1
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Zhang M, Peng Z, Huang Z, Fang J, Li X, Qiu X. Functional Diversity and Engineering of the Adenylation Domains in Nonribosomal Peptide Synthetases. Mar Drugs 2024; 22:349. [PMID: 39195464 DOI: 10.3390/md22080349] [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: 07/04/2024] [Revised: 07/23/2024] [Accepted: 07/27/2024] [Indexed: 08/29/2024] Open
Abstract
Nonribosomal peptides (NRPs) are biosynthesized by nonribosomal peptide synthetases (NRPSs) and are widely distributed in both terrestrial and marine organisms. Many NRPs and their analogs are biologically active and serve as therapeutic agents. The adenylation (A) domain is a key catalytic domain that primarily controls the sequence of a product during the assembling of NRPs and thus plays a predominant role in the structural diversity of NRPs. Engineering of the A domain to alter substrate specificity is a potential strategy for obtaining novel NRPs for pharmaceutical studies. On the basis of introducing the catalytic mechanism and multiple functions of the A domains, this article systematically describes several representative NRPS engineering strategies targeting the A domain, including mutagenesis of substrate-specificity codes, substitution of condensation-adenylation bidomains, the entire A domain or its subdomains, domain insertion, and whole-module rearrangements.
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Affiliation(s)
- Mengli Zhang
- College of Food Science and Engineering, Ningbo University, Ningbo 315800, China
| | - Zijing Peng
- College of Food Science and Engineering, Ningbo University, Ningbo 315800, China
| | - Zhenkuai Huang
- College of Food Science and Engineering, Ningbo University, Ningbo 315800, China
| | - Jiaqi Fang
- College of Food Science and Engineering, Ningbo University, Ningbo 315800, China
| | - Xinhai Li
- College of Food Science and Engineering, Ningbo University, Ningbo 315800, China
| | - Xiaoting Qiu
- College of Food Science and Engineering, Ningbo University, Ningbo 315800, China
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2
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Folger IB, Frota NF, Pistofidis A, Niquille DL, Hansen DA, Schmeing TM, Hilvert D. High-throughput reprogramming of an NRPS condensation domain. Nat Chem Biol 2024; 20:761-769. [PMID: 38308044 PMCID: PMC11142918 DOI: 10.1038/s41589-023-01532-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 12/19/2023] [Indexed: 02/04/2024]
Abstract
Engineered biosynthetic assembly lines could revolutionize the sustainable production of bioactive natural product analogs. Although yeast display is a proven, powerful tool for altering the substrate specificity of gatekeeper adenylation domains in nonribosomal peptide synthetases (NRPSs), comparable strategies for other components of these megaenzymes have not been described. Here we report a high-throughput approach for engineering condensation (C) domains responsible for peptide elongation. We show that a 120-kDa NRPS module, displayed in functional form on yeast, can productively interact with an upstream module, provided in solution, to produce amide products tethered to the yeast surface. Using this system to screen a large C-domain library, we reprogrammed a surfactin synthetase module to accept a fatty acid donor, increasing catalytic efficiency for this noncanonical substrate >40-fold. Because C domains can function as selectivity filters in NRPSs, this methodology should facilitate the precision engineering of these molecular assembly lines.
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Affiliation(s)
- Ines B Folger
- Laboratory of Organic Chemistry, ETH Zurich, Zurich, Switzerland
| | - Natália F Frota
- Department of Biochemistry and Centre de Recherche en Biologie Structurale, McGill University, Montréal, Quebec, Canada
| | - Angelos Pistofidis
- Department of Biochemistry and Centre de Recherche en Biologie Structurale, McGill University, Montréal, Quebec, Canada
| | - David L Niquille
- Laboratory of Organic Chemistry, ETH Zurich, Zurich, Switzerland
| | - Douglas A Hansen
- Laboratory of Organic Chemistry, ETH Zurich, Zurich, Switzerland
| | - T Martin Schmeing
- Department of Biochemistry and Centre de Recherche en Biologie Structurale, McGill University, Montréal, Quebec, Canada
| | - Donald Hilvert
- Laboratory of Organic Chemistry, ETH Zurich, Zurich, Switzerland.
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3
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Peng H, Schmiederer J, Chen X, Panagiotou G, Kries H. Controlling Substrate- and Stereospecificity of Condensation Domains in Nonribosomal Peptide Synthetases. ACS Chem Biol 2024; 19:599-606. [PMID: 38395426 PMCID: PMC10949931 DOI: 10.1021/acschembio.3c00678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 01/30/2024] [Accepted: 02/09/2024] [Indexed: 02/25/2024]
Abstract
Nonribosomal peptide synthetases (NRPSs) are sophisticated molecular machines that biosynthesize peptide drugs. In attempts to generate new bioactive compounds, some parts of NRPSs have been successfully manipulated, but especially the influence of condensation (C-)domains on substrate specificity remains enigmatic and poorly controlled. To understand the influence of C-domains on substrate preference, we extensively evaluated the peptide formation of C-domain mutants in a bimodular NRPS system. Thus, we identified three key mutations that govern the preference for stereoconfiguration and side-chain identity. These mutations show similar effects in three different C-domains (GrsB1, TycB1, and SrfAC) when di- or pentapeptides are synthesized in vitro or in vivo. Strikingly, mutation E386L allows the stereopreference to be switched from d- to l-configured donor substrates. Our findings provide valuable insights into how cryptic specificity filters in C-domains can be re-engineered to clear roadblocks for NRPS engineering and enable the production of novel bioactive compounds.
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Affiliation(s)
- Huiyun Peng
- Junior
Research Group Biosynthetic Design of Natural Products, Leibniz Institute for Natural Product Research and
Infection Biology (HKI), Beutenbergstr. 11a, 07745 Jena, Germany
| | - Julian Schmiederer
- Junior
Research Group Biosynthetic Design of Natural Products, Leibniz Institute for Natural Product Research and
Infection Biology (HKI), Beutenbergstr. 11a, 07745 Jena, Germany
| | - Xiuqiang Chen
- Department
of Microbiome Dynamics, Leibniz Institute
for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745 Jena, Germany
| | - Gianni Panagiotou
- Department
of Microbiome Dynamics, Leibniz Institute
for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745 Jena, Germany
- Faculty
of Biological Sciences, Friedrich Schiller
University, 07745 Jena, Germany
- Department
of Medicine, The University of Hong Kong, 999999 Hong Kong
SAR, China
| | - Hajo Kries
- Junior
Research Group Biosynthetic Design of Natural Products, Leibniz Institute for Natural Product Research and
Infection Biology (HKI), Beutenbergstr. 11a, 07745 Jena, Germany
- Department
of Chemistry, University of Bayreuth, Universitätsstr. 30, 95440 Bayreuth, Germany
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4
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Stephan P, Langley C, Winkler D, Basquin J, Caputi L, O'Connor SE, Kries H. Directed Evolution of Piperazic Acid Incorporation by a Nonribosomal Peptide Synthetase. Angew Chem Int Ed Engl 2023; 62:e202304843. [PMID: 37326625 DOI: 10.1002/anie.202304843] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 06/12/2023] [Accepted: 06/13/2023] [Indexed: 06/17/2023]
Abstract
Engineering of biosynthetic enzymes is increasingly employed to synthesize structural analogues of antibiotics. Of special interest are nonribosomal peptide synthetases (NRPSs) responsible for the production of important antimicrobial peptides. Here, directed evolution of an adenylation domain of a Pro-specific NRPS module completely switched substrate specificity to the non-standard amino acid piperazic acid (Piz) bearing a labile N-N bond. This success was achieved by UPLC-MS/MS-based screening of small, rationally designed mutant libraries and can presumably be replicated with a larger number of substrates and NRPS modules. The evolved NRPS produces a Piz-derived gramicidin S analogue. Thus, we give new impetus to the too-early dismissed idea that widely accessible low-throughput methods can switch the specificity of NRPSs in a biosynthetically useful fashion.
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Affiliation(s)
- Philipp Stephan
- Junior Research Group Biosynthetic Design of Natural Products, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
| | - Chloe Langley
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Hans-Knöll-Str. 8, 07745, Jena, Germany
| | - Daniela Winkler
- Junior Research Group Biosynthetic Design of Natural Products, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
| | - Jérôme Basquin
- Department of Structural Cell Biology, Max Planck Institute for Biochemistry, Am Klopferspitz 18, 82152, Planegg Martinsried, Germany
| | - Lorenzo Caputi
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Hans-Knöll-Str. 8, 07745, Jena, Germany
| | - Sarah E O'Connor
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Hans-Knöll-Str. 8, 07745, Jena, Germany
| | - Hajo Kries
- Junior Research Group Biosynthetic Design of Natural Products, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
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5
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Puja H, Mislin GLA, Rigouin C. Engineering Siderophore Biosynthesis and Regulation Pathways to Increase Diversity and Availability. Biomolecules 2023; 13:959. [PMID: 37371539 PMCID: PMC10296737 DOI: 10.3390/biom13060959] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 05/23/2023] [Accepted: 06/01/2023] [Indexed: 06/29/2023] Open
Abstract
Siderophores are small metal chelators synthesized by numerous organisms to access iron. These secondary metabolites are ubiquitously present on Earth, and because their production represents the main strategy to assimilate iron, they play an important role in both positive and negative interactions between organisms. In addition, siderophores are used in biotechnology for diverse applications in medicine, agriculture and the environment. The generation of non-natural siderophore analogs provides a new opportunity to create new-to-nature chelating biomolecules that can offer new properties to expand applications. This review summarizes the main strategies of combinatorial biosynthesis that have been used to generate siderophore analogs. We first provide a brief overview of siderophore biosynthesis, followed by a description of the strategies, namely, precursor-directed biosynthesis, the design of synthetic or heterologous pathways and enzyme engineering, used in siderophore biosynthetic pathways to create diversity. In addition, this review highlights the engineering strategies that have been used to improve the production of siderophores by cells to facilitate their downstream utilization.
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Affiliation(s)
- Hélène Puja
- CNRS-UMR7242, Biotechnologie et Signalisation Cellulaire, 300 Bld Sébastien Brant, 67412 Illkirch, France (G.L.A.M.)
- Institut de Recherche de l’Ecole de Biotechnologie de Strasbourg (IREBS), Université de Strasbourg, 300 Bld Sébastien Brant, 67412 Illkirch, France
| | - Gaëtan L. A. Mislin
- CNRS-UMR7242, Biotechnologie et Signalisation Cellulaire, 300 Bld Sébastien Brant, 67412 Illkirch, France (G.L.A.M.)
