1
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Peng YJ, Chen Y, Zhou CZ, Miao W, Jiang YL, Zeng X, Zhang CC. Modular catalytic activity of nonribosomal peptide synthetases depends on the dynamic interaction between adenylation and condensation domains. Structure 2024; 32:440-452.e4. [PMID: 38340732 DOI: 10.1016/j.str.2024.01.010] [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: 11/16/2023] [Revised: 12/22/2023] [Accepted: 01/16/2024] [Indexed: 02/12/2024]
Abstract
Nonribosomal peptide synthetases (NRPSs) are large multidomain enzymes for the synthesis of a variety of bioactive peptides in a modular and pipelined fashion. Here, we investigated how the condensation (C) domain and the adenylation (A) domain cooperate with each other for the efficient catalytic activity in microcystin NRPS modules. We solved two crystal structures of the microcystin NRPS modules, representing two different conformations in the NRPS catalytic cycle. Our data reveal that the dynamic interaction between the C and the A domains in these modules is mediated by the conserved "RXGR" motif, and this interaction is important for the adenylation activity. Furthermore, the "RXGR" motif-mediated dynamic interaction and its functional regulation are prevalent in different NRPSs modules possessing both the A and the C domains. This study provides new insights into the catalytic mechanism of NRPSs and their engineering strategy for synthetic peptides with different structures and properties.
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Affiliation(s)
- Ye-Jun Peng
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, People's Republic of China; University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Yuxing Chen
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, People's Republic of China
| | - Cong-Zhao Zhou
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, People's Republic of China
| | - Wei Miao
- Key Laboratory of Lake and Watershed Science for Water Security, Chinese Academy of Sciences, Nanjing 210008, People's Republic of China; Hubei Hongshan Laboratory, Wuhan 430070, People's Republic of China
| | - Yong-Liang Jiang
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, People's Republic of China.
| | - Xiaoli Zeng
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, People's Republic of China; Key Laboratory of Lake and Watershed Science for Water Security, Chinese Academy of Sciences, Nanjing 210008, People's Republic of China.
| | - Cheng-Cai Zhang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, People's Republic of China; Key Laboratory of Lake and Watershed Science for Water Security, Chinese Academy of Sciences, Nanjing 210008, People's Republic of China; Hubei Hongshan Laboratory, Wuhan 430070, People's Republic of China.
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2
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Li R, Lichstrahl MS, Zandi TA, Kahlert L, Townsend CA. The dabABC operon is a marker of C4-alkylated monobactam biosynthesis and responsible for ( 2S, 3R)-diaminobutyrate production. iScience 2024; 27:109202. [PMID: 38433893 PMCID: PMC10906522 DOI: 10.1016/j.isci.2024.109202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/12/2024] [Accepted: 02/07/2024] [Indexed: 03/05/2024] Open
Abstract
Non-ribosomal peptide synthetases (NRPSs) assemble metabolites of medicinal and commercial value. Both serine and threonine figure prominently in these processes and separately can be converted to the additional NRPS building blocks 2,3-diaminopropionate (Dap) and 2,3-diaminobutyrate (Dab). Here we bring extensive bioinformatics, in vivo and in vitro experimentation to compose a unified view of the biosynthesis of these widely distributed non-canonical amino acids that both derive by pyridoxal-mediated β-elimination of the activated O-phosphorylated substrates followed by β-addition of an amine donor. By examining monobactam biosynthesis in Pseudomonas and in Burkholderia species where it is silent, we show that (2S,3R)-Dab synthesis depends on an l-threonine kinase (DabA), a β-replacement reaction with l-aspartate (DabB) and an argininosuccinate lyase-like protein (DabC). The growing clinical importance of monobactams to both withstand Ambler Class B metallo-β-lactamases and retain their antibiotic activity make reprogrammed precursor and NRPS synthesis of modified monobactams a feasible and attractive goal.
