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Feng S, Guo Y, Wang Q, Meng M, Liu X, Zhang C, Zheng H, Guo H, Lu R, Li D, Su Z, Song H, Liang Y. UPLC/Q-TOF-MS-based metabolomics and molecular docking analysis of Bifidobacterium adolescentis exposure to levofloxacin. Biomed Chromatogr 2024; 38:e5862. [PMID: 38684194 DOI: 10.1002/bmc.5862] [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: 11/02/2023] [Revised: 02/04/2024] [Accepted: 02/26/2024] [Indexed: 05/02/2024]
Abstract
Antibiotic-associated diarrhea is a common adverse reaction caused by the widespread use of antibiotics. The decrease in probiotics is one of the reasons why antibiotics cause drug-induced diarrhea. However, few studies have addressed the intrinsic mechanism of antibiotics inhibiting probiotics. To investigate the underlying mechanism of levofloxacin against Bifidobacterium adolescentis, we used a metabolomics mass spectrometry-based approach and molecular docking analysis for a levofloxacin-induced B. adolescentis injury model. The results showed that levofloxacin reduced the survival rate of B. adolescentis and decreased the number of B. adolescentis. The untargeted metabolomics analysis identified 27 potential biomarkers, and many of these metabolites are involved in energy metabolism, amino acid metabolism and the lipid metabolism pathway. Molecular docking showed that levofloxacin can bind with aminoacyl-tRNA synthetase and lactic acid dehydrogenase. This result provides a novel insight into the mechanism of the adverse reactions of levofloxacin.
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Affiliation(s)
- Shisui Feng
- Pharmaceutical College, Guangxi Medical University, Nanning, China
- The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Yue Guo
- Pharmaceutical College, Guangxi Medical University, Nanning, China
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Qianyi Wang
- Department of pharmacy, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Mingwei Meng
- Pharmaceutical College, Guangxi Medical University, Nanning, China
| | - Xi Liu
- Pharmaceutical College, Guangxi Medical University, Nanning, China
| | - Chi Zhang
- Pharmaceutical College, Guangxi Medical University, Nanning, China
| | - Hua Zheng
- Life Sciences Institute, Guangxi Medical University, Nanning, China
| | - Hongwei Guo
- Pharmaceutical College, Guangxi Medical University, Nanning, China
| | - Rigang Lu
- Guangxi Institute for Food and Drug Control, Nanning, China
| | - Danfeng Li
- Guangxi Institute for Food and Drug Control, Nanning, China
| | - Zhiheng Su
- Pharmaceutical College, Guangxi Medical University, Nanning, China
| | - Hui Song
- Pharmaceutical College, Guangxi Medical University, Nanning, China
| | - Yonghong Liang
- Pharmaceutical College, Guangxi Medical University, Nanning, China
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2
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Bobrovs R, Bolsakova J, Buitrago JAR, Varaceva L, Skvorcova M, Kanepe I, Rudnickiha A, Parisini E, Jirgensons A. Structure-based identification of salicylic acid derivatives as malarial threonyl tRNA-synthetase inhibitors. PLoS One 2024; 19:e0296995. [PMID: 38558084 PMCID: PMC10984466 DOI: 10.1371/journal.pone.0296995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 12/21/2023] [Indexed: 04/04/2024] Open
Abstract
Emerging resistance to existing antimalarial drugs drives the search for new antimalarials, and protein translation is a promising pathway to target. Threonyl t-RNA synthetase (ThrRS) is one of the enzymes involved in this pathway, and it has been validated as an anti-malarial drug target. Here, we present 9 structurally diverse low micromolar Plasmodium falciparum ThrRS inhibitors that were identified using high-throughput virtual screening (HTVS) and were verified in a FRET enzymatic assay. Salicylic acid-based compound (LE = 0.34) was selected as a most perspective hit and was subjected to hit-to-lead optimisation. A total of 146 hit analogues were synthesised or obtained from commercial vendors and were tested. Structure-activity relationship study was supported by the crystal structure of the complex of a salicylic acid analogue with a close homologue of the plasmodium target, E. coli ThrRS (EcThrRS). Despite the availability of structural information, the hit identified via virtual screening remained one of the most potent PfThrRS inhibitors within this series. However, the compounds presented herein provide novel scaffolds for ThrRS inhibitors, which could serve as starting points for further medicinal chemistry projects targeting ThrRSs or structurally similar enzymes.
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Affiliation(s)
| | | | | | | | | | - Iveta Kanepe
- Latvian Institute of Organic Synthesis, Riga, Latvia
| | | | - Emilio Parisini
- Latvian Institute of Organic Synthesis, Riga, Latvia
- Department of Chemistry “G. Ciamician”, University of Bologna, Bologna, Italy
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3
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Chen X, Guo Y, Shi J, Wang Y, Guo X, Wu G, Li S, Zhang T. Structural basis for substrate and antibiotic recognition by Helicobacter pylori isoleucyl-tRNA synthetase. FEBS Lett 2024; 598:521-536. [PMID: 38246751 DOI: 10.1002/1873-3468.14805] [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: 10/28/2023] [Revised: 12/12/2023] [Accepted: 12/21/2023] [Indexed: 01/23/2024]
Abstract
Helicobacter pylori infection is a global health concern, affecting over half of the world's population. Acquiring structural information on pharmacological targets is crucial to facilitate inhibitor design. Here, we have determined the crystal structures of H. pylori isoleucyl-tRNA synthetase (HpIleRS) in apo form as well as in complex with various substrates (Ile, Ile-AMP, Val, and Val-AMP) or an inhibitor (mupirocin). Our results provide valuable insights into substrate specificity, recognition, and the mechanism by which HpIleRS is inhibited by an antibiotic. Moreover, we identified Asp641 as a prospective regulatory site and conducted biochemical analyses to investigate its regulatory mechanism. The detailed structural information acquired from this research holds promise for the development of highly selective and effective inhibitors against H. pylori infection.
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Affiliation(s)
- Xiaobao Chen
- Institute of Geriatrics, Affiliated Nantong Hospital of Shanghai University, Sixth People's Hospital of Nantong, Shanghai Engineering Research Center of Organ Repair, School of Medicine, Shanghai University, 500 Yonghe Road, Nantong, China
| | - Yu Guo
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai, China
- Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jiawen Shi
- Institute of Geriatrics, Affiliated Nantong Hospital of Shanghai University, Sixth People's Hospital of Nantong, Shanghai Engineering Research Center of Organ Repair, School of Medicine, Shanghai University, 500 Yonghe Road, Nantong, China
| | - Yilun Wang
- Institute of Geriatrics, Affiliated Nantong Hospital of Shanghai University, Sixth People's Hospital of Nantong, Shanghai Engineering Research Center of Organ Repair, School of Medicine, Shanghai University, 500 Yonghe Road, Nantong, China
| | - Xinyi Guo
- Institute of Geriatrics, Affiliated Nantong Hospital of Shanghai University, Sixth People's Hospital of Nantong, Shanghai Engineering Research Center of Organ Repair, School of Medicine, Shanghai University, 500 Yonghe Road, Nantong, China
| | - Guihua Wu
- Institute of Geriatrics, Affiliated Nantong Hospital of Shanghai University, Sixth People's Hospital of Nantong, Shanghai Engineering Research Center of Organ Repair, School of Medicine, Shanghai University, 500 Yonghe Road, Nantong, China
| | - Sheng Li
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai, China
- Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, China
| | - Tianlong Zhang
- Institute of Geriatrics, Affiliated Nantong Hospital of Shanghai University, Sixth People's Hospital of Nantong, Shanghai Engineering Research Center of Organ Repair, School of Medicine, Shanghai University, 500 Yonghe Road, Nantong, China
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4
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Cheuka PM, Njaria P, Mayoka G, Funjika E. Emerging Drug Targets for Antimalarial Drug Discovery: Validation and Insights into Molecular Mechanisms of Function. J Med Chem 2024; 67:838-863. [PMID: 38198596 DOI: 10.1021/acs.jmedchem.3c01828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
Approximately 619,000 malaria deaths were reported in 2021, and resistance to recommended drugs, including artemisinin-combination therapies (ACTs), threatens malaria control. Treatment failure with ACTs has been found to be as high as 93% in northeastern Thailand, and parasite mutations responsible for artemisinin resistance have already been reported in some African countries. Therefore, there is an urgent need to identify alternative treatments with novel targets. In this Perspective, we discuss some promising antimalarial drug targets, including enzymes involved in proteolysis, DNA and RNA metabolism, protein synthesis, and isoprenoid metabolism. Other targets discussed are transporters, Plasmodium falciparum acetyl-coenzyme A synthetase, N-myristoyltransferase, and the cyclic guanosine monophosphate-dependent protein kinase G. We have outlined mechanistic details, where these are understood, underpinning the biological roles and hence druggability of such targets. We believe that having a clear understanding of the underlying chemical interactions is valuable to medicinal chemists in their quest to design appropriate inhibitors.
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Affiliation(s)
- Peter Mubanga Cheuka
- Department of Chemistry, School of Natural Sciences, University of Zambia, P.O. Box 32379, Lusaka 10101, Zambia
| | - Paul Njaria
- Department of Pharmacognosy and Pharmaceutical Chemistry, Kenyatta University, P.O. Box 14548-00400, Nairobi 00100, Kenya
| | - Godfrey Mayoka
- Department of Pharmacology and Pharmacognosy, School of Pharmacy, Jomo Kenyatta University of Agriculture and Technology, P.O. Box 62000-00200, Nairobi 00100, Kenya
| | - Evelyn Funjika
- Department of Chemistry, School of Natural Sciences, University of Zambia, P.O. Box 32379, Lusaka 10101, Zambia
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Abaya A, Zaro GC, De la Mora Pena A, Hsiang T, Goodwin PH. Phenotypic and Genotypic Variation of Cultivated Panax quinquefolius. PLANTS (BASEL, SWITZERLAND) 2024; 13:300. [PMID: 38276757 PMCID: PMC10821518 DOI: 10.3390/plants13020300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 01/09/2024] [Accepted: 01/11/2024] [Indexed: 01/27/2024]
Abstract
American ginseng (Panax quinquefolius) is widely used due to its medicinal properties. Ontario is a major producer of cultivated American ginseng, where seeds were originally collected from the wild without any subsequent scientific selection, and thus the crop is potentially very diverse. A collection of 162 American ginseng plants was harvested from a small area in a commercial garden and phenotyped for morphological traits, such as root grade, stem length, and fresh and dry weights of roots, leaves, stems, and seeds. All of the traits showed a range of values, and correlations were observed between root and stem weights, root dry weight and leaf dry weight, as well as root and leaf fresh weights. The plants were also genotyped using single nucleotide polymorphisms (SNPs) at the PW16 locus. SNP analysis revealed 22 groups based on sequence relatedness with some groups showing no SNPs and others being more diverse. The SNP groups correlated with significant differences in some traits, such as stem length and leaf weight. This study provides insights into the genetic and phenotypic diversity of cultivated American ginseng grown under similar environmental conditions, and the relationship between different phenotypes, as well as genotype and phenotype, will aid in future selection programs to develop American ginseng cultivars with desirable agronomic traits.
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Affiliation(s)
| | | | | | | | - Paul H. Goodwin
- School of Environmental Sciences, University of Guelph, Guelph, ON N1G 2W1, Canada; (A.A.); (G.C.Z.); (A.D.l.M.P.); (T.H.)
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6
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Narsimulu B, Jakkula P, Qureshi R, Nasim F, Qureshi IA. Inhibition and structural insights of leishmanial glutamyl-tRNA synthetase for designing potent therapeutics. Int J Biol Macromol 2024; 254:127756. [PMID: 37907177 DOI: 10.1016/j.ijbiomac.2023.127756] [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: 07/12/2023] [Revised: 10/08/2023] [Accepted: 10/27/2023] [Indexed: 11/02/2023]
Abstract
Aminoacyl-tRNA synthetases (aaRSs), essential components of the protein synthesizing machinery, have been often chosen for devising therapeutics against parasitic diseases. Due to their relevance in drug development, the current study was designed to explore functional and structural aspects of Leishmania donovani glutamyl-tRNA synthetase (LdGluRS). Hence, LdGluRS was cloned into an expression vector and purified to homogeneity using chromatographic techniques. Purified protein showed maximum enzymatic activity at physiological pH, with more binding capacity towards its cofactor (Adenosine triphosphate, 0.06 ± 0.01 mM) than the cognate substrate (L-glutamate, 9.5 ± 0.5 mM). Remarkably, salicylate inhibited LdGluRS competitively with respect to L-glutamate and exhibited druglikeness with negligible effect on human macrophages. The protein possessed more α-helices (43 %) than β-sheets (12 %), whereas reductions in thermal stability and cofactor-binding affinity, along with variation in mode of inhibition after mutation signified the role of histidine (H60) as a catalytic residue. LdGluRS could also generate a pro-inflammatory milieu in human macrophages by upregulating cytokines. The docking study demonstrated the placement of salicylate into LdGluRS substrate-binding site, and the complex was found to be stable during molecular dynamics (MD) simulation. Altogether, our study highlights the understanding of molecular inhibition and structural features of glutamyl-tRNA synthetase from kinetoplastid parasites.
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Affiliation(s)
- Bandigi Narsimulu
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Prof. C.R. Rao Road, Hyderabad 500046, India
| | - Pranay Jakkula
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Prof. C.R. Rao Road, Hyderabad 500046, India
| | - Rahila Qureshi
- Centre for DNA Fingerprinting and Diagnostics, Hyderabad 500039, India
| | - Fouzia Nasim
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Prof. C.R. Rao Road, Hyderabad 500046, India
| | - Insaf Ahmed Qureshi
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Prof. C.R. Rao Road, Hyderabad 500046, India.
