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Zong G, Fu J, Zhang P, Zhang W, Xu Y, Cao G, Zhang R. Use of elicitors to enhance or activate the antibiotic production in streptomyces. Crit Rev Biotechnol 2021; 42:1260-1283. [PMID: 34706600 DOI: 10.1080/07388551.2021.1987856] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Streptomyces is the largest and most significant genus of Actinobacteria, comprising 961 species. These Gram-positive bacteria produce many versatile and important bioactive compounds; of these, antibiotics, specifically the enhancement or activation of their production, have received extensive research attention. Recently, various biotic and abiotic elicitors have been reported to modify the antibiotic metabolism of Streptomyces, which promotes the production of new antibiotics and bioactive metabolites for improvement in the yields of endogenous products. However, some elicitors that obviously contribute to secondary metabolite production have not yet received sufficient attention. In this study, we have reviewed the functions and mechanisms of chemicals, novel microbial metabolic elicitors, microbial interactions, enzymes, enzyme inhibitors, environmental factors, and novel combination methods regarding antibiotic production in Streptomyces. This review has aimed to identify potentially valuable elicitors for stimulating the production of latent antibiotics or enhancing the synthesis of subsistent antibiotics in Streptomyces. Future applications and challenges in the discovery of new antibiotics and enhancement of existing antibiotic production using elicitors are discussed.
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Affiliation(s)
- Gongli Zong
- Key Laboratory of Industrial Biotechnology of Ministry of Education & School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China.,Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, China
| | - Jiafang Fu
- Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, China
| | - Peipei Zhang
- Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, China
| | - Wenchi Zhang
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Yan Xu
- Key Laboratory of Industrial Biotechnology of Ministry of Education & School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Guangxiang Cao
- Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, China
| | - Rongzhen Zhang
- Key Laboratory of Industrial Biotechnology of Ministry of Education & School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
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2
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Brown AS, Owen JG, Jung J, Baker EN, Ackerley DF. Inhibition of Indigoidine Synthesis as a High-Throughput Colourimetric Screen for Antibiotics Targeting the Essential Mycobacterium tuberculosis Phosphopantetheinyl Transferase PptT. Pharmaceutics 2021; 13:pharmaceutics13071066. [PMID: 34371757 PMCID: PMC8309046 DOI: 10.3390/pharmaceutics13071066] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/07/2021] [Accepted: 07/09/2021] [Indexed: 11/16/2022] Open
Abstract
A recently-validated and underexplored drug target in Mycobacterium tuberculosis is PptT, an essential phosphopantetheinyl transferase (PPTase) that plays a critical role in activating enzymes for both primary and secondary metabolism. PptT possesses a deep binding pocket that does not readily accept labelled coenzyme A analogues that have previously been used to screen for PPTase inhibitors. Here we report on the development of a high throughput, colourimetric screen that monitors the PptT-mediated activation of the non-ribosomal peptide synthetase BpsA to a blue pigment (indigoidine) synthesising form in vitro. This screen uses unadulterated coenzyme A, avoiding analogues that may interfere with inhibitor binding, and requires only a single-endpoint measurement. We benchmark the screen using the well-characterised Library of Pharmaceutically Active Compounds (LOPAC1280) collection and show that it is both sensitive and able to distinguish weak from strong inhibitors. We further show that the BpsA assay can be applied to quantify the level of inhibition and generate consistent EC50 data. We anticipate these tools will facilitate both the screening of established chemical collections to identify new anti-mycobacterial drug leads and to guide the exploration of structure-activity landscapes to improve existing PPTase inhibitors.
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Affiliation(s)
- Alistair S. Brown
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand; (A.S.B.); (J.G.O.)
- Centre for Biodiscovery, Victoria University of Wellington, Wellington 6012, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1142, New Zealand; (J.J.); (E.N.B.)
| | - Jeremy G. Owen
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand; (A.S.B.); (J.G.O.)
- Centre for Biodiscovery, Victoria University of Wellington, Wellington 6012, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1142, New Zealand; (J.J.); (E.N.B.)
| | - James Jung
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1142, New Zealand; (J.J.); (E.N.B.)
- School of Biological Sciences, University of Auckland, Auckland 1142, New Zealand
| | - Edward N. Baker
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1142, New Zealand; (J.J.); (E.N.B.)
- School of Biological Sciences, University of Auckland, Auckland 1142, New Zealand
| | - David F. Ackerley
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand; (A.S.B.); (J.G.O.)
- Centre for Biodiscovery, Victoria University of Wellington, Wellington 6012, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1142, New Zealand; (J.J.); (E.N.B.)
