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Juby S, Soumya P, Jayachandran K, Radhakrishnan EK. Morphological, Metabolomic and Genomic Evidences on Drought Stress Protective Functioning of the Endophyte Bacillus safensis Ni7. Curr Microbiol 2024; 81:209. [PMID: 38834921 DOI: 10.1007/s00284-024-03720-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 04/26/2024] [Indexed: 06/06/2024]
Abstract
The metabolomic and genomic characterization of an endophytic Bacillus safensis Ni7 was carried out in this study. This strain has previously been isolated from the xerophytic plant Nerium indicum L. and reported to enhance the drought tolerance in Capsicum annuum L. seedlings. The effects of drought stress on the morphology, biofilm production, and metabolite production of B. safensis Ni7 are analyzed in the current study. From the results obtained, the organism was found to have multiple strategies such as aggregation and clumping, robust biofilm production, and increased production of surfactin homologues under the drought induced condition when compared to non-stressed condition. Further the whole genome sequencing (WGS) based analysis has demonstrated B. safensis Ni7 to have a genome size of 3,671,999 bp, N50 value of 3,527,239, and a mean G+C content of 41.58%. Interestingly the organism was observed to have the presence of various stress-responsive genes (13, 20U, 16U,160, 39, 17M, 18, 26, and ctc) and genes responsible for surfactin production (srfAA, srfAB, srfAC, and srfAD), biofilm production (epsD, epsE, epsF, epsG, epsH, epsI, epsK, epsL, epsM, epsN, and pel), chemotaxis (cheB_1, cheB_2, cheB_3, cheW_1, cheW_2 cheR, cheD, cheC, cheA, cheY, cheV, and cheB_4), flagella synthesis (flgG_1, flgG_2, flgG_3, flgC, and flgB) as supportive to the drought tolerance. Besides these, the genes responsible for plant growth promotion (PGP), including the genes for nitrogen (nasA, nasB, nasC, nasD, and nasE) and sulfur assimilation (cysL_1&L_2, cysI) and genes for phosphate solubilization (phoA, phoP_1& phoP_2, and phoR) could also be predicted. Along with the same, the genes for catalase, superoxide dismutase, protein homeostasis, cellular fitness, osmoprotectants production, and protein folding could also be predicted from its WGS data. Further pan-genome analysis with plant associated B. safensis strains available in the public databases revealed B. safensis Ni7 to have the presence of a total of 5391 gene clusters. Among these, 3207 genes were identified as core genes, 954 as shell genes and 1230 as cloud genes. This variation in gene content could be taken as an indication of evolution of strains of Bacillus safensis as per specific conditions and hence in the case of B. safensis Ni7 its role in habitat adaptation of plant is well expected. This diversity in endophytic bacterial genes may attribute its role to support the plant system to cope up with stress conditions. Overall, the study provides genomic evidence on Bacillus safensis Ni7 as a stress alleviating microbial partner in plants.
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Affiliation(s)
- Silju Juby
- School of Biosciences, Mahatma Gandhi University, Kottayam, India
| | - P Soumya
- School of Biosciences, Mahatma Gandhi University, Kottayam, India
| | - K Jayachandran
- School of Biosciences, Mahatma Gandhi University, Kottayam, India
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Tasdemir D, Scarpato S, Utermann-Thüsing C, Jensen T, Blümel M, Wenzel-Storjohann A, Welsch C, Echelmeyer VA. Epiphytic and endophytic microbiome of the seagrass Zostera marina: Do they contribute to pathogen reduction in seawater? THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 908:168422. [PMID: 37956849 DOI: 10.1016/j.scitotenv.2023.168422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 10/27/2023] [Accepted: 11/06/2023] [Indexed: 11/15/2023]
Abstract
Seagrass meadows provide crucial ecosystem services for coastal environments and were shown to reduce the abundance of waterborne pathogens linked to infections in humans and marine organisms in their vicinity. Among potential drivers, seagrass phenolics released into seawater have been linked to pathogen suppression, but the potential involvement of the seagrass microbiome has not been investigated. We hypothesized that the microbiome of the eelgrass Zostera marina, especially the leaf epiphytes that are at direct interface between the seagrass host and the surrounding seawater, inhibit waterborne pathogens thereby contributing to their removal. Using a culture-dependent approach, we isolated 88 bacteria and fungi associated with the surfaces and inner tissues of the eelgrass leaves (healthy and decaying) and the roots. We assessed the antibiotic activity of microbial extracts against a large panel of common aquatic, human (fecal) and plant pathogens, and mined the metabolome of the most active extracts. The healthy leaf epibiotic bacteria, particularly Streptomyces sp. strain 131, displayed broad-spectrum antibiotic activity superior to some control drugs. Gram-negative bacteria abundant on healthy leaf surfaces, and few endosphere-associated bacteria and fungi also displayed remarkable activities. UPLC-MS/MS-based untargeted metabolomics analyses showed rich specialized metabolite repertoires with low annotation rates, indicating the presence of many undescribed antimicrobials in the extracts. This study contributes to our understanding on microbial and chemical ecology of seagrasses, implying potential involvement of the seagrass microbiome in suppression of pathogens in seawater. Such effect is beneficial for the health of ocean and human, especially in the context of climate change that is expected to exacerbate all infectious diseases. It may also assist future seagrass conservation and management strategies.
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Affiliation(s)
- Deniz Tasdemir
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel 24106, Germany; Faculty of Mathematics and Natural Sciences, Kiel University, Kiel 24118, Germany.
| | - Silvia Scarpato
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel 24106, Germany
| | - Caroline Utermann-Thüsing
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel 24106, Germany
| | - Timo Jensen
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel 24106, Germany
| | - Martina Blümel
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel 24106, Germany
| | - Arlette Wenzel-Storjohann
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel 24106, Germany
| | - Claudia Welsch
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel 24106, Germany
| | - Vivien Anne Echelmeyer
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel 24106, Germany
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Keeler AM, Petruzziello PE, Boger EG, D'Ambrosio HK, Derbyshire ER. Exploring the Chain Release Mechanism from an Atypical Apicomplexan Polyketide Synthase. Biochemistry 2023; 62:2677-2688. [PMID: 37556730 DOI: 10.1021/acs.biochem.3c00272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/11/2023]
Abstract
Polyketide synthases (PKSs) are megaenzymes that form chemically diverse polyketides and are found within the genomes of nearly all classes of life. We recently discovered the type I PKS from the apicomplexan parasite Toxoplasma gondii, TgPKS2, which contains a unique putative chain release mechanism that includes ketosynthase (KS) and thioester reductase (TR) domains. Our bioinformatic analysis of the thioester reductase of TgPKS2, TgTR, suggests differences compared to other systems and hints at a possibly conserved release mechanism within the apicomplexan subclass Coccidia. To evaluate this release module, we first isolated TgTR and observed that it is capable of 4 electron (4e-) reduction of octanoyl-CoA to the primary alcohol, octanol, utilizing NADH. TgTR was also capable of generating octanol in the presence of octanal and NADH, but no reactions were observed when NADPH was supplied as a cofactor. To biochemically characterize the protein, we measured the catalytic efficiency of TgTR using a fluorescence assay and determined the TgTR binding affinity for cofactor and substrates using isothermal titration calorimetry (ITC). We additionally show that TgTR is capable of reducing an acyl carrier protein (ACP)-tethered substrate by liquid chromatography mass spectrometry and determine that TgTR binds to holo-TgACP4, its predicted cognate ACP, with a KD of 5.75 ± 0.77 μM. Finally, our transcriptional analysis shows that TgPKS2 is upregulated ∼4-fold in the parasite's cyst-forming bradyzoite stage compared to tachyzoites. Our study identifies features that distinguish TgPKS2 from well-characterized systems in bacteria and fungi and suggests it aids the T. gondii cyst stage.
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Affiliation(s)
- Aaron M Keeler
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Porter E Petruzziello
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Elizabeth G Boger
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Hannah K D'Ambrosio
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Emily R Derbyshire
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, United States
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Pal A, Das KM, Thakur A. Microwave-Assisted Synthesis of E-Aldimines, N-Heterocycles, and H 2 by Dehydrogenative Coupling of Benzyl Alcohol and Aniline Derivatives Using CoCl 2 as a Catalyst. J Org Chem 2023. [PMID: 37294694 DOI: 10.1021/acs.joc.3c00682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The acceptorless dehydrogenative coupling (ADC) between alcohols and amines to produce imines has been achieved mostly by employing precious-metal-based complexes or complexes of earth-abundant metal ions with sensitive and complicated ligand systems as catalysts mostly under harsh reaction conditions. Methodologies using readily available earth-abundant metal salts as catalysts without the requirement of ligand, oxidant, or any external additives are not explored. We report an unprecedented microwave-assisted CoCl2-catalyzed acceptorless dehydrogenative coupling of benzyl alcohol and amine for the synthesis of E-aldimines, N-heterocycles, and H2 under mild condition, without any complicated exogenous ligand template, oxidant, or other additives. This environmentally benign methodology exhibits broad substrate scope (43 including 7 new products) with fair functional-group tolerance on the aniline ring. Detection of metal-associated intermediate by gas chromatography (GC) and HRMS, H2 detection by GC, and kinetic isotope effect reveal the mechanism of this CoCl2-catalyzed reaction to be via ADC. Furthermore, kinetic experiments and Hammett analysis with variation in the nature of substituents over the aniline ring reveal the insight into the reaction mechanism with different substituents.
