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Liang X, Yang JF, Huang ZH, Ma X, Yan Y, Qi SH. New Antibacterial Peptaibiotics against Plant and Fish Pathogens from the Deep-Sea-Derived Fungus Simplicillium obclavatum EIODSF 020. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:6402-6413. [PMID: 38491989 DOI: 10.1021/acs.jafc.4c00493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/18/2024]
Abstract
Bacterial diseases could severely harm agricultural production. To develop new antibacterial agents, the secondary metabolites of a deep-sea-derived fungus Simplicillium obclavatum EIODSF 020 with antibacterial activities against plant and fish pathogens were investigated by a bioassay-guided approach, which led to the isolation of 11 new peptaibiotics, simplicpeptaibs A-K (1-11). They contain 16-19 residues, including β-alanine, tyrosine, or tyrosine O-sulfate, that were rarely present in peptaibiotics. Their structures were elucidated by spectroscopic analyses (NMR, HRMS, HRMS2, and ECD) and Marfey's method. The primary and secondary structures of novel sulfated peptaibiotic 9 were reconfirmed by single-crystal X-ray diffraction analysis. Genome sequencing of S. obclavatum EIODSF 020 allowed the detection of a gene cluster encoding two individual NRPSs (totally containing 19 modules) that was closely related to simplicpeptaib biosynthesis. Antibacterial investigations of 1-11 together with the previously isolated linear and cyclic peptides from this strain suggested the antibacterial property of this fungus was attributed to the peptaibiotics and cyclic lipopeptides. Among them, compounds 4, 6, 7, and 9 showed significant activity against the tobacco pathogen Ralstonia solanacearum or tilapia pathogens Streptococcus iniae and Streptococcus agalactiae. The antibacterial activity of 6 against R. solanacearum could be enhanced by the addition of 1% NaCl. The structure-bioactivity relationship of simplicpeptaibs was discussed.
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Affiliation(s)
- Xiao Liang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Jia-Fan Yang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhong-Hui Huang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Xuan Ma
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Yan Yan
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Shu-Hua Qi
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
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Pereira-Dias L, Oliveira-Pinto PR, Fernandes JO, Regalado L, Mendes R, Teixeira C, Mariz-Ponte N, Gomes P, Santos C. Peptaibiotics: Harnessing the potential of microbial secondary metabolites for mitigation of plant pathogens. Biotechnol Adv 2023; 68:108223. [PMID: 37536466 DOI: 10.1016/j.biotechadv.2023.108223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 07/28/2023] [Accepted: 07/31/2023] [Indexed: 08/05/2023]
Abstract
Agricultural systems are in need of low-cost, safe antibiotics to protect crops from pests and diseases. Peptaibiotics, a family of linear, membrane-active, amphipathic polypeptides, have been shown to exhibit antibacterial, antifungal, and antiviral activity, and to be inducers of plant resistance against a wide range of phytopathogens. Peptaibiotics belong to the new generation of alternatives to agrochemicals, aligned with the United Nations Sustainable Development Goals and the One Health approach toward ensuring global food security and safety. Despite that, these fungi-derived, non-ribosomal peptides remain surprisingly understudied, especially in agriculture, where only a small number has been tested against a reduced number of phytopathogens. This lack of adoption stems from peptaibiotics' poor water solubility and the difficulty to synthesize and purify them in vitro, which compromises their delivery and inclusion in formulations. In this review, we offer a comprehensive analysis of peptaibiotics' classification, biosynthesis, relevance to plant protection, and mode of action against phytopathogens, along with the techniques enabling researchers to extract, purify, and elucidate their structure, and the databases holding such valuable data. It is also discussed how chemical synthesis and ionic liquids could increase their solubility, how genetic engineering and epigenetics could boost in vitro production, and how omics can reduce screenings' workload through in silico selection of the best candidates. These strategies could turn peptaibiotics into effective, ultra-specific, biodegradable tools for phytopathogen control.
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Affiliation(s)
- Leandro Pereira-Dias
- iB(2) Laboratory, Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal; LAQV-REQUIMTE, Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal; Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, 46022, Valencia, Spain.
| | - Paulo R Oliveira-Pinto
- iB(2) Laboratory, Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal; LAQV-REQUIMTE, Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Juliana O Fernandes
- iB(2) Laboratory, Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal; LAQV-REQUIMTE, Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Laura Regalado
- iB(2) Laboratory, Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal; LAQV-REQUIMTE, Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Rafael Mendes
- iB(2) Laboratory, Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal; LAQV-REQUIMTE, Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Cátia Teixeira
- LAQV-REQUIMTE, Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal; Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal
| | - Nuno Mariz-Ponte
- iB(2) Laboratory, Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal; LAQV-REQUIMTE, Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Paula Gomes
- LAQV-REQUIMTE, Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal; Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal
| | - Conceição Santos
- iB(2) Laboratory, Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal; LAQV-REQUIMTE, Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
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Balázs D, Marik T, Szekeres A, Vágvölgyi C, Kredics L, Tyagi C. Structure-activity correlations for peptaibols obtained from clade Longibrachiatum of Trichoderma: A combined experimental and computational approach. Comput Struct Biotechnol J 2023; 21:1860-1873. [PMID: 36915379 PMCID: PMC10006723 DOI: 10.1016/j.csbj.2023.02.046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 02/23/2023] [Accepted: 02/23/2023] [Indexed: 03/06/2023] Open
Abstract
Integrated disease management and plant protection have been discussed with much fervor in the past decade due to the rising environmental concerns of using industrially produced pesticides. Members of the genus Trichoderma are a subject of considerable research today due to their several properties as biocontrol agents. In our study, the peptaibol production of Trichoderma longibrachiatum SZMC 1775, T. longibrachiatum f. bissettii SZMC 12546, T. reesei SZMC 22616, T. reesei SZMC 22614, T. saturnisporum SZMC 22606 and T. effusum SZMC 22611 were investigated to elucidate structure-activity relationships (SARs) between the properties of peptaibols and their 3D structures. The effects of peptaibol mixtures obtained from every Trichoderma strain were examined against nine commonly known bacteria. The lowest minimum inhibitory concentrations (MIC, mg ml-1) were exerted by T. longibrachiatum f. bissettii SZMC 12546 against Gram-positive bacteria, which was also able to inhibit the plant pathogenic Gram-negative Rhizobium radiobacter. Accelerated molecular dynamics (aMD) simulations were performed in aqueous solvent to explore the folding dynamics of 12 selected peptaibol sequences. The most characteristic difference between the peptaibols from group A and B relies in the 'Gly-Leu-Aib-Pro' and 'Gly-Aib-Aib-Pro' motifs ('Aib' stands for α-aminoisobutyric acid), which imparted a significant effect on the folding dynamics in water and might be correlated with their expressed bioactivity. In our aMD simulation experiments, Group A peptaibols showed more restricted folding dynamics with well-folded helical conformations as the most stable representative structures. This structural stability and dynamics may contribute to their bioactivity against the selected bacterial species.
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Affiliation(s)
- Dóra Balázs
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary.,Doctoral School of Biology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary
| | - Tamás Marik
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary
| | - András Szekeres
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary
| | - Csaba Vágvölgyi
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary
| | - László Kredics
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary
| | - Chetna Tyagi
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary
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Tyśkiewicz R, Nowak A, Ozimek E, Jaroszuk-Ściseł J. Trichoderma: The Current Status of Its Application in Agriculture for the Biocontrol of Fungal Phytopathogens and Stimulation of Plant Growth. Int J Mol Sci 2022; 23:2329. [PMID: 35216444 PMCID: PMC8875981 DOI: 10.3390/ijms23042329] [Citation(s) in RCA: 80] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 02/13/2022] [Accepted: 02/18/2022] [Indexed: 02/06/2023] Open
Abstract
Rhizosphere filamentous fungi of the genus Trichoderma, a dominant component of various soil ecosystem mycobiomes, are characterized by the ability to colonize plant roots. Detailed knowledge of the properties of Trichoderma, including metabolic activity and the type of interaction with plants and other microorganisms, can ensure its effective use in agriculture. The growing interest in the application of Trichoderma results from their direct and indirect biocontrol potential against a wide range of soil phytopathogens. They act through various complex mechanisms, such as mycoparasitism, the degradation of pathogen cell walls, competition for nutrients and space, and induction of plant resistance. With the constant exposure of plants to a variety of pathogens, especially filamentous fungi, and the increased resistance of pathogens to chemical pesticides, the main challenge is to develop biological protection alternatives. Among non-pathogenic microorganisms, Trichoderma seems to be the best candidate for use in green technologies due to its wide biofertilization and biostimulatory potential. Most of the species from the genus Trichoderma belong to the plant growth-promoting fungi that produce phytohormones and the 1-aminocyclopropane-1-carboxylate (ACC) deaminase enzyme. In the present review, the current status of Trichoderma is gathered, which is especially relevant in plant growth stimulation and the biocontrol of fungal phytopathogens.
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Affiliation(s)
- Renata Tyśkiewicz
- Analytical Laboratory, Łukasiewicz Research Network–New Chemical Syntheses Institute, Aleja Tysiąclecia Państwa Polskiego 13a, 24-110 Puławy, Poland
| | - Artur Nowak
- Department of Industrial and Environmental Microbiology, Faculty of Biology and Biotechnology, Institute of Biological Science, Maria-Curie Skłodowska University, Akademicka 19, 20-033 Lublin, Poland; (E.O.); (J.J.-Ś.)
| | - Ewa Ozimek
- Department of Industrial and Environmental Microbiology, Faculty of Biology and Biotechnology, Institute of Biological Science, Maria-Curie Skłodowska University, Akademicka 19, 20-033 Lublin, Poland; (E.O.); (J.J.-Ś.)
| | - Jolanta Jaroszuk-Ściseł
- Department of Industrial and Environmental Microbiology, Faculty of Biology and Biotechnology, Institute of Biological Science, Maria-Curie Skłodowska University, Akademicka 19, 20-033 Lublin, Poland; (E.O.); (J.J.-Ś.)