- Institut de Recherche de l’Ecole de Biotechnologie de Strasbourg (IREBS), Université de Strasbourg, 300 Bld Sébastien Brant, 67412 Illkirch, France
| | - Coraline Rigouin
- CNRS-UMR7242, Biotechnologie et Signalisation Cellulaire, 300 Bld Sébastien Brant, 67412 Illkirch, France (G.L.A.M.)
- Institut de Recherche de l’Ecole de Biotechnologie de Strasbourg (IREBS), Université de Strasbourg, 300 Bld Sébastien Brant, 67412 Illkirch, France
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6
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Dinglasan JLN, Sword TT, Barker JW, Doktycz MJ, Bailey CB. Investigating and Optimizing the Lysate-Based Expression of Nonribosomal Peptide Synthetases Using a Reporter System. ACS Synth Biol 2023; 12:1447-1460. [PMID: 37039644 PMCID: PMC11236431 DOI: 10.1021/acssynbio.2c00658] [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] [Indexed: 04/12/2023]
Abstract
Lysate-based cell-free expression (CFE) systems are accessible platforms for expressing proteins that are difficult to synthesize in vivo, such as nonribosomal peptide synthetases (NRPSs). NRPSs are large (>100 kDa), modular enzyme complexes that synthesize bioactive peptide natural products. This synthetic process is analogous to transcription/translation (TX/TL) in lysates, resulting in potential resource competition between NRPS expression and NRPS activity in cell-free environments. Moreover, CFE conditions depend on the size and structure of the protein. Here, a reporter system for rapidly investigating and optimizing reaction environments for NRPS CFE is described. This strategy is demonstrated in E. coli lysate reactions using blue pigment synthetase A (BpsA), a model NRPS, carrying a C-terminal tetracysteine (TC) tag which forms a fluorescent complex with the biarsenical dye, FlAsH. A colorimetric assay was adapted for lysate reactions to detect the blue pigment product, indigoidine, of cell-free expressed BpsA-TC, confirming that the tagged enzyme is catalytically active. An optimized protocol for end point TC/FlAsH complex measurements in reactions enables quick comparisons of full-length BpsA-TC expressed under different reaction conditions, defining unique requirements for NRPS expression that are related to the protein's catalytic activity and size. Importantly, these protein-dependent CFE conditions enable higher indigoidine titer and improve the expression of other monomodular NRPSs. Notably, these conditions differ from those used for the expression of superfolder GFP (sfGFP), a common reporter for optimizing lysate-based CFE systems, indicating the necessity for tailored reporters to optimize expression for specific enzyme classes. The reporter system is anticipated to advance lysate-based CFE systems for complex enzyme synthesis, enabling natural product discovery.
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Affiliation(s)
- Jaime Lorenzo N Dinglasan
- Graduate School of Genome Science & Technology, University of Tennessee-Knoxville, Knoxville, Tennessee 37996, United States
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Tien T Sword
- Department of Chemistry, University of Tennessee-Knoxville, Knoxville, Tennessee 37996, United States
| | - J William Barker
- Department of Chemistry, University of Tennessee-Knoxville, Knoxville, Tennessee 37996, United States
| | - Mitchel J Doktycz
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Constance B Bailey
- Department of Chemistry, University of Tennessee-Knoxville, Knoxville, Tennessee 37996, United States
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7
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Wang X, Gu Z, Wan J, Zhou X, Zhu K, Wang X, Cao X, Yu X, Peng X, Tang Y. dECM based dusal-responsive vascular graft with enzyme-controlled adenine release for long-term patency. Int J Biol Macromol 2023; 242:124618. [PMID: 37148948 DOI: 10.1016/j.ijbiomac.2023.124618] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 04/18/2023] [Accepted: 04/23/2023] [Indexed: 05/08/2023]
Abstract
Rapid occlusion is the culprit leading to implantation failure of biological blood vessels. Although adenosine is a clinical-proven drug to overcome the problem, its short half-life and turbulent burst-release limit its direct application. Thus, a pH/temperature dual-responsive blood vessel possessed controllable long-term adenosine secretion was constructed based on acellular matrix via compact crosslinking by oxidized chondroitin sulfate (OCSA) and functionalized with apyrase and acid phosphatase. These enzymes, as adenosine micro-generators, controlled the adenosine release amount by "real-time-responding" to acidity and temperature of vascular inflammation sites. Additionally, the macrophage phenotype was switched from M1 to M2, and related factors expression proved that adenosine release was effectively regulated with the severity of inflammation. What's more, the ultra-structure for degradation resisting and endothelialization accelerating was also preserved by their "double-crosslinking". Therefore, this work suggested a new feasible strategy providing a bright future of long-term patency for transplanted blood vessels.
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Affiliation(s)
- Xu Wang
- International Collaborative Centre on Big Science Plan for Purinergic Signaling, School of Acupuncture and Tuina, Chengdu University of Traditional Chinese Medicine, Chengdu 610075, China.
| | - Zhipeng Gu
- College of Polymer Science and Engineering, Sichuan University, Chengdu 610065, China
| | - Junyu Wan
- International Collaborative Centre on Big Science Plan for Purinergic Signaling, School of Acupuncture and Tuina, Chengdu University of Traditional Chinese Medicine, Chengdu 610075, China
| | - Xiong Zhou
- Department of Biomedical Engineering, City University of Hong Kong, 999077, Hong Kong, China
| | - Keli Zhu
- International Collaborative Centre on Big Science Plan for Purinergic Signaling, School of Acupuncture and Tuina, Chengdu University of Traditional Chinese Medicine, Chengdu 610075, China
| | - Xin Wang
- International Collaborative Centre on Big Science Plan for Purinergic Signaling, School of Acupuncture and Tuina, Chengdu University of Traditional Chinese Medicine, Chengdu 610075, China
| | - Xin Cao
- International Collaborative Centre on Big Science Plan for Purinergic Signaling, School of Acupuncture and Tuina, Chengdu University of Traditional Chinese Medicine, Chengdu 610075, China
| | - Xixun Yu
- College of Polymer Science and Engineering, Sichuan University, Chengdu 610065, China
| | - Xu Peng
- College of Polymer Science and Engineering, Sichuan University, Chengdu 610065, China.
| | - Yong Tang
- International Collaborative Centre on Big Science Plan for Purinergic Signaling, School of Acupuncture and Tuina, Chengdu University of Traditional Chinese Medicine, Chengdu 610075, China; Acupuncture & Chronobiology Key Laboratory of Sichuan Province, School of Health and Rehabilitation, Chengdu University of Traditional Chinese Medicine, Chengdu 610065, China.
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8
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Kahlert L, Lichstrahl MS, Townsend CA. Colorimetric Determination of Adenylation Domain Activity in Nonribosomal Peptide Synthetases by Using Chrome Azurol S. Chembiochem 2023; 24:e202200668. [PMID: 36511946 PMCID: PMC10041650 DOI: 10.1002/cbic.202200668] [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: 11/16/2022] [Revised: 12/12/2022] [Accepted: 12/13/2022] [Indexed: 12/15/2022]
Abstract
Adenylation domains are the main contributor to structural complexity among nonribosomal peptides due to their varied but stringent substrate selection. Several in vitro assays to determine the substrate specificity of these dedicated biocatalysts have been implemented, but high sensitivity is often accompanied by the cost of laborious procedures, expensive reagents or the requirement for auxiliary enzymes. Here, we describe a simple protocol that is based on the removal of ferric iron from a preformed chromogenic complex between ferric iron and Chrome Azurol S. Adenylation activity can be rapidly followed by a decrease in absorbance at 630 nm, visualized by a prominent color change from blue to orange.
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Affiliation(s)
- Lukas Kahlert
- Department of Chemistry, The Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland, 21218, USA
| | - Michael S Lichstrahl
- Department of Chemistry, The Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland, 21218, USA
| | - Craig A Townsend
- Department of Chemistry, The Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland, 21218, USA
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9
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Sreedharan SM, Rishi N, Singh R. Microbial Lipopeptides: Properties, Mechanics and Engineering for Novel Lipopeptides. Microbiol Res 2023; 271:127363. [PMID: 36989760 DOI: 10.1016/j.micres.2023.127363] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 12/04/2022] [Accepted: 03/11/2023] [Indexed: 03/17/2023]
Abstract
Microorganisms produce active surface agents called lipopeptides (LPs) which are amphiphilic in nature. They are cyclic or linear compounds and are predominantly isolated from Bacillus and Pseudomonas species. LPs show antimicrobial activity towards various plant pathogens and act by inhibiting the growth of these organisms. Several mechanisms are exhibited by LPs, such as cell membrane disruption, biofilm production, induced systematic resistance, improving plant growth, inhibition of spores, etc., making them suitable as biocontrol agents and highly advantageous for industrial utilization. The biosynthesis of lipopeptides involves large multimodular enzymes referred to as non-ribosomal peptide synthases. These enzymes unveil a broad range of engineering approaches through which lipopeptides can be overproduced and new LPs can be generated asserting high efficacy. Such approaches involve several synthetic biology systems and metabolic engineering techniques such as promotor engineering, enhanced precursor availability, condensation domain engineering, and adenylation domain engineering. Finally, this review provides an update of the applications of lipopeptides in various fields.
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10
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Zhang L, Wang C, Chen K, Zhong W, Xu Y, Molnár I. Engineering the biosynthesis of fungal nonribosomal peptides. Nat Prod Rep 2023; 40:62-88. [PMID: 35796260 DOI: 10.1039/d2np00036a] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Covering: 2011 up to the end of 2021.Fungal nonribosomal peptides (NRPs) and the related polyketide-nonribosomal peptide hybrid products (PK-NRPs) are a prolific source of bioactive compounds, some of which have been developed into essential drugs. The synthesis of these complex natural products (NPs) utilizes nonribosomal peptide synthetases (NRPSs), multidomain megaenzymes that assemble specific peptide products by sequential condensation of amino acids and amino acid-like substances, independent of the ribosome. NRPSs, collaborating polyketide synthase modules, and their associated tailoring enzymes involved in product maturation represent promising targets for NP structure diversification and the generation of small molecule unnatural products (uNPs) with improved or novel bioactivities. Indeed, reprogramming of NRPSs and recruiting of novel tailoring enzymes is the strategy by which nature evolves NRP products. The recent years have witnessed a rapid development in the discovery and identification of novel NRPs and PK-NRPs, and significant advances have also been made towards the engineering of fungal NRP assembly lines to generate uNP peptides. However, the intrinsic complexities of fungal NRP and PK-NRP biosynthesis, and the large size of the NRPSs still present formidable conceptual and technical challenges for the rational and efficient reprogramming of these pathways. This review examines key examples for the successful (and for some less-successful) re-engineering of fungal NRPS assembly lines to inform future efforts towards generating novel, biologically active peptides and PK-NRPs.
