1353846] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
Accuracy in protein biosynthesis is maintained through multiple pathways, with a critical checkpoint occurring at the tRNA aminoacylation step catalyzed by aminoacyl-tRNA synthetases (ARSs). In addition to the editing functions inherent to some synthetases, single-domain trans-editing factors, which are structurally homologous to ARS editing domains, have evolved as alternative mechanisms to correct mistakes in aminoacyl-tRNA synthesis. To date, ARS-like trans-editing domains have been shown to act on specific tRNAs that are mischarged with genetically encoded amino acids. However, structurally related non-protein amino acids are ubiquitous in cells and threaten the proteome. Here, we show that a previously uncharacterized homolog of the bacterial prolyl-tRNA synthetase (ProRS) editing domain edits a known ProRS aminoacylation error, Ala-tRNAPro, but displays even more robust editing of tRNAs misaminoacylated with the non-protein amino acid α-aminobutyrate (2-aminobutyrate, Abu) in vitro and in vivo. Our results indicate that editing by trans-editing domains such as ProXp-x studied here may offer advantages to cells, especially under environmental conditions where concentrations of non-protein amino acids may challenge the substrate specificity of ARSs.
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Affiliation(s)
- Jo Marie Bacusmo
- a Department of Chemistry and Biochemistry , The Ohio State University , Columbus , OH , USA.,b Center for RNA Biology , The Ohio State University , Columbus , OH , USA
| | - Alexandra B Kuzmishin
- a Department of Chemistry and Biochemistry , The Ohio State University , Columbus , OH , USA.,b Center for RNA Biology , The Ohio State University , Columbus , OH , USA
| | - William A Cantara
- a Department of Chemistry and Biochemistry , The Ohio State University , Columbus , OH , USA.,b Center for RNA Biology , The Ohio State University , Columbus , OH , USA
| | - Yuki Goto
- c Department of Chemistry , Graduate School of Science, The University of Tokyo , Bunkyo , Tokyo , Japan
| | - Hiroaki Suga
- c Department of Chemistry , Graduate School of Science, The University of Tokyo , Bunkyo , Tokyo , Japan
| | - Karin Musier-Forsyth
- a Department of Chemistry and Biochemistry , The Ohio State University , Columbus , OH , USA.,b Center for RNA Biology , The Ohio State University , Columbus , OH , USA
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31
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Peng S, Chu Z, Lu J, Li D, Wang Y, Yang S, Zhang Y. Heterologous Expression of Chaperones from Hyperthermophilic Archaea Inhibits Aminoglycoside-Induced Protein Misfolding in Escherichia coli. BIOCHEMISTRY (MOSCOW) 2017; 82:1169-1175. [PMID: 29037137 DOI: 10.1134/s0006297917100091] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Aminoglycoside antibiotics affect protein translation fidelity and lead to protein aggregation and an increase in intracellular oxidative stress level as well. The overexpression of the chaperonin GroEL/GroES system promotes short-term tolerance to aminoglycosides in Escherichia coli. Here, we demonstrated that the coexpression of prefoldin or Hsp60 originating from the hyperthermophilic archaeon Pyrococcus furiosus in E. coli cells can rescue cell growth and inhibit protein aggregation induced by streptomycin exposure. The results of our study show that hyperthermophilic chaperones endow E. coli with a higher tolerance to streptomycin than the GroEL/GroES system, and that they exert better effects on the reduction of intracellular protein misfolding, indicating that these chaperones have unique features and functions.
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Affiliation(s)
- S Peng
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China.
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32
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Ji QQ, Fang ZP, Ye Q, Chi CW, Wang ED. Self-protective responses to norvaline-induced stress in a leucyl-tRNA synthetase editing-deficient yeast strain. Nucleic Acids Res 2017; 45:7367-7381. [PMID: 28575390 PMCID: PMC5499588 DOI: 10.1093/nar/gkx487] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 05/24/2017] [Indexed: 12/23/2022] Open
Abstract
The editing function of aminoacyl-tRNA synthetases (aaRSs) is indispensible for formation of the correct aminoacyl-tRNAs. Editing deficiency may lead to growth inhibition and the pathogenesis of various diseases. Herein, we confirmed that norvaline (Nva) but not isoleucine or valine is the major threat to the editing function of Saccharomyces cerevisiae leucyl-tRNA synthetase (ScLeuRS), both in vitro and in vivo. Nva could be misincorporated into the proteome of the LeuRS editing-deficient yeast strain (D419A/ScΔleuS), potentially resulting in dysfunctional protein folding and growth delay. Furthermore, the exploration of the Nva-induced intracellular stress response mechanism in D419A/ScΔleuS revealed that Hsp70 chaperones were markedly upregulated in response to the potential protein misfolding. Additionally, proline (Pro), glutamate (Glu) and glutamine (Gln), which may accumulate due to the conversion of Nva, collectively contributed to the reduction of reactive oxygen species (ROS) levels in Nva-treated D419A/ScΔleuS cells. In conclusion, our study highlights the significance of the editing function of LeuRS and provides clues for understanding the intracellular stress protective mechanisms that are triggered in aaRS editing-deficient organisms.
