1
|
Qiao H, Wang Z, Yang H, Xia M, Yang G, Bai F, Wang J, Fang P. Specific glycine-dependent enzyme motion determines the potency of conformation selective inhibitors of threonyl-tRNA synthetase. Commun Biol 2024; 7:867. [PMID: 39014102 PMCID: PMC11252418 DOI: 10.1038/s42003-024-06559-x] [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: 02/26/2024] [Accepted: 07/05/2024] [Indexed: 07/18/2024] Open
Abstract
The function of proteins depends on their correct structure and proper dynamics. Understanding the dynamics of target proteins facilitates drug design and development. However, dynamic information is often hidden in the spatial structure of proteins. It is important but difficult to identify the specific residues that play a decisive role in protein dynamics. Here, we report that a critical glycine residue (Gly463) dominates the motion of threonyl-tRNA synthetase (ThrRS) and the sensitivity of the enzyme to antibiotics. Obafluorin (OB), a natural antibiotic, is a novel covalent inhibitor of ThrRS. The binding of OB induces a large conformational change in ThrRS. Through five crystal structures, biochemical and biophysical analyses, and computational simulations, we found that Gly463 plays an important role in the dynamics of ThrRS. Mutating this flexible residue into more rigid residues did not damage the enzyme's three-dimensional structure but significantly improved the thermal stability of the enzyme and suppressed its ability to change conformation. These mutations cause resistance of ThrRS to antibiotics that are conformationally selective, such as OB and borrelidin. This work not only elucidates the molecular mechanism of the self-resistance of OB-producing Pseudomonas fluorescens but also emphasizes the importance of backbone kinetics for aminoacyl-tRNA synthetase-targeting drug development.
Collapse
Affiliation(s)
- Hang Qiao
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, 200032, Shanghai, China
| | - Zilu Wang
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, 200032, Shanghai, China
| | - Hao Yang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, 201210, Shanghai, China
| | - Mingyu Xia
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, 200032, Shanghai, China
| | - Guang Yang
- School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, 1 Sub-lane Xiangshan, 310024, Hangzhou, China
| | - Fang Bai
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, 201210, Shanghai, China.
- School of Information Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, 201210, Shanghai, China.
- Shanghai Clinical Research and Trial Center, 201210, Shanghai, China.
| | - Jing Wang
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, 200032, Shanghai, China.
- School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, 1 Sub-lane Xiangshan, 310024, Hangzhou, China.
| | - Pengfei Fang
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, 200032, Shanghai, China.
- School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, 1 Sub-lane Xiangshan, 310024, Hangzhou, China.
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, 510006, Guangzhou, China.
| |
Collapse
|
2
|
Ivanesthi IR, Latifah E, Amrullah LF, Tseng YK, Chuang TH, Pan HC, Yang CS, Liu SY, Wang CC. Adaptation of a eukaryote-like ProRS to a prokaryote-like tRNAPro. Nucleic Acids Res 2024; 52:7158-7170. [PMID: 38842939 PMCID: PMC11229370 DOI: 10.1093/nar/gkae483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 05/22/2024] [Accepted: 05/24/2024] [Indexed: 07/09/2024] Open
Abstract
Prolyl-tRNA synthetases (ProRSs) are unique among aminoacyl-tRNA synthetases (aaRSs) in having two distinct structural architectures across different organisms: prokaryote-like (P-type) and eukaryote/archaeon-like (E-type). Interestingly, Bacillus thuringiensis harbors both types, with P-type (BtProRS1) and E-type ProRS (BtProRS2) coexisting. Despite their differences, both enzymes are constitutively expressed and functional in vivo. Similar to BtProRS1, BtProRS2 selectively charges the P-type tRNAPro and displays higher halofuginone tolerance than canonical E-type ProRS. However, these two isozymes recognize the primary identity elements of the P-type tRNAPro-G72 and A73 in the acceptor stem-through distinct mechanisms. Moreover, BtProRS2 exhibits significantly higher tolerance to stresses (such as heat, hydrogen peroxide, and dithiothreitol) than BtProRS1 does. This study underscores how an E-type ProRS adapts to a P-type tRNAPro and how it may contribute to the bacterium's survival under stress conditions.
Collapse
Affiliation(s)
- Indira Rizqita Ivanesthi
- Department of Life Sciences, National Central University, Zhongli District, Taoyuan 320317, Taiwan
| | - Emi Latifah
- Department of Life Sciences, National Central University, Zhongli District, Taoyuan 320317, Taiwan
| | - Luqman Fikri Amrullah
- Department of Life Sciences, National Central University, Zhongli District, Taoyuan 320317, Taiwan
| | - Yi-Kuan Tseng
- Graduate Institute of Statistics, National Central University, Zhongli District, Taoyuan320317, Taiwan
| | - Tsung-Hsien Chuang
- Immunology Research Center, National Health Research Institutes, Zhunan Town, Miaoli 35053, Taiwan
| | - Hung-Chuan Pan
- Department of Neurosurgery, Taichung Veterans General Hospital, Taichung 407219, Taiwan
| | - Chih-Shiang Yang
- Department of Life Sciences, National Central University, Zhongli District, Taoyuan 320317, Taiwan
| | - Shih-Yang Liu
- Department of Life Sciences, National Central University, Zhongli District, Taoyuan 320317, Taiwan
| | - Chien-Chia Wang
- Department of Life Sciences, National Central University, Zhongli District, Taoyuan 320317, Taiwan
| |
Collapse
|
3
|
Tang J, Li Z, Meng Q, Liu L, Huang T, Li C, Li Q, Chen T. CuH-Catalyzed Reductive Coupling of Nitroarenes with Phosphine Oxides for the Direct Synthesis of Phosphamides. J Org Chem 2024. [PMID: 38809686 DOI: 10.1021/acs.joc.4c00522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Abstract
A CuH-catalyzed reductive coupling of nitroarenes with phosphine oxides is developed, which produces a series of phosphamides in moderate to excellent yields with good functional group tolerance. Gram-scale synthesis and late-stage modification of nitro-aromatic functional molecule niclosamide are also successfully conducted. The mechanism study shows that the nitro group is transformed after being reduced to nitroso and a nucleophilic addition procedure is involved during the reaction.
Collapse
Affiliation(s)
- Jie Tang
- Hainan Provincial Key Laboratory of Fine Chemical, School of Chemistry and Chemical Engineering, Hainan University, Haikou, Hainan 570228, China
| | - Zhiyou Li
- Hainan Provincial Key Laboratory of Fine Chemical, School of Chemistry and Chemical Engineering, Hainan University, Haikou, Hainan 570228, China
| | - Qi Meng
- Hainan Provincial Key Laboratory of Fine Chemical, School of Chemistry and Chemical Engineering, Hainan University, Haikou, Hainan 570228, China
| | - Long Liu
- Hainan Provincial Key Laboratory of Fine Chemical, School of Chemistry and Chemical Engineering, Hainan University, Haikou, Hainan 570228, China
| | - Tianzeng Huang
- Hainan Provincial Key Laboratory of Fine Chemical, School of Chemistry and Chemical Engineering, Hainan University, Haikou, Hainan 570228, China
| | - Chunya Li
- Hainan Provincial Key Laboratory of Fine Chemical, School of Chemistry and Chemical Engineering, Hainan University, Haikou, Hainan 570228, China
| | - Qiang Li
- Shandong Provincial Key Laboratory of Chemical Energy Storage and Novel Cell Technology, School of Chemistry and Chemical Engineering, Liaocheng University, No. 1, Hunan Street, Liaocheng, Shandong 252000, China
| | - Tieqiao Chen
- Hainan Provincial Key Laboratory of Fine Chemical, School of Chemistry and Chemical Engineering, Hainan University, Haikou, Hainan 570228, China
| |
Collapse
|
4
|
Moréra S, Vigouroux A, Aumont-Nicaise M, Ahmar M, Meyer T, El Sahili A, Deicsics G, González-Mula A, Li S, Doré J, Sirigu S, Legrand P, Penot C, André F, Faure D, Soulère L, Queneau Y, Vial L. A highly conserved ligand-binding site for AccA transporters of antibiotic and quorum-sensing regulator in Agrobacterium leads to a different specificity. Biochem J 2024; 481:93-117. [PMID: 38058289 DOI: 10.1042/bcj20230273] [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: 06/29/2023] [Revised: 12/05/2023] [Accepted: 12/06/2023] [Indexed: 12/08/2023]
Abstract
Plants genetically modified by the pathogenic Agrobacterium strain C58 synthesize agrocinopines A and B, whereas those modified by the pathogenic strain Bo542 produce agrocinopines C and D. The four agrocinopines (A, B, C and D) serve as nutrients by agrobacteria and signaling molecule for the dissemination of virulence genes. They share the uncommon pyranose-2-phosphate motif, represented by the l-arabinopyranose moiety in agrocinopines A/B and the d-glucopyranose moiety in agrocinopines C/D, also found in the antibiotic agrocin 84. They are imported into agrobacterial cytoplasm via the Acc transport system, including the solute-binding protein AccA coupled to an ABC transporter. We have previously shown that unexpectedly, AccA from strain C58 (AccAC58) recognizes the pyranose-2-phosphate motif present in all four agrocinopines and agrocin 84, meaning that strain C58 is able to import agrocinopines C/D, originating from the competitor strain Bo542. Here, using agrocinopine derivatives and combining crystallography, affinity and stability measurements, modeling, molecular dynamics, in vitro and vivo assays, we show that AccABo542 and AccAC58 behave differently despite 75% sequence identity and a nearly identical ligand binding site. Indeed, strain Bo542 imports only compounds containing the d-glucopyranose-2-phosphate moiety, and with a lower affinity compared with strain C58. This difference in import efficiency makes C58 more competitive than Bo542 in culture media. We can now explain why Agrobacterium/Allorhizobium vitis strain S4 is insensitive to agrocin 84, although its genome contains a conserved Acc transport system. Overall, our work highlights AccA proteins as a case study, for which stability and dynamics drive specificity.