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Affiliation(s)
- Liwen Zhang
- Biotechnology Research Institute, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, P. R. China.
| | - Chen Wang
- Biotechnology Research Institute, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, P. R. China.
| | - Kang Chen
- Biotechnology Research Institute, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, P. R. China.
| | - Weimao Zhong
- Southwest Center for Natural Products Research, University of Arizona, 250 E. Valencia Rd., Tucson, AZ 85706, USA
| | - Yuquan Xu
- Biotechnology Research Institute, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, P. R. China.
| | - István Molnár
- Southwest Center for Natural Products Research, University of Arizona, 250 E. Valencia Rd., Tucson, AZ 85706, USA.,VTT Technical Research Centre of Finland, P.O. Box 1000, FI-02044 VTT, Espoo, Finland.
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11
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Wenski SL, Thiengmag S, Helfrich EJ. Complex peptide natural products: Biosynthetic principles, challenges and opportunities for pathway engineering. Synth Syst Biotechnol 2022; 7:631-647. [PMID: 35224231 PMCID: PMC8842026 DOI: 10.1016/j.synbio.2022.01.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/19/2022] [Accepted: 01/20/2022] [Indexed: 01/03/2023] Open
Abstract
Complex peptide natural products exhibit diverse biological functions and a wide range of physico-chemical properties. As a result, many peptides have entered the clinics for various applications. Two main routes for the biosynthesis of complex peptides have evolved in nature: ribosomally synthesized and post-translationally modified peptide (RiPP) biosynthetic pathways and non-ribosomal peptide synthetases (NRPSs). Insights into both bioorthogonal peptide biosynthetic strategies led to the establishment of universal principles for each of the two routes. These universal rules can be leveraged for the targeted identification of novel peptide biosynthetic blueprints in genome sequences and used for the rational engineering of biosynthetic pathways to produce non-natural peptides. In this review, we contrast the key principles of both biosynthetic routes and compare the different biochemical strategies to install the most frequently encountered peptide modifications. In addition, the influence of the fundamentally different biosynthetic principles on past, current and future engineering approaches is illustrated. Despite the different biosynthetic principles of both peptide biosynthetic routes, the arsenal of characterized peptide modifications encountered in RiPP and NRPS systems is largely overlapping. The continuous expansion of the biocatalytic toolbox of peptide modifying enzymes for both routes paves the way towards the production of complex tailor-made peptides and opens up the possibility to produce NRPS-derived peptides using the ribosomal route and vice versa.
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Affiliation(s)
- Sebastian L. Wenski
- Institute for Molecular Bio Science, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
- LOEWE Center for Translational Biodiversity Genomics (TBG), 60325, Frankfurt am Main, Germany
| | - Sirinthra Thiengmag
- Institute for Molecular Bio Science, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
- LOEWE Center for Translational Biodiversity Genomics (TBG), 60325, Frankfurt am Main, Germany
| | - Eric J.N. Helfrich
- Institute for Molecular Bio Science, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
- LOEWE Center for Translational Biodiversity Genomics (TBG), 60325, Frankfurt am Main, Germany
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12
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Soeriyadi AH, Ongley SE, Kehr JC, Pickford R, Dittmann E, Neilan BA. Tailoring Enzyme Stringency Masks the Multispecificity of a Lyngbyatoxin (Indolactam Alkaloid) Nonribosomal Peptide Synthetase. Chembiochem 2021; 23:e202100574. [PMID: 34850512 DOI: 10.1002/cbic.202100574] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 11/30/2021] [Indexed: 11/11/2022]
Abstract
Indolactam alkaloids are activators of protein kinase C (PKC) and are of pharmacological interest for the treatment of pathologies involving PKC dysregulation. The marine cyanobacterial nonribosomal peptide synthetase (NRPS) pathway for lyngbyatoxin biosynthesis, which we previously expressed in E. coli, was studied for its amenability towards the biosynthesis of indolactam variants. Modification of culture conditions for our E. coli heterologous expression host and analysis of pathway products suggested the native lyngbyatoxin pathway NRPS does possess a degree of relaxed specificity. Site-directed mutagenesis of two positions within the adenylation domain (A-domain) substrate-binding pocket was performed, resulting in an alteration of substrate preference between valine, isoleucine, and leucine. We observed relative congruence of in vitro substrate activation by the LtxA NRPS to in vivo product formation. While there was a preference for isoleucine over leucine, the substitution of alternative tailoring domains may unveil the true in vivo effects of the mutations introduced herein.
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Affiliation(s)
- Angela H Soeriyadi
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052, Australia
| | - Sarah E Ongley
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052, Australia.,School of Environmental and Life Sciences, University of Newcastle, Callaghan, 2308, Australia
| | - Jan-Christoph Kehr
- Department of Microbiology, Institute for Biochemistry and Biology, University of Potsdam, Potsdam-Golm, Germany
| | - Russel Pickford
- Bioanalytical Mass Spectrometry Facility, University of New South Wales, Sydney, 2052, Australia
| | - Elke Dittmann
- Department of Microbiology, Institute for Biochemistry and Biology, University of Potsdam, Potsdam-Golm, Germany
| | - Brett A Neilan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052, Australia.,School of Environmental and Life Sciences, University of Newcastle, Callaghan, 2308, Australia
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13
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Gene editing enables rapid engineering of complex antibiotic assembly lines. Nat Commun 2021; 12:6872. [PMID: 34824225 PMCID: PMC8616955 DOI: 10.1038/s41467-021-27139-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 11/02/2021] [Indexed: 11/08/2022] Open
Abstract
Re-engineering biosynthetic assembly lines, including nonribosomal peptide synthetases (NRPS) and related megasynthase enzymes, is a powerful route to new antibiotics and other bioactive natural products that are too complex for chemical synthesis. However, engineering megasynthases is very challenging using current methods. Here, we describe how CRISPR-Cas9 gene editing can be exploited to rapidly engineer one of the most complex megasynthase assembly lines in nature, the 2.0 MDa NRPS enzymes that deliver the lipopeptide antibiotic enduracidin. Gene editing was used to exchange subdomains within the NRPS, altering substrate selectivity, leading to ten new lipopeptide variants in good yields. In contrast, attempts to engineer the same NRPS using a conventional homologous recombination-mediated gene knockout and complementation approach resulted in only traces of new enduracidin variants. In addition to exchanging subdomains within the enduracidin NRPS, subdomains from a range of NRPS enzymes of diverse bacterial origins were also successfully utilized.
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14
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Iacovelli R, Bovenberg RAL, Driessen AJM. Nonribosomal peptide synthetases and their biotechnological potential in Penicillium rubens. J Ind Microbiol Biotechnol 2021; 48:6324005. [PMID: 34279620 PMCID: PMC8788816 DOI: 10.1093/jimb/kuab045] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 07/12/2021] [Indexed: 01/23/2023]
Abstract
Nonribosomal peptide synthetases (NRPS) are large multimodular enzymes that synthesize a diverse variety of peptides. Many of these are currently used as pharmaceuticals, thanks to their activity as antimicrobials (penicillin, vancomycin, daptomycin, echinocandin), immunosuppressant (cyclosporin) and anticancer compounds (bleomycin). Because of their biotechnological potential, NRPSs have been extensively studied in the past decades. In this review, we provide an overview of the main structural and functional features of these enzymes, and we consider the challenges and prospects of engineering NRPSs for the synthesis of novel compounds. Furthermore, we discuss secondary metabolism and NRP synthesis in the filamentous fungus Penicillium rubens and examine its potential for the production of novel and modified β-lactam antibiotics.
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Affiliation(s)
- Riccardo Iacovelli
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Roel A L Bovenberg
- Synthetic Biology and Cell Engineering, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands.,DSM Biotechnology Centre, 2613 AX Delft, The Netherlands
| | - Arnold J M Driessen
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
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15
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Stanišić A, Hüsken A, Stephan P, Niquille DL, Reinstein J, Kries H. Engineered Nonribosomal Peptide Synthetase Shows Opposite Amino Acid Loading and Condensation Specificity. ACS Catal 2021. [DOI: 10.1021/acscatal.1c01270] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Aleksa Stanišić
- Junior Research Group Biosynthetic Design of Natural Products, Leibniz Institute for Natural Product Research and Infection Biology (HKI) e.V., Beutenbergstr. 11a, 07745 Jena, Germany
| | - Annika Hüsken
- Junior Research Group Biosynthetic Design of Natural Products, Leibniz Institute for Natural Product Research and Infection Biology (HKI) e.V., Beutenbergstr. 11a, 07745 Jena, Germany
| | - Philipp Stephan
- Junior Research Group Biosynthetic Design of Natural Products, Leibniz Institute for Natural Product Research and Infection Biology (HKI) e.V., Beutenbergstr. 11a, 07745 Jena, Germany
| | - David L. Niquille
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, 500 Technology Square NE47-140, Cambridge, Massachusetts 02139, United States
| | - Jochen Reinstein
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Hajo Kries
- Junior Research Group Biosynthetic Design of Natural Products, Leibniz Institute for Natural Product Research and Infection Biology (HKI) e.V., Beutenbergstr. 11a, 07745 Jena, Germany
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16
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Niquille DL, Folger IB, Basler S, Hilvert D. Biosynthetic Functionalization of Nonribosomal Peptides. J Am Chem Soc 2021; 143:2736-2740. [PMID: 33570948 DOI: 10.1021/jacs.1c00925] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Nonribosomal peptides (NRPs) are a therapeutically important class of secondary metabolites that are produced by modular synthetases in assembly-line fashion. We previously showed that a single Trp-to-Ser mutation in the initial Phe-loading adenylation domain of tyrocidine synthetase completely switches the specificity toward clickable analogues. Here we report that this minimally invasive strategy enables efficient functionalization of the bioactive NRP on the pathway level. In a reconstituted tyrocidine synthetase, the W227S point mutation permitted selective incorporation of Phe analogues with alkyne, halogen, and benzoyl substituents by the initiation module. The respective W2742S mutation in module 4 similarly permits efficient incorporation of these functionalized substrate analogues at position 4, expanding this strategy to elongation modules. Efficient incorporation of an alkyne handle at position 1 or 4 of tyrocidine A allowed site-selective one-step fluorescent labeling of the corresponding tyrocidine analogues by Cu(I)-catalyzed alkyne-azide cycloaddition. By combining synthetic biology with bioorthogonal chemistry, this approach holds great potential for NRP isolation and molecular target elucidation as well as combinatorial optimization of NRP therapeutics.
