1
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Lu F, Xia K, Su J, Yi J, Luo Z, Xu J, Gu Q, Chen B, Zhou H. Biochemical and structural characterization of chlorhexidine as an ATP-assisted inhibitor against type 1 methionyl-tRNA synthetase from Gram-positive bacteria. Eur J Med Chem 2024; 268:116303. [PMID: 38458107 DOI: 10.1016/j.ejmech.2024.116303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 02/27/2024] [Accepted: 03/02/2024] [Indexed: 03/10/2024]
Abstract
Methionyl-tRNA synthetase (MetRS) catalyzes the attachment of l-methionine (l-Met) to tRNAMet to generate methionyl-tRNAMet, an essential substrate for protein translation within ribosome. Owing to its indispensable biological function and the structural discrepancies with human counterpart, bacterial MetRS is considered an ideal target for developing antibacterials. Herein, chlorhexidine (CHX) was identified as a potent binder of Staphylococcus aureus MetRS (SaMetRS) through an ATP-aided affinity screening. The co-crystal structure showed that CHX simultaneously occupies the enlarged l-Met pocket (EMP) and the auxiliary pocket (AP) of SaMetRS with its two chlorophenyl groups, while its central hexyl linker swings upwards to interact with some conserved hydrophobic residues. ATP adopts alternative conformations in the active site cavity, and forms ionic bonds and water-mediated hydrogen bonds with CHX. Consistent with this synergistic binding mode, ATP concentration-dependently enhanced the binding affinity of CHX to SaMetRS from 10.2 μM (no ATP) to 0.45 μM (1 mM ATP). While it selectively inhibited two representative type 1 MetRSs from S. aureus and Enterococcus faecalis, CHX did not show significant interactions with three tested type 2 MetRSs, including human cytoplasmic MetRS, in the enzyme inhibition and biophysical binding assays, probably due to the conformational differences between two types of MetRSs at their EMP and AP. Our findings on CHX may inspire the design of MetRS-directed antimicrobials in future.
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Affiliation(s)
- Feihu Lu
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China; Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Kaijiang Xia
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China; Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Jingtian Su
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China; Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Jia Yi
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China; Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Zhiteng Luo
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China; Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Jun Xu
- Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Qiong Gu
- Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Bingyi Chen
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China; Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China.
| | - Huihao Zhou
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China; Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China.
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2
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Luo X, Liu M, Wang S, Chen Y, Bao X, Lv Y, Zhang S, Xu B, Weng X, Bai X, Zeng M, Zhao C, Li J, Jia H, Yu B. Combining metabolomics and OCT to reveal plasma metabolic profiling and biomarkers of plaque erosion and plaque rupture in STEMI patients. Int J Cardiol 2023; 390:131223. [PMID: 37517782 DOI: 10.1016/j.ijcard.2023.131223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 01/15/2023] [Accepted: 02/26/2023] [Indexed: 08/01/2023]
Abstract
OBJECTIVE Plaque erosion (PE) and plaque rupture (PR) are the main subtypes of ST-segment elevation myocardial infarction (STEMI), the differences of metabolic patterns between PE and PR remain largely unknown. METHODS 132 STEMI patients were divided into training set (PR, n = 36; PE, n = 36) and test set (PR, n = 30; PE, n = 30), the plasma from patients were analyzed by liquid chromatography quadruple time-of-flight mass spectrometry. RESULTS We identified 56 and 28 differences in training and test set, respectively. Among these metabolites, it was found that docosahexaenoic acid (DHA), salicylic acid and proline were recognized in both tests. Receiver Operating Characteristic (ROC) analysis showed that the area under curve of docosahexaenoic acid (DHA) was 0.81 and 0.75 in training and test samples, respectively; proline was 0.67 and 0.74 in training and test samples, respectively; salicylic acid was 0.70 and 0.73 in training and test samples, respectively. CONCLUSIONS DHA, salicylic acid, and proline could be used as non-invasive biomarkers to differentiate PE and PR.
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Affiliation(s)
- Xing Luo
- Department of Cardiology, 2nd Affiliated Hospital of Harbin Medical University, Harbin 150001, PR China; Key Laboratory of Myocardial Ischemia, Ministry of Education, Harbin Medical University, Harbin 150001, PR China
| | - Minghao Liu
- Department of Cardiology, 2nd Affiliated Hospital of Harbin Medical University, Harbin 150001, PR China; Key Laboratory of Myocardial Ischemia, Ministry of Education, Harbin Medical University, Harbin 150001, PR China
| | - Shengfang Wang
- Department of Cardiology, 2nd Affiliated Hospital of Harbin Medical University, Harbin 150001, PR China; Key Laboratory of Myocardial Ischemia, Ministry of Education, Harbin Medical University, Harbin 150001, PR China
| | - Yuwu Chen
- Department of Cardiology, 2nd Affiliated Hospital of Harbin Medical University, Harbin 150001, PR China; Key Laboratory of Myocardial Ischemia, Ministry of Education, Harbin Medical University, Harbin 150001, PR China
| | - Xiaoyi Bao
- Department of Cardiology, 2nd Affiliated Hospital of Harbin Medical University, Harbin 150001, PR China; Key Laboratory of Myocardial Ischemia, Ministry of Education, Harbin Medical University, Harbin 150001, PR China
| | - Ying Lv
- Department of Cardiology, 2nd Affiliated Hospital of Harbin Medical University, Harbin 150001, PR China; Key Laboratory of Myocardial Ischemia, Ministry of Education, Harbin Medical University, Harbin 150001, PR China
| | - Shan Zhang
- Department of Cardiology, 2nd Affiliated Hospital of Harbin Medical University, Harbin 150001, PR China; Key Laboratory of Myocardial Ischemia, Ministry of Education, Harbin Medical University, Harbin 150001, PR China
| | - Biyi Xu
- Department of Cardiology, 2nd Affiliated Hospital of Harbin Medical University, Harbin 150001, PR China; Key Laboratory of Myocardial Ischemia, Ministry of Education, Harbin Medical University, Harbin 150001, PR China
| | - Xiuzhu Weng
- Department of Cardiology, 2nd Affiliated Hospital of Harbin Medical University, Harbin 150001, PR China; Key Laboratory of Myocardial Ischemia, Ministry of Education, Harbin Medical University, Harbin 150001, PR China
| | - Xiaoxuan Bai
- Department of Cardiology, 2nd Affiliated Hospital of Harbin Medical University, Harbin 150001, PR China; Key Laboratory of Myocardial Ischemia, Ministry of Education, Harbin Medical University, Harbin 150001, PR China
| | - Ming Zeng
- Department of Cardiology, 2nd Affiliated Hospital of Harbin Medical University, Harbin 150001, PR China; Key Laboratory of Myocardial Ischemia, Ministry of Education, Harbin Medical University, Harbin 150001, PR China
| | - Chen Zhao
- Department of Cardiology, 2nd Affiliated Hospital of Harbin Medical University, Harbin 150001, PR China; Key Laboratory of Myocardial Ischemia, Ministry of Education, Harbin Medical University, Harbin 150001, PR China
| | - Ji Li
- Department of Cardiology, 2nd Affiliated Hospital of Harbin Medical University, Harbin 150001, PR China; Key Laboratory of Myocardial Ischemia, Ministry of Education, Harbin Medical University, Harbin 150001, PR China
| | - Haibo Jia
- Department of Cardiology, 2nd Affiliated Hospital of Harbin Medical University, Harbin 150001, PR China; Key Laboratory of Myocardial Ischemia, Ministry of Education, Harbin Medical University, Harbin 150001, PR China.
| | - Bo Yu
- Department of Cardiology, 2nd Affiliated Hospital of Harbin Medical University, Harbin 150001, PR China; Key Laboratory of Myocardial Ischemia, Ministry of Education, Harbin Medical University, Harbin 150001, PR China.
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3
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Tijaro-Bulla S, Nyandwi SP, Cui H. Physiological and engineered tRNA aminoacylation. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1789. [PMID: 37042417 DOI: 10.1002/wrna.1789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 03/11/2023] [Accepted: 03/21/2023] [Indexed: 04/13/2023]
Abstract
Aminoacyl-tRNA synthetases form the protein family that controls the interpretation of the genetic code, with tRNA aminoacylation being the key chemical step during which an amino acid is assigned to a corresponding sequence of nucleic acids. In consequence, aminoacyl-tRNA synthetases have been studied in their physiological context, in disease states, and as tools for synthetic biology to enable the expansion of the genetic code. Here, we review the fundamentals of aminoacyl-tRNA synthetase biology and classification, with a focus on mammalian cytoplasmic enzymes. We compile evidence that the localization of aminoacyl-tRNA synthetases can be critical in health and disease. In addition, we discuss evidence from synthetic biology which made use of the importance of subcellular localization for efficient manipulation of the protein synthesis machinery. This article is categorized under: RNA Processing Translation > Translation Regulation RNA Processing > tRNA Processing RNA Export and Localization > RNA Localization.
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Affiliation(s)
| | | | - Haissi Cui
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
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4
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Mohler K, Moen JM, Rogulina S, Rinehart J. System-wide optimization of an orthogonal translation system with enhanced biological tolerance. Mol Syst Biol 2023; 19:e10591. [PMID: 37477096 PMCID: PMC10407733 DOI: 10.15252/msb.202110591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 07/05/2023] [Accepted: 07/05/2023] [Indexed: 07/22/2023] Open
Abstract
Over the past two decades, synthetic biological systems have revolutionized the study of cellular physiology. The ability to site-specifically incorporate biologically relevant non-standard amino acids using orthogonal translation systems (OTSs) has proven particularly useful, providing unparalleled access to cellular mechanisms modulated by post-translational modifications, such as protein phosphorylation. However, despite significant advances in OTS design and function, the systems-level biology of OTS development and utilization remains underexplored. In this study, we employ a phosphoserine OTS (pSerOTS) as a model to systematically investigate global interactions between OTS components and the cellular environment, aiming to improve OTS performance. Based on this analysis, we design OTS variants to enhance orthogonality by minimizing host process interactions and reducing stress response activation. Our findings advance understanding of system-wide OTS:host interactions, enabling informed design practices that circumvent deleterious interactions with host physiology while improving OTS performance and stability. Furthermore, our study emphasizes the importance of establishing a pipeline for systematically profiling OTS:host interactions to enhance orthogonality and mitigate mechanisms underlying OTS-mediated host toxicity.
