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Hoffmann G, Lukarska M, Clare RH, Masters EK, Johnston KL, Ford L, Turner JD, Ward SA, Taylor MJ, Jensen MR, Palencia A. Targeting a microbiota Wolbachian aminoacyl-tRNA synthetase to block its pathogenic host. SCIENCE ADVANCES 2024; 10:eado1453. [PMID: 38985862 PMCID: PMC11235159 DOI: 10.1126/sciadv.ado1453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 06/04/2024] [Indexed: 07/12/2024]
Abstract
The interplay between humans and their microbiome is crucial for various physiological processes, including nutrient absorption, immune defense, and maintaining homeostasis. Microbiome alterations can directly contribute to diseases or heighten their likelihood. This relationship extends beyond humans; microbiota play vital roles in other organisms, including eukaryotic pathogens causing severe diseases. Notably, Wolbachia, a bacterial microbiota, is essential for parasitic worms responsible for lymphatic filariasis and onchocerciasis, devastating human illnesses. Given the lack of rapid cures for these infections and the limitations of current treatments, new drugs are imperative. Here, we disrupt Wolbachia's symbiosis with pathogens using boron-based compounds targeting an unprecedented Wolbachia enzyme, leucyl-tRNA synthetase (LeuRS), effectively inhibiting its growth. Through a compound demonstrating anti-Wolbachia efficacy in infected cells, we use biophysical experiments and x-ray crystallography to elucidate the mechanism behind Wolbachia LeuRS inhibition. We reveal that these compounds form adenosine-based adducts inhibiting protein synthesis. Overall, our study underscores the potential of disrupting key microbiota to control infections.
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Affiliation(s)
- Guillaume Hoffmann
- Institute for Advanced Biosciences (IAB), Structural Biology of Novel Drug Targets in Human Diseases, INSERM U1209, CNRS UMR 5309, Université Grenoble-Alpes, Grenoble 38000, France
| | - Maria Lukarska
- Institute for Advanced Biosciences (IAB), Structural Biology of Novel Drug Targets in Human Diseases, INSERM U1209, CNRS UMR 5309, Université Grenoble-Alpes, Grenoble 38000, France
| | - Rachel H. Clare
- Centre for Drugs and Diagnostics, Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK
| | - Ellen K.G. Masters
- Centre for Drugs and Diagnostics, Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK
| | - Kelly L. Johnston
- Centre for Drugs and Diagnostics, Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK
| | - Louise Ford
- Centre for Drugs and Diagnostics, Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK
| | - Joseph D. Turner
- Centre for Drugs and Diagnostics, Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK
| | - Steve A. Ward
- Centre for Drugs and Diagnostics, Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK
| | - Mark J. Taylor
- Centre for Drugs and Diagnostics, Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK
| | | | - Andrés Palencia
- Institute for Advanced Biosciences (IAB), Structural Biology of Novel Drug Targets in Human Diseases, INSERM U1209, CNRS UMR 5309, Université Grenoble-Alpes, Grenoble 38000, France
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2
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Zheng WQ, Zhang JH, Li ZH, Liu X, Zhang Y, Huang S, Li J, Zhou B, Eriani G, Wang ED, Zhou XL. Mammalian mitochondrial translation infidelity leads to oxidative stress-induced cell cycle arrest and cardiomyopathy. Proc Natl Acad Sci U S A 2023; 120:e2309714120. [PMID: 37669377 PMCID: PMC10500172 DOI: 10.1073/pnas.2309714120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 08/08/2023] [Indexed: 09/07/2023] Open
Abstract
Proofreading (editing) of mischarged tRNAs by cytoplasmic aminoacyl-tRNA synthetases (aaRSs), whose impairment causes neurodegeneration and cardiac diseases, is of high significance for protein homeostasis. However, whether mitochondrial translation needs fidelity and the significance of editing by mitochondrial aaRSs have been unclear. Here, we show that mammalian cells critically depended on the editing of mitochondrial threonyl-tRNA synthetase (mtThrRS, encoded by Tars2), disruption of which accumulated Ser-tRNAThr and generated a large abundance of Thr-to-Ser misincorporated peptides in vivo. Such infidelity impaired mitochondrial translation and oxidative phosphorylation, causing oxidative stress and cell cycle arrest in the G0/G1 phase. Notably, reactive oxygen species (ROS) scavenging by N-acetylcysteine attenuated this abnormal cell proliferation. A mouse model of heart-specific defective mtThrRS editing was established. Increased ROS levels, blocked cardiomyocyte proliferation, contractile dysfunction, dilated cardiomyopathy, and cardiac fibrosis were observed. Our results elucidate that mitochondria critically require a high level of translational accuracy at Thr codons and highlight the cellular dysfunctions and imbalance in tissue homeostasis caused by mitochondrial mistranslation.
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Affiliation(s)
- Wen-Qiang Zheng
- Key Laboratory of RNA Science and Engineering, State Key Laboratory of Molecular Biology, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai200031, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai201210, China
| | - Jian-Hui Zhang
- Key Laboratory of RNA Science and Engineering, State Key Laboratory of Molecular Biology, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai200031, 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, Hangzhou310024, China
| | - Zi-Han Li
- Key Laboratory of RNA Science and Engineering, State Key Laboratory of Molecular Biology, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai200031, China
| | - Xiuxiu Liu
- Key Laboratory of RNA Science and Engineering, State Key Laboratory of Molecular Biology, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai200031, China
| | - Yong Zhang
- Key Laboratory of RNA Science and Engineering, State Key Laboratory of Molecular Biology, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai200031, China
| | - Shuo Huang
- Key Laboratory of RNA Science and Engineering, State Key Laboratory of Molecular Biology, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai200031, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai201210, China
| | - Jinsong Li
- Key Laboratory of RNA Science and Engineering, State Key Laboratory of Molecular Biology, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai200031, 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, Hangzhou310024, China
| | - Bin Zhou
- Key Laboratory of RNA Science and Engineering, State Key Laboratory of Molecular Biology, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai200031, 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, Hangzhou310024, China
| | - Gilbert Eriani
- Architecture et Réactivité de l’ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, Strasbourg67084, France
| | - En-Duo Wang
- Key Laboratory of RNA Science and Engineering, State Key Laboratory of Molecular Biology, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai200031, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai201210, China
| | - Xiao-Long Zhou
- Key Laboratory of RNA Science and Engineering, State Key Laboratory of Molecular Biology, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai200031, 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, Hangzhou310024, China
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3
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Sullivan JR, Courtine C, Taylor L, Solomon O, Behr MA. Loss of allosteric regulation in α-isopropylmalate synthase identified as an antimicrobial resistance mechanism. NPJ ANTIMICROBIALS AND RESISTANCE 2023; 1:7. [PMID: 38686213 PMCID: PMC11057210 DOI: 10.1038/s44259-023-00005-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 04/18/2023] [Indexed: 05/02/2024]
Abstract
Despite our best efforts to discover new antimicrobials, bacteria have evolved mechanisms to become resistant. Resistance to antimicrobials can be attributed to innate, inducible, and acquired mechanisms. Mycobacterium abscessus is one of the most antimicrobial resistant bacteria and is known to cause chronic pulmonary infections within the cystic fibrosis community. Previously, we identified epetraborole as an inhibitor against M. abscessus with in vitro and in vivo activities and that the efficacy of epetraborole could be improved with the combination of the non-proteinogenic amino acid norvaline. Norvaline demonstrated activity against the M. abscessus epetraborole resistant mutants thus, limiting resistance to epetraborole in wild-type populations. Here we show M. abscessus mutants with resistance to epetraborole can acquire resistance to norvaline in a leucyl-tRNA synthetase (LeuRS) editing-independent manner. After showing that the membrane hydrophobicity and efflux activity are not linked to norvaline resistance, whole-genome sequencing identified a mutation in the allosteric regulatory domain of α-isopropylmalate synthase (α-IPMS). We found that mutants with the α-IPMSA555V variant incorporated less norvaline in the proteome and produced more leucine than the parental strain. Furthermore, we found that leucine can rescue growth inhibition from norvaline challenge in the parental strain. Our results demonstrate that M. abscessus can modulate its metabolism through mutations in an allosteric regulatory site to upregulate the biosynthesis of the natural LeuRS substrate and outcompete norvaline. These findings emphasize the antimicrobial resistant nature of M. abscessus and describe a unique mechanism of substrate-inhibitor competition.
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Affiliation(s)
- Jaryd R. Sullivan
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1 Canada
- Department of Microbiology & Immunology, McGill University, Montreal, QC H3A 2B4 Canada
- McGill International TB Centre, Montreal, QC H4A 3S5 Canada
| | - Christophe Courtine
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1 Canada
- Department of Microbiology & Immunology, McGill University, Montreal, QC H3A 2B4 Canada
- Present Address: Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Hanover, NH 03755 USA
| | - Lorne Taylor
- Clinical Proteomics Platform, Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1 Canada
| | - Ori Solomon
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1 Canada
- Department of Microbiology & Immunology, McGill University, Montreal, QC H3A 2B4 Canada
- McGill International TB Centre, Montreal, QC H4A 3S5 Canada
| | - Marcel A. Behr
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1 Canada
- Department of Microbiology & Immunology, McGill University, Montreal, QC H3A 2B4 Canada
- McGill International TB Centre, Montreal, QC H4A 3S5 Canada
- Department of Medicine, McGill University Health Centre, Montreal, QC H3G 2M1 Canada
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4
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Sarmah P, Shang W, Origi A, Licheva M, Kraft C, Ulbrich M, Lichtenberg E, Wilde A, Koch HG. mRNA targeting eliminates the need for the signal recognition particle during membrane protein insertion in bacteria. Cell Rep 2023; 42:112140. [PMID: 36842086 PMCID: PMC10066597 DOI: 10.1016/j.celrep.2023.112140] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 01/10/2023] [Accepted: 02/02/2023] [Indexed: 02/26/2023] Open
Abstract
Signal-sequence-dependent protein targeting is essential for the spatiotemporal organization of eukaryotic and prokaryotic cells and is facilitated by dedicated protein targeting factors such as the signal recognition particle (SRP). However, targeting signals are not exclusively contained within proteins but can also be present within mRNAs. By in vivo and in vitro assays, we show that mRNA targeting is controlled by the nucleotide content and by secondary structures within mRNAs. mRNA binding to bacterial membranes occurs independently of soluble targeting factors but is dependent on the SecYEG translocon and YidC. Importantly, membrane insertion of proteins translated from membrane-bound mRNAs occurs independently of the SRP pathway, while the latter is strictly required for proteins translated from cytosolic mRNAs. In summary, our data indicate that mRNA targeting acts in parallel to the canonical SRP-dependent protein targeting and serves as an alternative strategy for safeguarding membrane protein insertion when the SRP pathway is compromised.
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Affiliation(s)
- Pinku Sarmah
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany; Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Wenkang Shang
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany; Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Andrea Origi
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany; Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Mariya Licheva
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany; Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Claudine Kraft
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany; CIBSS - Centre for Integrative Biological Signalling Studies, University Freiburg, 79104 Freiburg, Germany
| | - Maximilian Ulbrich
- Internal Medicine IV, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signaling Studies, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | | | - Annegret Wilde
- Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Hans-Georg Koch
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany.