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7
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Thakur S, Mehra R. Computational Insight into Substrate-Induced Conformational Changes in Methionyl-tRNA Synthetase of Mycobacterium Tuberculosis. Protein J 2023; 42:533-546. [PMID: 37402109 DOI: 10.1007/s10930-023-10135-3] [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: 06/26/2023] [Indexed: 07/05/2023]
Abstract
Tuberculosis caused by Mycobacterium tuberculosis (M.tb) has killed millions worldwide. Antibiotic resistance leads to the ineffectiveness of the current therapies. Aminoacyl tRNA synthetase (aaRS) class of proteins involved in protein synthesis are promising bacterial targets for developing new therapies. Here, we carried out a systematic comparative study on the aaRS sequences from M.tb and human. We listed important M.tb aaRS that could be explored as potential M.tb targets alongside the detailed conformational space analysis of methionyl-tRNA synthetase (MetRS) in apo- and substrate-bound form, which is among the proposed targets. Understanding the conformational dynamics is central to the mechanistic understanding of MetRS, as the substrate binding leads to the conformational changes causing the reaction to proceed. We performed the most complete simulation study of M.tb MetRS for 6 microseconds (2 systems × 3 runs × 1 microsecond) in the apo and substrate-bound states. Interestingly, we observed differential features, showing comparatively large dynamics for the holo simulations, whereas the apo structures became slightly compact with reduced solvent exposed area. In contrast, the ligand size decreased significantly in holo structures possibly to relax ligand conformation. Our findings correlate with experimental studies, thus validating our protocol. Adenosine monophosphate moiety of the substrate exhibited quite higher fluctuations than the methionine. His21 and Lys54 were found to be the important residues forming prominent hydrogen bond and salt-bridge interactions with the ligand. The ligand-protein affinity decreased during simulations as computed by MMGBSA analysis over the last 500 ns trajectories, which indicates the conformational changes upon ligand binding. These differential features could be further explored for designing new M.tb inhibitors.
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Affiliation(s)
- Shivani Thakur
- Department of Chemistry, Indian Institute of Technology Bhilai, Sejbahar, Raipur, Chhattisgarh, 492015, India
| | - Rukmankesh Mehra
- Department of Chemistry, Indian Institute of Technology Bhilai, Sejbahar, Raipur, Chhattisgarh, 492015, India.
- Department of Bioscience and Biomedical Engineering, Indian Institute of Technology Bhilai, Sejbahar, Raipur, Chhattisgarh, 492015, India.
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8
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Xie SC, Griffin MDW, Winzeler EA, Ribas de Pouplana L, Tilley L. Targeting Aminoacyl tRNA Synthetases for Antimalarial Drug Development. Annu Rev Microbiol 2023; 77:111-129. [PMID: 37018842 DOI: 10.1146/annurev-micro-032421-121210] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Infections caused by malaria parasites place an enormous burden on the world's poorest communities. Breakthrough drugs with novel mechanisms of action are urgently needed. As an organism that undergoes rapid growth and division, the malaria parasite Plasmodium falciparum is highly reliant on protein synthesis, which in turn requires aminoacyl-tRNA synthetases (aaRSs) to charge tRNAs with their corresponding amino acid. Protein translation is required at all stages of the parasite life cycle; thus, aaRS inhibitors have the potential for whole-of-life-cycle antimalarial activity. This review focuses on efforts to identify potent plasmodium-specific aaRS inhibitors using phenotypic screening, target validation, and structure-guided drug design. Recent work reveals that aaRSs are susceptible targets for a class of AMP-mimicking nucleoside sulfamates that target the enzymes via a novel reaction hijacking mechanism. This finding opens up the possibility of generating bespoke inhibitors of different aaRSs, providing new drug leads.
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Affiliation(s)
- Stanley C Xie
- Department of Biochemistry and Pharmacology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, Australia; , ,
| | - Michael D W Griffin
- Department of Biochemistry and Pharmacology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, Australia; , ,
| | - Elizabeth A Winzeler
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, California, USA;
| | - Lluis Ribas de Pouplana
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain;
- Catalan Institution for Research and Advanced Studies, Barcelona, Catalonia, Spain
| | - Leann Tilley
- Department of Biochemistry and Pharmacology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, Australia; , ,
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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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Engelhard CA, Khani S, Derdak S, Bilban M, Kornfeld JW. Nanopore sequencing unveils the complexity of the cold-activated murine brown adipose tissue transcriptome. iScience 2023; 26:107190. [PMID: 37564700 PMCID: PMC10410515 DOI: 10.1016/j.isci.2023.107190] [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: 01/30/2023] [Revised: 04/28/2023] [Accepted: 06/16/2023] [Indexed: 08/12/2023] Open
Abstract
Alternative transcription increases transcriptome complexity by expression of multiple transcripts per gene. Annotation and quantification of transcripts using short-read sequencing is non-trivial. Long-read sequencing aims at overcoming these problems by sequencing full-length transcripts. Activation of brown adipose tissue (BAT) thermogenesis involves major transcriptomic remodeling and positively affects metabolism via increased energy expenditure. We benchmark Oxford Nanopore Technology (ONT) long-read sequencing protocols to Illumina short-read sequencing assessing alignment characteristics, gene and transcript detection and quantification, differential gene and transcript expression, transcriptome reannotation, and differential transcript usage (DTU). We find ONT sequencing is superior to Illumina for transcriptome reassembly, reducing the risk of false-positive events by unambiguously mapping reads to transcripts. We identified novel isoforms of genes undergoing DTU in cold-activated BAT including Cars2, Adtrp, Acsl5, Scp2, Aldoa, and Pde4d, validated by real-time PCR. The reannotated murine BAT transcriptome established here provides a framework for future investigations into the regulation of BAT.
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Affiliation(s)
- Christoph Andreas Engelhard
- Department for Biochemistry and Molecular Biology (BMB), University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Sajjad Khani
- Max Planck Institute for Metabolism Research, Gleueler Strasse 50, 50931 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Ageing-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Sophia Derdak
- Core Facilities, Medical University of Vienna, Lazarettgasse 14, 1090 Vienna, Austria
| | - Martin Bilban
- Department of Laboratory Medicine & Core Facilities, Medical University of Vienna, Waehringer Guertel 18-20, 1090 Vienna, Austria
| | - Jan-Wilhelm Kornfeld
- Department for Biochemistry and Molecular Biology (BMB), University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
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Gan Z, Zhang X, Li M, Li X, Zhang X, Wang C, Xiao Y, Liu J, Fang Z. Seryl-tRNA Synthetase Shows a Noncanonical Activity of Upregulating Laccase Transcription in Trametes hirsuta AH28-2 Exposed to Copper Ion. Microbiol Spectr 2023; 11:e0076823. [PMID: 37395668 PMCID: PMC10433817 DOI: 10.1128/spectrum.00768-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 06/13/2023] [Indexed: 07/04/2023] Open
Abstract
The function of Seryl-tRNA synthetase in fungi during gene transcription regulation beyond translation has not been reported. Here, we report a seryl-tRNA synthetase, ThserRS, which can negatively regulate laccase lacA transcription in Trametes hirsuta AH28-2 under exposure to copper ion. ThserRS was obtained through yeast one-hybrid screening using a bait sequence of lacA promoter (-502 to -372 bp). ThserRS decreased while lacA increased at the transcription level in T. hirsuta AH28-2 in the first 36 h upon CuSO4 induction. Then, ThserRS was upregulated, and lacA was downregulated. ThserRS overexpression in T. hirsuta AH28-2 resulted in a decrement in lacA transcription and LacA activity. By comparison, ThserRS silencing led to increased LacA transcripts and activity. A minimum of a 32-bp DNA fragment containing two putative xenobiotic response elements could interact with ThserRS, with a dissociation constant of 919.9 nM. ThserRS localized in the cell cytoplasm and nucleus in T. hirsuta AH28-2 and was heterologously expressed in yeast. ThserRS overexpression also enhanced mycelial growth and oxidative stress resistance. The transcriptional level of several intracellular antioxidative enzymes in T. hirsuta AH28-2 was upregulated. Our results demonstrate a noncanonical activity of SerRS that acts as a transcriptional regulation factor to upregulate laccase expression at an early stage after exposure to copper ions. IMPORTANCE Seryl-tRNA synthetase is well known for the attachment of serine to the corresponding cognate tRNA during protein translation. In contrast, its functions beyond translation in microorganisms are underexplored. We performed in vitro and cell experiments to show that the seryl-tRNA synthetase in fungi with no UNE-S domain at the carboxyl terminus can enter the nucleus, directly interact with the promoter of the laccase gene, and negatively regulate the fungal laccase transcription early upon copper ion induction. Our study deepens our understanding of the Seryl-tRNA synthetase noncanonical activities in microorganisms. It also demonstrates a new transcription factor for fungal laccase transcription.
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Affiliation(s)
- Zhiwei Gan
- School of Life Sciences, Anhui University, Hefei, Anhui, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, Anhui, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, Anhui, China
| | - Xueping Zhang
- School of Life Sciences, Anhui University, Hefei, Anhui, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, Anhui, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, Anhui, China
| | - Mengke Li
- School of Life Sciences, Anhui University, Hefei, Anhui, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, Anhui, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, Anhui, China
| | - Xing Li
- School of Life Sciences, Anhui University, Hefei, Anhui, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, Anhui, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, Anhui, China
| | - Xinlei Zhang
- School of Life Sciences, Anhui University, Hefei, Anhui, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, Anhui, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, Anhui, China
| | - Chenkai Wang
- School of Life Sciences, Anhui University, Hefei, Anhui, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, Anhui, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, Anhui, China
| | - Yazhong Xiao
- School of Life Sciences, Anhui University, Hefei, Anhui, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, Anhui, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, Anhui, China
| | - Juanjuan Liu
- School of Life Sciences, Anhui University, Hefei, Anhui, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, Anhui, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, Anhui, China
| | - Zemin Fang
- School of Life Sciences, Anhui University, Hefei, Anhui, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, Anhui, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, Anhui, China
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12
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Buitrago JAR, Leitis G, Kaņepe-Lapsa I, Rudnickiha A, Parisini E, Jirgensons A. Synthesis and evaluation of an agrocin 84 toxic moiety (TM84) analogue as a malarial threonyl tRNA synthetase inhibitor. Org Biomol Chem 2023. [PMID: 37335076 DOI: 10.1039/d3ob00670k] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
Abstract
An analogue of a toxic moiety (TM84) of natural product agrocin 84 containing threonine amide instead of 2,3-dihydroxy-4-methylpentanamide was prepared and evaluated as a putative Plasmodium falciparum threonyl t-RNA synthetase (PfThrRS) inhibitor. This TM84 analogue features submicromolar inhibitory potency (IC50 = 440 nM) comparable to that of borrelidin (IC50 = 43 nM) and therefore complements chemotypes known to inhibit malarial PfThrRS, which are currently limited to borrelidin and its analogues. The crystal structure of the inhibitor in complex with the E. coli homologue enzyme (EcThrRS) was obtained, revealing crucial ligand-protein interactions that will pave the way for the design of novel ThrRS inhibitors.
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Affiliation(s)
| | - Gundars Leitis
- Latvian Institute of Organic Synthesis, Riga LV-1006, Latvia
| | | | | | - Emilio Parisini
- Latvian Institute of Organic Synthesis, Riga LV-1006, Latvia
- Department of Chemistry "G. Ciamician", University of Bologna, 40126, Bologna, Italy.
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13
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Meng C, Wang K, Zhang X, Zhu X. Effect of cadmium in the gonads of mussel (Mytilus coruscus): an ionomics and proteomics study. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:68373-68386. [PMID: 37120503 DOI: 10.1007/s11356-023-27208-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 04/20/2023] [Indexed: 05/27/2023]
Abstract
The mussel Mytilus coruscus is an important and very popular seafood in China and widespread along the eastern coast of China. In this study, we investigated the molecular response of mussel gonads to cadmium accumulation at two concentrations (80 and 200 µg/L) for 30 days using ionomics and proteomics techniques. The shrinkage of the cells and moderate hemocytic infiltration were observed in the Cd-treated groups. The strontium, selenium (Se), and zinc contents were significantly altered, and the relationships between iron, copper, Se, manganese, calcium, sodium, and magnesium were also significantly altered. Label-free quantitative proteomics analysis revealed a total of 227 differentially expressed proteins. These proteins were associated with multiple biological processes, including the tricarboxylic acid cycle, structural reorganization of cells, biosynthesis of amino acids, inflammatory response of cells, and tumorigenesis. Nonetheless, our ionomics and proteomics analysis revealed that mussels could partly alleviate the adverse effects of Cd by altering the metal contents and correlations between minerals, thereby enhancing the biosynthesis of some amino acids and activity of antioxidant enzymes. Overall, this study provides an insight into the mechanism underlying Cd toxicity in mussel gonads from a metal and protein perspective.
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Affiliation(s)
- Chunying Meng
- Laboratory of Aquatic Product Processing and Quality Safety, Zhejiang Marine Fisheries Research Institute, Zhoushan, 316100, People's Republic of China.
