1
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Dong J, Ning J, Tian Y, Li H, Chen H, Guan W. The involvement of multiple ABC transporters in daunorubicin efflux in Streptomyces coeruleorubidus. Microb Biotechnol 2024; 17:e70023. [PMID: 39375957 PMCID: PMC11458662 DOI: 10.1111/1751-7915.70023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Accepted: 09/15/2024] [Indexed: 10/09/2024] Open
Abstract
Streptomyces genus produces a large number of antibiotics, which are always synthesized by specific biosynthetic gene clusters (BGCs). To resist autotoxicity, transporters encoded by genes located within BGC occasionally pump antibiotic along with transporter encoded by gene located outside BGC. Daunorubicin is an anthracycline antibiotic biosynthesized by Streptomyces species, playing a crucial role in the treatment of leukaemia. In existing studies, only one two-component ATP-binding cassette (ABC) transporter, encoded by drrA1-drrB1 (abbreviated as drrAB1) and located within the daunorubicin BGC, has been proven to extrude daunorubicin. In this work, two other two-component ABC transporters, encoded by drrAB2 and drrAB3 and located outside the cluster, were found to play the complementary role in daunorubicin efflux in S. coeruleorubidus. Disruption of three drrABs resulted in a 94% decrease in daunorubicin production. Furthermore, drrAB2 is regulated by the TetR family regulator DrrR1, responding to the intracellular accumulation of daunorubicin and suggesting its role in stress response and self-resistance. Although the homologues of DrrAB1 are only found in three anthracycline BGCs, the homologues of DrrAB2 and DrrAB3 are spread in many Streptomyces strains which do not contain any known anthracycline BGC. This indicates that DrrAB2 and DrrAB3 may recognize and extrude a broader range of substrates besides daunorubicin, thus playing a more extensive role in cellular detoxification.
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Affiliation(s)
- Jianxin Dong
- The Fourth Affiliated Hospital & Institute of Pharmaceutical Biotechnology, School of MedicineZhejiang UniversityHangzhouChina
| | - Jiali Ning
- The Fourth Affiliated Hospital & Institute of Pharmaceutical Biotechnology, School of MedicineZhejiang UniversityHangzhouChina
| | - Yu Tian
- School of Biology, Food and EnvironmentHefei UniversityHefeiChina
| | - Han Li
- The Fourth Affiliated Hospital & Institute of Pharmaceutical Biotechnology, School of MedicineZhejiang UniversityHangzhouChina
| | - Hua Chen
- School of Biology, Food and EnvironmentHefei UniversityHefeiChina
| | - Wenjun Guan
- The Fourth Affiliated Hospital & Institute of Pharmaceutical Biotechnology, School of MedicineZhejiang UniversityHangzhouChina
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2
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Zhao M, Zhang W, Yang C, Zhang L, Huang H, Zhu Y, Ratnasekera D, Zhang C. Discovery of Kebanmycins with Antibacterial and Cytotoxic Activities from the Mangrove-Derived Streptomyces sp. SCSIO 40068. JOURNAL OF NATURAL PRODUCTS 2024; 87:1591-1600. [PMID: 38862138 DOI: 10.1021/acs.jnatprod.4c00232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2024]
Abstract
Mangrove derived actinomycetes are a rich reservoir of bioactive natural products and play important roles in pharmaceutical chemistry. In a screen of actinomycetes from mangrove rhizosphere sedimental environments, the isolated strain Streptomyces sp. SCSIO 40068 displayed strong antibacterial activity. Further fractionation of the extract yielded four new compounds kebanmycins A-D (1-4) and two known analogues FD-594 (5) and the aglycon (6). The structures of 1-6 were determined based on extensive spectroscopic data and single-crystal X-ray diffraction analysis. 1-3 featured a fused pyranonaphthaxanthene as an integral part of a 6/6/6/6/6/6 polycyclic motif, and showed bioactivity against a series of Gram-positive bacteria and cytotoxicity to several human tumor cells. In addition, the kebanmycins biosynthetic gene cluster (keb) was identified in Streptomyces sp. SCSIO 40068, and KebMT2 was biochemically characterized as a tailoring sugar-O-methyltransferase, leading to a proposed biosynthetic route to 1-6. This study paves the way to further investigate 1 as a potential lead compound.