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Affiliation(s)
- Rongfeng Li
- Department of Chemistry, The Johns Hopkins University, 3400 N Charles St, Baltimore, MD, USA
| | - Michael S. Lichstrahl
- Department of Chemistry, The Johns Hopkins University, 3400 N Charles St, Baltimore, MD, USA
| | - Trevor A. Zandi
- T. C. Jenkins Department of Biophysics, The Johns Hopkins University, Baltimore, MD, USA
| | - Lukas Kahlert
- Department of Chemistry, The Johns Hopkins University, 3400 N Charles St, Baltimore, MD, USA
| | - Craig A. Townsend
- Department of Chemistry, The Johns Hopkins University, 3400 N Charles St, Baltimore, MD, USA
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3
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Trottmann F, Ishida K, Franke J, Stanišić A, Ishida‐Ito M, Kries H, Pohnert G, Hertweck C. Sulfonium Acids Loaded onto an Unusual Thiotemplate Assembly Line Construct the Cyclopropanol Warhead of a
Burkholderia
Virulence Factor. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202003958] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Felix Trottmann
- Department of Biomolecular Chemistry Leibniz Institute for Natural Product Research and Infection Biology (HKI) Beutenbergstrasse 11a 07745 Jena Germany
| | - Keishi Ishida
- Department of Biomolecular Chemistry Leibniz Institute for Natural Product Research and Infection Biology (HKI) Beutenbergstrasse 11a 07745 Jena Germany
| | - Jakob Franke
- Institute of Botany Leibniz University Hannover 30419 Hannover Germany
| | - Aleksa Stanišić
- Junior Research Group Biosynthetic Design of Natural Products Leibniz Institute for Natural Product Research and Infection Biology (HKI) Beutenbergstrasse 11a 07745 Jena Germany
| | - Mie Ishida‐Ito
- Department of Biomolecular Chemistry Leibniz Institute for Natural Product Research and Infection Biology (HKI) Beutenbergstrasse 11a 07745 Jena Germany
| | - Hajo Kries
- Junior Research Group Biosynthetic Design of Natural Products Leibniz Institute for Natural Product Research and Infection Biology (HKI) Beutenbergstrasse 11a 07745 Jena Germany
| | - Georg Pohnert
- Institute for Inorganic and Analytical Chemistry Friedrich Schiller University Jena 07743 Jena Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry Leibniz Institute for Natural Product Research and Infection Biology (HKI) Beutenbergstrasse 11a 07745 Jena Germany
- Natural Product Chemistry Faculty of Biological Sciences Friedrich Schiller University Jena 07743 Jena Germany
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4
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Trottmann F, Ishida K, Franke J, Stanišić A, Ishida-Ito M, Kries H, Pohnert G, Hertweck C. Sulfonium Acids Loaded onto an Unusual Thiotemplate Assembly Line Construct the Cyclopropanol Warhead of a Burkholderia Virulence Factor. Angew Chem Int Ed Engl 2020; 59:13511-13515. [PMID: 32314848 PMCID: PMC7496086 DOI: 10.1002/anie.202003958] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Indexed: 12/13/2022]
Abstract
Pathogenic bacteria of the Burkholderia pseudomallei group cause severe infectious diseases such as glanders and melioidosis. Malleicyprols were identified as important bacterial virulence factors, yet the biosynthetic origin of their cyclopropanol warhead has remained enigmatic. By a combination of mutational analysis and metabolomics we found that sulfonium acids, dimethylsulfoniumpropionate (DMSP) and gonyol, known as osmolytes and as crucial components in the global organosulfur cycle, are key intermediates en route to the cyclopropanol unit. Functional genetics and in vitro analyses uncover a specialized pathway to DMSP involving a rare prokaryotic SET‐domain methyltransferase for a cryptic methylation, and show that DMSP is loaded onto the NRPS‐PKS hybrid assembly line by an adenylation domain dedicated to zwitterionic starter units. Then, the megasynthase transforms DMSP into gonyol, as demonstrated by heterologous pathway reconstitution in E. coli.
