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Zhang Y, Liu Z, Xiao G, Shi J, Liu B, Xiao N, Sun Z. Simultaneous DHA and organic selenium production by Schizochytrium sp.: a theoretical basis. Sci Rep 2023; 13:15607. [PMID: 37731016 PMCID: PMC10511486 DOI: 10.1038/s41598-023-42900-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 09/15/2023] [Indexed: 09/22/2023] Open
Abstract
Docosahexaenoic acid (DHA) and selenium (Se) are nutrients that confer several health benefits to both humans and animals. Widespread use of DHA in milk powder and health products requires large-scale mass production via Schizochytrium sp., while Se intended for human consumption is produced as organic Se via yeast. However, producing these nutrients on an industrial scale is constrained by various factors. We found that supplementing Schizochytrium sp. with Na2SeO3 (0.5 mg/L) improves its biomass and DHA production and also provides organic Se. De novo assembled transcriptome and biochemical indicators showed that Na2SeO3 promotes forming acetyl coenzyme A and L-cysteine via the glycerol kinase and cysteine synthase pathways, promoting DHA synthesis through the polyketide synthase pathway. However, high doses of Na2SeO3 (5 mg/L) limited the biomass of Schizochytrium sp. and DHA content. This study provided a theoretical basis for the simultaneous production of organic Se and DHA via Schizochytrium sp.
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Affiliation(s)
- Yunqiang Zhang
- Hunan Agricultural University Veterinary Faculty, No.1 Nongda Road, Furong District, Changsha City, 410000, Hunan, China
- Hunan Canzoho Biological Technology Co., Ltd., 321 Kangning Road, Changsha City, 410000, Hunan, China
| | - Zikui Liu
- Hunan Agricultural University Veterinary Faculty, No.1 Nongda Road, Furong District, Changsha City, 410000, Hunan, China
- Hunan Canzoho Biological Technology Co., Ltd., 321 Kangning Road, Changsha City, 410000, Hunan, China
| | - Gang Xiao
- Hunan Agricultural University Veterinary Faculty, No.1 Nongda Road, Furong District, Changsha City, 410000, Hunan, China
| | - Jiawei Shi
- Hunan Agricultural University Veterinary Faculty, No.1 Nongda Road, Furong District, Changsha City, 410000, Hunan, China
- Hunan Canzoho Biological Technology Co., Ltd., 321 Kangning Road, Changsha City, 410000, Hunan, China
| | - Baili Liu
- Hunan Canzoho Biological Technology Co., Ltd., 321 Kangning Road, Changsha City, 410000, Hunan, China
| | - Ning Xiao
- Hunan Agricultural University Veterinary Faculty, No.1 Nongda Road, Furong District, Changsha City, 410000, Hunan, China
| | - Zhiliang Sun
- Hunan Agricultural University Veterinary Faculty, No.1 Nongda Road, Furong District, Changsha City, 410000, Hunan, China.
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2
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West AKR, Bailey CB. Crosstalk between primary and secondary metabolism: Interconnected fatty acid and polyketide biosynthesis in prokaryotes. Bioorg Med Chem Lett 2023; 91:129377. [PMID: 37328038 PMCID: PMC11239236 DOI: 10.1016/j.bmcl.2023.129377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 06/03/2023] [Accepted: 06/11/2023] [Indexed: 06/18/2023]
Abstract
In primary metabolism, fatty acid synthases (FASs) biosynthesize fatty acids via sequential Claisen-like condensations of malonyl-CoA followed by reductive processing. Likewise, polyketide synthases (PKSs) share biosynthetic logic with FAS which includes utilizing the same precursors and cofactors. However, PKS biosynthesize structurally diverse, complex secondary metabolites, many of which are pharmaceutically relevant. This digest covers examples of interconnected biosynthesis between primary and secondary metabolism in fatty acid and polyketide metabolism. Taken together, further understanding the biosynthetic linkage between polyketide biosynthesis and fatty acid biosynthesis may lead to improved discovery and production of novel drug leads from polyketide metabolites.
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Affiliation(s)
- Anna-Kay R West
- Department of Chemistry, University of Tennessee-Knoxville, Knoxville, TN 37996, USA
| | - Constance B Bailey
- Department of Chemistry, University of Tennessee-Knoxville, Knoxville, TN 37996, USA; School of Chemistry, The University of Sydney, Camperdown, New South Wales 2006, Australia.
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3
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Paiva P, Medina FE, Viegas M, Ferreira P, Neves RPP, Sousa JPM, Ramos MJ, Fernandes PA. Animal Fatty Acid Synthase: A Chemical Nanofactory. Chem Rev 2021; 121:9502-9553. [PMID: 34156235 DOI: 10.1021/acs.chemrev.1c00147] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Fatty acids are crucial molecules for most living beings, very well spread and conserved across species. These molecules play a role in energy storage, cell membrane architecture, and cell signaling, the latter through their derivative metabolites. De novo synthesis of fatty acids is a complex chemical process that can be achieved either by a metabolic pathway built by a sequence of individual enzymes, such as in most bacteria, or by a single, large multi-enzyme, which incorporates all the chemical capabilities of the metabolic pathway, such as in animals and fungi, and in some bacteria. Here we focus on the multi-enzymes, specifically in the animal fatty acid synthase (FAS). We start by providing a historical overview of this vast field of research. We follow by describing the extraordinary architecture of animal FAS, a homodimeric multi-enzyme with seven different active sites per dimer, including a carrier protein that carries the intermediates from one active site to the next. We then delve into this multi-enzyme's detailed chemistry and critically discuss the current knowledge on the chemical mechanism of each of the steps necessary to synthesize a single fatty acid molecule with atomic detail. In line with this, we discuss the potential and achieved FAS applications in biotechnology, as biosynthetic machines, and compare them with their homologous polyketide synthases, which are also finding wide applications in the same field. Finally, we discuss some open questions on the architecture of FAS, such as their peculiar substrate-shuttling arm, and describe possible reasons for the emergence of large megasynthases during evolution, questions that have fascinated biochemists from long ago but are still far from answered and understood.
