1
|
Serrano R, González-Menéndez V, Tormo JR, Genilloud O. Development and Validation of a HTS Platform for the Discovery of New Antifungal Agents against Four Relevant Fungal Phytopathogens. J Fungi (Basel) 2023; 9:883. [PMID: 37754991 PMCID: PMC10532314 DOI: 10.3390/jof9090883] [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: 07/28/2023] [Revised: 08/22/2023] [Accepted: 08/25/2023] [Indexed: 09/28/2023] Open
Abstract
Fungal phytopathogens are the major agents responsible for causing severe damage to and losses in agricultural crops worldwide. Botrytis cinerea, Colletotrichum acutatum, Fusarium proliferatum, and Magnaporthe grisea are included in the top ten fungal phytopathogens that impose important plant diseases on a broad range of crops. Microbial natural products can be an attractive alternative for the biological control of phytopathogens. The objective of this work was to develop and validate a High-throughput Screening (HTS) platform to evaluate the antifungal potential of chemicals and natural products against these four important plant pathogens. Several experiments were performed to establish the optimal assay conditions that provide the best reproducibility and robustness. For this purpose, we have evaluated two media formulations (SDB and RPMI-1640), several inoculum concentrations (1 × 106, 5 × 105 and 5 × 106 conidia/mL), the germination curves for each strain, each strain's tolerance to dimethyl sulfoxide (DMSO), and the Dose Response Curves (DRC) of the antifungal control (Amphotericin B). The assays were performed in 96-well plate format, where absorbance at 620 nm was measured before and after incubation to evaluate growth inhibition, and fluorescence intensity at 570 nm excitation and 615 nm emission was monitored after resazurin addition for cell viability evaluation. Quality control parameters (RZ' Factors and Signal to Background (S/B) ratios) were determined for each assay batch. The assay conditions were finally validated by titrating 40 known relevant antifungal agents and testing 2400 microbial natural product extracts from the MEDINA Library through both HTS agar-based and HTS microdilution-based set-ups on the four phytopathogens.
Collapse
Affiliation(s)
- Rachel Serrano
- Fundación MEDINA, Av. Conocimiento 34, Health Sciences Technology Park, 18016 Granada, Spain; (J.R.T.); (O.G.)
| | - Víctor González-Menéndez
- Fundación MEDINA, Av. Conocimiento 34, Health Sciences Technology Park, 18016 Granada, Spain; (J.R.T.); (O.G.)
| | | | | |
Collapse
|
2
|
Ramesha KP, Chandra Mohana N, Chandra Nayaka S, Satish S. Epigenetic Modifiers Revamp Secondary Metabolite Production in Endophytic Nigrospora sphaerica. Front Microbiol 2021; 12:730355. [PMID: 34925254 PMCID: PMC8678036 DOI: 10.3389/fmicb.2021.730355] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 10/22/2021] [Indexed: 11/13/2022] Open
Abstract
During plant interaction, endophytes provide benefits to the host plant. Endophytes also contribute a variety of structural attributes with biological potential. Nigrospora sphaerica, which produces phomalactone from Adiantum philippense L., was subjected to epigenetic modification. High-performance liquid chromatography (HPLC) and Gas chromatography-mass spectrometry (GCMS) analysis were used to determine secondary metabolite profiling. Epigenetic modifiers like DNA Methyltransferase (DNMT) and Histone deacetylase (HDAC) inhibitors increased the expression of biosynthetic pathways. The activation of new metabolites was observed as a result of the activation of cryptic biosynthetic gene clusters, as well as the silencing of phomalactone in some treatments. When compared to DNMT treatments, HDAC treatments showed a significant increase in cryptic metabolite induction. The induction of cryptic metabolites with biological significance by HDAC treatment is supported by our findings.
Collapse
Affiliation(s)
- Kolathuru Puttamadaiah Ramesha
- Microbial Drug Technological Laboratory, Department of Studies in Microbiology, University of Mysore, Manasagangotri, Mysore, India
| | - Nagabhushana Chandra Mohana
- Microbial Drug Technological Laboratory, Department of Studies in Microbiology, University of Mysore, Manasagangotri, Mysore, India
| | | | - Sreedharamurthy Satish
- Microbial Drug Technological Laboratory, Department of Studies in Microbiology, University of Mysore, Manasagangotri, Mysore, India
| |
Collapse
|
3
|
Zhang Y, Ren J, Wang W, Chen B, Li E, Chen S. Siderophore and indolic acid production by Paenibacillus triticisoli BJ-18 and their plant growth-promoting and antimicrobe abilities. PeerJ 2020; 8:e9403. [PMID: 32742769 PMCID: PMC7367057 DOI: 10.7717/peerj.9403] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 06/01/2020] [Indexed: 12/22/2022] Open
Abstract
Paenibacillus triticisoli BJ-18, a N2-fixing bacterium, is able to promote plant growth, but the secondary metabolites that may play a role in promoting plant growth have never been characterized. In this study, untargeted metabolomics profiling of P. triticisoli BJ-18 indicated the existence of 101 known compounds, including N2-acetyl ornithine, which is the precursor of siderophores, plant growth regulators such as trehalose 6-phosphate, betaine and trigonelline, and other bioactive molecules such as oxymatrine, diosmetin, luotonin A, (-)-caryophyllene oxide and tetrahydrocurcumin. In addition, six compounds were also isolated from P. triticisoli BJ-18 using a combination of silica gel chromatography, sephadex LH-20, octadecyl silane (ODS), and high-performance liquid chromatography (HPLC). The compound structures were further analyzed by Nuclear Magnetic Resonance (NMR), Mass Spectrometry (MS), and Electronic Circular Dichroism (ECD). The six compounds included three classical siderophore fusarinines identified as deshydroxylferritriacetylfusigen, desferritriacetylfusigen, and triacetylfusigen, and three indolic acids identified as paenibacillic acid A, 3-indoleacetic acid (IAA), and 3-indolepropionic acid (IPA). Both deshydroxylferritriacetylfusigen and paenibacillic acid A have new structures. Fusarinines, which normally occur in fungi, were isolated from bacterium for the first time in this study. Both siderophores (compounds 1 and 2) showed antimicrobial activity against Escherichia coli, Staphylococcus aureus and Bacillus subtilis, but did not show obvious inhibitory activity against yeast Candida albicans, whereas triacetylfusigen (compound 3) showed no antibiosis activity against these test microorganisms. Paenibacillic acid A, IAA, and IPA were shown to promote the growth of plant shoots and roots, and paenibacillic acid A also showed antimicrobial activity against S. aureus. Our study demonstrates that siderophores and indolic acids may play an important role in plant growth promotion by P. triticisoli BJ-18.
