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Landeta C, Medina-Ortiz D, Escobar N, Valdez I, González-Troncoso MP, Álvares-Saravia D, Aldridge J, Gómez C, Lienqueo ME. Integrative workflows for the characterization of hydrophobin and cerato-platanin in the marine fungus Paradendryphiella salina. Arch Microbiol 2024; 206:385. [PMID: 39177836 DOI: 10.1007/s00203-024-04087-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Revised: 07/03/2024] [Accepted: 07/19/2024] [Indexed: 08/24/2024]
Abstract
Hydrophobins (HFBs) and cerato-platanins (CPs) are surface-active extracellular proteins produced by filamentous fungi. This study identified two HFB genes (pshyd1 and pshyd2) and one CP gene (pscp) in the marine fungus Paradendryphiella salina. The proteins PsCP, PsHYD2, and PsHYD1 had molecular weights of 12.70, 6.62, and 5.98 kDa, respectively, with isoelectric points below 7. PsHYD1 and PsHYD2 showed hydrophobicity (GRAVY score 0.462), while PsCP was hydrophilic (GRAVY score - 0.202). Stability indices indicated in-solution stability. Mass spectrometry identified 2,922 proteins, including CP but not HFB proteins. qPCR revealed differential gene expression influenced by developmental stage and substrate, with pshyd1 consistently expressed. These findings suggest P. salina's adaptation to marine ecosystems with fewer hydrophobin genes than other fungi but capable of producing surface-active proteins from seaweed carbohydrates. These proteins have potential applications in medical biocoatings, food industry foam stabilizers, and environmental bioremediation.
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Affiliation(s)
- Catalina Landeta
- Center for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology, and Materials, Faculty of Physical and Mathematical Sciences, University of Chile, Santiago, Beauchef, 851- 8370456, Chile
| | - David Medina-Ortiz
- Center for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology, and Materials, Faculty of Physical and Mathematical Sciences, University of Chile, Santiago, Beauchef, 851- 8370456, Chile
- Department of Computer Engineering, Faculty of Engineering, University of Magallanes, Av. Pdte. Manuel Bulnes 01855, Punta Arenas, Chile
| | - Natalia Escobar
- Microbiology, Department of Biology, Utrecht University, Utrecht, Netherlands
| | - Iván Valdez
- Microbiology, Department of Biology, Utrecht University, Utrecht, Netherlands
| | - María Paz González-Troncoso
- Center for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology, and Materials, Faculty of Physical and Mathematical Sciences, University of Chile, Santiago, Beauchef, 851- 8370456, Chile
| | - Diego Álvares-Saravia
- Teaching and Research Assistance Center, CADI, University of Magallanes, Av. los Flamencos, Punta Arenas, 01364, Chile
| | - Jacqueline Aldridge
- Department of Computer Engineering, Faculty of Engineering, University of Magallanes, Av. Pdte. Manuel Bulnes 01855, Punta Arenas, Chile
| | - Carlos Gómez
- Chemistry Department, University of Valle-Yumbo, Valle del Cauca, 760501, Chile
| | - María Elena Lienqueo
- Center for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology, and Materials, Faculty of Physical and Mathematical Sciences, University of Chile, Santiago, Beauchef, 851- 8370456, Chile.
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2
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Wingfield LK, Atcharawiriyakul J, Jitprasitporn N. Diversity and characterization of culturable fungi associated with the marine sea cucumber Holothuria scabra. PLoS One 2024; 19:e0296499. [PMID: 38165907 PMCID: PMC10760727 DOI: 10.1371/journal.pone.0296499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 12/14/2023] [Indexed: 01/04/2024] Open
Abstract
Fungi associated with the marine echinoderm, Holothuria scabra, produces extracellular enzymes and bioactive metabolites, and mycoviruses that could be used for biotechnological and pharmaceutical applications. The species identification based on molecular and morphological characteristics classified the culturable fungi into twenty-three genera belonging to eight orders, Chaetothyriales, Eurotiales, Hypocreales, Mucorales, Mycosphaerellales, Onygenales, Pleosporales and Venturiales, from four classes, Eurotiomycetes, Dothideomycetes, Mucoromycetes and Sordariomycetes of the two phyla Ascomycota and Mucoromycota. The most frequent genera were Aspergillus (relative frequency, 45.30%) and Penicillium (relative frequency, 22.68%). The Menhinick species richness and Shannon species diversity indices were 1.64 and 2.36, respectively, indicating a high diversity of fungi. An enzymatic production test revealed that sixteen isolates could produce proteases and amylases at different levels. The presence of mycoviruses was detected in eight isolates with different genomic profiles. Thirty-two of the 55 isolates produced antimicrobial metabolites which had an inhibitory effect on various microbial pathogens. Most of these active isolates were identified as Aspergillus, Penicillium and Trichoderma. Notably, Aspergillus terreus F10M7, Trichoderma harzianum F31M4 and T. harzianum F31M5 showed the most potent activity against both Gram-positive and Gram-negative bacteria and human pathogenic fungi. Our study represents the first report of the mycobiota associated with the marine echinoderm Holothuria scabra.
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Affiliation(s)
| | - Jirawalan Atcharawiriyakul
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Ninadia Jitprasitporn
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand
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3
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Liu P, Zhang H, Fan Y, Xu D. Microbially Influenced Corrosion of Steel in Marine Environments: A Review from Mechanisms to Prevention. Microorganisms 2023; 11:2299. [PMID: 37764143 PMCID: PMC10535020 DOI: 10.3390/microorganisms11092299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 08/25/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023] Open
Abstract
Microbially influenced corrosion (MIC) is a formidable challenge in the marine industry, resulting from intricate interactions among various biochemical reactions and microbial species. Many preventions used to mitigate biocorrosion fail due to ignorance of the MIC mechanisms. This review provides a summary of the current research on microbial corrosion in marine environments, including corrosive microbes and biocorrosion mechanisms. We also summarized current strategies for inhibiting MIC and proposed future research directions for MIC mechanisms and prevention. This review aims to comprehensively understand marine microbial corrosion and contribute to novel strategy developments for biocorrosion control in marine environments.
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Affiliation(s)
- Pan Liu
- Shenyang National Laboratory for Materials Science, Northeastern University, Shenyang 110819, China
| | - Haiting Zhang
- Shenyang National Laboratory for Materials Science, Northeastern University, Shenyang 110819, China
- College of Life and Health Sciences, Northeastern University, Shenyang 110819, China
| | - Yongqiang Fan
- Shenyang National Laboratory for Materials Science, Northeastern University, Shenyang 110819, China
- College of Life and Health Sciences, Northeastern University, Shenyang 110819, China
| | - Dake Xu
- Shenyang National Laboratory for Materials Science, Northeastern University, Shenyang 110819, China
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4
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Kempken F. Marine fungi: A treasure trove of novel natural products and for biological discovery. PLoS Pathog 2023; 19:e1011624. [PMID: 37733683 PMCID: PMC10513230 DOI: 10.1371/journal.ppat.1011624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/23/2023] Open
Affiliation(s)
- Frank Kempken
- Abteilung Botanische Genetik und Molekularbiologie, Botanisches Institut und Botanischer Garten, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
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5
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Labes A. Marine Resources Offer New Compounds and Strategies for the Treatment of Skin and Soft Tissue Infections. Mar Drugs 2023; 21:387. [PMID: 37504918 PMCID: PMC10381745 DOI: 10.3390/md21070387] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 06/26/2023] [Accepted: 06/28/2023] [Indexed: 07/29/2023] Open
Abstract
Bioprospecting of the marine environment for drug development has gained much attention in recent years owing to its massive chemical and biological diversity. Drugs for the treatment of skin and soft tissue infections have become part of the search, mainly with respect to enlarging the number of available antibiotics, with a special focus on multidrug-resistant Gram-positive bacteria, being the major causative agents in this field. Marine resources offer novel natural products with distinct biological activities of pharmaceutical importance, having the chance to provide new chemical scaffolds and new modes of action. New studies advance the field by proposing new strategies derived from an ecosystemic understanding for preventive activities against biofilms and new compounds suitable as disinfectants, which sustain the natural flora of the skin. Still, the development of new compounds is often stuck at the discovery level, as marine biotechnology also needs to overcome technological bottlenecks in drug development. This review summarizes its potential and shows these bottlenecks and new approaches.
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Affiliation(s)
- Antje Labes
- Department of Energy and Biotechnology, Flensburg University of Applied Sciences ZAiT, Kanzleistraße 91-93, D-24943 Flensburg, Germany
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6
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Elnaggar MS, Elissawy AM, Youssef FS, Kicsák M, Kurtán T, Singab ANB, Kalscheuer R. Austalide derivative from marine-derived Aspergillus sp. and evaluation of its cytotoxic and ADME/TOPKAT properties. RSC Adv 2023; 13:16480-16487. [PMID: 37274397 PMCID: PMC10233426 DOI: 10.1039/d3ra02632a] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 05/22/2023] [Indexed: 06/06/2023] Open
Abstract
In-depth chemical investigation of an ethyl acetate extract of Aspergillus sp. isolated from the soft coral Sinularia species resulted in the isolation of one new meroterpenoid, austalide Z (1), one known austalide W (2), six known prenylated indole diketopiperazine alkaloids (3-8), and phthalic acid and its ethyl derivative (9-10). The structures were established by means of 1D and 2D NMR (one- and two-dimensional nuclear magnetic resonance) experiments supported by UV analysis and ESI-MS (electrospray ionization mass spectrometry). In vitro cytotoxic evaluation was performed against the Caco-2 cancer cell line using the MTT assay, which showed that the examined compounds had weak to moderate activities, with the new meroterpenoid austalide Z (1) displaying an IC50 value of 51.6 μg mL-1. ADME/TOPKAT (absorption, distribution, metabolism, excretion, and toxicity) predication performed in silico showed that most of the isolated compounds possessed reasonable pharmacokinetic, pharmacodynamic, and toxicity properties. Thus, it can be concluded that Aspergillus sp. could act as a source of drug leads for cancer prevention with promising pharmacokinetic and pharmacodynamic properties and thus could be incorporated in pharmaceutical dosage forms.
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Affiliation(s)
- Mohamed S Elnaggar
- Department of Pharmacognosy, Faculty of Pharmacy, Ain Shams University Abbassia 11566 Cairo Egypt
- Institute of Pharmaceutical Biology and Biotechnology, Heinrich-Heine-Universität Düsseldorf 40225 Germany
| | - Ahmed M Elissawy
- Department of Pharmacognosy, Faculty of Pharmacy, Ain Shams University Abbassia 11566 Cairo Egypt
- Center of Drug Discovery Research and Development, Ain Shams University Abbassia 11566 Cairo Egypt
| | - Fadia S Youssef
- Department of Pharmacognosy, Faculty of Pharmacy, Ain Shams University Abbassia 11566 Cairo Egypt
| | - Máté Kicsák
- Department of Organic Chemistry, University of Debrecen Debrecen 4032 Hungary
| | - Tibor Kurtán
- Department of Organic Chemistry, University of Debrecen Debrecen 4032 Hungary
| | - Abdel Nasser B Singab
- Department of Pharmacognosy, Faculty of Pharmacy, Ain Shams University Abbassia 11566 Cairo Egypt
- Center of Drug Discovery Research and Development, Ain Shams University Abbassia 11566 Cairo Egypt
| | - Rainer Kalscheuer
- Institute of Pharmaceutical Biology and Biotechnology, Heinrich-Heine-Universität Düsseldorf 40225 Germany
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7
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Barazorda-Ccahuana HL, Ranilla LG, Candia-Puma MA, Cárcamo-Rodriguez EG, Centeno-Lopez AE, Davila-Del-Carpio G, Medina-Franco JL, Chávez-Fumagalli MA. PeruNPDB: the Peruvian Natural Products Database for in silico drug screening. Sci Rep 2023; 13:7577. [PMID: 37165197 PMCID: PMC10170056 DOI: 10.1038/s41598-023-34729-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 05/06/2023] [Indexed: 05/12/2023] Open
Abstract
Since the number of drugs based on natural products (NPs) represents a large source of novel pharmacological entities, NPs have acquired significance in drug discovery. Peru is considered a megadiverse country with many endemic species of plants, terrestrial, and marine animals, and microorganisms. NPs databases have a major impact on drug discovery development. For this reason, several countries such as Mexico, Brazil, India, and China have initiatives to assemble and maintain NPs databases that are representative of their diversity and ethnopharmacological usage. We describe the assembly, curation, and chemoinformatic evaluation of the content and coverage in chemical space, as well as the physicochemical attributes and chemical diversity of the initial version of the Peruvian Natural Products Database (PeruNPDB), which contains 280 natural products. Access to PeruNPDB is available for free ( https://perunpdb.com.pe/ ). The PeruNPDB's collection is intended to be used in a variety of tasks, such as virtual screening campaigns against various disease targets or biological endpoints. This emphasizes the significance of biodiversity protection both directly and indirectly on human health.
