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Karanth MN, Kirkpatrick JP, Krausze J, Schmelz S, Scrima A, Carlomagno T. The specificity of intermodular recognition in a prototypical nonribosomal peptide synthetase depends on an adaptor domain. SCIENCE ADVANCES 2024; 10:eadm9404. [PMID: 38896613 PMCID: PMC11186497 DOI: 10.1126/sciadv.adm9404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 05/14/2024] [Indexed: 06/21/2024]
Abstract
In the quest for new bioactive substances, nonribosomal peptide synthetases (NRPS) provide biodiversity by synthesizing nonproteinaceous peptides with high cellular activity. NRPS machinery consists of multiple modules, each catalyzing a unique series of chemical reactions. Incomplete understanding of the biophysical principles orchestrating these reaction arrays limits the exploitation of NRPSs in synthetic biology. Here, we use nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry to solve the conundrum of how intermodular recognition is coupled with loaded carrier protein specificity in the tomaymycin NRPS. We discover an adaptor domain that directly recruits the loaded carrier protein from the initiation module to the elongation module and reveal its mechanism of action. The adaptor domain of the type found here has specificity rules that could potentially be exploited in the design of engineered NRPS machinery.
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Affiliation(s)
- Megha N. Karanth
- Laboratory of Integrative Structural Biology, Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
- Institute of Organic Chemistry and Center of Biomolecular Drug Research, Leibniz University Hannover, Hannover D-30167, Germany
| | - John P. Kirkpatrick
- Institute of Organic Chemistry and Center of Biomolecular Drug Research, Leibniz University Hannover, Hannover D-30167, Germany
- Laboratory of Integrative Structural Biology, School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Birmingham B15 2TT, UK
- Department of Structure and Function of Proteins, Helmholtz Centre for Infection Research, Braunschweig D-38124, Germany
| | - Joern Krausze
- Institute of Organic Chemistry and Center of Biomolecular Drug Research, Leibniz University Hannover, Hannover D-30167, Germany
| | - Stefan Schmelz
- Department of Structure and Function of Proteins, Helmholtz Centre for Infection Research, Braunschweig D-38124, Germany
| | - Andrea Scrima
- Department of Structure and Function of Proteins, Helmholtz Centre for Infection Research, Braunschweig D-38124, Germany
| | - Teresa Carlomagno
- Laboratory of Integrative Structural Biology, Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
- Institute of Organic Chemistry and Center of Biomolecular Drug Research, Leibniz University Hannover, Hannover D-30167, Germany
- Laboratory of Integrative Structural Biology, School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Birmingham B15 2TT, UK
- Department of Structure and Function of Proteins, Helmholtz Centre for Infection Research, Braunschweig D-38124, Germany
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2
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Wei B, Luo X, Zhou ZY, Hu GA, Li L, Lin HW, Wang H. Discovering the secondary metabolic potential of Saccharothrix. Biotechnol Adv 2024; 70:108295. [PMID: 38052345 DOI: 10.1016/j.biotechadv.2023.108295] [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: 07/24/2023] [Revised: 11/08/2023] [Accepted: 11/25/2023] [Indexed: 12/07/2023]
Abstract
Rare actinomycetes are highly valued as potential sources of novel bioactive secondary metabolites. Among these rare actinomycetes, the genus Saccharothrix is particularly noteworthy due to its ability to produce a diverse range of bioactive secondary metabolites. With the continuous sequencing of bacterial genomes and the rapid development of bioinformatics technologies, our knowledge of the secondary metabolic potential of Saccharothrix can become more comprehensive, but this space has not been reviewed or explored. This review presents a detailed overview of the chemical structures and bioactivities of 138 Saccharothrix-derived secondary metabolites, which are classified into five distinct groups based on their biosynthetic pathways. Furthermore, we delve into experimentally characterized biosynthetic pathways of nine bioactive metabolites. By utilizing a combination of cheminformatic and bioinformatic approaches, we attempted to establish connections between the metabolite families and the biosynthetic gene cluster families encoded by Saccharothrix strains. Our analysis provides a comprehensive perspective on the secondary metabolites that can be linked to corresponding BGCs and highlights the underexplored biosynthetic potential of Saccharothrix. This review also provides guidance for the targeted discovery and biosynthesis of novel natural products from Saccharothrix.
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Affiliation(s)
- Bin Wei
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Xian Luo
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Zhen-Yi Zhou
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Gang-Ao Hu
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Lei Li
- Research Center for Marine Drugs, Department of Pharmacy, Ren Ji Hospital, School of Medicine, State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200127, China.
| | - Hou-Wen Lin
- Research Center for Marine Drugs, Department of Pharmacy, Ren Ji Hospital, School of Medicine, State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200127, China.
| | - Hong Wang
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China.