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Affiliation(s)
- Adwitiya Pal
- Department of Chemistry, Jadavpur University, Kolkata 700032, West Bengal, India
| | - Krishna Mohan Das
- Department of Chemistry, Jadavpur University, Kolkata 700032, West Bengal, India
| | - Arunabha Thakur
- Department of Chemistry, Jadavpur University, Kolkata 700032, West Bengal, India
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Wang Y, Zhao Q, Sun Z, Li Y, He H, Zhang Y, Yang X, Wang D, Dong B, Zhou H, Zhao M, Zheng H. Whole-genome analysis revealed the growth-promoting mechanism of endophytic bacterial strain Q2H1 in potato plants. Front Microbiol 2022; 13:1035901. [PMID: 36532474 PMCID: PMC9751815 DOI: 10.3389/fmicb.2022.1035901] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 11/03/2022] [Indexed: 01/09/2024] Open
Abstract
INTRODUCTION Endophytes are non-pathogenic inhabitants of healthy plant tissues and have been found to promote plant growth and health. The endophytic bacterial strain Q2H1 was isolated from the roots of the potato and was identified to exhibit growth-promoting effects in potato plants. METHODS Whole-genome sequencing was performed to reveal the mechanism underlying its growth-promoting effect. The obtained sequencing data of approximately 5.65 MB encompassed 5,533 coding sequences. Of note, nine secondary metabolite gene clusters, including siderophore gene clusters, closely associated with plant growth promotion (PGP) were predicted by antiSMASH software. Comparative genomic analysis revealed that Q2H1 belongs to the genus Peribacillus. By gene function annotation, those genes related to plant growth-promoting activities, including indole-3-acetic acid (IAA) synthesis in tryptophan metabolism, siderophore biosynthetic activity, phosphate solubilization, nitrogen fixation, and related genes, were summarized. IAA (14.4 μg/ml) was presumptively produced by Q2H1 using the Salkowski colorimetric method. A total of five genes, namely, phoU, pstB, pstA1, pstC, and pstS, were annotated for phosphate solubilization, which is associated with the ability of the Q2H1 strain to solubilize phosphate under in vitro conditions. RESULTS It is revealed that genes in the Q2H1 genome associated with nitrogen fixation belonged to three groups, namely, nitrogen fixation (nifU, sufU, salA, and nifS), nitrogen metabolism (nirA, nrtB, and nasA), and glutamate synthesis (glnA, gltB, gltD, and gudB), supported by evidence that Q2H1 grew on medium without nitrogen. We have also identified a siderophore gene cluster located on the chromosome of Q2H1, including seven genes (viz., rbsR, rhbf, rhbE, rhbD, rhbC, rhbA, ddc, and an unknown gene). In the in vitro assay, a prominent brown circle around the colony was produced on the chrome azurol S medium at 48 and 72 h post-inoculation, indicating that the siderophore gene cluster in Q2H1 harbored the ability to produce siderophores. CONCLUSION In summary, these findings implied that identifying strain-specific genes for their metabolic pathways in bacterial endophytes may reveal a variety of significant functions of plant growth-promoting mechanisms.
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Affiliation(s)
- Yuhu Wang
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
| | - Qianqian Zhao
- Institute of Agro-Food Technology, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Zhenqi Sun
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
| | - Yahui Li
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
| | - Hongtao He
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
| | - Yuanyu Zhang
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Xiangdong Yang
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Dong Wang
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
| | - Baozhu Dong
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
| | - Hongyou Zhou
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
| | - Mingmin Zhao
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
| | - Hongli Zheng
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
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Montecillo JAV, Bae H. In silico analysis of koranimine, a cyclic imine compound from Peribacillus frigoritolerans reveals potential nematicidal activity. Sci Rep 2022; 12:18883. [PMID: 36344604 PMCID: PMC9640594 DOI: 10.1038/s41598-022-20461-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 09/13/2022] [Indexed: 11/09/2022] Open
Abstract
Pine wilt disease (PWD) is a destructive vector-borne forest disease caused by the nematode Bursaphelenchus xylophilus. To date, several options are available for the management of pine wilt disease; however constant development and search for natural products with potential nematicidal activity are imperative to diversify management options and to cope with the possible future emergence of resistance in parasitic nematodes. Here, a combined metabolomics and genomics approach was employed to investigate the chemical repertoire and biosynthetic potential of the bacterial endophyte Peribacillus frigoritolerans BE93, previously characterized to exhibit nematicidal activity against B. xylophilus. Feature-based molecular networking revealed the presence of diverse secondary metabolites. A cyclic imine heptapeptide, koranimine, was found to be among the most abundant secondary metabolites produced. Genome mining displayed the presence of several putative biosynthetic gene clusters (BGCs), including a dedicated non-ribosomal peptide synthase (NRPS) BGC for koranimine. Given the non-ribosomal peptide nature of koranimine, in silico molecular docking analysis was conducted to investigate its potential nematicidal activity against the target receptor ivermectin-sensitive invertebrate α glutamate-gated chloride channel (GluCl). Results revealed the binding of koranimine at the allosteric site of the channel-the ivermectin binding site. Moreover, the ligand-receptor interactions observed were mostly shared between koranimine and ivermectin when bound to the α GluCl receptor thus, suggesting a possibly shared mechanism of potential nematicidal activity. This study highlights the efficiency of combined metabolomics and genomics approach in the identification of candidate compounds.
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Affiliation(s)
- Jake Adolf V. Montecillo
- grid.413028.c0000 0001 0674 4447Department of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk 38541 Republic of Korea
| | - Hanhong Bae
- grid.413028.c0000 0001 0674 4447Department of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk 38541 Republic of Korea
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Linardi D, She W, Zhang Q, Yu Y, Qian PY, Lam H. Proteomining-Based Elucidation of Natural Product Biosynthetic Pathways in Streptomyces. Front Microbiol 2022; 13:913756. [PMID: 35898901 PMCID: PMC9309509 DOI: 10.3389/fmicb.2022.913756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 05/30/2022] [Indexed: 11/24/2022] Open
Abstract
The genus Streptomyces is known to harbor numerous biosynthetic gene clusters (BGCs) of potential utility in synthetic biology applications. However, it is often difficult to link uncharacterized BGCs with the secondary metabolites they produce. Proteomining refers to the strategy of identifying active BGCs by correlating changes in protein expression with the production of secondary metabolites of interest. In this study, we devised a shotgun proteomics-based workflow to identify active BGCs during fermentation when a variety of compounds are being produced. Mycelia harvested during the non-producing growth phase served as the background. Proteins that were differentially expressed were clustered based on the proximity of the genes in the genome to highlight active BGCs systematically from label-free quantitative proteomics data. Our software tool is easy-to-use and requires only 1 point of comparison where natural product biosynthesis was significantly different. We tested our proteomining clustering method on three Streptomyces species producing different compounds. In Streptomyces coelicolor A3(2), we detected the BGCs of calcium-dependent antibiotic, actinorhodin, undecylprodigiosin, and coelimycin P1. In Streptomyces chrestomyceticus BCC24770, 7 BGCs were identified. Among them, we independently re-discovered the type II PKS for albofungin production previously identified by genome mining and tedious heterologous expression experiments. In Streptomyces tenebrarius, 5 BGCs were detected, including the known apramycin and tobramycin BGC as well as a newly discovered caerulomycin A BGC in this species. The production of caerulomycin A was confirmed by LC-MS and the inactivation of the caerulomycin A BGC surprisingly had a significant impact on the secondary metabolite regulation of S. tenebrarius. In conclusion, we developed an unbiased, high throughput proteomics-based method to complement genome mining methods for the identification of biosynthetic pathways in Streptomyces sp.
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Affiliation(s)
- Darwin Linardi
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China
| | - Weiyi She
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Hong Kong, Hong Kong SAR, China
- SZU-HKUST Joint PhD Program in Marine Environmental Science, Shenzhen University, Shenzhen, China
- Department of Ocean Science and Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China
| | - Qian Zhang
- Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Disease, Department of Gastroenterology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Yi Yu
- Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Disease, Department of Gastroenterology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Pei-Yuan Qian
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Hong Kong, Hong Kong SAR, China
- Department of Ocean Science and Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China
| | - Henry Lam
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China
- *Correspondence: Henry Lam,
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Jinno S, Senoo T, Mori K. Access to ortho-Hydroxyphenyl Ketimines via Imine Anion-Mediated Smiles Rearrangement. Org Lett 2022; 24:4140-4144. [PMID: 35670731 DOI: 10.1021/acs.orglett.2c01349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We have achieved a facile access to N-(2-halophenyl)-2-hydroxyphenylimine derivatives via imine anion-mediated Smiles rearrangement. When 2-(2-halophenoxy)benzonitriles were treated with 1.2-1.4 equiv of organolithium reagents, nucleophilic addition to the nitrile group followed by Smiles rearrangement occurred to give various N-(2-halophenyl)-2-hydroxyphenylimine derivatives, which are sometimes difficult to synthesize by the conventional acid-promoted condensation reaction between carbonyl compounds and aniline derivatives, in good to excellent chemical yields (up to 91%).
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Affiliation(s)
- Shunki Jinno
- Department of Applied Chemistry, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Nakacho, Koganei, Tokyo 184-8588, Japan
| | - Takahiro Senoo
- Department of Applied Chemistry, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Nakacho, Koganei, Tokyo 184-8588, Japan
| | - Keiji Mori
- Department of Applied Chemistry, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Nakacho, Koganei, Tokyo 184-8588, Japan
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Little RF, Hertweck C. Chain release mechanisms in polyketide and non-ribosomal peptide biosynthesis. Nat Prod Rep 2021; 39:163-205. [PMID: 34622896 DOI: 10.1039/d1np00035g] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Review covering up to mid-2021The structure of polyketide and non-ribosomal peptide natural products is strongly influenced by how they are released from their biosynthetic enzymes. As such, Nature has evolved a diverse range of release mechanisms, leading to the formation of bioactive chemical scaffolds such as lactones, lactams, diketopiperazines, and tetronates. Here, we review the enzymes and mechanisms used for chain release in polyketide and non-ribosomal peptide biosynthesis, how these mechanisms affect natural product structure, and how they could be utilised to introduce structural diversity into the products of engineered biosynthetic pathways.
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Affiliation(s)
- Rory F Little
- Leibniz Institute for Natural Product Research and Infection Biology, HKI, Germany.
| | - Christian Hertweck
- Leibniz Institute for Natural Product Research and Infection Biology, HKI, Germany.