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, 310018, People's Republic of China.
| | - Kuiwu Wang
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, 310018, People's Republic of China
| | - Xiaojun Zhang
- Laboratory of Aquatic Product Processing and Quality Safety, Zhejiang Marine Fisheries Research Institute, Zhoushan, 316100, People's Republic of China
| | - Xinyue Zhu
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, 310018, People's Republic of China
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14
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Nasim F, Qureshi IA. Aminoacyl tRNA Synthetases: Implications of Structural Biology in Drug Development against Trypanosomatid Parasites. ACS OMEGA 2023; 8:14884-14899. [PMID: 37151504 PMCID: PMC10157851 DOI: 10.1021/acsomega.3c00826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 03/29/2023] [Indexed: 05/09/2023]
Abstract
The ensemble of aminoacyl tRNA synthetases is regarded as a key component of the protein translation machinery. With the progressive increase in structure-based studies on tRNA synthetase-ligand complexes, the detailed picture of these enzymes is becoming clear. Having known their critical role in deciphering the genetic code in a living system, they have always been chosen as one of the important targets for development of antimicrobial drugs. Later on, the role of aminoacyl tRNA synthetases (aaRSs) on the survivability of trypanosomatids has also been validated. It became evident through several gene knockout studies that targeting even one of these enzymes affected parasitic growth drastically. Such successful studies have inspired researchers to search for inhibitors that could specifically target trypanosomal aaRSs, and their never-ending efforts have provided fruitful results. Taking all such studies into consideration, these macromolecules of prime importance deserve further investigation for the development of drugs that cure spectrum of infections caused by trypanosomatids. In this review, we have compiled advancements of over a decade that have taken place in the pursuit of devising drugs by using trypanosomatid aaRSs as a major target of interest. Several of these inhibitors work on an exemplary low concentration range without posing any threat to the mammalian cells which is a very critical aspect of the drug discovery process. Advancements have been made in terms of using structural biology as an important tool to analyze the architecture of the trypanosomatids aaRSs and concoction of inhibitors with augmented specificities toward their targets. Some of the inhibitors that have been tested on other parasites successfully but their efficacy has so far not been validated against these trypanosomatids have also been appended.
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15
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He M, Liu A, Shi J, Xu YJ, Liu Y. Multi-Omics Reveals the Effects of Cannabidiol on Gut Microbiota and Metabolic Phenotypes. Cannabis Cannabinoid Res 2023. [PMID: 37098174 DOI: 10.1089/can.2022.0331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/27/2023] Open
Abstract
Introduction: Cannabidiol (CBD) has important pharmacological activity, which includes antispasmodic, antioxidant, antithrombotic, and antianxiety properties. CBD has been applied as a health supplement to atherosclerosis. However, CBDs effect on gut microbiota and metabolic phenotype is unclear. Materials and Methods: We constructed a high production of cardiovascular risk factors, such as trimethylamine-N-oxide (TMAO) and phenylacetylglutamine (PAGln), in a mouse model using Clostridium sporogenes colonization. We used 16S ribosomal RNA (rRNA) gene sequencing and ultra-high performance liquid chromatography-quadrupole time-of flight mass spectrometry-based metabolomics to evaluate the effect of CBD on gut microbiota and plasma metabolites. Results: CBD decreased the levels of creatine kinase (CK), alanine transaminase (ALT), and low-density lipoprotein cholesterol and markedly increased high-density lipoprotein cholesterol. Furthermore, CBD treatment increased the abundance of beneficial bacteria, which include Lachnospiraceae_NK4A136 and Blautia in the gut, but it decreased the levels of TMAO and PAGln in the plasma. Conclusion: CBD might have beneficial effects for cardiovascular protection.
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Affiliation(s)
- Mengxue He
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, Wuxi, China
| | - Aiyang Liu
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, Wuxi, China
| | - Jiachen Shi
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, Wuxi, China
| | - Yong-Jiang Xu
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, Wuxi, China
| | - Yuanfa Liu
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, Wuxi, China
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16
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Narsimulu B, Qureshi R, Jakkula P, Singh P, Arifuddin M, Qureshi IA. Exploration of seryl tRNA synthetase to identify potent inhibitors against leishmanial parasites. Int J Biol Macromol 2023; 237:124118. [PMID: 36963547 DOI: 10.1016/j.ijbiomac.2023.124118] [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: 01/31/2023] [Revised: 03/13/2023] [Accepted: 03/17/2023] [Indexed: 03/26/2023]
Abstract
Aminoacyl-tRNA synthetases are crucial enzymes for cellular protein metabolism and have been considered as an attractive target for development of new antimicrobials. In the current study, seryl tRNA synthetase of Leishmania donovani (LdSerRS) and its mutants were purified and characterized through biochemical and structural methods. Purified LdSerRS was found to be enzymatically active and exhibited more alpha helices in secondary structure. The enzymatic activity of purified protein was observed as highest near physiological temperature and pH. Mutation in ATP binding residues (R295 and E297) demonstrated reduction in the affinity for cofactor with no significant deviation in secondary structure. In vitro inhibition studies with ureidosulfocoumarin derivatives helped to identify Comp 5l as a specific inhibitor for leishmanial SerRS that showed lesser potency towards purified HsSerRS. The identified compound presented competitive mode of inhibition for LdSerRS and also revealed druglikeness along with very low toxicity for human macrophages. Structural analysis of protein and ligand complex depicted the binding of Comp 5l into the cofactor binding site of LdSerRS with high affinity succeeded by validation employing molecular dynamics simulations. Altogether, our study presents a promising scaffold to explore small molecules to target the enzymatic activity of leishmanial SerRS to develop the specific therapeutics.
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Affiliation(s)
- Bandigi Narsimulu
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Prof. C.R. Rao Road, Hyderabad 500046, India
| | - Rahila Qureshi
- Centre for DNA Fingerprinting and Diagnostics, Hyderabad 500039, India
| | - Pranay Jakkula
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Prof. C.R. Rao Road, Hyderabad 500046, India
| | - Priti Singh
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad 500037, India
| | - Mohammed Arifuddin
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad 500037, India
| | - Insaf Ahmed Qureshi
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Prof. C.R. Rao Road, Hyderabad 500046, India.
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17
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Investigation into the anti-inflammatory mechanism of coffee leaf extract in LPS-induced Caco-2/U937 co-culture model through cytokines and NMR-based untargeted metabolomics analyses. Food Chem 2023; 404:134592. [DOI: 10.1016/j.foodchem.2022.134592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 08/15/2022] [Accepted: 10/10/2022] [Indexed: 11/07/2022]
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18
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He J, Liu XX, Ma MM, Lin JJ, Fu J, Chen YK, Xu GR, Xu LQ, Fu ZF, Xu D, Chen WF, Cao CY, Shi Y, Zeng YH, Zhang J, Chen XC, Zhang RX, Wang N, Kennerson M, Fan DS, Chen WJ. Heterozygous Seryl-tRNA Synthetase 1 Variants Cause Charcot-Marie-Tooth Disease. Ann Neurol 2023; 93:244-256. [PMID: 36088542 DOI: 10.1002/ana.26501] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 09/05/2022] [Accepted: 09/06/2022] [Indexed: 01/31/2023]
Abstract
OBJECTIVE Despite the increasing number of genes associated with Charcot-Marie-Tooth (CMT) disease, many patients currently still lack appropriate genetic diagnosis for this disease. Autosomal dominant mutations in aminoacyl-tRNA synthetases (ARSs) have been implicated in CMT. Here, we describe causal missense mutations in the gene encoding seryl-tRNA synthetase 1 (SerRS) for 3 families affected with CMT. METHODS Whole-exome sequencing was performed in 16 patients and 14 unaffected members of 3 unrelated families. The functional impact of the genetic variants identified was investigated using bioinformatic prediction tools and confirmed using cellular and biochemical assays. RESULTS Combined linkage analysis for the 3 families revealed significant linkage (Zmax LOD = 6.9) between the genomic co-ordinates on chromosome 1: 108681600-110300504. Within the linkage region, heterozygous SerRS missense variants segregated with the clinical phenotype in the 3 families. The mutant SerRS proteins exhibited reduced aminoacylation activity and abnormal SerRS dimerization, which suggests the impairment of total protein synthesis and induction of eIF2α phosphorylation. INTERPRETATION Our findings suggest the heterozygous SerRS variants identified represent a novel cause for autosomal dominant CMT. Mutant SerRS proteins are known to impact various molecular and cellular functions. Our findings provide significant advances on the current understanding of the molecular mechanisms associated with ARS-related CMT. ANN NEUROL 2023;93:244-256.
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Affiliation(s)
- Jin He
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, China
| | - Xiao-Xuan Liu
- Department of Neurology of Peking University Third Hospital, Key Laboratory for Neuroscience, National Health Commission/Ministry of Education, Peking University, Beijing, China
- Beijing Key Laboratory of Biomarker and Translational Research in Neurodegenerative Diseases, Peking University Third Hospital, Beijing, China
| | - Ming-Ming Ma
- Department of Neurology, Henan Provincial People's Hospital, Zhengzhou, China
| | - Jing-Jing Lin
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, China
| | - Jun Fu
- Department of Neurology, Henan Provincial People's Hospital, Zhengzhou, China
| | - Yi-Kun Chen
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, China
| | - Guo-Rong Xu
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, China
| | - Liu-Qing Xu
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, China
| | - Zhi-Fei Fu
- Public Technology Service Center, Fujian Medical University, Fuzhou, China
| | - Dan Xu
- Fujian Key Laboratory of Molecular Neurology, Institute of Neuroscience, Fujian Medical University, Fuzhou, China
| | - Wen-Feng Chen
- Institute of Life Sciences, College of Biological Science and Engineering, Fuzhou University, Fuzhou, China
| | - Chun-Yan Cao
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, China
| | - Yan Shi
- Fujian Key Laboratory of Molecular Neurology, Institute of Neuroscience, Fujian Medical University, Fuzhou, China
| | - Yi-Heng Zeng
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, China
| | - Jing Zhang
- Fujian Key Laboratory of Molecular Neurology, Institute of Neuroscience, Fujian Medical University, Fuzhou, China
| | - Xiao-Chun Chen
- Fujian Key Laboratory of Molecular Neurology, Institute of Neuroscience, Fujian Medical University, Fuzhou, China
| | - Ru-Xu Zhang
- Department of Neurology, Third Xiangya Hospital, Central South University, Changsha, China
| | - Ning Wang
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, China
| | - Marina Kennerson
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Sydney Local Health District and Faculty of Medicine and Health, University of Sydney, Sydney, Australia
| | - Dong-Sheng Fan
- Department of Neurology of Peking University Third Hospital, Key Laboratory for Neuroscience, National Health Commission/Ministry of Education, Peking University, Beijing, China
- Beijing Key Laboratory of Biomarker and Translational Research in Neurodegenerative Diseases, Peking University Third Hospital, Beijing, China
| | - Wan-Jin Chen
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, China
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19
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Lu AKM, Hsieh S, Yang CT, Wang XY, Lin SH. DNA methylation signature of psychological resilience in young adults: Constructing a methylation risk score using a machine learning method. Front Genet 2023; 13:1046700. [PMID: 36712885 PMCID: PMC9877348 DOI: 10.3389/fgene.2022.1046700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 12/29/2022] [Indexed: 01/15/2023] Open
Abstract
Resilience is a process associated with the ability to recover from stress and adversity. We aimed to explore the resilience-associated DNA methylation signatures and evaluate the abilities of methylation risk scores to discriminate low resilience (LR) individuals. The study recruited 78 young adults and used Connor-Davidson Resilience Scale (CD-RISC) to divide them into low and high resilience groups. We randomly allocated all participants of two groups to the discovery and validation sets. We used the blood DNA of the subjects to conduct a genome-wide methylation scan and identify the significant methylation differences of CpG Sites in the discovery set. Moreover, the classification accuracy of the DNA methylation probes was confirmed in the validation set by real-time quantitative methylation-specific polymerase chain reaction. In the genome-wide methylation profiling between LR and HR individuals, seventeen significantly differentially methylated probes were detected. In the validation set, nine DNA methylation signatures within gene coding regions were selected for verification. Finally, three methylation probes [cg18565204 (AARS), cg17682313 (FBXW7), and cg07167608 (LINC01107)] were included in the final model of the methylation risk score for LR versus HR. These methylation risk score models of low resilience demonstrated satisfactory discrimination by logistic regression and support vector machine, with an AUC of 0.81 and 0.93, accuracy of 72.3% and 87.1%, sensitivity of 75%, and 87.5%, and specificity of 70% and 80%. Our findings suggest that methylation signatures can be utilized to identify individuals with LR and establish risk score models that may contribute to the field of psychology.
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Affiliation(s)
- Andrew Ke-Ming Lu
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Shulan Hsieh
- Department of Psychology, College of Social Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Cheng-Ta Yang
- Department of Psychology, College of Social Sciences, National Cheng Kung University, Tainan, Taiwan,Graduate Institute of Mind, Brain, and Consciousness, Taipei Medical University, Taipei, Taiwan
| | - Xin-Yu Wang
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Sheng-Hsiang Lin
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan,Department of Public Health, College of Medicine, National Cheng Kung University, Tainan, Taiwan,Biostatistics Consulting Center, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan,*Correspondence: Sheng-Hsiang Lin,
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20
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Giant Viruses as a Source of Novel Enzymes for Biotechnological Application. Pathogens 2022; 11:pathogens11121453. [PMID: 36558786 PMCID: PMC9787589 DOI: 10.3390/pathogens11121453] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/24/2022] [Accepted: 11/28/2022] [Indexed: 12/05/2022] Open
Abstract
The global demand for industrial enzymes has been increasing in recent years, and the search for new sources of these biological products is intense, especially in microorganisms. Most known viruses have limited genetic machinery and, thus, have been overlooked by the enzyme industry for years. However, a peculiar group of viruses breaks this paradigm. Giant viruses of the phylum Nucleocytoviricota infect protists (i.e., algae and amoebae) and have complex genomes, reaching up to 2.7 Mb in length and encoding hundreds of genes. Different giant viruses have robust metabolic machinery, especially those in the Phycodnaviridae and Mimiviridae families. In this review, we present some peculiarities of giant viruses that infect protists and discuss why they should be seen as an outstanding source of new enzymes. We revisited the genomes of representatives of different groups of giant viruses and put together information about their enzymatic machinery, highlighting several genes to be explored in biotechnology involved in carbohydrate metabolism, DNA replication, and RNA processing, among others. Finally, we present additional evidence based on structural biology using chitinase as a model to reinforce the role of giant viruses as a source of novel enzymes for biotechnological application.