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Affiliation(s)
- Quan-Quan Ji
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, P. R. China
| | - Zhi-Peng Fang
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, P. R. China
| | - Qing Ye
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, P. R. China
| | - Cheng-Wu Chi
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, P. R. China
| | - En-Duo Wang
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, P. R. China.,School of Life Science and Technology, Shanghai Tech University, 100 Haike Road, Shanghai 201210, P. R. China
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33
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Ye Q, Ji QQ, Yan W, Yang F, Wang ED. Acetylation of lysine ϵ-amino groups regulates aminoacyl-tRNA synthetase activity in Escherichia coli. J Biol Chem 2017; 292:10709-10722. [PMID: 28455447 DOI: 10.1074/jbc.m116.770826] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 04/16/2017] [Indexed: 11/06/2022] Open
Abstract
Previous proteomic analyses have shown that aminoacyl-tRNA synthetases in many organisms can be modified by acetylation of Lys. In this present study, leucyl-tRNA synthetase and arginyl-tRNA synthetase from Escherichia coli (EcLeuRS and EcArgRS) were overexpressed and purified and found to be acetylated on Lys residues by MS. Gln scanning mutagenesis revealed that Lys619, Lys624, and Lys809 in EcLeuRS and Lys126 and Lys408 in EcArgRS might play important roles in enzyme activity. Furthermore, we utilized a novel protein expression system to obtain enzymes harboring acetylated Lys at specific sites and investigated their catalytic activity. Acetylation of these Lys residues could affect their aminoacylation activity by influencing amino acid activation and/or the affinity for tRNA. In vitro assays showed that acetyl-phosphate nonenzymatically acetylates EcLeuRS and EcArgRS and suggested that the sirtuin class deacetylase CobB might regulate acetylation of these two enzymes. These findings imply a potential regulatory role for Lys acetylation in controlling the activity of aminoacyl-tRNA synthetases and thus protein synthesis.
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Affiliation(s)
- Qing Ye
- From the State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Science, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China and
| | - Quan-Quan Ji
- From the State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Science, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China and
| | - Wei Yan
- From the State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Science, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China and
| | - Fang Yang
- From the State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Science, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China and
| | - En-Duo Wang
- From the State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Science, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China and .,the School of Life Science and Technology, Shanghai Tech University, Shanghai 201210, China
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34
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Shen DL, Liu TW, Zandberg W, Clark T, Eskandari R, Alteen MG, Tan HY, Zhu Y, Cecioni S, Vocadlo D. Catalytic Promiscuity of O-GlcNAc Transferase Enables Unexpected Metabolic Engineering of Cytoplasmic Proteins with 2-Azido-2-deoxy-glucose. ACS Chem Biol 2017; 12:206-213. [PMID: 27935279 DOI: 10.1021/acschembio.6b00876] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
O-GlcNAc transferase (OGT) catalyzes the installation of N-acetylglucosamine (GlcNAc) O-linked to nucleocytoplasmic proteins (O-GlcNAc) within multicellular eukaryotes. OGT shows surprising tolerance for structural changes in the sugar component of its nucleotide sugar donor substrate, uridine diphosphate N-acetylglucosamine (UDP-GlcNAc). Here, we find that OGT uses UDP-glucose to install O-linked glucose (O-Glc) onto proteins only 25-fold less efficiently than O-GlcNAc. Spurred by this observation, we show that OGT transfers 2-azido-2-deoxy-d-glucose (GlcAz) in vitro from UDP-GlcAz to proteins. Further, feeding cells with per-O-acetyl GlcAz (AcGlcAz), in combination with inhibition or inducible knockout of OGT, shows OGT-dependent modification of nuclear and cytoplasmic proteins with O-GlcAz as detected using microscopy, immunoblot, and proteomics. We find that O-GlcAz is reversible within cells, and an unidentified cellular enzyme exists to cleave O-Glc that can also process O-GlcAz. We anticipate that AcGlcAz will prove to be a useful tool to study the O-GlcNAc modification. We also speculate that, given the high concentration of UDP-Glc within certain mammalian tissues, O-Glc may exist within mammals and serve as a physiologically relevant modification.