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Affiliation(s)
- Felix Trottmann
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Keishi Ishida
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Jakob Franke
- Institute of Botany, Leibniz University Hannover, 30419, Hannover, Germany
| | - Aleksa Stanišić
- Junior Research Group Biosynthetic Design of Natural Products, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Mie Ishida-Ito
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Hajo Kries
- Junior Research Group Biosynthetic Design of Natural Products, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Georg Pohnert
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, 07743, Jena, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstrasse 11a, 07745, Jena, Germany.,Natural Product Chemistry, Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743, Jena, Germany
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5
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Stanišić A, Hüsken A, Kries H. HAMA: a multiplexed LC-MS/MS assay for specificity profiling of adenylate-forming enzymes. Chem Sci 2019; 10:10395-10399. [PMID: 32110329 PMCID: PMC6988596 DOI: 10.1039/c9sc04222a] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 09/13/2019] [Indexed: 01/04/2023] Open
Abstract
Adenylation enzymes are engineering targets in ribosomal and nonribosomal peptide synthesis. Through multiplexed LC-MS/MS measurement of hydroxamates, the HAMA assay records specificity profiles of these enzymes in a snap.
Adenylation enzymes selecting substrates for ribosomal and nonribosomal protein and peptide biosynthesis have been popular targets of enzyme engineering. Previous standard assays for adenylation specificity have been cumbersome and failed to reflect the competition conditions inside a cell because they measure substrates one at a time. We have developed an adenylation assay based on hydroxamate quenching and LC-MS/MS detection of hydroxamate products testing dozens of competing amino acid substrates in parallel. Streamlined specificity profiling of adenylation enzymes will facilitate engineering and directed evolution of ribosomal and nonribosomal peptide synthesis.
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Affiliation(s)
- Aleksa Stanišić
- Independent Junior Research Group Biosynthetic Design of Natural Products , Leibniz Institute for Natural Product Research and Infection Biology e.V. , Hans Knöll Institute (HKI Jena) , Beutenbergstr. 11a , 07745 Jena , Germany .
| | - Annika Hüsken
- Independent Junior Research Group Biosynthetic Design of Natural Products , Leibniz Institute for Natural Product Research and Infection Biology e.V. , Hans Knöll Institute (HKI Jena) , Beutenbergstr. 11a , 07745 Jena , Germany .
| | - Hajo Kries
- Independent Junior Research Group Biosynthetic Design of Natural Products , Leibniz Institute for Natural Product Research and Infection Biology e.V. , Hans Knöll Institute (HKI Jena) , Beutenbergstr. 11a , 07745 Jena , Germany .
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6
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Vassaux A, Meunier L, Vandenbol M, Baurain D, Fickers P, Jacques P, Leclère V. Nonribosomal peptides in fungal cell factories: from genome mining to optimized heterologous production. Biotechnol Adv 2019; 37:107449. [PMID: 31518630 DOI: 10.1016/j.biotechadv.2019.107449] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 09/06/2019] [Accepted: 09/09/2019] [Indexed: 12/15/2022]
Abstract
Fungi are notoriously prolific producers of secondary metabolites including nonribosomal peptides (NRPs). The structural complexity of NRPs grants them interesting activities such as antibiotic, anti-cancer, and anti-inflammatory properties. The discovery of these compounds with attractive activities can be achieved by using two approaches: either by screening samples originating from various environments for their biological activities, or by identifying the related clusters in genomic sequences thanks to bioinformatics tools. This genome mining approach has grown tremendously due to recent advances in genome sequencing, which have provided an incredible amount of genomic data from hundreds of microbial species. Regarding fungal organisms, the genomic data have revealed the presence of an unexpected number of putative NRP-related gene clusters. This highlights fungi as a goldmine for the discovery of putative novel bioactive compounds. Recent development of NRP dedicated bioinformatics tools have increased the capacity to identify these gene clusters and to deduce NRPs structures, speeding-up the screening process for novel metabolites discovery. Unfortunately, the newly identified compound is frequently not or poorly produced by native producers due to a lack of expression of the related genes cluster. A frequently employed strategy to increase production rates consists in transferring the related biosynthetic pathway in heterologous hosts. This review aims to provide a comprehensive overview about the topic of NRPs discovery, from gene cluster identification by genome mining to the heterologous production in fungal hosts. The main computational tools and methods for genome mining are herein presented with an emphasis on the particularities of the fungal systems. The different steps of the reconstitution of NRP biosynthetic pathway in heterologous fungal cell factories will be discussed, as well as the key factors to consider for maximizing productivity. Several examples will be developed to illustrate the potential of heterologous production to both discover uncharacterized novel compounds predicted in silico by genome mining, and to enhance the productivity of interesting bio-active natural products.
