1
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Yu Y, van der Donk WA. PEARL-Catalyzed Peptide Bond Formation after Chain Reversal by Ureido-Forming Condensation Domains. ACS CENTRAL SCIENCE 2024; 10:1242-1250. [PMID: 38947204 PMCID: PMC11212132 DOI: 10.1021/acscentsci.4c00044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 05/19/2024] [Accepted: 05/20/2024] [Indexed: 07/02/2024]
Abstract
A subset of nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs) are encoded in their biosynthetic gene clusters (BGCs) with enzymes annotated as lantibiotic dehydratases. The functions of these putative lantibiotic dehydratases remain unknown. Here, we characterize an NRPS-PKS BGC with a putative lantibiotic dehydratase from the bacterium Stackebrandtia nassauensis (sna). Heterologous expression revealed several metabolites produced by the BGC, and the omission of selected biosynthetic enzymes revealed the biosynthetic pathway toward these compounds. The final product is a bisarginyl ureidopeptide with an enone electrophile. The putative lantibiotic dehydratase catalyzes peptide bond formation to a Thr that extends the peptide scaffold opposite to the NRPS and PKS biosynthetic direction. The condensation domain of the NRPS SnaA catalyzes the formation of a ureido group, and bioinformatics analysis revealed a distinct active site signature EHHXXHDG of ureido-generating condensation (Curea) domains. This work demonstrates that the annotated lantibiotic dehydratase serves as a separate amide bond-forming machinery in addition to the NRPS, and that the lantibiotic dehydratase enzyme family possesses diverse catalytic activities in the biosynthesis of both ribosomal and nonribosomal natural products.
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Affiliation(s)
- Yue Yu
- Department
of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Wilfred A. van der Donk
- Department
of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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2
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Yu Y, van der Donk WA. PEARL-catalyzed peptide bond formation after chain reversal during the biosynthesis of non-ribosomal peptides. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.23.573212. [PMID: 38187666 PMCID: PMC10769383 DOI: 10.1101/2023.12.23.573212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
A subset of nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs) are encoded in their biosynthetic gene clusters (BGCs) with enzymes annotated as lantibiotic dehydratases. The functions of these putative lantibiotic dehydratases remain unknown. Here, we characterize an NRPS-PKS BGC with a putative lantibiotic dehydratase from the bacterium Stackebrandtia nassauensis (sna). Heterologous expression revealed several metabolites produced by the BGC, and the omission of selected biosynthetic enzymes revealed the biosynthetic sequence towards these compounds. The putative lantibiotic dehydratase catalyzes peptide bond formation that extends the peptide scaffold opposite to the NRPS and PKS biosynthetic direction. The condensation domain of the NRPS catalyzes the formation of a ureido group, and bioinformatics analysis revealed distinct active site residues of ureido-generating condensation (UreaC) domains. This work demonstrates that the annotated lantibiotic dehydratase serves as a separate amide bond-forming machinery in addition to the NRPS, and that the lantibiotic dehydratase enzyme family possesses diverse catalytic activities in the biosynthesis of both ribosomal and non-ribosomal natural products.
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Affiliation(s)
- Yue Yu
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Wilfred A van der Donk
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801
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3
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Zhong W, Aiosa N, Deutsch JM, Garg N, Agarwal V. Pseudobulbiferamides: Plasmid-Encoded Ureidopeptide Natural Products with Biosynthetic Gene Clusters Shared Among Marine Bacteria of Different Genera. JOURNAL OF NATURAL PRODUCTS 2023; 86:2414-2420. [PMID: 37713418 PMCID: PMC10616845 DOI: 10.1021/acs.jnatprod.3c00595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Indexed: 09/17/2023]
Abstract
Ureidopeptidic natural products possess a wide variety of favorable pharmacological properties. In addition, they have been shown to mediate core physiological functions in producer bacteria. Here, we report that similar ureidopeptidic natural products with conserved biosynthetic gene clusters are produced by different bacterial genera that coinhabit marine invertebrate microbiomes. We demonstrate that a Microbulbifer strain isolated from a marine sponge can produce two different classes of ureidopeptide natural products encoded by two different biosynthetic gene clusters that are positioned on the bacterial chromosome and on a plasmid. The plasmid encoded ureidopeptide natural products, which we term the pseudobulbiferamides (5-8), resemble the ureidopeptide natural products produced by Pseudovibrio, a different marine bacterial genus that is likewise present in marine sponge commensal microbiomes. Using imaging mass spectrometry, we find that the two classes of Microbulbifer-derived ureidopeptides occupy different physical spaces relative to the bacterial colony, perhaps implying different roles for these two compound classes in Microbulbifer physiology and environmental interactions.
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Affiliation(s)
- Weimao Zhong
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30332, United States
| | - Nicole Aiosa
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30332, United States
| | - Jessica M. Deutsch
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30332, United States
| | - Neha Garg
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30332, United States
- Center
for Microbial Dynamics and Infection, Georgia
Institute of Technology, Atlanta, Georgia 30332, United States
| | - Vinayak Agarwal
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30332, United States
- School
of Biological Sciences, Georgia Institute
of Technology, Atlanta, Georgia 30332, United States
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4
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Weisthal Algor S, Sukenik A, Carmeli S. Hydantoanabaenopeptins from Lake Kinneret Microcystis Bloom, Isolation, and Structure Elucidation of the Possible Intermediates in the Anabaenopeptins Biosynthesis. Mar Drugs 2023; 21:401. [PMID: 37504933 PMCID: PMC10381486 DOI: 10.3390/md21070401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 07/09/2023] [Accepted: 07/11/2023] [Indexed: 07/29/2023] Open
Abstract
Anabaenopeptins are common metabolites of cyanobacteria. In the course of reisolation of the known aeruginosins KT608A and KT608B for bioassay studies, we noticed the presence of some unknown anabaenopeptins in the extract of a Microcystis cell mass collected during the 2016 spring bloom event in Lake Kinneret, Israel. The 1H NMR spectra of some of these compounds presented a significant difference in the appearance of the ureido bridge protons, and their molecular masses did not match any one of the 152 known anabaenopeptins. Analyses of the 1D and 2D NMR, HRMS, and MS/MS spectra of the new compounds revealed their structures as the hydantoin derivatives of anabaenopeptins A, B, F, and 1[Dht]-anabaenopeptin A and oscillamide Y (1, 2, 3, 6, and 4, respectively) and a new anabaenopeptin, 1[Dht]-anabaenopeptin A (5). The known anabaenopeptins A, B, and F and oscillamide Y (7, 8, 9, and 10, respectively) were present in the extract as well. We propose that 1-4 and 6 are the possible missing intermediates in the previously proposed partial biosynthesis route to the anabaenopeptins. Compounds 1-6 were tested for inhibition of the serine proteases trypsin and chymotrypsin and found inactive at a final concentration of ca. 54 μM.
