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Li H, Li H, Chen S, Wu W, Sun P. Isolation and Identification of Pentalenolactone Analogs from Streptomyces sp. NRRL S-4. Molecules 2021; 26:molecules26237377. [PMID: 34885958 PMCID: PMC8659275 DOI: 10.3390/molecules26237377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/30/2021] [Accepted: 12/01/2021] [Indexed: 11/16/2022] Open
Abstract
Terpene synthases are widely distributed in Actinobacteria. Genome sequencing of Streptomyces sp. NRRL S-4 uncovered a biosynthetic gene cluster (BGC) that putatively synthesizes pentalenolactone type terpenes. Guided by genomic information, the S-4 strain was chemically investigated, resulting in the isolation of two new sesquiterpenoids, 1-deoxy-8α-hydroxypentalenic acid (1) and 1-deoxy-9β-hydroxy-11-oxopentalenic acid (2), as shunt metabolites of the pentalenolactone (3) biosynthesis pathway. Their structures and absolute configurations were elucidated by analyses of HRESIMS and NMR spectroscopic data as well as time-dependent density functional theory/electronic circular dichroism (TDDFT/ECD) calculations. Compounds 1 and 2 exhibited moderate antimicrobial activities against Gram-positive and Gram-negative bacteria. These results confirmed that the pentalenolactone pathway was functional in this organism and will facilitate efforts for exploring Actinobacteria using further genome mining strategies.
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Affiliation(s)
- Huanhuan Li
- Department of Phytochemistry, School of Pharmacy, Second Military Medical University, 325 Guo-He Road, Shanghai 200433, China; (H.L.); (H.L.); (S.C.)
- Department of Marine Bio-Pharmacology, College of Food Science and Technology, Shanghai Ocean University, 999 Huchenghuan Road, Shanghai 201306, China
| | - Hongji Li
- Department of Phytochemistry, School of Pharmacy, Second Military Medical University, 325 Guo-He Road, Shanghai 200433, China; (H.L.); (H.L.); (S.C.)
| | - Shuo Chen
- Department of Phytochemistry, School of Pharmacy, Second Military Medical University, 325 Guo-He Road, Shanghai 200433, China; (H.L.); (H.L.); (S.C.)
- Department of Marine Bio-Pharmacology, College of Food Science and Technology, Shanghai Ocean University, 999 Huchenghuan Road, Shanghai 201306, China
| | - Wenhui Wu
- Department of Marine Bio-Pharmacology, College of Food Science and Technology, Shanghai Ocean University, 999 Huchenghuan Road, Shanghai 201306, China
- Correspondence: (W.W.); (P.S.); Tel.: +86-21-81871259 (P.S.)
| | - Peng Sun
- Department of Phytochemistry, School of Pharmacy, Second Military Medical University, 325 Guo-He Road, Shanghai 200433, China; (H.L.); (H.L.); (S.C.)
- Correspondence: (W.W.); (P.S.); Tel.: +86-21-81871259 (P.S.)
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2
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Abstract
Covering: up to mid-2020 Terpenoids, also called isoprenoids, are the largest and most structurally diverse family of natural products. Found in all domains of life, there are over 80 000 known compounds. The majority of characterized terpenoids, which include some of the most well known, pharmaceutically relevant, and commercially valuable natural products, are produced by plants and fungi. Comparatively, terpenoids of bacterial origin are rare. This is counter-intuitive to the fact that recent microbial genomics revealed that almost all bacteria have the biosynthetic potential to create the C5 building blocks necessary for terpenoid biosynthesis. In this review, we catalogue terpenoids produced by bacteria. We collected 1062 natural products, consisting of both primary and secondary metabolites, and classified them into two major families and 55 distinct subfamilies. To highlight the structural and chemical space of bacterial terpenoids, we discuss their structures, biosynthesis, and biological activities. Although the bacterial terpenome is relatively small, it presents a fascinating dichotomy for future research. Similarities between bacterial and non-bacterial terpenoids and their biosynthetic pathways provides alternative model systems for detailed characterization while the abundance of novel skeletons, biosynthetic pathways, and bioactivies presents new opportunities for drug discovery, genome mining, and enzymology.
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Affiliation(s)
- Jeffrey D Rudolf
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, USA.
| | - Tyler A Alsup
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, USA.
| | - Baofu Xu
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, USA.
| | - Zining Li
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, USA.
