1
|
Paulo BS, Recchia MJJ, Lee S, Fergusson CH, Romanowski SB, Hernandez A, Krull N, Liu DY, Cavanagh H, Bos A, Gray CA, Murphy BT, Linington RG, Eustaquio AS. Discovery of megapolipeptins by genome mining of a Burkholderiales bacteria collection. Chem Sci 2024:d4sc03594a. [PMID: 39309087 PMCID: PMC11411415 DOI: 10.1039/d4sc03594a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Accepted: 09/11/2024] [Indexed: 09/25/2024] Open
Abstract
Burkholderiales bacteria have emerged as a promising source of structurally diverse natural products that are expected to play important ecological and industrial roles. This order ranks in the top three in terms of predicted natural product diversity from available genomes, warranting further genome sequencing efforts. However, a major hurdle in obtaining the predicted products is that biosynthetic genes are often 'silent' or poorly expressed. Here we report complementary strain isolation, genomics, metabolomics, and synthetic biology approaches to enable natural product discovery. First, we built a collection of 316 rhizosphere-derived Burkholderiales strains over the course of five years. We then selected 115 strains for sequencing using the mass spectrometry pipeline IDBac to avoid strain redundancy. After predicting and comparing the biosynthetic potential of each strain, a biosynthetic gene cluster that was silent in the native Paraburkholderia megapolitana and Paraburkholderia acidicola producers was cloned and activated by heterologous expression in a Burkholderia sp. host, yielding megapolipeptins A and B. Megapolipeptins are unusual polyketide, nonribosomal peptide, and polyunsaturated fatty acid hybrids that show low structural similarity to known natural products, highlighting the advantage of our Burkholderiales genomics-driven and synthetic biology-enabled pipeline to discover novel natural products.
Collapse
Affiliation(s)
- Bruno S Paulo
- 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
| | | | - Sanghoon Lee
- Department of Chemistry, Simon Fraser University Burnaby BC V5H 1S6 Canada
| | - Claire H Fergusson
- Department of Chemistry, Simon Fraser University Burnaby BC V5H 1S6 Canada
| | - Sean B Romanowski
- 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
| | - Antonio Hernandez
- 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
| | - Nyssa Krull
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago Chicago IL 60607 USA
| | - Dennis Y Liu
- Department of Chemistry, Simon Fraser University Burnaby BC V5H 1S6 Canada
| | - Hannah Cavanagh
- Department of Chemistry, Simon Fraser University Burnaby BC V5H 1S6 Canada
| | - Allyson Bos
- Department of Biological Sciences, University of New Brunswick Saint John New Brunswick E2L 4L5 Canada
| | - Christopher A Gray
- Department of Biological Sciences, University of New Brunswick Saint John New Brunswick E2L 4L5 Canada
| | - Brian T Murphy
- 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
| | - Roger G Linington
- Department of Chemistry, Simon Fraser University Burnaby BC V5H 1S6 Canada
| | - Alessandra S Eustaquio
- 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
| |
Collapse
|
2
|
Jian X, Pang F, Hobson C, Jenner M, Alkhalaf LM, Challis GL. Antibiotic Skeletal Diversification via Differential Enoylreductase Recruitment and Module Iteration in trans-Acyltransferase Polyketide Synthases. J Am Chem Soc 2024; 146:6114-6124. [PMID: 38389455 PMCID: PMC10921412 DOI: 10.1021/jacs.3c13667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 02/01/2024] [Accepted: 02/06/2024] [Indexed: 02/24/2024]
Abstract
Microorganisms are remarkable chemists capable of assembling complex molecular architectures that penetrate cells and bind biomolecular targets with exquisite selectivity. Consequently, microbial natural products have wide-ranging applications in medicine and agriculture. How the "blind watchmaker" of evolution creates skeletal diversity is a key question in natural products research. Comparative analysis of biosynthetic pathways to structurally related metabolites is an insightful approach to addressing this. Here, we report comparative biosynthetic investigations of gladiolin, a polyketide antibiotic from Burkholderia gladioli with promising activity against multidrug-resistant Mycobacterium tuberculosis, and etnangien, a structurally related antibiotic produced by Sorangium cellulosum. Although these metabolites have very similar macrolide cores, their C21 side chains differ significantly in both length and degree of saturation. Surprisingly, the trans-acyltransferase polyketide synthases (PKSs) that assemble these antibiotics are almost identical, raising intriguing questions about mechanisms underlying structural diversification in this important class of biosynthetic assembly line. In vitro reconstitution of key biosynthetic transformations using simplified substrate analogues, combined with gene deletion and complementation experiments, enabled us to elucidate the origin of all the structural differences in the C21 side chains of gladiolin and etnangien. The more saturated gladiolin side chain arises from a cis-acting enoylreductase (ER) domain in module 1 and in trans recruitment of a standalone ER to module 5 of the PKS. Remarkably, module 5 of the gladiolin PKS is intrinsically iterative in the absence of the standalone ER, accounting for the longer side chain in etnangien. These findings have important implications for biosynthetic engineering approaches to the creation of novel polyketide skeletons.