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Affiliation(s)
- David L Niquille
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Ines B Folger
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Sophie Basler
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Donald Hilvert
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
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17
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Combinatorial biosynthesis for the generation of new-to-nature peptide antimicrobials. Biochem Soc Trans 2021; 49:203-215. [PMID: 33439248 DOI: 10.1042/bst20200425] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 11/25/2020] [Accepted: 11/27/2020] [Indexed: 12/12/2022]
Abstract
Natural peptide products are a valuable source of important therapeutic agents, including antibiotics, antivirals and crop protection agents. Aided by an increased understanding of structure-activity relationships of these complex molecules and the biosynthetic machineries that produce them, it has become possible to re-engineer complete machineries and biosynthetic pathways to create novel products with improved pharmacological properties or modified structures to combat antimicrobial resistance. In this review, we will address the progress that has been made using non-ribosomally produced peptides and ribosomally synthesized and post-translationally modified peptides as scaffolds for designed biosynthetic pathways or combinatorial synthesis for the creation of novel peptide antimicrobials.
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18
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19
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Kaniusaite M, Kittilä T, Goode RJA, Schittenhelm RB, Cryle MJ. Redesign of Substrate Selection in Glycopeptide Antibiotic Biosynthesis Enables Effective Formation of Alternate Peptide Backbones. ACS Chem Biol 2020; 15:2444-2455. [PMID: 32794694 DOI: 10.1021/acschembio.0c00435] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Nonribosomal peptide synthesis is capable of utilizing a wide range of amino acid residues due to the selectivity of adenylation (A)-domains. Changing the selectivity of A-domains could lead to new bioactive nonribosomal peptides, although remodeling efforts of A-domains are often unsuccessful. Here, we explored and successfully reengineered the specificity of the module 3 A-domain from glycopeptide antibiotic biosynthesis to change the incorporation of 3,5-dihydroxyphenylglycine into 4-hydroxyphenylglycine. These engineered A-domains remain selective in a functioning peptide assembly line even under substrate competition conditions and indicate a possible application of these for the future redesign of GPA biosynthesis.
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Affiliation(s)
- Milda Kaniusaite
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
- EMBL Australia, Monash University, Clayton, Victoria 3800, Australia
| | - Tiia Kittilä
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Robert J. A. Goode
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
- Monash Proteomics and Metabolomics Facility, Monash University, Clayton, Victoria 3800, Australia
| | - Ralf B. Schittenhelm
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
- Monash Proteomics and Metabolomics Facility, Monash University, Clayton, Victoria 3800, Australia
| | - Max J. Cryle
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
- EMBL Australia, Monash University, Clayton, Victoria 3800, Australia
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20
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Kaniusaite M, Goode RJA, Tailhades J, Schittenhelm RB, Cryle MJ. Exploring modular reengineering strategies to redesign the teicoplanin non-ribosomal peptide synthetase. Chem Sci 2020; 11:9443-9458. [PMID: 34094211 PMCID: PMC8162109 DOI: 10.1039/d0sc03483e] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 08/22/2020] [Indexed: 12/24/2022] Open
Abstract
Non-ribosomal peptide synthesis is an important biosynthesis pathway in secondary metabolism. In this study we have investigated modularisation and redesign strategies for the glycopeptide antibiotic teicoplanin. Using the relocation or exchange of domains within the NRPS modules, we have identified how to initiate peptide biosynthesis and explored the requirements for the functional reengineering of both the condensation/adenylation domain and epimerisation/condensation domain interfaces. We have also demonstrated strategies that ensure communication between isolated NRPS modules, leading to new peptide assembly pathways. This provides important insights into NRPS reengineering of glycopeptide antibiotic biosynthesis and has broad implications for the redesign of other NRPS systems.
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Affiliation(s)
- Milda Kaniusaite
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University Clayton Victoria 3800 Australia
- EMBL Australia, Monash University Clayton Victoria 3800 Australia
- The Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Monash University Clayton Victoria 3800 Australia
| | - Robert J A Goode
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University Clayton Victoria 3800 Australia
- Monash Proteomics and Metabolomics Facility, Monash University Clayton Victoria 3800 Australia
| | - Julien Tailhades
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University Clayton Victoria 3800 Australia
- EMBL Australia, Monash University Clayton Victoria 3800 Australia
- The Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Monash University Clayton Victoria 3800 Australia
| | - Ralf B Schittenhelm
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University Clayton Victoria 3800 Australia
- Monash Proteomics and Metabolomics Facility, Monash University Clayton Victoria 3800 Australia
| | - Max J Cryle
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University Clayton Victoria 3800 Australia
- EMBL Australia, Monash University Clayton Victoria 3800 Australia
- The Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Monash University Clayton Victoria 3800 Australia
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21
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Zhang JJ, Moore BS. Site-Directed Mutagenesis of Large Biosynthetic Gene Clusters via Oligonucleotide Recombineering and CRISPR/Cas9 Targeting. ACS Synth Biol 2020; 9:1917-1922. [PMID: 32584552 DOI: 10.1021/acssynbio.0c00265] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Genetic engineering of natural product biosynthetic gene clusters represents an attractive approach to access new and complex bioactive small molecules. However, due to the large number and size of some genes involved in specialized metabolism, notably those encoding modular polyketide synthase and nonribosomal peptide synthetase megaproteins, it remains difficult to introduce precise genetic mutations to probe domain activity or alter chemical product formation. Here, we report the development and validation of a robust method combining oligonucleotide recombineering and CRISPR/Cas9 targeting for rapid site-directed mutagenesis of cloned pathways, which can be directly transferred to a heterologous host for expression. We rapidly generated 12 point mutations and identified several important determinants of successful mutagenesis, including the protospacer/PAM sequence and presence of regions of local homology. Our approach may be broadly applicable for researchers interested in probing natural product biosynthesis or performing pathway engineering.
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Affiliation(s)
- Jia Jia Zhang
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California 92037, United States
| | - Bradley S. Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California 92037, United States
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, California 92037, United States
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22
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Yuan Y, Xu QM, Yu SC, Sun HZ, Cheng JS, Yuan YJ. Control of the polymyxin analog ratio by domain swapping in the nonribosomal peptide synthetase of Paenibacillus polymyxa. J Ind Microbiol Biotechnol 2020; 47:551-562. [PMID: 32495197 DOI: 10.1007/s10295-020-02275-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Accepted: 04/15/2020] [Indexed: 11/26/2022]
Abstract
Polymyxins are used as the last-line therapy against multidrug-resistant bacteria. However, their further clinical development needs to solve problems related to the presence of heterogeneous analogs, but there is still no platform or methods that can regulate the biosynthesis of polymyxin analogs. In this study, we present an approach to swap domains in the polymyxin gene cluster to regulate the production of different analogs. Following adenylation domain swapping, the proportion of polymyxin B1 increased from 41.36 to 52.90%, while that of B1-1 decreased from 18.25 to 3.09%. The ratio of polymyxin B1 and B3 following starter condensation domain swapping changed from 41.36 and 16.99 to 55.03 and 6.39%, respectively. The two domain-swapping strains produced 62.96% of polymyxin B1, 6.70% of B3 and 3.32% of B1-1. This study also revealed the presence of overflow fluxes between acetoin, 2,3-butanediol and polymyxin. To our best knowledge, this is the first report of engineering the polymyxin synthetase gene cluster in situ to regulate the relative proportions of polymyxin analogs. This research paves a way for regulating lipopeptide analogs and will facilitate the development of novel lipopeptide derivatives.
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Affiliation(s)
- Ye Yuan
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, People's Republic of China
- SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, People's Republic of China
| | - Qiu-Man Xu
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Science, Tianjin Normal University, Binshuixi Road 393, Xiqing District, Tianjin, 300387, People's Republic of China.
| | - Si-Cen Yu
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, People's Republic of China
| | - Hui-Zhong Sun
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, People's Republic of China
- SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, People's Republic of China
| | - Jing-Sheng Cheng
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, People's Republic of China.
- SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, People's Republic of China.
| | - Ying-Jin Yuan
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, People's Republic of China
- SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, People's Republic of China
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23
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Kegler C, Bode HB. Artificial Splitting of a Non-Ribosomal Peptide Synthetase by Inserting Natural Docking Domains. Angew Chem Int Ed Engl 2020; 59:13463-13467. [PMID: 32329545 PMCID: PMC7496407 DOI: 10.1002/anie.201915989] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 03/18/2020] [Indexed: 12/13/2022]
Abstract
The interaction in multisubunit non‐ribosomal peptide synthetases (NRPSs) is mediated by docking domains that ensure the correct subunit‐to‐subunit interaction. We introduced natural docking domains into the three‐module xefoampeptide synthetase (XfpS) to create two to three artificial NRPS XfpS subunits. The enzymatic performance of the split biosynthesis was measured by absolute quantification of the products by HPLC‐ESI‐MS. The connecting role of the docking domains was probed by deleting integral parts of them. The peptide production data was compared to soluble protein amounts of the NRPS using SDS‐PAGE. Reduced peptide synthesis was not a result of reduced soluble NRPS concentration but a consequence of the deletion of vital docking domain parts. Splitting the xefoampeptide biosynthesis polypeptide by introducing docking domains was feasible and resulted in higher amounts of product in one of the two tested split‐module cases compared to the full‐length wild‐type enzyme.
