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Ballut L, Violot S, Kumar S, Aghajari N, Balaram H. GMP Synthetase: Allostery, Structure, and Function. Biomolecules 2023; 13:1379. [PMID: 37759779 PMCID: PMC10526850 DOI: 10.3390/biom13091379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 09/05/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
Glutamine amidotransferases (GATs) catalyze the hydrolysis of glutamine and transfer the generated ammonia to diverse metabolites. The two catalytic activities, glutaminolysis and the subsequent amination of the acceptor substrate, happen in two distinct catalytic pockets connected by a channel that facilitates the movement of ammonia. The de novo pathway for the synthesis of guanosine monophosphate (GMP) from xanthosine monophosphate (XMP) is enabled by the GAT GMP synthetase (GMPS). In most available crystal structures of GATs, the ammonia channel is evident in their native state or upon ligand binding, providing molecular details of the conduit. In addition, conformational changes that enable the coordination of the two catalytic chemistries are also informed by the available structures. In contrast, despite the first structure of a GMPS being published in 1996, the understanding of catalysis in the acceptor domain and inter-domain crosstalk became possible only after the structure of a glutamine-bound mutant of Plasmodium falciparum GMPS was determined. In this review, we present the current status of our understanding of the molecular basis of catalysis in GMPS, becoming the first comprehensive assessment of the biochemical function of this intriguing enzyme.
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Affiliation(s)
- Lionel Ballut
- Molecular Microbiology and Structural Biochemistry, CNRS, University of Lyon1, UMR5086, 7 Passage du Vercors, CEDEX 07, F-69367 Lyon, France; (L.B.); (S.V.)
| | - Sébastien Violot
- Molecular Microbiology and Structural Biochemistry, CNRS, University of Lyon1, UMR5086, 7 Passage du Vercors, CEDEX 07, F-69367 Lyon, France; (L.B.); (S.V.)
| | - Sanjeev Kumar
- Trivedi School of Biosciences, Ashoka University, Rajiv Gandhi Education City, Sonipat 131029, Haryana, India;
| | - Nushin Aghajari
- Molecular Microbiology and Structural Biochemistry, CNRS, University of Lyon1, UMR5086, 7 Passage du Vercors, CEDEX 07, F-69367 Lyon, France; (L.B.); (S.V.)
| | - Hemalatha Balaram
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur 560064, Bangalore, India
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Biology of Two-Spotted Spider Mite ( Tetranychus urticae): Ultrastructure, Photosynthesis, Guanine Transcriptomics, Carotenoids and Chlorophylls Metabolism, and Decoyinine as a Potential Acaricide. Int J Mol Sci 2023; 24:ijms24021715. [PMID: 36675229 PMCID: PMC9864819 DOI: 10.3390/ijms24021715] [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: 12/20/2022] [Revised: 01/13/2023] [Accepted: 01/13/2023] [Indexed: 01/17/2023] Open
Abstract
Two-Spotted Spider Mites (TSSMs, Tetranychus urticae Koch 1836 (Acari: Tetranychidae)) is one of the most important pests in many crop plants, and their feeding activity is based on sucking leaf cell contents. The purpose of this study was to evaluate the interaction between TSSMs and their host Lima bean (Phaseolus lunatus) by analyzing the metabolomics of leaf pigments and the transcriptomics of TSSM guanine production. We also used epifluorescence, confocal laser scanning, and transmission electron microscopies to study the morphology and structure of TSSMs and their excreta. Finally, we evaluated the potential photosynthetic ability of TSSMs and the activity and content of Ribulose-1,5-bisphosphate Carboxylase/Oxigenase (RubisCO). We found that TSSMs express several genes involved in guanine production, including Guanosine Monophosphate Synthetase (GMPS) and decoyinine (DCY), a potential inhibitor of GMPS, was found to reduce TSSMs proliferation in infested Lima bean leaves. Despite the presence of intact chloroplasts and chlorophyll in TSSMs, we demonstrate that TSSMs do not retain any photosynthetic activity. Our results show for the first time the transcriptomics of guanine production in TSSMs and provide new insight into the catabolic activity of TSSMs on leaf chlorophyll and carotenoids. Finally, we preliminary demonstrate that DCY has an acaricidal potential against TSSMs.
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Choudhary M, Kumar V, Naik B, Verma A, Saris PEJ, Kumar V, Gupta S. Antifungal metabolites, their novel sources, and targets to combat drug resistance. Front Microbiol 2022; 13:1061603. [PMID: 36532457 PMCID: PMC9755354 DOI: 10.3389/fmicb.2022.1061603] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 11/08/2022] [Indexed: 09/29/2023] Open
Abstract
Excessive antibiotic prescriptions as well as their misuse in agriculture are the main causes of antimicrobial resistance which poses a growing threat to public health. It necessitates the search for novel chemicals to combat drug resistance. Since ancient times, naturally occurring medicines have been employed and the enormous variety of bioactive chemicals found in nature has long served as an inspiration for researchers looking for possible therapeutics. Secondary metabolites from microorganisms, particularly those from actinomycetes, have made it incredibly easy to find new molecules. Different actinomycetes species account for more than 70% of naturally generated antibiotics currently used in medicine, and they also produce a variety of secondary metabolites, including pigments, enzymes, and anti-inflammatory compounds. They continue to be a crucial source of fresh chemical diversity and a crucial component of drug discovery. This review summarizes some uncommon sources of antifungal metabolites and highlights the importance of further research on these unusual habitats as a source of novel antimicrobial molecules.
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Affiliation(s)
- Megha Choudhary
- Himalayan School of Biosciences, Swami Rama Himalayan University, Dehradun, India
| | - Vijay Kumar
- Himalayan School of Biosciences, Swami Rama Himalayan University, Dehradun, India
| | - Bindu Naik
- Department of Life Sciences (Food Technology & Nutrition), Graphic Era (Deemed to be University), Dehradun, India
| | - Ankit Verma
- Himalayan School of Biosciences, Swami Rama Himalayan University, Dehradun, India
| | - Per Erik Joakim Saris
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland
| | - Vivek Kumar
- Himalayan School of Biosciences, Swami Rama Himalayan University, Dehradun, India
| | - Sanjay Gupta
- Himalayan School of Biosciences, Swami Rama Himalayan University, Dehradun, India
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Robbins N, Cowen LE. Antifungal discovery. Curr Opin Microbiol 2022; 69:102198. [PMID: 36037637 PMCID: PMC10726697 DOI: 10.1016/j.mib.2022.102198] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 07/29/2022] [Accepted: 08/02/2022] [Indexed: 11/30/2022]
Abstract
Fungi have a profound impact on human health, leading to billions of infections and millions of deaths worldwide each year. Exacerbating the public health burden is the continued emergence of drug-resistant fungal pathogens coupled with a dearth of treatment options to combat serious infections. Despite this health threat, scientific advances in chemistry, genetics, and biochemistry methodologies have enabled novel antifungal compounds to be discovered. Here, we describe current approaches for the discovery and characterization of novel antifungals, focusing on the identification of novel chemical matter and elucidation of the cellular target of bioactive compounds, followed by a review of the most promising emerging therapies in the antifungal-development pipeline.
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Affiliation(s)
- Nicole Robbins
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Leah E Cowen
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
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Robbins N, Cowen LE. Genomic Approaches to Antifungal Drug Target Identification and Validation. Annu Rev Microbiol 2022; 76:369-388. [PMID: 35650665 PMCID: PMC10727914 DOI: 10.1146/annurev-micro-041020-094524] [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] [Indexed: 11/09/2022]
Abstract
The last several decades have witnessed a surge in drug-resistant fungal infections that pose a serious threat to human health. While there is a limited arsenal of drugs that can be used to treat systemic infections, scientific advances have provided renewed optimism for the discovery of novel antifungals. The development of chemical-genomic assays using Saccharomyces cerevisiae has provided powerful methods to identify the mechanism of action of molecules in a living cell. Advances in molecular biology techniques have enabled complementary assays to be developed in fungal pathogens, including Candida albicans and Cryptococcus neoformans. These approaches enable the identification of target genes for drug candidates, as well as genes involved in buffering drug target pathways. Here, we examine yeast chemical-genomic assays and highlight how such resources can be utilized to predict the mechanisms of action of compounds, to study virulence attributes of diverse fungal pathogens, and to bolster the antifungal pipeline.
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Affiliation(s)
- Nicole Robbins
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada;
| | - Leah E Cowen
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada;
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Aron O, Otieno FJ, Tijjani I, Yang Z, Xu H, Weng S, Guo J, Lu S, Wang Z, Tang W. De novo purine nucleotide biosynthesis mediated by MoAde4 is required for conidiation, host colonization and pathogenicity in Magnaporthe oryzae. Appl Microbiol Biotechnol 2022; 106:5587-5602. [PMID: 35918446 DOI: 10.1007/s00253-022-12100-z] [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: 11/11/2021] [Revised: 07/18/2022] [Accepted: 07/21/2022] [Indexed: 11/02/2022]
Abstract
Amidophosphoribosyltransferase catalyzes the conversion of 5-phosphoribosyl-1-pyrophosphate into 5-phosphoribosyl-1-amine in the de novo purine biosynthetic pathway. Herein, we identified and characterized the functions of MoAde4, an orthologue of yeast Ade4 in Magnaporthe oryzae. MoAde4 is a 537-amino acid protein containing GATase_6 and pribosyltran domains. MoADE4 transcripts were highly expressed during the conidiation, early-infection, and late-infection stages of the fungus. Disruption of the MoADE4 gene resulted in ΔMoade4 exhibiting adenine, adenosine, and hypoxanthine auxotrophy on minimal medium. Conidia quantification assays showed that sporulation was significantly reduced in the ΔMoade4 mutant. The conidia of ΔMoade4 could still form appressoria but mostly failed to penetrate the rice cuticle. Pathogenicity tests showed that ΔMoade4 was completely nonpathogenic on rice and barley leaves, which was attributed to restricted infectious hyphal growth within the primary cells. The ΔMoade4 mutant was defective in the induction of strong host immunity. Exogenous adenine partially rescued conidiation, infectious hyphal growth, and the pathogenicity defects of the ΔMoade4 mutant on barley and rice leaves. Taken together, our results demonstrated that purine nucleotide biosynthesis orchestrated by MoAde4 is required for fungal development and pathogenicity in M. oryzae. These findings therefore act as a suitable target for antifungal development against recalcitrant plant fungal pathogens. KEY POINTS: • MoAde4 is crucial for de novo purine nucleotide biosynthesis. • MoAde4 is pivotal for conidiogenesis and appressorium development of M. oryzae. • MoAde4 is involoved in the pathogenicity of M. oryzae.
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Affiliation(s)
- Osakina Aron
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Frankine Jagero Otieno
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ibrahim Tijjani
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zifeng Yang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Huxiao Xu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Shuning Weng
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jiayuan Guo
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Songmao Lu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zonghua Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. .,Marine and Agricultural Biotechnology Laboratory, Institute of Oceanography, Minjiang University, Fuzhou, 350108, China.
| | - Wei Tang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. .,Fujian Key Laboratory for Monitoring and Integrated Management of Crop Pests, Fuzhou, 350013, China.
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Stuart AKDC, Furuie JL, Cataldi TR, Stuart RM, Zawadneak MAC, Labate CA, Pimentel IC. Fungal consortium of two Beauveria bassiana strains increases their virulence, growth, and resistance to stress: A metabolomic approach. PLoS One 2022; 17:e0271460. [PMID: 35834517 PMCID: PMC9282594 DOI: 10.1371/journal.pone.0271460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 06/28/2022] [Indexed: 11/18/2022] Open
Abstract
The use of two or more microorganisms in a microbial consortium has been increasingly applied in the biological control of diseases and pests. Beauveria bassiana is one of the most widely studied fungal species in biological control, yet little is known about its role in fungal consortiums. In a previous study, our group found that a consortium formed by two strains of B. bassiana had significantly greater biocontrol potential against the polyphagous caterpillars Duponchelia fovealis (Lepidoptera: Crambidae) than either strain on its own. In this study, we use GC-MS and LC-MS/MS to evaluate and discuss the metabolomics of the consortium. A total of 21 consortium biomarkers were identified, corresponding to 14 detected by LC-MS/MS and seven by GC-MS. Antioxidant and anti-inflammatory mechanisms are the main properties of the metabolites produced by the consortium. These metabolites can depress the insect’s immune system, increasing its vulnerability and, hence, the fungal virulence of the consortium. In light of these results, we propose an action model of insect mortality due to the metabolites secreted by the consortium. The model includes the inhibition of defense mechanisms such as pro-inflammatory interleukin secretion, cell migration, cell aggregation, Dif, Dorsal and Relish gene transcription, and JAK/STAT and JNK signaling pathways. It also promotes the cleaning of oxidative molecules, like ROS, NOS, and H2O2, and the induction of virulence factors.