Collapse
Affiliation(s)
- Solange Moréra
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Armelle Vigouroux
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Magali Aumont-Nicaise
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Mohammed Ahmar
- Univ Lyon, Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, CNRS, Université Lyon 1, INSA Lyon, CPE Lyon, ICBMS, UMR 5246; Université Claude Bernard, Bâtiment Lederer, 69622 Villeurbanne Cedex, France
| | - Thibault Meyer
- UMR Ecologie Microbienne, CNRS, INRAE, VetAgro Sup, UCBL, Université de Lyon, Villeurbanne, F-69622 Lyon, France
| | - Abbas El Sahili
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Grégory Deicsics
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Almudena González-Mula
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Sizhe Li
- Univ Lyon, Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, CNRS, Université Lyon 1, INSA Lyon, CPE Lyon, ICBMS, UMR 5246; Université Claude Bernard, Bâtiment Lederer, 69622 Villeurbanne Cedex, France
| | - Jeanne Doré
- UMR Ecologie Microbienne, CNRS, INRAE, VetAgro Sup, UCBL, Université de Lyon, Villeurbanne, F-69622 Lyon, France
| | - Serena Sirigu
- Synchrotron SOLEIL, HelioBio Group, 91190 Saint-Aubin, France
| | - Pierre Legrand
- Synchrotron SOLEIL, HelioBio Group, 91190 Saint-Aubin, France
| | - Camille Penot
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - François André
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Denis Faure
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Laurent Soulère
- Univ Lyon, Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, CNRS, Université Lyon 1, INSA Lyon, CPE Lyon, ICBMS, UMR 5246; Université Claude Bernard, Bâtiment Lederer, 69622 Villeurbanne Cedex, France
| | - Yves Queneau
- Univ Lyon, Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, CNRS, Université Lyon 1, INSA Lyon, CPE Lyon, ICBMS, UMR 5246; Université Claude Bernard, Bâtiment Lederer, 69622 Villeurbanne Cedex, France
| | - Ludovic Vial
- UMR Ecologie Microbienne, CNRS, INRAE, VetAgro Sup, UCBL, Université de Lyon, Villeurbanne, F-69622 Lyon, France
| |
Collapse
|
5
|
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.
Collapse
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; , ,
| |
Collapse
|
6
|
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.
Collapse
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.
| | | |
Collapse
|
7
|
Brown PJB, Chang JH, Fuqua C. Agrobacterium tumefaciens: a Transformative Agent for Fundamental Insights into Host-Microbe Interactions, Genome Biology, Chemical Signaling, and Cell Biology. J Bacteriol 2023; 205:e0000523. [PMID: 36892285 PMCID: PMC10127608 DOI: 10.1128/jb.00005-23] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2023] Open
Abstract
Agrobacterium tumefaciens incites the formation of readily visible macroscopic structures known as crown galls on plant tissues that it infects. Records from biologists as early as the 17th century noted these unusual plant growths and began examining the basis for their formation. These studies eventually led to isolation of the infectious agent, A. tumefaciens, and decades of study revealed the remarkable mechanisms by which A. tumefaciens causes crown gall through stable horizontal genetic transfer to plants. This fundamental discovery generated a barrage of applications in the genetic manipulation of plants that is still under way. As a consequence of the intense study of A. tumefaciens and its role in plant disease, this pathogen was developed as a model for the study of critical processes that are shared by many bacteria, including host perception during pathogenesis, DNA transfer and toxin secretion, bacterial cell-cell communication, plasmid biology, and more recently, asymmetric cell biology and composite genome coordination and evolution. As such, studies of A. tumefaciens have had an outsized impact on diverse areas within microbiology and plant biology that extend far beyond its remarkable agricultural applications. In this review, we attempt to highlight the colorful history of A. tumefaciens as a study system, as well as current areas that are actively demonstrating its value and utility as a model microorganism.
Collapse
Affiliation(s)
- Pamela J. B. Brown
- Division of Biological Sciences, University of Missouri, Columbia, Missouri, USA
| | - Jeff H. Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Clay Fuqua
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| |
Collapse
|
8
|
Hoffmann G, Le Gorrec M, Mestdach E, Cusack S, Salmon L, Jensen MR, Palencia A. Adenosine-Dependent Activation Mechanism of Prodrugs Targeting an Aminoacyl-tRNA Synthetase. J Am Chem Soc 2023; 145:800-810. [PMID: 36599057 PMCID: PMC9853866 DOI: 10.1021/jacs.2c04808] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Prodrugs have little or no pharmacological activity and are converted to active drugs in the body by enzymes, metabolic reactions, or through human-controlled actions. However, prodrugs promoting their chemical bioconversion without any of these processes have not been reported before. Here, we present an enzyme-independent prodrug activation mechanism by boron-based compounds (benzoxaboroles) targeting leucyl-tRNA synthetase (LeuRS), including an antibiotic that recently has completed phase II clinical trials to cure tuberculosis. We combine nuclear magnetic resonance spectroscopy and X-ray crystallography with isothermal titration calorimetry to show that these benzoxaboroles do not bind directly to their drug target LeuRS, instead they are prodrugs that activate their bioconversion by forming a highly specific and reversible LeuRS inhibition adduct with ATP, AMP, or the terminal adenosine of the tRNALeu. We demonstrate how the oxaborole group of the prodrugs cyclizes with the adenosine ribose at physiological concentrations to form the active molecule. This bioconversion mechanism explains the remarkably good druglike properties of benzoxaboroles showing efficacy against radically different human pathogens and fully explains the mechanism of action of these compounds. Thus, this adenosine-dependent activation mechanism represents a novel concept in prodrug chemistry that can be applied to improve the solubility, permeability and metabolic stability of challenging drugs.
