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Jia G, Liu J, Hou X, Jiang Y, Li X. Biological function and small molecule inhibitors of histone deacetylase 11. Eur J Med Chem 2024; 276:116634. [PMID: 38972077 DOI: 10.1016/j.ejmech.2024.116634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 06/16/2024] [Accepted: 06/25/2024] [Indexed: 07/09/2024]
Abstract
HDAC11, as a rising star in the histone deacetylase (HDAC) family, has attracted widespread interest in the biomedical field in recent years specially owing to its high defatty-acylase activity compared its innate deacetylase activity. Numerous studies have provided evidence indicating the crucial involvement of HDAC11 in cancers, immune responses, and metabolic processes. Several potent and selective HDAC11 inhibitors have been discovered and identified, which is crucial for exploring the function of HDAC11 and its potential therapeutic applications. Herein, we present a critical overview of the current advances in the biological function of HDAC11 and its inhibitors. We initially discuss the physiological functions of HDAC11 and its pathological roles in relevant diseases. Subsequently, our main focus centers on the design strategy and development process of HDAC11 inhibitors. Additionally, we address significant challenges and outline future directions in this field. This perspective may provide guidance for the further development of HDAC11 inhibitors and their prospects in disease treatment.
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Affiliation(s)
- Geng Jia
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Jinyu Liu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Xinlu Hou
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Yuqi Jiang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China.
| | - Xiaoyang Li
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China.
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Bai X, Chen H, Ren X, Zhong L, Wang X, Ji X, Zhang Y, Wang Y, Bian X. Heterologous Biosynthesis of Complex Bacterial Natural Products in Burkholderia gladioli. ACS Synth Biol 2023; 12:3072-3081. [PMID: 37708405 DOI: 10.1021/acssynbio.3c00389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/16/2023]
Abstract
Bacterial natural products (NPs) are an indispensable source of drugs and biopesticides. Heterologous expression is an essential method for discovering bacterial NPs and the efficient biosynthesis of valuable NPs, but the chassis for Gram-negative bacterial NPs remains inadequate. In this study, we built a Burkholderiales mutant Burkholderia gladioli Δgbn::attB by introducing an integrated site (attB) to inactivate the native gladiolin (gbn) biosynthetic gene cluster, which stabilizes large foreign gene clusters and reduces the native metabolite profile. The growth and successful heterologous production of high-value NPs such as phylogenetically close Burkholderiales-derived antitumor polyketides (PKs) rhizoxins, phylogenetically distant Gammaproteobacteria-derived anti-MRSA (methicillin-resistant Staphylococcus aureus) antibiotics WAP-8294As, and Deltaproteobacteria-derived antitumor PKs disorazols demonstrate that this strain is a potential chassis for Gram-negative bacterial NPs. We further improved the yields of WAP-8294As through promoter insertions and precursor pathway overexpression based on heterologous expression in this strain. This study provides a robust bacterial chassis for genome mining, efficient production, and molecular engineering of bacterial NPs.