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Probing Small-Angle Molecular Motions with EPR Spectroscopy: Dynamical Transition and Molecular Packing in Disordered Solids. MAGNETOCHEMISTRY 2022. [DOI: 10.3390/magnetochemistry8020019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Disordered molecular solids present a rather broad class of substances of different origin—amorphous polymers, materials for photonics and optoelectronics, amorphous pharmaceutics, simple molecular glass formers, and others. Frozen biological media in many respects also may be referred to this class. Theoretical description of dynamics and structure of disordered solids still does not exist, and only some phenomenological models can be developed to explain results of particular experiments. Among different experimental approaches, electron paramagnetic resonance (EPR) applied to spin probes and labels also can deliver useful information. EPR allows probing small-angle orientational molecular motions (molecular librations), which intrinsically are inherent to all molecular solids. EPR is employed in its conventional continuous wave (CW) and pulsed—electron spin echo (ESE)—versions. CW EPR spectra are sensitive to dynamical librations of molecules while ESE probes stochastic molecular librations. In this review, different manifestations of small-angle motions in EPR of spin probes and labels are discussed. It is shown that CW-EPR-detected dynamical librations provide information on dynamical transition in these media, similar to that explored with neutron scattering, and ESE-detected stochastic librations allow elucidating some features of nanoscale molecular packing. The possible EPR applications are analyzed for gel-phase lipid bilayers, for biological membranes interacting with proteins, peptides and cryoprotectants, for supercooled ionic liquids (ILs) and supercooled deep eutectic solvents (DESs), for globular proteins and intrinsically disordered proteins (IDPs), and for some other molecular solids.
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Trichoderma and Its Products From Laboratory to Patient Bedside in Medical Science: An Emerging Aspect. Fungal Biol 2022. [DOI: 10.1007/978-3-030-91650-3_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Lam YTH, Ricardo MG, Rennert R, Frolov A, Porzel A, Brandt W, Stark P, Westermann B, Arnold N. Rare Glutamic Acid Methyl Ester Peptaibols from Sepedonium ampullosporum Damon KSH 534 Exhibit Promising Antifungal and Anticancer Activity. Int J Mol Sci 2021; 22:ijms222312718. [PMID: 34884518 PMCID: PMC8657771 DOI: 10.3390/ijms222312718] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/17/2021] [Accepted: 11/23/2021] [Indexed: 01/29/2023] Open
Abstract
Fungal species of genus Sepedonium are rich sources of diverse secondary metabolites (e.g., alkaloids, peptaibols), which exhibit variable biological activities. Herein, two new peptaibols, named ampullosporin F (1) and ampullosporin G (2), together with five known compounds, ampullosporin A (3), peptaibolin (4), chrysosporide (5), c(Trp-Ser) (6) and c(Trp-Ala) (7), have been isolated from the culture of Sepedonium ampullosporum Damon strain KSH534. The structures of 1 and 2 were elucidated based on ESI-HRMSn experiments and intense 1D and 2D NMR analyses. The sequence of ampullosporin F (1) was determined to be Ac-Trp1-Ala2-Aib3-Aib4-Leu5-Aib6-Gln7-Aib8-Aib9-Aib10-GluOMe11-Leu12-Aib13-Gln14-Leuol15, while ampullosporin G (2) differs from 1 by exchanging the position of Gln7 with GluOMe11. Furthermore, the total synthesis of 1 and 2 was carried out on solid-phase to confirm the absolute configuration of all chiral amino acids as L. In addition, ampullosporin F (1) and G (2) showed significant antifungal activity against B. cinerea and P. infestans, but were inactive against S. tritici. Cell viability assays using human prostate (PC-3) and colorectal (HT-29) cancer cells confirmed potent anticancer activities of 1 and 2. Furthermore, a molecular docking study was performed in silico as an attempt to explain the structure-activity correlation of the characteristic ampullosporins (1–3).
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Affiliation(s)
- Yen T. H. Lam
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, D-06120 Halle (Saale), Germany; (Y.T.H.L.); (M.G.R.); (R.R.); (A.F.); (A.P.); (W.B.); (P.S.); (B.W.)
- Department of Organic Chemistry, Faculty of Chemistry, Hanoi National University of Education, Hanoi 100000, Vietnam
| | - Manuel G. Ricardo
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, D-06120 Halle (Saale), Germany; (Y.T.H.L.); (M.G.R.); (R.R.); (A.F.); (A.P.); (W.B.); (P.S.); (B.W.)
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, D-14476 Potsdam, Germany
| | - Robert Rennert
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, D-06120 Halle (Saale), Germany; (Y.T.H.L.); (M.G.R.); (R.R.); (A.F.); (A.P.); (W.B.); (P.S.); (B.W.)
| | - Andrej Frolov
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, D-06120 Halle (Saale), Germany; (Y.T.H.L.); (M.G.R.); (R.R.); (A.F.); (A.P.); (W.B.); (P.S.); (B.W.)
- Department of Biochemistry, Faculty of Biology, St. Petersburg State University, 199004 St. Petersburg, Russia
| | - Andrea Porzel
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, D-06120 Halle (Saale), Germany; (Y.T.H.L.); (M.G.R.); (R.R.); (A.F.); (A.P.); (W.B.); (P.S.); (B.W.)
| | - Wolfgang Brandt
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, D-06120 Halle (Saale), Germany; (Y.T.H.L.); (M.G.R.); (R.R.); (A.F.); (A.P.); (W.B.); (P.S.); (B.W.)
| | - Pauline Stark
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, D-06120 Halle (Saale), Germany; (Y.T.H.L.); (M.G.R.); (R.R.); (A.F.); (A.P.); (W.B.); (P.S.); (B.W.)
| | - Bernhard Westermann
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, D-06120 Halle (Saale), Germany; (Y.T.H.L.); (M.G.R.); (R.R.); (A.F.); (A.P.); (W.B.); (P.S.); (B.W.)
| | - Norbert Arnold
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, D-06120 Halle (Saale), Germany; (Y.T.H.L.); (M.G.R.); (R.R.); (A.F.); (A.P.); (W.B.); (P.S.); (B.W.)
- Correspondence: ; Tel.: +49-345-5582-1310
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Víglaš J, Dobiasová S, Viktorová J, Ruml T, Repiská V, Olejníková P, Gbelcová H. Peptaibol-Containing Extracts of Trichoderma atroviride and the Fight against Resistant Microorganisms and Cancer Cells. Molecules 2021; 26:molecules26196025. [PMID: 34641569 PMCID: PMC8512731 DOI: 10.3390/molecules26196025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 09/26/2021] [Accepted: 09/29/2021] [Indexed: 11/16/2022] Open
Abstract
Fighting resistance to antibiotics and chemotherapeutics has brought bioactive peptides to the fore. Peptaibols are short α-aminoisobutyric acid-containing peptides produced by Trichoderma species. Here, we studied the production of peptaibols by Trichoderma atroviride O1 and evaluated their antibacterial and anticancer activity against drug-sensitive and multidrug-resistant bacterium and cancer cell lines. This was substantiated by an analysis of the activity of the peptaibol synthetase-encoding gene. Atroviridins, 20-residue peptaibols were detected using MALDI-TOF mass spectrometry. Gram-positive bacteria were susceptible to peptaibol-containing extracts of T. atroviride O1. A synergic effect of extract constituents was possible, and the biolo-gical activity of extracts was pronounced in/after the peak of peptaibol synthetase activity. The growth of methicillin-resistant Staphylococcus aureus was reduced to just under 10% compared to the control. The effect of peptaibol-containing extracts was strongly modulated by the lipoteichoic acid and only slightly by the horse blood serum present in the cultivation medium. Peptaibol-containing extracts affected the proliferation of human breast cancer and human ovarian cancer cell lines in a 2D model, including the multidrug-resistant sublines. The peptaibols influenced the size and compactness of the cell lines in a 3D model. Our findings indicate the molecular basis of peptaibol production in T. atroviride O1 and the potential of its peptaibol-containing extracts as antimicrobial/anticancer agents.
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Affiliation(s)
- Ján Víglaš
- Institute of Biochemistry and Microbiology, Faculty of Food and Chemical Technology, Slovak University of Technology in Bratislava, 812 37 Bratislava, Slovakia;
- Correspondence:
| | - Simona Dobiasová
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, 166 28 Prague, Czech Republic; (S.D.); (J.V.); (T.R.)
| | - Jitka Viktorová
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, 166 28 Prague, Czech Republic; (S.D.); (J.V.); (T.R.)
| | - Tomáš Ruml
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, 166 28 Prague, Czech Republic; (S.D.); (J.V.); (T.R.)
| | - Vanda Repiská
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University in Bratislava, 813 72 Bratislava, Slovakia; (V.R.); (H.G.)
| | - Petra Olejníková
- Institute of Biochemistry and Microbiology, Faculty of Food and Chemical Technology, Slovak University of Technology in Bratislava, 812 37 Bratislava, Slovakia;
| | - Helena Gbelcová
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University in Bratislava, 813 72 Bratislava, Slovakia; (V.R.); (H.G.)
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Rush TA, Shrestha HK, Gopalakrishnan Meena M, Spangler MK, Ellis JC, Labbé JL, Abraham PE. Bioprospecting Trichoderma: A Systematic Roadmap to Screen Genomes and Natural Products for Biocontrol Applications. FRONTIERS IN FUNGAL BIOLOGY 2021; 2:716511. [PMID: 37744103 PMCID: PMC10512312 DOI: 10.3389/ffunb.2021.716511] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 08/10/2021] [Indexed: 09/26/2023]
Abstract
Natural products derived from microbes are crucial innovations that would help in reaching sustainability development goals worldwide while achieving bioeconomic growth. Trichoderma species are well-studied model fungal organisms used for their biocontrol properties with great potential to alleviate the use of agrochemicals in agriculture. However, identifying and characterizing effective natural products in novel species or strains as biological control products remains a meticulous process with many known challenges to be navigated. Integration of recent advancements in various "omics" technologies, next generation biodesign, machine learning, and artificial intelligence approaches could greatly advance bioprospecting goals. Herein, we propose a roadmap for assessing the potential impact of already known or newly discovered Trichoderma species for biocontrol applications. By screening publicly available Trichoderma genome sequences, we first highlight the prevalence of putative biosynthetic gene clusters and antimicrobial peptides among genomes as an initial step toward predicting which organisms could increase the diversity of natural products. Next, we discuss high-throughput methods for screening organisms to discover and characterize natural products and how these findings impact both fundamental and applied research fields.