Collapse
Affiliation(s)
- Yunzhi Zhang
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, People’s Republic of China
| | - Jinwei Ren
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Wenzhao Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Baosong Chen
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Erwei Li
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Sanfeng Chen
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, People’s Republic of China
| |
Collapse
|
4
|
Lan N, Perlatti B, Kvitek DJ, Wiemann P, Harvey CJB, Frisvad J, An Z, Bills GF. Acrophiarin (antibiotic S31794/F-1) from Penicillium arenicola shares biosynthetic features with both Aspergillus- and Leotiomycete-type echinocandins. Environ Microbiol 2020; 22:2292-2311. [PMID: 32239586 DOI: 10.1111/1462-2920.15004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 03/28/2020] [Indexed: 11/30/2022]
Abstract
The antifungal echinocandin lipopeptide, acrophiarin, was circumscribed in a patent in 1979. We confirmed that the producing strain NRRL 8095 is Penicillium arenicola and other strains of P. arenicola produced acrophiarin and acrophiarin analogues. Genome sequencing of NRRL 8095 identified the acrophiarin gene cluster. Penicillium arenicola and echinocandin-producing Aspergillus species belong to the family Aspergillaceae of the Eurotiomycetes, but several features of acrophiarin and its gene cluster suggest a closer relationship with echinocandins from Leotiomycete fungi. These features include hydroxy-glutamine in the peptide core instead of a serine or threonine residue, the inclusion of a non-heme iron, α-ketoglutarate-dependent oxygenase for hydroxylation of the C3 of the glutamine, and a thioesterase. In addition, P. arenicola bears similarity to Leotiomycete echinocandin-producing species because it exhibits self-resistance to exogenous echinocandins. Phylogenetic analysis of the genes of the echinocandin biosynthetic family indicated that most of the predicted proteins of acrophiarin gene cluster exhibited higher similarity to the predicted proteins of the pneumocandin gene cluster of the Leotiomycete Glarea lozoyensis than to those of the echinocandin B gene cluster from A. pachycristatus. The fellutamide gene cluster and related gene clusters are recognized as relatives of the echinocandins. Inclusion of the acrophiarin gene cluster into a comprehensive phylogenetic analysis of echinocandin gene clusters indicated the divergent evolutionary lineages of echinocandin gene clusters are descendants from a common ancestral progenitor. The minimal 10-gene cluster may have undergone multiple gene acquisitions or losses and possibly horizontal gene transfer after the ancestral separation of the two lineages.
Collapse
Affiliation(s)
- Nan Lan
- Texas Therapeutics Institute, The Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX, 77054, USA
| | - Bruno Perlatti
- Texas Therapeutics Institute, The Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX, 77054, USA
| | | | | | | | - Jens Frisvad
- Center for Microbial Biotechnology, Department of Systems Biology, Technical University of Denmark, DK-2800, Lyngby, Denmark
| | - Zhiqiang An
- Texas Therapeutics Institute, The Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX, 77054, USA
| | - Gerald F Bills
- Texas Therapeutics Institute, The Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX, 77054, USA
| |
Collapse
|
5
|
Perlatti B, Lan N, Jiang Y, An Z, Bills G. Identification of Secondary Metabolites from Aspergillus pachycristatus by Untargeted UPLC-ESI-HRMS/MS and Genome Mining. Molecules 2020; 25:molecules25040913. [PMID: 32085602 PMCID: PMC7071103 DOI: 10.3390/molecules25040913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 02/14/2020] [Indexed: 11/16/2022] Open
Abstract
Aspergillus pachycristatus is an industrially important fungus for the production of the antifungal echinocandin B and is closely related to model organism A. nidulans. Its secondary metabolism is largely unknown except for the production of echinocandin B and sterigmatocystin. We constructed mutants for three genes that regulate secondary metabolism in A. pachycristatus NRRL 11440, and evaluated the secondary metabolites produced by wild type and mutants strains. The secondary metabolism was explored by metabolic networking of UPLC-HRMS/MS data. The genes and metabolites of A. pachycristatus were compared to those of A.nidulans FGSC A4 as a reference to identify compounds and link them to their encoding genes. Major differences in chromatographic profiles were observable among the mutants. At least 28 molecules were identified in crude extracts that corresponded to nine characterized gene clusters. Moreover, metabolic networking revealed the presence of a yet unexplored array of secondary metabolites, including several undescribed fellutamides derivatives. Comparative reference to its sister species, A. nidulans, was an efficient way to dereplicate known compounds, whereas metabolic networking provided information that allowed prioritization of unknown compounds for further metabolic exploration. The mutation of global regulator genes proved to be a useful tool for expanding the expression of metabolic diversity in A. pachycristatus.
Collapse
Affiliation(s)
- Bruno Perlatti
- Texas Therapeutic Institute, The Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX 77054, USA; (N.L.); (Z.A.); (G.B.)
- Correspondence:
| | - Nan Lan
- Texas Therapeutic Institute, The Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX 77054, USA; (N.L.); (Z.A.); (G.B.)
| | - Yongying Jiang
- Institute for Applied Cancer Science, M.D. Anderson Cancer Center, Houston, TX 77054, USA;
| | - Zhiqiang An
- Texas Therapeutic Institute, The Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX 77054, USA; (N.L.); (Z.A.); (G.B.)
| | - Gerald Bills
- Texas Therapeutic Institute, The Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX 77054, USA; (N.L.); (Z.A.); (G.B.)
| |
Collapse
|
6
|
Jakubczyk D, Dussart F. Selected Fungal Natural Products with Antimicrobial Properties. Molecules 2020; 25:E911. [PMID: 32085562 PMCID: PMC7070998 DOI: 10.3390/molecules25040911] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 02/13/2020] [Accepted: 02/14/2020] [Indexed: 01/14/2023] Open
Abstract
Fungal natural products and their effects have been known to humankind for hundreds of years. For example, toxic ergot alkaloids produced by filamentous fungi growing on rye poisoned thousands of people and livestock throughout the Middle Ages. However, their later medicinal applications, followed by the discovery of the first class of antibiotics, penicillins and other drugs of fungal origin, such as peptidic natural products, terpenoids or polyketides, have altered the historically negative reputation of fungal "toxins". The development of new antimicrobial drugs is currently a major global challenge, mainly due to antimicrobial resistance phenomena. Therefore, the structures, biosynthesis and antimicrobial activity of selected fungal natural products are described here.