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3
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Galbiati A, Zana A, Conti P. Covalent inhibitors of GAPDH: From unspecific warheads to selective compounds. Eur J Med Chem 2020; 207:112740. [PMID: 32898762 DOI: 10.1016/j.ejmech.2020.112740] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 07/23/2020] [Accepted: 08/05/2020] [Indexed: 11/18/2022]
Abstract
Targeting glycolysis is an attractive approach for the treatment of a wide range of pathologies, such as various tumors and parasitic infections. Due to its pivotal role in the glycolysis, Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) represents a rate-limiting enzyme in those cells that mostly, or exclusively rely on this pathway for energy production. In this context, GAPDH inhibition can be a valuable approach for the development of anticancer and antiparasitic drugs. In addition to its glycolytic role, GAPDH possesses several moonlight functions, whose deregulation is involved in some pathological conditions. Covalent modification on different amino acids of GAPDH, in particular on cysteine residues, can lead to a modulation of the enzyme activity. The selectivity towards specific cysteine residues is essential to achieve a specific phenotypic effect. In this work we report an extensive overview of the latest advances on the numerous compounds able to inhibit GAPDH through the covalent binding to cysteine residues, ranging from endogenous metabolites and xenobiotics, which may serve as pharmacological tools to actual drug-like compounds with promising therapeutic perspectives. Furthermore, we focused on the potentialities of the different warheads, shedding light on the possibility to exploit a combination of a finely tuned electrophilic group with a well-designed recognition moiety. These findings can provide useful information for the rational design of novel covalent inhibitors of GAPDH, with the final goal to expand the current treatment options.
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Affiliation(s)
- Andrea Galbiati
- Department of Pharmaceutical Sciences, Università degli Studi di Milano, Via Mangiagalli 25, 20133, Milano, Italy.
| | - Aureliano Zana
- Department of Pharmaceutical Sciences, Università degli Studi di Milano, Via Mangiagalli 25, 20133, Milano, Italy
| | - Paola Conti
- Department of Pharmaceutical Sciences, Università degli Studi di Milano, Via Mangiagalli 25, 20133, Milano, Italy
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4
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Deng Q, Liu Y, Chen L, Xu M, Naowarojna N, Lee N, Chen L, Zhu D, Hong X, Deng Z, Liu P, Zhao C. Biochemical Characterization of a Multifunctional Mononuclear Nonheme Iron Enzyme (PtlD) in Neopentalenoketolactone Biosynthesis. Org Lett 2019; 21:7592-7596. [DOI: 10.1021/acs.orglett.9b02872] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Qian Deng
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Hubei 430072, People’s Republic of China
| | - Yang Liu
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Hubei 430072, People’s Republic of China
| | - Linyue Chen
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Hubei 430072, People’s Republic of China
| | - Meiling Xu
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Nathchar Naowarojna
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Norman Lee
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Li Chen
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Hubei 430072, People’s Republic of China
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Dongqing Zhu
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Hubei 430072, People’s Republic of China
| | - Xuechuan Hong
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Hubei 430072, People’s Republic of China
| | - Zixin Deng
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Hubei 430072, People’s Republic of China
| | - Pinghua Liu
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Changming Zhao
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Hubei 430072, People’s Republic of China
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5
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Tolmie C, Smit MS, Opperman DJ. Native roles of Baeyer–Villiger monooxygenases in the microbial metabolism of natural compounds. Nat Prod Rep 2019; 36:326-353. [DOI: 10.1039/c8np00054a] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Baeyer–Villiger monooxygenases function in the primary metabolism of atypical carbon sources, as well as the synthesis of complex microbial metabolites.
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Affiliation(s)
- Carmien Tolmie
- Department of Biotechnology
- University of the Free State
- Bloemfontein
- South Africa
| | - Martha S. Smit
- Department of Biotechnology
- University of the Free State
- Bloemfontein
- South Africa
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6
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Gao SS, Naowarojna N, Cheng R, Liu X, Liu P. Recent examples of α-ketoglutarate-dependent mononuclear non-haem iron enzymes in natural product biosyntheses. Nat Prod Rep 2018; 35:792-837. [PMID: 29932179 PMCID: PMC6093783 DOI: 10.1039/c7np00067g] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Covering: up to 2018 α-Ketoglutarate (αKG, also known as 2-oxoglutarate)-dependent mononuclear non-haem iron (αKG-NHFe) enzymes catalyze a wide range of biochemical reactions, including hydroxylation, ring fragmentation, C-C bond cleavage, epimerization, desaturation, endoperoxidation and heterocycle formation. These enzymes utilize iron(ii) as the metallo-cofactor and αKG as the co-substrate. Herein, we summarize several novel αKG-NHFe enzymes involved in natural product biosyntheses discovered in recent years, including halogenation reactions, amino acid modifications and tailoring reactions in the biosynthesis of terpenes, lipids, fatty acids and phosphonates. We also conducted a survey of the currently available structures of αKG-NHFe enzymes, in which αKG binds to the metallo-centre bidentately through either a proximal- or distal-type binding mode. Future structure-function and structure-reactivity relationship investigations will provide crucial information regarding how activities in this large class of enzymes have been fine-tuned in nature.