Collapse
Affiliation(s)
- Guillaume Hoffmann
- Institute
for Advanced Biosciences (IAB), Structural Biology of Novel Targets
in Human Diseases, INSERM U1209, CNRS UMR5309, Université Grenoble
Alpes, 38000 Grenoble, France
| | - Madalen Le Gorrec
- Institute
for Advanced Biosciences (IAB), Structural Biology of Novel Targets
in Human Diseases, INSERM U1209, CNRS UMR5309, Université Grenoble
Alpes, 38000 Grenoble, France
| | - Emeline Mestdach
- Centre
de Résonance Magnétique Nucléaire à Très
Hauts Champs, (CRMN), UMR 5082, CNRS, ENS Lyon, UCBL, Université
de Lyon, 69100 Villeurbanne, France
| | - Stephen Cusack
- European
Molecular Biology Laboratory, 38042 Grenoble, France
| | - Loïc Salmon
- Centre
de Résonance Magnétique Nucléaire à Très
Hauts Champs, (CRMN), UMR 5082, CNRS, ENS Lyon, UCBL, Université
de Lyon, 69100 Villeurbanne, France
| | | | - Andrés Palencia
- Institute
for Advanced Biosciences (IAB), Structural Biology of Novel Targets
in Human Diseases, INSERM U1209, CNRS UMR5309, Université Grenoble
Alpes, 38000 Grenoble, France,
| |
Collapse
|
9
|
Asenstorfer RE, Ryder MH, Jones GP. Agrocinopine C, a Ti-plasmid-coded enzyme-product, is a 2-O, 6-O linked phosphodiester of D-Glucose and sucrose. PHYTOCHEMISTRY 2022; 194:113013. [PMID: 34839131 DOI: 10.1016/j.phytochem.2021.113013] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 11/06/2021] [Accepted: 11/06/2021] [Indexed: 06/13/2023]
Abstract
Agrocinopine C is a small molecule found in crown gall tumours induced by pathogenic Agrobacterium radiobacter carrying the tumour-inducing plasmid pTi Bo542. This phosphodiester opine was isolated (at 0.02 g/100 g fresh wt.) from sunflower (Helianthus annuus L.) galls. It is structurally related to agrocinopine A and is a glucose-2-phosphodiester linked to the C6-hydroxy-methyl group of the glucose moiety of sucrose. Sugar-2-phosphates are uncommon in plant tissues, whether transformed by Agrobacterium or not. 1H and 31P NMR signal multiplicity indicates five-fold anomeric complexity of agrocinopine C in solution, implying that the permeases taking up these sucrose-phosphodiesters could recognise any one of the five anomers. Data suggests that the open chain aldehyde forms of the 2-phosphorylated opines agrocinopine C and agrocinopine A and the corresponding phosphorylated glucose-2-phosphoramidate component of the antibiotic agrocin 84 play a central role in agrocin's selective toxicity to certain strains of Agrobacterium after uptake via Ti plasmid-encoded permeases.
Collapse
Affiliation(s)
- Robert E Asenstorfer
- School of Agriculture, Food and Wine, University of Adelaide, Waite Research Institute, PMB 1, Glen Osmond, South Australia, 5064, Australia
| | - Maarten H Ryder
- School of Agriculture, Food and Wine, University of Adelaide, Waite Research Institute, PMB 1, Glen Osmond, South Australia, 5064, Australia.
| | - Graham P Jones
- School of Agriculture, Food and Wine, University of Adelaide, Waite Research Institute, PMB 1, Glen Osmond, South Australia, 5064, Australia
| |
Collapse
|
10
|
Zhu YY, Niu Y, Niu YN, Yang SD. Recent advances in the synthesis and applications of phosphoramides. Org Biomol Chem 2021; 19:10296-10313. [PMID: 34812834 DOI: 10.1039/d1ob01566d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Phosphoramide, as an important framework of many biologically active molecules, has attracted widespread attention in recent decades. It is not only widely used in pharmaceuticals because of its excellent biological activities, but it also shows good performance in organic dyes, flame retardants and extractors. Thus, it is of great significance to develop effective and convenient methods for the synthesis of phosphoramides. In this review, the recent advancements made in the synthesis routes and applications of phosphoramides are discussed. The synthetic strategies of phosphoramides can be separated into five categories: phosphorus halides as the substrate, phosphates as the substrate, phosphorus hydrogen as the substrate, azides as the substrate and other methods. The latest examples of these methods are provided and some representative mechanisms are also described.
Collapse
Affiliation(s)
- Yuan-Yuan Zhu
- State Key Laboratory of Applied Organic Chemistry, Lanzhou University, Lanzhou 730000, China.
| | - Yuan Niu
- State Key Laboratory of Applied Organic Chemistry, Lanzhou University, Lanzhou 730000, China.
| | - Yan-Ning Niu
- Department of Teaching and Research, Nanjing Forestry University, Huaian 223003, P. R. China
| | - Shang-Dong Yang
- State Key Laboratory of Applied Organic Chemistry, Lanzhou University, Lanzhou 730000, China.
| |
Collapse
|
11
|
Abstract
Organophosphorus compounds play a vital role as nucleic acids, nucleotide coenzymes, metabolic intermediates and are involved in many biochemical processes. They are part of DNA, RNA, ATP and a number of important biological elements of living organisms. Synthetic compounds of this class have found practical application as agrochemicals, pharmaceuticals, bioregulators, and othrs. In recent years, a large number of phosphorus compounds containing P-O, P-N, P-C bonds have been isolated from natural sources. Many of them have shown interesting biological properties and have become the objects of intensive scientific research. Most of these compounds contain asymmetric centers, the absolute configurations of which have a significant effect on the biological properties of the products of their transformations. This area of research on natural phosphorus compounds is still little-studied, that prompted us to analyze and discuss it in our review. Moreover natural organophosphorus compounds represent interesting models for the development of new biologically active compounds, and a number of promising drugs and agrochemicals have already been obtained on their basis. The review also discusses the history of the development of ideas about the role of organophosphorus compounds and stereochemistry in the origin of life on Earth, starting from the prebiotic period, that allows us in a new way to consider this most important problem of fundamental science.
Collapse
|
12
|
Travin DY, Severinov K, Dubiley S. Natural Trojan horse inhibitors of aminoacyl-tRNA synthetases. RSC Chem Biol 2021; 2:468-485. [PMID: 34382000 PMCID: PMC8323819 DOI: 10.1039/d0cb00208a] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 02/10/2021] [Indexed: 12/18/2022] Open
Abstract
For most antimicrobial compounds with intracellular targets, getting inside the cell is the major obstacle limiting their activity. To pass this barrier some antibiotics mimic the compounds of specific interest for the microbe (siderophores, peptides, carbohydrates, etc.) and hijack the transport systems involved in their active uptake followed by the release of a toxic warhead inside the cell. In this review, we summarize the information about the structures, biosynthesis, and transport of natural inhibitors of aminoacyl-tRNA synthetases (albomycin, microcin C-related compounds, and agrocin 84) that rely on such "Trojan horse" strategy to enter the cell. In addition, we provide new data on the composition and distribution of biosynthetic gene clusters reminiscent of those coding for known Trojan horse aminoacyl-tRNA synthetases inhibitors. The products of these clusters are likely new antimicrobials that warrant further investigation.
Collapse
Affiliation(s)
- Dmitrii Y Travin
- Center of Life Sciences, Skolkovo Institute of Science and Technology Moscow Russia
- Institute of Gene Biology, Russian Academy of Sciences Moscow Russia
| | - Konstantin Severinov
- Center of Life Sciences, Skolkovo Institute of Science and Technology Moscow Russia
- Institute of Gene Biology, Russian Academy of Sciences Moscow Russia
- Waksman Institute for Microbiology, Rutgers, Piscataway New Jersey USA
| | - Svetlana Dubiley
- Center of Life Sciences, Skolkovo Institute of Science and Technology Moscow Russia
- Institute of Gene Biology, Russian Academy of Sciences Moscow Russia
| |
Collapse
|
13
|
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.
Collapse
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;
| |
Collapse
|
14
|
Abstract
Aminoacyl-tRNA synthetases (AARSs) have been considered very attractive drug-targets for decades. This interest probably emerged with the identification of differences in AARSs between prokaryotic and eukaryotic species, which provided a rationale for the development of antimicrobials targeting bacterial AARSs with minimal effect on the homologous human AARSs. Today we know that AARSs are not only attractive, but also valid drug targets as they are housekeeping proteins that: (i) play a fundamental role in protein translation by charging the corresponding amino acid to its cognate tRNA and preventing mistranslation mistakes [1], a critical process during fast growing conditions of microbes; and (ii) present significant differences between microbes and humans that can be used for drug development [2]. Together with the vast amount of available data on both pathogenic and mammalian AARSs, it is expected that, in the future, the numerous reported inhibitors of AARSs will provide the basis to develop new therapeutics for the treatment of human diseases. In this chapter, a detailed summary on the state-of-the-art in drug discovery and drug development for each aminoacyl-tRNA synthetase will be presented.