Collapse
Affiliation(s)
- Dorota Jakubczyk
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznań, Poland
| | - Francois Dussart
- Department of Agriculture, Horticulture and Engineering Science, Scotland’s Rural College (SRUC), Edinburgh EH9 3JG, UK;
| |
Collapse
|
7
|
Alburae NA, Mohammed AE, Alorfi HS, Turki AJ, Asfour HZ, Alarif WM, Abdel-Lateff A. Nidulantes of Aspergillus (Formerly Emericella): A Treasure Trove of Chemical Diversity and Biological Activities. Metabolites 2020; 10:E73. [PMID: 32079311 PMCID: PMC7073611 DOI: 10.3390/metabo10020073] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Revised: 02/10/2020] [Accepted: 02/10/2020] [Indexed: 01/04/2023] Open
Abstract
The genus Emericella (Ascomycota) includes more than thirty species with worldwide distribution across many ecosystems. It is considered a rich source of diverse metabolites. The published classes of natural compounds that are discussed here are organized according to the following biosynthetic pathways: polyketides (azaphilones, cyclopentenone pigments, dicyanides, furan derivatives, phenolic ethers, and xanthones and anthraquinones); shikimate derivatives (bicoumarins); mevalonate derivatives (meroterpenes, sesquiterpenes, sesterterpenes and steroids) and amino acids derivatives (alkaloids (indole-derivatives, isoindolones, and piperazine) and peptides (depsipeptides)). These metabolites produce the wide array of biological effects associated with Emericella, including antioxidant, antiproliferative, antimalarial, antiviral, antibacterial, antioxidant, antihypertensive, anti-inflammatory, antifungal and kinase inhibitors. Careful and extensive study of the diversity and distribution of metabolites produced by the genus Emericella (either marine or terrestrial) revealed that, no matter the source of the fungus, the composition of the culture medium effectively controls the metabolites produced. The topic of this review is the diversity of metabolites that have been identified from Emericella, along with the contextual information on either their biological or geographic sources. This review presents 236 natural compounds, which were reported from marine and terrestrial Emericella. Amongst the reported compounds, only 70.2% were biologically assayed for their effects, including antimicrobial or cytotoxicity. This implies the need for substantial investigation of alternative activities. This review includes a full discussion of compound structures and disease management, based on materials published from 1982 through December 2019.
Collapse
Affiliation(s)
- Najla Ali Alburae
- Department of Biology, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia;
| | - Afrah E. Mohammed
- Department of Biology, Faculty of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia;
| | - Hajer Saeed Alorfi
- Department of Chemistry, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia;
| | - Adnan Jaman Turki
- Department of Marine Chemistry, Faculty of Marine Sciences, King Abdulaziz University, P.O. Box 80207, Jeddah 21589, Saudi Arabia;
| | - Hani Zakaria Asfour
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, Princess Al-Jawhara Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
| | - Walied Mohamed Alarif
- Department of Marine Chemistry, Faculty of Marine Sciences, King Abdulaziz University, P.O. Box 80207, Jeddah 21589, Saudi Arabia;
| | - Ahmed Abdel-Lateff
- Department of Natural Products and Alternative Medicine, Faculty of Pharmacy, King Abdulaziz University, P.O. Box 80260, Jeddah 21589, Saudi Arabia
- Department of Pharmacognosy, Faculty of Pharmacy, Minia University, Minia 61519, Egypt
| |
Collapse
|
8
|
Apc.LaeA and Apc.VeA of the velvet complex govern secondary metabolism and morphological development in the echinocandin-producing fungus Aspergillus pachycristatus. J Ind Microbiol Biotechnol 2019; 47:155-168. [PMID: 31758414 DOI: 10.1007/s10295-019-02250-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Accepted: 11/11/2019] [Indexed: 12/11/2022]
Abstract
The impact of the global secondary metabolite regulators LaeA and VeA on echinocandin B production and morphological development was evaluated in the industrial production strain Aspergillus pachycristatus NRRL 11440. Other representative secondary metabolites were examined as well to determine if the velvet complex functions as in A. nidulans and other species of fungi. Genetic methods used for gene manipulations in A. nidulans were applied to A. pachycristatus. Separate deletions of genes Apc.laeA and Apc.veA resulted in similar yet differing phenotypes in strain NRRL 11440. Disruption of Apc.laeA and Apc.veA significantly reduced, but did not eliminate, the production of echinocandin B. Similar to what has been observed in A. nidulans, the production of sterigmatocystin was nearly eliminated in both mutants. Quantitative reverse transcription PCR analyses confirmed that selected genes of both the echinocandin B and sterigmatocystin gene clusters were down-regulated in both mutant types. The two mutants differed with respect to growth of aerial hyphae, pigmentation, development of conidiophores, conidial germination rate, and ascospore maturation. Further functional annotation of key regulatory genes in A. pachycristatus and related Aspergillus species will improve our understanding of regulation of echinocandin production and co-produced metabolites.