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Affiliation(s)
- Shu-Shan Gao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | | | - Ronghai Cheng
- Department of Chemistry, Boston University, Boston, MA 02215, USA.
| | - Xueting Liu
- Department of Chemistry, Boston University, Boston, MA 02215, USA. and State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China.
| | - Pinghua Liu
- Department of Chemistry, Boston University, Boston, MA 02215, USA.
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7
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Chen K, Wu S, Zhu L, Zhang C, Xiang W, Deng Z, Ikeda H, Cane DE, Zhu D. Substitution of a Single Amino Acid Reverses the Regiospecificity of the Baeyer-Villiger Monooxygenase PntE in the Biosynthesis of the Antibiotic Pentalenolactone. Biochemistry 2016; 55:6696-6704. [PMID: 27933799 DOI: 10.1021/acs.biochem.6b01040] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In the biosynthesis of pentalenolactone (1), PenE and PntE, orthologous proteins from Streptomyces exfoliatus and S. arenae, respectively, catalyze the flavin-dependent Baeyer-Villiger oxidation of 1-deoxy-11-oxopentalenic acid (4) to the lactone pentalenolactone D (5), in which the less-substituted methylene carbon has migrated. By contrast, the paralogous PtlE enzyme from S. avermitilis catalyzes the oxidation of 4 to neopentalenolactone D (6), in which the more substituted methane substitution has undergone migration. We report the design and analysis of 13 single and multiple mutants of PntE mutants to identify the key amino acids that contribute to the regiospecificity of these two classes of Baeyer-Villiger monooxygenases. The L185S mutation in PntE reversed the observed regiospecificity of PntE such that all recombinant PntE mutants harboring this L185S mutation acquired the characteristic regiospecificity of PtlE, catalyzing the conversion of 4 to 6 as the major product. The recombinant PntE mutant harboring R484L exhibited reduced regiospecificity, generating a mixture of lactones containing more than 17% of 6. These in vitro results were corroborated by analysis of the complementation of the S. avermitilis ΔptlED double deletion mutant with pntE mutants, such that pntE mutants harboring L185S produced 6 as the major product, whereas complemention of the ΔptlED deletion mutant with pntE mutants carrying the R484L mutation gave 6 as more than 33% of the total lactone product mixture.
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Affiliation(s)
- Ke Chen
- The Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), Wuhan University , Wuhan, Hubei Province 430071, China
| | - Shiwen Wu
- The Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), Wuhan University , Wuhan, Hubei Province 430071, China
| | - Lu Zhu
- The Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), Wuhan University , Wuhan, Hubei Province 430071, China
| | - Chengde Zhang
- The Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), Wuhan University , Wuhan, Hubei Province 430071, China
| | - Wensheng Xiang
- School of Life Science, Northeast Agricultural University , Harbin, Heilongjiang Province 150030, China
| | - Zixin Deng
- The Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), Wuhan University , Wuhan, Hubei Province 430071, China
| | - Haruo Ikeda
- Laboratory of Microbial Engineering, Kitasato Institute for Life Sciences, Kitasato University , 1-15-1 Kitasato, Sagamihara, Minami-ku, Kanagawa 252-0373, Japan
| | - David E Cane
- Department of Chemistry, Box H, Brown University , Providence, Rhode Island 02912-9108, United States
| | - Dongqing Zhu
- The Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), Wuhan University , Wuhan, Hubei Province 430071, China
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8
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Velázquez-Domínguez J, Marchat LA, López-Camarillo C, Mendoza-Hernández G, Sánchez-Espíndola E, Calzada F, Ortega-Hernández A, Sánchez-Monroy V, Ramírez-Moreno E. Effect of the sesquiterpene lactone incomptine A in the energy metabolism of Entamoeba histolytica. Exp Parasitol 2013; 135:503-10. [PMID: 23994114 DOI: 10.1016/j.exppara.2013.08.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Revised: 08/14/2013] [Accepted: 08/21/2013] [Indexed: 10/26/2022]
Abstract
Entamoeba histolytica is the causative agent of human amoebiasis, which mainly affects developing countries. Although several drugs are effective against E. histolytica trophozoites, the control of amoebiasis requires the development of new and better alternative therapies. Medicinal plants have been the source of new molecules with remarkable antiprotozoal activity. Incomptine A isolated from Decachaeta incompta leaves, is a sesquiterpene lactone of the heliangolide type which has the major in vitro activity against E. histolytica trophozoites. However the molecular mechanisms involved in its antiprotozoal activity are still unknown. Using a proteomic approach based on two-dimensional gel electrophoresis and mass spectrometry (ESI-MS/MS) analysis, we evidenced that 21 E. histolytica proteins were differentially expressed in response to incomptine A treatment. Notably, three glycolytic enzymes, namely enolase, pyruvate:ferredoxin oxidoreductase and fructose-1,6-biphosphate aldolase, were down-regulated. Moreover, ultrastructural analysis of trophozoites through electronic microscopy showed an increased number of glycogen granules. Taken together, our data suggested that incomptine A could affect E. histolytica growth through alteration of its energy metabolism.