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Affiliation(s)
- Pedro Paiva
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Fabiola E Medina
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello, Autopista Concepción-Talcahuano, 7100 Talcahuano, Chile
| | - Matilde Viegas
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Pedro Ferreira
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Rui P P Neves
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - João P M Sousa
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Maria J Ramos
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Pedro A Fernandes
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
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4
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Liu X, Currens GC, Xue L, Cheng YQ. Origin and bioactivities of thiosulfinated FK228. MEDCHEMCOMM 2019; 10:538-542. [PMID: 31057733 DOI: 10.1039/c9md00060g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 03/14/2019] [Indexed: 11/21/2022]
Abstract
During a large laboratory-scale purification of FK228 from the fermentation broth of Burkholderia thailandensis MSMB43, a small amount of thiosulfinated FK228 (TS-FK228) was unexpectedly purified only after the broth was mixed with silica gel. Evidence supports the postulations that TS-FK228 was derived from FK228 through spontaneous chemical reaction with silica gel, and TS-FK228 existed as two isomers 1 and 2. TS-FK228 demonstrated similar inhibitory activity and profile against human class I histone deacetylases but exhibited a much higher antiproliferative activity against representative human cancer cell lines when compared to FK228.
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Affiliation(s)
- Xiangyang Liu
- UNT System College of Pharmacy , University of North Texas Health Science Center , 3500 Camp Bowie Blvd , Fort Worth , TX 76107 , USA . ; ; Tel: +817 735 0165
| | - Grant C Currens
- UNT System College of Pharmacy , University of North Texas Health Science Center , 3500 Camp Bowie Blvd , Fort Worth , TX 76107 , USA . ; ; Tel: +817 735 0165
| | - Liang Xue
- Alcon NMR laboratory at Novartis , 6201 South Fwy , Fort Worth , TX 76134 , USA
| | - Yi-Qiang Cheng
- UNT System College of Pharmacy , University of North Texas Health Science Center , 3500 Camp Bowie Blvd , Fort Worth , TX 76107 , USA . ; ; Tel: +817 735 0165
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Discovery of 16-Demethylrifamycins by Removing the Predominant Polyketide Biosynthesis Pathway in Micromonospora sp. Strain TP-A0468. Appl Environ Microbiol 2019; 85:AEM.02597-18. [PMID: 30530711 DOI: 10.1128/aem.02597-18] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 11/27/2018] [Indexed: 12/13/2022] Open
Abstract
A number of strategies have been developed to mine novel natural products based on biosynthetic gene clusters and there have been dozens of successful cases facilitated by the development of genomic sequencing. During our study on biosynthesis of the antitumor polyketide kosinostatin (KST), we found that the genome of Micromonospora sp. strain TP-A0468, the producer of KST, contains other potential polyketide gene clusters, with no encoded products detected. Deletion of kst cluster led to abolishment of KST and the enrichment of several new compounds, which were isolated and characterized as 16-demethylrifamycins (referred to here as compounds 3 to 6). Transcriptional analysis demonstrated that the expression of the essential genes related to the biosynthesis of compounds 3 to 6 was comparable to the level in the wild-type and in the kst cluster deletion strain. This indicates that the accumulation of these compounds was due to the redirection of metabolic flux rather than transcriptional activation. Genetic disruption, chemical complementation, and bioinformatic analysis revealed that the production of compounds 3 to 6 was accomplished by cross talk between the two distantly placed polyketide gene clusters pks3 and M-rif This finding not only enriches the analogue pool and the biosynthetic diversity of rifamycins but also provides an auxiliary strategy for natural product discovery through genome mining in polyketide-producing microorganisms.IMPORTANCE Natural products are essential in the development of novel clinically used drugs. Discovering new natural products and modifying known compounds are still the two main ways to generate new candidates. Here, we have discovered several rifamycins with varied skeleton structures by redirecting the metabolic flux from the predominant polyketide biosynthetic pathway to the rifamycin pathway in the marine actinomycetes species Micromonospora sp. strain TP-A0468. Rifamycins are indispensable chemotherapeutics in the treatment of various diseases such as tuberculosis, leprosy, and AIDS-related mycobacterial infections. This study exemplifies a useful method for the discovery of cryptic natural products in genome-sequenced microbes. Moreover, the 16-demethylrifamycins and their genetically manipulable producer provide a new opportunity in the construction of novel rifamycin derivates to aid in the defense against the ever-growing drug resistance of Mycobacterium tuberculosis.
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6
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Liu X, Xie F, Doughty LB, Wang Q, Zhang L, Liu X, Cheng YQ. Genomics-guided discovery of a new and significantly better source of anticancer natural drug FK228. Synth Syst Biotechnol 2018; 3:268-274. [PMID: 30417143 PMCID: PMC6222137 DOI: 10.1016/j.synbio.2018.10.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 10/23/2018] [Accepted: 10/26/2018] [Indexed: 11/28/2022] Open
Abstract
FK228 is an FDA-approved anticancer drug naturally produced by Chromobacterium violaceum No. 968 up to 19 mg/L in a pilot industry-scale batch fermentation. Here we report a genomics-guided discovery of Burkholderia thailandensis MSMB43 as a new and significantly better source of FK228. The genome of B. thailandensis MSMB43 was found to contain a functional biosynthetic gene cluster highly homologous to that of FK228 in C. violaceum No. 968, and the bacterium indeed produces authentic FK228. By simple fermentation in shaking flasks in a preferred M8 medium, B. thailandensis MSMB43 produced FK228 up to 67.7 mg/L; by fed-batch fermentation in a 20-L fermentor in M8 medium, B. thailandensis MSMB43 produced FK228 up to 115.9 mg/L, which is 95 fold higher than that of C. violaceum No. 968 under the same laboratory fermentation conditions. RT-PCR analysis indicated that the high FK228 yield of B. thailandensis MSMB43 was due to high expression of biosynthetic genes, represented by Bth_depA, during the fermentation process. Further genetic manipulation resulted in a recombinant strain, B. thailandensis MSMB43/pBMTL3-tdpR, which harbors a broad host-range vector expressing the thailandepsin biosynthetic pathway regulatory gene tdpR. This engineered strain produced up to 168.5 mg/L of FK228 in fed-batch fermentation in a 20-L fermentor in M8 medium. Therefore, the wild-type B. thailandensis MSMB43 or its engineered derivative could potentially be a good starting point for an industrial process to improve FK228 production for its expanding use in therapy.