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Affiliation(s)
- Carsten Kegler
- Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt, Max-von-Laue-Straße 9, 60438, Frankfurt am Main, Germany
| | - Helge B Bode
- Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt, Max-von-Laue-Straße 9, 60438, Frankfurt am Main, Germany.,Buchmann Institute for Molecular Life Sciences (BMLS), Goethe-Universität Frankfurt, 60438, Frankfurt, Germany.,Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, 60325, Frankfurt, Germany
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24
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Kegler C, Bode HB. Artificial Splitting of a Non‐Ribosomal Peptide Synthetase by Inserting Natural Docking Domains. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201915989] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Carsten Kegler
- Molekulare Biotechnologie, Fachbereich Biowissenschaften Goethe Universität Frankfurt Max-von-Laue-Straße 9 60438 Frankfurt am Main Germany
| | - Helge B. Bode
- Molekulare Biotechnologie, Fachbereich Biowissenschaften Goethe Universität Frankfurt Max-von-Laue-Straße 9 60438 Frankfurt am Main Germany
- Buchmann Institute for Molecular Life Sciences (BMLS) Goethe-Universität Frankfurt 60438 Frankfurt Germany
- Senckenberg Gesellschaft für Naturforschung Senckenberganlage 25 60325 Frankfurt Germany
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25
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Hwang S, Lee N, Cho S, Palsson B, Cho BK. Repurposing Modular Polyketide Synthases and Non-ribosomal Peptide Synthetases for Novel Chemical Biosynthesis. Front Mol Biosci 2020; 7:87. [PMID: 32500080 PMCID: PMC7242659 DOI: 10.3389/fmolb.2020.00087] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 04/16/2020] [Indexed: 12/16/2022] Open
Abstract
In nature, various enzymes govern diverse biochemical reactions through their specific three-dimensional structures, which have been harnessed to produce many useful bioactive compounds including clinical agents and commodity chemicals. Polyketide synthases (PKSs) and non-ribosomal peptide synthetases (NRPSs) are particularly unique multifunctional enzymes that display modular organization. Individual modules incorporate their own specific substrates and collaborate to assemble complex polyketides or non-ribosomal polypeptides in a linear fashion. Due to the modular properties of PKSs and NRPSs, they have been attractive rational engineering targets for novel chemical production through the predictable modification of each moiety of the complex chemical through engineering of the cognate module. Thus, individual reactions of each module could be separated as a retro-biosynthetic biopart and repurposed to new biosynthetic pathways for the production of biofuels or commodity chemicals. Despite these potentials, repurposing attempts have often failed owing to impaired catalytic activity or the production of unintended products due to incompatible protein–protein interactions between the modules and structural perturbation of the enzyme. Recent advances in the structural, computational, and synthetic tools provide more opportunities for successful repurposing. In this review, we focused on the representative strategies and examples for the repurposing of modular PKSs and NRPSs, along with their advantages and current limitations. Thereafter, synthetic biology tools and perspectives were suggested for potential further advancement, including the rational and large-scale high-throughput approaches. Ultimately, the potential diverse reactions from modular PKSs and NRPSs would be leveraged to expand the reservoir of useful chemicals.
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Affiliation(s)
- Soonkyu Hwang
- Systems and Synthetic Biology Laboratory, Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Namil Lee
- Systems and Synthetic Biology Laboratory, Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Suhyung Cho
- Systems and Synthetic Biology Laboratory, Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Bernhard Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States.,Department of Pediatrics, University of California, San Diego, La Jolla, CA, United States.,The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Byung-Kwan Cho
- Systems and Synthetic Biology Laboratory, Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.,Intelligent Synthetic Biology Center, Daejeon, South Korea
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26
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Reimer JM, Eivaskhani M, Harb I, Guarné A, Weigt M, Schmeing TM. Structures of a dimodular nonribosomal peptide synthetase reveal conformational flexibility. Science 2020; 366:366/6466/eaaw4388. [PMID: 31699907 DOI: 10.1126/science.aaw4388] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 06/04/2019] [Accepted: 10/10/2019] [Indexed: 01/01/2023]
Abstract
Nonribosomal peptide synthetases (NRPSs) are biosynthetic enzymes that synthesize natural product therapeutics using a modular synthetic logic, whereby each module adds one aminoacyl substrate to the nascent peptide. We have determined five x-ray crystal structures of large constructs of the NRPS linear gramicidin synthetase, including a structure of a full core dimodule in conformations organized for the condensation reaction and intermodular peptidyl substrate delivery. The structures reveal differences in the relative positions of adjacent modules, which are not strictly coupled to the catalytic cycle and are consistent with small-angle x-ray scattering data. The structures and covariation analysis of homologs allowed us to create mutants that improve the yield of a peptide from a module-swapped dimodular NRPS.
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Affiliation(s)
- Janice M Reimer
- Department of Biochemistry and Center de Recherche en Biologie Structurale, McGill University, Montréal, QC H3G 0B1, Canada
| | - Maximilian Eivaskhani
- Department of Biochemistry and Center de Recherche en Biologie Structurale, McGill University, Montréal, QC H3G 0B1, Canada
| | - Ingrid Harb
- Department of Biochemistry and Center de Recherche en Biologie Structurale, McGill University, Montréal, QC H3G 0B1, Canada
| | - Alba Guarné
- Department of Biochemistry and Center de Recherche en Biologie Structurale, McGill University, Montréal, QC H3G 0B1, Canada
| | - Martin Weigt
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, F-75005 Paris, France
| | - T Martin Schmeing
- Department of Biochemistry and Center de Recherche en Biologie Structurale, McGill University, Montréal, QC H3G 0B1, Canada.
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27
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Ishikawa F, Nohara M, Nakamura S, Nakanishi I, Tanabe G. Precise Probing of Residue Roles by NRPS Code Swapping: Mutation, Enzymatic Characterization, Modeling, and Substrate Promiscuity of Aryl Acid Adenylation Domains. Biochemistry 2020; 59:351-363. [PMID: 31894971 DOI: 10.1021/acs.biochem.9b00748] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Aryl acids are most commonly found in iron-scavenging siderophores but are not limited to them. The nonribosomal peptide synthetase (NRPS) codes of aryl acids remain poorly elucidated relative to those of amino acids. Here, we defined more precisely the role of active-site residues in aryl acid adenylation domains (A-domains) by gradually grafting the NRPS codes used for salicylic acid (Sal) into an archetypal aryl acid A-domain, EntE [specific for the substrate 2,3-dihydroxybenzoic acid (DHB)]. Enzyme kinetics and modeling studies of these EntE variants demonstrated that the NRPS code residues at positions 236, 240, and 339 collectively regulate the substrate specificity toward DHB and Sal. Furthermore, the EntE variants exhibited the ability to activate the non-native aryl acids 3-hydroxybenzoic acid, 3-aminobenzoic acid, 3-fluorobenzoic acid, and 3-chlorobenzoic acid. These studies enhance our knowledge of the NRPS codes of aryl acids and could be exploited to reprogram aryl acid A-domains for non-native aryl acids.
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Affiliation(s)
- Fumihiro Ishikawa
- Laboratory of Pharmaceutical Organic Chemistry, Faculty of Pharmacy , Kindai University , 3-4-1 Kowakae , Higashi-Osaka , Osaka 577-8502 , Japan
| | - Maya Nohara
- Laboratory of Pharmaceutical Organic Chemistry, Faculty of Pharmacy , Kindai University , 3-4-1 Kowakae , Higashi-Osaka , Osaka 577-8502 , Japan
| | - Shinya Nakamura
- Laboratory of Computational Drug Design and Discovery, Faculty of Pharmacy , Kindai University , 3-4-1 Kowakae , Higashi-Osaka , Osaka 577-8502 , Japan
| | - Isao Nakanishi
- Laboratory of Computational Drug Design and Discovery, Faculty of Pharmacy , Kindai University , 3-4-1 Kowakae , Higashi-Osaka , Osaka 577-8502 , Japan
| | - Genzoh Tanabe
- Laboratory of Pharmaceutical Organic Chemistry, Faculty of Pharmacy , Kindai University , 3-4-1 Kowakae , Higashi-Osaka , Osaka 577-8502 , Japan
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Lundy TA, Mori S, Garneau-Tsodikova S. Lessons learned in engineering interrupted adenylation domains when attempting to create trifunctional enzymes from three independent monofunctional ones. RSC Adv 2020; 10:34299-34307. [PMID: 35519055 PMCID: PMC9056781 DOI: 10.1039/d0ra05490a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 09/07/2020] [Indexed: 11/21/2022] Open
Abstract
Interrupted adenylation (A) domains are fascinating examples of multifunctional enzymes. They are found in nonribosomal peptide synthetases (NRPSs), which biosynthesize nonribosomal peptides (NRPs), a major class of medically relevant natural products (NPs). Interrupted A domains contain the catalytic portion of another domain within them, typically a methylation (M) domain, thus combining both adenylation and methylation capabilities. In recent years, interrupted A domains have demonstrated tremendous enzyme engineering potential as they are able to be constructed artificially in a laboratory setting by combining the A and M domains of two separate NRPS proteins. A recent discovery and characterization of a naturally occurring interrupted A domain that harbored two M domains back-to-back, a trifunctional protein, showed the ingenuity of Nature to both N- and O-methylate amino acids, the building blocks of NRPs. Since we have shown that a single M domain could be added to an uninterrupted A domain to create an artificial interrupted A domain, we set out to investigate if: (i) an A domain could be engineered to contain two back-to-back M domains and (ii) the added M domains would have to reflect the pattern in Nature, a side chain (O-) methylating M domain (Ms) followed by a backbone (N-) methylating M domain (Mb), or if the order of the M domains could be reversed. To address these questions, we set out to create our own AMsMbA and AMbMsA engineered interrupted A domains. We evaluated these engineered proteins connected (in cis) and/or disconnected (in trans) from the native thiolation (T) domain, through a series of radiometric assays, high performance liquid chromatography (HPLC), and mass spectrometry (MS) for adenylation, loading, and methylation ability. We found that although adenylation activity was preserved in both versions (AMsMbA and AMbMsA), addition of the M domains, in natural and unnatural order, did not result in the desired added methylation capability. This study offers valuable insights into the limits of constructing engineered interrupted A domains as potential tools for modifications of NRPs. Interrupted adenylation (A) domains are fascinating examples of multifunctional enzymes with high potential for engineering. Here, limits were established in engineering trifunctional interrupted A domains.![]()
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Affiliation(s)
- Taylor A. Lundy
- Department of Pharmaceutical Sciences
- University of Kentucky
- College of Pharmacy
- Lexington
- USA
| | - Shogo Mori
- Department of Pharmaceutical Sciences
- University of Kentucky
- College of Pharmacy
- Lexington
- USA
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29
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Steiniger C, Hoffmann S, Süssmuth RD. Probing Exchange Units for Combining Iterative and Linear Fungal Nonribosomal Peptide Synthetases. Cell Chem Biol 2019; 26:1526-1534.e2. [DOI: 10.1016/j.chembiol.2019.08.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 07/08/2019] [Accepted: 08/09/2019] [Indexed: 11/30/2022]
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Pass-back chain extension expands multimodular assembly line biosynthesis. Nat Chem Biol 2019; 16:42-49. [PMID: 31636431 PMCID: PMC6917876 DOI: 10.1038/s41589-019-0385-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 09/06/2019] [Indexed: 11/26/2022]
Abstract
Modular nonribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) enzymatic assembly lines are large and dynamic protein machines that generally effect a linear sequence of catalytic cycles. Here we report the heterologous reconstitution and comprehensive characterization of two hybrid NRPS-PKS assembly lines that defy many standard rules of assembly line biosynthesis to generate a large combinatorial library of cyclic lipodepsipeptide protease inhibitors called thalassospiramides. We generate a series of precise domain-inactivating mutations in thalassospiramide assembly lines and present evidence for an unprecedented biosynthetic model that invokes inter-module substrate activation and tailoring, module skipping, and pass-back chain extension, whereby the ability to pass the growing chain back to a preceding module is flexible and substrate-driven. Expanding bidirectional inter-module domain interactions could represent a viable mechanism for generating chemical diversity without increasing the size of biosynthetic assembly lines and challenges our understanding of the potential elasticity of multi-modular megaenzymes.