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Affiliation(s)
- Haruna L Barazorda-Ccahuana
- Computational Biology and Chemistry Research Group, Vicerrectorado de Investigación, Universidad Católica de Santa María, 04000, Arequipa, Peru
| | - Lena Gálvez Ranilla
- Laboratory of Research in Food Science, Universidad Catolica de Santa Maria, 04000, Arequipa, Peru
- Escuela Profesional de Ingeniería de Industria Alimentaria, Facultad de Ciencias e Ingenierías Biológicas y Químicas, Universidad Catolica de Santa Maria, 04000, Arequipa, Peru
| | - Mayron Antonio Candia-Puma
- Computational Biology and Chemistry Research Group, Vicerrectorado de Investigación, Universidad Católica de Santa María, 04000, Arequipa, Peru
- Facultad de Ciencias Farmacéuticas, Bioquímicas y Biotecnológicas, Universidad Católica de Santa María, 04000, Arequipa, Peru
| | - Eymi Gladys Cárcamo-Rodriguez
- Computational Biology and Chemistry Research Group, Vicerrectorado de Investigación, Universidad Católica de Santa María, 04000, Arequipa, Peru
- Facultad de Ciencias Farmacéuticas, Bioquímicas y Biotecnológicas, Universidad Católica de Santa María, 04000, Arequipa, Peru
| | - Angela Emperatriz Centeno-Lopez
- Computational Biology and Chemistry Research Group, Vicerrectorado de Investigación, Universidad Católica de Santa María, 04000, Arequipa, Peru
- Facultad de Ciencias Farmacéuticas, Bioquímicas y Biotecnológicas, Universidad Católica de Santa María, 04000, Arequipa, Peru
| | - Gonzalo Davila-Del-Carpio
- Facultad de Ciencias Farmacéuticas, Bioquímicas y Biotecnológicas, Universidad Católica de Santa María, 04000, Arequipa, Peru
| | - José L Medina-Franco
- DIFACQUIM Research Group, Department of Pharmacy, School of Chemistry, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Miguel Angel Chávez-Fumagalli
- Computational Biology and Chemistry Research Group, Vicerrectorado de Investigación, Universidad Católica de Santa María, 04000, Arequipa, Peru.
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8
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CNN_FunBar: Advanced Learning Technique for Fungi ITS Region Classification. Genes (Basel) 2023; 14:genes14030634. [PMID: 36980906 PMCID: PMC10048311 DOI: 10.3390/genes14030634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/28/2022] [Accepted: 01/09/2023] [Indexed: 03/06/2023] Open
Abstract
Fungal species identification from metagenomic data is a highly challenging task. Internal Transcribed Spacer (ITS) region is a potential DNA marker for fungi taxonomy prediction. Computational approaches, especially deep learning algorithms, are highly efficient for better pattern recognition and classification of large datasets compared to in silico techniques such as BLAST and machine learning methods. Here in this study, we present CNN_FunBar, a convolutional neural network-based approach for the classification of fungi ITS sequences from UNITE+INSDC reference datasets. Effects of convolution kernel size, filter numbers, k-mer size, degree of diversity and category-wise frequency of ITS sequences on classification performances of CNN models have been assessed at all taxonomic levels (species, genus, family, order, class and phylum). It is observed that CNN models can produce >93% average accuracy for classifying ITS sequences from balanced datasets with 500 sequences per category and 6-mer frequency features at all levels. The comparative study has revealed that CNN_FunBar can outperform machine learning-based algorithms (SVM, KNN, Naïve-Bayes and Random Forest) as well as existing fungal taxonomy prediction software (funbarRF, Mothur, RDP Classifier and SINTAX). The present study will be helpful for fungal taxonomy classification using large metagenomic datasets.
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9
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Xie M, Gao M, Yun Y, Malmsten M, Rotello VM, Zboril R, Akhavan O, Kraskouski A, Amalraj J, Cai X, Lu J, Zheng H, Li R. Antibacterial Nanomaterials: Mechanisms, Impacts on Antimicrobial Resistance and Design Principles. Angew Chem Int Ed Engl 2023; 62:e202217345. [PMID: 36718001 DOI: 10.1002/anie.202217345] [Citation(s) in RCA: 63] [Impact Index Per Article: 63.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 01/27/2023] [Accepted: 01/30/2023] [Indexed: 02/01/2023]
Abstract
Antimicrobial resistance (AMR) is one of the biggest threats to the environment and health. AMR rapidly invalidates conventional antibiotics, and antimicrobial nanomaterials have been increasingly explored as alternatives. Interestingly, several antimicrobial nanomaterials show AMR-independent antimicrobial effects without detectable new resistance and have therefore been suggested to prevent AMR evolution. In contrast, some are found to trigger the evolution of AMR. Given these seemingly conflicting findings, a timely discussion of the two faces of antimicrobial nanomaterials is urgently needed. This review systematically compares the killing mechanisms and structure-activity relationships of antibiotics and antimicrobial nanomaterials. We then focus on nano-microbe interactions to elucidate the impacts of molecular initiating events on AMR evolution. Finally, we provide an outlook on future antimicrobial nanomaterials and propose design principles for the prevention of AMR evolution.
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Affiliation(s)
- Maomao Xie
- State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X), Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Suzhou Medical College, Soochow University, Suzhou, 215123, Jiangsu, China
| | - Meng Gao
- State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X), Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Suzhou Medical College, Soochow University, Suzhou, 215123, Jiangsu, China
| | - Yang Yun
- College of Environmental & Resource Sciences, Shanxi University, Taiyuan, 030006, Shanxi, China
| | - Martin Malmsten
- Department of Pharmacy, University of Copenhagen, 2100, Copenhagen, Denmark.,Department of Physical Chemistry 1, University of Lund, 22100, Lund, Sweden
| | - Vincent M Rotello
- Department of Chemistry, University of Massachusetts Amherst, 710 N. Pleasant St., Amherst, USA
| | - Radek Zboril
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 241/27, Olomouc, 783 71, Czech Republic.,Nanotechnology Centre, Centre of Energy and Environmental Technologies, VŠB-Technical University of Ostrava, 17. listopadu 2172/15, Ostrava-Poruba, 708 00, Czech Republic
| | - Omid Akhavan
- Condensed Matter National Laboratory, P.O. Box 1956838861, Tehran, Iran
| | - Aliaksandr Kraskouski
- Department of Physicochemistry of Thin Film Materials, Institute of Chemistry of New Materials of NAS of Belarus, 36 F. Skaryna Str., 220084, Minsk, Belarus
| | - John Amalraj
- Laboratory of Materials Science, Instituto de Química de Recursos Naturales, Universidad de Talca, P.O. Box 747, Talca, Chile
| | - Xiaoming Cai
- School of Public Health, Suzhou Medical College, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Jianmei Lu
- College of Chemistry, Chemical Engineering and Materials Science, National Center for International Research on Intelligent Nano-Materials and Detection Technology in Environmental Protection, Soochow University, Suzhou, 215123, China
| | - Huizhen Zheng
- State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X), Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Suzhou Medical College, Soochow University, Suzhou, 215123, Jiangsu, China
| | - Ruibin Li
- State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X), Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Suzhou Medical College, Soochow University, Suzhou, 215123, Jiangsu, China
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10
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Munusamy M, Tan K, Nge CE, Gakuubi MM, Crasta S, Kanagasundaram Y, Ng SB. Diversity and Biosynthetic Potential of Fungi Isolated from St. John's Island, Singapore. Int J Mol Sci 2023; 24:1033. [PMID: 36674548 PMCID: PMC9861175 DOI: 10.3390/ijms24021033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 12/01/2022] [Accepted: 12/13/2022] [Indexed: 01/06/2023] Open
Abstract
Adaptation to a wide variety of habitats allows fungi to develop unique abilities to produce diverse secondary metabolites with diverse bioactivities. In this study, 30 Ascomycetes fungi isolated from St. John's Island, Singapore were investigated for their general biosynthetic potential and their ability to produce antimicrobial secondary metabolites (SMs). All the 30 fungal isolates belong to the Phylum Ascomycota and are distributed into 6 orders and 18 genera with Order Hypocreales having the highest number of representative (37%). Screening for polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) genes using degenerate PCR led to the identification of 23 polyketide synthases (PKSs) and 5 nonribosomal peptide synthetases (NRPSs) grouped into nine distinct clades based on their reduction capabilities. Some of the identified PKSs genes share high similarities between species and known reference genes, suggesting the possibility of conserved biosynthesis of closely related compounds from different fungi. Fungal extracts were tested for their antimicrobial activity against S. aureus, Methicillin-resistant S. aureus (MRSA), and Candida albicans. Bioassay-guided fractionation of the active constituents from two promising isolates resulted in the isolation of seven compounds: Penilumamides A, D, and E from strain F4335 and xanthomegnin, viomellein, pretrichodermamide C and vioxanthin from strain F7180. Vioxanthin exhibited the best antibacterial activity with IC50 values of 3.0 μM and 1.6 μM against S. aureus and MRSA respectively. Viomellein revealed weak antiproliferative activity against A549 cells with an IC50 of 42 μM. The results from this study give valuable insights into the diversity and biosynthetic potential of fungi from this unique habitat and forms a background for an in-depth analysis of the biosynthetic capability of selected strains of interest with the aim of discovering novel fungal natural products.
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Affiliation(s)
- Madhaiyan Munusamy
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02 Nanos, Singapore 138669, Singapore
| | - Kenneth Tan
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02 Nanos, Singapore 138669, Singapore
| | - Choy Eng Nge
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02 Nanos, Singapore 138669, Singapore
| | - Martin Muthee Gakuubi
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02 Nanos, Singapore 138669, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Sharon Crasta
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02 Nanos, Singapore 138669, Singapore
| | - Yoganathan Kanagasundaram
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02 Nanos, Singapore 138669, Singapore
| | - Siew Bee Ng
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02 Nanos, Singapore 138669, Singapore
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11
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Zhu Y, Ouyang Z, Du H, Wang M, Wang J, Sun H, Kong L, Xu Q, Ma H, Sun Y. New opportunities and challenges of natural products research: When target identification meets single-cell multiomics. Acta Pharm Sin B 2022; 12:4011-4039. [PMID: 36386472 PMCID: PMC9643300 DOI: 10.1016/j.apsb.2022.08.022] [Citation(s) in RCA: 147] [Impact Index Per Article: 73.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 07/06/2022] [Accepted: 08/22/2022] [Indexed: 12/12/2022] Open
Abstract
Natural products, and especially the active ingredients found in traditional Chinese medicine (TCM), have a thousand-year-long history of clinical use and a strong theoretical basis in TCM. As such, traditional remedies provide shortcuts for the development of original new drugs in China, and increasing numbers of natural products are showing great therapeutic potential in various diseases. This paper reviews the molecular mechanisms of action of natural products from different sources used in the treatment of inflammatory diseases and cancer, introduces the methods and newly emerging technologies used to identify and validate the targets of natural active ingredients, enumerates the expansive list of TCM used to treat inflammatory diseases and cancer, and summarizes the patterns of action of emerging technologies such as single-cell multiomics, network pharmacology, and artificial intelligence in the pharmacological studies of natural products to provide insights for the development of innovative natural product-based drugs. Our hope is that we can make use of advances in target identification and single-cell multiomics to obtain a deeper understanding of actions of mechanisms of natural products that will allow innovation and revitalization of TCM and its swift industrialization and internationalization.