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Affiliation(s)
- Kyle Mohler
- Department of Cellular & Molecular PhysiologyYale School of MedicineNew HavenCTUSA
- Systems Biology InstituteYale UniversityNew HavenCTUSA
| | - Jack M Moen
- Quantitative Biosciences Institute (QBI)University of California, San FranciscoSan FranciscoCAUSA
- 2QBI Coronavirus Research Group (QCRG)San FranciscoCAUSA
- Department of Cellular and Molecular PharmacologyUniversity of California, San FranciscoSan FranciscoCAUSA
| | - Svetlana Rogulina
- Department of Cellular & Molecular PhysiologyYale School of MedicineNew HavenCTUSA
- Systems Biology InstituteYale UniversityNew HavenCTUSA
| | - Jesse Rinehart
- Department of Cellular & Molecular PhysiologyYale School of MedicineNew HavenCTUSA
- Systems Biology InstituteYale UniversityNew HavenCTUSA
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5
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Jakubowski H. Proteomic Exploration of Paraoxonase 1 Function in Health and Disease. Int J Mol Sci 2023; 24:ijms24097764. [PMID: 37175471 PMCID: PMC10178420 DOI: 10.3390/ijms24097764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/08/2023] [Accepted: 04/14/2023] [Indexed: 05/15/2023] Open
Abstract
High-density lipoprotein (HDL) exhibits cardio- and neuro-protective properties, which are thought to be promoted by paraoxonase 1 (PON1), a hydrolytic enzyme associated with an HDL subfraction also enriched with an anticoagulant protein (PROS1) and amyloid beta-transport protein clusterin (CLU, APOJ). Reduced levels of PON1 activity, characterized biochemically by elevated levels of homocysteine (Hcy)-thiolactone, oxidized lipids, and proteins modified by these metabolites in humans and mice, are associated with pathological abnormalities affecting the cardiovascular system (atherothrombosis) and the central nervous system (cognitive impairment, Alzheimer's disease). The molecular bases of these abnormalities have been largely unknown. Proteomic and metabolic studies over the past decade have significantly contributed to our understanding of PON1 function and the mechanisms by which PON1 deficiency can lead to disease. Recent studies discussed in this review highlight the involvement of dysregulated proteostasis in the pro-oxidative, pro-atherothrombotic, and pro-amyloidogenic phenotypes associated with low PON1 activity.
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Affiliation(s)
- Hieronim Jakubowski
- Department of Biochemistry and Biotechnology, University of Life Sciences, 60-637 Poznań, Poland
- Department of Microbiology, Biochemistry and Molecular Genetics, International Center for Public Health, New Jersey Medical School, Rutgers University, Newark, NJ 07103, USA
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6
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Parker MD, Karbstein K. Quality control ensures fidelity in ribosome assembly and cellular health. J Cell Biol 2023; 222:213871. [PMID: 36790396 PMCID: PMC9960125 DOI: 10.1083/jcb.202209115] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 01/09/2023] [Accepted: 02/02/2023] [Indexed: 02/16/2023] Open
Abstract
The coordinated integration of ribosomal RNA and protein into two functional ribosomal subunits is safeguarded by quality control checkpoints that ensure ribosomes are correctly assembled and functional before they engage in translation. Quality control is critical in maintaining the integrity of ribosomes and necessary to support healthy cell growth and prevent diseases associated with mistakes in ribosome assembly. Its importance is demonstrated by the finding that bypassing quality control leads to misassembled, malfunctioning ribosomes with altered translation fidelity, which change gene expression and disrupt protein homeostasis. In this review, we outline our understanding of quality control within ribosome synthesis and how failure to enforce quality control contributes to human disease. We first provide a definition of quality control to guide our investigation, briefly present the main assembly steps, and then examine stages of assembly that test ribosome function, establish a pass-fail system to evaluate these functions, and contribute to altered ribosome performance when bypassed, and are thus considered "quality control."
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Affiliation(s)
- Melissa D. Parker
- The Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, La Jolla, CA, USA,University of Florida—Scripps Biomedical Research, Jupiter, FL, USA
| | - Katrin Karbstein
- The Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, La Jolla, CA, USA,University of Florida—Scripps Biomedical Research, Jupiter, FL, USA,Howard Hughes Medical Institute Faculty Scholar, Howard Hughes Medical Institute, Chevy Chase, MD, USA,Correspondence to Katrin Karbstein:
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7
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Giegé R, Eriani G. The tRNA identity landscape for aminoacylation and beyond. Nucleic Acids Res 2023; 51:1528-1570. [PMID: 36744444 PMCID: PMC9976931 DOI: 10.1093/nar/gkad007] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 12/21/2022] [Accepted: 01/03/2023] [Indexed: 02/07/2023] Open
Abstract
tRNAs are key partners in ribosome-dependent protein synthesis. This process is highly dependent on the fidelity of tRNA aminoacylation by aminoacyl-tRNA synthetases and relies primarily on sets of identities within tRNA molecules composed of determinants and antideterminants preventing mischarging by non-cognate synthetases. Such identity sets were discovered in the tRNAs of a few model organisms, and their properties were generalized as universal identity rules. Since then, the panel of identity elements governing the accuracy of tRNA aminoacylation has expanded considerably, but the increasing number of reported functional idiosyncrasies has led to some confusion. In parallel, the description of other processes involving tRNAs, often well beyond aminoacylation, has progressed considerably, greatly expanding their interactome and uncovering multiple novel identities on the same tRNA molecule. This review highlights key findings on the mechanistics and evolution of tRNA and tRNA-like identities. In addition, new methods and their results for searching sets of multiple identities on a single tRNA are discussed. Taken together, this knowledge shows that a comprehensive understanding of the functional role of individual and collective nucleotide identity sets in tRNA molecules is needed for medical, biotechnological and other applications.
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Affiliation(s)
- Richard Giegé
- Correspondence may also be addressed to Richard Giegé.
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8
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Witucki Ł, Borowczyk K, Suszyńska-Zajczyk J, Warzych E, Pawlak P, Jakubowski H. Deletion of the Homocysteine Thiolactone Detoxifying Enzyme Bleomycin Hydrolase, in Mice, Causes Memory and Neurological Deficits and Worsens Alzheimer's Disease-Related Behavioral and Biochemical Traits in the 5xFAD Model of Alzheimer's Disease. J Alzheimers Dis 2023; 95:1735-1755. [PMID: 37718819 PMCID: PMC10578231 DOI: 10.3233/jad-230578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/05/2023] [Indexed: 09/19/2023]
Abstract
BACKGROUND Bleomycin hydrolase (BLMH), a homocysteine (Hcy)-thiolactone detoxifying enzyme, is attenuated in Alzheimer's disease (AD) brains. Blmh loss causes astrogliosis in mice while the loss of histone demethylase Phf8, which controls mTOR signaling, causes neuropathy in mice and humans. OBJECTIVE To examine how Blmh gene deletion affects the Phf8/H4K20me1/mTOR/autophagy pathway, amyloid-β (Aβ) accumulation, and cognitive/neuromotor performance in mice. METHODS We generated a new mouse model of AD, the Blmh-/-5xFAD mouse. Behavioral assessments were conducted by cognitive/neuromotor testing. Blmh and Phf8 genes were silenced in mouse neuroblastoma N2a-APPswe cells by RNA interference. mTOR- and autophagy-related proteins, and AβPP were quantified by western blotting and the corresponding mRNAs by RT-qPCR. Aβ was quantified by western blotting (brains) and by confocal microscopy (cells). RESULTS Behavioral testing showed cognitive/neuromotor deficits in Blmh-/- and Blmh-/-5xFAD mice. Phf8 was transcriptionally downregulated in Blmh-/- and Blmh-/-5xFAD brains. H4K20me1, mTOR, phospho-mTOR, and AβPP were upregulated while autophagy markers Becn1, Atg5, and Atg7 were downregulated in Blmh-/- and Blmh-/-5xFAD brains. Aβ was elevated in Blmh-/-5xFAD brains. These biochemical changes were recapitulated in Blmh-silenced N2a-APPswe cells, which also showed increased H4K20me1-mTOR promoter binding and impaired autophagy flux (Lc3-I, Lc3-II, p62). Phf8-silencing or treatments with Hcy-thiolactone or N-Hcy-protein, metabolites elevated in Blmh-/- mice, induced biochemical changes in N2a-APPswe cells like those induced by the Blmh-silencing. However, Phf8-silencing elevated Aβ without affecting AβPP. CONCLUSIONS Our findings show that Blmh interacts with AβPP and the Phf8/H4K20me1/mTOR/autophagy pathway, and that disruption of those interactions causes Aβ accumulation and cognitive/neuromotor deficits.
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Affiliation(s)
- Łukasz Witucki
- Department of Biochemistry and Biotechnology, Poznań University of Life Sciences, Poznań, Poland
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers University, New Jersey Medical School, International Center for Public Health, Newark, NJ, USA
| | - Kamila Borowczyk
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers University, New Jersey Medical School, International Center for Public Health, Newark, NJ, USA
| | - Joanna Suszyńska-Zajczyk
- Department of Biochemistry and Biotechnology, Poznań University of Life Sciences, Poznań, Poland
| | - Ewelina Warzych
- Department of Genetics and Animal Breeding, Poznań University of Life Sciences, Poznań, Poland
| | - Piotr Pawlak
- Department of Genetics and Animal Breeding, Poznań University of Life Sciences, Poznań, Poland
| | - Hieronim Jakubowski
- Department of Biochemistry and Biotechnology, Poznań University of Life Sciences, Poznań, Poland
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers University, New Jersey Medical School, International Center for Public Health, Newark, NJ, USA
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9
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Chen SM, Tang XQ. Homocysteinylation and Sulfhydration in Diseases. Curr Neuropharmacol 2022; 20:1726-1735. [PMID: 34951391 PMCID: PMC9881069 DOI: 10.2174/1570159x20666211223125448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 11/02/2021] [Accepted: 12/18/2021] [Indexed: 11/22/2022] Open
Abstract
Homocysteine (Hcy) is an important intermediate in methionine metabolism and generation of one-carbon units, and its dysfunction is associated with many pathological states. Although Hcy is a non-protein amino acid, many studies have demonstrated protein-related homocysteine metabolism and possible mechanisms underlying homocysteinylation. Homocysteinylated proteins lose their original biological function and have a negative effect on the various disease phenotypes. Hydrogen sulfide (H2S) has been recognized as an important gaseous signaling molecule with mounting physiological properties. H2S modifies small molecules and proteins via sulfhydration, which is supposed to be essential in the regulation of biological functions and signal transduction in human health and disorders. This review briefly introduces Hcy and H2S, further discusses pathophysiological consequences of homocysteine modification and sulfhydryl modification, and ultimately makes a prediction that H2S might exert a protective effect on the toxicity of homocysteinylation of target protein via sulfhydration. The highlighted information here yields new insights into the role of protein modification by Hcy and H2S in diseases.
