1
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Dolan SK, Duong AT, Whiteley M. Convergent evolution in toxin detection and resistance provides evidence for conserved bacterial-fungal interactions. Proc Natl Acad Sci U S A 2024; 121:e2304382121. [PMID: 39088389 PMCID: PMC11317636 DOI: 10.1073/pnas.2304382121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 06/12/2024] [Indexed: 08/03/2024] Open
Abstract
Microbes rarely exist in isolation and instead form complex polymicrobial communities. As a result, microbes have developed intricate offensive and defensive strategies that enhance their fitness in these complex communities. Thus, identifying and understanding the molecular mechanisms controlling polymicrobial interactions is critical for understanding the function of microbial communities. In this study, we show that the gram-negative opportunistic human pathogen Pseudomonas aeruginosa, which frequently causes infection alongside a plethora of other microbes including fungi, encodes a genetic network which can detect and defend against gliotoxin, a potent, disulfide-containing antimicrobial produced by the ubiquitous filamentous fungus Aspergillus fumigatus. We show that gliotoxin exposure disrupts P. aeruginosa zinc homeostasis, leading to transcriptional activation of a gene encoding a previously uncharacterized dithiol oxidase (herein named as DnoP), which detoxifies gliotoxin and structurally related toxins. Despite sharing little homology to the A. fumigatus gliotoxin resistance protein (GliT), the enzymatic mechanism of DnoP from P. aeruginosa appears to be identical that used by A. fumigatus. Thus, DnoP and its transcriptional induction by low zinc represent a rare example of both convergent evolution of toxin defense and environmental cue sensing across kingdoms. Collectively, these data provide compelling evidence that P. aeruginosa has evolved to survive exposure to an A. fumigatus disulfide-containing toxin in the natural environment.
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Affiliation(s)
- Stephen K. Dolan
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA30310
- Department of Genetics and Biochemistry, Eukaryotic Pathogens Innovation Center, Clemson University, Clemson, SC29634
- Emory-Children’s Cystic Fibrosis Center, Atlanta, GA30310
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA30310
| | - Ashley T. Duong
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA30310
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA30310
| | - Marvin Whiteley
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA30310
- Emory-Children’s Cystic Fibrosis Center, Atlanta, GA30310
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA30310
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2
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Balamurugan C, Steenwyk JL, Goldman GH, Rokas A. The evolution of the gliotoxin biosynthetic gene cluster in Penicillium fungi. G3 (BETHESDA, MD.) 2024; 14:jkae063. [PMID: 38507596 PMCID: PMC11075534 DOI: 10.1093/g3journal/jkae063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 12/27/2023] [Accepted: 03/11/2024] [Indexed: 03/22/2024]
Abstract
Fungi biosynthesize diverse secondary metabolites, small organic bioactive molecules with key roles in fungal ecology. Fungal secondary metabolites are often encoded by physically clustered genes known as biosynthetic gene clusters (BGCs). Fungi in the genus Penicillium produce a cadre of secondary metabolites, some of which are useful (e.g. the antibiotic penicillin and the cholesterol-lowering drug mevastatin) and others harmful (e.g. the mycotoxin patulin and the immunosuppressant gliotoxin) to human affairs. Fungal genomes often also encode resistance genes that confer protection against toxic secondary metabolites. Some Penicillium species, such as Penicillium decumbens, are known to produce gliotoxin, a secondary metabolite with known immunosuppressant activity. To investigate the evolutionary conservation of homologs of the gliotoxin BGC and of genes involved in gliotoxin resistance in Penicillium, we analyzed 35 Penicillium genomes from 23 species. Homologous, lesser fragmented gliotoxin BGCs were found in 12 genomes, mostly fragmented remnants of the gliotoxin BGC were found in 21 genomes, whereas the remaining 2 Penicillium genomes lacked the gliotoxin BGC altogether. In contrast, broad conservation of homologs of resistance genes that reside outside the BGC across Penicillium genomes was observed. Evolutionary rate analysis revealed that BGCs with higher numbers of genes evolve slower than BGCs with few genes, suggestive of constraint and potential functional significance or more recent decay. Gene tree-species tree reconciliation analyses suggested that the history of homologs in the gliotoxin BGC across the genus Penicillium likely involved multiple duplications, losses, and horizontal gene transfers. Our analyses suggest that genes encoded in BGCs can have complex evolutionary histories and be retained in genomes long after the loss of secondary metabolite biosynthesis.