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Cheng S, Fahmi NA, Park M, Sun J, Thao K, Yeh HS, Zhang W, Yong J. mTOR Contributes to the Proteome Diversity through Transcriptome-Wide Alternative Splicing. Int J Mol Sci 2022; 23:ijms232012416. [PMID: 36293270 PMCID: PMC9604279 DOI: 10.3390/ijms232012416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/30/2022] [Accepted: 10/04/2022] [Indexed: 11/16/2022] Open
Abstract
The mammalian target of rapamycin (mTOR) pathway is crucial in energy metabolism and cell proliferation. Previously, we reported transcriptome-wide 3′-untranslated region (UTR) shortening by alternative polyadenylation upon mTOR activation and its impact on the proteome. Here, we further interrogated the mTOR-activated transcriptome and found that hyperactivation of mTOR promotes transcriptome-wide exon skipping/exclusion, producing short isoform transcripts from genes. This widespread exon skipping confers multifarious regulations in the mTOR-controlled functional proteomics: AS in coding regions widely affects the protein length and functional domains. They also alter the half-life of proteins and affect the regulatory post-translational modifications. Among the RNA processing factors differentially regulated by mTOR signaling, we found that SRSF3 mechanistically facilitates exon skipping in the mTOR-activated transcriptome. This study reveals a role of mTOR in AS regulation and demonstrates that widespread AS is a multifaceted modulator of the mTOR-regulated functional proteome.
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Affiliation(s)
- Sze Cheng
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN 55445, USA
| | - Naima Ahmed Fahmi
- Department of Computer Science, University of Central Florida, Orlando, FL 32816, USA
| | - Meeyeon Park
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN 55445, USA
| | - Jiao Sun
- Department of Computer Science, University of Central Florida, Orlando, FL 32816, USA
| | - Kaitlyn Thao
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN 55445, USA
| | - Hsin-Sung Yeh
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN 55445, USA
| | - Wei Zhang
- Department of Computer Science, University of Central Florida, Orlando, FL 32816, USA
- Correspondence: (W.Z.); (J.Y.); Tel.: +1-407-823-2763 (W.Z.); +1-612-626-2420 (J.Y.)
| | - Jeongsik Yong
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN 55445, USA
- Correspondence: (W.Z.); (J.Y.); Tel.: +1-407-823-2763 (W.Z.); +1-612-626-2420 (J.Y.)
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22
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Pang L, Zanki V, Strelkov SV, Van Aerschot A, Gruic-Sovulj I, Weeks SD. Partitioning of the initial catalytic steps of leucyl-tRNA synthetase is driven by an active site peptide-plane flip. Commun Biol 2022; 5:883. [PMID: 36038645 PMCID: PMC9424281 DOI: 10.1038/s42003-022-03825-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 08/09/2022] [Indexed: 12/29/2022] Open
Abstract
To correctly aminoacylate tRNALeu, leucyl-tRNA synthetase (LeuRS) catalyzes three reactions: activation of leucine by ATP to form leucyl-adenylate (Leu-AMP), transfer of this amino acid to tRNALeu and post-transfer editing of any mischarged product. Although LeuRS has been well characterized biochemically, detailed structural information is currently only available for the latter two stages of catalysis. We have solved crystal structures for all enzymatic states of Neisseria gonorrhoeae LeuRS during Leu-AMP formation. These show a cycle of dramatic conformational changes, involving multiple domains, and correlate with an energetically unfavorable peptide-plane flip observed in the active site of the pre-transition state structure. Biochemical analyses, combined with mutant structural studies, reveal that this backbone distortion acts as a trigger, temporally compartmentalizing the first two catalytic steps. These results unveil the remarkable effect of this small structural alteration on the global dynamics and activity of the enzyme.
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Affiliation(s)
- Luping Pang
- grid.5596.f0000 0001 0668 7884Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49 – Box 822, 3000 Leuven, Belgium ,grid.5596.f0000 0001 0668 7884Medicinal Chemistry, Rega Institute for Medical Research, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49 – Box 1041, 3000 Leuven, Belgium ,grid.207374.50000 0001 2189 3846Research Center of Basic Medicine, Academy of Medical Sciences, College of Medicine, Zhengzhou University, Zhengzhou, Henan 450001 China
| | - Vladimir Zanki
- grid.4808.40000 0001 0657 4636Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia
| | - Sergei V. Strelkov
- grid.5596.f0000 0001 0668 7884Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49 – Box 822, 3000 Leuven, Belgium
| | - Arthur Van Aerschot
- grid.5596.f0000 0001 0668 7884Medicinal Chemistry, Rega Institute for Medical Research, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49 – Box 1041, 3000 Leuven, Belgium
| | - Ita Gruic-Sovulj
- grid.4808.40000 0001 0657 4636Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia
| | - Stephen D. Weeks
- grid.5596.f0000 0001 0668 7884Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49 – Box 822, 3000 Leuven, Belgium ,Pledge Therapeutics, Gaston Geenslaan 1, 3001 Leuven, Belgium
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Kushwaha V, Capalash N. Aminoacyl-tRNA synthetase (AARS) as an attractive drug target in neglected tropical trypanosomatid diseases-Leishmaniasis, Human African Trypanosomiasis and Chagas disease. Mol Biochem Parasitol 2022; 251:111510. [PMID: 35988745 DOI: 10.1016/j.molbiopara.2022.111510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 08/09/2022] [Accepted: 08/16/2022] [Indexed: 10/15/2022]
Abstract
TriTryp diseases (Leishmaniasis, Human African Trypanosomiasis (HAT), and Chagas disease) are devastating parasitic neglected tropical diseases (NTDs) that affect billions of people in developing countries, cause high mortality in humans, and impose a large socio-economic burden. The current treatment options against tritryp diseases are suboptimal and challenging due to the emergence of resistance against available tritryp drugs. Hence, designing and developing effective anti-tritryp drugs with novel targets are required. Aminoacyl-tRNA synthetases (AARSs) involved in specific aminoacylation of transfer RNAs (tRNAs), interrupt protein synthesis through inhibitors, and retard the parasite growth. AaRSs have long been studied as therapeutic targets in bacteria, and three aaRS inhibitors, mupirocin (against IleRS), tavaborole AN2690 (against LeuRS), and halofuginone (against ProRS), are already in clinical practice. The structural differences between tritryp and human aaRSs and the presence of unique sequences (N-terminal domain/C-terminal domain/catalytic domain) make them potential target for developing selective inhibitors. Drugs based on a single aaRS target developed by high-throughput screening (HTS) are less effective due to the emergence of resistance. However, designing multi-targeted drugs may be a better strategy for resistance development. In this perspective, we discuss the characteristics of tritryp aaRSs, sequence conservation in their orthologs and their peculiarities, recent advancements towards the single-target and multi-target aaRS inhibitors developed through rational design.
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Affiliation(s)
- Vikas Kushwaha
- Department of Biotechnology, Panjab University, Sector-25, South Campus, Chandigarh 160025, India.
| | - Neena Capalash
- Department of Biotechnology, Panjab University, Sector-25, South Campus, Chandigarh 160025, India.
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Vafaee-Shahi M, Farhadi M, Razmara E, Morovvati S, Ghasemi S, Abedini SS, Bagher Z, Alizadeh R, Falah M. Novel phenotype and genotype spectrum of NARS2 and literature review of previous mutations. Ir J Med Sci 2022; 191:1877-1890. [PMID: 34374940 DOI: 10.1007/s11845-021-02736-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 07/30/2021] [Indexed: 01/19/2023]
Abstract
BACKGROUND Mutations in NARS2 (MIM: 612803) are associated with combined oxidative phosphorylation deficiency 24 (COXPD24; MIM: 616239) that is a rare mitochondrial and a multisystem autosomal recessive disorder. AIMS We aimed to detect the underlying genetic factors in two siblings with progressive ataxia, epilepsy, and severe-to-profound hearing impairment. METHODS After doing medical assessments and pertinent tests (i.e., auditory brainstem responses, pure tone otoacoustic emission test, cardiac examinations, computed tomography, and electroencephalogram), because of the clinical and probable genetic heterogeneity, whole-exome sequencing was performed, and co-segregation analysis was confirmed by Sanger sequencing. Biological impacts of the novel variant were evaluated using sequence-to-function bioinformatics tools. RESULTS A novel homozygous missense variant, NM_024678.6:c.545 T > A; p.(Ile182Lys), in exon 5 of NARS2 was identified in both patients and verified by Sanger sequencing. In silico analyses introduced this variant as pathogenic. Mitral valve prolapses with mild regurgitation, brachymetatarsia, severe hallux valgus, and clubbed fingers were reported as novel manifestations in association with NARS2 gene. By doing a literature review, we also underscored the high heterogeneity of disease phenotype. CONCLUSIONS Herein, we report some novel phenotype and genotype features of two female patients in an Iranian consanguineous family with COXPD24, caused by a variant in NARS2-NM_024678.6: c.545 T > A; p.(Ile182Lys). Moreover, our data expanded the phenotype and genotype spectrum of NARS2-related disorder and confirmed an unpredictable nature of genotype-phenotype correlation in COXPD24.
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Affiliation(s)
- Mohammad Vafaee-Shahi
- ENT and Head and Neck Research Center and Department, The Five Senses Health Institute, Hazrat Rasoul Akram Hospital, Iran University of Medical Sciences, Tehran, Iran
- Pediatric Growth and Development Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad Farhadi
- ENT and Head and Neck Research Center and Department, The Five Senses Health Institute, Hazrat Rasoul Akram Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Ehsan Razmara
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Saeid Morovvati
- Department of Genetics, Faculty of Advanced Sciences and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Saeide Ghasemi
- Ali Asghar Children's Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Seyedeh Sedigheh Abedini
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Zohreh Bagher
- ENT and Head and Neck Research Center and Department, The Five Senses Health Institute, Hazrat Rasoul Akram Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Rafieh Alizadeh
- ENT and Head and Neck Research Center and Department, The Five Senses Health Institute, Hazrat Rasoul Akram Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Masoumeh Falah
- ENT and Head and Neck Research Center and Department, The Five Senses Health Institute, Hazrat Rasoul Akram Hospital, Iran University of Medical Sciences, Tehran, Iran.
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Liu Q, Lin F. Lentivirus-induced knockdown of IARS2 expression inhibits the proliferation and promotes the apoptosis of human osteosarcoma cells. Oncol Lett 2022; 24:262. [PMID: 35765273 PMCID: PMC9219035 DOI: 10.3892/ol.2022.13382] [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: 09/14/2021] [Accepted: 03/09/2022] [Indexed: 11/19/2022] Open
Abstract
Isoleucyl-tRNA synthetase 2 (IARS2), distributed in mitochondria, is an IARS involved in protein synthesis. Notably, IARS2 has been reported to be associated with tumor progression; however, the relationship between osteosarcoma (OS) and IARS2 remains unclear. To investigate the role of IARS2 in human OS, the expression and relationship of IARS2 with survival were firstly analyzed using the Gene Expression Profiling Interactive Analysis 2 database. Subsequently, an IARS2-short hairpin RNA lentiviral vector was established and used to infect the MNNG/HOS and U2OS cell lines. Reverse transcription-quantitative PCR (RT-qPCR) and western blotting were applied to determine the efficiency of IARS2 knockdown. The effects of IARS2 knockdown on cell proliferation, colony formation and apoptosis were evaluated by Celigo, MTT assays, colony formation assays and flow cytomeric analysis. In the present study, IARS2 tends to be high expressed in OS tissue and was associated with survival but this was not significant. The results of RT-qPCR and western blotting showed that the expression of IARS2 was effectively knocked down in the MNNG/HOS and U2OS cell lines. Celigo, MTT and colony formation assays showed that IARS2 knockdown in MNNG/HOS and U2OS cell lines inhibited cell proliferation and colony formation compared with in the control group. Flow cytometric analysis revealed that IARS2 knockdown increased apoptosis. These results suggested that IARS2 may be critical for the proliferation and apoptosis of OS cells.
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Affiliation(s)
- Qi Liu
- Department of Oncology, The Eighth People's Hospital of Shanghai, Shanghai 200235, P.R. China
| | - Feng Lin
- Department of Oncology, The Eighth People's Hospital of Shanghai, Shanghai 200235, P.R. China
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Identification of dual-targeted Mycobacterium tuberculosis aminoacyl-tRNA synthetase inhibitors using machine learning. Future Med Chem 2022; 14:1223-1237. [PMID: 35876255 DOI: 10.4155/fmc-2022-0085] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Background: The most serious challenge in the treatment of tuberculosis is the multidrug resistance of Mycobacterium tuberculosis to existing antibiotics. As a strategy to overcome resistance we used a multitarget drug design approach. The purpose of the work was to discover dual-targeted inhibitors of mycobacterial LeuRS and MetRS with machine learning. Methods: The artificial neural networks were built using module nnet from R 3.6.1. The inhibitory activity of compounds toward LeuRS and MetRS was investigated in aminoacylation assays. Results: Using a machine-learning approach, we identified dual-targeted inhibitors of LeuRS and MetRS among 2-(quinolin-2-ylsulfanyl)-acetamide derivatives. The most active compound inhibits MetRS and LeuRS with IC50 values of 33 μm and 23.9 μm, respectively. Conclusion: 2-(Quinolin-2-ylsulfanyl)-acetamide scaffold can be useful for further research.
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27
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Mayoka G, Woodland JG, Chibale K. Thwarting protein synthesis leads to malaria parasite paralysis. Trends Parasitol 2022; 38:719-721. [PMID: 35843778 DOI: 10.1016/j.pt.2022.07.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 07/04/2022] [Indexed: 11/25/2022]
Abstract
Inhibiting translation presents a tantalizing strategy to tackle the most virulent human malaria parasite. Xie et al. disclose a compound that binds selectively to Plasmodium falciparum tyrosine aminoacyl-tRNA synthetase, preventing the incorporation of tyrosine into nascent proteins and paving the way for a new generation of safe, effective antimalarials.