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Affiliation(s)
- Xiangyang Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, PR China.,UNT System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, TX, 76107, USA
| | - Feng Xie
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Leah B Doughty
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, 53201, USA
| | - Qi Wang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Lixin Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, PR China.,CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Xueting Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, PR China
| | - Yi-Qiang Cheng
- UNT System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, TX, 76107, USA.,Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, 53201, USA
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7
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Son S, Hong YS, Futamura Y, Jang M, Lee JK, Heo KT, Ko SK, Lee JS, Takahashi S, Osada H, Jang JH, Ahn JS. Catenulisporolides, Glycosylated Triene Macrolides from the Chemically Underexploited Actinomycete Catenulispora Species. Org Lett 2018; 20:7234-7238. [DOI: 10.1021/acs.orglett.8b03160] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Sangkeun Son
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea
| | - Young-Soo Hong
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea
- Department of Biomolecular Science, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon 34113, Korea
| | - Yushi Futamura
- Chemical Biology Research Group, RIKEN Center for Sustainable Research Science, Saitama 351-0198, Japan
| | - Mina Jang
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea
- Department of Biomolecular Science, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon 34113, Korea
| | - Jae Kyoung Lee
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea
| | - Kyung Taek Heo
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea
- Department of Biomolecular Science, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon 34113, Korea
| | - Sung-Kyun Ko
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea
- Department of Biomolecular Science, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon 34113, Korea
| | - Jung Sook Lee
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Korea
| | - Shunji Takahashi
- RIKEN-KRIBB Joint Research Unit, RIKEN Center for Sustainable Research Science, Saitama 351-0198, Japan
| | - Hiroyuki Osada
- Chemical Biology Research Group, RIKEN Center for Sustainable Research Science, Saitama 351-0198, Japan
| | - Jae-Hyuk Jang
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea
- Department of Biomolecular Science, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon 34113, Korea
| | - Jong Seog Ahn
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea
- Department of Biomolecular Science, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon 34113, Korea
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8
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Skiba MA, Sikkema AP, Moss NA, Lowell AN, Su M, Sturgis RM, Gerwick L, Gerwick WH, Sherman DH, Smith JL. Biosynthesis of t-Butyl in Apratoxin A: Functional Analysis and Architecture of a PKS Loading Module. ACS Chem Biol 2018; 13:1640-1650. [PMID: 29701944 PMCID: PMC6003868 DOI: 10.1021/acschembio.8b00252] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The unusual feature of a t-butyl group is found in several marine-derived natural products including apratoxin A, a Sec61 inhibitor produced by the cyanobacterium Moorea bouillonii PNG 5-198. Here, we determine that the apratoxin A t-butyl group is formed as a pivaloyl acyl carrier protein (ACP) by AprA, the polyketide synthase (PKS) loading module of the apratoxin A biosynthetic pathway. AprA contains an inactive "pseudo" GCN5-related N-acetyltransferase domain (ΨGNAT) flanked by two methyltransferase domains (MT1 and MT2) that differ distinctly in sequence. Structural, biochemical, and precursor incorporation studies reveal that MT2 catalyzes unusually coupled decarboxylation and methylation reactions to transform dimethylmalonyl-ACP, the product of MT1, to pivaloyl-ACP. Further, pivaloyl-ACP synthesis is primed by the fatty acid synthase malonyl acyltransferase (FabD), which compensates for the ΨGNAT and provides the initial acyl-transfer step to form AprA malonyl-ACP. Additionally, images of AprA from negative stain electron microscopy reveal multiple conformations that may facilitate the individual catalytic steps of the multienzyme module.
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Affiliation(s)
- Meredith A Skiba
- Life Sciences Institute , University of Michigan , Ann Arbor , Michigan 48109 , United States
- Department of Biological Chemistry , University of Michigan , Ann Arbor Michigan 48109 , United States
| | - Andrew P Sikkema
- Life Sciences Institute , University of Michigan , Ann Arbor , Michigan 48109 , United States
- Department of Biological Chemistry , University of Michigan , Ann Arbor Michigan 48109 , United States
| | - Nathan A Moss
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography , University of California, San Diego , La Jolla , California 92093 , United States
| | - Andrew N Lowell
- Life Sciences Institute , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Min Su
- Life Sciences Institute , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Rebecca M Sturgis
- Life Sciences Institute , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Lena Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography , University of California, San Diego , La Jolla , California 92093 , United States
| | - William H Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography , University of California, San Diego , La Jolla , California 92093 , United States
- Skaggs School of Pharmacy and Pharmaceutical Sciences , University of California, San Diego , La Jolla , California 92093 , United States
| | - David H Sherman
- Life Sciences Institute , University of Michigan , Ann Arbor , Michigan 48109 , United States
- Department of Medicinal Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
- Department of Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
- Department of Microbiology and Immunology , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Janet L Smith
- Life Sciences Institute , University of Michigan , Ann Arbor , Michigan 48109 , United States
- Department of Biological Chemistry , University of Michigan , Ann Arbor Michigan 48109 , United States
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Mechanistic studies of DepR in regulating FK228 biosynthesis in Chromobacterium violaceum no. 968. PLoS One 2018; 13:e0196173. [PMID: 29672625 PMCID: PMC5908139 DOI: 10.1371/journal.pone.0196173] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 04/06/2018] [Indexed: 12/12/2022] Open
Abstract
DepR, a LysR-type transcriptional regulator encoded by the last gene of the putative min operon (orf21-20-19-depR) located at the downstream region of the anticancer agent FK228 biosynthetic gene cluster in Chromobacterium violaceum No. 968, positively regulates the biosynthesis of FK228. In this work, the mechanism underlining this positive regulation was probed by multiple approaches. Electrophoretic mobility shift assay (EMSA) and DNase I footprinting assay (DIFA) identified a conserved 35-nt DNA segment in the orf21-orf22 intergenic region where the purified recombinant DepR binds to. Quantitative reverse transcription PCR (RT-qPCR) and green fluorescent protein (GFP) promoter probe assays established that transcription of phasin gene orf22 increases in the depR deletion mutant of C. violaceum (CvΔdepR) compared to the wild-type strain. FK228 production in the orf22-overexpressed strain C. violaceum was reduced compared with the wild-type strain. DepR has two conserved cysteine residues C199 and C208 presumed to form a disulfide bridge upon sensing oxidative stress. C199X point mutations that locked DepR in a reduced conformation decreased the DNA-binding affinity of DepR; T232A or R278A mutation also had a negative impact on DNA binding of DepR. Complementation of CvΔdepR with any of those versions of depR carrying a single codon mutation was not able to restore FK228 production to the level of wild-type strain. All evidences collectively suggested that DepR positively regulates the biosynthesis of FK228 through indirect metabolic networking.