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Lasch C, Stierhof M, Estévez MR, Myronovskyi M, Zapp J, Luzhetskyy A. Bonsecamin: A New Cyclic Pentapeptide Discovered through Heterologous Expression of a Cryptic Gene Cluster. Microorganisms 2021; 9:microorganisms9081640. [PMID: 34442719 PMCID: PMC8400726 DOI: 10.3390/microorganisms9081640] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 07/27/2021] [Accepted: 07/28/2021] [Indexed: 11/16/2022] Open
Abstract
The intriguing structural complexity of molecules produced by natural organisms is uncontested. Natural scaffolds serve as an important basis for the development of molecules with broad applications, e.g., therapeutics or agrochemicals. Research in recent decades has demonstrated that by means of classic metabolite extraction from microbes only a small portion of natural products can be accessed. The use of genome mining and heterologous expression approaches represents a promising way to discover new natural compounds. In this paper we report the discovery of a novel cyclic pentapeptide called bonsecamin through the heterologous expression of a cryptic NRPS gene cluster from Streptomyces albus ssp. chlorinus NRRL B-24108 in Streptomyces albus Del14. The new compound was successfully isolated and structurally characterized using NMR. The minimal set of genes required for bonsecamin production was determined through bioinformatic analysis and gene deletion experiments. A biosynthetic route leading to the production of bonsecamin is proposed in this paper.
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Affiliation(s)
- Constanze Lasch
- Department of Pharmaceutical Biotechnology, Saarland University, 66123 Saarbruecken, Germany; (C.L.); (M.S.); (M.R.E.); (M.M.)
| | - Marc Stierhof
- Department of Pharmaceutical Biotechnology, Saarland University, 66123 Saarbruecken, Germany; (C.L.); (M.S.); (M.R.E.); (M.M.)
| | - Marta Rodríguez Estévez
- Department of Pharmaceutical Biotechnology, Saarland University, 66123 Saarbruecken, Germany; (C.L.); (M.S.); (M.R.E.); (M.M.)
| | - Maksym Myronovskyi
- Department of Pharmaceutical Biotechnology, Saarland University, 66123 Saarbruecken, Germany; (C.L.); (M.S.); (M.R.E.); (M.M.)
| | - Josef Zapp
- Department of Pharmaceutical Biology, Saarland University, 66123 Saarbruecken, Germany;
| | - Andriy Luzhetskyy
- Department of Pharmaceutical Biotechnology, Saarland University, 66123 Saarbruecken, Germany; (C.L.); (M.S.); (M.R.E.); (M.M.)
- Helmholtz Institute for Pharmaceutical Research Saarland, 66123 Saarbruecken, Germany
- Correspondence: ; Tel.: +49-681-302-70200
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Adrover-Castellano ML, Schmidt JJ, Sherman DH. Biosynthetic Cyclization Catalysts for the Assembly of Peptide and Polyketide Natural Products. ChemCatChem 2021; 13:2095-2116. [PMID: 34335987 PMCID: PMC8320681 DOI: 10.1002/cctc.202001886] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Indexed: 12/13/2022]
Abstract
Many biologically active natural products are synthesized by nonribosomal peptide synthetases (NRPSs), polyketide synthases (PKSs) and their hybrids. These megasynthetases contain modules possessing distinct catalytic domains that allow for substrate initiation, chain extension, processing and termination. At the end of a module, a terminal domain, usually a thioesterase (TE), is responsible for catalyzing the release of the NRPS or PKS as a linear or cyclized product. In this review, we address the general cyclization mechanism of the TE domain, including oligomerization and the fungal C-C bond forming Claisen-like cyclases (CLCs). Additionally, we include examples of cyclization catalysts acting within or at the end of a module. Furthermore, condensation-like (CT) domains, terminal reductase (R) domains, reductase-like domains that catalyze Dieckmann condensation (RD), thioesterase-like Dieckmann cyclases, trans-acting TEs from the penicillin binding protein (PBP) enzyme family, product template (PT) domains and others will also be reviewed. The studies summarized here highlight the remarkable diversity of NRPS and PKS cyclization catalysts for the production of biologically relevant, complex cyclic natural products and related compounds.
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Affiliation(s)
| | - Jennifer J Schmidt
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109-2216 (USA)
| | - David H Sherman
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109-2216 (USA)
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12
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Akulov AA, Varaksin MV, Mampuys P, Charushin VN, Chupakhin ON, Maes BUW. C(sp 2)-H functionalization in non-aromatic azomethine-based heterocycles. Org Biomol Chem 2021; 19:297-312. [PMID: 33026389 DOI: 10.1039/d0ob01580f] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Direct C(sp2)-H functionalization of the endocyclic azomethine and aldonitrone moieties in non-aromatic azaheterocycles has established itself as a promising methodology over the last decade. Transition metal-catalyzed cross-coupling reactions, α-metalation-electrophile quenching protocols, and (metal-free) nucleophilic substitution of hydrogen reactions (SNH) are the major routes applied on cyclic imines and their derivatives. In this overview, we show the tangible progress made in this area during the period from 2008 to 2020.
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Affiliation(s)
- Alexey A Akulov
- Department of Organic & Biomolecular Chemistry, Ural Federal University, 19 Mira Str., 620002 Ekaterinburg, Russia.
| | - Mikhail V Varaksin
- Department of Organic & Biomolecular Chemistry, Ural Federal University, 19 Mira Str., 620002 Ekaterinburg, Russia. and Institute of Organic Synthesis, Ural Branch of the Russian Academy of Sciences, 22 S. Kovalevskaya Str., 620990 Ekaterinburg, Russia
| | - Pieter Mampuys
- Division of Organic Synthesis, Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, B-2020, Antwerp, Belgium.
| | - Valery N Charushin
- Department of Organic & Biomolecular Chemistry, Ural Federal University, 19 Mira Str., 620002 Ekaterinburg, Russia. and Institute of Organic Synthesis, Ural Branch of the Russian Academy of Sciences, 22 S. Kovalevskaya Str., 620990 Ekaterinburg, Russia
| | - Oleg N Chupakhin
- Department of Organic & Biomolecular Chemistry, Ural Federal University, 19 Mira Str., 620002 Ekaterinburg, Russia. and Institute of Organic Synthesis, Ural Branch of the Russian Academy of Sciences, 22 S. Kovalevskaya Str., 620990 Ekaterinburg, Russia
| | - Bert U W Maes
- Division of Organic Synthesis, Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, B-2020, Antwerp, Belgium.
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13
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Maglangit F, Yu Y, Deng H. Bacterial pathogens: threat or treat (a review on bioactive natural products from bacterial pathogens). Nat Prod Rep 2021; 38:782-821. [PMID: 33119013 DOI: 10.1039/d0np00061b] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Covering: up to the second quarter of 2020 Threat or treat? While pathogenic bacteria pose significant threats, they also represent a huge reservoir of potential pharmaceuticals to treat various diseases. The alarming antimicrobial resistance crisis and the dwindling clinical pipeline urgently call for the discovery and development of new antibiotics. Pathogenic bacteria have an enormous potential for natural products drug discovery, yet they remained untapped and understudied. Herein, we review the specialised metabolites isolated from entomopathogenic, phytopathogenic, and human pathogenic bacteria with antibacterial and antifungal activities, highlighting those currently in pre-clinical trials or with potential for drug development. Selected unusual biosynthetic pathways, the key roles they play (where known) in various ecological niches are described. We also provide an overview of the mode of action (molecular target), activity, and minimum inhibitory concentration (MIC) towards bacteria and fungi. The exploitation of pathogenic bacteria as a rich source of antimicrobials, combined with the recent advances in genomics and natural products research methodology, could pave the way for a new golden age of antibiotic discovery. This review should serve as a compendium to communities of medicinal chemists, organic chemists, natural product chemists, biochemists, clinical researchers, and many others interested in the subject.
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Affiliation(s)
- Fleurdeliz Maglangit
- Department of Biology and Environmental Science, College of Science, University of the Philippines Cebu, Lahug, Cebu City, 6000, Philippines. and Department of Chemistry, University of Aberdeen, Aberdeen AB24 3UE, UK.
| | - Yi Yu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (MOE), Hubei Province Engineering and Technology Research Centre for Fluorinated Pharmaceuticals, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China.
| | - Hai Deng
- Department of Chemistry, University of Aberdeen, Aberdeen AB24 3UE, UK.
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14
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Reguera L, Rivera DG. Macrocyclic Iminopeptides Diversify To Better Target Proteins. ChemMedChem 2020; 15:1111-1112. [DOI: 10.1002/cmdc.202000261] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 05/28/2020] [Indexed: 01/16/2023]
Affiliation(s)
- Leslie Reguera
- Faculty of ChemistryUniversity of Havana, Zapata y G Havana 10400 Cuba
| | - Daniel G. Rivera
- Faculty of ChemistryUniversity of Havana, Zapata y G Havana 10400 Cuba
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15
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Wu H, Gu Q, Xie Y, Lou Z, Xue P, Fang L, Yu C, Jia D, Huang G, Zhu B, Schneider A, Blom J, Lasch P, Borriss R, Gao X. Cold-adapted Bacilli isolated from the Qinghai-Tibetan Plateau are able to promote plant growth in extreme environments. Environ Microbiol 2019; 21:3505-3526. [PMID: 31233661 DOI: 10.1111/1462-2920.14722] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 06/17/2019] [Accepted: 06/18/2019] [Indexed: 12/13/2022]
Abstract
Nearly 1400 Bacillus strains growing in the plant rhizosphere were sampled from different sites on the Qinghai-Tibetan Plateau. Forty-five of the isolates, selected due to their biocontrol activity, were genome-sequenced and their taxonomic identification revealed that they were representatives of the Bacillus subtilis species complex (20) and the Bacillus cereus group (9). Majority of the remaining strains were found closely related to Bacillus pumilus, but their average nucleotide identity based on BLAST and electronic DNA/DNA hybridization values excluded closer taxonomic identification. A total of 45 different gene clusters involved in synthesis of secondary metabolites were detected by mining the genomes of the 45 selected strains. Except eight mesophilic strains, the 37 remaining strains were found either cold-adapted or psychrophilic, able to propagate at 10°C and below (Bacillus wiedmannii NMSL88 and Bacillus sp. RJGP41). Pot experiments performed at 10°C with winter wheat seedlings revealed that cold-adapted representatives of B. pumilus, B. safensis and B. atrophaeus promoted growth of the seedlings under cold conditions, suggesting that these bacilli isolated from a cold environment are promising candidates for developing of bioformulations useful for application in sustainable agriculture under environmental conditions unfavourable for the mesophilic bacteria presently in use.
