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Sharma K, Ghiffary MR, Lee G, Kim HU. Efficient production of an antitumor precursor actinocin and other medicinal molecules from kynurenine pathway in Escherichia coli. Metab Eng 2024; 81:144-156. [PMID: 38043641 DOI: 10.1016/j.ymben.2023.11.008] [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: 09/02/2023] [Revised: 11/17/2023] [Accepted: 11/27/2023] [Indexed: 12/05/2023]
Abstract
Kynurenine pathway has a potential to convert L-tryptophan into multiple medicinal molecules. This study aims to explore the biosynthetic potential of kynurenine pathway for the efficient production of actinocin, an antitumor precursor selected as a proof-of-concept target molecule. Kynurenine pathway is first constructed in Escherichia coli by testing various combinations of biosynthetic genes from four different organisms. Metabolic engineering strategies are next performed to improve the production by inhibiting a competing pathway, and enhancing intracellular supply of a cofactor S-adenosyl-L-methionine, and ultimately to produce actinocin from glucose. Metabolome analysis further suggests additional gene overexpression targets, which finally leads to the actinocin titer of 719 mg/L. E. coli strain engineered to produce actinocin is further successfully utilized to produce 350 mg/L of kynurenic acid, a neuroprotectant, and 1401 mg/L of 3-hydroxyanthranilic acid, an antioxidant, also from glucose. These competitive production titers demonstrate the biosynthetic potential of kynurenine pathway as a source of multiple medicinal molecules. The approach undertaken in this study can be useful for the sustainable production of molecules derived from kynurenine pathway, which are otherwise chemically synthesized.
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Affiliation(s)
- Komal Sharma
- Systems Biology and Medicine Laboratory, Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Mohammad Rifqi Ghiffary
- Systems Biology and Medicine Laboratory, Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - GaRyoung Lee
- Systems Biology and Medicine Laboratory, Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Hyun Uk Kim
- Systems Biology and Medicine Laboratory, Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea; Graduate School of Engineering Biology, KAIST, Daejeon, 34141, Republic of Korea; BioProcess Engineering Research Center and BioInformatics Research Center, KAIST, Daejeon, 34141, Republic of Korea.
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2
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Yan JX, Wu Q, Maity M, Braun DR, Alas I, Wang X, Yin X, Zhu Y, Bell BA, Rajski SR, Ge Y, Richardson DD, Zhong W, Bugni TS. Rapid Unambiguous Structure Elucidation of Streptnatamide A, a New Cyclic Peptide Isolated from A Marine-derived Streptomyces sp. Chemistry 2023; 29:e202301813. [PMID: 37452377 PMCID: PMC10592287 DOI: 10.1002/chem.202301813] [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: 06/15/2023] [Revised: 07/14/2023] [Accepted: 07/14/2023] [Indexed: 07/18/2023]
Abstract
Cyclic peptides have been excellent source of drug leads. With the advances in discovery platforms, the pharmaceutical industry has a growing interest in cyclic peptides and has pushed several into clinical trials. However, structural complexity of cyclic peptides brings extreme challenges for structure elucidation efforts. Isotopic fine structure analysis, Nuclear magnetic resonance (NMR), and detailed tandem mass spectrometry rapidly provided peptide sequence for streptnatamide A, a cyclic peptide isolated from a marine-derived Streptomyces sp. Marfey's analysis determined the stereochemistry of all amino acids, enabling the unambiguous structure determination of this compound. A non-ribosomal peptide synthetase biosynthetic gene cluster (stp) was tentatively identified and annotated for streptnatamide A based on the in silico analysis of whole genome sequencing data. These analytical tools will be powerful tools to overcome the challenges for cyclic peptide structure elucidation and accelerate the development of bioactive cyclic peptides.
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Affiliation(s)
- Jia-Xuan Yan
- Merck & Co., Inc., 126 E. Lincoln Ave, 07065, Rahway, NJ, USA
- Pharmaceutical Sciences Division, University of Wisconsin-Madison, 777 Highland Ave, 53705, Madison, WI, USA
| | - Qihao Wu
- Pharmaceutical Sciences Division, University of Wisconsin-Madison, 777 Highland Ave, 53705, Madison, WI, USA
- Current address: Department of Chemistry, Institute of Biomolecular Design & Discovery, Yale University, 06516, West Haven, CT, USA
| | - Mitasree Maity
- Pharmaceutical Sciences Division, University of Wisconsin-Madison, 777 Highland Ave, 53705, Madison, WI, USA
| | - Doug R Braun
- Pharmaceutical Sciences Division, University of Wisconsin-Madison, 777 Highland Ave, 53705, Madison, WI, USA
| | - Imraan Alas
- Pharmaceutical Sciences Division, University of Wisconsin-Madison, 777 Highland Ave, 53705, Madison, WI, USA
| | - Xiao Wang
- Merck & Co., Inc., 126 E. Lincoln Ave, 07065, Rahway, NJ, USA
| | - Xing Yin
- Merck & Co., Inc., 126 E. Lincoln Ave, 07065, Rahway, NJ, USA
| | - Yanlong Zhu
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, 1111 Highland Ave, 53705, Madison, WI, USA
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, 1111 Highland Ave, 53705, Madison, WI, USA
| | - Bailey A Bell
- Pharmaceutical Sciences Division, University of Wisconsin-Madison, 777 Highland Ave, 53705, Madison, WI, USA
| | - Scott R Rajski
- Pharmaceutical Sciences Division, University of Wisconsin-Madison, 777 Highland Ave, 53705, Madison, WI, USA
| | - Ying Ge
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, 1111 Highland Ave, 53705, Madison, WI, USA
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, 1111 Highland Ave, 53705, Madison, WI, USA
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave, 53706, Madison, WI, USA
| | | | - Wendy Zhong
- Merck & Co., Inc., 126 E. Lincoln Ave, 07065, Rahway, NJ, USA
| | - Tim S Bugni
- Pharmaceutical Sciences Division, University of Wisconsin-Madison, 777 Highland Ave, 53705, Madison, WI, USA
- Lachman Institute for Pharmaceutical Development, University of Wisconsin-Madison, 600 Highland Ave, 53792, Madison, WI, USA
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3
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Gade P, Erlandson A, Ullah A, Chen X, Mathews II, Mera PE, Kim CY. Structural and functional analyses of the echinomycin resistance conferring protein Ecm16 from Streptomyces lasalocidi. Sci Rep 2023; 13:7980. [PMID: 37198233 PMCID: PMC10192343 DOI: 10.1038/s41598-023-34437-9] [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: 09/14/2022] [Accepted: 04/29/2023] [Indexed: 05/19/2023] Open
Abstract
Echinomycin is a natural product DNA bisintercalator antibiotic. The echinomycin biosynthetic gene cluster in Streptomyces lasalocidi includes a gene encoding the self-resistance protein Ecm16. Here, we present the 2.0 Å resolution crystal structure of Ecm16 bound to adenosine diphosphate. The structure of Ecm16 closely resembles that of UvrA, the DNA damage sensor component of the prokaryotic nucleotide excision repair system, but Ecm16 lacks the UvrB-binding domain and its associated zinc-binding module found in UvrA. Mutagenesis study revealed that the insertion domain of Ecm16 is required for DNA binding. Furthermore, the specific amino acid sequence of the insertion domain allows Ecm16 to distinguish echinomycin-bound DNA from normal DNA and link substrate binding to ATP hydrolysis activity. Expression of ecm16 in the heterologous host Brevibacillus choshinensis conferred resistance against echinomycin and other quinomycin antibiotics, including thiocoraline, quinaldopeptin, and sandramycin. Our study provides new insight into how the producers of DNA bisintercalator antibiotics fend off the toxic compounds that they produce.