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Affiliation(s)
- Mengran Zhao
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- Sanya Institute of Ocean Eco-Environmental Engineering, Sanya 572000, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenjun Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- Sanya Institute of Ocean Eco-Environmental Engineering, Sanya 572000, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chunfang Yang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- Sanya Institute of Ocean Eco-Environmental Engineering, Sanya 572000, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liping Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- Sanya Institute of Ocean Eco-Environmental Engineering, Sanya 572000, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huarong Huang
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, China
| | - Yiguang Zhu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- Sanya Institute of Ocean Eco-Environmental Engineering, Sanya 572000, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Disna Ratnasekera
- Department of Agricultural Biology, Faculty of Agriculture, University of Ruhuna, Kamburupitiya 81000, Sri Lanka
| | - Changsheng Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- Sanya Institute of Ocean Eco-Environmental Engineering, Sanya 572000, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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3
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Wang R, Nguyen J, Hecht J, Schwartz N, Brown KV, Ponomareva LV, Niemczura M, van Dissel D, van Wezel GP, Thorson JS, Metsä-Ketelä M, Shaaban KA, Nybo SE. A BioBricks Metabolic Engineering Platform for the Biosynthesis of Anthracyclinones in Streptomyces coelicolor. ACS Synth Biol 2022; 11:4193-4209. [PMID: 36378506 PMCID: PMC9764417 DOI: 10.1021/acssynbio.2c00498] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Actinomycetes produce a variety of clinically indispensable molecules, such as antineoplastic anthracyclines. However, the actinomycetes are hindered in their further development as genetically engineered hosts for the synthesis of new anthracycline analogues due to their slow growth kinetics associated with their mycelial life cycle and the lack of a comprehensive genetic toolbox for combinatorial biosynthesis. In this report, we tackled both issues via the development of the BIOPOLYMER (BIOBricks POLYketide Metabolic EngineeRing) toolbox: a comprehensive synthetic biology toolbox consisting of engineered strains, promoters, vectors, and biosynthetic genes for the synthesis of anthracyclinones. An improved derivative of the production host Streptomyces coelicolor M1152 was created by deleting the matAB gene cluster that specifies extracellular poly-β-1,6-N-acetylglucosamine (PNAG). This resulted in a loss of mycelial aggregation, with improved biomass accumulation and anthracyclinone production. We then leveraged BIOPOLYMER to engineer four distinct anthracyclinone pathways, identifying optimal combinations of promoters, genes, and vectors to produce aklavinone, 9-epi-aklavinone, auramycinone, and nogalamycinone at titers between 15-20 mg/L. Optimization of nogalamycinone production strains resulted in titers of 103 mg/L. We structurally characterized six anthracyclinone products from fermentations, including new compounds 9,10-seco-7-deoxy-nogalamycinone and 4-O-β-d-glucosyl-nogalamycinone. Lastly, we tested the antiproliferative activity of the anthracyclinones in a mammalian cancer cell viability assay, in which nogalamycinone, auramycinone, and aklavinone exhibited moderate cytotoxicity against several cancer cell lines. We envision that BIOPOLYMER will serve as a foundational platform technology for the synthesis of designer anthracycline analogues.
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Affiliation(s)
- Rongbin Wang
- Department
of Life Technologies, University of Turku, FIN-20014 Turku, Finland
| | - Jennifer Nguyen
- Department
of Pharmaceutical Sciences, College of Pharmacy, Ferris State University, Big Rapids, Michigan 49307, United States
| | - Jacob Hecht
- Department
of Pharmaceutical Sciences, College of Pharmacy, Ferris State University, Big Rapids, Michigan 49307, United States
| | - Nora Schwartz
- Department
of Pharmaceutical Sciences, College of Pharmacy, Ferris State University, Big Rapids, Michigan 49307, United States
| | - Katelyn V. Brown
- Department
of Pharmaceutical Sciences, College of Pharmacy, Ferris State University, Big Rapids, Michigan 49307, United States
| | - Larissa V. Ponomareva
- §Center for Pharmaceutical
Research and Innovation, ∥Department of Pharmaceutical Sciences,
College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Magdalena Niemczura
- Department
of Life Technologies, University of Turku, FIN-20014 Turku, Finland
| | - Dino van Dissel
- Institute
of Biology, Leiden University, Sylviusweg 72, 2333
BE Leiden, The Netherlands,Department
of Biotechnology and Nanomedicine, SINTEF
AS, P.O. Box 4760 Torgarden, NO-7465 Trondheim, Norway
| | - Gilles P. van Wezel
- Institute
