1
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Khushboo, Dubey KK. Enhanced Production of Lipstatin Through NTG Treatment of Streptomyces toxytricini KD18 at 5 L Bioreactor Level. Appl Biochem Biotechnol 2023; 195:6881-6892. [PMID: 36951941 DOI: 10.1007/s12010-023-04442-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/15/2023] [Indexed: 03/24/2023]
Abstract
Lipstatin, natural inhibitor of pancreatic lipase produced by Streptomyces toxytricini and used as an anti-obesity drug. Chemical mutagenesis was performed with different concentrations of N-methyl-N'-nitro-N-nitrosoguanidine (NTG) for strain improvement to obtain high yield of lipstatin. It was observed that the potential of the wild type strain to produce lipstatin (1.09 g/L) was very low. Selected mutants produced lipstatin in the range of 1.20-2.23 g/L at the flask level where maximum amount of lipstatin was produced by M5 mutant. For comparative study, both the parent and M5 mutant strain of S. toxytricini were grown at the lab scale bioreactor with suitable sources of carbon and nitrogen. Significant increase in the production of lipstatin was observed at the bioreactor level where the wild type strain produced 2.4 g/L of lipstatin, while through the NTG mutation, the production of lipstatin was 5.35 g/L. However, Dry Cell Weight (DCW) of the mutant strain was less in comparison with wild type strain and significant morphological differences were observed. Nearly 5 times increase in the production of lipstatin was achieved through NTG mutation and bioreactor-controlled conditions. It was determined that the NTG treatment might be beneficial for strain improvement to get a better candidate for lipstatin production on commercial scale.
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Affiliation(s)
- Khushboo
- Department of Biotechnology, Central University of Haryana, Haryana, 123031, Mahendergarh, India
| | - Kashyap Kumar Dubey
- Biomanufacturing and Process Development Laboratory, School of Biotechnology, Jawaharlal Nehru University, 110067, New Delhi, India.
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2
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He H, Huang J, Zhao Z, Du P, Li J, Xin J, Xu H, Feng W, Zheng X. Whole genome analysis of Streptomyces sp. RerS4, a Rehmannia glutinosa rhizosphere microbe producing a new lipopeptide. Heliyon 2023; 9:e19543. [PMID: 37681179 PMCID: PMC10480658 DOI: 10.1016/j.heliyon.2023.e19543] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 08/06/2023] [Accepted: 08/25/2023] [Indexed: 09/09/2023] Open
Abstract
Rehmannia glutinosa, a valuable medicinal plant, is threatened by ring rot, a condition that greatly affects its yield and quality. Interactions between plant and the rhizosphere soil microbiome in the context of pathogen invasion are generally more specific, with recruitment of specialized microbes potentially antagonistic to a certain pathogen. Isolation of microorganisms from rhizosphere soil of healthy and ring rot-infected R. glutinosa was carried out to screen antifungal microbes. A strain designated RerS4 isolated from ring rot-infected R. glutinosa rhizosphere soil with strong antifungal activities was selected for further study. RerS4 was taxonomically characterized as the genus Streptomyces according to its morphology and 16S rRNA sequences that were most closely related to Streptomyces racemochromogenes NRRL B-5430T (99.72%) and Streptomyces polychromogenes NBRC 13072T (99.72%). A new lipopeptide isolated from RerS4 showed restrained proliferation, but was devoid of significant antibacterial and antioxidant activity with minimum inhibitory concentration (MIC) values of 20.3 ± 2.5 and 70.8 ± 3.7 μg/mL and half-maximal inhibitory concentration (IC50) values of 23.3 ± 0.8 and 58.8 ± 2.9 μg/mL, respectively. In addition, we report the complete genome sequence of Streptomyces sp. RerS4, which consists of a 7,301,482 bp linear chromosome and a 242,139 bp plasmid. Genome analysis revealed that Streptomyces sp. RerS4 contained 25 biosynthetic gene clusters (BGCs) for secondary metabolites, among which 68% had low similarities with known BGCs, leading us to believe that Streptomyces sp. RerS4 could produce valuable bioactive compounds.
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Affiliation(s)
- Hairong He
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, 450046, China
| | - Jiarui Huang
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, 450046, China
| | - Zhenzhu Zhao
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, 450046, China
| | - Pengqiang Du
- College of Plant Protection, Henan Agricultural University, Zhengzhou, 450046, China
| | - Jiansong Li
- Institute of Applied Biotechnology, School of Medicine and Pharmaceutical Engineering, Taizhou Vocational and Technical College, Taizhou, 318000, China
| | - Jile Xin
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, 450046, China
| | - Huifang Xu
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, 450046, China
| | - Weisheng Feng
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, 450046, China
| | - Xiaoke Zheng
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, 450046, China
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3
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Thakur M, Kumar P, Rajput D, Yadav V, Dhaka N, Shukla R, Kumar Dubey K. Genome-guided approaches and evaluation of the strategies to influence bioprocessing assisted morphological engineering of Streptomyces cell factories. BIORESOURCE TECHNOLOGY 2023; 376:128836. [PMID: 36898554 DOI: 10.1016/j.biortech.2023.128836] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/02/2023] [Accepted: 03/04/2023] [Indexed: 06/18/2023]
Abstract
Streptomyces genera serve as adaptable cell factories for secondary metabolites with various and distinctive chemical structures that are relevant to the pharmaceutical industry. Streptomyces' complex life cycle necessitated a variety of tactics to enhance metabolite production. Identification of metabolic pathways, secondary metabolite clusters, and their controls have all been accomplished using genomic methods. Besides this, bioprocess parameters were also optimized for the regulation of morphology. Kinase families were identified as key checkpoints in the metabolic manipulation (DivIVA, Scy, FilP, matAB, and AfsK) and morphology engineering of Streptomyces. This review illustrates the role of different physiological variables during fermentation in the bioeconomy coupled with genome-based molecular characterization of biomolecules responsible for secondary metabolite production at different developmental stages of the Streptomyces life cycle.
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Affiliation(s)
- Mony Thakur
- Department of Microbiology, Central University of Haryana, Mahendergarh 123031, India
| | - Punit Kumar
- Department of Morphology and Physiology, Karaganda Medical University, Karaganda 100008 Kazakhstan
| | - Deepanshi Rajput
- Bioprocess Engineering Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Vinod Yadav
- Department of Microbiology, Central University of Haryana, Mahendergarh 123031, India
| | - Namrata Dhaka
- Department of Biotechnology, Central University of Haryana, Mahendergarh 123031, India
| | - Rishikesh Shukla
- Department of Biotechnology, Institute of Applied Sciences and Humanities, GLA University, Mathura- 281406, U.P., India
| | - Kashyap Kumar Dubey
- Bioprocess Engineering Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India.