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Affiliation(s)
- Yuyu Zhu
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Zijun Ouyang
- Institute of Marine Biomedicine, School of Food and Drug, Shenzhen Polytechnic, Shenzhen 518055, China
| | - Haojie Du
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science, Nanjing University, Nanjing 210023, China
| | - Meijing Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science, Nanjing University, Nanjing 210023, China
| | - Jiaojiao Wang
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Haiyan Sun
- Institute of Marine Biomedicine, School of Food and Drug, Shenzhen Polytechnic, Shenzhen 518055, China
| | - Lingdong Kong
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science, Nanjing University, Nanjing 210023, China
| | - Qiang Xu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science, Nanjing University, Nanjing 210023, China
| | - Hongyue Ma
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Yang Sun
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science, Nanjing University, Nanjing 210023, China
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou 221004, China
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12
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Luo L, Yang J, Wang C, Wu J, Li Y, Zhang X, Li H, Zhang H, Zhou Y, Lu A, Chen S. Natural products for infectious microbes and diseases: an overview of sources, compounds, and chemical diversities. SCIENCE CHINA. LIFE SCIENCES 2022; 65:1123-1145. [PMID: 34705221 PMCID: PMC8548270 DOI: 10.1007/s11427-020-1959-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 07/27/2021] [Indexed: 12/13/2022]
Abstract
As coronavirus disease 2019 (COVID-19) threatens human health globally, infectious disorders have become one of the most challenging problem for the medical community. Natural products (NP) have been a prolific source of antimicrobial agents with widely divergent structures and a range vast biological activities. A dataset comprising 618 articles, including 646 NP-based compounds from 672 species of natural sources with biological activities against 21 infectious pathogens from five categories, was assembled through manual selection of published articles. These data were used to identify 268 NP-based compounds classified into ten groups, which were used for network pharmacology analysis to capture the most promising lead-compounds such as agelasine D, dicumarol, dihydroartemisinin and pyridomycin. The distribution of maximum Tanimoto scores indicated that compounds which inhibited parasites exhibited low diversity, whereas the chemistries inhibiting bacteria, fungi, and viruses showed more structural diversity. A total of 331 species of medicinal plants with compounds exhibiting antimicrobial activities were selected to classify the family sources. The family Asteraceae possesses various compounds against C. neoformans, the family Anacardiaceae has compounds against Salmonella typhi, the family Cucurbitacea against the human immunodeficiency virus (HIV), and the family Ancistrocladaceae against Plasmodium. This review summarizes currently available data on NP-based antimicrobials against refractory infections to provide information for further discovery of drugs and synthetic strategies for anti-infectious agents.
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Affiliation(s)
- Lu Luo
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Jun Yang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Cheng Wang
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100006, China
| | - Jie Wu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Yafang Li
- Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Xu Zhang
- weMED Health, Houston, 77054, USA
| | - Hui Li
- Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Hui Zhang
- Akupunktur Akademiet, Aabyhoej, Aarhus, 8230, Denmark
| | - Yumei Zhou
- The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Guangzhou, 518033, China
| | - Aiping Lu
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, 999077, China
| | - Shilin Chen
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
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13
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Xu Y, Du X, Yu X, Jiang Q, Zheng K, Xu J, Wang P. Recent Advances in the Heterologous Expression of Biosynthetic Gene Clusters for Marine Natural Products. Mar Drugs 2022; 20:341. [PMID: 35736144 PMCID: PMC9225448 DOI: 10.3390/md20060341] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 05/11/2022] [Accepted: 05/20/2022] [Indexed: 12/29/2022] Open
Abstract
Marine natural products (MNPs) are an important source of biologically active metabolites, particularly for therapeutic agent development after terrestrial plants and nonmarine microorganisms. Sequencing technologies have revealed that the number of biosynthetic gene clusters (BGCs) in marine microorganisms and the marine environment is much higher than expected. Unfortunately, the majority of them are silent or only weakly expressed under traditional laboratory culture conditions. Furthermore, the large proportion of marine microorganisms are either uncultivable or cannot be genetically manipulated. Efficient heterologous expression systems can activate cryptic BGCs and increase target compound yield, allowing researchers to explore more unknown MNPs. When developing heterologous expression of MNPs, it is critical to consider heterologous host selection as well as genetic manipulations for BGCs. In this review, we summarize current progress on the heterologous expression of MNPs as a reference for future research.
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Affiliation(s)
- Yushan Xu
- Ocean College, Zhejiang University, Zhoushan 316021, China; (Y.X.); (X.D.); (X.Y.); (Q.J.); (K.Z.); (J.X.)
| | - Xinhua Du
- Ocean College, Zhejiang University, Zhoushan 316021, China; (Y.X.); (X.D.); (X.Y.); (Q.J.); (K.Z.); (J.X.)
| | - Xionghui Yu
- Ocean College, Zhejiang University, Zhoushan 316021, China; (Y.X.); (X.D.); (X.Y.); (Q.J.); (K.Z.); (J.X.)
| | - Qian Jiang
- Ocean College, Zhejiang University, Zhoushan 316021, China; (Y.X.); (X.D.); (X.Y.); (Q.J.); (K.Z.); (J.X.)
| | - Kaiwen Zheng
- Ocean College, Zhejiang University, Zhoushan 316021, China; (Y.X.); (X.D.); (X.Y.); (Q.J.); (K.Z.); (J.X.)
| | - Jinzhong Xu
- Ocean College, Zhejiang University, Zhoushan 316021, China; (Y.X.); (X.D.); (X.Y.); (Q.J.); (K.Z.); (J.X.)
| | - Pinmei Wang
- Ocean College, Zhejiang University, Zhoushan 316021, China; (Y.X.); (X.D.); (X.Y.); (Q.J.); (K.Z.); (J.X.)
- State Key Laboratory of Motor Vehicle Biofuel Technology, Zhejiang University, Zhoushan 316021, China
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14
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Sen K, Sen B, Wang G. Diversity, Abundance, and Ecological Roles of Planktonic Fungi in Marine Environments. J Fungi (Basel) 2022; 8:jof8050491. [PMID: 35628747 PMCID: PMC9147564 DOI: 10.3390/jof8050491] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Revised: 05/03/2022] [Accepted: 05/04/2022] [Indexed: 02/07/2023] Open
Abstract
Fungi are considered terrestrial and oceans are a “fungal desert”. However, with the considerable progress made over past decades, fungi have emerged as morphologically, phylogenetically, and functionally diverse components of the marine water column. Although their communities are influenced by a plethora of environmental factors, the most influential include salinity, temperature, nutrients, and dissolved oxygen, suggesting that fungi respond to local environmental gradients. The biomass carbon of planktonic fungi exhibits spatiotemporal dynamics and can reach up to 1 μg CL−1 of seawater, rivaling bacteria on some occasions, which suggests their active and important role in the water column. In the nutrient-rich coastal water column, there is increasing evidence for their contribution to biogeochemical cycling and food web dynamics on account of their saprotrophic, parasitic, hyper-parasitic, and pathogenic attributes. Conversely, relatively little is known about their function in the open-ocean water column. Interestingly, methodological advances in sequencing and omics approach, the standardization of sequence data analysis tools, and integration of data through network analyses are enhancing our current understanding of the ecological roles of these multifarious and enigmatic members of the marine water column. This review summarizes the current knowledge of the diversity and abundance of planktonic fungi in the world’s oceans and provides an integrated and holistic view of their ecological roles.
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Affiliation(s)
- Kalyani Sen
- Center for Marine Environmental Ecology, School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Biswarup Sen
- Center for Marine Environmental Ecology, School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Guangyi Wang
- Center for Marine Environmental Ecology, School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
- Center for Biosafety Research and Strategy, Tianjin University, Tianjin 300072, China
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15
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Marra R, Gutiérrez S, Woo SL, Bonanomi G, Vinale F. Editorial: Designing Bio-Formulations Based on Organic Amendments, Beneficial Microbes and Their Metabolites. Front Microbiol 2022; 12:832149. [PMID: 35116018 PMCID: PMC8803659 DOI: 10.3389/fmicb.2021.832149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 12/24/2021] [Indexed: 12/02/2022] Open
Affiliation(s)
- Roberta Marra
- Department of Agricultural Sciences, University of Naples Federico II, Naples, Italy
- Center for Studies on Bioinspired Agro-Environmental Technology (BAT Center), University of Naples Federico II, Naples, Italy
- *Correspondence: Roberta Marra
| | | | - Sheridan Lois Woo
- Center for Studies on Bioinspired Agro-Environmental Technology (BAT Center), University of Naples Federico II, Naples, Italy
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
- Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy
| | - Giuliano Bonanomi
- Department of Agricultural Sciences, University of Naples Federico II, Naples, Italy
- Center for Studies on Bioinspired Agro-Environmental Technology (BAT Center), University of Naples Federico II, Naples, Italy
- Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy
| | - Francesco Vinale
- Center for Studies on Bioinspired Agro-Environmental Technology (BAT Center), University of Naples Federico II, Naples, Italy
- Institute for Sustainable Plant Protection, National Research Council, Naples, Italy
- Department of Veterinary Medicine and Animal Productions, University of Naples Federico II, Naples, Italy
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16
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Dewi DAR, Thomas T, Ahmad Mokhtar AM, Mat Nanyan NS, Zulfigar SB, Salikin NH. Carbapenem Resistance among Marine Bacteria-An Emerging Threat to the Global Health Sector. Microorganisms 2021; 9:microorganisms9102147. [PMID: 34683467 PMCID: PMC8537846 DOI: 10.3390/microorganisms9102147] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/08/2021] [Accepted: 10/10/2021] [Indexed: 01/24/2023] Open
Abstract
The emergence of antibiotic resistance among pathogenic microorganisms is a major issue for global public health, as it results in acute or chronic infections, debilitating diseases, and mortality. Of particular concern is the rapid and common spread of carbapenem resistance in healthcare settings. Carbapenems are a class of critical antibiotics reserved for treatment against multidrug-resistant microorganisms, and resistance to this antibiotic may result in limited treatment against infections. In addition to in clinical facilities, carbapenem resistance has also been identified in aquatic niches, including marine environments. Various carbapenem-resistant genes (CRGs) have been detected in different marine settings, with the majority of the genes incorporated in mobile genetic elements, i.e., transposons or plasmids, which may contribute to efficient genetic transfer. This review highlights the potential of the marine environment as a reservoir for carbapenem resistance and provides a general overview of CRG transmission among marine microbes.
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Affiliation(s)
- Dewa A.P. Rasmika Dewi
- School of Medicine, International University of Health and Welfare, Narita 286-8686, Japan;
- Faculty of Medicine and Health Sciences, Udayana University, Bali 80232, Indonesia
| | - Torsten Thomas
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney 2052, Australia;
| | - Ana Masara Ahmad Mokhtar
- School of Industrial Technology, Universiti Sains Malaysia, Gelugor 11800, Penang, Malaysia; (A.M.A.M.); (N.S.M.N.); (S.B.Z.)
| | - Noreen Suliani Mat Nanyan
- School of Industrial Technology, Universiti Sains Malaysia, Gelugor 11800, Penang, Malaysia; (A.M.A.M.); (N.S.M.N.); (S.B.Z.)
| | - Siti Balqis Zulfigar
- School of Industrial Technology, Universiti Sains Malaysia, Gelugor 11800, Penang, Malaysia; (A.M.A.M.); (N.S.M.N.); (S.B.Z.)
| | - Nor Hawani Salikin
- School of Industrial Technology, Universiti Sains Malaysia, Gelugor 11800, Penang, Malaysia; (A.M.A.M.); (N.S.M.N.); (S.B.Z.)
- Correspondence: ; Tel.: +60-4-653-2241
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17
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Xing B, Yu J, Chi C, Ma X, Xu Q, Li A, Ge Y, Wang Z, Liu T, Jia H, Yin F, Guo J, Huang L, Yang D, Ma M. Functional characterization and structural bases of two class I diterpene synthases in pimarane-type diterpene biosynthesis. Commun Chem 2021; 4:140. [PMID: 36697656 PMCID: PMC9814573 DOI: 10.1038/s42004-021-00578-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 09/08/2021] [Indexed: 01/28/2023] Open
Abstract
Pimarane-type diterpenoids are widely distributed in all domains of life, but no structures or catalytic mechanisms of pimarane-type diterpene synthases (DTSs) have been characterized. Here, we report that two class I DTSs, Sat1646 and Stt4548, each accept copalyl diphosphate (CPP) as the substrate to produce isopimara-8,15-diene (1). Sat1646 can also accept syn-CPP and produce syn-isopimaradiene/pimaradiene analogues (2-7), among which 2 possesses a previously unreported "6/6/7" ring skeleton. We solve the crystal structures of Sat1646, Sat1646 complexed with magnesium ions, and Stt4548, thereby revealing the active sites of these pimarane-type DTSs. Substrate modeling and subsequent site-directed mutagenesis experiments demonstrate different structural bases of Sat1646 and Stt4548 for 1 production. Comparisons with previously reported DTSs reveal their distinct carbocation intermediate stabilization mechanisms, which control the conversion of a single substrate CPP into structurally diverse diterpene products. These results illustrate the structural bases for enzymatic catalyses of pimarane-type DTSs, potentially facilitating future DTS engineering and combinatorial biosynthesis.