- Correspondence: ; Tel.: +64-4-4635576
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3
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Zhang J, Liang Q, Xu Z, Cui M, Zhang Q, Abreu S, David M, Lejeune C, Chaminade P, Virolle MJ, Xu D. The Inhibition of Antibiotic Production in Streptomyces coelicolor Over-Expressing the TetR Regulator SCO3201 IS Correlated With Changes in the Lipidome of the Strain. Front Microbiol 2020; 11:1399. [PMID: 32655536 PMCID: PMC7324645 DOI: 10.3389/fmicb.2020.01399] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Accepted: 05/29/2020] [Indexed: 12/25/2022] Open
Abstract
In condition of over-expression, SCO3201, a regulator of the TetR family was previously shown to strongly inhibit antibiotic production and morphological differentiation in Streptomyces coelicolor M145. In order to elucidate the molecular processes underlying this interesting, but poorly understood phenomenon, a comparative analysis of the lipidomes and transcriptomes of the strain over-expressing sco3201 and of the control strain containing the empty plasmid, was carried out. This study revealed that the strain over-expressing sco3201 had a higher triacylglycerol content and a lower phospholipids content than the control strain. This was correlated with up- and down- regulation of some genes involved in fatty acids biosynthesis (fab) and degradation (fad) respectively, indicating a direct or indirect control of the expression of these genes by SCO3201. In some instances, indirect control might involve TetR regulators, whose encoding genes present in close vicinity of genes involved in lipid metabolism, were shown to be differentially expressed in the two strains. Direct interaction of purified His6-SCO3201 with the promoter regions of four of such TetR regulators encoding genes (sco0116, sco0430, sco4167, and sco6792) was demonstrated. Furthermore, fasR (sco2386), encoding the activator of the main fatty acid biosynthetic operon, sco2386-sco2390, has been shown to be an illegitimate positive regulatory target of SCO3201. Altogether our data demonstrated that the sco3201 over-expressing strain accumulates TAG and suggested that degradation of fatty acids was reduced in this strain. This is expected to result into a reduced acetyl-CoA availability that would impair antibiotic biosynthesis either directly or indirectly.
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Affiliation(s)
- Jun Zhang
- Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Department of Ecology, School of Life Sciences and Technology, Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Institute of Hydrobiology, Jinan University, Guangzhou, China
| | - Qiting Liang
- Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Department of Ecology, School of Life Sciences and Technology, Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Institute of Hydrobiology, Jinan University, Guangzhou, China
| | - Zhongheng Xu
- Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Department of Ecology, School of Life Sciences and Technology, Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Institute of Hydrobiology, Jinan University, Guangzhou, China
| | - Miao Cui
- Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Department of Ecology, School of Life Sciences and Technology, Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Institute of Hydrobiology, Jinan University, Guangzhou, China
| | - Qizhong Zhang
- Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Department of Ecology, School of Life Sciences and Technology, Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Institute of Hydrobiology, Jinan University, Guangzhou, China
| | - Sonia Abreu
- Université Paris-Saclay, Lipides, Systèmes Analytiques et Biologiques, Châtenay-Malabry, France
| | - Michelle David
- Group “Energetic Metabolism of Streptomyces”, Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, INRA, University Paris-Saclay, Gif-sur-Yvette, France
| | - Clara Lejeune
- Group “Energetic Metabolism of Streptomyces”, Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, INRA, University Paris-Saclay, Gif-sur-Yvette, France
| | - Pierre Chaminade
- Université Paris-Saclay, Lipides, Systèmes Analytiques et Biologiques, Châtenay-Malabry, France
| | - Marie-Joelle Virolle
- Group “Energetic Metabolism of Streptomyces”, Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, INRA, University Paris-Saclay, Gif-sur-Yvette, France
| | - Delin Xu
- Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Department of Ecology, School of Life Sciences and Technology, Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Institute of Hydrobiology, Jinan University, Guangzhou, China
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David M, Lejeune C, Abreu S, Thibessard A, Leblond P, Chaminade P, Virolle MJ. Negative Correlation between Lipid Content and Antibiotic Activity in Streptomyces: General Rule and Exceptions. Antibiotics (Basel) 2020; 9:E280. [PMID: 32466356 PMCID: PMC7344866 DOI: 10.3390/antibiotics9060280] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 05/19/2020] [Accepted: 05/20/2020] [Indexed: 12/26/2022] Open
Abstract
Streptomycetes are well known antibiotic producers and are among the rare prokaryotes able to store carbon as lipids. Previous comparative studies of the weak antibiotic producer Streptomyces lividans with its ppk mutant and with Streptomyces coelicolor, which both produce antibiotics, suggested the existence of a negative correlation between total lipid content and the ability to produce antibiotics. To determine whether such a negative correlation can be generalized to other Streptomyces species, fifty-four strains were picked randomly and grown on modified R2YE medium, limited in phosphate, with glucose or glycerol as the main carbon source. The total lipid content and antibiotic activity against Micrococcus luteus were assessed for each strain. This study revealed that the ability to accumulate lipids was not evenly distributed among strains and that glycerol was more lipogenic than glucose and had a negative impact on antibiotic biosynthesis. Furthermore, a statistically significant negative Pearson correlation between lipid content and antibiotic activity could be established for most strains, but a few strains escape this general law. These exceptions are likely due to limits and biases linked to the type of test used to determine antibiotic activity, which relies exclusively on Micrococcus luteus sensitivity. They are characterized either by high lipid content and high antibiotic activity or by low lipid content and undetectable antibiotic activity against Micrococcus luteus. Lastly, the comparative genomic analysis of two strains with contrasting lipid content, and both named Streptomyces antibioticus (DSM 41,481 and DSM 40,868, which we found to be phylogenetically related to Streptomyces lavenduligriseus), indicated that some genetic differences in various pathways related to the generation/consumption of acetylCoA could be responsible for such a difference.