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3
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Aubert C, Lavisse M, Roy S. Biosynthesis of [ 14 C]-11-De-O-Methyltomaymycin, a Precursor of Radiolabelled Antibody Drug Conjugates. Chembiochem 2021; 22:2424-2429. [PMID: 33973323 DOI: 10.1002/cbic.202100080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 05/06/2021] [Indexed: 02/03/2023]
Abstract
Antibody drug conjugates (ADCs) are one of the most promising technologies to treat cancer as they combine the specificity of an antibody with the high potency of a cytotoxic molecule such as tomaymycin derivatives, which are DNA-interactive antitumor antibiotics previously isolated from bacterial broth. The multistep chemical synthesis of some tomaymycin derivatives is complicated because their structures contain a reactive imine bond. Therefore, we turned to biosynthesis to obtain 14 C radiolabelled tomaymycin derivative to support ADME studies. Following Hurley's work (J. Antibiotics 1977, 30, 349-370; Antimicrob. Agents Chemother. 1979, 15, 42-45; Acc. Chem. Res. 1980, 13, 263-269), the 14 C radiolabel was incorporated efficiently in one step from radiolabelled tyrosine using the strain Streptomyces sp. FH6421. This process has been further optimized by using anthranilic acid as radiolabelled precursor, leading to one of the highest incorporation levels of radiochemical precursors published to date. This biosynthetic strategy is the fastest way to access such radiolabelled precursors.
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Affiliation(s)
- Catherine Aubert
- Integrated Drug Discovery, Isotope Chemistry, Sanofi R&D, 13 Quai Jules Guesde, 94403, Vitry sur Seine, France
| | - Mélanie Lavisse
- Integrated Drug Discovery, Isotope Chemistry, Sanofi R&D, 13 Quai Jules Guesde, 94403, Vitry sur Seine, France
| | - Sebastien Roy
- Integrated Drug Discovery, Isotope Chemistry, Sanofi R&D, 13 Quai Jules Guesde, 94403, Vitry sur Seine, France
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Adrover-Castellano ML, Schmidt JJ, Sherman DH. Biosynthetic Cyclization Catalysts for the Assembly of Peptide and Polyketide Natural Products. ChemCatChem 2021; 13:2095-2116. [PMID: 34335987 PMCID: PMC8320681 DOI: 10.1002/cctc.202001886] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Indexed: 12/13/2022]
Abstract
Many biologically active natural products are synthesized by nonribosomal peptide synthetases (NRPSs), polyketide synthases (PKSs) and their hybrids. These megasynthetases contain modules possessing distinct catalytic domains that allow for substrate initiation, chain extension, processing and termination. At the end of a module, a terminal domain, usually a thioesterase (TE), is responsible for catalyzing the release of the NRPS or PKS as a linear or cyclized product. In this review, we address the general cyclization mechanism of the TE domain, including oligomerization and the fungal C-C bond forming Claisen-like cyclases (CLCs). Additionally, we include examples of cyclization catalysts acting within or at the end of a module. Furthermore, condensation-like (CT) domains, terminal reductase (R) domains, reductase-like domains that catalyze Dieckmann condensation (RD), thioesterase-like Dieckmann cyclases, trans-acting TEs from the penicillin binding protein (PBP) enzyme family, product template (PT) domains and others will also be reviewed. The studies summarized here highlight the remarkable diversity of NRPS and PKS cyclization catalysts for the production of biologically relevant, complex cyclic natural products and related compounds.
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Affiliation(s)
| | - Jennifer J Schmidt
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109-2216 (USA)
| | - David H Sherman
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109-2216 (USA)
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Sakaine G, Ture A, Pedroni J, Smits G. Isolation, chemistry, and biology of pyrrolo[1,4]benzodiazepine natural products. Med Res Rev 2021; 42:5-55. [PMID: 33846985 DOI: 10.1002/med.21803] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 02/11/2021] [Accepted: 03/23/2021] [Indexed: 11/06/2022]
Abstract
The isolation of the antitumor antibiotic anthramycin in the 1960s prompted extensive research into pyrrolo[1,4]benzodiazepines (PBD) as potential therapeutics for the treatment of cancers. Since then, nearly 60 PBD natural products have been isolated and evaluated with regard to their biological activity. Synthetic studies and total syntheses have enabled access to PBD analogues, culminating in the development of highly potent anticancer agents. This review provides a summary of the occurrence and biological activity of PBD natural products and covers the strategies employed for their total syntheses.