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Affiliation(s)
- Xianping Bai
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Hanna Chen
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Xiangmei Ren
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Lin Zhong
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Xingyan Wang
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Xiaoqi Ji
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Youming Zhang
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Yan Wang
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, Shandong 266100, China
| | - Xiaoying Bian
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
- Key Laboratory of Tobacco Pest Monitoring & Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China
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Gong K, Wang M, Duan Q, Li G, Yong D, Ren C, Li Y, Zhang Q, Wang Z, Sun T, Zhang H, Tu Q, Wu C, Fu J, Li A, Song C, Zhang Y, Li R. High-yield production of FK228 and new derivatives in a Burkholderia chassis. Metab Eng 2023; 75:131-142. [PMID: 36528227 DOI: 10.1016/j.ymben.2022.12.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/30/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022]
Abstract
FK228 (romidepsin) is the only natural histone deacetylases (HDACs) inhibitor approved by FDA to treat cutaneous and peripheral T-cell lymphoma. However, the limited supply and severe cardiotoxicity of FK228 underscore the importance to develop an effective synthetic biology platform for the manufacturing and fine-tuning of this drug lead. In this work, we constructed a Burkholderia chassis for the high-yield production of FK228-family (unnatural) natural products. By virtue of the optimized Burkholderia-specific recombineering system, the biosynthetic gene cluster (BGC) encoding the FK228-like skeleton thailandepsins (tdp) in Burkholderia thailandensis E264 was replaced with an attB integration site to afford the basal chassis KOGC1. The tdp BGC directly captured from E264 was hybridized with the FK228-encoding BGC (dep) using the versatile Red/ET technology. The hybrid BGC (tdp-dep) was integrated into the attB site of KOGC1, resulting in the heterologous expression of FK228. Remarkably, the titer reached 581 mg/L, which is 30-fold higher than that of native producer Chromobacterium violaceum No. 968. This success encouraged us to further engineer the NRPS modules 4 or 6 of hybrid tdp-dep BGC by domain units swapping strategy, and eight new FK228 derivatives (1-8) varying in the composition of amino acids were generated. Especially, the titers of 2 and 3 in KOGC1 were up to 985 mg/L and 453 mg/L, respectively. 2 and 3 displayed stronger cytotoxic activity than FK228. All in all, this work established a robust platform to produce FK228 and its new derivatives in sufficient quantities for anticancer drug development.
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Affiliation(s)
- Kai Gong
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Maoqin Wang
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Qiong Duan
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Gang Li
- Department of Natural Medicinal Chemistry and Pharmacognosy, Qingdao University, Qingdao, Shandong, China
| | - Daojing Yong
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Cailing Ren
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Yue Li
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Qijun Zhang
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Zongjie Wang
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Tao Sun
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Huanyun Zhang
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Qiang Tu
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China; Chinese Academy of Sciences (CAS) Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Changsheng Wu
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Jun Fu
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Aiying Li
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Chaoyi Song
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China.
| | - Youming Zhang
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China; Chinese Academy of Sciences (CAS) Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
| | - Ruijuan Li
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China.
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Adaikpoh BI, Fernandez HN, Eustáquio AS. Biotechnology approaches for natural product discovery, engineering, and production based on Burkholderia bacteria. Curr Opin Biotechnol 2022; 77:102782. [PMID: 36049254 DOI: 10.1016/j.copbio.2022.102782] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 07/13/2022] [Accepted: 07/26/2022] [Indexed: 11/15/2022]
Abstract
Bacterial natural products (NPs) retain high value in discovery efforts for applications in medicine and agriculture. Burkholderia β-Proteobacteria are a promising source of NPs. In this review, we summarize the recently developed genetic manipulation techniques used to access silent/cryptic biosynthetic gene clusters from Burkholderia native producers. We also discuss the development of Burkholderia bacteria as heterologous hosts and the application of Burkholderia in industrial-scale production of NPs. Genetic engineering and fermentation media optimization have enabled the industrial-scale production of at least two Burkholderia NPs. The biotechnology approaches discussed here will continue to facilitate the discovery and development of NPs from Burkholderia.
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Affiliation(s)
- Barbara I Adaikpoh
- Department of Pharmaceutical Sciences and Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Hannah N Fernandez
- Department of Pharmaceutical Sciences and Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Alessandra S Eustáquio
- Department of Pharmaceutical Sciences and Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA.