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Affiliation(s)
- José Velázquez-Domínguez
- Posgrado en Biomedicina Molecular, ENMyH, Instituto Politécnico Nacional, México City 07320, Mexico
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9
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Product-mediated regulation of pentalenolactone biosynthesis in Streptomyces species by the MarR/SlyA family activators PenR and PntR. J Bacteriol 2013; 195:1255-66. [PMID: 23316039 DOI: 10.1128/jb.02079-12] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The orthologous penR and pntR genes from the pentalenolactone biosynthetic gene clusters of Streptomyces exfoliatus UC5319 and S. arenae TÜ469, respectively, were predicted to encode MarR/SlyA family transcriptional regulators, responsible for regulation of the biosynthesis of the sesquiterpenoid antibiotic pentalenolactone. The intrinsic target DNA sequences and small molecule ligands of purified recombinant PenR and PntR were identified by electrophoretic mobility shift assays. PenR bound to DNA from both the penR-gapN and penM-penH intergenic regions, while PntR bound only the corresponding pntR-gapR intergenic region. The targets of PenR and PntR were shown to be limited to conserved 37-bp DNA segments. Pentalenolactone and two late-stage biosynthetic intermediates, pentalenolactones D and F, act as ligands of both PenR and PntR, resulting in release of these proteins from their target DNA. The production of pentalenolactones was significantly decreased in the penR deletion mutant S. exfoliatus ΔpenR ZD27 but could be restored by complementation with either penR or pntR. Reverse transcription-PCR established that transcription of pentalenolactone biosynthetic and resistance genes decreased, while that of the penR gene itself increased in the penR deletion mutant S. exfoliatus ZD27 compared to the wild-type strain. The PenR protein thus serves as a positive regulator of pentalenolactone biosynthesis and self-resistance while acting as an autorepressor of penR.
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10
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Seo MJ, Zhu D, Endo S, Ikeda H, Cane DE. Genome mining in Streptomyces. Elucidation of the role of Baeyer-Villiger monooxygenases and non-heme iron-dependent dehydrogenase/oxygenases in the final steps of the biosynthesis of pentalenolactone and neopentalenolactone. Biochemistry 2011; 50:1739-54. [PMID: 21250661 DOI: 10.1021/bi1019786] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The pentalenolactone biosynthetic gene clusters have been cloned and sequenced from two known producers of the sesquiterpenoid antibiotic pentalenolactone, Streptomyces exfoliatus UC5319 and Streptomyces arenae TÜ469. The recombinant enzymes PenE and PntE, from S. exfoliatus and S. arenae, respectively, catalyze the flavin-dependent Baeyer-Villiger oxidation of 1-deoxy-11-oxopentalenic acid (7) to pentalenolactone D (8). Recombinant PenD, PntD, and PtlD, the latter from Streptomyces avermitilis, each catalyze the Fe(2+)-α-ketoglutarate-dependent oxidation of pentalenolactone D (8) to pentalenolactone E (15) and pentalenolactone F (16). Incubation of PenD, PntD, or PtlD with the isomeric neopentalenolactone D (9) gave PL308 (12) and a compound tentatively identified as neopentalenolactone E (14). These results are corroborated by analysis of the ΔpenD and ΔpntD mutants of S. exfoliatus and S. arenae, respectively, both of which accumulate pentalenolactone D but are blocked in production of pentalenolactone as well as the precursors pentalenolactones E and F. Finally, complementation of the previously described S. avermitilis ΔptlE ΔptlD deletion mutant with either penE or pntE gave pentalenolactone D (8), while complemention of the ΔptlE ΔptlD double mutant with pntE plus pntD or penE plus pntD gave pentalenolactone F (16).