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Affiliation(s)
- Guna Sakaine
- Latvian Institute of Organic Synthesis, Riga, Latvia
| | | | - Julia Pedroni
- Latvian Institute of Organic Synthesis, Riga, Latvia
| | - Gints Smits
- Latvian Institute of Organic Synthesis, Riga, Latvia
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6
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Groß S, Schnell B, Haack PA, Auerbach D, Müller R. In vivo and in vitro reconstitution of unique key steps in cystobactamid antibiotic biosynthesis. Nat Commun 2021; 12:1696. [PMID: 33727542 PMCID: PMC7966384 DOI: 10.1038/s41467-021-21848-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 02/13/2021] [Indexed: 01/31/2023] Open
Abstract
Cystobactamids are myxobacteria-derived topoisomerase inhibitors with potent anti-Gram-negative activity. They are formed by a non-ribosomal peptide synthetase (NRPS) and consist of tailored para-aminobenzoic acids, connected by a unique α-methoxy-L-isoasparagine or a β-methoxy-L-asparagine linker moiety. We describe the heterologous expression of the cystobactamid biosynthetic gene cluster (BGC) in Myxococcus xanthus. Targeted gene deletions produce several unnatural cystobactamids. Using in vitro experiments, we reconstitute the key biosynthetic steps of linker formation and shuttling via CysB to the NRPS. The biosynthetic logic involves a previously uncharacterized bifunctional domain found in the stand-alone NRPS module CysH, albicidin biosynthesis and numerous BGCs of unknown natural products. This domain performs either an aminomutase (AM) or an amide dehydratase (DH) type of reaction, depending on the activity of CysJ which hydroxylates CysH-bound L-asparagine. Furthermore, CysQ O-methylates hydroxyl-L-(iso)asparagine only in the presence of the AMDH domain. Taken together, these findings provide direct evidence for unique steps in cystobactamid biosynthesis.
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Affiliation(s)
- Sebastian Groß
- grid.11749.3a0000 0001 2167 7588Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany ,grid.11749.3a0000 0001 2167 7588Department of Pharmacy, Saarland University, 66123 Saarbrücken, Germany ,grid.452463.2DZIF - German Centre for Infection Research, Partnersite Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Bastien Schnell
- grid.11749.3a0000 0001 2167 7588Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany ,grid.11749.3a0000 0001 2167 7588Department of Pharmacy, Saarland University, 66123 Saarbrücken, Germany ,grid.452463.2DZIF - German Centre for Infection Research, Partnersite Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Patrick A. Haack
- grid.11749.3a0000 0001 2167 7588Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany ,grid.11749.3a0000 0001 2167 7588Department of Pharmacy, Saarland University, 66123 Saarbrücken, Germany ,grid.452463.2DZIF - German Centre for Infection Research, Partnersite Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - David Auerbach
- grid.11749.3a0000 0001 2167 7588Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany ,grid.11749.3a0000 0001 2167 7588Department of Pharmacy, Saarland University, 66123 Saarbrücken, Germany ,grid.452463.2DZIF - German Centre for Infection Research, Partnersite Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Rolf Müller
- grid.11749.3a0000 0001 2167 7588Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany ,grid.11749.3a0000 0001 2167 7588Department of Pharmacy, Saarland University, 66123 Saarbrücken, Germany ,grid.452463.2DZIF - German Centre for Infection Research, Partnersite Hannover-Braunschweig, 38124 Braunschweig, Germany
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7
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Lee SH, Kim B, Kim KJ. Crystal Structure and Regiospecificity of Catechol O-Methyltransferase from Niastella koreensis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:2531-2538. [PMID: 33596655 DOI: 10.1021/acs.jafc.0c07621] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Catechol O-methyltransferase (COMT) is an enzyme that transfers a methyl group to the catechol-derivative substrates using S-adenosyl-l-methionine (SAM) and Mg2+. We report the biochemical and structural analysis of COMT from Niastella koreensis (NkCOMT). NkCOMT showed the highest activity with Mg2+, although the enzyme also showed a significant level of activity with Cu2+ and Zn2+. NkCOMT structures complexed with SAH and Mg2+ elucidated how the enzyme stabilized the cosubstrate and the metal ion and revealed that the region near the SAM binding site undergoes conformational changes upon the binding of the cosubstrate and the metal ion. We also identified the catechol binding pocket of the enzyme and explained a broad substrate specificity of the bacterial enzyme and its ability to accommodate the catechol derivatives. In addition, we developed the NkCOMTE211R and NkCOMTE211K variants that showed both enhanced activities and regiospecificity for the production of the para-forms. Our study provides a structural basis for regiospecificity of NkCOMT, which is related with the conformational change upon binding of SAM and Mg2+.