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Affiliation(s)
- Shira Weisthal Algor
- Raymond and Beverly Sackler Faculty of Exact Sciences, School of Chemistry, Tel Aviv University, Tel Aviv 69978, Israel
| | - Assaf Sukenik
- The Yigal Allon Kinneret Limnological Laboratory, Israel Oceanographic & Limnological Research Institute, Migdal 49500, Israel
| | - Shmuel Carmeli
- Raymond and Beverly Sackler Faculty of Exact Sciences, School of Chemistry, Tel Aviv University, Tel Aviv 69978, Israel
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5
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Cui Z, Nguyen H, Bhardwaj M, Wang X, Büschleb M, Lemke A, Schütz C, Rohrbacher C, Junghanns P, Koppermann S, Ducho C, Thorson JS, Van Lanen SG. Enzymatic C β-H Functionalization of l-Arg and l-Leu in Nonribosomally Derived Peptidyl Natural Products: A Tale of Two Oxidoreductases. J Am Chem Soc 2021; 143:19425-19437. [PMID: 34767710 DOI: 10.1021/jacs.1c08177] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Muraymycins are peptidyl nucleoside antibiotics that contain two Cβ-modified amino acids, (2S,3S)-capreomycidine and (2S,3S)-β-OH-Leu. The former is also a component of chymostatins, which are aldehyde-containing peptidic protease inhibitors that─like muraymycin─are derived from nonribosomal peptide synthetases (NRPSs). Using feeding experiments and in vitro characterization of 12 recombinant proteins, the biosynthetic mechanism for both nonproteinogenic amino acids is now defined. The formation of (2S,3S)-capreomycidine is shown to involve an FAD-dependent dehydrogenase:cyclase that requires an NRPS-bound pathway intermediate as a substrate. This cryptic dehydrogenation strategy is both temporally and mechanistically distinct in comparison to the biosynthesis of other capreomycidine diastereomers, which has previously been shown to proceed by Cβ-hydroxylation of free l-Arg catalyzed by a member of the nonheme Fe2+- and α-ketoglutarate (αKG)-dependent dioxygenase family and (eventually) a dehydration-mediated cyclization process catalyzed by a distinct enzyme(s). Contrary to our initial expectation, the sole nonheme Fe2+- and αKG-dependent dioxygenase candidate Mur15 encoded within the muraymycin gene cluster is instead demonstrated to catalyze specific Cβ hydroxylation of the Leu residue to generate (2S,3S)-β-OH-Leu that is found in most muraymycin congeners. Importantly, and in contrast to known l-Arg-Cβ-hydroxylases, the Mur15-catalyzed reaction occurs after the NRPS-mediated assembly of the peptide scaffold. This late-stage functionalization affords the opportunity to exploit Mur15 as a biocatalyst, proof of concept of which is provided.
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Affiliation(s)
- Zheng Cui
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Han Nguyen
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Minakshi Bhardwaj
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Xiachang Wang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Martin Büschleb
- Department of Chemistry, Institute of Organic and Biomolecular Chemistry, Georg-August-University, GöTammannstr. 2, 37077 Göttingen, Germany
| | - Anke Lemke
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123 Saarbrücken, Germany
| | - Christian Schütz
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123 Saarbrücken, Germany
| | - Christian Rohrbacher
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123 Saarbrücken, Germany
| | - Pierre Junghanns
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123 Saarbrücken, Germany
| | - Stefan Koppermann
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123 Saarbrücken, Germany
| | - Christian Ducho
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123 Saarbrücken, Germany
| | - Jon S Thorson
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Steven G Van Lanen
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
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6
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Anabaenopeptins: What We Know So Far. Toxins (Basel) 2021; 13:toxins13080522. [PMID: 34437393 PMCID: PMC8402340 DOI: 10.3390/toxins13080522] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/19/2021] [Accepted: 05/25/2021] [Indexed: 12/14/2022] Open
Abstract
Cyanobacteria are microorganisms with photosynthetic mechanisms capable of colonizing several distinct environments worldwide. They can produce a vast spectrum of bioactive compounds with different properties, resulting in an improved adaptative capacity. Their richness in secondary metabolites is related to their unique and diverse metabolic apparatus, such as Non-Ribosomal Peptide Synthetases (NRPSs). One important class of peptides produced by the non-ribosomal pathway is anabaenopeptins. These cyclic hexapeptides demonstrated inhibitory activity towards phosphatases and proteases, which could be related to their toxicity and adaptiveness against zooplankters and crustaceans. Thus, this review aims to identify key features related to anabaenopeptins, including the diversity of their structure, occurrence, the biosynthetic steps for their production, ecological roles, and biotechnological applications.
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7
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Ióca LP, Dai Y, Kunakom S, Diaz‐Espinosa J, Krunic A, Crnkovic CM, Orjala J, Sanchez LM, Ferreira AG, Berlinck RGS, Eustáquio AS. A Family of Nonribosomal Peptides Modulate Collective Behavior in
Pseudovibrio
Bacteria Isolated from Marine Sponges**. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202017320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Laura P. Ióca
- Department of Pharmaceutical Sciences College of Pharmacy University of Illinois at Chicago Chicago IL 60607 USA
- Center for Biomolecular Sciences College of Pharmacy University of Illinois at Chicago Chicago IL 60607 USA
- Instituto de Química de São Carlos Universidade de São Paulo São Carlos SP 13560-970 Brazil
| | - Yitao Dai
- Department of Pharmaceutical Sciences College of Pharmacy University of Illinois at Chicago Chicago IL 60607 USA
- Center for Biomolecular Sciences College of Pharmacy University of Illinois at Chicago Chicago IL 60607 USA
| | - Sylvia Kunakom
- Department of Pharmaceutical Sciences College of Pharmacy University of Illinois at Chicago Chicago IL 60607 USA
- Center for Biomolecular Sciences College of Pharmacy University of Illinois at Chicago Chicago IL 60607 USA
| | - Jennifer Diaz‐Espinosa
- Department of Pharmaceutical Sciences College of Pharmacy University of Illinois at Chicago Chicago IL 60607 USA
- Center for Biomolecular Sciences College of Pharmacy University of Illinois at Chicago Chicago IL 60607 USA
| | - Aleksej Krunic
- Department of Pharmaceutical Sciences College of Pharmacy University of Illinois at Chicago Chicago IL 60607 USA
| | - Camila M. Crnkovic
- Department of Pharmaceutical Sciences College of Pharmacy University of Illinois at Chicago Chicago IL 60607 USA
- Center for Biomolecular Sciences College of Pharmacy University of Illinois at Chicago Chicago IL 60607 USA
| | - Jimmy Orjala
- Department of Pharmaceutical Sciences College of Pharmacy University of Illinois at Chicago Chicago IL 60607 USA
- Center for Biomolecular Sciences College of Pharmacy University of Illinois at Chicago Chicago IL 60607 USA
| | - Laura M. Sanchez
- Department of Pharmaceutical Sciences College of Pharmacy University of Illinois at Chicago Chicago IL 60607 USA
| | - Antonio G. Ferreira
- Departamento de Química Universidade Federal de São Carlos São Carlos SP 13565-905 Brazil
| | - Roberto G. S. Berlinck
- Instituto de Química de São Carlos Universidade de São Paulo São Carlos SP 13560-970 Brazil
| | - Alessandra S. Eustáquio
- Department of Pharmaceutical Sciences College of Pharmacy University of Illinois at Chicago Chicago IL 60607 USA
- Center for Biomolecular Sciences College of Pharmacy University of Illinois at Chicago Chicago IL 60607 USA
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8
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Ióca LP, Dai Y, Kunakom S, Diaz-Espinosa J, Krunic A, Crnkovic CM, Orjala J, Sanchez LM, Ferreira AG, Berlinck RGS, Eustáquio AS. A Family of Nonribosomal Peptides Modulate Collective Behavior in Pseudovibrio Bacteria Isolated from Marine Sponges*. Angew Chem Int Ed Engl 2021; 60:15891-15898. [PMID: 33961724 PMCID: PMC8269750 DOI: 10.1002/anie.202017320] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 04/01/2021] [Indexed: 11/08/2022]
Abstract
Although swarming motility and biofilms are opposed collective behaviors, both contribute to bacterial survival and host colonization. Pseudovibrio bacteria have attracted attention because they are part of the microbiome of healthy marine sponges. Two-thirds of Pseudovibrio genomes contain a member of a nonribosomal peptide synthetase-polyketide synthase gene cluster family, which is also found sporadically in Pseudomonas pathogens of insects and plants. After developing reverse genetics for Pseudovibrio, we isolated heptapeptides with an ureido linkage and related nonadepsipeptides we termed pseudovibriamides A and B, respectively. A combination of genetics and imaging mass spectrometry experiments showed heptapetides were excreted, promoting motility and reducing biofilm formation. In contrast to lipopeptides widely known to affect motility/biofilms, pseudovibriamides are not surfactants. Our results expand current knowledge on metabolites mediating bacterial collective behavior.