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Affiliation(s)
- Charu Balamurugan
- Department of Biological Sciences, Vanderbilt University, VU Station B #35-1634, Nashville, TN 37235, USA
- Vanderbilt Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - Jacob L Steenwyk
- Department of Biological Sciences, Vanderbilt University, VU Station B #35-1634, Nashville, TN 37235, USA
- Vanderbilt Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
- Howards Hughes Medical Institute and the Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Gustavo H Goldman
- Faculdade de Ciencias Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo CEP 14040-903, Brazil
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, VU Station B #35-1634, Nashville, TN 37235, USA
- Vanderbilt Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
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3
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Jojić K, Gherlone F, Cseresnyés Z, Bissell AU, Hoefgen S, Hoffmann S, Huang Y, Janevska S, Figge MT, Valiante V. The spatial organization of sphingofungin biosynthesis in Aspergillus fumigatus and its cross-interaction with sphingolipid metabolism. mBio 2024; 15:e0019524. [PMID: 38380921 PMCID: PMC10936153 DOI: 10.1128/mbio.00195-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 01/24/2024] [Indexed: 02/22/2024] Open
Abstract
Sphingofungins are sphinganine analog mycotoxins acting as inhibitors of serine palmitoyl transferases, enzymes responsible for the first step in the sphingolipid biosynthesis. Eukaryotic cells are highly organized with various structures and organelles to facilitate cellular processes and chemical reactions, including the ones occurring as part of the secondary metabolism. We studied how sphingofungin biosynthesis is compartmentalized in the human-pathogenic fungus Aspergillus fumigatus, and we observed that it takes place in the endoplasmic reticulum (ER), ER-derived vesicles, and the cytosol. This implies that sphingofungin and sphingolipid biosynthesis colocalize to some extent. Automated analysis of confocal microscopy images confirmed the colocalization of the fluorescent proteins. Moreover, we demonstrated that the cluster-associated aminotransferase (SphA) and 3-ketoreductase (SphF) play a bifunctional role, supporting sphingolipid biosynthesis, and thereby antagonizing the toxic effects caused by sphingofungin production.IMPORTANCEA balanced sphingolipid homeostasis is critical for the proper functioning of eukaryotic cells. To this end, sphingolipid inhibitors have therapeutic potential against diseases related to the deregulation of sphingolipid balance. In addition, some of them have significant antifungal activity, suggesting that sphingolipid inhibitors-producing fungi have evolved mechanisms to escape self-poisoning. Here, we propose a novel self-defense mechanism, with cluster-associated genes coding for enzymes that play a dual role, being involved in both sphingofungin and sphingolipid production.
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Affiliation(s)
- Katarina Jojić
- Biobricks of Microbial Natural Product Syntheses, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (Leibniz-HKI), Jena, Germany
- Faculty of Biological Sciences, Friedrich Schiller University Jena, Jena, Germany
| | - Fabio Gherlone
- Biobricks of Microbial Natural Product Syntheses, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (Leibniz-HKI), Jena, Germany
- Faculty of Biological Sciences, Friedrich Schiller University Jena, Jena, Germany
| | - Zoltán Cseresnyés
- Applied Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (Leibniz-HKI), Jena, Germany
| | - Alexander U. Bissell
- Biobricks of Microbial Natural Product Syntheses, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (Leibniz-HKI), Jena, Germany
| | - Sandra Hoefgen
- Biobricks of Microbial Natural Product Syntheses, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (Leibniz-HKI), Jena, Germany
| | - Stefan Hoffmann
- Faculty of Biological Sciences, Friedrich Schiller University Jena, Jena, Germany
- Applied Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (Leibniz-HKI), Jena, Germany
| | - Ying Huang
- Biobricks of Microbial Natural Product Syntheses, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (Leibniz-HKI), Jena, Germany
| | - Slavica Janevska
- (Epi-)Genetic Regulation of Fungal Virulence, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (Leibniz-HKI), Jena, Germany
| | - Marc Thilo Figge
- Faculty of Biological Sciences, Friedrich Schiller University Jena, Jena, Germany
- Applied Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (Leibniz-HKI), Jena, Germany
| | - Vito Valiante
- Biobricks of Microbial Natural Product Syntheses, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (Leibniz-HKI), Jena, Germany