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Jiang L, Huang P, Ren B, Song Z, Zhu G, He W, Zhang J, Oyeleye A, Dai H, Zhang L, Liu X. Antibacterial polyene-polyol macrolides and cyclic peptides from the marine-derived Streptomyces sp. MS110128. Appl Microbiol Biotechnol 2021; 105:4975-4986. [PMID: 34146138 DOI: 10.1007/s00253-021-11226-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 02/27/2021] [Accepted: 03/07/2021] [Indexed: 02/05/2023]
Abstract
Marine microbes provide an important resource to discover new chemical compounds with biological activities beneficial to drug discovery. In our study, two new polyene macrolides, pyranpolyenolides A (1) and B (2), and one new natural cyclic peptide (9), together with two known polyenes (7 and 8) and three known cyclic peptides (10-12), were isolated from a culture of the marine Streptomyces sp. MS110128. In addition, four new polyene macrolides, pyranpolyenolides C-F (3-6), were identified as olefin geometric isomers that were most likely produced by photochemical conversion during the cultivation or isolation procedures. The pyranpolyenolides are 32-membered macrolides endowed with a conjugated tetraene and several pairs of 1,3-dihydroxyl groups. Pyranpolyenolides that contain a hydropyran group have not been previously reported. Four cyclic peptides (9-12) showed significant activities against Bacillus subtilis, Staphylococcus aureus, and methicillin-resistant S. aureus with supporting MIC values ranging from 0.025 to 1.25 μg/mL. These cyclic peptides containing piperazic moieties showed moderate activities with MIC values of 12.5 μg/mL against Bacille Calmette Guerin (BCG), an attenuated form of the bovine. Additionally, cyclic peptide 12 showed moderate antifungal activity against Candida albicans with an MIC value of 12.5 μg/mL. KEY POINTS: • Discovery of new polyenes and cyclic peptides from a marine-derived Actinomycete. • Cyclic peptides containing piperazic moieties exhibited good antibacterial activity.
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Affiliation(s)
- Lan Jiang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Pei Huang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China.,Department of Pediatric Hematology/Oncology, Affiliated Hospital of Zunyi Medical University/Guizhou Children's Hospital, Zunyi, 563000, Guizhou, China
| | - Biao Ren
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Zhijun Song
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guoliang Zhu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Wenni He
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Jingyu Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Ayokunmi Oyeleye
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Malaysia
| | - Huanqin Dai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Lixin Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Xueting Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China.
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6
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Wei H, Ma W, Lu X, Liu H, Lin K, Wang Y, Ye Z, Sun L, Huang Z, Pan T, Zhou Z, Cheng EY, Zhang H, Gao P, Zhong X. KDELR2 promotes breast cancer proliferation via HDAC3-mediated cell cycle progression. Cancer Commun (Lond) 2021; 41:904-920. [PMID: 34146461 PMCID: PMC8441056 DOI: 10.1002/cac2.12180] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 04/22/2021] [Accepted: 06/01/2021] [Indexed: 12/15/2022] Open
Abstract
Background Histone deacetylases (HDACs) engage in the regulation of various cellular processes by controlling global gene expression. The dysregulation of HDACs leads to carcinogenesis, making HDACs ideal targets for cancer therapy. However, the use of HDAC inhibitors (HDACi) as single agents has been shown to have limited success in treating solid tumors in clinical studies. This study aimed to identify a novel downstream effector of HDACs to provide a potential target for combination therapy. Methods Transcriptome sequencing and bioinformatics analysis were performed to screen for genes responsive to HDACi in breast cancer cells. The effects of HDACi on cell viability were detected using the MTT assay. The mRNA and protein levels of genes were determined by quantitative reverse transcription‐PCR (qRT‐PCR) and Western blotting. Cell cycle distribution and apoptosis were analyzed by flow cytometry. The binding of CREB1 (cAMP‐response element binding protein 1) to the promoter of the KDELR (The KDEL (Lys‐Asp‐Glu‐Leu) receptor) gene was validated by the ChIP (chromatin immunoprecipitation assay). The association between KDELR2 and protein of centriole 5 (POC5) was detected by immunoprecipitation. A breast cancer‐bearing mouse model was employed to analyze the effect of the HDAC3‐KDELR2 axis on tumor growth. Results KDELR2 was identified as a novel target of HDAC3, and its aberrant expression indicated the poor prognosis of breast cancer patients. We found a strong correlation between the protein expression patterns of HADC3 and KDELR2 in tumor tissues from breast cancer patients. The results of the ChIP assay and qRT‐PCR analysis validated that HDAC3 transactivated KDELR2 via CREB1. The HDAC3‐KDELR2 axis accelerated the cell cycle progression of cancer cells by protecting the centrosomal protein POC5 from proteasomal degradation. Moreover, the HDAC3‐KDELR2 axis promoted breast cancer cell proliferation and tumorigenesis in vitro and in vivo. Conclusion Our results uncovered a previously unappreciated function of KDELR2 in tumorigenesis, linking a critical Golgi‐the endoplasmic reticulum traffic transport protein to HDAC‐controlled cell cycle progression on the path of cancer development and thus revealing a potential therapeutical target for breast cancer.