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Affiliation(s)
- Laura P. Ióca
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
- Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
- Instituto de Química de São Carlos, Universidade de São Paulo, São Carlos, SP 13560-970, Brazil
| | - Yitao Dai
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
- Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Sylvia Kunakom
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
- Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Jennifer Diaz-Espinosa
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
- Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Aleksej Krunic
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Camila M. Crnkovic
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
- Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Jimmy Orjala
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
- Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Laura M. Sanchez
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Antonio G. Ferreira
- Departamento de Química, Universidade Federal de São Carlos, São Carlos, SP 13565-905, Brazil
| | - Roberto G. S. Berlinck
- Instituto de Química de São Carlos, Universidade de São Paulo, São Carlos, SP 13560-970, Brazil
| | - Alessandra S. Eustáquio
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
- Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
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9
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McErlean M, Liu X, Cui Z, Gust B, Van Lanen SG. Identification and characterization of enzymes involved in the biosynthesis of pyrimidine nucleoside antibiotics. Nat Prod Rep 2021; 38:1362-1407. [PMID: 33404015 DOI: 10.1039/d0np00064g] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Covering: up to September 2020 Hundreds of nucleoside-based natural products have been isolated from various microorganisms, several of which have been utilized in agriculture as pesticides and herbicides, in medicine as therapeutics for cancer and infectious disease, and as molecular probes to study biological processes. Natural products consisting of structural modifications of each of the canonical nucleosides have been discovered, ranging from simple modifications such as single-step alkylations or acylations to highly elaborate modifications that dramatically alter the nucleoside scaffold and require multiple enzyme-catalyzed reactions. A vast amount of genomic information has been uncovered the past two decades, which has subsequently allowed the first opportunity to interrogate the chemically intriguing enzymatic transformations for the latter type of modifications. This review highlights (i) the discovery and potential applications of structurally complex pyrimidine nucleoside antibiotics for which genetic information is known, (ii) the established reactions that convert the canonical pyrimidine into a new nucleoside scaffold, and (iii) the important tailoring reactions that impart further structural complexity to these molecules.
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Affiliation(s)
- M McErlean
- Department of Pharmaceutical Science, College of Pharmacy, University of Kentucky, USA.
| | - X Liu
- Department of Pharmaceutical Science, College of Pharmacy, University of Kentucky, USA.
| | - Z Cui
- Department of Pharmaceutical Science, College of Pharmacy, University of Kentucky, USA.
| | - B Gust
- Pharmaceutical Institute, Department of Pharmaceutical Biology, University of Tübingen, Germany
| | - S G Van Lanen
- Department of Pharmaceutical Science, College of Pharmacy, University of Kentucky, USA.
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10
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Tsutsumi H, Tanaka K, Chia JY, Mihara H. Short self‐assembling peptides with a urea bond: A new type of supramolecular peptide hydrogel materials. Pept Sci (Hoboken) 2020. [DOI: 10.1002/pep2.24214] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Hiroshi Tsutsumi
- School of Life Science and Technology, Tokyo Institute of Technology Yokohama Kanagawa Japan
| | - Kunifumi Tanaka
- School of Life Science and Technology, Tokyo Institute of Technology Yokohama Kanagawa Japan
| | - Jyh Yea Chia
- School of Life Science and Technology, Tokyo Institute of Technology Yokohama Kanagawa Japan
| | - Hisakazu Mihara
- School of Life Science and Technology, Tokyo Institute of Technology Yokohama Kanagawa Japan
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11
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Juettner NE, Bogen JP, Bauer TA, Knapp S, Pfeifer F, Huettenhain SH, Meusinger R, Kraemer A, Fuchsbauer HL. Decoding the Papain Inhibitor from Streptomyces mobaraensis as Being Hydroxylated Chymostatin Derivatives: Purification, Structure Analysis, and Putative Biosynthetic Pathway. JOURNAL OF NATURAL PRODUCTS 2020; 83:2983-2995. [PMID: 32998509 DOI: 10.1021/acs.jnatprod.0c00201] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Streptomyces mobaraensis produces the papain inhibitor SPI consisting of a 12 kDa protein and small active compounds (SPIac). Purification of the papain inhibitory compounds resulted in four diverse chymostatin derivatives that were characterized by NMR and MS analysis. Chymostatins are hydrophobic tetrapeptide aldehydes from streptomycetes, e.g., S. lavendulae and S. hygroscopicus, that reverse chymosin-mediated angiotensin activation and inhibit other serine and cysteine proteases. Chymotrypsin and papain were both inhibited by the SPIac compounds in the low nanomolar range. SPIac differs from the characterized chymostatins by the exchange of phenylalanine for tyrosine. The crystal structure of one of these chymostatin variants confirmed its molecular structure and revealed a S-configured hemithioacetal bond with the catalytic Cys25 thiolate as well as close interactions with hydrophobic S1 and S2 subsite amino acids. A model for chymostatin biosynthesis is provided based on the discovery of clustered genes encoding several putative nonribosomal peptide synthetases; among them, there is the unusual CstF enzyme that accommodates two canonical amino acid activation domains as well as three peptide carrier protein domains.
