1
|
Gao Y, Liao L, Xu Y, Huang J, Gao J, Li L. Bioinformatic Approaches Identify Hybrid Antibiotics against Tuberculosis via d-Amino Acid-Activating Adenylation Domains from Cordyceps militaris. JOURNAL OF NATURAL PRODUCTS 2024. [PMID: 39052090 DOI: 10.1021/acs.jnatprod.4c00718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
Abstract
The development of tuberculosis (TB) therapy has been marked by the discovery of natural-product-derived streptomycin, followed by the introduction of NP-derived rifampicin, representing a significant milestone in the history of TB management. However, TB remains a global challenge, with the emergence of multidrug-resistant Mycobacterium tuberculosis highlighting the need for novel therapeutic agents. In this study, a bioinformatic approach was employed to investigate d-amino acid-activating adenylation domains, leading to the identification of cordysetin A (1), a novel trans-decalin tetramic acid antibiotic from the ascomycete fungi Cordyceps militaris. Cordysetin A (1) exhibits considerable activity against M. tuberculosis in vitro and in vivo while maintaining low cytotoxicity. These results reveal that the d-configuration of the amino acid within this hybrid polyketide-nonribosomal antibiotic is crucial for preserving its anti-tuberculosis efficacy. These findings emphasize the significant translational potential of cordysetin A as a promising candidate for TB treatment, furthering our understanding of bioinformatic approaches in the development of effective anti-tuberculosis agents.
Collapse
Affiliation(s)
- Yangle Gao
- Engineering Research Center of Industrial Microbiology, College of Life Sciences, Fujian Normal University, Fuzhou 350117, People's Republic of China
| | - Lijuan Liao
- Key BioAI Synthetica Lab for Natural Product Drug Discovery, College of Bee and Biomedical Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, People's Republic of China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, People's Republic of China
| | - Yuanteng Xu
- Department of Otorhinolaryngology-Head and Neck Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou 350004, People's Republic of China
| | - Jianzhong Huang
- Engineering Research Center of Industrial Microbiology, College of Life Sciences, Fujian Normal University, Fuzhou 350117, People's Republic of China
| | - Jiangtao Gao
- Key BioAI Synthetica Lab for Natural Product Drug Discovery, College of Bee and Biomedical Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, People's Republic of China
| | - Li Li
- Engineering Research Center of Industrial Microbiology, College of Life Sciences, Fujian Normal University, Fuzhou 350117, People's Republic of China
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
Ahmed MMA, Boudreau PD. LCMS-Metabolomic Profiling and Genome Mining of Delftia lacustris DSM 21246 Revealed Lipophilic Delftibactin Metallophores. JOURNAL OF NATURAL PRODUCTS 2024; 87:1384-1393. [PMID: 38739531 DOI: 10.1021/acs.jnatprod.4c00049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Bacteria have evolved various strategies to combat heavy metal stress, including the secretion of small molecules, known as metallophores. These molecules hold a potential role in the mitigation of toxic metal contamination from the environment (bioremediation). Herein, we employed combined comparative metabolomic and genomic analyses to study the metallophores excreted by Delftia lacustris DSM 21246. LCMS-metabolomic analysis of this bacterium cultured under iron limitation led to a suite of lipophilic metallophores exclusively secreted in response to iron starvation. Additionally, we conducted genome sequencing of the DSM 21246 strain using nanopore sequencing technology and employed antiSMASH to mine the genome, leading to the identification of a biosynthetic gene cluster (BGC) matching the known BGC responsible for delftibactin A production. The isolated suite of amphiphilic metallophores, termed delftibactins C-F (1-4), was characterized using various chromatographic, spectroscopic, and bioinformatic techniques. The planar structure of these compounds was elucidated through 1D and 2D NMR analyses, as well as LCMS/MS-based fragmentation studies. Notably, their structures differed from previously known delftibactins due to the presence of a lipid tail. Marfey's and bioinformatic analyses were employed to determine the absolute configuration of the peptide scaffold. Delftibactin A, a previously identified metallophore, has exhibited a gold biomineralizing property; compound 1 was tested for and also demonstrated this property.
Collapse
Affiliation(s)
- Mohammed M A Ahmed
- Boudreau Lab, Department of BioMolecular Science, School of Pharmacy, University of Mississippi, University, Mississippi 38677, United States
- Department of Pharmacognosy, Al-Azhar University, Cairo 11651, Egypt
| | - Paul D Boudreau
- Boudreau Lab, Department of BioMolecular Science, School of Pharmacy, University of Mississippi, University, Mississippi 38677, United States
| |
Collapse
|
4
|
Sani A, Qin WQ, Li JY, Liu YF, Zhou L, Yang SZ, Mu BZ. Structural diversity and applications of lipopeptide biosurfactants as biocontrol agents against phytopathogens: A review. Microbiol Res 2024; 278:127518. [PMID: 37897841 DOI: 10.1016/j.micres.2023.127518] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 10/10/2023] [Accepted: 10/10/2023] [Indexed: 10/30/2023]
Abstract
Amphipathic compounds known as biosurfactants are able to reduce surface and interfacial tensions. These substances produced by microbial organisms perform the same functions as chemical surfactants with several enhancements, the most significant of which is biocontrol activity. Lipopeptide is one of the five biosurfactants from natural resources and is identified as the best alternative for chemical surfactants and the major topic of interest for both scientific and industrial communities due to their increasingly growing potential applications in biological and commercial fields. These are the biological compounds with very less toxicity level that increase their importance in the pesticide industry. In this article we summarize the structural diversity of the microbial lipopeptide biosurfactants and focus on their applications as biocontrol agents in plants, covering (1) an intensive study of the structural diversity of lipopeptide biosurfactants originated primarily by the Bacillus, Pseudomonas, Cyanobacteria, and Actinomycetes species is presented, (2) the comparative study of advantages and disadvantages of characterization techniques and physicochemical properties which have a major role in biocontrol activity of microbial lipopeptides, and (3) their wide range biocontrol applications as systemic resistance inducers against different plant diseases, resistance against phytopathogens by alteration of wettability of plant surfaces and antimicrobial activities of important bioactive lipopeptides produced from Bacillus strains.
Collapse
Affiliation(s)
- Asma Sani
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China; Engineering Research Center for Microbial Enhanced Oil Recovery, Ministry of Education, East China University of Science and Technology, Shanghai 200237, China
| | - Wan-Qi Qin
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China; Engineering Research Center for Microbial Enhanced Oil Recovery, Ministry of Education, East China University of Science and Technology, Shanghai 200237, China
| | - Jia-Yi Li
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China; Engineering Research Center for Microbial Enhanced Oil Recovery, Ministry of Education, East China University of Science and Technology, Shanghai 200237, China
| | - Yi-Fan Liu
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China; Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai 200237, China; Engineering Research Center for Microbial Enhanced Oil Recovery, Ministry of Education, East China University of Science and Technology, Shanghai 200237, China
| | - Lei Zhou
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China; Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai 200237, China; Engineering Research Center for Microbial Enhanced Oil Recovery, Ministry of Education, East China University of Science and Technology, Shanghai 200237, China
| | - Shi-Zhong Yang
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China; Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai 200237, China; Engineering Research Center for Microbial Enhanced Oil Recovery, Ministry of Education, East China University of Science and Technology, Shanghai 200237, China
| | - Bo-Zhong Mu
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China; Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai 200237, China; Engineering Research Center for Microbial Enhanced Oil Recovery, Ministry of Education, East China University of Science and Technology, Shanghai 200237, China.
| |
Collapse
|
5
|
Wu Y, Wang M, Liu L. Advances on structure, bioactivity, and biosynthesis of amino acid-containing trans-AT polyketides. Eur J Med Chem 2023; 262:115890. [PMID: 37907023 DOI: 10.1016/j.ejmech.2023.115890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Revised: 10/01/2023] [Accepted: 10/19/2023] [Indexed: 11/02/2023]
Abstract
Trans-AT polyketides represent a class of natural compounds utilizing independent acyltransferase during their biosynthesis. They are well known for their diverse chemical structures and potent bioactivities. Trans-AT polyketides are synthesized through biosynthetic gene clusters predominantly composed of polyketide synthases (PKS), but often found in hybrid with non-ribosomal peptide synthetases (NRPS). This genetic hybridization results in the incorporation of amino acid residues into polyketide structures, significantly enhancing their structural diversity. Numerous amino acid-containing trans-AT polyketides have been identified, drawing significant attention to the mechanisms underlying amino acid incorporation and their impact on the biological activity of polyketides. Here, we discussed their origins, structures, biological activities, and the specific roles of amino acids in modulating both the bioactivity and biosynthesis of 38 trans-AT polyketides containing amino acids for the first time. This comprehensive analysis will serve as a crucial reference for the exploration of novel compounds and the improvement of structures and activities.
Collapse
Affiliation(s)
- Yunqiang Wu
- Health Science Center, Ningbo University, Ningbo, Zhejiang, 315211, China; Department of Marine Pharmacy, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang, 315832, China
| | - Min Wang
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, 529020, China.
| | - Liwei Liu
- Health Science Center, Ningbo University, Ningbo, Zhejiang, 315211, China; Department of Marine Pharmacy, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang, 315832, China.
| |
Collapse
|
6
|
Muangkaew P, De Roo V, Zhou L, Girard L, Cesa-Luna C, Höfte M, De Mot R, Madder A, Geudens N, Martins JC. Stereomeric Lipopeptides from a Single Non-Ribosomal Peptide Synthetase as an Additional Source of Structural and Functional Diversification in Pseudomonas Lipopeptide Biosynthesis. Int J Mol Sci 2023; 24:14302. [PMID: 37762605 PMCID: PMC10531924 DOI: 10.3390/ijms241814302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/11/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023] Open
Abstract
In Pseudomonas lipopeptides, the D-configuration of amino acids is generated by dedicated, dual-function epimerization/condensation (E/C) domains. The increasing attention to stereochemistry in lipopeptide structure elucidation efforts has revealed multiple examples where epimerization does not occur, even though an E/C-type domain is present. While the origin of the idle epimerization in those E/C-domains remains elusive, epimerization activity has so far shown a binary profile: it is either 'on' (active) or 'off' (inactive). Here, we report the unprecedented observation of an E/C-domain that acts 'on and off', giving rise to the production of two diastereoisomeric lipopeptides by a single non-ribosomal peptide synthetase system. Using dereplication based on solid-phase peptide synthesis and NMR fingerprinting, we first show that the two cyclic lipopeptides produced by Pseudomonas entomophila COR5 correspond to entolysin A and B originally described for P. entomophila L48. Next, we prove that both are diastereoisomeric homologues differing only in the configuration of a single amino acid. This configurational variability is maintained in multiple Pseudomonas strains and typically occurs in a 3:2 ratio. Bioinformatic analysis reveals a possible correlation with the composition of the flanking sequence of the N-terminal secondary histidine motif characteristic for dual-function E/C-type domains. In permeabilization assays, using propidium iodide entolysin B has a higher antifungal activity compared to entolysin A against Botrytis cinerea and Pyricularia oryzae spores. The fact that configurational homologues are produced by the same NRPS system in a Pseudomonas strain adds a new level of structural and functional diversification to those already known from substrate flexibility during the recruitment of the amino acids and fatty acids and underscores the importance of complete stereochemical elucidation of non-ribosomal lipopeptide structures.
Collapse
Affiliation(s)
- Penthip Muangkaew
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Faculty of Science, Ghent University, B-9000 Ghent, Belgium; (P.M.); (V.D.R.); (A.M.)
| | - Vic De Roo
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Faculty of Science, Ghent University, B-9000 Ghent, Belgium; (P.M.); (V.D.R.); (A.M.)