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Affiliation(s)
- Haoran Wei
- Hefei National Laboratory for Physical Sciences at Microscale, the Chinese Academy of Sciences Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, Anhui, 230027, P. R. China
| | - Wenhao Ma
- Hefei National Laboratory for Physical Sciences at Microscale, the Chinese Academy of Sciences Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, Anhui, 230027, P. R. China
| | - Xiaofei Lu
- Hefei National Laboratory for Physical Sciences at Microscale, the Chinese Academy of Sciences Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, Anhui, 230027, P. R. China
| | - Haiying Liu
- Hefei National Laboratory for Physical Sciences at Microscale, the Chinese Academy of Sciences Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, Anhui, 230027, P. R. China
| | - Kashuai Lin
- School of Medicine and Institutes for Life Sciences, South China University of Technology, Guangzhou, Guangdong, 510006, P. R. China
| | - Yinghui Wang
- School of Medicine and Institutes for Life Sciences, South China University of Technology, Guangzhou, Guangdong, 510006, P. R. China
| | - Zijian Ye
- School of Medicine and Institutes for Life Sciences, South China University of Technology, Guangzhou, Guangdong, 510006, P. R. China
| | - Linchong Sun
- School of Medicine and Institutes for Life Sciences, South China University of Technology, Guangzhou, Guangdong, 510006, P. R. China
| | - Zhitong Huang
- School of Medicine and Institutes for Life Sciences, South China University of Technology, Guangzhou, Guangdong, 510006, P. R. China
| | - Tingting Pan
- Division of Life Sciences and Medicine, The First Affiliated Hospital of University of Science and Technology of China, University of Science and Technology of China, Hefei, Anhui, 230027, P. R. China
| | - Zilong Zhou
- Hefei National Laboratory for Physical Sciences at Microscale, the Chinese Academy of Sciences Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, Anhui, 230027, P. R. China
| | - Eric Y Cheng
- College of Pharmacy, University of North Texas Health Science Center, Fort Worth, Texas, 76107, USA
| | - Huafeng Zhang
- Hefei National Laboratory for Physical Sciences at Microscale, the Chinese Academy of Sciences Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, Anhui, 230027, P. R. China
| | - Ping Gao
- Hefei National Laboratory for Physical Sciences at Microscale, the Chinese Academy of Sciences Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, Anhui, 230027, P. R. China.,School of Medicine and Institutes for Life Sciences, South China University of Technology, Guangzhou, Guangdong, 510006, P. R. China
| | - Xiuying Zhong
- Hefei National Laboratory for Physical Sciences at Microscale, the Chinese Academy of Sciences Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, Anhui, 230027, P. R. China.,School of Medicine and Institutes for Life Sciences, South China University of Technology, Guangzhou, Guangdong, 510006, P. R. China
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Zheng W, Wang X, Zhou H, Zhang Y, Li A, Bian X. Establishment of recombineering genome editing system in Paraburkholderia megapolitana empowers activation of silent biosynthetic gene clusters. Microb Biotechnol 2021; 13:397-405. [PMID: 32053291 PMCID: PMC7017819 DOI: 10.1111/1751-7915.13535] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 12/12/2019] [Accepted: 12/30/2019] [Indexed: 12/30/2022] Open
Abstract
The Burkholderiales are an emerging source of bioactive natural products. Their genomes contain a large number of cryptic biosynthetic gene clusters (BGCs), indicating great potential for novel structures. However, the lack of genetic tools for the most of Burkholderiales strains restricts the mining of these cryptic BGCs. We previously discovered novel phage recombinases Redαβ7029 from Burkholderiales strain DSM 7029 that could help in efficiently editing several Burkholderiales genomes and established the recombineering genome editing system in Burkholderialse species. Herein, we report the application of this phage recombinase system in another species Paraburkholderia megapolitana DSM 23488, resulting in activation of two silent non‐ribosomal peptide synthetase/polyketide synthase BGCs. A novel class of lipopeptide, haereomegapolitanin, was identified through spectroscopic characterization. Haereomegapolitanin A represents an unusual threonine‐tagged lipopeptide which is longer than the predicted NRPS assembly line. This recombineering‐mediated genome editing system shows great potential for genetic manipulation of more Burkholderiales species to activate silent BGCs for bioactive metabolites discovery.