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5
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Liu S, She P, Li Z, Li Y, Li L, Yang Y, Zhou L, Wu Y. Drug synergy discovery of tavaborole and aminoglycosides against Escherichia coli using high throughput screening. AMB Express 2022; 12:151. [PMID: 36454354 PMCID: PMC9715904 DOI: 10.1186/s13568-022-01488-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 11/01/2022] [Indexed: 12/05/2022] Open
Abstract
High incidences of urinary tract infection (UTI) of aminoglycosides-resistant E.coli causes a severe burden for public health. A new therapeutic strategy to ease this crisis is to repurpose non-antibacterial compounds to increase aminoglycosides sensibility against multidrug resistant E.coli pathogens. Based on high throughput screening technology, we profile the antimicrobial activity of tavaborole, a first antifungal benzoxaborole drug for onychomycosis treatment, and investigate the synergistic interaction between tavaborole and aminoglycosides, especially tobramycin and amikacin. Most importantly, by resistance accumulation assay, we found that, tavaborole not only slowed resistance occurrence of aminoglycosides, but also reduced invasiveness of E.coli in combination with tobramycin. Mechanistic studies preliminary explored that tavaborole and aminoglycosides lead to mistranslation, but would be still necessary to investigate more details for further research. In addition, tavaborole exhibited low systematic toxicity in vitro and in vivo, and enhanced aminoglycoside bactericidal activity in mice peritonitis model. Collectively, these results suggest the potential of tavaborole as a novel aminoglycosides adjuvant to tackle the clinically relevant drug resistant E. coli and encourages us to discover more benzoxaborole analogues for circumvention of recalcitrant infections.
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Affiliation(s)
- Shasha Liu
- grid.431010.7Department of Laboratory Medicine, The Third Xiangya Hospital, Central South University, Changsha, 410000 Hunan China
| | - Pengfei She
- grid.431010.7Department of Laboratory Medicine, The Third Xiangya Hospital, Central South University, Changsha, 410000 Hunan China
| | - Zehao Li
- grid.431010.7Department of Laboratory Medicine, The Third Xiangya Hospital, Central South University, Changsha, 410000 Hunan China
| | - Yimin Li
- grid.431010.7Department of Laboratory Medicine, The Third Xiangya Hospital, Central South University, Changsha, 410000 Hunan China
| | - Linhui Li
- grid.431010.7Department of Laboratory Medicine, The Third Xiangya Hospital, Central South University, Changsha, 410000 Hunan China
| | - Yifan Yang
- grid.431010.7Department of Laboratory Medicine, The Third Xiangya Hospital, Central South University, Changsha, 410000 Hunan China
| | - Linying Zhou
- grid.216417.70000 0001 0379 7164Department of Laboratory Medicine, The Affiliated Changsha Hospital of Xiangya School of Medicine, Central South University, Changsha, 410000 Hunan China
| | - Yong Wu
- grid.216417.70000 0001 0379 7164Department of Laboratory Medicine, The Affiliated Changsha Hospital of Xiangya School of Medicine, Central South University, Changsha, 410000 Hunan China
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6
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Pang L, Zanki V, Strelkov SV, Van Aerschot A, Gruic-Sovulj I, Weeks SD. Partitioning of the initial catalytic steps of leucyl-tRNA synthetase is driven by an active site peptide-plane flip. Commun Biol 2022; 5:883. [PMID: 36038645 PMCID: PMC9424281 DOI: 10.1038/s42003-022-03825-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 08/09/2022] [Indexed: 12/29/2022] Open
Abstract
To correctly aminoacylate tRNALeu, leucyl-tRNA synthetase (LeuRS) catalyzes three reactions: activation of leucine by ATP to form leucyl-adenylate (Leu-AMP), transfer of this amino acid to tRNALeu and post-transfer editing of any mischarged product. Although LeuRS has been well characterized biochemically, detailed structural information is currently only available for the latter two stages of catalysis. We have solved crystal structures for all enzymatic states of Neisseria gonorrhoeae LeuRS during Leu-AMP formation. These show a cycle of dramatic conformational changes, involving multiple domains, and correlate with an energetically unfavorable peptide-plane flip observed in the active site of the pre-transition state structure. Biochemical analyses, combined with mutant structural studies, reveal that this backbone distortion acts as a trigger, temporally compartmentalizing the first two catalytic steps. These results unveil the remarkable effect of this small structural alteration on the global dynamics and activity of the enzyme.
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Affiliation(s)
- Luping Pang
- grid.5596.f0000 0001 0668 7884Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49 – Box 822, 3000 Leuven, Belgium ,grid.5596.f0000 0001 0668 7884Medicinal Chemistry, Rega Institute for Medical Research, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49 – Box 1041, 3000 Leuven, Belgium ,grid.207374.50000 0001 2189 3846Research Center of Basic Medicine, Academy of Medical Sciences, College of Medicine, Zhengzhou University, Zhengzhou, Henan 450001 China
| | - Vladimir Zanki
- grid.4808.40000 0001 0657 4636Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia
| | - Sergei V. Strelkov
- grid.5596.f0000 0001 0668 7884Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49 – Box 822, 3000 Leuven, Belgium
| | - Arthur Van Aerschot
- grid.5596.f0000 0001 0668 7884Medicinal Chemistry, Rega Institute for Medical Research, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49 – Box 1041, 3000 Leuven, Belgium
| | - Ita Gruic-Sovulj
- grid.4808.40000 0001 0657 4636Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia
| | - Stephen D. Weeks
- grid.5596.f0000 0001 0668 7884Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49 – Box 822, 3000 Leuven, Belgium ,Pledge Therapeutics, Gaston Geenslaan 1, 3001 Leuven, Belgium
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7
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Leucyl-tRNA Synthetase Inhibitor, D-Norvaline, in Combination with Oxacillin, Is Effective against Methicillin-Resistant Staphylococcus aureus. Antibiotics (Basel) 2022; 11:antibiotics11050683. [PMID: 35625327 PMCID: PMC9137938 DOI: 10.3390/antibiotics11050683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 05/11/2022] [Accepted: 05/16/2022] [Indexed: 11/17/2022] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is a pathogenic bacterium that causes severe diseases in humans. For decades, MRSA has acquired substantial resistance against conventional antibiotics through regulatory adaptation, thereby posing a challenge for treating MRSA infection. One of the emerging strategies to combat MRSA is the combinatory use of antibacterial agents. Based on the dramatic change in phospholipid fatty acid (PLFA) composition of MRSA in previous results, this study investigated branched-chain amino acid derivatives (precursors of fatty acid synthesis of cell membrane) and discovered the antimicrobial potency of D-norvaline. The compound, which can act synergistically with oxacillin, is among the three leucine-tRNA synthetase inhibitors with high potency to inhibit MRSA cell growth and biofilm formation. PLFA analysis and membrane properties revealed that D-norvaline decreased the overall amount of PLFA, increasing the fluidity and decreasing the hydrophobicity of the bacterial cell membrane. Additionally, we observed genetic differences to explore the response to D-norvaline. Furthermore, deletion mutants and clinically isolated MRSA strains were treated with D-norvaline. The study revealed that D-norvaline, with low concentrations of oxacillin, was effective in killing several MRSA strains. In summary, our findings provide a new combination of aminoacyl-tRNA synthetase inhibitor D-norvaline and oxacillin, which is effective against MRSA.
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8
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Zivkovic I, Ivkovic K, Cvetesic N, Marsavelski A, Gruic-Sovulj I. Negative catalysis by the editing domain of class I aminoacyl-tRNA synthetases. Nucleic Acids Res 2022; 50:4029-4041. [PMID: 35357484 PMCID: PMC9023258 DOI: 10.1093/nar/gkac207] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 03/14/2022] [Accepted: 03/28/2022] [Indexed: 11/19/2022] Open
Abstract
Aminoacyl-tRNA synthetases (AARS) translate the genetic code by loading tRNAs with the cognate amino acids. The errors in amino acid recognition are cleared at the AARS editing domain through hydrolysis of misaminoacyl-tRNAs. This ensures faithful protein synthesis and cellular fitness. Using Escherichia coli isoleucyl-tRNA synthetase (IleRS) as a model enzyme, we demonstrated that the class I editing domain clears the non-cognate amino acids well-discriminated at the synthetic site with the same rates as the weakly-discriminated fidelity threats. This unveiled low selectivity suggests that evolutionary pressure to optimize the rates against the amino acids that jeopardize translational fidelity did not shape the editing site. Instead, we propose that editing was shaped to safeguard cognate aminoacyl-tRNAs against hydrolysis. Misediting is prevented by the residues that promote negative catalysis through destabilisation of the transition state comprising cognate amino acid. Such powerful design allows broad substrate acceptance of the editing domain along with its exquisite specificity in the cognate aminoacyl-tRNA rejection. Editing proceeds by direct substrate delivery to the editing domain (in cis pathway). However, we found that class I IleRS also releases misaminoacyl-tRNAIle and edits it in trans. This minor editing pathway was up to now recognized only for class II AARSs.
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Affiliation(s)
- Igor Zivkovic
- Department of Chemistry, Faculty of Science, University of Zagreb, Zagreb 10000, Croatia
| | - Kate Ivkovic
- Department of Chemistry, Faculty of Science, University of Zagreb, Zagreb 10000, Croatia
| | - Nevena Cvetesic
- Institute for Clinical Sciences, Faculty of Medicine, Imperial College London and MRC London Institute of Medical Sciences, London, SW7 2AZ, UK
| | - Aleksandra Marsavelski
- Department of Chemistry, Faculty of Science, University of Zagreb, Zagreb 10000, Croatia
| | - Ita Gruic-Sovulj
- Department of Chemistry, Faculty of Science, University of Zagreb, Zagreb 10000, Croatia
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9
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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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10
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Rayevsky A, Sharifi M, Demianenko E, Volochnyuk D, Tukalo M. Effect of Charge Distribution in a Modified tRNA Substrate on Pre-Reaction Protein-tRNA Complex Geometry. ACS OMEGA 2021; 6:4227-4235. [PMID: 33644545 PMCID: PMC7906584 DOI: 10.1021/acsomega.0c05143] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 01/21/2021] [Indexed: 06/12/2023]
Abstract
An important aspect of molecular mechanics simulations of a protein structure and ligand binding often involves the generation of reliable force fields for nonstandard residues and ligands. We consider the aminoacyl-tRNA synthetase (AaRS) system that involves nucleic acid and amino acid derivatives, obtaining force field atomic charges using the restrained electrostatic potential (RESP) approach. These charges are shown to predict observed properties of the post-transfer editing reaction in this system, in contrast to simulations performed using approximate charges conceived based upon standard charges for related systems present in force field databases. In particular, the simulations predicted key properties induced by mutation. The approach taken for generating the RESP charges retains established charges for known fragments, defining new charges only for the novel chemical features present in the modified residues. This approach is of general relevance for the design of force fields for pharmacological applications, and indeed the AaRS target system is itself relevant to antibiotics development.