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The secreted metabolome of Streptomyces chartreusis and implications for bacterial chemistry. Proc Natl Acad Sci U S A 2018; 115:2490-2495. [PMID: 29463727 DOI: 10.1073/pnas.1715713115] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Actinomycetes are known for producing diverse secondary metabolites. Combining genomics with untargeted data-dependent tandem MS and molecular networking, we characterized the secreted metabolome of the tunicamycin producer Streptomyces chartreusis NRRL 3882. The genome harbors 128 predicted biosynthetic gene clusters. We detected >1,000 distinct secreted metabolites in culture supernatants, only 22 of which were identified based on standards and public spectral libraries. S. chartreusis adapts the secreted metabolome to cultivation conditions. A number of metabolites are produced iron dependently, among them 17 desferrioxamine siderophores aiding in iron acquisition. Eight previously unknown members of this long-known compound class are described. A single desferrioxamine synthesis gene cluster was detected in the genome, yet different sets of desferrioxamines are produced in different media. Additionally, a polyether ionophore, differentially produced by the calcimycin biosynthesis cluster, was discovered. This illustrates that metabolite output of a single biosynthetic machine can be exquisitely regulated not only with regard to product quantity but also with regard to product range. Compared with chemically defined medium, in complex medium, total metabolite abundance was higher, structural diversity greater, and the average molecular weight almost doubled. Tunicamycins, for example, were only produced in complex medium. Extrapolating from this study, we anticipate that the larger part of bacterial chemistry, including chemical structures, ecological functions, and pharmacological potential, is yet to be uncovered.
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11
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Pait IGU, Kitani S, Roslan FW, Ulanova D, Arai M, Ikeda H, Nihira T. Discovery of a new diol-containing polyketide by heterologous expression of a silent biosynthetic gene cluster from Streptomyces lavendulae FRI-5. J Ind Microbiol Biotechnol 2017; 45:77-87. [PMID: 29255990 DOI: 10.1007/s10295-017-1997-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Accepted: 12/09/2017] [Indexed: 11/29/2022]
Abstract
The genome of streptomycetes has the ability to produce many novel and potentially useful bioactive compounds, but most of which are not produced under standard laboratory cultivation conditions and are referred to as silent/cryptic secondary metabolites. Streptomyces lavendulae FRI-5 produces several types of bioactive compounds. However, this strain may also have the potential to biosynthesize more useful secondary metabolites. Here, we activated a silent biosynthetic gene cluster of an uncharacterized compound from S. lavendulae FRI-5 using heterologous expression. The engineered strain carrying the silent gene cluster produced compound 5, which was undetectable in the culture broth of S. lavendulae FRI-5. Using various spectroscopic analyses, we elucidated the chemical structure of compound 5 (named lavendiol) as a new diol-containing polyketide. The proposed assembly line of lavendiol shows a unique biosynthetic mechanism for polyketide compounds. The results of this study suggest the possibility of discovering more silent useful compounds from streptomycetes by genome mining and heterologous expression.
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Affiliation(s)
- Ivy Grace Umadhay Pait
- International Center for Biotechnology, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Shigeru Kitani
- International Center for Biotechnology, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Farah Wahidah Roslan
- International Center for Biotechnology, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Dana Ulanova
- International Center for Biotechnology, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan.,Department of Marine Resource Science, Faculty of Agriculture and Marine Science, Kochi University, 200 Otsu, Monobe, Nankoku, Kochi, 783-8502, Japan
| | - Masayoshi Arai
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Haruo Ikeda
- Kitasato Institute for Life Sciences, Kitasato University, 1-15-1 Kitasato, Sagamihara, Kanagawa, 252-0373, Japan
| | - Takuya Nihira
- International Center for Biotechnology, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan. .,MU-OU Collaborative Research Center for Bioscience and Biotechnology, Faculty of Science, Mahidol University, Rama VI Rd, Bangkok, 10400, Thailand.
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12
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Timmermans ML, Paudel YP, Ross AC. Investigating the Biosynthesis of Natural Products from Marine Proteobacteria: A Survey of Molecules and Strategies. Mar Drugs 2017; 15:E235. [PMID: 28762997 PMCID: PMC5577590 DOI: 10.3390/md15080235] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2017] [Revised: 07/21/2017] [Accepted: 07/24/2017] [Indexed: 02/07/2023] Open
Abstract
The phylum proteobacteria contains a wide array of Gram-negative marine bacteria. With recent advances in genomic sequencing, genome analysis, and analytical chemistry techniques, a whole host of information is being revealed about the primary and secondary metabolism of marine proteobacteria. This has led to the discovery of a growing number of medically relevant natural products, including novel leads for the treatment of multidrug-resistant Staphylococcus aureus (MRSA) and cancer. Of equal interest, marine proteobacteria produce natural products whose structure and biosynthetic mechanisms differ from those of their terrestrial and actinobacterial counterparts. Notable features of secondary metabolites produced by marine proteobacteria include halogenation, sulfur-containing heterocycles, non-ribosomal peptides, and polyketides with unusual biosynthetic logic. As advances are made in the technology associated with functional genomics, such as computational sequence analysis, targeted DNA manipulation, and heterologous expression, it has become easier to probe the mechanisms for natural product biosynthesis. This review will focus on genomics driven approaches to understanding the biosynthetic mechanisms for natural products produced by marine proteobacteria.