- Faculty of Biological Sciences, Friedrich Schiller University Jena, Jena, Germany
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4
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Alves de Castro P, Figueiredo Pinzan C, Dos Reis TF, Valero C, Van Rhijn N, Menegatti C, de Freitas Migliorini IL, Bromley M, Fleming AB, Traynor AM, Sarikaya-Bayram Ö, Bayram Ö, Malavazi I, Ebel F, Barbosa JCJ, Fill T, Pupo MT, Goldman GH. Aspergillus fumigatus mitogen-activated protein kinase MpkA is involved in gliotoxin production and self-protection. Nat Commun 2024; 15:33. [PMID: 38167253 PMCID: PMC10762094 DOI: 10.1038/s41467-023-44329-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 12/08/2023] [Indexed: 01/05/2024] Open
Abstract
Aspergillus fumigatus is a saprophytic fungus that can cause a variety of human diseases known as aspergillosis. Mycotoxin gliotoxin (GT) production is important for its virulence and must be tightly regulated to avoid excess production and toxicity to the fungus. GT self-protection by GliT oxidoreductase and GtmA methyltransferase activities is related to the subcellular localization of these enzymes and how GT can be sequestered from the cytoplasm to avoid increased cell damage. Here, we show that GliT:GFP and GtmA:GFP are localized in the cytoplasm and in vacuoles during GT production. The Mitogen-Activated Protein kinase MpkA is essential for GT production and self-protection, interacts physically with GliT and GtmA and it is necessary for their regulation and subsequent presence in the vacuoles. The sensor histidine kinase SlnASln1 is important for modulation of MpkA phosphorylation. Our work emphasizes the importance of MpkA and compartmentalization of cellular events for GT production and self-defense.
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Affiliation(s)
- Patrícia Alves de Castro
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Camila Figueiredo Pinzan
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Thaila Fernanda Dos Reis
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Clara Valero
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
- Manchester Fungal Infection Group, Division of Evolution, Infection and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Norman Van Rhijn
- Manchester Fungal Infection Group, Division of Evolution, Infection and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Carla Menegatti
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | | | - Michael Bromley
- Manchester Fungal Infection Group, Division of Evolution, Infection and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Alastair B Fleming
- Department of Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin, Ireland
| | - Aimee M Traynor
- Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland
| | | | - Özgür Bayram
- Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland.
| | - Iran Malavazi
- Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | - Frank Ebel
- Institut für Infektionsmedizin und Zoonosen, Medizinische Fakultät, LMU, 80539, München, Germany
| | | | - Taícia Fill
- Instituto de Química, Universidade Estadual de Campinas, Campinas, Brazil
| | - Monica Tallarico Pupo
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Gustavo H Goldman
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil.
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5
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Son YE, Han J, Lee KT, Park HS. Pleiotropic functions of SscA on the asexual spore of the human pathogenic fungus Aspergillus fumigatus. Mycology 2023; 15:238-254. [PMID: 38813476 PMCID: PMC11132850 DOI: 10.1080/21501203.2023.2294061] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 12/06/2023] [Indexed: 05/31/2024] Open
Abstract
Asexual spores, called conidia, are key reproductive fungal particles that enable survival in harsh environmental conditions or host systems. The conidia can infect humans, animals, and plants to cause various fungal diseases. Transcription factors, including VosA, WetA, and SscA, have key roles in conidia formation and long-term survival in Aspergillus nidulans. Herein, we report the pleiotropic functions of SscA in the conidia of the human pathogen A. fumigatus. The deletion of sscA increased conidia formation despite decreased fungal growth. Absence of sscA impaired long-term survival and reduced spore resistance to various stresses, including heat, UV, and oxidation. Transcriptomic analyses showed that SscA involved the mRNA expression of cell wall organisation-related genes. Importantly, the sscA deletion mutant conidia contained an increased amount of β-glucan and chitin compared to wild type conidia. In addition, conidial gliotoxin production was decreased in the sscA deletion strain. Overall, SscA has pleiotropic roles in conidia formation, maturation and dormancy and mycotoxin production in A. fumigatus.