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31
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Throckmorton K, Vinnik V, Chowdhury R, Cook T, Chevrette MG, Maranas C, Pfleger B, Thomas MG. Directed Evolution Reveals the Functional Sequence Space of an Adenylation Domain Specificity Code. ACS Chem Biol 2019; 14:2044-2054. [PMID: 31430120 DOI: 10.1021/acschembio.9b00532] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Nonribosomal peptides are important natural products biosynthesized by nonribosomal peptide synthetases (NRPSs). Adenylation (A) domains of NRPSs are highly specific for the substrate they recognize. This recognition is determined by 10 residues in the substrate-binding pocket, termed the specificity code. This finding led to the proposal that nonribosomal peptides could be altered by specificity code swapping. Unfortunately, this approach has proven, with few exceptions, to be unproductive; changing the specificity code typically results in broadened specificity or poor function. To enhance our understanding of A domain substrate selectivity, we carried out a detailed analysis of the specificity code from the A domain of EntF, an NRPS involved in enterobactin biosynthesis in Escherichia coli. Using directed evolution and a genetic selection, we determined which sites in the code have strict residue requirements and which are tolerant of variation. We showed that the EntF A domain, and other l-Ser-specific A domains, have a functional sequence space for l-Ser recognition, rather than a single code. This functional space is more expansive than the aggregate of all characterized l-Ser-specific A domains: we identified 152 new l-Ser specificity codes. Together, our data provide essential insights into how to overcome the barriers that prevent rational changes to A domain specificity.
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Affiliation(s)
- Kurt Throckmorton
- Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Vladimir Vinnik
- Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Ratul Chowdhury
- Department of Chemical Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Taylor Cook
- Department of Chemical and Biological Engineering, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Marc G. Chevrette
- Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
- Department of Genetics, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Costas Maranas
- Department of Chemical Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Brian Pfleger
- Department of Chemical and Biological Engineering, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Michael George Thomas
- Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
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32
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Brown AS, Calcott MJ, Owen JG, Ackerley DF. Structural, functional and evolutionary perspectives on effective re-engineering of non-ribosomal peptide synthetase assembly lines. Nat Prod Rep 2019; 35:1210-1228. [PMID: 30069573 DOI: 10.1039/c8np00036k] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Covering: up to May 2018 Non-ribosomal peptide synthetases (NRPSs) are mega-enzymes that form modular templates to assemble specific peptide products, independent of the ribosome. The autonomous nature of the modules in the template offers prospects for re-engineering NRPS enzymes to generate modified peptide products. Although this has clearly been a primary mechanism of natural product diversification throughout evolution, equivalent strategies have proven challenging to implement in the laboratory. In this review we examine key examples of successful and less-successful re-engineering of NRPS templates to generate novel peptides, with the aim of extracting practical guidelines to inform future efforts. We emphasise the importance of maintaining effective protein-protein interactions in recombinant NRPS templates, and identify strengths and limitations of diverse strategies for achieving different engineering outcomes.
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Affiliation(s)
- Alistair S Brown
- School of Biological Sciences, Victoria University of Wellington, New Zealand.
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33
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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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34
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Alanjary M, Cano-Prieto C, Gross H, Medema MH. Computer-aided re-engineering of nonribosomal peptide and polyketide biosynthetic assembly lines. Nat Prod Rep 2019; 36:1249-1261. [PMID: 31259995 DOI: 10.1039/c9np00021f] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Covering: 2014 to 2019Nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs) have been the subject of engineering efforts for multiple decades. Their modular assembly line architecture potentially allows unlocking vast chemical space for biosynthesis. However, attempts thus far are often met with mixed success, due to limited molecular compatibility of the parts used for engineering. Now, new engineering strategies, increases in genomic data, and improved computational tools provide more opportunities for major progress. In this review we highlight some of the challenges and progressive strategies for the re-design of NRPSs & type I PKSs and survey useful computational tools and approaches to attain the ultimate goal of semi-automated and design-based engineering of novel peptide and polyketide products.
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Affiliation(s)
- Mohammad Alanjary
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands.
| | - Carolina Cano-Prieto
- Department of Pharmaceutical Biology, Pharmaceutical Institute, Eberhard Karls Universität Tübingen, Tübingen, Germany.
| | - Harald Gross
- Department of Pharmaceutical Biology, Pharmaceutical Institute, Eberhard Karls Universität Tübingen, Tübingen, Germany.
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands.
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35
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Morgan GL, Kretsch AM, Santa Maria KC, Weeks SJ, Li B. Specificity of Nonribosomal Peptide Synthetases in the Biosynthesis of the Pseudomonas virulence factor. Biochemistry 2019; 58:5249-5254. [PMID: 31243997 DOI: 10.1021/acs.biochem.9b00360] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The Pseudomonas virulence factor (pvf) biosynthetic operon has been implicated in bacterial virulence and signaling. We identified 308 bacterial strains containing pvf homologues that likely produce signaling molecules with distinct structures and biological activities. Several homologues of the nonribosomal peptide synthetase (NRPS), PvfC, were biochemically characterized and shown to activate l-Val or l-Leu. The amino acid selectivity of PvfC and its homologues likely direct pvf signaling activity. We explored the natural diversity of the active site residues present in 92% of the adenylation domains of PvfC homologues and identified key residues for substrate selection and catalysis. Sequence similarity network (SSN) analysis revealed grouping of PvfC homologues that harbor the same active site residues and activate the same amino acids. Our work identified PvfC as a gatekeeper for the structure and bioactivity of the pvf-produced signaling molecules. The combination of active site residue identification and SSN analysis can improve the prediction of aliphatic amino acid substrates for NRPS adenylation domains.
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Affiliation(s)
- Gina L Morgan
- Department of Chemistry , The University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Ashley M Kretsch
- Department of Chemistry , The University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Kevin C Santa Maria
- Department of Chemistry , The University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Savannah J Weeks
- Department of Chemistry , The University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Bo Li
- Department of Chemistry , The University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
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36
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Modification and de novo design of non-ribosomal peptide synthetases using specific assembly points within condensation domains. Nat Chem 2019; 11:653-661. [PMID: 31182822 DOI: 10.1038/s41557-019-0276-z] [Citation(s) in RCA: 107] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Accepted: 04/26/2019] [Indexed: 11/09/2022]
Abstract
Non-ribosomal peptide synthetases (NRPSs) are giant enzyme machines that activate amino acids in an assembly line fashion. As NRPSs are not restricted to the incorporation of the 20 proteinogenic amino acids, their efficient manipulation would enable microbial production of a diverse range of peptides; however, the structural requirements for reprogramming NRPSs to facilitate the production of new peptides are not clear. Here we describe a new fusion point inside the condensation domains of NRPSs that results in the development of the exchange unit condensation domain (XUC) concept, which enables the efficient production of peptides, even containing non-natural amino acids, in yields up to 280 mg l-1. This allows the generation of more specific NRPSs, reducing the number of unwanted peptide derivatives, but also the generation of peptide libraries. The XUC might therefore be suitable for the future optimization of peptide production and the identification of bioactive peptide derivatives for pharmaceutical and other applications.
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37
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Ishikawa F, Miyanaga A, Kitayama H, Nakamura S, Nakanishi I, Kudo F, Eguchi T, Tanabe G. An Engineered Aryl Acid Adenylation Domain with an Enlarged Substrate Binding Pocket. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201900318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Fumihiro Ishikawa
- Faculty of PharmacyKindai University 3-4-1 Kowakae, Higashi-Osaka Osaka 577- 8502 Japan
| | - Akimasa Miyanaga
- Department of ChemistryTokyo Institute of Technology 2-12-1 O-okayama, Meguro-ku Tokyo 152-8551 Japan
| | - Hinano Kitayama
- Faculty of PharmacyKindai University 3-4-1 Kowakae, Higashi-Osaka Osaka 577- 8502 Japan
| | - Shinya Nakamura
- Faculty of PharmacyKindai University 3-4-1 Kowakae, Higashi-Osaka Osaka 577- 8502 Japan
| | - Isao Nakanishi
- Faculty of PharmacyKindai University 3-4-1 Kowakae, Higashi-Osaka Osaka 577- 8502 Japan
| | - Fumitaka Kudo
- Department of ChemistryTokyo Institute of Technology 2-12-1 O-okayama, Meguro-ku Tokyo 152-8551 Japan
| | - Tadashi Eguchi
- Department of ChemistryTokyo Institute of Technology 2-12-1 O-okayama, Meguro-ku Tokyo 152-8551 Japan
| | - Genzoh Tanabe
- Faculty of PharmacyKindai University 3-4-1 Kowakae, Higashi-Osaka Osaka 577- 8502 Japan
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38
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Ishikawa F, Miyanaga A, Kitayama H, Nakamura S, Nakanishi I, Kudo F, Eguchi T, Tanabe G. An Engineered Aryl Acid Adenylation Domain with an Enlarged Substrate Binding Pocket. Angew Chem Int Ed Engl 2019; 58:6906-6910. [PMID: 30945421 DOI: 10.1002/anie.201900318] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 03/04/2019] [Indexed: 12/27/2022]
Abstract
Adenylation (A) domains act as the gatekeepers of non-ribosomal peptide synthetases (NRPSs), ensuring the activation and thioesterification of the correct amino acid/aryl acid building blocks. Aryl acid building blocks are most commonly observed in iron-chelating siderophores, but are not limited to them. Very little is known about the reprogramming of aryl acid A-domains. We show that a single asparagine-to-glycine mutation in an aryl acid A-domain leads to an enzyme that tolerates a wide range of non-native aryl acids. The engineered catalyst is capable of activating non-native aryl acids functionalized with nitro, cyano, bromo, and iodo groups, even though no enzymatic activity of wild-type enzyme was observed toward these substrates. Co-crystal structures with non-hydrolysable aryl-AMP analogues revealed the origins of this expansion of substrate promiscuity, highlighting an enlargement of the substrate binding pocket of the enzyme. Our findings may be exploited to produce diversified aryl acid containing natural products and serve as a template for further directed evolution in combinatorial biosynthesis.