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Affiliation(s)
- Andressa Katiski da Costa Stuart
- Departamento de Patologia Básica, Setor de Ciências Biológicas, Laboratório de Microbiologia e Biologia Molecular (LabMicro), Universidade Federal do Paraná, Curitiba, Paraná, Brazil
- * E-mail:
| | - Jason Lee Furuie
- Departamento de Patologia Básica, Setor de Ciências Biológicas, Laboratório de Microbiologia e Biologia Molecular (LabMicro), Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - Thais Regiani Cataldi
- Departamento de Genética, Laboratório de Genética de Plantas Max Feffer, Escola Superior de Agronomia Luiz de Queiroz – Esalq/USP, Piracicaba, São Paulo, Brazil
| | - Rodrigo Makowiecky Stuart
- Departamento de Patologia Básica, Setor de Ciências Biológicas, Laboratório de Microbiologia e Biologia Molecular (LabMicro), Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - Maria Aparecida Cassilha Zawadneak
- Departamento de Patologia Básica, Setor de Ciências Biológicas, Laboratório de Microbiologia e Biologia Molecular (LabMicro), Universidade Federal do Paraná, Curitiba, Paraná, Brazil
- Departamento de Fitotecnia e Fitossanitaríssimo, Programa de Pós-graduação em Agronomia Produção Vegetal, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - Carlos Alberto Labate
- Departamento de Genética, Laboratório de Genética de Plantas Max Feffer, Escola Superior de Agronomia Luiz de Queiroz – Esalq/USP, Piracicaba, São Paulo, Brazil
| | - Ida Chapaval Pimentel
- Departamento de Patologia Básica, Setor de Ciências Biológicas, Laboratório de Microbiologia e Biologia Molecular (LabMicro), Universidade Federal do Paraná, Curitiba, Paraná, Brazil
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Huang F, Abbas F, Fiaz S, Imran M, Yanguo K, Hassan W, Ashraf U, He Y, Cai X, Wang Z, Yu L, Ye X, Chen X. Comprehensive characterization of Guanosine monophosphate synthetase in Nicotiana tabacum. Mol Biol Rep 2022; 49:5265-5272. [PMID: 34689282 DOI: 10.1007/s11033-021-06718-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 09/27/2021] [Indexed: 02/06/2023]
Abstract
BACKGROUND Guanosine monophosphate (GMP) synthetase is an enzyme that converts xanthosine monophosphate to GMP. GMP plays an essential role in plant development and responses to internal and external stimuli. It also plays a crucial role in several plant physiochemical processes, such as stomata closure, cation flux regulation, pathogen responses and chloroplast development. METHODS AND RESULTS The mRNA sequences of NtGMP synthase in tobacco (Nicotiana tabacum) were rapidly amplified from cDNA. The GMP synthase open reading frame contains a 1617 bp sequence encoding 538 amino acids. A sequence analysis showed that this sequence shares high homology with that of Nicotiana sylvestris, Nicotiana attenuata, N. tomentosiformis, Solanum tuberosum, Lycopersicon pennellii, L. esculentum, Capsicum annuum, C. chinense and C. baccatum GMP synthase. A BLAST analysis with a tobacco high-throughput genomic sequence database revealed that the tobacco GMP synthase gene has five introns and six exons. A phylogenetic analysis showed a close genetic evolutionary relationship with N. sylvestris GMP synthase. The tissue-specific expression profile was evaluated using quantitative real-time PCR. The data showed that NtGMP synthase was highly expressed in leaves and moderately expressed in roots, flowers, and stems. The subcellular localization was predicted using the WOLF PSORT webserver, which strongly suggested that it might be localized to the cytoplasm. CONCLUSIONS In the current study, we cloned and comprehensively characterized GMP synthase in tobacco (Nicotiana tabacum). Our results establish a basis for further research to explore the precise role of this enzyme in tobacco.
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Affiliation(s)
- Feiyan Huang
- College of Agriculture and Life Sciences, Yunnan Urban Agricultural Engineering & Technological Research Center, Kunming University, Kunming, China
| | - Farhat Abbas
- The Research Center for Ornamental Plants, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
| | - Sajid Fiaz
- Department of Plant Breeding and Genetics, University of Haripur, Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Imran
- Department of Crop Science and Technology, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Ke Yanguo
- College of Agriculture and Life Sciences, Yunnan Urban Agricultural Engineering & Technological Research Center, Kunming University, Kunming, China.
- College of Economics and Management, Kunming University, Kunming, China.
| | - Waseem Hassan
- Institute of Environment and Sustainable Development in Agricultural, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Umair Ashraf
- Department of Botany, Division of Science and Technology, University of Education Lahore, Punjab, Pakistan
| | - Yuansheng He
- Lincang Tobacco Corporation of Yunnan Province, Kunming, China
| | - Xuanjie Cai
- Material Procurement Center, Shanghai Tobacco Group Co., Ltd, Shanghai, 200082, China
| | - Zhijiang Wang
- Kunming Tobacco Corporation of Yunnan Province, Kunming, 650021, China
| | - Lei Yu
- College of Agriculture and Life Sciences, Yunnan Urban Agricultural Engineering & Technological Research Center, Kunming University, Kunming, China
| | - Xianwen Ye
- Kunming Tobacco Corporation of Yunnan Province, Kunming, 650021, China.
| | - Xiaolong Chen
- Tobacco Leaf Technology Centre, China Tobacco Henan Industrial Co., Ltd, Zhengzhou, 450000, China.
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Nguyen S, Jovcevski B, Pukala TL, Bruning JB. Structural insights into the antifungal drug target guanosine monophosphate synthase from Aspergillus fumigatus. ACTA CRYSTALLOGRAPHICA SECTION D STRUCTURAL BIOLOGY 2022; 78:248-259. [DOI: 10.1107/s2059798321012031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 11/11/2021] [Indexed: 11/10/2022]
Abstract
Purine biosynthesis is a fundamental cellular process that sustains life by maintaining the intracellular pool of purines for DNA/RNA synthesis and signal transduction. As an integral determinant of fungal survival and virulence, the enzymes in this metabolic pathway have been pursued as potential antifungal targets. Guanosine monophosphate (GMP) synthase has been identified as an attractive target as it is essential for virulence in the clinically prominent fungal pathogens Aspergillus fumigatus, Candida albicans and Cryptococcus neoformans. However, a lack of structural information on GMP synthase has hindered drug-design efforts. Here, the first structure of a GMP synthase of fungal origin, that from A. fumigatus (at 2.3 Å resolution), is presented. Structural analysis of GMP synthase shows a distinct absence of the D1 dimerization domain that is present in the human homologue. Interestingly, A. fumigatus GMP synthase adopts a dimeric state, as determined by native mass spectrometry and gel-filtration chromatography, in contrast to the monomeric human homologue. Analysis of the substrate-binding pockets of A. fumigatus GMP synthase reveals key differences in the ATP- and XMP-binding sites that can be exploited for species-specific inhibitor drug design. Furthermore, the inhibitory activities of the glutamine analogues acivicin (IC50 = 16.6 ± 2.4 µM) and 6-diazo-5-oxo-L-norleucine (IC50 = 29.6 ± 5.6 µM) against A. fumigatus GMP synthase are demonstrated. Together, these data provide crucial structural information required for specifically targeting A. fumigatus GMP synthase for future antifungal drug-discovery endeavours.
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Nan J, Zhang S, Zhan P, Jiang L. Discovery of Novel GMPS Inhibitors of Candidatus Liberibacter Asiaticus by Structure Based Design and Enzyme Kinetic. BIOLOGY 2021; 10:biology10070594. [PMID: 34203217 PMCID: PMC8301025 DOI: 10.3390/biology10070594] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/24/2021] [Accepted: 06/25/2021] [Indexed: 12/12/2022]
Abstract
Simple Summary The spread of citrus Huanglongbing caused significant damage to the world’s citrus industry. Thermotherapy and chemical agents were used to control this disease; however, the effectiveness of these treatments is frequently inconsistent. In addition, CLas cannot be cultured in vitro. Therefore, structure-based virtual screening is a novel method to find compounds that work against CLas. This study used CLas GMPS as a target for high-throughput screening and selected some compounds which have a higher binding affinity to test their inhibition of CLas GMPS. Finally, two molecules were identified as the lead compound to control citrus HLB. Abstract Citrus production is facing an unprecedented problem because of huanglongbing (HLB) disease. Presently, no effective HLB-easing method is available when citrus becomes infected. Guanosine 5′-monophosphate synthetase (GMPS) is a key protein in the de novo synthesis of guanine nucleotides. GMPS is used as an attractive target for developing agents that are effective against the patogen infection. In this research, homology modeling, structure-based virtual screening, and molecular docking were used to discover the new inhibitors against CLas GMPS. Enzyme assay showed that folic acid and AZD1152 showed high inhibition at micromole concentrations, with AZD1152 being the most potent molecule. The inhibition constant (Ki) value of folic acid and AZD1152 was 51.98 µM and 4.05 µM, respectively. These results suggested that folic acid and AZD1152 could be considered as promising candidates for the development of CLas agents.
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Affiliation(s)
- Jing Nan
- Ministry of Education Key Laboratory of Plant Biology, Huazhong Agricultural University, Wuhan 430070, China; (J.N.); (P.Z.)
| | - Shaoran Zhang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China;
| | - Ping Zhan
- Ministry of Education Key Laboratory of Plant Biology, Huazhong Agricultural University, Wuhan 430070, China; (J.N.); (P.Z.)
| | - Ling Jiang
- Ministry of Education Key Laboratory of Plant Biology, Huazhong Agricultural University, Wuhan 430070, China; (J.N.); (P.Z.)
- Correspondence:
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Garcia-Ceron D, Dawson CS, Faou P, Bleackley MR, Anderson MA. Size-exclusion chromatography allows the isolation of EVs from the filamentous fungal plant pathogen Fusarium oxysporum f. sp. vasinfectum (Fov). Proteomics 2021; 21:e2000240. [PMID: 33609009 DOI: 10.1002/pmic.202000240] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 02/01/2021] [Accepted: 02/03/2021] [Indexed: 12/11/2022]
Abstract
Extracellular vesicles (EVs) are nano-sized compartments involved in cell communication and macromolecule transport that are well characterized in mammalian organisms. Fungal EVs transport virulence-related cargo and modulate the host immune response, but most work has been focused on human yeast pathogens. Additionally, the study of EVs from filamentous fungi has been hindered by the lack of protein markers and efficient isolation methods. In this study we performed the isolation and proteomic characterization of EVs from the filamentous cotton pathogen Fusarium oxysporum f. sp. vasinfectum (Fov). EVs were recovered from two different growth media, Czapek Dox and Saboraud's dextrose broth, and purified by size-exclusion chromatography. Our results show that the EV proteome changes depending on the growth medium but EV production remains constant. EVs contained proteins involved in polyketide synthesis, cell wall modifications, proteases and potential effectors. These results support a role in modulation of host-pathogen interactions for Fov EVs.
