1
|
Bozhüyük KAJ, Präve L, Kegler C, Schenk L, Kaiser S, Schelhas C, Shi YN, Kuttenlochner W, Schreiber M, Kandler J, Alanjary M, Mohiuddin TM, Groll M, Hochberg GKA, Bode HB. Evolution-inspired engineering of nonribosomal peptide synthetases. Science 2024; 383:eadg4320. [PMID: 38513038 DOI: 10.1126/science.adg4320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 02/09/2024] [Indexed: 03/23/2024]
Abstract
Many clinically used drugs are derived from or inspired by bacterial natural products that often are produced through nonribosomal peptide synthetases (NRPSs), megasynthetases that activate and join individual amino acids in an assembly line fashion. In this work, we describe a detailed phylogenetic analysis of several bacterial NRPSs that led to the identification of yet undescribed recombination sites within the thiolation (T) domain that can be used for NRPS engineering. We then developed an evolution-inspired "eXchange Unit between T domains" (XUT) approach, which allows the assembly of NRPS fragments over a broad range of GC contents, protein similarities, and extender unit specificities, as demonstrated for the specific production of a proteasome inhibitor designed and assembled from five different NRPS fragments.
Collapse
Affiliation(s)
- Kenan A J Bozhüyük
- Max Planck Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043 Marburg, Germany
- Molecular Biotechnology, Department of Biosciences, Goethe-University Frankfurt, 60438 Frankfurt, Germany
- Myria Biosciences AG, Tech Park Basel, Hochbergstrasse 60C, 4057 Basel, Switzerland
| | - Leonard Präve
- Max Planck Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043 Marburg, Germany
- Molecular Biotechnology, Department of Biosciences, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Carsten Kegler
- Max Planck Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043 Marburg, Germany
- Molecular Biotechnology, Department of Biosciences, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Leonie Schenk
- Max Planck Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043 Marburg, Germany
- Molecular Biotechnology, Department of Biosciences, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Sebastian Kaiser
- Max Planck Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043 Marburg, Germany
- Evolutionary Biochemistry Group, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Christian Schelhas
- Max Planck Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043 Marburg, Germany
| | - Yan-Ni Shi
- Molecular Biotechnology, Department of Biosciences, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Wolfgang Kuttenlochner
- Chair of Biochemistry, Center for Protein Assemblies, Technical University of Munich, Ernst-Otto-Fischer-Straße 8, 85748 Garching, Germany
| | - Max Schreiber
- Max Planck Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043 Marburg, Germany
- Molecular Biotechnology, Department of Biosciences, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Joshua Kandler
- Molecular Biotechnology, Department of Biosciences, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Mohammad Alanjary
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| | - T M Mohiuddin
- Molecular Biotechnology, Department of Biosciences, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Michael Groll
- Chair of Biochemistry, Center for Protein Assemblies, Technical University of Munich, Ernst-Otto-Fischer-Straße 8, 85748 Garching, Germany
| | - Georg K A Hochberg
- Evolutionary Biochemistry Group, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Phillips University Marburg, 35043 Marburg, Germany
- Department of Chemistry, Phillips University Marburg, 35043 Marburg, Germany
| | - Helge B Bode
- Max Planck Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043 Marburg, Germany
- Molecular Biotechnology, Department of Biosciences, Goethe-University Frankfurt, 60438 Frankfurt, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Phillips University Marburg, 35043 Marburg, Germany
- Department of Chemistry, Phillips University Marburg, 35043 Marburg, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG) & Senckenberg Gesellschaft für Naturforschung, 60325 Frankfurt, Germany
| |
Collapse
|
2
|
Ishikawa F, Nakamura S, Nakanishi I, Tanabe G. Recent progress in the reprogramming of nonribosomal peptide synthetases. J Pept Sci 2024; 30:e3545. [PMID: 37721208 DOI: 10.1002/psc.3545] [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: 04/27/2023] [Revised: 08/27/2023] [Accepted: 08/28/2023] [Indexed: 09/19/2023]
Abstract
Nonribosomal peptide synthetases (NRPSs) biosynthesize nonribosomal peptide (NRP) natural products, which belong to the most promising resources for drug discovery and development because of their wide range of therapeutic applications. The results of genetic, biochemical, and bioinformatics analyses have enhanced our understanding of the mechanisms of the NRPS machinery. A major goal in NRP biosynthesis is to reprogram the NRPS machinery to enable the biosynthetic production of designed peptides. Reprogramming strategies for the NRPS machinery have progressed considerably in recent years, thereby increasing the yields and generating modified peptides. Here, the recent progress in NRPS reprogramming and its application in peptide synthesis are described.
Collapse
Affiliation(s)
| | | | | | - Genzoh Tanabe
- Faculty of Pharmacy, Kindai University, Osaka, Japan
| |
Collapse
|
3
|
Walls WG, Vagstad A, Delridge T, Piel J, Broderick WE, Broderick JB. Direct Detection of the α-Carbon Radical Intermediate Formed by OspD: Mechanistic Insights into Radical S-Adenosyl-l-methionine Peptide Epimerization. J Am Chem Soc 2024; 146:5550-5559. [PMID: 38364824 PMCID: PMC11302384 DOI: 10.1021/jacs.3c13829] [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] [Indexed: 02/18/2024]
Abstract
OspD is a radical S-adenosyl-l-methionine (SAM) peptide epimerase that converts an isoleucine (Ile) and valine (Val) of the OspA substrate to d-amino acids during biosynthesis of the ribosomally synthesized and post-translationally modified peptide (RiPP) natural product landornamide A. OspD is proposed to carry out this reaction via α-carbon (Cα) H-atom abstraction to form a peptidyl Cα radical that is stereospecifically quenched by hydrogen atom transfer (HAT) from a conserved cysteine (Cys). Here we use site-directed mutagenesis, freeze-quench trapping, isotopic labeling, and electron paramagnetic resonance (EPR) spectroscopy to provide new insights into the OspD catalytic mechanism including the direct observation of the substrate peptide Cα radical intermediate. The putative quenching Cys334 was changed to serine to generate an OspD C334S variant impaired in HAT quenching. The reaction of reduced OspD C334S with SAM and OspA freeze-quenched at 15 s exhibits a doublet EPR signal characteristic of a Cα radical coupled to a single β-H. Using isotopologues of OspA deuterated at either Ile or Val, or both Ile and Val, reveals that the initial Cα radical intermediate forms exclusively on the Ile of OspA. Time-dependent freeze quench coupled with EPR spectroscopy provided evidence for loss of the Ile Cα radical concomitant with gain of a Val Cα radical, directly demonstrating the N-to-C directionality of epimerization by OspD. These results provide direct evidence for the aforementioned OspD-catalyzed peptide epimerization mechanism via a central Cα radical intermediate during RiPP maturation of OspA, a mechanism that may extend to other proteusin peptide epimerases.