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Affiliation(s)
- Seul Hoo Lee
- School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea
- KNU Institute for Microorganisms, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Bongsang Kim
- School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea
- KNU Institute for Microorganisms, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Kyung-Jin Kim
- School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea
- KNU Institute for Microorganisms, Kyungpook National University, Daegu 41566, Republic of Korea
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8
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Hai Y, Jenner M, Tang Y. Fungal siderophore biosynthesis catalysed by an iterative nonribosomal peptide synthetase. Chem Sci 2020; 11:11525-11530. [PMID: 34094397 PMCID: PMC8162485 DOI: 10.1039/d0sc03627g] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Siderophores play a vital role in the viability of fungi and are essential for the virulence of many pathogenic fungal species. Despite their importance in fungal physiology and pathogenesis, the programming rule of siderophore assembly by fungal nonribosomal peptide synthetases (NRPSs) remains unresolved. Here, we report the characterization of the bimodular fungal NRPS, SidD, responsible for construction of the extracellular siderophore fusarinine C. The use of intact protein mass spectrometry, together with in vitro biochemical assays of native and dissected enzymes, provided snapshots of individual biosynthetic steps during NPRS catalysis. The adenylation and condensation domain of SidD can iteratively load and condense the amino acid building block cis-AMHO, respectively, to synthesize fusarinine C. Our study showcases the iterative programming features of fungal siderophore-producing NRPSs.
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Affiliation(s)
- Yang Hai
- Department of Chemical and Biomolecular Engineering, University of California Los Angeles California 90095 USA
| | - Matthew Jenner
- Department of Chemistry, Warwick Integrative Synthetic Biology Center, University of Warwick Coventry UK
- Warwick Integrative Synthetic Biology (WISB) Centre, University of Warwick Coventry UK
| | - Yi Tang
- Department of Chemical and Biomolecular Engineering, University of California Los Angeles California 90095 USA
- Department of Chemistry and Biochemistry, University of California Los Angeles California 90095 USA
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9
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Alexander EM, Kreitler DF, Guidolin V, Hurben AK, Drake E, Villalta PW, Balbo S, Gulick AM, Aldrich CC. Biosynthesis, Mechanism of Action, and Inhibition of the Enterotoxin Tilimycin Produced by the Opportunistic Pathogen Klebsiella oxytoca. ACS Infect Dis 2020; 6:1976-1997. [PMID: 32485104 PMCID: PMC7354218 DOI: 10.1021/acsinfecdis.0c00326] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Tilimycin is an enterotoxin produced by the opportunistic pathogen Klebsiella oxytoca that causes antibiotic-associated hemorrhagic colitis (AAHC). This pyrrolobenzodiazepine (PBD) natural product is synthesized by a bimodular nonribosomal peptide synthetase (NRPS) pathway composed of three proteins: NpsA, ThdA, and NpsB. We describe the functional and structural characterization of the fully reconstituted NRPS system and report the steady-state kinetic analysis of all natural substrates and cofactors as well as the structural characterization of both NpsA and ThdA. The mechanism of action of tilimycin was confirmed using DNA adductomics techniques through the detection of putative N-2 guanine alkylation after tilimycin exposure to eukaryotic cells, providing the first structural characterization of a PBD-DNA adduct formed in cells. Finally, we report the rational design of small-molecule inhibitors that block tilimycin biosynthesis in whole cell K. oxytoca (IC50 = 29 ± 4 μM) through the inhibition of NpsA (KD = 29 ± 4 nM).