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4
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Xiao J, Wang G, Liu H, Dai X. Application of composted lipstatin fermentation residue as organic fertilizer: Temporal changes in soil characteristics and bacterial community. CHEMOSPHERE 2022; 306:135637. [PMID: 35810867 DOI: 10.1016/j.chemosphere.2022.135637] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 06/27/2022] [Accepted: 07/04/2022] [Indexed: 06/15/2023]
Abstract
Lipstatin fermentation residue (LFR) is a byproduct of the pharmaceutical industry that may be disposed through land application after composting due to its high organic matter content. The effect of composted LFR application on the soil properties and microbial community still needs to be investigated before field application to verify its suitability and safety. Over a three months laboratory soil incubation experiment, the impacts of composted and raw LFR on soil properties, enzyme activities and bacterial community were investigated. The results indicated that the pH value of the soil fertilized with composted LFR decreased slightly, but the EC value increased significantly. It was worth noting that there was no measurable accumulation of lipstatin with LFR fertilization. The soil nutrients including available phosphorus, available potassium, organic matter and soluble organic matter were significantly increased in composted LFR-fertilized soil. In addition, the culturable microorganisms and enzymes were not inhibited throughout the incubation of composted LFR in soil. The composted LFR improved the soil fertility, environment and microbial biomass, which demonstrated its potential as a fertilizer. This study will provide a theoretical basis for the resource utilization of LFR.
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Affiliation(s)
- Jinhong Xiao
- College of Environmental and Chemical Engineering, Shanghai University of Electric Power, Shanghai, 200090, China
| | - Gang Wang
- School of Environmental and Material Engineering, Yantai University, Yantai, 264005, China
| | - Huiling Liu
- College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China.
| | - Xiaohu Dai
- College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China
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5
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Zhang F, Ramos Alvarenga RF, Throckmorton K, Chanana S, Braun DR, Fossen J, Zhao M, McCrone S, Harper MK, Rajski SR, Rose WE, Andes DR, Thomas MG, Bugni TS. Genome Mining and Metabolomics Unveil Pseudonochelin: A Siderophore Containing 5-Aminosalicylate from a Marine-Derived Pseudonocardia sp. Bacterium. Org Lett 2022; 24:3998-4002. [PMID: 35649263 DOI: 10.1021/acs.orglett.2c01408] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Pseudonochelin (1), a siderophore from a marine-derived Pseudonocardia sp. bacterium, was discovered using genome mining and metabolomics technologies. A 5-aminosalicylic acid (5-ASA) unit, not previously found in siderophore natural products, was identified in 1. Annotation of a putative psn biosynthetic gene cluster combined with bioinformatics and isotopic enrichment studies enabled us to propose the biosynthesis of 1. Moreover, 1 was found to display in vitro and in vivo antibacterial activity in an iron-dependent fashion.
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Affiliation(s)
- Fan Zhang
- Pharmaceutical Sciences Division, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - René F Ramos Alvarenga
- Pharmaceutical Sciences Division, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Kurt Throckmorton
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Shaurya Chanana
- Pharmaceutical Sciences Division, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Doug R Braun
- Pharmaceutical Sciences Division, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Jen Fossen
- Department of Medicine, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Miao Zhao
- Department of Medicine, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Sue McCrone
- Pharmacy Practice Division, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Mary Kay Harper
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Scott R Rajski
- Pharmaceutical Sciences Division, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Warren E Rose
- Pharmacy Practice Division, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - David R Andes
- Department of Medicine, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Michael G Thomas
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Tim S Bugni
- Pharmaceutical Sciences Division, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
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6
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Gene Cluster Analysis of Marine Bacteria Seeking for Natural Anticancer Products. Jundishapur J Nat Pharm Prod 2021. [DOI: 10.5812/jjnpp.104665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Background: In the past decade, metabolites of marine microorganisms have been increasingly used for their various biological activities. An intense effort has been dedicated to assessing the therapeutic efficacy of the marine natural products and metabolites obtained from marine bacteria in cancer therapy. Fast and reliable analytical bacterial genome sequencing provides specialized bioinformatic tools to identify potential gene clusters in bacteria for obtaining secondary metabolites. Objectives: This study aimed to analyze the genome sequences of marine bacteria to recognize bioactive compounds with anti-cancer properties. Methods: Marine bacteria with the genomic sequences registered in the National Center for Biotechnology Information (NCBI) genome database were used in this study. The genome was analyzed for proteins, tRNAs, and rRNAs from GenBank entries by Feature Extract 1.2L Server. The Anti-SMASH webserver was used for the analysis of unique marine bacterial metabolites of the marine bacterial genome, available from the NCBI database. Results: A number of marine bacterial species, including Salinispora arenicola, Salinispora tropica, Crocosphaera watsonii, and Blastopirellula marina encoded metabolites belonging to the polyketide and nonribosomal peptide (NRP) families, showing anti-cancer properties. Among the marine species described, S. tropica and S. arenicola are richer in the genes encoding polyketide and NRP with potential antitumor activities. Conclusions: Marine bacteria are an excellent and exceptional source of anti-cancer compounds. In silico genome analysis of marine bacteria provided an opportunity to evaluate gene clusters for known natural products. Like this chemical engineering approaches for pharmaceutical application are useful in clinical evaluation of cancer treatment.
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Engelbrecht A, Saad H, Gross H, Kaysser L. Natural Products from Nocardia and Their Role in Pathogenicity. Microb Physiol 2021; 31:217-232. [PMID: 34139700 DOI: 10.1159/000516864] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 04/26/2021] [Indexed: 11/19/2022]
Abstract
Nocardia spp. are filamentous Actinobacteria of the order Corynebacteriales and mostly known for their ability to cause localized and systemic infections in humans. However, the onset and progression of nocardiosis is only poorly understood, in particular the mechanisms of strain-specific presentations. Recent genome sequencing has revealed an extraordinary capacity for the production of specialized small molecules. Such secondary metabolites are often crucial for the producing microbe to survive the challenges of different environmental conditions. An interesting question thus concerns the role of these natural products in Nocardia-associated pathogenicity and immune evasion in a human host. In this review, a summary and discussion of Nocardia metabolites is presented, which may play a part in nocardiosis because of their cytotoxic, immunosuppressive and metal-chelating properties or otherwise vitally important functions. This review also contains so far unpublished data concerning the biosynthesis of these molecules that were obtained by detailed bioinformatic analyses.