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Affiliation(s)
- Michelle David
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette, France; (M.D.); (C.L.)
| | - Clara Lejeune
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette, France; (M.D.); (C.L.)
| | - Sonia Abreu
- Lipides, Systèmes Analytiques et Biologiques, Université Paris-Saclay, 92296 Châtenay-Malabry, France; (S.A.); (P.C.)
| | | | - Pierre Leblond
- Université de Lorraine, INRAE, DynAMic, F-54000 Nancy, France; (A.T.); (P.L.)
| | - Pierre Chaminade
- Lipides, Systèmes Analytiques et Biologiques, Université Paris-Saclay, 92296 Châtenay-Malabry, France; (S.A.); (P.C.)
| | - Marie-Joelle Virolle
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette, France; (M.D.); (C.L.)
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5
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Houšť J, Spížek J, Havlíček V. Antifungal Drugs. Metabolites 2020; 10:metabo10030106. [PMID: 32178468 PMCID: PMC7143493 DOI: 10.3390/metabo10030106] [Citation(s) in RCA: 113] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 03/08/2020] [Accepted: 03/10/2020] [Indexed: 12/26/2022] Open
Abstract
We reviewed the licensed antifungal drugs and summarized their mechanisms of action, pharmacological profiles, and susceptibility to specific fungi. Approved antimycotics inhibit 1,3-β-d-glucan synthase, lanosterol 14-α-demethylase, protein, and deoxyribonucleic acid biosynthesis, or sequestrate ergosterol. Their most severe side effects are hepatotoxicity, nephrotoxicity, and myelotoxicity. Whereas triazoles exhibit the most significant drug–drug interactions, echinocandins exhibit almost none. The antifungal resistance may be developed across most pathogens and includes drug target overexpression, efflux pump activation, and amino acid substitution. The experimental antifungal drugs in clinical trials are also reviewed. Siderophores in the Trojan horse approach or the application of siderophore biosynthesis enzyme inhibitors represent the most promising emerging antifungal therapies.
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6
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Streptomyces Differentiation in Liquid Cultures as a Trigger of Secondary Metabolism. Antibiotics (Basel) 2018; 7:antibiotics7020041. [PMID: 29757948 PMCID: PMC6022995 DOI: 10.3390/antibiotics7020041] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 05/09/2018] [Accepted: 05/09/2018] [Indexed: 02/08/2023] Open
Abstract
Streptomyces is a diverse group of gram-positive microorganisms characterised by a complex developmental cycle. Streptomycetes produce a number of antibiotics and other bioactive compounds used in the clinic. Most screening campaigns looking for new bioactive molecules from actinomycetes have been performed empirically, e.g., without considering whether the bacteria are growing under the best developmental conditions for secondary metabolite production. These screening campaigns were extremely productive and discovered a number of new bioactive compounds during the so-called “golden age of antibiotics” (until the 1980s). However, at present, there is a worrying bottleneck in drug discovery, and new experimental approaches are needed to improve the screening of natural actinomycetes. Streptomycetes are still the most important natural source of antibiotics and other bioactive compounds. They harbour many cryptic secondary metabolite pathways not expressed under classical laboratory cultures. Here, we review the new strategies that are being explored to overcome current challenges in drug discovery. In particular, we focus on those aimed at improving the differentiation of the antibiotic-producing mycelium stage in the laboratory.
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7
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Ishikawa F, Tanabe G, Kakeya H. Activity-Based Protein Profiling of Non-ribosomal Peptide Synthetases. Curr Top Microbiol Immunol 2018; 420:321-349. [PMID: 30178264 DOI: 10.1007/82_2018_133] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Non-ribosomal peptide (NRP) natural products are one of the most promising resources for drug discovery and development because of their wide-ranging of therapeutic potential, and their behavior as virulence factors and signaling molecules. The NRPs are biosynthesized independently of the ribosome by enzyme assembly lines known as the non-ribosomal peptide synthetase (NRPS) machinery. Genetic, biochemical, and bioinformatics analyses have provided a detailed understanding of the mechanism of NRPS catalysis. However, proteomic techniques for natural product biosynthesis remain a developing field. New strategies are needed to investigate the proteomes of diverse producer organisms and directly analyze the endogenous NRPS machinery. Advanced platforms should verify protein expression, protein folding, and activities and also enable the profiling of the NRPS machinery in biological samples from wild-type, heterologous, and engineered bacterial systems. Here, we focus on activity-based protein profiling strategies that have been recently developed for studies aimed at visualizing and monitoring the NRPS machinery and also for rapid labeling, identification, and biochemical analysis of NRPS enzyme family members as required for proteomic chemistry in natural product sciences.