Collapse
Affiliation(s)
- William G. Walls
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, United States
| | - Anna Vagstad
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, Zürich 8093, Switzerland
| | - Tyler Delridge
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, United States
| | - Jörn Piel
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, Zürich 8093, Switzerland
| | - William E. Broderick
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, United States
| | - Joan B. Broderick
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, United States
| |
Collapse
|
4
|
Duan J, Yuan B, Jia F, Li X, Chen C, Li G. Development of an Efficient and Seamless Genetic Manipulation Method for Xenorhabdus and Its Application for Enhancing the Production of Fabclavines. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:274-283. [PMID: 38109418 DOI: 10.1021/acs.jafc.3c04136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
Xenorhabdus can produce numerous natural products, but their development has been hampered by the lack of a seamless genetic manipulation method. In this study, we compared several lethal genes and determined the sacB gene as the most effective counter-selection marker and then established a dual selection/counter-selection system by integrating neo and sacB genes into one cassette. This provides an efficient and seamless genetic manipulation method for Xenorhabdus. Using this method, DNA fragments ranging from 205 to 47,788 bp in length were seamlessly knocked out or replaced with impressively high positive rates of 80 to 100% in Xenorhabdus budapestensis XBD8. In addition, the method was successfully applied with good efficiency (45-100%) in Xenorhabdus nematophila CB6. To further validate the method, different constitutive promoters were used to replace the native fclC promoter in a batch experiment. The positivity rate remained consistently high, at 46.3%. In comparison to WT XBD8, the recombinant strain MX14 demonstrated a significant increase in the production of fabclavine 7 and fabclavine 8 by 4.97-fold and 3.22-fold, respectively, while the overall production of fabclavines was enhanced by 3.52-fold.
Collapse
Affiliation(s)
- Jiaqi Duan
- State Key Laboratory for Biology of Plant Diseases and Insect Pests/Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agri-Product Quality and Safety, Ministry of Agriculture, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Baoming Yuan
- State Key Laboratory for Biology of Plant Diseases and Insect Pests/Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agri-Product Quality and Safety, Ministry of Agriculture, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Fenglian Jia
- State Key Laboratory for Biology of Plant Diseases and Insect Pests/Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agri-Product Quality and Safety, Ministry of Agriculture, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xiaohui Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests/Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agri-Product Quality and Safety, Ministry of Agriculture, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Chang Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests/Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agri-Product Quality and Safety, Ministry of Agriculture, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Beijing Green Agricultural Science and Technology Group Co., Ltd, Beijing 100193, China
| | - Guangyue Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests/Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agri-Product Quality and Safety, Ministry of Agriculture, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| |
Collapse
|
5
|
Abbood N, Effert J, Bozhueyuek KAJ, Bode HB. Guidelines for Optimizing Type S Nonribosomal Peptide Synthetases. ACS Synth Biol 2023; 12:2432-2443. [PMID: 37523786 PMCID: PMC10443035 DOI: 10.1021/acssynbio.3c00295] [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: 05/08/2023] [Indexed: 08/02/2023]
Abstract
Bacterial biosynthetic assembly lines, such as nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs), play a crucial role in the synthesis of natural products that have significant therapeutic potential. The ability to engineer these biosynthetic assembly lines offers opportunities to produce artificial nonribosomal peptides, polyketides, and their hybrids with improved properties. In this study, we introduced a synthetic NRPS variant, termed type S NRPS, which simplifies the engineering process and enables biocombinatorial approaches for generating nonribosomal peptide libraries in a parallelized high-throughput manner. However, initial generations of type S NRPSs exhibited a bottleneck that led to significantly reduced production yields. To address this challenge, we employed two optimization strategies. First, we truncated SYNZIPs from the N- and/or C-terminus of the NRPS. SYNZIPs comprise a large set of well-characterized synthetic protein interaction reagents. Second, we incorporated a structurally flexible glycine-serine linker between the NRPS protein and the attached SYNZIP, aiming to improve dynamic domain-domain interactions. Through an iterative optimization process, we achieved remarkable improvements in production yields, with titer increases of up to 55-fold compared to the nonoptimized counterparts. These optimizations successfully restored production levels of type S NRPSs to those observed in wild-type NRPSs and even surpassed them. Overall, our findings demonstrate the potential of engineering bacterial biosynthetic assembly lines for the production of artificial nonribosomal peptides. In addition, optimizing the SYNZIP toolbox can have valuable implications for diverse applications in synthetic biology, such as metabolic engineering, cell signaling studies, or engineering of other multienzyme complexes, such as PKSs.
Collapse
Affiliation(s)
- Nadya Abbood
- Max-Planck-Institute
for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043 Marburg, Germany
- Molecular
Biotechnology, Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Juliana Effert
- Max-Planck-Institute
for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043 Marburg, Germany
| | - Kenan A. J. Bozhueyuek
- Max-Planck-Institute
for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043 Marburg, Germany
- Molecular
Biotechnology, Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
- Myria
Biosciences AG, Mattenstrasse
26, 4058 Basel, Switzerland
| | - Helge B. Bode
- Max-Planck-Institute
for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043 Marburg, Germany
- Molecular
Biotechnology, Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
- Chemical
Biology, Department of Chemistry, Philipps-University
Marburg, 35043 Marburg, Germany
- Senckenberg
Gesellschaft für Naturforschung, 60325 Frankfurt am Main, Germany
- Center for
Synthetic Microbiology (SYNMIKRO), Phillips
University Marburg, 35043 Marburg, Germany
| |
Collapse
|
6
|
Abbood N, Duy Vo T, Watzel J, Bozhueyuek KAJ, Bode HB. Type S Non‐Ribosomal Peptide Synthetases for the Rapid Generation of Tailormade Peptide Libraries**. Chemistry 2022; 28:e202103963. [PMID: 35176184 PMCID: PMC9315016 DOI: 10.1002/chem.202103963] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Indexed: 11/23/2022]
Abstract
Bacterial natural products in general, and non‐ribosomally synthesized peptides in particular, are structurally diverse and provide us with a broad range of pharmaceutically relevant bioactivities. Yet, traditional natural product research suffers from rediscovering the same scaffolds and has been stigmatized as inefficient, time‐, labour‐ and cost‐intensive. Combinatorial chemistry, on the other hand, can produce new molecules in greater numbers, cheaper and in less time than traditional natural product discovery, but also fails to meet current medical needs due to the limited biologically relevant chemical space that can be addressed. Consequently, methods for the high throughput generation of new natural products would offer a new approach to identifying novel bioactive chemical entities for the hit to lead phase of drug discovery programs. As a follow‐up to our previously published proof‐of‐principle study on generating bipartite type S non‐ribosomal peptide synthetases (NRPSs), we now envisaged the de novo generation of non‐ribosomal peptides (NRPs) on an unreached scale. Using synthetic zippers, we split NRPSs in up to three subunits and rapidly generated different bi‐ and tripartite NRPS libraries to produce 49 peptides, peptide derivatives, and de novo peptides at good titres up to 145 mg L−1. A further advantage of type S NRPSs not only is the possibility to easily expand the created libraries by re‐using previously created type S NRPS, but that functions of individual domains as well as domain‐domain interactions can be studied and assigned rapidly.