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Affiliation(s)
- Alicia Engelbrecht
- Department of Pharmaceutical Biology, University of Tübingen, Tübingen, Germany
| | - Hamada Saad
- Department of Pharmaceutical Biology, University of Tübingen, Tübingen, Germany.,Department of Phytochemistry and Plant Systematics, Division of Pharmaceutical Industries, National Research Centre, Cairo, Egypt
| | - Harald Gross
- Department of Pharmaceutical Biology, University of Tübingen, Tübingen, Germany
| | - Leonard Kaysser
- Department of Pharmaceutical Biology, University of Tübingen, Tübingen, Germany.,Institute for Drug Discovery, University of Leipzig, Leipzig, Germany
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8
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Smith MD, Tassoulas LJ, Biernath TA, Richman JE, Aukema KG, Wackett LP. p-Nitrophenyl esters provide new insights and applications for the thiolase enzyme OleA. Comput Struct Biotechnol J 2021; 19:3087-3096. [PMID: 34141132 PMCID: PMC8180931 DOI: 10.1016/j.csbj.2021.05.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 05/18/2021] [Accepted: 05/19/2021] [Indexed: 11/21/2022] Open
Abstract
The OleA enzyme is distinct amongst thiolase enzymes in binding two long (≥C8) acyl chains into structurally-opposed hydrophobic channels, denoted A and B, to carry out a non-decarboxylative Claisen condensation reaction and initiate the biosynthesis of membrane hydrocarbons and β-lactone natural products. OleA has now been identified in hundreds of diverse bacteria via bioinformatics and high-throughput screening using p-nitrophenyl alkanoate esters as surrogate substrates. In the present study, p-nitrophenyl esters were used to probe the reaction mechanism of OleA and shown to be incorporated into Claisen condensation products for the first time. p-Nitrophenyl alkanoate substrates alone were shown not to undergo Claisen condensation, but co-incubation of p-nitrophenyl esters and CoA thioesters produced mixed Claisen products. Mixed product reactions were shown to initiate via acyl group transfer from a p-nitrophenyl carrier to the enzyme active site cysteine, C143. Acyl chains esterified to p-nitrophenol were synthesized and shown to undergo Claisen condensation with an acyl-CoA substrate, showing potential to greatly expand the range of possible Claisen products. Using p-nitrophenyl 1-13C-decanoate, the Channel A bound thioester chain was shown to act as the Claisen nucleophile, representing the first direct evidence for the directionality of the Claisen reaction in any OleA enzyme. These results both provide new insights into OleA catalysis and open a path for making unnatural hydrocarbon and β-lactone natural products for biotechnological applications using cheap and easily synthesized p-nitrophenyl esters.
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Affiliation(s)
- Megan D. Smith
- Biotechnology Institute, University of Minnesota, St Paul, MN, USA
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN, USA
- Microbial and Plant Genomics Institute, University of Minnesota, St Paul, MN, USA
| | - Lambros J. Tassoulas
- Biotechnology Institute, University of Minnesota, St Paul, MN, USA
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St Paul, MN, USA
| | - Troy A. Biernath
- Biotechnology Institute, University of Minnesota, St Paul, MN, USA
| | - Jack E. Richman
- Biotechnology Institute, University of Minnesota, St Paul, MN, USA
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St Paul, MN, USA
| | - Kelly G. Aukema
- Biotechnology Institute, University of Minnesota, St Paul, MN, USA
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St Paul, MN, USA
| | - Lawrence P. Wackett
- Biotechnology Institute, University of Minnesota, St Paul, MN, USA
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St Paul, MN, USA
- Microbial and Plant Genomics Institute, University of Minnesota, St Paul, MN, USA
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9
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Exploring the Chemical Space of Macro- and Micro-Algae Using Comparative Metabolomics. Microorganisms 2021; 9:microorganisms9020311. [PMID: 33546180 PMCID: PMC7913273 DOI: 10.3390/microorganisms9020311] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 01/26/2021] [Accepted: 01/30/2021] [Indexed: 02/08/2023] Open
Abstract
With more than 156,000 described species, eukaryotic algae (both macro- and micro-algae) are a rich source of biological diversity, however their chemical diversity remains largely unexplored. Specialised metabolites with promising biological activities have been widely reported for seaweeds, and more recently extracts from microalgae have exhibited activity in anticancer, antimicrobial, and antioxidant screens. However, we are still missing critical information on the distinction of chemical profiles between macro- and microalgae, as well as the chemical space these metabolites cover. This study has used an untargeted comparative metabolomics approach to explore the chemical diversity of seven seaweeds and 36 microalgal strains. A total of 1390 liquid chromatography-mass spectrometry (LC-MS) features were detected, representing small organic algal metabolites, with no overlap between the seaweeds and microalgae. An in-depth analysis of four Dunaliella tertiolecta strains shows that environmental factors may play a larger role than phylogeny when classifying their metabolomic profiles.
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10
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Chandra P, Enespa, Singh R, Arora PK. Microbial lipases and their industrial applications: a comprehensive review. Microb Cell Fact 2020; 19:169. [PMID: 32847584 PMCID: PMC7449042 DOI: 10.1186/s12934-020-01428-8] [Citation(s) in RCA: 258] [Impact Index Per Article: 64.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 08/17/2020] [Indexed: 12/12/2022] Open
Abstract
Lipases are very versatile enzymes, and produced the attention of the several industrial processes. Lipase can be achieved from several sources, animal, vegetable, and microbiological. The uses of microbial lipase market is estimated to be USD 425.0 Million in 2018 and it is projected to reach USD 590.2 Million by 2023, growing at a CAGR of 6.8% from 2018. Microbial lipases (EC 3.1.1.3) catalyze the hydrolysis of long chain triglycerides. The microbial origins of lipase enzymes are logically dynamic and proficient also have an extensive range of industrial uses with the manufacturing of altered molecules. The unique lipase (triacylglycerol acyl hydrolase) enzymes catalyzed the hydrolysis, esterification and alcoholysis reactions. Immobilization has made the use of microbial lipases accomplish its best performance and hence suitable for several reactions and need to enhance aroma to the immobilization processes. Immobilized enzymes depend on the immobilization technique and the carrier type. The choice of the carrier concerns usually the biocompatibility, chemical and thermal stability, and insolubility under reaction conditions, capability of easy rejuvenation and reusability, as well as cost proficiency. Bacillus spp., Achromobacter spp., Alcaligenes spp., Arthrobacter spp., Pseudomonos spp., of bacteria and Penicillium spp., Fusarium spp., Aspergillus spp., of fungi are screened large scale for lipase production. Lipases as multipurpose biological catalyst has given a favorable vision in meeting the needs for several industries such as biodiesel, foods and drinks, leather, textile, detergents, pharmaceuticals and medicals. This review represents a discussion on microbial sources of lipases, immobilization methods increased productivity at market profitability and reduce logistical liability on the environment and user.