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Affiliation(s)
- Donovan Garcia-Ceron
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, Australia
| | - Charlotte S Dawson
- Cambridge Centre for Proteomics, Department of Biochemistry, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, United Kingdom
| | - Pierre Faou
- La Trobe Comprehensive Proteomics Platform, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, Australia
| | - Mark R Bleackley
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, Australia
| | - Marilyn A Anderson
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, Australia
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Nguyen S, Truong JQ, Bruning JB. Targeting Unconventional Pathways in Pursuit of Novel Antifungals. Front Mol Biosci 2021; 7:621366. [PMID: 33511160 PMCID: PMC7835888 DOI: 10.3389/fmolb.2020.621366] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 12/11/2020] [Indexed: 01/31/2023] Open
Abstract
The impact of invasive fungal infections on human health is a serious, but largely overlooked, public health issue. Commonly affecting the immunocompromised community, fungal infections are predominantly caused by species of Candida, Cryptococcus, and Aspergillus. Treatments are reliant on the aggressive use of pre-existing antifungal drug classes that target the fungal cell wall and membrane. Despite their frequent use, these drugs are subject to unfavorable drug-drug interactions, can cause undesirable side-effects and have compromised efficacy due to the emergence of antifungal resistance. Hence, there is a clear need to develop novel classes of antifungal drugs. A promising approach involves exploiting the metabolic needs of fungi by targeted interruption of essential metabolic pathways. This review highlights potential antifungal targets including enolase, a component of the enolase-plasminogen complex, and enzymes from the mannitol biosynthesis and purine nucleotide biosynthesis pathways. There has been increased interest in the enzymes that comprise these particular pathways and further investigation into their merits as antifungal targets and roles in fungal survival and virulence are warranted. Disruption of these vital processes by targeting unconventional pathways with small molecules or antibodies may serve as a promising approach to discovering novel classes of antifungals.
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Affiliation(s)
- Stephanie Nguyen
- Institute of Photonics and Advanced Sensing (IPAS), School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia
| | - Jia Q Truong
- School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia
| | - John B Bruning
- Institute of Photonics and Advanced Sensing (IPAS), School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia
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13
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Nguyen S, Jovcevski B, Pukala TL, Bruning JB. Nucleoside selectivity of Aspergillus fumigatus nucleoside-diphosphate kinase. FEBS J 2020; 288:2398-2417. [PMID: 33089641 DOI: 10.1111/febs.15607] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 10/06/2020] [Accepted: 10/19/2020] [Indexed: 11/29/2022]
Abstract
Aspergillus fumigatus infections are rising at a disconcerting rate in tandem with antifungal resistance rates. Efforts to develop novel antifungals have been hindered by the limited knowledge of fundamental biological and structural mechanisms of A. fumigatus propagation. Biosynthesis of NTPs, the building blocks of DNA and RNA, is catalysed by NDK. An essential enzyme in A. fumigatus, NDK poses as an attractive target for novel antifungals. NDK exhibits broad substrate specificity across species, using both purines and pyrimidines, but the selectivity of such nucleosides in A. fumigatus NDK is unknown, impeding structure-guided inhibitor design. Structures of NDK in unbound- and NDP-bound states were solved, and NDK activity was assessed in the presence of various NTP substrates. We present the first instance of a unique substrate binding mode adopted by CDP and TDP specific to A. fumigatus NDK that illuminates the structural determinants of selectivity. Analysis of the oligomeric state reveals that A. fumigatus NDK adopts a hexameric assembly in both unbound- and NDP-bound states, contrary to previous reports suggesting it is tetrameric. Kinetic analysis revealed that ATP exhibited the greatest turnover rate (321 ± 33.0 s-1 ), specificity constant (626 ± 110.0 mm-1 ·s-1 ) and binding free energy change (-37.0 ± 3.5 kcal·mol-1 ). Comparatively, cytidine nucleosides displayed the slowest turnover rate (53.1 ± 3.7 s-1 ) and lowest specificity constant (40.2 ± 4.4 mm-1 ·s-1 ). We conclude that NDK exhibits nucleoside selectivity whereby adenine nucleosides are used preferentially compared to cytidine nucleosides, and these insights can be exploited to guide drug design. ENZYMES: Nucleoside-diphosphate kinase (EC 2.7.4.6). DATABASE: Structural data are available in the PDB database under the accession numbers: Unbound-NDK (6XP4), ADP-NDK (6XP7), GDP-NDK (6XPS), IDP-NDK (6XPU), UDP-NDK (6XPT), CDP-NDK (6XPW), TDP-NDK (6XPV).
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Affiliation(s)
- Stephanie Nguyen
- Institute of Photonics and Advanced Sensing (IPAS), School of Biological Sciences, The University of Adelaide, Australia
| | - Blagojce Jovcevski
- Adelaide Proteomics Centre, School of Physical Sciences, The University of Adelaide, Australia.,School of Agriculture, Food and Wine, The University of Adelaide, Australia
| | - Tara L Pukala
- Adelaide Proteomics Centre, School of Physical Sciences, The University of Adelaide, Australia
| | - John B Bruning
- Institute of Photonics and Advanced Sensing (IPAS), School of Biological Sciences, The University of Adelaide, Australia
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Shivakumaraswamy S, Pandey N, Ballut L, Violot S, Aghajari N, Balaram H. Helices on Interdomain Interface Couple Catalysis in the ATPPase Domain with Allostery in Plasmodium falciparum GMP Synthetase. Chembiochem 2020; 21:2805-2817. [PMID: 32358899 DOI: 10.1002/cbic.202000158] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 04/30/2020] [Indexed: 11/07/2022]
Abstract
GMP synthetase catalyses the conversion of XMP to GMP through a series of reactions that include hydrolysis of Gln to generate ammonia in the glutamine amidotransferase (GATase) domain, activation of XMP to adenyl-XMP intermediate in the ATP pyrophosphatase (ATPPase) domain and reaction of ammonia with the intermediate to generate GMP. The functioning of GMP synthetases entails bidirectional domain crosstalk, which leads to allosteric activation of the GATase domain, synchronization of catalytic events and tunnelling of ammonia. Herein, we have taken recourse to the analysis of structures of GMP synthetases, site-directed mutagenesis and steady-state and transient kinetics on the Plasmodium falciparum enzyme to decipher the molecular basis of catalysis in the ATPPase domain and domain crosstalk. Our results suggest an arrangement at the interdomain interface, of helices with residues that play roles in ATPPase catalysis as well as domain crosstalk enabling the coupling of ATPPase catalysis with GATase activation. Overall, the study enhances our understanding of GMP synthetases, which are drug targets in many infectious pathogens.
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Affiliation(s)
- Santosh Shivakumaraswamy
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, Karnataka, 560064, India
| | - Nivedita Pandey
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, Karnataka, 560064, India
| | - Lionel Ballut
- Biocrystallography and Structural Biology of Therapeutic Targets Molecular Microbiology and Structural Biochemistry UMR 5086 CNRS -, University of Lyon 1, 7 passage du Vercors, 69367, Lyon Cedex 07, France
| | - Sébastien Violot
- Biocrystallography and Structural Biology of Therapeutic Targets Molecular Microbiology and Structural Biochemistry UMR 5086 CNRS -, University of Lyon 1, 7 passage du Vercors, 69367, Lyon Cedex 07, France
| | - Nushin Aghajari
- Biocrystallography and Structural Biology of Therapeutic Targets Molecular Microbiology and Structural Biochemistry UMR 5086 CNRS -, University of Lyon 1, 7 passage du Vercors, 69367, Lyon Cedex 07, France
| | - Hemalatha Balaram
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, Karnataka, 560064, India
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15
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Liu ZW, Li H, Liu JX, Wang Y, Zhuang J. Integrative transcriptome, proteome, and microRNA analysis reveals the effects of nitrogen sufficiency and deficiency conditions on theanine metabolism in the tea plant ( Camellia sinensis). HORTICULTURE RESEARCH 2020; 7:65. [PMID: 32377356 PMCID: PMC7192918 DOI: 10.1038/s41438-020-0290-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 02/13/2020] [Accepted: 03/02/2020] [Indexed: 05/18/2023]
Abstract
Nitrogen (N) is associated with amino acid metabolism in higher plants. Theanine is an important amino acid in tea plants. To explore the relationship between theanine metabolism and N conditions, we examined the differentially expressed genes (DEGs), proteins (DEPs), and microRNAs (DEMs) involved in theanine metabolism in tea plant shoots and roots under N sufficiency and deficiency conditions. Transcriptome, proteome, and microRNA analyses were performed on tea plant shoots and roots under N sufficiency and deficiency conditions. The contents of theanine, expression levels of genes involved in theanine metabolism, contents of proteinogenic amino acids, and activity of enzymes were analyzed. The DEP-DEG correlation pairs and negative DEM-DEG interactions related to theanine metabolism were identified based on correlation analyses. The expression profiles of DEGs and negative DEM-DEG pairs related to theanine biosynthesis were consistent with the sequencing results. Our results suggest that the molecular and physiological mechanism of theanine accumulation is significantly affected by N sufficiency and deficiency conditions. The DEGs, DEPs, and DEMs and the activity of the enzymes involved in theanine biosynthesis might play vital roles in theanine accumulation under N sufficiency and deficiency conditions in the shoots and roots of tea plants.
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Affiliation(s)
- Zhi-Wei Liu
- Tea Science Research Institute, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, 210095 Nanjing, China
| | - Hui Li
- Tea Science Research Institute, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, 210095 Nanjing, China
| | - Jie-Xia Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 210095 Nanjing, China
| | - Yu Wang
- Tea Science Research Institute, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, 210095 Nanjing, China
| | - Jing Zhuang
- Tea Science Research Institute, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, 210095 Nanjing, China
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16
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Muthamil S, Prasath KG, Priya A, Precilla P, Pandian SK. Global proteomic analysis deciphers the mechanism of action of plant derived oleic acid against Candida albicans virulence and biofilm formation. Sci Rep 2020; 10:5113. [PMID: 32198447 PMCID: PMC7083969 DOI: 10.1038/s41598-020-61918-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 03/02/2020] [Indexed: 01/04/2023] Open
Abstract
Candida albicans is a commensal fungus in humans, mostly found on the mucosal surfaces of the mouth, gut, vagina and skin. Incidence of ever increasing invasive candidiasis in immunocompromised patients, alarming occurrence of antifungal resistance and insufficient diagnostic methods demand more focused research into C. albicans pathogenicity. Consequently, in the present study, oleic acid from Murraya koenigii was shown to have the efficacy to inhibit biofilm formation and virulence of Candida spp. Results of in vitro virulence assays and gene expression analysis, impelled to study the protein targets which are involved in the molecular pathways of C. albicans pathogenicity. Proteomic studies of differentially expressed proteins reveals that oleic acid induces oxidative stress responses and mainly targets the proteins involved in glucose metabolism, ergosterol biosynthesis, lipase production, iron homeostasis and amino acid biosynthesis. The current study emphasizes anti-virulent potential of oleic acid which can be used as a therapeutic agent to treat Candida infections.
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Affiliation(s)
- Subramanian Muthamil
- Department of Biotechnology Science Campus Alagappa University Karaikudi, 630 003, Tamil Nadu, India
| | - Krishnan Ganesh Prasath
- Department of Biotechnology Science Campus Alagappa University Karaikudi, 630 003, Tamil Nadu, India
| | - Arumugam Priya
- Department of Biotechnology Science Campus Alagappa University Karaikudi, 630 003, Tamil Nadu, India
| | - Pitchai Precilla
- Department of Biotechnology Science Campus Alagappa University Karaikudi, 630 003, Tamil Nadu, India
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17
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Chemogenomic Profiling of the Fungal Pathogen Candida albicans. Antimicrob Agents Chemother 2018; 62:AAC.02365-17. [PMID: 29203491 PMCID: PMC5786791 DOI: 10.1128/aac.02365-17] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 11/30/2017] [Indexed: 12/19/2022] Open
Abstract
There is currently a small number of classes of antifungal drugs, and these drugs are known to target a very limited set of cellular functions. We derived a set of approximately 900 nonessential, transactivator-defective disruption strains from the tetracycline-regulated GRACE collection of strains of the fungal pathogen Candida albicans This strain set was screened against classic antifungal drugs to identify gene inactivations that conferred either enhanced sensitivity or increased resistance to the compounds. We examined two azoles, fluconazole and posaconazole; two echinocandins, caspofungin and anidulafungin; and a polyene, amphotericin B. Overall, the chemogenomic profiles within drug classes were highly similar, but there was little overlap between classes, suggesting that the different drug classes interacted with discrete networks of genes in C. albicans We also tested two pyridine amides, designated GPI-LY7 and GPI-C107; these drugs gave very similar profiles that were distinct from those of the echinocandins, azoles, or polyenes, supporting the idea that they target a distinct cellular function. Intriguingly, in cases where these gene sets can be compared to genetic disruptions conferring drug sensitivity in other fungi, we find very little correspondence in genes. Thus, even though the drug targets are the same in the different species, the specific genetic profiles that can lead to drug sensitivity are distinct. This implies that chemogenomic screens of one organism may be poorly predictive of the profiles found in other organisms and that drug sensitivity and resistance profiles can differ significantly among organisms even when the apparent target of the drug is the same.