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Affiliation(s)
- Ye-Eun Son
- School of Food Science and Biotechnology, Kyungpook National University, Daegu, Republic of Korea
| | - Jiwoo Han
- Korea Zoonosis Research Institute, Jeonbuk National University, Iksan, Republic of Korea
| | - Kyung-Tae Lee
- Korea Zoonosis Research Institute, Jeonbuk National University, Iksan, Republic of Korea
| | - Hee-Soo Park
- School of Food Science and Biotechnology, Kyungpook National University, Daegu, Republic of Korea
- Department of Integrative Biology, Kyungpook National University, Daegu, Republic of Korea
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6
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Downes SG, Owens RA, Walshe K, Fitzpatrick DA, Dorey A, Jones GW, Doyle S. Gliotoxin-mediated bacterial growth inhibition is caused by specific metal ion depletion. Sci Rep 2023; 13:16156. [PMID: 37758814 PMCID: PMC10533825 DOI: 10.1038/s41598-023-43300-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 09/21/2023] [Indexed: 09/29/2023] Open
Abstract
Overcoming antimicrobial resistance represents a formidable challenge and investigating bacterial growth inhibition by fungal metabolites may yield new strategies. Although the fungal non-ribosomal peptide gliotoxin (GT) is known to exhibit antibacterial activity, the mechanism(s) of action are unknown, although reduced gliotoxin (dithiol gliotoxin; DTG) is a zinc chelator. Furthermore, it has been demonstrated that GT synergises with vancomycin to inhibit growth of Staphylococcus aureus. Here we demonstrate, without precedent, that GT-mediated growth inhibition of both Gram positive and negative bacterial species is reversed by Zn2+ or Cu2+ addition. Both GT, and the known zinc chelator TPEN, mediate growth inhibition of Enterococcus faecalis which is reversed by zinc addition. Moreover, zinc also reverses the synergistic growth inhibition of E. faecalis observed in the presence of both GT and vancomycin (4 µg/ml). As well as zinc chelation, DTG also appears to chelate Cu2+, but not Mn2+ using a 4-(2-pyridylazo)resorcinol assay system and Zn2+ as a positive control. DTG also specifically reacts in Fe3+-containing Siderotec™ assays, most likely by Fe3+ chelation from test reagents. GSH or DTT show no activity in these assays. Confirmatory high resolution mass spectrometry, in negative ion mode, confirmed, for the first time, the presence of both Cu[DTG] and Fe[DTG]2 chelates. Label free quantitative proteomic analysis further revealed major intracellular proteomic remodelling within E. faecalis in response to GT exposure for 30-180 min. Globally, 4.2-7.2% of detectable proteins exhibited evidence of either unique presence/increased abundance or unique absence/decreased abundance (n = 994-1160 total proteins detected), which is the first demonstration that GT affects the bacterial proteome in general, and E. faecalis, specifically. Unique detection of components of the AdcABC and AdcA-II zinc uptake systems was observed, along with apparent ribosomal reprofiling to zinc-free paralogs in the presence of GT. Overall, we hypothesise that GT-mediated bacterial growth inhibition appears to involve intracellular zinc depletion or reduced bioavailability, and based on in vitro chelate formation, may also involve dysregulation of Cu2+ homeostasis.
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Affiliation(s)
- Shane G Downes
- Department of Biology, Maynooth University, Co. Kildare, Ireland
| | - Rebecca A Owens
- Department of Biology, Maynooth University, Co. Kildare, Ireland
| | | | | | - Amber Dorey
- Molecular Parasitology, University of Galway, Galway, Ireland
| | - Gary W Jones
- Centre for Biomedical Science Research, School of Health, Leeds-Beckett University, Leeds, UK.
| | - Sean Doyle
- Department of Biology, Maynooth University, Co. Kildare, Ireland.