of Biology, Leiden University, Sylviusweg 72, 2333
BE Leiden, The Netherlands
| | - Jon S. Thorson
- §Center for Pharmaceutical
Research and Innovation, ∥Department of Pharmaceutical Sciences,
College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Mikko Metsä-Ketelä
- Department
of Life Technologies, University of Turku, FIN-20014 Turku, Finland,
| | - Khaled A. Shaaban
- §Center for Pharmaceutical
Research and Innovation, ∥Department of Pharmaceutical Sciences,
College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States,
| | - S. Eric Nybo
- Department
of Pharmaceutical Sciences, College of Pharmacy, Ferris State University, Big Rapids, Michigan 49307, United States,
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4
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Zhao S, Xia Y, Liu H, Cui T, Fu P, Zhu W. A Cyclohexapeptide and Its Rare Glycosides from Marine Sponge-Derived Streptomyces sp. OUCMDZ-4539. Org Lett 2022; 24:6750-6754. [PMID: 36073973 DOI: 10.1021/acs.orglett.2c02520] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Pyridapeptide A (1), a cyclohexapeptide containing hexahydropyridazine-3-carboxylic acid (HPDA), 5-hydroxytetrahydropyridazine-3-carboxylic acid (γ-OH-TPDA), and (2S,3R,4E,6E)-2-amino-3-hydroxy-8-methylnona-4,6-dienoic acid residues, and its four glycopeptides, pyridapeptides B-E (2-5, respectively), were isolated from the fermentation broth of the marine sponge-derived Streptomyces sp. OUCMDZ-4539. Their structures were determined on the basis of spectroscopic analysis and chemical methods. Pyridapeptides B-E have one or more 2,3,6-trideoxyhexose sugar units glycosylated at the γ-OH-TPDA residue. The biosynthetic pathways were proposed on the basis of gene cluster analysis. Compounds 4 and 5, containing four sugar groups, displayed significant antiproliferative activity against five human cancer cell lines (PC9, MKN45, HepG2, HCT-116, and K562).
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Affiliation(s)
- Shuige Zhao
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Yuwei Xia
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Haishan Liu
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China.,School of Biological Science and Technology, University of Jinan, Jinan 250022, China
| | - Tongxu Cui
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Peng Fu
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China.,Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China
| | - Weiming Zhu
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China.,Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China
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5
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Hu X, Tang Y, Liu Y, Pei X, Huang Z, Song F, Zhang H. Comprehensive Genomic Analysis of Marine Strain Streptomyces sp. 891, an Excellent Producer of Chrysomycin A with Therapeutic Potential. Mar Drugs 2022; 20:287. [PMID: 35621938 PMCID: PMC9144908 DOI: 10.3390/md20050287] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 04/20/2022] [Accepted: 04/22/2022] [Indexed: 11/29/2022] Open
Abstract
Chrysomycin A is one of the most promising therapeutic candidates for treating infections caused by multidrug-resistant Gram-positive bacteria. By hybridizing next-step generation (Illumina) and third-generation (PacBio) sequencing technologies, a high-quality chromosome-level genome together with a plasmid was firstly assembled for chrysomycin A-producing marine strain 891. Phylogenetic analysis of the 16S rRNA gene and genome sequences revealed that this strain unambiguously belonged to the genus Streptomyces, and its genomic features and functional genes were comprehensively analyzed and annotated. AntiSMASH analysis of this strain unveiled one key biosynthetic gene cluster, T2PKS, responsible for the biosynthesis of chrysomycin, the biosynthesis pathway of which was putatively proposed. These findings definitely shed light on further investigation for construction of a robust industrial strain with high-yield chrysomycin A production using genetic engineering techniques and combinatorial biology approaches.
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Affiliation(s)
- Xu Hu
- School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, China; (X.H.); (Y.T.); (Y.L.); (X.P.); (Z.H.)
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Yuqi Tang
- School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, China; (X.H.); (Y.T.); (Y.L.); (X.P.); (Z.H.)
| | - Yuanyuan Liu
- School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, China; (X.H.); (Y.T.); (Y.L.); (X.P.); (Z.H.)
| | - Xinwei Pei
- School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, China; (X.H.); (Y.T.); (Y.L.); (X.P.); (Z.H.)
| | - Ziwei Huang
- School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, China; (X.H.); (Y.T.); (Y.L.); (X.P.); (Z.H.)
| | - Fuhang Song
- School of Light Industry, Beijing Technology and Business University, Beijing 100048, China;
| | - Huawei Zhang
- School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, China; (X.H.); (Y.T.); (Y.L.); (X.P.); (Z.H.)