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Affiliation(s)
- Wentao Zheng
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
| | - Xue Wang
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
| | - Haibo Zhou
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
| | - Youming Zhang
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
| | - Aiying Li
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
| | - Xiaoying Bian
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
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8
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Pojani E, Barlocco D. Romidepsin (FK228), A Histone Deacetylase Inhibitor and its Analogues in Cancer Chemotherapy. Curr Med Chem 2021; 28:1290-1303. [PMID: 32013816 DOI: 10.2174/0929867327666200203113926] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 11/24/2019] [Accepted: 12/17/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND Human HDACs represent a group of enzymes able to modify histone and non-histone proteins, which interact with DNA to generate chromatin. The correlation between irregular covalent modification of histones and tumor development has been proved over the last decades. Therefore, HDAC inhibitors are considered as potential drugs in cancer treatment. Romidepsin (FK228), Belinostat (PXD-101), Vorinostat (SAHA), Panobinostat (LBH-589) and Chidamide were approved by FDA as novel antitumor agents. OBJECTIVE The aim of this review article is to highlight the structure-activity relationships of several FK228 analogues as HDAC inhibitors. In addition, the synergistic effects of a dual HDAC/PI3K inhibition by some derivatives have been investigated. MATERIALS AND METHODS PubMed, MEDLINE, CAPLUS, SciFinder Scholar database were considered by selecting articles which fulfilled the objectives of this review, dating from 2015 till present time. RESULTS HDAC inhibitors have a significant role in cancer pathogenesis and evolution. Class I HDAC isoforms are expressed in many tumor types, therefore, potent and selective Class I HDAC inhibitors are of great interest as candidate therapeutic agents with limited side effects. By structurebased optimization, several FK228 analogues [15 (FK-A5), 22, 23 and 26 (FK-A11)] were identified, provided with significant activity against Class I HDAC enzymes and dose dependent antitumor activity. Compound 26 was recognized as an interesting HDAC/PI3K dual inhibitor (IC50 against p110α of 6.7 μM while for HDAC1 inhibitory activity IC50 was 0.64 nM). CONCLUSION Romidepsin analogues HDAC inhibitors have been confirmed as useful anticancer agents. In addition, dual HDAC/PI3K inhibition showed by some of them exhibited synergistic effects in inducing apoptosis in human cancer cells. Further studies on FK228 analogues may positively contribute to the availability of potent agents in tumor treatment.