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Affiliation(s)
- Fumihiro Ishikawa
- Faculty of Pharmacy, Kindai University, 3-4-1 Kowakae, Higashi-Osaka, Osaka, 577-8502, Japan.
| | - Genzoh Tanabe
- Faculty of Pharmacy, Kindai University, 3-4-1 Kowakae, Higashi-Osaka, Osaka, 577-8502, Japan
| | - Hideaki Kakeya
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto, 606-8501, Japan.
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Zhang B, Tian W, Wang S, Yan X, Jia X, Pierens GK, Chen W, Ma H, Deng Z, Qu X. Activation of Natural Products Biosynthetic Pathways via a Protein Modification Level Regulation. ACS Chem Biol 2017; 12:1732-1736. [PMID: 28562006 DOI: 10.1021/acschembio.7b00225] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Natural products are critical for drug discovery and development; however their discovery is challenged by the wide inactivation or silence of microbial biosynthetic pathways. Currently strategies targeting this problem are mainly concentrated on chromosome dissembling, transcription, and translation-stage regulations as well as chemical stimulation. In this study, we developed a novel approach to awake cryptic/silenced microbial biosynthetic pathways through augmentation of the conserved protein modification step-phosphopantetheinylation of carrier proteins. Overexpression of phosphopantetheinyl transferase (Pptase) genes into 33 Actinomycetes achieved a significantly high activation ratio at which 23 (70%) strains produced new metabolites. Genetic and biochemical studies on the mode-of-action revealed that exogenous PPtases triggered the activation of carrier proteins and subsequent production of metabolites. With this approach we successfully identified five oviedomycin and halichomycin-like compounds from two strains. This study provides a novel approach to efficiently activate cryptic/silenced biosynthetic pathways which will be useful for natural products discovery.
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Affiliation(s)
- Benyin Zhang
- Key
Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry
of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan, Hubei, China, 430072
- State
Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, China
| | - Wenya Tian
- Key
Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry
of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan, Hubei, China, 430072
| | - Shuwen Wang
- Key
Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry
of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan, Hubei, China, 430072
| | - Xiaoli Yan
- Key
Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry
of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan, Hubei, China, 430072
| | - Xinying Jia
- Centre
for Advanced Imaging, The University of Queensland, Brisbane, Queensland, Australia
| | - Gregory K. Pierens
- Centre
for Advanced Imaging, The University of Queensland, Brisbane, Queensland, Australia
| | - Wenqing Chen
- Key
Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry
of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan, Hubei, China, 430072
| | - Hongmin Ma
- Key
Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry
of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan, Hubei, China, 430072
| | - Zixin Deng
- Key
Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry
of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan, Hubei, China, 430072
| | - Xudong Qu
- Key
Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry
of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan, Hubei, China, 430072
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing, Jiangsu, China
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Strong antibiotic production is correlated with highly active oxidative metabolism in Streptomyces coelicolor M145. Sci Rep 2017; 7:200. [PMID: 28298624 PMCID: PMC5427975 DOI: 10.1038/s41598-017-00259-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 02/10/2017] [Indexed: 11/08/2022] Open
Abstract
The Streptomyces genus is well known for its ability to produce bio-active secondary metabolites of great medical interest. However, the metabolic features accompanying these bio-productions remain to be defined. In this study, the comparison of related model strains producing differing levels of actinorhoddin (ACT), showed that S. lividans, a weak producer, had high TriAcylGlycerol (TAG) content indicative of a glycolytic metabolism. In contrast, the strong producer, S. coelicolor, was characterized by low TAG content, active consumption of its polyphosphate (PolyP) stores and extremely high ATP/ADP ratios. This indicated highly active oxidative metabolism that was correlated with induction of ACT biosynthesis. Interestingly, in conditions of phosphate limitation, the ppk mutant had TAG content and ACT production levels intermediary between those of S. lividans and S. coelicolor. This strain was characterized by high ADP levels indicating that Ppk was acting as an Adenosine Di Phosphate Kinase. Its absence resulted in energetic stress that is proposed to trigger an activation of oxidative metabolism to restore its energetic balance. This process, which is correlated with ACT biosynthesis, requires acetylCoA to fuel the Krebs cycle and phosphate for ATP generation by the ATP synthase coupled to the respiratory chain, resulting in low TAG and polyP content of the ACT producing strains.