Collapse
Affiliation(s)
- Nadya Abbood
- Max-Planck-Institute for Terrestrial Microbiology Department of Natural Products in Organismic Interactions 35043 Marburg Germany
- Molecular Biotechnology Institute of Molecular Biosciences Goethe University Frankfurt 60438 Frankfurt am Main Germany
| | - Tien Duy Vo
- Molecular Biotechnology Institute of Molecular Biosciences Goethe University Frankfurt 60438 Frankfurt am Main Germany
| | - Jonas Watzel
- Molecular Biotechnology Institute of Molecular Biosciences Goethe University Frankfurt 60438 Frankfurt am Main Germany
| | - Kenan A. J. Bozhueyuek
- Max-Planck-Institute for Terrestrial Microbiology Department of Natural Products in Organismic Interactions 35043 Marburg Germany
- Molecular Biotechnology Institute of Molecular Biosciences Goethe University Frankfurt 60438 Frankfurt am Main Germany
| | - Helge B. Bode
- Max-Planck-Institute for Terrestrial Microbiology Department of Natural Products in Organismic Interactions 35043 Marburg Germany
- Molecular Biotechnology Institute of Molecular Biosciences Goethe University Frankfurt 60438 Frankfurt am Main Germany
- Senckenberg Gesellschaft für Naturforschung 60325 Frankfurt am Main Germany
| |
Collapse
|
7
|
Bozhueyuek KAJ, Watzel J, Abbood N, Bode HB. Synthetic Zippers as an Enabling Tool for Engineering of Non-Ribosomal Peptide Synthetases*. Angew Chem Int Ed Engl 2021; 60:17531-17538. [PMID: 34015175 PMCID: PMC8362031 DOI: 10.1002/anie.202102859] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 03/31/2021] [Indexed: 12/29/2022]
Abstract
Non‐ribosomal peptide synthetases (NRPSs) are the origin of a wide range of natural products, including many clinically used drugs. Efficient engineering of these often giant biosynthetic machineries to produce novel non‐ribosomal peptides (NRPs) is an ongoing challenge. Here we describe a cloning and co‐expression strategy to functionally combine NRPS fragments of Gram‐negative and ‐positive origin, synthesising novel peptides at titres up to 220 mg L−1. Extending from the recently introduced definition of eXchange Units (XUs), we inserted synthetic zippers (SZs) to split single protein NRPSs into independently expressed and translated polypeptide chains. These synthetic type of NRPS (type S) enables easier access to engineering, overcomes cloning limitations, and provides a simple and rapid approach to building peptide libraries via the combination of different NRPS subunits.
Collapse
Affiliation(s)
- Kenan A J Bozhueyuek
- Molecular Biotechnology, Institute of Molecular Biosciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - Jonas Watzel
- Molecular Biotechnology, Institute of Molecular Biosciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - Nadya Abbood
- Molecular Biotechnology, Institute of Molecular Biosciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany.,Max-Planck-Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043, Marburg, Germany
| | - Helge B Bode
- Molecular Biotechnology, Institute of Molecular Biosciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany.,Max-Planck-Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043, Marburg, Germany.,Senckenberg Gesellschaft für Naturforschung, 60325, Frankfurt am Main, Germany
| |
Collapse
|
8
|
Bozhueyuek KAJ, Watzel J, Abbood N, Bode HB. Synthetic Zippers as an Enabling Tool for Engineering of Non‐Ribosomal Peptide Synthetases**. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202102859] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Kenan A. J. Bozhueyuek
- Molecular Biotechnology Institute of Molecular Biosciences Goethe University Frankfurt 60438 Frankfurt am Main Germany
| | - Jonas Watzel
- Molecular Biotechnology Institute of Molecular Biosciences Goethe University Frankfurt 60438 Frankfurt am Main Germany
| | - Nadya Abbood
- Molecular Biotechnology Institute of Molecular Biosciences Goethe University Frankfurt 60438 Frankfurt am Main Germany
- Max-Planck-Institute for Terrestrial Microbiology Department of Natural Products in Organismic Interactions 35043 Marburg Germany
| | - Helge B. Bode
- Molecular Biotechnology Institute of Molecular Biosciences Goethe University Frankfurt 60438 Frankfurt am Main Germany
- Max-Planck-Institute for Terrestrial Microbiology Department of Natural Products in Organismic Interactions 35043 Marburg Germany
- Senckenberg Gesellschaft für Naturforschung 60325 Frankfurt am Main Germany
| |
Collapse
|
9
|
Zhao L, Le Chapelain C, Brachmann AO, Kaiser M, Groll M, Bode HB. Activation, Structure, Biosynthesis and Bioactivity of Glidobactin-like Proteasome Inhibitors from Photorhabdus laumondii. Chembiochem 2021; 22:1582-1588. [PMID: 33452852 PMCID: PMC8248439 DOI: 10.1002/cbic.202100014] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Indexed: 12/22/2022]
Abstract
The glidobactin-like natural products (GLNPs) glidobactin A and cepafungin I have been reported to be potent proteasome inhibitors and are regarded as promising candidates for anticancer drug development. Their biosynthetic gene cluster (BGC) plu1881-1877 is present in entomopathogenic Photorhabdus laumondii but silent under standard laboratory conditions. Here we show the largest subset of GLNPs, which are produced and identified after activation of the silent BGC in the native host and following heterologous expression of the BGC in Escherichia coli. Their chemical diversity results from a relaxed substrate specificity and flexible product release in the assembly line of GLNPs. Crystal structure analysis of the yeast proteasome in complex with new GLNPs suggests that the degree of unsaturation and the length of the aliphatic tail are critical for their bioactivity. The results in this study provide the basis to engineer the BGC for the generation of new GLNPs and to optimize these natural products resulting in potential drugs for cancer therapy.