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Affiliation(s)
- Godfrey Mayoka
- Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa; Department of Pharmacology and Pharmacognosy, School of Pharmacy, Jomo Kenyatta University of Agriculture and Technology, PO BOX 62000-00200, Nairobi, Kenya
| | - John G Woodland
- Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa; Holistic Drug Discovery and Development (H3D) Centre, University of Cape Town, Rondebosch 7701, South Africa; South African Medical Research Council Drug Discovery and Development Research Unit, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch 7701, South Africa
| | - Kelly Chibale
- Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa; Holistic Drug Discovery and Development (H3D) Centre, University of Cape Town, Rondebosch 7701, South Africa; South African Medical Research Council Drug Discovery and Development Research Unit, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch 7701, South Africa.
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Polyphenols and IUGR Pregnancies: Effects of the Antioxidant Hydroxytyrosol on the Hippocampus Proteome in a Porcine Model. Antioxidants (Basel) 2022; 11:antiox11061135. [PMID: 35740029 PMCID: PMC9219860 DOI: 10.3390/antiox11061135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/04/2022] [Accepted: 06/07/2022] [Indexed: 12/13/2022] Open
Abstract
Supplementation of a mother’s diet with antioxidants such as hydroxytyrosol (HTX) has been proposed to ameliorate the adverse phenotypes of foetuses affected by intrauterine growth restriction (IUGR). Our previous studies showed, in a porcine model of IUGR, an effect of maternal HTX supplementation on the neurotransmitter profile of several brain areas and the morphology of the hippocampus in 100 days old foetuses. The present study analyzed the impact of maternal HTX supplementation on the hippocampus proteome at this foetal age by TMT10plex labelling. Eleven differentially abundant proteins were identified by comparing both conditions, and eight of them downregulated and three upregulated in the HTX-treated group. The downregulated proteins were mainly involved in protein synthesis and RNA metabolism and may explain the differences in neuron differentiation in the HTX-treated group. The upregulated proteins were related to cell detoxification and could represent a potential mechanism to explain the neuroprotective effect of HTX.
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Galindo-Feria AS, Notarnicola A, Lundberg IE, Horuluoglu B. Aminoacyl-tRNA Synthetases: On Anti-Synthetase Syndrome and Beyond. Front Immunol 2022; 13:866087. [PMID: 35634293 PMCID: PMC9136399 DOI: 10.3389/fimmu.2022.866087] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 03/28/2022] [Indexed: 12/20/2022] Open
Abstract
Anti-synthetase syndrome (ASSD) is an autoimmune disease characterized by the presence of autoantibodies targeting one of several aminoacyl t-RNA synthetases (aaRSs) along with clinical features including interstitial lung disease, myositis, Raynaud’s phenomenon, arthritis, mechanic’s hands, and fever. The family of aaRSs consists of highly conserved cytoplasmic and mitochondrial enzymes, one for each amino acid, which are essential for the RNA translation machinery and protein synthesis. Along with their main functions, aaRSs are involved in the development of immune responses, regulation of transcription, and gene-specific silencing of translation. During the last decade, these proteins have been associated with cancer, neurological disorders, infectious responses, and autoimmune diseases including ASSD. To date, several aaRSs have been described to be possible autoantigens in different diseases. The most commonly described are histidyl (HisRS), threonyl (ThrRS), alanyl (AlaRS), glycyl (GlyRS), isoleucyl (IleRS), asparaginyl (AsnRS), phenylalanyl (PheRS), tyrosyl (TyrRS), lysyl (LysRS), glutaminyl (GlnRS), tryptophanyl (TrpRS), and seryl (SerRS) tRNA synthetases. Autoantibodies against the first eight autoantigens listed above have been associated with ASSD while the rest have been associated with other diseases. This review will address what is known about the function of the aaRSs with a focus on their autoantigenic properties. We will also describe the anti-aaRSs autoantibodies and their association to specific clinical manifestations, and discuss their potential contribution to the pathogenesis of ASSD.
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Affiliation(s)
- Angeles S. Galindo-Feria
- Division of Rheumatology, Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, and Karolinska University Hospital Solna, Stockholm, Sweden
| | - Antonella Notarnicola
- Center for Molecular Medicine, Karolinska Institutet, and Karolinska University Hospital Solna, Stockholm, Sweden
| | - Ingrid E. Lundberg
- Division of Rheumatology, Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, and Karolinska University Hospital Solna, Stockholm, Sweden
| | - Begum Horuluoglu
- Division of Rheumatology, Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, and Karolinska University Hospital Solna, Stockholm, Sweden
- *Correspondence: Begum Horuluoglu,
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30
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Novel NARS2 variant causing leigh syndrome with normal lactate levels. Hum Genome Var 2022; 9:12. [PMID: 35508527 PMCID: PMC9068749 DOI: 10.1038/s41439-022-00191-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 03/20/2022] [Accepted: 03/26/2022] [Indexed: 01/15/2023] Open
Abstract
Leigh syndrome is the most genetically heterogenous phenotype of mitochondrial disease. We describe a patient with Leigh syndrome whose diagnosis had not been confirmed because of normal metabolic screening results at the initial presentation. Whole-exome sequencing identified pathogenic variants in NARS2, the gene encoding a mitochondrial asparaginyl-tRNA synthetase. One of the biallelic variants was novel. This highlights the essential role of genetic testing for a definite diagnosis of Leigh syndrome.
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31
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Damoiseaux J, Mammen AL, Piette Y, Benveniste O, Allenbach Y. 256th ENMC international workshop: Myositis specific and associated autoantibodies (MSA-ab): Amsterdam, The Netherlands, 8-10 October 2021. Neuromuscul Disord 2022; 32:594-608. [DOI: 10.1016/j.nmd.2022.05.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/12/2022] [Accepted: 05/17/2022] [Indexed: 10/18/2022]
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32
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Yao H, Xu H, Qiu S, Chen J, Lin Z, Zhu J, Sun X, Gao Q, Chen X, Xi C, Huang D, Zhang F, Gao S, Wang Z, Zhang J, Liu X, Ren G, Tao X, Li M, Chen W. Choline deficiency-related multi-omics characteristics are susceptible factors for chemotherapy-induced thrombocytopenia. Pharmacol Res 2022; 178:106155. [DOI: 10.1016/j.phrs.2022.106155] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 01/24/2022] [Accepted: 03/01/2022] [Indexed: 02/06/2023]
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Shah RM, Stephenson S, Crosswell J, Gorman D, Hillyer KE, Palombo EA, Jones OAH, Cook S, Bodrossy L, van de Kamp J, Walsh TK, Bissett A, Steven ADL, Beale DJ. Omics-based ecosurveillance uncovers the influence of estuarine macrophytes on sediment microbial function and metabolic redundancy in a tropical ecosystem. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 809:151175. [PMID: 34699819 DOI: 10.1016/j.scitotenv.2021.151175] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/18/2021] [Accepted: 10/19/2021] [Indexed: 06/13/2023]
Abstract
Vertical zonation within estuarine ecosystems can strongly influence microbial diversity and function by regulating competition, predation, and environmental stability. The degree to which microbial communities exhibit horizontal patterns through an estuary has received comparatively less attention. Here, we take a multi-omics ecosurveillance approach to study environmental gradients created by the transition between dominant vegetation types along a near pristine tropical river system (Wenlock River, Far North Queensland, Australia). The study sites included intertidal mudflats fringed by saltmarsh, mangrove or mixed soft substrata habitats. Collected sediments were analyzed for eukaryotes and prokaryotes using small sub-unit (SSU) rRNA gene amplicons to profile the relative taxonomic composition. Central carbon metabolism metabolites and other associated organic polar metabolites were analyzed using established metabolomics-based approaches, coupled with total heavy metals analysis. Eukaryotic taxonomic information was found to be more informative of habitat type. Bacterial taxonomy and community composition also showed habitat-specificity, with phyla Proteobacteria and Cyanobacteria strongly linked to mangroves and saltmarshes, respectively. In contrast, metabolite profiling was critical for understanding the biochemical pathways and expressed functional outputs in these systems that were tied to predicted microbial gene function (16S rRNA). A high degree of metabolic redundancy was observed in the bacterial communities, with the metabolomics data suggesting varying degrees of metabolic criticality based on habitat type. The predicted functions of the bacterial taxa combined with annotated metabolites accounted for the conservative perspective of microbial community redundancy against the putative metabolic pathway impacts in the metabolomics data. Coupling these data demonstrates that habitat-mediated estuarine gradients drive patterns of community diversity and metabolic function and highlights the real redundancy potential of habitat microbiomes. This information is useful as a point of comparison for these sensitive ecosystems and provides a framework for identifying potentially vulnerable or at-risk systems before they are significantly degraded.
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Affiliation(s)
- Rohan M Shah
- Land and Water, Commonwealth Scientific and Industrial Research Organisation, Dutton Park, QLD 4102, Australia; Department of Chemistry and Biotechnology, School of Science, Computing and Engineering Technologies, Swinburne University of Technology, Hawthorn, VIC 3122, Australia
| | - Sarah Stephenson
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Lucas Heights, NSW 2234, Australia
| | - Joseph Crosswell
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Dutton Park, QLD 4102, Australia
| | - Daniel Gorman
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Indian Ocean Marine Research Centre, Crawley, WA 6009, Australia
| | - Katie E Hillyer
- Land and Water, Commonwealth Scientific and Industrial Research Organisation, Dutton Park, QLD 4102, Australia
| | - Enzo A Palombo
- Department of Chemistry and Biotechnology, School of Science, Computing and Engineering Technologies, Swinburne University of Technology, Hawthorn, VIC 3122, Australia
| | - Oliver A H Jones
- Australian Centre for Research on Separation Science (ACROSS), School of Science, RMIT University, Bundoora West Campus, PO Box 71, Bundoora, VIC 3083, Australia
| | - Stephen Cook
- Land and Water, Commonwealth Scientific and Industrial Research Organisation, Berrimah, NT 0828, Australia
| | - Levente Bodrossy
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Battery Point, TAS 7004, Australia
| | - Jodie van de Kamp
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Battery Point, TAS 7004, Australia
| | - Thomas K Walsh
- Land and Water, Commonwealth Scientific and Industrial Research Organisation, Acton, ACT 2601, Australia
| | - Andrew Bissett
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Battery Point, TAS 7004, Australia
| | - Andrew D L Steven
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Dutton Park, QLD 4102, Australia
| | - David J Beale
- Land and Water, Commonwealth Scientific and Industrial Research Organisation, Dutton Park, QLD 4102, Australia.
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Fu Z, Han F, Huang K, Zhang J, Qin JG, Chen L, Li E. Impact of imidacloprid exposure on the biochemical responses, transcriptome, gut microbiota and growth performance of the Pacific white shrimp Litopenaeus vannamei. JOURNAL OF HAZARDOUS MATERIALS 2022; 424:127513. [PMID: 34687996 DOI: 10.1016/j.jhazmat.2021.127513] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 10/01/2021] [Accepted: 10/13/2021] [Indexed: 06/13/2023]
Abstract
The widespread use of neonicotinoid insecticides, such as imidacloprid, in agriculture is one of the key factors for the drop in the survival of invertebrates, including decapod crustaceans. However, there is currently a lack of comprehensive studies on the chronic toxicity mechanisms in decapod crustaceans. Here, the concentration-dependent effects of imidacloprid on the physiology and biochemistry, gut microbiota and transcriptome of L. vannamei , and the interaction between imidacloprid, gut microbiota and genes were studied. Imidacloprid caused oxidative stress, leading to reduced growth and to immunity and tissue damage in L. vannamei . Imidacloprid increased the gut pathogenic microbiota abundance and broke the steady state of the gut microbiota interaction network, resulting in microbiota function disorders. Chronic imidacloprid exposure induced overall transcriptome changes in L. vannamei . Specifically, imidacloprid caused a large number of differentially expressed genes (DEGs) to be significantly downregulated. The inhibition of autophagy-related pathways revealed the toxic process of imidacloprid to L. vannamei . The changes in phase I and II detoxification gene expression clarified the formation of a detoxification mechanism in L. vannamei . The disturbance of circadian rhythm (CLOCK) caused by imidacloprid is one of the reasons for the increase in gut pathogenic microbiota abundance.
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Affiliation(s)
- Zhenqiang Fu
- Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan Province, Hainan Aquaculture Breeding Engineering Research Center, College of Marine Sciences, Hainan University, Haikou, Hainan 570228, China
| | - Fenglu Han
- Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan Province, Hainan Aquaculture Breeding Engineering Research Center, College of Marine Sciences, Hainan University, Haikou, Hainan 570228, China
| | - Kaiqi Huang
- Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan Province, Hainan Aquaculture Breeding Engineering Research Center, College of Marine Sciences, Hainan University, Haikou, Hainan 570228, China
| | - Jiliang Zhang
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, Hainan, China
| | - Jian G Qin
- School of Biological Sciences, Flinders University, Adelaide, SA 5001, Australia
| | - Liqiao Chen
- School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Erchao Li
- Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan Province, Hainan Aquaculture Breeding Engineering Research Center, College of Marine Sciences, Hainan University, Haikou, Hainan 570228, China.
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35
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Noureldin NA, Richards J, Kothayer H, Baraka MM, Eladl SM, Wootton M, Simons C. Phenylalanyl tRNA synthetase (PheRS) substrate mimics: design, synthesis, molecular dynamics and antimicrobial evaluation. RSC Adv 2022; 12:2511-2524. [PMID: 35425259 PMCID: PMC8979089 DOI: 10.1039/d1ra06439h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 01/05/2022] [Indexed: 11/21/2022] Open
Abstract
Nineteen novel compounds were designed to mimic Phe-AMP, as a new hope to find novel antibacterial agents and combat the antibiotic resistance. E. faecalis PheS homology model was constructed to study the mimics–enzyme interactions in more detail.