- NMR and Structure Analysis Unit, Department of Organic and Macromolecular Chemistry, Faculty of Science, Ghent University, B-9000 Ghent, Belgium
| | - Lu Zhou
- Laboratory of Phytopathology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, B-9000 Ghent, Belgium; (L.Z.); (M.H.)
| | - Léa Girard
- Centre of Microbial and Plant Genetics, Faculty of Bioscience Engineering, Katholieke Universiteit Leuven, B-3001 Heverlee, Belgium; (L.G.); (C.C.-L.); (R.D.M.)
| | - Catherine Cesa-Luna
- Centre of Microbial and Plant Genetics, Faculty of Bioscience Engineering, Katholieke Universiteit Leuven, B-3001 Heverlee, Belgium; (L.G.); (C.C.-L.); (R.D.M.)
| | - Monica Höfte
- Laboratory of Phytopathology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, B-9000 Ghent, Belgium; (L.Z.); (M.H.)
| | - René De Mot
- Centre of Microbial and Plant Genetics, Faculty of Bioscience Engineering, Katholieke Universiteit Leuven, B-3001 Heverlee, Belgium; (L.G.); (C.C.-L.); (R.D.M.)
| | - Annemieke Madder
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Faculty of Science, Ghent University, B-9000 Ghent, Belgium; (P.M.); (V.D.R.); (A.M.)
| | - Niels Geudens
- NMR and Structure Analysis Unit, Department of Organic and Macromolecular Chemistry, Faculty of Science, Ghent University, B-9000 Ghent, Belgium
| | - José C. Martins
- NMR and Structure Analysis Unit, Department of Organic and Macromolecular Chemistry, Faculty of Science, Ghent University, B-9000 Ghent, Belgium
| |
Collapse
|
7
|
Park J, Kim J, Hwang S, Oh D, Du YE, Nam SJ, Park HG, Lee MJ, Oh DC. Sadopeptins A and B, Sulfoxide- and Piperidone-Containing Cyclic Heptapeptides with Proteasome Inhibitory Activity from a Streptomyces sp. JOURNAL OF NATURAL PRODUCTS 2023; 86:612-620. [PMID: 36921317 DOI: 10.1021/acs.jnatprod.2c00978] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
New sulfur-bearing natural products, sadopeptins A and B (1 and 2), were discovered from Streptomyces sp. YNK18 based on a targeted search using the characteristic isotopic signature of sulfur in mass spectrometry analysis. Compounds 1 and 2 were determined to be new cyclic heptapeptides, bearing methionine sulfoxide [Met(O)] and 3-amino-6-hydroxy-2-piperidone (Ahp), based on 1D and 2D NMR spectroscopy along with IR, UV, and MS. The configurations of sadopeptins A and B (1 and 2) were established via the analysis of the ROESY NMR correlation, oxidation, Marfey's method, and circular dichroism (CD) spectroscopy. The bioinformatics analysis of the full Streptomyces sp. YNK18 genome identified a nonribosomal peptide synthetase (NRPS) biosynthetic gene cluster (BGC), and a putative biosynthetic pathway is proposed. Sadopeptins A and B displayed proteasome-inhibitory activity without affecting cellular autophagic flux.
Collapse
Affiliation(s)
- Jiyoon Park
- Natural Products Research Institute, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Jiseong Kim
- Department of Biomedical Sciences, College of Medicine, Seoul National University, 103 Daehak-ro, Jongno-gu, Seoul 03080, Republic of Korea
| | - Sunghoon Hwang
- Natural Products Research Institute, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Daehyun Oh
- Research Institute of Pharmaceutical Sciences and College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Young Eun Du
- Natural Products Research Institute, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Sang-Jip Nam
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Hyeung-Geun Park
- Research Institute of Pharmaceutical Sciences and College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Min Jae Lee
- Department of Biomedical Sciences, College of Medicine, Seoul National University, 103 Daehak-ro, Jongno-gu, Seoul 03080, Republic of Korea
| | - Dong-Chan Oh
- Natural Products Research Institute, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| |
Collapse
|
8
|
Sreedharan SM, Rishi N, Singh R. Microbial Lipopeptides: Properties, Mechanics and Engineering for Novel Lipopeptides. Microbiol Res 2023; 271:127363. [PMID: 36989760 DOI: 10.1016/j.micres.2023.127363] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 12/04/2022] [Accepted: 03/11/2023] [Indexed: 03/17/2023]
Abstract
Microorganisms produce active surface agents called lipopeptides (LPs) which are amphiphilic in nature. They are cyclic or linear compounds and are predominantly isolated from Bacillus and Pseudomonas species. LPs show antimicrobial activity towards various plant pathogens and act by inhibiting the growth of these organisms. Several mechanisms are exhibited by LPs, such as cell membrane disruption, biofilm production, induced systematic resistance, improving plant growth, inhibition of spores, etc., making them suitable as biocontrol agents and highly advantageous for industrial utilization. The biosynthesis of lipopeptides involves large multimodular enzymes referred to as non-ribosomal peptide synthases. These enzymes unveil a broad range of engineering approaches through which lipopeptides can be overproduced and new LPs can be generated asserting high efficacy. Such approaches involve several synthetic biology systems and metabolic engineering techniques such as promotor engineering, enhanced precursor availability, condensation domain engineering, and adenylation domain engineering. Finally, this review provides an update of the applications of lipopeptides in various fields.
Collapse
|
9
|
Pistorius D, Buntin K, Richard E, Rust M, Bouquet C, Wollbrett S, Weber E, Dietschin D, Bruccoleri R, Oakeley E, Petersen F. Valhidepsin Lipopeptides from Chromobacterium vaccinii: Structures, Biosynthesis, and Coregulation with FR900359 Production. JOURNAL OF NATURAL PRODUCTS 2023; 86:246-255. [PMID: 36745695 DOI: 10.1021/acs.jnatprod.2c00825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Microbial secondary metabolites continue to provide a valuable source of both chemical matter and inspiration for drug discovery in a broad range of therapeutic areas. Beyond this, the corresponding microorganisms represent a sustainable modality for biotechnological production of structurally complex molecules at the quantities required for drug development or even commercial manufacturing. Chromobacterium vaccinii, which has recently been reported as a producer of the pharmacologically highly important Gq inhibitor FR900359 (FR), represents such an example. The characterization of an orphan biosynthetic gene cluster (BGC) located directly downstream of the frs BCG led to the discovery of eight new lipopeptides, valhidepsins A-H (1-8), produced by C. vaccinii. Their chemical structures were elucidated through analysis of 1D and 2D NMR data and high-resolution MS/MS fragmentation methods. The valhidepsins did not display significant antibiotic nor cytotoxic activities but showed surfactant properties. The cluster-compound correlation was demonstrated by generation of a knockout mutant, which abolished production of valhidepsins. This knockout mutant yielded a significantly increased isolated yield of FR.
Collapse
Affiliation(s)
- Dominik Pistorius
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, 4056 Basel, Switzerland
| | - Kathrin Buntin
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, 4056 Basel, Switzerland
| | - Etienne Richard
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, 4056 Basel, Switzerland
| | - Michael Rust
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, 4056 Basel, Switzerland
| | - Caroline Bouquet
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, 4056 Basel, Switzerland
| | - Séverine Wollbrett
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, 4056 Basel, Switzerland
| | - Eric Weber
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, 4056 Basel, Switzerland
| | - Daniele Dietschin
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, 4056 Basel, Switzerland
| | | | - Edward Oakeley
- Chemical Biology & Therapeutics, Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, 4056 Basel, Switzerland
| | - Frank Petersen
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, 4056 Basel, Switzerland
| |
Collapse
|
10
|
Abstract
A major source of pseudomonad-specialized metabolites is the nonribosomal peptide synthetases (NRPSs) assembling siderophores and lipopeptides. Cyclic lipopeptides (CLPs) of the Mycin and Peptin families are frequently associated with, but not restricted to, phytopathogenic species. We conducted an in silico analysis of the NRPSs encoded by lipopeptide biosynthetic gene clusters in nonpathogenic Pseudomonas genomes, covering 13 chemically diversified families. This global assessment of lipopeptide production capacity revealed it to be confined to the Pseudomonas fluorescens lineage, with most strains synthesizing a single type of CLP. Whereas certain lipopeptide families are specific for a taxonomic subgroup, others are found in distant groups. NRPS activation domain-guided peptide predictions enabled reliable family assignments, including identification of novel members. Focusing on the two most abundant lipopeptide families (Viscosin and Amphisin), a portion of their uncharted diversity was mapped, including characterization of two novel Amphisin family members (nepenthesin and oakridgin). Using NMR fingerprint matching, known Viscosin-family lipopeptides were identified in 15 (type) species spread across different taxonomic groups. A bifurcate genomic organization predominates among Viscosin-family producers and typifies Xantholysin-, Entolysin-, and Poaeamide-family producers but most families feature a single NRPS gene cluster embedded between cognate regulator and transporter genes. The strong correlation observed between NRPS system phylogeny and rpoD-based taxonomic affiliation indicates that much of the structural diversity is linked to speciation, providing few indications of horizontal gene transfer. The grouping of most NRPS systems in four superfamilies based on activation domain homology suggests extensive module dynamics driven by domain deletions, duplications, and exchanges. IMPORTANCE Pseudomonas species are prominent producers of lipopeptides that support proliferation in a multitude of environments and foster varied lifestyles. By genome mining of biosynthetic gene clusters (BGCs) with lipopeptide-specific organization, we mapped the global Pseudomonas lipopeptidome and linked its staggering diversity to taxonomy of the producers, belonging to different groups within the major Pseudomonas fluorescens lineage. Activation domain phylogeny of newly mined lipopeptide synthetases combined with previously characterized enzymes enabled assignment of predicted BGC products to specific lipopeptide families. In addition, novel peptide sequences were detected, showing the value of substrate specificity analysis for prioritization of BGCs for further characterization. NMR fingerprint matching proved an excellent tool to unequivocally identify multiple lipopeptides bioinformatically assigned to the Viscosin family, by far the most abundant one in Pseudomonas and with stereochemistry of all its current members elucidated. In-depth analysis of activation domains provided insight into mechanisms driving lipopeptide structural diversification.
Collapse
|
11
|
Velilla JA, Kenney GE, Gaudet R. Structure and function of prodrug-activating peptidases. Biochimie 2023; 205:124-135. [PMID: 36803695 PMCID: PMC10030199 DOI: 10.1016/j.biochi.2022.07.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 07/25/2022] [Indexed: 11/11/2022]
Abstract
Bacteria protect themselves from the toxicity of antimicrobial metabolites they produce through several strategies. In one resistance mechanism, bacteria assemble a non-toxic precursor on an N-acyl-d-asparagine prodrug motif in the cytoplasm, then export it to the periplasm where a dedicated d-amino peptidase hydrolyzes the prodrug motif. These prodrug-activating peptidases contain an N-terminal periplasmic S12 hydrolase domain and C-terminal transmembrane domains (TMDs) of varying lengths: type I peptidases contain three transmembrane helices, and type II peptidases have an additional C-terminal ABC half-transporter. We review studies which have addressed the role of the TMD in function, the substrate specificity, and the biological assembly of ClbP, the type I peptidase that activates colibactin. We use modeling and sequence analyses to extend those insights to other prodrug-activating peptidases and ClbP-like proteins which are not part of prodrug resistance gene clusters. These ClbP-like proteins may play roles in the biosynthesis or degradation of other natural products, including antibiotics, may adopt different TMD folds, and have different substrate specificity compared to prodrug-activating homologs. Finally, we review the data supporting the long-standing hypothesis that ClbP interacts with transporters in the cell and that this association is important for the export of other natural products. Future investigations of this hypothesis as well as of the structure and function of type II peptidases will provide a complete account of the role of prodrug-activating peptidases in the activation and secretion of bacterial toxins.
Collapse
Affiliation(s)
- José A Velilla
- Department of Molecular and Cellular Biology, Harvard University, 52 Oxford St, Cambridge, MA, 02138, USA
| | - Grace E Kenney
- Department of Chemistry and Chemical Biology, Harvard University, 38 Oxford St, Cambridge, MA, USA
| | - Rachelle Gaudet
- Department of Molecular and Cellular Biology, Harvard University, 52 Oxford St, Cambridge, MA, 02138, USA.
| |
Collapse
|
12
|
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
|
13
|
Büttner H, Pidot SJ, Scherlach K, Hertweck C. Endofungal bacteria boost anthelminthic host protection with the biosurfactant symbiosin. Chem Sci 2022; 14:103-112. [PMID: 36605741 PMCID: PMC9769094 DOI: 10.1039/d2sc04167g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 11/20/2022] [Indexed: 11/22/2022] Open
Abstract
Effective protection of soil fungi from predators is crucial for their survival in the niche. Thus, fungi have developed efficient defence strategies. We discovered that soil beneficial Mortierella fungi employ a potent cytotoxin (necroxime) against fungivorous nematodes. Interestingly, this anthelminthic agent is produced by bacterial endosymbionts (Candidatus Mycoavidus necroximicus) residing within the fungus. Analysis of the symbiont's genome indicated a rich biosynthetic potential, yet nothing has been known about additional metabolites and their potential synergistic functions. Here we report that two distinct Mortierella endosymbionts produce a novel cyclic lipodepsipeptide (symbiosin), that is clearly of bacterial origin, but has striking similarities to various fungal specialized metabolites. The structure and absolute configuration of symbiosin were fully elucidated. By comparative genomics of symbiosin-positive strains and in silico analyses of the deduced non-ribosomal synthetases, we assigned the (sym) biosynthetic gene cluster and proposed an assembly line model. Bioassays revealed that symbiosin is not only an antibiotic, in particular against mycobacteria, but also exhibits marked synergistic effects with necroxime in anti-nematode tests. By functional analyses and substitution experiments we found that symbiosin is a potent biosurfactant and that this particular property confers a boost in the anthelmintic action, similar to formulations of therapeutics in human medicine. Our findings illustrate that "combination therapies" against parasites already exist in ecological contexts, which may inspire the development of biocontrol agents and therapeutics.