Collapse
Affiliation(s)
- Xinyun Jian
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, U.K.
- Warwick
Integrative Synthetic Biology Centre, University
of Warwick, Coventry CV4 7AL, U.K.
- Department
of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
- ARC
Centre of Excellence for Innovations in Protein and Peptide Science, Monash University, Clayton, VIC 3800, Australia
| | - Fang Pang
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, U.K.
| | - Christian Hobson
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, U.K.
| | - Matthew Jenner
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, U.K.
- Warwick
Integrative Synthetic Biology Centre, University
of Warwick, Coventry CV4 7AL, U.K.
| | - Lona M. Alkhalaf
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, U.K.
| | - Gregory L. Challis
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, U.K.
- Warwick
Integrative Synthetic Biology Centre, University
of Warwick, Coventry CV4 7AL, U.K.
- Department
of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
- ARC
Centre of Excellence for Innovations in Protein and Peptide Science, Monash University, Clayton, VIC 3800, Australia
| |
Collapse
|
3
|
Steinmetz T, Lombe BK, Nett M. Intermediates and shunt products of massiliachelin biosynthesis in Massilia sp. NR 4-1. Beilstein J Org Chem 2023; 19:909-917. [PMID: 37377775 PMCID: PMC10291242 DOI: 10.3762/bjoc.19.69] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023] Open
Abstract
Siderophores are small molecules secreted by microorganisms in order to scavenge iron from the environment. An example is the thiazoline-containing natural product massiliachelin, which is produced by Massilia sp. NR 4-1 under iron-deficient conditions. Based on experimental evidence and genome analysis, it was suspected that this bacterium synthesizes further iron-chelating molecules. After a thorough inspection of its metabolic profile, six previously overlooked compounds were isolated that were active in the chrome azurol S (CAS) assay. Mass spectrometric measurements and nuclear magnetic resonance spectroscopic analyses identified these compounds as possible biosynthetic intermediates or shunt products of massiliachelin. Their bioactivity was tested against one Gram-positive and three Gram-negative bacteria.
Collapse
Affiliation(s)
- Till Steinmetz
- Department of Biochemical and Chemical Engineering, Laboratory of Technical Biology, TU Dortmund University, Emil-Figge-Strasse 66, 44227 Dortmund, Germany
| | - Blaise Kimbadi Lombe
- Department of Biochemical and Chemical Engineering, Laboratory of Technical Biology, TU Dortmund University, Emil-Figge-Strasse 66, 44227 Dortmund, Germany
| | - Markus Nett
- Department of Biochemical and Chemical Engineering, Laboratory of Technical Biology, TU Dortmund University, Emil-Figge-Strasse 66, 44227 Dortmund, Germany
| |
Collapse
|
4
|
Abstract
Peptide natural products constitute a major class of secondary metabolites produced by microorganisms (mostly bacteria and fungi). In the past several decades, researchers have gained extensive knowledge about nonribosomal peptides (NRPs) generated by ribosome-independent systems, namely, NRP synthetases (NRPSs). NRPSs are multifunctional enzymes consisting of semiautonomous domains that form a peptide backbone. Using a thiotemplate mechanism that employs assembly-line logic with multiple modules, NRPSs activate, tether, and modify amino acid building blocks, sequentially elongating the peptide chain before releasing the complete peptide. Adenylation, thiolation, condensation, and thioesterase domains play central roles in these reactions. This chapter focuses on the current understanding of these central domains in NRPS assembly-line enzymology.