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Affiliation(s)
- Fumihiro Ishikawa
- Faculty of Pharmacy, Kindai University, 3-4-1 Kowakae, Higashi-Osaka, Osaka 577-, 8502, Japan
| | - Akimasa Miyanaga
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo, 152-8551, Japan
| | - Hinano Kitayama
- Faculty of Pharmacy, Kindai University, 3-4-1 Kowakae, Higashi-Osaka, Osaka 577-, 8502, Japan
| | - Shinya Nakamura
- Faculty of Pharmacy, Kindai University, 3-4-1 Kowakae, Higashi-Osaka, Osaka 577-, 8502, Japan
| | - Isao Nakanishi
- Faculty of Pharmacy, Kindai University, 3-4-1 Kowakae, Higashi-Osaka, Osaka 577-, 8502, Japan
| | - Fumitaka Kudo
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo, 152-8551, Japan
| | - Tadashi Eguchi
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo, 152-8551, Japan
| | - Genzoh Tanabe
- Faculty of Pharmacy, Kindai University, 3-4-1 Kowakae, Higashi-Osaka, Osaka 577-, 8502, Japan
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39
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Lundy TA, Mori S, Garneau-Tsodikova S. Probing the limits of interrupted adenylation domains by engineering a trifunctional enzyme capable of adenylation, N-, and S-methylation. Org Biomol Chem 2019; 17:1169-1175. [PMID: 30644493 DOI: 10.1039/c8ob02996b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The adenylation (A) domains found in nonribosomal peptide synthetases (NRPSs) exhibit tremendous plasticity. Some A domains have been shown to display the ability to contain within them the catalytic portion of an auxiliary domain, most commonly that of a methyltransferase (M) enzyme. This unique feature of A domains interrupted by M domains allows them to possess bifunctionality, where they can both adenylate and methylate an amino acid substrate. Additionally, these types of inserted M domains are able to selectively carry out either backbone or side chain methylation of amino acids. Interruptions with M domains are naturally found to occur either between the a2-a3 or the a8-a9 of the ten conserved motifs of A domains. Herein, we set out to answer the following question: Can one A domain support two different M domain interruptions occurring in two different locations (a2-a3 and a8-a9) of the A domain and possess the ability to adenylate an amino acid and methylate it on both its side chain and backbone? To answer this question we added a backbone methylating M3S domain from TioS(A3aM3SA3b) between the a8-a9 region of a mono-interrupted A domain, TioN(AaMNAb), that already contained a side chain methylating MN domain between its a2-a3 region. We evaluated the di-interrupted A domain TioN(AMNAM3SA) with a series of radiometric and mass spectrometry assays and found that this engineered enzyme was indeed capable of all three activities. These findings show that production of an active trifunctional di-interrupted A domain is possible and represents an exciting new avenue for future nonribosomal peptide (NRP) derivatization.
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Affiliation(s)
- Taylor A Lundy
- University of Kentucky, Department of Pharmaceutical Sciences, College of Pharmacy, Lexington, KY 40536-0596, USA.
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40
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Stanišić A, Kries H. Adenylation Domains in Nonribosomal Peptide Engineering. Chembiochem 2019; 20:1347-1356. [DOI: 10.1002/cbic.201800750] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Indexed: 11/10/2022]
Affiliation(s)
- Aleksa Stanišić
- Independent Junior Research GroupBiosynthetic Design of Natural ProductsLeibniz Institute for Natural Product Research and Infection BiologyHans Knöll Institute (HKI Jena) Beutenbergstrasse 11a 07745 Jena Germany
| | - Hajo Kries
- Independent Junior Research GroupBiosynthetic Design of Natural ProductsLeibniz Institute for Natural Product Research and Infection BiologyHans Knöll Institute (HKI Jena) Beutenbergstrasse 11a 07745 Jena Germany
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41
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Structural basis of the nonribosomal codes for nonproteinogenic amino acid selective adenylation enzymes in the biosynthesis of natural products. ACTA ACUST UNITED AC 2019; 46:515-536. [DOI: 10.1007/s10295-018-2084-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 09/25/2018] [Indexed: 01/09/2023]
Abstract
Abstract
Nonproteinogenic amino acids are the unique building blocks of nonribosomal peptides (NRPs) and hybrid nonribosomal peptide–polyketides (NRP–PKs) and contribute to their diversity of chemical structures and biological activities. In the biosynthesis of NRPs and NRP–PKs, adenylation enzymes select and activate an amino acid substrate as an aminoacyl adenylate, which reacts with the thiol of the holo form of the carrier protein to afford an aminoacyl thioester as the electrophile for the condensation reaction. Therefore, the substrate specificity of adenylation enzymes is a key determinant of the structure of NRPs and NRP–PKs. Here, we focus on nonproteinogenic amino acid selective adenylation enzymes, because understanding their unique selection mechanisms will lead to accurate functional predictions and protein engineering toward the rational biosynthesis of designed molecules containing amino acids. Based on recent progress in the structural analysis of adenylation enzymes, we discuss the nonribosomal codes of nonproteinogenic amino acid selective adenylation enzymes.
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42
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Zhu M, Wang L, He J. Chemical Diversification Based on Substrate Promiscuity of a Standalone Adenylation Domain in a Reconstituted NRPS System. ACS Chem Biol 2019; 14:256-265. [PMID: 30673204 DOI: 10.1021/acschembio.8b00938] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
A nonribosomal peptide synthetase (NRPS) assembly line ( sfa) in Streptomyces thioluteus that directs the formation of the diisonitrile chalkophore SF2768 (1) has been characterized by heterologous expression and directed gene knockouts. Herein, differential metabolic analysis of the heterologous expression strain and the original host led to the isolation of an SF2768 analogue (2, a byproduct of sfa) that possesses N-isovaleryl rather than 3-isocyanobutyryl side chains. The proposed biosynthetic logic of sfa and the structural difference between 1 and 2 suggested substrate promiscuity of the adenylate-forming enzyme SfaB. Further substrate scope investigation of SfaB and a successfully reconstituted NRPS system including a four-enzyme cascade enabled incorporation of diverse carboxylic acid building blocks into peptide scaffolds, and 30 unnatural products were thus generated. This structural diversification strategy based on substrate flexibility of the adenylation domain and in vitro reconstitution can be applied to other adenylation-priming pathways, thus providing a supplementary method for diversity-oriented total synthesis. Additionally, the biocatalytic process of the putative lysine δ-hydroxylase SfaE was validated through the derivatization of two key aldehyde intermediates (2a and 2b), thereby expanding the toolkit of enzymatic C-H bond activation.
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Affiliation(s)
- Mengyi Zhu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Lijuan Wang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, RNAM Center for Marine Microbiology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, P. R. China
| | - Jing He
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
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43
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Greule A, Charkoudian LK, Cryle MJ. Studying trans-acting enzymes that target carrier protein-bound amino acids during nonribosomal peptide synthesis. Methods Enzymol 2019; 617:113-154. [PMID: 30784400 DOI: 10.1016/bs.mie.2018.12.008] [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] [Indexed: 03/10/2023]
Abstract
Nonribosomal peptide biosynthesis is a complex enzymatic assembly responsible for producing a great diversity of bioactive peptide natural products. Due to the recurring arrangement of catalytic domains within these machineries, great interest has been shown in reengineering these pathways to produce novel, designer peptide products. However, in order to realize such ambitions, it is first necessary to develop a comprehensive understanding of the selectivity, mechanisms, and structure of these complex enzymes, which in turn requires significant in vitro experiments. Within nonribosomal biosynthesis, some modifications are performed by enzymatic domains that are not linked to the main nonribosomal peptide synthetase but rather act in trans: these systems offer great potential for redesign, but in turn require detailed study. In this chapter, we present an overview of in vitro experiments that can be used to characterize examples of such trans-interacting enzymes from nonribosomal peptide biosynthesis: Cytochrome P450 monooxygenases and flavin-dependent halogenases.
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Affiliation(s)
- Anja Greule
- Department of Biochemistry and Molecular Biology and ARC Centre of Excellence in Advanced Molecular Imaging, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia; EMBL Australia, Monash University, Clayton, VIC, Australia
| | | | - Max J Cryle
- Department of Biochemistry and Molecular Biology and ARC Centre of Excellence in Advanced Molecular Imaging, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia; EMBL Australia, Monash University, Clayton, VIC, Australia.
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44
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Schoppet M, Peschke M, Kirchberg A, Wiebach V, Süssmuth RD, Stegmann E, Cryle MJ. The biosynthetic implications of late-stage condensation domain selectivity during glycopeptide antibiotic biosynthesis. Chem Sci 2019; 10:118-133. [PMID: 30713624 PMCID: PMC6333238 DOI: 10.1039/c8sc03530j] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 10/10/2018] [Indexed: 01/27/2023] Open
Abstract
Non-ribosomal peptide synthesis is a highly important biosynthetic pathway for the formation of many secondary metabolites of medical relevance. Due to the challenges associated with the chemical synthesis of many of the products of these assembly lines, understanding the activity and selectivity of non-ribosomal peptide synthetase (NRPS) machineries is an essential step towards the redesign of such machineries to produce new bioactive peptides. Whilst the selectivity of the adenylation domains responsible for amino acid activation during NRPS synthesis has been widely studied, the selectivity of the essential peptide bond forming domains - known as condensation domains - is not well understood. Here, we present the results of a combination of in vitro and in vivo investigations into the final condensation domain from the NRPS machinery that produces the glycopeptide antibiotics (GPAs). Our results show that this condensation domain is tolerant for a range of peptide substrates and even those with unnatural stereochemistry of the peptide C-terminus, which is in contrast to the widely ascribed role of these domains as a stereochemical gatekeeper during NRPS synthesis. Furthermore, we show that this condensation domain has a significant preference for linear peptide substrates over crosslinked peptides, which indicates that the GPA crosslinking cascade targets the heptapeptide bound to the final module of the NRPS machinery and reinforces the role of the unique GPA X-domain in this process. Finally, we demonstrate that the peptide bond forming activity of this condensation domain is coupled to the rate of amino acid activation performed by the subsequent adenylation domain. This is a significant result with implications for NRPS redesign, as it indicates that the rate of amino acid activation of modified adenylation domains must be maintained to prevent unwanted peptide hydrolysis from the NRPS due to a loss of the productive coupling of amino acid selection and peptide bond formation. Taken together, our results indicate that assessing condensation domain activity is a vital step in not only understanding the biosynthetic logic and timing of NRPS-mediated peptide assembly, but also the rules which redesign efforts must obey in order to successfully produce functional, modified NRPS assembly lines.
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Affiliation(s)
- Melanie Schoppet
- The Monash Biomedicine Discovery Institute , Department of Biochemistry and Molecular Biology , EMBL Australia , Monash University , Clayton , Victoria 3800 , Australia .