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Affiliation(s)
- Priyanka Gade
- Department of Chemistry and Biochemistry, The University of Texas at El Paso, El Paso, TX, USA
| | - Amanda Erlandson
- Department of Microbiology, School of Molecular and Cellular Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Anwar Ullah
- Department of Chemistry and Biochemistry, The University of Texas at El Paso, El Paso, TX, USA
| | - Xi Chen
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an, 710127, China
| | - Irimpan I Mathews
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Paola E Mera
- Department of Microbiology, School of Molecular and Cellular Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA.
| | - Chu-Young Kim
- Department of Chemistry and Biochemistry, The University of Texas at El Paso, El Paso, TX, USA.
- Department of Biochemistry, School of Molecular and Cellular Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA.
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4
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Erlandson A, Gade P, Menikpurage IP, Kim CY, Mera PE. The UvrA-like protein Ecm16 requires ATPase activity to render resistance against echinomycin. Mol Microbiol 2022; 117:1434-1446. [PMID: 35534931 PMCID: PMC9328131 DOI: 10.1111/mmi.14918] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 05/05/2022] [Accepted: 05/07/2022] [Indexed: 12/02/2022]
Abstract
Bacteria use various strategies to become antibiotic resistant. The molecular details of these strategies are not fully understood. We can increase our understanding by investigating the same strategies found in antibiotic‐producing bacteria. In this work, we characterize the self‐resistance protein Ecm16 encoded by echinomycin‐producing bacteria. Ecm16 is a structural homolog of the nucleotide excision repair protein UvrA. Expression of ecm16 in the heterologous system Escherichia coli was sufficient to render resistance against echinomycin. Ecm16 binds DNA (double‐stranded and single‐stranded) using a nucleotide‐independent binding mode. Ecm16’s binding affinity for DNA increased by 1.7‐fold when the DNA is intercalated with echinomycin. Ecm16 can render resistance against echinomycin toxicity independently of the nucleotide excision repair system. Similar to UvrA, Ecm16 has ATPase activity, and this activity is essential for Ecm16’s ability to render echinomycin resistance. Notably, UvrA and Ecm16 were unable to complement each other's function. Together, our findings identify new mechanistic details of how a refurbished DNA repair protein Ecm16 can specifically render resistance to the DNA intercalator echinomycin.
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Affiliation(s)
- Amanda Erlandson
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Molecular Biology Program, New Mexico State University, Las Cruces, NM, USA
| | - Priyanka Gade
- Department of Chemistry and Biochemistry, The University of Texas at El Paso, El Paso, TX, USA
| | - Inoka P Menikpurage
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Chu-Young Kim
- Department of Chemistry and Biochemistry, The University of Texas at El Paso, El Paso, TX, USA.,Border Biomedical Research Center, The University of Texas at El Paso, El Paso, TX, USA
| | - Paola E Mera
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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5
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Shi X, Huang L, Song K, Zhao G, Liu Y, Lv L, Du Y. Enzymatic Tailoring in Luzopeptin Biosynthesis Involves Cytochrome P450‐Mediated Carbon–Nitrogen Bond Desaturation for Hydrazone Formation. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202105312] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Xinjie Shi
- Institute of Pharmaceutical Biotechnology and The First Affiliated Hospital Zhejiang University School of Medicine 310058 Hangzhou China
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases The First Affiliated Hospital Zhejiang University 310003 Hangzhou China
| | - Liming Huang
- Institute of Pharmaceutical Biotechnology and The First Affiliated Hospital Zhejiang University School of Medicine 310058 Hangzhou China
| | - Kaihui Song
- Institute of Pharmaceutical Biotechnology and The First Affiliated Hospital Zhejiang University School of Medicine 310058 Hangzhou China
| | - Guiyun Zhao
- Institute of Pharmaceutical Biotechnology and The First Affiliated Hospital Zhejiang University School of Medicine 310058 Hangzhou China
| | - Yu Liu
- College of Life Sciences Zhejiang University 310058 Hangzhou China
| | - Longxian Lv
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases The First Affiliated Hospital Zhejiang University 310003 Hangzhou China
| | - Yi‐Ling Du
- Institute of Pharmaceutical Biotechnology and The First Affiliated Hospital Zhejiang University School of Medicine 310058 Hangzhou China
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases The First Affiliated Hospital Zhejiang University 310003 Hangzhou China
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6
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Little RF, Hertweck C. Chain release mechanisms in polyketide and non-ribosomal peptide biosynthesis. Nat Prod Rep 2021; 39:163-205. [PMID: 34622896 DOI: 10.1039/d1np00035g] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Review covering up to mid-2021The structure of polyketide and non-ribosomal peptide natural products is strongly influenced by how they are released from their biosynthetic enzymes. As such, Nature has evolved a diverse range of release mechanisms, leading to the formation of bioactive chemical scaffolds such as lactones, lactams, diketopiperazines, and tetronates. Here, we review the enzymes and mechanisms used for chain release in polyketide and non-ribosomal peptide biosynthesis, how these mechanisms affect natural product structure, and how they could be utilised to introduce structural diversity into the products of engineered biosynthetic pathways.