Collapse
Affiliation(s)
- Chitose Maruyama
- Graduate School of Bioscience and Biotechnology, Fukui Prefectural University, Fukui, Japan
- Fukui Bioincubation Center (FBIC), Fukui Prefectural University, Fukui, Japan
| | - Yoshimitsu Hamano
- Graduate School of Bioscience and Biotechnology, Fukui Prefectural University, Fukui, Japan.
- Fukui Bioincubation Center (FBIC), Fukui Prefectural University, Fukui, Japan.
| |
Collapse
|
5
|
Adaikpoh BI, Fernandez HN, Eustáquio AS. Biotechnology approaches for natural product discovery, engineering, and production based on Burkholderia bacteria. Curr Opin Biotechnol 2022; 77:102782. [PMID: 36049254 DOI: 10.1016/j.copbio.2022.102782] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 07/13/2022] [Accepted: 07/26/2022] [Indexed: 11/15/2022]
Abstract
Bacterial natural products (NPs) retain high value in discovery efforts for applications in medicine and agriculture. Burkholderia β-Proteobacteria are a promising source of NPs. In this review, we summarize the recently developed genetic manipulation techniques used to access silent/cryptic biosynthetic gene clusters from Burkholderia native producers. We also discuss the development of Burkholderia bacteria as heterologous hosts and the application of Burkholderia in industrial-scale production of NPs. Genetic engineering and fermentation media optimization have enabled the industrial-scale production of at least two Burkholderia NPs. The biotechnology approaches discussed here will continue to facilitate the discovery and development of NPs from Burkholderia.
Collapse
Affiliation(s)
- Barbara I Adaikpoh
- Department of Pharmaceutical Sciences and Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Hannah N Fernandez
- Department of Pharmaceutical Sciences and Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Alessandra S Eustáquio
- Department of Pharmaceutical Sciences and Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA.
| |
Collapse
|
6
|
Reitz ZL, Medema MH. Genome mining strategies for metallophore discovery. Curr Opin Biotechnol 2022; 77:102757. [PMID: 35914390 DOI: 10.1016/j.copbio.2022.102757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/17/2022] [Accepted: 06/21/2022] [Indexed: 11/03/2022]
Abstract
Many bacteria use small-molecule chelators called metallophores to acquire trace metals from their environment. These molecules play a central role in interactions between bacteria, plants, and animals. Hence, knowing their full diversity is key to combatting infectious diseases as well as harnessing beneficial microbial communities. Metallophore discovery has been streamlined by advances in genome mining, where genomes are scanned for genes involved in metallophore biosynthesis. This review highlights recent trends and advances in predicting the presence and structure of metallophores based solely on genomic information. Recent work suggests new families of metallophores remain hidden from current homology-based approaches. Their discovery will require new genome mining approaches that move beyond biosynthesis to consider metallophore transporters, regulation, and evolution.
Collapse
Affiliation(s)
- Zachary L Reitz
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands.