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Affiliation(s)
- Nada A. Noureldin
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Cardiff CF10 3NB, UK
- Department of Medicinal Chemistry, Faculty of Pharmacy, Zagazig University, Zagazig P. C., 44519, Egypt
| | - Jennifer Richards
- Specialist Antimicrobial Chemotherapy Unit, University Hospital of Wales, Heath Park, Cardiff CF14 4XW, UK
| | - Hend Kothayer
- Department of Medicinal Chemistry, Faculty of Pharmacy, Zagazig University, Zagazig P. C., 44519, Egypt
| | - Mohammed M. Baraka
- Department of Medicinal Chemistry, Faculty of Pharmacy, Zagazig University, Zagazig P. C., 44519, Egypt
| | - Sobhy M. Eladl
- Department of Medicinal Chemistry, Faculty of Pharmacy, Zagazig University, Zagazig P. C., 44519, Egypt
| | - Mandy Wootton
- Specialist Antimicrobial Chemotherapy Unit, University Hospital of Wales, Heath Park, Cardiff CF14 4XW, UK
| | - Claire Simons
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Cardiff CF10 3NB, UK
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Wang D, Guo D, Tang Y, Qi M, Fang J, Zhang Y, Chai Y, Cao Y, Lv D. A multi-omics study of the anti-cancer effect of a ferulic acid derivative FA-30. Mol Omics 2022; 18:805-813. [DOI: 10.1039/d2mo00025c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The active ingredients of Traditional Chinese Medicine are an important source of bioactive molecules and play an important role in the research and development of innovative drugs.
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Affiliation(s)
- Dongyao Wang
- Shanghai Key Laboratory for Pharmaceutical Metabolite Research, School of Pharmacy, Second Military Medical University, Shanghai, 200433, China
| | - Dandan Guo
- Shanghai Key Laboratory for Pharmaceutical Metabolite Research, School of Pharmacy, Second Military Medical University, Shanghai, 200433, China
| | - Yuxiao Tang
- Department of nutrition, Second Military Medical University, Shanghai, China
| | - Minyu Qi
- Shanghai Key Laboratory for Pharmaceutical Metabolite Research, School of Pharmacy, Second Military Medical University, Shanghai, 200433, China
| | - Jiahao Fang
- Shanghai Key Laboratory for Pharmaceutical Metabolite Research, School of Pharmacy, Second Military Medical University, Shanghai, 200433, China
| | - Ying Zhang
- Shanghai Key Laboratory for Pharmaceutical Metabolite Research, School of Pharmacy, Second Military Medical University, Shanghai, 200433, China
| | - Yifeng Chai
- Shanghai Key Laboratory for Pharmaceutical Metabolite Research, School of Pharmacy, Second Military Medical University, Shanghai, 200433, China
| | - Yan Cao
- Shanghai Key Laboratory for Pharmaceutical Metabolite Research, School of Pharmacy, Second Military Medical University, Shanghai, 200433, China
| | - Diya Lv
- Shanghai Key Laboratory for Pharmaceutical Metabolite Research, School of Pharmacy, Second Military Medical University, Shanghai, 200433, China
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37
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Noureldin NA, Richards J, Kothayer H, Baraka MM, Eladl SM, Wootton M, Simons C. Design, computational studies, synthesis and in vitro antimicrobial evaluation of benzimidazole based thio-oxadiazole and thio-thiadiazole analogues. BMC Chem 2021; 15:58. [PMID: 34711258 PMCID: PMC8555319 DOI: 10.1186/s13065-021-00785-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 10/20/2021] [Indexed: 01/16/2023] Open
Abstract
Background Two series of benzimidazole based thio-oxadiazole and thio-thiadiazole analogues were designed and synthesised as novel antimicrobial drugs through inhibition of phenylalanyl-tRNA synthetase (PheRS), which is a promising antimicrobial target. Compounds were designed to mimic the structural features of phenylalanyl adenylate (Phe-AMP) the PheRS natural substrate. Methods A 3D conformational alignment for the designed compounds and the PheRS natural substrate revealed a high level of conformational similarity, and a molecular docking study indicated the ability of the designed compounds to occupy both Phe-AMP binding pockets. A molecular dynamics (MD) simulation comparative study was performed to understand the binding interactions with PheRS from different bacterial microorganisms. The synthetic pathway of the designed compounds proceeded in five steps starting from benzimidazole. The fourteen synthesised compounds 5a-d, 6a-c, 8a-d and 9a-c were purified, fully characterised and obtained in high yield. Results In vitro antimicrobial evaluation against five bacterial strains showed a moderate activity of compound 8b with MIC value of 32 μg/mL against S. aureus, while all the synthesised compounds showed weak activity against both E. faecalis and P. aeruginosa (MIC 128 μg/mL). Conclusion Compound 8b provides a lead compound for further structural development to obtain high affinity PheRS inhibitors. Supplementary Information The online version contains supplementary material available at 10.1186/s13065-021-00785-8.
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Affiliation(s)
- Nada A Noureldin
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Cardiff, CF10 3NB, UK. .,Department of Medicinal Chemistry, Faculty of Pharmacy, Zagazig University, Zagazig, P.C. 44519, Egypt.
| | - Jennifer Richards
- Specialist Antimicrobial Chemotherapy Unit, University Hospital of Wales, Heath Park, Cardiff, CF14 4XW, UK
| | - Hend Kothayer
- Department of Medicinal Chemistry, Faculty of Pharmacy, Zagazig University, Zagazig, P.C. 44519, Egypt
| | - Mohammed M Baraka
- Department of Medicinal Chemistry, Faculty of Pharmacy, Zagazig University, Zagazig, P.C. 44519, Egypt
| | - Sobhy M Eladl
- Department of Medicinal Chemistry, Faculty of Pharmacy, Zagazig University, Zagazig, P.C. 44519, Egypt
| | - Mandy Wootton
- Specialist Antimicrobial Chemotherapy Unit, University Hospital of Wales, Heath Park, Cardiff, CF14 4XW, UK
| | - Claire Simons
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Cardiff, CF10 3NB, UK
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38
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Ravel JM, Dreumont N, Mosca P, Smith DEC, Mendes MI, Wiedemann A, Coelho D, Schmitt E, Rivière JB, Tran Mau-Them F, Thevenon J, Kuentz P, Polivka M, Fuchs SA, Kok G, Thauvin-Robinet C, Guéant JL, Salomons GS, Faivre L, Feillet F. A bi-allelic loss-of-function SARS1 variant in children with neurodevelopmental delay, deafness, cardiomyopathy, and decompensation during fever. Hum Mutat 2021; 42:1576-1583. [PMID: 34570399 DOI: 10.1002/humu.24285] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 09/01/2021] [Accepted: 09/23/2021] [Indexed: 11/08/2022]
Abstract
Aminoacyl-tRNA synthetases (aaRS) are ubiquitously expressed enzymes responsible for ligating amino acids to their cognate tRNA molecules through an aminoacylation reaction. The resulting aminoacyl-tRNA is delivered to ribosome elongation factors to participate in protein synthesis. Seryl-tRNA synthetase (SARS1) is one of the cytosolic aaRSs and catalyzes serine attachment to tRNASer . SARS1 deficiency has already been associated with moderate intellectual disability, ataxia, muscle weakness, and seizure in one family. We describe here a new clinical presentation including developmental delay, central deafness, cardiomyopathy, and metabolic decompensation during fever leading to death, in a consanguineous Turkish family, with biallelic variants (c.638G>T, p.(Arg213Leu)) in SARS1. This missense variant was shown to lead to protein instability, resulting in reduced protein level and enzymatic activity. Our results describe a new clinical entity and expand the clinical and mutational spectrum of SARS1 and aaRS deficiencies.
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Affiliation(s)
- Jean-Marie Ravel
- Reference Centre of Inborn Metabolism Diseases, Université de Lorraine, CHRU-Nancy, Nancy, France.,NGERE, Université de Lorraine, Inserm, Nancy, France
| | | | - Pauline Mosca
- NGERE, Université de Lorraine, Inserm, Nancy, France
| | - Desiree E C Smith
- Metabolic Unit, Department of Clinical Chemistry, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Marisa I Mendes
- Metabolic Unit, Department of Clinical Chemistry, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | | | - David Coelho
- NGERE, Université de Lorraine, Inserm, Nancy, France
| | | | - Jean-Baptiste Rivière
- Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, CHU Dijon Bourgogne, Dijon, France.,Centre de Génétique, Centre de Référence Anomalies du Développement et Syndromes Malformatifs, Centre de Compétence Maladies Mitochondriales, FHU TRANSLAD, Hôpital d'Enfants, CHU de Dijon, France.,INSERM UMR1231, Equipe Génétique des Anomalies du Développement, Université de Bourgogne, Dijon, France
| | - Frédéric Tran Mau-Them
- Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, CHU Dijon Bourgogne, Dijon, France.,Centre de Génétique, Centre de Référence Anomalies du Développement et Syndromes Malformatifs, Centre de Compétence Maladies Mitochondriales, FHU TRANSLAD, Hôpital d'Enfants, CHU de Dijon, France.,INSERM UMR1231, Equipe Génétique des Anomalies du Développement, Université de Bourgogne, Dijon, France
| | - Julien Thevenon
- Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, CHU Dijon Bourgogne, Dijon, France.,Centre de Génétique, Centre de Référence Anomalies du Développement et Syndromes Malformatifs, Centre de Compétence Maladies Mitochondriales, FHU TRANSLAD, Hôpital d'Enfants, CHU de Dijon, France.,INSERM UMR1231, Equipe Génétique des Anomalies du Développement, Université de Bourgogne, Dijon, France
| | - Paul Kuentz
- Centre de Génétique, Centre de Référence Anomalies du Développement et Syndromes Malformatifs, Centre de Compétence Maladies Mitochondriales, FHU TRANSLAD, Hôpital d'Enfants, CHU de Dijon, France.,INSERM UMR1231, Equipe Génétique des Anomalies du Développement, Université de Bourgogne, Dijon, France
| | - Marc Polivka
- Department of Pathology, Hôpital Lariboisière, Paris, France
| | - Sabine A Fuchs
- Department of Metabolic Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, The Netherlands.,Regenerative Medicine Center Utrecht, Regenerative Medicine Utrecht, Utrecht, The Netherlands.,On behalf of "United for Metabolic Diseases,", Amsterdam, the Netherlands
| | - Gautam Kok
- Department of Pathology, Hôpital Lariboisière, Paris, France
| | - Christel Thauvin-Robinet
- Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, CHU Dijon Bourgogne, Dijon, France.,Centre de Génétique, Centre de Référence Anomalies du Développement et Syndromes Malformatifs, Centre de Compétence Maladies Mitochondriales, FHU TRANSLAD, Hôpital d'Enfants, CHU de Dijon, France.,INSERM UMR1231, Equipe Génétique des Anomalies du Développement, Université de Bourgogne, Dijon, France
| | - Jean-Louis Guéant
- Reference Centre of Inborn Metabolism Diseases, Université de Lorraine, CHRU-Nancy, Nancy, France.,NGERE, Université de Lorraine, Inserm, Nancy, France
| | - Gajja S Salomons
- Metabolic Unit, Department of Clinical Chemistry, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Laurence Faivre
- Centre de Génétique, Centre de Référence Anomalies du Développement et Syndromes Malformatifs, Centre de Compétence Maladies Mitochondriales, FHU TRANSLAD, Hôpital d'Enfants, CHU de Dijon, France.,INSERM UMR1231, Equipe Génétique des Anomalies du Développement, Université de Bourgogne, Dijon, France
| | - François Feillet
- Reference Centre of Inborn Metabolism Diseases, Université de Lorraine, CHRU-Nancy, Nancy, France.,NGERE, Université de Lorraine, Inserm, Nancy, France
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39
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Jha SG, Borowsky AT, Cole BJ, Fahlgren N, Farmer A, Huang SSC, Karia P, Libault M, Provart NJ, Rice SL, Saura-Sanchez M, Agarwal P, Ahkami AH, Anderton CR, Briggs SP, Brophy JAN, Denolf P, Di Costanzo LF, Exposito-Alonso M, Giacomello S, Gomez-Cano F, Kaufmann K, Ko DK, Kumar S, Malkovskiy AV, Nakayama N, Obata T, Otegui MS, Palfalvi G, Quezada-Rodríguez EH, Singh R, Uhrig RG, Waese J, Van Wijk K, Wright RC, Ehrhardt DW, Birnbaum KD, Rhee SY. Vision, challenges and opportunities for a Plant Cell Atlas. eLife 2021; 10:e66877. [PMID: 34491200 PMCID: PMC8423441 DOI: 10.7554/elife.66877] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 08/26/2021] [Indexed: 02/06/2023] Open
Abstract
With growing populations and pressing environmental problems, future economies will be increasingly plant-based. Now is the time to reimagine plant science as a critical component of fundamental science, agriculture, environmental stewardship, energy, technology and healthcare. This effort requires a conceptual and technological framework to identify and map all cell types, and to comprehensively annotate the localization and organization of molecules at cellular and tissue levels. This framework, called the Plant Cell Atlas (PCA), will be critical for understanding and engineering plant development, physiology and environmental responses. A workshop was convened to discuss the purpose and utility of such an initiative, resulting in a roadmap that acknowledges the current knowledge gaps and technical challenges, and underscores how the PCA initiative can help to overcome them.