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Affiliation(s)
- Evan M. Alexander
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Dale F. Kreitler
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences University at Buffalo, Buffalo, New York 14203, USA
| | - Valeria Guidolin
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, 55455, USA
- Division of Environmental Health Sciences, School of Public Health, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Alexander K. Hurben
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Eric Drake
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences University at Buffalo, Buffalo, New York 14203, USA
| | - Peter W. Villalta
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Silvia Balbo
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, 55455, USA
- Division of Environmental Health Sciences, School of Public Health, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Andrew M. Gulick
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences University at Buffalo, Buffalo, New York 14203, USA
| | - Courtney C. Aldrich
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA
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10
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Steiningerova L, Kamenik Z, Gazak R, Kadlcik S, Bashiri G, Man P, Kuzma M, Pavlikova M, Janata J. Different Reaction Specificities of F 420H 2-Dependent Reductases Facilitate Pyrrolobenzodiazepines and Lincomycin To Fit Their Biological Targets. J Am Chem Soc 2020; 142:3440-3448. [PMID: 31944685 DOI: 10.1021/jacs.9b11234] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Antitumor pyrrolobenzodiazepines (PBDs), lincosamide antibiotics, quorum-sensing molecule hormaomycin, and antimicrobial griselimycin are structurally and functionally diverse groups of actinobacterial metabolites. The common feature of these compounds is the incorporation of l-tyrosine- or l-leucine-derived 4-alkyl-l-proline derivatives (APDs) in their structures. Here, we report that the last reaction in the biosynthetic pathway of APDs, catalyzed by F420H2-dependent Apd6 reductases, contributes to the structural diversity of APD precursors. Specifically, the heterologous overproduction of six Apd6 enzymes demonstrated that Apd6 from the biosynthesis of PBDs and hormaomycin can reduce only an endocyclic imine double bond, whereas Apd6 LmbY and partially GriH from the biosyntheses of lincomycin and griselimycin, respectively, also reduce the more inert exocyclic double bond of the same 4-substituted Δ1-pyrroline-2-carboxylic acid substrate, making LmbY and GriH unusual, if not unique, among reductases. Furthermore, the differences in the reaction specificity of the Apd6 reductases determine the formation of the fully saturated APD moiety of lincomycin versus the unsaturated APD moiety of PBDs, providing molecules with optimal shapes to bind their distinct biological targets. Moreover, the Apd6 reductases establish the first F420H2-dependent enzymes from the luciferase-like hydride transferase protein superfamily in the biosynthesis of bioactive molecules. Finally, our bioinformatics analysis demonstrates that Apd6 and their homologues, widely distributed within several bacterial phyla, play a role in the formation of novel yet unknown natural products with incorporated l-proline-like precursors and likely in the microbial central metabolism.
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Affiliation(s)
- Lucie Steiningerova
- Institute of Microbiology, v.v.i., Czech Academy of Sciences , Videnska 1083 , 142 20 Praha 4 , Czech Republic.,Department of Genetics and Microbiology, Faculty of Science , Charles University in Prague , Vinicna 5 , 128 00 Praha 2 , Czech Republic
| | - Zdenek Kamenik
- Institute of Microbiology, v.v.i., Czech Academy of Sciences , Videnska 1083 , 142 20 Praha 4 , Czech Republic.,Institute of Microbiology, v.v.i., BIOCEV, Czech Academy of Sciences , 252 50 Vestec , Czech Republic
| | - Radek Gazak
- Institute of Microbiology, v.v.i., Czech Academy of Sciences , Videnska 1083 , 142 20 Praha 4 , Czech Republic
| | - Stanislav Kadlcik
- Institute of Microbiology, v.v.i., Czech Academy of Sciences , Videnska 1083 , 142 20 Praha 4 , Czech Republic
| | - Ghader Bashiri
- Laboratory of Structural Biology and Maurice Wilkins Center for Molecular Biodiscovery, School of Biological Sciences , University of Auckland , Auckland 1010 , New Zealand
| | - Petr Man
- Institute of Microbiology, v.v.i., BIOCEV, Czech Academy of Sciences , 252 50 Vestec , Czech Republic
| | - Marek Kuzma
- Institute of Microbiology, v.v.i., Czech Academy of Sciences , Videnska 1083 , 142 20 Praha 4 , Czech Republic
| | - Magdalena Pavlikova
- Institute of Microbiology, v.v.i., Czech Academy of Sciences , Videnska 1083 , 142 20 Praha 4 , Czech Republic
| | - Jiri Janata
- Institute of Microbiology, v.v.i., Czech Academy of Sciences , Videnska 1083 , 142 20 Praha 4 , Czech Republic
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11
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Ishikawa F, Tanabe G. Chemical Strategies for Visualizing and Analyzing Endogenous Nonribosomal Peptide Synthetase (NRPS) Megasynthetases. Chembiochem 2019; 20:2032-2040. [PMID: 31134733 DOI: 10.1002/cbic.201900186] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 05/27/2019] [Indexed: 12/22/2022]
Abstract
Nonribosomal peptide (NRP) natural products are among the most promising resources for drug discovery and development, owing to their wide range of biological activities and therapeutic applications. These peptide metabolites are biosynthesized by large multienzyme machinery known as NRP synthetases (NRPSs). The structural complexity of a number of NRPs poses an enormous challenge in their synthesis. A major issue in this field is reprogramming NRPS machineries to allow the biosynthetic production of artificial peptides. NRPS adenylation (A) domains are responsible for the incorporation of a wide variety of amino acids and can be considered as reprogramming sites; therefore, advanced methods to accelerate the functional prediction and assessment of A-domains are required. This Concept article demonstrates that activity-based protein profiling of NRPSs offers a simple, rapid, and robust analytical platform for A-domains and provides insights into enzyme-substrate candidates and active-site microenvironments. It also describes the background associated with the development and application of a method to analyze endogenous NRPS machinery in its natural environment.