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Affiliation(s)
- Antoine Vassaux
- TERRA Teaching and Research Centre, Microbial Processes and Interactions, Gembloux Agro-Bio Tech, University of Liege, Avenue de la Faculté d'Agronomie, B5030 Gembloux, Belgium; Univ. Lille, INRA, ISA, Univ. Artois, Univ. Littoral Côte d'Opale, EA 7394-ICV-Institut Charles Viollette, F-59000 Lille, France
| | - Loïc Meunier
- TERRA Teaching and Research Centre, Microbial Processes and Interactions, Gembloux Agro-Bio Tech, University of Liege, Avenue de la Faculté d'Agronomie, B5030 Gembloux, Belgium; InBioS-PhytoSYSTEMS, Eukaryotic Phylogenomics, University of Liege, Boulevard du Rectorat 27, B-4000 Liège, Belgium
| | - Micheline Vandenbol
- TERRA Teaching and Research Centre, Microbiologie et Génomique, Gembloux Agro-Bio Tech, University of Liege, Avenue de la Faculté d'Agronomie, B5030 Gembloux, Belgium
| | - Denis Baurain
- InBioS-PhytoSYSTEMS, Eukaryotic Phylogenomics, University of Liege, Boulevard du Rectorat 27, B-4000 Liège, Belgium
| | - Patrick Fickers
- TERRA Teaching and Research Centre, Microbial Processes and Interactions, Gembloux Agro-Bio Tech, University of Liege, Avenue de la Faculté d'Agronomie, B5030 Gembloux, Belgium
| | - Philippe Jacques
- TERRA Teaching and Research Centre, Microbial Processes and Interactions, Gembloux Agro-Bio Tech, University of Liege, Avenue de la Faculté d'Agronomie, B5030 Gembloux, Belgium
| | - Valérie Leclère
- Univ. Lille, INRA, ISA, Univ. Artois, Univ. Littoral Côte d'Opale, EA 7394-ICV-Institut Charles Viollette, F-59000 Lille, France.
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7
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Robinson SL, Christenson JK, Richman JE, Jenkins DJ, Neres J, Fonseca DR, Aldrich CC, Wackett LP. Mechanism of a Standalone β-Lactone Synthetase: New Continuous Assay for a Widespread ANL Superfamily Enzyme. Chembiochem 2019; 20:1701-1711. [PMID: 30856684 DOI: 10.1002/cbic.201800821] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 03/09/2019] [Indexed: 12/11/2022]
Abstract
Enzyme-catalyzed β-lactone formation from β-hydroxy acids is a crucial step in bacterial biosynthesis of β-lactone natural products and membrane hydrocarbons. We developed a novel, continuous assay for β-lactone synthetase activity using synthetic β-hydroxy acid substrates with alkene or alkyne moieties. β-Lactone formation is followed by rapid decarboxylation to form a conjugated triene chromophore for real-time evaluation by UV/Vis spectroscopy. The assay was used to determine steady-state kinetics of a long-chain β-lactone synthetase, OleC, from the plant pathogen Xanthomonas campestris. Site-directed mutagenesis was used to test the involvement of conserved active site residues in Mg2+ and ATP binding. A previous report suggested OleC adenylated the substrate hydroxy group. Here we present several lines of evidence, including hydroxylamine trapping of the AMP intermediate, to demonstrate the substrate carboxyl group is adenylated prior to making the β-lactone final product. A panel of nine substrate analogues were used to investigate the substrate specificity of X. campestris OleC by HPLC and GC-MS. Stereoisomers of 2-hexyl-3hydroxyoctanoic acid were synthesized and OleC preferred the (2R,3S) diastereomer consistent with the stereo-preference of upstream and downstream pathway enzymes. This biochemical knowledge was used to guide phylogenetic analysis of the β-lactone synthetases to map their functional diversity within the acyl-CoA synthetase, NRPS adenylation domain, and luciferase superfamily.