Collapse
Affiliation(s)
- Maria Lukarska
- Institute for Advanced Biosciences (IAB), Structural Biology of Novel Drug Targets in Human Diseases, INSERM U1209, CNRS UMR 5309, University Grenoble Alpes, Grenoble, France
| | - Andrés Palencia
- Institute for Advanced Biosciences (IAB), Structural Biology of Novel Drug Targets in Human Diseases, INSERM U1209, CNRS UMR 5309, University Grenoble Alpes, Grenoble, France.
| |
Collapse
|
15
|
Zhang P, Ma S. Recent development of leucyl-tRNA synthetase inhibitors as antimicrobial agents. MEDCHEMCOMM 2019; 10:1329-1341. [PMID: 31534653 PMCID: PMC6727470 DOI: 10.1039/c9md00139e] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 05/26/2019] [Indexed: 12/14/2022]
Abstract
Aminoacyl-tRNA synthetases (aaRSs) widely exist in organisms and mediate protein synthesis. Inhibiting these synthetases can lead to the termination of protein synthesis and subsequently achieve antibacterial and antiparasitic purposes. Moreover, the structures of aaRSs found in eukaryotes have considerable structural differences compared to those in prokaryotes, based on which it is possible to develop highly selective inhibitors. Leucyl-tRNA synthetase (LeuRS) with unique synthesis and editing sites is one of 20 kinds of aaRSs. Many inhibitors targeting LeuRS have been designed and synthesized, some of which have entered clinical use. For example, the benzoxaborole compound AN2690 has been approved by the FDA for the treatment of onychomycosis. AN3365 is suspended in the phase II clinical trial due to the rapid development of AN3365 resistance, but it may be used in combination with other antibiotics. The aaRSs, especially LeuRS, are being considered as targets of new potential anti-infective drugs for the treatment of not only bacterial or fungal infections but also infections by trypanosomes and malaria parasites. This review mainly describes the development of LeuRS inhibitors, focusing on their mechanisms of action, structure-activity relationships (SARs), and in vitro and in vivo activities.
Collapse
Affiliation(s)
- Panpan Zhang
- Department of Medicinal Chemistry , Key Laboratory of Chemical Biology , Ministry of Education , School of Pharmaceutical Sciences , Shandong University , 44, West Culture Road , Jinan 250012 , P. R. China . E mail:
| | - Shutao Ma
- Department of Medicinal Chemistry , Key Laboratory of Chemical Biology , Ministry of Education , School of Pharmaceutical Sciences , Shandong University , 44, West Culture Road , Jinan 250012 , P. R. China . E mail:
| |
Collapse
|
16
|
Petkowski JJ, Bains W, Seager S. Natural Products Containing 'Rare' Organophosphorus Functional Groups. Molecules 2019; 24:E866. [PMID: 30823503 PMCID: PMC6429109 DOI: 10.3390/molecules24050866] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 02/13/2019] [Accepted: 02/22/2019] [Indexed: 12/25/2022] Open
Abstract
Phosphorous-containing molecules are essential constituents of all living cells. While the phosphate functional group is very common in small molecule natural products, nucleic acids, and as chemical modification in protein and peptides, phosphorous can form P⁻N (phosphoramidate), P⁻S (phosphorothioate), and P⁻C (e.g., phosphonate and phosphinate) linkages. While rare, these moieties play critical roles in many processes and in all forms of life. In this review we thoroughly categorize P⁻N, P⁻S, and P⁻C natural organophosphorus compounds. Information on biological source, biological activity, and biosynthesis is included, if known. This review also summarizes the role of phosphorylation on unusual amino acids in proteins (N- and S-phosphorylation) and reviews the natural phosphorothioate (P⁻S) and phosphoramidate (P⁻N) modifications of DNA and nucleotides with an emphasis on their role in the metabolism of the cell. We challenge the commonly held notion that nonphosphate organophosphorus functional groups are an oddity of biochemistry, with no central role in the metabolism of the cell. We postulate that the extent of utilization of some phosphorus groups by life, especially those containing P⁻N bonds, is likely severely underestimated and has been largely overlooked, mainly due to the technological limitations in their detection and analysis.
Collapse
Affiliation(s)
- Janusz J Petkowski
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, 77 Mass. Ave., Cambridge, MA 02139, USA.
| | - William Bains
- Rufus Scientific, 37 The Moor, Melbourn, Royston, Herts SG8 6ED, UK.
| | - Sara Seager
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, 77 Mass. Ave., Cambridge, MA 02139, USA.
- Department of Physics, Massachusetts Institute of Technology, 77 Mass. Ave., Cambridge, MA 02139, USA.
- Department of Aeronautics and Astronautics, Massachusetts Institute of Technology, 77 Mass. Ave., Cambridge, MA 02139, USA.
| |
Collapse
|
17
|
Francklyn CS, Mullen P. Progress and challenges in aminoacyl-tRNA synthetase-based therapeutics. J Biol Chem 2019; 294:5365-5385. [PMID: 30670594 DOI: 10.1074/jbc.rev118.002956] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Aminoacyl-tRNA synthetases (ARSs) are universal enzymes that catalyze the attachment of amino acids to the 3' ends of their cognate tRNAs. The resulting aminoacylated tRNAs are escorted to the ribosome where they enter protein synthesis. By specifically matching amino acids to defined anticodon sequences in tRNAs, ARSs are essential to the physical interpretation of the genetic code. In addition to their canonical role in protein synthesis, ARSs are also involved in RNA splicing, transcriptional regulation, translation, and other aspects of cellular homeostasis. Likewise, aminoacylated tRNAs serve as amino acid donors for biosynthetic processes distinct from protein synthesis, including lipid modification and antibiotic biosynthesis. Thanks to the wealth of details on ARS structures and functions and the growing appreciation of their additional roles regulating cellular homeostasis, opportunities for the development of clinically useful ARS inhibitors are emerging to manage microbial and parasite infections. Exploitation of these opportunities has been stimulated by the discovery of new inhibitor frameworks, the use of semi-synthetic approaches combining chemistry and genome engineering, and more powerful techniques for identifying leads from the screening of large chemical libraries. Here, we review the inhibition of ARSs by small molecules, including the various families of natural products, as well as inhibitors developed by either rational design or high-throughput screening as antibiotics and anti-parasitic therapeutics.
Collapse
Affiliation(s)
- Christopher S Francklyn
- From the Department of Biochemistry, College of Medicine, University of Vermont, Burlington, Vermont 05405
| | - Patrick Mullen
- From the Department of Biochemistry, College of Medicine, University of Vermont, Burlington, Vermont 05405
| |
Collapse
|
18
|
Abstract
Inhibition of tRNA aminoacylation has proven to be an effective antimicrobial strategy, impeding an essential step of protein synthesis. Mupirocin, the well-known selective inhibitor of bacterial isoleucyl-tRNA synthetase, is one of three aminoacylation inhibitors now approved for human or animal use. However, design of novel aminoacylation inhibitors is complicated by the steadfast requirement to avoid off-target inhibition of protein synthesis in human cells. Here we review available data regarding known aminoacylation inhibitors as well as key amino-acid residues in aminoacyl-tRNA synthetases (aaRSs) and nucleotides in tRNA that determine the specificity and strength of the aaRS-tRNA interaction. Unlike most ligand-protein interactions, the aaRS-tRNA recognition interaction represents coevolution of both the tRNA and aaRS structures to conserve the specificity of aminoacylation. This property means that many determinants of tRNA recognition in pathogens have diverged from those of humans-a phenomenon that provides a valuable source of data for antimicrobial drug development.