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Affiliation(s)
- Alexey Rayevsky
- Department
of Protein Synthesis Enzymology, Institute
of Molecular Biology and Genetics National Academy of Sciences of
Ukraine, Osipovskogo
st. 2a, Kyiv, UA 03143, Ukraine
- Laboratory
of Bioinformatics and Structural Biology, Institute of Food Biotechnology and Genomics National Academy of
Sciences, Osipovskogo 2a Str., Kyiv, 04123, Ukraine
| | - Mohsen Sharifi
- RockGen
Therapeutics, #831 Bioventure,
4301 W. Markham St., Little Rock, Arkansas 72205, United
States
| | - Eugeniy Demianenko
- Chuiko
Institute of Surface Chemistry of National Academy of Sciences of
Ukraine, 17 General Naumov Str., Kyiv 03164, Ukraine
| | - Dmitriy Volochnyuk
- Department
of Biologically Active Compounds, Institute
of Organic Chemistry NASU, Murmanskaya 5 str, Kyiv, 02660, Ukraine
- Enamine
Ltd, 78 Chervonotkatska
Str, Kyiv, UA 02660, Ukraine
| | - Michael Tukalo
- Department
of Protein Synthesis Enzymology, Institute
of Molecular Biology and Genetics National Academy of Sciences of
Ukraine, Osipovskogo
st. 2a, Kyiv, UA 03143, Ukraine
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11
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Mazeed M, Singh R, Kumar P, Roy A, Raman B, Kruparani SP, Sankaranarayanan R. Recruitment of archaeal DTD is a key event toward the emergence of land plants. SCIENCE ADVANCES 2021; 7:7/6/eabe8890. [PMID: 33536220 PMCID: PMC7857688 DOI: 10.1126/sciadv.abe8890] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 12/16/2020] [Indexed: 06/09/2023]
Abstract
Streptophyte algae emerged as a land plant with adaptations that eventually led to terrestrialization. Land plants encounter a range of biotic and abiotic stresses that elicit anaerobic stress responses. Here, we show that acetaldehyde, a toxic metabolite of anaerobic stress, targets and generates ethyl adducts on aminoacyl-tRNA, a central component of the translation machinery. However, elongation factor thermo unstable (EF-Tu) safeguards l-aminoacyl-tRNA, but not d-aminoacyl-tRNA, from being modified by acetaldehyde. We identified a unique activity of archaeal-derived chiral proofreading module, d-aminoacyl-tRNA deacylase 2 (DTD2), that removes N-ethyl adducts formed on d-aminoacyl-tRNAs (NEDATs). Thus, the study provides the molecular basis of ethanol and acetaldehyde hypersensitivity in DTD2 knockout plants. We uncovered an important gene transfer event from methanogenic archaea to the ancestor of land plants. While missing in other algal lineages, DTD2 is conserved from streptophyte algae to land plants, suggesting its role toward the emergence and evolution of land plants.
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Affiliation(s)
- Mohd Mazeed
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500007, India
| | - Raghvendra Singh
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500007, India
| | - Pradeep Kumar
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500007, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-CCMB campus, Uppal Road, Hyderabad 500007, India
| | - Ankit Roy
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500007, India
| | - Bakthisaran Raman
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500007, India
| | - Shobha P Kruparani
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500007, India
| | - Rajan Sankaranarayanan
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500007, India.
- Academy of Scientific and Innovative Research (AcSIR), CSIR-CCMB campus, Uppal Road, Hyderabad 500007, India
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12
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Deciphering the interaction of benzoxaborole inhibitor AN2690 with connective polypeptide 1 (CP1) editing domain of Leishmania donovani leucyl-tRNA synthetase. J Biosci 2020. [DOI: 10.1007/s12038-020-00031-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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13
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Kelly P, Kavoor A, Ibba M. Fine-Tuning of Alanyl-tRNA Synthetase Quality Control Alleviates Global Dysregulation of the Proteome. Genes (Basel) 2020; 11:genes11101222. [PMID: 33081015 PMCID: PMC7603204 DOI: 10.3390/genes11101222] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 10/10/2020] [Accepted: 10/15/2020] [Indexed: 11/16/2022] Open
Abstract
One integral step in the transition from a nucleic acid encoded-genome to functional proteins is the aminoacylation of tRNA molecules. To perform this activity, aminoacyl-tRNA synthetases (aaRSs) activate free amino acids in the cell forming an aminoacyl-adenylate before transferring the amino acid on to its cognate tRNA. These newly formed aminoacyl-tRNA (aa-tRNA) can then be used by the ribosome during mRNA decoding. In Escherichia coli, there are twenty aaRSs encoded in the genome, each of which corresponds to one of the twenty proteinogenic amino acids used in translation. Given the shared chemicophysical properties of many amino acids, aaRSs have evolved mechanisms to prevent erroneous aa-tRNA formation with non-cognate amino acid substrates. Of particular interest is the post-transfer proofreading activity of alanyl-tRNA synthetase (AlaRS) which prevents the accumulation of Ser-tRNAAla and Gly-tRNAAla in the cell. We have previously shown that defects in AlaRS proofreading of Ser-tRNAAla lead to global dysregulation of the E. coli proteome, subsequently causing defects in growth, motility, and antibiotic sensitivity. Here we report second-site AlaRS suppressor mutations that alleviate the aforementioned phenotypes, revealing previously uncharacterized residues within the AlaRS proofreading domain that function in quality control.
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Affiliation(s)
- Paul Kelly
- The Ohio State University Molecular, Cellular and Developmental Biology Program, The Ohio State University, Columbus, OH 43210, USA; (P.K.); (A.K.)
| | - Arundhati Kavoor
- The Ohio State University Molecular, Cellular and Developmental Biology Program, The Ohio State University, Columbus, OH 43210, USA; (P.K.); (A.K.)
| | - Michael Ibba
- The Ohio State University Molecular, Cellular and Developmental Biology Program, The Ohio State University, Columbus, OH 43210, USA; (P.K.); (A.K.)
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
- Department of Microbiology, The Ohio State University, 318 West 12th Avenue, Columbus, OH 43210, USA
- Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA
- Correspondence: ; Tel.: +1-714-516-5235
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14
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Abstract
Aminoacyl-tRNA synthetases (AARSs) have been considered very attractive drug-targets for decades. This interest probably emerged with the identification of differences in AARSs between prokaryotic and eukaryotic species, which provided a rationale for the development of antimicrobials targeting bacterial AARSs with minimal effect on the homologous human AARSs. Today we know that AARSs are not only attractive, but also valid drug targets as they are housekeeping proteins that: (i) play a fundamental role in protein translation by charging the corresponding amino acid to its cognate tRNA and preventing mistranslation mistakes [1], a critical process during fast growing conditions of microbes; and (ii) present significant differences between microbes and humans that can be used for drug development [2]. Together with the vast amount of available data on both pathogenic and mammalian AARSs, it is expected that, in the future, the numerous reported inhibitors of AARSs will provide the basis to develop new therapeutics for the treatment of human diseases. In this chapter, a detailed summary on the state-of-the-art in drug discovery and drug development for each aminoacyl-tRNA synthetase will be presented.
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Affiliation(s)
- Maria Lukarska
- Institute for Advanced Biosciences (IAB), Structural Biology of Novel Drug Targets in Human Diseases, INSERM U1209, CNRS UMR 5309, University Grenoble Alpes, Grenoble, France
| | - Andrés Palencia
- Institute for Advanced Biosciences (IAB), Structural Biology of Novel Drug Targets in Human Diseases, INSERM U1209, CNRS UMR 5309, University Grenoble Alpes, Grenoble, France.
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15
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Kuzmishin Nagy AB, Bakhtina M, Musier-Forsyth K. Trans-editing by aminoacyl-tRNA synthetase-like editing domains. Enzymes 2020; 48:69-115. [PMID: 33837712 DOI: 10.1016/bs.enz.2020.07.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Aminoacyl-tRNA synthetases (aaRS) are ubiquitous enzymes responsible for aminoacyl-tRNA (aa-tRNA) synthesis. Correctly formed aa-tRNAs are necessary for proper decoding of mRNA and accurate protein synthesis. tRNAs possess specific nucleobases that promote selective recognition by cognate aaRSs. Selecting the cognate amino acid can be more challenging because all amino acids share the same peptide backbone and several are isosteric or have similar side chains. Thus, aaRSs can misactivate non-cognate amino acids and produce mischarged aa-tRNAs. If left uncorrected, mischarged aa-tRNAs deliver their non-cognate amino acid to the ribosome resulting in misincorporation into the nascent polypeptide chain. This changes the primary protein sequence and potentially causes misfolding or formation of non-functional proteins that impair cell survival. A variety of proofreading or editing pathways exist to prevent and correct mistakes in aa-tRNA formation. Editing may occur before the amino acid transfer step of aminoacylation via hydrolysis of the aminoacyl-adenylate. Alternatively, post-transfer editing, which occurs after the mischarged aa-tRNA is formed, may be carried out via a distinct editing site on the aaRS where the mischarged aa-tRNA is deacylated. In recent years, it has become clear that most organisms also encode factors that lack aminoacylation activity but resemble aaRS editing domains and function to clear mischarged aa-tRNAs in trans. This review focuses on these trans-editing factors, which are encoded in all three domains of life and function together with editing domains present within aaRSs to ensure that the accuracy of protein synthesis is sufficient for cell survival.
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Affiliation(s)
- Alexandra B Kuzmishin Nagy
- Department of Chemistry and Biochemistry and Center for RNA Biology, The Ohio State University, Columbus, OH, United States
| | - Marina Bakhtina
- Department of Chemistry and Biochemistry and Center for RNA Biology, The Ohio State University, Columbus, OH, United States
| | - Karin Musier-Forsyth
- Department of Chemistry and Biochemistry and Center for RNA Biology, The Ohio State University, Columbus, OH, United States.
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16
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Tawfik DS, Gruic-Sovulj I. How evolution shapes enzyme selectivity - lessons from aminoacyl-tRNA synthetases and other amino acid utilizing enzymes. FEBS J 2020; 287:1284-1305. [PMID: 31891445 DOI: 10.1111/febs.15199] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Revised: 12/08/2019] [Accepted: 12/30/2019] [Indexed: 12/21/2022]
Abstract
Aminoacyl-tRNA synthetases (AARSs) charge tRNA with their cognate amino acids. Many other enzymes use amino acids as substrates, yet discrimination against noncognate amino acids that threaten the accuracy of protein translation is a hallmark of AARSs. Comparing AARSs to these other enzymes allowed us to recognize patterns in molecular recognition and strategies used by evolution for exercising selectivity. Overall, AARSs are 2-3 orders of magnitude more selective than most other amino acid utilizing enzymes. AARSs also reveal the physicochemical limits of molecular discrimination. For example, amino acids smaller by a single methyl moiety present a discrimination ceiling of ~200, while larger ones can be discriminated by up to 105 -fold. In contrast, substrates larger by a hydroxyl group challenge AARS selectivity, due to promiscuous H-bonding with polar active site groups. This 'hydroxyl paradox' is resolved by editing. Indeed, when the physicochemical discrimination limits are reached, post-transfer editing - hydrolysis of tRNAs charged with noncognate amino acids, evolved. The editing site often selectively recognizes the edited noncognate substrate using the very same feature that the synthetic site could not efficiently discriminate against. Finally, the comparison to other enzymes also reveals that the selectivity of AARSs is an explicitly evolved trait, showing some clear examples of how selection acted not only to optimize catalytic efficiency with the target substrate, but also to abolish activity with noncognate threat substrates ('negative selection').