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Affiliation(s)
- Si-Min Chen
- Emergency Intensive Care Unit, Department of Emergency, Xiangtan Central Hospital, Xiangtan, 411100, Hunan, P.R. China; ,The First Affiliated Hospital, Institute of Neurology, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, P.R. China; ,Institute of Neuroscience, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, P.R. China
| | - Xiao-Qing Tang
- The First Affiliated Hospital, Institute of Neurology, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, P.R. China; ,Institute of Neuroscience, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, P.R. China,Address correspondence to this author at the The First Affiliated Hospital, Institute of Neurology, Hengyang Medical School, University of South China 69 Chuanshan Road, Hengyang 421001, Hunan Province, P.R. China; E-mails: ;
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10
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Yi J, Cai Z, Qiu H, Lu F, Luo Z, Chen B, Gu Q, Xu J, Zhou H. Fragment screening and structural analyses highlight the ATP-assisted ligand binding for inhibitor discovery against type 1 methionyl-tRNA synthetase. Nucleic Acids Res 2022; 50:4755-4768. [PMID: 35474479 PMCID: PMC9071491 DOI: 10.1093/nar/gkac285] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 04/05/2022] [Accepted: 04/13/2022] [Indexed: 12/24/2022] Open
Abstract
Methionyl-tRNA synthetase (MetRS) charges tRNAMet with l-methionine (L-Met) to decode the ATG codon for protein translation, making it indispensable for all cellular lives. Many gram-positive bacteria use a type 1 MetRS (MetRS1), which is considered a promising antimicrobial drug target due to its low sequence identity with human cytosolic MetRS (HcMetRS, which belongs to MetRS2). Here, we report crystal structures of a representative MetRS1 from Staphylococcus aureus (SaMetRS) in its apo and substrate-binding forms. The connecting peptide (CP) domain of SaMetRS differs from HcMetRS in structural organization and dynamic movement. We screened 1049 chemical fragments against SaMetRS preincubated with or without substrate ATP, and ten hits were identified. Four cocrystal structures revealed that the fragments bound to either the L-Met binding site or an auxiliary pocket near the tRNA CCA end binding site of SaMetRS. Interestingly, fragment binding was enhanced by ATP in most cases, suggesting a potential ATP-assisted ligand binding mechanism in MetRS1. Moreover, co-binding with ATP was also observed in our cocrystal structure of SaMetRS with a class of newly reported inhibitors that simultaneously occupied the auxiliary pocket, tRNA site and L-Met site. Our findings will inspire the development of new MetRS1 inhibitors for fighting microbial infections.
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Affiliation(s)
| | | | - Haipeng Qiu
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China,Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Feihu Lu
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China,Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Zhiteng Luo
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China,Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Bingyi Chen
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China,Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Qiong Gu
- Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Jun Xu
- Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Huihao Zhou
- To whom correspondence should be addressed. Tel: +86 20 39943350;
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11
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Zhang Z, Liao D, Ma Y, Jia B, Yuan Y. Orthogonality of Redesigned
tRNA
Molecules with Three Stop Codons. CHINESE J CHEM 2022. [DOI: 10.1002/cjoc.202100759] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Zhao‐Yang Zhang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology Tianjin University Tianjin 300072 China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Tianjin University Tianjin 300072 China
| | - Dan‐Ni Liao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology Tianjin University Tianjin 300072 China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Tianjin University Tianjin 300072 China
| | - Yu‐Xin Ma
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology Tianjin University Tianjin 300072 China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Tianjin University Tianjin 300072 China
| | - Bin Jia
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology Tianjin University Tianjin 300072 China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Tianjin University Tianjin 300072 China
| | - Ying‐Jin Yuan
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology Tianjin University Tianjin 300072 China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Tianjin University Tianjin 300072 China
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12
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Fankhauser D, Alissandratos A, Liutkus M, Easton CJ. Easy Production of "Difficult Peptides" Using Cell-Free Protein Synthesis and a New Methionine Analogue as a Latent Peptide Cleavage Site. Chemistry 2021; 27:17487-17494. [PMID: 34651362 DOI: 10.1002/chem.202103161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Indexed: 11/08/2022]
Abstract
Aliphatic γ-chloro-α-amino acids incorporated in place of their canonical analogues through cell-free protein synthesis act as heat-labile linkers, offering a useful strategy for the straightforward production of target peptides as fusion proteins, from which the targets are readily released. Until now, the natural abundance of aliphatic amino acids in peptides has limited the scope of the method, as it leads to undesired cleavage sites in synthesized products, but here the authors report the development of a new cleavable chloro amino acid that incorporates in place of the relatively rare amino acid methionine, thus greatly expanding the scope of producible targets. This new strategy is employed for simplified peptide synthesis with a methionine-free fusion partner, allowing single-site incorporation of the cleavable linker for clean release and easy purification of the target peptide. Its utility is demonstrated through the straightforward preparation of two peptides reported to be challenging targets and not accessible through standard solid-phase chemical methodologies, as well as analogues.
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Affiliation(s)
- Daniel Fankhauser
- Research School of Chemistry, Australian National University, 137 Sullivans Creek Road, Acton, ACT 2601, Australia
| | - Apostolos Alissandratos
- Research School of Chemistry, Australian National University, 137 Sullivans Creek Road, Acton, ACT 2601, Australia
| | - Mantas Liutkus
- Research School of Chemistry, Australian National University, 137 Sullivans Creek Road, Acton, ACT 2601, Australia
| | - Christopher J Easton
- Research School of Chemistry, Australian National University, 137 Sullivans Creek Road, Acton, ACT 2601, Australia
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13
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Metabolic Reprogramming of Colorectal Cancer Cells and the Microenvironment: Implication for Therapy. Int J Mol Sci 2021; 22:ijms22126262. [PMID: 34200820 PMCID: PMC8230539 DOI: 10.3390/ijms22126262] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/07/2021] [Accepted: 06/08/2021] [Indexed: 12/20/2022] Open
Abstract
Colorectal carcinoma (CRC) is one of the most frequently diagnosed carcinomas and one of the leading causes of cancer-related death worldwide. Metabolic reprogramming, a hallmark of cancer, is closely related to the initiation and progression of carcinomas, including CRC. Accumulating evidence shows that activation of oncogenic pathways and loss of tumor suppressor genes regulate the metabolic reprogramming that is mainly involved in glycolysis, glutaminolysis, one-carbon metabolism and lipid metabolism. The abnormal metabolic program provides tumor cells with abundant energy, nutrients and redox requirements to support their malignant growth and metastasis, which is accompanied by impaired metabolic flexibility in the tumor microenvironment (TME) and dysbiosis of the gut microbiota. The metabolic crosstalk between the tumor cells, the components of the TME and the intestinal microbiota further facilitates CRC cell proliferation, invasion and metastasis and leads to therapy resistance. Hence, to target the dysregulated tumor metabolism, the TME and the gut microbiota, novel preventive and therapeutic applications are required. In this review, the dysregulation of metabolic programs, molecular pathways, the TME and the intestinal microbiota in CRC is addressed. Possible therapeutic strategies, including metabolic inhibition and immune therapy in CRC, as well as modulation of the aberrant intestinal microbiota, are discussed.
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14
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Jakubowski H. Proteomic exploration of cystathionine β-synthase deficiency: implications for the clinic. Expert Rev Proteomics 2021; 17:751-765. [PMID: 33320032 DOI: 10.1080/14789450.2020.1865160] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Introduction: Homocystinuria due to cystathionine β-synthase (CBS) deficiency, the most frequent inborn error of sulfur amino acid metabolism, is characterized biochemically by severely elevated homocysteine (Hcy) and related metabolites, such as Hcy-thiolactone and N-Hcy-protein. CBS deficiency reduces life span and causes pathological abnormalities affecting most organ systems in the human body, including the cardiovascular (thrombosis, stroke), skeletal/connective tissue (osteoporosis, thin/non-elastic skin, thin hair), and central nervous systems (mental retardation, seizures), as well as the liver (fatty changes), and the eye (ectopia lentis, myopia). Molecular basis of these abnormalities were largely unknown and available treatments remain ineffective. Areas covered: Proteomic and transcriptomic studies over the past decade or so, have significantly contributed to our understanding of mechanisms by which the CBS enzyme deficiency leads to clinical manifestations associated with it. Expert opinion: Recent findings, discussed in this review, highlight the involvement of dysregulated proteostasis in pathologies associated with CBS deficiency, including thromboembolism, stroke, neurologic impairment, connective tissue/collagen abnormalities, hair defects, and hepatic toxicity. To ameliorate these pathologies, pharmacological, enzyme replacement, and gene transfer therapies are being developed.
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Affiliation(s)
- Hieronim Jakubowski
- Department of Biochemistry and Biotechnology, Poznań University of Life Sciences , Poznań, Poland.,Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers University-New Jersey Medical School, International Center for Public Health , Newark, NJ USA
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15
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Howitz N, Su T, Lazazzera BA. Meta-Tyrosine Induces Cytotoxic Misregulation of Metabolism in Escherichia coli. J Mol Biol 2020; 432:166716. [PMID: 33220263 DOI: 10.1016/j.jmb.2020.11.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 11/09/2020] [Accepted: 11/12/2020] [Indexed: 12/16/2022]
Abstract
The non-protein amino acid meta-Tyrosine (m-Tyr) is produced in cells under conditions of oxidative stress, and m-Tyr has been shown to be toxic to a broad range of biological systems. However, the mechanism by which m-Tyr damages cells is unclear. In E. coli, the quality control (QC) function of phenyalanyl-tRNA synthetase (PheRS) is required for resistantce to m-Tyr. To determine the mechanism of m-Tyr toxicity, we utilitized a strain of E. coli that expresses a QC-defective PheRS. The global responses of E. coli cells to m-Tyr were assessed by RNA-seq, and >500 genes were differentially expressed after the addition of m-Tyr. The most strongly up-regulated genes are involved in unfolded-protein stress response, and cells exposed to m-Tyr contained large, electron-dense protein aggregates, indicating that m-Tyr destabilized a large fraction of the proteome. Additionally, we observed that amino acid biosynthesis and transport regulons, controlled by ArgR, TrpR, and TyrR, and the stringent-response regulon, controlled by DksA/ppGpp, were differentially expressed. m-Tyr resistant mutants were isolated and found to have altered a promoter to increase expression of the enzymes for Phe production or to have altered transporters, which likely result in less uptake or increased efflux of m-Tyr. These findings indicate that when m-Tyr has passed the QC checkpoint by the PheRS, this toxicity of m-Tyr may result from interfering with amino acid metabolism, destabalizing a large number of proteins, and the formation of protein aggregates.
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Affiliation(s)
- Nathaniel Howitz
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA 90095, USA
| | - Trent Su
- Department of Biological Chemistry, University of California, Los Angeles, CA 90095, USA; Institute for Quantitative and Computational Biology, University of California, Los Angeles, CA 90095, USA
| | - Beth A Lazazzera
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA.
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16
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De Ruysscher D, Pang L, Lenders SMG, Cappoen D, Cos P, Rozenski J, Strelkov SV, Weeks SD, Van Aerschot A. Synthesis and structure-activity studies of novel anhydrohexitol-based Leucyl-tRNA synthetase inhibitors. Eur J Med Chem 2020; 211:113021. [PMID: 33248851 DOI: 10.1016/j.ejmech.2020.113021] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 10/20/2020] [Accepted: 11/10/2020] [Indexed: 12/01/2022]
Abstract
Leucyl-tRNA synthetase (LeuRS) is a clinically validated target for the development of antimicrobials. This enzyme catalyzes the formation of charged tRNALeu molecules, an essential substrate for protein translation. In the first step of catalysis LeuRS activates leucine using ATP, forming a leucyl-adenylate intermediate. Bi-substrate inhibitors that mimic this chemically labile phosphoanhydride-linked nucleoside have proven to be potent inhibitors of different members of the aminoacyl-tRNA synthetase family but, to date, they have demonstrated poor antibacterial activity. We synthesized a small series of 1,5-anhydrohexitol-based analogues coupled to a variety of triazoles and performed detailed structure-activity relationship studies with bacterial LeuRS. In an in vitro assay, Kiapp values in the nanomolar range were demonstrated. Inhibitory activity differences between the compounds revealed that the polarity and size of the triazole substituents affect binding. X-ray crystallographic studies of N. gonorrhoeae LeuRS in complex with all the inhibitors highlighted the crucial interactions defining their relative enzyme inhibitory activities. We further examined their in vitro antimicrobial properties by screening against several bacterial and yeast strains. While only weak antibacterial activity against M. tuberculosis was detected, the extensive structural data which were obtained could make these LeuRS inhibitors a suitable starting point towards further antibiotic development.