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10
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Zimhony O, Schwarz A, Raitses-Gurevich M, Peleg Y, Dym O, Albeck S, Burstein Y, Shakked Z. AcpM, the meromycolate extension acyl carrier protein of Mycobacterium tuberculosis, is activated by the 4'-phosphopantetheinyl transferase PptT, a potential target of the multistep mycolic acid biosynthesis. Biochemistry 2015; 54:2360-71. [PMID: 25785780 DOI: 10.1021/bi501444e] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Modification of acyl carrier proteins (ACP) or domains by the covalent binding of a 4'-phosphopantetheine (4'-PP) moiety is a fundamental condition for activation of fatty acid synthases (FASes) and polyketide synthases (PKSes). Binding of 4'-PP is mediated by 4' phosphopantetheinyl transfersases (PPTases). Mycobacterium tuberculosis (Mtb) possesses two essential PPTases: acyl carrier protein synthase (Mtb AcpS), which activates the multidomain fatty acid synthase I (FAS I), and Mtb PptT, an Sfp-type broad spectrum PPTase that activates PKSes. To date, it has not been determined which of the two Mtb PPTases, AcpS or PptT, activates the meromycolate extension ACP, Mtb AcpM, en route to the production of mycolic acids, the main components of the mycobacterial cell wall. In this study, we tested the enzymatic activation of a highly purified Mtb apo-AcpM to Mtb holo-AcpM by either Mtb PptT or Mtb AcpS. By using SDS-PAGE band shift assay and mass spectrometry analysis, we found that Mtb PptT is the PPTase that activates Mtb AcpM. We measured the catalytic activity of Mtb PptT toward CoA, using an activation assay of a blue pigment synthase, BpsA (a nonribosomal peptide synthase, NRPS). BpsA activation by Mtb PptT was inhibited by Mtb apo-AcpM through competition for CoA, in accord with Mtb AcpM activation. A structural model of the putative interaction between Mtb PptT and Mtb AcpM suggests that both hydrophobic and electrostatic interactions stabilize this complex. To conclude, activation of Mtb AcpM by Mtb PptT reveals a potential target of the multistep mycolic acid biosynthesis.
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Affiliation(s)
- Oren Zimhony
- †Kaplan Medical Center, Affiliated to the School of Medicine, Hebrew University of Jerusalem and Hadassah Medical Center, POB1 Rehovot 76100, Israel
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11
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Liu P, Cooks RG, Chen H. Nuclear Magnetic Resonance Structure Elucidation of Peptideb2Ions. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201410250] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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12
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Liu P, Cooks RG, Chen H. Nuclear magnetic resonance structure elucidation of peptide b2 ions. Angew Chem Int Ed Engl 2014; 54:1547-50. [PMID: 25504444 DOI: 10.1002/anie.201410250] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2014] [Indexed: 11/06/2022]
Abstract
Tandem mass spectrometry (MS/MS) is powerful for chemical identification but it is still insufficient for explicit ion structure determination. A strategy is introduced to elucidate MS fragment ion structures using NMR spectroscopy for the first time. In our experiments, precursor ions are dissociated at atmospheric pressure and the resulting fragment ions are identified by mass spectrometry but collected outside the mass spectrometer, making the subsequent NMR measurements possible. This new strategy has been applied to determine the chemical structure of the characteristic b2 fragment ion, a subject of longstanding debate in MS-based proteomics.
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Affiliation(s)
- Pengyuan Liu
- Center for Intelligent Chemical Instrumentation, Department of Chemistry and Biochemistry & Edison Biotechnology Institute, Ohio University, Athens, OH 45701 (USA)
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13
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Kosa NM, Pham KM, Burkart MD. Chemoenzymatic exchange of phosphopantetheine on protein and peptide. Chem Sci 2014; 5:1179-1186. [PMID: 26998215 PMCID: PMC4795179 DOI: 10.1039/c3sc53154f] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Evaluation of new acyl carrier protein hydrolase (AcpH, EC 3.1.4.14) homologs from proteobacteria and cyanobacteria reveals significant variation in substrate selectivity and kinetic parameters for phosphopantetheine hydrolysis from carrier proteins. Evaluation with carrier proteins from both primary and secondary metabolic pathways reveals an overall preference for acyl carrier protein (ACP) substrates from type II fatty acid synthases, as well as variable activity for polyketide synthase ACPs and peptidyl carrier proteins (PCP) from non-ribosomal peptide synthases. We also demonstrate the kinetic parameters of these homologs for AcpP and the 11-mer peptide substrate YbbR. These findings enable the fully reversible labeling of all three classes of natural product synthase carrier proteins as well as full and minimal fusion protein constructs.