Collapse
Affiliation(s)
- Lei Zhao
- Molecular BiotechnologyDepartment of BiosciencesGoethe University Frankfurt60438Frankfurt am MainGermany
- Institute of BotanyJiangsu Province and Chinese Academy of Sciences210014NanjingP. R. China
| | - Camille Le Chapelain
- Center for Integrated Protein Science Munich (CIPSM)Department of ChemistryTechnical University of Munich85748GarchingGermany
| | - Alexander O. Brachmann
- Molecular BiotechnologyDepartment of BiosciencesGoethe University Frankfurt60438Frankfurt am MainGermany
| | - Marcel Kaiser
- Swiss Tropical and Public Health Institute4002BaselSwitzerland
| | - Michael Groll
- Center for Integrated Protein Science Munich (CIPSM)Department of ChemistryTechnical University of Munich85748GarchingGermany
| | - Helge B. Bode
- Molecular BiotechnologyDepartment of BiosciencesGoethe University Frankfurt60438Frankfurt am MainGermany
- Buchmann Institute for Molecular Life Sciences (BMLS)Goethe University Frankfurt60438Frankfurt am MainGermany
- Senckenberg Gesellschaft für Naturforschung60325Frankfurt am MainGermany
- Department of Natural Products in Organismic InteractionsMax-Planck-Institute for Terrestrial Microbiology35043MarburgGermany
| |
Collapse
|
10
|
Liu S, Wang T, Lu Q, Li F, Wu G, Jiang Z, Habden X, Liu L, Zhang X, Lukianov DA, Osterman IA, Sergiev PV, Dontsova OA, Sun C. Bioprospecting of Soil-Derived Actinobacteria Along the Alar-Hotan Desert Highway in the Taklamakan Desert. Front Microbiol 2021; 12:604999. [PMID: 33790875 PMCID: PMC8005632 DOI: 10.3389/fmicb.2021.604999] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 02/22/2021] [Indexed: 02/04/2023] Open
Abstract
Taklamakan desert is known as the largest dunefield in China and as the second largest shifting sand desert in the world. Although with long history and glorious culture, the Taklamakan desert remains largely unexplored and numerous microorganisms have not been harvested in culture or taxonomically identified yet. The main objective of this study is to explore the diversity, novelty, and pharmacological potential of the cultivable actinomycetes from soil samples at various sites along the Alar-Hotan desert highway in the Taklamakan desert. A total of 590 actinobacterial strains were recovered by the culture-dependent approach. Phylogenetic analysis based on 16S ribosomal RNA (rRNA) gene sequences unveiled a significant level of actinobacterial diversity with 55 genera distributed in 27 families of 12 orders. Thirty-six strains showed relatively low 16S rRNA similarities (<98.65%) with validly described species, among which four strains had already been characterized as novel taxa by our previous research. One hundred and forty-six actinobacterial isolates were selected as representatives to evaluate the antibacterial activities and mechanism of action by the paper-disk diffusion method and a double fluorescent protein reporter "pDualrep2" system, respectively. A total of 61 isolates exhibited antagonistic activity against the tested "ESKAPE" pathogens, among which seven strains could produce bioactive metabolites either to be able to block translation machinery or to induce SOS-response in the pDualrep2 system. Notably, Saccharothrix sp. 16Sb2-4, harboring a promising antibacterial potential with the mechanism of interfering with protein translation, was analyzed in detail to gain deeper insights into its bioactive metabolites. Through ultra-performance liquid chromatography (UPLC)-quadrupole time-of-flight (QToF)-MS/MS based molecular networking analysis and databases identification, four families of compounds (1-16) were putatively identified. Subsequent bioassay-guided separation resulted in purification of four 16-membered macrolide antibiotics, aldgamycin H (8), aldgamycin K (9), aldgamycin G (10), and swalpamycin B (11), and their structures were elucidated by HR-electrospray ionization source (ESI)-MS and NMR spectroscopy. All compounds 8-11 displayed antibacterial activities by inhibiting protein synthesis in the pDualrep2 system. In conclusion, this work demonstrates that Taklamakan desert is a potentially unique reservoir of versatile actinobacteria, which can be a promising source for discovery of novel species and diverse bioactive compounds.
Collapse
Affiliation(s)
- Shaowei Liu
- Department of Microbial Chemistry, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Ting Wang
- Department of Microbial Chemistry, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Qinpei Lu
- Department of Microbial Chemistry, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Feina Li
- Department of Microbial Chemistry, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Gang Wu
- Department of Microbial Chemistry, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Zhongke Jiang
- Department of Microbial Chemistry, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Xugela Habden
- College of Life Science, Xinjiang Normal University, Urumchi, China
| | - Lin Liu
- School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Xiaolin Zhang
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
| | - Dmitry A. Lukianov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Ilya A. Osterman
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
- Department of Chemistry, A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Petr V. Sergiev
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
- Department of Chemistry, A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Olga A. Dontsova
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
- Department of Chemistry, A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Chenghang Sun
- Department of Microbial Chemistry, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| |
Collapse
|
11
|
Pérez-Victoria I. Co-occurring Congeners Reveal the Position of Enantiomeric Amino Acids in Nonribosomal Peptides. Chembiochem 2021; 22:2087-2092. [PMID: 33440038 DOI: 10.1002/cbic.202000805] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/11/2021] [Indexed: 11/09/2022]
Abstract
The absolute configuration of the constituent amino acids in microbial nonribosomal peptides is typically determined by Marfey's method after total hydrolysis of the peptide. A challenge to structure elucidation arises when both d and l enantiomeric configurations of an amino acid are present. Determining the actual position of each amino acid enantiomer within the peptide sequence typically requires laborious approaches based on peptide partial hydrolysis or even total synthesis of the possible diastereomers. Herein, an alternative solution is discussed based on the homogeneous backbone chirality that governs all peptides biosynthesized by a common nonribosomal peptide synthetase. The information on configuration provided by Marfey's analysis of co-occurring minor congeners can reveal unequivocally the stereochemical sequence of the whole peptide family.
Collapse
Affiliation(s)
- Ignacio Pérez-Victoria
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía Parque Tecnológico de Ciencias de la Salud, Avda. del Conocimiento 34, 18016, Armilla, Granada, Spain
| |
Collapse
|
12
|
Zhao L, Bode HB. Production of a photohexapeptide library from entomopathogenic Photorhabdus asymbiotica PB68.1. Org Biomol Chem 2019; 17:7858-7862. [PMID: 31403156 DOI: 10.1039/c9ob01489f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new natural product compound library, photohexapeptide library, was identified from entomopathogenic Photorhabdus asymbiotica PB68.1 after the NRPS-encoding gene phpS was activated via promoter exchange. Peptide structures, including the absolute configurations of amino acids, were determined by using a combination of bioinformatics analysis and isotopic labelling experiments followed by detailed HPLC-MS analysis. Additionally, their structures were confirmed by chemical synthesis and NMR after preparative isolation. The chemical diversity of the photohexapeptides results from promiscuous adenylation domain specificity being an excellent example of how to create libraries in nature.