Collapse
|
9
|
Sharma V, Singamaneni V, Sharma N, Kumar A, Arora D, Kushwaha M, Bhushan S, Jaglan S, Gupta P. Valproic acid induces three novel cytotoxic secondary metabolites in Diaporthe sp., an endophytic fungus from Datura inoxia Mill. Bioorg Med Chem Lett 2018; 28:2217-2221. [DOI: 10.1016/j.bmcl.2018.04.018] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 03/29/2018] [Accepted: 04/09/2018] [Indexed: 11/29/2022]
|
10
|
Maciá-Vicente JG, Shi YN, Cheikh-Ali Z, Grün P, Glynou K, Kia SH, Piepenbring M, Bode HB. Metabolomics-based chemotaxonomy of root endophytic fungi for natural products discovery. Environ Microbiol 2018; 20:1253-1270. [DOI: 10.1111/1462-2920.14072] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 02/09/2018] [Indexed: 12/01/2022]
Affiliation(s)
- Jose G. Maciá-Vicente
- Institute of Ecology, Evolution and Diversity, Goethe Universität Frankfurt, Max-von-Laue-Str. 13; Frankfurt am Main 60438 Germany
- Integrative Fungal Research Cluster (IPF); Frankfurt am Main Germany
| | - Yan-Ni Shi
- Merck Stiftungsprofessur für Molekulare Biotechnologie, Fachbereich Biowissenschaften; Goethe Universität Frankfurt; Frankfurt am Main 60438 Germany
| | - Zakaria Cheikh-Ali
- Integrative Fungal Research Cluster (IPF); Frankfurt am Main Germany
- Merck Stiftungsprofessur für Molekulare Biotechnologie, Fachbereich Biowissenschaften; Goethe Universität Frankfurt; Frankfurt am Main 60438 Germany
| | - Peter Grün
- Merck Stiftungsprofessur für Molekulare Biotechnologie, Fachbereich Biowissenschaften; Goethe Universität Frankfurt; Frankfurt am Main 60438 Germany
| | - Kyriaki Glynou
- Institute of Ecology, Evolution and Diversity, Goethe Universität Frankfurt, Max-von-Laue-Str. 13; Frankfurt am Main 60438 Germany
- Integrative Fungal Research Cluster (IPF); Frankfurt am Main Germany
| | - Sevda Haghi Kia
- Institute of Ecology, Evolution and Diversity, Goethe Universität Frankfurt, Max-von-Laue-Str. 13; Frankfurt am Main 60438 Germany
- Integrative Fungal Research Cluster (IPF); Frankfurt am Main Germany
| | - Meike Piepenbring
- Institute of Ecology, Evolution and Diversity, Goethe Universität Frankfurt, Max-von-Laue-Str. 13; Frankfurt am Main 60438 Germany
- Integrative Fungal Research Cluster (IPF); Frankfurt am Main Germany
| | - Helge B. Bode
- Integrative Fungal Research Cluster (IPF); Frankfurt am Main Germany
- Merck Stiftungsprofessur für Molekulare Biotechnologie, Fachbereich Biowissenschaften; Goethe Universität Frankfurt; Frankfurt am Main 60438 Germany
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe Universität Frankfurt; Frankfurt am Main 60438 Germany
| |
Collapse
|
11
|
Hüttel W. Structural diversity in echinocandin biosynthesis: the impact of oxidation steps and approaches toward an evolutionary explanation. ACTA ACUST UNITED AC 2017; 72:1-20. [PMID: 27705900 DOI: 10.1515/znc-2016-0156] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 08/28/2016] [Indexed: 11/15/2022]
Abstract
Echinocandins are an important group of cyclic non-ribosomal peptides with strong antifungal activity produced by filamentous fungi from Aspergillaceae and Leotiomycetes. Their structure is characterized by numerous hydroxylated non-proteinogenic amino acids. Biosynthetic clusters discovered in the last years contain up to six oxygenases, all of which are involved in amino acid modifications. Especially, variations in the oxidation pattern induced by these enzymes account for a remarkable structural diversity among the echinocandins. This review provides an overview of the current knowledge of echinocandin biosynthesis with a special focus on diversity-inducing oxidation steps. The emergence of metabolic diversity is further discussed on the basis of a comprehensive overview of the structurally characterized echinocandins, their producer strains and biosynthetic clusters. For the pneumocandins, echinocandins produced by Glarea lozoyensis, the formation of metabolic diversity in a single organism is analyzed. It is compared to two common models for the evolution of secondary metabolism: the 'target-based' approach and the 'diversity-based' model. Whereas the early phase of pneumocandin biosynthesis supports the target-based model, the diversity-inducing late steps and most oxidation reactions best fit the diversity-based approach. Moreover, two types of diversity-inducing steps can be distinguished. Although incomplete hydroxylation is a common phenomenon in echinocandin production and secondary metabolite biosynthesis in general, the incorporation of diverse hydroxyprolines at position 6 is apparently a unique feature of pneumocandin biosynthesis, which stands in stark contrast to the strict selectivity found in echinocandin biosynthesis by Aspergillaceae. The example of echinocandin biosynthesis shows that the existing models for the evolution of secondary metabolism can be well applied to parts of the pathway; however, thus far, there is no comprehensive theory that could explain the entire biosynthesis.
Collapse
Affiliation(s)
- Wolfgang Hüttel
- Wolfgang Hüttel, Institute of Pharmaceutical Sciences, University of Freiburg, Albertstrasse 25, 79104 Freiburg, Germany
| |
Collapse
|
12
|
Time-Dependent Production of the Bioactive Peptides Endolides A and B and the Polyketide Mariline A from the Sponge-Derived Fungus Stachylidium bicolor 293K04. FERMENTATION-BASEL 2017. [DOI: 10.3390/fermentation3030045] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
|
13
|
Gonzalez-Menendez V, Martin J, Siles JA, Gonzalez-Tejero MR, Reyes F, Platas G, Tormo JR, Genilloud O. Biodiversity and chemotaxonomy of Preussia isolates from the Iberian Peninsula. Mycol Prog 2017. [DOI: 10.1007/s11557-017-1305-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
|
14
|
Serrano R, González-Menéndez V, Rodríguez L, Martín J, Tormo JR, Genilloud O. Co-culturing of Fungal Strains Against Botrytis cinerea as a Model for the Induction of Chemical Diversity and Therapeutic Agents. Front Microbiol 2017; 8:649. [PMID: 28469610 PMCID: PMC5396503 DOI: 10.3389/fmicb.2017.00649] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 03/29/2017] [Indexed: 01/10/2023] Open
Abstract
New fungal SMs (SMs) have been successfully described to be produced by means of in vitro-simulated microbial community interactions. Co-culturing of fungi has proved to be an efficient way to induce cell–cell interactions that can promote the activation of cryptic pathways, frequently silent when the strains are grown in laboratory conditions. Filamentous fungi represent one of the most diverse microbial groups known to produce bioactive natural products. Triggering the production of novel antifungal compounds in fungi could respond to the current needs to fight health compromising pathogens and provide new therapeutic solutions. In this study, we have selected the fungus Botrytis cinerea as a model to establish microbial interactions with a large set of fungal strains related to ecosystems where they can coexist with this phytopathogen, and to generate a collection of extracts, obtained from their antagonic microbial interactions and potentially containing new bioactive compounds. The antifungal specificity of the extracts containing compounds induced after B. cinerea interaction was determined against two human fungal pathogens (Candida albicans and Aspergillus fumigatus) and three phytopathogens (Colletotrichum acutatum, Fusarium proliferatum, and Magnaporthe grisea). In addition, their cytotoxicity was also evaluated against the human hepatocellular carcinoma cell line (HepG2). We have identified by LC-MS the production of a wide variety of known compounds induced from these fungal interactions, as well as novel molecules that support the potential of this approach to generate new chemical diversity and possible new therapeutic agents.