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Affiliation(s)
- Nicolas M. Kosa
- Department of Chemistry and Biochemistry, University of California, San Diego (UCSD), La Jolla, California, USA
| | - Kevin M. Pham
- Department of Chemistry and Biochemistry, University of California, San Diego (UCSD), La Jolla, California, USA
| | - Michael D. Burkart
- Department of Chemistry and Biochemistry, University of California, San Diego (UCSD), La Jolla, California, USA
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14
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Foley TL, Rai G, Yasgar A, Daniel T, Baker HL, Attene-Ramos M, Kosa NM, Leister W, Burkart MD, Jadhav A, Simeonov A, Maloney DJ. 4-(3-Chloro-5-(trifluoromethyl)pyridin-2-yl)-N-(4-methoxypyridin-2-yl)piperazine-1-carbothioamide (ML267), a potent inhibitor of bacterial phosphopantetheinyl transferase that attenuates secondary metabolism and thwarts bacterial growth. J Med Chem 2014; 57:1063-78. [PMID: 24450337 PMCID: PMC3983359 DOI: 10.1021/jm401752p] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
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4′-Phosphopantetheinyl
transferases (PPTases) catalyze a post-translational modification
essential to bacterial cell viability and virulence. We present the
discovery and medicinal chemistry optimization of 2-pyridinyl-N-(4-aryl)piperazine-1-carbothioamides, which exhibit submicromolar
inhibition of bacterial Sfp-PPTase with no activity toward the human
orthologue. Moreover, compounds within this class possess antibacterial
activity in the absence of a rapid cytotoxic response in human cells.
An advanced analogue of this series, ML267 (55), was
found to attenuate production of an Sfp-PPTase-dependent metabolite
when applied to Bacillus subtilis at
sublethal doses. Additional testing revealed antibacterial activity
against methicillin-resistant Staphylococcus aureus, and chemical genetic studies implicated efflux as a mechanism for
resistance in Escherichia coli. Additionally,
we highlight the in vitro absorption, distribution, metabolism, and
excretion and in vivo pharmacokinetic profiles of compound 55 to further demonstrate the potential utility of this small-molecule
inhibitor.
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Affiliation(s)
- Timothy L Foley
- National Center for Advancing Translational Sciences, National Institutes of Health , 9800 Medical Center Drive, Rockville, Maryland 20850, United States
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15
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Beld J, Sonnenschein EC, Vickery CR, Noel JP, Burkart MD. The phosphopantetheinyl transferases: catalysis of a post-translational modification crucial for life. Nat Prod Rep 2014; 31:61-108. [PMID: 24292120 PMCID: PMC3918677 DOI: 10.1039/c3np70054b] [Citation(s) in RCA: 240] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Covering: up to 2013. Although holo-acyl carrier protein synthase, AcpS, a phosphopantetheinyl transferase (PPTase), was characterized in the 1960s, it was not until the publication of the landmark paper by Lambalot et al. in 1996 that PPTases garnered wide-spread attention being classified as a distinct enzyme superfamily. In the past two decades an increasing number of papers have been published on PPTases ranging from identification, characterization, structure determination, mutagenesis, inhibition, and engineering in synthetic biology. In this review, we comprehensively discuss all current knowledge on this class of enzymes that post-translationally install a 4'-phosphopantetheine arm on various carrier proteins.
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Affiliation(s)
- Joris Beld
- Department of Chemistry and Biochemistry, University of California-San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA.
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16
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Yoon V, Nodwell JR. Activating secondary metabolism with stress and chemicals. J Ind Microbiol Biotechnol 2013; 41:415-24. [PMID: 24326978 DOI: 10.1007/s10295-013-1387-y] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Accepted: 11/22/2013] [Indexed: 10/25/2022]
Abstract
The available literature on the secondary or nonessential metabolites of the streptomycetes bacteria suggests that there may be poorly expressed or "cryptic" compounds that have yet to be identified and that may have significant medical utility. In addition, it is clear that there is a large and complex regulatory network that controls the production of these molecules in the laboratory and in nature. Two approaches that have been taken to manipulating the yields of secondary metabolites are the use of various stress responses and, more recently, the use of precision chemical probes. Here, we review the status of this work and outline the challenges and opportunities afforded by each of them.
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Affiliation(s)
- Vanessa Yoon
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada
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17
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Kosa NM, Foley TL, Burkart MD. Fluorescent techniques for discovery and characterization of phosphopantetheinyl transferase inhibitors. J Antibiot (Tokyo) 2013; 67:113-20. [PMID: 24192555 DOI: 10.1038/ja.2013.106] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Revised: 08/26/2013] [Accepted: 09/13/2013] [Indexed: 11/09/2022]
Abstract
Phosphopantetheinyl transferase (PPTase; E.C. 2.7.8.-) activates biosynthetic pathways that synthesize both primary and secondary metabolites in bacteria. Inhibitors of these enzymes have the potential to serve as antibiotic compounds that function through a unique mode of action and possess clinical utility. Here we report a direct and continuous assay for this enzyme class based upon monitoring polarization of a fluorescent phosphopantetheine analog as it is transferred from a low-molecular weight CoA substrate to higher-molecular weight protein acceptor. We demonstrate the utility of this method for the biochemical characterization of PPTase Sfp, a canonical representative from this class. We also establish the portability of this technique to other homologs by adapting the assay to function with the human PPTase, a target for which a microplate detection method does not currently exist. Comparison of these targets provides a basis to predict the therapeutic index of inhibitor candidates and offers a valuable characterization of enzyme activity.