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18
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Peng Y, Zhang H, Xu M, Tan MW. A Tet-Off gene expression system for validation of antifungal drug targets in a murine invasive pulmonary aspergillosis model. Sci Rep 2018; 8:443. [PMID: 29323188 PMCID: PMC5765126 DOI: 10.1038/s41598-017-18868-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 12/18/2017] [Indexed: 12/20/2022] Open
Abstract
Aspergillus fumigatus is one of the major causes of invasive pulmonary aspergillosis in immunocompromised patients. Novel antifungal therapy is in urgent need due to emerging resistance and adverse toxicity of current antifungal drugs. Gene products that are essential for Aspergillus viability during infection are attractive drug targets. To characterize these genes in vivo we developed a Tet-Off gene expression system in A. fumigatus, whereby the administration of doxycycline resulted in down regulation of the gene whose expression is under the control of the Tet-Off promoter. We tested the system on two potential drug targets, inosine 5′-monophosphate dehydrogenase (IMPDH) and L-ornithine N5-oxygenase (sidA) in a murine invasive pulmonary aspergillosis model. We show that depletion of IMPDH attenuated but did not completely abolish virulence in vivo whereas turning off the expression of sidA, which is required for iron acquisition, resulted in avirulence. We also investigated whether sidA expression could be controlled in a time-dependent manner in mice. Our results demonstrated that timing of doxycycline administration dramatically affects survival rate, suggesting that this genetic system can be used for testing whether an antifungal drug target is critical for fungal growth post-infection.
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Affiliation(s)
- Yutian Peng
- Infectious Diseases Department, Genentech Inc., South San Francisco, California, 94080, USA.
| | - Hua Zhang
- Translational Immunology Department, Genentech Inc., South San Francisco, California, 94080, USA
| | - Min Xu
- Translational Immunology Department, Genentech Inc., South San Francisco, California, 94080, USA
| | - Man-Wah Tan
- Infectious Diseases Department, Genentech Inc., South San Francisco, California, 94080, USA.
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19
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Cai X, Zhang X, Li X, Liu M, Liu X, Wang X, Zhang H, Zheng X, Zhang Z. The Atypical Guanylate Kinase MoGuk2 Plays Important Roles in Asexual/Sexual Development, Conidial Septation, and Pathogenicity in the Rice Blast Fungus. Front Microbiol 2017; 8:2467. [PMID: 29321770 PMCID: PMC5732230 DOI: 10.3389/fmicb.2017.02467] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 11/28/2017] [Indexed: 01/28/2023] Open
Abstract
Guanylate kinases (GKs), which convert guanosine monophosphate into guanosine diphosphate (GDP), are important for growth and mannose outer chain elongation of cell wall N-linked glycoproteins in yeast. Here, we identified the ortholog of Saccharomyces cerevisiae GK Guk1, named MoGuk1 and a novel family of fungal GKs MoGuk2 in the rice blast fungus Magnaporthe oryzae. MoGuk1 contains 242 aa with an C-terminal GuKc domain that very similar to yeast Guk1. MoGuk2 contains 810 amino acids with a C-terminal GuKc domain and an additional N-terminal efThoc1 domain. Expression of either MoGuk1 or MoGuk2 in heterozygote yeast guk1 mutant could increase its GDP level. To investigate the biological role of MoGuk1 and MoGuk2 in M. oryzae, the gene replacement vectors were constructed. We obtained the ΔMoguk2 but not ΔMoguk1 mutant by screening over 1,000 transformants, indicating MoGuk1 might be essential for M. oryzae. The ΔMoguk2 mutant showed weak reductions in vegetative growth, conidial germination, appressorial formation, and appressorial turgor, and showed significant reductions in sporulation and pathogenicity. Moreover, the ΔMoguk2 mutant failed to produce perithecia and was sensitive to neomycin and a mixture of neomycin-tunicamycin. Exogenous GDP and ATP partially rescued the defects in conidial germination, appressorial formation, and infectious growth of the mutant. Further analysis revealed that intracellular GDP and GTP level was decreased, and GMP level was increased in the mutant, suggesting that MoGuk2 exhibits enzymatic activity. Structural analysis proved that the efThoc1, GuKc, and P-loop domains are essential for the full function of MoGuk2. Taken together, our data suggest that the guanylate kinase MoGuk2 is involved in the de novo GTP biosynthesis pathway and is important for infection-related morphogenesis in the rice blast fungus.
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Affiliation(s)
- Xingjia Cai
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China
| | - Xi Zhang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China
| | - Xinrui Li
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China
| | - Muxing Liu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China
| | - Xinyu Liu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China
| | - Xiaoli Wang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China
| | - Haifeng Zhang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China
| | - Xiaobo Zheng
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China
| | - Zhengguang Zhang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China
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20
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Chitty JL, Fraser JA. Purine Acquisition and Synthesis by Human Fungal Pathogens. Microorganisms 2017; 5:microorganisms5020033. [PMID: 28594372 PMCID: PMC5488104 DOI: 10.3390/microorganisms5020033] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 06/06/2017] [Accepted: 06/06/2017] [Indexed: 01/13/2023] Open
Abstract
While members of the Kingdom Fungi are found across many of the world's most hostile environments, only a limited number of species can thrive within the human host. The causative agents of the most common invasive fungal infections are Candida albicans, Aspergillus fumigatus, and Cryptococcus neoformans. During the infection process, these fungi must not only combat the host immune system while adapting to dramatic changes in temperature and pH, but also acquire sufficient nutrients to enable growth and dissemination in the host. One class of nutrients required by fungi, which is found in varying concentrations in their environmental niches and the human host, is the purines. These nitrogen-containing heterocycles are one of the most abundant organic molecules in nature and are required for roles as diverse as signal transduction, energy metabolism and DNA synthesis. The most common life-threatening fungal pathogens can degrade, salvage and synthesize de novo purines through a number of enzymatic steps that are conserved. While these enable them to adapt to the changing purine availability in the environment, only de novo purine biosynthesis is essential during infection and therefore an attractive antimycotic target.
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Affiliation(s)
- Jessica L Chitty
- Australian Infectious Diseases Research Centre, School of Chemistry & Molecular Biosciences, the University of Queensland, St Lucia, Queensland 4072, Australia.
- Institute for Molecular Bioscience, the University of Queensland, St Lucia, Queensland 4072, Australia.
| | - James A Fraser
- Australian Infectious Diseases Research Centre, School of Chemistry & Molecular Biosciences, the University of Queensland, St Lucia, Queensland 4072, Australia.
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21
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Chitty JL, Blake KL, Blundell RD, Koh YQAE, Thompson M, Robertson AAB, Butler MS, Cooper MA, Kappler U, Williams SJ, Kobe B, Fraser JA. Cryptococcus neoformans ADS lyase is an enzyme essential for virulence whose crystal structure reveals features exploitable in antifungal drug design. J Biol Chem 2017; 292:11829-11839. [PMID: 28559277 DOI: 10.1074/jbc.m117.787994] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 05/03/2017] [Indexed: 01/09/2023] Open
Abstract
There is significant clinical need for new antifungal agents to manage infections with pathogenic species such as Cryptococcus neoformans Because the purine biosynthesis pathway is essential for many metabolic processes, such as synthesis of DNA and RNA and energy generation, it may represent a potential target for developing new antifungals. Within this pathway, the bifunctional enzyme adenylosuccinate (ADS) lyase plays a role in the formation of the key intermediates inosine monophosphate and AMP involved in the synthesis of ATP and GTP, prompting us to investigate ADS lyase in C. neoformans. Here, we report that ADE13 encodes ADS lyase in C. neoformans. We found that an ade13Δ mutant is an adenine auxotroph and is unable to successfully cause infections in a murine model of virulence. Plate assays revealed that production of a number of virulence factors essential for dissemination and survival of C. neoformans in a host environment was compromised even with the addition of exogenous adenine. Purified recombinant C. neoformans ADS lyase shows catalytic activity similar to its human counterpart, and its crystal structure, the first fungal ADS lyase structure determined, shows a high degree of structural similarity to that of human ADS lyase. Two potentially important amino acid differences are identified in the C. neoformans crystal structure, in particular a threonine residue that may serve as an additional point of binding for a fungal enzyme-specific inhibitor. Besides serving as an antimicrobial target, C. neoformans ADS lyase inhibitors may also serve as potential therapeutics for metabolic disease; rather than disrupt ADS lyase, compounds that improve the stability the enzyme may be used to treat ADS lyase deficiency disease.
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Affiliation(s)
- Jessica L Chitty
- Australian Infectious Diseases Research Centre, School of Chemistry & Molecular Biosciences, University of Queensland, St. Lucia, Queensland 4072; Institute for Molecular Bioscience, University of Queensland, St. Lucia, Queensland 4072
| | - Kirsten L Blake
- Australian Infectious Diseases Research Centre, School of Chemistry & Molecular Biosciences, University of Queensland, St. Lucia, Queensland 4072
| | - Ross D Blundell
- Australian Infectious Diseases Research Centre, School of Chemistry & Molecular Biosciences, University of Queensland, St. Lucia, Queensland 4072
| | - Y Q Andre E Koh
- Australian Infectious Diseases Research Centre, School of Chemistry & Molecular Biosciences, University of Queensland, St. Lucia, Queensland 4072
| | - Merinda Thompson
- Australian Infectious Diseases Research Centre, School of Chemistry & Molecular Biosciences, University of Queensland, St. Lucia, Queensland 4072
| | - Avril A B Robertson
- Institute for Molecular Bioscience, University of Queensland, St. Lucia, Queensland 4072
| | - Mark S Butler
- Institute for Molecular Bioscience, University of Queensland, St. Lucia, Queensland 4072
| | - Matthew A Cooper
- Australian Infectious Diseases Research Centre, School of Chemistry & Molecular Biosciences, University of Queensland, St. Lucia, Queensland 4072; Institute for Molecular Bioscience, University of Queensland, St. Lucia, Queensland 4072
| | - Ulrike Kappler
- Australian Infectious Diseases Research Centre, School of Chemistry & Molecular Biosciences, University of Queensland, St. Lucia, Queensland 4072; Centre for Metals in Biology, University of Queensland, St. Lucia, Queensland 4072
| | - Simon J Williams
- Australian Infectious Diseases Research Centre, School of Chemistry & Molecular Biosciences, University of Queensland, St. Lucia, Queensland 4072; Research School of Biology, Australian National University, Acton, Australian Capital Territory 2601 Australia
| | - Bostjan Kobe
- Australian Infectious Diseases Research Centre, School of Chemistry & Molecular Biosciences, University of Queensland, St. Lucia, Queensland 4072; Institute for Molecular Bioscience, University of Queensland, St. Lucia, Queensland 4072
| | - James A Fraser
- Australian Infectious Diseases Research Centre, School of Chemistry & Molecular Biosciences, University of Queensland, St. Lucia, Queensland 4072.