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6
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Liu Q, Zhang L, Wang Y, Zhang C, Liu T, Duan C, Bian X, Guo Z, Long Q, Tang Y, Du J, Liu A, Dai L, Li D, Chen W. Enhancement of edeine production in Brevibacillus brevis X23 via in situ promoter engineering. Microb Biotechnol 2022; 15:577-589. [PMID: 34310825 PMCID: PMC8867987 DOI: 10.1111/1751-7915.13825] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 04/22/2021] [Accepted: 04/26/2021] [Indexed: 11/28/2022] Open
Abstract
Edeines, a group of cationic antimicrobial peptides produced by the soil bacterium Brevibacillus, have broad biological effects, such as antimicrobial, anticancer and immunosuppressive activities. However, the yield of edeines in wild-type (WT) Brevibacillus is extremely low, and chemical synthesis of edeines is a time-consuming process. Genetic engineering has proven to be an effective approach to produce antibiotics with high yield. In this study, the edeine biosynthetic gene cluster (ede BGC), which is involved in edeine production, was identified and characterized in Brevibacillus brevis X23. To improve edeine production in B. brevis X23, the ede BGC promoter was replaced with six different promoters, Pmwp , Pspc , PxylA , Pshuttle-09 , Pgrac or P43 , through double-crossover homologous recombination. The new promoters significantly increased the expression of the ede BGC as well as edeine production by 2.9 ± 0.4 to 20.5 ± 1.2-fold and 3.6 ± 0.1to 8.7 ± 0.7-fold respectively. The highest yield of edeines (83.6 mg l-1 ) was obtained in B. brevis X23 with the Pmwp promoter. This study provides a practical approach for producing high yields of edeines in B. brevis.
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Affiliation(s)
- Qingshu Liu
- College of Plant ProtectionHunan Agricultural UniversityChangsha410128China
- Hunan Province Engineering Research Center for Agricultural Microbiology ApplicationHunan Institute of MicrobiologyChangsha410009China
| | - Liang Zhang
- College of Plant ProtectionHunan Agricultural UniversityChangsha410128China
- College of AgronomyHunan Agricultural UniversityChangsha410128China
| | - Yunsheng Wang
- College of Plant ProtectionHunan Agricultural UniversityChangsha410128China
| | - Cuiyang Zhang
- Hunan Province Engineering Research Center for Agricultural Microbiology ApplicationHunan Institute of MicrobiologyChangsha410009China
| | - Tianbo Liu
- College of Plant ProtectionHunan Agricultural UniversityChangsha410128China
| | - Caichen Duan
- Hunan Province Engineering Research Center for Agricultural Microbiology ApplicationHunan Institute of MicrobiologyChangsha410009China
| | - Xiaoying Bian
- Helmholtz International Lab for Anti‐Infectives, Shandong University‐Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial TechnologyShandong UniversityQingdao266237China
| | - Zhaohui Guo
- Hunan Province Engineering Research Center for Agricultural Microbiology ApplicationHunan Institute of MicrobiologyChangsha410009China
| | - Qingshan Long
- Hunan Province Engineering Research Center for Agricultural Microbiology ApplicationHunan Institute of MicrobiologyChangsha410009China
| | - Ying Tang
- Hunan Province Engineering Research Center for Agricultural Microbiology ApplicationHunan Institute of MicrobiologyChangsha410009China
| | - Jie Du
- Hunan Province Engineering Research Center for Agricultural Microbiology ApplicationHunan Institute of MicrobiologyChangsha410009China
| | - Aiyu Liu
- College of AgronomyHunan Agricultural UniversityChangsha410128China
| | - Liangying Dai
- College of Plant ProtectionHunan Agricultural UniversityChangsha410128China
| | - Dingjun Li
- College of Plant ProtectionHunan Agricultural UniversityChangsha410128China
- Hunan University of Technology and BusinessChangsha410205China
| | - Wu Chen
- College of Plant ProtectionHunan Agricultural UniversityChangsha410128China
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7
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Abdul Kader S, Dib S, Achkar IW, Thareja G, Suhre K, Rafii A, Halama A. Defining the landscape of metabolic dysregulations in cancer metastasis. Clin Exp Metastasis 2021; 39:345-362. [PMID: 34921655 PMCID: PMC8971193 DOI: 10.1007/s10585-021-10140-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 12/10/2021] [Indexed: 02/07/2023]
Abstract