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Affiliation(s)
- Suryatapa Ghosh Jha
- Department of Plant Biology, Carnegie Institution for ScienceStanfordUnited States
| | - Alexander T Borowsky
- Department of Botany and Plant Sciences, University of California, RiversideRiversideUnited States
| | - Benjamin J Cole
- Joint Genome Institute, Lawrence Berkeley National LaboratoryWalnut CreekUnited States
| | - Noah Fahlgren
- Donald Danforth Plant Science CenterSt. LouisUnited States
| | - Andrew Farmer
- National Center for Genome ResourcesSanta FeUnited States
| | | | - Purva Karia
- Department of Plant Biology, Carnegie Institution for ScienceStanfordUnited States
- Department of Cell and Systems Biology, University of TorontoTorontoCanada
| | - Marc Libault
- Department of Agronomy and Horticulture, University of Nebraska-LincolnLincolnUnited States
| | - Nicholas J Provart
- Department of Cell and Systems Biology and the Centre for the Analysis of Genome Evolution and Function, University of TorontoTorontoCanada
| | - Selena L Rice
- Department of Plant Biology, Carnegie Institution for ScienceStanfordUnited States
| | - Maite Saura-Sanchez
- Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura, Facultad de Agronomía, Universidad de Buenos AiresBuenos AiresArgentina
| | - Pinky Agarwal
- National Institute of Plant Genome ResearchNew DelhiIndia
| | - Amir H Ahkami
- Environmental Molecular Sciences Division, Pacific Northwest National LaboratoryRichlandUnited States
| | - Christopher R Anderton
- Environmental Molecular Sciences Division, Pacific Northwest National LaboratoryRichlandUnited States
| | - Steven P Briggs
- Department of Biological Sciences, University of California, San DiegoSan DiegoUnited States
| | | | | | - Luigi F Di Costanzo
- Department of Agricultural Sciences, University of Naples Federico IINapoliItaly
| | - Moises Exposito-Alonso
- Department of Plant Biology, Carnegie Institution for ScienceStanfordUnited States
- Department of Plant Biology, Carnegie Institution for ScienceTübingenGermany
| | | | - Fabio Gomez-Cano
- Department of Biochemistry and Molecular Biology, Michigan State UniversityEast LansingUnited States
| | - Kerstin Kaufmann
- Department for Plant Cell and Molecular Biology, Institute for Biology, Humboldt-Universitaet zu BerlinBerlinGermany
| | - Dae Kwan Ko
- Great Lakes Bioenergy Research Center, Michigan State UniversityEast LansingUnited States
| | - Sagar Kumar
- Department of Plant Breeding & Genetics, Mata Gujri College, Fatehgarh Sahib, Punjabi UniversityPatialaIndia
| | - Andrey V Malkovskiy
- Department of Plant Biology, Carnegie Institution for ScienceStanfordUnited States
| | - Naomi Nakayama
- Department of Bioengineering, Imperial College LondonLondonUnited Kingdom
| | - Toshihiro Obata
- Department of Biochemistry, University of Nebraska-LincolnMadisonUnited States
| | - Marisa S Otegui
- Department of Botany, University of Wisconsin-MadisonMadisonUnited States
| | - Gergo Palfalvi
- Division of Evolutionary Biology, National Institute for Basic BiologyOkazakiJapan
| | - Elsa H Quezada-Rodríguez
- Ciencias Agrogenómicas, Escuela Nacional de Estudios Superiores Unidad León, Universidad Nacional Autónoma de MéxicoLeónMexico
| | - Rajveer Singh
- School of Agricultural Biotechnology, Punjab Agricultural UniversityLudhianaIndia
| | - R Glen Uhrig
- Department of Science, University of AlbertaEdmontonCanada
| | - Jamie Waese
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of TorontoTorontoCanada
| | - Klaas Van Wijk
- School of Integrated Plant Science, Plant Biology Section, Cornell UniversityIthacaUnited States
| | - R Clay Wright
- Department of Biological Systems Engineering, Virginia TechBlacksburgUnited States
| | - David W Ehrhardt
- Department of Plant Biology, Carnegie Institution for ScienceStanfordUnited States
| | - Kenneth D Birnbaum
- Center for Genomics and Systems Biology, New York UniversityNew YorkUnited States
| | - Seung Y Rhee
- Department of Plant Biology, Carnegie Institution for ScienceStanfordUnited States
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40
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Destruxin A Interacts with Aminoacyl tRNA Synthases in Bombyx mori. J Fungi (Basel) 2021; 7:jof7080593. [PMID: 34436132 PMCID: PMC8396844 DOI: 10.3390/jof7080593] [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: 07/02/2021] [Revised: 07/20/2021] [Accepted: 07/22/2021] [Indexed: 11/16/2022] Open
Abstract
Destruxin A (DA), a hexa-cyclodepsipeptidic mycotoxin produced by the entomopathogenic fungus Metarhizium anisopliae, exhibits insecticidal activities in a wide range of pests and is known as an innate immunity inhibitor. However, its mechanism of action requires further investigation. In this research, the interactions of DA with the six aminoacyl tRNA synthetases (ARSs) of Bombyx mori, BmAlaRS, BmCysRS, BmMetRS, BmValRS, BmIleRS, and BmGluProRS, were analyzed. The six ARSs were expressed and purified. The BLI (biolayer interferometry) results indicated that DA binds these ARSs with the affinity indices (KD) of 10−4 to 10−5 M. The molecular docking suggested a similar interaction mode of DA with ARSs, whereby DA settled into a pocket through hydrogen bonds with Asn, Arg, His, Lys, and Tyr of ARSs. Furthermore, DA treatments decreased the contents of soluble protein and free amino acids in Bm12 cells, which suggested that DA impedes protein synthesis. Lastly, the ARSs in Bm12 cells were all downregulated by DA stress. This study sheds light on exploring and answering the molecular target of DA against target insects.
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41
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Sopko B, Tejral G, Bitti G, Abate M, Medvedikova M, Hajduch M, Chloupek J, Fajmonova J, Skoric M, Amler E, Erban T. Glyphosate Interaction with eEF1α1 Indicates Altered Protein Synthesis: Evidence for Reduced Spermatogenesis and Cytostatic Effect. ACS OMEGA 2021; 6:14848-14857. [PMID: 34151066 PMCID: PMC8209799 DOI: 10.1021/acsomega.1c00449] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 05/18/2021] [Indexed: 06/13/2023]
Abstract
The broad-spectrum herbicide, glyphosate, is considered safe for animals because it selectively affects the shikimate pathway that is specific to plants and microorganisms. We sought a previously unknown mechanism to explain the concerns that glyphosate exposure can negatively affect animals, including humans. Computer modeling showed a probable interaction between glyphosate and eukaryotic translation elongation factor 1 subunit alpha 1 (eEF1α1), which was confirmed by microcalorimetry. Only restricted, nondisrupted spermatogenesis in rats was observed after chronic glyphosate treatments (0.7 and 7 mg/L). Cytostatic and antiproliferative effects of glyphosate in GC-1 and SUP-B15 cells were indicated. Meta-analysis of public health data suggested a possible effect of glyphosate use on sperm count. The in silico, in vitro, and in vivo experimental results as well as the metastatistics indicate side effects of chronic glyphosate exposure. Together, these findings indicate that glyphosate delays protein synthesis through an interaction with eEF1α1, thereby suppressing spermatogenesis and cell growth.
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Affiliation(s)
- Bruno Sopko
- Crop
Research Institute, Prague 161 06, Czechia
- Department
of Medical Chemistry and Clinical Biochemistry, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Prague 150 06, Czechia
- Laboratory
of Tissue Engineering, Institute of Experimental
Medicine, Academy of Sciences of the Czech Republic, Prague 142 20, Czechia
- Biomedicine
and Advanced Biomaterials Department, University Center for Energy
Efficient Buildings, The Czech Technical
University in Prague, Prague, Bustehrad 273 43, Czechia
| | - Gracian Tejral
- Laboratory
of Tissue Engineering, Institute of Experimental
Medicine, Academy of Sciences of the Czech Republic, Prague 142 20, Czechia
- Biomedicine
and Advanced Biomaterials Department, University Center for Energy
Efficient Buildings, The Czech Technical
University in Prague, Prague, Bustehrad 273 43, Czechia
- Department
of Biophysics, 2nd Faculty of Medicine, Charles University, Prague 150 06, Czechia
| | - Guissepe Bitti
- Laboratory
of Tissue Engineering, Institute of Experimental
Medicine, Academy of Sciences of the Czech Republic, Prague 142 20, Czechia
- Biomedicine
and Advanced Biomaterials Department, University Center for Energy
Efficient Buildings, The Czech Technical
University in Prague, Prague, Bustehrad 273 43, Czechia
| | - Marianna Abate
- Department
of Precision Medicine, University of Campania
“Luigi Vanvitelli”, Naples 80131, Italy
| | - Martina Medvedikova
- Institute
of Molecular and Translation Medicine, Faculty of Medicine and Dentistry, Palacky University, Olomouc 779 00, Czechia
| | - Marian Hajduch
- Institute
of Molecular and Translation Medicine, Faculty of Medicine and Dentistry, Palacky University, Olomouc 779 00, Czechia
| | - Jan Chloupek
- Department
of Pharmacology and Pharmacy, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences
Brno, Brno 612 42, Czechia
| | - Jolana Fajmonova
- Department
of Pharmacology and Pharmacy, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences
Brno, Brno 612 42, Czechia
| | - Misa Skoric
- Department
of Pathological Morphology and Parasitology, Faculty of Veterinary
Medicine, University of Veterinary and Pharmaceutical
Sciences Brno, Brno 612 42, Czechia
| | - Evzen Amler
- Biomedicine
and Advanced Biomaterials Department, University Center for Energy
Efficient Buildings, The Czech Technical
University in Prague, Prague, Bustehrad 273 43, Czechia
- Department
of Biophysics, 2nd Faculty of Medicine, Charles University, Prague 150 06, Czechia
| | - Tomas Erban
- Crop
Research Institute, Prague 161 06, Czechia
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42
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Vinogradova ES, Nikonov OS, Nikonova EY. Associations between Neurological Diseases and Mutations in the Human Glycyl-tRNA Synthetase. BIOCHEMISTRY (MOSCOW) 2021; 86:S12-S23. [PMID: 33827397 PMCID: PMC7905983 DOI: 10.1134/s0006297921140029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Aminoacyl-RNA synthetases (aaRSs) are among the key enzymes of protein biosynthesis. They are responsible for conducting the first step in the protein biosynthesis, namely attaching amino acids to the corresponding tRNA molecules both in cytoplasm and mitochondria. More and more research demonstrates that mutations in the genes encoding aaRSs lead to the development of various neurodegenerative diseases, such as incurable Charcot–Marie–Tooth disease (CMT) and distal spinal muscular atrophy. Some mutations result in the loss of tRNA aminoacylation activity, while other mutants retain their classical enzyme activity. In the latter case, disease manifestations are associated with additional neuron-specific functions of aaRSs. At present, seven aaRSs (GlyRS, TyrRS, AlaRS, HisRS, TrpRS, MetRS, and LysRS) are known to be involved in the CMT etiology with glycyl-tRNA synthetase (GlyRS) being the most studied of them.
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Affiliation(s)
| | - Oleg S Nikonov
- Institute of Protein Research, Pushchino, Moscow Region, 142290, Russia
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43
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Rybak MY, Balanda AO, Yatsyshyna AP, Kotey IM, Starosyla SA, Bdzhola VG, Lukash LL, Yarmoluk SM, Tukalo MA, Volynets GP. Discovery of novel antituberculosis agents among 3-phenyl-5-(1-phenyl-1H-[1,2,3]triazol-4-yl)-[1,2,4]oxadiazole derivatives targeting aminoacyl-tRNA synthetases. Sci Rep 2021; 11:7162. [PMID: 33785838 PMCID: PMC8010095 DOI: 10.1038/s41598-021-86562-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 03/17/2021] [Indexed: 02/05/2023] Open
Abstract
Antibiotic resistance is a major problem of tuberculosis treatment. This provides the stimulus for the search of novel molecular targets and approaches to reduce or forestall resistance emergence in Mycobacterium tuberculosis. Earlier, we discovered a novel small-molecular inhibitor among 3-phenyl-5-(1-phenyl-1H-[1,2,3]triazol-4-yl)-[1,2,4]oxadiazoles targeting simultaneously two enzymes—mycobacterial leucyl-tRNA synthetase (LeuRS) and methionyl-tRNA synthetase (MetRS), which are promising molecular targets for antibiotic development. Unfortunately, the identified inhibitor does not reveal antibacterial activity toward M. tuberculosis. This study aims to develop novel aminoacyl-tRNA synthetase inhibitors among this chemical class with antibacterial activity toward resistant strains of M. tuberculosis. We performed molecular docking of the library of 3-phenyl-5-(1-phenyl-1H-[1,2,3]triazol-4-yl)-[1,2,4]oxadiazole derivatives and selected 41 compounds for investigation of their inhibitory activity toward MetRS and LeuRS in aminoacylation assay and antibacterial activity toward M. tuberculosis strains using microdilution assay. In vitro screening resulted in 10 compounds active against MetRS and 3 compounds active against LeuRS. Structure-related relationships (SAR) were established. The antibacterial screening revealed 4 compounds active toward M. tuberculosis mono-resistant strains in the range of concentrations 2–20 mg/L. Among these compounds, only one compound 27 has significant enzyme inhibitory activity toward mycobacterial MetRS (IC50 = 148.5 µM). The MIC for this compound toward M. tuberculosis H37Rv strain is 12.5 µM. This compound is not cytotoxic to human HEK293 and HepG2 cell lines. Therefore, 3-phenyl-5-(1-phenyl-1H-[1,2,3]triazol-4-yl)-[1,2,4]oxadiazole derivatives can be used for further chemical optimization and biological research to find non-toxic antituberculosis agents with a novel mechanism of action.