Collapse
Affiliation(s)
- Rachel Serrano
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en AndalucíaGranada, Spain
| | - Víctor González-Menéndez
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en AndalucíaGranada, Spain
| | - Lorena Rodríguez
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en AndalucíaGranada, Spain
| | - Jesús Martín
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en AndalucíaGranada, Spain
| | - José R Tormo
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en AndalucíaGranada, Spain
| | - Olga Genilloud
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en AndalucíaGranada, Spain
| |
Collapse
|
15
|
Chen AJ, Frisvad JC, Sun BD, Varga J, Kocsubé S, Dijksterhuis J, Kim DH, Hong SB, Houbraken J, Samson RA. Aspergillus section Nidulantes (formerly Emericella): Polyphasic taxonomy, chemistry and biology. Stud Mycol 2016; 84:1-118. [PMID: 28050053 PMCID: PMC5198626 DOI: 10.1016/j.simyco.2016.10.001] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
Aspergillus section Nidulantes includes species with striking morphological characters, such as biseriate conidiophores with brown-pigmented stipes, and if present, the production of ascomata embedded in masses of Hülle cells with often reddish brown ascospores. The majority of species in this section have a sexual state, which were named Emericella in the dual name nomenclature system. In the present study, strains belonging to subgenus Nidulantes were subjected to multilocus molecular phylogenetic analyses using internal transcribed spacer region (ITS), partial β-tubulin (BenA), calmodulin (CaM) and RNA polymerase II second largest subunit (RPB2) sequences. Nine sections are accepted in subgenus Nidulantes including the new section Cavernicolus. A polyphasic approach using morphological characters, extrolites, physiological characters and phylogeny was applied to investigate the taxonomy of section Nidulantes. Based on this approach, section Nidulantes is subdivided in seven clades and 65 species, and 10 species are described here as new. Morphological characters including colour, shape, size, and ornamentation of ascospores, shape and size of conidia and vesicles, growth temperatures are important for identifying species. Many species of section Nidulantes produce the carcinogenic mycotoxin sterigmatocystin. The most important mycotoxins in Aspergillus section Nidulantes are aflatoxins, sterigmatocystin, emestrin, fumitremorgins, asteltoxins, and paxillin while other extrolites are useful drugs or drug lead candidates such as echinocandins, mulundocandins, calbistrins, varitriols, variecolins and terrain. Aflatoxin B1 is produced by four species: A. astellatus, A. miraensis, A. olivicola, and A. venezuelensis.
Collapse
Affiliation(s)
- A J Chen
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, PR China; CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| | - J C Frisvad
- Department of Systems Biology, Søltofts Plads B. 221, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - B D Sun
- China General Microbiological Culture Collection Centre, Institute of Microbiology, Chinese Academy of Sciences, Beichen West Road, Chaoyang District, Beijing, 100101, PR China
| | - J Varga
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, H-6726, Szeged, Hungary
| | - S Kocsubé
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, H-6726, Szeged, Hungary
| | - J Dijksterhuis
- CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| | - D H Kim
- Division of Forest Environment Protection, Kangwon National University, Chuncheon, 24341, Republic of Korea
| | - S-B Hong
- Korean Agricultural Culture Collection, National Institute of Agricultural Science, 166, Nongsaengmyeong-ro, Iseo-myeon, Wanju-gun, Jeollabuk-do, 55365, Republic of Korea
| | - J Houbraken
- CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| | - R A Samson
- CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| |
Collapse
|
16
|
Multicomponent Analysis of the Differential Induction of Secondary Metabolite Profiles in Fungal Endophytes. Molecules 2016; 21:molecules21020234. [PMID: 26901184 PMCID: PMC6272891 DOI: 10.3390/molecules21020234] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Revised: 02/10/2016] [Accepted: 02/13/2016] [Indexed: 11/29/2022] Open
Abstract
Small molecule histone deacetylase (HDAC) and DNA methyltransferase (DNMT) inhibitors are commonly used to perturb the production of fungal metabolites leading to the induction of the expression of silent biosynthetic pathways. Several reports have described the variable effects observed in natural product profiles in fungi treated with HDAC and DNMT inhibitors, such as enhanced chemical diversity and/or the induction of new molecules previously unknown to be produced by the strain. Fungal endophytes are known to produce a wide variety of secondary metabolites (SMs) involved in their adaptation and survival within higher plants. The plant-microbe interaction may influence the expression of some biosynthetic pathways, otherwise cryptic in these fungi when grown in vitro. The aim of this study was to setup a systematic approach to evaluate and identify the possible effects of HDAC and DNMT inhibitors on the metabolic profiles of wild type fungal endophytes, including the chemical identification and characterization of the most significant SMs induced by these epigenetic modifiers.
Collapse
|
17
|
Epigenetic Activation of Antibacterial Property of an Endophytic Streptomyces coelicolor Strain AZRA 37 and Identification of the Induced Protein Using MALDI TOF MS/MS. PLoS One 2016; 11:e0147876. [PMID: 26844762 PMCID: PMC4742224 DOI: 10.1371/journal.pone.0147876] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 01/08/2016] [Indexed: 12/27/2022] Open
Abstract
The endophytic Streptomyces coelicolor strain AZRA 37 was isolated from the surface sterilized root of Azadirachta indica A. Juss., commonly known as neem plant in India. Since only a few reports are available regarding epigenetic modulations of microbial entities, S. coelicolor was treated with different concentrations of 5-azacytidine for this purpose and evaluated for its antibacterial potential against five human pathogenic bacteria (Aeromonas hydrophila IMS/GN11, Enterococcus faecalis IMS/GN7, Salmonella typhi MTCC 3216, Shigella flexneri ATCC 12022 and Staphylococcus aureus ATCC 25923). The crude extract obtained from cultures treated with 25 μM concentration of 5-azacytidine, was found effective against all five pathogenic bacteria tested while the untreated control was only active against 3 pathogenic bacteria. HPLC analysis of crude compounds from treated cultures showed a greater number of compounds than that of the control. Extraction of whole cell protein and its SDS PAGE analysis showed an additional major protein band in 25 μM 5-azacytidine treated culture and MALDI TOF MS/MS analysis revealed that this protein belongs to the porin family.