Collapse
Affiliation(s)
- Hannah Büttner
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute (Leibniz-HKI)Beutenbergstrasse 11a07745 JenaGermany
| | - Sacha J. Pidot
- Department of Microbiology and Immunology, Doherty Institute792 Elizabeth StreetMelbourne3000Australia
| | - Kirstin Scherlach
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute (Leibniz-HKI)Beutenbergstrasse 11a07745 JenaGermany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute (Leibniz-HKI)Beutenbergstrasse 11a07745 JenaGermany,Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University Jena07743 JenaGermany
| |
Collapse
|
14
|
Gnann AD, Xia Y, Soule J, Barthélemy C, Mawani JS, Musoke SN, Castellano BM, Brignole EJ, Frueh DP, Dowling DP. High-resolution structures of a siderophore-producing cyclization domain from Yersinia pestis offer a refined proposal of substrate binding. J Biol Chem 2022; 298:102454. [PMID: 36063993 PMCID: PMC9547227 DOI: 10.1016/j.jbc.2022.102454] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 08/27/2022] [Accepted: 08/29/2022] [Indexed: 01/01/2023] Open
Abstract
Nonribosomal peptide synthetase heterocyclization (Cy) domains generate biologically important oxazoline/thiazoline groups found in natural products, including pharmaceuticals and virulence factors such as some siderophores. Cy domains catalyze consecutive condensation and cyclodehydration reactions, although the mechanism is unknown. To better understand Cy domain catalysis, here we report the crystal structure of the second Cy domain (Cy2) of yersiniabactin synthetase from the causative agent of the plague, Yersinia pestis. Our high-resolution structure of Cy2 adopts a conformation that enables exploration of interactions with the extended thiazoline-containing cyclodehydration intermediate and the acceptor carrier protein (CP) to which it is tethered. We also report complementary electrostatic interfaces between Cy2 and its donor CP that mediate donor binding. Finally, we explored domain flexibility through normal mode analysis and identified small-molecule fragment-binding sites that may inform future antibiotic design targeting Cy function. Our results suggest how CP binding may influence global Cy conformations, with consequences for active-site remodeling to facilitate the separate condensation and cyclodehydration steps as well as potential inhibitor development.
Collapse
Affiliation(s)
- Andrew D. Gnann
- Department of Chemistry, University of Massachusetts Boston, Boston, Massachusetts, USA
| | - Yuan Xia
- Department of Chemistry, University of Massachusetts Boston, Boston, Massachusetts, USA
| | - Jess Soule
- Department of Chemistry, University of Massachusetts Boston, Boston, Massachusetts, USA
| | - Clara Barthélemy
- Department of Chemistry, University of Massachusetts Boston, Boston, Massachusetts, USA
| | - Jayata S. Mawani
- Department of Chemistry, University of Massachusetts Boston, Boston, Massachusetts, USA
| | - Sarah Nzikoba Musoke
- Department of Chemistry, University of Massachusetts Boston, Boston, Massachusetts, USA
| | - Brian M. Castellano
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Edward J. Brignole
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Dominique P. Frueh
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Daniel P. Dowling
- Department of Chemistry, University of Massachusetts Boston, Boston, Massachusetts, USA,For correspondence: Daniel P. Dowling
| |
Collapse
|
15
|
De Roo V, Verleysen Y, Kovács B, De Vleeschouwer M, Muangkaew P, Girard L, Höfte M, De Mot R, Madder A, Geudens N, Martins JC. An Nuclear Magnetic Resonance Fingerprint Matching Approach for the Identification and Structural Re-Evaluation of Pseudomonas Lipopeptides. Microbiol Spectr 2022; 10:e0126122. [PMID: 35876524 PMCID: PMC9431178 DOI: 10.1128/spectrum.01261-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 06/26/2022] [Indexed: 01/21/2023] Open
Abstract
Cyclic lipopeptides (CLiPs) are secondary metabolites secreted by a range of bacterial phyla. CLiPs from Pseudomonas in particular, display diverse structural variations in terms of the number of amino acid residues, macrocycle size, amino acid identity, and stereochemistry (e.g., d- versus l-amino acids). Reports detailing the discovery of novel or already characterized CLiPs from new sources appear regularly in literature. Increasingly, however, the lack of detailed characterization threatens to cause considerable confusion, especially if configurational heterogeneity is present for one or more amino acids. Using Pseudomonas CLiPs from the Bananamide, Orfamide, and Xantholysin groups as test cases, we demonstrate and validate that the combined 1H and 13C Nuclear Magnetic Resonance (NMR) chemical shifts of CLiPs constitute a spectral fingerprint that is sufficiently sensitive to differentiate between possible diastereomers of a particular sequence even when they only differ in a single d/l configuration. Rapid screening, involving simple matching of the NMR fingerprint of a newly isolated CLiP with that of a reference CLiP of known stereochemistry, can then be applied to resolve dead-ends in configurational characterization and avoid the much more cumbersome chemical characterization protocols. Even when the stereochemistry of a particular reference CLiP remains to be established, its spectral fingerprint allows to quickly verify whether a newly isolated CLiP is novel or already present in the reference collection. We show NMR fingerprinting leads to a simple approach for early on dereplication which should become more effective as more fingerprints are collected. To benefit research involving CLiPs, we have made a publicly available data repository accompanied by a 'knowledge base' at https://www.rhizoclip.be, where we present an overview of published NMR fingerprint data of characterized CLiPs, together with literature data on the originally determined structures. IMPORTANCE Pseudomonas CLiPs are ubiquitous specialized metabolites, impacting the producer's lifestyle and interactions with the (a)biotic environment. Consequently, they generate interest for agricultural and clinical applications. Establishing structure-activity relationships as a premise to their development is hindered because full structural characterization including stereochemical information requires labor-intensive analyses, without guarantee for success. Moreover, increasing use of superficial comparison with previously characterized CLiPs introduces or propagates erroneous attributions, clouding further scientific progress. We provide a generally applicable characterization methodology based on matching NMR spectral fingerprints of newly isolated CLiPs to natural and synthetic reference compounds with (un)known stereochemistry. In addition, NMR fingerprinting is shown to provide a suitable basis for structural dereplication. A publicly available reference compound repository promises to facilitate participation of the lipopeptide research community in structural assessment and dereplication of newly isolated CLiPs, which should also support further developments in genome mining for novel CLiPs.
Collapse
Affiliation(s)
- Vic De Roo
- NMR and Structure Analysis Unit, Ghent University, Department of Organic and Macromolecular Chemistry, Ghent, Belgium
| | - Yentl Verleysen
- NMR and Structure Analysis Unit, Ghent University, Department of Organic and Macromolecular Chemistry, Ghent, Belgium
- Organic and Biomimetic Chemistry Research Group, Ghent University, Department of Organic and Macromolecular Chemistry, Ghent, Belgium
| | - Benjámin Kovács
- NMR and Structure Analysis Unit, Ghent University, Department of Organic and Macromolecular Chemistry, Ghent, Belgium
| | - Matthias De Vleeschouwer
- NMR and Structure Analysis Unit, Ghent University, Department of Organic and Macromolecular Chemistry, Ghent, Belgium
- Organic and Biomimetic Chemistry Research Group, Ghent University, Department of Organic and Macromolecular Chemistry, Ghent, Belgium
| | - Penthip Muangkaew
- Organic and Biomimetic Chemistry Research Group, Ghent University, Department of Organic and Macromolecular Chemistry, Ghent, Belgium
| | - Léa Girard
- Centre for Microbial and Plant Genetics, Faculty of Bioscience Engineering, KULeuven, Heverlee-Leuven, Belgium
| | - Monica Höfte
- Laboratory of Phytopathology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent, Belgium
| | - René De Mot
- Centre for Microbial and Plant Genetics, Faculty of Bioscience Engineering, KULeuven, Heverlee-Leuven, Belgium
| | - Annemieke Madder
- Organic and Biomimetic Chemistry Research Group, Ghent University, Department of Organic and Macromolecular Chemistry, Ghent, Belgium
| | - Niels Geudens
- NMR and Structure Analysis Unit, Ghent University, Department of Organic and Macromolecular Chemistry, Ghent, Belgium
| | - José C. Martins
- NMR and Structure Analysis Unit, Ghent University, Department of Organic and Macromolecular Chemistry, Ghent, Belgium
| |
Collapse
|
16
|
Patteson JB, Fortinez CM, Putz AT, Rodriguez-Rivas J, Bryant LH, Adhikari K, Weigt M, Schmeing TM, Li B. Structure and Function of a Dehydrating Condensation Domain in Nonribosomal Peptide Biosynthesis. J Am Chem Soc 2022; 144:14057-14070. [PMID: 35895935 DOI: 10.1021/jacs.1c13404] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Dehydroamino acids are important structural motifs and biosynthetic intermediates for natural products. Many bioactive natural products of nonribosomal origin contain dehydroamino acids; however, the biosynthesis of dehydroamino acids in most nonribosomal peptides is not well understood. Here, we provide biochemical and bioinformatic evidence in support of the role of a unique class of condensation domains in dehydration (CmodAA). We also obtain the crystal structure of a CmodAA domain, which is part of the nonribosomal peptide synthetase AmbE in the biosynthesis of the antibiotic methoxyvinylglycine. Biochemical analysis reveals that AmbE-CmodAA modifies a peptide substrate that is attached to the donor carrier protein. Mutational studies of AmbE-CmodAA identify several key residues for activity, including four residues that are mostly conserved in the CmodAA subfamily. Alanine mutation of these conserved residues either significantly increases or decreases AmbE activity. AmbE exhibits a dimeric conformation, which is uncommon and could enable transfer of an intermediate between different protomers. Our discovery highlights a central dehydrating function for CmodAA domains that unifies dehydroamino acid biosynthesis in diverse nonribosomal peptide pathways. Our work also begins to shed light on the mechanism of CmodAA domains. Understanding CmodAA domain function may facilitate identification of new natural products that contain dehydroamino acids and enable engineering of dehydroamino acids into nonribosomal peptides.
Collapse
Affiliation(s)
- Jon B Patteson
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Camille Marie Fortinez
- Department of Biochemistry and Centre de recherche en biologie structurale, McGill University, Montréal, Canada H3G 0B1
| | - Andrew T Putz
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Juan Rodriguez-Rivas
- Sorbonne Université, CNRS, Institut de Biologie Paris Seine, Biologie Computationnelle et Quantitative - LCQB, Paris 75005, France
| | - L Henry Bryant
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Kamal Adhikari
- Department of Biochemistry and Centre de recherche en biologie structurale, McGill University, Montréal, Canada H3G 0B1
| | - Martin Weigt
- Sorbonne Université, CNRS, Institut de Biologie Paris Seine, Biologie Computationnelle et Quantitative - LCQB, Paris 75005, France
| | - T Martin Schmeing
- Department of Biochemistry and Centre de recherche en biologie structurale, McGill University, Montréal, Canada H3G 0B1
| | - Bo Li
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| |
Collapse
|
17
|
Cui J, Kim E, Moon DH, Kim TH, Kang I, Lim Y, Shin D, Hwang S, Du YE, Song MC, Bae M, Cho JC, Jang J, Lee SK, Yoon YJ, Oh DC. Taeanamides A and B, Nonribosomal Lipo-Decapeptides Isolated from an Intertidal-Mudflat-Derived Streptomyces sp. Mar Drugs 2022; 20:md20060400. [PMID: 35736203 PMCID: PMC9229766 DOI: 10.3390/md20060400] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 06/10/2022] [Accepted: 06/13/2022] [Indexed: 12/04/2022] Open
Abstract
Two new lipo-decapeptides, namely taeanamides A and B (1 and 2), were discovered from the Gram-positive bacterium Streptomyces sp. AMD43, which was isolated from a mudflat sample from Anmyeondo, Korea. The exact molecular masses of 1 and 2 were revealed by high-resolution mass spectrometry, and the planar structures of 1 and 2 were elucidated using NMR spectroscopy. The absolute configurations of 1 and 2 were determined using a combined analysis of 1H-1H coupling constants and ROESY correlations, the advanced Marfey’s method, and bioinformatics. The putative nonribosomal peptide synthetase pathway for the taeanamides was identified by analyzing the full genome sequence data of Streptomyces sp. AMD43. We also found that taeanamide A exhibited mild anti-tuberculosis bioactivity, whereas taeanamide B showed significant bioactivity against several cancer cell lines.