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Affiliation(s)
- Myung-Ji Seo
- Department of Chemistry, Box H, Brown University, Providence, Rhode Island 02912-9108, United States
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11
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Jiang J, Tetzlaff CN, Takamatsu S, Iwatsuki M, Komatsu M, Ikeda H, Cane DE. Genome mining in Streptomyces avermitilis: A biochemical Baeyer-Villiger reaction and discovery of a new branch of the pentalenolactone family tree. Biochemistry 2009; 48:6431-40. [PMID: 19485417 DOI: 10.1021/bi900766w] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Incubation of 1-deoxy-11-oxopentalenic acid (12) with recombinant PtlE protein from Streptomyces avermitilis in the presence of NADPH and catalytic FAD gave the Baeyer-Villiger oxidation product, the previously unknown compound neopentalenolactone D (13), representing a new branch of the pentalenolactone biosynthetic pathway. The structure and stereochemistry of the derived neopentalenolactone D methyl ester (13-Me) were fully assigned by a combination of GC-MS and NMR analysis and confirmed by X-ray crystallography. Neopentalenolactone D (13) was also isolated from engineered cultures of S. avermitilis from which the ptlD gene within the 13.4-kb (neo)-ptl biosynthetic gene cluster had been deleted. The DeltaptlEDeltaptlD double deletion mutant accumulated 12, the substrate for the ptlE gene product, while the corresponding single DeltaptlE mutant produced 12 as well as the related oxidation products 14 and 15. Engineered strains of S. avermitilis, SUKA5 and pKU462::ermRp-ptl cluster, harboring the complete (neo)ptl cluster produced the oxidized lactone 18 and the closely related seco acid hydrolysis products 16 and 17.
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Affiliation(s)
- Jiaoyang Jiang
- Department of Chemistry, Box H, Brown University, Providence, Rhode Island 02912-9108, USA
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12
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You Z, Omura S, Ikeda H, Cane DE, Jogl G. Crystal structure of the non-heme iron dioxygenase PtlH in pentalenolactone biosynthesis. J Biol Chem 2007; 282:36552-60. [PMID: 17942405 PMCID: PMC3010413 DOI: 10.1074/jbc.m706358200] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The non-heme iron dioxygenase PtlH from the soil organism Streptomyces avermitilis is a member of the iron(II)/alpha-ketoglutarate-dependent dioxygenase superfamily and catalyzes an essential reaction in the biosynthesis of the sesquiterpenoid antibiotic pentalenolactone. To investigate the structural basis for substrate recognition and catalysis, we have determined the x-ray crystal structure of PtlH in several complexes with the cofactors iron, alpha-ketoglutarate, and the non-reactive enantiomer of the substrate, ent-1-deoxypentalenic acid, in four different crystal forms to up to 1.31 A resolution. The overall structure of PtlH forms a double-stranded barrel helix fold, and the cofactor-binding site for iron and alpha-ketoglutarate is similar to other double-stranded barrel helix fold enzymes. Additional secondary structure elements that contribute to the substrate-binding site in PtlH are not conserved in other double-stranded barrel helix fold enzymes. Binding of the substrate enantiomer induces a reorganization of the monoclinic crystal lattice leading to a disorder-order transition of a C-terminal alpha-helix. The newly formed helix blocks the major access to the active site and effectively traps the bound substrate. Kinetic analysis of wild type and site-directed mutant proteins confirms a critical function of two arginine residues in substrate binding, while simulated docking of the enzymatic reaction product reveals the likely orientation of bound substrate.
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Affiliation(s)
- Zheng You
- Department of Chemistry, Brown University, Box H, Providence, RI 02912-9108, USA
| | - Satoshi Omura
- The Kitasato Institute, 9-1, Shirokane 5-chome, Minato-ku, Tokyo 108-8642, Japan
| | - Haruo Ikeda
- Kitasato Institute for Life Sciences, Kitasato University, 1-15-1, Kitasato, Sagamihara, Kanagawa 228-8555, Japan
| | - David E. Cane
- Department of Chemistry, Brown University, Box H, Providence, RI 02912-9108, USA
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Box G, Providence, RI 02912, USA
| | - Gerwald Jogl
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Box G, Providence, RI 02912, USA
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13
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Tetzlaff CN, You Z, Cane DE, Takamatsu S, Omura S, Ikeda H. A gene cluster for biosynthesis of the sesquiterpenoid antibiotic pentalenolactone in Streptomyces avermitilis. Biochemistry 2006; 45:6179-86. [PMID: 16681390 PMCID: PMC2518623 DOI: 10.1021/bi060419n] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Streptomyces avermitilis, an industrial organism responsible for the production of the anthelminthic avermectins, harbors a 13.4 kb gene cluster containing 13 unidirectionally transcribed open reading frames corresponding to the apparent biosynthetic operon for the sesquiterpene antibiotic pentalenolactone. The advanced intermediate pentalenolactone F, along with the shunt metabolite pentalenic acid, could be isolated from cultures of S. avermitilis, thereby establishing that the pentalenolactone biosynthetic pathway is functional in S. avermitilis. Deletion of the entire 13.4 kb cluster from S. avermitilis abolished formation of pentalenolactone metabolites, while transfer of the intact cluster to the pentalenolactone nonproducer Streptomyces lividans 1326 resulted in production of pentalenic acid. Direct evidence for the biochemical function of the individual biosynthetic genes came from expression of the ptlA gene (SAV2998) in Escherichia coli. Assay of the resultant protein established that PtlA is a pentalenene synthase, catalyzing the cyclization of farnesyl diphosphate to pentalenene, the parent hydrocarbon of the pentalenolactone family of metabolites. The most upstream gene in the cluster, gap1 (SAV2990), was shown to correspond to the pentalenolactone resistance gene, based on expression in E. coli and demonstration that the resulting glyceraldehyde-3-phosphate dehydrogenase, the normal target of pentalenolactone, was insensitive to the antibiotic. Furthermore, a second GAPDH isozyme (gap2, SAV6296) has been expressed in E. coli and shown to be inactivated by pentalenolactone.