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Affiliation(s)
- Tomás A. Rush
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN, United States
| | - Him K. Shrestha
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN, United States
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Knoxville, TN, United States
| | | | - Margaret K. Spangler
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN, United States
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - J. Christopher Ellis
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN, United States
| | - Jesse L. Labbé
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN, United States
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Paul E. Abraham
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN, United States
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Knoxville, TN, United States
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van Bohemen AI, Ruiz N, Zalouk-Vergnoux A, Michaud A, Robiou du Pont T, Druzhinina I, Atanasova L, Prado S, Bodo B, Meslet-Cladiere L, Cochereau B, Bastide F, Maslard C, Marchi M, Guillemette T, Pouchus YF. Pentadecaibins I-V: 15-Residue Peptaibols Produced by a Marine-Derived Trichoderma sp. of the Harzianum Clade. JOURNAL OF NATURAL PRODUCTS 2021; 84:1271-1282. [PMID: 33600182 DOI: 10.1021/acs.jnatprod.0c01355] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
In the course of investigations on peptaibol chemodiversity from marine-derived Trichoderma spp., five new 15-residue peptaibols named pentadecaibins I-V (1-5) were isolated from the solid culture of the strain Trichoderma sp. MMS1255 belonging to the T. harzianum species complex. Phylogenetic analyses allowed precise positioning of the strain close to T. lentiforme lineage inside the Harzianum clade. Peptaibol sequences were elucidated on the basis of their MS/MS fragmentation and extensive 2D NMR experiments. Amino acid configurations were determined by Marfey's analyses. The pentadecaibins are based on the sequences Ac-Aib1-Gly2-Ala3-Leu4-Aib/Iva5-Gln6-Aib/Iva7-Val/Leu8-Aib9-Ala10-Aib11-Aib12-Aib13-Gln14-Pheol15. Characteristic of the pentadecaibin sequences is the lack of the Aib-Pro motif commonly present in peptaibols produced by Trichoderma spp. Genome sequencing of Trichoderma sp. MMS1255 allowed the detection of a 15-module NRPS-encoding gene closely associated with pentadecaibin biosynthesis. Pentadecaibins were assessed for their potential antiproliferative and antimicrobial activities.
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Affiliation(s)
| | - Nicolas Ruiz
- Université de Nantes, MMS - EA2160, 44000 Nantes, France
| | | | - Aurore Michaud
- Université de Nantes, MMS - EA2160, 44000 Nantes, France
| | | | - Irina Druzhinina
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, 1040 Vienna, Austria
- Fungal Genomics Laboratory (FungiG), Nanjing Agricultural University, 210095 Nanjing, China
| | - Lea Atanasova
- Department of Food Science and Technology, University of Natural Resources and Life Sciences - BOKU, 1190 Vienna, Austria
| | - Soizic Prado
- Muséum National d'Histoire Naturelle, Unité Molécules de Communication et Adaptation des Micro-organismes, UMR 7245, CP 54, 57 Rue Cuvier, 75005 Paris, France
| | - Bernard Bodo
- Muséum National d'Histoire Naturelle, Unité Molécules de Communication et Adaptation des Micro-organismes, UMR 7245, CP 54, 57 Rue Cuvier, 75005 Paris, France
| | - Laurence Meslet-Cladiere
- Université de Brest, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, 29280 Plouzané, France
| | - Bastien Cochereau
- Université de Nantes, MMS - EA2160, 44000 Nantes, France
- Université de Brest, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, 29280 Plouzané, France
| | - Franck Bastide
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, 49071 Beaucouzé, France
| | - Corentin Maslard
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, 49071 Beaucouzé, France
| | - Muriel Marchi
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, 49071 Beaucouzé, France
| | - Thomas Guillemette
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, 49071 Beaucouzé, France
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11
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Sphaerostilbellins, New Antimicrobial Aminolipopeptide Peptaibiotics from Sphaerostilbella toxica. Biomolecules 2020; 10:biom10101371. [PMID: 32993102 PMCID: PMC7600149 DOI: 10.3390/biom10101371] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 09/18/2020] [Accepted: 09/25/2020] [Indexed: 02/07/2023] Open
Abstract
Sphaerostilbella toxica is a mycoparasitic fungus that can be found parasitizing wood-decay basidiomycetes in the southern USA. Organic solvent extracts of fermented strains of S. toxica exhibited potent antimicrobial activity, including potent growth inhibition of human pathogenic yeasts Candida albicans and Cryptococcus neoformans, the respiratory pathogenic fungus Aspergillus fumigatus, and the Gram-positive bacterium Staphylococcus aureus. Bioassay-guided separations led to the purification and structure elucidation of new peptaibiotics designated as sphaerostilbellins A and B. Their structures were established mainly by analysis of NMR and HRMS data, verification of amino acid composition by Marfey's method, and by comparison with published data of known compounds. They incorporate intriguing structural features, including an N-terminal 2-methyl-3-oxo-tetradecanoyl (MOTDA) residue and a C-terminal putrescine residue. The minimal inhibitory concentrations for sphaerostilbellins A and B were measured as 2 μM each for C. neoformans, 1 μM each for A. fumigatus, and 4 and 2 μM, respectively, for C. albicans. Murine macrophage cells were unaffected at these concentrations.
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12
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Khan RAA, Najeeb S, Hussain S, Xie B, Li Y. Bioactive Secondary Metabolites from Trichoderma spp. against Phytopathogenic Fungi. Microorganisms 2020; 8:E817. [PMID: 32486107 PMCID: PMC7356054 DOI: 10.3390/microorganisms8060817] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 05/05/2020] [Accepted: 05/28/2020] [Indexed: 01/06/2023] Open
Abstract
Phytopathogenic fungi, causing significant economic and production losses, are becoming a serious threat to global food security. Due to an increase in fungal resistance and the hazardous effects of chemical fungicides to human and environmental health, scientists are now engaged to explore alternate non-chemical and ecofriendly management strategies. The use of biocontrol agents and their secondary metabolites (SMs) is one of the potential approaches used today. Trichoderma spp. are well known biocontrol agents used globally. Many Trichoderma species are the most prominent producers of SMs with antimicrobial activity against phytopathogenic fungi. Detailed information about these secondary metabolites, when grouped together, enhances the understanding of their efficient utilization and further exploration of new bioactive compounds for the management of plant pathogenic fungi. The current literature provides the information about SMs of Trichoderma spp. in a different context. In this review, we summarize and group different antifungal SMs of Trichoderma spp. against phytopathogenic fungi along with a comprehensive overview of some aspects related to their chemistry and biosynthesis. Moreover, a brief overview of the biosynthesis pathway, action mechanism, and different approaches for the analysis of SMs and the factors affecting the regulation of SMs in Trichoderma is also discussed.
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Affiliation(s)
- Raja Asad Ali Khan
- Institute of Vegetables and Flowers (Plant Pathology Lab), Chinese Academy of Agricultural Sciences, Beijing 100081, China; (R.A.A.K.); (S.N.)
| | - Saba Najeeb
- Institute of Vegetables and Flowers (Plant Pathology Lab), Chinese Academy of Agricultural Sciences, Beijing 100081, China; (R.A.A.K.); (S.N.)
| | - Shaukat Hussain
- Department of Plant Pathology, The University of Agriculture Peshawar, Peshawar 25130, Pakistan;
| | - Bingyan Xie
- Institute of Vegetables and Flowers (Plant Pathology Lab), Chinese Academy of Agricultural Sciences, Beijing 100081, China; (R.A.A.K.); (S.N.)
| | - Yan Li
- Institute of Vegetables and Flowers (Plant Pathology Lab), Chinese Academy of Agricultural Sciences, Beijing 100081, China; (R.A.A.K.); (S.N.)
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13
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Changes in Peptaibol Production of Trichoderma Species during In Vitro Antagonistic Interactions with Fungal Plant Pathogens. Biomolecules 2020; 10:biom10050730. [PMID: 32392805 PMCID: PMC7277233 DOI: 10.3390/biom10050730] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Revised: 05/05/2020] [Accepted: 05/05/2020] [Indexed: 02/06/2023] Open
Abstract
Trichoderma species are widely used as biofungicides for the control of fungal plant pathogens. Several studies have been performed to identify the main genes and compounds involved in Trichoderma–plant–microbial pathogen cross-talks. However, there is not much information about the exact mechanism of this profitable interaction. Peptaibols secreted mainly by Trichoderma species are linear, 5–20 amino acid residue long, non-ribosomally synthesized peptides rich in α-amino isobutyric acid, which seem to be effective in Trichoderma–plant pathogenic fungus interactions. In the present study, reversed phase (RP) high-performance liquid chromatography (HPLC) coupled with electrospray ionization (ESI) mass spectrometry (MS) was used to detect peptaibol profiles of Trichoderma strains during interactions with fungal plant pathogens. MS investigations of the crude extracts deriving from in vitro confrontations of Trichoderma asperellum and T. longibrachiatum with different plant pathogenic fungi (Fusarium moniliforme, F. culmorum, F. graminearum, F. oxysporum species complex, Alternaria solani and Rhizoctonia solani) were performed to get a better insight into the role of these non-ribosomal antimicrobial peptides. The results revealed an increase in the total amount of peptaibols produced during the interactions, as well as some differences in the peptaibol profiles between the confrontational and control tests. Detection of the expression level of the peptaibol synthetase tex1 by qRT-PCR showed a significant increase in T. asperellum/R. solani interaction in comparison to the control. In conclusion, the interaction with plant pathogens highly influenced the peptaibol production of the examined Trichoderma strains.
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Antifungal compounds with anticancer potential from Trichoderma sp. P8BDA1F1, an endophytic fungus from Begonia venosa. Braz J Microbiol 2020; 51:989-997. [PMID: 32333271 DOI: 10.1007/s42770-020-00270-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 04/07/2020] [Indexed: 01/28/2023] Open
Abstract
Fungi in the genus Trichoderma are notorious producers of secondary metabolites with diverse applications, such as antibacterial, antifungal, and plant growth-promoting properties. Peptaibols are linear peptides produced by such fungi, with more than 440 compounds described to date, including tricholongins, longibrachins, trichobrachins, and trichovirins. Peptaibols are synthesized by non-ribosomal peptide synthetases and they have several biological activities. Our research group isolated four peptaibols (6DP2, 6DP3, 6DP4, and 6DP5) with antifungal activity against the plant pathogen Colletotrichum gloeosporioides and the proteasome (a cancer chemotherapy target) from Trichoderma sp. P8BDA1F1, an endophytic fungus from Begonia venosa. The ethyl acetate extract of this endophyte showed activity of 6.01% and 75% against C. gloeosporioides and the proteasome, respectively. The isolated compounds were identified by MS/MS and compared to literature data, suggesting the presence of trilongins BI, BII, BIII, and BIV, which are peptaibols containing 20 amino acid residues. The minimum inhibitory concentration against C. gloeosporioides was 40 μM for trilongin BI, 320 μM for trilongin BII, 160 μM for trilongin BIII, and 310 μM for trilongin BIV. BI-BIV trilongins inhibited proteasome ChTL activity, with IC50 values of 6.5 ± 2.7; 4.7 ± 1.8; 6.3 ± 2.2; and 2.7 ± 0.5 μM, respectively. The compounds were tested ex vivo against the intracellular amastigotes of Leishmania (L.) infantum but showed no selectivity. It is the first report of trilongins BI-BIV with antifungal activity against C. gloeosporioides and the proteasome target.