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Affiliation(s)
- Serina L Robinson
- BioTechnology Institute, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN, 55108, USA
| | - James K Christenson
- BioTechnology Institute, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN, 55108, USA.,Present address: Department of Chemistry, Bethel University, 3900 Bethel Drive, Saint Paul, MN, 55112, USA
| | - Jack E Richman
- BioTechnology Institute, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN, 55108, USA
| | - Dominick J Jenkins
- BioTechnology Institute, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN, 55108, USA
| | - João Neres
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard St. SE, Minneapolis, MN, 55455, USA.,Present address: UCB Biopharma, Chemin du Foriest, 1420, Braine-l'Alleud, Belgium
| | - Dallas R Fonseca
- BioTechnology Institute, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN, 55108, USA
| | - Courtney C Aldrich
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard St. SE, Minneapolis, MN, 55455, USA
| | - Lawrence P Wackett
- BioTechnology Institute, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN, 55108, USA
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8
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Sinha S, Nge CE, Leong CY, Ng V, Crasta S, Alfatah M, Goh F, Low KN, Zhang H, Arumugam P, Lezhava A, Chen SL, Kanagasundaram Y, Ng SB, Eisenhaber F, Eisenhaber B. Genomics-driven discovery of a biosynthetic gene cluster required for the synthesis of BII-Rafflesfungin from the fungus Phoma sp. F3723. BMC Genomics 2019; 20:374. [PMID: 31088369 PMCID: PMC6518819 DOI: 10.1186/s12864-019-5762-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 05/02/2019] [Indexed: 12/20/2022] Open
Abstract
Background Phomafungin is a recently reported broad spectrum antifungal compound but its biosynthetic pathway is unknown. We combed publicly available Phoma genomes but failed to find any putative biosynthetic gene cluster that could account for its biosynthesis. Results Therefore, we sequenced the genome of one of our Phoma strains (F3723) previously identified as having antifungal activity in a high-throughput screen. We found a biosynthetic gene cluster that was predicted to synthesize a cyclic lipodepsipeptide that differs in the amino acid composition compared to Phomafungin. Antifungal activity guided isolation yielded a new compound, BII-Rafflesfungin, the structure of which was determined. Conclusions We describe the NRPS-t1PKS cluster ‘BIIRfg’ compatible with the synthesis of the cyclic lipodepsipeptide BII-Rafflesfungin [HMHDA-L-Ala-L-Glu-L-Asn-L-Ser-L-Ser-D-Ser-D-allo-Thr-Gly]. We report new Stachelhaus codes for Ala, Glu, Asn, Ser, Thr, and Gly. We propose a mechanism for BII-Rafflesfungin biosynthesis, which involves the formation of the lipid part by BIIRfg_PKS followed by activation and transfer of the lipid chain by a predicted AMP-ligase on to the first PCP domain of the BIIRfg_NRPS gene. Electronic supplementary material The online version of this article (10.1186/s12864-019-5762-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Swati Sinha
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore.
| | - Choy-Eng Nge
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore
| | - Chung Yan Leong
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore
| | - Veronica Ng
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore
| | - Sharon Crasta
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore
| | - Mohammad Alfatah
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore
| | - Falicia Goh
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore
| | - Kia-Ngee Low
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore
| | - Huibin Zhang
- Genome Institue of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, #02-01 Genome, Singapore, 138672, Republic of Singapore
| | - Prakash Arumugam
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore
| | - Alexander Lezhava
- Genome Institue of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, #02-01 Genome, Singapore, 138672, Republic of Singapore
| | - Swaine L Chen
- Genome Institue of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, #02-01 Genome, Singapore, 138672, Republic of Singapore.,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, 1E Kent Ridge Road, NUHS Tower Block, Level 10, Singapore, 119228, Republic of Singapore
| | - Yoganathan Kanagasundaram
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore
| | - Siew Bee Ng
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore
| | - Frank Eisenhaber
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore.,School of Computer Science and Engineering (SCSE), Nanyang Technological University (NTU), 50 Nanyang Drive, Singapore, 637553, Republic of Singapore
| | - Birgit Eisenhaber
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore.