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Affiliation(s)
- David L. Shen
- Department
of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
- Department
of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Ta-Wei Liu
- Department
of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
- Department
of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Wesley Zandberg
- Department
of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Tom Clark
- Department
of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Razieh Eskandari
- Department
of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Matthew G. Alteen
- Department
of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Hong Yee Tan
- Department
of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Yanping Zhu
- Department
of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
- Department
of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Samy Cecioni
- Department
of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - David Vocadlo
- Department
of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
- Department
of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
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35
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Rewiring protein synthesis: From natural to synthetic amino acids. Biochim Biophys Acta Gen Subj 2017; 1861:3024-3029. [PMID: 28095316 DOI: 10.1016/j.bbagen.2017.01.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 01/11/2017] [Accepted: 01/12/2017] [Indexed: 11/21/2022]
Abstract
BACKGROUND The protein synthesis machinery uses 22 natural amino acids as building blocks that faithfully decode the genetic information. Such fidelity is controlled at multiple steps and can be compromised in nature and in the laboratory to rewire protein synthesis with natural and synthetic amino acids. SCOPE OF REVIEW This review summarizes the major quality control mechanisms during protein synthesis, including aminoacyl-tRNA synthetases, elongation factors, and the ribosome. We will discuss evolution and engineering of such components that allow incorporation of natural and synthetic amino acids at positions that deviate from the standard genetic code. MAJOR CONCLUSIONS The protein synthesis machinery is highly selective, yet not fixed, for the correct amino acids that match the mRNA codons. Ambiguous translation of a codon with multiple amino acids or complete reassignment of a codon with a synthetic amino acid diversifies the proteome. GENERAL SIGNIFICANCE Expanding the genetic code with synthetic amino acids through rewiring protein synthesis has broad applications in synthetic biology and chemical biology. Biochemical, structural, and genetic studies of the translational quality control mechanisms are not only crucial to understand the physiological role of translational fidelity and evolution of the genetic code, but also enable us to better design biological parts to expand the proteomes of synthetic organisms. This article is part of a Special Issue entitled "Biochemistry of Synthetic Biology - Recent Developments" Guest Editor: Dr. Ilka Heinemann and Dr. Patrick O'Donoghue.
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36
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Schwartz MH, Pan T. Function and origin of mistranslation in distinct cellular contexts. Crit Rev Biochem Mol Biol 2017; 52:205-219. [PMID: 28075177 DOI: 10.1080/10409238.2016.1274284] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Mistranslation describes errors during protein synthesis that prevent the amino acid sequences specified in the genetic code from being reflected within proteins. For a long time, mistranslation has largely been considered an aberrant cellular process that cells actively avoid at all times. However, recent evidence has demonstrated that cells from all three domains of life not only tolerate certain levels and forms of mistranslation, but actively induce mistranslation under certain circumstances. To this end, dedicated biological mechanisms have recently been found to reduce translational fidelity, which indicates that mistranslation is not exclusively an erroneous process and can even benefit cells in particular cellular contexts. There currently exists a spectrum of mistranslational processes that differ not only in their origins, but also in their molecular and cellular effects. These findings suggest that the optimal degree of translational fidelity largely depends on a specific cellular context. This review aims to conceptualize the basis and functional consequence of the diverse types of mistranslation that have been described so far.
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Affiliation(s)
- Michael H Schwartz
- a Department of Biochemistry and Molecular Biology , University of Chicago, Chicago , IL , USA
| | - Tao Pan
- a Department of Biochemistry and Molecular Biology , University of Chicago, Chicago , IL , USA
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37
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Zhou XL, Chen Y, Fang ZP, Ruan ZR, Wang Y, Liu RJ, Xue MQ, Wang ED. Translational Quality Control by Bacterial Threonyl-tRNA Synthetases. J Biol Chem 2016; 291:21208-21221. [PMID: 27542414 DOI: 10.1074/jbc.m116.740472] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Indexed: 11/06/2022] Open
Abstract
Translational fidelity mediated by aminoacyl-tRNA synthetases ensures the generation of the correct aminoacyl-tRNAs, which is critical for most species. Threonyl-tRNA synthetase (ThrRS) contains multiple domains, including an N2 editing domain. Of the ThrRS domains, N1 is the last to be assigned a function. Here, we found that ThrRSs from Mycoplasma species exhibit differences in their domain composition and editing active sites compared with the canonical ThrRSs. The Mycoplasma mobile ThrRS, the first example of a ThrRS naturally lacking the N1 domain, displays efficient post-transfer editing activity. In contrast, the Mycoplasma capricolum ThrRS, which harbors an N1 domain and a degenerate N2 domain, is editing-defective. Only editing-capable ThrRSs were able to support the growth of a yeast thrS deletion strain (ScΔthrS), thus suggesting that ScΔthrS is an excellent tool for studying the in vivo editing of introduced bacterial ThrRSs. On the basis of the presence or absence of an N1 domain, we further revealed the crucial importance of the only absolutely conserved residue within the N1 domain in regulating editing by mediating an N1-N2 domain interaction in Escherichia coli ThrRS. Our results reveal the translational quality control of various ThrRSs and the role of the N1 domain in translational fidelity.