Metastasis is the primary cause of cancer related deaths due to the limited number of efficient druggable targets. Signatures of dysregulated cancer metabolism could serve as a roadmap for the determination of new treatment strategies. However, the metabolic signatures of metastatic cells remain vastly elusive. Our aim was to determine metabolic dysregulations associated with high metastatic potential in breast cancer cell lines. We have selected 5 triple negative breast cancer (TNBC) cell lines including three with high metastatic potential (HMP) (MDA-MB-231, MDA-MB-436, MDA-MB-468) and two with low metastatic potential (LMP) (BT549, HCC1143). The normal epithelial breast cell line (hTERT-HME1) was also investigated. The untargeted metabolic profiling of cells and growth media was conducted and total of 479 metabolites were quantified. First we characterized metabolic features differentiating TNBC cell lines from normal cells as well as identified cell line specific metabolic fingerprints. Next, we determined 92 metabolites in cells and 22 in growth medium that display significant differences between LMP and HMP. The HMP cell lines had elevated level of molecules involved in glycolysis, TCA cycle and lipid metabolism. We identified metabolic advantages of cell lines with HMP beyond enhanced glycolysis by pinpointing the role of branched chain amino acids (BCAA) catabolism as well as molecules supporting coagulation and platelet activation as important contributors to the metastatic cascade. The landscape of metabolic dysregulations, characterized in our study, could serve as a roadmap for the identification of treatment strategies targeting cancer cells with enhanced metastatic potential.
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Affiliation(s)
- Sara Abdul Kader
- Department of Physiology and Biophysics, Weill Cornell Medicine-Qatar, 24144, Doha, Qatar
- University of Paris-Saclay, 91190, Gif-sur-Yvette, France
| | - Shaima Dib
- Department of Physiology and Biophysics, Weill Cornell Medicine-Qatar, 24144, Doha, Qatar
| | - Iman W Achkar
- Department of Physiology and Biophysics, Weill Cornell Medicine-Qatar, 24144, Doha, Qatar
| | - Gaurav Thareja
- Department of Physiology and Biophysics, Weill Cornell Medicine-Qatar, 24144, Doha, Qatar
- University of Paris-Saclay, 91190, Gif-sur-Yvette, France
| | - Karsten Suhre
- Department of Physiology and Biophysics, Weill Cornell Medicine-Qatar, 24144, Doha, Qatar
- Department of Biophysics and Physiology, Weill Cornell Medicine, New York, USA
| | - Arash Rafii
- Department of Genetic Medicine, Weill Cornell Medicine, New York, USA
- Genetic Intelligence Laboratory, Weill Cornell Medicine in Qatar, Qatar Foundation, Doha, Qatar
| | - Anna Halama
- Department of Physiology and Biophysics, Weill Cornell Medicine-Qatar, 24144, Doha, Qatar.
- Department of Biophysics and Physiology, Weill Cornell Medicine, New York, USA.
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8
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Reductive inactivation of the hemiaminal pharmacophore for resistance against tetrahydroisoquinoline antibiotics. Nat Commun 2021; 12:7085. [PMID: 34873166 PMCID: PMC8648761 DOI: 10.1038/s41467-021-27404-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 11/11/2021] [Indexed: 12/24/2022] Open
Abstract
Antibiotic resistance is becoming one of the major crises, among which hydrolysis reaction is widely employed by bacteria to destroy the reactive pharmacophore. Correspondingly, antibiotic producer has canonically co-evolved this approach with the biosynthetic capability for self-resistance. Here we discover a self-defense strategy featuring with reductive inactivation of hemiaminal pharmacophore by short-chain dehydrogenases/reductases (SDRs) NapW and homW, which are integrated with the naphthyridinomycin biosynthetic pathway. We determine the crystal structure of NapW·NADPH complex and propose a catalytic mechanism by molecular dynamics simulation analysis. Additionally, a similar detoxification strategy is identified in the biosynthesis of saframycin A, another member of tetrahydroisoquinoline (THIQ) antibiotics. Remarkably, similar SDRs are widely spread in bacteria and able to inactive other THIQ members including the clinical anticancer drug, ET-743. These findings not only fill in the missing intracellular events of temporal-spatial shielding mode for cryptic self-resistance during THIQs biosynthesis, but also exhibit a sophisticated damage-control in secondary metabolism and general immunity toward this family of antibiotics. Antibiotic-producing organisms need to co-evolve self-protection mechanisms to avoid any damage to themselves caused by the antibiotic pharmacophore (the reactive part of the compound). In this study, the authors report a self-defense strategy in naphthyridinomycin (NDM)-producing Streptomyces lusitanus, that comprises reductive inactivation of the hemiaminal pharmacophore by short-chain dehydrogenases/reductases (SDRs) NapW and HomW.