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Affiliation(s)
- Rory F Little
- Leibniz Institute for Natural Product Research and Infection Biology, HKI, Germany.
| | - Christian Hertweck
- Leibniz Institute for Natural Product Research and Infection Biology, HKI, Germany.
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7
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Shi X, Huang L, Song K, Zhao G, Liu Y, Lv L, Du YL. Enzymatic Tailoring in Luzopeptin Biosynthesis Involves Cytochrome P450-Mediated Carbon-Nitrogen Bond Desaturation for Hydrazone Formation. Angew Chem Int Ed Engl 2021; 60:19821-19828. [PMID: 34180113 DOI: 10.1002/anie.202105312] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 06/04/2021] [Indexed: 01/15/2023]
Abstract
Luzopeptins and related decadepsipeptides are bisintercalator nonribosomal peptides featuring rare acyl-substituted tetrahydropyridazine-3-carboxylic acid (Thp) subunits that are critical to their biological activities. Herein, we reconstitute the biosynthetic tailoring pathway in luzopeptin A biosynthesis through in vivo genetic and in vitro biochemical approaches. Significantly, we revealed a multitasking cytochrome P450 enzyme that catalyzes four consecutive oxidations including the highly unusual carbon-nitrogen bond desaturation, forming the hydrazone-bearing 4-OH-Thp residues. Moreover, we identified a membrane-bound acyltransferase that likely mediates the subsequent O-acetylation extracellularly, as a potential self-protective strategy for the producer strain. Further genome mining of novel decadepsipeptides and an associated P450 enzyme have provided mechanistic insights into the P450-mediated carbon-nitrogen bond desaturation. Our results not only reveal the molecular basis of pharmacophore formation in bisintercalator decadepsipeptides, but also expand the catalytic versatility of P450 family enzymes.
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Affiliation(s)
- Xinjie Shi
- Institute of Pharmaceutical Biotechnology and The First Affiliated Hospital, Zhejiang University School of Medicine, 310058, Hangzhou, China.,State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University, 310003, Hangzhou, China
| | - Liming Huang
- Institute of Pharmaceutical Biotechnology and The First Affiliated Hospital, Zhejiang University School of Medicine, 310058, Hangzhou, China
| | - Kaihui Song
- Institute of Pharmaceutical Biotechnology and The First Affiliated Hospital, Zhejiang University School of Medicine, 310058, Hangzhou, China
| | - Guiyun Zhao
- Institute of Pharmaceutical Biotechnology and The First Affiliated Hospital, Zhejiang University School of Medicine, 310058, Hangzhou, China
| | - Yu Liu
- College of Life Sciences, Zhejiang University, 310058, Hangzhou, China
| | - Longxian Lv
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University, 310003, Hangzhou, China
| | - Yi-Ling Du
- Institute of Pharmaceutical Biotechnology and The First Affiliated Hospital, Zhejiang University School of Medicine, 310058, Hangzhou, China.,State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University, 310003, Hangzhou, China
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8
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Shi Y, Jiang Z, Hu X, Hu X, Gu R, Jiang B, Zuo L, Li X, Sun H, Zhang C, Wang L, Wu L, Hong B. The Cytochrome P450 Catalyzing C−S Bond Formation in
S
‐Heterocyclization of Chuangxinmycin Biosynthesis. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202015814] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Yuanyuan Shi
- NHC Key Laboratory of Biotechnology of Antibiotics CAMS Key Laboratory of Synthetic Biology for Drug Innovation Institute of Medicinal Biotechnology Chinese Academy of Medical Sciences & Peking Union Medical College No.1 Tiantan Xili Beijing 100050 China
| | - Zhibo Jiang
- NHC Key Laboratory of Biotechnology of Antibiotics CAMS Key Laboratory of Synthetic Biology for Drug Innovation Institute of Medicinal Biotechnology Chinese Academy of Medical Sciences & Peking Union Medical College No.1 Tiantan Xili Beijing 100050 China
| | - Xiaowen Hu
- NHC Key Laboratory of Biotechnology of Antibiotics CAMS Key Laboratory of Synthetic Biology for Drug Innovation Institute of Medicinal Biotechnology Chinese Academy of Medical Sciences & Peking Union Medical College No.1 Tiantan Xili Beijing 100050 China
| | - Xiaomin Hu
- NHC Key Laboratory of Biotechnology of Antibiotics CAMS Key Laboratory of Synthetic Biology for Drug Innovation Institute of Medicinal Biotechnology Chinese Academy of Medical Sciences & Peking Union Medical College No.1 Tiantan Xili Beijing 100050 China
| | - Renjie Gu
- NHC Key Laboratory of Biotechnology of Antibiotics CAMS Key Laboratory of Synthetic Biology for Drug Innovation Institute of Medicinal Biotechnology Chinese Academy of Medical Sciences & Peking Union Medical College No.1 Tiantan Xili Beijing 100050 China
| | - Bingya Jiang
- NHC Key Laboratory of Biotechnology of Antibiotics CAMS Key Laboratory of Synthetic Biology for Drug Innovation Institute of Medicinal Biotechnology Chinese Academy of Medical Sciences & Peking Union Medical College No.1 Tiantan Xili Beijing 100050 China
| | - Lijie Zuo
- NHC Key Laboratory of Biotechnology of Antibiotics CAMS Key Laboratory of Synthetic Biology for Drug Innovation Institute of Medicinal Biotechnology Chinese Academy of Medical Sciences & Peking Union Medical College No.1 Tiantan Xili Beijing 100050 China
| | - Xingxing Li
- NHC Key Laboratory of Biotechnology of Antibiotics CAMS Key Laboratory of Synthetic Biology for Drug Innovation Institute of Medicinal Biotechnology Chinese Academy of Medical Sciences & Peking Union Medical College No.1 Tiantan Xili Beijing 100050 China
| | - Hongmin Sun
- NHC Key Laboratory of Biotechnology of Antibiotics CAMS Key Laboratory of Synthetic Biology for Drug Innovation Institute of Medicinal Biotechnology Chinese Academy of Medical Sciences & Peking Union Medical College No.1 Tiantan Xili Beijing 100050 China
| | - Cong Zhang
- NHC Key Laboratory of Biotechnology of Antibiotics CAMS Key Laboratory of Synthetic Biology for Drug Innovation Institute of Medicinal Biotechnology Chinese Academy of Medical Sciences & Peking Union Medical College No.1 Tiantan Xili Beijing 100050 China
| | - Lifei Wang
- NHC Key Laboratory of Biotechnology of Antibiotics CAMS Key Laboratory of Synthetic Biology for Drug Innovation Institute of Medicinal Biotechnology Chinese Academy of Medical Sciences & Peking Union Medical College No.1 Tiantan Xili Beijing 100050 China