Collapse
|
18
|
Exploitation of Fungal Biodiversity for Discovery of Novel Antibiotics. Curr Top Microbiol Immunol 2016; 398:303-338. [PMID: 27422786 DOI: 10.1007/82_2016_496] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Fungi were among the first sources for antibiotics. The discovery and development of the penicillin-type and cephalosporin-type β-lactams and their synthetic versions were transformative in emergence of the modern pharmaceutical industry. They remain some of the most important antibiotics, even 70 years after their discovery. Meanwhile, thousands of fungal metabolites have been discovered, yet these metabolites have only contributed a few additional compounds that have entered clinical development. Substantial expansion in fungal biodiversity assessment along with the availability of modern "-OMICS" technology and revolutionary developments in fungal biotechnology have been made in the last 15 years subsequent to the exit of most of the big Pharma companies from the field of novel antibiotics discovery. Therefore, the timing seems opportune to revisit these fascinating chemically rich organisms as a reservoir of small-molecule templates for lead discovery. This review will describe ongoing interdisciplinary scenarios in which specialists in fungal biology collaborate with chemists, pharmacologists and biochemical and process engineers in order to reveal and make new antibiotics. The utility of a pre-selection process based on phylogenetic data and distribution of secondary metabolite encoding gene cluster will be highlighted. Examples of novel bioactive metabolites from fungi derived from special ecological groups and new phylogenetic lineages will also be discussed.
Collapse
|
19
|
Aspergillus mulundensis sp. nov., a new species for the fungus producing the antifungal echinocandin lipopeptides, mulundocandins. J Antibiot (Tokyo) 2015; 69:141-8. [DOI: 10.1038/ja.2015.105] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Revised: 09/05/2015] [Accepted: 09/11/2015] [Indexed: 01/06/2023]
|
20
|
Fedorenko V, Genilloud O, Horbal L, Marcone GL, Marinelli F, Paitan Y, Ron EZ. Antibacterial Discovery and Development: From Gene to Product and Back. BIOMED RESEARCH INTERNATIONAL 2015; 2015:591349. [PMID: 26339625 PMCID: PMC4538407 DOI: 10.1155/2015/591349] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 12/30/2014] [Accepted: 01/13/2015] [Indexed: 12/23/2022]
Abstract
Concern over the reports of antibiotic-resistant bacterial infections in hospitals and in the community has been publicized in the media, accompanied by comments on the risk that we may soon run out of antibiotics as a way to control infectious disease. Infections caused by Enterococcus faecium, Staphylococcus aureus, Klebsiella species, Clostridium difficile, Acinetobacter baumannii, Pseudomonas aeruginosa, Escherichia coli, and other Enterobacteriaceae species represent a major public health burden. Despite the pharmaceutical sector's lack of interest in the topic in the last decade, microbial natural products continue to represent one of the most interesting sources for discovering and developing novel antibacterials. Research in microbial natural product screening and development is currently benefiting from progress that has been made in other related fields (microbial ecology, analytical chemistry, genomics, molecular biology, and synthetic biology). In this paper, we review how novel and classical approaches can be integrated in the current processes for microbial product screening, fermentation, and strain improvement.
Collapse
Affiliation(s)
- Victor Fedorenko
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Lviv 79005, Ukraine
| | - Olga Genilloud
- Fundación MEDINA, Health Sciences Technology Park, 18016 Granada, Spain
| | - Liliya Horbal
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Lviv 79005, Ukraine
| | - Giorgia Letizia Marcone
- Department of Biotechnology and Life Sciences, University of Insubria, 21100 Varese, Italy
- The Protein Factory, Interuniversity Centre Politecnico di Milano, ICRM CNR Milano, and University of Insubria, 21100 Varese, Italy
| | - Flavia Marinelli
- Department of Biotechnology and Life Sciences, University of Insubria, 21100 Varese, Italy
- The Protein Factory, Interuniversity Centre Politecnico di Milano, ICRM CNR Milano, and University of Insubria, 21100 Varese, Italy
| | - Yossi Paitan
- Clinical Microbiology Laboratory, Meir Medical Center, 44281 Kfar Saba, Israel
| | - Eliora Z. Ron
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, 6997801 Tel Aviv, Israel
- Galilee Research Institute (MIGAL), 11016 Kiryat Shmona, Israel
| |
Collapse
|
21
|
Evolution of Chemical Diversity in Echinocandin Lipopeptide Antifungal Metabolites. EUKARYOTIC CELL 2015; 14:698-718. [PMID: 26024901 DOI: 10.1128/ec.00076-15] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2015] [Accepted: 05/19/2015] [Indexed: 11/20/2022]
Abstract
The echinocandins are a class of antifungal drugs that includes caspofungin, micafungin, and anidulafungin. Gene clusters encoding most of the structural complexity of the echinocandins provided a framework for hypotheses about the evolutionary history and chemical logic of echinocandin biosynthesis. Gene orthologs among echinocandin-producing fungi were identified. Pathway genes, including the nonribosomal peptide synthetases (NRPSs), were analyzed phylogenetically to address the hypothesis that these pathways represent descent from a common ancestor. The clusters share cooperative gene contents and linkages among the different strains. Individual pathway genes analyzed in the context of similar genes formed unique echinocandin-exclusive phylogenetic lineages. The echinocandin NRPSs, along with the NRPS from the inp gene cluster in Aspergillus nidulans and its orthologs, comprise a novel lineage among fungal NRPSs. NRPS adenylation domains from different species exhibited a one-to-one correspondence between modules and amino acid specificity that is consistent with models of tandem duplication and subfunctionalization. Pathway gene trees and Ascomycota phylogenies are congruent and consistent with the hypothesis that the echinocandin gene clusters have a common origin. The disjunct Eurotiomycete-Leotiomycete distribution appears to be consistent with a scenario of vertical descent accompanied by incomplete lineage sorting and loss of the clusters from most lineages of the Ascomycota. We present evidence for a single evolutionary origin of the echinocandin family of gene clusters and a progression of structural diversification in two fungal classes that diverged approximately 290 to 390 million years ago. Lineage-specific gene cluster evolution driven by selection of new chemotypes contributed to diversification of the molecular functionalities.