Collapse
Affiliation(s)
- Joanne M Ho
- a Department of BioSciences , Rice University , Houston , TX , United States
| | | | - Dieter Söll
- c Departments of Molecular Biophysics & Biochemistry , Yale University , New Haven , CT , United States.,d Department of Chemistry , Yale University , New Haven , CT , United States
| | | |
Collapse
|
19
|
Soprano AS, Smetana JHC, Benedetti CE. Regulation of tRNA biogenesis in plants and its link to plant growth and response to pathogens. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2017; 1861:344-353. [PMID: 29222070 DOI: 10.1016/j.bbagrm.2017.12.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 11/29/2017] [Accepted: 12/03/2017] [Indexed: 12/23/2022]
Abstract
The field of tRNA biology, encompassing the functional and structural complexity of tRNAs, has fascinated scientists over the years and is continuously growing. Besides their fundamental role in protein translation, new evidence indicates that tRNA-derived molecules also regulate gene expression and protein synthesis in all domains of life. This review highlights some of the recent findings linking tRNA transcription and modification with plant cell growth and response to pathogens. In fact, mutations in proteins directly involved in tRNA synthesis and modification most often lead to pleiotropic effects on plant growth and immunity. As plants need to optimize and balance their energy and nutrient resources towards growth and defense, regulatory pathways that play a central role in integrating tRNA transcription and protein translation with cell growth control and organ development, such as the auxin-TOR signaling pathway, also influence the plant immune response against pathogens. As a consequence, distinct pathogens employ an array of effector molecules including tRNA fragments to target such regulatory pathways to exploit the plant's translational capacity, gain access to nutrients and evade defenses. An example includes the RNA polymerase III repressor MAF1, a conserved component of the TOR signaling pathway that controls ribosome biogenesis and tRNA synthesis required for plant growth and which is targeted by a pathogen effector molecule to promote disease. This article is part of a Special Issue entitled: SI: Regulation of tRNA synthesis and modification in physiological conditions and disease edited by Dr. Boguta Magdalena.
Collapse
Affiliation(s)
- Adriana Santos Soprano
- Brazilian Nacional Biosciences Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 13083-100 Campinas, SP, Brazil
| | - Juliana Helena Costa Smetana
- Brazilian Nacional Biosciences Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 13083-100 Campinas, SP, Brazil
| | - Celso Eduardo Benedetti
- Brazilian Nacional Biosciences Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 13083-100 Campinas, SP, Brazil.
| |
Collapse
|
20
|
Characterization of tRNALeu binding interactions with Cu2+ and Pb2+ and their biological implications. J Inorg Biochem 2017; 171:90-99. [DOI: 10.1016/j.jinorgbio.2017.03.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 02/12/2017] [Accepted: 03/19/2017] [Indexed: 11/17/2022]
|
21
|
Structural characterization of human aminoacyl-tRNA synthetases for translational and nontranslational functions. Methods 2017; 113:83-90. [DOI: 10.1016/j.ymeth.2016.11.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Revised: 11/14/2016] [Accepted: 11/21/2016] [Indexed: 11/18/2022] Open
|
22
|
Structural characterization of antibiotic self-immunity tRNA synthetase in plant tumour biocontrol agent. Nat Commun 2016; 7:12928. [PMID: 27713402 PMCID: PMC5059758 DOI: 10.1038/ncomms12928] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 08/16/2016] [Indexed: 01/08/2023] Open
Abstract
Antibiotic-producing microbes evolved self-resistance mechanisms to avoid suicide. The biocontrol Agrobacterium radiobacter K84 secretes the Trojan Horse antibiotic agrocin 84 that is selectively transported into the plant pathogen A. tumefaciens and processed into the toxin TM84. We previously showed that TM84 employs a unique tRNA-dependent mechanism to inhibit leucyl-tRNA synthetase (LeuRS), while the TM84-producer prevents self-poisoning by expressing a resistant LeuRS AgnB2. We now identify a mechanism by which the antibiotic-producing microbe resists its own toxin. Using a combination of structural, biochemical and biophysical approaches, we show that AgnB2 evolved structural changes so as to resist the antibiotic by eliminating the tRNA-dependence of TM84 binding. Mutagenesis of key resistance determinants results in mutants adopting an antibiotic-sensitive phenotype. This study illuminates the evolution of resistance in self-immunity genes and provides mechanistic insights into a fascinating tRNA-dependent antibiotic with applications for the development of anti-infectives and the prevention of biocontrol emasculation.
The bacterium Agrobacterium radiobacter K84 secretes an antibiotic that is transported into the plant pathogen A. tumefaciens and processed into the toxin TM84. Here, the authors identify a mechanism whereby the antibiotic-producing microbe resists its own toxin.
Collapse
|
23
|
Aleksandrov A, Palencia A, Cusack S, Field M. Aminoacetylation Reaction Catalyzed by Leucyl-tRNA Synthetase Operates via a Self-Assisted Mechanism Using a Conserved Residue and the Aminoacyl Substrate. J Phys Chem B 2016; 120:4388-98. [PMID: 27115861 DOI: 10.1021/acs.jpcb.6b02387] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Leucyl-tRNA synthetase catalyzes attachment of leucine amino acid to its cognate tRNA. During the second, aminoacetylation, step of the reaction, the leucyl moiety is transferred from leucyl-adenylate to the terminal A76 adenosine of tRNA. In this work, we have investigated the aminoacetylation step catalyzed by leucyl-tRNA synthase, using ab initio quantum chemical/molecular mechanical hybrid potentials in conjunction with reaction-path-location algorithms and molecular dynamics free energy simulations. We have modeled reaction mechanisms arising from both crystallographic studies and computational work. We invoke various groups as potential proton acceptors-namely, the phosphate and leucyl amino groups of leucyl-adenylate, the A76 base of tRNA, and the Asp80 and Glu532 residues of the protein-and consider both metal-assisted and metal-free reactions. Free energy calculations indicate that both the phosphate group of leucyl adenylate and Glu532 are not strong bases. This agrees with the results of the quantum chemical/molecular mechanical reaction path calculations which give high free energy barriers for the studied pathways involving these groups. A self-assisted mechanism with the leucyl amino group and Asp80 as proton acceptors is the most likely. Furthermore, in this mechanism the presence of a metal ion coordinated by the phosphate group and Glu532 strongly activates the reaction.
Collapse
Affiliation(s)
- Alexey Aleksandrov
- Laboratoire de Biochimie, UMR 7654, Ecole Polytechnique, CNRS , F-91128 Palaiseau Cedex, France
| | - Andrés Palencia
- European Molecular Biology Laboratory (EMBL), Grenoble Outstation and Unit of Virus Host-Cell Interactions, University of Grenoble-EMBL-CNRS , 38044 Grenoble, France
| | - Stephen Cusack
- European Molecular Biology Laboratory (EMBL), Grenoble Outstation and Unit of Virus Host-Cell Interactions, University of Grenoble-EMBL-CNRS , 38044 Grenoble, France
| | - Martin Field
- Dynamo Team, DYNAMOP Group, UMR 5075, Université Grenoble 1, CNRS, CEA, Institut de Biologie Structurale , 71 Avenue des Martyrs, CS 10090, 38044 Grenoble Cedex 9, France
| |
Collapse
|
24
|
Abstract
Aminoacyl-tRNA synthetases (aaRSs) are modular enzymes globally conserved in the three kingdoms of life. All catalyze the same two-step reaction, i.e., the attachment of a proteinogenic amino acid on their cognate tRNAs, thereby mediating the correct expression of the genetic code. In addition, some aaRSs acquired other functions beyond this key role in translation. Genomics and X-ray crystallography have revealed great structural diversity in aaRSs (e.g., in oligomery and modularity, in ranking into two distinct groups each subdivided in 3 subgroups, by additional domains appended on the catalytic modules). AaRSs show huge structural plasticity related to function and limited idiosyncrasies that are kingdom or even species specific (e.g., the presence in many Bacteria of non discriminating aaRSs compensating for the absence of one or two specific aaRSs, notably AsnRS and/or GlnRS). Diversity, as well, occurs in the mechanisms of aaRS gene regulation that are not conserved in evolution, notably between distant groups such as Gram-positive and Gram-negative Bacteria. The review focuses on bacterial aaRSs (and their paralogs) and covers their structure, function, regulation, and evolution. Structure/function relationships are emphasized, notably the enzymology of tRNA aminoacylation and the editing mechanisms for correction of activation and charging errors. The huge amount of genomic and structural data that accumulated in last two decades is reviewed, showing how the field moved from essentially reductionist biology towards more global and integrated approaches. Likewise, the alternative functions of aaRSs and those of aaRS paralogs (e.g., during cell wall biogenesis and other metabolic processes in or outside protein synthesis) are reviewed. Since aaRS phylogenies present promiscuous bacterial, archaeal, and eukaryal features, similarities and differences in the properties of aaRSs from the three kingdoms of life are pinpointed throughout the review and distinctive characteristics of bacterium-like synthetases from organelles are outlined.