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9
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Hong Z, Bolard A, Giraud C, Prévost S, Genta‐Jouve G, Deregnaucourt C, Häussler S, Jeannot K, Li Y. Azetidine‐Containing Alkaloids Produced by a Quorum‐Sensing Regulated Nonribosomal Peptide Synthetase Pathway in
Pseudomonas aeruginosa. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201809981] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Zhilai Hong
- Unité Molécules de Communication et Adaptation des Microorganismes (MCAM)Muséum National d'Histoire Naturelle (MNHN)Centre National de la Recherche Scientifique (CNRS), CP 54 57 rue Cuvier 75005 Paris France
| | - Arnaud Bolard
- Laboratoire de BactériologieCentre National de Référence (CNR) de la Résistance aux Antibiotiques, Centre Hospitalier Régional Universitaire (CHRU) de Besançon, UMR4269 “Chrono-Environnement” Boulevard Fleming 25030 Besançon France
| | - Caroline Giraud
- U2RM Stress/VirulenceNormandy University, UNICAEN 14000 Caen France
| | - Sébastien Prévost
- Laboratoire de Synthèse Organique, UMR 7652CNRS, Ecole PolytechniqueENSTA ParisTechUniversité Paris-Saclay 828 Bd des Maréchaux 91128 Palaiseau France
| | - Grégory Genta‐Jouve
- Unité Molécules de Communication et Adaptation des Microorganismes (MCAM)Muséum National d'Histoire Naturelle (MNHN)Centre National de la Recherche Scientifique (CNRS), CP 54 57 rue Cuvier 75005 Paris France
- C-TAC, UMR 8638, CNRSFaculté de Pharmacie de ParisUniversité Paris Descartes, Sorbonne Paris Cité 4 Avenue de l'Observatoire 75006 Paris France
| | - Christiane Deregnaucourt
- Unité Molécules de Communication et Adaptation des Microorganismes (MCAM)Muséum National d'Histoire Naturelle (MNHN)Centre National de la Recherche Scientifique (CNRS), CP 54 57 rue Cuvier 75005 Paris France
| | - Susanne Häussler
- Institute for Molecular Bacteriology, TWINCORECentre for Experimental and Clinical Infection Research Hannover Germany
- Department of Molecular BacteriologyHelmholtz Centre for Infection Research Braunschweig Germany
| | - Katy Jeannot
- Laboratoire de BactériologieCentre National de Référence (CNR) de la Résistance aux Antibiotiques, Centre Hospitalier Régional Universitaire (CHRU) de Besançon, UMR4269 “Chrono-Environnement” Boulevard Fleming 25030 Besançon France
| | - Yanyan Li
- Unité Molécules de Communication et Adaptation des Microorganismes (MCAM)Muséum National d'Histoire Naturelle (MNHN)Centre National de la Recherche Scientifique (CNRS), CP 54 57 rue Cuvier 75005 Paris France
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10
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Hong Z, Bolard A, Giraud C, Prévost S, Genta-Jouve G, Deregnaucourt C, Häussler S, Jeannot K, Li Y. Azetidine-Containing Alkaloids Produced by a Quorum-Sensing Regulated Nonribosomal Peptide Synthetase Pathway in Pseudomonas aeruginosa. Angew Chem Int Ed Engl 2019; 58:3178-3182. [PMID: 30548135 DOI: 10.1002/anie.201809981] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 11/08/2018] [Indexed: 12/26/2022]
Abstract
Pseudomonas aeruginosa displays an impressive metabolic versatility, which ensures its survival in diverse environments. Reported herein is the identification of rare azetidine-containing alkaloids from P. aeruginosa PAO1, termed azetidomonamides, which are derived from a conserved, quorum-sensing regulated nonribosomal peptide synthetase (NRPS) pathway. Biosynthesis of the azetidine motif has been elucidated by gene inactivation, feeding experiments, and biochemical characterization in vitro, which involves a new S-adenosylmethionine-dependent enzyme to produce azetidine 2-carboxylic acid as an unusual building block of NRPS. The mutants of P. aeruginosa unable to produce azetidomonamides had an advantage in growth at high cell density in vitro and displayed rapid virulence in Galleria mellonella model, inferring functional roles of azetidomonamides in the host adaptation. This work opens the avenue to study the biological functions of azetidomonamides and related compounds in pathogenic and environmental bacteria.