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Affiliation(s)
- Dan S Tawfik
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Ita Gruic-Sovulj
- Department of Chemistry, Faculty of Science, University of Zagreb, Croatia
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17
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Kovalenko OP, Volynets GP, Rybak MY, Starosyla SA, Gudzera OI, Lukashov SS, Bdzhola VG, Yarmoluk SM, Boshoff HI, Tukalo MA. Dual-target inhibitors of mycobacterial aminoacyl-tRNA synthetases among N-benzylidene- N'-thiazol-2-yl-hydrazines. MEDCHEMCOMM 2019; 10:2161-2169. [PMID: 32206244 PMCID: PMC7069510 DOI: 10.1039/c9md00347a] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 11/09/2019] [Indexed: 12/19/2022]
Abstract
Effective treatment of tuberculosis is challenged by the rapid development of Mycobacterium tuberculosis (Mtb) multidrug resistance that presumably could be overcome with novel multi-target drugs. Aminoacyl-tRNA synthetases (AARSs) are an essential part of protein biosynthesis machinery and attractive targets for drug discovery. Here, we experimentally verify a hypothesis of simultaneous targeting of structurally related AARSs by a single inhibitor. We previously identified a new class of mycobacterial leucyl-tRNA synthetase inhibitors, N-benzylidene-N'-thiazol-2-yl-hydrazines. Molecular docking of a library of novel N-benzylidene-N'-thiazol-2-yl-hydrazine derivatives into active sites of M. tuberculosis LeuRS (MtbLeuRS) and MetRS (MtbMetRS) resulted in a panel of the best ranking compounds, which were then evaluated for enzymatic potency. Screening data revealed 11 compounds active against MtbLeuRS and 28 compounds active against MtbMetRS. The hit compounds display dual inhibitory potency as demonstrated by IC50 values for both enzymes. Compound 3 is active against Mtb H37Rv cells in in vitro bioassays.
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Affiliation(s)
- Oksana P Kovalenko
- Department of Protein Synthesis Enzymology , Institute of Molecular Biology and Genetics , The NAS of Ukraine , 150 Zabolotnogo St , 03143 Kyiv , Ukraine . ; ; ; Tel: +38 044 5265589
| | - Galyna P Volynets
- Department of Medicinal Chemistry , Institute of Molecular Biology and Genetics , The NAS of Ukraine , 150 Zabolotnogo St , 03143 Kyiv , Ukraine
| | - Mariia Yu Rybak
- Department of Protein Synthesis Enzymology , Institute of Molecular Biology and Genetics , The NAS of Ukraine , 150 Zabolotnogo St , 03143 Kyiv , Ukraine . ; ; ; Tel: +38 044 5265589
| | - Sergiy A Starosyla
- Department of Medicinal Chemistry , Institute of Molecular Biology and Genetics , The NAS of Ukraine , 150 Zabolotnogo St , 03143 Kyiv , Ukraine
| | - Olga I Gudzera
- Department of Protein Synthesis Enzymology , Institute of Molecular Biology and Genetics , The NAS of Ukraine , 150 Zabolotnogo St , 03143 Kyiv , Ukraine . ; ; ; Tel: +38 044 5265589
| | - Sergiy S Lukashov
- Department of Medicinal Chemistry , Institute of Molecular Biology and Genetics , The NAS of Ukraine , 150 Zabolotnogo St , 03143 Kyiv , Ukraine
| | - Volodymyr G Bdzhola
- Department of Medicinal Chemistry , Institute of Molecular Biology and Genetics , The NAS of Ukraine , 150 Zabolotnogo St , 03143 Kyiv , Ukraine
| | - Sergiy M Yarmoluk
- Department of Medicinal Chemistry , Institute of Molecular Biology and Genetics , The NAS of Ukraine , 150 Zabolotnogo St , 03143 Kyiv , Ukraine
| | - Helena I Boshoff
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology , National Institute of Allergy and Infectious Disease , National Institute of Health , 5601 Fishers Lane, MSC 9806 , Bethesda , MD 20892-9806 , Maryland , USA
| | - Michael A Tukalo
- Department of Protein Synthesis Enzymology , Institute of Molecular Biology and Genetics , The NAS of Ukraine , 150 Zabolotnogo St , 03143 Kyiv , Ukraine . ; ; ; Tel: +38 044 5265589
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18
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Zivkovic I, Moschner J, Koksch B, Gruic‐Sovulj I. Mechanism of discrimination of isoleucyl‐tRNA synthetase against nonproteinogenic α‐aminobutyrate and its fluorinated analogues. FEBS J 2019; 287:800-813. [DOI: 10.1111/febs.15053] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 07/12/2019] [Accepted: 08/30/2019] [Indexed: 11/29/2022]
Affiliation(s)
- Igor Zivkovic
- Department of Chemistry Faculty of Science University of Zagreb Croatia
| | - Johann Moschner
- Institute of Chemistry and Biochemistry – Organic Chemistry Freie Universitat Berlin Germany
| | - Beate Koksch
- Institute of Chemistry and Biochemistry – Organic Chemistry Freie Universitat Berlin Germany
| | - Ita Gruic‐Sovulj
- Department of Chemistry Faculty of Science University of Zagreb Croatia
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19
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Oxidation of phenylalanyl-tRNA synthetase positively regulates translational quality control. Proc Natl Acad Sci U S A 2019; 116:10058-10063. [PMID: 31036643 DOI: 10.1073/pnas.1901634116] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Accurate translation of the genetic code is maintained in part by aminoacyl-tRNA synthetases (aaRS) proofreading mechanisms that ensure correct attachment of a cognate amino acid to a transfer RNA (tRNA). During environmental stress, such as oxidative stress, demands on aaRS proofreading are altered by changes in the availability of cytoplasmic amino acids. For example, oxidative stress increases levels of cytotoxic tyrosine isomers, noncognate amino acids normally excluded from translation by the proofreading activity of phenylalanyl-tRNA synthetase (PheRS). Here we show that oxidation of PheRS induces a conformational change, generating a partially unstructured protein. This conformational change does not affect Phe or Tyr activation or the aminoacylation activity of PheRS. However, in vitro and ex vivo analyses reveal that proofreading activity to hydrolyze Tyr-tRNAPhe is increased during oxidative stress, while the cognate Phe-tRNAPhe aminoacylation activity is unchanged. In HPX-, Escherichia coli that lack reactive oxygen-scavenging enzymes and accumulate intracellular H2O2, we found that PheRS proofreading is increased by 11%, thereby providing potential protection against hazardous cytoplasmic m-Tyr accumulation. These findings show that in response to oxidative stress, PheRS proofreading is positively regulated without negative effects on the enzyme's housekeeping activity in translation. Our findings also illustrate that while the loss of quality control and mistranslation may be beneficial under some conditions, increased proofreading provides a mechanism for the cell to appropriately respond to environmental changes during oxidative stress.
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20
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Liang Z, Yu X, Zhong W. Peptide Sequence Influence on the Differentiation of Valine and Norvaline by Hot Electron Capture Dissociation. Anal Chem 2019; 91:4381-4387. [PMID: 30786210 DOI: 10.1021/acs.analchem.8b04808] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Isomeric amino acid residues such as valine (Val) and norvaline (Nva) are common in recombinant proteins. The mis-incorporation of Nva for leucine (Leu) causes heterogeneity and in some cases even toxicity. Previous studies have shown that hot electron capture dissociation (HECD) is able to differentiate Val from Nva by producing diagnostic w ions on custom designed synthetic model peptides. To broaden the utilization of HECD in proteomic studies and to define the critical structural features, a thorough investigation was performed on representative peptides including specifically designed synthetic peptides as well as biological peptides bearing tryptic digest-like features and peptides with post-translational modifications. Experimental evidence confirmed that the formation of a w ion is directly dependent upon the presence of the corresponding z ion. The results suggested that a charge carrier residue at the C-terminus is promoting the formation of diagnostic w ions for Nva. Thus, peptides resulting from trypsin digestion, with arginine (Arg) or lysine (Lys) at the C-terminus, can be analyzed using the HECD method. Post-translational modification (PTM) such as phosphorylation did not prevent the generation of the requisite side chain fragmentation w ions. These results suggest the general applicability of HECD for unambiguous identification of Val and Nva especially in structure characterization of therapeutic proteins.
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Affiliation(s)
- Zhidan Liang
- Analytical Research & Development, Merck Research Laboratories , Merck & Co., Inc. , Rahway , New Jersey 07065 , United States
| | - Xiang Yu
- Department of Pharmacokinetics, Pharmacodynamics, & Drug Metabolism (PPDM), Merck Research Laboratories , Merck & Co., Inc. , West Point , Pennsylvania 19486 , United States
| | - Wendy Zhong
- Analytical Research & Development, Merck Research Laboratories , Merck & Co., Inc. , Rahway , New Jersey 07065 , United States
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21
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Boël G, Danot O, de Lorenzo V, Danchin A. Omnipresent Maxwell's demons orchestrate information management in living cells. Microb Biotechnol 2019; 12:210-242. [PMID: 30806035 PMCID: PMC6389857 DOI: 10.1111/1751-7915.13378] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The development of synthetic biology calls for accurate understanding of the critical functions that allow construction and operation of a living cell. Besides coding for ubiquitous structures, minimal genomes encode a wealth of functions that dissipate energy in an unanticipated way. Analysis of these functions shows that they are meant to manage information under conditions when discrimination of substrates in a noisy background is preferred over a simple recognition process. We show here that many of these functions, including transporters and the ribosome construction machinery, behave as would behave a material implementation of the information-managing agent theorized by Maxwell almost 150 years ago and commonly known as Maxwell's demon (MxD). A core gene set encoding these functions belongs to the minimal genome required to allow the construction of an autonomous cell. These MxDs allow the cell to perform computations in an energy-efficient way that is vastly better than our contemporary computers.
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Affiliation(s)
- Grégory Boël
- UMR 8261 CNRS‐University Paris DiderotInstitut de Biologie Physico‐Chimique13 rue Pierre et Marie Curie75005ParisFrance
| | - Olivier Danot
- Institut Pasteur25‐28 rue du Docteur Roux75724Paris Cedex 15France
| | - Victor de Lorenzo
- Molecular Environmental Microbiology LaboratorySystems Biology ProgrammeCentro Nacional de BiotecnologiaC/Darwin n° 3, Campus de Cantoblanco28049MadridEspaña
| | - Antoine Danchin
- Institute of Cardiometabolism and NutritionHôpital de la Pitié‐Salpêtrière47 Boulevard de l'Hôpital75013ParisFrance
- The School of Biomedical SciencesLi Kashing Faculty of MedicineHong Kong University21, Sassoon RoadPokfulamSAR Hong Kong
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22
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Bilus M, Semanjski M, Mocibob M, Zivkovic I, Cvetesic N, Tawfik DS, Toth-Petroczy A, Macek B, Gruic-Sovulj I. On the Mechanism and Origin of Isoleucyl-tRNA Synthetase Editing against Norvaline. J Mol Biol 2019; 431:1284-1297. [PMID: 30711543 DOI: 10.1016/j.jmb.2019.01.029] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Revised: 01/20/2019] [Accepted: 01/22/2019] [Indexed: 11/17/2022]
Abstract
Aminoacyl-tRNA synthetases (aaRSs), the enzymes responsible for coupling tRNAs to their cognate amino acids, minimize translational errors by intrinsic hydrolytic editing. Here, we compared norvaline (Nva), a linear amino acid not coded for protein synthesis, to the proteinogenic, branched valine (Val) in their propensity to mistranslate isoleucine (Ile) in proteins. We show that in the synthetic site of isoleucyl-tRNA synthetase (IleRS), Nva and Val are activated and transferred to tRNA at similar rates. The efficiency of the synthetic site in pre-transfer editing of Nva and Val also appears to be similar. Post-transfer editing was, however, more rapid with Nva and consequently IleRS misaminoacylates Nva-tRNAIle at slower rate than Val-tRNAIle. Accordingly, an Escherichia coli strain lacking IleRS post-transfer editing misincorporated Nva and Val in the proteome to a similar extent and at the same Ile positions. However, Nva mistranslation inflicted higher toxicity than Val, in agreement with IleRS editing being optimized for hydrolysis of Nva-tRNAIle. Furthermore, we found that the evolutionary-related IleRS, leucyl- and valyl-tRNA synthetases (I/L/VRSs), all efficiently hydrolyze Nva-tRNAs even when editing of Nva seems redundant. We thus hypothesize that editing of Nva-tRNAs had already existed in the last common ancestor of I/L/VRSs, and that the editing domain of I/L/VRSs had primarily evolved to prevent infiltration of Nva into modern proteins.