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Affiliation(s)
- Norbert E Juettner
- The Department of Chemical Engineering and Biotechnology, University of Applied Sciences of Darmstadt, Stephanstraße 7, 64295 Darmstadt, Germany
- The Department of Biology, Technische Universität Darmstadt, Schnittspahnstraße 10, 64287 Darmstadt, Germany
| | - Jan P Bogen
- The Department of Chemical Engineering and Biotechnology, University of Applied Sciences of Darmstadt, Stephanstraße 7, 64295 Darmstadt, Germany
| | - Tobias A Bauer
- The Department of Chemical Engineering and Biotechnology, University of Applied Sciences of Darmstadt, Stephanstraße 7, 64295 Darmstadt, Germany
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Max-von-Laue-Straße 15, 60438 Frankfurt am Main, Germany
| | - Felicitas Pfeifer
- The Department of Biology, Technische Universität Darmstadt, Schnittspahnstraße 10, 64287 Darmstadt, Germany
| | - Stefan H Huettenhain
- The Department of Chemical Engineering and Biotechnology, University of Applied Sciences of Darmstadt, Stephanstraße 7, 64295 Darmstadt, Germany
| | - Reinhard Meusinger
- The Department of Chemistry, Technische Universität Darmstadt, Alarich-Weiss-Straße 8, 64287 Darmstadt, Germany
| | - Andreas Kraemer
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438 Frankfurt am Main, Germany
| | - Hans-Lothar Fuchsbauer
- The Department of Chemical Engineering and Biotechnology, University of Applied Sciences of Darmstadt, Stephanstraße 7, 64295 Darmstadt, Germany
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12
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Arbour CA, Imperiali B. Uridine natural products: Challenging targets and inspiration for novel small molecule inhibitors. Bioorg Med Chem 2020; 28:115661. [PMID: 32828427 DOI: 10.1016/j.bmc.2020.115661] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 07/18/2020] [Indexed: 12/16/2022]
Abstract
Nucleoside derivatives, in particular those featuring uridine, are familiar components of the nucleoside family of bioactive natural products. The structural complexity and biological activities of these compounds have inspired research from organic chemistry and chemical biology communities seeking to develop novel approaches to assemble the challenging molecular targets, to gain inspiration for enzyme inhibitor development and to fuel antibiotic discovery efforts. This review will present recent case studies describing the total synthesis and biosynthesis of uridine natural products, and de novo synthetic efforts exploiting features of the natural products to produce simplified scaffolds. This research has culminated in the development of complementary strategies that can lead to effective uridine-based inhibitors and antibiotics. The strengths and challenges of the juxtaposing methods will be illustrated by examining select uridine natural products. Moreover, structure-activity relationships (SAR) for each natural product-inspired scaffold will be discussed, highlighting the impact on inhibitor development, with the aim of future uridine-based small molecule expansion.
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Affiliation(s)
- Christine A Arbour
- Department of Biology and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Barbara Imperiali
- Department of Biology and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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13
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Kaysser L. Built to bind: biosynthetic strategies for the formation of small-molecule protease inhibitors. Nat Prod Rep 2019; 36:1654-1686. [DOI: 10.1039/c8np00095f] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The discovery and characterization of natural product protease inhibitors has inspired the development of numerous pharmaceutical agents.
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Affiliation(s)
- Leonard Kaysser
- Department of Pharmaceutical Biology
- University of Tübingen
- 72076 Tübingen
- Germany
- German Centre for Infection Research (DZIF)
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Mullowney MW, McClure RA, Robey MT, Kelleher NL, Thomson RJ. Natural products from thioester reductase containing biosynthetic pathways. Nat Prod Rep 2018; 35:847-878. [PMID: 29916519 PMCID: PMC6146020 DOI: 10.1039/c8np00013a] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Covering: up to 2018 Thioester reductase domains catalyze two- and four-electron reductions to release natural products following assembly on nonribosomal peptide synthetases, polyketide synthases, and their hybrid biosynthetic complexes. This reductive off-loading of a natural product yields an aldehyde or alcohol, can initiate the formation of a macrocyclic imine, and contributes to important intermediates in a variety of biosyntheses, including those for polyketide alkaloids and pyrrolobenzodiazepines. Compounds that arise from reductase-terminated biosynthetic gene clusters are often reactive and exhibit biological activity. Biomedically important examples include the cancer therapeutic Yondelis (ecteinascidin 743), peptide aldehydes that inspired the first therapeutic proteasome inhibitor bortezomib, and numerous synthetic derivatives and antibody drug conjugates of the pyrrolobenzodiazepines. Recent advances in microbial genomics, metabolomics, bioinformatics, and reactivity-based labeling have facilitated the detection of these compounds for targeted isolation. Herein, we summarize known natural products arising from this important category, highlighting their occurrence in Nature, biosyntheses, biological activities, and the technologies used for their detection and identification. Additionally, we review publicly available genomic data to highlight the remaining potential for novel reductively tailored compounds and drug leads from microorganisms. This thorough retrospective highlights various molecular families with especially privileged bioactivity while illuminating challenges and prospects toward accelerating the discovery of new, high value natural products.
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Affiliation(s)
- Michael W Mullowney
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA.
| | - Ryan A McClure
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA.
| | - Matthew T Robey
- Department of Molecular Biosciences, Northwestern University, 2205 Tech Drive, Evanston, IL 60208, USA
| | - Neil L Kelleher
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA. and Department of Molecular Biosciences, Northwestern University, 2205 Tech Drive, Evanston, IL 60208, USA
| | - Regan J Thomson
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA.
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15
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Huang F, Tang J, He L, Ding X, Huang S, Zhang Y, Sun Y, Xia L. Heterologous expression and antitumor activity analysis of syringolin from Pseudomonas syringae pv. syringae B728a. Microb Cell Fact 2018; 17:31. [PMID: 29482589 PMCID: PMC6389232 DOI: 10.1186/s12934-018-0859-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 01/15/2018] [Indexed: 12/20/2022] Open
Abstract
Background Syringolin, synthesized by a mixed non-ribosomal peptide synthetase/polyketide synthetase in Pseudomonas syringae pv. syringae (Pss) B728a, is a novel eukaryotic proteasome inhibitor. Meanwhile, directly modifying large fragments in the PKS/NRPS gene cluster through traditional DNA engineering techniques is very difficult. In this study, we directly cloned the syl gene cluster from Pss B301D-R via Red/ET recombineering to effectively express syringolin in heterologous hosts. Results A 22 kb genomic fragment containing the sylA–sylE gene cluster was cloned into the pASK vector, and the obtained recombinant plasmid was transferred into Streptomyces coelicolor and Streptomyces lividans for the heterologous expression of syringolin. Transcriptional levels of recombinant syl gene in S. coelicolor M145 and S. lividans TK24 were evaluated via RT-PCR and the production of syringolin compounds was detected via LC–MS analysis. The extracts of the engineered bacteria showed cytotoxic activity to B16, 4T1, Meth-A, and HeLa tumor cells. It is noteworthy that the syringolin displayed anticancer activity against C57BL/6 mice with B16 murine melanoma tumor cells. Together, our results herein demonstrate the potential of syrinolin as effective antitumor agent that can treat various cancers without apparent adverse effects. Conclusions This present study is the first to report the heterologous expression of the entire syl gene cluster in Streptomyces strains and the successful expression of syringolin in both S. coelicolor M145 and S. lividans TK24. Syringolin derivatives demonstrated high cytotoxicity in vitro and in vivo. Hence, this paper provided an important foundation for the discovery and production of new antitumor compounds.