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15
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Singh VP, Pathania AS, Kushwaha M, Singh S, Sharma V, Malik FA, Khan IA, Kumar A, Singh D, Vishwakarma RA. 14-Residue peptaibol velutibol A from Trichoderma velutinum: its structural and cytotoxic evaluation. RSC Adv 2020; 10:31233-31242. [PMID: 35520634 PMCID: PMC9056410 DOI: 10.1039/d0ra05780k] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 08/08/2020] [Indexed: 11/21/2022] Open
Abstract
Velutibol A (1), a new 14-residue peptaibol was isolated from the Himalayan cold habitat fungus Trichoderma velutinum. The structural characterization was carried out by 1D and 2D NMR studies, and tandem mass studies, and Marfey's method aided in determining the stereochemistry of the amino acids. The CD analysis revealed folding of the peptide in a 310-helical conformation. The intramolecular H-bonding was determined by an NMR-VT experiment. Cytotoxic evaluation was carried out against a panel of cancer cell lines. The cell cycle assay was carried out on human myeloid leukaemia (HL-60) cells and revealed the formation of apoptotic bodies and DNA damage in a dose-dependent manner. Three other peptaibols namely velutibol B (2), velutibol C (3), and velutibol D (4) were also isolated in trace amounts from the psychotropic fungus and characterized through tandem mass spectroscopy and Marfey's analysis. Velutibol A (1), a new 14-residue peptaibol isolated from the Himalayan cold habitat fungus Trichoderma velutinum.![]()
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Affiliation(s)
- Varun Pratap Singh
- Medicinal Chemistry Division
- CSIR-Indian Institute of Integrative Medicine
- Jammu 180 001
- India
- Department of Biotechnology
| | - Anup Singh Pathania
- Pharmacology Division
- CSIR-Indian Institute of Integrative Medicine
- Jammu 180 001
- India
| | - Manoj Kushwaha
- Quality Control & Quality Assurance Division
- CSIR-Indian Institute of Integrative Medicine
- Jammu 180 001
- India
| | - Samsher Singh
- Clinical Microbiology Division
- CSIR-Indian Institute of Integrative Medicine
- Jammu 180 001
- India
| | - Vandana Sharma
- Quality Control & Quality Assurance Division
- CSIR-Indian Institute of Integrative Medicine
- Jammu 180 001
- India
- Academy of Scientific and Innovative Research
| | - Fayaz A. Malik
- Pharmacology Division
- CSIR-Indian Institute of Integrative Medicine
- Jammu 180 001
- India
| | - Inshad A. Khan
- Clinical Microbiology Division
- CSIR-Indian Institute of Integrative Medicine
- Jammu 180 001
- India
- Department of Microbiology
| | - Anil Kumar
- Department of Biotechnology
- Faculty of Sciences
- Shri Mata Vaishno Devi University
- India
| | - Deepika Singh
- Medicinal Chemistry Division
- CSIR-Indian Institute of Integrative Medicine
- Jammu 180 001
- India
- Quality Control & Quality Assurance Division
| | - Ram A. Vishwakarma
- Medicinal Chemistry Division
- CSIR-Indian Institute of Integrative Medicine
- Jammu 180 001
- India
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16
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Rashad YM, Abdel-Azeem AM. Recent Progress on Trichoderma Secondary Metabolites. Fungal Biol 2020. [DOI: 10.1007/978-3-030-41870-0_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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17
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Brückner H, Fox S, Degenkolb T. Sequences of Acretocins, Peptaibiotics Containing the Rare 1-Aminocyclopropanecarboxylic Acid, from Acremonium crotocinigenum CBS 217.70. Chem Biodivers 2019; 16:e1900276. [PMID: 31336036 DOI: 10.1002/cbdv.201900276] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 07/18/2019] [Indexed: 11/06/2022]
Affiliation(s)
- Hans Brückner
- Interdisciplinary Research Center for BioSystems, Land Use and Nutrition (IFZ), Department of Food Sciences, Institute of Nutritional Science, Justus-Liebig University of Giessen, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Stefan Fox
- Institute of Chemistry, Department of Bioinorganic Chemistry, University of Hohenheim, Garbenstr. 30, 70599, Stuttgart, Germany
| | - Thomas Degenkolb
- Interdisciplinary Research Center for BioSystems, Land Use and Nutrition (IFZ), Department of Food Sciences, Institute of Nutritional Science, Justus-Liebig University of Giessen, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany.,Present address: Institute of Insect Biotechnology, Department of Applied Entomology, IFZ, Justus-Liebig University Giessen, Heinrich-Buff-Ring 26-32, Giessen, Germany
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18
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Trichoderma atroviride: an isolate from forest environment with secondary metabolites with high antimicrobial potential. ACTA CHIMICA SLOVACA 2019. [DOI: 10.2478/acs-2019-0008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Abstract
This work was focused on the characterization of novel isolate of Trichoderma atroviride O1, found in the forest around the village of Zázrivá (the Northern Slovakia, region Orava). The isolate was identified by sequencing its internal transcribed spacer (ITS) region of rDNA. T. atroviride O1 stimulated the development of lateral roots of model plant Lepidium sativum. Simultaneously, the isolate has proved its high mycoparasitic potential as it displayed the ability to attack colonies of phytopathogenic fungi (Alternaria alternata, Fusarium culmorum, Botrytis cinerea). This isolate produced secondary metabolites, which were isolated and tested for the antimicrobial activity against gram-positive bacteria Staphylococcus epidermidis and Staphylococcus aureus. The growth of these bacteria was suppressed to 10 % and 40 %, respectively. The suppression of the growth of two Candida species was also strong (10 % growth). However, growth parameters of three phytopathogenic fungi (Alternaria alternata, Botrytis cinerea and Fusarium culmorum) were less affected (75 % growth in comparison with the control). Attempts were made to characterize secondary metabolites isolated from T. atroviride O1. Known peptaibols, 20—21 amino acid long, but also shorter peptides, were detected by MALDI-TOF mass spectrometry. Thus, this study demonstrates the plant growth promotion, strong mycoparasitic potential and antimicrobial activity of the isolate T. atroviride O1, which could be in part ascribed to the production of secondary metabolites. This isolate does have a potential in the biocontrol in eco-farming. Further study, particularly, the identification of produced secondary metabolites, is needed.
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19
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Oberlies NH, Knowles SL, Amrine CSM, Kao D, Kertesz V, Raja HA. Droplet probe: coupling chromatography to the in situ evaluation of the chemistry of nature. Nat Prod Rep 2019; 36:944-959. [PMID: 31112181 PMCID: PMC6640111 DOI: 10.1039/c9np00019d] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Covering: up to 2019The chemistry of nature can be beautiful, inspiring, beneficial and poisonous, depending on perspective. Since the isolation of the first secondary metabolites roughly two centuries ago, much of the chemical research on natural products has been both reductionist and static. Typically, compounds were isolated and characterized from the extract of an entire organism from a single time point. While there could be subtexts to that approach, the general premise has been to determine the chemistry with very little in the way of tools to differentiate spatial and/or temporal changes in secondary metabolite profiles. However, the past decade has seen exponential advances in our ability to observe, measure, and visualize the chemistry of nature in situ. Many of those techniques have been reviewed in this journal, and most are tapping into the power of mass spectrometry to analyze a plethora of sample types. In nearly all of the other techniques used to study chemistry in situ, the element of chromatography has been eliminated, instead using various ionization sources to coax ions of the secondary metabolites directly into the mass spectrometer as a mixture. Much of that science has been driven by the great advances in ambient ionization techniques used with a suite of mass spectrometry platforms, including the alphabet soup from DESI to LAESI to MALDI. This review discusses the one in situ analysis technique that incorporates chromatography, being the droplet-liquid microjunction-surface sampling probe, which is more easily termed "droplet probe". In addition to comparing and contrasting the droplet probe with other techniques, we provide perspective on why scientists, particularly those steeped in natural products chemistry training, may want to include chromatography in in situ analyses. Moreover, we provide justification for droplet sampling, especially for samples with delicate and/or non-uniform topographies. Furthermore, while the droplet probe has been used the most in the analysis of fungal cultures, we digest a variety of other applications, ranging from cyanobacteria, to plant parts, and even delicate documents, such as herbarium specimens.
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Affiliation(s)
- Nicholas H Oberlies
- Department of Chemistry & Biochemistry, University of North Carolina at Greensboro, Greensboro, North Carolina, USA.
| | - Sonja L Knowles
- Department of Chemistry & Biochemistry, University of North Carolina at Greensboro, Greensboro, North Carolina, USA.
| | - Chiraz Soumia M Amrine
- Department of Chemistry & Biochemistry, University of North Carolina at Greensboro, Greensboro, North Carolina, USA.
| | - Diana Kao
- Department of Chemistry & Biochemistry, University of North Carolina at Greensboro, Greensboro, North Carolina, USA.
| | - Vilmos Kertesz
- Mass Spectrometry and Laser Spectroscopy Group, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Huzefa A Raja
- Department of Chemistry & Biochemistry, University of North Carolina at Greensboro, Greensboro, North Carolina, USA.
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20
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Marik T, Tyagi C, Balázs D, Urbán P, Szepesi Á, Bakacsy L, Endre G, Rakk D, Szekeres A, Andersson MA, Salonen H, Druzhinina IS, Vágvölgyi C, Kredics L. Structural Diversity and Bioactivities of Peptaibol Compounds From the Longibrachiatum Clade of the Filamentous Fungal Genus Trichoderma. Front Microbiol 2019; 10:1434. [PMID: 31293557 PMCID: PMC6606783 DOI: 10.3389/fmicb.2019.01434] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 06/06/2019] [Indexed: 01/18/2023] Open
Abstract
This study examined the structural diversity and bioactivity of peptaibol compounds produced by species from the phylogenetically separated Longibrachiatum Clade of the filamentous fungal genus Trichoderma, which contains several biotechnologically, agriculturally and clinically important species. HPLC-ESI-MS investigations of crude extracts from 17 species of the Longibrachiatum Clade (T. aethiopicum, T. andinense, T. capillare, T. citrinoviride, T. effusum, T. flagellatum, T. ghanense, T. konilangbra, T. longibrachiatum, T. novae-zelandiae, T. pinnatum, T. parareesei, T. pseudokoningii, T. reesei, T. saturnisporum, T. sinensis, and T. orientale) revealed several new and recurrent 20-residue peptaibols related to trichobrachins, paracelsins, suzukacillins, saturnisporins, trichoaureocins, trichocellins, longibrachins, hyporientalins, trichokonins, trilongins, metanicins, trichosporins, gliodeliquescins, alamethicins and hypophellins, as well as eight 19-residue sequences from a new subfamily of peptaibols named brevicelsins. Non-ribosomal peptide synthetase genes were mined from the available genome sequences of the Longibrachiatum Clade. Their annotation and product prediction were performed in silico and revealed full agreement in 11 out of 20 positions regarding the amino acids predicted based on the signature sequences and the detected amino acids incorporated. Molecular dynamics simulations were performed for structural characterization of four selected peptaibol sequences: paracelsins B, H and their 19-residue counterparts brevicelsins I and IV. Loss of position R6 in brevicelsins resulted in smaller helical structures with higher atomic fluctuation for every residue than the structures formed by paracelsins. We observed the formation of highly bent, almost hairpin-like, helical structures throughout the trajectory, along with linear conformation. Bioactivity tests were performed on the purified peptaibol extract of T. reesei on clinically and phytopathologically important filamentous fungi, mammalian cells, and Arabidopsis thaliana seedlings. Porcine kidney cells and boar spermatozoa proved to be sensitive to the purified peptaibol extract. Peptaibol concentrations ≥0.3 mg ml−1 deterred the growth of A. thaliana. However, negative effects to plants were not detected at concentrations below 0.1 mg ml−1, which could still inhibit plant pathogenic filamentous fungi, suggesting that those peptaibols reported here may have applications for plant protection.