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22
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Bills GF, Platas G, Overy DP, Collado J, Fillola A, Jiménez MR, Martín J, del Val AG, Vicente F, Tormo JR, Peláez F, Calati K, Harris G, Parish C, Xu D, Roemer T. Discovery of the parnafungins, antifungal metabolites that inhibit mRNA polyadenylation, from theFusarium larvarumcomplex and other Hypocrealean fungi. Mycologia 2017; 101:449-72. [DOI: 10.3852/08-163] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Fernando Peláez
- Centro de Investigación Básica, Merck, Sharp & Dohme de España S. A., Josefa Valcárcel 38, Madrid, E-28027, Spain
| | | | | | | | | | - Terry Roemer
- Merck Research Laboratories, 126 E. Lincoln Avenue, Rahway, New Jersey 07065
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23
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Chitty JL, Tatzenko TL, Williams SJ, Koh YQAE, Corfield EC, Butler MS, Robertson AAB, Cooper MA, Kappler U, Kobe B, Fraser JA. GMP Synthase Is Required for Virulence Factor Production and Infection by Cryptococcus neoformans. J Biol Chem 2017; 292:3049-3059. [PMID: 28062578 DOI: 10.1074/jbc.m116.767533] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 01/04/2017] [Indexed: 11/06/2022] Open
Abstract
Over the last four decades the HIV pandemic and advances in medical treatments that also cause immunosuppression have produced an ever-growing cohort of individuals susceptible to opportunistic pathogens. Of these, AIDS patients are particularly vulnerable to infection by the encapsulated yeast Cryptococcus neoformans Most commonly found in the environment in purine-rich bird guano, C. neoformans experiences a drastic change in nutrient availability during host infection, ultimately disseminating to colonize the purine-poor central nervous system. Investigating the consequences of this challenge, we have characterized C. neoformans GMP synthase, the second enzyme in the guanylate branch of de novo purine biosynthesis. We show that in the absence of GMP synthase, C. neoformans becomes a guanine auxotroph, the production of key virulence factors is compromised, and the ability to infect nematodes and mice is abolished. Activity assays performed using recombinant protein unveiled differences in substrate binding between the C. neoformans and human enzymes, with structural insights into these kinetic differences acquired via homology modeling. Collectively, these data highlight the potential of GMP synthase to be exploited in the development of new therapeutic agents for the treatment of disseminated, life-threatening fungal infections.
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Affiliation(s)
- Jessica L Chitty
- From the Australian Infectious Diseases Research Centre, School of Chemistry & Molecular Biosciences.,the Institute for Molecular Bioscience, and
| | - Tayla L Tatzenko
- From the Australian Infectious Diseases Research Centre, School of Chemistry & Molecular Biosciences
| | - Simon J Williams
- From the Australian Infectious Diseases Research Centre, School of Chemistry & Molecular Biosciences.,the ANU Research School of Biology, Australian National University, Acton, ACT 2601, Australia
| | - Y Q Andre E Koh
- From the Australian Infectious Diseases Research Centre, School of Chemistry & Molecular Biosciences
| | - Elizabeth C Corfield
- From the Australian Infectious Diseases Research Centre, School of Chemistry & Molecular Biosciences
| | | | | | - Matthew A Cooper
- From the Australian Infectious Diseases Research Centre, School of Chemistry & Molecular Biosciences.,the Institute for Molecular Bioscience, and
| | - Ulrike Kappler
- From the Australian Infectious Diseases Research Centre, School of Chemistry & Molecular Biosciences.,the Centre for Metals in Biology, University of Queensland, St. Lucia, Queensland 4072, Australia and
| | - Bostjan Kobe
- From the Australian Infectious Diseases Research Centre, School of Chemistry & Molecular Biosciences.,the Institute for Molecular Bioscience, and
| | - James A Fraser
- From the Australian Infectious Diseases Research Centre, School of Chemistry & Molecular Biosciences,
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24
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Serpi M, Ferrari V, Pertusati F. Nucleoside Derived Antibiotics to Fight Microbial Drug Resistance: New Utilities for an Established Class of Drugs? J Med Chem 2016; 59:10343-10382. [PMID: 27607900 DOI: 10.1021/acs.jmedchem.6b00325] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Novel antibiotics are urgently needed to combat the rise of infections due to drug-resistant microorganisms. Numerous natural nucleosides and their synthetically modified analogues have been reported to have moderate to good antibiotic activity against different bacterial and fungal strains. Nucleoside-based compounds target several crucial processes of bacterial and fungal cells such as nucleoside metabolism and cell wall, nucleic acid, and protein biosynthesis. Nucleoside analogues have also been shown to target many other bacterial and fungal cellular processes although these are not well characterized and may therefore represent opportunities to discover new drugs with unique mechanisms of action. In this Perspective, we demonstrate that nucleoside analogues, cornerstones of anticancer and antiviral treatments, also have great potential to be repurposed as antibiotics so that an old drug can learn new tricks.
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Affiliation(s)
- Michaela Serpi
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University , Redwood Building, King Edward VII Avenue, CF10 3NB Cardiff, United Kingdom
| | - Valentina Ferrari
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University , Redwood Building, King Edward VII Avenue, CF10 3NB Cardiff, United Kingdom
| | - Fabrizio Pertusati
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University , Redwood Building, King Edward VII Avenue, CF10 3NB Cardiff, United Kingdom
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25
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Utilizing yeast chemogenomic profiles for the prediction of pharmacogenomic associations in humans. Sci Rep 2016; 6:23703. [PMID: 27025271 PMCID: PMC4812343 DOI: 10.1038/srep23703] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 03/10/2016] [Indexed: 01/29/2023] Open
Abstract
Understanding the genetic basis underlying individual responses to drug treatment is a fundamental task with implications to drug development and administration. Pharmacogenomics is the study of the genes that affect drug response. The study of pharmacogenomic associations between a drug and a gene that influences the interindividual drug response, which is only beginning, holds much promise and potential. Although relatively few pharmacogenomic associations between drugs and specific genes were mapped in humans, large systematic screens have been carried out in the yeast Saccharomyces cerevisiae, motivating the constructing of a projection method. We devised a novel approach for the prediction of pharmacogenomic associations in humans using genome-scale chemogenomic data from yeast. We validated our method using both cross-validation and comparison to known drug-gene associations extracted from multiple data sources, attaining high AUC scores. We show that our method outperforms a previous technique, as well as a similar method based on known human associations. Last, we analyze the predictions and demonstrate their biological relevance to understanding drug response.
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26
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Pérez-Torrado R, Querol A. Opportunistic Strains of Saccharomyces cerevisiae: A Potential Risk Sold in Food Products. Front Microbiol 2016; 6:1522. [PMID: 26779173 PMCID: PMC4705302 DOI: 10.3389/fmicb.2015.01522] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 12/17/2015] [Indexed: 12/28/2022] Open
Abstract
In recent decades, fungal infections have emerged as an important health problem associated with more people who present deficiencies in the immune system, such as HIV or transplanted patients. Saccharomyces cerevisiae is one of the emerging fungal pathogens with a unique characteristic: its presence in many food products. S. cerevisiae has an impeccably good food safety record compared to other microorganisms like virus, bacteria and some filamentous fungi. However, humans unknowingly and inadvertently ingest large viable populations of S. cerevisiae (home-brewed beer or dietary supplements that contain yeast). In the last few years, researchers have studied the nature of S. cerevisiae strains and the molecular mechanisms related to infections. Here we review the last advance made in this emerging pathogen and we discuss the implication of using this species in food products.
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Affiliation(s)
- Roberto Pérez-Torrado
- Food Biotechnology Department, Instituto de Agroquímica y Tecnología de los Alimentos - Consejo Superior de Investigaciones Científicas Valencia, Spain
| | - Amparo Querol
- Food Biotechnology Department, Instituto de Agroquímica y Tecnología de los Alimentos - Consejo Superior de Investigaciones Científicas Valencia, Spain
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27
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Bianchi-Smiraglia A, Wawrzyniak JA, Bagati A, Marvin EK, Ackroyd J, Moparthy S, Bshara W, Fink EE, Foley CE, Morozevich GE, Berman AE, Shewach DS, Nikiforov MA. Pharmacological targeting of guanosine monophosphate synthase suppresses melanoma cell invasion and tumorigenicity. Cell Death Differ 2015; 22:1858-64. [PMID: 25909885 PMCID: PMC4648332 DOI: 10.1038/cdd.2015.47] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Revised: 03/12/2015] [Accepted: 03/16/2015] [Indexed: 12/20/2022] Open
Abstract
Malignant melanoma possesses one of the highest metastatic potentials among human cancers. Acquisition of invasive phenotypes is a prerequisite for melanoma metastases. Elucidation of the molecular mechanisms underlying melanoma invasion will greatly enhance the design of novel agents for melanoma therapeutic intervention. Here, we report that guanosine monophosphate synthase (GMPS), an enzyme required for the de novo biosynthesis of GMP, has a major role in invasion and tumorigenicity of cells derived from either BRAF(V600E) or NRAS(Q61R) human metastatic melanomas. Moreover, GMPS levels are increased in metastatic human melanoma specimens compared with primary melanomas arguing that GMPS is an attractive candidate for anti-melanoma therapy. Accordingly, for the first time we demonstrate that angustmycin A, a nucleoside-analog inhibitor of GMPS produced by Streptomyces hygroscopius efficiently suppresses melanoma cell invasion in vitro and tumorigenicity in immunocompromised mice. Our data identify GMPS as a powerful driver of melanoma cell invasion and warrant further investigation of angustmycin A as a novel anti-melanoma agent.
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Affiliation(s)
- A Bianchi-Smiraglia
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - J A Wawrzyniak
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - A Bagati
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - E K Marvin
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - J Ackroyd
- Department of Pharmacology, University of Michigan, Ann Arbor, MI 48109, USA
| | - S Moparthy
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - W Bshara
- Department of Pathology, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - E E Fink
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - C E Foley
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - G E Morozevich
- Orekhovich Institute of Biomedical Chemistry, Moscow 119121, Russia
| | - A E Berman
- Orekhovich Institute of Biomedical Chemistry, Moscow 119121, Russia
| | - D S Shewach
- Department of Pharmacology, University of Michigan, Ann Arbor, MI 48109, USA
| | - M A Nikiforov
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
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28
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Balibar CJ, Roemer T. Yeast: a microbe with macro-implications to antimicrobial drug discovery. Brief Funct Genomics 2015; 15:147-54. [PMID: 26443612 DOI: 10.1093/bfgp/elv038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Paramount to any rational discovery of new antibiotics displaying novel mechanisms of action is a deep knowledge of the genetic basis of microbial growth, division and virulence. The bakers' yeast,Saccharomyces cerevisiae, illustrates the highest understanding of the genetic underpinnings of microbial life, and from this framework, a systems biology paradigm has evolved, begging to be emulated in antibacterial discovery. Here, we review landmark events in the history of yeast genomics that provide this new foundation for antibacterial drug discovery.
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29
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Application of chemical biology in target identification and drug discovery. Arch Pharm Res 2015; 38:1642-50. [PMID: 26242900 DOI: 10.1007/s12272-015-0643-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 07/29/2015] [Indexed: 10/23/2022]
Abstract
Drug discovery and development is vital to the well-being of mankind and sustainability of the pharmaceutical industry. Using chemical biology approaches to discover drug leads has become a widely accepted path partially because of the completion of the Human Genome Project. Chemical biology mainly solves biological problems through searching previously unknown targets for pharmacologically active small molecules or finding ligands for well-defined drug targets. It is a powerful tool to study how these small molecules interact with their respective targets, as well as their roles in signal transduction, molecular recognition and cell functions. There have been an increasing number of new therapeutic targets being identified and subsequently validated as a result of advances in functional genomics, which in turn led to the discovery of numerous active small molecules via a variety of high-throughput screening initiatives. In this review, we highlight some applications of chemical biology in the context of drug discovery.