| | - Linzhuan Wu
- NHC Key Laboratory of Biotechnology of Antibiotics CAMS Key Laboratory of Synthetic Biology for Drug Innovation Institute of Medicinal Biotechnology Chinese Academy of Medical Sciences & Peking Union Medical College No.1 Tiantan Xili Beijing 100050 China
| | - Bin Hong
- NHC Key Laboratory of Biotechnology of Antibiotics CAMS Key Laboratory of Synthetic Biology for Drug Innovation Institute of Medicinal Biotechnology Chinese Academy of Medical Sciences & Peking Union Medical College No.1 Tiantan Xili Beijing 100050 China
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9
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Shi Y, Jiang Z, Hu X, Hu X, Gu R, Jiang B, Zuo L, Li X, Sun H, Zhang C, Wang L, Wu L, Hong B. The Cytochrome P450 Catalyzing C−S Bond Formation in
S
‐Heterocyclization of Chuangxinmycin Biosynthesis. Angew Chem Int Ed Engl 2021; 60:15399-15404. [DOI: 10.1002/anie.202015814] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 04/08/2021] [Indexed: 11/10/2022]
Affiliation(s)
- Yuanyuan Shi
- NHC Key Laboratory of Biotechnology of Antibiotics CAMS Key Laboratory of Synthetic Biology for Drug Innovation Institute of Medicinal Biotechnology Chinese Academy of Medical Sciences & Peking Union Medical College No.1 Tiantan Xili Beijing 100050 China
| | - Zhibo Jiang
- NHC Key Laboratory of Biotechnology of Antibiotics CAMS Key Laboratory of Synthetic Biology for Drug Innovation Institute of Medicinal Biotechnology Chinese Academy of Medical Sciences & Peking Union Medical College No.1 Tiantan Xili Beijing 100050 China
| | - Xiaowen Hu
- NHC Key Laboratory of Biotechnology of Antibiotics CAMS Key Laboratory of Synthetic Biology for Drug Innovation Institute of Medicinal Biotechnology Chinese Academy of Medical Sciences & Peking Union Medical College No.1 Tiantan Xili Beijing 100050 China
| | - Xiaomin Hu
- NHC Key Laboratory of Biotechnology of Antibiotics CAMS Key Laboratory of Synthetic Biology for Drug Innovation Institute of Medicinal Biotechnology Chinese Academy of Medical Sciences & Peking Union Medical College No.1 Tiantan Xili Beijing 100050 China
| | - Renjie Gu
- NHC Key Laboratory of Biotechnology of Antibiotics CAMS Key Laboratory of Synthetic Biology for Drug Innovation Institute of Medicinal Biotechnology Chinese Academy of Medical Sciences & Peking Union Medical College No.1 Tiantan Xili Beijing 100050 China
| | - Bingya Jiang
- NHC Key Laboratory of Biotechnology of Antibiotics CAMS Key Laboratory of Synthetic Biology for Drug Innovation Institute of Medicinal Biotechnology Chinese Academy of Medical Sciences & Peking Union Medical College No.1 Tiantan Xili Beijing 100050 China
| | - Lijie Zuo
- NHC Key Laboratory of Biotechnology of Antibiotics CAMS Key Laboratory of Synthetic Biology for Drug Innovation Institute of Medicinal Biotechnology Chinese Academy of Medical Sciences & Peking Union Medical College No.1 Tiantan Xili Beijing 100050 China
| | - Xingxing Li
- NHC Key Laboratory of Biotechnology of Antibiotics CAMS Key Laboratory of Synthetic Biology for Drug Innovation Institute of Medicinal Biotechnology Chinese Academy of Medical Sciences & Peking Union Medical College No.1 Tiantan Xili Beijing 100050 China
| | - Hongmin Sun
- NHC Key Laboratory of Biotechnology of Antibiotics CAMS Key Laboratory of Synthetic Biology for Drug Innovation Institute of Medicinal Biotechnology Chinese Academy of Medical Sciences & Peking Union Medical College No.1 Tiantan Xili Beijing 100050 China
| | - Cong Zhang
- NHC Key Laboratory of Biotechnology of Antibiotics CAMS Key Laboratory of Synthetic Biology for Drug Innovation Institute of Medicinal Biotechnology Chinese Academy of Medical Sciences & Peking Union Medical College No.1 Tiantan Xili Beijing 100050 China
| | - Lifei Wang
- NHC Key Laboratory of Biotechnology of Antibiotics CAMS Key Laboratory of Synthetic Biology for Drug Innovation Institute of Medicinal Biotechnology Chinese Academy of Medical Sciences & Peking Union Medical College No.1 Tiantan Xili Beijing 100050 China
| | - Linzhuan Wu
- NHC Key Laboratory of Biotechnology of Antibiotics CAMS Key Laboratory of Synthetic Biology for Drug Innovation Institute of Medicinal Biotechnology Chinese Academy of Medical Sciences & Peking Union Medical College No.1 Tiantan Xili Beijing 100050 China
| | - Bin Hong
- NHC Key Laboratory of Biotechnology of Antibiotics CAMS Key Laboratory of Synthetic Biology for Drug Innovation Institute of Medicinal Biotechnology Chinese Academy of Medical Sciences & Peking Union Medical College No.1 Tiantan Xili Beijing 100050 China
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10
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Komaki H, Tamura T. Reclassification of Streptomyces diastaticus subsp. ardesiacus, Streptomyces gougerotii and Streptomyces rutgersensis. Int J Syst Evol Microbiol 2020; 70:4291-4297. [PMID: 32644916 DOI: 10.1099/ijsem.0.004287] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
We investigated the taxonomic relationships among Streptomyces diastaticus subsp. ardesiacus, Streptomyces diastaticus subsp. diastaticus, Streptomyces gougerotii and Streptomyces rutgersensis. The 16S rRNA gene sequence similarity between S. diastaticus subsp. ardesiacus and S. diastaticus subsp. diastaticus was 97.7 %, whereas S. diastaticus subsp. diastaticus, S. gougerotii and S. rutgersensis showed 100 % nucleotide sequence identity. In addition, S. diastaticus subsp. diastaticus, S. gougerotii and S. rutgersensis formed a single clade in the phylogenetic tree. Digital DNA-DNA relatedness between S. diastaticus subsp. diastaticus and S. diastaticus subsp. ardesiacus was only 22.8%, indicative of different species. In comparison, DNA-DNA relatedness values for S. diastaticus subsp. diastaticus, S. gougerotii and S. rutgersensis ranged from 95.8 to 97.2 %, suggesting the three taxa belong to the same genomospecies. Previously reported phenotypic data also supported synonymy. Therefore, we propose that S. diastaticus subsp. ardesiacus should be classified as an independent species, Streptomyces ardesiacus sp. nov. The type strain is NBRC 13412T (=ATCC 3315T=CBS 713.72T=DSM 40496T=ISP 5496T=JCM 4745T=NBRC 3714T=NRRL B-1241T=RIA 1373T). Our data also suggests that S. rutgersensis and S. gougerotii should be reclassified as later heterotypic synonyms of S. diastaticus.