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Affiliation(s)
- Baiying Xing
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing, 100191, China
| | - Jiahui Yu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing, 100191, China
| | - Changbiao Chi
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing, 100191, China
| | - Xueyang Ma
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing, 100191, China
| | - Qingxia Xu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing, 100191, China
| | - Annan Li
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing, 100191, China
| | - Yuanjie Ge
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing, 100191, China
| | - Zhengdong Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing, 100191, China
| | - Tan Liu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing, 100191, China
| | - Hongli Jia
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing, 100191, China
| | - Fuling Yin
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing, 100191, China
| | - Juan Guo
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Luqi Huang
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Donghui Yang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing, 100191, China.
| | - Ming Ma
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing, 100191, China.
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18
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de Carvalho Silveira T, Gomes WE, Tonon GC, Beatto TG, Spogis N, Cunha LHD, Lattaro BP, Nogueira AB, Mendes RK, Alvarenga DO, Etchegaray A. Residual biomass from surfactin production is a source of arginase and adsorbed surfactin that is useful for environmental remediation. World J Microbiol Biotechnol 2021; 37:123. [PMID: 34160683 DOI: 10.1007/s11274-021-03094-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 06/01/2021] [Indexed: 10/21/2022]
Abstract
Lipopeptides are important secondary metabolites produced by microbes. They find applications in environmental decontamination and in the chemical, pharmaceutical and food industries. However, their production is expensive. In the present work we propose three strategies to lower the production costs of surfactin. First, the coproduction of surfactin and arginase in a single growth. Second, extract the fraction of surfactin that adsorbs to the biomass and is removed from the growth medium through centrifugation. Third, use microbial biomass for the remediation of organic and inorganic contaminants. The coproduction of surfactin and arginase was evaluated by factorial design experiments using the LB medium supplemented with arginine. The best conditions for surfactin production were 22 h of growth at 37 °C using LB supplemented with arginine 7.3 g/L. Almost similar conditions were found to produce highest levels of arginase, 24 h and 6.45 g/L arginine. Decontamination of phenol and copper from artificial samples was attained by treatment with residues from lipopeptide production. Thus, cell suspensions and wash-waters used to extract surfactin from the biomass. Cell suspensions were used to successfully remove hydroquinone. Cell suspensions and wash-waters containing surfactin were successfully used to recover copper from solution. Specific monitoring methods were used for phenol and metal solutions, respectively a biosensor based on tyrosinase and either atomic absorption flame ionization spectrometry or absorbance coupled to the Arduino™ platform. Therefore, we report three alternative strategies to lower the production costs in lipopeptide production, which include the effective recovery of copper and phenol from contaminated waters using residues from surfactin production. Sustainable and profitable production of surfactin can be achieved by a coproduction strategy of lipopeptides and enzymes. Lipopeptides are collected in the supernatant and enzymes in the biomass. In addition, lipopeptides that coprecipitate with biomass can be recovered by washing. Lipopeptide wash-waters find applications in remediation and cells can also be used for environmental decontamination.
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Affiliation(s)
- Thais de Carvalho Silveira
- Programa de Pós-Graduação em Ciências da Saúde, Centro de Ciências da Vida, Pontifícia Universidade Católica de Campinas, Campinas, SP, Brasil
| | - Wyllerson Evaristo Gomes
- Programa de Pós-Graduação em Sistemas de Infraestrutura Urbana, Centro de Ciências Ambientais e de Tecnologias, Pontifícia Universidade Católica de Campinas, Campinas, SP, Brasil
| | - Giovana Chinaglia Tonon
- Faculdade de Química, Centro de Ciências Ambientais e de Tecnologias, Pontifícia Universidade Católica de Campinas (PUC-Campinas), Rua Professor Doutor Euryclides de Jesus Zerbini n° 1.516, Parque Rural Fazenda Santa Cândida, CEP 13087571, Campinas, SP, Brasil
| | - Thainá Godoy Beatto
- Programa de Pós-Graduação em Sistemas de Infraestrutura Urbana, Centro de Ciências Ambientais e de Tecnologias, Pontifícia Universidade Católica de Campinas, Campinas, SP, Brasil.,Faculdade de Química, Centro de Ciências Ambientais e de Tecnologias, Pontifícia Universidade Católica de Campinas (PUC-Campinas), Rua Professor Doutor Euryclides de Jesus Zerbini n° 1.516, Parque Rural Fazenda Santa Cândida, CEP 13087571, Campinas, SP, Brasil
| | - Nicolas Spogis
- Faculdade de Química, Centro de Ciências Ambientais e de Tecnologias, Pontifícia Universidade Católica de Campinas (PUC-Campinas), Rua Professor Doutor Euryclides de Jesus Zerbini n° 1.516, Parque Rural Fazenda Santa Cândida, CEP 13087571, Campinas, SP, Brasil
| | - Luiz Henrique Dallan Cunha
- Faculdade de Química, Centro de Ciências Ambientais e de Tecnologias, Pontifícia Universidade Católica de Campinas (PUC-Campinas), Rua Professor Doutor Euryclides de Jesus Zerbini n° 1.516, Parque Rural Fazenda Santa Cândida, CEP 13087571, Campinas, SP, Brasil
| | - Bruno Pera Lattaro
- Faculdade de Química, Centro de Ciências Ambientais e de Tecnologias, Pontifícia Universidade Católica de Campinas (PUC-Campinas), Rua Professor Doutor Euryclides de Jesus Zerbini n° 1.516, Parque Rural Fazenda Santa Cândida, CEP 13087571, Campinas, SP, Brasil
| | - Alessandra Borin Nogueira
- Faculdade de Química, Centro de Ciências Ambientais e de Tecnologias, Pontifícia Universidade Católica de Campinas (PUC-Campinas), Rua Professor Doutor Euryclides de Jesus Zerbini n° 1.516, Parque Rural Fazenda Santa Cândida, CEP 13087571, Campinas, SP, Brasil
| | - Renata Kelly Mendes
- Programa de Pós-Graduação em Sistemas de Infraestrutura Urbana, Centro de Ciências Ambientais e de Tecnologias, Pontifícia Universidade Católica de Campinas, Campinas, SP, Brasil.,Faculdade de Química, Centro de Ciências Ambientais e de Tecnologias, Pontifícia Universidade Católica de Campinas (PUC-Campinas), Rua Professor Doutor Euryclides de Jesus Zerbini n° 1.516, Parque Rural Fazenda Santa Cândida, CEP 13087571, Campinas, SP, Brasil
| | | | - Augusto Etchegaray
- Programa de Pós-Graduação em Ciências da Saúde, Centro de Ciências da Vida, Pontifícia Universidade Católica de Campinas, Campinas, SP, Brasil. .,Faculdade de Química, Centro de Ciências Ambientais e de Tecnologias, Pontifícia Universidade Católica de Campinas (PUC-Campinas), Rua Professor Doutor Euryclides de Jesus Zerbini n° 1.516, Parque Rural Fazenda Santa Cândida, CEP 13087571, Campinas, SP, Brasil.
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19
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Zhang B, Zhang T, Xu J, Lu J, Qiu P, Wang T, Ding L. Marine Sponge-Associated Fungi as Potential Novel Bioactive Natural Product Sources for Drug Discovery: A Review. Mini Rev Med Chem 2021; 20:1966-2010. [PMID: 32851959 DOI: 10.2174/1389557520666200826123248] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/26/2020] [Accepted: 07/20/2020] [Indexed: 11/22/2022]
Abstract
Marine sponge-associated fungi are promising sources of structurally interesting and bioactive secondary metabolites. Great plenty of natural products have been discovered from spongeassociated fungi in recent years. Here reviewed are 571 new compounds isolated from marine fungi associated with sponges in 2010-2018. These molecules comprised eight different structural classes, including alkaloids, polyketides, terpenoids, meroterpenoids, etc. Moreover, most of these compounds demonstrated profoundly biological activities, such as antimicrobial, antiviral, cytotoxic, etc. This review systematically summarized the structural diversity, biological function, and future potential of these novel bioactive natural products for drug discovery.
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Affiliation(s)
- Bin Zhang
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315832, China
| | - Ting Zhang
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315832, China
| | - Jianzhou Xu
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315832, China
| | - Jian Lu
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315832, China
| | - Panpan Qiu
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315832, China
| | - Tingting Wang
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315832, China
| | - Lijian Ding
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315832, China
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20
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Süntar I, Çetinkaya S, Haydaroğlu ÜS, Habtemariam S. Bioproduction process of natural products and biopharmaceuticals: Biotechnological aspects. Biotechnol Adv 2021; 50:107768. [PMID: 33974980 DOI: 10.1016/j.biotechadv.2021.107768] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 04/30/2021] [Accepted: 05/05/2021] [Indexed: 02/07/2023]
Abstract
Decades of research have been put in place for developing sustainable routes of bioproduction of high commercial value natural products (NPs) on the global market. In the last few years alone, we have witnessed significant advances in the biotechnological production of NPs. The development of new methodologies has resulted in a better understanding of the metabolic flux within the organisms, which have driven manipulations to improve production of the target product. This was further realised due to the recent advances in the omics technologies such as genomics, transcriptomics, proteomics, metabolomics and secretomics, as well as systems and synthetic biology. Additionally, the combined application of novel engineering strategies has made possible avenues for enhancing the yield of these products in an efficient and economical way. Invention of high-throughput technologies such as next generation sequencing (NGS) and toolkits for genome editing Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated 9 (CRISPR/Cas9) have been the game changers and provided unprecedented opportunities to generate rationally designed synthetic circuits which can produce complex molecules. This review covers recent advances in the engineering of various hosts for the production of bioactive NPs and biopharmaceuticals. It also highlights general approaches and strategies to improve their biosynthesis with higher yields in a perspective of plants and microbes (bacteria, yeast and filamentous fungi). Although there are numerous reviews covering this topic on a selected species at a time, our approach herein is to give a comprehensive understanding about state-of-art technologies in different platforms of organisms.
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Affiliation(s)
- Ipek Süntar
- Department of Pharmacognosy, Faculty of Pharmacy, Gazi University, 06330 Etiler, Ankara, Turkey.
| | - Sümeyra Çetinkaya
- Biotechnology Research Center of Ministry of Agriculture and Forestry, 06330 Yenimahalle, Ankara, Turkey
| | - Ülkü Selcen Haydaroğlu
- Biotechnology Research Center of Ministry of Agriculture and Forestry, 06330 Yenimahalle, Ankara, Turkey
| | - Solomon Habtemariam
- Pharmacognosy Research Laboratories & Herbal Analysis Services UK, University of Greenwich, Chatham-Maritime, Kent ME4 4TB, United Kingdom
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The pentose phosphate pathway in industrially relevant fungi: crucial insights for bioprocessing. Appl Microbiol Biotechnol 2021; 105:4017-4031. [PMID: 33950280 PMCID: PMC8140973 DOI: 10.1007/s00253-021-11314-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 03/04/2021] [Accepted: 04/20/2021] [Indexed: 11/12/2022]
Abstract
Abstract The pentose phosphate pathway (PPP) is one of the most targeted pathways in metabolic engineering. This pathway is the primary source of NADPH, and it contributes in fungi to the production of many compounds of interest such as polyols, biofuels, carotenoids, or antibiotics. However, the regulatory mechanisms of the PPP are still not fully known. This review provides an insight into the current comprehension of the PPP in fungi and the limitations of this current understanding. It highlights how this knowledge contributes to targeted engineering of the PPP and thus to better performance of industrially used fungal strains. Key points • Type of carbon and nitrogen source as well as oxidative stress influence the PPP. • A complex network of transcription factors regulates the PPP. • Improved understanding of the PPP will allow to increase yields of bioprocesses.