Collapse
Affiliation(s)
- Richard Giegé
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, 67084 Strasbourg, France
| | - Mathias Springer
- Université Paris Diderot, Sorbonne Cité, UPR9073 CNRS, IBPC, 75005 Paris, France
| |
Collapse
|
25
|
Fang P, Guo M. Evolutionary Limitation and Opportunities for Developing tRNA Synthetase Inhibitors with 5-Binding-Mode Classification. Life (Basel) 2015; 5:1703-25. [PMID: 26670257 PMCID: PMC4695845 DOI: 10.3390/life5041703] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2015] [Revised: 11/24/2015] [Accepted: 11/25/2015] [Indexed: 12/30/2022] Open
Abstract
Aminoacyl-tRNA synthetases (aaRSs) are enzymes that catalyze the transfer of amino acids to their cognate tRNAs as building blocks for translation. Each of the aaRS families plays a pivotal role in protein biosynthesis and is indispensable for cell growth and survival. In addition, aaRSs in higher species have evolved important non-translational functions. These translational and non-translational functions of aaRS are attractive for developing antibacterial, antifungal, and antiparasitic agents and for treating other human diseases. The interplay between amino acids, tRNA, ATP, EF-Tu and non-canonical binding partners, had shaped each family with distinct pattern of key sites for regulation, with characters varying among species across the path of evolution. These sporadic variations in the aaRSs offer great opportunity to target these essential enzymes for therapy. Up to this day, growing numbers of aaRS inhibitors have been discovered and developed. Here, we summarize the latest developments and structural studies of aaRS inhibitors, and classify them with distinct binding modes into five categories.
Collapse
Affiliation(s)
- Pengfei Fang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China.
- Department of Cancer Biology, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA.
| | - Min Guo
- Department of Cancer Biology, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA.
| |
Collapse
|
26
|
Ornithine Transcarbamylase ArgK Plays a Dual role for the Self-defense of Phaseolotoxin Producing Pseudomonas syringae pv. phaseolicola. Sci Rep 2015; 5:12892. [PMID: 26256666 PMCID: PMC4530439 DOI: 10.1038/srep12892] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 07/14/2015] [Indexed: 12/19/2022] Open
Abstract
Pseudomonas syringae is a phytopathogenic bacterium widely spread on terrestrial plants. Sulfodiaminophosphinyl tripeptide Phaseolotoxins (PHTs), produced by P. syringae pv. phaseolicola and P. syringae pv. actinidiae, represent a kind of antimetabolic phytotoxins. PHTs inhibit host cell Ornithine transcarbamylase (OTCase) activity and induce Arginine auxotrophic phenotype. The biosynthesis of PHT is temperature dependent, being optically produced at around 18 °C, while blocked above 28 °C. PHT resistant OTCase ArgK acts as a functional replacement of housekeeping OTCase ArgF, which is the acting target of PHT, to confer PHT producers with self-resistance. It was postulated that argK might be regulated directly by a PHT biosynthetic precursor and indirectly by temperature with an unknown manner. Neither transcriptional regulator nor thermal regulation related protein encoding gene was detected from PHT biosynthetic gene cluster. The tripeptide, Cit-Ala-hArg, was identified to be a by-product of PHT biosynthetic pathway in this report. Formation of Cit-Ala-hArg was catalyzed by ArgK with tripeptide Orn-Ala-hArg and carbamyl phosphate as substrates. It showed that ArgK not only provided alternative Arginine source as reported previously, but also controlled the production of PHTs by converting PHT biosynthetic precursors to nontoxic Cit-Ala-hArg reservoir for producers’ self-defense.
Collapse
|
27
|
El Sahili A, Li SZ, Lang J, Virus C, Planamente S, Ahmar M, Guimaraes BG, Aumont-Nicaise M, Vigouroux A, Soulère L, Reader J, Queneau Y, Faure D, Moréra S. A Pyranose-2-Phosphate Motif Is Responsible for Both Antibiotic Import and Quorum-Sensing Regulation in Agrobacterium tumefaciens. PLoS Pathog 2015; 11:e1005071. [PMID: 26244338 PMCID: PMC4526662 DOI: 10.1371/journal.ppat.1005071] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 07/06/2015] [Indexed: 11/18/2022] Open
Abstract
Periplasmic binding proteins (PBPs) in association with ABC transporters select and import a wide variety of ligands into bacterial cytoplasm. They can also take up toxic molecules, as observed in the case of the phytopathogen Agrobacterium tumefaciens strain C58. This organism contains a PBP called AccA that mediates the import of the antibiotic agrocin 84, as well as the opine agrocinopine A that acts as both a nutrient and a signalling molecule for the dissemination of virulence genes through quorum-sensing. Here, we characterized the binding mode of AccA using purified agrocin 84 and synthetic agrocinopine A by X-ray crystallography at very high resolution and performed affinity measurements. Structural and affinity analyses revealed that AccA recognizes an uncommon and specific motif, a pyranose-2-phosphate moiety which is present in both imported molecules via the L-arabinopyranose moiety in agrocinopine A and the D-glucopyranose moiety in agrocin 84. We hypothesized that AccA is a gateway allowing the import of any compound possessing a pyranose-2-phosphate motif at one end. This was structurally and functionally confirmed by experiments using four synthetic compounds: agrocinopine 3'-O-benzoate, L-arabinose-2-isopropylphosphate, L-arabinose-2-phosphate and D-glucose-2-phosphate. By combining affinity measurements and in vivo assays, we demonstrated that both L-arabinose-2-phosphate and D-glucose-2-phosphate, which are the AccF mediated degradation products of agrocinopine A and agrocin 84 respectively, interact with the master transcriptional regulator AccR and activate the quorum-sensing signal synthesis and Ti plasmid transfer in A. tumefaciens C58. Our findings shed light on the role of agrocinopine and antibiotic agrocin 84 on quorum-sensing regulation in A. tumefaciens and reveal how the PBP AccA acts as vehicle for the importation of both molecules by means of a key-recognition motif. It also opens future possibilities for the rational design of antibiotic and anti-virulence compounds against A. tumefaciens or other pathogens possessing similar PBPs.