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Affiliation(s)
- Mirna Bilus
- Department of Chemistry, Faculty of Science, University of Zagreb, Zagreb 10000, Croatia
| | - Maja Semanjski
- Proteome Center Tuebingen, University of Tuebingen, Tuebingen 72076, Germany
| | - Marko Mocibob
- Department of Chemistry, Faculty of Science, University of Zagreb, Zagreb 10000, Croatia
| | - Igor Zivkovic
- Department of Chemistry, Faculty of Science, University of Zagreb, Zagreb 10000, Croatia
| | - Nevena Cvetesic
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, and the MRC London Institute of Medical Sciences, London, W12 0NN, United Kingdom
| | - Dan S Tawfik
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Agnes Toth-Petroczy
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden 01307, Germany
| | - Boris Macek
- Proteome Center Tuebingen, University of Tuebingen, Tuebingen 72076, Germany
| | - Ita Gruic-Sovulj
- Department of Chemistry, Faculty of Science, University of Zagreb, Zagreb 10000, Croatia.
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23
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Samardzic K, Rodgers KJ. Cytotoxicity and mitochondrial dysfunction caused by the dietary supplement l-norvaline. Toxicol In Vitro 2019; 56:163-171. [PMID: 30703532 DOI: 10.1016/j.tiv.2019.01.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 01/14/2019] [Accepted: 01/26/2019] [Indexed: 02/07/2023]
Abstract
In addition to the 20 protein amino acids that are encoded for protein synthesis, hundreds of other naturally occurring amino acids, known as non-proteinogenic amino acids (NPAAs) exist. It is well known that some NPAAs are toxic through their ability to mimic protein amino acids, either in protein synthesis or in other metabolic pathways, and this property is utilised by some plants to inhibit the growth of other plants or kill herbivores. L-norvaline is an NPAA readily available for purchase as a dietary supplement. In light of previous evidence of l-norvaline's antifungal, antimicrobial and herbicidal activity, we examined the toxicity of l-norvaline to mammalian cells in vitro and showed that l-norvaline decreased cell viability at concentrations as low as 125 μM, caused necrotic cell death and significant changes to mitochondrial morphology and function. Furthermore, toxicity was reduced in the presence of structurally similar 'protein' amino acids, suggesting l-norvaline's cytotoxicity could be attributed to protein amino acid mimicry.
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Affiliation(s)
- Kate Samardzic
- School of Life Sciences, University of Technology Sydney, Harris Street, Sydney, NSW 2007, Australia
| | - Kenneth J Rodgers
- School of Life Sciences, University of Technology Sydney, Harris Street, Sydney, NSW 2007, Australia.
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24
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Ho DH, Kim H, Nam D, Sim H, Kim J, Kim HG, Son I, Seol W. LRRK2 impairs autophagy by mediating phosphorylation of leucyl-tRNA synthetase. Cell Biochem Funct 2018; 36:431-442. [PMID: 30411383 DOI: 10.1002/cbf.3364] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Revised: 09/19/2018] [Accepted: 10/06/2018] [Indexed: 02/05/2023]
Abstract
Leucine-rich repeat kinase 2 (LRRK2) is a causal gene of Parkinson disease. G2019S pathogenic mutation increases its kinase activity. LRRK2 regulates various phenotypes including autophagy, neurite outgrowth, and vesicle trafficking. Leucyl-tRNA synthetase (LRS) attaches leucine to tRNALeu and activates mTORC1. Down-regulation of LRS induces autophagy. We investigated the relationship between LRRK2 and LRS in regulating autophagy and observed interaction between endogenous LRRK2 and LRS proteins and LRS phosphorylation by LRRK2. Mutation studies implicated that T293 in the LRS editing domain was a putative phosphorylation site. Phospho-Thr in LRS was increased in cells overexpressing G2019S and dopaminergic neurons differentiated from induced pluripotent stem (iPS) cells of a G2019S carrier. It was decreased by treatment with an LRRK2 kinase inhibitor (GSK2578215A). Phosphomimetic T293D displayed lower leucine bindings than wild type (WT), suggesting its defective editing function. Cellular expression of T293D increased expression of GRP78/BiP, LC3B-II, and p62 proteins and number of LC3 puncta. Increase of GRP78 and phosphorylated LRS was diminished by treatment with GSK2578215A. Levels of LC3B, GRP78/BiP, p62, and α-synuclein proteins were also increased in G2019S transgenic (TG) mice. These data suggest that LRRK2-mediated LRS phosphorylation impairs autophagy by increasing protein misfolding and endoplasmic reticulum stress mediated by LRS editing defect. SIGNIFICANCE OF THE STUDY: Leucine-rich repeat kinase 2 (LRRK2) is the most common genetic cause of Parkinson disease (PD), and the most prevalent pathogenic mutation, G2019S, increases its kinase activity. In this study, we elucidated that leucyl-tRNA synthetase (LRS) was an LRRK2 kinase substrate and identified T293 as an LRRK2 phosphorylation site. LRRK2-meidated LRS phosphorylation or G2019S can lead to impairment of LRS editing, increased ER stress, and accumulation of autophagy markers. These results demonstrate that LRRK2 kinase activity can facilitate accumulation of misfolded protein, suggesting that LRRK2 kinase might be a potential PD therapeutic target along with previous studies.
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Affiliation(s)
- Dong Hwan Ho
- InAm Neuroscience Research Center, Sanbon Medical Center, College of Medicine, Wonkwang University, Gunpo, Republic of Korea
| | - Hyejung Kim
- InAm Neuroscience Research Center, Sanbon Medical Center, College of Medicine, Wonkwang University, Gunpo, Republic of Korea
| | - Daleum Nam
- InAm Neuroscience Research Center, Sanbon Medical Center, College of Medicine, Wonkwang University, Gunpo, Republic of Korea
| | - Hyuna Sim
- Stem Cell Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea.,Korea University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Janghwan Kim
- Stem Cell Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea.,Korea University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Hyung Gun Kim
- Department of Pharmacology, College of Medicine, Dankook University, Cheonan, Republic of Korea
| | - Ilhong Son
- InAm Neuroscience Research Center, Sanbon Medical Center, College of Medicine, Wonkwang University, Gunpo, Republic of Korea.,Department of Neurology, Sanbon Medical Center, College of Medicine, Wonkwang University, Gunpo, Republic of Korea
| | - Wongi Seol
- InAm Neuroscience Research Center, Sanbon Medical Center, College of Medicine, Wonkwang University, Gunpo, Republic of Korea
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25
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Noda-Garcia L, Liebermeister W, Tawfik DS. Metabolite–Enzyme Coevolution: From Single Enzymes to Metabolic Pathways and Networks. Annu Rev Biochem 2018; 87:187-216. [DOI: 10.1146/annurev-biochem-062917-012023] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
How individual enzymes evolved is relatively well understood. However, individual enzymes rarely confer a physiological advantage on their own. Judging by its current state, the emergence of metabolism seemingly demanded the simultaneous emergence of many enzymes. Indeed, how multicomponent interlocked systems, like metabolic pathways, evolved is largely an open question. This complexity can be unlocked if we assume that survival of the fittest applies not only to genes and enzymes but also to the metabolites they produce. This review develops our current knowledge of enzyme evolution into a wider hypothesis of pathway and network evolution. We describe the current models for pathway evolution and offer an integrative metabolite–enzyme coevolution hypothesis. Our hypothesis addresses the origins of new metabolites and of new enzymes and the order of their recruitment. We aim to not only survey established knowledge but also present open questions and potential ways of addressing them.
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Affiliation(s)
- Lianet Noda-Garcia
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel;,
| | - Wolfram Liebermeister
- INRA, Unité MaIAGE, 78352 Jouy en Josas, France
- Institute of Biochemistry, Charité Universitätsmedizin, Berlin, 10117 Berlin, Germany
| | - Dan S. Tawfik
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel;,
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26
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A molecular dynamics simulation study of amino acid selectivity of LeuRS editing domain from Thermus thermophilus. J Mol Graph Model 2018; 84:74-81. [PMID: 29935476 DOI: 10.1016/j.jmgm.2018.06.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 05/13/2018] [Accepted: 06/14/2018] [Indexed: 11/20/2022]
Abstract
The accuracy of protein synthesis is provided by the editing functions of aminoacyl-tRNA synthetases (aaRSs), a mechanism that eliminates misactivated amino acids or mischarged tRNAs. Despite research efforts, some molecular bases of these mechanisms are still unclear. The post-transfer editing pathway of leucyl-tRNA synthetase (LeuRS) carried out in a special insertion domain (the Connective Polypeptide 1 or CP1), as editing domain. Recently, it was shown by in vivo studies and was supported by mutagenesis, and the kinetics approaches that the CP1 domain of LeuRS has discriminatory power for different substrates. The goal of this work is to investigate the structural basis for amino acid recognition of LeuRS post-transfer editing processes with molecular dynamics (MD) simulation method. To pursue this aim, the molecular modeling studies on Thermus thermophiles LeuRS (LeuRSTT) with two post-transfer substrates (norvalyl-tRNALeu and isoleucyl-tRNALeu) was performed. Our results revealed that post-transfer substrate norvalyl-tRNALeu is more favorable. Moreover, the MD simulations show that branched side chain of Ile-A76 cannot allow water molecules to get close, which leads to a significant decrease in the rate of hydrolysis. Finally, the study showed that site mutation Asp347Ala has elucidated a number of fine structural differences in the binding mode of two post-transfer substrates to the active centre of LeuRS editing domain and two conserved threonines, namely Thr247 and Thr248, are responsible for the amino acid selection through the interaction with substrates.
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27
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Reitz C, Fan Q, Neubauer P. Synthesis of non-canonical branched-chain amino acids in Escherichia coli and approaches to avoid their incorporation into recombinant proteins. Curr Opin Biotechnol 2018; 53:248-253. [PMID: 29870877 DOI: 10.1016/j.copbio.2018.05.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Revised: 05/05/2018] [Accepted: 05/10/2018] [Indexed: 12/14/2022]
Abstract
In E. coli the non-canonical amino acids acids norvaline, norleucine, and β-methylnorleucine, which derive from an off-pathway of the branched-chain amino acid synthesis route are synthesized and incorporated into cellular and recombinant proteins. The synthesis of these amino acids is supported by a high flux of glucose through the glycolytic pathway in combination with a derepression of the enzymes of the branched chain amino acid pathway, for example, when leucine-rich proteins are produced. Avoiding the synthesis and misincorporation of these amino acids has been challenging, especially in large-scale pharmaceutical processes where the problem is boosted by the typical fed-batch production and the technical limitation of mass transfer in the bioreactors. Despite its industrial importance, so far this issue has not been discussed comprehensively. Therefore this paper reviews, firstly, the specific pathway of the non-canonical branched chain amino acids starting at pyruvate, secondly, the molecular factors for their misincorporation, and thirdly, approaches to avoid this misincoporation. While the synthesis of these amino acids is difficult to prevent due to the broad promiscuity of the connected enzymes, recent studies on the control mechanisms of aminoacyl tRNA synthetases open new opportunities to avoid this misincorporation.