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Affiliation(s)
- Fumihiro Ishikawa
- Faculty of Pharmacy, Kindai University, 3-4-1 Kowakae, Higashi-Osaka, Osaka, 577-8502, Japan
| | - Genzoh Tanabe
- Faculty of Pharmacy, Kindai University, 3-4-1 Kowakae, Higashi-Osaka, Osaka, 577-8502, Japan
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12
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Shi YM, Bode HB. Chemical language and warfare of bacterial natural products in bacteria-nematode-insect interactions. Nat Prod Rep 2019; 35:309-335. [PMID: 29359226 DOI: 10.1039/c7np00054e] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Covering: up to November 2017 Organismic interaction is one of the fundamental principles for survival in any ecosystem. Today, numerous examples show the interaction between microorganisms like bacteria and higher eukaryotes that can be anything between mutualistic to parasitic/pathogenic symbioses. There is also increasing evidence that microorganisms are used by higher eukaryotes not only for the supply of essential factors like vitamins but also as biological weapons to protect themselves or to kill other organisms. Excellent examples for such systems are entomopathogenic nematodes of the genera Heterorhabditis and Steinernema that live in mutualistic symbiosis with bacteria of the genera Photorhabdus and Xenorhabdus, respectively. Although these systems have been used successfully in organic farming on an industrial scale, it was only shown during the last 15 years that several different natural products (NPs) produced by the bacteria play key roles in the complex life cycle of the bacterial symbionts, the nematode host and the insect prey that is killed by and provides nutrients for the nematode-bacteria pair. Since the bacteria can switch from mutualistic to pathogenic lifestyle, interacting with two different types of higher eukaryotes, and since the full system with all players can be established in the lab, they are promising model systems to elucidate the natural function of microbial NPs. This review summarizes the current knowledge as well as open questions for NPs from Photorhabdus and Xenorhabdus and tries to assign their roles in the tritrophic relationship.
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Affiliation(s)
- Yi-Ming Shi
- Merck-Stiftungsprofessur für Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt, Frankfurt am Main 60438, Germany
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Lee S, Kang J, Kim J. Structural and biochemical characterization of Rv0187, an O-methyltransferase from Mycobacterium tuberculosis. Sci Rep 2019; 9:8059. [PMID: 31147608 PMCID: PMC6543040 DOI: 10.1038/s41598-019-44592-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 05/20/2019] [Indexed: 01/05/2023] Open
Abstract
Catechol O-methyltransferase (COMT) is widely distributed in nature and installs a methyl group onto one of the vicinal hydroxyl groups of a catechol derivative. Enzymes belonging to this family require two cofactors for methyl transfer: S-adenosyl-l-methionine as a methyl donor and a divalent metal cation for regiospecific binding and activation of a substrate. We have determined two high-resolution crystal structures of Rv0187, one of three COMT paralogs from Mycobacterium tuberculosis, in the presence and absence of cofactors. The cofactor-bound structure clearly locates strontium ions and S-adenosyl-l-homocysteine in the active site, and together with the complementary structure of the ligand-free form, it suggests conformational dynamics induced by the binding of cofactors. Examination of in vitro activities revealed promiscuous substrate specificity and relaxed regioselectivity against various catechol-like compounds. Unexpectedly, mutation of the proposed catalytic lysine residue did not abolish activity but altered the overall landscape of regiospecific methylation.
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Affiliation(s)
- Sanghyun Lee
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju, 61005, Republic of Korea
| | - Jihoon Kang
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju, 61005, Republic of Korea
| | - Jungwook Kim
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju, 61005, Republic of Korea.