Collapse
Affiliation(s)
- Jinsheng Cui
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Korea; (J.C.); (E.K.); (D.H.M.); (D.S.); (S.H.); (Y.E.D.); (M.C.S.); (S.K.L.)
| | - Eunji Kim
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Korea; (J.C.); (E.K.); (D.H.M.); (D.S.); (S.H.); (Y.E.D.); (M.C.S.); (S.K.L.)
| | - Dong Hyun Moon
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Korea; (J.C.); (E.K.); (D.H.M.); (D.S.); (S.H.); (Y.E.D.); (M.C.S.); (S.K.L.)
| | - Tae Ho Kim
- Molecular Mechanism of Antibiotics, Division of Life Science, Department of Bio & Medical Big Data (BK4 Program), Research Institute of Life Science, Gyeongsang National University, Jinju 52828, Korea; (T.H.K.); (J.J.)
| | - Ilnam Kang
- Department of Biological Sciences, Inha University, Incheon 22212, Korea; (I.K.); (Y.L.); (J.-C.C.)
| | - Yeonjung Lim
- Department of Biological Sciences, Inha University, Incheon 22212, Korea; (I.K.); (Y.L.); (J.-C.C.)
| | - Daniel Shin
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Korea; (J.C.); (E.K.); (D.H.M.); (D.S.); (S.H.); (Y.E.D.); (M.C.S.); (S.K.L.)
| | - Sunghoon Hwang
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Korea; (J.C.); (E.K.); (D.H.M.); (D.S.); (S.H.); (Y.E.D.); (M.C.S.); (S.K.L.)
| | - Young Eun Du
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Korea; (J.C.); (E.K.); (D.H.M.); (D.S.); (S.H.); (Y.E.D.); (M.C.S.); (S.K.L.)
| | - Myoung Chong Song
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Korea; (J.C.); (E.K.); (D.H.M.); (D.S.); (S.H.); (Y.E.D.); (M.C.S.); (S.K.L.)
| | - Munhyung Bae
- College of Pharmacy, Gachon University, Incheon 21936, Korea;
| | - Jang-Cheon Cho
- Department of Biological Sciences, Inha University, Incheon 22212, Korea; (I.K.); (Y.L.); (J.-C.C.)
| | - Jichan Jang
- Molecular Mechanism of Antibiotics, Division of Life Science, Department of Bio & Medical Big Data (BK4 Program), Research Institute of Life Science, Gyeongsang National University, Jinju 52828, Korea; (T.H.K.); (J.J.)
| | - Sang Kook Lee
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Korea; (J.C.); (E.K.); (D.H.M.); (D.S.); (S.H.); (Y.E.D.); (M.C.S.); (S.K.L.)
| | - Yeo Joon Yoon
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Korea; (J.C.); (E.K.); (D.H.M.); (D.S.); (S.H.); (Y.E.D.); (M.C.S.); (S.K.L.)
- Correspondence: (Y.J.Y.); (D.-C.O.); Tel.: +82-2-880-2379 (Y.J.Y.); +82-2-880-2491 (D.-C.O.); Fax: +82-2-762-8322 (D.-C.O.)
| | - Dong-Chan Oh
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Korea; (J.C.); (E.K.); (D.H.M.); (D.S.); (S.H.); (Y.E.D.); (M.C.S.); (S.K.L.)
- Correspondence: (Y.J.Y.); (D.-C.O.); Tel.: +82-2-880-2379 (Y.J.Y.); +82-2-880-2491 (D.-C.O.); Fax: +82-2-762-8322 (D.-C.O.)
| |
Collapse
|
18
|
Nonribosomal Peptide Synthesis Definitely Working Out of the Rules. Microorganisms 2022; 10:microorganisms10030577. [PMID: 35336152 PMCID: PMC8949500 DOI: 10.3390/microorganisms10030577] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [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
|
19
|
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] [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
|
20
|
Isolation and Purification of a Hydrophobic Non-Ribosomal Peptide from an Escherichia coli Fermentation Broth. SEPARATIONS 2021. [DOI: 10.3390/separations8120241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Non-ribosomal peptide synthases (NRPSs) generate versatile bioactive peptides by incorporating non-proteinogenic amino acids and catalyzing diverse modifications. Here, we developed an efficient downstream process for the capture, intermediate purification and polishing of a rhabdopeptide (RXP) produced by the NRPS VietABC. Many typical unit operations were unsuitable due to the similar physical and chemical properties of the RXP and related byproducts. However, we were able to capture the RXP from a fermentation broth using a hydrophobic resin (XAD-16N), resulting in a 14-fold increase in concentration while removing salts as well as polar and weak non-polar impurities. We then used ultra-high-performance liquid chromatography (UHPLC) for intermediate purification, with optimized parameters determined using statistical experimental designs, resulting in the complete removal of hydrophobic impurities. Finally, the UHPLC eluents were removed by evaporation. Our three-step downstream process achieved an overall product recovery of 81.7 ± 8.4%.
Collapse
|
21
|
Koutinas M, Kyriakou M, Andreou K, Hadjicharalambous M, Kaliviotis E, Pasias D, Kazamias G, Varavvas C, Vyrides I. Enhanced biodegradation and valorization of drilling wastewater via simultaneous production of biosurfactants and polyhydroxyalkanoates by Pseudomonas citronellolis SJTE-3. BIORESOURCE TECHNOLOGY 2021; 340:125679. [PMID: 34364084 DOI: 10.1016/j.biortech.2021.125679] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 07/25/2021] [Accepted: 07/26/2021] [Indexed: 06/13/2023]
Abstract
Pseudomonas citronellolis SJTE-3 was isolated as a highly efficient microorganism for biodegradation and valorization of drilling fluids (DF) wastewater. The strain metabolised DF and oily mud exhibiting up to 93%, 86%, 85% and 88% of chemical oxygen demand (COD), n-dodecane, n-tetradecane and naphthalene removal efficiency respectively. Enhanced bioconversion was enabled through production of biosurfactants that reduced the surface tension of water by 53% and resulted in 43.3% emulsification index (E24), while synthesizing 24% of dry cell weight (DCW) as medium-chain-length polyhydroxyalkanoates (PHA). Expression from the main pathways for alkanes and naphthalene biodegradation as well as biosurfactants and PHA biosynthesis revealed that although the alkanes and naphthalene biodegradation routes were actively expressed even at stationary phase, PHA production was stimulated at late stationary phase and putisolvin could comprise the biosurfactant synthesized. The bioconversion of toxic petrochemical residues to added-value thermoelastomers and biosurfactants indicate the high industrial significance of P. citronellolis SJTE-3.
Collapse
Affiliation(s)
- Michalis Koutinas
- Department of Chemical Engineering, Cyprus University of Technology, 30 Archbishop Kyprianou Str., 3036, Limassol, Cyprus.
| | - Maria Kyriakou
- Department of Chemical Engineering, Cyprus University of Technology, 30 Archbishop Kyprianou Str., 3036, Limassol, Cyprus
| | - Kostas Andreou
- Department of Chemical Engineering, Cyprus University of Technology, 30 Archbishop Kyprianou Str., 3036, Limassol, Cyprus
| | - Michalis Hadjicharalambous
- Innovating Environmental Solutions Center (IESC) Ltd, 33 Spyrou Kyprianou Str., 3(rd) Industrial Area, Agios Sylas, 4193, Ypsonas, Limassol, Cyprus
| | - Efstathios Kaliviotis
- Department of Mechanical Engineering and Material Science and Engineering, Cyprus University of Technology, 45 Kitiou Kyprianou Str., 3041, Limassol, Cyprus
| | - Dimitris Pasias
- Department of Mechanical Engineering and Material Science and Engineering, Cyprus University of Technology, 45 Kitiou Kyprianou Str., 3041, Limassol, Cyprus
| | - George Kazamias
- Innovating Environmental Solutions Center (IESC) Ltd, 33 Spyrou Kyprianou Str., 3(rd) Industrial Area, Agios Sylas, 4193, Ypsonas, Limassol, Cyprus
| | - Costas Varavvas
- Innovating Environmental Solutions Center (IESC) Ltd, 33 Spyrou Kyprianou Str., 3(rd) Industrial Area, Agios Sylas, 4193, Ypsonas, Limassol, Cyprus
| | - Ioannis Vyrides
- Department of Chemical Engineering, Cyprus University of Technology, 30 Archbishop Kyprianou Str., 3036, Limassol, Cyprus
| |
Collapse
|
22
|
Yu J, Song J, Chi C, Liu T, Geng T, Cai Z, Dong W, Shi C, Ma X, Zhang Z, Ma X, Xing B, Jin H, Zhang L, Dong S, Yang D, Ma M. Functional Characterization and Crystal Structure of the Bifunctional Thioesterase Catalyzing Epimerization and Cyclization in Skyllamycin Biosynthesis. ACS Catal 2021. [DOI: 10.1021/acscatal.1c03064] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Jiahui Yu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Juan Song
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Changbiao Chi
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Tan Liu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Tongtong Geng
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Zonghui Cai
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Weidong Dong
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Cheng Shi
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Xueyang Ma
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Zhongyi Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Xiaojie Ma
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Baiying Xing
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Hongwei Jin
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Liangren Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Suwei Dong
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Donghui Yang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Ming Ma
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| |
Collapse
|
23
|
Fage CD, Kosol S, Jenner M, Öster C, Gallo A, Kaniusaite M, Steinbach R, Staniforth M, Stavros VG, Marahiel MA, Cryle MJ, Lewandowski JR. Communication Breakdown: Dissecting the COM Interfaces between the Subunits of Nonribosomal Peptide Synthetases. ACS Catal 2021. [DOI: 10.1021/acscatal.1c02113] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Christopher D. Fage
- Department of Chemistry/Biochemistry, Philipps-Universität Marburg, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany
- Department of Chemistry, University of Warwick, Gibbet Hill, Coventry CV4 7AL, U.K
| | - Simone Kosol
- Department of Chemistry, University of Warwick, Gibbet Hill, Coventry CV4 7AL, U.K
| | - Matthew Jenner
- Department of Chemistry, University of Warwick, Gibbet Hill, Coventry CV4 7AL, U.K
- Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry CV4 7AL, U.K
| | - Carl Öster
- Department of Chemistry, University of Warwick, Gibbet Hill, Coventry CV4 7AL, U.K
| | - Angelo Gallo
- Department of Chemistry, University of Warwick, Gibbet Hill, Coventry CV4 7AL, U.K
| | - Milda Kaniusaite
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
- EMBL Australia, Monash University, Clayton, Victoria 3800, Australia
| | - Roman Steinbach
- Department of Chemistry/Biochemistry, Philipps-Universität Marburg, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany
| | - Michael Staniforth
- Department of Chemistry, University of Warwick, Gibbet Hill, Coventry CV4 7AL, U.K
| | - Vasilios G. Stavros
- Department of Chemistry, University of Warwick, Gibbet Hill, Coventry CV4 7AL, U.K
| | - Mohamed A. Marahiel
- Department of Chemistry/Biochemistry, Philipps-Universität Marburg, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany
| | - Max J. Cryle
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
- EMBL Australia, Monash University, Clayton, Victoria 3800, Australia
| | - Józef R. Lewandowski
- Department of Chemistry, University of Warwick, Gibbet Hill, Coventry CV4 7AL, U.K
| |
Collapse
|
24
|
Mapping the biosynthetic pathway of a hybrid polyketide-nonribosomal peptide in a metazoan. Nat Commun 2021; 12:4912. [PMID: 34389721 PMCID: PMC8363725 DOI: 10.1038/s41467-021-24682-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 06/30/2021] [Indexed: 11/10/2022] Open
Abstract
Polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) hybrid systems typically use complex protein-protein interactions to facilitate direct transfer of intermediates between these multimodular megaenzymes. In the canal-associated neurons (CANs) of Caenorhabditis elegans, PKS-1 and NRPS-1 produce the nemamides, the only known hybrid polyketide-nonribosomal peptides biosynthesized by animals, through a poorly understood mechanism. Here, we use genome editing and mass spectrometry to map the roles of individual PKS-1 and NRPS-1 enzymatic domains in nemamide biosynthesis. Furthermore, we show that nemamide biosynthesis requires at least five additional enzymes expressed in the CANs that are encoded by genes distributed across the worm genome. We identify the roles of these enzymes and discover a mechanism for trafficking intermediates between a PKS and an NRPS. Specifically, the enzyme PKAL-1 activates an advanced polyketide intermediate as an adenylate and directly loads it onto a carrier protein in NRPS-1. This trafficking mechanism provides a means by which a PKS-NRPS system can expand its biosynthetic potential and is likely important for the regulation of nemamide biosynthesis. The only known animal polyketide-nonribosomal peptides, the nemamides, are biosynthesized by two megasynthetases in the canal-associated neurons (CANs) of C. elegans. Here, the authors map the biosynthetic roles of individual megasynthetase domains and identify additional enzymes in the CANs required for nemamide biosynthesis.
Collapse
|
25
|
Oestreich AM, Suli MI, Gerlach D, Fan R, Czermak P. Media development and process parameter optimization using statistical experimental designs for the production of nonribosomal peptides in Escherichia coli. ELECTRON J BIOTECHN 2021. [DOI: 10.1016/j.ejbt.2021.05.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
|
26
|
Evolutionary and functional analysis of an NRPS condensation domain integrates β-lactam, ᴅ-amino acid, and dehydroamino acid synthesis. Proc Natl Acad Sci U S A 2021; 118:2026017118. [PMID: 33893237 DOI: 10.1073/pnas.2026017118] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Nonribosomal peptide synthetases (NRPSs) are large, multidomain biosynthetic enzymes involved in the assembly-line-like synthesis of numerous peptide natural products. Among these are clinically useful antibiotics including three classes of β-lactams: the penicillins/cephalosporins, the monobactams, and the monocyclic nocardicins, as well as the vancomycin family of glycopeptides and the depsipeptide daptomycin. During NRPS synthesis, peptide bond formation is catalyzed by condensation (C) domains, which couple the nascent peptide with the next programmed amino acid of the sequence. A growing number of additional functions are linked to the activity of C domains. In the biosynthesis of the nocardicins, a specialized C domain prepares the embedded β-lactam ring from a serine residue. Here, we examine the evolutionary descent of this unique β-lactam-synthesizing C domain. Guided by its ancestry, we predict and demonstrate in vitro that this C domain alternatively performs peptide bond formation when a single stereochemical change is introduced into its peptide starting material. Remarkably, the function of the downstream thioesterase (TE) domain also changes. Natively, the TE directs C terminus epimerization prior to hydrolysis when the β-lactam is made but catalyzes immediate release of the alternative peptide. In addition, we investigate the roles of C-domain histidine residues in light of clade-specific sequence motifs, refining earlier mechanistic proposals of both β-lactam formation and canonical peptide synthesis. Finally, expanded phylogenetic analysis reveals unifying connections between β-lactam synthesis and allied C domains associated with the appearance of ᴅ-amino acid and dehydroamino acid residues in other NRPS-derived natural products.