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Affiliation(s)
- Dries De Ruysscher
- Medicinal Chemistry, Rega Institute for Medical Research, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49 - Box 1030, 3000, Leuven, Belgium
| | - Luping Pang
- Medicinal Chemistry, Rega Institute for Medical Research, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49 - Box 1030, 3000, Leuven, Belgium; Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49 - Box 822, 3000, Leuven, Belgium
| | - Stijn M G Lenders
- Medicinal Chemistry, Rega Institute for Medical Research, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49 - Box 1030, 3000, Leuven, Belgium
| | - Davie Cappoen
- Laboratory of Microbiology, Parasitology and Hygiene, Department of Pharmaceutical Sciences, University of Antwerp, Universiteitsplein 1, 2610, Wilrijk, Belgium
| | - Paul Cos
- Laboratory of Microbiology, Parasitology and Hygiene, Department of Pharmaceutical Sciences, University of Antwerp, Universiteitsplein 1, 2610, Wilrijk, Belgium
| | - Jef Rozenski
- Medicinal Chemistry, Rega Institute for Medical Research, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49 - Box 1030, 3000, Leuven, Belgium
| | - Sergei V Strelkov
- Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49 - Box 822, 3000, Leuven, Belgium
| | - Stephen D Weeks
- Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49 - Box 822, 3000, Leuven, Belgium.
| | - Arthur Van Aerschot
- Medicinal Chemistry, Rega Institute for Medical Research, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49 - Box 1030, 3000, Leuven, Belgium.
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17
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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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18
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Abstract
The aminoacyl-tRNA synthetases are an essential and universally distributed family of enzymes that plays a critical role in protein synthesis, pairing tRNAs with their cognate amino acids for decoding mRNAs according to the genetic code. Synthetases help to ensure accurate translation of the genetic code by using both highly accurate cognate substrate recognition and stringent proofreading of noncognate products. While alterations in the quality control mechanisms of synthetases are generally detrimental to cellular viability, recent studies suggest that in some instances such changes facilitate adaption to stress conditions. Beyond their central role in translation, synthetases are also emerging as key players in an increasing number of other cellular processes, with far-reaching consequences in health and disease. The biochemical versatility of the synthetases has also proven pivotal in efforts to expand the genetic code, further emphasizing the wide-ranging roles of the aminoacyl-tRNA synthetase family in synthetic and natural biology.
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Affiliation(s)
- Miguel Angel Rubio Gomez
- Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, USA Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, USA
| | - Michael Ibba
- Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, USA Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, USA
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19
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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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20
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Levi O, Garin S, Arava Y. RNA mimicry in post-transcriptional regulation by aminoacyl tRNA synthetases. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 11:e1564. [PMID: 31414576 DOI: 10.1002/wrna.1564] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 07/10/2019] [Accepted: 07/25/2019] [Indexed: 12/15/2022]
Abstract
Aminoacyl tRNA synthetases (aaRS) are well studied for their roles in tRNA charging with cognate amino acid. Nevertheless, numerous lines of evidence indicate that these proteins have roles other than tRNA charging. These include coordination of cellular signaling cascades, induction of cytokines outside the cell and transcription regulation. Herein, we focus on their roles in post-transcriptional regulation of mRNA expression. We describe functions that are related to antitermination of transcription, RNA splicing and mRNA translation. Cases were recognition of mRNA by the aaRS involves recognition of tRNA-like structures are described. Such recognition may be achieved by repurposing tRNA-binding domains or through domains added to the aaRS later in evolution. Furthermore, we describe cases in which binding by aaRS is implicated in autogenous regulation of expression. Overall, we propose RNA-mimicry as a common mode of interaction between aaRS and mRNA which allows efficient expression regulation. This article is categorized under: RNA Processing > tRNA Processing RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications Translation > Translation Regulation.
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Affiliation(s)
- Ofri Levi
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - Shahar Garin
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - Yoav Arava
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
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21
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Dysregulation of Epigenetic Mechanisms of Gene Expression in the Pathologies of Hyperhomocysteinemia. Int J Mol Sci 2019; 20:ijms20133140. [PMID: 31252610 PMCID: PMC6651274 DOI: 10.3390/ijms20133140] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 06/21/2019] [Accepted: 06/25/2019] [Indexed: 02/07/2023] Open
Abstract
Hyperhomocysteinemia (HHcy) exerts a wide range of biological effects and is associated with a number of diseases, including cardiovascular disease, dementia, neural tube defects, and cancer. Although mechanisms of HHcy toxicity are not fully uncovered, there has been a significant progress in their understanding. The picture emerging from the studies of homocysteine (Hcy) metabolism and pathophysiology is a complex one, as Hcy and its metabolites affect biomolecules and processes in a tissue- and sex-specific manner. Because of their connection to one carbon metabolism and editing mechanisms in protein biosynthesis, Hcy and its metabolites impair epigenetic control of gene expression mediated by DNA methylation, histone modifications, and non-coding RNA, which underlies the pathology of human disease. In this review we summarize the recent evidence showing that epigenetic dysregulation of gene expression, mediated by changes in DNA methylation and histone N-homocysteinylation, is a pathogenic consequence of HHcy in many human diseases. These findings provide new insights into the mechanisms of human disease induced by Hcy and its metabolites, and suggest therapeutic targets for the prevention and/or treatment.
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22
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Santos M, Fidalgo A, Varanda AS, Oliveira C, Santos MAS. tRNA Deregulation and Its Consequences in Cancer. Trends Mol Med 2019; 25:853-865. [PMID: 31248782 DOI: 10.1016/j.molmed.2019.05.011] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 05/24/2019] [Accepted: 05/28/2019] [Indexed: 02/06/2023]
Abstract
The expression of transfer RNAs (tRNAs) is deregulated in cancer cells but the mechanisms and functional meaning of such deregulation are poorly understood. The proteome of cancer cells is not fully encoded by their transcriptome, however, the contribution of mRNA translation to such diversity remains to be elucidated. We review data supporting the hypothesis that tRNA expression deregulation and translational error rate is an important contributor to proteome diversity and cell population heterogeneity, genome instability, and drug resistance in tumors. This hypothesis is aligned with recent data in various model organisms, showing unanticipated adaptive roles of translational errors (adaptive mistranslation), expression control of specific gene subsets by tRNAs, and proteome diversification by elevation of translational error rates in tumors.
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Affiliation(s)
- Mafalda Santos
- Expression Regulation in Cancer, Instituto de Investigação e Inovação em Saúde, University of Porto, Portugal; Institute of Molecular Pathology and Immunology University of Porto (IPATIMUP), Porto, Portugal; Department of Medical Sciences and Institute of Biomedicine - iBiMED, University of Aveiro, Aveiro, Portugal
| | - Ana Fidalgo
- Department of Medical Sciences and Institute of Biomedicine - iBiMED, University of Aveiro, Aveiro, Portugal
| | - A Sofia Varanda
- Expression Regulation in Cancer, Instituto de Investigação e Inovação em Saúde, University of Porto, Portugal; Institute of Molecular Pathology and Immunology University of Porto (IPATIMUP), Porto, Portugal; Department of Medical Sciences and Institute of Biomedicine - iBiMED, University of Aveiro, Aveiro, Portugal
| | - Carla Oliveira
- Expression Regulation in Cancer, Instituto de Investigação e Inovação em Saúde, University of Porto, Portugal; Institute of Molecular Pathology and Immunology University of Porto (IPATIMUP), Porto, Portugal; Department of Pathology, Medical Faculty of Porto, Porto, Portugal.
| | - Manuel A S Santos
- Department of Medical Sciences and Institute of Biomedicine - iBiMED, University of Aveiro, Aveiro, Portugal.
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23
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Jakubowski H. Homocysteine Modification in Protein Structure/Function and Human Disease. Physiol Rev 2019; 99:555-604. [PMID: 30427275 DOI: 10.1152/physrev.00003.2018] [Citation(s) in RCA: 135] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Epidemiological studies established that elevated homocysteine, an important intermediate in folate, vitamin B12, and one carbon metabolism, is associated with poor health, including heart and brain diseases. Earlier studies show that patients with severe hyperhomocysteinemia, first identified in the 1960s, exhibit neurological and cardiovascular abnormalities and premature death due to vascular complications. Although homocysteine is considered to be a nonprotein amino acid, studies over the past 2 decades have led to discoveries of protein-related homocysteine metabolism and mechanisms by which homocysteine can become a component of proteins. Homocysteine-containing proteins lose their biological function and acquire cytotoxic, proinflammatory, proatherothrombotic, and proneuropathic properties, which can account for the various disease phenotypes associated with hyperhomocysteinemia. This review describes mechanisms by which hyperhomocysteinemia affects cellular proteostasis, provides a comprehensive account of the biological chemistry of homocysteine-containing proteins, and discusses pathophysiological consequences and clinical implications of their formation.
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Affiliation(s)
- Hieronim Jakubowski
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers-New Jersey Medical School, International Center for Public Health , Newark, New Jersey ; and Department of Biochemistry and Biotechnology, Poznań University of Life Sciences , Poznań , Poland
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24
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Borowczyk K, Piechocka J, Głowacki R, Dhar I, Midtun Ø, Tell GS, Ueland PM, Nygård O, Jakubowski H. Urinary excretion of homocysteine thiolactone and the risk of acute myocardial infarction in coronary artery disease patients: the WENBIT trial. J Intern Med 2019; 285:232-244. [PMID: 30193001 PMCID: PMC6378604 DOI: 10.1111/joim.12834] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVES No individual homocysteine (Hcy) metabolite has been studied as a risk marker for coronary artery disease (CAD). Our objective was to examine Hcy-thiolactone, a chemically reactive metabolite generated by methionyl-tRNA synthetase and cleared by the kidney, as a risk predictor of incident acute myocardial infarction (AMI) in the Western Norway B-Vitamin Intervention Trial. DESIGN Single centre, prospective double-blind clinical intervention study, randomized in a 2 × 2 factorial design. SUBJECTS AND METHODS Patients with suspected CAD (n = 2049, 69.8% men; 61.2-year-old) were randomized to groups receiving daily (i) folic acid (0.8 mg)/vitamin B12 (0.4 mg)/vitamin B6 (40 mg); (ii) folic acid/vitamin B12 ; (iii) vitamin B6 or (iv) placebo. Urinary Hcy-thiolactone was quantified at baseline, 12 and 38 months. RESULTS Baseline urinary Hcy-thiolactone/creatinine was significantly associated with plasma tHcy, ApoA1, glomerular filtration rate, potassium and pyridoxal 5'-phosphate (positively) and with age, hypertension, smoking, urinary creatinine, plasma bilirubin and kynurenine (negatively). During median 4.7-years, 183 patients (8.9%) suffered an AMI. In Cox regression analysis, Hcy-thiolactone/creatinine was associated with AMI risk (hazard ratio = 1.58, 95% confidence interval = 1.10-2.26, P = 0.012 for trend; adjusted for age, gender, tHcy). This association was confined to patients with pyridoxic acid below median (adjusted HR = 2.72, 95% CI = 1.47-5.03, P = 0.0001; Pinteraction = 0.020). B-vitamin/folate treatments did not affect Hcy-thiolactone/creatinine and its AMI risk association. CONCLUSIONS Hcy-thiolactone/creatinine ratio is a novel AMI risk predictor in patients with suspected CAD, independent of traditional risk factors and tHcy, but modified by vitamin B6 catabolism. These findings lend a support to the hypothesis that Hcy-thiolactone is mechanistically involved in cardiovascular disease.