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Affiliation(s)
- Tamás Marik
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Chetna Tyagi
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Dóra Balázs
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Péter Urbán
- Department of General and Environmental Microbiology, Faculty of Sciences, and Szentágothai Research Center, University of Pécs, Pécs, Hungary
| | - Ágnes Szepesi
- Department of Plant Biology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - László Bakacsy
- Department of Plant Biology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Gábor Endre
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Dávid Rakk
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - András Szekeres
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | | | - Heidi Salonen
- Department of Civil Engineering, Aalto University, Espoo, Finland
| | - Irina S Druzhinina
- Research Area Biochemical Technology, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria.,Jiangsu Provincial Key Laboratory of Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - Csaba Vágvölgyi
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - László Kredics
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
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21
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Gessmann R, Brückner H, Berg A, Petratos K. The crystal structure of the lipoaminopeptaibol helioferin, an antibiotic peptide from Mycogone rosea. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2018; 74:315-320. [PMID: 29652258 DOI: 10.1107/s2059798318001857] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 01/30/2018] [Indexed: 11/10/2022]
Abstract
The crystal structure of the natural nonapeptide antibiotic helioferin has been determined and refined to 0.9 Å resolution. Helioferin consists of helioferin A and B, which contain 2-(2'-aminopropyl)aminoethanol (Apae) and 2-[(2'-aminopropyl)methylamino]ethanol (Amae) at their respective alkanolamine termini. In addition, helioferin contains the unusual amino-acid residues α-aminoisobutyric acid (Aib) and (2S,4S,6S)-2-amino-6-hydroxy-4-methyl-8-oxodecanoic acid (Ahmod). The amino-terminus is capped with 2-methyl-n-1-octanoic acid (M8a). The peptide crystallizes with a 1:1 molar ratio of helioferin A and B in the monoclinic space group C2, with unit-cell parameters a = 34.711, b = 10.886, c = 17.150 Å, β = 93.05°. The peptide backbone folds in a regular right-handed α-helical conformation, with eight intramolecular hydrogen bonds, all but one forming 5→1 interactions. The two aliphatic chains of the fatty-acyl (M8a) and the second residue (Ahmod) extend out of the α-helical structure in opposite directions and lead to a corkscrew-like shape of the peptide molecule. Halogen anions (Cl- and F-) have been co-crystallized with the peptide molecules, implying a positive charge at the aminoalcohol end of the peptide. In the tightly packed crystal the helices are linked head to tail via the anions by electrostatic, hydrogen-bond and van der Waals interactions, forming continuous helical rods. Two nonparallel rods (forming an angle of 118°) interact directly via hydrogen bonds and via the anions, forming a double layer. Successive double layers are held together only via van der Waals contacts. The helical axes of successive double layers are also related by an angle of 118°. The structure of helioferin reported here and the previously determined structure of the homologous leucinostatin A have a total straight length of about 21 Å, indicating a different membrane-modifying bioactivity from that of long-chain, amphiphilic peptaibols.
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Affiliation(s)
| | - Hans Brückner
- Research Center for BioSystems, Land Use and Nutrition (IFZ), Institute of Nutritional Science, Department of Food Sciences, Heinrich-Buff-Ring 26-32, 65392 Giessen, Germany
| | - Albrecht Berg
- Innovent e.V., Prüssingstrasse 27B, 07745 Jena, Germany
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22
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Singh VP, Yedukondalu N, Sharma V, Kushwaha M, Sharma R, Chaubey A, Kumar A, Singh D, Vishwakarma RA. Lipovelutibols A-D: Cytotoxic Lipopeptaibols from the Himalayan Cold Habitat Fungus Trichoderma velutinum. JOURNAL OF NATURAL PRODUCTS 2018; 81:219-226. [PMID: 29373791 DOI: 10.1021/acs.jnatprod.6b00873] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Four novel lipovelutibols A (1), B (2), C (3), and D (4) containing six amino acid residues with leucinol at the C-terminus and a fatty acyl moiety (n-octanoyl) at its N-terminus were isolated from the psychrotrophic fungus Trichoderma velutinum collected from the Himalayan cold habitat. The structures (1-4) were determined by NMR and MS/MS, and the stereochemistry of amino acids by Marfey's method. Lipopeptaibols 2 and 4 were found to contain d-isovaline, a nonproteinogenic amino acid, but lacked α-aminoisobutyric acid, characteristic of peptaibols. Cytotoxic activity of 2 and 4 was observed against HL-60, LS180, MDA-MB-231, and A549 cancer cell lines.
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Affiliation(s)
- Varun Pratap Singh
- Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine , Canal Road, Jammu 180 001, India
- Department of Biotechnology, Faculty of Sciences, Shri Mata Vaishno Devi University , Katra, Jammu and Kashmir 182320, India
| | - Nalli Yedukondalu
- Academy of Scientific and Innovative Research , Jammu 180 001, India
- Natural Product Chemistry Division, CSIR-Indian Institute of Integrative Medicine , Canal Road, Jammu 180 001, India
| | - Vandana Sharma
- Quality Control and Quality Assurance, CSIR-Indian Institute of Integrative Medicine , Canal Road, Jammu 180 001, India
| | - Manoj Kushwaha
- Quality Control and Quality Assurance, CSIR-Indian Institute of Integrative Medicine , Canal Road, Jammu 180 001, India
| | - Richa Sharma
- Academy of Scientific and Innovative Research , Jammu 180 001, India
- Fermentation Technology Division, CSIR-Indian Institute of Integrative Medicine , Canal Road, Jammu 180 001, India
| | - Asha Chaubey
- Academy of Scientific and Innovative Research , Jammu 180 001, India
- Fermentation Technology Division, CSIR-Indian Institute of Integrative Medicine , Canal Road, Jammu 180 001, India
| | - Anil Kumar
- Department of Biotechnology, Faculty of Sciences, Shri Mata Vaishno Devi University , Katra, Jammu and Kashmir 182320, India
| | - Deepika Singh
- Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine , Canal Road, Jammu 180 001, India
- Academy of Scientific and Innovative Research , Jammu 180 001, India
- Quality Control and Quality Assurance, CSIR-Indian Institute of Integrative Medicine , Canal Road, Jammu 180 001, India
| | - Ram A Vishwakarma
- Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine , Canal Road, Jammu 180 001, India
- Academy of Scientific and Innovative Research , Jammu 180 001, India
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23
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Syryamina VN, De Zotti M, Toniolo C, Formaggio F, Dzuba SA. Alamethicin self-assembling in lipid membranes: concentration dependence from pulsed EPR of spin labels. Phys Chem Chem Phys 2018; 20:3592-3601. [DOI: 10.1039/c7cp07298h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The antimicrobial action of the peptide antibiotic alamethicin (Alm) is commonly related to peptide self-assembling resulting in the formation of voltage-dependent channels in bacterial membranes, which induces ion permeation.
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Affiliation(s)
- Victoria N. Syryamina
- Institute of Chemical Kinetics and Combustion
- RAS
- Novosibirsk 630090
- Russian Federation
- Novosibirsk State University
| | - Marta De Zotti
- Department of Chemical Sciences
- University of Padova
- 35131 Padova
- Italy
| | - Claudio Toniolo
- Department of Chemical Sciences
- University of Padova
- 35131 Padova
- Italy
- Institute of Biomolecular Chemistry
| | - Fernando Formaggio
- Department of Chemical Sciences
- University of Padova
- 35131 Padova
- Italy
- Institute of Biomolecular Chemistry
| | - Sergei A. Dzuba
- Institute of Chemical Kinetics and Combustion
- RAS
- Novosibirsk 630090
- Russian Federation
- Novosibirsk State University
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24
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Sica VP, Rees ER, Raja HA, Rivera-Chávez J, Burdette JE, Pearce CJ, Oberlies NH. In situ mass spectrometry monitoring of fungal cultures led to the identification of four peptaibols with a rare threonine residue. PHYTOCHEMISTRY 2017; 143:45-53. [PMID: 28772192 PMCID: PMC5603414 DOI: 10.1016/j.phytochem.2017.07.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 07/14/2017] [Accepted: 07/19/2017] [Indexed: 05/03/2023]
Abstract
Peptaibols are an intriguing class of fungal metabolites due both to their wide range of reported bioactivities and to the structural variability that can be generated by the exchange of variable amino acid building blocks. In an effort to streamline the discovery of structurally diverse peptaibols, a mass spectrometry surface sampling technique was applied to screen the chemistry of fungal cultures in situ. Four previously undescribed peptaibols, all containing a rare threonine residue, were identified from a fungal culture (MSX53554), which was identified as Nectriopsis Maire (Bionectriaceae, Hypocreales, Ascomycota). These compounds not only increased the known threonine-containing peptaibols by nearly 20%, but also, the threonine residue was situated in a unique place compared to the other reported threonine-containing peptaibols. After the initial in situ detection and characterization, a large-scale solid fermentation culture was grown. The four peptaibols were isolated and characterized by mass spectrometry. In addition, one of the peptaibols was fully characterized by NMR and amino acid analysis using Marfey's reagent and exhibited moderate in vitro anticancer activity.
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Affiliation(s)
- Vincent P Sica
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC 27402, United States
| | - Evan R Rees
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC 27402, United States
| | - Huzefa A Raja
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC 27402, United States
| | - José Rivera-Chávez
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC 27402, United States
| | - Joanna E Burdette
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612, United States
| | - Cedric J Pearce
- Mycosynthetix, Inc., 505 Meadowlands Dr., Suite103, Hillsborough, NC 27278, United States
| | - Nicholas H Oberlies
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC 27402, United States.