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Affiliation(s)
- Christian Reitz
- Technische Universität Berlin, Institute of Biotechnology, Department of Bioprocess Engineering, Ackerstr. 76, D-13355 Berlin, Germany
| | - Qin Fan
- Technische Universität Berlin, Institute of Biotechnology, Department of Bioprocess Engineering, Ackerstr. 76, D-13355 Berlin, Germany
| | - Peter Neubauer
- Technische Universität Berlin, Institute of Biotechnology, Department of Bioprocess Engineering, Ackerstr. 76, D-13355 Berlin, Germany.
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28
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Dulic M, Cvetesic N, Zivkovic I, Palencia A, Cusack S, Bertosa B, Gruic-Sovulj I. Kinetic Origin of Substrate Specificity in Post-Transfer Editing by Leucyl-tRNA Synthetase. J Mol Biol 2018; 430:1-16. [DOI: 10.1016/j.jmb.2017.10.024] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 10/02/2017] [Accepted: 10/08/2017] [Indexed: 10/18/2022]
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29
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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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30
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Kelly P, Ibba M. Aminoacyl-tRNA Quality Control Provides a Speedy Solution to Discriminate Right from Wrong. J Mol Biol 2017; 430:17-19. [PMID: 29111345 DOI: 10.1016/j.jmb.2017.10.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 10/25/2017] [Indexed: 11/26/2022]
Affiliation(s)
- Paul Kelly
- Department of Microbiology, The Ohio State University, 318 West 12th Avenue, Columbus, OH 43210, United States; Molecular, Cellular, and Developmental Biology Program, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, United States
| | - Michael Ibba
- Department of Microbiology, The Ohio State University, 318 West 12th Avenue, Columbus, OH 43210, United States; Molecular, Cellular, and Developmental Biology Program, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, United States.
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31
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Wong HE, Huang CJ, Zhang Z. Amino acid misincorporation in recombinant proteins. Biotechnol Adv 2017; 36:168-181. [PMID: 29107148 DOI: 10.1016/j.biotechadv.2017.10.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 09/12/2017] [Accepted: 10/24/2017] [Indexed: 11/26/2022]
Abstract
Proteins provide the molecular basis for cellular structure, catalytic activity, signal transduction, and molecular transport in biological systems. Recombinant protein expression is widely used to prepare and manufacture novel proteins that serve as the foundation of many biopharmaceutical products. However, protein translation bioprocesses are inherently prone to low-level errors. These sequence variants caused by amino acid misincorporation have been observed in both native and recombinant proteins. Protein sequence variants impact product quality, and their presence can be exacerbated through cellular stress, overexpression, and nutrient starvation. Therefore, the cell line selection process, which is used in the biopharmaceutical industry, is not only directed towards maximizing productivity, but also focuses on selecting clones which yield low sequence variant levels, thereby proactively avoiding potentially inauspicious patient safety and efficacy outcomes. Here, we summarize a number of hallmark studies aimed at understanding the mechanisms of amino acid misincorporation, as well as exacerbating factors, and mitigation strategies. We also describe key advances in analytical technologies in the identification and quantification of sequence variants, and some practical considerations when using LC-MS/MS for detecting sequence variants.
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Affiliation(s)
- H Edward Wong
- Process Development, Amgen Inc., 1 Amgen Center Drive, Thousand Oaks, CA 91320, United States
| | - Chung-Jr Huang
- Process Development, Amgen Inc., 1 Amgen Center Drive, Thousand Oaks, CA 91320, United States
| | - Zhongqi Zhang
- Process Development, Amgen Inc., 1 Amgen Center Drive, Thousand Oaks, CA 91320, United States.
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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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Rayevsky AV, Sharifi M, Tukalo MA. Molecular modeling and molecular dynamics simulation study of archaeal leucyl-tRNA synthetase in complex with different mischarged tRNA in editing conformation. J Mol Graph Model 2017; 76:289-295. [PMID: 28743072 DOI: 10.1016/j.jmgm.2017.06.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 06/07/2017] [Accepted: 06/23/2017] [Indexed: 12/20/2022]
Abstract
Aminoacyl-tRNA synthetases (aaRSs) play important roles in maintaining the accuracy of protein synthesis. Some aaRSs accomplish this via editing mechanisms, among which leucyl-tRNA synthetase (LeuRS) edits non-cognate amino acid norvaline mainly by post-transfer editing. However, the molecular basis for this pathway for eukaryotic and archaeal LeuRS remain unclear. In this study, a complex of archaeal P. horikoshii LeuRS (PhLeuRS) with misacylated tRNALeu was modeled wherever tRNA's acceptor stem was oriented directly into the editing site. To understand the distinctive features of organization we reconstructed a complex of PhLeuRS with tRNA and visualize post-transfer editing interactions mode by performing molecular dynamics (MD) simulation studies. To study molecular basis for substrate selectivity by PhLeuRS's editing site we utilized MD simulation of the entire LeuRS complexes using a diverse charged form of tRNAs, namely norvalyl-tRNALeu and isoleucyl-tRNALeu. In general, the editing site organization of LeuRS from P.horikoshii has much in common with bacterial LeuRS. The MD simulation results revealed that the post-transfer editing substrate norvalyl-A76, binds more strongly than isoleucyl-A76. Moreover, the branched side chain of isoleucine prevents water molecules from being closer and hence the hydrolysis reaction slows significantly. To investigate a possible mechanism of the post-transfer editing reaction, by PhLeuRS we have determined that two water molecules (the attacking and assisting water molecules) are localized near the carbonyl group of the amino acid to be cleaved off. These water molecules approach the substrate from the opposite side to that observed for Thermus thermophilus LeuRS (TtLeuRS). Based on the results obtained, it was suggested that the post-transfer editing mechanism of PhLeuRS differs from that of prokaryotic TtLeuRS.
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Affiliation(s)
- A V Rayevsky
- Institute of Molecular Biology and Genetics, NAS of Ukraine, 150 Academician Zabolotny Str., Kyiv 03680, Ukraine.
| | - M Sharifi
- Medway School of Pharmacy, Universities of Kent and Greenwich, Kent ME4 4TB, UK
| | - M A Tukalo
- Institute of Molecular Biology and Genetics, NAS of Ukraine, 150 Academician Zabolotny Str., Kyiv 03680, Ukraine.
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34
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Characterization of tRNALeu binding interactions with Cu2+ and Pb2+ and their biological implications. J Inorg Biochem 2017; 171:90-99. [DOI: 10.1016/j.jinorgbio.2017.03.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 02/12/2017] [Accepted: 03/19/2017] [Indexed: 11/17/2022]
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35
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Pawar KI, Suma K, Seenivasan A, Kuncha SK, Routh SB, Kruparani SP, Sankaranarayanan R. Role of D-aminoacyl-tRNA deacylase beyond chiral proofreading as a cellular defense against glycine mischarging by AlaRS. eLife 2017; 6. [PMID: 28362257 PMCID: PMC5409826 DOI: 10.7554/elife.24001] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 03/30/2017] [Indexed: 12/18/2022] Open
Abstract
Strict L-chiral rejection through Gly-cisPro motif during chiral proofreading underlies the inability of D-aminoacyl-tRNA deacylase (DTD) to discriminate between D-amino acids and achiral glycine. The consequent Gly-tRNAGly ‘misediting paradox’ is resolved by EF-Tu in the cell. Here, we show that DTD’s active site architecture can efficiently edit mischarged Gly-tRNAAla species four orders of magnitude more efficiently than even AlaRS, the only ubiquitous cellular checkpoint known for clearing the error. Also, DTD knockout in AlaRS editing-defective background causes pronounced toxicity in Escherichia coli even at low-glycine levels which is alleviated by alanine supplementation. We further demonstrate that DTD positively selects the universally invariant tRNAAla-specific G3•U70. Moreover, DTD’s activity on non-cognate Gly-tRNAAla is conserved across all bacteria and eukaryotes, suggesting DTD’s key cellular role as a glycine deacylator. Our study thus reveals a hitherto unknown function of DTD in cracking the universal mechanistic dilemma encountered by AlaRS, and its physiological importance. DOI:http://dx.doi.org/10.7554/eLife.24001.001 Proteins are made up of many different building blocks called amino acids, which are linked together in chains. The exact order of amino acids in a protein chain is important for the protein to work properly. When a cell makes proteins, molecules known as transfer ribonucleic acids (or tRNAs for short) bind to specific amino acids to guide them to the growing protein chains in the correct order. Most amino acids – except one called glycine – have two forms that are mirror images of one another, known as left-handed (L-amino acids) and right-handed (D-amino acids). However, only L-amino acids and glycine are used to make proteins. This is because of the presence of multiple quality control checkpoints in the cell that prevent D-amino acids from being involved. One such checkpoint is an enzyme called D-amino acid deacylase (DTD), which removes D-amino acids that are attached to tRNAs. Other enzymes are responsible for linking a particular amino acid to its correct tRNA. Along with mistaking D-amino acids for L-amino acids, these enzymes can also make errors when they have to distinguish between amino acids that are similar in shape and size. For example, the enzyme that attaches L-alanine to its tRNA can also mistakenly attach larger L-serine or smaller glycine to it instead. Previous research has shown that attaching L-serine to this tRNA can lead to neurodegeneration in mice, whereas attaching glycine does not seem to cause any harm. It is not clear why this is the case. Pawar et al. investigated how incorrectly attaching glycine or L-serine to the tRNA that usually binds to L-alanine affects a bacterium called Escherichia coli. The experiments show that, if the mistake is not corrected, glycine can be just as harmful to the cells as L-serine. The reason that glycine appears to be less of a problem is that the DTD enzyme is able to remove glycine, but not L-serine, from the tRNA. Further experiments show that DTD can play a similar role in a variety of organisms from bacteria to mammals. The findings of Pawar et al. extend the role of DTD beyond preventing D-amino acids from being incorporated into proteins. The next step is to understand the role of this enzyme in humans and other multicellular organisms, especially in the context of nerve cells, where it is present at high levels. DOI:http://dx.doi.org/10.7554/eLife.24001.002
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Affiliation(s)
| | - Katta Suma
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
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36
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Jakubowski H. Homocysteine Editing, Thioester Chemistry, Coenzyme A, and the Origin of Coded Peptide Synthesis †. Life (Basel) 2017; 7:life7010006. [PMID: 28208756 PMCID: PMC5370406 DOI: 10.3390/life7010006] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 02/03/2017] [Indexed: 12/22/2022] Open
Abstract
Aminoacyl-tRNA synthetases (AARSs) have evolved “quality control” mechanisms which prevent tRNA aminoacylation with non-protein amino acids, such as homocysteine, homoserine, and ornithine, and thus their access to the Genetic Code. Of the ten AARSs that possess editing function, five edit homocysteine: Class I MetRS, ValRS, IleRS, LeuRS, and Class II LysRS. Studies of their editing function reveal that catalytic modules of these AARSs have a thiol-binding site that confers the ability to catalyze the aminoacylation of coenzyme A, pantetheine, and other thiols. Other AARSs also catalyze aminoacyl-thioester synthesis. Amino acid selectivity of AARSs in the aminoacyl thioesters formation reaction is relaxed, characteristic of primitive amino acid activation systems that may have originated in the Thioester World. With homocysteine and cysteine as thiol substrates, AARSs support peptide bond synthesis. Evolutionary origin of these activities is revealed by genomic comparisons, which show that AARSs are structurally related to proteins involved in coenzyme A/sulfur metabolism and non-coded peptide bond synthesis. These findings suggest that the extant AARSs descended from ancestral forms that were involved in non-coded Thioester-dependent peptide synthesis, functionally similar to the present-day non-ribosomal peptide synthetases.