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Affiliation(s)
- Xiao-Long Zhou
- From the State Key Laboratory of Molecular Biology, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031 Shanghai, China and
| | - Yun Chen
- From the State Key Laboratory of Molecular Biology, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031 Shanghai, China and
| | - Zhi-Peng Fang
- From the State Key Laboratory of Molecular Biology, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031 Shanghai, China and
| | - Zhi-Rong Ruan
- From the State Key Laboratory of Molecular Biology, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031 Shanghai, China and
| | - Yong Wang
- the School of Life Science and Technology, ShanghaiTech University, 200031 Shanghai, China
| | - Ru-Juan Liu
- From the State Key Laboratory of Molecular Biology, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031 Shanghai, China and
| | - Mei-Qin Xue
- From the State Key Laboratory of Molecular Biology, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031 Shanghai, China and
| | - En-Duo Wang
- From the State Key Laboratory of Molecular Biology, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031 Shanghai, China and the School of Life Science and Technology, ShanghaiTech University, 200031 Shanghai, China
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38
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Abstract
Our genome is protected from the introduction of mutations by high fidelity replication and an extensive network of DNA damage response and repair mechanisms. However, the expression of our genome, via RNA and protein synthesis, allows for more diversity in translating genetic information. In addition, the splicing process has become less stringent over evolutionary time allowing for a substantial increase in the diversity of transcripts generated. The result is a diverse transcriptome and proteome that harbor selective advantages over a more tightly regulated system. Here, we describe mechanisms in place that both safeguard the genome and promote translational diversity, with emphasis on post-transcriptional RNA processing.
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Affiliation(s)
- Brian Magnuson
- Department of Radiation Oncology, University of Michigan Comprehensive Cancer Center, and Translational Oncology Program, University of Michigan, Ann Arbor, USA; Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, USA
| | - Karan Bedi
- Department of Radiation Oncology, University of Michigan Comprehensive Cancer Center, and Translational Oncology Program, University of Michigan, Ann Arbor, USA
| | - Mats Ljungman
- Department of Radiation Oncology, University of Michigan Comprehensive Cancer Center, and Translational Oncology Program, University of Michigan, Ann Arbor, USA; Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, USA.
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39
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Wang X, Pan T. Stress Response and Adaptation Mediated by Amino Acid Misincorporation during Protein Synthesis. Adv Nutr 2016; 7:773S-9S. [PMID: 27422514 PMCID: PMC4942860 DOI: 10.3945/an.115.010991] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Translation of genetic information into functional proteins is critical for all cellular life. Accurate protein synthesis relies on proper aminoacylation of transfer RNAs (tRNAs) and decoding of mRNAs by the ribosome with the use of aminoacyl-tRNAs. Mistranslation can lead to pathologic consequences. All cells contain elaborate quality control mechanisms in translation, although translational fidelity may be regulated by various factors such as nutrient limitation or reactive oxygen species. Translation fidelity is maintained via the accuracy of tRNA aminoacylation by the aminoacyl-tRNA synthetases and matching of the mRNA codon with the tRNA anticodon by the ribosome. Stringent substrate discrimination and proofreading are critical in aminoacylating tRNAs with their cognate amino acid to maintain high accuracy of translation. Although the composition of the cellular proteome generally adheres to the genetic code, accumulating evidence indicates that cells can also deliberately mistranslate; they synthesize mutant proteins that deviate from the genetic code in response to stress or environmental changes. Mistranslation with tRNA charged with noncognate amino acids can expand the proteome to enhance stress response and help adaptation. Here, we review current knowledge on mistranslation through tRNA misacylation and describe advances in our understanding of translational control in the regulation of stress response and human diseases.
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Affiliation(s)
- Xiaoyun Wang
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL
| | - Tao Pan
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL
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40
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p53-Dependent DNA damage response sensitive to editing-defective tRNA synthetase in zebrafish. Proc Natl Acad Sci U S A 2016; 113:8460-5. [PMID: 27402763 DOI: 10.1073/pnas.1608139113] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Brain and heart pathologies are caused by editing defects of transfer RNA (tRNA) synthetases, which preserve genetic code fidelity by removing incorrect amino acids misattached to tRNAs. To extend understanding of the broader impact of synthetase editing reactions on organismal homeostasis, and based on effects in bacteria ostensibly from small amounts of mistranslation of components of the replication apparatus, we investigated the sensitivity to editing of the vertebrate genome. We show here that in zebrafish embryos, transient overexpression of editing-defective valyl-tRNA synthetase (ValRS(ED)) activated DNA break-responsive H2AX and p53-responsive downstream proteins, such as cyclin-dependent kinase (CDK) inhibitor p21, which promotes cell-cycle arrest at DNA damage checkpoints, and Gadd45 and p53R2, with pivotal roles in DNA repair. In contrast, the response of these proteins to expression of ValRS(ED) was abolished in p53-deficient fish. The p53-activated downstream signaling events correlated with suppression of abnormal morphological changes caused by the editing defect and, in adults, reversed a shortened life span (followed for 2 y). Conversely, with normal editing activities, p53-deficient fish have a normal life span and few morphological changes. Whole-fish deep sequencing showed genomic mutations associated with the editing defect. We suggest that the sensitivity of p53 to expression of an editing-defective tRNA synthetase has a critical role in promoting genome integrity and organismal homeostasis.