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Affiliation(s)
- Charles N. Tetzlaff
- Department of Chemistry, Box H, Brown University, Providence, RI 02912-9108, USA; The Kitasato Institute, 9-1, Shirokane 5-chome, Minato-ku, Tokyo 108-8642, Japan
| | - Zheng You
- Department of Chemistry, Box H, Brown University, Providence, RI 02912-9108, USA; The Kitasato Institute, 9-1, Shirokane 5-chome, Minato-ku, Tokyo 108-8642, Japan
| | - David E. Cane
- Department of Chemistry, Box H, Brown University, Providence, RI 02912-9108, USA; The Kitasato Institute, 9-1, Shirokane 5-chome, Minato-ku, Tokyo 108-8642, Japan
- Address correspondence to: David E. Cane, Department of Chemistry, Box H, Brown University, Providence, RI 02912-9108, USA; Tel: 401-863-3588; Fax: 401-863-9368; E-mail:
| | - Satoshi Takamatsu
- Kitasato Institute for Life Sciences, Kitasato University, 1-151-1, Kitasato, Sagamihara, Kanagawa 228-8555, Japan
| | - Satoshi Omura
- Department of Chemistry, Box H, Brown University, Providence, RI 02912-9108, USA; The Kitasato Institute, 9-1, Shirokane 5-chome, Minato-ku, Tokyo 108-8642, Japan
| | - Haruo Ikeda
- Kitasato Institute for Life Sciences, Kitasato University, 1-151-1, Kitasato, Sagamihara, Kanagawa 228-8555, Japan
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14
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Ikeda M, Fukuda A, Takagi M, Morita M, Shimada Y. Inhibitory effect of pentalenolactone on vascular smooth muscle cell proliferation. Eur J Pharmacol 2001; 411:45-53. [PMID: 11137857 DOI: 10.1016/s0014-2999(00)00894-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The effect of pentalenolactone, an inhibitor of glyceraldehyde-3-phosphate dehydrogenase, on rat vascular smooth muscle cell proliferation was studied. Addition of pentalenolactone together with serum to quiescent cells dose-dependently inhibited cell proliferation and DNA synthesis. This inhibition was not associated with cell death. When quiescent cells were stimulated with serum and then treated with pentalenolactone, the inhibitory effect on the DNA synthesis declined gradually. A similar result was obtained when PD 98059 (2'-amino-3'-methoxyflavone), an inhibitor of extracellular signal-regulated kinase1/2 (ERK1/2) kinase (MEK1/2), was added to the cells after serum stimulation. Pentalenolactone inhibited serum or protein kinase C activator (phorbol 12,13-dibutyrate)-induced phosphorylation of ERK1/2 and MEK1/2. In contrast, pentalenolactone had little effect on platelet-derived growth factor receptor autophosphorylation. Taken together, these results indicate that pentalenolactone inhibits vascular smooth muscle cell proliferation, and that this inhibition appears to be mediated by inhibition of the ERK1/2 cascade.