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Affiliation(s)
- Mariia Yu Rybak
- Department of Protein Synthesis Enzymology, Institute of Molecular Biology and Genetics of the NAS of Ukraine, Kyiv, Ukraine.
| | - Anatoliy O Balanda
- Department of Medicinal Chemistry, Institute of Molecular Biology and Genetics of the NAS of Ukraine, Kyiv, Ukraine
| | - Anna P Yatsyshyna
- Department of Human Genetics, Institute of Molecular Biology and Genetics of the NAS of Ukraine, Kyiv, Ukraine
| | - Igor M Kotey
- Department of Medicinal Chemistry, Institute of Molecular Biology and Genetics of the NAS of Ukraine, Kyiv, Ukraine
| | - Sergiy A Starosyla
- Department of Medicinal Chemistry, Institute of Molecular Biology and Genetics of the NAS of Ukraine, Kyiv, Ukraine
| | - Volodymyr G Bdzhola
- Department of Medicinal Chemistry, Institute of Molecular Biology and Genetics of the NAS of Ukraine, Kyiv, Ukraine
| | - Lubov L Lukash
- Department of Human Genetics, Institute of Molecular Biology and Genetics of the NAS of Ukraine, Kyiv, Ukraine
| | - Sergiy M Yarmoluk
- Department of Medicinal Chemistry, Institute of Molecular Biology and Genetics of the NAS of Ukraine, Kyiv, Ukraine
| | - Michael A Tukalo
- Department of Protein Synthesis Enzymology, Institute of Molecular Biology and Genetics of the NAS of Ukraine, Kyiv, Ukraine
| | - Galyna P Volynets
- Department of Medicinal Chemistry, Institute of Molecular Biology and Genetics of the NAS of Ukraine, Kyiv, Ukraine
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44
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Zhao L, Yang X, Feng C, Wang Y, Wang Q, Pei J, Wu J, Li S, Zhang H, Cao X. Triple-negative breast cancer cells respond to T cells severely at the alternative splicing layer. ELECTRON J BIOTECHN 2021. [DOI: 10.1016/j.ejbt.2021.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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45
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Pang L, Weeks SD, Van Aerschot A. Aminoacyl-tRNA Synthetases as Valuable Targets for Antimicrobial Drug Discovery. Int J Mol Sci 2021; 22:1750. [PMID: 33578647 PMCID: PMC7916415 DOI: 10.3390/ijms22041750] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/04/2021] [Accepted: 02/06/2021] [Indexed: 12/20/2022] Open
Abstract
Aminoacyl-tRNA synthetases (aaRSs) catalyze the esterification of tRNA with a cognate amino acid and are essential enzymes in all three kingdoms of life. Due to their important role in the translation of the genetic code, aaRSs have been recognized as suitable targets for the development of small molecule anti-infectives. In this review, following a concise discussion of aaRS catalytic and proof-reading activities, the various inhibitory mechanisms of reported natural and synthetic aaRS inhibitors are discussed. Using the expanding repository of ligand-bound X-ray crystal structures, we classified these compounds based on their binding sites, focusing on their ability to compete with the association of one, or more of the canonical aaRS substrates. In parallel, we examined the determinants of species-selectivity and discuss potential resistance mechanisms of some of the inhibitor classes. Combined, this structural perspective highlights the opportunities for further exploration of the aaRS enzyme family as antimicrobial targets.
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Affiliation(s)
- Luping Pang
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49–box 1041, 3000 Leuven, Belgium;
- KU Leuven, Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, Herestraat 49–box 822, 3000 Leuven, Belgium
| | | | - Arthur Van Aerschot
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49–box 1041, 3000 Leuven, Belgium;
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Misincorporation Proteomics Technologies: A Review. Proteomes 2021; 9:proteomes9010002. [PMID: 33494504 PMCID: PMC7924376 DOI: 10.3390/proteomes9010002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/11/2021] [Accepted: 01/18/2021] [Indexed: 12/15/2022] Open
Abstract
Proteinopathies are diseases caused by factors that affect proteoform conformation. As such, a prevalent hypothesis is that the misincorporation of noncanonical amino acids into a proteoform results in detrimental structures. However, this hypothesis is missing proteomic evidence, specifically the detection of a noncanonical amino acid in a peptide sequence. This review aims to outline the current state of technology that can be used to investigate mistranslations and misincorporations whilst framing the pursuit as Misincorporation Proteomics (MiP). The current availability of technologies explored herein is mass spectrometry, sample enrichment/preparation, data analysis techniques, and the hyphenation of approaches. While many of these technologies show potential, our review reveals a need for further development and refinement of approaches is still required.
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Guarnaccia AD, Rose KL, Wang J, Zhao B, Popay TM, Wang CE, Guerrazzi K, Hill S, Woodley CM, Hansen TJ, Lorey SL, Shaw JG, Payne WG, Weissmiller AM, Olejniczak ET, Fesik SW, Liu Q, Tansey WP. Impact of WIN site inhibitor on the WDR5 interactome. Cell Rep 2021; 34:108636. [PMID: 33472061 PMCID: PMC7871196 DOI: 10.1016/j.celrep.2020.108636] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 11/17/2020] [Accepted: 12/21/2020] [Indexed: 01/08/2023] Open
Abstract
The chromatin-associated protein WDR5 is a promising pharmacological target in cancer, with most drug discovery efforts directed against an arginine-binding cavity in WDR5 called the WIN site. Despite a clear expectation that WIN site inhibitors will alter the repertoire of WDR5 interaction partners, their impact on the WDR5 interactome remains unknown. Here, we use quantitative proteomics to delineate how the WDR5 interactome is changed by WIN site inhibition. We show that the WIN site inhibitor alters the interaction of WDR5 with dozens of proteins, including those linked to phosphatidylinositol 3-kinase (PI3K) signaling. As proof of concept, we demonstrate that the master kinase PDPK1 is a bona fide high-affinity WIN site binding protein that engages WDR5 to modulate transcription of genes expressed in the G2 phase of the cell cycle. This dataset expands our understanding of WDR5 and serves as a resource for deciphering the action of WIN site inhibitors.
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Affiliation(s)
- Alissa D Guarnaccia
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Kristie L Rose
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Jing Wang
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Bin Zhao
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Tessa M Popay
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Christina E Wang
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Kiana Guerrazzi
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Salisha Hill
- Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Chase M Woodley
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Tyler J Hansen
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Shelly L Lorey
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - J Grace Shaw
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - William G Payne
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - April M Weissmiller
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Edward T Olejniczak
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Stephen W Fesik
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Department of Chemistry, Vanderbilt University, Nashville, TN 37232, USA
| | - Qi Liu
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - William P Tansey
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.
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Panigrahi GC, Qureshi R, Jakkula P, Kumar KA, Khan N, Qureshi IA. Leishmanial aspartyl-tRNA synthetase: Biochemical, biophysical and structural insights. Int J Biol Macromol 2020; 165:2869-2885. [PMID: 33736288 DOI: 10.1016/j.ijbiomac.2020.10.140] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 10/04/2020] [Accepted: 10/16/2020] [Indexed: 11/18/2022]
Abstract
Aminoacyl tRNA synthetases (aaRSs) are integral components of protein biosynthesis along with several non-canonical cellular processes. Inhibition studies of aaRSs presented these enzymes as promising drug targets in many pathogens, however aspartyl tRNA synthetase has not been studied in trypanosomatids despite its essentiality. Hence, full-length ORF of Leishmania donovani aspartyl tRNA synthetase (LdaspRS) was cloned and purified to homogeneity followed by molecular mass determination. The aminoacylation assay established that the purified protein performs its function optimally at physiological pH and temperature. The kinetic parameters of LdaspRS revealed the affinity of l-aspartate towards the enzyme to be very much lower than the cofactor. Our study also highlights the moonlighting function of LdaspRS to stimulate the pro-inflammatory cytokines and nitric oxide generation by host macrophage. Furthermore, CD and intrinsic tryptophan fluorescence measurements showed the changes in structural conformation at varying pH, denaturants and ligands. The modelled LdaspRS structure presented all the specific characteristics of class II aaRSs, while in silico study suggested binding of pyrimidine-derived inhibitors in its cofactor binding site with high affinity followed by validation using MD simulation. Altogether, this study could provide a platform for exploring LdaspRS to develop potential therapeutics against leishmaniasis.
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Affiliation(s)
- Girish Ch Panigrahi
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500046, Telangana, India
| | - Rahila Qureshi
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad 500046, Telangana, India
| | - Pranay Jakkula
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500046, Telangana, India
| | - K Amith Kumar
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500046, Telangana, India
| | - Nooruddin Khan
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad 500046, Telangana, India
| | - Insaf Ahmed Qureshi
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500046, Telangana, India.
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49
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Lee KM, Hwang EH, Kang SE, Lee CH, Lee H, Oh HJ, Kim K, Koh J, Ryu HS. Tryptophanyl-tRNA Synthetase Sensitizes Hormone Receptor-Positive Breast Cancer to Docetaxel-Based Chemotherapy. J Breast Cancer 2020; 23:599-609. [PMID: 33408886 PMCID: PMC7779724 DOI: 10.4048/jbc.2020.23.e67] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 12/06/2020] [Indexed: 12/24/2022] Open
Abstract
Purpose A relatively low response to chemotherapy has been reported for hormone receptor (HR)-positive breast cancer. In this study, we investigated the role of tryptophanyl-transfer RNA synthetase (WARS) in the chemotherapeutic response of HR-positive breast cancer. Methods Pre-chemotherapeutic needle biopsy samples of 45 HR-positive breast cancer patients undergoing the same chemotherapeutic regimen were subjected to immunohistochemistry. To investigate the biological functions of WARS in HR-positive breast cancer, we conducted cell viability assay, flow cytometry analysis, caspase activity assay, Quantitative real-time polymerase chain reaction, and western blotting using WARS gene-modulated HR-positive breast cancer cells (T47D, ZR-75-1, and MCF7). Results WARS overexpression in HR-positive breast cancer patients showed a significant correlation with favorable chemotherapy response. Downregulation of WARS increased cell viability following docetaxel treatment in tumor cell lines. On the other hand, WARS overexpression sensitized the therapeutic response to docetaxel. Additionally, downregulation of WARS caused a decrease in the number of apoptotic cell populations by docetaxel. Poly (ADP-ribose) polymerase cleavage and caspase 3/7 activity were increased in docetaxel-treated tumor cells with WARS overexpression. Conclusion Our results suggest that WARS might be a potential predictor for chemotherapy response in patients with HR-positive breast cancer as well as a novel molecular target to improve chemosensitivity.
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Affiliation(s)
- Kyung-Min Lee
- Center for Medical Innovation, Biomedical Research Institute, Seoul National University Hospital, Seoul, Korea
| | - Eun Hye Hwang
- Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Seong Eun Kang
- Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Cheng Hyun Lee
- Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Hyebin Lee
- Department of Radiation Oncology, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Korea
| | - Hyeon Jeong Oh
- Department of Pathology, Seoul National University Bundang Hospital, 82 Gumi-ro 173, Bundang-gu, Seongnam, Korea
| | - Kwangsoo Kim
- Transdisciplinary Department of Medicine & Advanced Technology, Seoul National University Hospital, Seoul, Korea
| | - Jiwon Koh
- Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Han Suk Ryu
- Center for Medical Innovation, Biomedical Research Institute, Seoul National University Hospital, Seoul, Korea.,Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
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50
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Yuan S, Yong X, Zhao T, Li Y, Liu J. Research Progress of the Biosynthesis of Natural Bio-Antibacterial Agent Pulcherriminic Acid in Bacillus. Molecules 2020; 25:E5611. [PMID: 33260656 PMCID: PMC7731078 DOI: 10.3390/molecules25235611] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 11/13/2020] [Accepted: 11/15/2020] [Indexed: 11/16/2022] Open
Abstract
Pulcherriminic acid is a cyclic dipeptide found mainly in Bacillus and yeast. Due to the ability of pulcherriminic acid to chelate Fe3+ to produce reddish brown pulcherrimin, microorganisms capable of synthesizing pulcherriminic acid compete with other microorganisms for environmental iron ions to achieve bacteriostatic effects. Therefore, studying the biosynthetic pathway and their enzymatic catalysis, gene regulation in the process of synthesis of pulcherriminic acid in Bacillus can facilitate the industrial production, and promote the wide application in food, agriculture and medicine industries. After initially discussing, this review summarizes current research on the synthesis of pulcherriminic acid by Bacillus, which includes the crystallization of key enzymes, molecular catalytic mechanisms, regulation of synthetic pathways, and methods to improve efficiency in synthesizing pulcherriminic acid and its precursors. Finally, possible applications of pulcherriminic acid in the fermented food, such as Chinese Baijiu, applying combinatorial biosynthesis will be summarized.
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Affiliation(s)
- Siqi Yuan
- Sichuan University of Science & Engineering, Xueyuan Street 180#, Huixing Rd., Zigong 643000, China; (S.Y.); (X.Y.); (T.Z.)
- Luzhou Laojiao Group Co. Ltd., Airentang Square, Jiangyang District, Luzhou 646000, China
| | - Xihao Yong
- Sichuan University of Science & Engineering, Xueyuan Street 180#, Huixing Rd., Zigong 643000, China; (S.Y.); (X.Y.); (T.Z.)
| | - Ting Zhao
- Sichuan University of Science & Engineering, Xueyuan Street 180#, Huixing Rd., Zigong 643000, China; (S.Y.); (X.Y.); (T.Z.)
| | - Yuan Li
- Sichuan University of Science & Engineering, Xueyuan Street 180#, Huixing Rd., Zigong 643000, China; (S.Y.); (X.Y.); (T.Z.)
| | - Jun Liu
- Sichuan University of Science & Engineering, Xueyuan Street 180#, Huixing Rd., Zigong 643000, China; (S.Y.); (X.Y.); (T.Z.)
- Wuliangye Group Co. Ltd., No. 150 Minjiang West Road, Yibin 644000, China
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