| |
Collapse
|
7
|
Zhang H, Zhang C, Li Q, Ma J, Ju J. Metabolic Blockade-Based Genome Mining Reveals Lipochain-Linked Dihydro-β-alanine Synthetases Involved in Autucedine Biosynthesis. Org Lett 2022; 24:5535-5540. [PMID: 35876054 DOI: 10.1021/acs.orglett.2c01957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Huaran Zhang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No.1119, Haibin Rd., Nansha District, Guangzhou 511458, China
- College of Oceanology, University of Chinese Academy of Sciences, Qingdao 266400, China
| | - Chunyan Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Qinglian Li
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No.1119, Haibin Rd., Nansha District, Guangzhou 511458, China
- College of Oceanology, University of Chinese Academy of Sciences, Qingdao 266400, China
| | - Junying Ma
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No.1119, Haibin Rd., Nansha District, Guangzhou 511458, China
- College of Oceanology, University of Chinese Academy of Sciences, Qingdao 266400, China
| | - Jianhua Ju
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No.1119, Haibin Rd., Nansha District, Guangzhou 511458, China
- College of Oceanology, University of Chinese Academy of Sciences, Qingdao 266400, China
| |
Collapse
|
8
|
Duban M, Cociancich S, Leclère V. Nonribosomal Peptide Synthesis Definitely Working Out of the Rules. Microorganisms 2022; 10:577. [PMID: 35336152 PMCID: PMC8949500 DOI: 10.3390/microorganisms10030577] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/02/2022] [Accepted: 03/03/2022] [Indexed: 12/04/2022] Open
Abstract
Nonribosomal peptides are microbial secondary metabolites exhibiting a tremendous structural diversity and a broad range of biological activities useful in the medical and agro-ecological fields. They are built up by huge multimodular enzymes called nonribosomal peptide synthetases. These synthetases are organized in modules constituted of adenylation, thiolation, and condensation core domains. As such, each module governs, according to the collinearity rule, the incorporation of a monomer within the growing peptide. The release of the peptide from the assembly chain is finally performed by a terminal core thioesterase domain. Secondary domains with modifying catalytic activities such as epimerization or methylation are sometimes included in the assembly lines as supplementary domains. This assembly line structure is analyzed by bioinformatics tools to predict the sequence and structure of the final peptides according to the sequence of the corresponding synthetases. However, a constantly expanding literature unravels new examples of nonribosomal synthetases exhibiting very rare domains and noncanonical organizations of domains and modules, leading to several amazing strategies developed by microorganisms to synthesize nonribosomal peptides. In this review, through several examples, we aim at highlighting these noncanonical pathways in order for the readers to perceive their complexity.
Collapse
Affiliation(s)
- Matthieu Duban
- Université de Lille, Université de Liège, UMRT 1158 BioEcoAgro, Métabolites Secondaires d’origine Microbienne, Institut Charles Viollette, F-59000 Lille, France;
| | - Stéphane Cociancich
- CIRAD, UMR PHIM, F-34398 Montpellier, France;
- PHIM, Université Montpellier, CIRAD, INRAE, Institut Agro, IRD, F-34398 Montpellier, France
| | - Valérie Leclère
- Université de Lille, Université de Liège, UMRT 1158 BioEcoAgro, Métabolites Secondaires d’origine Microbienne, Institut Charles Viollette, F-59000 Lille, France;
| |
Collapse
|
9
|
Wenski SL, Thiengmag S, Helfrich EJ. Complex peptide natural products: Biosynthetic principles, challenges and opportunities for pathway engineering. Synth Syst Biotechnol 2022; 7:631-647. [PMID: 35224231 PMCID: PMC8842026 DOI: 10.1016/j.synbio.2022.01.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/19/2022] [Accepted: 01/20/2022] [Indexed: 01/03/2023] Open
Abstract
Complex peptide natural products exhibit diverse biological functions and a wide range of physico-chemical properties. As a result, many peptides have entered the clinics for various applications. Two main routes for the biosynthesis of complex peptides have evolved in nature: ribosomally synthesized and post-translationally modified peptide (RiPP) biosynthetic pathways and non-ribosomal peptide synthetases (NRPSs). Insights into both bioorthogonal peptide biosynthetic strategies led to the establishment of universal principles for each of the two routes. These universal rules can be leveraged for the targeted identification of novel peptide biosynthetic blueprints in genome sequences and used for the rational engineering of biosynthetic pathways to produce non-natural peptides. In this review, we contrast the key principles of both biosynthetic routes and compare the different biochemical strategies to install the most frequently encountered peptide modifications. In addition, the influence of the fundamentally different biosynthetic principles on past, current and future engineering approaches is illustrated. Despite the different biosynthetic principles of both peptide biosynthetic routes, the arsenal of characterized peptide modifications encountered in RiPP and NRPS systems is largely overlapping. The continuous expansion of the biocatalytic toolbox of peptide modifying enzymes for both routes paves the way towards the production of complex tailor-made peptides and opens up the possibility to produce NRPS-derived peptides using the ribosomal route and vice versa.