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9
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Zhuang W, Yu X, Hu R, Luo Z, Liu X, Zheng X, Xiao F, Peng Y, He Q, Tian Y, Yang T, Wang S, Shu L, Yan Q, Wang C, He Z. Diversity, function and assembly of mangrove root-associated microbial communities at a continuous fine-scale. NPJ Biofilms Microbiomes 2020; 6:52. [PMID: 33184266 PMCID: PMC7665043 DOI: 10.1038/s41522-020-00164-6] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 10/19/2020] [Indexed: 12/13/2022] Open
Abstract
Mangrove roots harbor a repertoire of microbial taxa that contribute to important ecological functions in mangrove ecosystems. However, the diversity, function, and assembly of mangrove root-associated microbial communities along a continuous fine-scale niche remain elusive. Here, we applied amplicon and metagenome sequencing to investigate the bacterial and fungal communities among four compartments (nonrhizosphere, rhizosphere, episphere, and endosphere) of mangrove roots. We found different distribution patterns for both bacterial and fungal communities in all four root compartments, which could be largely due to niche differentiation along the root compartments and exudation effects of mangrove roots. The functional pattern for bacterial and fungal communities was also divergent within the compartments. The endosphere harbored more genes involved in carbohydrate metabolism, lipid transport, and methane production, and fewer genes were found to be involved in sulfur reduction compared to other compartments. The dynamics of root-associated microbial communities revealed that 56-74% of endosphere bacterial taxa were derived from nonrhizosphere, whereas no fungal OTUs of nonrhizosphere were detected in the endosphere. This indicates that roots may play a more strictly selective role in the assembly of the fungal community compared to the endosphere bacterial community, which is consistent with the projections established in an amplification-selection model. This study reveals the divergence in the diversity and function of root-associated microbial communities along a continuous fine-scale niche, thereby highlighting a strictly selective role of soil-root interfaces in shaping the fungal community structure in the mangrove root systems.
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Affiliation(s)
- Wei Zhuang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), South China Sea Institution, Sun Yat-sen University, 510006, Guangzhou, China
| | - Xiaoli Yu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), South China Sea Institution, Sun Yat-sen University, 510006, Guangzhou, China
| | - Ruiwen Hu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), South China Sea Institution, Sun Yat-sen University, 510006, Guangzhou, China
| | - Zhiwen Luo
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), South China Sea Institution, Sun Yat-sen University, 510006, Guangzhou, China
| | - Xingyu Liu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), South China Sea Institution, Sun Yat-sen University, 510006, Guangzhou, China
| | - Xiafei Zheng
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), South China Sea Institution, Sun Yat-sen University, 510006, Guangzhou, China
| | - Fanshu Xiao
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), South China Sea Institution, Sun Yat-sen University, 510006, Guangzhou, China
| | - Yisheng Peng
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), South China Sea Institution, Sun Yat-sen University, 510006, Guangzhou, China
| | - Qiang He
- Department of Civil and Environmental Engineering, The University of Tennessee, Knoxville, TN, 37996, USA
| | - Yun Tian
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, 361102, Xiamen, China
| | - Tony Yang
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, S9H 3×2, Canada
| | - Shanquan Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), South China Sea Institution, Sun Yat-sen University, 510006, Guangzhou, China
| | - Longfei Shu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), South China Sea Institution, Sun Yat-sen University, 510006, Guangzhou, China
| | - Qingyun Yan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), South China Sea Institution, Sun Yat-sen University, 510006, Guangzhou, China
| | - Cheng Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), South China Sea Institution, Sun Yat-sen University, 510006, Guangzhou, China.
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), South China Sea Institution, Sun Yat-sen University, 510006, Guangzhou, China.
- College of Agronomy, Hunan Agricultural University, 410128, Changsha, China.
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