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Affiliation(s)
- Prem Chandra
- Food Microbiology & Toxicology, Department of Microbiology, School for Biomedical and Pharmaceutical Sciences, Babasaheb Bhimrao Ambedkar University (A Central) University, Lucknow, Uttar Pradesh 226025 India
| | - Enespa
- Department of Plant Pathology, School for Agriculture, SMPDC, University of Lucknow, Lucknow, 226007 U.P. India
| | - Ranjan Singh
- Department of Environmental Science, School for Environmental Science, Babasaheb Bhimrao Ambedkar University (A Central) University, Lucknow, U.P. India
| | - Pankaj Kumar Arora
- Department of Microbiology, School for Biomedical and Pharmaceutical Sciences, Babasaheb Bhimrao Ambedkar University (A Central) University, Lucknow, U.P. India
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11
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Robinson SL, Terlouw BR, Smith MD, Pidot SJ, Stinear TP, Medema MH, Wackett LP. Global analysis of adenylate-forming enzymes reveals β-lactone biosynthesis pathway in pathogenic Nocardia. J Biol Chem 2020; 295:14826-14839. [PMID: 32826316 DOI: 10.1074/jbc.ra120.013528] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 08/07/2020] [Indexed: 12/31/2022] Open
Abstract
Enzymes that cleave ATP to activate carboxylic acids play essential roles in primary and secondary metabolism in all domains of life. Class I adenylate-forming enzymes share a conserved structural fold but act on a wide range of substrates to catalyze reactions involved in bioluminescence, nonribosomal peptide biosynthesis, fatty acid activation, and β-lactone formation. Despite their metabolic importance, the substrates and functions of the vast majority of adenylate-forming enzymes are unknown without tools available to accurately predict them. Given the crucial roles of adenylate-forming enzymes in biosynthesis, this also severely limits our ability to predict natural product structures from biosynthetic gene clusters. Here we used machine learning to predict adenylate-forming enzyme function and substrate specificity from protein sequences. We built a web-based predictive tool and used it to comprehensively map the biochemical diversity of adenylate-forming enzymes across >50,000 candidate biosynthetic gene clusters in bacterial, fungal, and plant genomes. Ancestral phylogenetic reconstruction and sequence similarity networking of enzymes from these clusters suggested divergent evolution of the adenylate-forming superfamily from a core enzyme scaffold most related to contemporary CoA ligases toward more specialized functions including β-lactone synthetases. Our classifier predicted β-lactone synthetases in uncharacterized biosynthetic gene clusters conserved in >90 different strains of Nocardia. To test our prediction, we purified a candidate β-lactone synthetase from Nocardia brasiliensis and reconstituted the biosynthetic pathway in vitro to link the gene cluster to the β-lactone natural product, nocardiolactone. We anticipate that our machine learning approach will aid in functional classification of enzymes and advance natural product discovery.
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Affiliation(s)
- Serina L Robinson
- BioTechnology Institute, University of Minnesota, Saint Paul, Minnesota, USA; Graduate Program in Bioinformatics and Computational Biology, University of Minnesota, Rochester, Minnesota, USA; Graduate Program in Microbiology, Immunology, and Cancer Biology, University of Minnesota, Minneapolis, Minnesota, USA.
| | - Barbara R Terlouw
- Bioinformatics Group, Wageningen University & Research, Wageningen, The Netherlands
| | - Megan D Smith
- BioTechnology Institute, University of Minnesota, Saint Paul, Minnesota, USA; Graduate Program in Microbiology, Immunology, and Cancer Biology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Sacha J Pidot
- Department of Microbiology and Immunology at the Doherty Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - Timothy P Stinear
- Department of Microbiology and Immunology at the Doherty Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University & Research, Wageningen, The Netherlands
| | - Lawrence P Wackett
- BioTechnology Institute, University of Minnesota, Saint Paul, Minnesota, USA; Graduate Program in Bioinformatics and Computational Biology, University of Minnesota, Rochester, Minnesota, USA; Graduate Program in Microbiology, Immunology, and Cancer Biology, University of Minnesota, Minneapolis, Minnesota, USA
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12
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Kitadokoro K, Tanaka M, Hikima T, Okuno Y, Yamamoto M, Kamitani S. Crystal structure of pathogenic Staphylococcus aureus lipase complex with the anti-obesity drug orlistat. Sci Rep 2020; 10:5469. [PMID: 32214208 PMCID: PMC7096528 DOI: 10.1038/s41598-020-62427-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 03/11/2020] [Indexed: 12/26/2022] Open
Abstract
Staphylococcus aureus lipase (SAL), a triacylglycerol esterase, is an important virulence factor and may be a therapeutic target for infectious diseases. Herein, we determined the 3D structure of native SAL, the mutated S116A inactive form, and the inhibitor complex using the anti-obesity drug orlistat to aid in drug development. The determined crystal structures showed a typical α/β hydrolase motif with a dimeric form. Fatty acids bound near the active site in native SAL and inactive S116A mutant structures. We found that orlistat potently inhibits SAL activity, and it covalently bound to the catalytic Ser116 residue. This is the first report detailing orlistat–lipase binding. It provides structure-based information on the production of potent anti-SAL drugs and lipase inhibitors. These results also indicated that orlistat can be repositioned to treat bacterial diseases.
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Affiliation(s)
- Kengo Kitadokoro
- Faculty of Molecular Chemistry and Engineering, Graduate School of Science and Technology, Kyoto Institute of Technology, Hashigami-cho, Matsugasaki, Sakyo-ku, Kyoto, 606-8585, Japan.
| | - Mutsumi Tanaka
- Faculty of Molecular Chemistry and Engineering, Graduate School of Science and Technology, Kyoto Institute of Technology, Hashigami-cho, Matsugasaki, Sakyo-ku, Kyoto, 606-8585, Japan
| | - Takaaki Hikima
- SR Life Science Instrumentation Team, Life Science Research Infrastructure Group, Advanced Photon Technology Division, RIKEN SPring-8 Center, 1-1-1, Koto, Sayo-cho, Sayo-gun, Hyogo, 679-6148, Japan
| | - Yukiko Okuno
- Medical Research Support Center, Graduate School of Medicine, Kyoto University, Yoshidakonoe, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Masaki Yamamoto
- SR Life Science Instrumentation Team, Life Science Research Infrastructure Group, Advanced Photon Technology Division, RIKEN SPring-8 Center, 1-1-1, Koto, Sayo-cho, Sayo-gun, Hyogo, 679-6148, Japan
| | - Shigeki Kamitani
- Graduate School of Comprehensive Rehabilitation, College of Health and Human Sciences, Osaka Prefecture University, 3-7-30 Habikino, Habikino, 583-8555, Osaka, Japan
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13
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Smith MD, Robinson SL, Molomjamts M, Wackett LP. In Vivo Assay Reveals Microbial OleA Thiolases Initiating Hydrocarbon and β-Lactone Biosynthesis. mBio 2020; 11:e00111-20. [PMID: 32156808 PMCID: PMC7064751 DOI: 10.1128/mbio.00111-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 01/22/2020] [Indexed: 12/29/2022] Open
Abstract
OleA, a member of the thiolase superfamily, is known to catalyze the Claisen condensation of long-chain acyl coenzyme A (acyl-CoA) substrates, initiating metabolic pathways in bacteria for the production of membrane lipids and β-lactone natural products. OleA homologs are found in diverse bacterial phyla, but to date, only one homodimeric OleA has been successfully purified to homogeneity and characterized in vitro A major impediment for the identification of new OleA enzymes has been protein instability and time-consuming in vitro assays. Here, we developed a bioinformatic pipeline to identify OleA homologs and a new rapid assay to screen OleA enzyme activity in vivo and map their taxonomic diversity. The screen is based on the discovery that OleA displayed surprisingly high rates of p-nitrophenyl ester hydrolysis, an activity not shared by other thiolases, including FabH. The high rates allowed activity to be determined in vitro and with heterologously expressed OleA in vivo via the release of the yellow p-nitrophenol product. Seventy-four putative oleA genes identified in the genomes of diverse bacteria were heterologously expressed in Escherichia coli, and 25 showed activity with p-nitrophenyl esters. The OleA proteins tested were encoded in variable genomic contexts from seven different phyla and are predicted to function in distinct membrane lipid and β-lactone natural product metabolic pathways. This study highlights the diversity of unstudied OleA proteins and presents a rapid method for their identification and characterization.IMPORTANCE Microbially produced β-lactones are found in antibiotic, antitumor, and antiobesity drugs. Long-chain olefinic membrane hydrocarbons have potential utility as fuels and specialty chemicals. The metabolic pathway to both end products share bacterial enzymes denoted as OleA, OleC, and OleD that transform acyl-CoA cellular intermediates into β-lactones. Bacteria producing membrane hydrocarbons via the Ole pathway additionally express a β-lactone decarboxylase, OleB. Both β-lactone and olefin biosynthesis pathways are initiated by OleA enzymes that define the overall structure of the final product. There is currently very limited information on OleA enzymes apart from the single representative from Xanthomonas campestris In this study, bioinformatic analysis identified hundreds of new, putative OleA proteins, 74 proteins were screened via a rapid whole-cell method, leading to the identification of 25 stably expressed OleA proteins representing seven bacteria phyla.