Collapse
Affiliation(s)
- Sebastian L. Wenski
- Institute for Molecular Bio Science, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
- LOEWE Center for Translational Biodiversity Genomics (TBG), 60325, Frankfurt am Main, Germany
| | - Sirinthra Thiengmag
- Institute for Molecular Bio Science, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
- LOEWE Center for Translational Biodiversity Genomics (TBG), 60325, Frankfurt am Main, Germany
| | - Eric J.N. Helfrich
- Institute for Molecular Bio Science, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
- LOEWE Center for Translational Biodiversity Genomics (TBG), 60325, Frankfurt am Main, Germany
| |
Collapse
|
10
|
Bach E, Passaglia LMP, Jiao J, Gross H. Burkholderia in the genomic era: from taxonomy to the discovery of new antimicrobial secondary metabolites. Crit Rev Microbiol 2021; 48:121-160. [PMID: 34346791 DOI: 10.1080/1040841x.2021.1946009] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Species of Burkholderia are highly versatile being found not only abundantly in soil, but also as plants and animals' commensals or pathogens. Their complex multireplicon genomes harbour an impressive number of polyketide synthase (PKS) and nonribosomal peptide-synthetase (NRPS) genes coding for the production of antimicrobial secondary metabolites (SMs), which have been successfully deciphered by genome-guided tools. Moreover, genome metrics supported the split of this genus into Burkholderia sensu stricto (s.s.) and five new other genera. Here, we show that the successful antimicrobial SMs producers belong to Burkholderia s.s. Additionally, we reviewed the occurrence, bioactivities, modes of action, structural, and biosynthetic information of thirty-eight Burkholderia antimicrobial SMs shedding light on their diversity, complexity, and uniqueness as well as the importance of genome-guided strategies to facilitate their discovery. Several Burkholderia NRPS and PKS display unusual features, which are reflected in their structural diversity, important bioactivities, and varied modes of action. Up to now, it is possible to observe a general tendency of Burkholderia SMs being more active against fungi. Although the modes of action and biosynthetic gene clusters of many SMs remain unknown, we highlight the potential of Burkholderia SMs as alternatives to fight against new diseases and antibiotic resistance.
Collapse
Affiliation(s)
- Evelise Bach
- Departamento de Genética and Programa de Pós-graduação em Genética e Biologia Molecular, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Luciane Maria Pereira Passaglia
- Departamento de Genética and Programa de Pós-graduação em Genética e Biologia Molecular, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Junjing Jiao
- Department for Pharmaceutical Biology, Pharmaceutical Institute, University of Tübingen, Tübingen, Germany
| | - Harald Gross
- Department for Pharmaceutical Biology, Pharmaceutical Institute, University of Tübingen, Tübingen, Germany
| |
Collapse
|
11
|
He HY, Ryan KS. Glycine-derived nitronates bifurcate to O-methylation or denitrification in bacteria. Nat Chem 2021; 13:599-606. [PMID: 33782561 DOI: 10.1038/s41557-021-00656-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 02/08/2021] [Indexed: 02/01/2023]
Abstract
Natural products with rare functional groups are likely to be constructed by unique biosynthetic enzymes. One such rare functional group is the O-methyl nitronate, which can undergo [3 + 2] cycloaddition reactions with olefins in mild conditions. O-methyl nitronates are found in some natural products; however, how such O-methyl nitronates are assembled biosynthetically is unknown. Here we show that the assembly of the O-methyl nitronate in the natural product enteromycin carboxamide occurs via activation of glycine on a peptidyl carrier protein, followed by reaction with a diiron oxygenase to give a nitronate intermediate and then with a methyltransferase to give an O-methyl nitronate. Guided by the discovery of this pathway, we then identify related cryptic biosynthetic gene cassettes in other bacteria and show that these alternative gene cassettes can, instead, facilitate oxidative denitrification of glycine-derived nitronates. Altogether, our work reveals bifurcating pathways from a central glycine-derived nitronate intermediate in bacteria.