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MESH Headings
- 3T3 Cells
- Animals
- Anti-Bacterial Agents/pharmacology
- Calcium-Calmodulin-Dependent Protein Kinases/antagonists & inhibitors
- Cell Division/drug effects
- Cell Movement/drug effects
- Cells, Cultured
- Cyclin-Dependent Kinases/antagonists & inhibitors
- DNA/biosynthesis
- DNA/drug effects
- Dose-Response Relationship, Drug
- Enzyme Inhibitors/pharmacology
- Flavonoids/pharmacology
- Glyceraldehyde-3-Phosphate Dehydrogenases/antagonists & inhibitors
- Glycolysis/drug effects
- Kinetin
- MAP Kinase Kinase 1
- MAP Kinase Kinase 2
- Mice
- Mitogen-Activated Protein Kinase 1/drug effects
- Mitogen-Activated Protein Kinase 1/metabolism
- Mitogen-Activated Protein Kinase 3
- Mitogen-Activated Protein Kinase Kinases/drug effects
- Mitogen-Activated Protein Kinase Kinases/metabolism
- Mitogen-Activated Protein Kinases/drug effects
- Mitogen-Activated Protein Kinases/metabolism
- Muscle, Smooth, Vascular/cytology
- Muscle, Smooth, Vascular/drug effects
- Muscle, Smooth, Vascular/metabolism
- Phosphorylation/drug effects
- Protein Serine-Threonine Kinases/drug effects
- Protein Serine-Threonine Kinases/metabolism
- Protein-Tyrosine Kinases/drug effects
- Protein-Tyrosine Kinases/metabolism
- Purines/pharmacology
- Rats
- Rats, Sprague-Dawley
- Receptors, Platelet-Derived Growth Factor/drug effects
- Receptors, Platelet-Derived Growth Factor/metabolism
- Sesquiterpenes/pharmacology
- Time Factors
- Tyrosine/drug effects
- Tyrosine/metabolism
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Affiliation(s)
- M Ikeda
- Department of Veterinary Pharmacology, Faculty of Agriculture, Miyazaki University, 1-1 Gakuenkibanadai-nishi, 889-2192, Miyazaki, Japan
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15
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Fröhlich KU, Wiedmann M, Lottspeich F, Mecke D. Substitution of a pentalenolactone-sensitive glyceraldehyde-3-phosphate dehydrogenase by a genetically distinct resistant isoform accompanies pentalenolactone production in Streptomyces arenae. J Bacteriol 1989; 171:6696-702. [PMID: 2592349 PMCID: PMC210565 DOI: 10.1128/jb.171.12.6696-6702.1989] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Pentalenolactone (PL), an antibiotic produced by Streptomyces arenae, is a potent inhibitor of glyceraldehyde-3-phosphate dehydrogenase (GAPDH). The producer strain contains different isoforms of GAPDH: a PL-sensitive enzyme on nonproduction media and a PL-insensitive enzyme on production media. After induction of PL synthesis, the sensitive GAPDH disappears parallel to the disappearance of its activity, as shown by Western (immunoblot) hybridization. The two isoenzymes exhibit little immunological cross-reactivity and differ in size, amino acid composition, and several amino acid residues of their amino termini. Two different types of plasmids from a S. arenae genomic library, named pBRPLR1 and pBRPLR2, were cloned in Escherichia coli by selection for enhanced PL resistance. Both contain a GAPDH structural gene. Plasmid pBRPLR1 increases E. coli PL tolerance 7-fold, and plasmid pBRPLR2 increases it 30-fold. GAPDH from pBRPLR1 transformants shows biphasic PL inactivation kinetics. These cells contain PL-sensitive GAPDH from both E. coli and S. arenae. GAPDH from pBRPLR2 transformants tolerates higher PL concentrations than either E. coli or S. arenae PL-sensitive GAPDH but is less resistant than S. arenae PL-insensitive GAPDH. Nondenaturing polyacrylamide electrophoresis showed this GAPDH to be a hybrid of E. coli and S. arenae PL-insensitive GAPDH. The hybrid enzyme could be purified to homogeneity. Induction of the lacZ promoter of pUC subclones of both GAPDH genes had only a small effect on raising the level of intracellular GAPDH.
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Affiliation(s)
- K U Fröhlich
- Physiologisch-chemisches Institut, Universität Tübingen, Federal Republic of Germany
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16
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Cane DE, Sohng JK. Inhibition of glyceraldehyde-3-phosphate dehydrogenase by pentalenolactone: kinetic and mechanistic studies. Arch Biochem Biophys 1989; 270:50-61. [PMID: 2930199 DOI: 10.1016/0003-9861(89)90006-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Incubation of rabbit muscle glyceraldehyde-3-phosphate dehydrogenase (GAPDH) with the antibiotic pentalenolactone (1) resulted in time-dependent, irreversible inhibition of GAPDH. The kinetics of inactivation were biphasic, exhibiting an initial rapid phase and a slower second phase. Pentalenolactone methyl ester (2) also irreversibly inactivated GADPH, albeit at a slower rate and with a higher KI. The substrate glyceraldehyde-3-phosphate (G-3-P) afforded protection against inactivation by 1, whereas the presence of NAD+ in the incubation mixture stimulated the inactivation by increasing the apparent affinity of the enzyme for the inhibitor. In steady-state kinetic experiments, 1 acted as a competitive inhibitor of GAPDH with respect to G-3-P but exhibited uncompetitive inhibition with respect to NAD+. Inactivation of NAD+-free apo-GAPDH by 1 showed simple pseudo-first-order kinetics. By titrating the free thiol residues of partially inactivated GAPDH, it was found that both pentalenolactone and pentalenolactone methyl ester react with all four Cys-SH residues of the tetrameric GAPDH.