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Affiliation(s)
- K Borowczyk
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers-New Jersey Medical School, International Center for Public Health, Newark, NJ, USA.,Department of Environmental Chemistry, Faculty of Chemistry, University of Łódź, Łódź, Poland
| | - J Piechocka
- Department of Environmental Chemistry, Faculty of Chemistry, University of Łódź, Łódź, Poland
| | - R Głowacki
- Department of Environmental Chemistry, Faculty of Chemistry, University of Łódź, Łódź, Poland
| | - I Dhar
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | | | - G S Tell
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,Division of Mental and Physical Health, Norwegian Institute of Public Health, Bergen, Norway
| | - P M Ueland
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - O Nygård
- Department of Clinical Science, University of Bergen, Bergen, Norway.,Department of Heart Disease, Haukeland University Hospital, Institute of Medicine, University of Bergen, Bergen, Norway
| | - H Jakubowski
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers-New Jersey Medical School, International Center for Public Health, Newark, NJ, USA.,Department of Biochemistry and Biotechnology, Poznań University of Life Sciences, Poznań, Poland
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25
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Zimmerman SM, Kon Y, Hauke AC, Ruiz BY, Fields S, Phizicky EM. Conditional accumulation of toxic tRNAs to cause amino acid misincorporation. Nucleic Acids Res 2018; 46:7831-7843. [PMID: 30007351 PMCID: PMC6125640 DOI: 10.1093/nar/gky623] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 06/22/2018] [Accepted: 07/01/2018] [Indexed: 12/16/2022] Open
Abstract
To develop a system for conditional amino acid misincorporation, we engineered tRNAs in the yeast Saccharomyces cerevisiae to be substrates of the rapid tRNA decay (RTD) pathway, such that they accumulate when RTD is turned off. We used this system to test the effects on growth of a library of tRNASer variants with all possible anticodons, and show that many are lethal when RTD is inhibited and the tRNA accumulates. Using mass spectrometry, we measured serine misincorporation in yeast containing each of six tRNA variants, and for five of them identified hundreds of peptides with serine substitutions at the targeted amino acid sites. Unexpectedly, we found that there is not a simple correlation between toxicity and the level of serine misincorporation; in particular, high levels of serine misincorporation can occur at cysteine residues without obvious growth defects. We also showed that toxic tRNAs can be used as a tool to identify sequence variants that reduce tRNA function. Finally, we generalized this method to another tRNA species, and generated conditionally toxic tRNATyr variants in a similar manner. This method should facilitate the study of tRNA biology and provide a tool to probe the effects of amino acid misincorporation on cellular physiology.
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Affiliation(s)
| | - Yoshiko Kon
- Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester School of Medicine, Rochester, NY 14642, USA
| | - Alayna C Hauke
- Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester School of Medicine, Rochester, NY 14642, USA
| | - Bianca Y Ruiz
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Stanley Fields
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Eric M Phizicky
- Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester School of Medicine, Rochester, NY 14642, USA
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26
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de Farias ST, Antonino D, Rêgo TG, José MV. Structural evolution of Glycyl-tRNA synthetases alpha subunit and its implication in the initial organization of the decoding system. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2018; 142:43-50. [PMID: 30142371 DOI: 10.1016/j.pbiomolbio.2018.08.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 07/13/2018] [Accepted: 08/14/2018] [Indexed: 11/27/2022]
Abstract
The origin and evolution of the genetic code is a fundamental challenge in modern biology. At the center of this problem is the correct interaction between amino acids and tRNAs. Aminoacyl-tRNA synthetase is the enzyme responsible for the correct binding between amino acids and tRNAs. Among the 20 canonical amino acid, glycine was the most abundant in prebiotic condition and it must have been one of the first to be incorporated into the genetic code. In this work, we derive the ancestral sequence of Glycyl-tRNA synthetase (GlyRS) and predict its 3D-structure. We show, via molecular docking experiments, the capacity of ancestral GlyRS to bind the tRNA anticodon stem loop, cofactors and substrates. These bindings exhibit high affinity and specificity. We propose that the primordial function of these interactions was to stabilize both compounds to make possible the catalysis. In this context, the anticodon stem loop did contribute to the encoding system and just with the emergence of the mRNA it was co-opted for codification. Thus, we present a model for the origin of the genetic code in which the operational and the anticodon codes did not evolve independently.
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Affiliation(s)
- Savio Torres de Farias
- Laboratório de Genética Evolutiva Paulo Leminsk, Departamento de Biologia Molecular, Universidade Federal da Paraíba, João Pessoa, Brazil.
| | - Daniel Antonino
- Laboratório de Genética Evolutiva Paulo Leminsk, Departamento de Biologia Molecular, Universidade Federal da Paraíba, João Pessoa, Brazil
| | - Thais Gaudêncio Rêgo
- Departamento de Informática, Universidade Federal da Paraíba, João Pessoa, Brazil
| | - Marco V José
- Theoretical Biology Group, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México CDMX, C.P. 04510, Mexico.
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27
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Zamacona R, Chavero PN, Medellin E, Hu Y, Hughes CA, Quach N, Keniry M, Bullard JM. Identification and Characterization of Chemical Compounds that Inhibit Leucyl-tRNA Synthetase from Pseudomonas aeruginosa. Curr Drug Discov Technol 2018; 17:119-130. [PMID: 30088448 DOI: 10.2174/1570163815666180808095600] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 07/20/2018] [Accepted: 08/01/2018] [Indexed: 11/22/2022]
Abstract
BACKGROUND Pseudomonas aeruginosa is an opportunistic multi-drug resistance pathogen implicated as the causative agent in a high-percentage of nosocomial and community acquired bacterial infections. The gene encoding leucyl-tRNA synthetase (LeuRS) from P. aeruginosa was overexpressed in Escherichia coli and the resulting protein was characterized. METHODS LeuRS was kinetically evaluated and the KM values for interactions with leucine, ATP and tRNA were 6.5, 330, and 3.0 μM, respectively. LeuRS was developed into a screening platform using scintillation proximity assay (SPA) technology and used to screen over 2000 synthetic and natural chemical compounds. RESULTS The initial screen resulted in the identification of two inhibitory compounds, BT03C09 and BT03E07. IC50s against LeuRS observed for BT03C09 and BT03E07 were 23 and 15 μM, respectively. The minimum inhibitory concentrations (MIC) were determined against nine clinically relevant bacterial strains. In time-kill kinetic analysis, BT03C09 was observed to inhibit bacterial growth in a bacteriostatic manner, while BT03E07 acted as a bactericidal agent. Neither compound competed with leucine or ATP for binding LeuRS. Limited inhibition was observed in aminoacylation assays with the human mitochondrial form of LeuRS, however when tested in cultures of human cell line, BT03C09 was toxic at all concentration whereas BT03E07 only showed toxic effects at elevated concentrations. CONCLUSION Two compounds were identified as inhibitors of LeuRS in a screen of over 2000 natural and synthetic compounds. After characterization one compound (BT03E07) exhibited broad spectrum antibacterial activity while maintaining low toxicity against human mitochondrial LeuRS as well as against human cell cultures.
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Affiliation(s)
- Regina Zamacona
- Chemistry Department, The University of Texas-RGV, 1201 W. University Drive, Edinburg, TX 78541, United States
| | - Pamela N Chavero
- Chemistry Department, The University of Texas-RGV, 1201 W. University Drive, Edinburg, TX 78541, United States
| | - Eduardo Medellin
- Chemistry Department, The University of Texas-RGV, 1201 W. University Drive, Edinburg, TX 78541, United States
| | - Yanmei Hu
- Chemistry Department, The University of Texas-RGV, 1201 W. University Drive, Edinburg, TX 78541, United States.,Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, Arizona 85721, United States
| | - Casey A Hughes
- Chemistry Department, The University of Texas-RGV, 1201 W. University Drive, Edinburg, TX 78541, United States
| | - Nathalie Quach
- Chemistry Department, The University of Texas-RGV, 1201 W. University Drive, Edinburg, TX 78541, United States
| | - Megan Keniry
- Biology Department, The University of Texas-RGV, 1201 W. University Drive, Edinburg, TX 78541, United States
| | - James M Bullard
- Chemistry Department, The University of Texas-RGV, 1201 W. University Drive, Edinburg, TX 78541, United States
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Stephen P, Ye S, Zhou M, Song J, Zhang R, Wang ED, Giegé R, Lin SX. Structure of Escherichia coli Arginyl-tRNA Synthetase in Complex with tRNA Arg: Pivotal Role of the D-loop. J Mol Biol 2018; 430:1590-1606. [PMID: 29678554 DOI: 10.1016/j.jmb.2018.04.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 03/16/2018] [Accepted: 04/10/2018] [Indexed: 10/17/2022]
Abstract
Aminoacyl-tRNA synthetases are essential components in protein biosynthesis. Arginyl-tRNA synthetase (ArgRS) belongs to the small group of aminoacyl-tRNA synthetases requiring cognate tRNA for amino acid activation. The crystal structure of Escherichia coli (Eco) ArgRS has been solved in complex with tRNAArg at 3.0-Å resolution. With this first bacterial tRNA complex, we are attempting to bridge the gap existing in structure-function understanding in prokaryotic tRNAArg recognition. The structure shows a tight binding of tRNA on the synthetase through the identity determinant A20 from the D-loop, a tRNA recognition snapshot never elucidated structurally. This interaction of A20 involves 5 amino acids from the synthetase. Additional contacts via U20a and U16 from the D-loop reinforce the interaction. The importance of D-loop recognition in EcoArgRS functioning is supported by a mutagenesis analysis of critical amino acids that anchor tRNAArg on the synthetase; in particular, mutations at amino acids interacting with A20 affect binding affinity to the tRNA and specificity of arginylation. Altogether the structural and functional data indicate that the unprecedented ArgRS crystal structure represents a snapshot during functioning and suggest that the recognition of the D-loop by ArgRS is an important trigger that anchors tRNAArg on the synthetase. In this process, A20 plays a major role, together with prominent conformational changes in several ArgRS domains that may eventually lead to the mature ArgRS:tRNA complex and the arginine activation. Functional implications that could be idiosyncratic to the arginine identity of bacterial ArgRSs are discussed.