Collapse
Affiliation(s)
- Lei Zhao
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany.
| | | |
Collapse
|
13
|
Shi YM, Bode HB. Chemical language and warfare of bacterial natural products in bacteria-nematode-insect interactions. Nat Prod Rep 2019; 35:309-335. [PMID: 29359226 DOI: 10.1039/c7np00054e] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Covering: up to November 2017 Organismic interaction is one of the fundamental principles for survival in any ecosystem. Today, numerous examples show the interaction between microorganisms like bacteria and higher eukaryotes that can be anything between mutualistic to parasitic/pathogenic symbioses. There is also increasing evidence that microorganisms are used by higher eukaryotes not only for the supply of essential factors like vitamins but also as biological weapons to protect themselves or to kill other organisms. Excellent examples for such systems are entomopathogenic nematodes of the genera Heterorhabditis and Steinernema that live in mutualistic symbiosis with bacteria of the genera Photorhabdus and Xenorhabdus, respectively. Although these systems have been used successfully in organic farming on an industrial scale, it was only shown during the last 15 years that several different natural products (NPs) produced by the bacteria play key roles in the complex life cycle of the bacterial symbionts, the nematode host and the insect prey that is killed by and provides nutrients for the nematode-bacteria pair. Since the bacteria can switch from mutualistic to pathogenic lifestyle, interacting with two different types of higher eukaryotes, and since the full system with all players can be established in the lab, they are promising model systems to elucidate the natural function of microbial NPs. This review summarizes the current knowledge as well as open questions for NPs from Photorhabdus and Xenorhabdus and tries to assign their roles in the tritrophic relationship.
Collapse
Affiliation(s)
- Yi-Ming Shi
- Merck-Stiftungsprofessur für Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt, Frankfurt am Main 60438, Germany
| | | |
Collapse
|
14
|
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.
Collapse
|
15
|
Vagstad AL, Kuranaga T, Püntener S, Pattabiraman VR, Bode JW, Piel J. Introduction of
d
‐Amino Acids in Minimalistic Peptide Substrates by an
S
‐Adenosyl‐
l
‐Methionine Radical Epimerase. Angew Chem Int Ed Engl 2019; 58:2246-2250. [DOI: 10.1002/anie.201809508] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 11/08/2018] [Indexed: 02/02/2023]
Affiliation(s)
- Anna L. Vagstad
- Institute of MicrobiologyEidgenössische Technische Hochschule (ETH) Zurich Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Takefumi Kuranaga
- Graduate School of Pharmaceutical SciencesKyoto University Kyoto 606-8501 Japan
| | - Salome Püntener
- Institute of MicrobiologyEidgenössische Technische Hochschule (ETH) Zurich Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Vijaya R. Pattabiraman
- Laboratory of Organic ChemistryEidgenössische Technische Hochschule (ETH) Zurich Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
| | - Jeffrey W. Bode
- Laboratory of Organic ChemistryEidgenössische Technische Hochschule (ETH) Zurich Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
| | - Jörn Piel
- Institute of MicrobiologyEidgenössische Technische Hochschule (ETH) Zurich Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| |
Collapse
|
16
|
Vagstad AL, Kuranaga T, Püntener S, Pattabiraman VR, Bode JW, Piel J. Introduction of d
-Amino Acids in Minimalistic Peptide Substrates by an S
-Adenosyl-l
-Methionine Radical Epimerase. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201809508] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Anna L. Vagstad
- Institute of Microbiology; Eidgenössische Technische Hochschule (ETH) Zurich; Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Takefumi Kuranaga
- Graduate School of Pharmaceutical Sciences; Kyoto University; Kyoto 606-8501 Japan
| | - Salome Püntener
- Institute of Microbiology; Eidgenössische Technische Hochschule (ETH) Zurich; Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Vijaya R. Pattabiraman
- Laboratory of Organic Chemistry; Eidgenössische Technische Hochschule (ETH) Zurich; Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
| | - Jeffrey W. Bode
- Laboratory of Organic Chemistry; Eidgenössische Technische Hochschule (ETH) Zurich; Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
| | - Jörn Piel
- Institute of Microbiology; Eidgenössische Technische Hochschule (ETH) Zurich; Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| |
Collapse
|
17
|
Radical S-Adenosylmethionine Peptide Epimerases: Detection of Activity and Characterization of d-Amino Acid Products. Methods Enzymol 2018; 604:237-257. [DOI: 10.1016/bs.mie.2018.01.033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
|
18
|
De novo design and engineering of non-ribosomal peptide synthetases. Nat Chem 2017; 10:275-281. [PMID: 29461518 DOI: 10.1038/nchem.2890] [Citation(s) in RCA: 130] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 10/06/2017] [Indexed: 01/20/2023]
Abstract
Peptides derived from non-ribosomal peptide synthetases (NRPSs) represent an important class of pharmaceutically relevant drugs. Methods to generate novel non-ribosomal peptides or to modify peptide natural products in an easy and predictable way are therefore of great interest. However, although the overall modular structure of NRPSs suggests the possibility of adjusting domain specificity and selectivity, only a few examples have been reported and these usually show a severe drop in production titre. Here we report a new strategy for the modification of NRPSs that uses defined exchange units (XUs) and not modules as functional units. XUs are fused at specific positions that connect the condensation and adenylation domains and respect the original specificity of the downstream module to enable the production of the desired peptides. We also present the use of internal condensation domains as an alternative to other peptide-chain-releasing domains for the production of cyclic peptides.
Collapse
|
19
|
Tobias NJ, Wolff H, Djahanschiri B, Grundmann F, Kronenwerth M, Shi YM, Simonyi S, Grün P, Shapiro-Ilan D, Pidot SJ, Stinear TP, Ebersberger I, Bode HB. Natural product diversity associated with the nematode symbionts Photorhabdus and Xenorhabdus. Nat Microbiol 2017; 2:1676-1685. [PMID: 28993611 DOI: 10.1038/s41564-017-0039-9] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 09/08/2017] [Indexed: 12/25/2022]
Abstract
Xenorhabdus and Photorhabdus species dedicate a large amount of resources to the production of specialized metabolites derived from non-ribosomal peptide synthetase (NRPS) or polyketide synthase (PKS). Both bacteria undergo symbiosis with nematodes, which is followed by an insect pathogenic phase. So far, the molecular basis of this tripartite relationship and the exact roles that individual metabolites and metabolic pathways play have not been well understood. To close this gap, we have significantly expanded the database for comparative genomics studies in these bacteria. Clustering the genes encoded in the individual genomes into hierarchical orthologous groups reveals a high-resolution picture of functional evolution in this clade. It identifies groups of genes-many of which are involved in secondary metabolite production-that may account for the niche specificity of these bacteria. Photorhabdus and Xenorhabdus appear very similar at the DNA sequence level, which indicates their close evolutionary relationship. Yet, high-resolution mass spectrometry analyses reveal a huge chemical diversity in the two taxa. Molecular network reconstruction identified a large number of previously unidentified metabolite classes, including the xefoampeptides and tilivalline. Here, we apply genomic and metabolomic methods in a complementary manner to identify and elucidate additional classes of natural products. We also highlight the ability to rapidly and simultaneously identify potentially interesting bioactive products from NRPSs and PKSs, thereby augmenting the contribution of molecular biology techniques to the acceleration of natural product discovery.