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Jiang G, Zuo R, Zhang Y, Powell MM, Zhang P, Hylton SM, Loria R, Ding Y. One-Pot Biocombinatorial Synthesis of Herbicidal Thaxtomins. ACS Catal 2018. [DOI: 10.1021/acscatal.8b03317] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Guangde Jiang
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, Florida 32610, United States
| | - Ran Zuo
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, Florida 32610, United States
| | - Yi Zhang
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, Florida 32610, United States
| | - Magan M. Powell
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, Florida 32610, United States
| | - Peilan Zhang
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, Florida 32610, United States
| | - Sarah M. Hylton
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, Florida 32610, United States
| | - Rosemary Loria
- Department of Plant Pathology, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida 32611, United States
| | - Yousong Ding
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, Florida 32610, United States
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Mullowney MW, McClure RA, Robey MT, Kelleher NL, Thomson RJ. Natural products from thioester reductase containing biosynthetic pathways. Nat Prod Rep 2018; 35:847-878. [PMID: 29916519 PMCID: PMC6146020 DOI: 10.1039/c8np00013a] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Covering: up to 2018 Thioester reductase domains catalyze two- and four-electron reductions to release natural products following assembly on nonribosomal peptide synthetases, polyketide synthases, and their hybrid biosynthetic complexes. This reductive off-loading of a natural product yields an aldehyde or alcohol, can initiate the formation of a macrocyclic imine, and contributes to important intermediates in a variety of biosyntheses, including those for polyketide alkaloids and pyrrolobenzodiazepines. Compounds that arise from reductase-terminated biosynthetic gene clusters are often reactive and exhibit biological activity. Biomedically important examples include the cancer therapeutic Yondelis (ecteinascidin 743), peptide aldehydes that inspired the first therapeutic proteasome inhibitor bortezomib, and numerous synthetic derivatives and antibody drug conjugates of the pyrrolobenzodiazepines. Recent advances in microbial genomics, metabolomics, bioinformatics, and reactivity-based labeling have facilitated the detection of these compounds for targeted isolation. Herein, we summarize known natural products arising from this important category, highlighting their occurrence in Nature, biosyntheses, biological activities, and the technologies used for their detection and identification. Additionally, we review publicly available genomic data to highlight the remaining potential for novel reductively tailored compounds and drug leads from microorganisms. This thorough retrospective highlights various molecular families with especially privileged bioactivity while illuminating challenges and prospects toward accelerating the discovery of new, high value natural products.
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Affiliation(s)
- Michael W Mullowney
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA.
| | - Ryan A McClure
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA.
| | - Matthew T Robey
- Department of Molecular Biosciences, Northwestern University, 2205 Tech Drive, Evanston, IL 60208, USA
| | - Neil L Kelleher
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA. and Department of Molecular Biosciences, Northwestern University, 2205 Tech Drive, Evanston, IL 60208, USA
| | - Regan J Thomson
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA.
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Pavlikova M, Kamenik Z, Janata J, Kadlcik S, Kuzma M, Najmanova L. Novel pathway of 3-hydroxyanthranilic acid formation in limazepine biosynthesis reveals evolutionary relation between phenazines and pyrrolobenzodiazepines. Sci Rep 2018; 8:7810. [PMID: 29773836 PMCID: PMC5958127 DOI: 10.1038/s41598-018-26179-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 05/04/2018] [Indexed: 02/06/2023] Open
Abstract
Natural pyrrolobenzodiazepines (PBDs) form a large and structurally diverse group of antitumour microbial metabolites produced through complex pathways, which are encoded within biosynthetic gene clusters. We sequenced the gene cluster of limazepines and proposed their biosynthetic pathway based on comparison with five available gene clusters for the biosynthesis of other PBDs. Furthermore, we tested two recombinant proteins from limazepine biosynthesis, Lim5 and Lim6, with the expected substrates in vitro. The reactions monitored by LC-MS revealed that limazepine biosynthesis involves a new way of 3-hydroxyanthranilic acid formation, which we refer to as the chorismate/DHHA pathway and which represents an alternative to the kynurenine pathway employed for the formation of the same precursor in the biosynthesis of other PBDs. The chorismate/DHHA pathway is presumably also involved in the biosynthesis of PBD tilivalline, several natural products unrelated to PBDs, and its part is shared also with phenazine biosynthesis. The similarities between limazepine and phenazine biosynthesis indicate tight evolutionary links between these groups of compounds.
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Affiliation(s)
- Magdalena Pavlikova
- Institute of Microbiology of the Czech Academy of Sciences, 142 20, Prague 4, Czech Republic
| | - Zdenek Kamenik
- Institute of Microbiology of the Czech Academy of Sciences, 142 20, Prague 4, Czech Republic
| | - Jiri Janata
- Institute of Microbiology of the Czech Academy of Sciences, 142 20, Prague 4, Czech Republic
| | - Stanislav Kadlcik
- Institute of Microbiology of the Czech Academy of Sciences, 142 20, Prague 4, Czech Republic
| | - Marek Kuzma
- Institute of Microbiology of the Czech Academy of Sciences, 142 20, Prague 4, Czech Republic
| | - Lucie Najmanova
- Institute of Microbiology of the Czech Academy of Sciences, 142 20, Prague 4, Czech Republic.