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25
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Rivera-Chávez J, Raja HA, Graf TN, Gallagher JM, Metri P, Xue D, Pearce CJ, Oberlies NH. Prealamethicin F50 and related peptaibols from Trichoderma arundinaceum: Validation of their authenticity via in situ chemical analysis. RSC Adv 2017; 7:45733-45751. [PMID: 29379602 PMCID: PMC5786278 DOI: 10.1039/c7ra09602j] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
In the field of natural products chemistry, a common question pertains to the authenticity of an isolated compound, i.e. are the interesting side chains biosynthesized naturally or an artefact of the isolation/purification processes? The droplet-liquid microjunction-surface sampling probe (droplet-LMJ-SSP) coupled to a hyphenated system (UPLC-UV-HRESIMS) empowers the analysis of natural product sources in situ, providing data on the biosynthetic timing and spatial distribution of secondary metabolites. In this study the droplet-LMJ-SSP was utilized to validate the authenticity of two new peptaibols (2 and 3) as biosynthesized secondary metabolites, even though both them had structural features that could be perceived as artefacts. Compounds 2 and 3 were isolated from the scaled up fermentation of Trichoderma arundinaceum (strain MSX70741), along with a new member of the trichobrevin BIII complex (1), and four known compounds (4-7). The structures of the isolates were established using a set of spectroscopic and spectrometric methods, and their absolute configurations were determined by Marfey's analysis. The cytotoxic activity of compounds 1, 3, 4 and 6 was evaluated against a panel of cancer cell lines, where cytotoxic activity in the single digit μM range was observed.
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Affiliation(s)
- José Rivera-Chávez
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC 27402, USA
| | - Huzefa A Raja
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC 27402, USA
| | - Tyler N Graf
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC 27402, USA
| | - Jacklyn M Gallagher
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC 27402, USA
| | - Prashant Metri
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
| | - Ding Xue
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
| | | | - Nicholas H Oberlies
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC 27402, USA
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26
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Abstract
Mycoparasitism is a lifestyle where one fungus establishes parasitic interactions with other fungi. Species of the genus Trichoderma together with Clonostachys rosea are among the most studied fungal mycoparasites. They have wide host ranges comprising several plant pathogens and are used for biological control of plant diseases. Trichoderma as well as C. rosea mycoparasites efficiently overgrow and kill their fungal prey by using infection structures and by applying lytic enzymes and toxic metabolites. Most of our knowledge on the putative signals and signaling pathways involved in prey recognition and activation of the mycoparasitic response is derived from studies with Trichoderma. These fungi rely on G-protein signaling, the cAMP pathway, and mitogen-activated protein kinase cascades during growth and development as well as during mycoparasitism. The signals being recognized by the mycoparasite may include surface molecules and surface properties as well as secondary metabolites and other small molecules released from the prey. Their exact nature, however, remains elusive so far. Recent genomics-based studies of mycoparasitic fungi of the order Hypocreales, i.e., Trichoderma species, C. rosea, Tolypocladium ophioglossoides, and Escovopsis weberi, revealed not only several gene families with a mycoparasitism-related expansion of gene paralogue numbers, but also distinct differences between the different mycoparasites. We use this information to illustrate the biological principles and molecular basis of necrotrophic mycoparasitism and compare the mycoparasitic strategies of Trichoderma as a "model" mycoparasite with the behavior and special features of C. rosea, T. ophioglossoides, and E. weberi.
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27
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McMullin DR, Renaud JB, Barasubiye T, Sumarah MW, Miller JD. Metabolites of Trichoderma species isolated from damp building materials. Can J Microbiol 2017; 63:621-632. [DOI: 10.1139/cjm-2017-0083] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Buildings that have been flooded often have high concentrations of Trichoderma spores in the air while drying. Inhaled spores and spore and mycelial fragments contain large amounts of fungal glucan and natural products that contribute to the symptoms associated with indoor mould exposures. In this study, we considered both small molecules and peptaibol profiles of T. atroviride, T. koningiopsis, T. citrinoviride, and T. harzianum strains obtained from damp buildings in eastern Canada. Twenty-residue peptaibols and sorbicillin-derived metabolites (1–6) including a new structure, (R)-vertinolide (1), were characterized from T. citrinoviride. Trichoderma koningiopsis produced several koninginins (7–10), trikoningin KA V, and the 11-residue lipopeptaibols trikoningin KB I and trikoningin KB II. Trichoderma atroviride biosynthesized a mixture of 19-residue trichorzianine-like peptaibols, whereas T. harzianum produced 18-residue trichokindin-like peptaibols and the 11-residue harzianin HB I that was subsequently identified from the studied T. citrinoviride strain. Two α-pyrones, 6-pentyl-pyran-2-one (11) and an oxidized analog (12), were produced by both T. atroviride and T. harzianum. Aside from exposure to low molecular weight natural products, inhalation of Trichoderma spores and mycelial fragments may result in exposure to membrane-disrupting peptaibols. This investigation contributes to a more comprehensive understanding of the biologically active natural products produced by fungi commonly found in damp buildings.
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Affiliation(s)
- David R. McMullin
- Ottawa Carleton Institute of Chemistry, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Justin B. Renaud
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON N5V 4T3, Canada
| | - Tharcisse Barasubiye
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada
| | - Mark W. Sumarah
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON N5V 4T3, Canada
| | - J. David Miller
- Ottawa Carleton Institute of Chemistry, Carleton University, Ottawa, ON K1S 5B6, Canada
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28
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Rivera-Chávez J, Raja HA, Graf TN, Burdette JE, Pearce CJ, Oberlies NH. Biosynthesis of Fluorinated Peptaibols Using a Site-Directed Building Block Incorporation Approach. JOURNAL OF NATURAL PRODUCTS 2017; 80:1883-1892. [PMID: 28594169 PMCID: PMC5485375 DOI: 10.1021/acs.jnatprod.7b00189] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Indexed: 05/20/2023]
Abstract
Synthetic biological approaches, such as site-directed biosynthesis, have contributed to the expansion of the chemical space of natural products, making possible the biosynthesis of unnatural metabolites that otherwise would be difficult to access. Such methods may allow the incorporation of fluorine, an atom rarely found in nature, into complex secondary metabolites. Organofluorine compounds and secondary metabolites have both played pivotal roles in the development of drugs; however, their discovery and development are often via nonintersecting tracks. In this context, we used the biosynthetic machinery of Trichoderma arundinaceum (strain MSX70741) to incorporate a fluorine atom into peptaibol-type molecules in a site-selective manner. Thus, fermentation of strain MSX70741 in media containing ortho- and meta-F-phenylalanine resulted in the biosynthesis of two new fluorine-containing alamethicin F50 derivatives. The fluorinated products were characterized using spectroscopic (1D and 2D NMR, including 19F) and spectrometric (HRESIMS/MSn) methods, and their absolute configurations were established by Marfey's analysis. Fluorine-containing alamethicin F50 derivatives exhibited potency analogous to the nonfluorinated parent when evaluated against a panel of human cancer cell lines. Importantly, the biosynthesis of fluorinated alamethicin F50 derivatives by strain MSX70741 was monitored in situ using a droplet-liquid microjunction-surface sampling probe coupled to a hyphenated system.
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Affiliation(s)
- José Rivera-Chávez
- Department
of Chemistry and Biochemistry, University
of North Carolina at Greensboro, P.O. Box 26170, Greensboro, North Carolina 27412, United States
| | - Huzefa A. Raja
- Department
of Chemistry and Biochemistry, University
of North Carolina at Greensboro, P.O. Box 26170, Greensboro, North Carolina 27412, United States
| | - Tyler N. Graf
- Department
of Chemistry and Biochemistry, University
of North Carolina at Greensboro, P.O. Box 26170, Greensboro, North Carolina 27412, United States
| | - Joanna E. Burdette
- Department
of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Cedric J. Pearce
- Mycosynthetix, Inc., 505 Meadowlands Drive, Suite 103, Hillsborough, North Carolina 27278, United States
| | - Nicholas H. Oberlies
- Department
of Chemistry and Biochemistry, University
of North Carolina at Greensboro, P.O. Box 26170, Greensboro, North Carolina 27412, United States
- E-mail: . Tel: 336-334-5474
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29
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Marik T, Urbán P, Tyagi C, Szekeres A, Leitgeb B, Vágvölgyi M, Manczinger L, Druzhinina IS, Vágvölgyi C, Kredics L. Diversity Profile and Dynamics of Peptaibols Produced by Green Mould Trichoderma Species in Interactions with Their Hosts Agaricus bisporus and Pleurotus ostreatus. Chem Biodivers 2017; 14. [PMID: 28261948 DOI: 10.1002/cbdv.201700033] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 02/27/2017] [Indexed: 11/06/2022]
Abstract
Certain Trichoderma species are causing serious losses in mushroom production worldwide. Trichoderma aggressivum and Trichoderma pleuroti are among the major causal agents of the green mould diseases affecting Agaricus bisporus and Pleurotus ostreatus, respectively. The genus Trichoderma is well-known for the production of bioactive secondary metabolites, including peptaibols, which are short, linear peptides containing unusual amino acid residues and being synthesised via non-ribosomal peptide synthetases (NRPSs). The aim of this study was to get more insight into the peptaibol production of T. aggressivum and T. pleuroti. HPLC/MS-based methods revealed the production of peptaibols closely related to hypomurocins B by T. aggressivum, while tripleurins representing a new group of 18-residue peptaibols were identified in T. pleuroti. Putative NRPS genes enabling the biosynthesis of the detected peptaibols could be found in the genomes of both Trichoderma species. In vitro experiments revealed that peptaibols are potential growth inhibitors of mushroom mycelia, and that the host mushrooms may have an influence on the peptaibol profiles of green mould agents.