Collapse
|
27
|
Uchiyama C, Fukuda A, Mukaiyama M, Nakazawa Y, Kuramochi Y, Muguruma K, Arimoto M, Ninomiya A, Kako K, Katsuyama Y, Konno S, Taguchi A, Takayama K, Taniguchi A, Nagumo Y, Usui T, Hayashi Y. Structural Revision of Natural Cyclic Depsipeptide MA026 Established by Total Synthesis and Biosynthetic Gene Cluster Analysis. Angew Chem Int Ed Engl 2021; 60:8792-8797. [PMID: 33533101 DOI: 10.1002/anie.202015193] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 01/16/2021] [Indexed: 11/06/2022]
Abstract
A revised structure of natural 14-mer cyclic depsipeptide MA026, isolated from Pseudomonas sp. RtlB026 in 2002 was established by physicochemical analysis with HPLC, MS/MS, and NMR and confirmed by total solid-phase synthesis. The revised structure differs from that previously reported in that two amino acid residues, assigned in error, have been replaced. Synthesized MA026 with the revised structure showed a tight junction (TJ) opening activity like that of the natural one in a cell-based TJ opening assay. Bioinformatic analysis of the putative MA026 biosynthetic gene cluster (BGC) of RtIB026 demonstrated that the stereochemistry of each amino acid residue in the revised structure can be reasonably explained. Phylogenetic analysis with xantholysin BGC indicates an exceptionally high homology (ca. 90 %) between xantholysin and MA026. The TJ opening activity of MA026 when binding to claudin-1 is a key to new avenues for transdermal administration of large hydrophilic biologics.
Collapse
Affiliation(s)
- Chihiro Uchiyama
- Department of Medicinal Chemistry, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan
| | - Akane Fukuda
- Department of Medicinal Chemistry, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan
| | - Minagi Mukaiyama
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan
| | - Yoshiki Nakazawa
- Department of Medicinal Chemistry, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan
| | - Yuka Kuramochi
- Department of Medicinal Chemistry, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan
| | - Kyohei Muguruma
- Department of Medicinal Chemistry, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan.,Present address: Department of Chemical Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, Tokyo, 152-8552, Japan
| | - Mitsue Arimoto
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan
| | - Akihiro Ninomiya
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan
| | - Koichiro Kako
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan
| | - Yohei Katsuyama
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Sho Konno
- Department of Medicinal Chemistry, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan
| | - Akihiro Taguchi
- Department of Medicinal Chemistry, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan
| | - Kentaro Takayama
- Department of Medicinal Chemistry, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan
| | - Atsuhiko Taniguchi
- Department of Medicinal Chemistry, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan
| | - Yoko Nagumo
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan
| | - Takeo Usui
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan
| | - Yoshio Hayashi
- Department of Medicinal Chemistry, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan
| |
Collapse
|
28
|
Uchiyama C, Fukuda A, Mukaiyama M, Nakazawa Y, Kuramochi Y, Muguruma K, Arimoto M, Ninomiya A, Kako K, Katsuyama Y, Konno S, Taguchi A, Takayama K, Taniguchi A, Nagumo Y, Usui T, Hayashi Y. Structural Revision of Natural Cyclic Depsipeptide MA026 Established by Total Synthesis and Biosynthetic Gene Cluster Analysis. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202015193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Chihiro Uchiyama
- Department of Medicinal Chemistry School of Pharmacy Tokyo University of Pharmacy and Life Sciences 1432-1 Horinouchi Hachioji Tokyo 192-0392 Japan
| | - Akane Fukuda
- Department of Medicinal Chemistry School of Pharmacy Tokyo University of Pharmacy and Life Sciences 1432-1 Horinouchi Hachioji Tokyo 192-0392 Japan
| | - Minagi Mukaiyama
- Graduate School of Life and Environmental Sciences University of Tsukuba 1-1-1 Tennodai Tsukuba Ibaraki 305-8572 Japan
| | - Yoshiki Nakazawa
- Department of Medicinal Chemistry School of Pharmacy Tokyo University of Pharmacy and Life Sciences 1432-1 Horinouchi Hachioji Tokyo 192-0392 Japan
| | - Yuka Kuramochi
- Department of Medicinal Chemistry School of Pharmacy Tokyo University of Pharmacy and Life Sciences 1432-1 Horinouchi Hachioji Tokyo 192-0392 Japan
| | - Kyohei Muguruma
- Department of Medicinal Chemistry School of Pharmacy Tokyo University of Pharmacy and Life Sciences 1432-1 Horinouchi Hachioji Tokyo 192-0392 Japan
- Present address: Department of Chemical Science and Engineering School of Materials and Chemical Technology Tokyo Institute of Technology Tokyo 152-8552 Japan
| | - Mitsue Arimoto
- Graduate School of Life and Environmental Sciences University of Tsukuba 1-1-1 Tennodai Tsukuba Ibaraki 305-8572 Japan
| | - Akihiro Ninomiya
- Graduate School of Life and Environmental Sciences University of Tsukuba 1-1-1 Tennodai Tsukuba Ibaraki 305-8572 Japan
| | - Koichiro Kako
- Graduate School of Life and Environmental Sciences University of Tsukuba 1-1-1 Tennodai Tsukuba Ibaraki 305-8572 Japan
| | - Yohei Katsuyama
- Department of Biotechnology Graduate School of Agricultural and Life Sciences The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku Tokyo 113-8657 Japan
- Collaborative Research Institute for Innovative Microbiology The University of Tokyo Bunkyo-ku Tokyo 113-8657 Japan
| | - Sho Konno
- Department of Medicinal Chemistry School of Pharmacy Tokyo University of Pharmacy and Life Sciences 1432-1 Horinouchi Hachioji Tokyo 192-0392 Japan
| | - Akihiro Taguchi
- Department of Medicinal Chemistry School of Pharmacy Tokyo University of Pharmacy and Life Sciences 1432-1 Horinouchi Hachioji Tokyo 192-0392 Japan
| | - Kentaro Takayama
- Department of Medicinal Chemistry School of Pharmacy Tokyo University of Pharmacy and Life Sciences 1432-1 Horinouchi Hachioji Tokyo 192-0392 Japan
| | - Atsuhiko Taniguchi
- Department of Medicinal Chemistry School of Pharmacy Tokyo University of Pharmacy and Life Sciences 1432-1 Horinouchi Hachioji Tokyo 192-0392 Japan
| | - Yoko Nagumo
- Graduate School of Life and Environmental Sciences University of Tsukuba 1-1-1 Tennodai Tsukuba Ibaraki 305-8572 Japan
| | - Takeo Usui
- Graduate School of Life and Environmental Sciences University of Tsukuba 1-1-1 Tennodai Tsukuba Ibaraki 305-8572 Japan
| | - Yoshio Hayashi
- Department of Medicinal Chemistry School of Pharmacy Tokyo University of Pharmacy and Life Sciences 1432-1 Horinouchi Hachioji Tokyo 192-0392 Japan
| |
Collapse
|
29
|
Pérez-Victoria I. Co-occurring Congeners Reveal the Position of Enantiomeric Amino Acids in Nonribosomal Peptides. Chembiochem 2021; 22:2087-2092. [PMID: 33440038 DOI: 10.1002/cbic.202000805] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/11/2021] [Indexed: 11/09/2022]
Abstract
The absolute configuration of the constituent amino acids in microbial nonribosomal peptides is typically determined by Marfey's method after total hydrolysis of the peptide. A challenge to structure elucidation arises when both d and l enantiomeric configurations of an amino acid are present. Determining the actual position of each amino acid enantiomer within the peptide sequence typically requires laborious approaches based on peptide partial hydrolysis or even total synthesis of the possible diastereomers. Herein, an alternative solution is discussed based on the homogeneous backbone chirality that governs all peptides biosynthesized by a common nonribosomal peptide synthetase. The information on configuration provided by Marfey's analysis of co-occurring minor congeners can reveal unequivocally the stereochemical sequence of the whole peptide family.
Collapse
Affiliation(s)
- Ignacio Pérez-Victoria
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía Parque Tecnológico de Ciencias de la Salud, Avda. del Conocimiento 34, 18016, Armilla, Granada, Spain
| |
Collapse
|
30
|
Fukuda TTH, Pereira CF, Melo WGP, Menegatti C, Andrade PHM, Groppo M, Lacava PT, Currie CR, Pupo MT. Insights Into the Ecological Role of Pseudomonas spp. in an Ant-plant Symbiosis. Front Microbiol 2021; 12:621274. [PMID: 33597940 PMCID: PMC7882492 DOI: 10.3389/fmicb.2021.621274] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 01/08/2021] [Indexed: 11/13/2022] Open
Abstract
In the myrmecophytic mutualistic relationship between Azteca ants and Cecropia plants both species receive protection and exchange nutrients. The presence of microorganisms in this symbiotic system has been reported, and the symbiotic role of some fungi involved in the myrmecophytic interactions has been described. In this work we focus on bacteria within this mutualism, conducting isolations and screening for antimicrobial activities, genome sequencing, and biochemical characterization. We show that Pantoea, Rhizobium, Methylobacterium, Streptomyces and Pseudomonas are the most common cultivable genera of bacteria. Interestingly, Pseudomonas spp. isolates showed potent activity against 83% of the pathogens tested in our antimicrobial activity assays, including a phytopathogenic fungus isolated from Cecropia samples. Given the predicted nitrogen limitations associated with the fungal patches within this myrmecophyte, we performed nitrogen fixation analyses on the bacterial isolates within the Proteobacteria and show the potential for nitrogen fixation in Pseudomonas strains. The genome of one Pseudomonas strain was sequenced and analyzed. The gene cluster involved in the biosynthesis of cyclic lipodepsipeptides (CLPs) was identified, and we found mutations that may be related to the loss of function in the dual epimerization/condensation domains. The compound was isolated, and its structure was determined, corresponding to the antifungal viscosinamide. Our findings of diazotrophy and production of viscosinamide in multiple Pseudomonas isolates suggests that this bacterial genus may play an important role in the Cecropia-Azteca symbiosis.
Collapse
Affiliation(s)
- Taise T H Fukuda
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Camila F Pereira
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Weilan G P Melo
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Carla Menegatti
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Paulo H M Andrade
- Laboratory of Microbiology and Biomolecules, Department of Morphology and Pathology, Center for Biological and Health Sciences, Federal University of São Carlos, São Carlos, Brazil
| | - Milton Groppo
- Laboratory of Plant Systematics, Department of Biology, Faculty of Philosophy, Sciences and Letters at Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Paulo T Lacava
- Laboratory of Microbiology and Biomolecules, Department of Morphology and Pathology, Center for Biological and Health Sciences, Federal University of São Carlos, São Carlos, Brazil
| | - Cameron R Currie
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States
| | - Mônica T Pupo
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| |
Collapse
|
31
|
Kirchner N, Cano-Prieto C, Schulz-Fincke AC, Gütschow M, Ortlieb N, Moschny J, Niedermeyer THJ, Horak J, Lämmerhofer M, van der Voort M, Raaijmakers JM, Gross H. Discovery of Thanafactin A, a Linear, Proline-Containing Octalipopeptide from Pseudomonas sp. SH-C52, Motivated by Genome Mining. JOURNAL OF NATURAL PRODUCTS 2021; 84:101-109. [PMID: 33382250 DOI: 10.1021/acs.jnatprod.0c01174] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Genome mining of the bacterial strains Pseudomonas sp. SH-C52 and Pseudomonas fluorescens DSM 11579 showed that both strains contained a highly similar gene cluster encoding an octamodular nonribosomal peptide synthetase (NRPS) system which was not associated with a known secondary metabolite. Insertional mutagenesis of an NRPS component followed by comparative profiling led to the discovery of the corresponding novel linear octalipopeptide thanafactin A, which was subsequently isolated and its structure determined by two-dimensional NMR and further spectroscopic and chromatographic methods. In bioassays, thanafactin A exhibited weak protease inhibitory activity and was found to modulate swarming motility in a strain-specific manner.