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Affiliation(s)
- Hieronim Jakubowski
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, NJ 07103, USA.
- Department of Biochemistry and Biotechnology, University of Life Sciences, Poznan 60-632, Poland.
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Kermgard E, Yang Z, Michel AM, Simari R, Wong J, Ibba M, Lazazzera BA. Quality Control by Isoleucyl-tRNA Synthetase of Bacillus subtilis Is Required for Efficient Sporulation. Sci Rep 2017; 7:41763. [PMID: 28139725 PMCID: PMC5282499 DOI: 10.1038/srep41763] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 12/22/2016] [Indexed: 11/11/2022] Open
Abstract
Isoleucyl-tRNA synthetase (IleRS) is an aminoacyl-tRNA synthetase whose essential function is to aminoacylate tRNAIle with isoleucine. Like some other aminoacyl-tRNA synthetases, IleRS can mischarge tRNAIle and correct this misacylation through a separate post-transfer editing function. To explore the biological significance of this editing function, we created a ileS(T233P) mutant of Bacillus subtilis that allows tRNAIle mischarging while retaining wild-type Ile-tRNAIle synthesis activity. As seen in other species defective for aminoacylation quality control, the growth rate of the ileS(T233P) strain was not significantly different from wild-type. When the ileS(T233P) strain was assessed for its ability to promote distinct phenotypes in response to starvation, the ileS(T233P) strain was observed to exhibit a significant defect in formation of environmentally resistant spores. The sporulation defect ranged from 3-fold to 30-fold and was due to a delay in activation of early sporulation genes. The loss of aminoacylation quality control in the ileS(T233P) strain resulted in the inability to compete with a wild-type strain under selective conditions that required sporulation. These data show that the quality control function of IleRS is required in B. subtilis for efficient sporulation and suggests that editing by aminoacyl-tRNA synthetases may be important for survival under starvation/nutrient limitation conditions.
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Affiliation(s)
- Elizabeth Kermgard
- Department of Microbiology, Immunology and Molecular Genetics University of California, Los Angeles, California 90095, USA
| | - Zhou Yang
- Department of Microbiology, Immunology and Molecular Genetics University of California, Los Angeles, California 90095, USA
| | - Annika-Marisa Michel
- Department of Microbiology, Immunology and Molecular Genetics University of California, Los Angeles, California 90095, USA.,Technische Universität Braunschweig, Institut of Microbiology, Braunschweig, Germany
| | - Rachel Simari
- Ohio State Biochemistry Program, Ohio State University, Columbus, Ohio 43210, USA
| | - Jacqueline Wong
- Department of Microbiology, Immunology and Molecular Genetics University of California, Los Angeles, California 90095, USA
| | - Michael Ibba
- Ohio State Biochemistry Program, Ohio State University, Columbus, Ohio 43210, USA.,Department of Microbiology, Ohio State University, Columbus, Ohio 43210, USA.,Center for RNA Biology, Ohio State University, Columbus, Ohio 43210, USA
| | - Beth A Lazazzera
- Department of Microbiology, Immunology and Molecular Genetics University of California, Los Angeles, California 90095, USA.,Molecular Biology Institute, University of California, Los Angeles, California 90095, USA
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38
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Cvetesic N, Gruic-Sovulj I. Synthetic and editing reactions of aminoacyl-tRNA synthetases using cognate and non-cognate amino acid substrates. Methods 2016; 113:13-26. [PMID: 27713080 DOI: 10.1016/j.ymeth.2016.09.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 09/29/2016] [Accepted: 09/29/2016] [Indexed: 11/19/2022] Open
Abstract
The covalent coupling of cognate amino acid-tRNA pairs by corresponding aminoacyl-tRNA synthetases (aaRS) defines the genetic code and provides aminoacylated tRNAs for ribosomal protein synthesis. Besides the cognate substrate, some non-cognate amino acids may also compete for tRNA aminoacylation. However, their participation in protein synthesis is generally prevented by an aaRS proofreading activity located in the synthetic site and in a separate editing domain. These mechanisms, coupled with the ability of certain aaRSs to discriminate well against non-cognate amino acids in the synthetic reaction alone, define the accuracy of the aminoacylation reaction. aaRS quality control may also act as a gatekeeper for the standard genetic code and prevents infiltration by natural amino acids that are not normally coded for protein biosynthesis. This latter finding has reinforced interest in understanding the principles that govern discrimination against a range of potential non-cognate amino acids. This paper presents an overview of the kinetic assays that have been established for monitoring synthetic and editing reactions with cognate and non-cognate amino acid substrates. Taking into account the peculiarities of non-cognate reactions, the specific controls needed and the dedicated experimental designs are discussed in detail. Kinetic partitioning within the synthetic and editing sites controls the balance between editing and aminoacylation. We describe in detail steady-state and single-turnover approaches for the analysis of synthetic and editing reactions, which ultimately enable mechanisms of amino acid discrimination to be determined.
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Affiliation(s)
- Nevena Cvetesic
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia
| | - Ita Gruic-Sovulj
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia.
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Cryptosporidium and Toxoplasma Parasites Are Inhibited by a Benzoxaborole Targeting Leucyl-tRNA Synthetase. Antimicrob Agents Chemother 2016; 60:5817-27. [PMID: 27431220 PMCID: PMC5038320 DOI: 10.1128/aac.00873-16] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 07/07/2016] [Indexed: 11/20/2022] Open
Abstract
The apicomplexan parasites Cryptosporidium and Toxoplasma are serious threats to human health. Cryptosporidiosis is a severe diarrheal disease in malnourished children and immunocompromised individuals, with the only FDA-approved drug treatment currently being nitazoxanide. The existing therapies for toxoplasmosis, an important pathology in immunocompromised individuals and pregnant women, also have serious limitations. With the aim of developing alternative therapeutic options to address these health problems, we tested a number of benzoxaboroles, boron-containing compounds shown to be active against various infectious agents, for inhibition of the growth of Cryptosporidium parasites in mammalian cells. A 3-aminomethyl benzoxaborole, AN6426, with activity in the micromolar range and with activity comparable to that of nitazoxanide, was identified and further characterized using biophysical measurements of affinity and crystal structures of complexes with the editing domain of Cryptosporidium leucyl-tRNA synthetase (LeuRS). The same compound was shown to be active against Toxoplasma parasites, with the activity being enhanced in the presence of norvaline, an amino acid that can be mischarged by LeuRS. Our observations are consistent with AN6426 inhibiting protein synthesis in both Cryptosporidium and Toxoplasma by forming a covalent adduct with tRNA(Leu) in the LeuRS editing active site and suggest that further exploitation of the benzoxaborole scaffold is a valid strategy to develop novel, much needed antiparasitic agents.
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40
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Proteome-wide measurement of non-canonical bacterial mistranslation by quantitative mass spectrometry of protein modifications. Sci Rep 2016; 6:28631. [PMID: 27377007 PMCID: PMC4932531 DOI: 10.1038/srep28631] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 06/06/2016] [Indexed: 01/06/2023] Open
Abstract
The genetic code is virtually universal in biology and was likely established before the advent of cellular life. The extent to which mistranslation occurs is poorly understood and presents a fundamental question in basic research and production of recombinant proteins. Here we used shotgun proteomics combined with unbiased protein modification analysis to quantitatively analyze in vivo mistranslation in an E. coli strain with a defect in the editing mechanism of leucyl-tRNA synthetase. We detected the misincorporation of a non-proteinogenic amino acid norvaline on 10% of all measured leucine residues under microaerobic conditions and revealed preferential deployment of a tRNA(Leu)(CAG) isoacceptor during norvaline misincorporation. The strain with the norvalylated proteome demonstrated a substantial reduction in cell fitness under both prolonged aerobic and microaerobic cultivation. Unlike norvaline, isoleucine did not substitute for leucine even under harsh error-prone conditions. Our study introduces shotgun proteomics as a powerful tool in quantitative analysis of mistranslation.
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41
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Moghal A, Hwang L, Faull K, Ibba M. Multiple Quality Control Pathways Limit Non-protein Amino Acid Use by Yeast Cytoplasmic Phenylalanyl-tRNA Synthetase. J Biol Chem 2016; 291:15796-805. [PMID: 27226603 DOI: 10.1074/jbc.m116.726828] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Indexed: 11/06/2022] Open
Abstract
Non-protein amino acids, particularly isomers of the proteinogenic amino acids, present a threat to proteome integrity if they are mistakenly inserted into proteins. Quality control during aminoacyl-tRNA synthesis reduces non-protein amino acid incorporation by both substrate discrimination and proofreading. For example phenylalanyl-tRNA synthetase (PheRS) proofreads the non-protein hydroxylated phenylalanine derivative m-Tyr after its attachment to tRNA(Phe) We now show in Saccharomyces cerevisiae that PheRS misacylation of tRNA(Phe) with the more abundant Phe oxidation product o-Tyr is limited by kinetic discrimination against o-Tyr-AMP in the transfer step followed by o-Tyr-AMP release from the synthetic active site. This selective rejection of a non-protein aminoacyl-adenylate is in addition to known kinetic discrimination against certain non-cognates in the activation step as well as catalytic hydrolysis of mispaired aminoacyl-tRNA(Phe) species. We also report an unexpected resistance to cytotoxicity by a S. cerevisiae mutant with ablated post-transfer editing activity when supplemented with o-Tyr, cognate Phe, or Ala, the latter of which is not a substrate for activation by this enzyme. Our phenotypic, metabolomic, and kinetic analyses indicate at least three modes of discrimination against non-protein amino acids by S. cerevisiae PheRS and support a non-canonical role for SccytoPheRS post-transfer editing in response to amino acid stress.
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Affiliation(s)
- Adil Moghal
- From the Ohio State Biochemistry Program, Department of Microbiology, The Ohio State University, Columbus, Ohio 43210 and
| | - Lin Hwang
- Pasarow Mass Spectrometry Laboratory, Semel Institute of Neuroscience and Human Behavior, University of California, Los Angeles, California 90095
| | - Kym Faull
- Pasarow Mass Spectrometry Laboratory, Semel Institute of Neuroscience and Human Behavior, University of California, Los Angeles, California 90095
| | - Michael Ibba
- From the Ohio State Biochemistry Program, Department of Microbiology, The Ohio State University, Columbus, Ohio 43210 and
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Yu X, Zhong W. Differentiation of Norvaline and Valine in Peptides by Hot Electron Capture Dissociation. Anal Chem 2016; 88:5914-9. [DOI: 10.1021/acs.analchem.6b00823] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Xiang Yu
- Department of Pharmacokinetics, Pharmacodynamics, & Drug Metabolism (PPDM), Merck Research Laboratories, 770 Sumneytown Pike, West Point, Pennsylvania 19486, United States
| | - Wendy Zhong
- Process/Analytical
Chemistry, Merck Research Laboratories, 126 East Lincoln Avenue, Rahway, New Jersey 07065, United States
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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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44
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Cvetesic N, Dulic M, Bilus M, Sostaric N, Lenhard B, Gruic-Sovulj I. Naturally Occurring Isoleucyl-tRNA Synthetase without tRNA-dependent Pre-transfer Editing. J Biol Chem 2016; 291:8618-31. [PMID: 26921320 PMCID: PMC4861432 DOI: 10.1074/jbc.m115.698225] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Indexed: 11/23/2022] Open
Abstract
Isoleucyl-tRNA synthetase (IleRS) is unusual among aminoacyl-tRNA synthetases in having a tRNA-dependent pre-transfer editing activity. Alongside the typical bacterial IleRS (such as Escherichia coli IleRS), some bacteria also have the enzymes (eukaryote-like) that cluster with eukaryotic IleRSs and exhibit low sensitivity to the antibiotic mupirocin. Our phylogenetic analysis suggests that the ileS1 and ileS2 genes of contemporary bacteria are the descendants of genes that might have arisen by an ancient duplication event before the separation of bacteria and archaea. We present the analysis of evolutionary constraints of the synthetic and editing reactions in eukaryotic/eukaryote-like IleRSs, which share a common origin but diverged through adaptation to different cell environments. The enzyme from the yeast cytosol exhibits tRNA-dependent pre-transfer editing analogous to E. coli IleRS. This argues for the presence of this proofreading in the common ancestor of both IleRS types and an ancient origin of the synthetic site-based quality control step. Yet surprisingly, the eukaryote-like enzyme from Streptomyces griseus IleRS lacks this capacity; at the same time, its synthetic site displays the 103-fold drop in sensitivity to antibiotic mupirocin relative to the yeast enzyme. The discovery that pre-transfer editing is optional in IleRSs lends support to the notion that the conserved post-transfer editing domain is the main checkpoint in these enzymes. We substantiated this by showing that under error-prone conditions S. griseus IleRS is able to rescue the growth of an E. coli lacking functional IleRS, providing the first evidence that tRNA-dependent pre-transfer editing in IleRS is not essential for cell viability.