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41
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Abstract
Aminoacyl-tRNA synthetases (aaRSs) are modular enzymes globally conserved in the three kingdoms of life. All catalyze the same two-step reaction, i.e., the attachment of a proteinogenic amino acid on their cognate tRNAs, thereby mediating the correct expression of the genetic code. In addition, some aaRSs acquired other functions beyond this key role in translation. Genomics and X-ray crystallography have revealed great structural diversity in aaRSs (e.g., in oligomery and modularity, in ranking into two distinct groups each subdivided in 3 subgroups, by additional domains appended on the catalytic modules). AaRSs show huge structural plasticity related to function and limited idiosyncrasies that are kingdom or even species specific (e.g., the presence in many Bacteria of non discriminating aaRSs compensating for the absence of one or two specific aaRSs, notably AsnRS and/or GlnRS). Diversity, as well, occurs in the mechanisms of aaRS gene regulation that are not conserved in evolution, notably between distant groups such as Gram-positive and Gram-negative Bacteria. The review focuses on bacterial aaRSs (and their paralogs) and covers their structure, function, regulation, and evolution. Structure/function relationships are emphasized, notably the enzymology of tRNA aminoacylation and the editing mechanisms for correction of activation and charging errors. The huge amount of genomic and structural data that accumulated in last two decades is reviewed, showing how the field moved from essentially reductionist biology towards more global and integrated approaches. Likewise, the alternative functions of aaRSs and those of aaRS paralogs (e.g., during cell wall biogenesis and other metabolic processes in or outside protein synthesis) are reviewed. Since aaRS phylogenies present promiscuous bacterial, archaeal, and eukaryal features, similarities and differences in the properties of aaRSs from the three kingdoms of life are pinpointed throughout the review and distinctive characteristics of bacterium-like synthetases from organelles are outlined.
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Affiliation(s)
- Richard Giegé
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, 67084 Strasbourg, France
| | - Mathias Springer
- Université Paris Diderot, Sorbonne Cité, UPR9073 CNRS, IBPC, 75005 Paris, France
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42
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Wang Y, Zhou XL, Ruan ZR, Liu RJ, Eriani G, Wang ED. A Human Disease-causing Point Mutation in Mitochondrial Threonyl-tRNA Synthetase Induces Both Structural and Functional Defects. J Biol Chem 2016; 291:6507-20. [PMID: 26811336 DOI: 10.1074/jbc.m115.700849] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Indexed: 11/06/2022] Open
Abstract
Mitochondria require all translational components, including aminoacyl-tRNA synthetases (aaRSs), to complete organelle protein synthesis. Some aaRS mutations cause mitochondrial disorders, including human mitochondrial threonyl-tRNA synthetase (hmtThrRS) (encoded by TARS2), the P282L mutation of which causes mitochondrial encephalomyopathies. However, its catalytic and structural consequences remain unclear. Herein, we cloned TARS2 and purified the wild-type and P282L mutant hmtThrRS. hmtThrRS misactivates non-cognate Ser and uses post-transfer editing to clear erroneously synthesized products. In vitro and in vivo analyses revealed that the mutation induces a decrease in Thr activation, aminoacylation, and proofreading activities and a change in the protein structure and/or stability, which might cause reduced catalytic efficiency. We also identified a splicing variant of TARS2 mRNA lacking exons 8 and 9, the protein product of which is targeted into mitochondria. In HEK293T cells, the variant does not dimerize and cannot complement the ThrRS knock-out strain in yeast, suggesting that the truncated protein is inactive and might have a non-canonical function, as observed for other aaRS fragments. The present study describes the aminoacylation and editing properties of hmtThrRS, clarifies the molecular consequences of the P282L mutation, and shows that the yeast ThrRS-deletion model is suitable to test pathology-associated point mutations or alternative splicing variants of mammalian aaRS mRNAs.