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Affiliation(s)
- Huijun Wu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, People's Republic of China
| | - Qin Gu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, People's Republic of China
| | - Yongli Xie
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, People's Republic of China
| | - Zhiying Lou
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, People's Republic of China
| | - Pengqi Xue
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, People's Republic of China
| | - Liu Fang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, People's Republic of China
| | - Chenjie Yu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, People's Republic of China
| | - Dandan Jia
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, People's Republic of China
| | - Guochao Huang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, People's Republic of China
| | - Bichun Zhu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, People's Republic of China
| | - Andy Schneider
- Proteomics and Spectroscopy Unit (ZBS6) at the Centre for Biological Threats and Special Pathogens, Robert Koch-Institute, Berlin, Germany
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig Universität Giessen, Giessen, Germany
| | - Peter Lasch
- Proteomics and Spectroscopy Unit (ZBS6) at the Centre for Biological Threats and Special Pathogens, Robert Koch-Institute, Berlin, Germany
| | - Rainer Borriss
- Nordreet UG, Greifswald, Germany.,Institute of Marine Biotechnology e.V. (IMaB), Greifswald, Germany
| | - Xuewen Gao
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, People's Republic of China
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16
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Copper amine oxidases catalyze the oxidative deamination and hydrolysis of cyclic imines. Nat Commun 2019; 10:413. [PMID: 30679427 PMCID: PMC6345859 DOI: 10.1038/s41467-018-08280-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 12/28/2018] [Indexed: 01/26/2023] Open
Abstract
Although cyclic imines are present in various bioactive secondary metabolites, their degradative metabolism remains unknown. Here, we report that copper amine oxidases, which are important in metabolism of primary amines, catalyze a cyclic imine cleavage reaction. We isolate a microorganism (Arthrobacter sp. C-4A) which metabolizes a β-carboline alkaloid, harmaline. The harmaline-metabolizing enzyme (HarA) purified from strain C-4A is found to be copper amine oxidase and catalyze a ring-opening reaction of cyclic imine within harmaline, besides oxidative deamination of amines. Growth experiments on strain C-4A and Western blot analysis indicate that the HarA expression is induced by harmaline. We propose a reaction mechanism of the cyclic imine cleavage by HarA containing a post-translationally-synthesized cofactor, topaquinone. Together with the above results, the finding of the same activity of copper amine oxidase from E. coli suggests that, in many living organisms, these enzymes may play crucial roles in metabolism of ubiquitous cyclic imines.
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17
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De Leon Rodriguez LM, Williams ET, Brimble MA. Chemical Synthesis of Bioactive Naturally Derived Cyclic Peptides Containing Ene‐Like Rigidifying Motifs. Chemistry 2018; 24:17869-17880. [DOI: 10.1002/chem.201802533] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Indexed: 12/12/2022]
Affiliation(s)
| | - Elyse T. Williams
- School of Chemical SciencesThe University of Auckland 23 Symonds St. Auckland 1142 New Zealand
| | - Margaret A. Brimble
- School of Biological SciencesThe University of Auckland 3 Symonds St. Auckland 1142 New Zealand
- School of Chemical SciencesThe University of Auckland 23 Symonds St. Auckland 1142 New Zealand
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18
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Mullowney MW, McClure RA, Robey MT, Kelleher NL, Thomson RJ. Natural products from thioester reductase containing biosynthetic pathways. Nat Prod Rep 2018; 35:847-878. [PMID: 29916519 PMCID: PMC6146020 DOI: 10.1039/c8np00013a] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Covering: up to 2018 Thioester reductase domains catalyze two- and four-electron reductions to release natural products following assembly on nonribosomal peptide synthetases, polyketide synthases, and their hybrid biosynthetic complexes. This reductive off-loading of a natural product yields an aldehyde or alcohol, can initiate the formation of a macrocyclic imine, and contributes to important intermediates in a variety of biosyntheses, including those for polyketide alkaloids and pyrrolobenzodiazepines. Compounds that arise from reductase-terminated biosynthetic gene clusters are often reactive and exhibit biological activity. Biomedically important examples include the cancer therapeutic Yondelis (ecteinascidin 743), peptide aldehydes that inspired the first therapeutic proteasome inhibitor bortezomib, and numerous synthetic derivatives and antibody drug conjugates of the pyrrolobenzodiazepines. Recent advances in microbial genomics, metabolomics, bioinformatics, and reactivity-based labeling have facilitated the detection of these compounds for targeted isolation. Herein, we summarize known natural products arising from this important category, highlighting their occurrence in Nature, biosyntheses, biological activities, and the technologies used for their detection and identification. Additionally, we review publicly available genomic data to highlight the remaining potential for novel reductively tailored compounds and drug leads from microorganisms. This thorough retrospective highlights various molecular families with especially privileged bioactivity while illuminating challenges and prospects toward accelerating the discovery of new, high value natural products.
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Affiliation(s)
- Michael W Mullowney
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA.
| | - Ryan A McClure
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA.
| | - Matthew T Robey
- Department of Molecular Biosciences, Northwestern University, 2205 Tech Drive, Evanston, IL 60208, USA
| | - Neil L Kelleher
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA. and Department of Molecular Biosciences, Northwestern University, 2205 Tech Drive, Evanston, IL 60208, USA
| | - Regan J Thomson
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA.
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19
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Du C, van Wezel GP. Mining for Microbial Gems: Integrating Proteomics in the Postgenomic Natural Product Discovery Pipeline. Proteomics 2018; 18:e1700332. [PMID: 29708658 PMCID: PMC6175363 DOI: 10.1002/pmic.201700332] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 04/09/2018] [Indexed: 12/23/2022]
Abstract
Natural products (NPs) are a major source of compounds for medical, agricultural, and biotechnological industries. Many of these compounds are of microbial origin, and, in particular, from Actinobacteria or filamentous fungi. To successfully identify novel compounds that correlate to a bioactivity of interest, or discover new enzymes with desired functions, systematic multiomics approaches have been developed over the years. Bioinformatics tools harness the rapidly expanding wealth of genome sequence information, revealing previously unsuspected biosynthetic diversity. Varying growth conditions or application of elicitors are applied to activate cryptic biosynthetic gene clusters, and metabolomics provide detailed insights into the NPs they specify. Combining these technologies with proteomics-based approaches to profile the biosynthetic enzymes provides scientists with insights into the full biosynthetic potential of microorganisms. The proteomics approaches include enrichment strategies such as employing activity-based probes designed by chemical biology, as well as unbiased (quantitative) proteomics methods. In this review, the opportunities and challenges in microbial NP research are discussed, and, in particular, the application of proteomics to link biosynthetic enzymes to the molecules they produce, and vice versa.
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Affiliation(s)
- Chao Du
- Microbial Biotechnology & Health Programme Institute of BiologyLeiden UniversitySylviusweg 722333 BELeidenThe Netherlands
| | - Gilles P. van Wezel
- Microbial Biotechnology & Health Programme Institute of BiologyLeiden UniversitySylviusweg 722333 BELeidenThe Netherlands
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20
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Palazzotto E, Weber T. Omics and multi-omics approaches to study the biosynthesis of secondary metabolites in microorganisms. Curr Opin Microbiol 2018; 45:109-116. [PMID: 29656009 DOI: 10.1016/j.mib.2018.03.004] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 03/28/2018] [Accepted: 03/30/2018] [Indexed: 10/17/2022]
Abstract
Natural products produced by microorganisms represent the main source of bioactive molecules. The development of high-throughput (omics) techniques have importantly contributed to the renaissance of new antibiotic discovery increasing our understanding of complex mechanisms controlling the expression of biosynthetic gene clusters (BGCs) encoding secondary metabolites. In this context this review highlights recent progress in the use and integration of 'omics' approaches with focuses on genomics, transcriptomics, proteomics metabolomics meta-omics and combined omics as powerful strategy to discover new antibiotics.
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Affiliation(s)
- Emilia Palazzotto
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet bygning 220, 2800 Kgs., Lyngby, Denmark
| | - Tilmann Weber
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet bygning 220, 2800 Kgs., Lyngby, Denmark.
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21
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Wilson TA, Tokarski RJ, Sullivan P, Demoret RM, Orjala J, Rakotondraibe LH, Fuchs JR. Total Synthesis of Scytonemide A Employing Weinreb AM Solid-Phase Resin. JOURNAL OF NATURAL PRODUCTS 2018; 81:534-542. [PMID: 29400964 PMCID: PMC5866229 DOI: 10.1021/acs.jnatprod.7b00912] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The human 20S proteasome inhibitor scytonemide A (1), a macrocyclic imine originally isolated from the cyanobacterium Scytonema hofmanni, was synthesized via a biomimetic solid-phase peptide synthesis (SPPS) approach employing the Weinreb AM resin. Utilizing this approach, cyclization of the protected heptapeptide via formation of the imine bond occurred spontaneously upon cleavage from the resin in the presence of a reducing agent and subsequent aqueous workup. The final deprotection step necessary to produce the natural product was accomplished under slightly basic conditions, facilitating cleavage of the silyl ether group while leaving the macrocycle intact. Purification of the synthetic scytonemide A was accomplished via normal-phase flash column chromatography, potentially facilitating larger scale preparation of the compound necessary for future mechanistic and SAR studies. The structure of the target compound was confirmed by NMR spectroscopy, which also shed light on differences in the spectroscopic data obtained for the synthetic and natural scytonemide A samples for some of the amide and alcohol signals in the 1H NMR spectrum.