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Affiliation(s)
- Nicolas M Kosa
- Department of Chemistry and Biochemistry, University of California, San Diego (UCSD), La Jolla, CA, USA
| | - Timothy L Foley
- Department of Chemistry and Biochemistry, University of California, San Diego (UCSD), La Jolla, CA, USA
| | - Michael D Burkart
- Department of Chemistry and Biochemistry, University of California, San Diego (UCSD), La Jolla, CA, USA
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18
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Craney A, Ahmed S, Nodwell J. Towards a new science of secondary metabolism. J Antibiot (Tokyo) 2013; 66:387-400. [PMID: 23612726 DOI: 10.1038/ja.2013.25] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Revised: 01/12/2013] [Accepted: 02/12/2013] [Indexed: 12/20/2022]
Abstract
Secondary metabolites are a reliable and very important source of medicinal compounds. While these molecules have been mined extensively, genome sequencing has suggested that there is a great deal of chemical diversity and bioactivity that remains to be discovered and characterized. A central challenge to the field is that many of the novel or poorly understood molecules are expressed at low levels in the laboratory-such molecules are often described as the 'cryptic' secondary metabolites. In this review, we will discuss evidence that research in this field has provided us with sufficient knowledge and tools to express and purify any secondary metabolite of interest. We will describe 'unselective' strategies that bring about global changes in secondary metabolite output as well as 'selective' strategies where a specific biosynthetic gene cluster of interest is manipulated to enhance the yield of a single product.
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Affiliation(s)
- Arryn Craney
- Department of Biochemistry and Biomedical Sciences, McMaster University, Michael Degroote Institute for Infectious Diseases Research, Hamilton, Ontario, Canada
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19
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Leblanc C, Prudhomme T, Tabouret G, Ray A, Burbaud S, Cabantous S, Mourey L, Guilhot C, Chalut C. 4'-Phosphopantetheinyl transferase PptT, a new drug target required for Mycobacterium tuberculosis growth and persistence in vivo. PLoS Pathog 2012; 8:e1003097. [PMID: 23308068 PMCID: PMC3534377 DOI: 10.1371/journal.ppat.1003097] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Accepted: 11/08/2012] [Indexed: 11/18/2022] Open
Abstract
The cell envelope of Mycobacterium tuberculosis, the causative agent of tuberculosis in humans, contains lipids with unusual structures. These lipids play a key role in both virulence and resistance to the various hostile environments encountered by the bacteria during infection. They are synthesized by complex enzymatic systems, including type-I polyketide synthases and type-I and -II fatty acid synthases, which require a post-translational modification to become active. This modification consists of the covalent attachment of the 4′-phosphopantetheine moiety of Coenzyme A catalyzed by phosphopantetheinyl transferases (PPTases). PptT, one of the two PPTases produced by mycobacteria, is involved in post-translational modification of various type-I polyketide synthases required for the formation of both mycolic acids and lipid virulence factors in mycobacteria. Here we identify PptT as a new target for anti-tuberculosis drugs; we address all the critical issues of target validation to demonstrate that PptT can be used to search for new drugs. We confirm that PptT is essential for the growth of M. bovis BCG in vitro and show that it is required for persistence of M. bovis BCG in both infected macrophages and immunodeficient mice. We generated a conditional expression mutant of M. tuberculosis, in which the expression of the pptT gene is tightly regulated by tetracycline derivatives. We used this construct to demonstrate that PptT is required for the replication and survival of the tubercle bacillus during the acute and chronic phases of infection in mice. Finally, we developed a robust and miniaturized assay based on scintillation proximity assay technology to search for inhibitors of PPTases, and especially of PptT, by high-throughput screening. Our various findings indicate that PptT meets the key criteria for being a therapeutic target for the treatment of mycobacterial infections. Mycobacterium tuberculosis, the causative agent of human tuberculosis, is responsible for more than 8 million new cases and 1.5 million deaths every year. Despite the existence of effective treatments, the emergence of resistance makes the need for new anti-tuberculosis drugs urgent. The cell envelope of the tubercle bacillus undoubtedly plays a key role in pathogenicity. The envelope has very high lipid content and contains lipids with unusual structures. Some of these lipids are synthesized by complex enzymatic systems that can only become functional after post-translational modification by a 4′-phosphopantetheinyl transferase named PptT. We report that PptT is essential for the viability of M. tuberculosis in vitro and of M. tuberculosis and its close relative M. bovis BCG in both macrophages and the mouse model. Our findings demonstrate that PptT plays a key role in multiplication and persistence of the tubercle bacillus and is therefore an attractive target for drug discovery. We also developed an in vitro assay that promises to be a powerful tool for high-throughput screening of PptT inhibitors.