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Affiliation(s)
- Preyesh Stephen
- Laboratory of Molecular Endocrinology, CHU Research Center and Laval University, Québec, Canada
| | - Sheng Ye
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Ming Zhou
- Laboratory of Molecular Endocrinology, CHU Research Center and Laval University, Québec, Canada
| | - Jian Song
- Laboratory of Molecular Endocrinology, CHU Research Center and Laval University, Québec, Canada
| | - Rongguang Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China; Shanghai Institutes of Biochemistry and Cell Biology, SIBS, Shanghai, China.
| | - En-Duo Wang
- Shanghai Institutes of Biochemistry and Cell Biology, SIBS, Shanghai, China.
| | - Richard Giegé
- Institut de Biologie Moléculaire et Cellulaire, CNRS and Université de Strasbourg, Strasbourg Cedex, France
| | - Sheng-Xiang Lin
- Laboratory of Molecular Endocrinology, CHU Research Center and Laval University, Québec, Canada; Shanghai Institutes of Biochemistry and Cell Biology, SIBS, Shanghai, China.
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Borowczyk K, Suliburska J, Jakubowski H. Demethylation of methionine and keratin damage in human hair. Amino Acids 2018; 50:537-546. [PMID: 29480334 PMCID: PMC5917003 DOI: 10.1007/s00726-018-2545-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 02/20/2018] [Indexed: 12/23/2022]
Abstract
Growing human head hair contains a history of keratin and provides a unique model for studies of protein damage. Here, we examined mechanism of homocysteine (Hcy) accumulation and keratin damage in human hair. We found that the content of Hcy-keratin increased along the hair fiber, with levels 5-10-fold higher levels in older sections at the hair's tip than in younger sections at hair's base. The accumulation of Hcy led to a complete loss of keratin solubility in sodium dodecyl sulfate. The increase in Hcy-keratin was accompanied by a decrease in methionine-keratin. Levels of Hcy-keratin were correlated with hair copper and iron in older hair. These relationships were recapitulated in model experiments in vitro, in which Hcy generation from Met exhibited a similar dependence on copper or iron. Taken together, these findings suggest that Hcy-keratin accumulation is due to copper/iron-catalyzed demethylation of methionine residues and contributes to keratin damage in human hair.
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Affiliation(s)
- Kamila Borowczyk
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers-New Jersey Medical School, International Center for Public Health, 225 Warren Street, Newark, NJ, 07103, USA.,Department of Environmental Chemistry, University of Łódź, 90-236, Łódź, Poland
| | - Joanna Suliburska
- Department of Human Nutrition and Hygiene, Poznań University of Life Sciences, 60-632, Poznań, Poland
| | - Hieronim Jakubowski
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers-New Jersey Medical School, International Center for Public Health, 225 Warren Street, Newark, NJ, 07103, USA. .,Department of Biochemistry and Biotechnology, Poznań University of Life Sciences, 60-632, Poznań, Poland.
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30
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A tRNA's fate is decided at its 3' end: Collaborative actions of CCA-adding enzyme and RNases involved in tRNA processing and degradation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1861:433-441. [PMID: 29374586 DOI: 10.1016/j.bbagrm.2018.01.012] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 01/15/2018] [Accepted: 01/19/2018] [Indexed: 02/07/2023]
Abstract
tRNAs are key players in translation and are additionally involved in a wide range of distinct cellular processes. The vital importance of tRNAs becomes evident in numerous diseases that are linked to defective tRNA molecules. It is therefore not surprising that the structural intactness of tRNAs is continuously scrutinized and defective tRNAs are eliminated. In this process, erroneous tRNAs are tagged with single-stranded RNA sequences that are recognized by degrading exonucleases. Recent discoveries have revealed that the CCA-adding enzyme - actually responsible for the de novo synthesis of the 3'-CCA end - plays an indispensable role in tRNA quality control by incorporating a second CCA triplet that is recognized as a degradation tag. In this review, we give an update on the latest findings regarding tRNA quality control that turns out to represent an interplay of the CCA-adding enzyme and RNases involved in tRNA degradation and maturation. In particular, the RNase-induced turnover of the CCA end is now recognized as a trigger for the CCA-adding enzyme to repeatedly scrutinize the structural intactness of a tRNA. This article is part of a Special Issue entitled: SI: Regulation of tRNA synthesis and modification in physiological conditions and disease edited by Dr. Boguta Magdalena.
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31
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Grube CD, Roy H. A continuous assay for monitoring the synthetic and proofreading activities of multiple aminoacyl-tRNA synthetases for high-throughput drug discovery. RNA Biol 2017; 15:659-666. [PMID: 29168435 PMCID: PMC6103669 DOI: 10.1080/15476286.2017.1397262] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Aminoacyl-tRNA synthetases (aaRSs) catalyze the aminoacylation of tRNAs to produce the aminoacyl-tRNAs (aa-tRNAs) required by ribosomes for translation of the genetic message into proteins. To ensure the accuracy of tRNA aminoacylation, and consequently the fidelity of protein synthesis, some aaRSs exhibit a proofreading (editing) site, distinct from the aa-tRNA synthetic site. The aaRS editing site hydrolyzes misacylated products formed when a non-cognate amino acid is used during tRNA charging. Because aaRSs play a central role in protein biosynthesis and cellular life, these proteins represent longstanding targets for therapeutic drug development to combat infectious diseases. Most existing aaRS inhibitors target the synthetic site, and it is only recently that drugs targeting the proofreading site have been considered. In the present study, we developed a robust assay for the high-throughput screening of libraries of inhibitors targeting both the synthetic and the proofreading sites of up to four aaRSs simultaneously. Thus, this assay allows for screening of eight distinct enzyme active sites in a single experiment. aaRSs from several prominent human pathogens (i.e., Mycobacterium tuberculosis, Plasmodium falciparum, and Escherichia coli) were used for development of this assay.
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Affiliation(s)
- Christopher D Grube
- a Burnett School of Biomedical Sciences, College of Medicine , University of Central Florida , Orlando , Florida , United States of America
| | - Hervé Roy
- a Burnett School of Biomedical Sciences, College of Medicine , University of Central Florida , Orlando , Florida , United States of America
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32
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Antikainen H, Driscoll M, Haspel G, Dobrowolski R. TOR-mediated regulation of metabolism in aging. Aging Cell 2017; 16:1219-1233. [PMID: 28971552 PMCID: PMC5676073 DOI: 10.1111/acel.12689] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/03/2017] [Indexed: 01/06/2023] Open
Abstract
Cellular metabolism is regulated by the mTOR kinase, a key component of the molecular nutrient sensor pathway that plays a central role in cellular survival and aging. The mTOR pathway promotes protein and lipid synthesis and inhibits autophagy, a process known for its contribution to longevity in several model organisms. The nutrient‐sensing pathway is regulated at the lysosomal membrane by a number of proteins for which deficiency triggers widespread aging phenotypes in tested animal models. In response to environmental cues, this recently discovered lysosomal nutrient‐sensing complex regulates autophagy transcriptionally through conserved factors, such as the transcription factors TFEB and FOXO, associated with lifespan extension. This key metabolic pathway strongly depends on nucleocytoplasmic compartmentalization, a cellular phenomenon gradually lost during aging. In this review, we discuss the current progress in understanding the contribution of mTOR‐regulating factors to autophagy and longevity. Furthermore, we review research on the regulation of metabolism conducted in multiple aging models, including Caenorhabditis elegans, Drosophila and mouse, and human iPSCs. We suggest that conserved molecular pathways have the strongest potential for the development of new avenues for treatment of age‐related diseases.
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Affiliation(s)
- Henri Antikainen
- Federated Department of Biological Sciences New Jersey Institute of Technology Rutgers University Newark NJ 07102 USA
| | - Monica Driscoll
- Department of Molecular Biology and Biochemistry Rutgers University Piscataway NJ 08854 USA
| | - Gal Haspel
- Federated Department of Biological Sciences New Jersey Institute of Technology Rutgers University Newark NJ 07102 USA
| | - Radek Dobrowolski
- Federated Department of Biological Sciences New Jersey Institute of Technology Rutgers University Newark NJ 07102 USA
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33
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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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Genoud V, Quintana PG, Gionco S, Baldessari A, Quintana I. Structural changes of fibrinogen molecule mediated by the N-homocysteinylation reaction. J Thromb Thrombolysis 2017; 45:66-76. [DOI: 10.1007/s11239-017-1574-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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35
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Mechanistic Insights Into Catalytic RNA-Protein Complexes Involved in Translation of the Genetic Code. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2017. [PMID: 28683922 DOI: 10.1016/bs.apcsb.2017.04.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
The contemporary world is an "RNA-protein world" rather than a "protein world" and tracing its evolutionary origins is of great interest and importance. The different RNAs that function in close collaboration with proteins are involved in several key physiological processes, including catalysis. Ribosome-the complex megadalton cellular machinery that translates genetic information encoded in nucleotide sequence to amino acid sequence-epitomizes such an association between RNA and protein. RNAs that can catalyze biochemical reactions are known as ribozymes. They usually employ general acid-base catalytic mechanism, often involving the 2'-OH of RNA that activates and/or stabilizes a nucleophile during the reaction pathway. The protein component of such RNA-protein complexes (RNPCs) mostly serves as a scaffold which provides an environment conducive for the RNA to function, or as a mediator for other interacting partners. In this review, we describe those RNPCs that are involved at different stages of protein biosynthesis and in which RNA performs the catalytic function; the focus of the account is on highlighting mechanistic aspects of these complexes. We also provide a perspective on such associations in the context of proofreading during translation of the genetic code. The latter aspect is not much appreciated and recent works suggest that this is an avenue worth exploring, since an understanding of the subject can provide useful insights into how RNAs collaborate with proteins to ensure fidelity during these essential cellular processes. It may also aid in comprehending evolutionary aspects of such associations.
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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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Mohler K, Aerni HR, Gassaway B, Ling J, Ibba M, Rinehart J. MS-READ: Quantitative measurement of amino acid incorporation. Biochim Biophys Acta Gen Subj 2017; 1861:3081-3088. [PMID: 28130155 DOI: 10.1016/j.bbagen.2017.01.025] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 01/18/2017] [Indexed: 10/20/2022]
Abstract
Ribosomal protein synthesis results in the genetically programmed incorporation of amino acids into a growing polypeptide chain. Faithful amino acid incorporation that accurately reflects the genetic code is critical to the structure and function of proteins as well as overall proteome integrity. Errors in protein synthesis are generally detrimental to cellular processes yet emerging evidence suggest that proteome diversity generated through mistranslation may be beneficial under certain conditions. Cumulative translational error rates have been determined at the organismal level, however codon specific error rates and the spectrum of misincorporation errors from system to system remain largely unexplored. In particular, until recently technical challenges have limited the ability to detect and quantify comparatively rare amino acid misincorporation events, which occur orders of magnitude less frequently than canonical amino acid incorporation events. We now describe a technique for the quantitative analysis of amino acid incorporation that provides the sensitivity necessary to detect mistranslation events during translation of a single codon at frequencies as low as 1 in 10,000 for all 20 proteinogenic amino acids, as well as non-proteinogenic and modified amino acids. This article is part of a Special Issue entitled "Biochemistry of Synthetic Biology - Recent Developments" Guest Editor: Dr. Ilka Heinemann and Dr. Patrick O'Donoghue.