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Affiliation(s)
- Hisayuki Komaki
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC), Chiba 292-0818, Japan
| | - Tomohiko Tamura
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC), Chiba 292-0818, Japan
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11
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Ogawara H. Comparison of Antibiotic Resistance Mechanisms in Antibiotic-Producing and Pathogenic Bacteria. Molecules 2019; 24:E3430. [PMID: 31546630 PMCID: PMC6804068 DOI: 10.3390/molecules24193430] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 09/18/2019] [Accepted: 09/20/2019] [Indexed: 12/13/2022] Open
Abstract
Antibiotic resistance poses a tremendous threat to human health. To overcome this problem, it is essential to know the mechanism of antibiotic resistance in antibiotic-producing and pathogenic bacteria. This paper deals with this problem from four points of view. First, the antibiotic resistance genes in producers are discussed related to their biosynthesis. Most resistance genes are present within the biosynthetic gene clusters, but some genes such as paromomycin acetyltransferases are located far outside the gene cluster. Second, when the antibiotic resistance genes in pathogens are compared with those in the producers, resistance mechanisms have dependency on antibiotic classes, and, in addition, new types of resistance mechanisms such as Eis aminoglycoside acetyltransferase and self-sacrifice proteins in enediyne antibiotics emerge in pathogens. Third, the relationships of the resistance genes between producers and pathogens are reevaluated at their amino acid sequence as well as nucleotide sequence levels. Pathogenic bacteria possess other resistance mechanisms than those in antibiotic producers. In addition, resistance mechanisms are little different between early stage of antibiotic use and the present time, e.g., β-lactam resistance in Staphylococcus aureus. Lastly, guanine + cytosine (GC) barrier in gene transfer to pathogenic bacteria is considered. Now, the resistance genes constitute resistome composed of complicated mixture from divergent environments.
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Affiliation(s)
- Hiroshi Ogawara
- HO Bio Institute, 33-9, Yushima-2, Bunkyo-ku, Tokyo 113-0034, Japan.
- Department of Biochemistry, Meiji Pharmaceutical University, 522-1, Noshio-2, Kiyose, Tokyo 204-8588, Japan.
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12
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Ratnayake AS, Chang LP, Tumey LN, Loganzo F, Chemler JA, Wagenaar M, Musto S, Li F, Janso JE, Ballard TE, Rago B, Steele GL, Ding W, Feng X, Hosselet C, Buklan V, Lucas J, Koehn FE, O'Donnell CJ, Graziani EI. Natural Product Bis-Intercalator Depsipeptides as a New Class of Payloads for Antibody-Drug Conjugates. Bioconjug Chem 2018; 30:200-209. [PMID: 30543418 DOI: 10.1021/acs.bioconjchem.8b00843] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A potent class of DNA-damaging agents, natural product bis-intercalator depsipeptides (NPBIDs), was evaluated as ultrapotent payloads for use in antibody-drug conjugates (ADCs). Detailed investigation of potency (both in cells and via biophysical characterization of DNA binding), chemical tractability, and in vitro and in vivo stability of the compounds in this class eliminated a number of potential candidates, greatly reducing the complexity and resources required for conjugate preparation and evaluation. This effort yielded a potent, stable, and efficacious ADC, PF-06888667, consisting of the bis-intercalator, SW-163D, conjugated via an N-acetyl-lysine-valine-citrulline- p-aminobenzyl alcohol- N, N-dimethylethylenediamine (AcLysValCit-PABC-DMAE) linker to an engineered variant of the anti-Her2 mAb, trastuzumab, catalyzed by transglutaminase.