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Affiliation(s)
- Fan Huang
- Hunan Provincial Key Laboratory of Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, People's Republic of China
| | - Jianli Tang
- Hunan Provincial Key Laboratory of Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, People's Republic of China
| | - Lian He
- Hunan Provincial Key Laboratory of Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, People's Republic of China
| | - Xuezhi Ding
- Hunan Provincial Key Laboratory of Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, People's Republic of China
| | - Shaoya Huang
- Hunan Provincial Key Laboratory of Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, People's Republic of China
| | - Youming Zhang
- Hunan Provincial Key Laboratory of Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, People's Republic of China
| | - Yunjun Sun
- Hunan Provincial Key Laboratory of Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, People's Republic of China
| | - Liqiu Xia
- Hunan Provincial Key Laboratory of Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, People's Republic of China.
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16
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Maxson T, Tietz JI, Hudson GA, Guo XR, Tai HC, Mitchell DA. Targeting Reactive Carbonyls for Identifying Natural Products and Their Biosynthetic Origins. J Am Chem Soc 2016; 138:15157-15166. [PMID: 27797509 DOI: 10.1021/jacs.6b06848] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Natural products (NPs) serve important roles as drug candidates and as tools for chemical biology. However, traditional NP discovery, largely based on bioassay-guided approaches, is biased toward abundant compounds and rediscovery rates are high. Orthogonal methods to facilitate discovery of new NPs are thus needed, and herein we describe an isotope tag-based expansion of reactivity-based NP screening to address these shortcomings. Reactivity-based screening is a directed discovery approach in which a specific reactive handle on the NP is targeted by a chemoselective probe to enable its detection by mass spectrometry. In this study, we have developed an aminooxy-containing probe to guide the discovery of aldehyde- and ketone-containing NPs. To facilitate the detection of labeling events, the probe was dibrominated, imparting a unique isotopic signature to distinguish labeled metabolites from spectral noise. As a proof of concept, the probe was then utilized to screen a collection of bacterial extracts, leading to the identification of a new analogue of antipain, deimino-antipain. The bacterial producer of deimino-antipain was sequenced and the responsible biosynthetic gene cluster was identified by bioinformatic analysis and heterologous expression. These data reveal the previously undetermined genetic basis for a well-known family of aldehyde-containing, peptidic protease inhibitors, including antipain, chymostatin, leupeptin, elastatinal, and microbial alkaline protease inhibitor, which have been widely used for over 40 years.
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Affiliation(s)
- Tucker Maxson
- Department of Chemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Jonathan I Tietz
- Department of Chemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Graham A Hudson
- Department of Chemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Xiao Rui Guo
- Department of Chemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Hua-Chia Tai
- Department of Chemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Douglas A Mitchell
- Department of Chemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States.,Department of Microbiology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
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17
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Steele AD, Knouse KW, Keohane CE, Wuest WM. Total synthesis and biological investigation of (-)-promysalin. J Am Chem Soc 2015; 137:7314-7. [PMID: 26024439 DOI: 10.1021/jacs.5b04767] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Compounds that specifically target pathogenic bacteria are greatly needed, and identifying the method by which they act would provide new avenues of treatment. Herein we report the concise, high-yielding total synthesis (eight steps, 35% yield) of promysalin, a natural product that displays antivirulence phenotypes against pathogenic bacteria. Guided by bioinformatics, four diastereomers were synthesized, and the relative and absolute stereochemistries were confirmed by spectral and biological analysis. Finally, we show for the first time that promysalin displays two antivirulence phenotypes: the dispersion of mature biofilms and the inhibition of pyoverdine production, hinting at a unique pathogenic-specific mechanism of action.
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Affiliation(s)
- Andrew D Steele
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Kyle W Knouse
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Colleen E Keohane
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - William M Wuest
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
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18
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Production of proteasome inhibitor syringolin A by the endophyte Rhizobium sp. strain AP16. Appl Environ Microbiol 2014; 80:3741-8. [PMID: 24727275 DOI: 10.1128/aem.00395-14] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Syringolin A, the product of a mixed nonribosomal peptide synthetase/polyketide synthase encoded by the syl gene cluster, is a virulence factor secreted by certain Pseudomonas syringae strains. Together with the glidobactins produced by a number of beta- and gammaproteobacterial human and animal pathogens, it belongs to the syrbactins, a structurally novel class of proteasome inhibitors. In plants, proteasome inhibition by syringolin A-producing P. syringae strains leads to the suppression of host defense pathways requiring proteasome activity, such as the ones mediated by salicylic acid and jasmonic acid. Here we report the discovery of a syl-like gene cluster with some unusual features in the alphaproteobacterial endophyte Rhizobium sp. strain AP16 that encodes a putative syringolin A-like synthetase whose components share 55% to 65% sequence identity (72% to 79% similarity) at the amino acid level. As revealed by average nucleotide identity (ANI) calculations, this strain likely belongs to the same species as biocontrol strain R. rhizogenes K84 (formely known as Agrobacterium radiobacter K84), which, however, carries a nonfunctional deletion remnant of the syl-like gene cluster. Here we present a functional analysis of the syl-like gene cluster of Rhizobium sp. strain AP16 and demonstrate that this endophyte synthesizes syringolin A and some related minor variants, suggesting that proteasome inhibition by syrbactin production can be important not only for pathogens but also for endophytic bacteria in the interaction with their hosts.
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19
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Sidda JD, Song L, Poon V, Al-Bassam M, Lazos O, Buttner MJ, Challis GL, Corre C. Discovery of a family of γ-aminobutyrate ureas via rational derepression of a silent bacterial gene cluster. Chem Sci 2014. [DOI: 10.1039/c3sc52536h] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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20
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Dudler R. The role of bacterial phytotoxins in inhibiting the eukaryotic proteasome. Trends Microbiol 2013; 22:28-35. [PMID: 24284310 DOI: 10.1016/j.tim.2013.10.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Revised: 10/25/2013] [Accepted: 10/30/2013] [Indexed: 11/19/2022]
Abstract
The ubiquitin-26S proteasome degradation system (UPS) plays a pivotal role in almost all aspects of plant life, including defending against pathogens. Although the proteasome is important for plant immunity, it has been found to be also exploited by pathogens using effectors to increase their virulence. Recent work on the XopJ effector and syringolin A/syrbactins has highlighted host proteasome inhibition as a virulence strategy of pathogens. This review will focus on these recent developments.
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Affiliation(s)
- Robert Dudler
- Institute of Plant Biology, University of Zurich, Zollikerstrasse 107, CH-8008 Zurich, Switzerland.