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Affiliation(s)
- Kyle Mohler
- Department of Microbiology, The Ohio State University, 318 West 12th Avenue, Columbus, OH 43210, USA; Center for RNA Biology, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA
| | - Hans-Rudolf Aerni
- Systems Biology Institute, Yale University, West Haven, CT 06516, USA; Department of Cellular & Molecular Physiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Brandon Gassaway
- Systems Biology Institute, Yale University, West Haven, CT 06516, USA; Department of Cellular & Molecular Physiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Jiqiang Ling
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Michael Ibba
- Department of Microbiology, The Ohio State University, 318 West 12th Avenue, Columbus, OH 43210, USA; Center for RNA Biology, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA
| | - Jesse Rinehart
- Systems Biology Institute, Yale University, West Haven, CT 06516, USA; Department of Cellular & Molecular Physiology, Yale University School of Medicine, New Haven, CT 06520, USA.
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Khayati K, Antikainen H, Bonder EM, Weber GF, Kruger WD, Jakubowski H, Dobrowolski R. The amino acid metabolite homocysteine activates mTORC1 to inhibit autophagy and form abnormal proteins in human neurons and mice. FASEB J 2016; 31:598-609. [PMID: 28148781 DOI: 10.1096/fj.201600915r] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 10/11/2016] [Indexed: 11/11/2022]
Abstract
The molecular mechanisms leading to and responsible for age-related, sporadic Alzheimer's disease (AD) remain largely unknown. It is well documented that aging patients with elevated levels of the amino acid metabolite homocysteine (Hcy) are at high risk of developing AD. We investigated the impact of Hcy on molecular clearance pathways in mammalian cells, including in vitro cultured induced pluripotent stem cell-derived forebrain neurons and in vivo neurons in mouse brains. Exposure to Hcy resulted in up-regulation of the mechanistic target of rapamycin complex 1 (mTORC1) activity, one of the major kinases in cells that is tightly linked to anabolic and catabolic pathways. Hcy is sensed by a constitutive protein complex composed of leucyl-tRNA-synthetase and folliculin, which regulates mTOR tethering to lysosomal membranes. In hyperhomocysteinemic human cells and cystathionine β-synthase-deficient mouse brains, we find an acute and chronic inhibition of the molecular clearance of protein products resulting in a buildup of abnormal proteins, including β-amyloid and phospho-Tau. Formation of these protein aggregates leads to AD-like neurodegeneration. This pathology can be prevented by inhibition of mTORC1 or by induction of autophagy. We conclude that an increase of intracellular Hcy levels predisposes neurons to develop abnormal protein aggregates, which are hallmarks of AD and its associated onset and pathophysiology with age.-Khayati, K., Antikainen, H., Bonder, E. M., Weber, G. F., Kruger, W. D., Jakubowski, H., Dobrowolski, R. The amino acid metabolite homocysteine activates mTORC1 to inhibit autophagy and form abnormal proteins in human neurons and mice.
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Affiliation(s)
- Khoosheh Khayati
- Federated Department of Biological Sciences, Rutgers University/New Jersey Institute of Technology, Newark, New Jersey, USA
| | - Henri Antikainen
- Federated Department of Biological Sciences, Rutgers University/New Jersey Institute of Technology, Newark, New Jersey, USA
| | - Edward M Bonder
- Federated Department of Biological Sciences, Rutgers University/New Jersey Institute of Technology, Newark, New Jersey, USA
| | - Gregory F Weber
- Federated Department of Biological Sciences, Rutgers University/New Jersey Institute of Technology, Newark, New Jersey, USA
| | | | - Hieronim Jakubowski
- Department of Microbiology, Biochemistry, and Molecular Genetics, International Center for Public Health, Rutgers-New Jersey Medical School, Newark, New Jersey, USA.,Institute of Bioorganic Chemistry, Poznań, Poland; and.,Department of Biochemistry and Biotechnology, University of Life Sciences, Poznań, Poland
| | - Radek Dobrowolski
- Federated Department of Biological Sciences, Rutgers University/New Jersey Institute of Technology, Newark, New Jersey, USA;
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Wang X, Pan T. Stress Response and Adaptation Mediated by Amino Acid Misincorporation during Protein Synthesis. Adv Nutr 2016; 7:773S-9S. [PMID: 27422514 PMCID: PMC4942860 DOI: 10.3945/an.115.010991] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Translation of genetic information into functional proteins is critical for all cellular life. Accurate protein synthesis relies on proper aminoacylation of transfer RNAs (tRNAs) and decoding of mRNAs by the ribosome with the use of aminoacyl-tRNAs. Mistranslation can lead to pathologic consequences. All cells contain elaborate quality control mechanisms in translation, although translational fidelity may be regulated by various factors such as nutrient limitation or reactive oxygen species. Translation fidelity is maintained via the accuracy of tRNA aminoacylation by the aminoacyl-tRNA synthetases and matching of the mRNA codon with the tRNA anticodon by the ribosome. Stringent substrate discrimination and proofreading are critical in aminoacylating tRNAs with their cognate amino acid to maintain high accuracy of translation. Although the composition of the cellular proteome generally adheres to the genetic code, accumulating evidence indicates that cells can also deliberately mistranslate; they synthesize mutant proteins that deviate from the genetic code in response to stress or environmental changes. Mistranslation with tRNA charged with noncognate amino acids can expand the proteome to enhance stress response and help adaptation. Here, we review current knowledge on mistranslation through tRNA misacylation and describe advances in our understanding of translational control in the regulation of stress response and human diseases.
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Affiliation(s)
- Xiaoyun Wang
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL
| | - Tao Pan
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL
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40
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Chang CY, Chien CI, Chang CP, Lin BC, Wang CC. A WHEP Domain Regulates the Dynamic Structure and Activity of Caenorhabditis elegans Glycyl-tRNA Synthetase. J Biol Chem 2016; 291:16567-75. [PMID: 27298321 DOI: 10.1074/jbc.m116.730812] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Indexed: 11/06/2022] Open
Abstract
WHEP domains exist in certain eukaryotic aminoacyl-tRNA synthetases and play roles in tRNA or protein binding. We present evidence herein that cytoplasmic and mitochondrial forms of Caenorhabditis elegans glycyl-tRNA synthetase (CeGlyRS) are encoded by the same gene (CeGRS1) through alternative initiation of translation. The cytoplasmic form possessed an N-terminal WHEP domain, whereas its mitochondrial isoform possessed an extra N-terminal sequence consisting of an mitochondrial targeting signal and an appended domain. Cross-species complementation assays showed that CeGRS1 effectively rescued the cytoplasmic and mitochondrial defects of a yeast GRS1 knock-out strain. Although both forms of CeGlyRS efficiently charged the cytoplasmic tRNAs(Gly) of C. elegans, the mitochondrial form was much more efficient than its cytoplasmic counterpart in charging the mitochondrial tRNA(Gly) isoacceptor, which carries a defective TψC hairpin. Despite the WHEP domain per se lacking tRNA binding activity, deletion of this domain reduced the catalytic efficiency of the enzyme. Most interestingly, the deletion mutant possessed a higher thermal stability and a somewhat lower structural flexibility. Our study suggests a role for the WHEP domain as a regulator of the dynamic structure and activity of the enzyme.
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Affiliation(s)
- Chih-Yao Chang
- From the Department of Life Sciences, National Central University, Taoyuan 32001, Taiwan
| | - Chin-I Chien
- From the Department of Life Sciences, National Central University, Taoyuan 32001, Taiwan
| | - Chia-Pei Chang
- From the Department of Life Sciences, National Central University, Taoyuan 32001, Taiwan
| | - Bo-Chun Lin
- From the Department of Life Sciences, National Central University, Taoyuan 32001, Taiwan
| | - Chien-Chia Wang
- From the Department of Life Sciences, National Central University, Taoyuan 32001, Taiwan
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41
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Abstract
Aminoacyl-tRNA synthetases (aaRSs) are modular enzymes globally conserved in the three kingdoms of life. All catalyze the same two-step reaction, i.e., the attachment of a proteinogenic amino acid on their cognate tRNAs, thereby mediating the correct expression of the genetic code. In addition, some aaRSs acquired other functions beyond this key role in translation. Genomics and X-ray crystallography have revealed great structural diversity in aaRSs (e.g., in oligomery and modularity, in ranking into two distinct groups each subdivided in 3 subgroups, by additional domains appended on the catalytic modules). AaRSs show huge structural plasticity related to function and limited idiosyncrasies that are kingdom or even species specific (e.g., the presence in many Bacteria of non discriminating aaRSs compensating for the absence of one or two specific aaRSs, notably AsnRS and/or GlnRS). Diversity, as well, occurs in the mechanisms of aaRS gene regulation that are not conserved in evolution, notably between distant groups such as Gram-positive and Gram-negative Bacteria. The review focuses on bacterial aaRSs (and their paralogs) and covers their structure, function, regulation, and evolution. Structure/function relationships are emphasized, notably the enzymology of tRNA aminoacylation and the editing mechanisms for correction of activation and charging errors. The huge amount of genomic and structural data that accumulated in last two decades is reviewed, showing how the field moved from essentially reductionist biology towards more global and integrated approaches. Likewise, the alternative functions of aaRSs and those of aaRS paralogs (e.g., during cell wall biogenesis and other metabolic processes in or outside protein synthesis) are reviewed. Since aaRS phylogenies present promiscuous bacterial, archaeal, and eukaryal features, similarities and differences in the properties of aaRSs from the three kingdoms of life are pinpointed throughout the review and distinctive characteristics of bacterium-like synthetases from organelles are outlined.
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Affiliation(s)
- Richard Giegé
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, 67084 Strasbourg, France
| | - Mathias Springer
- Université Paris Diderot, Sorbonne Cité, UPR9073 CNRS, IBPC, 75005 Paris, France
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42
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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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43
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Jakubowski H. Aminoacyl-tRNA synthetases and the evolution of coded peptide synthesis: the Thioester World. FEBS Lett 2016; 590:469-81. [PMID: 26831912 DOI: 10.1002/1873-3468.12085] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 01/12/2016] [Accepted: 01/13/2016] [Indexed: 11/10/2022]
Abstract
Coded peptide synthesis must have been preceded by a prebiotic stage, in which thioesters played key roles. Fossils of the Thioester World are found in extant aminoacyl-tRNA synthetases (AARSs). Indeed, studies of the editing function reveal that AARSs have a thiol-binding site in their catalytic modules. The thiol-binding site confers the ability to catalyze aminoacyl~coenzyme A thioester synthesis and peptide bond formation. Genomic comparisons show that AARSs are structurally related to proteins involved in sulfur and coenzyme A metabolisms and peptide bond synthesis. These findings point to the origin of the amino acid activation and peptide bond synthesis functions in the Thioester World and suggest that the present-day AARSs had originated from ancestral forms that were involved in noncoded thioester-dependent peptide synthesis.