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Affiliation(s)
- Megan D Smith
- Biotechnology Institute, University of Minnesota, St. Paul, Minnesota, USA
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Serina L Robinson
- Biotechnology Institute, University of Minnesota, St. Paul, Minnesota, USA
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Mandkhai Molomjamts
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Lawrence P Wackett
- Biotechnology Institute, University of Minnesota, St. Paul, Minnesota, USA
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
- Microbial and Plant Genomics Institute, University of Minnesota, St. Paul, Minnesota, USA
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14
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Robinson SL, Christenson JK, Wackett LP. Biosynthesis and chemical diversity of β-lactone natural products. Nat Prod Rep 2019; 36:458-475. [PMID: 30191940 DOI: 10.1039/c8np00052b] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Covering: up to 2018 β-Lactones are strained rings that are useful organic synthons and pharmaceutical warheads. Over 30 core scaffolds of β-lactone natural products have been described to date, many with potent bioactivity against bacteria, fungi, or human cancer cell lines. β-Lactone natural products are chemically diverse and have high clinical potential, but production of derivatized drug leads has been largely restricted to chemical synthesis partly due to gaps in biochemical knowledge about β-lactone biosynthesis. Here we review recent discoveries in enzymatic β-lactone ring closure via ATP-dependent synthetases, intramolecular cyclization from seven-membered rings, and thioesterase-mediated cyclization during release from nonribosomal peptide synthetase assembly lines. We also comprehensively cover the diversity and taxonomy of source organisms for β-lactone natural products including their isolation from bacteria, fungi, plants, insects, and marine sponges. This work identifies computational and experimental bottlenecks and highlights future directions for genome-based discovery of biosynthetic gene clusters that may produce novel compounds with β-lactone rings.
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Affiliation(s)
- Serina L Robinson
- BioTechnology Institute, University of Minnesota - Twin Cities 140 Gortner Laboratory, 1479 Gortner Avenue, Saint Paul, MN 55108, USA.
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15
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Robinson SL, Christenson JK, Richman JE, Jenkins DJ, Neres J, Fonseca DR, Aldrich CC, Wackett LP. Mechanism of a Standalone β-Lactone Synthetase: New Continuous Assay for a Widespread ANL Superfamily Enzyme. Chembiochem 2019; 20:1701-1711. [PMID: 30856684 DOI: 10.1002/cbic.201800821] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 03/09/2019] [Indexed: 12/11/2022]
Abstract
Enzyme-catalyzed β-lactone formation from β-hydroxy acids is a crucial step in bacterial biosynthesis of β-lactone natural products and membrane hydrocarbons. We developed a novel, continuous assay for β-lactone synthetase activity using synthetic β-hydroxy acid substrates with alkene or alkyne moieties. β-Lactone formation is followed by rapid decarboxylation to form a conjugated triene chromophore for real-time evaluation by UV/Vis spectroscopy. The assay was used to determine steady-state kinetics of a long-chain β-lactone synthetase, OleC, from the plant pathogen Xanthomonas campestris. Site-directed mutagenesis was used to test the involvement of conserved active site residues in Mg2+ and ATP binding. A previous report suggested OleC adenylated the substrate hydroxy group. Here we present several lines of evidence, including hydroxylamine trapping of the AMP intermediate, to demonstrate the substrate carboxyl group is adenylated prior to making the β-lactone final product. A panel of nine substrate analogues were used to investigate the substrate specificity of X. campestris OleC by HPLC and GC-MS. Stereoisomers of 2-hexyl-3hydroxyoctanoic acid were synthesized and OleC preferred the (2R,3S) diastereomer consistent with the stereo-preference of upstream and downstream pathway enzymes. This biochemical knowledge was used to guide phylogenetic analysis of the β-lactone synthetases to map their functional diversity within the acyl-CoA synthetase, NRPS adenylation domain, and luciferase superfamily.
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Affiliation(s)
- Serina L Robinson
- BioTechnology Institute, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN, 55108, USA
| | - James K Christenson
- BioTechnology Institute, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN, 55108, USA.,Present address: Department of Chemistry, Bethel University, 3900 Bethel Drive, Saint Paul, MN, 55112, USA
| | - Jack E Richman
- BioTechnology Institute, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN, 55108, USA
| | - Dominick J Jenkins
- BioTechnology Institute, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN, 55108, USA
| | - João Neres
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard St. SE, Minneapolis, MN, 55455, USA.,Present address: UCB Biopharma, Chemin du Foriest, 1420, Braine-l'Alleud, Belgium
| | - Dallas R Fonseca
- BioTechnology Institute, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN, 55108, USA
| | - Courtney C Aldrich
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard St. SE, Minneapolis, MN, 55455, USA
| | - Lawrence P Wackett
- BioTechnology Institute, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN, 55108, USA
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16
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Zhang D, Zhang F, Liu W. A KAS-III Heterodimer in Lipstatin Biosynthesis Nondecarboxylatively Condenses C 8 and C 14 Fatty Acyl-CoA Substrates by a Variable Mechanism during the Establishment of a C 22 Aliphatic Skeleton. J Am Chem Soc 2019; 141:3993-4001. [PMID: 30763089 DOI: 10.1021/jacs.8b12843] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
β-Ketoacyl-acyl carrier protein synthase-III (KAS-III) and its homologues are thiolase-fold proteins that typically behave as homodimers functioning in diverse thioester-based reactions for C-C, C-O, or C-N bond formation. Here, we report an exception observed in the biosynthesis of lipstatin. During the establishment of the C22 aliphatic skeleton of this β-lactone lipase inhibitor, LstA and LstB, which both are KAS-III homologues but phylogenetically distinct from each other, function together by forming an unusual heterodimer to catalyze a nondecarboxylating Claisen condensation of C8 and C14 fatty acyl-CoA substrates. The resulting C22 α-alkyl β-ketoacid, which is unstable and tends to be spontaneously decarboxylated to a shunt C21 hydrocarbon product, is transformed by the stereoselective β-ketoreductase LstD into a relatively stable C22 α-alkyl β-hydroxyacid for further transformation. LstAB activity tolerates changes in the stereochemistry, saturation degree, and thioester form of both long-chain fatty acyl-CoA substrates. This flexibility, along with the characterization of catalytic residues, benefits our investigations into the individual roles of the two KAS-III homologues in the heterodimer-catalyzed reactions. The large subunit LstA contains a characteristic Cys-His-Asn triad and likely reacts with C8 acyl-CoA to form an acyl-Cys enzyme intermediate. In contrast, the small subunit LstB lacks this triad but possesses a catalytic Glu residue, which can act on the C8 acyl-Cys enzyme intermediate in a substrate-dependent manner, either as a base for Cα deprotonation or as a nucleophile for a Michael-type addition-initiated cascade reaction, to produce an enolate anion for head-to-head assembly with C14 acyl-CoA through a unidirectional nucleophilic substitution. Uncovering LstAB catalysis draws attention to thiolase-fold proteins that are noncanonical in both active form and catalytic reaction/mechanism. LstAB homologues are widespread in bacteria and remain to be functionally assigned, generating great interest in their corresponding products and associated biological functions.