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Affiliation(s)
- Tyler A. Wilson
- Division of Medicinal Chemistry & Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH 43210, United States
| | - Robert J. Tokarski
- Division of Medicinal Chemistry & Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH 43210, United States
| | - Peter Sullivan
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612, United States
| | - Robert M. Demoret
- Division of Medicinal Chemistry & Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH 43210, United States
| | - Jimmy Orjala
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612, United States
| | - L. Harinantenaina Rakotondraibe
- Division of Medicinal Chemistry & Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH 43210, United States
| | - James R. Fuchs
- Division of Medicinal Chemistry & Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH 43210, United States
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22
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Malins LR, deGruyter JN, Robbins KJ, Scola PM, Eastgate MD, Ghadiri MR, Baran PS. Peptide Macrocyclization Inspired by Non-Ribosomal Imine Natural Products. J Am Chem Soc 2017; 139:5233-5241. [PMID: 28326777 PMCID: PMC5391502 DOI: 10.1021/jacs.7b01624] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
A thermodynamic approach to peptide macrocyclization inspired by the cyclization of non-ribosomal peptide aldehydes is presented. The method provides access to structurally diverse macrocycles by exploiting the reactivity of transient macrocyclic peptide imines toward inter- and intramolecular nucleophiles. Reactions are performed in aqueous media, in the absence of side chain protecting groups, and are tolerant of all proteinogenic functional groups. Macrocyclic products bearing non-native and rigidifying structural motifs, isotopic labels, and a variety of bioorthogonal handles are prepared, along with analogues of four distinct natural products. Structural interrogation of the linear and macrocyclic peptides using variable-temperature NMR and circular dichroism suggests that preorganization of linear substrates is not a prerequisite for macrocyclization.
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Affiliation(s)
- Lara R Malins
- Department of Chemistry, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Justine N deGruyter
- Department of Chemistry, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Kevin J Robbins
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development , 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Paul M Scola
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development , 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Martin D Eastgate
- Chemical Development, Bristol-Myers Squibb , One Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - M Reza Ghadiri
- Department of Chemistry, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Phil S Baran
- Department of Chemistry, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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23
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Dinesh R, Srinivasan V, T E S, Anandaraj M, Srambikkal H. Endophytic actinobacteria: Diversity, secondary metabolism and mechanisms to unsilence biosynthetic gene clusters. Crit Rev Microbiol 2017; 43:546-566. [PMID: 28358596 DOI: 10.1080/1040841x.2016.1270895] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Endophytic actinobacteria, which reside in the inner tissues of host plants, are gaining serious attention due to their capacity to produce a plethora of secondary metabolites (e.g. antibiotics) possessing a wide variety of biological activity with diverse functions. This review encompasses the recent reports on endophytic actinobacterial species diversity, in planta habitats and mechanisms underlying their mode of entry into plants. Besides, their metabolic potential, novel bioactive compounds they produce and mechanisms to unravel their hidden metabolic repertoire by activation of cryptic or silent biosynthetic gene clusters (BGCs) for eliciting novel secondary metabolite production are discussed. The study also reviews the classical conservative techniques (chemical/biological/physical elicitation, co-culturing) as well as modern microbiology tools (e.g. next generation sequencing) that are being gainfully employed to uncover the vast hidden scaffolds for novel secondary metabolites produced by these endophytes, which would subsequently herald a revolution in drug engineering. The potential role of these endophytes in the agro-environment as promising biological candidates for inhibition of phytopathogens and the way forward to thoroughly exploit this unique microbial community by inducing expression of cryptic BGCs for encoding unseen products with novel therapeutic properties are also discussed.
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Affiliation(s)
- Raghavan Dinesh
- a ICAR-Indian Institute of Spices Research , Kozhikode, Kerala , India
| | | | - Sheeja T E
- a ICAR-Indian Institute of Spices Research , Kozhikode, Kerala , India
| | | | - Hamza Srambikkal
- a ICAR-Indian Institute of Spices Research , Kozhikode, Kerala , India
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24
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Synergism of proteomics and mRNA sequencing for enzyme discovery. J Biotechnol 2016; 235:132-8. [DOI: 10.1016/j.jbiotec.2015.12.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 12/07/2015] [Accepted: 12/14/2015] [Indexed: 12/14/2022]
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25
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Henke MT, Soukup AA, Goering AW, McClure RA, Thomson RJ, Keller NP, Kelleher NL. New Aspercryptins, Lipopeptide Natural Products, Revealed by HDAC Inhibition in Aspergillus nidulans. ACS Chem Biol 2016; 11:2117-23. [PMID: 27310134 PMCID: PMC5119465 DOI: 10.1021/acschembio.6b00398] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Unlocking the biochemical stores of fungi is key for developing future pharmaceuticals. Through reduced expression of a critical histone deacetylase in Aspergillus nidulans, increases of up to 100-fold were observed in the levels of 15 new aspercryptins, recently described lipopeptides with two noncanonical amino acids derived from octanoic and dodecanoic acids. In addition to two NMR-verified structures, MS/MS networking helped uncover an additional 13 aspercryptins. The aspercryptins break the conventional structural orientation of lipopeptides and appear "backward" when compared to known compounds of this class. We have also confirmed the 14-gene aspercryptin biosynthetic gene cluster, which encodes two fatty acid synthases and several enzymes to convert saturated octanoic and dodecanoic acid to α-amino acids.
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Affiliation(s)
- Matthew T. Henke
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
| | - Alexandra A. Soukup
- Department of Genetics, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Anthony W. Goering
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
| | - Ryan A. McClure
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Regan J. Thomson
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Nancy P. Keller
- Department of Genetics, University of Wisconsin, Madison, Wisconsin 53706, United States
- Department of Bacteriology, University of Wisconsin, Madison, Wisconsin 53706, United States
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Neil L. Kelleher
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
- Feinberg School of Medicine, Northwestern University, Evanston, Illinois 60208, United States
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26
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Biosynthesis of Antibiotic Leucinostatins in Bio-control Fungus Purpureocillium lilacinum and Their Inhibition on Phytophthora Revealed by Genome Mining. PLoS Pathog 2016; 12:e1005685. [PMID: 27416025 PMCID: PMC4946873 DOI: 10.1371/journal.ppat.1005685] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2016] [Accepted: 05/18/2016] [Indexed: 12/18/2022] Open
Abstract
Purpureocillium lilacinum of Ophiocordycipitaceae is one of the most promising and commercialized agents for controlling plant parasitic nematodes, as well as other insects and plant pathogens. However, how the fungus functions at the molecular level remains unknown. Here, we sequenced two isolates (PLBJ-1 and PLFJ-1) of P. lilacinum from different places Beijing and Fujian. Genomic analysis showed high synteny of the two isolates, and the phylogenetic analysis indicated they were most related to the insect pathogen Tolypocladium inflatum. A comparison with other species revealed that this fungus was enriched in carbohydrate-active enzymes (CAZymes), proteases and pathogenesis related genes. Whole genome search revealed a rich repertoire of secondary metabolites (SMs) encoding genes. The non-ribosomal peptide synthetase LcsA, which is comprised of ten C-A-PCP modules, was identified as the core biosynthetic gene of lipopeptide leucinostatins, which was specific to P. lilacinum and T. ophioglossoides, as confirmed by phylogenetic analysis. Furthermore, gene expression level was analyzed when PLBJ-1 was grown in leucinostatin-inducing and non-inducing medium, and 20 genes involved in the biosynthesis of leucionostatins were identified. Disruption mutants allowed us to propose a putative biosynthetic pathway of leucinostatin A. Moreover, overexpression of the transcription factor lcsF increased the production (1.5-fold) of leucinostatins A and B compared to wild type. Bioassays explored a new bioactivity of leucinostatins and P. lilacinum: inhibiting the growth of Phytophthora infestans and P. capsici. These results contribute to our understanding of the biosynthetic mechanism of leucinostatins and may allow us to utilize P. lilacinum better as bio-control agent. Purpureocillium lilacinum, a well-known bio-control agent against various plant pathogens in agriculture, can produce antibiotic leucinostatins—peptaibiotic with extensive biological activities, including antimalarial, antiviral, antibacterial, antifungal, and antitumor activities, as well as phytotoxic. We have sequenced the genomes of two P. lilacinum isolates, and compared them with other fungi, focusing on their bio-control characteristics. We discovered a rich repertoire of CAZymes, proteases, SMs and pathogenesis related genes. We also identified a gene cluster containing 20 genes involved in the leucinostatins A and B biosynthesis by gene deletion, qRT-PCR and RNA-seq analyses. A transcription factor in the pathway was overexpressed, resulting in the upregulation of the related genes and a 1.5-fold increase in leucinostatins A and B. A new bioactivity of leucinostatins, inhibition of the growth of the notorious Phytophthora, was identified in this study by confronting incubation with P. lilacinum. These results provided new strategies for the agricultural development of leucinostatins and improving P. lilacinum strains.
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Bandyopadhyay A, Gao J. Iminoboronate-Based Peptide Cyclization That Responds to pH, Oxidation, and Small Molecule Modulators. J Am Chem Soc 2016; 138:2098-101. [PMID: 26859098 DOI: 10.1021/jacs.5b12301] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
As a rich source of therapeutic agents, peptide natural products usually adopt a cyclic or multicyclic scaffold that minimizes structural flexibility to favor target binding. Inspired by nature, chemists have been interested in developing synthetic cyclic and multicyclic peptides that serve as biological probes and potential therapeutics. Herein we describe a novel strategy for peptide cyclization in which intramolecular iminoboronate formation allows spontaneous cyclization under physiologic conditions to yield monocyclic and bicyclic peptides. Importantly the iminoboronate-based cyclization can be rapidly reversed in response to multiple stimuli, including pH, oxidation, and small molecules. This highly versatile strategy for peptide cyclization should find applications in many areas of chemical biology.
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Affiliation(s)
- Anupam Bandyopadhyay
- Department of Chemistry, Merkert Chemistry Center, Boston College , 2609 Beacon Street, Chestnut Hill, Massachusetts 02467, United States
| | - Jianmin Gao
- Department of Chemistry, Merkert Chemistry Center, Boston College , 2609 Beacon Street, Chestnut Hill, Massachusetts 02467, United States
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Chen Y, McClure RA, Kelleher NL. Screening for Expressed Nonribosomal Peptide Synthetases and Polyketide Synthases Using LC-MS/MS-Based Proteomics. Methods Mol Biol 2016; 1401:135-47. [PMID: 26831706 DOI: 10.1007/978-1-4939-3375-4_9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Liquid chromatography-mass spectrometry (LC-MS)-based proteomics is a powerful technique for the profiling of protein expression in cells in a high-throughput fashion. Herein we report a protocol using LC-MS/MS-based proteomics for the screening of enzymes involved in natural product biosynthesis, such as nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs) from bacterial strains. Taking advantage of the large size of modular NRPSs and PKSs (often >200 kDa), size-based separation (SDS-PAGE) is employed prior to LC-MS/MS analysis. Based upon the protein identifications obtained through software search, we can accurately pinpoint the expressed NRPS and/or PKS gene clusters from a given strain and growth condition. The proteomics screening result can be used to guide the discovery of potentially new nonribosomal peptide and polyketide natural products.