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Affiliation(s)
- Yong Wang
- From the State Key Laboratory of Molecular Biology, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China, the School of Life Science and Technology, ShanghaiTech University, 319 Yue Yang Road, Shanghai 200031, China, and
| | - Xiao-Long Zhou
- From the State Key Laboratory of Molecular Biology, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China,
| | - Zhi-Rong Ruan
- From the State Key Laboratory of Molecular Biology, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Ru-Juan Liu
- From the State Key Laboratory of Molecular Biology, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Gilbert Eriani
- the Architecture et Réactivité de l'ARN, UPR9002 CNRS, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, 15 rue René Descartes, 67084 Strasbourg, France
| | - En-Duo Wang
- From the State Key Laboratory of Molecular Biology, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China, the School of Life Science and Technology, ShanghaiTech University, 319 Yue Yang Road, Shanghai 200031, China, and
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43
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Homologous trans-editing factors with broad tRNA specificity prevent mistranslation caused by serine/threonine misactivation. Proc Natl Acad Sci U S A 2015; 112:6027-32. [PMID: 25918376 DOI: 10.1073/pnas.1423664112] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Aminoacyl-tRNA synthetases (ARSs) establish the rules of the genetic code, whereby each amino acid is attached to a cognate tRNA. Errors in this process lead to mistranslation, which can be toxic to cells. The selective forces exerted by species-specific requirements and environmental conditions potentially shape quality-control mechanisms that serve to prevent mistranslation. A family of editing factors that are homologous to the editing domain of bacterial prolyl-tRNA synthetase includes the previously characterized trans-editing factors ProXp-ala and YbaK, which clear Ala-tRNA(Pro) and Cys-tRNA(Pro), respectively, and three additional homologs of unknown function, ProXp-x, ProXp-y, and ProXp-z. We performed an in vivo screen of 230 conditions in which an Escherichia coli proXp-y deletion strain was grown in the presence of elevated levels of amino acids and specific ARSs. This screen, together with the results of in vitro deacylation assays, revealed Ser- and Thr-tRNA deacylase function for this homolog. A similar activity was demonstrated for Bordetella parapertussis ProXp-z in vitro. These proteins, now renamed "ProXp-ST1" and "ProXp-ST2," respectively, recognize multiple tRNAs as substrates. Taken together, our data suggest that these free-standing editing domains have the ability to prevent mistranslation errors caused by a number of ARSs, including lysyl-tRNA synthetase, threonyl-tRNA synthetase, seryl-tRNA synthetase, and alanyl-tRNA synthetase. The expression of these multifunctional enzymes is likely to provide a selective growth advantage to organisms subjected to environmental stresses and other conditions that alter the amino acid pool.
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44
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Novoa EM, Vargas-Rodriguez O, Lange S, Goto Y, Suga H, Musier-Forsyth K, Ribas de Pouplana L. Ancestral AlaX editing enzymes for control of genetic code fidelity are not tRNA-specific. J Biol Chem 2015; 290:10495-503. [PMID: 25724653 DOI: 10.1074/jbc.m115.640060] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Indexed: 01/15/2023] Open
Abstract
Accurate protein synthesis requires the hydrolytic editing of tRNAs incorrectly aminoacylated by aminoacyl-tRNA synthetases (ARSs). Recognition of cognate tRNAs by ARS is less error-prone than amino acid recognition, and, consequently, editing domains are generally believed to act only on the tRNAs cognate to their related ARSs. For example, the AlaX family of editing domains, including the editing domain of alanyl-tRNA synthetase and the related free-standing trans-editing AlaX enzymes, are thought to specifically act on tRNA(Ala), whereas the editing domains of threonyl-tRNA synthetases are specific for tRNA(Thr). Here we show that, contrary to this belief, AlaX-S, the smallest of the extant AlaX enzymes, deacylates Ser-tRNA(Thr) in addition to Ser-tRNA(Ala) and that a single residue is important to determine this behavior. Our data indicate that promiscuous forms of AlaX are ancestral to tRNA-specific AlaXs. We propose that former AlaX domains were used to maintain translational fidelity in earlier stages of genetic code evolution when mis-serylation of several tRNAs was possible.
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Affiliation(s)
- Eva Maria Novoa
- From the Institute for Research in Biomedicine, c/ Baldiri Reixac 10, 08028 Barcelona, Catalonia, Spain
| | - Oscar Vargas-Rodriguez
- the Department of Chemistry and Biochemistry, Center for RNA Biology, Ohio State University, Columbus, Ohio 43210
| | - Stefanie Lange
- From the Institute for Research in Biomedicine, c/ Baldiri Reixac 10, 08028 Barcelona, Catalonia, Spain
| | - Yuki Goto
- the Department of Chemistry, Graduate School of Science, University of Tokyo, Tokyo 113-0033, Japan, and
| | - Hiroaki Suga
- the Department of Chemistry, Graduate School of Science, University of Tokyo, Tokyo 113-0033, Japan, and
| | - Karin Musier-Forsyth
- the Department of Chemistry and Biochemistry, Center for RNA Biology, Ohio State University, Columbus, Ohio 43210
| | - Lluís Ribas de Pouplana
- From the Institute for Research in Biomedicine, c/ Baldiri Reixac 10, 08028 Barcelona, Catalonia, Spain, the Catalan Institution for Research and Advanced Studies, Passeig Lluís Companys 23, 08010 Barcelona, Catalonia, Spain
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45
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Fan Y, Wu J, Ung MH, De Lay N, Cheng C, Ling J. Protein mistranslation protects bacteria against oxidative stress. Nucleic Acids Res 2015; 43:1740-8. [PMID: 25578967 PMCID: PMC4330365 DOI: 10.1093/nar/gku1404] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Accurate flow of genetic information from DNA to protein requires faithful translation. An increased level of translational errors (mistranslation) has therefore been widely considered harmful to cells. Here we demonstrate that surprisingly, moderate levels of mistranslation indeed increase tolerance to oxidative stress in Escherichia coli. Our RNA sequencing analyses revealed that two antioxidant genes katE and osmC, both controlled by the general stress response activator RpoS, were upregulated by a ribosomal error-prone mutation. Mistranslation-induced tolerance to hydrogen peroxide required rpoS, katE and osmC. We further show that both translational and post-translational regulation of RpoS contribute to peroxide tolerance in the error-prone strain, and a small RNA DsrA, which controls translation of RpoS, is critical for the improved tolerance to oxidative stress through mistranslation. Our work thus challenges the prevailing view that mistranslation is always detrimental, and provides a mechanism by which mistranslation benefits bacteria under stress conditions.