Collapse
Affiliation(s)
- Hai-Yan He
- Department of Chemistry, The University of British Columbia, Vancouver, British Columbia, Canada.,Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China
| | - Katherine S Ryan
- Department of Chemistry, The University of British Columbia, Vancouver, British Columbia, Canada.
| |
Collapse
|
12
|
Genomics-Driven Activation of Silent Biosynthetic Gene Clusters in Burkholderia gladioli by Screening Recombineering System. Molecules 2021; 26:molecules26030700. [PMID: 33572733 PMCID: PMC7866175 DOI: 10.3390/molecules26030700] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 01/19/2021] [Accepted: 01/21/2021] [Indexed: 01/10/2023] Open
Abstract
The Burkholderia genus possesses ecological and metabolic diversities. A large number of silent biosynthetic gene clusters (BGCs) in the Burkholderia genome remain uncharacterized and represent a promising resource for new natural product discovery. However, exploitation of the metabolomic potential of Burkholderia is limited by the absence of efficient genetic manipulation tools. Here, we screened a bacteriophage recombinase system Redγ-BAS, which was functional for genome modification in the plant pathogen Burkholderia gladioli ATCC 10248. By using this recombineering tool, the constitutive promoters were precisely inserted in the genome, leading to activation of two silent nonribosomal peptide synthetase gene clusters (bgdd and hgdd) and production of corresponding new classes of lipopeptides, burriogladiodins A–H (1–8) and haereogladiodins A–B (9–10). Structure elucidation revealed an unnatural amino acid Z- dehydrobutyrine (Dhb) in 1–8 and an E-Dhb in 9–10. Notably, compounds 2–4 and 9 feature an unusual threonine tag that is longer than the predicted collinearity assembly lines. The structural diversity of burriogladiodins was derived from the relaxed substrate specificity of the fifth adenylation domain as well as chain termination conducted by water or threonine. The recombinase-mediating genome editing system is not only applicable in B. gladioli, but also possesses great potential for mining meaningful silent gene clusters from other Burkholderia species.
Collapse
|
13
|
Dose B, Ross C, Niehs SP, Scherlach K, Bauer JP, Hertweck C. Food-Poisoning Bacteria Employ a Citrate Synthase and a Type II NRPS To Synthesize Bolaamphiphilic Lipopeptide Antibiotics*. Angew Chem Int Ed Engl 2020; 59:21535-21540. [PMID: 32780428 PMCID: PMC7756705 DOI: 10.1002/anie.202009107] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Indexed: 12/21/2022]
Abstract
Mining the genome of the food-spoiling bacterium Burkholderia gladioli pv. cocovenenans revealed five nonribosomal peptide synthetase (NRPS) gene clusters, including an orphan gene locus (bol). Gene inactivation and metabolic profiling linked the bol gene cluster to novel bolaamphiphilic lipopeptides with antimycobacterial activity. A combination of chemical analysis and bioinformatics elucidated the structures of bolagladin A and B, lipocyclopeptides featuring an unusual dehydro-β-alanine enamide linker fused to an unprecedented tricarboxylic fatty acid tail. Through a series of targeted gene deletions, we proved the involvement of a designated citrate synthase (CS), priming ketosynthases III (KS III), a type II NRPS, including a novel desaturase for enamide formation, and a multimodular NRPS in generating the cyclopeptide. Network analyses revealed the evolutionary origin of the CS and identified cryptic CS/NRPS gene loci in various bacterial genomes.