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Affiliation(s)
- Cécile Leblanc
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), Toulouse, France
- Université de Toulouse, UPS, IPBS, Toulouse, France
| | - Thomas Prudhomme
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), Toulouse, France
- Université de Toulouse, UPS, IPBS, Toulouse, France
| | - Guillaume Tabouret
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), Toulouse, France
- Université de Toulouse, UPS, IPBS, Toulouse, France
| | - Aurélie Ray
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), Toulouse, France
- Université de Toulouse, UPS, IPBS, Toulouse, France
| | - Sophie Burbaud
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), Toulouse, France
- Université de Toulouse, UPS, IPBS, Toulouse, France
| | - Stéphanie Cabantous
- Centre de Recherche en Cancérologie (CRCT), UMR 1037 INSERM-CNRS-UPS Institut Claudius Regaud, Toulouse, France
| | - Lionel Mourey
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), Toulouse, France
- Université de Toulouse, UPS, IPBS, Toulouse, France
| | - Christophe Guilhot
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), Toulouse, France
- Université de Toulouse, UPS, IPBS, Toulouse, France
- * E-mail: (CC); (CG)
| | - Christian Chalut
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), Toulouse, France
- Université de Toulouse, UPS, IPBS, Toulouse, France
- * E-mail: (CC); (CG)
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20
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Kosa NM, Haushalter RW, Smith AR, Burkart MD. Reversible labeling of native and fusion-protein motifs. Nat Methods 2012; 9:981-4. [PMID: 22983458 PMCID: PMC4128096 DOI: 10.1038/nmeth.2175] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Accepted: 08/23/2012] [Indexed: 11/09/2022]
Abstract
The reversible covalent attachment of chemical probes to proteins has long been sought as a means to visualize and manipulate proteins. Here we demonstrate the full reversibility of post-translational custom pantetheine modification of Escherichia coli acyl carrier protein for visualization and functional studies. We use this iterative enzymatic methodology in vitro to reversibly label acyl carrier protein variants and apply these tools to NMR structural studies of protein-substrate interactions.
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Affiliation(s)
- Nicolas M. Kosa
- University of California San Diego, La Jolla, California, USA
| | | | - Andrew R. Smith
- University of California San Diego, La Jolla, California, USA
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21
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Rapid and flexible biochemical assays for evaluating 4′-phosphopantetheinyl transferase activity. Biochem J 2011; 436:709-17. [DOI: 10.1042/bj20110321] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
PPTases (phosphopantetheinyl transferases) are of great interest owing to their essential roles in activating fatty acid, polyketide and non-ribosomal peptide synthetase enzymes for both primary and secondary metabolism, as well as an increasing number of biotechnological applications. However, existing techniques for PPTase characterization and development are cumbersome and technically challenging. To address this, we have developed the indigoidine-synthesizing non-ribosomal peptide synthetase BpsA as a reporter for PPTase activity. Simple co-transformation allows rapid assessment of the ability of a PPTase candidate to activate BpsA in vivo. Kinetic parameters with respect to either CoA or BpsA as variable substrate can then be derived in vitro by continuously measuring the rate of indigoidine synthesis as the PPTase progressively converts BpsA from its apo into holo form. Subsequently, a competition assay, in which BpsA and purified carrier proteins compete for a limited pool of CoA, enables elucidation of kinetic parameters for a PPTase with those carrier proteins. We used this system to conduct a rapid characterization of three different PPTase enzymes: Sfp of Bacillus subtilis A.T.C.C.6633, PcpS of Pseudomonas aeruginosa PAO1, and the putative PPTase PP1183 of Ps. putida KT2440. We also demonstrate the utility of this system for discovery and characterization of PPTase inhibitors.
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22
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Allen G, Bromley M, Kaye SJ, Keszenman-Pereyra D, Zucchi TD, Price J, Birch M, Oliver JD, Turner G. Functional analysis of a mitochondrial phosphopantetheinyl transferase (PPTase) gene pptB in Aspergillus fumigatus. Fungal Genet Biol 2011; 48:456-64. [DOI: 10.1016/j.fgb.2010.12.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2010] [Revised: 12/13/2010] [Accepted: 12/13/2010] [Indexed: 11/28/2022]
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23
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Foley TL, Yasgar A, Garcia CJ, Jadhav A, Simeonov A, Burkart MD. Preparation of FRET reporters to support chemical probe development. Org Biomol Chem 2010; 8:4601-6. [PMID: 20725690 DOI: 10.1039/c0ob00322k] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In high throughput screening (HTS) campaigns, the quality and cost of commercial reagents suitable for pilot studies often create obstacles upon scale-up to a full screen. We faced such challenges in our efforts to implement an HTS for inhibitors of the phosphopantetheinyl transferase Sfp using an assay that had been validated using commercially available reagents. Here we demonstrate a facile route to the synthetic preparation of reactive tetraethylrhodamine and quencher probes, and their application to economically produce fluorescent and quencher-modified substrates. These probes were prepared on a scale that would allow a full, quantitative HTS of more than 350,000 compounds.
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Affiliation(s)
- Timothy L Foley
- Department of Chemistry and Biochemistry, University of California-San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA
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