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Affiliation(s)
- Zhilai Hong
- Unité Molécules de Communication et Adaptation des Microorganismes (MCAM), Muséum National d'Histoire Naturelle (MNHN), Centre National de la Recherche Scientifique (CNRS), CP 54, 57 rue Cuvier, 75005, Paris, France
| | - Arnaud Bolard
- Laboratoire de Bactériologie, Centre National de Référence (CNR) de la Résistance aux Antibiotiques, Centre Hospitalier Régional Universitaire (CHRU) de Besançon, UMR4269 "Chrono-Environnement", Boulevard Fleming, 25030, Besançon, France
| | - Caroline Giraud
- U2RM Stress/Virulence, Normandy University, UNICAEN, 14000, Caen, France
| | - Sébastien Prévost
- Laboratoire de Synthèse Organique, UMR 7652, CNRS, Ecole Polytechnique, ENSTA ParisTech, Université Paris-Saclay, 828 Bd des Maréchaux, 91128, Palaiseau, France
| | - Grégory Genta-Jouve
- Unité Molécules de Communication et Adaptation des Microorganismes (MCAM), Muséum National d'Histoire Naturelle (MNHN), Centre National de la Recherche Scientifique (CNRS), CP 54, 57 rue Cuvier, 75005, Paris, France.,C-TAC, UMR 8638, CNRS, Faculté de Pharmacie de Paris, Université Paris Descartes, Sorbonne Paris Cité, 4 Avenue de l'Observatoire, 75006, Paris, France
| | - Christiane Deregnaucourt
- Unité Molécules de Communication et Adaptation des Microorganismes (MCAM), Muséum National d'Histoire Naturelle (MNHN), Centre National de la Recherche Scientifique (CNRS), CP 54, 57 rue Cuvier, 75005, Paris, France
| | - Susanne Häussler
- Institute for Molecular Bacteriology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany.,Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Katy Jeannot
- Laboratoire de Bactériologie, Centre National de Référence (CNR) de la Résistance aux Antibiotiques, Centre Hospitalier Régional Universitaire (CHRU) de Besançon, UMR4269 "Chrono-Environnement", Boulevard Fleming, 25030, Besançon, France
| | - Yanyan Li
- Unité Molécules de Communication et Adaptation des Microorganismes (MCAM), Muséum National d'Histoire Naturelle (MNHN), Centre National de la Recherche Scientifique (CNRS), CP 54, 57 rue Cuvier, 75005, Paris, France
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Ronnebaum TA, McFarlane JS, Prisinzano TE, Booker SJ, Lamb AL. Stuffed Methyltransferase Catalyzes the Penultimate Step of Pyochelin Biosynthesis. Biochemistry 2018; 58:665-678. [PMID: 30525512 DOI: 10.1021/acs.biochem.8b00716] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Nonribosomal peptide synthetases use tailoring domains to incorporate chemical diversity into the final natural product. A structurally unique set of tailoring domains are found to be stuffed within adenylation domains and have only recently begun to be characterized. PchF is the NRPS termination module in pyochelin biosynthesis and includes a stuffed methyltransferase domain responsible for S-adenosylmethionine (AdoMet)-dependent N-methylation. Recent studies of stuffed methyltransferase domains propose a model in which methylation occurs on amino acids after adenylation and thiolation rather than after condensation to the nascent peptide chain. Herein, we characterize the adenylation and stuffed methyltransferase didomain of PchF through the synthesis and use of substrate analogues, steady-state kinetics, and onium chalcogen effects. We provide evidence that methylation occurs through an SN2 reaction after thiolation, condensation, cyclization, and reduction of the module substrate cysteine and is the penultimate step in pyochelin biosynthesis.