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Affiliation(s)
- Daozhong Zhang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry , University of Chinese Academy of Sciences , 345 Lingling Road , Shanghai 200032 , China
| | - Fang Zhang
- Innovation Research Institute of Traditional Chinese Medicine , Shanghai University of Traditional Chinese Medicine , 1200 Cailun Road , Shanghai 201203 , China
| | - Wen Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry , University of Chinese Academy of Sciences , 345 Lingling Road , Shanghai 200032 , China.,Huzhou Center of Bio-Synthetic Innovation , 1366 Hongfeng Road , Huzhou 313000 , China
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17
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Kaysser L. Built to bind: biosynthetic strategies for the formation of small-molecule protease inhibitors. Nat Prod Rep 2019; 36:1654-1686. [DOI: 10.1039/c8np00095f] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The discovery and characterization of natural product protease inhibitors has inspired the development of numerous pharmaceutical agents.
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Affiliation(s)
- Leonard Kaysser
- Department of Pharmaceutical Biology
- University of Tübingen
- 72076 Tübingen
- Germany
- German Centre for Infection Research (DZIF)
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18
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Abstract
Enzymes in biosynthetic pathways, especially in plant and microbial metabolism, generate structural and functional group complexity in small molecules by conversion of acyclic frameworks to cyclic scaffolds via short, efficient routes. The distinct chemical logic used by several distinct classes of cyclases, oxidative and non-oxidative, has recently been elucidated by genome mining, heterologous expression, and genetic and mechanistic analyses. These include enzymes performing pericyclic transformations, pyran synthases, tandem acting epoxygenases, and epoxide "hydrolases", as well as oxygenases and radical S-adenosylmethionine enzymes that involve rearrangements of substrate radicals under aerobic or anaerobic conditions.
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Affiliation(s)
- Christopher T. Walsh
- Stanford University Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford University, Stanford, CA
| | - Yi Tang
- Department of Chemical and Biomolecular Engineering and Department of Chemistry and Biochemistry, University of California, Los Angeles, CA
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19
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Híreš M, Rapavá N, Šimkovič M, Varečka Ľ, Berkeš D, Kryštofová S. Development and Optimization of a High-Throughput Screening Assay for Rapid Evaluation of Lipstatin Production by Streptomyces Strains. Curr Microbiol 2017; 75:580-587. [PMID: 29256008 DOI: 10.1007/s00284-017-1420-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 12/11/2017] [Indexed: 11/24/2022]
Abstract
Pancreatic lipase inhibitors, such as tetrahydrolipstatin (orlistat), are used in anti-obesity treatments. Orlistat is the only anti-obesity drug approved by the European Medicines Agency (EMA). The drug is synthesized by saturation of lipstatin, a β-lactone compound, isolated from Streptomyces toxytricini and S. virginiae. To identify producers of novel pancreatic lipase inhibitors or microbial strains with improved lipstatin production and higher chemical purity remains still a priority. In this study, a high-throughput screening method to identify Streptomyces strains producing potent pancreatic lipase inhibitors was established. The assay was optimized and validated using S. toxytricini NRRL 15443 and its mutants. Strains grew in 24-well titer plates. Lipstatin levels were assessed directly in culture medium at the end of cultivation by monitoring lipolytic activity in the presence of a chromogenic substrate, 1,2-Di-O-lauryl-rac-glycero-3-glutaric acid 6-methylresorufin ester (DGGR). The lipase activity decreased in response to lipstatin production, and this was demonstrated by accumulation of red-purple methylresorufin, a product of DGGR digestion. The sensitivity of the assay was achieved by adding a lipase of high lipolytic activity and sensitivity to lipstatin to the reaction mixture. In the assay, the fungal lipase from Mucor javanicus was used as an alternative to the human pancreatic lipase. Many fungal lipases preserve high lipolytic activity in extreme conditions and are not colipase dependent. The assay proved to be reliable in differentiation of strains with high and low lipstatin productivity.
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Affiliation(s)
- Michal Híreš
- Institute of Biochemistry and Microbiology, Slovak University of Technology, Radlinského 9, 81 237, Bratislava, Slovakia.
| | - Nora Rapavá
- Institute of Biochemistry and Microbiology, Slovak University of Technology, Radlinského 9, 81 237, Bratislava, Slovakia
| | - Martin Šimkovič
- Institute of Biochemistry and Microbiology, Slovak University of Technology, Radlinského 9, 81 237, Bratislava, Slovakia
| | - Ľudovít Varečka
- Institute of Biochemistry and Microbiology, Slovak University of Technology, Radlinského 9, 81 237, Bratislava, Slovakia
| | - Dušan Berkeš
- Department of Organic Chemistry, Slovak University of Technology, Radlinského 9, 81 237, Bratislava, Slovakia
| | - Svetlana Kryštofová
- Institute of Biochemistry and Microbiology, Slovak University of Technology, Radlinského 9, 81 237, Bratislava, Slovakia
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20
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β-Lactone formation during product release from a nonribosomal peptide synthetase. Nat Chem Biol 2017; 13:737-744. [PMID: 28504677 DOI: 10.1038/nchembio.2374] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 03/07/2017] [Indexed: 11/09/2022]
Abstract
Nonribosomal peptide synthetases (NRPSs) are multidomain modular biosynthetic assembly lines that polymerize amino acids into a myriad of biologically active nonribosomal peptides (NRPs). NRPS thioesterase (TE) domains employ diverse release strategies for off-loading thioester-tethered polymeric peptides from termination modules typically via hydrolysis, aminolysis, or cyclization to provide mature antibiotics as carboxylic acids/esters, amides, and lactams/lactones, respectively. Here we report the enzyme-catalyzed formation of a highly strained β-lactone ring during TE-mediated cyclization of a β-hydroxythioester to release the antibiotic obafluorin (Obi) from an NRPS assembly line. The Obi NRPS (ObiF) contains a type I TE domain with a rare catalytic cysteine residue that plays a direct role in β-lactone ring formation. We present a detailed genetic and biochemical characterization of the entire Obi biosynthetic gene cluster in plant-associated Pseudomonas fluorescens ATCC 39502 that establishes a general strategy for β-lactone biogenesis.