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Affiliation(s)
- D E Cane
- Department of Chemistry, Brown University, Providence, Rhode Island 02912
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17
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Duszenko M, Mecke D. Inhibition of glyceraldehyde-3-phosphate dehydrogenase by pentalenolactone in Trypanosoma brucei. Mol Biochem Parasitol 1986; 19:223-9. [PMID: 3736593 DOI: 10.1016/0166-6851(86)90004-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Pentalenolactone (PL), an antibiotic produced by several strains of Streptomycetes, is a specific irreversible inhibitor of glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12). The effect of this antibiotic was studied in Trypanosoma brucei. In infected mice, due to the rapid metabolic inactivation of PL in vivo, trypanosomes were not affected by concentrations that were lethal to the host. Bloodstream trypanosomes in vitro were killed by low concentrations of PL (1.5 microgram ml-1), suggesting that there is no alternative to the glycolytic pathway for the generation of ATP in the bloodstream forms. In contrast, even high concentrations of PL (75 micrograms ml-1) were unable to inhibit growth of the procyclic form in vitro, presumably due to their ability to generate ATP independently of the glycolytic pathway.
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18
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Nagle WA, Moss AJ, Henle KJ. Sensitization of cultured Chinese hamster cells to 42 degrees C hyperthermia by pentalenolactone, an inhibitor of glycolytic ATP synthesis. INTERNATIONAL JOURNAL OF RADIATION BIOLOGY AND RELATED STUDIES IN PHYSICS, CHEMISTRY, AND MEDICINE 1985; 48:821-35. [PMID: 3877019 DOI: 10.1080/09553008514551921] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The antibiotic pentalenolactone, a specific inhibitor of glyceraldehydephosphate dehydrogenase, was used to investigate the effect of glycolytic adenosine triphosphate (ATP) synthesis on the survival response of aerobic and hypoxic Chinese hamster cells treated with 42 degrees C hyperthermia. Data obtained with aerobic cells, incubated in balanced salt solutions supplemented with different substrates for ATP production, showed that 50 microM pentalenolactone blocked ATP synthesis via glycolysis but not by oxidative phosphorylation. The glycolytic inhibition was reversed upon transfer of the cells to antibiotic-free medium, and minimal cytotoxicity (less than 20 per cent) was observed. Hypoxic cultures were obtained by incubating dense cell suspensions (2 X 10(6)/ml) to produce metabolic oxygen depletion. Concomitant with the development of hypoxia, pentalenolactone-treated cells became ATP-depleted; cellular ATP levels were reduced by about 70-fold as compared to hypoxic cells in the antibiotic-free medium. The ATP-depleted cells were more sensitive to killing by hyperthermia. Comparison of the 42 degrees C survival curves for control and the antibiotic-treated hypoxic cells yielded a dose-modifying factor of 4 (5 per cent survival level). The results indicate that inhibition of glycolytic ATP synthesis, for example by pentalenolactone, can selectively sensitize hypoxic cells to the lethal effects of mild hyperthermia.
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19
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Maurer KH, Pfeiffer F, Zehender H, Mecke D. Characterization of two glyceraldehyde-3-phosphate dehydrogenase isoenzymes from the pentalenolactone producer Streptomyces arenae. J Bacteriol 1983; 153:930-6. [PMID: 6822480 PMCID: PMC221716 DOI: 10.1128/jb.153.2.930-936.1983] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Pentalenolactone (PL) irreversibly inactivates the enzyme glyceraldehyde-3-phosphate dehydrogenase [D-glyceraldehyde-3-phosphate:NAD+ oxidoreductase (phosphorylating)] (EC 1.2.1.12) and thus is a potent inhibitor of glycolysis in both procaryotic and eucaryotic cells. We showed that PL-producing strain Streptomyces arenae TU469 contains a PL-insensitive glyceraldehyde-3-phosphate dehydrogenase under conditions of PL production. In complex media no PL production was observed, and a PL-sensitive glyceraldehyde-3-phosphate dehydrogenase, rather than the insensitive enzyme, could be detected. The enzymes had the same substrate specificity but different catalytic and molecular properties. The apparent Km values of the PL-insensitive and PL-sensitive enzymes for glyceraldehyde-3-phosphate were 100 and 250 microM, respectively, and the PL-sensitive enzyme was strongly inhibited by PL under conditions in which the PL-insensitive enzyme was not inhibited. The physical properties of the PL-insensitive enzyme suggest that the protein is an octamer, whereas the PL-sensitive enzyme, like other glyceraldehyde-3-phosphate dehydrogenases, appears to be a tetramer.
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