Collapse
Affiliation(s)
- Norbert Kirchner
- Pharmaceutical Institute, Department of Pharmaceutical Biology, University of Tübingen, 72076 Tübingen, Germany
| | - Carolina Cano-Prieto
- Pharmaceutical Institute, Department of Pharmaceutical Biology, University of Tübingen, 72076 Tübingen, Germany
| | | | - Michael Gütschow
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, 53121 Bonn, Germany
| | - Nico Ortlieb
- Department of Microbiology and Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, Eberhard Karls University Tübingen, 72076 Tübingen, Germany
- German Centre for Infection Research (DZIF), Partner Site Tübingen, 72076 Tübingen, Germany
| | - Julia Moschny
- Department of Microbiology and Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, Eberhard Karls University Tübingen, 72076 Tübingen, Germany
| | - Timo H J Niedermeyer
- Department of Microbiology and Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, Eberhard Karls University Tübingen, 72076 Tübingen, Germany
- German Centre for Infection Research (DZIF), Partner Site Tübingen, 72076 Tübingen, Germany
| | - Jeannie Horak
- Pharmaceutical Institute, Department of Pharmaceutical Analysis and Bioanalysis, University of Tübingen, 72076 Tübingen, Germany
- Dr. von Hauner Children's Hospital, Department of Metabolic and Nutritional Medicine, University of Munich Medical Center, Campus Innenstadt, 80337 Muenchen, Germany
| | - Michael Lämmerhofer
- Pharmaceutical Institute, Department of Pharmaceutical Analysis and Bioanalysis, University of Tübingen, 72076 Tübingen, Germany
| | - Menno van der Voort
- Laboratory of Phytopathology, Wageningen University, Wageningen, Netherlands
| | - Jos M Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Harald Gross
- Pharmaceutical Institute, Department of Pharmaceutical Biology, University of Tübingen, 72076 Tübingen, Germany
- German Centre for Infection Research (DZIF), Partner Site Tübingen, 72076 Tübingen, Germany
| |
Collapse
|
32
|
Dekimpe S, Masschelein J. Beyond peptide bond formation: the versatile role of condensation domains in natural product biosynthesis. Nat Prod Rep 2021; 38:1910-1937. [DOI: 10.1039/d0np00098a] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Condensation domains perform highly diverse functions during natural product biosynthesis and are capable of generating remarkable chemical diversity.
Collapse
Affiliation(s)
- Sofie Dekimpe
- Laboratory for Biomolecular Discovery & Engineering
- Department of Biology
- KU Leuven
- Leuven
- Belgium
| | - Joleen Masschelein
- Laboratory for Biomolecular Discovery & Engineering
- Department of Biology
- KU Leuven
- Leuven
- Belgium
| |
Collapse
|
33
|
Girard L, Höfte M, De Mot R. Lipopeptide families at the interface between pathogenic and beneficial Pseudomonas-plant interactions. Crit Rev Microbiol 2020; 46:397-419. [PMID: 32885723 DOI: 10.1080/1040841x.2020.1794790] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Lipopeptides (LPs) are a prominent class of molecules among the steadily growing spectrum of specialized metabolites retrieved from Pseudomonas, in particular soil-dwelling and plant-associated isolates. Among the multiple LP families, pioneering research focussed on phytotoxic and antimicrobial cyclic lipopeptides (CLPs) of the ubiquitous plant pathogen Pseudomonas syringae (syringomycin and syringopeptin). Their non-ribosomal peptide synthetases (NRPSs) are embedded in biosynthetic gene clusters (BGCs) that are tightly co-clustered on a pathogenicity island. Other members of the P. syringae group (Pseudomonas cichorii) and some species of the Pseudomonas asplenii group and Pseudomonas fluorescens complex have adopted these biosynthetic strategies to co-produce their own mycin and peptin variants, in some strains supplemented with an analogue of the P. syringae linear LP (LLP), syringafactin. This capacity is not confined to phytopathogens but also occurs in some biocontrol strains, which indicates that these LP families not solely function as general virulence factors. We address this issue by scrutinizing the structural diversity and bioactivities of LPs from the mycin, peptin, and factin families in a phylogenetic and evolutionary perspective. BGC functional organization (including associated regulatory and transport genes) and NRPS modular architectures in known and candidate LP producers were assessed by genome mining.
Collapse
Affiliation(s)
- Léa Girard
- Centre of Microbial and Plant Genetics, Faculty of Bioscience Engineering, KU Leuven, Heverlee-Leuven, Belgium
| | - Monica Höfte
- Department of Plants and Crops, Laboratory of Phytopathology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - René De Mot
- Centre of Microbial and Plant Genetics, Faculty of Bioscience Engineering, KU Leuven, Heverlee-Leuven, Belgium
| |
Collapse
|
34
|
Covas C, Almeida B, Esteves AC, Lourenço J, Domingues P, Caetano T, Mendo S. Peptone from casein, an antagonist of nonribosomal peptide synthesis: a case study of pedopeptins produced by Pedobacter lusitanus NL19. N Biotechnol 2020; 60:62-71. [PMID: 32891869 DOI: 10.1016/j.nbt.2020.07.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 07/20/2020] [Accepted: 07/25/2020] [Indexed: 01/30/2023]
Abstract
Novel natural products are urgently needed to address the worldwide incidence of bacterial resistance to antibiotics. Extreme environments are a major source of novel compounds with unusual chemical structures. Pedobacter lusitanus NL19 is a new bacterial species that was isolated from one such environment and which produces compounds with potent activity against relevant microorganisms in the clinical, food, veterinary and aquaculture areas. The production of antimicrobials by P. lusitanus NL19 was identified in tryptic soy agar (TSA), but not in its equivalent broth (TSB). It was observed that in TSB medium a high concentration of casein peptone (PC) repressed the production of antibacterial compounds. HPLC, MS and MS/MS spectra with de novo sequencing revealed that the bioactivity of P. lusitanus NL19 was due to the production of pedopeptins. Hence, biosynthesis of pedopeptins is inhibited by high concentrations of PC in the broth medium. Furthermore, a nonribosomal peptide synthetase (NRPS) gene cluster was identified in the genome of NL19 encoding the biosynthesis of the peptides. qPCR analysis confirmed that the transcription of these genes is repressed in cells cultivated in high concentrations of PC. It is shown that pedopeptins are nonribosomal peptides with a broad-spectrum activity, including against Gram-positive and Gram-negative bacteria and yeasts.
Collapse
Affiliation(s)
- Cláudia Covas
- CESAM and Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - Beatriz Almeida
- CESAM and Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - Ana Cristina Esteves
- CESAM and Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal; Universidade Católica Portuguesa, Faculty of Dental Medicine, Center for Interdisciplinary Research in Health (CIIS), Portugal
| | - Joana Lourenço
- CESAM and Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - Pedro Domingues
- Mass Spectrometry Centre and LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, Aveiro, 3810-193, Portugal
| | - Tânia Caetano
- CESAM and Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - Sónia Mendo
- CESAM and Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal.
| |
Collapse
|
35
|
Oni FE, Geudens N, Adiobo A, Omoboye OO, Enow EA, Onyeka JT, Salami AE, De Mot R, Martins JC, Höfte M. Biosynthesis and Antimicrobial Activity of Pseudodesmin and Viscosinamide Cyclic Lipopeptides Produced by Pseudomonads Associated with the Cocoyam Rhizosphere. Microorganisms 2020; 8:microorganisms8071079. [PMID: 32698413 PMCID: PMC7409209 DOI: 10.3390/microorganisms8071079] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 07/13/2020] [Accepted: 07/15/2020] [Indexed: 01/26/2023] Open
Abstract
Pseudomonas cyclic lipopeptides (CLPs) are encoded non-ribosomally by biosynthetic gene clusters (BGCs) and possess diverse biological activities. In this study, we conducted chemical structure and BGC analyses with antimicrobial activity assays for two CLPs produced by Pseudomonas strains isolated from the cocoyam rhizosphere in Cameroon and Nigeria. LC-MS and NMR analyses showed that the Pseudomonas sp. COR52 and A2W4.9 produce pseudodesmin and viscosinamide, respectively. These CLPs belong to the Viscosin group characterized by a nonapeptidic moiety with a 7-membered macrocycle. Similar to other Viscosin-group CLPs, the initiatory non-ribosomal peptide synthetase (NRPS) gene of the viscosinamide BGC is situated remotely from the other two NRPS genes. In contrast, the pseudodesmin genes are all clustered in a single genomic locus. Nano- to micromolar levels of pseudodesmin and viscosinamide led to the hyphal distortion and/or disintegration of Rhizoctonia solani AG2-2 and Pythium myriotylum CMR1, whereas similar levels of White Line-Inducing Principle (WLIP), another member of the Viscosin group, resulted in complete lysis of both soil-borne phytopathogens. In addition to the identification of the biosynthetic genes of these two CLPs and the demonstration of their interaction with soil-borne pathogens, this study provides further insights regarding evolutionary divergence within the Viscosin group.
Collapse
Affiliation(s)
- Feyisara E. Oni
- Laboratory of Phytopathology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium; (F.E.O.); (O.O.O.); (E.A.E.)
- Unit for Environmental Sciences and Management, Faculty of Natural and Agricultural Sciences, North-West University, 2520 Potchefstroom, South Africa
| | - Niels Geudens
- NMR and Structure Analysis Unit, Department of Organic and Macromolecular Chemistry, Faculty of Science, Ghent University, Krijgslaan 281, B-9000 Gent, Belgium; (N.G.); (J.C.M.)
| | - Amayana Adiobo
- Jay PJ Biotechnology Laboratory, Institute of Agricultural Research for Development (IRAD), Ekona, P. M. B 25 Buea, Cameroon;
| | - Olumide O. Omoboye
- Laboratory of Phytopathology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium; (F.E.O.); (O.O.O.); (E.A.E.)
- Department of Microbiology, Obafemi Awolowo University, 220005 Ile-Ife, Osun State, Nigeria
| | - Elsie A. Enow
- Laboratory of Phytopathology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium; (F.E.O.); (O.O.O.); (E.A.E.)
| | - Joseph T. Onyeka
- Plant Pathology Unit, National Root Crops Research Institute (NRCRI), 440001 Umudike, Abia State, Nigeria;
| | - Ayodeji E. Salami
- Faculty of Agriculture, Department of Crop, Horticulture and Landscape Design, Ekiti State University (EKSU), 360211 Ado-Ekiti, Nigeria;
| | - René De Mot
- Centre of Microbial and Plant Genetics, Faculty of Bioscience Engineering, KU Leuven, 3001 Heverlee, Belgium;
| | - José C. Martins
- NMR and Structure Analysis Unit, Department of Organic and Macromolecular Chemistry, Faculty of Science, Ghent University, Krijgslaan 281, B-9000 Gent, Belgium; (N.G.); (J.C.M.)
| | - Monica Höfte
- Laboratory of Phytopathology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium; (F.E.O.); (O.O.O.); (E.A.E.)
- Correspondence: ; Tel.: +32-9-264-6017
| |
Collapse
|
36
|
Yamanaka K, Fukumoto H, Takehara M, Hamano Y, Oikawa T. The Stereocontrolled Biosynthesis of Mirror-Symmetric 2,4-Diaminobutyric Acid Homopolymers Is Critically Governed by Adenylation Activations. ACS Chem Biol 2020; 15:1964-1973. [PMID: 32484328 DOI: 10.1021/acschembio.0c00321] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Among the four bioactive cationic homo-poly(amino acids) discovered in nature, two are mirror-image isomers of poly(2,4-diaminobutyric acid) (poly-Dab) whose biosynthesis has long been unexplained. Their structural analogy plausibly suggested that they could share a common biosynthetic pathway utilizing ε-poly(l-lysine) synthetase-like enzymology but with an unprecedented process for enantiomeric inversion of polymer building blocks. To investigate this possibility, we comparatively explored the biosynthesis of poly-l-Dab and its mirror-image isomer poly-d-Dab in Streptomyces celluloflavus USE31 and Streptoalloteichus hindustanus NBRC15115, respectively, through genome mining, genetic inactivation, and heterologous expression combined with biochemical assays. While they shared the same biosynthetic pathway, the poly-d-Dab biosynthetic gene cluster additionally harbored the racemase gene. The critical finding that poly-d-Dab synthetase, in contrast to the synthetase generating the l-isomer, selectively activated d-Dab through adenylation conclusively demonstrated that free diffusible d-Dab preactivationally generated by the racemase is directly activated to be incorporated into the polymer. Our study thus represents the first demonstration of the stereoselective biosynthesis of a nonribosomal peptide governed by adenylation activity for a d-amino acid other than alanine. In silico sequence comparison between poly-Dab synthetases allowed us to identify amino acid residues potentially responsible for the discrimination of Dab enantiomers. Our results will provide significant insight not only for the future discovery of novel bioactive cationic poly(amino acids) but also for the creation of designer nonribosomal peptides with d-configuration.