Collapse
Affiliation(s)
- Nicholas J Tobias
- Fachbereich Biowissenschaften, Merck Stiftungsprofessur für Molekulare Biotechnologie, Goethe-Universität Frankfurt, Frankfurt am Main, 60438, Germany
| | - Hendrik Wolff
- Fachbereich Biowissenschaften, Merck Stiftungsprofessur für Molekulare Biotechnologie, Goethe-Universität Frankfurt, Frankfurt am Main, 60438, Germany
| | - Bardya Djahanschiri
- Department of Applied Bioinformatics, Institute for Cell Biology and Neuroscience, Goethe-Universität Frankfurt, Frankfurt am Main, 60438, Germany
| | - Florian Grundmann
- Fachbereich Biowissenschaften, Merck Stiftungsprofessur für Molekulare Biotechnologie, Goethe-Universität Frankfurt, Frankfurt am Main, 60438, Germany
| | - Max Kronenwerth
- Fachbereich Biowissenschaften, Merck Stiftungsprofessur für Molekulare Biotechnologie, Goethe-Universität Frankfurt, Frankfurt am Main, 60438, Germany
| | - Yi-Ming Shi
- Fachbereich Biowissenschaften, Merck Stiftungsprofessur für Molekulare Biotechnologie, Goethe-Universität Frankfurt, Frankfurt am Main, 60438, Germany
| | - Svenja Simonyi
- Fachbereich Biowissenschaften, Merck Stiftungsprofessur für Molekulare Biotechnologie, Goethe-Universität Frankfurt, Frankfurt am Main, 60438, Germany
| | - Peter Grün
- Fachbereich Biowissenschaften, Merck Stiftungsprofessur für Molekulare Biotechnologie, Goethe-Universität Frankfurt, Frankfurt am Main, 60438, Germany
| | - David Shapiro-Ilan
- USDA-ARS, SEA, SE Fruit and Tree Nut Research Unit, 21 Dunbar Road, Byron, GA, 31008, USA
| | - Sacha J Pidot
- Department of Microbiology and Immunology, University of Melbourne, at the Doherty Institute for Infection and Immunity, Parkville, Victoria, 3010, Australia
| | - Timothy P Stinear
- Department of Microbiology and Immunology, University of Melbourne, at the Doherty Institute for Infection and Immunity, Parkville, Victoria, 3010, Australia
| | - Ingo Ebersberger
- Department of Applied Bioinformatics, Institute for Cell Biology and Neuroscience, Goethe-Universität Frankfurt, Frankfurt am Main, 60438, Germany.,Senckenberg Climate and Research Centre (BIK-F), Frankfurt am Main, 60325, Germany
| | - Helge B Bode
- Fachbereich Biowissenschaften, Merck Stiftungsprofessur für Molekulare Biotechnologie, Goethe-Universität Frankfurt, Frankfurt am Main, 60438, Germany. .,Buchmann Institute for Molecular Life Sciences, Goethe-Universität Frankfurt, Frankfurt am Main, 60438, Germany.
| |
Collapse
|
20
|
Heinrich AK, Hirschmann M, Neubacher N, Bode HB. LuxS-dependent AI-2 production is not involved in global regulation of natural product biosynthesis in Photorhabdus and Xenorhabdus. PeerJ 2017; 5:e3471. [PMID: 28663937 PMCID: PMC5488855 DOI: 10.7717/peerj.3471] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 05/26/2017] [Indexed: 01/06/2023] Open
Abstract
The Gram-negative bacteria Photorhabdus and Xenorhabdus are known to produce a variety of different natural products (NP). These compounds play different roles since the bacteria live in symbiosis with nematodes and are pathogenic to insect larvae in the soil. Thus, a fine tuned regulatory system controlling NP biosynthesis is indispensable. Global regulators such as Hfq, Lrp, LeuO and HexA have been shown to influence NP production of Photorhabdus and Xenorhabdus. Additionally, photopyrones as quorum sensing (QS) signals were demonstrated to be involved in the regulation of NP production in Photorhabdus. In this study, we investigated the role of another possible QS signal, autoinducer-2 (AI-2), in regulation of NP production. The AI-2 synthase (LuxS) is widely distributed within the bacterial kingdom and has a dual role as a part of the activated methyl cycle pathway, as well as being responsible for AI-2 precursor production. We deleted luxS in three different entomopathogenic bacteria and compared NP levels in the mutant strains to the wild type (WT) but observed no difference to the WT strains. Furthermore, the absence of the small regulatory RNA micA, which is encoded directly upstream of luxS, did not influence NP levels. Phenotypic differences between the P. luminescens luxS deletion mutant and an earlier described luxS deficient strain of P. luminescens suggested that two phenotypically different strains have evolved in different laboratories.