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Affiliation(s)
- Tamás Marik
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726, Szeged, Hungary
| | - Péter Urbán
- Department of General and Environmental Microbiology, Faculty of Sciences, and Szentágothai Research Center, University of Pécs, Ifjúság útja 6, H-7624, Pécs, Hungary
| | - Chetna Tyagi
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726, Szeged, Hungary
| | - András Szekeres
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726, Szeged, Hungary
| | - Balázs Leitgeb
- Institute of Biophysics, Biological Research Centre of the Hungarian Academy of Sciences, Temesvári krt. 62, H-6726, Szeged, Hungary
| | - Máté Vágvölgyi
- Institute of Pharmacognosy, University of Szeged, Eötvös u. 6, H-6720, Szeged, Hungary
| | - László Manczinger
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726, Szeged, Hungary
| | - Irina S Druzhinina
- Research Area Biochemical Technology, Institute of Chemical and Biological Engineering, TU Wien, Getreidemarkt 9/166, A-1060, Vienna, Austria
| | - Csaba Vágvölgyi
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726, Szeged, Hungary
| | - László Kredics
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726, Szeged, Hungary
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30
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Raja H, Miller AN, Pearce CJ, Oberlies NH. Fungal Identification Using Molecular Tools: A Primer for the Natural Products Research Community. JOURNAL OF NATURAL PRODUCTS 2017; 80:756-770. [PMID: 28199101 PMCID: PMC5368684 DOI: 10.1021/acs.jnatprod.6b01085] [Citation(s) in RCA: 373] [Impact Index Per Article: 53.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Indexed: 05/17/2023]
Abstract
Fungi are morphologically, ecologically, metabolically, and phylogenetically diverse. They are known to produce numerous bioactive molecules, which makes them very useful for natural products researchers in their pursuit of discovering new chemical diversity with agricultural, industrial, and pharmaceutical applications. Despite their importance in natural products chemistry, identification of fungi remains a daunting task for chemists, especially those who do not work with a trained mycologist. The purpose of this review is to update natural products researchers about the tools available for molecular identification of fungi. In particular, we discuss (1) problems of using morphology alone in the identification of fungi to the species level; (2) the three nuclear ribosomal genes most commonly used in fungal identification and the potential advantages and limitations of the ITS region, which is the official DNA barcoding marker for species-level identification of fungi; (3) how to use NCBI-BLAST search for DNA barcoding, with a cautionary note regarding its limitations; (4) the numerous curated molecular databases containing fungal sequences; (5) the various protein-coding genes used to augment or supplant ITS in species-level identification of certain fungal groups; and (6) methods used in the construction of phylogenetic trees from DNA sequences to facilitate fungal species identification. We recommend that, whenever possible, both morphology and molecular data be used for fungal identification. Our goal is that this review will provide a set of standardized procedures for the molecular identification of fungi that can be utilized by the natural products research community.
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Affiliation(s)
- Huzefa
A. Raja
- Department
of Chemistry and Biochemistry, University
of North Carolina at Greensboro, Greensboro, North Carolina 27402, United States
| | - Andrew N. Miller
- Illinois
Natural History Survey, University of Illinois, Champaign, Illinois 61820, United States
| | - Cedric J. Pearce
- Mycosynthetix,
Inc., 505 Meadowland
Drive, Suite 103, Hillsborough, North Carolina 27278, United States
| | - Nicholas H. Oberlies
- Department
of Chemistry and Biochemistry, University
of North Carolina at Greensboro, Greensboro, North Carolina 27402, United States
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31
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Degenkolb T, Götze L, von Döhren H, Vilcinskas A, Brückner H. Sequences of stilboflavin C: towards the peptaibiome of the filamentous fungus Stilbella (= Trichoderma) flavipes. J Pept Sci 2017; 22:517-24. [PMID: 27443977 DOI: 10.1002/psc.2897] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 04/26/2016] [Accepted: 05/09/2016] [Indexed: 01/30/2023]
Abstract
Filamentous fungi of the genus Stilbella are recognized as an abundant source of naturally occurring α-aminoisobutyric acid-containing peptides. The culture broth of Stilbella (Trichoderma) flavipes CBS 146.81 yielded a mixture of peptides named stilboflavins (SF), and these were isolated and separated by preparative TLC into groups named SF-A, SF-B, and SF-C. Although all three of these groups resolved as single spots on thin-layer chromatograms, HPLC analysis revealed that each of the groups represents very microheterogeneous mixtures of closely related peptides. Here, we report on the sequence analysis of SF-C peptides, formerly isolated by preparative TLC. HPLC coupled to QqTOF-ESI-HRMS provided the sequences of 10 16-residue peptides and five 19-residue peptides, all of which were N-terminally acetylated. In contrast to the previously described SF-A and SF-B peptaibols, SF-C peptaibols contain Ser-Alaol or Ser-Leuol, which are rarely found as C-termini, and repetitive Leu-Aib-Gly sequences, which have not been detected in peptaibols before. Taking the previously determined sequences of SF-A and SF-B into account, the entirety of peptides produced by S. flavipes (the 'peptaibiome') approaches or exceeds 100 non-ribosomally biosynthesized peptaibiotics. Copyright © 2016 European Peptide Society and John Wiley & Sons, Ltd.
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Affiliation(s)
- Thomas Degenkolb
- Institute for Insect Biotechnology, Department of Applied Entomology, Interdisciplinary Research Center for BioSystems, Land Use and Nutrition (IFZ), Justus-Liebig-University of Giessen, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Lutz Götze
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Winchester Strasse 2, 35394, Giessen, Germany
| | - Hans von Döhren
- Biochemistry and Molecular Biology OE 2, Institute of Chemistry, Technical University of Berlin, Franklinstrasse 29, 10587, Berlin, Germany.,Schillerstrasse 34, 10627, Berlin, Germany
| | - Andreas Vilcinskas
- Institute for Insect Biotechnology, Department of Applied Entomology, Interdisciplinary Research Center for BioSystems, Land Use and Nutrition (IFZ), Justus-Liebig-University of Giessen, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany.,Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Winchester Strasse 2, 35394, Giessen, Germany
| | - Hans Brückner
- Institute for Insect Biotechnology, Department of Applied Entomology, Interdisciplinary Research Center for BioSystems, Land Use and Nutrition (IFZ), Justus-Liebig-University of Giessen, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
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Gessmann R, Axford D, Brückner H, Berg A, Petratos K. A natural, single-residue substitution yields a less active peptaibiotic: the structure of bergofungin A at atomic resolution. Acta Crystallogr F Struct Biol Commun 2017; 73:95-100. [PMID: 28177320 PMCID: PMC5297930 DOI: 10.1107/s2053230x17001236] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 01/24/2017] [Indexed: 11/11/2022] Open
Abstract
Bergofungin is a peptide antibiotic that is produced by the ascomycetous fungus Emericellopsis donezkii HKI 0059 and belongs to peptaibol subfamily 2. The crystal structure of bergofungin A has been determined and refined to 0.84 Å resolution. This is the second crystal structure of a natural 15-residue peptaibol, after that of samarosporin I. The amino-terminal phenylalanine residue in samarosporin I is exchanged to a valine residue in bergofungin A. According to agar diffusion tests, this results in a nearly inactive antibiotic peptide compared with the moderately active samarosporin I. Crystals were obtained from methanol solutions of purified bergofungin mixed with water. Although there are differences in the intramolecular hydrogen-bonding scheme of samarosporin I, the overall folding is very similar for both peptaibols, namely 310-helical at the termini and α-helical in the middle of the molecules. Bergofungin A and samarosporin I molecules are arranged in a similar way in both lattices. However, the packing of bergofungin A exhibits a second solvent channel along the twofold axis. This latter channel occurs in the vicinity of the N-terminus, where the natural substitution resides.
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Affiliation(s)
| | - Danny Axford
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - Hans Brückner
- Department of Food Science, Institute of Nutritional Science, Research Center for BioSystems, Land Use and Nutrition (IFZ), Heinrich-Buff-Ring 26-32, 65392 Giessen, Germany
| | - Albrecht Berg
- Innovent e.V., Prüssingstrasse 27B, 07745 Jena, Germany
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Zeilinger S, Gruber S, Bansal R, Mukherjee PK. Secondary metabolism in Trichoderma – Chemistry meets genomics. FUNGAL BIOL REV 2016. [DOI: 10.1016/j.fbr.2016.05.001] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Mohamed-Benkada M, François Pouchus Y, Vérité P, Pagniez F, Caroff N, Ruiz N. Identification and Biological Activities of Long-Chain Peptaibols Produced by a Marine-Derived Strain ofTrichoderma longibrachiatum. Chem Biodivers 2016; 13:521-30. [DOI: 10.1002/cbdv.201500159] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2015] [Accepted: 12/11/2015] [Indexed: 11/09/2022]
Affiliation(s)
- Mustapha Mohamed-Benkada
- Département de Biotechnologie; Faculté des Sciences de la Nature et de la Vie; Université des Sciences et de la Technologie d'Oran-Mohamed Boudiaf (USTO-MB); El Mnaouar, B.P. 1505 Bir El Djir 31000 Oran Algeria
| | | | - Philippe Vérité
- Laboratoire de Chimie Analytique; Faculté de Médecine et Pharmacie; Université de Rouen; FR-76000 Rouen
| | - Fabrice Pagniez
- Laboratoire de Parasitologie et Mycologie Médicale, IICiMed; Faculté de Pharmacie; Université de Nantes; FR-44000 Nantes
| | - Nathalie Caroff
- Laboratoire Thérapeutiques Cliniques et Expérimentales des Infections; Faculté de Médecine; Université de Nantes; FR-44000 Nantes
| | - Nicolas Ruiz
- Faculté de Pharmacie, MMS; Université de Nantes; FR-44000 Nantes
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Holzlechner M, Reitschmidt S, Gruber S, Zeilinger S, Marchetti-Deschmann M. Visualizing fungal metabolites during mycoparasitic interaction by MALDI mass spectrometry imaging. Proteomics 2016; 16:1742-6. [PMID: 26959280 PMCID: PMC4982067 DOI: 10.1002/pmic.201500510] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 01/25/2016] [Accepted: 02/17/2016] [Indexed: 11/09/2022]
Abstract
Studying microbial interactions by MALDI mass spectrometry imaging (MSI) directly from growing media is a difficult task if high sensitivity is demanded. We present a quick and robust sample preparation strategy for growing fungi (Trichoderma atroviride, Rhizoctonia solani) on glass slides to establish a miniaturized confrontation assay. By this we were able to visualize metabolite distributions by MALDI MSI after matrix deposition with a home-built sublimation device and thorough recrystallization. We present for the first time MALDI MSI data for secondary metabolite release during active mycoparasitism.