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21
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Wolf F, Bauer JS, Bendel TM, Kulik A, Kalinowski J, Gross H, Kaysser L. Die Biosynthese der β-Lacton-haltigen Proteasominhibitoren Belactosin und Cystargolid. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201612076] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Felix Wolf
- Abteilung Pharmazeutische Biologie; Pharmazeutisches Institut; Universität Tübingen; 72076 Tübingen Deutschland
- Deutsches Zentrum für Infektionsforschung (DZIF); Standort Tübingen; 72076 Tübingen Deutschland
| | - Judith S. Bauer
- Abteilung Pharmazeutische Biologie; Pharmazeutisches Institut; Universität Tübingen; 72076 Tübingen Deutschland
- Deutsches Zentrum für Infektionsforschung (DZIF); Standort Tübingen; 72076 Tübingen Deutschland
| | - Theresa M. Bendel
- Abteilung Pharmazeutische Biologie; Pharmazeutisches Institut; Universität Tübingen; 72076 Tübingen Deutschland
- Deutsches Zentrum für Infektionsforschung (DZIF); Standort Tübingen; 72076 Tübingen Deutschland
| | - Andreas Kulik
- Interfaculty Institute for Microbiology and Infection Medicine, Tübingen (IMIT); Mikrobiologie/Biotechnologie; Universität Tübingen; 72076 Tübingen Deutschland
| | - Jörn Kalinowski
- Center for Biotechnology (CeBiTec); Universität Bielefeld; 33615 Bielefeld Deutschland
| | - Harald Gross
- Abteilung Pharmazeutische Biologie; Pharmazeutisches Institut; Universität Tübingen; 72076 Tübingen Deutschland
- Deutsches Zentrum für Infektionsforschung (DZIF); Standort Tübingen; 72076 Tübingen Deutschland
| | - Leonard Kaysser
- Abteilung Pharmazeutische Biologie; Pharmazeutisches Institut; Universität Tübingen; 72076 Tübingen Deutschland
- Deutsches Zentrum für Infektionsforschung (DZIF); Standort Tübingen; 72076 Tübingen Deutschland
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22
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Wolf F, Bauer JS, Bendel TM, Kulik A, Kalinowski J, Gross H, Kaysser L. Biosynthesis of the β-Lactone Proteasome Inhibitors Belactosin and Cystargolide. Angew Chem Int Ed Engl 2017; 56:6665-6668. [PMID: 28452105 DOI: 10.1002/anie.201612076] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Indexed: 01/06/2023]
Abstract
Belactosins and cystargolides are natural product proteasome inhibitors from Actinobacteria. Both feature dipeptidic backbones and a unique β-lactone building block. Herein, we present a detailed investigation of their biosynthesis. Identification and analysis of the corresponding gene clusters indicated that both compounds are assembled by rare single-enzyme amino acid ligases. Feeding experiments with isotope-labeled precursors and in vitro biochemistry showed that the formation of the β-lactone warhead is unprecedented and reminiscent of leucine biosynthesis, and that it involves the action of isopropylmalate synthase homologues.
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Affiliation(s)
- Felix Wolf
- Department of Pharmaceutical Biology, Pharmaceutical Institute, University of Tuebingen, 72076, Tuebingen, Germany.,German Centre for Infection Research (DZIF), partner site Tuebingen, 72076, Tuebingen, Germany
| | - Judith S Bauer
- Department of Pharmaceutical Biology, Pharmaceutical Institute, University of Tuebingen, 72076, Tuebingen, Germany.,German Centre for Infection Research (DZIF), partner site Tuebingen, 72076, Tuebingen, Germany
| | - Theresa M Bendel
- Department of Pharmaceutical Biology, Pharmaceutical Institute, University of Tuebingen, 72076, Tuebingen, Germany.,German Centre for Infection Research (DZIF), partner site Tuebingen, 72076, Tuebingen, Germany
| | - Andreas Kulik
- Interfaculty Institute for Microbiology and Infection Medicine Tuebingen (IMIT), Microbiology/Biotechnology, University of Tuebingen, 72076, Tuebingen, Germany
| | - Jörn Kalinowski
- Center for Biotechnology (CeBiTec), University of Bielefeld, 33615, Bielefeld, Germany
| | - Harald Gross
- Department of Pharmaceutical Biology, Pharmaceutical Institute, University of Tuebingen, 72076, Tuebingen, Germany.,German Centre for Infection Research (DZIF), partner site Tuebingen, 72076, Tuebingen, Germany
| | - Leonard Kaysser
- Department of Pharmaceutical Biology, Pharmaceutical Institute, University of Tuebingen, 72076, Tuebingen, Germany.,German Centre for Infection Research (DZIF), partner site Tuebingen, 72076, Tuebingen, Germany
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23
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Active Multienzyme Assemblies for Long-Chain Olefinic Hydrocarbon Biosynthesis. J Bacteriol 2017; 199:JB.00890-16. [PMID: 28223313 DOI: 10.1128/jb.00890-16] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 02/10/2017] [Indexed: 12/14/2022] Open
Abstract
Bacteria from different phyla produce long-chain olefinic hydrocarbons derived from an OleA-catalyzed Claisen condensation of two fatty acyl coenzyme A (acyl-CoA) substrates, followed by reduction and oxygen elimination reactions catalyzed by the proteins OleB, OleC, and OleD. In this report, OleA, OleB, OleC, and OleD were individually purified as soluble proteins, and all were found to be essential for reconstituting hydrocarbon biosynthesis. Recombinant coexpression of tagged OleABCD proteins from Xanthomonas campestris in Escherichia coli and purification over His6 and FLAG columns resulted in OleA separating, while OleBCD purified together, irrespective of which of the four Ole proteins were tagged. Hydrocarbon biosynthetic activity of copurified OleBCD assemblies could be reconstituted by adding separately purified OleA. Immunoblots of nondenaturing gels using anti-OleC reacted with X. campestris crude protein lysate indicated the presence of a large protein assembly containing OleC in the native host. Negative-stain electron microscopy of recombinant OleBCD revealed distinct large structures with diameters primarily between 24 and 40 nm. Assembling OleB, OleC, and OleD into a complex may be important to maintain stereochemical integrity of intermediates, facilitate the movement of hydrophobic metabolites between enzyme active sites, and protect the cell against the highly reactive β-lactone intermediate produced by the OleC-catalyzed reaction.IMPORTANCE Bacteria biosynthesize hydrophobic molecules to maintain a membrane, store carbon, and for antibiotics that help them survive in their niche. The hydrophobic compounds are often synthesized by a multidomain protein or by large multienzyme assemblies. The present study reports on the discovery that long-chain olefinic hydrocarbons made by bacteria from different phyla are produced by multienzyme assemblies in X. campestris The OleBCD multienzyme assemblies are thought to compartmentalize and sequester olefin biosynthesis from the rest of the cell. This system provides additional insights into how bacteria control specific biosynthetic pathways.