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Affiliation(s)
- Anokha S Ratnayake
- Medicine Design , Pfizer Worldwide Research and Development , 445 Eastern Point Road , Groton , Connecticut 06340 , United States
| | - Li-Ping Chang
- Medicine Design , Pfizer Worldwide Research and Development , 445 Eastern Point Road , Groton , Connecticut 06340 , United States
| | - L Nathan Tumey
- Medicine Design , Pfizer Worldwide Research and Development , 445 Eastern Point Road , Groton , Connecticut 06340 , United States
| | - Frank Loganzo
- Oncology Research , Pfizer Worldwide Research and Development , 401 North Middletown Road , Pearl River , New York 10965 , United States
| | - Joseph A Chemler
- Medicine Design , Pfizer Worldwide Research and Development , 445 Eastern Point Road , Groton , Connecticut 06340 , United States
| | - Melissa Wagenaar
- Medicine Design , Pfizer Worldwide Research and Development , 445 Eastern Point Road , Groton , Connecticut 06340 , United States
| | - Sylvia Musto
- Oncology Research , Pfizer Worldwide Research and Development , 401 North Middletown Road , Pearl River , New York 10965 , United States
| | - Fengping Li
- Medicine Design , Pfizer Worldwide Research and Development , 445 Eastern Point Road , Groton , Connecticut 06340 , United States
| | - Jeffrey E Janso
- Medicine Design , Pfizer Worldwide Research and Development , 445 Eastern Point Road , Groton , Connecticut 06340 , United States
| | - T Eric Ballard
- Medicine Design , Pfizer Worldwide Research and Development , 445 Eastern Point Road , Groton , Connecticut 06340 , United States
| | - Brian Rago
- Medicine Design , Pfizer Worldwide Research and Development , 445 Eastern Point Road , Groton , Connecticut 06340 , United States
| | - Greg L Steele
- Medicine Design , Pfizer Worldwide Research and Development , 445 Eastern Point Road , Groton , Connecticut 06340 , United States
| | - WeiDong Ding
- Medicine Design , Pfizer Worldwide Research and Development , 445 Eastern Point Road , Groton , Connecticut 06340 , United States
| | - Xidong Feng
- Medicine Design , Pfizer Worldwide Research and Development , 445 Eastern Point Road , Groton , Connecticut 06340 , United States
| | - Christine Hosselet
- Oncology Research , Pfizer Worldwide Research and Development , 401 North Middletown Road , Pearl River , New York 10965 , United States
| | - Vlad Buklan
- Oncology Research , Pfizer Worldwide Research and Development , 401 North Middletown Road , Pearl River , New York 10965 , United States
| | - Judy Lucas
- Oncology Research , Pfizer Worldwide Research and Development , 401 North Middletown Road , Pearl River , New York 10965 , United States
| | - Frank E Koehn
- Medicine Design , Pfizer Worldwide Research and Development , 445 Eastern Point Road , Groton , Connecticut 06340 , United States
| | - Christopher J O'Donnell
- Medicine Design , Pfizer Worldwide Research and Development , 445 Eastern Point Road , Groton , Connecticut 06340 , United States
| | - Edmund I Graziani
- Medicine Design , Pfizer Worldwide Research and Development , 445 Eastern Point Road , Groton , Connecticut 06340 , United States
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13
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Structural basis for backbone N-methylation by an interrupted adenylation domain. Nat Chem Biol 2018; 14:428-430. [PMID: 29556104 DOI: 10.1038/s41589-018-0014-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 12/29/2017] [Indexed: 12/11/2022]
Abstract
Interrupted adenylation domains are enigmatic fusions, in which one enzyme is inserted into another to form a highly unusual bifunctional enzyme. We present the first crystal structure of an interrupted adenylation domain that reveals a unique embedded methyltransferase. The structure and functional data provide insight into how these enzymes N-methylate amino acid precursors en route to nonribosomal peptides.
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14
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Mori S, Shrestha SK, Fernández J, Álvarez San Millán M, Garzan A, Al-Mestarihi AH, Lombó F, Garneau-Tsodikova S. Activation and Loading of the Starter Unit during Thiocoraline Biosynthesis. Biochemistry 2017; 56:4457-4467. [DOI: 10.1021/acs.biochem.7b00661] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Shogo Mori
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536-0596, United States
| | - Sanjib K. Shrestha
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536-0596, United States
| | - Javier Fernández
- Departamento
de Biología Funcional e Instituto Universitario de Oncología
del Principado de Asturias, Universidad de Oviedo, Oviedo 33006, Spain
| | - María Álvarez San Millán
- Departamento
de Biología Funcional e Instituto Universitario de Oncología
del Principado de Asturias, Universidad de Oviedo, Oviedo 33006, Spain
| | - Atefeh Garzan
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536-0596, United States
| | - Ahmad H. Al-Mestarihi
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536-0596, United States
| | - Felipe Lombó
- Departamento
de Biología Funcional e Instituto Universitario de Oncología
del Principado de Asturias, Universidad de Oviedo, Oviedo 33006, Spain
| | - Sylvie Garneau-Tsodikova
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536-0596, United States
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15
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Losada AA, Cano-Prieto C, García-Salcedo R, Braña AF, Méndez C, Salas JA, Olano C. Caboxamycin biosynthesis pathway and identification of novel benzoxazoles produced by cross-talk in Streptomyces sp. NTK 937. Microb Biotechnol 2017; 10:873-885. [PMID: 28417606 PMCID: PMC5481532 DOI: 10.1111/1751-7915.12716] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 03/01/2017] [Accepted: 03/20/2017] [Indexed: 12/13/2022] Open
Abstract
Streptomyces sp. NTK937, producer of benzoxazole antibiotic caboxamycin, produces in addition a methyl ester derivative, O‐methylcaboxamycin. Caboxamycin cluster, comprising one regulatory and nine structural genes, has been delimited, and each gene has been individually inactivated to demonstrate its role in the biosynthetic process. The O‐methyltransferase potentially responsible for O‐methylcaboxamycin synthesis would reside outside this cluster. Five of the genes, cbxR, cbxA, cbxB, cbxD and cbxE, encoding a SARP transcriptional regulator, salicylate synthase, 3‐oxoacyl‐ACP‐synthase, ACP and amidohydrolase, respectively, have been found to be essential for caboxamycin biosynthesis. The remaining five structural genes were found to have paralogues distributed throughout the genome, capable of partaking in the process when their cluster homologue is inactivated. Two of such paralogues, cbxC’ and cbxI’, coding an AMP‐dependent synthetase‐ligase and an anthranilate synthase, respectively, have been identified. However, the other three genes might simultaneously have more than one paralogue, given that cbxF (DAHP synthase), cbxG (2,3‐dihydro‐2,3‐dihydroxybenzoate dehydrogenase) and cbxH (isochorismatase) have three, three and five putative paralogue genes, respectively, of similar function within the genome. As a result of genetic manipulation, a novel benzoxazole (3′‐hydroxycaboxamycin) has been identified in the salicylate synthase‐deficient mutant strain ΔcbxA. 3′‐hydroxycaboxamycin derives from the cross‐talk between the caboxamycin and enterobactin pathways.