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Affiliation(s)
- Nevena Cvetesic
- From the Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia and
| | - Morana Dulic
- From the Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia and
| | - Mirna Bilus
- From the Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia and
| | - Nikolina Sostaric
- From the Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia and
| | - Boris Lenhard
- the Computational Regulatory Genomics Group, MRC Clinical Sciences Centre, Imperial College London, London W12 0NN, United Kingdom
| | - Ita Gruic-Sovulj
- From the Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia and
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45
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Soldà G, Caccia S, Robusto M, Chiereghin C, Castorina P, Ambrosetti U, Duga S, Asselta R. First independent replication of the involvement of LARS2 in Perrault syndrome by whole-exome sequencing of an Italian family. J Hum Genet 2015; 61:295-300. [PMID: 26657938 PMCID: PMC4817218 DOI: 10.1038/jhg.2015.149] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 11/09/2015] [Accepted: 11/10/2015] [Indexed: 11/24/2022]
Abstract
Perrault syndrome (MIM #233400) is a rare autosomal recessive disorder characterized by ovarian dysgenesis and primary ovarian insufficiency in females, and progressive hearing loss in both genders. Recently, mutations in five genes (HSD17B4, HARS2, CLPP, LARS2, and C10ORF2) were found to be responsible for Perrault syndrome, although they do not account for all cases of this genetically heterogeneous condition. We used whole-exome sequencing to identify pathogenic variants responsible for Perrault syndrome in an Italian pedigree with two affected siblings. Both patients were compound heterozygous for two novel missense variants within the mitochondrial leucyl-tRNA synthetase (LARS2), NM_015340.3:c.899C>T(p.Thr300Met) and c.1912G>A(p.Glu638Lys). Both variants co-segregated with the phenotype in the family. p.Thr300 and p.Glu638 are evolutionary conserved residues, and are located respectively within the editing domain and immediately before the catalytically important KMSKS motif. Homology modeling using as template the E. coli leucyl-tRNA synthetase provided further insights on the possible pathogenic effects of the identified variants. This represents the first independent replication of the involvement of LARS2 mutations in Perrault syndrome, contributing valuable information for the further understanding of this disease.
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Affiliation(s)
- Giulia Soldà
- Department of Biomedical Sciences, Humanitas University, Milan, Italy.,Humanitas Clinical and Research Center, Milan, Italy
| | - Sonia Caccia
- Department of Biomedical and Clinical Sciences "Luigi Sacco", Università degli Studi di Milano - LITA Vialba, Milan, Italy
| | - Michela Robusto
- Department of Biomedical Sciences, Humanitas University, Milan, Italy.,Humanitas Clinical and Research Center, Milan, Italy
| | - Chiara Chiereghin
- Department of Biomedical Sciences, Humanitas University, Milan, Italy.,Humanitas Clinical and Research Center, Milan, Italy
| | - Pierangela Castorina
- UO Audiologia, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Umberto Ambrosetti
- UO Audiologia, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milan, Italy.,Dipartimento di Scienze Cliniche e di Comunità, Università degli Studi di Milano, Milan, Italy
| | - Stefano Duga
- Department of Biomedical Sciences, Humanitas University, Milan, Italy.,Humanitas Clinical and Research Center, Milan, Italy
| | - Rosanna Asselta
- Department of Biomedical Sciences, Humanitas University, Milan, Italy.,Humanitas Clinical and Research Center, Milan, Italy
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46
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Ye Q, Wang M, Fang ZP, Ruan ZR, Ji QQ, Zhou XL, Wang ED. Degenerate connective polypeptide 1 (CP1) domain from human mitochondrial leucyl-tRNA synthetase. J Biol Chem 2015; 290:24391-402. [PMID: 26272616 DOI: 10.1074/jbc.m115.672824] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Indexed: 11/06/2022] Open
Abstract
The connective polypeptide 1 (CP1) editing domain of leucyl-tRNA synthetase (LeuRS) from various species either harbors a conserved active site to exclude tRNA mis-charging with noncognate amino acids or is evolutionarily truncated or lost because there is no requirement for high translational fidelity. However, human mitochondrial LeuRS (hmtLeuRS) contains a full-length but degenerate CP1 domain that has mutations in some residues important for post-transfer editing. The significance of such an inactive CP1 domain and a translational accuracy mechanism with different noncognate amino acids are not completely understood. Here, we identified the essential role of the evolutionarily divergent CP1 domain in facilitating hmtLeuRS's catalytic efficiency and endowing enzyme with resistance to AN2690, a broad-spectrum drug acting on LeuRSs. In addition, the canonical core of hmtLeuRS is not stringent for noncognate norvaline (Nva) and valine (Val). hmtLeuRS has a very weak tRNA-independent pre-transfer editing activity for Nva, which is insufficient to remove mis-activated Nva. Moreover, hmtLeuRS chimeras fused with a functional CP1 domain from LeuRSs of other species, regardless of origin, showed restored post-transfer editing activity and acquired fidelity during aminoacylation. This work offers a novel perspective on the role of the CP1 domain in optimizing aminoacylation efficiency.
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Affiliation(s)
- Qing Ye
- From the 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 and
| | - Meng Wang
- From the 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 and
| | - Zhi-Peng Fang
- From the 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 and
| | - Zhi-Rong Ruan
- From the 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 and
| | - Quan-Quan Ji
- From the 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 and
| | - Xiao-Long Zhou
- From the 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 and
| | - En-Duo Wang
- From the 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 and the School of Life Science and Technology, ShanghaiTech University, 319 Yue Yang Road, Shanghai 200031, China
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47
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Fang P, Han H, Wang J, Chen K, Chen X, Guo M. Structural Basis for Specific Inhibition of tRNA Synthetase by an ATP Competitive Inhibitor. ACTA ACUST UNITED AC 2015; 22:734-44. [PMID: 26074468 DOI: 10.1016/j.chembiol.2015.05.007] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 05/03/2015] [Accepted: 05/09/2015] [Indexed: 01/26/2023]
Abstract
Pharmaceutical inhibitors of aminoacyl-tRNA synthetases demand high species and family specificity. The antimalarial ATP-mimetic cladosporin selectively inhibits Plasmodium falciparum LysRS (PfLysRS). How the binding to a universal ATP site achieves the specificity is unknown. Here we report three crystal structures of cladosporin with human LysRS, PfLysRS, and a Pf-like human LysRS mutant. In all three structures, cladosporin occupies the class defining ATP-binding pocket, replacing the adenosine portion of ATP. Three residues holding the methyltetrahydropyran moiety of cladosporin are critical for the specificity of cladosporin against LysRS over other class II tRNA synthetase families. The species-exclusive inhibition of PfLysRS is linked to a structural divergence beyond the active site that mounts a lysine-specific stabilizing response to binding cladosporin. These analyses reveal that inherent divergence of tRNA synthetase structural assembly may allow for highly specific inhibition even through the otherwise universal substrate binding pocket and highlight the potential for structure-driven drug development.
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Affiliation(s)
- Pengfei Fang
- Department of Cancer Biology, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA.
| | - Hongyan Han
- Department of Cancer Biology, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA; School of Biology and Basic Medical Sciences, Soochow University, Suzhou 215123, People's Republic of China
| | - Jing Wang
- Department of Cancer Biology, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Kaige Chen
- Department of Cancer Biology, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Xin Chen
- Department of Cancer Biology, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Min Guo
- Department of Cancer Biology, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA; Department of Cell and Molecular Biology, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA.
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48
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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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Cvetesic N, Bilus M, Gruic-Sovulj I. The tRNA A76 Hydroxyl Groups Control Partitioning of the tRNA-dependent Pre- and Post-transfer Editing Pathways in Class I tRNA Synthetase. J Biol Chem 2015; 290:13981-91. [PMID: 25873392 DOI: 10.1074/jbc.m115.648568] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Indexed: 11/06/2022] Open
Abstract
Aminoacyl-tRNA synthetases catalyze ATP-dependent covalent coupling of cognate amino acids and tRNAs for ribosomal protein synthesis. Escherichia coli isoleucyl-tRNA synthetase (IleRS) exploits both the tRNA-dependent pre- and post-transfer editing pathways to minimize errors in translation. However, the molecular mechanisms by which tRNA(Ile) organizes the synthetic site to enhance pre-transfer editing, an idiosyncratic feature of IleRS, remains elusive. Here we show that tRNA(Ile) affects both the synthetic and editing reactions localized within the IleRS synthetic site. In a complex with cognate tRNA, IleRS exhibits a 10-fold faster aminoacyl-AMP hydrolysis and a 10-fold drop in amino acid affinity relative to the free enzyme. Remarkably, the specificity against non-cognate valine was not improved by the presence of tRNA in either of these processes. Instead, amino acid specificity is determined by the protein component per se, whereas the tRNA promotes catalytic performance of the synthetic site, bringing about less error-prone and kinetically optimized isoleucyl-tRNA(Ile) synthesis under cellular conditions. Finally, the extent to which tRNA(Ile) modulates activation and pre-transfer editing is independent of the intactness of its 3'-end. This finding decouples aminoacylation and pre-transfer editing within the IleRS synthetic site and further demonstrates that the A76 hydroxyl groups participate in post-transfer editing only. The data are consistent with a model whereby the 3'-end of the tRNA remains free to sample different positions within the IleRS·tRNA complex, whereas the fine-tuning of the synthetic site is attained via conformational rearrangement of the enzyme through the interactions with the remaining parts of the tRNA body.
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Affiliation(s)
- Nevena Cvetesic
- From the Department of Chemistry, University of Zagreb, Faculty of Science, Horvatovac 102a, 10000 Zagreb, Croatia
| | - Mirna Bilus
- From the Department of Chemistry, University of Zagreb, Faculty of Science, Horvatovac 102a, 10000 Zagreb, Croatia
| | - Ita Gruic-Sovulj
- From the Department of Chemistry, University of Zagreb, Faculty of Science, Horvatovac 102a, 10000 Zagreb, Croatia
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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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