Collapse
Affiliation(s)
- Kazuya Yamanaka
- Department of Life Science and Biotechnology, Graduate School of Science and Engineering, Kansai University, 3-3-35 Yamate-Cho, Suita, Osaka 564-8680, Japan
| | - Hibiki Fukumoto
- Department of Life Science and Biotechnology, Graduate School of Science and Engineering, Kansai University, 3-3-35 Yamate-Cho, Suita, Osaka 564-8680, Japan
| | - Munenori Takehara
- Department of Materials Science, The University of Shiga Prefecture, 2500 Hassaka-cho, Hikone, Shiga 522-8533, Japan
| | - Yoshimitsu Hamano
- Department of Bioscience and Biotechnology, Fukui Prefectural University, 4-1-1 Matsuoka-Kenjojima, Eiheiji-cho, Yoshida-gun, Fukui 910-1195, Japan
| | - Tadao Oikawa
- Department of Life Science and Biotechnology, Graduate School of Science and Engineering, Kansai University, 3-3-35 Yamate-Cho, Suita, Osaka 564-8680, Japan
| |
Collapse
|
37
|
Li Y, Liu L, Zhang G, He N, Guo W, Hong B, Xie Y. Potashchelins, a Suite of Lipid Siderophores Bearing Both L- threo and L- erythro Beta-Hydroxyaspartic Acids, Acquired From the Potash-Salt-Ore-Derived Extremophile Halomonas sp. MG34. Front Chem 2020; 8:197. [PMID: 32266214 PMCID: PMC7100376 DOI: 10.3389/fchem.2020.00197] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 03/03/2020] [Indexed: 12/12/2022] Open
Abstract
Four new lipid siderophores bearing both L-threo- and L-erythro-β-hydroxyaspartic acids, potashchelins A-D (1-4), were isolated from the potash-salt-ore-derived extremophile Halomonas sp. MG34. The planar structures of 1-4 were elucidated on the basis of extensive 1D and 2D NMR studies and MS/MS data. Potashchelins 1-4 contain a hydrophilic nonapeptide headgroup sequentially consisting of β-hydroxyaspartic acid, serine, glycine, serine, serine, β-hydroxyaspartic acid, threonine, serine, and cyclic N(δ)-hydroxy-ornithine, which is appended by one of a series of fatty acids ranging from dodecanoic acid to tetradecanoic acid. The absolute configurations of the amino acids of potashchelins 1-4 were determined by C3 and advanced Marfey's reaction, partial hydrolysis, and bioinformatics analysis, which revealed that potashchelins 1-4 bear both L-threo- and L-erythro-β-hydroxyaspartic acid. Phylogenetic analysis showed that the stand-alone β-hydroxylase, PtcA, and the fused domain with β-hydroxylase activity in PtcB are expected to be responsible for the formation of L-erythro and L-threo diastereomers, respectively. Additionally, utilizing a comparative genomics approach, we revealed an evolutionary mechanism for lipid siderophores in Halomonas involving horizontal transfer. Bioassays showed that potashchelin A and D had weak antibacterial activity against B. subtilis CPCC 100029 with an MIC value of 64 μg/mL.
Collapse
Affiliation(s)
- Yihong Li
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Li Liu
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Gengxin Zhang
- Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, China Academy of Sciences, Beijing, China
| | - Ning He
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Wenqiang Guo
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Bin Hong
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.,NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yunying Xie
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| |
Collapse
|
38
|
Götze S, Stallforth P. Structure elucidation of bacterial nonribosomal lipopeptides. Org Biomol Chem 2020; 18:1710-1727. [DOI: 10.1039/c9ob02539a] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We provide a summary of the tools, which allow elucidate the structures of nonribosomal lipopetides.
Collapse
Affiliation(s)
- Sebastian Götze
- Department of Paleobiotechnology
- Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute (HKI)
- 07745 Jena
- Germany
| | - Pierre Stallforth
- Department of Paleobiotechnology
- Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute (HKI)
- 07745 Jena
- Germany
| |
Collapse
|
39
|
Götze S, Stallforth P. Structure, properties, and biological functions of nonribosomal lipopeptides from pseudomonads. Nat Prod Rep 2020; 37:29-54. [DOI: 10.1039/c9np00022d] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Bacteria of the genusPseudomonasdisplay a fascinating metabolic diversity. In this review, we focus our attention on the natural product class of nonribosomal lipopeptides, which help pseudomonads to colonize a wide range of ecological niches.
Collapse
Affiliation(s)
- Sebastian Götze
- Faculty 7: Natural and Environmental Sciences
- Institute for Environmental Sciences
- University Koblenz Landau
- 76829 Landau
- Germany
| | - Pierre Stallforth
- Junior Research Group Chemistry of Microbial Communication
- Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute (HKI)
- 07745 Jena
- Germany
| |
Collapse
|
40
|
Modification and de novo design of non-ribosomal peptide synthetases using specific assembly points within condensation domains. Nat Chem 2019; 11:653-661. [PMID: 31182822 DOI: 10.1038/s41557-019-0276-z] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Accepted: 04/26/2019] [Indexed: 11/09/2022]
Abstract
Non-ribosomal peptide synthetases (NRPSs) are giant enzyme machines that activate amino acids in an assembly line fashion. As NRPSs are not restricted to the incorporation of the 20 proteinogenic amino acids, their efficient manipulation would enable microbial production of a diverse range of peptides; however, the structural requirements for reprogramming NRPSs to facilitate the production of new peptides are not clear. Here we describe a new fusion point inside the condensation domains of NRPSs that results in the development of the exchange unit condensation domain (XUC) concept, which enables the efficient production of peptides, even containing non-natural amino acids, in yields up to 280 mg l-1. This allows the generation of more specific NRPSs, reducing the number of unwanted peptide derivatives, but also the generation of peptide libraries. The XUC might therefore be suitable for the future optimization of peptide production and the identification of bioactive peptide derivatives for pharmaceutical and other applications.
Collapse
|
41
|
Sinha S, Nge CE, Leong CY, Ng V, Crasta S, Alfatah M, Goh F, Low KN, Zhang H, Arumugam P, Lezhava A, Chen SL, Kanagasundaram Y, Ng SB, Eisenhaber F, Eisenhaber B. Genomics-driven discovery of a biosynthetic gene cluster required for the synthesis of BII-Rafflesfungin from the fungus Phoma sp. F3723. BMC Genomics 2019; 20:374. [PMID: 31088369 PMCID: PMC6518819 DOI: 10.1186/s12864-019-5762-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 05/02/2019] [Indexed: 12/20/2022] Open
Abstract
Background Phomafungin is a recently reported broad spectrum antifungal compound but its biosynthetic pathway is unknown. We combed publicly available Phoma genomes but failed to find any putative biosynthetic gene cluster that could account for its biosynthesis. Results Therefore, we sequenced the genome of one of our Phoma strains (F3723) previously identified as having antifungal activity in a high-throughput screen. We found a biosynthetic gene cluster that was predicted to synthesize a cyclic lipodepsipeptide that differs in the amino acid composition compared to Phomafungin. Antifungal activity guided isolation yielded a new compound, BII-Rafflesfungin, the structure of which was determined. Conclusions We describe the NRPS-t1PKS cluster ‘BIIRfg’ compatible with the synthesis of the cyclic lipodepsipeptide BII-Rafflesfungin [HMHDA-L-Ala-L-Glu-L-Asn-L-Ser-L-Ser-D-Ser-D-allo-Thr-Gly]. We report new Stachelhaus codes for Ala, Glu, Asn, Ser, Thr, and Gly. We propose a mechanism for BII-Rafflesfungin biosynthesis, which involves the formation of the lipid part by BIIRfg_PKS followed by activation and transfer of the lipid chain by a predicted AMP-ligase on to the first PCP domain of the BIIRfg_NRPS gene. Electronic supplementary material The online version of this article (10.1186/s12864-019-5762-6) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Swati Sinha
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore.
| | - Choy-Eng Nge
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore
| | - Chung Yan Leong
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore
| | - Veronica Ng
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore
| | - Sharon Crasta
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore
| | - Mohammad Alfatah
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore
| | - Falicia Goh
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore
| | - Kia-Ngee Low
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore
| | - Huibin Zhang
- Genome Institue of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, #02-01 Genome, Singapore, 138672, Republic of Singapore
| | - Prakash Arumugam
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore
| | - Alexander Lezhava
- Genome Institue of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, #02-01 Genome, Singapore, 138672, Republic of Singapore
| | - Swaine L Chen
- Genome Institue of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, #02-01 Genome, Singapore, 138672, Republic of Singapore.,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, 1E Kent Ridge Road, NUHS Tower Block, Level 10, Singapore, 119228, Republic of Singapore
| | - Yoganathan Kanagasundaram
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore
| | - Siew Bee Ng
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore
| | - Frank Eisenhaber
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore.,School of Computer Science and Engineering (SCSE), Nanyang Technological University (NTU), 50 Nanyang Drive, Singapore, 637553, Republic of Singapore
| | - Birgit Eisenhaber
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore.
| |
Collapse
|
42
|
Lundy TA, Mori S, Garneau-Tsodikova S. Probing the limits of interrupted adenylation domains by engineering a trifunctional enzyme capable of adenylation, N-, and S-methylation. Org Biomol Chem 2019; 17:1169-1175. [PMID: 30644493 DOI: 10.1039/c8ob02996b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The adenylation (A) domains found in nonribosomal peptide synthetases (NRPSs) exhibit tremendous plasticity. Some A domains have been shown to display the ability to contain within them the catalytic portion of an auxiliary domain, most commonly that of a methyltransferase (M) enzyme. This unique feature of A domains interrupted by M domains allows them to possess bifunctionality, where they can both adenylate and methylate an amino acid substrate. Additionally, these types of inserted M domains are able to selectively carry out either backbone or side chain methylation of amino acids. Interruptions with M domains are naturally found to occur either between the a2-a3 or the a8-a9 of the ten conserved motifs of A domains. Herein, we set out to answer the following question: Can one A domain support two different M domain interruptions occurring in two different locations (a2-a3 and a8-a9) of the A domain and possess the ability to adenylate an amino acid and methylate it on both its side chain and backbone? To answer this question we added a backbone methylating M3S domain from TioS(A3aM3SA3b) between the a8-a9 region of a mono-interrupted A domain, TioN(AaMNAb), that already contained a side chain methylating MN domain between its a2-a3 region. We evaluated the di-interrupted A domain TioN(AMNAM3SA) with a series of radiometric and mass spectrometry assays and found that this engineered enzyme was indeed capable of all three activities. These findings show that production of an active trifunctional di-interrupted A domain is possible and represents an exciting new avenue for future nonribosomal peptide (NRP) derivatization.
Collapse
Affiliation(s)
- Taylor A Lundy
- University of Kentucky, Department of Pharmaceutical Sciences, College of Pharmacy, Lexington, KY 40536-0596, USA.
| | | | | |
Collapse
|
43
|
Jahanshah G, Yan Q, Gerhardt H, Pataj Z, Lämmerhofer M, Pianet I, Josten M, Sahl HG, Silby MW, Loper JE, Gross H. Discovery of the Cyclic Lipopeptide Gacamide A by Genome Mining and Repair of the Defective GacA Regulator in Pseudomonas fluorescens Pf0-1. JOURNAL OF NATURAL PRODUCTS 2019; 82:301-308. [PMID: 30666877 DOI: 10.1021/acs.jnatprod.8b00747] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Genome mining of the Gram-negative bacterium Pseudomonas fluorescens Pf0-1 showed that the strain possesses a silent NRPS-based biosynthetic gene cluster encoding a new lipopeptide; its activation required the repair of the global regulator system. In this paper, we describe the genomics-driven discovery and characterization of the associated secondary metabolite gacamide A, a lipodepsipeptide that forms a new family of Pseudomonas lipopeptides. The compound has a moderate, narrow-spectrum antibiotic activity and facilitates bacterial surface motility.