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21
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Dudler R. Manipulation of host proteasomes as a virulence mechanism of plant pathogens. ANNUAL REVIEW OF PHYTOPATHOLOGY 2013; 51:521-42. [PMID: 23725468 DOI: 10.1146/annurev-phyto-082712-102312] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The ubiquitin-26S proteasome degradation system (UPS) in plants is involved in the signal transduction of many cellular processes, including host immune responses triggered by pathogen attack. Attacking pathogens produce effectors that are translocated into host cells, where they interfere with the host's defense signaling in very specific ways. Perhaps not surprising in view of the broad involvement of the host proteasome in plant immunity, certain bacterial effectors exploit or require the host UPS for their action, as currently best studied in Pseudomonas syringae. Intriguingly, some P. syringae strains also secrete the virulence factor syringolin A, which irreversibly inhibits the proteasome by a novel mechanism. Here, the role of the UPS in plant defense and its exploitation by effectors are summarized, and the biology, taxonomic distribution, and emerging implications for virulence strategies of syringolin A and similar compounds are discussed.
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Affiliation(s)
- Robert Dudler
- Institute of Plant Biology, University of Zurich, 8008 Zurich, Switzerland.
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22
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Dudnik A, Bigler L, Dudler R. Heterologous expression of a Photorhabdus luminescens syrbactin-like gene cluster results in production of the potent proteasome inhibitor glidobactin A. Microbiol Res 2012; 168:73-6. [PMID: 23079192 DOI: 10.1016/j.micres.2012.09.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Revised: 08/20/2012] [Accepted: 09/18/2012] [Indexed: 02/03/2023]
Abstract
Syrbactins are cyclic peptide derivatives which are known to inhibit the eukaryotic proteasome by irreversible covalent binding to its catalytic sites. The only two members of this family characterized to date, syringolin A and glidobactin A, are secreted by certain strains of Pseudomonas syringae pv. syringae and strain K481-B101 from the order Burkholderiales, respectively. Syrbactins are the products of mixed non-ribosomal peptide/polyketide synthases encoded by gene clusters with a characteristic architecture. Similar, but not identical gene clusters are present in several other bacterial genomes, including that of Photorhabdus luminescens subsp. laumondii TT01, which is therefore hypothesized to be able to produce a syrbactin-type proteasome inhibitor. Here we report the cloning of the putative syrbactins synthetase encoding gene cluster of Ph. luminescens into a cosmid vector and its heterologous expression in Pseudomonas putida. Analysis of culture supernatants of transformed Ps. putida by HPLC and mass spectrometry revealed the presence of glidobactin A, indicating that the syrbactins-like gene cluster of Ph. luminescens encodes a glidobactin A synthetase and that this organism has the capacity to synthesize glidobactin A.
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Affiliation(s)
- Alexey Dudnik
- Institute of Plant Biology, University of Zurich, Zollikerstrasse 107, CH-8008 Zurich, Switzerland
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23
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Condurso HL, Bruner SD. Structure and noncanonical chemistry of nonribosomal peptide biosynthetic machinery. Nat Prod Rep 2012; 29:1099-110. [PMID: 22729219 PMCID: PMC3442147 DOI: 10.1039/c2np20023f] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Structural biology has provided significant insights into the complex chemistry and macromolecular organization of nonribosomal peptide synthetases. In addition, novel pathways are continually described, expanding the knowledge of known biosynthetic chemistry.
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Affiliation(s)
- Heather L. Condurso
- Department of Chemistry, University of Florida, Gainesville, Florida, 32611, USA. Fax: 352 392 8758; Tel: 352 392 0525
| | - Steven D. Bruner
- Department of Chemistry, University of Florida, Gainesville, Florida, 32611, USA. Fax: 352 392 8758; Tel: 352 392 0525
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24
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Ramel C, Baechler N, Hildbrand M, Meyer M, Schädeli D, Dudler R. Regulation of biosynthesis of syringolin A, a Pseudomonas syringae virulence factor targeting the host proteasome. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2012; 25:1198-1208. [PMID: 22852810 DOI: 10.1094/mpmi-03-12-0070-r] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Many strains of the phytopathogenic bacterium Pseudomonas syringae pv. syringae synthesize the virulence factor syringolin A, which irreversibly inactivates the eukaryotic proteasome. Syringolin A, a peptide derivative, is synthesized by a mixed nonribosomal peptide/polyketide synthetase encoded by five clustered genes, sylA to sylE. Biosynthesis of syringolin A, previously shown to be dependent on the GacS/GacA two-component system, occurs in planta and in vitro but only under still culture conditions in a defined medium. Here, we show that the sylC, sylD, and sylE genes of P. syringae pv. syringae B301D-R form an operon transcribed by promoter sequences located between the sylCDE operon and the sylB gene residing on opposite strands. Assays of overlapping sylB and sylCDE promoter deletions translationally fused to the lacZ gene defined promoter sequences required for gene activity both in vitro and in planta. Activation of both promoters depended on the sylA gene encoding a helix-turn-helix (HTH) LuxR-type transcription factor which was shown to directly bind to the promoters. Activity of the sylA gene, in turn, required a functional salA gene, which also encodes an HTH LuxR-type transcription factor. Furthermore, evidence is presented that acyl-homoserine lactone-mediated quorum-sensing regulation is not involved in syringolin A biosynthesis but that oxygen concentration appears to play a role.
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25
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Bian X, Huang F, Stewart FA, Xia L, Zhang Y, Müller R. Direct Cloning, Genetic Engineering, and Heterologous Expression of the Syringolin Biosynthetic Gene Cluster inE. colithrough Red/ET Recombineering. Chembiochem 2012; 13:1946-52. [DOI: 10.1002/cbic.201200310] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2012] [Indexed: 11/11/2022]
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26
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Kehr JC, Gatte Picchi D, Dittmann E. Natural product biosyntheses in cyanobacteria: A treasure trove of unique enzymes. Beilstein J Org Chem 2011; 7:1622-35. [PMID: 22238540 PMCID: PMC3252866 DOI: 10.3762/bjoc.7.191] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2011] [Accepted: 09/19/2011] [Indexed: 11/25/2022] Open
Abstract
Cyanobacteria are prolific producers of natural products. Investigations into the biochemistry responsible for the formation of these compounds have revealed fascinating mechanisms that are not, or only rarely, found in other microorganisms. In this article, we survey the biosynthetic pathways of cyanobacteria isolated from freshwater, marine and terrestrial habitats. We especially emphasize modular nonribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) pathways and highlight the unique enzyme mechanisms that were elucidated or can be anticipated for the individual products. We further include ribosomal natural products and UV-absorbing pigments from cyanobacteria. Mechanistic insights obtained from the biochemical studies of cyanobacterial pathways can inspire the development of concepts for the design of bioactive compounds by synthetic-biology approaches in the future.