Collapse
Affiliation(s)
- Benjamin Dose
- Leibniz Institute for Natural Product Research and Infection Biology, HKIBeutenbergstrasse 11a07745JenaGermany
| | - Claudia Ross
- Leibniz Institute for Natural Product Research and Infection Biology, HKIBeutenbergstrasse 11a07745JenaGermany
| | - Sarah P. Niehs
- Leibniz Institute for Natural Product Research and Infection Biology, HKIBeutenbergstrasse 11a07745JenaGermany
| | - Kirstin Scherlach
- Leibniz Institute for Natural Product Research and Infection Biology, HKIBeutenbergstrasse 11a07745JenaGermany
| | - Johanna P. Bauer
- Leibniz Institute for Natural Product Research and Infection Biology, HKIBeutenbergstrasse 11a07745JenaGermany
| | - Christian Hertweck
- Leibniz Institute for Natural Product Research and Infection Biology, HKIBeutenbergstrasse 11a07745JenaGermany
- Faculty of Biological SciencesFriedrich Schiller University Jena07743JenaGermany
| |
Collapse
|
14
|
Nakou IT, Jenner M, Dashti Y, Romero‐Canelón I, Masschelein J, Mahenthiralingam E, Challis GL. Genomics-Driven Discovery of a Novel Glutarimide Antibiotic from Burkholderia gladioli Reveals an Unusual Polyketide Synthase Chain Release Mechanism. Angew Chem Int Ed Engl 2020; 59:23145-23153. [PMID: 32918852 PMCID: PMC7756379 DOI: 10.1002/anie.202009007] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/18/2020] [Indexed: 11/07/2022]
Abstract
A gene cluster encoding a cryptic trans‐acyl transferase polyketide synthase (PKS) was identified in the genomes of Burkholderia gladioli BCC0238 and BCC1622, both isolated from the lungs of cystic fibrosis patients. Bioinfomatics analyses indicated the PKS assembles a novel member of the glutarimide class of antibiotics, hitherto only isolated from Streptomyces species. Screening of a range of growth parameters led to the identification of gladiostatin, the metabolic product of the PKS. NMR spectroscopic analysis revealed that gladiostatin, which has promising activity against several human cancer cell lines and inhibits tumor cell migration, contains an unusual 2‐acyl‐4‐hydroxy‐3‐methylbutenolide in addition to the glutarimide pharmacophore. An AfsA‐like domain at the C‐terminus of the PKS was shown to catalyze condensation of 3‐ketothioesters with dihydroxyacetone phosphate, thus indicating it plays a key role in polyketide chain release and butenolide formation.
Collapse
Affiliation(s)
- Ioanna T. Nakou
- Department of ChemistryUniversity of WarwickCoventryCV4 7ALUK
| | - Matthew Jenner
- Department of ChemistryUniversity of WarwickCoventryCV4 7ALUK
- Warwick Integrative Synthetic Biology CentreUniversity of WarwickCoventryCV4 7ALUK
| | - Yousef Dashti
- Department of ChemistryUniversity of WarwickCoventryCV4 7ALUK
- Current Address: The Centre for Bacterial Cell Biology, Biosciences InstituteMedical SchoolNewcastle UniversityNewcastle upon TyneNE2 4AXUK
| | - Isolda Romero‐Canelón
- Institute of Clinical SciencesSchool of PharmacyUniversity of BirminghamBirminghamB15 2TTUK
| | - Joleen Masschelein
- Department of ChemistryUniversity of WarwickCoventryCV4 7ALUK
- Current Address: Laboratory for Biomolecular Discovery &, EngineeringVIB-KU Leuven Center for MicrobiologyDepartment of BiologyKU Leuven3001LeuvenBelgium
| | - Eshwar Mahenthiralingam
- Organisms and Environment DivisionCardiff School of BiosciencesCardiff UniversityCardiffCF10 3ATUK
| | - Gregory L. Challis
- Department of ChemistryUniversity of WarwickCoventryCV4 7ALUK
- Warwick Integrative Synthetic Biology CentreUniversity of WarwickCoventryCV4 7ALUK
- Department of Biochemistry and Molecular BiologyARC Centre of Excellence for Innovations in Peptide and Protein ScienceMonash UniversityVictoria3800Australia
| |
Collapse
|