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Affiliation(s)
| | - Yagya P Paudel
- Department of Chemistry, Queen's University, Kingston, ON K7L 3N6, Canada.
| | - Avena C Ross
- Department of Chemistry, Queen's University, Kingston, ON K7L 3N6, Canada.
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13
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Masschelein J, Jenner M, Challis GL. Antibiotics from Gram-negative bacteria: a comprehensive overview and selected biosynthetic highlights. Nat Prod Rep 2017. [PMID: 28650032 DOI: 10.1039/c7np00010c] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Covering: up to 2017The overwhelming majority of antibiotics in clinical use originate from Gram-positive Actinobacteria. In recent years, however, Gram-negative bacteria have become increasingly recognised as a rich yet underexplored source of novel antimicrobials, with the potential to combat the looming health threat posed by antibiotic resistance. In this article, we have compiled a comprehensive list of natural products with antimicrobial activity from Gram-negative bacteria, including information on their biosynthetic origin(s) and molecular target(s), where known. We also provide a detailed discussion of several unusual pathways for antibiotic biosynthesis in Gram-negative bacteria, serving to highlight the exceptional biocatalytic repertoire of this group of microorganisms.
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Affiliation(s)
- J Masschelein
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, UK.
| | - M Jenner
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, UK.
| | - G L Challis
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, UK.
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14
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Yurkovich ME, Jenkins R, Sun Y, Tosin M, Leadlay PF. The polyketide backbone of thiolactomycin is assembled by an unusual iterative polyketide synthase. Chem Commun (Camb) 2017; 53:2182-2185. [DOI: 10.1039/c6cc09934c] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Thiotetronate polyketide assembly by an unusual iterative synthase is reconstructed via in vitro enzymology and chemical probes.
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Affiliation(s)
| | | | - Yuhui Sun
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University)
- Ministry of Education
- Wuhan University School of Pharmaceutical Sciences
- Wuhan 430071
- People's Republic of China
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15
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Ishikawa F, Sugimoto H, Kakeya H. In Vitro Investigation of Crosstalk between Fatty Acid and Polyketide Synthases in the Andrimid Biosynthetic Assembly Line. Chembiochem 2016; 17:2137-2142. [DOI: 10.1002/cbic.201600410] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Indexed: 11/11/2022]
Affiliation(s)
- Fumihiro Ishikawa
- Department of System Chemotherapy and Molecular Sciences; Division of Bioinformatics and Chemical Genomics; Graduate School of Pharmaceutical Sciences; Kyoto University; Sakyo Kyoto 606-8501 Japan
| | - Hiroyasu Sugimoto
- Department of System Chemotherapy and Molecular Sciences; Division of Bioinformatics and Chemical Genomics; Graduate School of Pharmaceutical Sciences; Kyoto University; Sakyo Kyoto 606-8501 Japan
| | - Hideaki Kakeya
- Department of System Chemotherapy and Molecular Sciences; Division of Bioinformatics and Chemical Genomics; Graduate School of Pharmaceutical Sciences; Kyoto University; Sakyo Kyoto 606-8501 Japan
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16
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Xiao K, Li YP, Wang C, Ahmad S, Vu M, Kuma K, Cheng YQ, Lam KS. Disulfide cross-linked micelles of novel HDAC inhibitor thailandepsin A for the treatment of breast cancer. Biomaterials 2015. [PMID: 26218744 DOI: 10.1016/j.biomaterials.2015.07.033] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Histone deacetylase (HDAC) inhibitors are an emerging class of targeted therapy against cancers. Thailandepsin A (TDP-A) is a recently discovered class I HDAC inhibitor with broad anti-proliferative activities. In the present study, we aimed to investigate the potential of TDP-A in the treatment of breast cancer. We demonstrated that TDP-A inhibited cell proliferation and induced apoptosis in breast cancer cells at low nanomolar concentrations. TDP-A activated the intrinsic apoptotic pathway through increase of pro-apoptotic protein Bax, decrease of anti-apoptotic Bcl-2, and cleavage of caspase-3 and poly (ADP-ribose) polymerase (PARP). TDP-A also induced cell cycle arrest at the G2/M phase, and promoted the production of reactive oxygen species (ROS). We have successfully encapsulated TDP-A into our recently developed disulfide cross-linked micelles (DCMs), improving its water solubility and targeted delivery. TDP-A loaded DCMs (TDP-A/DCMs) possess the characteristics of high loading capacity (>20%, w/w), optimal and monodisperse particle size (16 ± 4 nm), outstanding stability with redox stimuli-responsive disintegration, sustained drug release, and preferential uptake in breast tumors. In the MDA-MB-231 breast cancer xenograft model, TDP-A/DCMs were more efficacious than the FDA-approved FK228 at well-tolerated doses. Furthermore, TDP-A/DCMs exhibited synergistic anticancer effects when combined with the proteasome inhibitor bortezomib (BTZ) loaded DCMs (BTZ/DCMs). Our results indicate that TDP-A nanoformulation alone or in combination with BTZ nanoformulation are efficacious against breast cancer.