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Affiliation(s)
- Yongqiang Fan
- Department of Microbiology and Molecular Genetics, Medical School, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Jiang Wu
- Department of Microbiology and Molecular Genetics, Medical School, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Matthew H Ung
- Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Nicholas De Lay
- Department of Microbiology and Molecular Genetics, Medical School, University of Texas Health Science Center, Houston, TX 77030, USA Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Chao Cheng
- Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Jiqiang Ling
- Department of Microbiology and Molecular Genetics, Medical School, University of Texas Health Science Center, Houston, TX 77030, USA Graduate School of Biomedical Sciences, Houston, TX 77030, USA
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46
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Deficiencies in tRNA synthetase editing activity cause cardioproteinopathy. Proc Natl Acad Sci U S A 2014; 111:17570-5. [PMID: 25422440 DOI: 10.1073/pnas.1420196111] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Misfolded proteins are an emerging hallmark of cardiac diseases. Although some misfolded proteins, such as desmin, are associated with mutations in the genes encoding these disease-associated proteins, little is known regarding more general mechanisms that contribute to the generation of misfolded proteins in the heart. Reduced translational fidelity, caused by a hypomorphic mutation in the editing domain of alanyl-tRNA synthetase (AlaRS), resulted in accumulation of misfolded proteins in specific mouse neurons. By further genetic modulation of the editing activity of AlaRS, we generated mouse models with broader phenotypes, the severity of which was directly related to the degree of compromised editing. Severe disruption of the editing activity of AlaRS caused embryonic lethality, whereas an intermediate reduction in AlaRS editing efficacy resulted in ubiquitinated protein aggregates and mitochondrial defects in cardiomyocytes that were accompanied by progressive cardiac fibrosis and dysfunction. In addition, autophagic vacuoles accumulated in mutant cardiomyocytes, suggesting that autophagy is insufficient to eliminate misfolded proteins. These findings demonstrate that the pathological consequences of diminished tRNA synthetase editing activity, and thus translational infidelity, are dependent on the cell type and the extent of editing disruption, and provide a previously unidentified mechanism underlying cardiac proteinopathy.
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47
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Bullwinkle T, Lazazzera B, Ibba M. Quality Control and Infiltration of Translation by Amino Acids Outside of the Genetic Code. Annu Rev Genet 2014; 48:149-66. [DOI: 10.1146/annurev-genet-120213-092101] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Tammy Bullwinkle
- Department of Microbiology, Ohio State University, Columbus, Ohio 43210
| | - Beth Lazazzera
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, California 90095
| | - Michael Ibba
- Department of Microbiology, Ohio State University, Columbus, Ohio 43210
- Ohio State Biochemistry Program and Center for RNA Biology, Ohio State University, Columbus, Ohio 43210;
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48
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Zhou XL, Ruan ZR, Wang M, Fang ZP, Wang Y, Chen Y, Liu RJ, Eriani G, Wang ED. A minimalist mitochondrial threonyl-tRNA synthetase exhibits tRNA-isoacceptor specificity during proofreading. Nucleic Acids Res 2014; 42:13873-86. [PMID: 25414329 PMCID: PMC4267643 DOI: 10.1093/nar/gku1218] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Yeast mitochondria contain a minimalist threonyl-tRNA synthetase (ThrRS) composed only of the catalytic core and tRNA binding domain but lacking the entire editing domain. Besides the usual tRNAThr2, some budding yeasts, such as Saccharomyces cerevisiae, also contain a non-canonical tRNAThr1 with an enlarged 8-nucleotide anticodon loop, reprograming the usual leucine CUN codons to threonine. This raises interesting questions about the aminoacylation fidelity of such ThrRSs and the possible contribution of the two tRNAThrs during editing. Here, we found that, despite the absence of the editing domain, S. cerevisiae mitochondrial ThrRS (ScmtThrRS) harbors a tRNA-dependent pre-transfer editing activity. Remarkably, only the usual tRNAThr2 stimulated pre-transfer editing, thus, establishing the first example of a synthetase exhibiting tRNA-isoacceptor specificity during pre-transfer editing. We also showed that the failure of tRNAThr1 to stimulate tRNA-dependent pre-transfer editing was due to the lack of an editing domain. Using assays of the complementation of a ScmtThrRS gene knockout strain, we showed that the catalytic core and tRNA binding domain of ScmtThrRS co-evolved to recognize the unusual tRNAThr1. In combination, the results provide insights into the tRNA-dependent editing process and suggest that tRNA-dependent pre-transfer editing takes place in the aminoacylation catalytic core.