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Affiliation(s)
- Jan-Christoph Kehr
- University of Potsdam, Institute for Biochemistry and Biology, Karl-Liebknecht-Str. 24/25, 14476 Potsdam-Golm, Germany
| | - Douglas Gatte Picchi
- University of Potsdam, Institute for Biochemistry and Biology, Karl-Liebknecht-Str. 24/25, 14476 Potsdam-Golm, Germany
| | - Elke Dittmann
- University of Potsdam, Institute for Biochemistry and Biology, Karl-Liebknecht-Str. 24/25, 14476 Potsdam-Golm, Germany
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27
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Walsh CT, Zhang W. Chemical logic and enzymatic machinery for biological assembly of peptidyl nucleoside antibiotics. ACS Chem Biol 2011; 6:1000-7. [PMID: 21851099 DOI: 10.1021/cb200284p] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Peptidyl nucleoside antibiotics are a group of natural products targeting MraY, a bacterial translocase involved in the lipid-linked cycle in peptidoglycan biosynthesis. In this Perspective, we explore how Nature builds complex peptidyl nucleoside antibiotics scaffolds from simple nucleoside and amino acid building blocks. We discuss the current stage of research on biosynthetic pathways for peptidyl nucleoside antibiotics, primarily focusing on chemical logic and enzymatic machinery for uridine transformation and coupling to peptides. We further survey the nonribosomal biosynthetic paradigm for a subgroup of uridyl peptide antibiotics represented by pacidamycins, concluded by diversification opportunities for antibiotic optimization.
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Affiliation(s)
- Christopher T. Walsh
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Wenjun Zhang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
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28
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Krahn D, Ottmann C, Kaiser M. The chemistry and biology of syringolins, glidobactins and cepafungins (syrbactins). Nat Prod Rep 2011; 28:1854-67. [PMID: 21904761 DOI: 10.1039/c1np00048a] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Syrbactin is a subordinate term for the syringolin, glidobactin and cepafungin natural product families. Their grouping is based on their related molecular frameworks, similar biosynthesis pathways and, most importantly, identical modes-of-action, being irreversible proteasome inhibition. With this report, we aim to review their chemical biology, describing their common, but also differential characteristics.
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Affiliation(s)
- Daniel Krahn
- Zentrum für Medizinische Biotechnologie, Universität Duisburg-Essen, Germany
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29
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Wuest WM, Krahn D, Kaiser M, Walsh CT. Enzymatic timing and tailoring of macrolactamization in syringolin biosynthesis. Org Lett 2011; 13:4518-21. [PMID: 21812451 DOI: 10.1021/ol2016687] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The enzymatic activation of 3,4-dehydrolysine and subsequent formation of the 12-membered syringolin macrolactam were investigated. The timing of the desaturation was elucidated through the analysis of the initial adenylation domain of SylD. The SylD-TTE didomain was characterized and demonstrated to be the catalyst for formation of 12-membered macrocycles. When the SylD thioesterase domain was reacted with a family of acyclic CoA both natural and unnatural macrocycles were generated.
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Affiliation(s)
- William M Wuest
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
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30
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Imker HJ, Krahn D, Clerc J, Kaiser M, Walsh CT. N-acylation during glidobactin biosynthesis by the tridomain nonribosomal peptide synthetase module GlbF. ACTA ACUST UNITED AC 2011; 17:1077-83. [PMID: 21035730 DOI: 10.1016/j.chembiol.2010.08.007] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2010] [Revised: 07/30/2010] [Accepted: 08/04/2010] [Indexed: 10/18/2022]
Abstract
Glidobactins are hybrid NRPS-PKS natural products that function as irreversible proteasome inhibitors. A variety of medium chain 2(E),4(E)-diene fatty acids N-acylate the peptidolactam core and contribute significantly to the potency of proteasome inhibition. We have expressed the initiation NRPS module GlbF (C-A-T) in Escherichia coli and observe soluble active protein only on coexpression with the 8 kDa MbtH-like protein, GlbE. Following adenylation and installation of Thr as a T-domain thioester, the starter condensation domain utilizes fatty acyl-CoA donors to acylate the Thr(1) amino group and generate the fatty acyl-Thr(1)-S-pantetheinyl-GlbF intermediate to be used in subsequent chain elongation. Previously proposed to be mediated via acyl carrier protein fatty acid donors, direct utilization of fatty acyl-CoA donors for N-acylation of T-domain tethered amino acids is likely a common strategy for chain initiation in NRPS-mediated lipopeptide biosynthesis.
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Affiliation(s)
- Heidi J Imker
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
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Kolodziejek I, Misas-Villamil JC, Kaschani F, Clerc J, Gu C, Krahn D, Niessen S, Verdoes M, Willems LI, Overkleeft HS, Kaiser M, van der Hoorn RA. Proteasome activity imaging and profiling characterizes bacterial effector syringolin A. PLANT PHYSIOLOGY 2011; 155:477-89. [PMID: 21045122 PMCID: PMC3075764 DOI: 10.1104/pp.110.163733] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2010] [Accepted: 11/01/2010] [Indexed: 05/20/2023]
Abstract
Syringolin A (SylA) is a nonribosomal cyclic peptide produced by the bacterial pathogen Pseudomonas syringae pv syringae that can inhibit the eukaryotic proteasome. The proteasome is a multisubunit proteolytic complex that resides in the nucleus and cytoplasm and contains three subunits with different catalytic activities: β1, β2, and β5. Here, we studied how SylA targets the plant proteasome in living cells using activity-based profiling and imaging. We further developed this technology by introducing new, more selective probes and establishing procedures of noninvasive imaging in living Arabidopsis (Arabidopsis thaliana) cells. These studies showed that SylA preferentially targets β2 and β5 of the plant proteasome in vitro and in vivo. Structure-activity analysis revealed that the dipeptide tail of SylA contributes to β2 specificity and identified a nonreactive SylA derivative that proved essential for imaging experiments. Interestingly, subcellular imaging with probes based on epoxomicin and SylA showed that SylA accumulates in the nucleus of the plant cell and suggests that SylA targets the nuclear proteasome. Furthermore, subcellular fractionation studies showed that SylA labels nuclear and cytoplasmic proteasomes. The selectivity of SylA for the catalytic subunits and subcellular compartments is discussed, and the subunit selectivity is explained by crystallographic data.