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Affiliation(s)
- Armando A Losada
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, 33006, Oviedo, Spain
| | - Carolina Cano-Prieto
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, 33006, Oviedo, Spain
| | - Raúl García-Salcedo
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, 33006, Oviedo, Spain
| | - Alfredo F Braña
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, 33006, Oviedo, Spain
| | - Carmen Méndez
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, 33006, Oviedo, Spain
| | - José A Salas
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, 33006, Oviedo, Spain
| | - Carlos Olano
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, 33006, Oviedo, Spain
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16
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Bakal T, Goo KS, Najmanova L, Plhackova K, Kadlcik S, Ulanova D. Comparative analysis of oligonucleotide primers for high-throughput screening of genes encoding adenylation domains of nonribosomal peptide synthetases in actinomycetes. Antonie van Leeuwenhoek 2015; 108:1267-74. [PMID: 26296377 DOI: 10.1007/s10482-015-0557-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 08/12/2015] [Indexed: 10/23/2022]
Abstract
In the biosynthesis of diverse natural bioactive products the adenylation domains (ADs) of nonribosomal peptide synthetases select specific precursors from the cellular pool and activate them for further incorporation into the scaffold of the final compound. Therefore, the drug discovery programs employing PCR-based screening studies of microbial collections or metagenomic libraries often use AD-coding genes as markers of relevant biosynthetic gene clusters. However, due to significant sequence diversity of ADs, the conventional approach using only one primer pair in a single screening experiment could be insufficient for maximal coverage of AD abundance. In this study, the widely used primer pair A3F/A7R was compared with the newly designed aa194F/aa413R one by 454 pyrosequencing of two sets of actinomycete strains from highly dissimilar environments: subseafloor sediments and forest soil. Individually, none of the primer pairs was able to cover the overall diversity of ADs. However, due to slightly shifted specificity of the primer pairs, the total number and diversity of identified ADs were noticeably extended when both primer pairs were used in a single assay. Additionally, the efficiency of AD detection by different primer combinations was confirmed on the model of Salinispora tropica genomic DNA of known sequence.
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Affiliation(s)
- Tomas Bakal
- Institute of Microbiology AS CR, Videnska 1083, 142 00, Prague 4, Czech Republic
| | - Kian-Sim Goo
- Evaluation and Support Organization for Young Researchers, Kochi University, Kohasu, Oko-cho, Nankoku, Kochi, 783-8505, Japan
| | - Lucie Najmanova
- Institute of Microbiology AS CR, Videnska 1083, 142 00, Prague 4, Czech Republic
| | - Kamila Plhackova
- Institute of Microbiology AS CR, Videnska 1083, 142 00, Prague 4, Czech Republic
| | - Stanislav Kadlcik
- Institute of Microbiology AS CR, Videnska 1083, 142 00, Prague 4, Czech Republic
| | - Dana Ulanova
- Oceanography Section, Science Research Center, Kochi University, IMT-MEXT, Kohasu, Oko-cho, Nankoku, Kochi, 783-8505, Japan.
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17
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Al-Mestarihi AH, Villamizar G, Fernández J, Zolova OE, Lombó F, Garneau-Tsodikova S. Adenylation and S-methylation of cysteine by the bifunctional enzyme TioN in thiocoraline biosynthesis. J Am Chem Soc 2014; 136:17350-4. [PMID: 25409494 DOI: 10.1021/ja510489j] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The antitumor agent thiocoraline is a nonribosomally biosynthesized bisintercalator natural product, which contains in its peptidic backbone two S-methylated l-cysteine residues. S-Methylation occurs very rarely in nature, and is observed extremely rarely in nonribosomal peptide scaffolds. We have proposed that during thiocoraline biosynthesis, TioN, a stand-alone adenylation domain interrupted by the S-adenosyl-l-methionine binding region of a methyltransferase enzyme, is capable of performing two functions: the adenylation and S-methylation of l-cysteine. Herein, by preparation of knockouts of TioN and its MbtH-like protein partner TioT, we confirmed their role in thiocoraline biosynthesis. We also co-expressed recombinant TioN and TioT and biochemically investigated three potential pathways involving activation, methylation, and loading of l-cysteine onto the TioN partner thiolation domain, TioS(T4). The valuable insights gained into the pathway(s) followed for the production of S-Me-l-Cys-S-TioS(T4) will serve as a guide for the development of novel engineered interrupted adenylation enzymes for combinatorial biosynthesis.
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Affiliation(s)
- Ahmad H Al-Mestarihi
- Department of Pharmaceutical Sciences, University of Kentucky , Lexington, Kentucky 40536-0596, United States
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18
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Fernández J, Marín L, Alvarez-Alonso R, Redondo S, Carvajal J, Villamizar G, Villar CJ, Lombó F. Biosynthetic modularity rules in the bisintercalator family of antitumor compounds. Mar Drugs 2014; 12:2668-99. [PMID: 24821625 PMCID: PMC4052310 DOI: 10.3390/md12052668] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Revised: 04/09/2014] [Accepted: 04/11/2014] [Indexed: 12/05/2022] Open
Abstract
Diverse actinomycetes produce a family of structurally and biosynthetically related non-ribosomal peptide compounds which belong to the chromodepsipeptide family. These compounds act as bisintercalators into the DNA helix. They give rise to antitumor, antiparasitic, antibacterial and antiviral bioactivities. These compounds show a high degree of conserved modularity (chromophores, number and type of amino acids). This modularity and their high sequence similarities at the genetic level imply a common biosynthetic origin for these pathways. Here, we describe insights about rules governing this modular biosynthesis, taking advantage of the fact that nowadays five of these gene clusters have been made public (thiocoraline, triostin, SW-163 and echinomycin/quinomycin). This modularity has potential application for designing and producing novel genetic engineered derivatives, as well as for developing new chemical synthesis strategies. These would facilitate their clinical development.