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30
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Li Q, Leija C, Rijo-Ferreira F, Chen J, Cestari I, Stuart K, Tu BP, Phillips MA. GMP synthase is essential for viability and infectivity of Trypanosoma brucei despite a redundant purine salvage pathway. Mol Microbiol 2015; 97:1006-20. [PMID: 26043892 DOI: 10.1111/mmi.13083] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/04/2015] [Indexed: 12/28/2022]
Abstract
The causative agent of human African trypanosomiasis, Trypanosoma brucei, lacks de novo purine biosynthesis and depends on purine salvage from the host. The purine salvage pathway is redundant and contains two routes to guanosine-5'-monophosphate (GMP) formation: conversion from xanthosine-5'-monophosphate (XMP) by GMP synthase (GMPS) or direct salvage of guanine by hypoxanthine-guanine phosphoribosyltransferase (HGPRT). We show recombinant T. brucei GMPS efficiently catalyzes GMP formation. Genetic knockout of GMPS in bloodstream parasites led to depletion of guanine nucleotide pools and was lethal. Growth of gmps null cells was only rescued by supraphysiological guanine concentrations (100 μM) or by expression of an extrachromosomal copy of GMPS. Hypoxanthine was a competitive inhibitor of guanine rescue, consistent with a common uptake/metabolic conversion mechanism. In mice, gmps null parasites were unable to establish an infection demonstrating that GMPS is essential for virulence and that plasma guanine is insufficient to support parasite purine requirements. These data validate GMPS as a potential therapeutic target for treatment of human African trypanosomiasis. The ability to strategically inhibit key metabolic enzymes in the purine pathway unexpectedly bypasses its functional redundancy by exploiting both the nature of pathway flux and the limited nutrient environment of the parasite's extracellular niche.
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Affiliation(s)
- Qiong Li
- Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, 6001 Forest Park Rd, Dallas, TX, 75390-9041, USA
| | - Christopher Leija
- Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, 6001 Forest Park Rd, Dallas, TX, 75390-9041, USA
| | - Filipa Rijo-Ferreira
- Department of Neuroscience, University of Texas Southwestern Medical Center at Dallas, 6001 Forest Park Rd, Dallas, TX, 75390-9041, USA.,Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal.,Graduate Program in Areas of Basic and Applied Biology, Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Jun Chen
- Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, 6001 Forest Park Rd, Dallas, TX, 75390-9041, USA
| | - Igor Cestari
- Seattle Biomedical Research Institute, 307 Westlake Avenue North, Suite 500, Seattle, WA, 98109-5219, USA
| | - Kenneth Stuart
- Seattle Biomedical Research Institute, 307 Westlake Avenue North, Suite 500, Seattle, WA, 98109-5219, USA
| | - Benjamin P Tu
- Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, 6001 Forest Park Rd, Dallas, TX, 75390-9041, USA
| | - Margaret A Phillips
- Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, 6001 Forest Park Rd, Dallas, TX, 75390-9041, USA
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31
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Pérez-Torrado R, Llopis S, Perrone B, Gómez-Pastor R, Hube B, Querol A. Comparative genomic analysis reveals a critical role of de novo nucleotide biosynthesis for Saccharomyces cerevisiae virulence. PLoS One 2015; 10:e0122382. [PMID: 25816288 PMCID: PMC4376706 DOI: 10.1371/journal.pone.0122382] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 02/23/2015] [Indexed: 12/22/2022] Open
Abstract
In recent years, the number of human infection cases produced by the food related species Saccharomyces cerevisiae has increased. Whereas many strains of this species are considered safe, other 'opportunistic' strains show a high degree of potential virulence attributes and can cause infections in immunocompromised patients. Here we studied the genetic characteristics of selected opportunistic strains isolated from dietary supplements and also from patients by array comparative genomic hybridization. Our results show increased copy numbers of IMD genes in opportunistic strains, which are implicated in the de novo biosynthesis of the purine nucleotides pathway. The importance of this pathway for virulence of S. cerevisiae was confirmed by infections in immunodeficient murine models using a GUA1 mutant, a key gene of this pathway. We show that exogenous guanine, an end product of this pathway in its triphosphorylated form, increases the survival of yeast strains in ex vivo blood infections. Finally, we show the importance of the DNA damage response that activates dNTP biosynthesis in yeast cells during ex vivo blood infections. We conclude that opportunistic yeasts may use an enhanced de novo biosynthesis of the purine nucleotides pathway to increase survival and favor infections in the host.
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Affiliation(s)
| | - Silvia Llopis
- Instituto de Agroquímica y Tecnología de los Alimentos, CSIC, Valencia, Spain
| | - Benedetta Perrone
- Instituto de Agroquímica y Tecnología de los Alimentos, CSIC, Valencia, Spain
- Department of Agricultural, Forest and Food Sciences Microbiology and Food Technologies Unit University of Torino, Torino, Italy
| | - Rocío Gómez-Pastor
- Instituto de Agroquímica y Tecnología de los Alimentos, CSIC, Valencia, Spain
| | - Bernhard Hube
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knoell-Institute (HKI), Jena, Germany
- Friedrich Schiller University, Jena, Germany
| | - Amparo Querol
- Instituto de Agroquímica y Tecnología de los Alimentos, CSIC, Valencia, Spain
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32
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Abstract
Very few chemically novel agents have been approved for antibacterial chemotherapies during the last 50 yr. Yet new antibacterial drugs are needed to reduce the impact on global health of an increasing number of drug-resistant infections, including highly drug-resistant forms of tuberculosis. This review discusses how genetic approaches can be used to study the mechanism of action of whole-cell screening hits and facilitate target-driven strategies for antimicrobial drug development.
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Affiliation(s)
- Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York 10065
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33
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Mann PA, McLellan CA, Koseoglu S, Si Q, Kuzmin E, Flattery A, Harris G, Sher X, Murgolo N, Wang H, Devito K, de Pedro N, Genilloud O, Kahn JN, Jiang B, Costanzo M, Boone C, Garlisi CG, Lindquist S, Roemer T. Chemical Genomics-Based Antifungal Drug Discovery: Targeting Glycosylphosphatidylinositol (GPI) Precursor Biosynthesis. ACS Infect Dis 2015; 1:59-72. [PMID: 26878058 PMCID: PMC4739577 DOI: 10.1021/id5000212] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Steadily increasing antifungal drug resistance and persistent high rates of fungal-associated mortality highlight the dire need for the development of novel antifungals. Characterization of inhibitors of one enzyme in the GPI anchor pathway, Gwt1, has generated interest in the exploration of targets in this pathway for further study. Utilizing a chemical genomics-based screening platform referred to as the Candida albicans fitness test (CaFT), we have identified novel inhibitors of Gwt1 and a second enzyme in the glycosylphosphatidylinositol (GPI) cell wall anchor pathway, Mcd4. We further validate these targets using the model fungal organism Saccharomyces cerevisiae and demonstrate the utility of using the facile toolbox that has been compiled in this species to further explore target specific biology. Using these compounds as probes, we demonstrate that inhibition of Mcd4 as well as Gwt1 blocks the growth of a broad spectrum of fungal pathogens and exposes key elicitors of pathogen recognition. Interestingly, a strong chemical synergy is also observed by combining Gwt1 and Mcd4 inhibitors, mirroring the demonstrated synthetic lethality of combining conditional mutants of GWT1 and MCD4. We further demonstrate that the Mcd4 inhibitor M720 is efficacious in a murine infection model of systemic candidiasis. Our results establish Mcd4 as a promising antifungal target and confirm the GPI cell wall anchor synthesis pathway as a promising antifungal target area by demonstrating that effects of inhibiting it are more general than previously recognized.
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Affiliation(s)
- Paul A. Mann
- Merck Research
Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Catherine A. McLellan
- Whitehead Institute
for Biomedical Research, 9 Cambridge
Center, Cambridge, Massachusetts 02142, United States
- Howard
Hughes Medical Institute and Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Sandra Koseoglu
- Merck Research
Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Qian Si
- Merck Research
Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Elena Kuzmin
- Banting and
Best Department of Medical Research, Terrance Donnally Centre of Cellular
and Biomedical Research, University of Toronto, Toronto, Ontario, Canada
| | - Amy Flattery
- Merck Research
Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Guy Harris
- Merck Research
Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Xinwei Sher
- Merck Research
Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Nicholas Murgolo
- Merck Research
Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Hao Wang
- Merck Research
Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Kristine Devito
- Merck Research
Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Nuria de Pedro
- Fundación
Centro de Excelencia en Investigación de Medicamentos Innovadores
en Andalucı́a, Medina, Parque Tecnológico de Ciencias de la Salud , Avenida Conocimiento 34, 18016 Grenada, Spain
| | - Olga Genilloud
- Fundación
Centro de Excelencia en Investigación de Medicamentos Innovadores
en Andalucı́a, Medina, Parque Tecnológico de Ciencias de la Salud , Avenida Conocimiento 34, 18016 Grenada, Spain
| | - Jennifer Nielsen Kahn
- Merck Research
Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Bo Jiang
- Merck Research
Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Michael Costanzo
- Banting and
Best Department of Medical Research, Terrance Donnally Centre of Cellular
and Biomedical Research, University of Toronto, Toronto, Ontario, Canada
| | - Charlie Boone
- Banting and
Best Department of Medical Research, Terrance Donnally Centre of Cellular
and Biomedical Research, University of Toronto, Toronto, Ontario, Canada
| | - Charles G. Garlisi
- Merck Research
Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Susan Lindquist
- Whitehead Institute
for Biomedical Research, 9 Cambridge
Center, Cambridge, Massachusetts 02142, United States
- Howard
Hughes Medical Institute and Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Terry Roemer
- Merck Research
Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
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34
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Oliver JC, Linger RS, Chittur SV, Davisson VJ. Substrate activation and conformational dynamics of guanosine 5'-monophosphate synthetase. Biochemistry 2013; 52:5225-35. [PMID: 23841499 DOI: 10.1021/bi3017075] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Glutamine amidotransferases catalyze the amination of a wide range of molecules using the amide nitrogen of glutamine. The family provides numerous examples for study of multi-active-site regulation and interdomain communication in proteins. Guanosine 5'-monophosphate synthetase (GMPS) is one of three glutamine amidotransferases in de novo purine biosynthesis and is responsible for the last step in the guanosine branch of the pathway, the amination of xanthosine 5'-monophosphate (XMP). In several amidotransferases, the intramolecular path of ammonia from glutamine to substrate is understood; however, the crystal structure of GMPS only hinted at the details of such transfer. Rapid kinetics studies provide insight into the mechanism of the substrate-induced changes in this complex enzyme. Rapid mixing of GMPS with substrates also manifests absorbance changes that report on the kinetics of formation of a reactive intermediate as well as steps in the process of rapid transfer of ammonia to this intermediate. Isolation and use of the adenylylated nucleotide intermediate allowed the study of the amido transfer reaction distinct from the ATP-dependent reaction. Changes in intrinsic tryptophan fluorescence upon mixing of enzyme with XMP suggest a conformational change upon substrate binding, likely the ordering of a highly conserved loop in addition to global domain motions. In the GMPS reaction, all forward rates before product release appear to be faster than steady-state turnover, implying that release is likely rate-limiting. These studies establish the functional role of a substrate-induced conformational change in the GMPS catalytic cycle and provide a kinetic context for the formation of an ammonia channel linking the distinct active sites.
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Affiliation(s)
- Justin C Oliver
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University , West Lafayette, Indiana 47907, United States
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35
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Cools HJ, Hammond-Kosack KE. Exploitation of genomics in fungicide research: current status and future perspectives. MOLECULAR PLANT PATHOLOGY 2013; 14:197-210. [PMID: 23157348 PMCID: PMC6638899 DOI: 10.1111/mpp.12001] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Every year, fungicide use to control plant disease caused by pathogenic fungi increases. The global fungicide market is now worth more than £5.3 billion, second only to the herbicide market in importance. In the UK, over 5500 tonnes of fungicide were applied to crops in 2010 (The Food and Environment Research Agency, Pesticide Usage Statistics), with 95.5% of the wheat-growing area receiving three fungicide sprays. Although dependence on fungicides to produce food securely, reliably and cheaply may be moderated in the future by further developments in crop biotechnology, modern crop protection will continue to require a diversity of solutions, including effective and safe chemical control. Therefore, investment in exploiting the increasingly available genome sequences of the most devastating fungal and oomycete phytopathogenic species should bring an array of new opportunities for chemical intervention. To date, the impact of whole genome research on the development, introduction and stewardship of fungicides has been limited, but ongoing improvements in computational analysis, molecular biology, chemical genetics, genome sequencing and transcriptomics will facilitate the development and registration of the future suite of crop protection chemicals.