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Martinelli L, Redou V, Cochereau B, Delage L, Hymery N, Poirier E, Le Meur C, Le Foch G, Cladiere L, Mehiri M, Demont-Caulet N, Meslet-Cladiere L. Identification and Characterization of a New Type III Polyketide Synthase from a Marine Yeast, Naganishia uzbekistanensis. Mar Drugs 2020; 18:E637. [PMID: 33322429 PMCID: PMC7763939 DOI: 10.3390/md18120637] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 12/02/2020] [Accepted: 12/09/2020] [Indexed: 01/22/2023] Open
Abstract
A putative Type III Polyketide synthase (PKSIII) encoding gene was identified from a marine yeast, Naganishia uzbekistanensis strain Mo29 (UBOCC-A-208024) (formerly named as Cryptococcus sp.) isolated from deep-sea hydrothermal vents. This gene is part of a distinct phylogenetic branch compared to all known terrestrial fungal sequences. This new gene encodes a C-terminus extension of 74 amino acids compared to other known PKSIII proteins like Neurospora crassa. Full-length and reduced versions of this PKSIII were successfully cloned and overexpressed in a bacterial host, Escherichia coli BL21 (DE3). Both proteins showed the same activity, suggesting that additional amino acid residues at the C-terminus are probably not required for biochemical functions. We demonstrated by LC-ESI-MS/MS that these two recombinant PKSIII proteins could only produce tri- and tetraketide pyrones and alkylresorcinols using only long fatty acid chain from C8 to C16 acyl-CoAs as starter units, in presence of malonyl-CoA. In addition, we showed that some of these molecules exhibit cytotoxic activities against several cancer cell lines.
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Affiliation(s)
- Laure Martinelli
- Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, University Brest, F-29280 Plouzané, France; (L.M.); (V.R.); (B.C.); (N.H.); (E.P.); (C.L.M.); (G.L.F.)
| | - Vanessa Redou
- Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, University Brest, F-29280 Plouzané, France; (L.M.); (V.R.); (B.C.); (N.H.); (E.P.); (C.L.M.); (G.L.F.)
| | - Bastien Cochereau
- Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, University Brest, F-29280 Plouzané, France; (L.M.); (V.R.); (B.C.); (N.H.); (E.P.); (C.L.M.); (G.L.F.)
| | - Ludovic Delage
- Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR),CNRS, UMR8227, Sorbonne Université, 29680 Roscoff, France; (L.D.); (L.C.)
| | - Nolwenn Hymery
- Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, University Brest, F-29280 Plouzané, France; (L.M.); (V.R.); (B.C.); (N.H.); (E.P.); (C.L.M.); (G.L.F.)
| | - Elisabeth Poirier
- Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, University Brest, F-29280 Plouzané, France; (L.M.); (V.R.); (B.C.); (N.H.); (E.P.); (C.L.M.); (G.L.F.)
| | - Christophe Le Meur
- Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, University Brest, F-29280 Plouzané, France; (L.M.); (V.R.); (B.C.); (N.H.); (E.P.); (C.L.M.); (G.L.F.)
| | - Gaetan Le Foch
- Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, University Brest, F-29280 Plouzané, France; (L.M.); (V.R.); (B.C.); (N.H.); (E.P.); (C.L.M.); (G.L.F.)
| | - Lionel Cladiere
- Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR),CNRS, UMR8227, Sorbonne Université, 29680 Roscoff, France; (L.D.); (L.C.)
| | - Mohamed Mehiri
- Marine Natural Products Team, CNRS, UMR 7272, Institut de Chimie de Nice, Université Côte d’Azur, 06108 Nice, France;
| | - Nathalie Demont-Caulet
- UMR ECOSYS, INRAE, INRAE, University of Paris, 78026 Versailles, France;
- AgroParisTech, Université Paris-Saclay, 78026 Versailles, France
| | - Laurence Meslet-Cladiere
- Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, University Brest, F-29280 Plouzané, France; (L.M.); (V.R.); (B.C.); (N.H.); (E.P.); (C.L.M.); (G.L.F.)
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Marine invasive species for high-value products' exploration – Unveiling the antimicrobial potential of Asparagopsis armata against human pathogens. ALGAL RES 2020. [DOI: 10.1016/j.algal.2020.102091] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Tamminen A, Happonen P, Barth D, Holmström S, Wiebe MG. High throughput, small scale methods to characterise the growth of marine fungi. PLoS One 2020; 15:e0236822. [PMID: 32764772 PMCID: PMC7413501 DOI: 10.1371/journal.pone.0236822] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 07/14/2020] [Indexed: 11/26/2022] Open
Abstract
Various marine fungi have been shown to produce interesting, bioactive compounds, but scaling up the production of these compounds can be challenging, particularly because little is generally known about how the producing organisms grow. Here we assessed the suitability of using 100-well BioScreen plates or 96-well plates incubated in a robot hotel to cultivate eight filamentous marine fungi, six sporulating and two non-sporulating, to obtain data on growth and substrate (glucose, xylose, galactose or glycerol) utilisation in a high throughput manner. All eight fungi grew in both cultivation systems, but growth was more variable and with more noise in the data in the Cytomat plate hotel than in the BioScreen. Specific growth rates between 0.01 (no added substrate) and 0.07 h-1 were measured for strains growing in the BioScreen and between 0.01 and 0.27 h-1 for strains in the plate hotel. Three strains, Dendryphiella salina LF304, Penicillium chrysogenum KF657 and Penicillium pinophilum LF458, consistently had higher specific growth rates on glucose and xylose in the plate hotel than in the BioScreen, but otherwise results were similar in the two systems. However, because of the noise in data from the plate hotel, the data obtained from it could only be used to distinguish between substrates which did or did not support growth, whereas data from BioScreen also provided information on substrate preference. Glucose was the preferred substrate for all strains, followed by xylose and galactose. Five strains also grew on glycerol. Therefore it was important to minimise the amount of glycerol introduced with the inoculum to avoid misinterpreting the results for growth on poor substrates. We concluded that both systems could provide physiological data with filamentous fungi, provided sufficient replicates are included in the measurements.
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Affiliation(s)
- Anu Tamminen
- VTT Technical Research Centre of Finland Ltd, Espoo, Finland
| | - Petrus Happonen
- VTT Technical Research Centre of Finland Ltd, Espoo, Finland
| | - Dorothee Barth
- VTT Technical Research Centre of Finland Ltd, Espoo, Finland
| | - Sami Holmström
- VTT Technical Research Centre of Finland Ltd, Espoo, Finland
| | - Marilyn G. Wiebe
- VTT Technical Research Centre of Finland Ltd, Espoo, Finland
- * E-mail:
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Vidgren V, Halinen S, Tamminen A, Olenius S, Wiebe MG. Engineering marine fungi for conversion of D-galacturonic acid to mucic acid. Microb Cell Fact 2020; 19:156. [PMID: 32736636 PMCID: PMC7393721 DOI: 10.1186/s12934-020-01411-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 07/20/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Two marine fungi, a Trichoderma sp. and a Coniochaeta sp., which can grow on D-galacturonic acid and pectin, were selected as hosts to engineer for mucic acid production, assessing the suitability of marine fungi for production of platform chemicals. The pathway for biotechnologcial production of mucic (galactaric) acid from D-galacturonic acid is simple and requires minimal modification of the genome, optimally one deletion and one insertion. D-Galacturonic acid, the main component of pectin, is a potential substrate for bioconversion, since pectin-rich waste is abundant. RESULTS Trichoderma sp. LF328 and Coniochaeta sp. MF729 were engineered using CRISPR-Cas9 to oxidize D-galacturonic acid to mucic acid, disrupting the endogenous pathway for D-galacturonic acid catabolism when inserting a gene encoding bacterial uronate dehydrogenase. The uronate dehydrogenase was expressed under control of a synthetic expression system, which fucntioned in both marine strains. The marine Trichoderma transformants produced 25 g L-1 mucic acid from D-galacturonic acid in equimolar amounts: the yield was 1.0 to 1.1 g mucic acid [g D-galacturonic acid utilized]-1. D-Xylose and lactose were the preferred co-substrates. The engineered marine Trichoderma sp. was more productive than the best Trichoderma reesei strain (D-161646) described in the literature to date, that had been engineered to produce mucic acid. With marine Coniochaeta transformants, D-glucose was the preferred co-substrate, but the highest yield was 0.82 g g-1: a portion of D-galacturonic acid was still metabolized. Coniochaeta sp. transformants produced adequate pectinases to produce mucic acid from pectin, but Trichoderma sp. transformants did not. CONCLUSIONS Both marine species were successfully engineered using CRISPR-Cas9 and the synthetic expression system was functional in both species. Although Coniochaeta sp. transformants produced mucic acid directly from pectin, the metabolism of D-galacturonic acid was not completely disrupted and mucic acid amounts were low. The D-galacturonic pathway was completely disrupted in the transformants of the marine Trichoderma sp., which produced more mucic acid than a previously constructed T. reesei mucic acid producing strain, when grown under similar conditions. This demonstrated that marine fungi may be useful as production organisms, not only for native enzymes or bioactive compounds, but also for other compounds.
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Affiliation(s)
- Virve Vidgren
- VTT Technical Research Centre of Finland Ltd, Tietotie 2, P.O. Box 1000, 02044, Espoo, Finland.
| | - Satu Halinen
- VTT Technical Research Centre of Finland Ltd, Tietotie 2, P.O. Box 1000, 02044, Espoo, Finland
| | - Anu Tamminen
- VTT Technical Research Centre of Finland Ltd, Tietotie 2, P.O. Box 1000, 02044, Espoo, Finland
| | - Susanna Olenius
- VTT Technical Research Centre of Finland Ltd, Tietotie 2, P.O. Box 1000, 02044, Espoo, Finland
| | - Marilyn G Wiebe
- VTT Technical Research Centre of Finland Ltd, Tietotie 2, P.O. Box 1000, 02044, Espoo, Finland
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Acacia senegal Extract Rejuvenates the Activity of Phenicols on Selected Enterobacteriaceae Multi Drug Resistant Strains. Antibiotics (Basel) 2020; 9:antibiotics9060323. [PMID: 32545716 PMCID: PMC7344600 DOI: 10.3390/antibiotics9060323] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 06/08/2020] [Accepted: 06/09/2020] [Indexed: 11/24/2022] Open
Abstract
This study reported the phytochemical composition of two hydroethanolic extracts of Acacia senegal and Acacia seyal trees from Burkina Faso and their activities, alone or in combination with selected antibiotics, against multidrug resistant bacteria. High performance thin layer chromatography (HPTLC) method was used for phytochemical screening. Total phenolic and total flavonoid ant tannins in leaves extracts contents were assessed by spectrophotometric method. The minimal inhibitory concentrations (MICs) of plant extracts and antibiotics were determined using the microdilution method and p-iodonitrotetrazolium chloride. Combinations of extracts and antibiotics were studied using checkerboard assays. Screening revealed the presence of phenolic compounds, flavonoids, and tannins in the hydroethanolic extract (HE) of the leaves. The HE of A. seyal showed the highest total phenolic (571.30 ± 6.97 mg GAE/g), total flavonoids (140.41 ± 4.01 mg RTE/g), and tannins (24.72 ± 0.14%, condensed; 35.77 ± 0.19%, hydrolysable tannins). However, the HE of A. senegal showed the lowest total phenolic (69.84 ± 3.54 mg GAE/g), total flavonoids (27.32 ± 0.57 mg RTE/g), and tannins (14.60 ± 0.01%, condensed; 3.09 ± 0.02%, hydrolysable). The MICs for HE and antibiotics were in the range of 2–512 and 0.008–1024 mg/L, respectively. All tested HE presented an MIC greater than 512 mg/L except HE of A. senegal. The lowest MIC value (128 mg/L) was obtained with HE of A. senegal against Klebsiella aerogenes EA298 and Escherichia coli AG100A. Interesting restoring effects on chloramphenicol and florphenicol activity were detected with alcoholic extracts of A. senegal against resistant E. coli and K. aerogenes strains that overproduce AcrAB or FloR pumps. The adjuvant effect of HE of A. senegal suggests that the crude extract of leaves could be a potential source of molecules for improving the susceptibility of bacteria to phenicols antibiotics.