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Kaysser L, Tang X, Wemakor E, Sedding K, Hennig S, Siebenberg S, Gust B. Identification of a Napsamycin Biosynthesis Gene Cluster by Genome Mining. Chembiochem 2010; 12:477-87. [PMID: 21290549 DOI: 10.1002/cbic.201000460] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2010] [Indexed: 11/11/2022]
Affiliation(s)
- Leonard Kaysser
- Eberhard-Karls-Universität Tübingen, Pharmazeutische Biologie, Auf der Morgenstelle 8, 72076 Tübingen, Germany
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Rackham EJ, Grüschow S, Ragab AE, Dickens S, Goss RJM. Pacidamycin biosynthesis: identification and heterologous expression of the first uridyl peptide antibiotic gene cluster. Chembiochem 2010; 11:1700-9. [PMID: 20665770 DOI: 10.1002/cbic.201000200] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The pacidamycins are antimicrobial nucleoside antibiotics produced by Streptomyces coeruleorubidus that inhibit translocase I, an essential bacterial enzyme yet to be clinically targeted. The novel pacidamycin scaffold is composed of a pseudopeptide backbone linked by a unique exocyclic enamide to an atypical 3'-deoxyuridine nucleoside. In addition, the peptidyl chain undergoes a double inversion caused by the incorporation of a diamino acid residue and a rare internal ureido moiety. The pacidamycin gene cluster was identified and sequenced, thereby providing the first example of a biosynthetic cluster for a member of the uridyl peptide family of antibiotics. Analysis of the 22 ORFs provided an insight into the biosynthesis of the unique structural features of the pacidamycins. Heterologous expression in Streptomyces lividans resulted in the production of pacidamycin D and the newly identified pacidamycin S, thus confirming the identity of the pacidamycin biosynthetic gene cluster. Identification of this cluster will enable the generation of new uridyl peptide antibiotics through combinatorial biosynthesis. The concise cluster will provide a useful model system through which to gain a fundamental understanding of the way in which nonribosomal peptide synthetases interact.
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Affiliation(s)
- Emma J Rackham
- School of Chemistry, University of East Anglia, Earlham Road, Norwich NR4 7TJ, UK
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Schellenberg B, Ramel C, Dudler R. Pseudomonas syringae virulence factor syringolin A counteracts stomatal immunity by proteasome inhibition. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2010; 23:1287-93. [PMID: 20831408 DOI: 10.1094/mpmi-04-10-0094] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The peptide derivative syringolin A, a product of a mixed nonribosomal peptide and polyketide synthetase, is secreted by certain strains of the phytopathogenic bacterium Pseudomonas syringae pv. syringae. Syringolin A was shown to be a virulence factor for P. syringae pv. syringae B728a because disease symptoms on its host Phaseolus vulgaris (bean) were greatly reduced upon inoculation with syringolin A-negative mutants. Syringolin A's mode of action was recently shown to be irreversible proteasome inhibition. Here, we report that syringolin A-producing bacteria are able to open stomata and, thus, counteract stomatal innate immunity in bean and Arabidopsis. Syringolin A-negative mutants, which induce stomatal closure, can be complemented by exogenous addition of not only syringolin A but also MG132, a well-characterized and structurally unrelated proteasome inhibitor. This demonstrates that proteasome activity is crucial for guard cell function. In Arabidopsis, stomatal immunity was salicylic acid (SA)-dependent and required NPR1, a key regulator of the SA-dependent defense pathway whose proteasome-dependent turnover has been reported to be essential for its function. Thus, elimination of NPR1 turnover through proteasome inhibition by syringolin A is an attractive hypothesis to explain the observed inhibition of stomatal immunity by syringolin A.
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Identification of the biosynthetic gene cluster for the pacidamycin group of peptidyl nucleoside antibiotics. Proc Natl Acad Sci U S A 2010; 107:16828-33. [PMID: 20826445 DOI: 10.1073/pnas.1011557107] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Pacidamycins are a family of uridyl tetra/pentapeptide antibiotics that act on the translocase MraY to block bacterial cell wall assembly. To elucidate the biosynthetic logic of pacidamcyins, a putative gene cluster was identified by 454 shotgun genome sequencing of the producer Streptomyces coeruleorubidus NRRL 18370. The 31-kb gene cluster encodes 22 proteins (PacA-V), including highly dissociated nonribosomal peptide synthetase (NRPS) modules and a variety of tailoring enzymes. Gene deletions confirmed that two NRPSs, PacP and PacO, are required for the biosynthesis of pacidamycins. Heterologous expression and in vitro assays of PacL, PacO, and PacP established reversible formation of m-Tyr-AMP, l-Ala-AMP, and diaminopropionyl-AMP, respectively, consistent with the amino acids found in pacidamycin scaffolds. The unusual Ala(4)-Phe(5) dipeptidyl ureido linkage was formed during in vitro assays containing purified PacL, PacJ, PacN, and PacO. Both the genetic and enzymatic studies validate identification of the biosynthetic genes for this subclass of uridyl peptide antibiotics and provide the basis for future mechanistic study of their biosynthesis.
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Abstract
Total syntheses of two recently discovered proteasome inhibitors, syringolin A and B, are reported. The key to our approach was creation of the alpha,beta-unsaturated 12-membered lactam via intramolecular Horner-Wadsworth-Emmons reaction. Such reactions have been broadly used to prepared macrolactones, but this work presents a rarer example of its application to macrolactams. The final steps involved attachment of the bis(valinyl)urea side chain using peptide coupling procedures, including a method based on the unprotected valine N-carboxy anhydride. The additional alkene of syringolin A was created through cross-metathesis.
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Affiliation(s)
- Michael C Pirrung
- Department of Chemistry, University of California, Riverside, California 92521, USA.
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Rouhiainen L, Jokela J, Fewer DP, Urmann M, Sivonen K. Two alternative starter modules for the non-ribosomal biosynthesis of specific anabaenopeptin variants in Anabaena (Cyanobacteria). ACTA ACUST UNITED AC 2010; 17:265-73. [PMID: 20338518 DOI: 10.1016/j.chembiol.2010.01.017] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2009] [Revised: 01/27/2010] [Accepted: 01/28/2010] [Indexed: 11/25/2022]
Abstract
Anabaenopeptins are a diverse family of cyclic hexapeptide protease inhibitors produced by cyanobacteria that contain a conserved ureido bond and D-Lys moiety. Here we demonstrate that anabaenopeptins are assembled on a nonribosomal peptide synthetase enzyme complex encoded by a 32 kb apt gene cluster in the cyanobacterium Anabaena sp. strain 90. Surprisingly, the gene cluster encoded two alternative starter modules organized in separate bimodular proteins. The starter modules display high substrate specificity for L-Arg/L-Lys and L-Tyr, respectively, and allow the specific biosynthesis of different anabaenopeptin variants. The two starter modules were found also in other Anabaena strains. However, just a single module was present in the anabaenopeptin gene clusters of Nostoc and Nodularia, respectively. The organization of the apt gene cluster in Anabaena represents an exception to the established colinearity rule of linear non-ribosomal peptide synthetases.
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Affiliation(s)
- Leo Rouhiainen
- Department of Food and Environmental Sciences, P.O. Box 56, Viikki Biocenter, Viikinkaari 9, FIN-00014, University of Helsinki, Finland
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Erol Ö, Schäberle TF, Schmitz A, Rachid S, Gurgui C, El Omari M, Lohr F, Kehraus S, Piel J, Müller R, König GM. Biosynthesis of the Myxobacterial Antibiotic Corallopyronin A. Chembiochem 2010; 11:1253-65. [DOI: 10.1002/cbic.201000085] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Clerc J, Schellenberg B, Groll M, Bachmann AS, Huber R, Dudler R, Kaiser M. Convergent Synthesis and Biological Evaluation of Syringolin A and Derivatives as Eukaryotic 20S Proteasome Inhibitors. European J Org Chem 2010. [DOI: 10.1002/ejoc.201000317] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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