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Affiliation(s)
- Javier Fernández
- Research Group BITTEN, Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, C/Julián Clavería 7, Facultad de Medicina, Oviedo 33006, Spain.
| | - Laura Marín
- Research Group BITTEN, Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, C/Julián Clavería 7, Facultad de Medicina, Oviedo 33006, Spain.
| | - Raquel Alvarez-Alonso
- Research Group BITTEN, Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, C/Julián Clavería 7, Facultad de Medicina, Oviedo 33006, Spain.
| | - Saúl Redondo
- Research Group BITTEN, Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, C/Julián Clavería 7, Facultad de Medicina, Oviedo 33006, Spain.
| | - Juan Carvajal
- Research Group BITTEN, Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, C/Julián Clavería 7, Facultad de Medicina, Oviedo 33006, Spain.
| | - Germán Villamizar
- Research Group BITTEN, Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, C/Julián Clavería 7, Facultad de Medicina, Oviedo 33006, Spain.
| | - Claudio J Villar
- Research Group BITTEN, Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, C/Julián Clavería 7, Facultad de Medicina, Oviedo 33006, Spain.
| | - Felipe Lombó
- Research Group BITTEN, Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, C/Julián Clavería 7, Facultad de Medicina, Oviedo 33006, Spain.
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19
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Baltz RH. MbtH homology codes to identify gifted microbes for genome mining. ACTA ACUST UNITED AC 2014; 41:357-69. [DOI: 10.1007/s10295-013-1360-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2013] [Accepted: 09/30/2013] [Indexed: 11/24/2022]
Abstract
Abstract
Advances in DNA sequencing technologies have made it possible to sequence large numbers of microbial genomes rapidly and inexpensively. In recent years, genome sequencing initiatives have demonstrated that actinomycetes with large genomes generally have the genetic potential to produce many secondary metabolites, most of which remain cryptic. Since the numbers of new and novel pathways vary considerably among actinomycetes, and the correct assembly of secondary metabolite pathways containing type I polyketide synthase or nonribosomal peptide synthetase (NRPS) genes is costly and time consuming, it would be advantageous to have simple genetic predictors for the number and potential novelty of secondary metabolite pathways in targeted microorganisms. For secondary metabolite pathways that utilize NRPS mechanisms, the small chaperone-like proteins related to MbtH encoded by Mycobacterium tuberculosis offer unique probes or beacons to identify gifted microbes encoding large numbers of diverse NRPS pathways because of their unique function(s) and small size. The small size of the mbtH-homolog genes makes surveying large numbers of genomes straight-forward with less than ten-fold sequencing coverage. Multiple MbtH orthologs and paralogs have been coupled to generate a 24-mer multiprobe to assign numerical codes to individual MbtH homologs by BLASTp analysis. This multiprobe can be used to identify gifted microbes encoding new and novel secondary metabolites for further focused exploration by extensive DNA sequencing, pathway assembly and annotation, and expression studies in homologous or heterologous hosts.
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Affiliation(s)
- Richard H Baltz
- CognoGen Biotechnology Consulting 7636 Andora Drive 34238 Sarasota FL USA
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20
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Zhang C, Kong L, Liu Q, Lei X, Zhu T, Yin J, Lin B, Deng Z, You D. In vitro characterization of echinomycin biosynthesis: formation and hydroxylation of L-tryptophanyl-S-enzyme and oxidation of (2S,3S) β-hydroxytryptophan. PLoS One 2013; 8:e56772. [PMID: 23437232 PMCID: PMC3578932 DOI: 10.1371/journal.pone.0056772] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2012] [Accepted: 01/14/2013] [Indexed: 11/30/2022] Open
Abstract
Quinoxaline-2-carboxylic acid (QXC) and 3-hydroxyquinaldic acid (HQA) feature in quinomycin family and confer anticancer activity. In light of the significant potency against cancer, the biosynthetic gene clusters have been reported from many different Streptomyces strains, and the biosynthetic pathway were proposed mainly based on the in vivo feeding experiment with isotope labeled putative intermediates. Herein we report another gene cluster from Streptomyces griseovariabilis subsp. bandungensis subsp. nov responsible for the biosynthesis of echinomycin (a member of quinomycin family, also named quinomycin A) and presented in vitro evidence to corroborate the previous hypothesis on QXC biosynthesis, showing that only with the assistance of a MbtH-like protein Qui5, did the didomain NRPS protein (Qui18) perform the loading of a L-tryptophan onto its own PCP domain. Particularly, it was found that Qui5 and Qui18 subunits form a functional tetramer through size exclusion chromatography. The subsequent hydroxylation on β-carbon of the loaded L-tryptophan proved in vitro to be completed by cytochrome P450-dependent hydroxylase Qui15. Importantly, only the Qui18 loaded L-tryptophan can be hydroxylated by Qui15 and the enzyme was inactive on free L-tryptophan. Additionally, the chemically synthesized (2S,3S) β-hydroxytryptophan was detected to be converted by the tryptophan 2,3-dioxygenase Qui17 through LC-MS, which enriched our previous knowledge that tryptophan 2,3-dioxygenase nearly exclusively acted on L-tryptophan and 6-fluoro-tryptophan.
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Affiliation(s)
- Chen Zhang
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Lingxin Kong
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Qian Liu
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Xuan Lei
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Tao Zhu
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Jun Yin
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Birun Lin
- Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Guangzhou, People’s Republic of China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Delin You
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
- * E-mail:
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21
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Hirose Y, Watanabe K, Minami A, Nakamura T, Oguri H, Oikawa H. Involvement of common intermediate 3-hydroxy-L-kynurenine in chromophore biosynthesis of quinomycin family antibiotics. J Antibiot (Tokyo) 2010; 64:117-22. [DOI: 10.1038/ja.2010.142] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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22
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Zolova OE, Mady ASA, Garneau-Tsodikova S. Recent developments in bisintercalator natural products. Biopolymers 2010; 93:777-90. [DOI: 10.1002/bip.21489] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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23
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Watanabe K, Hotta K, Praseuth AP, Searcey M, Wang CCC, Oguri H, Oikawa H. Rationally engineered total biosynthesis of a synthetic analogue of a natural quinomycin depsipeptide in Escherichia coli. Chembiochem 2009; 10:1965-8. [PMID: 19588480 DOI: 10.1002/cbic.200900260] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Kenji Watanabe
- Research Core for Interdisciplinary Sciences, Okayama University, Okayama 700-8530 (Japan).
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24
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Kumar Ray A, Diederichsen U. Syntheses of Triostin A Antibiotic and Nucleobase-Functionalized Analogs as New DNA Binders. European J Org Chem 2009. [DOI: 10.1002/ejoc.200900530] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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