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Affiliation(s)
- Hans J Cools
- Department of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK.
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36
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Struntz NB, Hu T, White BR, Olson ME, Harki DA. Inhibition of guanosine monophosphate synthetase by the substrate enantiomer L-XMP. Chembiochem 2012; 13:2517-20. [PMID: 23097382 DOI: 10.1002/cbic.201200503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2012] [Indexed: 11/12/2022]
Affiliation(s)
- Nicholas B Struntz
- Department of Medicinal Chemistry, University of Minnesota, 717 Delaware Street S.E., Minneapolis, MN 55414, USA
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37
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Sun Z, Sun Y, Zhou Y, Wan Y. Yeast Genomics Technique for High-Throughput Drug Target Discovery. Drug Dev Res 2012. [DOI: 10.1002/ddr.21030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Zijun Sun
- The Key Laboratory of Developmental Genes and Human Disease; Ministry of Education; Institute of Life Sciences; Southeast University; Nanjing; 210096; China
| | - Yanyan Sun
- The Key Laboratory of Developmental Genes and Human Disease; Ministry of Education; Institute of Life Sciences; Southeast University; Nanjing; 210096; China
| | - Yaxian Zhou
- The Key Laboratory of Developmental Genes and Human Disease; Ministry of Education; Institute of Life Sciences; Southeast University; Nanjing; 210096; China
| | - Yakun Wan
- The Key Laboratory of Developmental Genes and Human Disease; Ministry of Education; Institute of Life Sciences; Southeast University; Nanjing; 210096; China
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38
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Morrow CA, Valkov E, Stamp A, Chow EWL, Lee IR, Wronski A, Williams SJ, Hill JM, Djordjevic JT, Kappler U, Kobe B, Fraser JA. De novo GTP biosynthesis is critical for virulence of the fungal pathogen Cryptococcus neoformans. PLoS Pathog 2012; 8:e1002957. [PMID: 23071437 PMCID: PMC3469657 DOI: 10.1371/journal.ppat.1002957] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2012] [Accepted: 08/26/2012] [Indexed: 01/01/2023] Open
Abstract
We have investigated the potential of the GTP synthesis pathways as chemotherapeutic targets in the human pathogen Cryptococcus neoformans, a common cause of fatal fungal meningoencephalitis. We find that de novo GTP biosynthesis, but not the alternate salvage pathway, is critical to cryptococcal dissemination and survival in vivo. Loss of inosine monophosphate dehydrogenase (IMPDH) in the de novo pathway results in slow growth and virulence factor defects, while loss of the cognate phosphoribosyltransferase in the salvage pathway yielded no phenotypes. Further, the Cryptococcus species complex displays variable sensitivity to the IMPDH inhibitor mycophenolic acid, and we uncover a rare drug-resistant subtype of C. gattii that suggests an adaptive response to microbial IMPDH inhibitors in its environmental niche. We report the structural and functional characterization of IMPDH from Cryptococcus, revealing insights into the basis for drug resistance and suggesting strategies for the development of fungal-specific inhibitors. The crystal structure reveals the position of the IMPDH moveable flap and catalytic arginine in the open conformation for the first time, plus unique, exploitable differences in the highly conserved active site. Treatment with mycophenolic acid led to significantly increased survival times in a nematode model, validating de novo GTP biosynthesis as an antifungal target in Cryptococcus.
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Affiliation(s)
- Carl A. Morrow
- Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland, Australia
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Eugene Valkov
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Anna Stamp
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Eve W. L. Chow
- Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland, Australia
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - I. Russel Lee
- Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland, Australia
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Ania Wronski
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Simon J. Williams
- Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland, Australia
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Justine M. Hill
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
- Centre for Advanced Imaging, University of Queensland, Brisbane, Queensland, Australia
| | - Julianne T. Djordjevic
- Centre for Infectious Diseases and Microbiology, Westmead Millennium Institute, University of Sydney at Westmead Hospital, Sydney, New South Wales, Australia
| | - Ulrike Kappler
- Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland, Australia
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Bostjan Kobe
- Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland, Australia
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - James A. Fraser
- Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland, Australia
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
- * E-mail:
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Azad MA, Wright GD. Determining the mode of action of bioactive compounds. Bioorg Med Chem 2012; 20:1929-39. [DOI: 10.1016/j.bmc.2011.10.088] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2011] [Revised: 10/14/2011] [Accepted: 10/30/2011] [Indexed: 10/14/2022]
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Cong F, Cheung AK, Huang SMA. Chemical Genetics–Based Target Identification in Drug Discovery. Annu Rev Pharmacol Toxicol 2012; 52:57-78. [DOI: 10.1146/annurev-pharmtox-010611-134639] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Feng Cong
- Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139;
| | - Atwood K. Cheung
- Global Discovery Chemistry – Chemogenetics and Proteomics, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139
| | - Shih-Min A. Huang
- Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139;
- Current address: Sanofi-Aventis Oncology, Cambridge, Massachusetts 02139
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Andrusiak K, Piotrowski JS, Boone C. Chemical-genomic profiling: systematic analysis of the cellular targets of bioactive molecules. Bioorg Med Chem 2011; 20:1952-60. [PMID: 22261022 DOI: 10.1016/j.bmc.2011.12.023] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2011] [Revised: 12/05/2011] [Accepted: 12/13/2011] [Indexed: 11/17/2022]
Abstract
Chemical-genomic (CG) profiling of bioactive compounds is a powerful approach for drug target identification and mode of action studies. Within the last decade, research focused largely on the development and application of CG approaches in the model yeast Saccharomyces cerevisiae. The success of these methods has sparked interest in transitioning CG profiling to other biological systems to extend clinical and evolutionary relevance. Additionally, CG profiling has proven to enhance drug-synergy screens for developing combinatorial therapies. Herein, we briefly review CG profiling, focusing on emerging cross-species technologies and novel drug-synergy applications, as well as outlining needs within the field.
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Affiliation(s)
- Kerry Andrusiak
- Banting and Best Department of Medical Research and Department of Molecular Genetics, Donnelly Centre, University of Toronto, 160 College St., Toronto, ON, Canada M5S 3E1
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Abstract
The serendipitous discovery of penicillin inspired intensive research into how small molecules affect basic cellular processes and their potential to treat disease. Biochemical and genetic approaches have been fundamental for clarifying small-molecule modes of action. Genomic technologies have permitted the use of chemical-genetic strategies that comprehensively study compound-target relationships in the context of a living cell, providing a systems biology view of both the cellular targets and the interdependent networks that respond to chemical stress. These studies highlight the fact that in vitro determinations of mechanism rarely translate into a complete understanding of drug behavior in the cell. Here, we review key discoveries that gave rise to the field of chemical genetics, with particular attention to chemical-genetic strategies developed for bakers' yeast, their extension to clinically relevant microbial pathogens, and the potential of these approaches to affect antimicrobial drug discovery.
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Franco TMA, Rostirolla DC, Ducati RG, Lorenzini DM, Basso LA, Santos DS. Biochemical characterization of recombinant guaA-encoded guanosine monophosphate synthetase (EC 6.3.5.2) from Mycobacterium tuberculosis H37Rv strain. Arch Biochem Biophys 2011; 517:1-11. [PMID: 22119138 DOI: 10.1016/j.abb.2011.11.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Revised: 11/08/2011] [Accepted: 11/09/2011] [Indexed: 12/29/2022]
Abstract
Administration of the current tuberculosis (TB) vaccine to newborns is not a reliable route for preventing TB in adults. The conversion of XMP to GMP is catalyzed by guaA-encoded GMP synthetase (GMPS), and deletions in the Shiguella flexneri guaBA operon led to an attenuated auxotrophic strain. Here we present the cloning, expression, and purification of recombinant guaA-encoded GMPS from Mycobacterium tuberculosis (MtGMPS). Mass spectrometry data, oligomeric state determination, steady-state kinetics, isothermal titration calorimetry (ITC), and multiple sequence alignment are also presented. The homodimeric MtGMPS catalyzes the conversion of XMP, MgATP, and glutamine into GMP, ADP, PP(i), and glutamate. XMP, NH(4)(+), and Mg(2+) displayed positive homotropic cooperativity, whereas ATP and glutamine displayed hyperbolic saturation curves. The activity of ATP pyrophosphatase domain is independent of glutamine amidotransferase domain, whereas the latter cannot catalyze hydrolysis of glutamine to NH(3) and glutamate in the absence of substrates. ITC data suggest random order of binding of substrates, and PP(i) is the last product released. Sequence comparison analysis showed conservation of both Cys-His-Glu catalytic triad of N-terminal Class I amidotransferase and of amino acid residues of the P-loop of the N-type ATP pyrophosphatase family.
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Affiliation(s)
- Tathyana Mar A Franco
- Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, RS, Brazil
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Xu D, Ondeyka J, Harris GH, Zink D, Kahn JN, Wang H, Bills G, Platas G, Wang W, Szewczak AA, Liberator P, Roemer T, Singh SB. Isolation, structure, and biological activities of Fellutamides C and D from an undescribed Metulocladosporiella (Chaetothyriales) using the genome-wide Candida albicans fitness test. JOURNAL OF NATURAL PRODUCTS 2011; 74:1721-1730. [PMID: 21761939 DOI: 10.1021/np2001573] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
In a whole-cell mechanism of action (MOA)-based screening strategy for discovery of antifungal agents, Candida albicans was used, followed by testing of active extracts in the C. albicans fitness test (CaFT), which provides insight into the mechanism of action. A fermentation extract of an undescribed species of Metulocladosporiella that inhibited proteasome activity in a C. albicans fitness test was identified. The chemical genomic profile of the extract contained hypersensitivity of heterozygous deletion strains (strains that had one of the genes of the diploid genes knocked down) of genes represented by multiple subunits of the 25S proteasome. Two structurally related peptide aldehydes, named fellutamides C and D, were isolated from the extract. Fellutamides were active against C. albicans and Aspergillus fumigatus with MICs ranging from 4 to 16 μg/mL and against fungal proteasome (IC₅₀ 0.2 μg/mL). Both compounds showed proteasome activity against human tumor cell lines, potently inhibiting the growth of PC-3 prostate carcinoma cells, but not A549 lung carcinoma cells. In PC-3 cells compound treatment produced a G2M cell cycle block and induced apoptosis. Preliminary SAR studies indicated that the aldehyde group is critical for the antifungal activity and that the two hydroxy groups are quantitatively important for potency.
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Affiliation(s)
- Deming Xu
- Department of Natural Products and Medicinal Chemistry, Merck Research Laboratories, Rahway, New Jersey 07065, USA
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Duke SO, Dayan FE. Modes of action of microbially-produced phytotoxins. Toxins (Basel) 2011; 3:1038-1064. [PMID: 22069756 PMCID: PMC3202864 DOI: 10.3390/toxins3081038] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2011] [Revised: 08/15/2011] [Accepted: 08/17/2011] [Indexed: 01/17/2023] Open
Abstract
Some of the most potent phytotoxins are synthesized by microbes. A few of these share molecular target sites with some synthetic herbicides, but many microbial toxins have unique target sites with potential for exploitation by the herbicide industry. Compounds from both non-pathogenic and pathogenic microbes are discussed. Microbial phytotoxins with modes of action the same as those of commercial herbicides and those with novel modes of action of action are covered. Examples of the compounds discussed are tentoxin, AAL-toxin, auscaulitoxin aglycone, hydantocidin, thaxtomin, and tabtoxin.