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Wolff H, Bode HB. The benzodiazepine-like natural product tilivalline is produced by the entomopathogenic bacterium Xenorhabdus eapokensis. PLoS One 2018; 13:e0194297. [PMID: 29596433 PMCID: PMC5875774 DOI: 10.1371/journal.pone.0194297] [Citation(s) in RCA: 12] [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: 12/18/2017] [Accepted: 02/28/2018] [Indexed: 01/05/2023] Open
Abstract
The pyrrolobenzodiazepine tilivalline (1) was originally identified in the human gut pathobiont Klebsiella oxytoca, the causative agent of antibiotic-associated hemorrhagic colitis. Here we show the identification of tilivalline and analogs thereof in the entomopathogenic bacterium Xenorhabdus eapokensis as well as the identification of its biosynthesis gene cluster encoding a bimodular non-ribosomal peptide synthetase. Heterologous expression of both genes in E. coli resulted in the production of 1 and from mutasynthesis and precursor directed biosynthesis 11 new tilivalline analogs were identified in X. eapokensis. These results allowed the prediction of the tilivalline biosynthesis being similar to that in K. oxytoca.
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Affiliation(s)
- Hendrik Wolff
- Fachbereich Biowissenschaften, Merck Stiftungsprofessur für Molekulare Biotechnologie, Goethe-Universität Frankfurt, Frankfurt am Main, Germany
| | - Helge B. Bode
- Fachbereich Biowissenschaften, Merck Stiftungsprofessur für Molekulare Biotechnologie, Goethe-Universität Frankfurt, Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe-Universität Frankfurt, Frankfurt am Main, Germany
- * E-mail:
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von Tesmar A, Hoffmann M, Abou Fayad A, Hüttel S, Schmitt V, Herrmann J, Müller R. Biosynthesis of the Klebsiella oxytoca Pathogenicity Factor Tilivalline: Heterologous Expression, in Vitro Biosynthesis, and Inhibitor Development. ACS Chem Biol 2018; 13:812-819. [PMID: 29389112 DOI: 10.1021/acschembio.7b00990] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Tilvalline is a pyrrolo[4,2]benzodiazepine derivative produced by the pathobiont Klebsiella oxytoca and is the causative toxin in antibiotic associated hemorrhagic colitis (AAHC). Heterologous expression of the tilivalline biosynthetic gene cluster along with in vitro reconstitution of the respective NRPS (NpsA, ThdA, NpsB) was employed to reveal a nonenzymatic indole incorporation via a spontaneous Friedel-Crafts-like alkylation reaction. Furthermore, the heterologous system was used to generate novel tilivalline derivatives by supplementation of respective anthranilate and indole precursors. Finally, it could be shown that salicylic and acetylsalicylic acid inhibit the biosynthesis of tilivalline in K. oxytoca liquid culture, presumably by blocking the peptidyl carrier protein ThdA, pointing toward a potential application in combination therapy to prevent or alleviate the symptoms of AAHC.
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Affiliation(s)
- Alexander von Tesmar
- Department of Microbial Natural Products (MINS), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, 66123 Saarbrücken, Germany
| | - Michael Hoffmann
- Department of Microbial Natural Products (MINS), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, 66123 Saarbrücken, Germany
| | - Antoine Abou Fayad
- Department of Microbial Natural Products (MINS), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, 66123 Saarbrücken, Germany
| | - Stephan Hüttel
- Department of Microbial Drugs, Helmholtz Centre for Infection Research and German Centre for Infection Research (DZIF), partner site Hannover/Braunschweig, Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - Viktoria Schmitt
- Department of Microbial Natural Products (MINS), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, 66123 Saarbrücken, Germany
| | - Jennifer Herrmann
- Department of Microbial Natural Products (MINS), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, 66123 Saarbrücken, Germany
| | - Rolf Müller
- Department of Microbial Natural Products (MINS), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, 66123 Saarbrücken, Germany
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19
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Janata J, Kamenik Z, Gazak R, Kadlcik S, Najmanova L. Biosynthesis and incorporation of an alkylproline-derivative (APD) precursor into complex natural products. Nat Prod Rep 2018. [DOI: 10.1039/c7np00047b] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
This review covers the biosynthetic and evolutionary aspects of lincosamide antibiotics, antitumour pyrrolobenzodiazepines (PBDs) and the quorum-sensing molecule hormaomycin.
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Affiliation(s)
- J. Janata
- Institute of Microbiology
- Czech Academy of Sciences
- BIOCEV
- Vestec
- Czech Republic
| | - Z. Kamenik
- Institute of Microbiology
- Czech Academy of Sciences
- BIOCEV
- Vestec
- Czech Republic
| | - R. Gazak
- Institute of Microbiology
- Czech Academy of Sciences
- BIOCEV
- Vestec
- Czech Republic
| | - S. Kadlcik
- Institute of Microbiology
- Czech Academy of Sciences
- BIOCEV
- Vestec
- Czech Republic
| | - L. Najmanova
- Institute of Microbiology
- Czech Academy of Sciences
- BIOCEV
- Vestec
- Czech Republic
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