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Affiliation(s)
- Xiao-Long Zhou
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, The Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, China
| | - Zhi-Rong Ruan
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, The Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, China
| | - Meng Wang
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, The Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, China
| | - Zhi-Peng Fang
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, The Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, China
| | - Yong Wang
- School of Life Science and Technology, ShanghaiTech University, 319 Yue Yang Road, 200031 Shanghai, China
| | - Yun Chen
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, The Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, China
| | - Ru-Juan Liu
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, The Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, China
| | - Gilbert Eriani
- Architecture et Réactivité de l'ARN, Université de Strasbourg, UPR9002 CNRS, Institut de Biologie Moléculaire et Cellulaire, 15 rue René Descartes, 67084 Strasbourg, France
| | - En-Duo Wang
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, The Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, China School of Life Science and Technology, ShanghaiTech University, 319 Yue Yang Road, 200031 Shanghai, China
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49
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Ribas de Pouplana L, Santos MAS, Zhu JH, Farabaugh PJ, Javid B. Protein mistranslation: friend or foe? Trends Biochem Sci 2014; 39:355-62. [PMID: 25023410 DOI: 10.1016/j.tibs.2014.06.002] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Revised: 06/06/2014] [Accepted: 06/12/2014] [Indexed: 01/03/2023]
Abstract
The translation of genes into functional proteins involves error. Mistranslation is a known cause of disease, but, surprisingly, recent studies suggest that certain organisms from all domains of life have evolved diverse pathways that increase their tolerance of translational error. Although the reason for these high error rates are not yet clear, evidence suggests that increased mistranslation may have a role in the generation of diversity within the proteome and other adaptive functions. Error rates are regulated, and there appears to be an optimal mistranslation rate that varies by organism and environmental condition. Advances in unbiased interrogation of error types and experiments involving wild organisms may help our understanding of the potentially adaptive roles for protein translation errors.
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Affiliation(s)
- Liuís Ribas de Pouplana
- Institute for Research in Biomedicine (IRB Barcelona), c/Baldiri Reixac 10, Barcelona, 08028, Catalonia, Spain; Catalan Institution for Research and Advanced Studies (ICREA), Pg. Lluís Companys 23, Barcelona, 08010, Catalonia, Spain
| | - Manuel A S Santos
- RNA Biology Laboratory, Department of Biology and CESAM, University of Aveiro, Aveiro, Portugal
| | - Jun-Hao Zhu
- Centre for Infectious Diseases Research, Tsinghua University School of Medicine, Beijing, China
| | - Philip J Farabaugh
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD, USA
| | - Babak Javid
- Centre for Infectious Diseases Research, Tsinghua University School of Medicine, Beijing, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, Hangzhou, China.
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50
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Wu J, Fan Y, Ling J. Mechanism of oxidant-induced mistranslation by threonyl-tRNA synthetase. Nucleic Acids Res 2014; 42:6523-31. [PMID: 24744241 PMCID: PMC4041444 DOI: 10.1093/nar/gku271] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Aminoacyl-tRNA synthetases maintain the fidelity during protein synthesis by selective activation of cognate amino acids at the aminoacylation site and hydrolysis of misformed aminoacyl-tRNAs at the editing site. Threonyl-tRNA synthetase (ThrRS) misactivates serine and utilizes an editing site cysteine (C182 in Escherichia coli) to hydrolyze Ser-tRNAThr. Hydrogen peroxide oxidizes C182, leading to Ser-tRNAThr production and mistranslation of threonine codons as serine. The mechanism of C182 oxidation remains unclear. Here we used a chemical probe to demonstrate that C182 was oxidized to sulfenic acid by air, hydrogen peroxide and hypochlorite. Aminoacylation experiments in vitro showed that air oxidation increased the Ser-tRNAThr level in the presence of elongation factor Tu. C182 forms a putative metal binding site with three conserved histidine residues (H73, H77 and H186). We showed that H73 and H186, but not H77, were critical for activating C182 for oxidation. Addition of zinc or nickel ions inhibited C182 oxidation by hydrogen peroxide. These results led us to propose a model for C182 oxidation, which could serve as a paradigm for the poorly understood activation mechanisms of protein cysteine residues. Our work also suggests that bacteria may use ThrRS editing to sense the oxidant levels in the environment.
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Affiliation(s)
- Jiang Wu
- Department of Microbiology and Molecular Genetics, Medical School, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Yongqiang Fan
- Department of Microbiology and Molecular Genetics, Medical School, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Jiqiang Ling
- Department of Microbiology and Molecular Genetics, Medical School, University of Texas Health Science Center, Houston, TX 77030, USA Graduate School of Biomedical Sciences, University of Texas, Houston, TX 77030, USA
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