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Marchese P, Garzoli L, Gnavi G, O'Connell E, Bouraoui A, Mehiri M, Murphy JM, Varese GC. Diversity and bioactivity of fungi associated with the marine sea cucumber Holothuria poli: disclosing the strains potential for biomedical applications. J Appl Microbiol 2020; 129:612-625. [PMID: 32274883 DOI: 10.1111/jam.14659] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 03/07/2020] [Accepted: 03/31/2020] [Indexed: 01/01/2023]
Abstract
AIMS Identification of the mycobiota associated to the marine echinoderm Holothuria poli and investigation of cytotoxic and pro-osteogenic potential of isolated strains. METHODS AND RESULTS Fungal strains were isolated from the animal's body-wall, intestine and faeces. The species identification was based on DNA barcoding and morphophysiological observations. Forty-seven species were identified, all are Ascomycota and mainly belonging to Aspergillus and Penicillium genera. Sixteen strains were grown on three media for chemical extraction. Cytotoxic activity was tested on a hepatic cancer cell line (HepG2), the cells viability was evaluated after treatment using a resazurin based assay (AlamarBlue). Pro-osteogenic activity was tested on human Mesenchymal stem cell, differentiation was measured as the alkaline phosphatase production through reaction with p-nitrophenylphosphate or as the cells ability to mineralize calcium using a colorimetric kit (StanBio). Cytotoxic activity was recorded for four fungal species while five of 48 extracts highlighted bioactivity towards human mesenchymal stem cells. CONCLUSIONS The presence of relevant animal-associated mycobiota was observed in H. poli and selected strains showed cytotoxic potential and pro-osteogenic activity. SIGNIFICANCE AND IMPACT OF THE STUDY Our work represents the first report of a Mediterranean Sea cucumber mycobiota and highlights the isolates potential to synthetize compounds of pharmaceutical interest for regenerative medicine.
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Affiliation(s)
- P Marchese
- Regenerative Medicine Institute, School of Medicine, National University of Ireland Galway, Galway, Ireland.,Department of Life Sciences and Systems Biology, Mycotheca Universitatis Taurinensis, University of Turin, Turin, Italy
| | - L Garzoli
- Department of Life Sciences and Systems Biology, Mycotheca Universitatis Taurinensis, University of Turin, Turin, Italy
| | - G Gnavi
- Department of Life Sciences and Systems Biology, Mycotheca Universitatis Taurinensis, University of Turin, Turin, Italy
| | - E O'Connell
- Genomics and Screening Core, National University of Ireland Galway, Galway, Ireland
| | - A Bouraoui
- Laboratoire de dévelopement chimique, galénique et pharmacologique des médicaments, Universite de Monastir, Monastir, Tunisia
| | - M Mehiri
- Marine Natural Products Team, Institute of Chemistry of Nice, University Nice Sophia Antipolis, Nice, France
| | - J M Murphy
- Regenerative Medicine Institute, School of Medicine, National University of Ireland Galway, Galway, Ireland
| | - G C Varese
- Department of Life Sciences and Systems Biology, Mycotheca Universitatis Taurinensis, University of Turin, Turin, Italy
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Du L, Gao B, Liang J, Wang Y, Xiao Y, Zhu D. Microparticle-enhanced Chaetomium globosum DX-THS3 β-d-glucuronidase production by controlled fungal morphology in submerged fermentation. 3 Biotech 2020; 10:100. [PMID: 32099741 PMCID: PMC7005231 DOI: 10.1007/s13205-020-2068-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 01/10/2020] [Indexed: 11/29/2022] Open
Abstract
Glycyrrhetinic acid monoglucuronide (GAMG) is a novel and low-calorie sweetener that is widely applied in the food industry. This study aimed to enhance the production of fungal β-d-glucuronidase (GUS) via a novel fermentation technique by evaluating the effects of the various microparticles on Chaetomium globosum DX-THS3 GUS production. Results showed that the silica microparticle greatly affected the morphology of DX-THS3 strain relative to the other microparticles. Microbial structure imaging results showed that the smallest average diameter of fungal pellets was achieved (0.7 ± 0.1 mm) by adding 10 g/L (600 mesh) of silica. The diameter of the control was 3.0 ± 0.5 mm in shake flask fermentation. The GUS activity and biomass of DX-THS3 reached 680 U/mL and 4.2 g/L, respectively, with the use of 10 g/L of silica microparticles, whereas those of the control were 210 U/mL and 2.8 g/L via shake flask fermentation. The findings in this study may provide a potential strategy for designing the morphology of filamentous fungi using microparticles in the industrial production of GAMG.
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Affiliation(s)
- Liangqing Du
- Key Lab of Bioprocess Engineering of Jiangxi Province, College of life Sciences, Jiangxi Science and Technology Normal University, Nanchang, 330013 China
| | - Boliang Gao
- Key Lab of Bioprocess Engineering of Jiangxi Province, College of life Sciences, Jiangxi Science and Technology Normal University, Nanchang, 330013 China
| | - JinFeng Liang
- Key Lab of Bioprocess Engineering of Jiangxi Province, College of life Sciences, Jiangxi Science and Technology Normal University, Nanchang, 330013 China
| | - Ya Wang
- Key Lab of Bioprocess Engineering of Jiangxi Province, College of life Sciences, Jiangxi Science and Technology Normal University, Nanchang, 330013 China
| | - Yiwen Xiao
- Key Lab of Bioprocess Engineering of Jiangxi Province, College of life Sciences, Jiangxi Science and Technology Normal University, Nanchang, 330013 China
| | - Du Zhu
- Key Lab of Bioprocess Engineering of Jiangxi Province, College of life Sciences, Jiangxi Science and Technology Normal University, Nanchang, 330013 China
- Key Laboratory of Protection and Utilization of Subtropic Plant Resources of Jiangxi Province, Jiangxi Normal University, Nanchang, 330022 China
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Vinale F, Salvatore MM, Nicoletti R, Staropoli A, Manganiello G, Venneri T, Borrelli F, DellaGreca M, Salvatore F, Andolfi A. Identification of the Main Metabolites of a Marine-Derived Strain of Penicillium brevicompactum Using LC and GC MS Techniques. Metabolites 2020; 10:metabo10020055. [PMID: 32019164 PMCID: PMC7074196 DOI: 10.3390/metabo10020055] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 01/21/2020] [Accepted: 01/27/2020] [Indexed: 11/16/2022] Open
Abstract
Marine-derived fungi are an important source of many valuable compounds with original structures and diverse physico-chemical properties. In this work, the metabolomic profile of a strain of Penicillium brevicompactum, recovered from a snakelocks sea anemone (Anemonia sulcata), was investigated through the parallel application of LC-ESI-HRMS, GC-MS, and NMR. Our strategy allowed the identification of mycophenolic acid, brevianamide A, and several compounds belonging to the thiosilvatins. Among the latter, five products are reported for the first time in this species. The main product of this series, cis-bis(methylthio)silvatin, was also tested for antiproliferative activity on both cancer and non-tumoral colon cell lines.
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Affiliation(s)
- Francesco Vinale
- Department of Veterinary Medicine and Animal Productions, University of Naples Federico II, 80137 Naples, Italy;
- Institute for Sustainable Plant Protection, National Research Council, 80055 Portici (NA), Italy;
| | - Maria Michela Salvatore
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy; (M.M.S.); (M.D.); (F.S.)
| | - Rosario Nicoletti
- Council for Agricultural Research and Economics, Research Centre for Olive, Citrus and Tree Fruit, 81100 Caserta, Italy;
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici (NA), Italy;
| | - Alessia Staropoli
- Institute for Sustainable Plant Protection, National Research Council, 80055 Portici (NA), Italy;
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici (NA), Italy;
| | - Gelsomina Manganiello
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici (NA), Italy;
| | - Tommaso Venneri
- Department of Pharmacy, School of Medicine and Surgery, University of Naples Federico II, 80131 Naples, Italy; (T.V.); (F.B.)
| | - Francesca Borrelli
- Department of Pharmacy, School of Medicine and Surgery, University of Naples Federico II, 80131 Naples, Italy; (T.V.); (F.B.)
| | - Marina DellaGreca
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy; (M.M.S.); (M.D.); (F.S.)
| | - Francesco Salvatore
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy; (M.M.S.); (M.D.); (F.S.)
| | - Anna Andolfi
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy; (M.M.S.); (M.D.); (F.S.)
- Correspondence: ; Tel.: +39-081-2539179
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Venkateskumar K, Parasuraman S, Chuen LY, Ravichandran V, Balamurgan S. Exploring Antimicrobials from the Flora and Fauna of Marine: Opportunities and Limitations. Curr Drug Discov Technol 2020; 17:507-514. [PMID: 31424372 DOI: 10.2174/1570163816666190819141344] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 04/24/2019] [Accepted: 07/11/2019] [Indexed: 06/10/2023]
Abstract
About 95% of earth living space lies deep below the ocean's surface and it harbors extraordinary diversity of marine organisms. Marine biodiversity is an exceptional reservoir of natural products, bioactive compounds, nutraceuticals and other potential compounds of commercial value. Timeline for the development of the drug from a plant, synthetic and other alternative sources is too lengthy. Exploration of the marine environment for potential bioactive compounds has gained focus and huge opportunity lies ahead for the exploration of such vast resources in the ocean. Further, the evolution of superbugs with increasing resistance to the currently available drugs is alarming and it needs coordinated efforts to resolve them. World Health Organization recommends the need and necessity to develop effective bioactive compounds to combat problems associated with antimicrobial resistance. Based on these factors, it is imperative to shift the focus towards the marine environment for potential bioactive compounds that could be utilized to tackle antimicrobial resistance. Current research trends also indicate the huge strides in research involving marine environment for drug discovery. The objective of this review article is to provide an overview of marine resources, recently reported research from marine resources, challenges, future research prospects in the marine environment.
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Affiliation(s)
| | - Subramani Parasuraman
- Faculty of Pharmacy, AIMST University, Jalan Bedong-Semeling, 08100 Bedong, Kedah, Malaysia
| | - Leow Y Chuen
- Faculty of Pharmacy, AIMST University, Jalan Bedong-Semeling, 08100 Bedong, Kedah, Malaysia
| | - Veerasamy Ravichandran
- Faculty of Pharmacy, AIMST University, Jalan Bedong-Semeling, 08100 Bedong, Kedah, Malaysia
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Carney RL, Labbate M, Siboni N, Tagg KA, Mitrovic SM, Seymour JR. Urban beaches are environmental hotspots for antibiotic resistance following rainfall. WATER RESEARCH 2019; 167:115081. [PMID: 31574348 DOI: 10.1016/j.watres.2019.115081] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 09/09/2019] [Accepted: 09/10/2019] [Indexed: 06/10/2023]
Abstract
To reveal the occurrence and mechanisms for dispersal of antibiotic resistance (AbR) among the microbial assemblages inhabiting impacted coastal environments, we performed a weekly, two-year duration time-series study at two urban beaches between 2014 and 2016. We combined quantitative PCR and multiplex PCR/reverse line blot techniques to track patterns in the occurrence of 31 AbR genes, including genes that confer resistance to antibiotics that are critically important antimicrobials for human medicine. Patterns in the abundance of these genes were linked to specific microbial groups and environmental parameters by coupling qPCR and 16S rRNA amplicon sequencing data with network analysis. Up to 100-fold increases in the abundance of several AbR genes, including genes conferring resistance to quinolones, trimethoprim, sulfonamides, tetracycline, vancomycin and carbapenems, occurred following storm-water and modelled wet-weather sewer overflow events. The abundance of AbR genes strongly and significantly correlated with several potentially pathogenic bacterial OTUs regularly associated with wastewater infrastructure, such as Arcobacter, Acinetobacter, Aeromonas and Cloacibacterium. These high-resolution observations provide clear links between storm-water discharge and sewer overflow events and the occurrence of AbR in the coastal microbial assemblages inhabiting urban beaches, highlighting a direct mechanism for potentially significant AbR exposure risks to humans.
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Affiliation(s)
- Richard L Carney
- Climate Change Cluster, University of Technology Sydney, Australia
| | - Maurizio Labbate
- School of Life Sciences, University of Technology Sydney, Australia
| | - Nachshon Siboni
- Climate Change Cluster, University of Technology Sydney, Australia
| | - Kaitlin A Tagg
- Westmead Institute for Medical Research, University of Sydney, NSW, Australia; IHRC, Inc., Atlanta, GA, USA
| | - Simon M Mitrovic
- School of Life Sciences, University of Technology Sydney, Australia
| | - Justin R Seymour
- Climate Change Cluster, University of Technology Sydney, Australia.