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Affiliation(s)
- Kai Xiao
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy, Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, PR China; Department of Biochemistry & Molecular Medicine, UC Davis Cancer Center, University of California Davis, Sacramento, CA 95817, USA.
| | - Yuan-Pei Li
- Department of Biochemistry & Molecular Medicine, UC Davis Cancer Center, University of California Davis, Sacramento, CA 95817, USA
| | - Cheng Wang
- UNT System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, Texas 76107, USA
| | - Sarah Ahmad
- Department of Biochemistry & Molecular Medicine, UC Davis Cancer Center, University of California Davis, Sacramento, CA 95817, USA
| | - Michael Vu
- Department of Biochemistry & Molecular Medicine, UC Davis Cancer Center, University of California Davis, Sacramento, CA 95817, USA
| | - Krishneel Kuma
- Department of Biochemistry & Molecular Medicine, UC Davis Cancer Center, University of California Davis, Sacramento, CA 95817, USA
| | - Yi-Qiang Cheng
- UNT System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, Texas 76107, USA
| | - Kit S Lam
- Department of Biochemistry & Molecular Medicine, UC Davis Cancer Center, University of California Davis, Sacramento, CA 95817, USA.
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17
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Shah GR, Wesener SR, Cheng YQ. Engineered Production of Tryprostatins in E. coli through Reconstitution of a Partial ftm Biosynthetic Gene Cluster from Aspergillus sp. JACOBS JOURNAL OF BIOTECHNOLOGY AND BIOENGINEERING 2015; 2:009. [PMID: 26640821 PMCID: PMC4670043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Tryprostatin A and B are indole alkaloid-based fungal products that inhibit mammalian cell cycle at the G2/M phase. They are biosynthetic intermediates of fumitremorgins produced by a complex pathway involving a nonribosomal peptide synthetase (FtmA), a prenyltransferase (FtmB), a cytochrome P450 hydroxylase (FtmC), an O-methyltransferase (FtmD), and several additional enzymes. A partial fumitremorgin biosynthetic gene cluster (ftmABCD) from Aspergillus sp. was reconstituted in Escherichia coli BL21(DE3) cells, with or without the co-expression of an Sfp-type phosphopantetheinyltransferase gene (Cv_sfp) from Chromobacterium violaceum No. 968. Several recombinant E. coli strains produced tryprostatin B up to 106 mg/l or tryprostatin A up to 76 mg/l in the fermentation broth under aerobic condition, providing an effective way to prepare those pharmaceutically important natural products biologically.
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Affiliation(s)
- Gopitkumar R Shah
- Department of Biological Sciences, University of Wisconsin–Milwaukee, PO Box 413, Milwaukee, Wisconsin 53201, USA
| | - Shane R. Wesener
- Department of Biological Sciences, University of Wisconsin–Milwaukee, PO Box 413, Milwaukee, Wisconsin 53201, USA
| | - Yi-Qiang Cheng
- Department of Biological Sciences, University of Wisconsin–Milwaukee, PO Box 413, Milwaukee, Wisconsin 53201, USA
- UNT System College of Pharmacy, University of North Texas Health Science Center, 3500 Camp Bowie Boulevard, Fort Worth, Texas 76107, USA
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18
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Genetic determinants of reutericyclin biosynthesis in Lactobacillus reuteri. Appl Environ Microbiol 2015; 81:2032-41. [PMID: 25576609 DOI: 10.1128/aem.03691-14] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Reutericyclin is a unique antimicrobial tetramic acid produced by some strains of Lactobacillus reuteri. This study aimed to identify the genetic determinants of reutericyclin biosynthesis. Comparisons of the genomes of reutericyclin-producing L. reuteri strains with those of non-reutericyclin-producing strains identified a genomic island of 14 open reading frames (ORFs) including genes coding for a nonribosomal peptide synthetase (NRPS), a polyketide synthase (PKS), homologues of PhlA, PhlB, and PhlC, and putative transport and regulatory proteins. The protein encoded by rtcN is composed of a condensation domain, an adenylation domain likely specific for d-leucine, and a thiolation domain. rtcK codes for a PKS that is composed of a ketosynthase domain, an acyl-carrier protein domain, and a thioesterase domain. The products of rtcA, rtcB, and rtcC are homologous to the diacetylphloroglucinol-biosynthetic proteins PhlABC and may acetylate the tetramic acid moiety produced by RtcN and RtcK, forming reutericyclin. Deletion of rtcN or rtcABC in L. reuteri TMW1.656 abrogated reutericyclin production but did not affect resistance to reutericyclin. Genes coding for transport and regulatory proteins could be deleted only in the reutericyclin-negative L. reuteri strain TMW1.656ΔrtcN, and these deletions eliminated reutericyclin resistance. The genomic analyses suggest that the reutericyclin genomic island was horizontally acquired from an unknown source during a unique event. The combination of PhlABC homologues with both an NRPS and a PKS has also been identified in the lactic acid bacteria Streptococcus mutans and Lactobacillus plantarum, suggesting that the genes in these organisms and those in L. reuteri share an evolutionary origin.
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19
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Identification and characterization of the spiruchostatin biosynthetic gene cluster enable yield improvement by overexpressing a transcriptional activator. J Ind Microbiol Biotechnol 2014; 41:1457-65. [PMID: 24973954 DOI: 10.1007/s10295-014-1474-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 06/10/2014] [Indexed: 01/05/2023]
Abstract
Spiruchostatins A and B are members of the FK228-family of natural products with potent histone deacetylase inhibitory activities and antineoplastic activities. However, their production in the wild-type strain of Pseudomonas sp. Q71576 is low. To improve the yield, the spiruchostatin biosynthetic gene cluster (spi) was first identified by rapid genome sequencing and characterized by genetic mutations. This spi gene cluster encodes a hybrid biosynthetic pathway similar to that encoded by the FK228 biosynthetic gene cluster (dep) in Chromobacterium violaceum No. 968. Each gene cluster contains a pathway regulatory gene (spiR vs. depR), but these two genes encode transcriptional activators of different classes. Overexpression of native spiR or heterologous depR in the wild-type strain of Pseudomonas sp. Q71576 resulted in 268 or 1,285 % increase of the combined titer of spiruchostatins A and B, respectively. RT-PCR analysis indicates that overexpression of heterologous depR upregulates the expression of native spiR.