Collapse
Affiliation(s)
- Antje K. Heinrich
- Fachbereich Biowissenschaften, Merck Stiftungsprofessur für Molekulare Biotechnologie, Goethe-Universität Frankfurt, Frankfurt am Main, Germany
| | - Merle Hirschmann
- Fachbereich Biowissenschaften, Merck Stiftungsprofessur für Molekulare Biotechnologie, Goethe-Universität Frankfurt, Frankfurt am Main, Germany
| | - Nick Neubacher
- Fachbereich Biowissenschaften, Merck Stiftungsprofessur für Molekulare Biotechnologie, Goethe-Universität Frankfurt, Frankfurt am Main, Germany
| | - Helge B. Bode
- Fachbereich Biowissenschaften, Merck Stiftungsprofessur für Molekulare Biotechnologie, Goethe-Universität Frankfurt, Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences, Goethe-Universität Frankfurt, Frankfurt am Main, Germany
| |
Collapse
|
21
|
Engel Y, Windhorst C, Lu X, Goodrich-Blair H, Bode HB. The Global Regulators Lrp, LeuO, and HexA Control Secondary Metabolism in Entomopathogenic Bacteria. Front Microbiol 2017; 8:209. [PMID: 28261170 PMCID: PMC5313471 DOI: 10.3389/fmicb.2017.00209] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 01/30/2017] [Indexed: 11/13/2022] Open
Abstract
Photorhabdus luminescens TTO1 and Xenorhabdus nematophila HGB081 are insect pathogenic bacteria and producers of various structurally diverse bioactive natural products. In these entomopathogenic bacteria we investigated the role of the global regulators Lrp, LeuO, and HexA in the production of natural products. Lrp is a general activator of natural product biosynthesis in X. nematophila and for most compounds in TTO1. Microarray analysis confirmed these results in X. nematophila and enabled the identification of additional biosynthesis gene clusters (BGC) regulated by Lrp. Moreover, when promoters of two X. nematophila BGC were analyzed, transcriptional activation by Lrp was observed. In contrast, LeuO in X. nematophila and P. luminescens has both repressing and activating features, depending on the natural product examined. Furthermore, heterologous overexpression of leuO from X. nematophila in the closely related Xenorhabdus szentirmaii resulted in overproduction of several natural products including novel compounds. The presented findings could be of importance for establishing a tool for overproduction of secondary metabolites and subsequent identification of novel compounds.
Collapse
Affiliation(s)
- Yvonne Engel
- Merck-Stiftungsprofessur Molekulare Biotechnologie, Molekulare Biowissenschaften, Goethe Universität Frankfurt Frankfurt am Main, Germany
| | - Carina Windhorst
- Merck-Stiftungsprofessur Molekulare Biotechnologie, Molekulare Biowissenschaften, Goethe Universität Frankfurt Frankfurt am Main, Germany
| | - Xiaojun Lu
- Department of Bacteriology, University of Wisconsin-Madison, Madison WI, USA
| | - Heidi Goodrich-Blair
- Department of Bacteriology, University of Wisconsin-Madison, MadisonWI, USA; Department of Microbiology, University of Tennessee, Knoxville, KnoxvilleTN, USA
| | - Helge B Bode
- Merck-Stiftungsprofessur Molekulare Biotechnologie, Molekulare Biowissenschaften, Goethe Universität FrankfurtFrankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences (BMLS), Goethe Universität FrankfurtFrankfurt am Main, Germany
| |
Collapse
|
22
|
Fichtner M, Voigt K, Schuster S. The tip and hidden part of the iceberg: Proteinogenic and non-proteinogenic aliphatic amino acids. Biochim Biophys Acta Gen Subj 2017; 1861:3258-3269. [DOI: 10.1016/j.bbagen.2016.08.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 07/14/2016] [Accepted: 08/15/2016] [Indexed: 12/26/2022]
|
23
|
Morinaka BI, Verest M, Freeman MF, Gugger M, Piel J. An Orthogonal D
2
O‐Based Induction System that Provides Insights into
d
‐Amino Acid Pattern Formation by Radical S‐Adenosylmethionine Peptide Epimerases. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201609469] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Brandon I. Morinaka
- Institute of Microbiology Eigenössische Technische Hochschule (ETH) Zurich Vladimir-Prelog-Weg 1-5/10 8093 Zurich Switzerland
| | - Marjan Verest
- Institute of Microbiology Eigenössische Technische Hochschule (ETH) Zurich Vladimir-Prelog-Weg 1-5/10 8093 Zurich Switzerland
| | - Michael F. Freeman
- Institute of Microbiology Eigenössische Technische Hochschule (ETH) Zurich Vladimir-Prelog-Weg 1-5/10 8093 Zurich Switzerland
| | - Muriel Gugger
- Insitut Pasteur, Collection des Cyanobactéries Département de Microbiologie 75015 Paris France
| | - Jörn Piel
- Institute of Microbiology Eigenössische Technische Hochschule (ETH) Zurich Vladimir-Prelog-Weg 1-5/10 8093 Zurich Switzerland
| |
Collapse
|
24
|
Morinaka BI, Verest M, Freeman MF, Gugger M, Piel J. An Orthogonal D
2
O‐Based Induction System that Provides Insights into
d
‐Amino Acid Pattern Formation by Radical S‐Adenosylmethionine Peptide Epimerases. Angew Chem Int Ed Engl 2016; 56:762-766. [DOI: 10.1002/anie.201609469] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Brandon I. Morinaka
- Institute of Microbiology Eigenössische Technische Hochschule (ETH) Zurich Vladimir-Prelog-Weg 1-5/10 8093 Zurich Switzerland
| | - Marjan Verest
- Institute of Microbiology Eigenössische Technische Hochschule (ETH) Zurich Vladimir-Prelog-Weg 1-5/10 8093 Zurich Switzerland
| | - Michael F. Freeman
- Institute of Microbiology Eigenössische Technische Hochschule (ETH) Zurich Vladimir-Prelog-Weg 1-5/10 8093 Zurich Switzerland
| | - Muriel Gugger
- Insitut Pasteur, Collection des Cyanobactéries Département de Microbiologie 75015 Paris France
| | - Jörn Piel
- Institute of Microbiology Eigenössische Technische Hochschule (ETH) Zurich Vladimir-Prelog-Weg 1-5/10 8093 Zurich Switzerland
| |
Collapse
|
25
|
Identification of the Sfp-Type PPTase EppA from the Lichenized Fungus Evernia prunastri. PLoS One 2016; 11:e0145624. [PMID: 26784935 PMCID: PMC4718654 DOI: 10.1371/journal.pone.0145624] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 12/07/2015] [Indexed: 01/12/2023] Open
Abstract
In the last decades, natural products from lichens have gained more interest for pharmaceutical application due to the broad range of their biological activity. However, isolation of the compounds of interest directly from the lichen is neither feasible nor sustainable due to slow growth of many lichens. In order to develop a pipeline for heterologous expression of lichen biosynthesis gene clusters and thus the sustainable production of their bioactive compounds we have identified and characterized the phosphopantheteinyl transferase (PPTase) EppA from the lichen Evernia prunastri. The Sfp-type PPTase EppA was functionally characterized through heterologous expression in E. coli using the production of the blue pigment indigoidine as readout and by complementation of a lys5 deletion in S. cerevisiae.