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Affiliation(s)
- Eftiola Pojani
- Department of the Chemical-Toxicological and Pharmacological Evaluation of Drugs, Faculty of Pharmacy, Catholic University "Our Lady of Good Counsel", Tirana, Albania
| | - Daniela Barlocco
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, University of Milan, L. Mangiagalli 25, Milan 20133, Italy
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Genome-based mining of new antimicrobial meroterpenoids from the phytopathogenic fungus Bipolaris sorokiniana strain 11134. Appl Microbiol Biotechnol 2020; 104:3835-3846. [PMID: 32215711 DOI: 10.1007/s00253-020-10522-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/21/2020] [Accepted: 03/03/2020] [Indexed: 01/14/2023]
Abstract
Polyketide-terpenoid hybrid compounds are one of the largest families of meroterpenoids, with great potential for drug development for resistant pathogens. Genome sequence analysis of secondary metabolite gene clusters of a phytopathogenic fungus, Bipolaris sorokiniana 11134, revealed a type I polyketide gene cluster, consisting of highly reducing polyketide synthase, non-reducing polyketide synthase, and adjacent prenyltransferase. MS- and UV-guided isolations led to the isolation of ten meroterpenoids, including two new compounds: 19-dehydroxyl-3-epi-arthripenoid A (1) and 12-keto-cochlioquinone A (2). The structures of 1-10 were elucidated by the analysis of NMR and high-resolution electrospray ionization mass spectroscopy data. Compounds 5-8 and 10 showed moderate activity against common Staphylococcus aureus and methicillin-resistant S. aureus, with minimum inhibitory concentration (MIC) values of 12.5-100 μg/mL. Compound 5 also exhibited activity against four clinical resistant S. aureus strains and synergistic antifungal activity against Candida albicans with MIC values of 12.5-25 μg/mL. The biosynthetic gene cluster of the isolated compounds and their putative biosynthetic pathway are also proposed. KEY POINTS: • Ten meroterpenoids were identified from B. sorokiniana, including two new compounds. • Cochlioquinone B (5) showed activity against MRSA and synergistic activity against C. albicans. • The biosynthetic gene cluster and biosynthetic pathway of meroterpenoids are proposed. • Genome mining provided a new direction to uncover the diversity of meroterpenoids.
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Abstract
Burkholderia bacteria are multifaceted organisms that are ecologically and metabolically diverse. The Burkholderia genus has gained prominence because it includes human pathogens; however, many strains are nonpathogenic and have desirable characteristics such as beneficial plant associations and degradation of pollutants. The diversity of the Burkholderia genus is reflected within the large genomes that feature multiple replicons. Burkholderia genomes encode a plethora of natural products with potential therapeutic relevance and biotechnological applications. This review highlights Burkholderia as an emerging source of natural products. An overview of the taxonomy of the Burkholderia genus, which is currently being revised, is provided. We then present a curated compilation of natural products isolated from Burkholderia sensu lato and analyze their characteristics in terms of biosynthetic class, discovery method, and bioactivity. Finally, we describe and discuss genome characteristics and highlight the biosynthesis of a select number of natural products that are encoded in unusual biosynthetic gene clusters. The availability of >1000 Burkholderia genomes in public databases provides an opportunity to realize the genetic potential of this underexplored taxon for natural product discovery.
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Affiliation(s)
- Sylvia Kunakom
- Department of Medicinal Chemistry and Pharmacognosy and Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Alessandra S. Eustáquio
- Department of Medicinal Chemistry and Pharmacognosy and Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
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11
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Genome- and MS-based mining of antibacterial chlorinated chromones and xanthones from the phytopathogenic fungus Bipolaris sorokiniana strain 11134. Appl Microbiol Biotechnol 2019; 103:5167-5181. [PMID: 31001746 DOI: 10.1007/s00253-019-09821-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 03/29/2019] [Accepted: 04/01/2019] [Indexed: 12/18/2022]
Abstract
Halogen substituents are important for biological activity in many compounds. Genome-based mining of halogenase along with its biosynthetic gene cluster provided an efficient approach for the discovery of naturally occurring organohalogen compounds. Analysis of the genome sequence of a phytopathogenic fungus Bipolaris sorokiniana 11134 revealed a polyketide gene cluster adjacent to a flavin-dependent halogenase capable of encoding halogenated polyketides, which are rarely reported in phytopathogenic fungi. Furthermore, MS- and UV-guided isolation and purification led to the identification of five chlorine-containing natural products together with seven other chromones and xanthones. Two of the chlorinated compounds and four chromones are new compounds. Their structures were elucidated by NMR spectroscopic analysis and HRESIMS data. The biosynthetic gene clusters of isolated compounds and their putative biosynthetic pathway are also proposed. One new chlorinated compound showed activity against Staphylococcus aureus, methicillin-resistant S. aureus, and three clinical-resistant S. aureus strains with a shared minimum inhibitory concentration (MIC) of 12.5 μg/mL. Genome-based mining of halogenases combined with high-resolution MS- and UV-guided identification provides an efficient approach to discover new halogenated natural products from microorganisms.
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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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