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Teixeira TR, Santos GSD, Armstrong L, Colepicolo P, Debonsi HM. Antitumor Potential of Seaweed Derived-Endophytic Fungi. Antibiotics (Basel) 2019; 8:E205. [PMID: 31683523 PMCID: PMC6963884 DOI: 10.3390/antibiotics8040205] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 10/16/2019] [Accepted: 10/17/2019] [Indexed: 12/30/2022] Open
Abstract
The marine environment presents a high biodiversity and a valuable source of bioactive compounds with therapeutic and biotechnological potential. Among the organisms present in marine environment, the endophytic fungi isolated from seaweed stand out. These microorganisms have aroused interest in the scientific community regarding its various activities such as antiviral, antimicrobial, antioxidant, photoprotective, cytotoxic, genotoxic, anti-inflammatory, and anticancer, besides establishing important ecological relations with its hosts. Anticancer molecules derived from marine natural sources are a promising target against different types of cancer. The disease's high rates of morbidity and mortality affect millions of people world wild and the search for new therapeutic alternatives is needed. Thus, this review partially summarizes the methodologies for the isolation of seaweed-derived endophytic fungi, as well as describes the anticancer compounds isolated from such microorganisms, reported in the literature from 2009 to the present. In addition, it describes how some biotechnological processes can help in the discovery of bioactive compounds, especially with anticancer activity.
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Affiliation(s)
- Thaiz Rodrigues Teixeira
- Department of Physics and Chemistry, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, RibeirãoPreto, SP 14040903, Brazil.
| | - Gustavo Souza Dos Santos
- Department of Physics and Chemistry, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, RibeirãoPreto, SP 14040903, Brazil.
| | - Lorene Armstrong
- Department of Pharmaceutical Sciences, State University of Ponta Grossa, Ponta Grossa, PR 84030900, Brazil.
| | - Pio Colepicolo
- Department of Biochemistry, Chemistry Institute, University of São Paulo, São Paulo, SP 05508-000, Brazil.
| | - Hosana Maria Debonsi
- Department of Physics and Chemistry, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, RibeirãoPreto, SP 14040903, Brazil.
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Marine Fungi: Biotechnological Perspectives from Deep-Hypersaline Anoxic Basins. DIVERSITY 2019. [DOI: 10.3390/d11070113] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Deep-sea hypersaline anoxic basins (DHABs) are one of the most hostile environments on Earth. Even though DHABs have hypersaline conditions, anoxia and high hydrostatic pressure, they host incredible microbial biodiversity. Among eukaryotes inhabiting these systems, recent studies demonstrated that fungi are a quantitatively relevant component. Here, fungi can benefit from the accumulation of large amounts of organic material. Marine fungi are also known to produce bioactive molecules. In particular, halophilic and halotolerant fungi are a reservoir of enzymes and secondary metabolites with valuable applications in industrial, pharmaceutical, and environmental biotechnology. Here we report that among the fungal taxa identified from the Mediterranean and Red Sea DHABs, halotolerant halophilic species belonging to the genera Aspergillus and Penicillium can be used or screened for enzymes and bioactive molecules. Fungi living in DHABs can extend our knowledge about the limits of life, and the discovery of new species and molecules from these environments can have high biotechnological potential.
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Yousuf M, Jamil W, Mammadova K. Microbial Bioconversion: A Regio-specific Method for Novel Drug Design and Toxicological Study of Metabolites. Curr Pharm Biotechnol 2019; 20:1156-1162. [PMID: 31258075 DOI: 10.2174/1389201020666190618115821] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 04/12/2019] [Accepted: 05/20/2019] [Indexed: 11/22/2022]
Abstract
The methods of chemical structural alteration of small organic molecules by using microbes (fungi, bacteria, yeast, etc.) are gaining tremendous attention to obtain structurally novel and therapeutically potential leads. The regiospecific mild environmental friendly reaction conditions with the ability of novel chemical structural modification in compounds categorize this technique; a distinguished and unique way to obtain medicinally important drugs and their in vivo mimic metabolites with costeffective and timely manner. This review article shortly addresses the immense pharmaceutical importance of microbial transformation methods in drug designing and development as well as the role of CYP450 enzymes in fungi to obtain in vivo drug metabolites for toxicological studies.
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Affiliation(s)
- Maria Yousuf
- Dow College of Biotechnology, Department of Bioinformatics, Dow University of Health Sciences, Karachi, Pakistan
| | - Waqas Jamil
- Institute of Advanced Research Studies and Chemical Sciences, University of Sindh, Jamshoro, Pakistan
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Farha AK, Hatha AM. Bioprospecting potential and secondary metabolite profile of a novel sediment-derived fungus Penicillium sp. ArCSPf from continental slope of Eastern Arabian Sea. Mycology 2019; 10:109-117. [PMID: 31069124 PMCID: PMC6493292 DOI: 10.1080/21501203.2019.1572034] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 01/14/2019] [Indexed: 11/12/2022] Open
Abstract
Marine fungi, one of the major decomposers of marine environment, is found to produce potential enzymes and novel biomolecules. The present study explored bioprospecting potentials such as antimicrobial, anticancer and enzymatic activities of marine sediment-derived fungi isolated from continental slope of Eastern Arabian Sea. Morphology and ITS sequencing identified the fungus as Penicillium sp. ArCSPf. The fungal strain exhibited amylase, gelatinase, phytase, lipase and pectinase activity. The active fraction obtained from the ethyl acetate extract column fractionation (F2) of fungus showed antibacterial activity against both methicillin-resistant Staphylococcus aureus (MRSA) and Bacillus cereus. Minimum inhibitory concentrations of F2 were 125 μg/mL for MRSA and 62.5 μg/mL for B. cereus. The active fraction showed a significant anticancer activity (IC50 = 22.79 µg/mL) against MCF-7 breast cancer cells. The secondary metabolite (Z)-Octadec-9-enamide (oleamide, m/z 282.27 (M + H+)] was identified in the LC-MS/MS analysis of active fraction F2 in positive ionisation mode. To the best of our knowledge, this is the first report on exploring the bioprospecting potential of a sediment-derived fungus from continental slope of eastern Arabian Sea for the production of therapeutically active compounds.
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Affiliation(s)
- Arakkaveettil Kabeer Farha
- Department of Marine Biology Microbiology and Biochemistry, School of Marine Sciences, Cochin University of Science and Technology (CUSAT), Kochi, India
| | - Abdulla Mohamed Hatha
- Department of Marine Biology Microbiology and Biochemistry, School of Marine Sciences, Cochin University of Science and Technology (CUSAT), Kochi, India
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Raimundo I, Silva SG, Costa R, Keller-Costa T. Bioactive Secondary Metabolites from Octocoral-Associated Microbes-New Chances for Blue Growth. Mar Drugs 2018; 16:E485. [PMID: 30518125 PMCID: PMC6316421 DOI: 10.3390/md16120485] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Revised: 11/25/2018] [Accepted: 11/29/2018] [Indexed: 12/14/2022] Open
Abstract
Octocorals (Cnidaria, Anthozoa Octocorallia) are magnificent repositories of natural products with fascinating and unusual chemical structures and bioactivities of interest to medicine and biotechnology. However, mechanistic understanding of the contribution of microbial symbionts to the chemical diversity of octocorals is yet to be achieved. This review inventories the natural products so-far described for octocoral-derived bacteria and fungi, uncovering a true chemical arsenal of terpenes, steroids, alkaloids, and polyketides with antibacterial, antifungal, antiviral, antifouling, anticancer, anti-inflammatory, and antimalarial activities of enormous potential for blue growth. Genome mining of 15 bacterial associates (spanning 12 genera) cultivated from Eunicella spp. resulted in the identification of 440 putative and classifiable secondary metabolite biosynthetic gene clusters (BGCs), encompassing varied terpene-, polyketide-, bacteriocin-, and nonribosomal peptide-synthase BGCs. This points towards a widespread yet uncharted capacity of octocoral-associated bacteria to synthetize a broad range of natural products. However, to extend our knowledge and foster the near-future laboratory production of bioactive compounds from (cultivatable and currently uncultivatable) octocoral symbionts, optimal blending between targeted metagenomics, DNA recombinant technologies, improved symbiont cultivation, functional genomics, and analytical chemistry are required. Such a multidisciplinary undertaking is key to achieving a sustainable response to the urgent industrial demand for novel drugs and enzyme varieties.
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Affiliation(s)
- Inês Raimundo
- Institute for Bioengineering and Biosciences (iBB), Instituto Superior Técnico (IST), Universidade de Lisboa, 1049-001 Lisbon, Portugal.
| | - Sandra G Silva
- Institute for Bioengineering and Biosciences (iBB), Instituto Superior Técnico (IST), Universidade de Lisboa, 1049-001 Lisbon, Portugal.
| | - Rodrigo Costa
- Institute for Bioengineering and Biosciences (iBB), Instituto Superior Técnico (IST), Universidade de Lisboa, 1049-001 Lisbon, Portugal.
| | - Tina Keller-Costa
- Institute for Bioengineering and Biosciences (iBB), Instituto Superior Técnico (IST), Universidade de Lisboa, 1049-001 Lisbon, Portugal.
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Huang RH, Gou JY, Zhao DL, Wang D, Liu J, Ma GY, Li YQ, Zhang CS. Phytotoxicity and anti-phytopathogenic activities of marine-derived fungi and their secondary metabolites. RSC Adv 2018; 8:37573-37580. [PMID: 35558593 PMCID: PMC9089327 DOI: 10.1039/c8ra08047j] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 10/26/2018] [Indexed: 01/06/2023] Open
Abstract
To find new pesticides for agricultural use, 133 fungal strains were isolated from coastal marine habitats, from which 37 independent isolates were identified, belonging to 20 genera in nine orders, and the diversity of the isolated fungi were discussed. The phytotoxicity and anti-phytopathogenic fungal and bacterial activities of these 37 extracts, and two previously isolated fungal extracts were evaluated, displaying different levels of bioactivity. Based on the bioactive and chemical screening, an Alternaria sp. (P8) strain, which showed prominent bioactivity and contained abundant secondary metabolites was selected for further chemical investigation; one new compound, a benzopyranone (1), and seven known compounds (2-8) were obtained. Their structures were determined by analysing extensive NMR spectroscopic data and ECD comparisons. Compounds 1, 2, and 6-8 showed obvious phytotoxicity, especially against amaranth, and compound 1 also showed potent antifungal activity toward Alternaria brassicicola. To the best of our knowledge, this is the first report of the phytotoxicity of marine-derived fungi and their secondary metabolites. These studies should provide the foundation for future research into the use of such fungal extracts to combat weeds and diseases in agriculture.
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Affiliation(s)
- Rui-Huan Huang
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences Qingdao 266101 China +86-532-8870-2115
| | - Jian-Yu Gou
- Zunyi Branch, Guizhou Tobacco Company Zunyi 563000 China
| | - Dong-Lin Zhao
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences Qingdao 266101 China +86-532-8870-2115
| | - Dan Wang
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences Qingdao 266101 China +86-532-8870-2115
| | - Jing Liu
- Zunyi Branch, Guizhou Tobacco Company Zunyi 563000 China
| | - Guo-Yong Ma
- Zunyi Branch, Guizhou Tobacco Company Zunyi 563000 China
| | - Yi-Qiang Li
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences Qingdao 266101 China +86-532-8870-2115
| | - Cheng-Sheng Zhang
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences Qingdao 266101 China +86-532-8870-2115
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Akita H, Hayashi J, Sakuraba H, Ohshima T. Artificial Thermostable D-Amino Acid Dehydrogenase: Creation and Application. Front Microbiol 2018; 9:1760. [PMID: 30123202 PMCID: PMC6085447 DOI: 10.3389/fmicb.2018.01760] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 07/13/2018] [Indexed: 01/06/2023] Open
Abstract
Many kinds of NAD(P)+-dependent L-amino acid dehydrogenases have been so far found and effectively used for synthesis of L-amino acids and their analogs, and for their sensing. By contrast, similar biotechnological use of D-amino acid dehydrogenase (D-AADH) has not been achieved because useful D-AADH has not been found from natural resources. Recently, using protein engineering methods, an NADP+-dependent D-AADH was created from meso-diaminopimelate dehydrogenase (meso-DAPDH). The artificially created D-AADH catalyzed the reversible NADP+-dependent oxidative deamination of D-amino acids to 2-oxo acids. The enzyme, especially thermostable one from thermophiles, was efficiently applicable to synthesis of D-branched-chain amino acids (D-BCAAs), with high yields and optical purity, and was useful for the practical synthesis of 13C- and/or 15N-labeled D-BCAAs. The enzyme also made it possible to assay D-isoleucine selectively in a mixture of isoleucine isomers. Analyses of the three-dimensional structures of meso-DAPDH and D-AADH, and designed mutations based on the information obtained made it possible to markedly enhance enzyme activity and to create D-AADH homologs with desired reactivity profiles. The methods described here may be an effective approach to artificial creation of biotechnologically useful enzymes.