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20
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Liu X, Cheng YQ. Genome-guided discovery of diverse natural products from Burkholderia sp. J Ind Microbiol Biotechnol 2013; 41:275-84. [PMID: 24212473 DOI: 10.1007/s10295-013-1376-1] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Accepted: 10/24/2013] [Indexed: 01/09/2023]
Abstract
Burkholderia species have emerged as a new source of diverse natural products. This mini-review covers all of the natural products discovered in recent years from Burkholderia sp. by genome-guided approaches--these refer to the use of bacterial genome sequence as an entry point for in silico structural prediction, wet lab experimental design, and execution. While reliable structural prediction based on cryptic biosynthetic gene cluster sequence was not always possible due to noncanonical domains and/or module organization of a deduced biosynthetic pathway, a molecular genetic method was often employed to detect or alter the expression level of the gene cluster to achieve an observable phenotype, which facilitated downstream natural product purification and identification. Those examples of natural product discovery from Burkholderia sp. provide practical guidance for future exploration of Gram-negative bacteria as a new source of natural products.
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Affiliation(s)
- Xiangyang Liu
- UNT System College of Pharmacy, University of North Texas Health Science Center, 3500 Camp Bowie Boulevard, Fort Worth, TX, 76107, USA
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21
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Musiol EM, Greule A, Härtner T, Kulik A, Wohlleben W, Weber T. The AT₂ domain of KirCI loads malonyl extender units to the ACPs of the kirromycin PKS. Chembiochem 2013; 14:1343-52. [PMID: 23828654 DOI: 10.1002/cbic.201300211] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Indexed: 11/06/2022]
Abstract
The antibiotic kirromycin is assembled by a hybrid modular polyketide synthases (PKSs)/nonribosomal peptide synthetases (NRPSs). Five of six PKSs of this complex assembly line do not have acyltransferase (AT) and have to recruit this activity from discrete AT enzymes. Here, we show that KirCI is a discrete AT which is involved in kirromycin production and displays a rarely found three-domain architecture (AT₁-AT₂-ER). We demonstrate that the second AT domain, KirCI-AT₂, but not KirCI-AT₁, is the malonyl-CoA-specific AT which utilizes this precursor for loading the acyl carrier proteins (ACPs) of the trans-AT PKS in vitro. In the kirromycin biosynthetic pathway, ACP5 is exclusively loaded with ethylmalonate by the enzyme KirCII and is not recognized as a substrate by KirCI. Interestingly, the excised KirCI-AT₂ can also transfer malonate to ACP5 and thus has a relaxed ACP-specificity compared to the entire KirCI protein. The ability of KirCI-AT₂ to load different ACPs provides opportunities for AT engineering as a potential strategy for polyketide diversification.
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Affiliation(s)
- Ewa Maria Musiol
- Mikrobiologie/Biotechnologie, Interfakultäres Institut für Mikrobiologie und Infektionsmedizin, Eberhard-Karls-Universität Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
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22
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Liu XY, Wang C, Cheng YQ. FK228 from Burkholderia thailandensis MSMB43. Acta Crystallogr Sect E Struct Rep Online 2012; 68:o2757-8. [PMID: 22969639 PMCID: PMC3435793 DOI: 10.1107/s160053681203601x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Accepted: 08/16/2012] [Indexed: 11/10/2022]
Abstract
FK228 [systematic name: (1S,4S,7Z,10S,16E,21R)-7-ethyl-idene-4,21-di(propan-2-yl)-2-oxa-12,13-dithia-5,8,20,23-tetra-za--bicyclo[8.7.6]tricos-16-ene-3,6,9,19,22-pentone], C(24)H(36)N(4)O(6)S(2), also known as FR901228, depsipeptide, NSC 630176, romidepsin, and marketed as Istodax by Celgene Corporation, is crystallized from ethyl acetate in P2(1) as compared to the absolute configuration of FK228, first crystallized from methanol in P2(1)2(1)2(1) [Shigematsu et al. (1994 ▶). J. Anti-biot.47, 311-314]. A slight difference is observed between the absolute configuration of FK228 and the present structure. The molecular structure is stabilized by intramolecular N-H⋯O hydrogen bonds. In the crystal, molecules are linked via N-H⋯O hydrogen bonds.