Collapse
|
22
|
Nielsen KF, Larsen TO. The importance of mass spectrometric dereplication in fungal secondary metabolite analysis. Front Microbiol 2015; 6:71. [PMID: 25741325 PMCID: PMC4330896 DOI: 10.3389/fmicb.2015.00071] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 01/20/2015] [Indexed: 11/13/2022] Open
Abstract
Having entered the Genomic Era, it is now evident that the biosynthetic potential of filamentous fungi is much larger than was thought even a decade ago. Fungi harbor many cryptic gene clusters encoding for the biosynthesis of polyketides, non-ribosomal peptides, and terpenoids - which can all undergo extensive modifications by tailoring enzymes - thus potentially providing a large array of products from a single pathway. Elucidating the full chemical profile of a fungal species is a challenging exercise, even with elemental composition provided by high-resolution mass spectrometry (HRMS) used in combination with chemical databases (e.g., AntiBase) to dereplicate known compounds. This has led to a continuous effort to improve chromatographic separation in conjunction with improvement in HRMS detection. Major improvements have also occurred with 2D chromatography, ion-mobility, MS/MS and MS(3), stable isotope labeling feeding experiments, classic UV/Vis, and especially automated data-mining and metabolomics software approaches as the sheer amount of data generated is now the major challenge. This review will focus on the development and implementation of dereplication strategies and will highlight the importance of each stage of the process from sample preparation to chromatographic separation and finally toward both manual and more targeted methods for automated dereplication of fungal natural products using state-of-the art MS instrumentation.
Collapse
Affiliation(s)
- Kristian F Nielsen
- Department of Systems Biology, Technical University of Denmark, Kongens Lyngby Denmark
| | - Thomas O Larsen
- Department of Systems Biology, Technical University of Denmark, Kongens Lyngby Denmark
| |
Collapse
|
23
|
Bills G, Li Y, Chen L, Yue Q, Niu XM, An Z. New insights into the echinocandins and other fungal non-ribosomal peptides and peptaibiotics. Nat Prod Rep 2014; 31:1348-75. [PMID: 25156669 DOI: 10.1039/c4np00046c] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Non-ribosomal peptide synthetases (NRPSs) are a primary modality for fungal peptidic natural product assembly and are responsible for some of the best known, most useful, and most destructive fungal metabolites. Through genome sequencing and computer-assisted recognition of modular motifs of catalytic domains, one can now confidently identify most NRPS biosynthetic genes of a fungal strain. The biosynthetic gene clusters responsible for two of the most important classes of NRP fungal derived drugs, cyclosporine and the echinocandins, have been recently characterized by genomic sequencing and annotation. Complete biosynthetic gene clusters for the pneumocandins and echinocandins have been mapped at the genetic level and functionally characterized to some extent. Genomic sequencing of representative strains of most of the variants in the echinocandin family, including the wild-type of the three fungal strains employed for industrial-scale production of caspofungin, micafungin and anidulofungin, has enabled characterization of the basic architecture of the echinocandin NRPS pathways. A comparative analysis of how pathway genes cause variations in lipoinitiation, biosynthesis of the non-proteinogenic amino acids, amino acid substitutions, and hydroxylations and sulfonations of the core peptide and contribute to the molecular diversity of the family is presented. We also review new information on the natural functions of NRPs, the differences between fungal and bacterial NRPSs, and functional characterization of selected NRPS gene clusters. Continuing discovery of the new fungal nonribosomal peptides has contributed new structural diversity and potential insights into their biological functions among other natural peptides and peptaibiotics. We therefore provide an update on new peptides, depsipeptides and peptaibols discovered in the Fungi since 2009.
Collapse
Affiliation(s)
- Gerald Bills
- Texas Therapeutics Institute, The Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Centre at Houston, Houston, Texas 77054, USA.
| | | | | | | | | | | |
Collapse
|
24
|
González-Menéndez V, Asensio F, Moreno C, de Pedro N, Monteiro MC, de la Cruz M, Vicente F, Bills GF, Reyes F, Genilloud O, Tormo JR. Assessing the effects of adsorptive polymeric resin additions on fungal secondary metabolite chemical diversity. Mycology 2014; 5:179-191. [PMID: 25379340 PMCID: PMC4205895 DOI: 10.1080/21501203.2014.942406] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Accepted: 07/02/2014] [Indexed: 01/01/2023] Open
Abstract
Adsorptive polymeric resins have been occasionally described to enhance the production of specific secondary metabolites (SMs) of interest. Methods that induce the expression of new chemical entities in fungal fermentations may lead to the discovery of new bioactive molecules and should be addressed as possible tools for the creation of new microbial chemical libraries for drug lead discovery. Herein, we apply both biological activity and chemical evaluations to assess the use of adsorptive resins as tools for the differential expression of SMs in fungal strain sets. Data automation approaches were applied to ultra high performance liquid chromatography analysis of extracts to evaluate the general influence in generating new chemical entities or in changing the production of specific SMs by fungi grown in the presence of resins and different base media.