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Affiliation(s)
- Yunqiu Chen
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
| | - Ryan A McClure
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
| | - Neil L Kelleher
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA.
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Ishikawa F, Suzuki T, Dohmae N, Kakeya H. A Multiple-Labeling Strategy for Nonribosomal Peptide Synthetases Using Active-Site-Directed Proteomic Probes for Adenylation Domains. Chembiochem 2015; 16:2590-4. [PMID: 26467472 DOI: 10.1002/cbic.201500481] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Indexed: 11/07/2022]
Abstract
Genetic approaches have greatly contributed to our understanding of nonribosomal peptide biosynthetic machinery; however, proteomic investigations are limited. Here, we developed a highly sensitive detection strategy for multidomain nonribosomal peptide synthetases (NRPSs) by using a multiple-labeling technique with active-site-directed probes for adenylation domains. When applied to gramicidin S-producing and -nonproducing strains of Aneurinibacillus migulanus (DSM 5759 and DSM 2895, respectively), the multiple technique sensitively detected an active multidomain NRPS (GrsB) in lysates obtained from the organisms. This functional proteomics method revealed an unknown inactive precursor (or other inactive form) of GrsB in the nonproducing strain. This method provides a new option for the direct detection, functional analysis, and high-resolution identification of low-abundance active NRPS enzymes in native proteomic environments.
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Affiliation(s)
- Fumihiro Ishikawa
- Department of System Chemotherapy and Molecular Sciences, Division of Bioinformatics and Chemical Genomics, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto, 606-8501, Japan.
| | - Takehiro Suzuki
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Naoshi Dohmae
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Hideaki Kakeya
- Department of System Chemotherapy and Molecular Sciences, Division of Bioinformatics and Chemical Genomics, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto, 606-8501, Japan.
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Skinnider MA, Dejong CA, Rees PN, Johnston CW, Li H, Webster ALH, Wyatt MA, Magarvey NA. Genomes to natural products PRediction Informatics for Secondary Metabolomes (PRISM). Nucleic Acids Res 2015; 43:9645-62. [PMID: 26442528 PMCID: PMC4787774 DOI: 10.1093/nar/gkv1012] [Citation(s) in RCA: 130] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 09/24/2015] [Indexed: 12/05/2022] Open
Abstract
Microbial natural products are an invaluable source of evolved bioactive small molecules and pharmaceutical agents. Next-generation and metagenomic sequencing indicates untapped genomic potential, yet high rediscovery rates of known metabolites increasingly frustrate conventional natural product screening programs. New methods to connect biosynthetic gene clusters to novel chemical scaffolds are therefore critical to enable the targeted discovery of genetically encoded natural products. Here, we present PRISM, a computational resource for the identification of biosynthetic gene clusters, prediction of genetically encoded nonribosomal peptides and type I and II polyketides, and bio- and cheminformatic dereplication of known natural products. PRISM implements novel algorithms which render it uniquely capable of predicting type II polyketides, deoxygenated sugars, and starter units, making it a comprehensive genome-guided chemical structure prediction engine. A library of 57 tailoring reactions is leveraged for combinatorial scaffold library generation when multiple potential substrates are consistent with biosynthetic logic. We compare the accuracy of PRISM to existing genomic analysis platforms. PRISM is an open-source, user-friendly web application available at http://magarveylab.ca/prism/.
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Affiliation(s)
- Michael A Skinnider
- Departments of Biochemistry and Biomedical Sciences and Chemistry and Chemical Biology, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, L8S 4K1, Canada
| | - Chris A Dejong
- Departments of Biochemistry and Biomedical Sciences and Chemistry and Chemical Biology, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, L8S 4K1, Canada
| | - Philip N Rees
- Departments of Biochemistry and Biomedical Sciences and Chemistry and Chemical Biology, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, L8S 4K1, Canada
| | - Chad W Johnston
- Departments of Biochemistry and Biomedical Sciences and Chemistry and Chemical Biology, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, L8S 4K1, Canada
| | - Haoxin Li
- Departments of Biochemistry and Biomedical Sciences and Chemistry and Chemical Biology, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, L8S 4K1, Canada
| | - Andrew L H Webster
- Departments of Biochemistry and Biomedical Sciences and Chemistry and Chemical Biology, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, L8S 4K1, Canada
| | - Morgan A Wyatt
- Departments of Biochemistry and Biomedical Sciences and Chemistry and Chemical Biology, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, L8S 4K1, Canada
| | - Nathan A Magarvey
- Departments of Biochemistry and Biomedical Sciences and Chemistry and Chemical Biology, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, L8S 4K1, Canada
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Ishikawa F, Konno S, Suzuki T, Dohmae N, Kakeya H. Profiling Nonribosomal Peptide Synthetase Activities Using Chemical Proteomic Probes for Adenylation Domains. ACS Chem Biol 2015; 10:1989-97. [PMID: 26038981 DOI: 10.1021/acschembio.5b00097] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Nonribosomal peptide synthetases (NRPSs) and polyketide synthases are large diverse families of biosynthetic enzymes that catalyze the synthesis of natural products that display biologically important activities. Genetic investigations have greatly contributed to our understanding of these biosynthetic enzymes; however, proteomic studies are limited. Here we describe the application of active site-directed proteomic probes for adenylation (A) domains to profile the activity of NRPSs directly in native proteomic environments. Derivatization of a 5'-O-N-(aminoacyl)sulfamoyladenosine appended clickable benzophenone functionality enabled activity-based protein profiling of the A-domains in NRPSs in proteomic extracts. These probes were used to identify natural product producing microorganisms, optimize culture conditions, and profile the activity dynamics of NRPSs. Our proteomic approach offers a simple and versatile method to monitor NRPS expression at the protein level and will facilitate the identification of orphan enzymatic pathways involved in secondary metabolite production.
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Affiliation(s)
- Fumihiro Ishikawa
- Department
of System Chemotherapy and Molecular Sciences, Division of Bioinformatics
and Chemical Genomics, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Sho Konno
- Department
of System Chemotherapy and Molecular Sciences, Division of Bioinformatics
and Chemical Genomics, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Takehiro Suzuki
- Biomolecular
Characterization Unit, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Naoshi Dohmae
- Biomolecular
Characterization Unit, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Hideaki Kakeya
- Department
of System Chemotherapy and Molecular Sciences, Division of Bioinformatics
and Chemical Genomics, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan
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Maymon M, Martínez-Hidalgo P, Tran SS, Ice T, Craemer K, Anbarchian T, Sung T, Hwang LH, Chou M, Fujishige NA, Villella W, Ventosa J, Sikorski J, Sanders ER, Faull KF, Hirsch AM. Mining the phytomicrobiome to understand how bacterial coinoculations enhance plant growth. FRONTIERS IN PLANT SCIENCE 2015; 6:784. [PMID: 26442090 PMCID: PMC4585168 DOI: 10.3389/fpls.2015.00784] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 09/10/2015] [Indexed: 05/02/2023]
Abstract
In previous work, we showed that coinoculating Rhizobium leguminosarum bv. viciae 128C53 and Bacillus simplex 30N-5 onto Pisum sativum L. roots resulted in better nodulation and increased plant growth. We now expand this research to include another alpha-rhizobial species as well as a beta-rhizobium, Burkholderia tuberum STM678. We first determined whether the rhizobia were compatible with B. simplex 30N-5 by cross-streaking experiments, and then Medicago truncatula and Melilotus alba were coinoculated with B. simplex 30N-5 and Sinorhizobium (Ensifer) meliloti to determine the effects on plant growth. Similarly, B. simplex 30N-5 and Bu. tuberum STM678 were coinoculated onto Macroptilium atropurpureum. The exact mechanisms whereby coinoculation results in increased plant growth are incompletely understood, but the synthesis of phytohormones and siderophores, the improved solubilization of inorganic nutrients, and the production of antimicrobial compounds are likely possibilities. Because B. simplex 30N-5 is not widely recognized as a Plant Growth Promoting Bacterial (PGPB) species, after sequencing its genome, we searched for genes proposed to promote plant growth, and then compared these sequences with those from several well studied PGPB species. In addition to genes involved in phytohormone synthesis, we detected genes important for the production of volatiles, polyamines, and antimicrobial peptides as well as genes for such plant growth-promoting traits as phosphate solubilization and siderophore production. Experimental evidence is presented to show that some of these traits, such as polyamine synthesis, are functional in B. simplex 30N-5, whereas others, e.g., auxin production, are not.