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Affiliation(s)
- Xiang-Yang Liu
- Department of Biological Sciences, Department of Chemistry and Biochemistry, Univeristy of Wisconsin–Milwaukee, PO Box 413, Milwaukee, WI 53201, USA
| | - Cheng Wang
- Department of Biological Sciences, Department of Chemistry and Biochemistry, Univeristy of Wisconsin–Milwaukee, PO Box 413, Milwaukee, WI 53201, USA
| | - Yi-Qiang Cheng
- Department of Biological Sciences, Department of Chemistry and Biochemistry, Univeristy of Wisconsin–Milwaukee, PO Box 413, Milwaukee, WI 53201, USA
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23
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Busch B, Ueberschaar N, Sugimoto Y, Hertweck C. Interchenar Retrotransfer of Aureothin Intermediates in an Iterative Polyketide Synthase Module. J Am Chem Soc 2012; 134:12382-5. [DOI: 10.1021/ja304454r] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Benjamin Busch
- Leibniz Institute for
Natural Product Research and
Infection Biology, HKI, Beutenbergstrasse 11a, 07745 Jena, Germany,
and Friedrich Schiller University, Jena,
Germany
| | - Nico Ueberschaar
- Leibniz Institute for
Natural Product Research and
Infection Biology, HKI, Beutenbergstrasse 11a, 07745 Jena, Germany,
and Friedrich Schiller University, Jena,
Germany
| | - Yuki Sugimoto
- Leibniz Institute for
Natural Product Research and
Infection Biology, HKI, Beutenbergstrasse 11a, 07745 Jena, Germany,
and Friedrich Schiller University, Jena,
Germany
| | - Christian Hertweck
- Leibniz Institute for
Natural Product Research and
Infection Biology, HKI, Beutenbergstrasse 11a, 07745 Jena, Germany,
and Friedrich Schiller University, Jena,
Germany
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24
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Xu Y, Kersten RD, Nam SJ, Lu L, Al-Suwailem AM, Zheng H, Fenical W, Dorrestein PC, Moore BS, Qian PY. Bacterial biosynthesis and maturation of the didemnin anti-cancer agents. J Am Chem Soc 2012; 134:8625-32. [PMID: 22458477 PMCID: PMC3401512 DOI: 10.1021/ja301735a] [Citation(s) in RCA: 119] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The anti-neoplastic agent didemnin B from the Caribbean tunicate Trididemnum solidum was the first marine drug to be clinically tested in humans. Because of its limited supply and its complex cyclic depsipeptide structure, considerable challenges were encountered during didemnin B's development that continue to limit aplidine (dehydrodidemnin B), which is currently being evaluated in numerous clinical trials. Herein we show that the didemnins are bacterial products produced by the marine α-proteobacteria Tistrella mobilis and Tistrella bauzanensis via a unique post-assembly line maturation process. Complete genome sequence analysis of the 6,513,401 bp T. mobilis strain KA081020-065 with its five circular replicons revealed the putative didemnin biosynthetic gene cluster (did) on the 1,126,962 bp megaplasmid pTM3. The did locus encodes a 13-module hybrid non-ribosomal peptide synthetase-polyketide synthase enzyme complex organized in a collinear arrangement for the synthesis of the fatty acylglutamine ester derivatives didemnins X and Y rather than didemnin B as first anticipated. Imaging mass spectrometry of T. mobilis bacterial colonies captured the time-dependent extracellular conversion of the didemnin X and Y precursors to didemnin B, in support of an unusual post-synthetase activation mechanism. Significantly, the discovery of the didemnin biosynthetic gene cluster may provide a long-term solution to the supply problem that presently hinders this group of marine natural products and pave the way for the genetic engineering of new didemnin congeners.
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Affiliation(s)
- Ying Xu
- KAUST Global Collaborative Research, Division of Life Science, School of Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
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25
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Benelkebir H, Donlevy AM, Packham G, Ganesan A. Total synthesis and stereochemical assignment of burkholdac B, a depsipeptide HDAC inhibitor. Org Lett 2011; 13:6334-7. [PMID: 22091906 DOI: 10.1021/ol202197q] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Three diastereomers of burkholdac B were prepared by total synthesis, enabling the full stereochemical assignment of the natural product. It is proposed that burkholdac B is identical to thailandepsin A independently isolated by Cheng from the same strain of Burkholderia thailandensis . Burkholdac B is the most potent among depsipeptide histone deacetylase inhibitors in growth inhibition of the MCF7 breast cancer cell line with an IC(50) of 60 pM.
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Affiliation(s)
- Hanae Benelkebir
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom
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26
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Wang C, Henkes LM, Doughty LB, He M, Wang D, Meyer-Almes FJ, Cheng YQ. Thailandepsins: bacterial products with potent histone deacetylase inhibitory activities and broad-spectrum antiproliferative activities. JOURNAL OF NATURAL PRODUCTS 2011; 74:2031-8. [PMID: 21793558 PMCID: PMC3204160 DOI: 10.1021/np200324x] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Histone deacetylase (HDAC) inhibitors have emerged as a new class of anticancer drugs, with one synthetic compound, SAHA (vorinostat, Zolinza; 1), and one natural product, FK228 (depsipeptide, romidepsin, Istodax; 2), approved by FDA for clinical use. Our studies of FK228 biosynthesis in Chromobacterium violaceum no. 968 led to the identification of a cryptic biosynthetic gene cluster in the genome of Burkholderia thailandensis E264. Genome mining and genetic manipulation of this gene cluster further led to the discovery of two new products, thailandepsin A (6) and thailandepsin B (7). HDAC inhibition assays showed that thailandepsins have selective inhibition profiles different from that of FK228, with comparable inhibitory activities to those of FK228 toward human HDAC1, HDAC2, HDAC3, HDAC6, HDAC7, and HDAC9 but weaker inhibitory activities than FK228 toward HDAC4 and HDAC8, the latter of which could be beneficial. NCI-60 anticancer screening assays showed that thailandepsins possess broad-spectrum antiproliferative activities with GI50 for over 90% of the tested cell lines at low nanomolar concentrations and potent cytotoxic activities toward certain types of cell lines, particularly for those derived from colon, melanoma, ovarian, and renal cancers. Thailandepsins thus represent new naturally produced HDAC inhibitors that are promising for anticancer drug development.
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Affiliation(s)
- Cheng Wang
- Department of Biological Sciences, and Department of Chemistry and Biochemistry, University of Wisconsin–Milwaukee, P.O. Box 413, Milwaukee, WI 53201, United States
| | - Leonhard M. Henkes
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, 64287 Darmstadt, Germany
| | - Leah B. Doughty
- Department of Biological Sciences, and Department of Chemistry and Biochemistry, University of Wisconsin–Milwaukee, P.O. Box 413, Milwaukee, WI 53201, United States
| | - Min He
- Developmental Therapeutics Program, the US National Cancer Institute, Frederick, MD 21701, United States
| | - Difei Wang
- Laboratory of Cell Biology, the US National Cancer Institute, Bethesda, MD 20892, Unites States
| | - Franz-Josef Meyer-Almes
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, 64287 Darmstadt, Germany
| | - Yi-Qiang Cheng
- Department of Biological Sciences, and Department of Chemistry and Biochemistry, University of Wisconsin–Milwaukee, P.O. Box 413, Milwaukee, WI 53201, United States
- MoE Laboratory of Combinatorial Biosynthesis and New Drug Discovery, Wuhan University College of Pharmacy, Wuhan 430072, China
- Corresponding author: Tel: (414) 229-4739. Fax: (414) 229-3926.
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