Collapse
Affiliation(s)
- Víctor González-Menéndez
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía , Avda. del Conocimiento 3, Parque Tecnológico de Ciencias de la Salud, 18016 Granada , Spain
| | - Francisco Asensio
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía , Avda. del Conocimiento 3, Parque Tecnológico de Ciencias de la Salud, 18016 Granada , Spain
| | - Catalina Moreno
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía , Avda. del Conocimiento 3, Parque Tecnológico de Ciencias de la Salud, 18016 Granada , Spain
| | - Nuria de Pedro
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía , Avda. del Conocimiento 3, Parque Tecnológico de Ciencias de la Salud, 18016 Granada , Spain
| | - Maria Candida Monteiro
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía , Avda. del Conocimiento 3, Parque Tecnológico de Ciencias de la Salud, 18016 Granada , Spain
| | - Mercedes de la Cruz
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía , Avda. del Conocimiento 3, Parque Tecnológico de Ciencias de la Salud, 18016 Granada , Spain
| | - Francisca Vicente
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía , Avda. del Conocimiento 3, Parque Tecnológico de Ciencias de la Salud, 18016 Granada , Spain
| | - Gerald F Bills
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía , Avda. del Conocimiento 3, Parque Tecnológico de Ciencias de la Salud, 18016 Granada , Spain
| | - Fernando Reyes
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía , Avda. del Conocimiento 3, Parque Tecnológico de Ciencias de la Salud, 18016 Granada , Spain
| | - Olga Genilloud
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía , Avda. del Conocimiento 3, Parque Tecnológico de Ciencias de la Salud, 18016 Granada , Spain
| | - José R Tormo
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía , Avda. del Conocimiento 3, Parque Tecnológico de Ciencias de la Salud, 18016 Granada , Spain
| |
Collapse
|
25
|
Kildgaard S, Mansson M, Dosen I, Klitgaard A, Frisvad JC, Larsen TO, Nielsen KF. Accurate dereplication of bioactive secondary metabolites from marine-derived fungi by UHPLC-DAD-QTOFMS and a MS/HRMS library. Mar Drugs 2014; 12:3681-705. [PMID: 24955556 PMCID: PMC4071597 DOI: 10.3390/md12063681] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 05/23/2014] [Accepted: 06/11/2014] [Indexed: 12/23/2022] Open
Abstract
In drug discovery, reliable and fast dereplication of known compounds is essential for identification of novel bioactive compounds. Here, we show an integrated approach using ultra-high performance liquid chromatography-diode array detection-quadrupole time of flight mass spectrometry (UHPLC-DAD-QTOFMS) providing both accurate mass full-scan mass spectrometry (MS) and tandem high resolution MS (MS/HRMS) data. The methodology was demonstrated on compounds from bioactive marine-derived strains of Aspergillus, Penicillium, and Emericellopsis, including small polyketides, non-ribosomal peptides, terpenes, and meroterpenoids. The MS/HRMS data were then searched against an in-house MS/HRMS library of ~1300 compounds for unambiguous identification. The full scan MS data was used for dereplication of compounds not in the MS/HRMS library, combined with ultraviolet/visual (UV/Vis) and MS/HRMS data for faster exclusion of database search results. This led to the identification of four novel isomers of the known anticancer compound, asperphenamate. Except for very low intensity peaks, no false negatives were found using the MS/HRMS approach, which proved to be robust against poor data quality caused by system overload or loss of lock-mass. Only for small polyketides, like patulin, were both retention time and UV/Vis spectra necessary for unambiguous identification. For the ophiobolin family with many structurally similar analogues partly co-eluting, the peaks could be assigned correctly by combining MS/HRMS data and m/z of the [M + Na]+ ions.
Collapse
Affiliation(s)
- Sara Kildgaard
- Department of Systems Biology, Technical University of Denmark, Soeltofts Plads 221, Kgs. Lyngby DK-2800, Denmark.
| | - Maria Mansson
- Department of Systems Biology, Technical University of Denmark, Soeltofts Plads 221, Kgs. Lyngby DK-2800, Denmark.
| | - Ina Dosen
- Department of Systems Biology, Technical University of Denmark, Soeltofts Plads 221, Kgs. Lyngby DK-2800, Denmark.
| | - Andreas Klitgaard
- Department of Systems Biology, Technical University of Denmark, Soeltofts Plads 221, Kgs. Lyngby DK-2800, Denmark.
| | - Jens C Frisvad
- Department of Systems Biology, Technical University of Denmark, Soeltofts Plads 221, Kgs. Lyngby DK-2800, Denmark.
| | - Thomas O Larsen
- Department of Systems Biology, Technical University of Denmark, Soeltofts Plads 221, Kgs. Lyngby DK-2800, Denmark.
| | - Kristian F Nielsen
- Department of Systems Biology, Technical University of Denmark, Soeltofts Plads 221, Kgs. Lyngby DK-2800, Denmark.
| |
Collapse
|
26
|
Genilloud O. The re-emerging role of microbial natural products in antibiotic discovery. Antonie Van Leeuwenhoek 2014; 106:173-88. [PMID: 24923558 DOI: 10.1007/s10482-014-0204-6] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 05/23/2014] [Indexed: 11/28/2022]
Abstract
New classes of antibacterial compounds are urgently needed to respond to the high frequency of occurrence of resistances to all major classes of known antibiotics. Microbial natural products have been for decades one of the most successful sources of drugs to treat infectious diseases but today, the emerging unmet clinical need poses completely new challenges to the discovery of novel candidates with the desired properties to be developed as antibiotics. While natural products discovery programs have been gradually abandoned by the big pharma, smaller biotechnology companies and research organizations are taking over the lead in the discovery of novel antibacterials. Recent years have seen new approaches and technologies being developed and integrated in a multidisciplinary effort to further exploit microbial resources and their biosynthetic potential as an untapped source of novel molecules. New strategies to isolate novel species thought to be uncultivable, and synthetic biology approaches ranging from genome mining of microbial strains for cryptic biosynthetic pathways to their heterologous expression have been emerging in combination with high throughput sequencing platforms, integrated bioinformatic analysis, and on-site analytical detection and dereplication tools for novel compounds. These different innovative approaches are defining a completely new framework that is setting the bases for the future discovery of novel chemical scaffolds that should foster a renewed interest in the identification of novel classes of natural product antibiotics from the microbial world.
Collapse
Affiliation(s)
- Olga Genilloud
- Fundación MEDINA, Avda Conocimiento 3, Parque Tecnológico Ciencias de la Salud, 18016, Granada, Spain,
| |
Collapse
|
27
|
Bills GF, Gloer JB, An Z. Coprophilous fungi: antibiotic discovery and functions in an underexplored arena of microbial defensive mutualism. Curr Opin Microbiol 2013; 16:549-65. [DOI: 10.1016/j.mib.2013.08.001] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Revised: 08/01/2013] [Accepted: 08/06/2013] [Indexed: 01/24/2023]
|