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Affiliation(s)
- Stephen O. Duke
- United States Department of Agriculture, Agricultural Research Service, Natural Products Utilization Research Unit, P. O. Box 8048, MS 38677, USA;
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Roemer T, Xu D, Singh SB, Parish CA, Harris G, Wang H, Davies JE, Bills GF. Confronting the challenges of natural product-based antifungal discovery. ACTA ACUST UNITED AC 2011; 18:148-64. [PMID: 21338914 DOI: 10.1016/j.chembiol.2011.01.009] [Citation(s) in RCA: 109] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2010] [Revised: 12/28/2010] [Accepted: 01/03/2011] [Indexed: 12/21/2022]
Abstract
Starting with the discovery of penicillin, the pharmaceutical industry has relied extensively on natural products (NPs) as an unparalleled source of bioactive small molecules suitable for antibiotic development. However, the discovery of structurally novel and chemically tractable NPs with suitable pharmacological properties as antibiotic leads has waned in recent decades. Today, the repetitive "rediscovery" of previously known NP classes with limited antibiotic lead potential dominates most industrial efforts. This limited productivity, exacerbated by the significant financial and resource requirements of such activities, has led to a broad de-emphasis of NP research by most pharmaceutical companies, including most recently Merck. Here we review our strategies--both technological and philosophical--in addressing current antifungal discovery bottlenecks in target identification and validation and how such efforts may improve NP-based antimicrobial discoveries when aligned with NP screening and dereplication.
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Affiliation(s)
- Terry Roemer
- Department of Infectious Disease, Merck Frosst Canada Ltd., Montreal, QC, Canada.
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Cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action. Mol Syst Biol 2011; 6:451. [PMID: 21179023 PMCID: PMC3018166 DOI: 10.1038/msb.2010.107] [Citation(s) in RCA: 124] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2010] [Accepted: 11/09/2010] [Indexed: 12/01/2022] Open
Abstract
Chemogenomic screens were performed in both budding and fission yeasts, allowing for a cross-species comparison of drug–gene interaction networks. Drug–module interactions were more conserved than individual drug–gene interactions. Combination of data from both species can improve drug–module predictions and helps identify a compound's mode of action.
Understanding the molecular effects of chemical compounds in living cells is an important step toward rational therapeutics. Drug discovery aims to find compounds that will target a specific pathway or pathogen with minimal side effects. However, even when an effective drug is found, its mode of action (MoA) is typically not well understood. The lack of knowledge regarding a drug's MoA makes the drug discovery process slow and rational therapeutics incredibly difficult. More recently, different high-throughput methods have been developed that attempt to discern how a compound exerts its effects in cells. One of these methods relies on measuring the growth of cells carrying different mutations in the presence of the compounds of interest, commonly referred to as chemogenomics (Wuster and Babu, 2008). The differential growth of the different mutants provides clues as to what the compounds target in the cell (Figure 2). For example, if a drug inhibits a branch in a vital two-branch pathway, then mutations in the second branch might result in cell death if the mutants are grown in the presence of the drug (Figure 2C). As these compound–mutant functional interactions are expected to be relatively rare, one can assume that the growth rate of a mutant–drug combination should generally be equal to the product of the growth rate of the untreated mutant with the growth rate of the drug-treated wild type. This expectation is defined as the neutral model and deviations from this provide a quantitative score that allow us to make informed predictions regarding a drug's MoA (Figure 2B;Parsons et al, 2006). The availability of these high-throughput approaches now allows us to perform cross-species studies of functional interactions between compounds and genes. In this study, we have performed a quantitative analysis of compound–gene interactions for two fungal species (budding yeast (S. cerevisiae) and fission yeast (S. pombe)) that diverged from each other approximately 500–700 million years ago. A collection of 2957 compounds from the National Cancer Institute (NCI) were screened in both species for inhibition of wild-type cell growth. A total of 132 were found to be bioactive in both fungi and 9, along with 12 additional well-characterized drugs, were selected for subsequent screening. Mutant libraries of 727 and 438 gene deletions were used for S. cerevisiae and S. pombe, respectively, and these were selected based on availability of genetic interaction data from previous studies (Collins et al, 2007; Roguev et al, 2008; Fiedler et al, 2009) and contain an overlap of 190 one-to-one orthologs that can be directly compared. Deviations from the neutral expectation were quantified as drug–gene interactions scores (D-scores) for the 21 compounds against the deletion libraries. Replicates of both screens showed very high correlations (S. cerevisiae r=0.72, S. pombe r=0.76) and reproduced well previously known compound–gene interactions (Supplementary information). We then compared the D-scores for the 190 one-to-one orthologs present in the data set of both species. Despite the high reproducibility, we observed a very poor conservation of these compound–gene interaction scores across these species (r=0.13, Figure 4A). Previous work had shown that, across these same species, genetic interactions within protein complexes were much more conserved than average genetic interactions (Roguev et al, 2008). Similarly we observed a higher cross-species conservation of the compound–module (complex or pathway) interactions than the overall compound–gene interactions. Specifically, the data derived from fission yeast were a poor predictor of S. cerevisaie drug–gene interactions, but a good predictor of budding yeast compound–module connections (Figure 4B). Also, a combined score from both species improved the prediction of compound–module interactions, above the accuracy observed with the S. cerevisae information alone, but this improvement was not observed for the prediction of drug–gene interactions (Figure 4B). Data from both species were used to predict drug–module interactions, and one specific interaction (compound NSC-207895 interaction with DNA repair complexes) was experimentally verified by showing that the compound activates the DNA damage repair pathway in three species (S. cerevisiae, S. pombe and H. sapiens). To understand why the combination of chemogenomic data from two species might improve drug–module interaction predictions, we also analyzed previously published cross-species genetic–interaction data. We observed a significant correlation between the conservation of drug–gene and gene–gene interactions among the one-to-one orthologs (r=0.28, P-value=0.0078). Additionally, the strongest interactions of benomyl (a microtubule inhibitor) were to complexes that also had strong and conserved genetic interactions with microtubules (Figure 4C). We hypothesize that a significant number of the compound–gene interactions obtained from chemogenomic studies are not direct interactions with the physical target of the compounds, but include many indirect interactions that genetically interact with the main target(s). This would explain why the compound interaction networks show similar evolutionary patterns as the genetic interactions networks. In summary, these results shed some light on the interplay between the evolution of genetic networks and the evolution of drug response. Understanding how genetic variability across different species might result in different sensitivity to drugs should improve our capacity to design treatments. Concretely, we hope that this line of research might one day help us create drugs and drug combinations that specifically affect a pathogen or diseased tissue, but not the host. We present a cross-species chemogenomic screening platform using libraries of haploid deletion mutants from two yeast species, Saccharomyces cerevisiae and Schizosaccharomyces pombe. We screened a set of compounds of known and unknown mode of action (MoA) and derived quantitative drug scores (or D-scores), identifying mutants that are either sensitive or resistant to particular compounds. We found that compound–functional module relationships are more conserved than individual compound–gene interactions between these two species. Furthermore, we observed that combining data from both species allows for more accurate prediction of MoA. Finally, using this platform, we identified a novel small molecule that acts as a DNA damaging agent and demonstrate that its MoA is conserved in human cells.
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Combining functional genomics and chemical biology to identify targets of bioactive compounds. Curr Opin Chem Biol 2011; 15:66-78. [DOI: 10.1016/j.cbpa.2010.10.023] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2010] [Accepted: 10/20/2010] [Indexed: 01/08/2023]
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Oh J, Fung E, Schlecht U, Davis RW, Giaever G, St. Onge RP, Deutschbauer A, Nislow C. Gene annotation and drug target discovery in Candida albicans with a tagged transposon mutant collection. PLoS Pathog 2010; 6:e1001140. [PMID: 20949076 PMCID: PMC2951378 DOI: 10.1371/journal.ppat.1001140] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2010] [Accepted: 09/08/2010] [Indexed: 11/18/2022] Open
Abstract
Candida albicans is the most common human fungal pathogen, causing infections that can be lethal in immunocompromised patients. Although Saccharomyces cerevisiae has been used as a model for C. albicans, it lacks C. albicans' diverse morphogenic forms and is primarily non-pathogenic. Comprehensive genetic analyses that have been instrumental for determining gene function in S. cerevisiae are hampered in C. albicans, due in part to limited resources to systematically assay phenotypes of loss-of-function alleles. Here, we constructed and screened a library of 3633 tagged heterozygous transposon disruption mutants, using them in a competitive growth assay to examine nutrient- and drug-dependent haploinsufficiency. We identified 269 genes that were haploinsufficient in four growth conditions, the majority of which were condition-specific. These screens identified two new genes necessary for filamentous growth as well as ten genes that function in essential processes. We also screened 57 chemically diverse compounds that more potently inhibited growth of C. albicans versus S. cerevisiae. For four of these compounds, we examined the genetic basis of this differential inhibition. Notably, Sec7p was identified as the target of brefeldin A in C. albicans screens, while S. cerevisiae screens with this compound failed to identify this target. We also uncovered a new C. albicans-specific target, Tfp1p, for the synthetic compound 0136-0228. These results highlight the value of haploinsufficiency screens directly in this pathogen for gene annotation and drug target identification. Candida albicans is a normal inhabitant in our bodies, yet it can become pathogenic and cause infections that range from the superficial in healthy individuals to deadly in the immunocompromised. Comprehensive genetic analysis of C. albicans to identify mechanisms of virulence and new treatment strategies has been hampered by limited, publically accessible genomic resources. By combining the principles of Saccharomyces cerevisiae strain tagging with transposon mutagenesis to generate individually tagged mutants, we created the first entirely public resource that allows simultaneous measurement of strain fitness of ∼60% of the genome in a wide range of experimental treatments. By identifying genes that confer a fitness or growth defect when reduced in copy number, we uncovered genes whose protein products represent potential antifungal targets. Moreover, screening this strain collection with chemical compounds allowed us to identify anticandidal chemicals while concurrently gaining insight into their cellular mechanism of action. This resource, combined with straightforward screening methodology, provides powerful tools to generate hypotheses for functional annotation of the genome, and our results highlight the value of direct versus model-based pathogen studies.
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Affiliation(s)
- Julia Oh
- Department of Genetics, Stanford University, Palo Alto, California, United States of America
- Stanford Genome Technology Center, Palo Alto, California, United States of America
| | - Eula Fung
- Stanford Genome Technology Center, Palo Alto, California, United States of America
| | - Ulrich Schlecht
- Stanford Genome Technology Center, Palo Alto, California, United States of America
| | - Ronald W. Davis
- Department of Genetics, Stanford University, Palo Alto, California, United States of America
- Stanford Genome Technology Center, Palo Alto, California, United States of America
| | - Guri Giaever
- Department of Pharmaceutical Sciences, University of Toronto, Toronto, Ontario, Canada
- Banting and Best Department of Medical Research and Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Donnelley Center for Cellular and Biomolecular Research, Toronto, Ontario, Canada
| | - Robert P. St. Onge
- Stanford Genome Technology Center, Palo Alto, California, United States of America
| | - Adam Deutschbauer
- Physical Biosciences Division, Lawrence Berkeley National Lab, Berkeley, California, United States of America
- Virtual Institute for Microbial Stress and Survival, Lawrence Berkeley National Lab, Berkeley, California, United States of America
| | - Corey Nislow
- Banting and Best Department of Medical Research and Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Donnelley Center for Cellular and Biomolecular Research, Toronto, Ontario, Canada
- * E-mail:
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Staphylococcus aureus TargetArray: comprehensive differential essential gene expression as a mechanistic tool to profile antibacterials. Antimicrob Agents Chemother 2010; 54:3659-70. [PMID: 20547796 DOI: 10.1128/aac.00308-10] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The widespread emergence of antibiotic-resistant bacteria and a lack of new pharmaceutical development have catalyzed a need for new and innovative approaches for antibiotic drug discovery. One bottleneck in antibiotic discovery is the lack of a rapid and comprehensive method to identify compound mode of action (MOA). Since a hallmark of antibiotic action is as an inhibitor of essential cellular targets and processes, we identify a set of 308 essential genes in the clinically important pathogen Staphylococcus aureus. A total of 446 strains differentially expressing these genes were constructed in a comprehensive platform of sensitized and resistant strains. A subset of strains allows either target underexpression or target overexpression by heterologous promoter replacements with a suite of tetracycline-regulatable promoters. A further subset of 236 antisense RNA-expressing clones allows knockdown expression of cognate targets. Knockdown expression confers selective antibiotic hypersensitivity, while target overexpression confers resistance. The antisense strains were configured into a TargetArray in which pools of sensitized strains were challenged in fitness tests. A rapid detection method measures strain responses toward antibiotics. The TargetArray antibiotic fitness test results show mechanistically informative biological fingerprints that allow MOA elucidation.
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