Collapse
Affiliation(s)
- Abbas El Sahili
- Institute for Integrative Biology of the Cell (I2BC), Department of Biophysics, Biochemistry and Structural Biology, CNRS CEA University Paris-Sud, Gif-sur-Yvette, France
- Institute for Integrative Biology of the Cell (I2BC), Department of Microbiology, CNRS CEA University Paris-Sud, Gif-sur-Yvette, France
| | - Si-Zhe Li
- Institut de Chimie et de Biochimie Moléculaires et Supramoléculaires, ICBMS, Université de Lyon, INSA Lyon, UMR 5246, CNRS, Université Lyon 1, INSA Lyon, CPE-Lyon, Bât J. Verne, Villeurbanne, France
| | - Julien Lang
- Institute for Integrative Biology of the Cell (I2BC), Department of Microbiology, CNRS CEA University Paris-Sud, Gif-sur-Yvette, France
| | - Cornelia Virus
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Sara Planamente
- Institute for Integrative Biology of the Cell (I2BC), Department of Biophysics, Biochemistry and Structural Biology, CNRS CEA University Paris-Sud, Gif-sur-Yvette, France
- Institute for Integrative Biology of the Cell (I2BC), Department of Microbiology, CNRS CEA University Paris-Sud, Gif-sur-Yvette, France
| | - Mohammed Ahmar
- Institut de Chimie et de Biochimie Moléculaires et Supramoléculaires, ICBMS, Université de Lyon, INSA Lyon, UMR 5246, CNRS, Université Lyon 1, INSA Lyon, CPE-Lyon, Bât J. Verne, Villeurbanne, France
| | | | - Magali Aumont-Nicaise
- Institute for Integrative Biology of the Cell (I2BC), Protein-Protein Interaction Platform, CNRS CEA University Paris-Sud, Orsay, France
| | - Armelle Vigouroux
- Institute for Integrative Biology of the Cell (I2BC), Department of Biophysics, Biochemistry and Structural Biology, CNRS CEA University Paris-Sud, Gif-sur-Yvette, France
| | - Laurent Soulère
- Institut de Chimie et de Biochimie Moléculaires et Supramoléculaires, ICBMS, Université de Lyon, INSA Lyon, UMR 5246, CNRS, Université Lyon 1, INSA Lyon, CPE-Lyon, Bât J. Verne, Villeurbanne, France
| | - John Reader
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Yves Queneau
- Institut de Chimie et de Biochimie Moléculaires et Supramoléculaires, ICBMS, Université de Lyon, INSA Lyon, UMR 5246, CNRS, Université Lyon 1, INSA Lyon, CPE-Lyon, Bât J. Verne, Villeurbanne, France
- * E-mail: (YQ); (DF); (SM)
| | - Denis Faure
- Institute for Integrative Biology of the Cell (I2BC), Department of Microbiology, CNRS CEA University Paris-Sud, Gif-sur-Yvette, France
- * E-mail: (YQ); (DF); (SM)
| | - Solange Moréra
- Institute for Integrative Biology of the Cell (I2BC), Department of Biophysics, Biochemistry and Structural Biology, CNRS CEA University Paris-Sud, Gif-sur-Yvette, France
- * E-mail: (YQ); (DF); (SM)
| |
Collapse
|
28
|
Koh CY, Kallur Siddaramaiah L, Ranade RM, Nguyen J, Jian T, Zhang Z, Gillespie JR, Buckner FS, Verlinde CLMJ, Fan E, Hol WGJ. A binding hotspot in Trypanosoma cruzi histidyl-tRNA synthetase revealed by fragment-based crystallographic cocktail screens. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:1684-98. [PMID: 26249349 PMCID: PMC4528801 DOI: 10.1107/s1399004715007683] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 04/18/2015] [Indexed: 01/04/2023]
Abstract
American trypanosomiasis, commonly known as Chagas disease, is a neglected tropical disease caused by the protozoan parasite Trypanosoma cruzi. The chronic form of the infection often causes debilitating morbidity and mortality. However, the current treatment for the disease is typically inadequate owing to drug toxicity and poor efficacy, necessitating a continual effort to discover and develop new antiparasitic therapeutic agents. The structure of T. cruzi histidyl-tRNA synthetase (HisRS), a validated drug target, has previously been reported. Based on this structure and those of human cytosolic HisRS, opportunities for the development of specific inhibitors were identified. Here, efforts are reported to identify small molecules that bind to T. cruzi HisRS through fragment-based crystallographic screening in order to arrive at chemical starting points for the development of specific inhibitors. T. cruzi HisRS was soaked into 68 different cocktails from the Medical Structural Genomics of Pathogenic Protozoa (MSGPP) fragment library and diffraction data were collected to identify bound fragments after soaking. A total of 15 fragments were identified, all bound to the same site on the protein, revealing a fragment-binding hotspot adjacent to the ATP-binding pocket. On the basis of the initial hits, the design of reactive fragments targeting the hotspot which would be simultaneously covalently linked to a cysteine residue present only in trypanosomatid HisRS was initiated. Inhibition of T. cruzi HisRS was observed with the resultant reactive fragments and the anticipated binding mode was confirmed crystallographically. These results form a platform for the development of future generations of selective inhibitors for trypanosomatid HisRS.
Collapse
Affiliation(s)
- Cho Yeow Koh
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | | | - Ranae M. Ranade
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Jasmine Nguyen
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Tengyue Jian
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Zhongsheng Zhang
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | | | | | | | - Erkang Fan
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Wim G. J. Hol
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| |
Collapse
|
29
|
Mousa WK, Raizada MN. Biodiversity of genes encoding anti-microbial traits within plant associated microbes. FRONTIERS IN PLANT SCIENCE 2015; 6:231. [PMID: 25914708 PMCID: PMC4392301 DOI: 10.3389/fpls.2015.00231] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 03/23/2015] [Indexed: 05/10/2023]
Abstract
The plant is an attractive versatile home for diverse associated microbes. A subset of these microbes produces a diversity of anti-microbial natural products including polyketides, non-ribosomal peptides, terpenoids, heterocylic nitrogenous compounds, volatile compounds, bacteriocins, and lytic enzymes. In recent years, detailed molecular analysis has led to a better understanding of the underlying genetic mechanisms. New genomic and bioinformatic tools have permitted comparisons of orthologous genes between species, leading to predictions of the associated evolutionary mechanisms responsible for diversification at the genetic and corresponding biochemical levels. The purpose of this review is to describe the biodiversity of biosynthetic genes of plant-associated bacteria and fungi that encode selected examples of antimicrobial natural products. For each compound, the target pathogen and biochemical mode of action are described, in order to draw attention to the complexity of these phenomena. We review recent information of the underlying molecular diversity and draw lessons through comparative genomic analysis of the orthologous coding sequences (CDS). We conclude by discussing emerging themes and gaps, discuss the metabolic pathways in the context of the phylogeny and ecology of their microbial hosts, and discuss potential evolutionary mechanisms that led to the diversification of biosynthetic gene clusters.
Collapse
Affiliation(s)
- Walaa K. Mousa
- Department of Plant Agriculture, University of GuelphGuelph, ON, Canada
- Department of Pharmacognosy, Faculty of Pharmacy, Mansoura UniversityMansoura, Egypt
| | - Manish N. Raizada
- Department of Plant Agriculture, University of GuelphGuelph, ON, Canada
| |
Collapse
|
30
|
Abstract
Transfer RNAs (tRNAs) are central players in the protein translation machinery and as such are prominent targets for a large number of natural and synthetic antibiotics. This review focuses on the role of tRNAs in bacterial antibiosis. We will discuss examples of antibiotics that target multiple stages in tRNA biology from tRNA biogenesis and modification, mature tRNAs, aminoacylation of tRNA as well as prevention of proper tRNA function by small molecules binding to the ribosome. Finally, the role of deacylated tRNAs in the bacterial “stringent response” mechanism that can lead to bacteria displaying antibiotic persistence phenotypes will be discussed.
Collapse
|
31
|
Identification of borrelidin binding site on threonyl-tRNA synthetase. Biochem Biophys Res Commun 2014; 451:485-90. [PMID: 25128830 DOI: 10.1016/j.bbrc.2014.07.100] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 07/22/2014] [Indexed: 01/06/2023]
Abstract
Borrelidin exhibits a wide spectrum of biological activities and has been considered as a non-competitive inhibitor of threonyl-tRNA synthetase (ThrRS). However, the detailed mechanisms of borrelidin against ThrRS, especially borrelidin binding site on ThrRS, are still unclear, which limits the development of novel borrelidin derivatives and rational design of structure-based ThrRS inhibitors. In this study, the binding site of borrelidin on Escherichia coli ThrRS was predicted by molecular docking. To validate our speculations, the ThrRS mutants of E. coli (P424K, E458Δ, and G459Δ) were constructed and their sensitivity to borrelidin was compared to that of the wild-type ThrRS by enzyme kinetics and stopped-flow fluorescence analysis. The docking results showed that borrelidin binds the pocket outside but adjacent to the active site of ThrRS, consisting of residue Y313, R363, R375, P424, E458, G459, and K465. Site-directed mutagenesis results showed that sensitivities of P424K, E458Δ, and G459Δ ThrRSs to borrelidin were reduced markedly. All the results showed that residue Y313, P424, E458, and G459 play vital roles in the binding of borrelidin to ThrRS. It indicated that borrelidin may induce the cleft closure, which blocks the release of Thr-AMP and PPi, to inhibit activity of ThrRS rather than inhibit the binding of ATP and threonine. This study provides new insight into inhibitory mechanisms of borrelidin against ThrRS.