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24
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Christenson JK, Richman JE, Jensen MR, Neufeld JY, Wilmot CM, Wackett LP. β-Lactone Synthetase Found in the Olefin Biosynthesis Pathway. Biochemistry 2017; 56:348-351. [PMID: 28029240 PMCID: PMC5499249 DOI: 10.1021/acs.biochem.6b01199] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The first β-lactone synthetase enzyme is reported, creating an unexpected link between the biosynthesis of olefinic hydrocarbons and highly functionalized natural products. The enzyme OleC, involved in the microbial biosynthesis of long-chain olefinic hydrocarbons, reacts with syn- and anti-β-hydroxy acid substrates to yield cis- and trans-β-lactones, respectively. Protein sequence comparisons reveal that enzymes homologous to OleC are encoded in natural product gene clusters that generate β-lactone rings, suggesting a common mechanism of biosynthesis.
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Affiliation(s)
- James K. Christenson
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Min-nesota, 55455, United States
- BioTechnology Institute, University of Minnesota, St. Paul, Minnesota, 55108, United States
| | - Jack E. Richman
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Min-nesota, 55455, United States
- BioTechnology Institute, University of Minnesota, St. Paul, Minnesota, 55108, United States
| | - Matthew R. Jensen
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Min-nesota, 55455, United States
- BioTechnology Institute, University of Minnesota, St. Paul, Minnesota, 55108, United States
| | - Jennifer Y. Neufeld
- BioTechnology Institute, University of Minnesota, St. Paul, Minnesota, 55108, United States
| | - Carrie M. Wilmot
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Min-nesota, 55455, United States
- BioTechnology Institute, University of Minnesota, St. Paul, Minnesota, 55108, United States
| | - Lawrence P. Wackett
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Min-nesota, 55455, United States
- BioTechnology Institute, University of Minnesota, St. Paul, Minnesota, 55108, United States
- Microbial and Plant Genomic Institute, University of Minnesota, St. Paul, Minnesota, 55108, United States
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25
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Klementz D, Döring K, Lucas X, Telukunta KK, Erxleben A, Deubel D, Erber A, Santillana I, Thomas OS, Bechthold A, Günther S. StreptomeDB 2.0--an extended resource of natural products produced by streptomycetes. Nucleic Acids Res 2015; 44:D509-14. [PMID: 26615197 PMCID: PMC4702922 DOI: 10.1093/nar/gkv1319] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 11/10/2015] [Indexed: 12/03/2022] Open
Abstract
Over the last decades, the genus Streptomyces has stirred huge interest in the scientific community as a source of bioactive compounds. The majority of all known antibiotics is isolated from these bacterial strains, as well as a variety of other drugs such as antitumor agents, immunosuppressants and antifungals. To the best of our knowledge, StreptomeDB was the first database focusing on compounds produced by streptomycetes. The new version presented herein represents a major step forward: its content has been increased to over 4000 compounds and more than 2500 host organisms. In addition, we have extended the background information and included hundreds of new manually curated references to literature. The latest update features a unique scaffold-based navigation system, which enables the exploration of the chemical diversity of StreptomeDB on a structural basis. We have included a phylogenetic tree, based on 16S rRNA sequences, which comprises more than two-thirds of the included host organisms. It enables visualizing the frequency, appearance, and persistence of compounds and scaffolds in an evolutionary context. Additionally, we have included predicted MS- and NMR-spectra of thousands of compounds for assignment of experimental data. The database is freely accessible via http://www.pharmaceutical-bioinformatics.org/streptomedb.
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Affiliation(s)
- Dennis Klementz
- Pharmaceutical Bioinformatics, Institute of Pharmaceutical Sciences, Albert-Ludwigs-University, Hermann-Herder-Strasse 9, Freiburg 79104, Germany
| | - Kersten Döring
- Pharmaceutical Bioinformatics, Institute of Pharmaceutical Sciences, Albert-Ludwigs-University, Hermann-Herder-Strasse 9, Freiburg 79104, Germany
| | - Xavier Lucas
- Pharmaceutical Bioinformatics, Institute of Pharmaceutical Sciences, Albert-Ludwigs-University, Hermann-Herder-Strasse 9, Freiburg 79104, Germany School of Life Sciences, Division of Biological Chemistry and Drug Discovery, University of Dundee, James Black Centre, Dow Street, Dundee DD1 5EH, UK
| | - Kiran K Telukunta
- Pharmaceutical Bioinformatics, Institute of Pharmaceutical Sciences, Albert-Ludwigs-University, Hermann-Herder-Strasse 9, Freiburg 79104, Germany
| | - Anika Erxleben
- Pharmaceutical Bioinformatics, Institute of Pharmaceutical Sciences, Albert-Ludwigs-University, Hermann-Herder-Strasse 9, Freiburg 79104, Germany Chair for Bioinformatics, Department of Computer Science, University of Freiburg, Georges-Koehler-Allee 106, Freiburg 79110, Germany
| | - Denise Deubel
- Pharmaceutical Biology, Institute of Pharmaceutical Sciences, Albert-Ludwigs-University, 79104 Freiburg, Germany
| | - Astrid Erber
- Pharmaceutical Biology, Institute of Pharmaceutical Sciences, Albert-Ludwigs-University, 79104 Freiburg, Germany
| | - Irene Santillana
- Pharmaceutical Biology, Institute of Pharmaceutical Sciences, Albert-Ludwigs-University, 79104 Freiburg, Germany
| | - Oliver S Thomas
- Pharmaceutical Bioinformatics, Institute of Pharmaceutical Sciences, Albert-Ludwigs-University, Hermann-Herder-Strasse 9, Freiburg 79104, Germany
| | - Andreas Bechthold
- Pharmaceutical Biology, Institute of Pharmaceutical Sciences, Albert-Ludwigs-University, 79104 Freiburg, Germany
| | - Stefan Günther
- Pharmaceutical Bioinformatics, Institute of Pharmaceutical Sciences, Albert-Ludwigs-University, Hermann-Herder-Strasse 9, Freiburg 79104, Germany
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Kumar P, Dubey KK. Current trends and future prospects of lipstatin: a lipase inhibitor and pro-drug for obesity. RSC Adv 2015. [DOI: 10.1039/c5ra14892h] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
A review of the implications and causes of obesity, the status of antiobesity drugs, the mechanism of inhibition of pancreatic lipases, the biosynthesis of lipstatin and the present status of lipstatin production.
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Affiliation(s)
- Punit Kumar
- Microbial Biotechnology Laboratory
- University Institute of Engineering and Technology
- Maharshi Dayanand University
- Rohtak
- India
| | - Kashyap Kumar Dubey
- Microbial Biotechnology Laboratory
- University Institute of Engineering and Technology
- Maharshi Dayanand University
- Rohtak
- India
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