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Affiliation(s)
- Matthias Holzlechner
- Institute of Chemical Technologies and Analytics, Vienna University of Technology, Vienna, Austria
| | - Sonja Reitschmidt
- Institute of Chemical Technologies and Analytics, Vienna University of Technology, Vienna, Austria
| | - Sabine Gruber
- Institute of Microbiology, University of Innsbruck, Innsbruck, Austria
| | - Susanne Zeilinger
- Institute of Microbiology, University of Innsbruck, Innsbruck, Austria.,Institute of Chemical Engineering, Vienna University of Technology, Vienna, Austria
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Development and validation of LC–MS methods for peptaibol quantification in fungal extracts according to their lengths. J Chromatogr B Analyt Technol Biomed Life Sci 2016; 1009-1010:25-33. [DOI: 10.1016/j.jchromb.2015.11.039] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 10/20/2015] [Accepted: 11/21/2015] [Indexed: 01/31/2023]
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Tavano R, Malachin G, De Zotti M, Peggion C, Biondi B, Formaggio F, Papini E. Comparison of bactericidal and cytotoxic activities of trichogin analogs. Data Brief 2015; 6:359-67. [PMID: 26862583 PMCID: PMC4706618 DOI: 10.1016/j.dib.2015.12.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 11/30/2015] [Accepted: 12/04/2015] [Indexed: 11/29/2022] Open
Abstract
Peptaibiotics are a group of membrane active peptides of fungal origin. They typically contain α-aminoisobutyric acid (Aib; 1-letter code, U) and other non-coded residues (Toniolo and Brückner, 2009; Neumann et al., 2015; Benedett et al., 1982) [1], [2], [3] stabilizing their helical structure. Peptaibols are peptaibiotics carrying a 1, 2-aminoalcohol at the C-terminus. When a fatty acid chain (of 8–10 carbon atoms) is present at their N-terminus, they are called lipopeptaibols (Toniolo et al., 2001; Degenkolb et al., 2003) [4], [5]. We found (Tavano et al., 2015) [6] that the lipopeptaibol trichogin displays no antibacterial effects up to 64 µM, against both Gram− and Gram+ bacteria, but kills tumor and healthy human cells via a mechanism requiring both the C-terminal primary alcohol group and the N-terminal n-octanoyl moiety, with EC50s around 4–5 µM. However, the substitution of single Gly residues with Lys strongly improves anti-Gram+ activity (Tavano et al., 2015; De Zotti, Biondi, Park et al., 2012; De Zotti, Biondi, Peggion et al., 2012) [6], [7], [8]. To further characterize the activity of trichogin analogs as antibiotics and cytotoxic agents, we here manipulated the peptide helix amphipathicity by means of two different substitutions: (i) Aib to Leu (De Zotti et al., 2012) [7] or (ii) multiple Gly to Lys changes (Tavano et al., 2015; De Zotti, Biondi, Park et al., 2012; De Zotti, Biondi, Peggion, Formaggio et al., 2012; De Zotti, Biondi, Peggion, De Poli et al., 2012) [6], [7], [8], [9]. The antibacterial activity against four commensal or opportunistic bacterial species and the cytotoxicity against a panel of 9 healthy and tumor-derived eukaryotic cell types (including erythrocytes) are reported as MIC and EC50 (MTS - [3-(4, 5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)]-2H-tetrazolium- reduction and LDH - lactate dehydrogenase - release assay).
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Affiliation(s)
- Regina Tavano
- Department of Biomedical Sciences, University of Padova, Viale G. Colombo 3, 35121 Padova, Italy
| | - Giulia Malachin
- Department of Biomedical Sciences, University of Padova, Viale G. Colombo 3, 35121 Padova, Italy
| | - Marta De Zotti
- Institute of Biomolecular Chemistry, CNR, Padova Unit, Department of Chemistry, University of Padova, Via Marzolo 1, 35131 Padova, Italy
| | - Cristina Peggion
- Institute of Biomolecular Chemistry, CNR, Padova Unit, Department of Chemistry, University of Padova, Via Marzolo 1, 35131 Padova, Italy
| | - Barbara Biondi
- Institute of Biomolecular Chemistry, CNR, Padova Unit, Department of Chemistry, University of Padova, Via Marzolo 1, 35131 Padova, Italy
| | - Fernando Formaggio
- Institute of Biomolecular Chemistry, CNR, Padova Unit, Department of Chemistry, University of Padova, Via Marzolo 1, 35131 Padova, Italy
| | - Emanuele Papini
- Department of Biomedical Sciences, University of Padova, Viale G. Colombo 3, 35121 Padova, Italy
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Flissi A, Dufresne Y, Michalik J, Tonon L, Janot S, Noé L, Jacques P, Leclère V, Pupin M. Norine, the knowledgebase dedicated to non-ribosomal peptides, is now open to crowdsourcing. Nucleic Acids Res 2015; 44:D1113-8. [PMID: 26527733 PMCID: PMC4702827 DOI: 10.1093/nar/gkv1143] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 10/16/2015] [Indexed: 11/29/2022] Open
Abstract
Since its creation in 2006, Norine remains the unique knowledgebase dedicated to non-ribosomal peptides (NRPs). These secondary metabolites, produced by bacteria and fungi, harbor diverse interesting biological activities (such as antibiotic, antitumor, siderophore or surfactant) directly related to the diversity of their structures. The Norine team goal is to collect the NRPs and provide tools to analyze them efficiently. We have developed a user-friendly interface and dedicated tools to provide a complete bioinformatics platform. The knowledgebase gathers abundant and valuable annotations on more than 1100 NRPs. To increase the quantity of described NRPs and improve the quality of associated annotations, we are now opening Norine to crowdsourcing. We believe that contributors from the scientific community are the best experts to annotate the NRPs they work on. We have developed MyNorine to facilitate the submission of new NRPs or modifications of stored ones. This article presents MyNorine and other novelties of Norine interface released since the first publication. Norine is freely accessible from the following URL: http://bioinfo.lifl.fr/NRP.
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Affiliation(s)
- Areski Flissi
- University of Lille, CRIStAL, UMR CNRS 9189, cité scientifique-bat M3ext, 59650 Villeneuve d'Ascq, France Inria Lille Nord Europe, Bonsai team, Parc scientifique de la Haute Borne, 40, avenue Halley-Bt A, 59650 Villeneuve d'Ascq, France
| | - Yoann Dufresne
- University of Lille, CRIStAL, UMR CNRS 9189, cité scientifique-bat M3ext, 59650 Villeneuve d'Ascq, France Inria Lille Nord Europe, Bonsai team, Parc scientifique de la Haute Borne, 40, avenue Halley-Bt A, 59650 Villeneuve d'Ascq, France
| | - Juraj Michalik
- University of Lille, CRIStAL, UMR CNRS 9189, cité scientifique-bat M3ext, 59650 Villeneuve d'Ascq, France University of Lille, bilille, cité scientifique-bat M3ext, 59650 Villeneuve d'Ascq, France
| | - Laurie Tonon
- University of Lille, CRIStAL, UMR CNRS 9189, cité scientifique-bat M3ext, 59650 Villeneuve d'Ascq, France Inria Lille Nord Europe, Bonsai team, Parc scientifique de la Haute Borne, 40, avenue Halley-Bt A, 59650 Villeneuve d'Ascq, France
| | - Stéphane Janot
- University of Lille, CRIStAL, UMR CNRS 9189, cité scientifique-bat M3ext, 59650 Villeneuve d'Ascq, France Inria Lille Nord Europe, Bonsai team, Parc scientifique de la Haute Borne, 40, avenue Halley-Bt A, 59650 Villeneuve d'Ascq, France
| | - Laurent Noé
- University of Lille, CRIStAL, UMR CNRS 9189, cité scientifique-bat M3ext, 59650 Villeneuve d'Ascq, France Inria Lille Nord Europe, Bonsai team, Parc scientifique de la Haute Borne, 40, avenue Halley-Bt A, 59650 Villeneuve d'Ascq, France
| | - Philippe Jacques
- University of Lille, EA 7394, ICV-Institut Charles Viollette, ProBioGEM team, Polytech'Lille, avenue Langevin, 59655 Villeneuve d'Ascq, France
| | - Valérie Leclère
- University of Lille, CRIStAL, UMR CNRS 9189, cité scientifique-bat M3ext, 59650 Villeneuve d'Ascq, France Inria Lille Nord Europe, Bonsai team, Parc scientifique de la Haute Borne, 40, avenue Halley-Bt A, 59650 Villeneuve d'Ascq, France University of Lille, EA 7394, ICV-Institut Charles Viollette, ProBioGEM team, Polytech'Lille, avenue Langevin, 59655 Villeneuve d'Ascq, France
| | - Maude Pupin
- University of Lille, CRIStAL, UMR CNRS 9189, cité scientifique-bat M3ext, 59650 Villeneuve d'Ascq, France Inria Lille Nord Europe, Bonsai team, Parc scientifique de la Haute Borne, 40, avenue Halley-Bt A, 59650 Villeneuve d'Ascq, France University of Lille, bilille, cité scientifique-bat M3ext, 59650 Villeneuve d'Ascq, France
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Waghu FH, Barai RS, Gurung P, Idicula-Thomas S. CAMPR3: a database on sequences, structures and signatures of antimicrobial peptides. Nucleic Acids Res 2015; 44:D1094-7. [PMID: 26467475 PMCID: PMC4702787 DOI: 10.1093/nar/gkv1051] [Citation(s) in RCA: 428] [Impact Index Per Article: 47.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 10/01/2015] [Indexed: 12/31/2022] Open
Abstract
Antimicrobial peptides (AMPs) are known to have family-specific sequence composition, which can be mined for discovery and design of AMPs. Here, we present CAMPR3; an update to the existing CAMP database available online at www.camp3.bicnirrh.res.in. It is a database of sequences, structures and family-specific signatures of prokaryotic and eukaryotic AMPs. Family-specific sequence signatures comprising of patterns and Hidden Markov Models were generated for 45 AMP families by analysing 1386 experimentally studied AMPs. These were further used to retrieve AMPs from online sequence databases. More than 4000 AMPs could be identified using these signatures. AMP family signatures provided in CAMPR3 can thus be used to accelerate and expand the discovery of AMPs. CAMPR3 presently holds 10247 sequences, 757 structures and 114 family-specific signatures of AMPs. Users can avail the sequence optimization algorithm for rational design of AMPs. The database integrated with tools for AMP sequence and structure analysis will be a valuable resource for family-based studies on AMPs.
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Affiliation(s)
- Faiza Hanif Waghu
- Biomedical Informatics Centre of Indian Council of Medical Research, National Institute for Research in Reproductive Health, Mumbai 400012, Maharashtra, India
| | - Ram Shankar Barai
- Biomedical Informatics Centre of Indian Council of Medical Research, National Institute for Research in Reproductive Health, Mumbai 400012, Maharashtra, India
| | - Pratima Gurung
- Biomedical Informatics Centre of Indian Council of Medical Research, National Institute for Research in Reproductive Health, Mumbai 400012, Maharashtra, India
| | - Susan Idicula-Thomas
- Biomedical Informatics Centre of Indian Council of Medical Research, National Institute for Research in Reproductive Health, Mumbai 400012, Maharashtra, India
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Gas chromatographic separation of stereoisomers of non-protein amino acids on modified γ-cyclodextrin stationary phase. J Chromatogr A 2015; 1411:101-9. [DOI: 10.1016/j.chroma.2015.07.082] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 07/20/2015] [Accepted: 07/22/2015] [Indexed: 11/22/2022]
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