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Affiliation(s)
| | | | | | - Squire J Booker
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and the Howard Hughes Medical Institute , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
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12
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Barajas JF, Zargar A, Pang B, Benites VT, Gin J, Baidoo EEK, Petzold CJ, Hillson NJ, Keasling JD. Biochemical Characterization of β-Amino Acid Incorporation in Fluvirucin B 2 Biosynthesis. Chembiochem 2018; 19:1391-1395. [PMID: 29603548 DOI: 10.1002/cbic.201800169] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Indexed: 11/10/2022]
Abstract
Naturally occurring lactams, such as the polyketide-derived macrolactams, provide a diverse class of natural products that could enhance existing chemically produced lactams. Although β-amino acid loading in the fluvirucin B2 polyketide pathway was proposed by a previously identified putative biosynthetic gene cluster, biochemical characterization of the complete loading enzymes has not been described. Here we elucidate the complete biosynthetic pathway of the β-amino acid loading pathway in fluvirucin B2 biosynthesis. We demonstrate the promiscuity of the loading pathway to utilize a range of amino acids and further illustrate the ability to introduce non-native acyl transferases to selectively transfer β-amino acids onto a polyketide synthase (PKS) loading platform. The results presented here provide a detailed biochemical description of β-amino acid selection and will further aid in future efforts to develop engineered lactam-producing PKS platforms.
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Affiliation(s)
- Jesus F Barajas
- Department of Energy Agile BioFoundry, 5885 Hollis Street, 4th floor, Emeryville, CA, 94608, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Amin Zargar
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA.,Joint BioEnergy Institute, 5885 Hollis Street, 4th floor, Emeryville, CA, 94608, USA
| | - Bo Pang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA.,Joint BioEnergy Institute, 5885 Hollis Street, 4th floor, Emeryville, CA, 94608, USA
| | - Veronica T Benites
- Department of Energy Agile BioFoundry, 5885 Hollis Street, 4th floor, Emeryville, CA, 94608, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA.,Joint BioEnergy Institute, 5885 Hollis Street, 4th floor, Emeryville, CA, 94608, USA
| | - Jennifer Gin
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA.,Joint BioEnergy Institute, 5885 Hollis Street, 4th floor, Emeryville, CA, 94608, USA
| | - Edward E K Baidoo
- Department of Energy Agile BioFoundry, 5885 Hollis Street, 4th floor, Emeryville, CA, 94608, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA.,Joint BioEnergy Institute, 5885 Hollis Street, 4th floor, Emeryville, CA, 94608, USA
| | - Christopher J Petzold
- Department of Energy Agile BioFoundry, 5885 Hollis Street, 4th floor, Emeryville, CA, 94608, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA.,Joint BioEnergy Institute, 5885 Hollis Street, 4th floor, Emeryville, CA, 94608, USA
| | - Nathan J Hillson
- Department of Energy Agile BioFoundry, 5885 Hollis Street, 4th floor, Emeryville, CA, 94608, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA.,Joint BioEnergy Institute, 5885 Hollis Street, 4th floor, Emeryville, CA, 94608, USA
| | - Jay D Keasling
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA.,Joint BioEnergy Institute, 5885 Hollis Street, 4th floor, Emeryville, CA, 94608, USA.,QB3 Institute, University of California-Berkeley, 174 Stanley Hall, Berkeley, CA, 94720, USA.,Department of Chemical and Biomolecular Engineering, Department of Bioengineering, University of California-Berkeley, 201 Gilman Hall, Berkeley, CA, 94720, USA.,Novo Nordisk Foundation Center for Biosustainability, Technical University Denmark, 2800 kgs., Lingby, Denmark
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13
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Substrate-Induced Conformational Changes of the Tyrocidine Synthetase 1 Adenylation Domain Probed by Intrinsic Trp Fluorescence. Protein J 2017; 36:202-211. [DOI: 10.1007/s10930-017-9714-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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