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Affiliation(s)
- Hieronim Jakubowski
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers-New Jersey Medical School, International Center for Public Health, Newark, NJ, USA.,Institute of Bioorganic Chemistry, Poznań, Poland.,Department of Biochemistry and Biotechnology, University of Life Sciences, Poznań, Poland
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44
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Fortowsky GB, Simard DJ, Aboelnga MM, Gauld JW. Substrate-Assisted and Enzymatic Pretransfer Editing of Nonstandard Amino Acids by Methionyl-tRNA Synthetase. Biochemistry 2015; 54:5757-65. [PMID: 26322377 DOI: 10.1021/acs.biochem.5b00588] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Aminoacyl-tRNA synthetases (aaRSs) are central to a number of physiological processes, including protein biosynthesis. In particular, they activate and then transfer their corresponding amino acid to the cognate tRNA. This is achieved with a generally remarkably high fidelity by editing against incorrect standard and nonstandard amino acids. Using docking, molecular dynamics (MD), and hybrid quantum mechanical/molecular mechanics methods, we have investigated mechanisms by which methionyl-tRNA synthetase (MetRS) may edit against the highly toxic, noncognate, amino acids homocysteine (Hcy) and its oxygen analogue, homoserine (Hse). Substrate-assisted editing of Hcy-AMP in which its own phosphate acts as the mechanistic base occurs with a rate-limiting barrier of 98.2 kJ mol(-1). This step corresponds to nucleophilic attack of the Hcy side-chain sulfur at its own carbonyl carbon (CCarb). In contrast, a new possible editing mechanism is identified in which an active site aspartate (Asp259) acts as the base. The rate-limiting step is now rotation about the substrate's aminoacyl Cβ-Cγ bond with a barrier of 27.5 kJ mol(-1), while for Hse-AMP, the rate-limiting step is cleavage of the CCarb-OP bond with a barrier of 30.9 kJ mol(-1). A similarly positioned aspartate or glutamate also occurs in the homologous enzymes LeuRS, IleRS, and ValRS, which also discriminate against Hcy. Docking and MD studies suggest that at least in the case of LeuRS and ValRS, a similar editing mechanism may be possible.
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Affiliation(s)
- Grant B Fortowsky
- Department of Chemistry and Biochemistry, University of Windsor , Windsor, Ontario N9B 3P4, Canada
| | - Daniel J Simard
- Department of Chemistry and Biochemistry, University of Windsor , Windsor, Ontario N9B 3P4, Canada
| | - Mohamed M Aboelnga
- Department of Chemistry and Biochemistry, University of Windsor , Windsor, Ontario N9B 3P4, Canada
| | - James W Gauld
- Department of Chemistry and Biochemistry, University of Windsor , Windsor, Ontario N9B 3P4, Canada
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45
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Konovalova S, Hilander T, Loayza-Puch F, Rooijers K, Agami R, Tyynismaa H. Exposure to arginine analog canavanine induces aberrant mitochondrial translation products, mitoribosome stalling, and instability of the mitochondrial proteome. Int J Biochem Cell Biol 2015; 65:268-74. [DOI: 10.1016/j.biocel.2015.06.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 06/01/2015] [Accepted: 06/22/2015] [Indexed: 10/23/2022]
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46
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Wilusz JE. Controlling translation via modulation of tRNA levels. WILEY INTERDISCIPLINARY REVIEWS-RNA 2015; 6:453-70. [PMID: 25919480 DOI: 10.1002/wrna.1287] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 03/13/2015] [Accepted: 04/06/2015] [Indexed: 12/22/2022]
Abstract
Transfer RNAs (tRNAs) are critical adaptor molecules that carry amino acids to a messenger RNA (mRNA) template during protein synthesis. Although tRNAs have commonly been viewed as abundant 'house-keeping' RNAs, it is becoming increasingly clear that tRNA expression is tightly regulated. Depending on a cell's proliferative status, the pool of active tRNAs is rapidly changed, enabling distinct translational programs to be expressed in differentiated versus proliferating cells. Here, I highlight several post-transcriptional regulatory mechanisms that allow the expression or functions of tRNAs to be altered. Modulating the modification status or structural stability of individual tRNAs can cause those specific tRNA transcripts to selectively accumulate or be degraded. Decay generally occurs via the rapid tRNA decay pathway or by the nuclear RNA surveillance machinery. In addition, the CCA-adding enzyme plays a critical role in determining the fate of a tRNA. The post-transcriptional addition of CCA to the 3' ends of stable tRNAs generates the amino acid attachment site, whereas addition of CCACCA to unstable tRNAs prevents aminoacylation and marks the tRNA for degradation. In response to various stresses, tRNAs can accumulate in the nucleus or be further cleaved into small RNAs, some of which inhibit translation. By implementing these various post-transcriptional control mechanisms, cells are able to fine-tune tRNA levels to regulate subsets of mRNAs as well as overall translation rates.
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Affiliation(s)
- Jeremy E Wilusz
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
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47
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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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48
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Naganathan A, Wood MP, Moore SD. The large ribosomal subunit protein L9 enables the growth of EF-P deficient cells and enhances small subunit maturation. PLoS One 2015; 10:e0120060. [PMID: 25879934 PMCID: PMC4399890 DOI: 10.1371/journal.pone.0120060] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 02/03/2015] [Indexed: 01/08/2023] Open
Abstract
The loss of the large ribosomal protein L9 causes a reduction in translation fidelity by an unknown mechanism. To identify pathways affected by L9, we identified mutants of E. coli that require L9 for fitness. In a prior study, we characterized L9-dependent mutations in the essential GTPase Der (EngA). Here, we describe a second class of L9-dependent mutations that either compromise or inactivate elongation factor P (EF-P, eIF5A in eukaryotes). Without L9, Δefp cells are practically inviable. Cell fractionation studies revealed that, in both the Der and EF-P mutant cases, L9's activity reduces immature 16S rRNA in 30S particles and partially restores the abundance of monosomes. Inspired by these findings, we discovered that L9 also enhances 16S maturation in wild-type cells. Surprisingly, although the amount of immature 16S in 30S particles was found to be elevated in ΔrplI cells, the amount in polysomes was low and inversely correlated with the immature 16S abundance. These findings provide an explanation for the observed fitness increases afforded by L9 in these mutants and reveal particular physiological conditions in which L9 becomes critical. Additionally, L9 may affect the partitioning of small subunits containing immature 16S rRNA.
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Affiliation(s)
- Anusha Naganathan
- The Burnett School of Biomedical Sciences, College of Medicine, The University of Central Florida, Orlando, FL, 32816, United States of America
| | - Matthew P. Wood
- Seattle Biomed, 307 Westlake Ave N, Suite 500, Seattle, WA, 98109, United States of America
- Department of Global Health, University of Washington, 1510 N.E. San Juan Road, Seattle, WA, 98195, United States of America
| | - Sean D. Moore
- The Burnett School of Biomedical Sciences, College of Medicine, The University of Central Florida, Orlando, FL, 32816, United States of America
- * E-mail:
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49
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Homocysteine thiolactone and N-homocysteinylated protein induce pro-atherogenic changes in gene expression in human vascular endothelial cells. Amino Acids 2015; 47:1319-39. [PMID: 25802182 PMCID: PMC4458266 DOI: 10.1007/s00726-015-1956-7] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 03/04/2015] [Indexed: 12/11/2022]
Abstract
Genetic or nutritional deficiencies in homocysteine (Hcy) metabolism lead to hyperhomocysteinemia (HHcy) and cause endothelial dysfunction, a hallmark of atherosclerosis. In addition to Hcy, related metabolites accumulate in HHcy but their role in endothelial dysfunction is unknown. Here, we examine how Hcy-thiolactone, N-Hcy-protein, and Hcy affect gene expression and molecular pathways in human umbilical vein endothelial cells. We used microarray technology, real-time quantitative polymerase chain reaction, and bioinformatic analysis with PANTHER, DAVID, and Ingenuity Pathway Analysis (IPA) resources. We identified 47, 113, and 30 mRNAs regulated by N-Hcy-protein, Hcy-thiolactone, and Hcy, respectively, and found that each metabolite induced a unique pattern of gene expression. Top molecular pathways affected by Hcy-thiolactone were chromatin organization, one-carbon metabolism, and lipid-related processes [−log(P value) = 20–31]. Top pathways affected by N-Hcy-protein and Hcy were blood coagulation, sulfur amino acid metabolism, and lipid metabolism [−log(P value)] = 4–11; also affected by Hcy-thiolactone, [−log(P value) = 8–14]. Top disease related to Hcy-thiolactone, N-Hcy-protein, and Hcy was ‘atherosclerosis, coronary heart disease’ [−log(P value) = 9–16]. Top-scored biological networks affected by Hcy-thiolactone (score = 34–40) were cardiovascular disease and function; those affected by N-Hcy-protein (score = 24–35) were ‘small molecule biochemistry, neurological disease,’ and ‘cardiovascular system development and function’; and those affected by Hcy (score = 25–37) were ‘amino acid metabolism, lipid metabolism,’ ‘cellular movement, and cardiovascular and nervous system development and function.’ These results indicate that each Hcy metabolite uniquely modulates gene expression in pathways important for vascular homeostasis and identify new genes and pathways that are linked to HHcy-induced endothelial dysfunction and vascular disease.
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50
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Borisov OV, Alvarez M, Carroll JA, Brown PW. Sequence Variants and Sequence Variant Analysis in Biotherapeutic Proteins. ACS SYMPOSIUM SERIES 2015. [DOI: 10.1021/bk-2015-1201.ch002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Oleg V. Borisov
- Novavax, Inc., Gaithersburg, Maryland 20878, United States
- Roche Group Member, Genentech, Inc., South San Francisco, California 94080, United States
- Pfizer Worldwide Research & Development, Chesterfield, Missouri 63017, United States
| | - Melissa Alvarez
- Novavax, Inc., Gaithersburg, Maryland 20878, United States
- Roche Group Member, Genentech, Inc., South San Francisco, California 94080, United States
- Pfizer Worldwide Research & Development, Chesterfield, Missouri 63017, United States
| | - James A. Carroll
- Novavax, Inc., Gaithersburg, Maryland 20878, United States
- Roche Group Member, Genentech, Inc., South San Francisco, California 94080, United States
- Pfizer Worldwide Research & Development, Chesterfield, Missouri 63017, United States
| | - Paul W. Brown
- Novavax, Inc., Gaithersburg, Maryland 20878, United States
- Roche Group Member, Genentech, Inc., South San Francisco, California 94080, United States
- Pfizer Worldwide Research & Development, Chesterfield, Missouri 63017, United States
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