Collapse
|
32
|
In silico discovery of aminoacyl-tRNA synthetase inhibitors. Int J Mol Sci 2014; 15:1358-73. [PMID: 24447926 PMCID: PMC3907873 DOI: 10.3390/ijms15011358] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Revised: 01/02/2014] [Accepted: 01/07/2014] [Indexed: 11/17/2022] Open
Abstract
Aminoacyl-tRNA synthetases (aaRSs) are enzymes that catalyze the transfer of amino acids to their cognate tRNA. They play a pivotal role in protein synthesis and are essential for cell growth and survival. The aaRSs are one of the leading targets for development of antibiotic agents. In this review, we mainly focused on aaRS inhibitor discovery and development using in silico methods including virtual screening and structure-based drug design. These computational methods are relatively fast and cheap, and are proving to be of great benefit for the rational development of more potent aaRS inhibitors and other pharmaceutical agents that may usher in a much needed generation of new antibiotics.
Collapse
|
33
|
Agarwal V, Vondenhoff G, Gadakh B, Severinov K, Van Aerschot A, Nair SK. Exploring the substrate promiscuity of an antibiotic inactivating enzyme. MEDCHEMCOMM 2014. [DOI: 10.1039/c4md00204k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Peptide–nucleotide conjugates have been extensively studied as scaffolds for the development of new antibiotics.
Collapse
Affiliation(s)
- Vinayak Agarwal
- Center for Biophysics and Computational Biology and Institute for Genomic Biology
- University of Illinois at Urbana Champaign
- USA
| | - Gaston Vondenhoff
- Rega Institute for Medical Research, Medicinal Chemistry
- KU Leuven
- Belgium
| | - Bharat Gadakh
- Rega Institute for Medical Research, Medicinal Chemistry
- KU Leuven
- Belgium
| | - Konstantin Severinov
- Saint Petersburg State Polytechnical University
- St. Petersburg, Russia
- Institute of Molecular Genetics
- Russian Academy of Sciences
- Moscow, Russia
| | | | - Satish K. Nair
- Center for Biophysics and Computational Biology and Institute for Genomic Biology
- University of Illinois at Urbana Champaign
- USA
| |
Collapse
|
34
|
Tarkowski P, Vereecke D. Threats and opportunities of plant pathogenic bacteria. Biotechnol Adv 2013; 32:215-29. [PMID: 24216222 DOI: 10.1016/j.biotechadv.2013.11.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Revised: 10/22/2013] [Accepted: 11/03/2013] [Indexed: 02/08/2023]
Abstract
Plant pathogenic bacteria can have devastating effects on plant productivity and yield. Nevertheless, because these often soil-dwelling bacteria have evolved to interact with eukaryotes, they generally exhibit a strong adaptivity, a versatile metabolism, and ingenious mechanisms tailored to modify the development of their hosts. Consequently, besides being a threat for agricultural practices, phytopathogens may also represent opportunities for plant production or be useful for specific biotechnological applications. Here, we illustrate this idea by reviewing the pathogenic strategies and the (potential) uses of five very different (hemi)biotrophic plant pathogenic bacteria: Agrobacterium tumefaciens, A. rhizogenes, Rhodococcus fascians, scab-inducing Streptomyces spp., and Pseudomonas syringae.
Collapse
Affiliation(s)
- Petr Tarkowski
- Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 11, CZ-78371 Olomouc, Czech Republic.
| | - Danny Vereecke
- Department of Applied Biosciences, Faculty of Bioscience Engineering, Ghent University, Valentin Vaerwyckweg 1, BE-9000 Ghent, Belgium.
| |
Collapse
|
35
|
Li L, Carter CW. Full implementation of the genetic code by tryptophanyl-tRNA synthetase requires intermodular coupling. J Biol Chem 2013; 288:34736-45. [PMID: 24142809 DOI: 10.1074/jbc.m113.510958] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Tryptophanyl-tRNA Synthetase (TrpRS) Urzyme (fragments A and C), a 130-residue construct containing only secondary structures positioning the HIGH and KMSKS active site signatures and the specificity helix, accelerates tRNA(Trp) aminoacylation with ∼10-fold specificity toward tryptophan, relative to structurally related tyrosine. We proposed that including the 76-residue connecting peptide 1 insertion (Fragment B) might enhance tryptophan affinity and hence amino acid specificity, because that subdomain constrains the orientation of the specificity helix. We test that hypothesis by characterizing two new constructs: the catalytic domain (fragments A-C) and the Urzyme supplemented with the anticodon-binding domain (fragments A, C, and D). The three constructs, together with the full-length enzyme (fragments A-D), comprise a factorial experiment from which we deduce individual and combined contributions of the two modules to the steady-state kinetics parameters for tryptophan-dependent (32)PPi exchange, specificity for tryptophan versus tyrosine, and aminoacylation of tRNA(Trp). Factorial design directly measures the energetic coupling between the two more recent modules in the contemporary enzyme and demonstrates its functionality. Combining the TrpRS Urzyme individually in cis with each module affords an analysis of long term evolution of amino acid specificity and tRNA aminoacylation, both essential for expanding the genetic code. Either module significantly enhances tryptophan activation but unexpectedly eliminates amino acid specificity for tryptophan, relative to tyrosine, and significantly reduces tRNA aminoacylation. Exclusive dependence of both enhanced functionalities of full-length TrpRS on interdomain coupling energies between the two new modules argues that independent recruitment of connecting peptide 1 and the anticodon-binding domain during evolutionary development of Urzymes would have entailed significant losses of fitness.
Collapse
Affiliation(s)
- Li Li
- From the Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7260
| | | |
Collapse
|
36
|
Dewan V, Reader J, Forsyth KM. Role of aminoacyl-tRNA synthetases in infectious diseases and targets for therapeutic development. Top Curr Chem (Cham) 2013; 344:293-329. [PMID: 23666077 DOI: 10.1007/128_2013_425] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Aminoacyl-tRNA synthetases (AARSs) play a pivotal role in protein synthesis and cell viability. These 22 "housekeeping" enzymes (1 for each standard amino acid plus pyrrolysine and o-phosphoserine) are specifically involved in recognizing and aminoacylating their cognate tRNAs in the cellular pool with the correct amino acid prior to delivery of the charged tRNA to the protein synthesis machinery. Besides serving this canonical function, higher eukaryotic AARSs, some of which are organized in the cytoplasm as a multisynthetase complex of nine enzymes plus additional cellular factors, have also been implicated in a variety of non-canonical roles. AARSs are involved in the regulation of transcription, translation, and various signaling pathways, thereby ensuring cell survival. Based in part on their versatility, AARSs have been recruited by viruses to perform essential functions. For example, host synthetases are packaged into some retroviruses and are required for their replication. Other viruses mimic tRNA-like structures in their genomes, and these motifs are aminoacylated by the host synthetase as part of the viral replication cycle. More recently, it has been shown that certain large DNA viruses infecting animals and other diverse unicellular eukaryotes encode tRNAs, AARSs, and additional components of the protein-synthesis machinery. This chapter will review our current understanding of the role of host AARSs and tRNA-like structures in viruses and discuss their potential as anti-viral drug targets. The identification and development of compounds that target bacterial AARSs, thereby serving as novel antibiotics, will also be discussed. Particular attention will be given to recent work on a number of tRNA-dependent AARS inhibitors and to advances in a new class of natural "pro-drug" antibiotics called Trojan Horse inhibitors. Finally, we will explore how bacteria that naturally produce AARS-targeting antibiotics must protect themselves against cell suicide using naturally antibiotic resistant AARSs, and how horizontal gene transfer of these AARS genes to pathogens may threaten the future use of this class of antibiotics.
Collapse
Affiliation(s)
- Varun Dewan
- Department of Chemistry and Biochemistry, Ohio State Biochemistry Program, Center for RNA Biology, and Center for Retroviral Research, The Ohio State University, Columbus, OH, 43210, USA
| | | | | |
Collapse
|