Collapse
|
26
|
Antimicrobials and the Natural Biology of a Bacterial-Nematode Symbiosis. ADVANCES IN ENVIRONMENTAL MICROBIOLOGY 2016. [DOI: 10.1007/978-3-319-28068-4_5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
|
27
|
Rinkel J, Dickschat JS. Recent highlights in biosynthesis research using stable isotopes. Beilstein J Org Chem 2015; 11:2493-508. [PMID: 26734097 PMCID: PMC4685789 DOI: 10.3762/bjoc.11.271] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 11/23/2015] [Indexed: 02/03/2023] Open
Abstract
The long and successful history of isotopic labeling experiments within natural products research has both changed and deepened our understanding of biosynthesis. As demonstrated in this article, the usage of isotopes is not at all old-fashioned, but continues to give important insights into biosynthetic pathways of secondary metabolites. This review with 85 cited references is structured by separate discussions of compounds from different classes including polyketides, non-ribosomal peptides, their hybrids, terpenoids, and aromatic compounds formed via the shikimate pathway. The text does not aim at a comprehensive overview, but instead a selection of recent important examples of isotope usage within biosynthetic studies is presented, with a special emphasis on mechanistic surprises.
Collapse
Affiliation(s)
- Jan Rinkel
- Kekulé-Institute of Organic Chemistry and Biochemistry, Gerhard-Domagk-Str. 1, 53121 Bonn, Germany
| | - Jeroen S Dickschat
- Kekulé-Institute of Organic Chemistry and Biochemistry, Gerhard-Domagk-Str. 1, 53121 Bonn, Germany
| |
Collapse
|
28
|
Bode HB, Brachmann AO, Jadhav KB, Seyfarth L, Dauth C, Fuchs SW, Kaiser M, Waterfield NR, Sack H, Heinemann SH, Arndt HD. Structure Elucidation and Activity of Kolossin A, theD-/L-Pentadecapeptide Product of a Giant Nonribosomal Peptide Synthetase. Angew Chem Int Ed Engl 2015; 54:10352-5. [DOI: 10.1002/anie.201502835] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Indexed: 01/09/2023]
|
29
|
Strukturaufklärung und Aktivität des aus einer riesigen nicht- ribosomalen Peptidsynthetase stammendenD-/L-Pentadecapeptids Kolossin A. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201502835] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|
30
|
Nollmann FI, Dauth C, Mulley G, Kegler C, Kaiser M, Waterfield NR, Bode HB. Insect-specific production of new GameXPeptides in photorhabdus luminescens TTO1, widespread natural products in entomopathogenic bacteria. Chembiochem 2014; 16:205-8. [PMID: 25425189 DOI: 10.1002/cbic.201402603] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2014] [Indexed: 12/31/2022]
Abstract
Discovery of new natural products by heterologous expression reaches its limits, especially when specific building blocks are missing in the heterologous host or the production medium. Here, we describe the insect-specific production of the new GameXPeptides E-H (5-8) from Photorhabdus luminescens TTO1, which can be produced heterologously from expression of the GameXPeptide synthetase GxpS only upon supplementation of the production media with the missing building blocks, and thus must be regarded as the true natural products under natural conditions.
Collapse
Affiliation(s)
- Friederike I Nollmann
- Merck Stiftungsprofessur für Molekulare Biotechnologie, Fachbereich der Biowissenschaften, Goethe Universität Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt am Main (Germany)
| | | | | | | | | | | | | |
Collapse
|
31
|
Role of secondary metabolites in establishment of the mutualistic partnership between Xenorhabdus nematophila and the entomopathogenic nematode Steinernema carpocapsae. Appl Environ Microbiol 2014; 81:754-64. [PMID: 25398871 DOI: 10.1128/aem.02650-14] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Xenorhabdus nematophila engages in a mutualistic partnership with the nematode Steinernema carpocapsae, which invades insects, migrates through the gut, and penetrates into the hemocoel (body cavity). We showed previously that during invasion of Manduca sexta, the gut microbe Staphylococcus saprophyticus appeared transiently in the hemocoel, while Enterococcus faecalis proliferated as X. nematophila became dominant. X. nematophila produces diverse secondary metabolites, including the major water-soluble antimicrobial xenocoumacin. Here, we study the role of X. nematophila antimicrobials in interspecies competition under biologically relevant conditions using strains lacking either xenocoumacin (ΔxcnKL strain), xenocoumacin and the newly discovered antibiotic F (ΔxcnKL:F strain), or all ngrA-derived secondary metabolites (ngrA strain). Competition experiments were performed in Grace's insect medium, which is based on lepidopteran hemolymph. S. saprophyticus was eliminated when inoculated into growing cultures of either the ΔxcnKL strain or ΔxcnKL:F strain but grew in the presence of the ngrA strain, indicating that ngrA-derived antimicrobials, excluding xenocoumacin or antibiotic F, were required to eliminate the competitor. In contrast, S. saprophyticus was eliminated when coinjected into M. sexta with either the ΔxcnKL or ngrA strain, indicating that ngrA-derived antimicrobials were not required to eliminate the competitor in vivo. E. faecalis growth was facilitated when coinjected with either of the mutant strains. Furthermore, nematode reproduction in M. sexta naturally infected with infective juveniles colonized with the ngrA strain was markedly reduced relative to the level of reproduction when infective juveniles were colonized with the wild-type strain. These findings provide new insights into interspecies competition in a host environment and suggest that ngrA-derived compounds serve as signals for in vivo nematode reproduction.
Collapse
|
32
|
Barra L, Schulz B, Dickschat JS. Pogostol Biosynthesis by the Endophytic FungusGeniculosporium. Chembiochem 2014; 15:2379-83. [DOI: 10.1002/cbic.201402298] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Indexed: 11/11/2022]
|
33
|
Reimer D, Nollmann FI, Schultz K, Kaiser M, Bode HB. Xenortide Biosynthesis by Entomopathogenic Xenorhabdus nematophila. JOURNAL OF NATURAL PRODUCTS 2014; 77:1976-1980. [PMID: 25080196 DOI: 10.1021/np500390b] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The biosynthesis gene cluster of the xenortides and a new derivative, xenortide D, which is produced in only trace amounts, was identified in Xenorhabdus nematophila. The structure of xenortide D was elucidated using a combination of labeling experiments followed by MS analysis and was confirmed by synthesis. Bioactivity tests revealed a weak activity of tryptamine-carrying xenortides against Plasmodium falciparum and Trypanosoma brucei.
Collapse
Affiliation(s)
- Daniela Reimer
- Merck Stiftungsprofessur für Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt , 60438 Frankfurt am Main, Germany
| | - Friederike I Nollmann
- Merck Stiftungsprofessur für Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt , 60438 Frankfurt am Main, Germany
| | - Katharina Schultz
- Merck Stiftungsprofessur für Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt , 60438 Frankfurt am Main, Germany
| | - Marcel Kaiser
- Swiss Tropical and Public Health Institute , Parasite Chemotherapy Socinstraße 57, P.O. Box, CH-4002 Basel, Switzerland
| | - Helge B Bode
- Merck Stiftungsprofessur für Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt , 60438 Frankfurt am Main, Germany
| |
Collapse
|