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Affiliation(s)
- Maskit Maymon
- Departments of Molecular, Cell, and Developmental Biology, University of California, Los AngelesLos Angeles, CA, USA
| | - Pilar Martínez-Hidalgo
- Departments of Molecular, Cell, and Developmental Biology, University of California, Los AngelesLos Angeles, CA, USA
| | - Stephen S. Tran
- Bioinformatics, University of California, Los AngelesLos Angeles, CA, USA
| | - Tyler Ice
- Departments of Molecular, Cell, and Developmental Biology, University of California, Los AngelesLos Angeles, CA, USA
| | - Karena Craemer
- Departments of Molecular, Cell, and Developmental Biology, University of California, Los AngelesLos Angeles, CA, USA
| | - Teni Anbarchian
- Departments of Molecular, Cell, and Developmental Biology, University of California, Los AngelesLos Angeles, CA, USA
| | - Tiffany Sung
- Departments of Molecular, Cell, and Developmental Biology, University of California, Los AngelesLos Angeles, CA, USA
| | - Lin H. Hwang
- Pasarow Mass Spectrometry Laboratory, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine at UCLA, Semel Institute for Neuroscience and Human Behavior, University of California, Los AngelesLos Angeles, CA, USA
| | - Minxia Chou
- Departments of Molecular, Cell, and Developmental Biology, University of California, Los AngelesLos Angeles, CA, USA
| | - Nancy A. Fujishige
- Departments of Molecular, Cell, and Developmental Biology, University of California, Los AngelesLos Angeles, CA, USA
| | - William Villella
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los AngelesLos Angeles, CA, USA
| | - Jérôme Ventosa
- Biotechnology, Plants, and Microorganisms Biology, University of Montpellier IIMontpellier, France
| | - Johannes Sikorski
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbHBraunschweig, Germany
| | - Erin R. Sanders
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los AngelesLos Angeles, CA, USA
| | - Kym F. Faull
- Pasarow Mass Spectrometry Laboratory, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine at UCLA, Semel Institute for Neuroscience and Human Behavior, University of California, Los AngelesLos Angeles, CA, USA
- Molecular Biology Institute, University of California, Los AngelesLos Angeles, CA, USA
| | - Ann M. Hirsch
- Departments of Molecular, Cell, and Developmental Biology, University of California, Los AngelesLos Angeles, CA, USA
- Molecular Biology Institute, University of California, Los AngelesLos Angeles, CA, USA
- *Correspondence: Ann M. Hirsch, Departments of Molecular, Cell, and Developmental Biology and Molecular Biology Institute, University of California, Los Angeles, 621 Charles Young Drive South, Los Angeles, CA 90095-1606, USA
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Cho K, Evans BS, Wood BM, Kumar R, Erb TJ, Warlick BP, Gerlt JA, Sweedler JV. Integration of untargeted metabolomics with transcriptomics reveals active metabolic pathways. Metabolomics 2014; 2014. [PMID: 25705145 PMCID: PMC4334135 DOI: 10.1007/s11306-014-0713-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
While recent advances in metabolomic measurement technologies have been dramatic, extracting biological insight from complex metabolite profiles remains a challenge. We present an analytical strategy that uses data obtained from high resolution liquid chromatography-mass spectrometry and a bioinformatics toolset for detecting actively changing metabolic pathways upon external perturbation. We begin with untargeted metabolite profiling to nominate altered metabolites and identify pathway candidates, followed by validation of those pathways with transcriptomics. Using the model organisms Rhodospirillum rubrum and Bacillus subtilis, our results reveal metabolic pathways that are interconnected with methionine salvage. The rubrum-type methionine salvage pathway is interconnected with the active methyl cycle in which re-methylation, a key reaction for recycling methionine from homocysteine, is unexpectedly suppressed; instead, homocysteine is catabolized by the transsulfuration pathway. Notably, the non-mevalonate pathway is repressed, whereas the rubrum-type methionine salvage pathway contributes to isoprenoid biosynthesis upon 5'-methylthioadenosine feeding. In this process, glutathione functions as a coenzyme in vivo when 1-methylthio-d-xylulose 5-phosphate (MTXu 5-P) methylsulfurylase catalyzes dethiomethylation of MTXu 5-P. These results clearly show that our analytical approach enables unexpected metabolic pathways to be uncovered.
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Affiliation(s)
- Kyuil Cho
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801 USA
| | - Bradley S. Evans
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801 USA
| | - B. McKay Wood
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
| | - Ritesh Kumar
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
| | - Tobias J. Erb
- Institute for Microbiology, Swiss Federal Institute of Technology (ETH) Zurich, CH-8093 Zurich, Switzerland
| | - Benjamin P. Warlick
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
| | - John A. Gerlt
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801 USA
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
| | - Jonathan V. Sweedler
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801 USA
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Ma J, Vannam R, Terwilliger DW, Peczuh MW. Synthesis, structure and reactivity of a macrocyclic imine: aza-[13]-macrodiolides. Tetrahedron Lett 2014. [DOI: 10.1016/j.tetlet.2014.05.081] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Emerging strategies and integrated systems microbiology technologies for biodiscovery of marine bioactive compounds. Mar Drugs 2014; 12:3516-59. [PMID: 24918453 PMCID: PMC4071589 DOI: 10.3390/md12063516] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 05/21/2014] [Accepted: 05/22/2014] [Indexed: 12/30/2022] Open
Abstract
Marine microorganisms continue to be a source of structurally and biologically novel compounds with potential use in the biotechnology industry. The unique physiochemical properties of the marine environment (such as pH, pressure, temperature, osmolarity) and uncommon functional groups (such as isonitrile, dichloroimine, isocyanate, and halogenated functional groups) are frequently found in marine metabolites. These facts have resulted in the production of bioactive substances with different properties than those found in terrestrial habitats. In fact, the marine environment contains a relatively untapped reservoir of bioactivity. Recent advances in genomics, metagenomics, proteomics, combinatorial biosynthesis, synthetic biology, screening methods, expression systems, bioinformatics, and the ever increasing availability of sequenced genomes provides us with more opportunities than ever in the discovery of novel bioactive compounds and biocatalysts. The combination of these advanced techniques with traditional techniques, together with the use of dereplication strategies to eliminate known compounds, provides a powerful tool in the discovery of novel marine bioactive compounds. This review outlines and discusses the emerging strategies for the biodiscovery of these bioactive compounds.
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Szcześniak P, Stecko S, Staszewska-Krajewska O, Furman B. Sugar-derived cyclic imines: one-pot synthesis and direct functionalization. Tetrahedron 2014. [DOI: 10.1016/j.tet.2014.01.039] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Bekkaye M, Masson G. Cerium(IV) ammonium nitrate mediated three-component α-allylation of imine surrogates. Org Lett 2014; 16:1510-3. [PMID: 24568134 DOI: 10.1021/ol5004143] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
A general and practical CAN-mediated oxidative radical α-coupling reaction of various imine surrogates with allylsilanes has been described. This multicomponent process affords β-allylated α-carbamido ethers as stable imine precursors in respectable yields under mild conditions.
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Affiliation(s)
- Mathieu Bekkaye
- Centre de Recherche de Gif, Institut de Chimie des Substances Naturelles, CNRS , 91198 Gif-sur-Yvette Cedex, France
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Schofield MM, Sherman DH. Meta-omic characterization of prokaryotic gene clusters for natural product biosynthesis. Curr Opin Biotechnol 2013; 24:1151-8. [PMID: 23731715 PMCID: PMC3797859 DOI: 10.1016/j.copbio.2013.05.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Revised: 04/14/2013] [Accepted: 05/07/2013] [Indexed: 01/04/2023]
Abstract
Microorganisms produce a remarkable selection of bioactive small molecules. The study and exploitation of these secondary metabolites have traditionally been restricted to the cultivable minority of bacteria. Rapid advances in meta-omics challenge this paradigm. Breakthroughs in metagenomic library methodologies, direct sequencing, single cell genomics, and natural product-specific bioinformatic tools now facilitate the retrieval of previously inaccessible biosynthetic gene clusters. Similarly, metaproteomic developments enable the direct study of biosynthetic enzymes from complex microbial communities. Additional methods within and beyond meta-omics are also in development. This review discusses recent reports in these arenas and how they can be utilized to characterize natural product biosynthetic gene clusters and pathways.
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Affiliation(s)
- Michael M. Schofield
- Life Sciences Institute and Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - David H. Sherman
- Life Sciences Institute and Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
- Departments of Medicinal Chemistry, and Chemistry, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109
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Albright JC, Goering AW, Doroghazi JR, Metcalf WW, Kelleher NL. Strain-specific proteogenomics accelerates the discovery of natural products via their biosynthetic pathways. J Ind Microbiol Biotechnol 2013; 41:451-9. [PMID: 24242000 DOI: 10.1007/s10295-013-1373-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2013] [Accepted: 10/18/2013] [Indexed: 11/27/2022]
Abstract
The use of proteomics for direct detection of expressed pathways producing natural products has yielded many new compounds, even when used in a screening mode without a bacterial genome sequence available. Here we quantify the advantages of having draft DNA-sequence available for strain-specific proteomics using the latest in ultrahigh-resolution mass spectrometry for both proteins and the small molecules they generate. Using the draft sequence of Streptomyces lilacinus NRRL B-1968, we show a >tenfold increase in the number of peptide identifications vs. using publicly available databases. Detected in this strain were six expressed gene clusters with varying homology to those known. To date, we have identified three of these clusters as encoding for the production of griseobactin (known), rakicidin D (an orphan NRPS/PKS hybrid cluster), and a putative thr and DHB-containing siderophore produced by a new non-ribosomal peptide sythetase gene cluster. The remaining three clusters show lower homology to those known, and likely encode enzymes for production of novel compounds. Using an interpreted strain-specific DNA sequence enables deep proteomics for the detection of multiple pathways and their encoded natural products in a single cultured bacterium.
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Affiliation(s)
- Jessica C Albright
- Departments of Chemistry, Molecular Biosciences, and the Feinberg School of Medicine, Northwestern University, 2170 Campus Drive, Evanston, IL, 60208, USA
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Deane CD, Mitchell DA. Lessons learned from the transformation of natural product discovery to a genome-driven endeavor. J Ind Microbiol Biotechnol 2013; 41:315-31. [PMID: 24142337 DOI: 10.1007/s10295-013-1361-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2013] [Accepted: 09/30/2013] [Indexed: 12/24/2022]
Abstract
Natural product discovery is currently undergoing a transformation from a phenotype-driven field to a genotype-driven one. The increasing availability of genome sequences, coupled with improved techniques for identifying biosynthetic gene clusters, has revealed that secondary metabolomes are strikingly vaster than previously thought. New approaches to correlate biosynthetic gene clusters with the compounds they produce have facilitated the production and isolation of a rapidly growing collection of what we refer to as "reverse-discovered" natural products, in analogy to reverse genetics. In this review, we present an extensive list of reverse-discovered natural products and discuss seven important lessons for natural product discovery by genome-guided methods: structure prediction, accurate annotation, continued study of model organisms, avoiding genome-size bias, genetic manipulation, heterologous expression, and potential engineering of natural product analogs.