- Department of Biomolecular Mechanisms , Max Planck Institute for Medical Research , Jahnstrasse 29, 69120 Heidelberg , Germany
| | - Madeleine Peschke
- Department of Biomolecular Mechanisms , Max Planck Institute for Medical Research , Jahnstrasse 29, 69120 Heidelberg , Germany
| | - Anja Kirchberg
- The Monash Biomedicine Discovery Institute , Department of Biochemistry and Molecular Biology , EMBL Australia , Monash University , Clayton , Victoria 3800 , Australia .
| | - Vincent Wiebach
- Institut für Chemie , Technische Universität Berlin , Strasse des 17. Juni 124 , 10623 Berlin , Germany
| | - Roderich D Süssmuth
- Institut für Chemie , Technische Universität Berlin , Strasse des 17. Juni 124 , 10623 Berlin , Germany
| | - Evi Stegmann
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen , Microbiology/Biotechnology , University of Tübingen , Auf der Morgenstelle 28, 72076 Tübingen , Germany .
- German Centre for Infection Research (DZIF) , Partner Site Tübingen, Tübingen , Germany
| | - Max J Cryle
- The Monash Biomedicine Discovery Institute , Department of Biochemistry and Molecular Biology , EMBL Australia , Monash University , Clayton , Victoria 3800 , Australia .
- Department of Biomolecular Mechanisms , Max Planck Institute for Medical Research , Jahnstrasse 29, 69120 Heidelberg , Germany
- ARC Centre of Excellence in Advanced Molecular Imaging , Monash University , Clayton , Victoria 3800 , Australia
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45
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Guzmán-Chávez F, Zwahlen RD, Bovenberg RAL, Driessen AJM. Engineering of the Filamentous Fungus Penicillium chrysogenum as Cell Factory for Natural Products. Front Microbiol 2018; 9:2768. [PMID: 30524395 PMCID: PMC6262359 DOI: 10.3389/fmicb.2018.02768] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 10/29/2018] [Indexed: 12/14/2022] Open
Abstract
Penicillium chrysogenum (renamed P. rubens) is the most studied member of a family of more than 350 Penicillium species that constitute the genus. Since the discovery of penicillin by Alexander Fleming, this filamentous fungus is used as a commercial β-lactam antibiotic producer. For several decades, P. chrysogenum was subjected to a classical strain improvement (CSI) program to increase penicillin titers. This resulted in a massive increase in the penicillin production capacity, paralleled by the silencing of several other biosynthetic gene clusters (BGCs), causing a reduction in the production of a broad range of BGC encoded natural products (NPs). Several approaches have been used to restore the ability of the penicillin production strains to synthetize the NPs lost during the CSI. Here, we summarize various re-activation mechanisms of BGCs, and how interference with regulation can be used as a strategy to activate or silence BGCs in filamentous fungi. To further emphasize the versatility of P. chrysogenum as a fungal production platform for NPs with potential commercial value, protein engineering of biosynthetic enzymes is discussed as a tool to develop de novo BGC pathways for new NPs.
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Affiliation(s)
- Fernando Guzmán-Chávez
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands.,Synthetic Biology and Cell Engineering, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Reto D Zwahlen
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands.,Synthetic Biology and Cell Engineering, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Roel A L Bovenberg
- Synthetic Biology and Cell Engineering, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands.,DSM Biotechnology Centre, Delft, Netherlands
| | - Arnold J M Driessen
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands.,Synthetic Biology and Cell Engineering, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
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46
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Winn M, Francis D, Micklefield J. De novo Biosynthesis of “Non-Natural” Thaxtomin Phytotoxins. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201801525] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Michael Winn
- School of Chemistry; Manchester Institute of Biotechnology; The University of Manchester; 131 Princess Street Manchester M1 7DN UK
| | - Daniel Francis
- School of Chemistry; Manchester Institute of Biotechnology; The University of Manchester; 131 Princess Street Manchester M1 7DN UK
| | - Jason Micklefield
- School of Chemistry; Manchester Institute of Biotechnology; The University of Manchester; 131 Princess Street Manchester M1 7DN UK
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47
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Winn M, Francis D, Micklefield J. De novo Biosynthesis of "Non-Natural" Thaxtomin Phytotoxins. Angew Chem Int Ed Engl 2018; 57:6830-6833. [PMID: 29603527 PMCID: PMC6001691 DOI: 10.1002/anie.201801525] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Indexed: 02/04/2023]
Abstract
Thaxtomins are diketopiperazine phytotoxins produced by Streptomyces scabies and other actinobacterial plant pathogens that inhibit cellulose biosynthesis in plants. Due to their potent bioactivity and novel mode of action there has been considerable interest in developing thaxtomins as herbicides for crop protection. To address the need for more stable derivatives, we have developed a new approach for structural diversification of thaxtomins. Genes encoding the thaxtomin NRPS from S. scabies, along with genes encoding a promiscuous tryptophan synthase (TrpS) from Salmonella typhimurium, were assembled in a heterologous host Streptomyces albus. Upon feeding indole derivatives to the engineered S. albus strain, tryptophan intermediates with alternative substituents are biosynthesized and incorporated by the NRPS to deliver a series of thaxtomins with different functionalities in place of the nitro group. The approach described herein, demonstrates how genes from different pathways and different bacterial origins can be combined in a heterologous host to create a de novo biosynthetic pathway to "non-natural" product target compounds.
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Affiliation(s)
- Michael Winn
- School of ChemistryManchester Institute of BiotechnologyThe University of Manchester131 Princess StreetManchesterM1 7DNUK
| | - Daniel Francis
- School of ChemistryManchester Institute of BiotechnologyThe University of Manchester131 Princess StreetManchesterM1 7DNUK
| | - Jason Micklefield
- School of ChemistryManchester Institute of BiotechnologyThe University of Manchester131 Princess StreetManchesterM1 7DNUK
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48
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Lundy TA, Mori S, Garneau-Tsodikova S. Engineering Bifunctional Enzymes Capable of Adenylating and Selectively Methylating the Side Chain or Core of Amino Acids. ACS Synth Biol 2018; 7:399-404. [PMID: 29393631 DOI: 10.1021/acssynbio.7b00426] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nonribosomal peptides (NRPs) are known sources of therapeutics. Some nonribosomal peptide synthetase assembly lines contain unique functional interrupted adenylation (A) domains, where nature has combined two different functional domains into one bifunctional enzyme. Most often these interrupted A domains contain a part of a methylation (M) domain embedded in their sequence. Herein, we aimed to emulate nature and create fully functional interrupted A domains by inserting two different noncognate M domains, KtzH(MH) and TioS(M3S), into a naturally occurring uninterrupted A domain, Ecm6(A1T1). We evaluated the engineered enzymes, Ecm6(A1aMHA1bT1) and Ecm6(A1aM3SA1bT1), by a series of radiometric assays and found that not only do they maintain A domain activity, but also they gain the site-specific methylation patterns observed in the parent M domain donors. These findings provide an exciting proof-of-concept for generating interrupted A domains as future tools to modify NRPs and increase the diversity and activity of potential therapeutics.
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Affiliation(s)
- Taylor A. Lundy
- Department of Pharmaceutical
Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536-0596, United States
| | - Shogo Mori
- Department of Pharmaceutical
Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536-0596, United States
| | - Sylvie Garneau-Tsodikova
- Department of Pharmaceutical
Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536-0596, United States
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49
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Hossain GS, Nadarajan SP, Zhang L, Ng TK, Foo JL, Ling H, Choi WJ, Chang MW. Rewriting the Metabolic Blueprint: Advances in Pathway Diversification in Microorganisms. Front Microbiol 2018; 9:155. [PMID: 29483901 PMCID: PMC5816047 DOI: 10.3389/fmicb.2018.00155] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 01/23/2018] [Indexed: 11/13/2022] Open
Abstract
Living organisms have evolved over millions of years to fine tune their metabolism to create efficient pathways for producing metabolites necessary for their survival. Advancement in the field of synthetic biology has enabled the exploitation of these metabolic pathways for the production of desired compounds by creating microbial cell factories through metabolic engineering, thus providing sustainable routes to obtain value-added chemicals. Following the past success in metabolic engineering, there is increasing interest in diversifying natural metabolic pathways to construct non-natural biosynthesis routes, thereby creating possibilities for producing novel valuable compounds that are non-natural or without elucidated biosynthesis pathways. Thus, the range of chemicals that can be produced by biological systems can be expanded to meet the demands of industries for compounds such as plastic precursors and new antibiotics, most of which can only be obtained through chemical synthesis currently. Herein, we review and discuss novel strategies that have been developed to rewrite natural metabolic blueprints in a bid to broaden the chemical repertoire achievable in microorganisms. This review aims to provide insights on recent approaches taken to open new avenues for achieving biochemical production that are beyond currently available inventions.
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Affiliation(s)
- Gazi Sakir Hossain
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Saravanan Prabhu Nadarajan
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Lei Zhang
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Tee-Kheang Ng
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Jee Loon Foo
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Hua Ling
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Won Jae Choi
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore, Singapore
- Agency for Science, Technology and Research (ASTAR), Institute of Chemical and Engineering Sciences, Singapore, Singapore
| | - Matthew Wook Chang
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore, Singapore
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50
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Ishikawa F, Tanabe G, Kakeya H. Activity-Based Protein Profiling of Non-ribosomal Peptide Synthetases. Curr Top Microbiol Immunol 2018; 420:321-349. [PMID: 30178264 DOI: 10.1007/82_2018_133] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Non-ribosomal peptide (NRP) natural products are one of the most promising resources for drug discovery and development because of their wide-ranging of therapeutic potential, and their behavior as virulence factors and signaling molecules. The NRPs are biosynthesized independently of the ribosome by enzyme assembly lines known as the non-ribosomal peptide synthetase (NRPS) machinery. Genetic, biochemical, and bioinformatics analyses have provided a detailed understanding of the mechanism of NRPS catalysis. However, proteomic techniques for natural product biosynthesis remain a developing field. New strategies are needed to investigate the proteomes of diverse producer organisms and directly analyze the endogenous NRPS machinery. Advanced platforms should verify protein expression, protein folding, and activities and also enable the profiling of the NRPS machinery in biological samples from wild-type, heterologous, and engineered bacterial systems. Here, we focus on activity-based protein profiling strategies that have been recently developed for studies aimed at visualizing and monitoring the NRPS machinery and also for rapid labeling, identification, and biochemical analysis of NRPS enzyme family members as required for proteomic chemistry in natural product sciences.
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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
| | - Hideaki Kakeya
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto, 606-8501, Japan.
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