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Affiliation(s)
- Hironaga Akita
- Research Institute for Sustainable Chemistry, National Institute of Advanced Industrial Science and Technology (AIST), Hiroshima, Japan
| | - Junji Hayashi
- Department of Biotechnology, College of Life Sciences, Ritsumeikan University Biwako-Kusatsu Campus, Shiga, Japan
| | - Haruhiko Sakuraba
- Department of Applied Biological Science, Faculty of Agriculture, Kagawa University, Kagawa, Japan
| | - Toshihisa Ohshima
- Department of Biomedical Engineering, Faculty of Engineering, Osaka Institute of Technology, Osaka, Japan
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Ali SM, Siddiqui R, Khan NA. Antimicrobial discovery from natural and unusual sources. ACTA ACUST UNITED AC 2018; 70:1287-1300. [PMID: 30003546 DOI: 10.1111/jphp.12976] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 06/15/2018] [Indexed: 01/30/2023]
Abstract
OBJECTIVES Whether vertebrates/invertebrates living in polluted environments are an additional source of antimicrobials. KEY FINDINGS Majority of antimicrobials have been discovered from prokaryotes and those which are of eukaryotic origin are derived mainly from fungal and plant sources. With this in mind, it is important to note that pests, such as cockroaches come across pathogenic bacteria routinely, yet thrive in polluted environments. Other animals, such as snakes thrive from feeding on germ-infested rodents. Logically, such species must have developed an approach to protect themselves from these pathogens, yet they have largely been ignored as a potential source of antimicrobials despite their remarkable capability to fight disease-causing organisms. SUMMARY Animals living in polluted environments are an underutilized source for potential antimicrobials, hence it is believed that several novel bioactive molecule(s) will be identified from these sources to counter increasingly resistant bacterial infections. Further research will be necessary in the development of novel antimicrobial(s) from these unusual sources which will have huge clinical impact worldwide.
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Affiliation(s)
- Salwa Mansur Ali
- Department of Biological Sciences, School of Science and Technology, Sunway University, Subang Jaya, Selangor, Malaysia
| | - Ruqaiyyah Siddiqui
- Department of Biological Sciences, School of Science and Technology, Sunway University, Subang Jaya, Selangor, Malaysia
| | - Naveed Ahmed Khan
- Department of Biological Sciences, School of Science and Technology, Sunway University, Subang Jaya, Selangor, Malaysia
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Adnan M, Alshammari E, Patel M, Amir Ashraf S, Khan S, Hadi S. Significance and potential of marine microbial natural bioactive compounds against biofilms/biofouling: necessity for green chemistry. PeerJ 2018; 6:e5049. [PMID: 29967730 PMCID: PMC6026461 DOI: 10.7717/peerj.5049] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 06/01/2018] [Indexed: 12/17/2022] Open
Abstract
Natural products from the unique environments of sea water and oceans represent a largely unfamiliar source for isolation of new microbes, which are potent producers of secondary bioactive metabolites. These unique life-forms from the marine ecosphere have served as an important source of drugs since ancient times and still offer a valuable resource for novel findings by providing remedial treatments. Therefore, it can be expected that many naturally bioactive marine microbial compounds with novel structures and bioactivities against those from terrestrial environments may be found among marine metabolites. Biofilms in aquatic environment possess serious problems to naval forces and oceanic industries around the globe. Current anti-biofilm or anti-biofouling technology is based on the use of toxic substances that can be harmful to their surrounding natural locales. Comprehensive research has been done to examine the bioactive potential of marine microbes. Results are remarkably varied and dynamic, but there is an urgent need for bioactive compounds with environmentally friendly or "green" chemical activities. Marine microbes have the potential as upcoming and promising source of non-toxic compounds with sustainable anti-biofouling/anti-biofilm properties as they can produce substances that can inhibit not only the chemical components required for biofilm production but also the attachment, microorganism growth, and/or cell-cell communication.
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Affiliation(s)
- Mohd Adnan
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hail, Hail, Saudi Arabia
| | - Eyad Alshammari
- Department of Clinical Nutrition, College of Applied Medical Sciences, University of Hail, Hail, Saudi Arabia
| | - Mitesh Patel
- Department of Biosciences, Bapalal Vaidhya Botanical Research Centre, Veer Narmad South Gujarat University, Surat, India
| | - Syed Amir Ashraf
- Department of Clinical Nutrition, College of Applied Medical Sciences, University of Hail, Hail, Saudi Arabia
| | - Saif Khan
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hail, Hail, Saudi Arabia
| | - Sibte Hadi
- School of Forensic and Applied Sciences, University of Central Lancashire, Preston, UK
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Fernández-Cabezón L, Galán B, García JL. New Insights on Steroid Biotechnology. Front Microbiol 2018; 9:958. [PMID: 29867863 PMCID: PMC5962712 DOI: 10.3389/fmicb.2018.00958] [Citation(s) in RCA: 105] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2017] [Accepted: 04/24/2018] [Indexed: 01/10/2023] Open
Abstract
Nowadays steroid manufacturing occupies a prominent place in the pharmaceutical industry with an annual global market over $10 billion. The synthesis of steroidal active pharmaceutical ingredients (APIs) such as sex hormones (estrogens, androgens, and progestogens) and corticosteroids is currently performed by a combination of microbiological and chemical processes. Several mycobacterial strains capable of naturally metabolizing sterols (e.g., cholesterol, phytosterols) are used as biocatalysts to transform phytosterols into steroidal intermediates (synthons), which are subsequently used as key precursors to produce steroidal APIs in chemical processes. These synthons can also be modified by other microbial strains capable of introducing regio- and/or stereospecific modifications (functionalization) into steroidal molecules. Most of the industrial microbial strains currently available have been improved through traditional technologies based on physicochemical mutagenesis and selection processes. Surprisingly, Synthetic Biology and Systems Biology approaches have hardly been applied for this purpose. This review attempts to highlight the most relevant research on Steroid Biotechnology carried out in last decades, focusing specially on those works based on recombinant DNA technologies, as well as outlining trends and future perspectives. In addition, the need to construct new microbial cell factories (MCF) to design more robust and bio-sustainable bioprocesses with the ultimate aim of producing steroids à la carte is discussed.
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Affiliation(s)
- Lorena Fernández-Cabezón
- Department of Environmental Biology, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid, Spain.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Beatriz Galán
- Department of Environmental Biology, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - José L García
- Department of Environmental Biology, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
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Morshed MT, Vuong D, Crombie A, Lacey AE, Karuso P, Lacey E, Piggott AM. Expanding antibiotic chemical space around the nidulin pharmacophore. Org Biomol Chem 2018; 16:3038-3051. [DOI: 10.1039/c8ob00545a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Reinvestigating antibiotic scaffolds that were identified during the Golden Age of antibiotic discovery, but have long since been “forgotten”, has proven to be an effective strategy for delivering next-generation antibiotics capable of combatting multidrug-resistant superbugs.
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Affiliation(s)
| | - Daniel Vuong
- Microbial Screening Technologies Pty. Ltd
- Australia
| | | | | | - Peter Karuso
- Department of Molecular Sciences
- Macquarie University
- Australia
| | - Ernest Lacey
- Department of Molecular Sciences
- Macquarie University
- Australia
- Microbial Screening Technologies Pty. Ltd
- Australia
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Wu X, Chen Z, Ding W, Liu Y, Ma Z. Chemical constituents of the fermentative extracts of marine fungi Phoma sp. CZD-F11 and Aspergillus sp. CZD-F18 from Zhoushan Archipelago, China. Nat Prod Res 2017; 32:1562-1566. [DOI: 10.1080/14786419.2017.1389929] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Xiaomei Wu
- Institute of Marine Biology, Ocean College, Zhejiang University, Zhoushan, China
| | - Zhe Chen
- Zhejiang Key Laboratory of Gastrointestinal Pathophysiology, Chinese Traditional Medicine Hospital of Zhejiang Province, Hangzhou, China
| | - Wanjing Ding
- Institute of Marine Biology, Ocean College, Zhejiang University, Zhoushan, China
| | - Yu Liu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Zhongjun Ma
- Institute of Marine Biology, Ocean College, Zhejiang University, Zhoushan, China
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47
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Tasdemir D. Marine fungi in the spotlight: opportunities and challenges for marine fungal natural product discovery and biotechnology. Fungal Biol Biotechnol 2017. [PMCID: PMC5611562 DOI: 10.1186/s40694-017-0034-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The marine fungal natural products (MaFNaP) Consortium, a scientific network founded in 2014, aims to fuel systematic research on marine fungi and their secondary metabolites. The 2nd international conference of marine fungal natural products (MaFNaP_2017) that was held in Kiel (Germany) and hosted by GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech) in June 2017 brought together scientists working all relevant aspects of marine fungi. This conference report highlights the topics discussed in the conference and suggestions for future work on marine fungal compounds. One of the major aims is to attract scientists working on terrestrial fungi in tackling the common bottlenecks and to move marine fungal biodiscovery and biotechnology research forward.
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Auckloo BN, Pan C, Akhter N, Wu B, Wu X, He S. Stress-Driven Discovery of Novel Cryptic Antibiotics from a Marine Fungus Penicillium sp. BB1122. Front Microbiol 2017; 8:1450. [PMID: 28824581 PMCID: PMC5540946 DOI: 10.3389/fmicb.2017.01450] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 07/17/2017] [Indexed: 11/13/2022] Open
Abstract
Standard laboratory cultures have long been known to hinder activation of specific gene clusters which in turn hamper production of secondary metabolites with unique properties due to lack of innovation or the inability to trigger cryptic gene clusters’ expression. Due to challenges related to the avoidance of the isolation of replicated metabolites, resistance-developing pathogens are to be addressed by the scientific community worldwide in order to progress with novel and potent compounds which could further be developed in the future for pharmaceutical usage. This study reports the isolation of novel cryptic antibiotics from a marine fungus Penicillium sp. BB1122 collected from Zhoushan coast by applying the “metal-stress” strategy, here referring to the heavy metal cobalt (6 mM). High-performance liquid chromatography-guided isolation of four novel and four known compounds belonging to the polyketide class has been carried out where their relative as well as absolute configurations have been determined using spectroscopic analysis techniques as well as by the comparison of theoretically calculated ECD spectrum and the experimental ECD spectrum, respectively. The structures of novel compounds 7 and 8 represent the first example of 2,5-dioxabicyclo[2.2.1]heptane pyrone backbone bearing a migrated polyene chain. The novel compounds 7, 8, and 5 exhibited impressive antibiotic properties against methicillin resistant Staphylococcus aureus (MRSA) with MIC value of around 0.5 and 1 μg/mL, respectively. Moreover, the new compounds 1, 7, and 8 displayed potent antibiotic activities with MIC values of around 4 μg/mL against the pathogenic Pseudomonas aeruginosa. Moreover, the MBC of the different potent compounds ranged from 1 to 128 μg/mL against MRSA, P. aeruginosa, and Klebsiella pneumoniae. In addition, the cytotoxic activities were also evaluated where new antibiotics 7 and 8 were not obviously harmful toward normal liver cell lines LO2, showing IC50 values above 100 μg/mL. As a consequence, the results from this study unveiled that cobalt stress is an effective strategy to discover novel antibiotics from microorganisms.
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Affiliation(s)
| | | | | | - Bin Wu
- Ocean College, Zhejiang UniversityHangzhou, China
| | - Xiaodan Wu
- Center of Analysis and Measurement, Zhejiang UniversityHangzhou, China
| | - Shan He
- Laboratory of Marine Natural Products, School of Marine Sciences, Ningbo UniversityNingbo, China
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