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Affiliation(s)
- Caitlin D Deane
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
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Bologa CG, Ursu O, Oprea TI, Melançon CE, Tegos GP. Emerging trends in the discovery of natural product antibacterials. Curr Opin Pharmacol 2013; 13:678-87. [PMID: 23890825 DOI: 10.1016/j.coph.2013.07.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Revised: 06/11/2013] [Accepted: 07/01/2013] [Indexed: 10/26/2022]
Abstract
This article highlights current trends and advances in exploiting natural sources for the deployment of novel and potent anti-infective countermeasures. The key challenge is to therapeutically target bacterial pathogens that exhibit a variety of puzzling and evolutionarily complex resistance mechanisms. Special emphasis is given to the strengths, weaknesses, and opportunities in the natural product antibacterial drug discovery arena, and to emerging applications driven by advances in bioinformatics, chemical biology, and synthetic biology in concert with exploiting bacterial phenotypes. These efforts have identified a critical mass of natural product antibacterial lead compounds and discovery technologies with high probability of successful implementation against emerging bacterial pathogens.
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Affiliation(s)
- Cristian G Bologa
- Center for Molecular Discovery, University of New Mexico, Albuquerque, USA; Translational Informatics Division, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
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42
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Chen Y, McClure RA, Zheng Y, Thomson RJ, Kelleher NL. Proteomics guided discovery of flavopeptins: anti-proliferative aldehydes synthesized by a reductase domain-containing non-ribosomal peptide synthetase. J Am Chem Soc 2013; 135:10449-56. [PMID: 23763305 DOI: 10.1021/ja4031193] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Due to the importance of proteases in regulating cellular processes, the development of protease inhibitors has garnered great attention. Peptide-based aldehydes are a class of compounds that exhibit inhibitory activities against various proteases and proteasomes in the context of anti-proliferative treatments for cancer and other diseases. More than a dozen peptide-based natural products containing aldehydes have been discovered such as chymostatin, leupeptin, and fellutamide; however, the biosynthetic origin of the aldehyde functionality has yet to be elucidated. Herein we describe the discovery of a new group of lipopeptide aldehydes, the flavopeptins, and the corresponding biosynthetic pathway arising from an orphan gene cluster in Streptomyces sp. NRRL-F6652, a close relative of Streptomyces flavogriseus ATCC 33331. This research was initiated using a proteomics approach that screens for expressed enzymes involved in secondary metabolism in microorganisms. Flavopeptins are synthesized through a non-ribosomal peptide synthetase containing a terminal NAD(P)H-dependent reductase domain likely for the reductive release of the peptide with a C-terminal aldehyde. Solid-phase peptide synthesis of several flavopeptin species and derivatives enabled structural verification and subsequent screening of biological activity. Flavopeptins exhibit sub-micromolar inhibition activities against cysteine proteases such as papain and calpain as well as the human 20S proteasome. They also show anti-proliferative activities against multiple myeloma and lymphoma cell lines.
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Affiliation(s)
- Yunqiu Chen
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
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Evans BS, Zhao C, Gao J, Evans CM, Ju KS, Doroghazi JR, van der Donk WA, Kelleher NL, Metcalf WW. Discovery of the antibiotic phosacetamycin via a new mass spectrometry-based method for phosphonic acid detection. ACS Chem Biol 2013; 8:908-13. [PMID: 23474169 DOI: 10.1021/cb400102t] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Naturally occurring phosphonates such as phosphinothricin (Glufosinate, a commercially used herbicide) and fosfomycin (Monurol, a clinically used antibiotic) have proved to be potent and useful biocides. Yet this class of natural products is still an under explored family of secondary metabolites. Discovery of the biosynthetic pathways responsible for the production of these compounds has been simplified by using gene based screening approaches, but detection and identification of the natural products the genes produce have been hampered by a lack of high-throughput methods for screening potential producers under various culture conditions. Here, we present an efficient mass-spectrometric method for the selective detection of natural products containing phosphonate and phosphinate functional groups. We have used this method to identify a new phosphonate metabolite, phosacetamycin, whose structure, biological activity, and biosynthetic gene cluster are reported.
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Affiliation(s)
| | | | | | | | | | | | | | - Neil L. Kelleher
- Northwestern University, Evanston, Illinois 60208, United States
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Jiang W, Cacho RA, Chiou G, Garg NK, Tang Y, Walsh CT. EcdGHK are three tailoring iron oxygenases for amino acid building blocks of the echinocandin scaffold. J Am Chem Soc 2013; 135:4457-66. [PMID: 23451921 PMCID: PMC3628723 DOI: 10.1021/ja312572v] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The echinocandins are a small group of fungal N-acylated cyclic hexapeptides that are fungicidal for candida strains and fungistatic for aspergilli by targeting cell wall 1,3-β-glucan synthases. The side chains of all six amino acid building blocks have hydroxyl groups, including the nonproteinogenic 4R,5R-dihydroxy-Orn1, 4R-OH-Pro3, 3S,4S-dihydroxy-homoTyr4, and 3S-OH-4S-Me-Pro6. The echinocandin (ecd) gene cluster contains two predicted nonheme mononuclear iron oxygenase genes (ecdG,K) and one encoding a P450 type heme protein (ecdH). Deletion of the ecdH gene in the producing strain Emericella rugulosa generates an echinocandin scaffold (echinocandin D) lacking both hydroxyl groups on Orn1. Correspondingly, the ΔecdG strain failed to hydroxylate C3 of the homoTyr residue, and purified EcdG hydroxylated free L-homoTyr at C3. The ΔecdK strain failed to generate mature echinocandin unless supplemented with either 4R-Me-Pro or 3S-OH-4S-Me-Pro, indicating blockage of a step upstream of Me-Pro formation. Purified EcdK is a Leu 5-hydroxylase, acting iteratively at C5 to yield γ-Me-Glu-γ-semialdehyde in equilibrium with the cyclic imine product. Evaluation of deshydroxyechinocandin scaffolds in the in vitro anticandidal assays revealed up to a 3-fold loss of potency for the ΔecdG scaffolds, but a 3-fold gain of potency for the ΔecdH scaffold, in line with prior results on deoxyechinocandin homologues.
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Affiliation(s)
- Wei Jiang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
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Chen Y, Unger M, Ntai I, McClure RA, Albright JC, Thomson RJ, Kelleher NL. Gobichelin A and B: Mixed-Ligand Siderophores Discovered Using Proteomics. MEDCHEMCOMM 2012; 4:233-238. [PMID: 23336063 DOI: 10.1039/c2md20232h] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
"Omic" strategies have been increasingly applied to natural product discovery processes, with (meta-)genome sequencing and mining implemented in many laboratories to date. Using the proteomics-based discovery platform called PrISM (Proteomic Investigation of Secondary Metabolism), we discovered two new siderophores gobichelin A and B from Streptomyces sp. NRRL F-4415, a strain without a sequenced genome. Using the proteomics information as a guide, the 37 kb gene cluster responsible for production of gobichelins was sequenced and its 20 open reading frames interpreted into a biosynthetic scheme. This led to the targeted detection and structure elucidation of the new compounds produced by nonribosomal peptide (NRP) synthesis.
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Affiliation(s)
- Yunqiu Chen
- Department of Chemistry and Chemistry of Life Processes Institute, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208
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Sasso S, Pohnert G, Lohr M, Mittag M, Hertweck C. Microalgae in the postgenomic era: a blooming reservoir for new natural products. FEMS Microbiol Rev 2012; 36:761-85. [DOI: 10.1111/j.1574-6976.2011.00304.x] [Citation(s) in RCA: 115] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2011] [Accepted: 08/29/2011] [Indexed: 01/20/2023] Open
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Gomez-Escribano JP, Song L, Fox DJ, Yeo V, Bibb MJ, Challis GL. Structure and biosynthesis of the unusual polyketide alkaloid coelimycin P1, a metabolic product of the cpk gene cluster of Streptomyces coelicolor M145. Chem Sci 2012. [DOI: 10.1039/c2sc20410j] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Chen Y, Ntai I, Ju KS, Unger M, Zamdborg L, Robinson SJ, Doroghazi JR, Labeda DP, Metcalf WW, Kelleher NL. A proteomic survey of nonribosomal peptide and polyketide biosynthesis in actinobacteria. J Proteome Res 2011; 11:85-94. [PMID: 21978092 DOI: 10.1021/pr2009115] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Actinobacteria such as streptomycetes are renowned for their ability to produce bioactive natural products including nonribosomal peptides (NRPs) and polyketides (PKs). The advent of genome sequencing has revealed an even larger genetic repertoire for secondary metabolism with most of the small molecule products of these gene clusters still unknown. Here, we employed a "protein-first" method called PrISM (Proteomic Investigation of Secondary Metabolism) to screen 26 unsequenced actinomycetes using mass spectrometry-based proteomics for the targeted detection of expressed nonribosomal peptide synthetases or polyketide synthases. Improvements to the original PrISM screening approach (Nat. Biotechnol. 2009, 27, 951-956), for example, improved de novo peptide sequencing, have enabled the discovery of 10 NRPS/PKS gene clusters from 6 strains. Taking advantage of the concurrence of biosynthetic enzymes and the secondary metabolites they generate, two natural products were associated with their previously "orphan" gene clusters. This work has demonstrated the feasibility of a proteomics-based strategy for use in screening for NRP/PK production in actinomycetes (often >8 Mbp, high GC genomes) versus the bacilli (2-4 Mbp genomes) used previously.
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Affiliation(s)
- Yunqiu Chen
- Department of Chemistry, Northwestern University, Evanston, Illinois, 60208, United States
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49
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Qu X, Lei C, Liu W. Transcriptome mining of active biosynthetic pathways and their associated products in Streptomyces flaveolus. Angew Chem Int Ed Engl 2011; 50:9651-4. [PMID: 21948600 DOI: 10.1002/anie.201103085] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2011] [Revised: 07/30/2011] [Indexed: 01/08/2023]
Affiliation(s)
- Xudong Qu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Rd., Shanghai 200032, China
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50
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Qu X, Lei C, Liu W. Transcriptome Mining of Active Biosynthetic Pathways and Their Associated Products in Streptomyces flaveolus. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201103085] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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