Collapse
Affiliation(s)
- Gahzaleh Jahanshah
- Pharmaceutical Institute, Department of Pharmaceutical Biology , University of Tübingen , 72076 Tübingen , Germany
- German Centre for Infection Research (DZIF) , partner site Tübingen , 72076 Tübingen , Germany
| | - Qing Yan
- Department of Botany and Plant Pathology , Oregon State University , Corvallis , Oregon 97331 , United States
| | - Heike Gerhardt
- Pharmaceutical Institute, Department of Pharmaceutical Analysis and Bioanalysis , University of Tübingen , 72076 Tübingen , Germany
- UMR 5060, IRAMAT-CRP2A, Esplanade des Antilles , F-33600 Pessac , France
| | - Zoltán Pataj
- Pharmaceutical Institute, Department of Pharmaceutical Analysis and Bioanalysis , University of Tübingen , 72076 Tübingen , Germany
- UMR 5060, IRAMAT-CRP2A, Esplanade des Antilles , F-33600 Pessac , France
| | - Michael Lämmerhofer
- Pharmaceutical Institute, Department of Pharmaceutical Analysis and Bioanalysis , University of Tübingen , 72076 Tübingen , Germany
- UMR 5060, IRAMAT-CRP2A, Esplanade des Antilles , F-33600 Pessac , France
| | - Isabelle Pianet
- CESAMO-ISM, UMR 5255, CNRS , Université Bordeaux I , 351 Cours de la Libération , F-33405 Talence , France
| | - Michaele Josten
- Institute for Medical Microbiology, Immunology and Parasitology (IMMIP), Pharmaceutical Microbiology Unit , University of Bonn , 53115 Bonn , Germany
- German Centre for Infection Research (DZIF) , partner site Bonn-Cologne , 53115 Bonn , Germany
| | - Hans-Georg Sahl
- Institute for Medical Microbiology, Immunology and Parasitology (IMMIP), Pharmaceutical Microbiology Unit , University of Bonn , 53115 Bonn , Germany
- German Centre for Infection Research (DZIF) , partner site Bonn-Cologne , 53115 Bonn , Germany
| | - Mark W Silby
- Department of Biology , University of Massachusetts Dartmouth , North Dartmouth , Massachusetts 02747 , United States
| | - Joyce E Loper
- Department of Botany and Plant Pathology , Oregon State University , Corvallis , Oregon 97331 , United States
- Agricultural Research Service , U.S. Department of Agriculture , Corvallis , Oregon 97331 , United States
| | - Harald Gross
- Pharmaceutical Institute, Department of Pharmaceutical Biology , University of Tübingen , 72076 Tübingen , Germany
- German Centre for Infection Research (DZIF) , partner site Tübingen , 72076 Tübingen , Germany
| |
Collapse
|
44
|
Rai J. Peptide and protein mimetics by retro and retroinverso analogs. Chem Biol Drug Des 2019; 93:724-736. [PMID: 30582286 DOI: 10.1111/cbdd.13472] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 12/10/2018] [Accepted: 12/16/2018] [Indexed: 12/19/2022]
Abstract
Retroinverso analog of a natural polypeptide can sometimes mimic the structure and function of the natural peptide. The additional advantage of using retroinverso analog is that it is resistant to proteolysis. The retroinverso analogs have peptide sequence in reverse direction with respect to natural peptide and also have chirality of amino acid inverted from L to D. The D amino acids cannot be recognized by common proteases of the body; therefore, these peptides will not be degraded easily and have a longer-lasting effect as vaccine and inhibitor drugs. There have been many contested propositions about the geometric relationship between a peptide and its retro, inverso, or retroinverso analog. A retroinverso analog sometimes fails to adopt the structure that can mimic the function of the natural peptide. In such cases, partial retroinverso analog and other modifications can help in achieving the desired structure and function. Here, we review the theory, major experimental attempts, prediction methods, and alternative strategies related to retroinverso peptidomimetics.
Collapse
|
45
|
Guzmán-Chávez F, Zwahlen RD, Bovenberg RAL, Driessen AJM. Engineering of the Filamentous Fungus Penicillium chrysogenum as Cell Factory for Natural Products. Front Microbiol 2018; 9:2768. [PMID: 30524395 PMCID: PMC6262359 DOI: 10.3389/fmicb.2018.02768] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 10/29/2018] [Indexed: 12/14/2022] Open
Abstract
Penicillium chrysogenum (renamed P. rubens) is the most studied member of a family of more than 350 Penicillium species that constitute the genus. Since the discovery of penicillin by Alexander Fleming, this filamentous fungus is used as a commercial β-lactam antibiotic producer. For several decades, P. chrysogenum was subjected to a classical strain improvement (CSI) program to increase penicillin titers. This resulted in a massive increase in the penicillin production capacity, paralleled by the silencing of several other biosynthetic gene clusters (BGCs), causing a reduction in the production of a broad range of BGC encoded natural products (NPs). Several approaches have been used to restore the ability of the penicillin production strains to synthetize the NPs lost during the CSI. Here, we summarize various re-activation mechanisms of BGCs, and how interference with regulation can be used as a strategy to activate or silence BGCs in filamentous fungi. To further emphasize the versatility of P. chrysogenum as a fungal production platform for NPs with potential commercial value, protein engineering of biosynthetic enzymes is discussed as a tool to develop de novo BGC pathways for new NPs.
Collapse
Affiliation(s)
- Fernando Guzmán-Chávez
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands.,Synthetic Biology and Cell Engineering, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Reto D Zwahlen
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands.,Synthetic Biology and Cell Engineering, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Roel A L Bovenberg
- Synthetic Biology and Cell Engineering, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands.,DSM Biotechnology Centre, Delft, Netherlands
| | - Arnold J M Driessen
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands.,Synthetic Biology and Cell Engineering, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| |
Collapse
|
46
|
Esmaeel Q, Pupin M, Jacques P, Leclère V. Nonribosomal peptides and polyketides of Burkholderia: new compounds potentially implicated in biocontrol and pharmaceuticals. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:29794-29807. [PMID: 28547376 DOI: 10.1007/s11356-017-9166-3] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 05/01/2017] [Indexed: 06/07/2023]
Abstract
Bacteria belonging to the genus Burkholderia live in various ecological niches and present a significant role in the environments through the excretion of a wide variety of secondary metabolites including modular nonribosomal peptides (NRPs) and polyketides (PKs). These metabolites represent a widely distributed biomedically and biocontrol important class of natural products including antibiotics, siderophores, and anticancers as well as biopesticides that are considered as a novel source that can be used to defend ecological niche from competitors and to promote plant growth. The aim of this review is to present all NRPs produced or potentially produced by strains of Burkholderia, as NRPs represent a major source of active compounds implicated in biocontrol. The review is a compilation of results from a large screening we have performed on 48 complete sequenced genomes available in NCBI to identify NRPS gene clusters, and data found in the literature mainly because some interesting compounds are produced by strains not yet sequenced. In addition to NRPs, hybrids NRPs/PKs are also included. Specific features about biosynthetic gene clusters and structures of the modular enzymes responsible for the synthesis, the biological activities, and the potential uses in agriculture and pharmaceutical of NRPs and hybrids NRPs/PKs will also be discussed.
Collapse
Affiliation(s)
- Qassim Esmaeel
- University Lille, INRA, ISA, University Artois, University Littoral Côte d'Opale, EA 7394-ICV- Institut Charles Viollette, F-59000, Lille, France
- Laboratoire de Stress, Défenses et Reproduction des Plantes URVVC-EA 4707, UFR Sciences Exactes et Naturelles, University of Reims-Champagne-Ardenne, Reims, France
| | - Maude Pupin
- University Lille, CNRS, Centrale Lille, UMR 9189- CRIStAL- Centre de Recherche en Informatique Signal et Automatique de Lille, F-59000, Lille, France
- Inria-Lille Nord Europe, Bonsai team, F-59655, Villeneuve d'Ascq Cedex, France
| | - Philippe Jacques
- University Lille, INRA, ISA, University Artois, University Littoral Côte d'Opale, EA 7394-ICV- Institut Charles Viollette, F-59000, Lille, France
- TERRA Research Centre, Microbial Processes and Interactions (MiPI), Gembloux Agro-Bio Tech University of Liege, B-5030, Gembloux, Belgium
| | - Valérie Leclère
- University Lille, INRA, ISA, University Artois, University Littoral Côte d'Opale, EA 7394-ICV- Institut Charles Viollette, F-59000, Lille, France.
- University Lille, CNRS, Centrale Lille, UMR 9189- CRIStAL- Centre de Recherche en Informatique Signal et Automatique de Lille, F-59000, Lille, France.
- Inria-Lille Nord Europe, Bonsai team, F-59655, Villeneuve d'Ascq Cedex, France.
| |
Collapse
|
47
|
Geng H, Huang PQ. Rapid Generation of Molecular Complexity by Chemical Synthesis: Highly Efficient Total Synthesis of Hexacyclic Alkaloid (-)-Chaetominine and Its Biosynthetic Implications. CHEM REC 2018; 19:523-533. [PMID: 30252197 DOI: 10.1002/tcr.201800079] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 08/17/2018] [Indexed: 12/20/2022]
Abstract
The efficiency becomes a key issue in today's natural product total synthesis. While biomimetic synthesis is one of the most elegant strategies to achieve synthetic efficiency and thus to approach the ideal synthesis, most biogenetic pathways are unknown or unconfirmed. In this account, we demonstrate, through the shortest and also the most efficient asymmetric total syntheses of the hexacyclic alkaloid (-)-chaetominine to date, that on the basis of biogenetic thinking, one can develop quite efficient bio-inspired total synthesis, which in turn serves to suggest and chemically validate plausible biosynthetic routes for the natural product. The synthetic strategy thus developed is also inspiring for the development of other synthetic methods and efficient total synthesis of other natural products.
Collapse
Affiliation(s)
- Hui Geng
- Department of Chemistry Fujian Provincial Key Laboratory of Chemical BiologyiChEM (Collaborative Innovation Center of Chemistry for Energy Materials), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian, 361005, P. R. China
| | - Pei-Qiang Huang
- Department of Chemistry Fujian Provincial Key Laboratory of Chemical BiologyiChEM (Collaborative Innovation Center of Chemistry for Energy Materials), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian, 361005, P. R. China
| |
Collapse
|
48
|
Ganley JG, Carr G, Ioerger TR, Sacchettini JC, Clardy J, Derbyshire ER. Discovery of Antimicrobial Lipodepsipeptides Produced by aSerratiasp. within Mosquito Microbiomes. Chembiochem 2018; 19:1590-1594. [DOI: 10.1002/cbic.201800124] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Indexed: 11/06/2022]
Affiliation(s)
- Jack G. Ganley
- Department of Chemistry; Duke University; 124 Science Drive Durham NC 27708-0346 USA
| | - Gavin Carr
- Department of Biological Chemistry and Molecular Pharmacology; Harvard Medical School; 240 Longwood Avenue Boston MA 02115 USA
| | - Thomas R. Ioerger
- Department of Computer Science; Texas A&M University; College Station TX 77843 USA
| | - James C. Sacchettini
- Department of Biochemistry and Biophysics; Texas A&M University; College Station TX 77843 USA
| | - Jon Clardy
- Department of Biological Chemistry and Molecular Pharmacology; Harvard Medical School; 240 Longwood Avenue Boston MA 02115 USA
| | - Emily R. Derbyshire
- Department of Chemistry; Duke University; 124 Science Drive Durham NC 27708-0346 USA
| |
Collapse
|
49
|
Greene NP, Kaplan E, Crow A, Koronakis V. Antibiotic Resistance Mediated by the MacB ABC Transporter Family: A Structural and Functional Perspective. Front Microbiol 2018; 9:950. [PMID: 29892271 PMCID: PMC5985334 DOI: 10.3389/fmicb.2018.00950] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 04/24/2018] [Indexed: 12/18/2022] Open
Abstract
The MacB ABC transporter forms a tripartite efflux pump with the MacA adaptor protein and TolC outer membrane exit duct to expel antibiotics and export virulence factors from Gram-negative bacteria. Here, we review recent structural and functional data on MacB and its homologs. MacB has a fold that is distinct from other structurally characterized ABC transporters and uses a unique molecular mechanism termed mechanotransmission. Unlike other bacterial ABC transporters, MacB does not transport substrates across the inner membrane in which it is based, but instead couples cytoplasmic ATP hydrolysis with transmembrane conformational changes that are used to perform work in the extra-cytoplasmic space. In the MacAB-TolC tripartite pump, mechanotransmission drives efflux of antibiotics and export of a protein toxin from the periplasmic space via the TolC exit duct. Homologous tripartite systems from pathogenic bacteria similarly export protein-like signaling molecules, virulence factors and siderophores. In addition, many MacB-like ABC transporters do not form tripartite pumps, but instead operate in diverse cellular processes including antibiotic sensing, cell division and lipoprotein trafficking.
Collapse
Affiliation(s)
- Nicholas P Greene
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Elise Kaplan
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Allister Crow
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Vassilis Koronakis
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| |
Collapse
|
50
|
Resistance to nonribosomal peptide antibiotics mediated by D-stereospecific peptidases. Nat Chem Biol 2018; 14:381-387. [PMID: 29483640 DOI: 10.1038/s41589-018-0009-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 12/27/2017] [Indexed: 12/26/2022]
Abstract
Nonribosomal peptide antibiotics, including polymyxin, vancomycin, and teixobactin, most of which contain D-amino acids, are highly effective against multidrug-resistant bacteria. However, overusing antibiotics while ignoring the risk of resistance arising has inexorably led to widespread emergence of resistant bacteria. Therefore, elucidation of the emerging mechanisms of resistance to nonribosomal peptide antibiotics is critical to their implementation. Here we describe a networking-associated genome-mining platform for linking biosynthetic building blocks to resistance components associated with biosynthetic gene clusters. By applying this approach to 5,585 complete bacterial genomes spanning the entire domain of bacteria, with subsequent chemical and enzymatic analyses, we demonstrate a mechanism of resistance toward nonribosomal peptide antibiotics that is based on hydrolytic cleavage by D-stereospecific peptidases. Our finding reveals both the widespread distribution and broad-spectrum resistance potential of D-stereospecific peptidases, providing a potential early indicator of antibiotic resistance to nonribosomal peptide antibiotics.
Collapse
|