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7
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Downes SG, Doyle S, Jones GW, Owens RA. Gliotoxin and related metabolites as zinc chelators: implications and exploitation to overcome antimicrobial resistance. Essays Biochem 2023; 67:769-780. [PMID: 36876884 PMCID: PMC10500201 DOI: 10.1042/ebc20220222] [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: 12/21/2022] [Revised: 02/03/2023] [Accepted: 02/06/2023] [Indexed: 03/07/2023]
Abstract
Antimicrobial resistance (AMR) is a major global problem and threat to humanity. The search for new antibiotics is directed towards targeting of novel microbial systems and enzymes, as well as augmenting the activity of pre-existing antimicrobials. Sulphur-containing metabolites (e.g., auranofin and bacterial dithiolopyrrolones [e.g., holomycin]) and Zn2+-chelating ionophores (PBT2) have emerged as important antimicrobial classes. The sulphur-containing, non-ribosomal peptide gliotoxin, biosynthesised by Aspergillus fumigatus and other fungi exhibits potent antimicrobial activity, especially in the dithiol form (dithiol gliotoxin; DTG). Specifically, it has been revealed that deletion of the enzymes gliotoxin oxidoreductase GliT, bis-thiomethyltransferase GtmA or the transporter GliA dramatically sensitise A. fumigatus to gliotoxin presence. Indeed, the double deletion strain A. fumigatus ΔgliTΔgtmA is especially sensitive to gliotoxin-mediated growth inhibition, which can be reversed by Zn2+ presence. Moreover, DTG is a Zn2+ chelator which can eject zinc from enzymes and inhibit activity. Although multiple studies have demonstrated the potent antibacterial effect of gliotoxin, no mechanistic details are available. Interestingly, reduced holomycin can inhibit metallo-β-lactamases. Since holomycin and gliotoxin can chelate Zn2+, resulting in metalloenzyme inhibition, we propose that this metal-chelating characteristic of these metabolites requires immediate investigation to identify new antibacterial drug targets or to augment the activity of existing antimicrobials. Given that (i) gliotoxin has been shown in vitro to significantly enhance vancomycin activity against Staphylococcus aureus, and (ii) that it has been independently proposed as an ideal probe to dissect the central 'Integrator' role of Zn2+ in bacteria - we contend such studies are immediately undertaken to help address AMR.
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Affiliation(s)
- Shane G Downes
- Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland
| | - Sean Doyle
- Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland
| | - Gary W Jones
- Centre for Biomedical Science Research, School of Health, Leeds Beckett University, Leeds LS1 3HE, U.K
| | - Rebecca A Owens
- Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland
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8
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Traynor AM, Sarikaya-Bayram Ö, Bayram Ö, Antonio Calera J, Doyle S. Proteomic dissection of the role of GliZ in gliotoxin biosynthesis in Aspergillus fumigatus. Fungal Genet Biol 2023; 166:103795. [PMID: 37023941 DOI: 10.1016/j.fgb.2023.103795] [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: 11/17/2022] [Revised: 03/30/2023] [Accepted: 03/31/2023] [Indexed: 04/08/2023]
Abstract
Gliotoxin (GT) biosynthesis in fungi is encoded by the gli biosynthetic gene cluster. While GT addition autoinduces biosynthesis, Zn2+ has been shown to attenuate cluster activity, and it was speculated that identification of Zn2Cys6 binuclear transcription factor GliZ binding partners might provide insight into this observation. Using the Tet-ON induction system, doxycycline (DOX) presence induced GliZ fusion protein expression in, and recovery of GT biosynthesis by, A. fumigatus ΔgliZ::HA-gliZ and ΔgliZ::TAP-gliZ strains, respectively. Quantitative RT-PCR confirmed that DOX induces gli cluster gene expression (n = 5) in both A. fumigatus HA-GliZ and TAP-GliZ strains. GT biosynthesis was evident in Czapek-Dox and in Sabouraud media, however tagged GliZ protein expression was more readily detected in Sabouraud media. Unexpectedly, Zn2+ was essential for GliZ fusion protein expression in vivo, following 3 h DOX induction. Moreover, HA-GliZ abundance was significantly higher in either DOX/GT or DOX/Zn2+, compared to DOX-only. This suggests that while GT induction is still intact, Zn2+ inhibition of HA-GliZ production in vivo is lost. Co-immunoprecipitation revealed that GT oxidoreductase GliT associates with GliZ in the presence of GT, suggesting a potential protective role. Additional putative HA-GliZ interacting proteins included cystathionine gamma lyase, ribosomal protein L15 and serine hydroxymethyltransferase (SHMT). Total mycelial quantitative proteomic data revealed that GliT and GtmA, as well as several other gli cluster proteins, are increased in abundance or uniquely expressed with GT addition. Proteins involved in sulphur metabolism are also differentially expressed with GT or Zn2+ presence. Overall, we disclose that under DOX induction GliZ functionality is unexpectedly evident in zinc-replete media, subject to GT induction and that GliT appears to associate with GliZ, potentially to prevent DTG-mediated GliZ inactivation by zinc ejection.
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Affiliation(s)
- Aimee M Traynor
- Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland
| | | | - Özgür Bayram
- Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland
| | - José Antonio Calera
- Instituto de Biología Funcional y Genómica (IBFG-CSIC), Universidad de Salamanca, Salamanca, Spain, Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
| | - Sean Doyle
- Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland.
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9
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Balamurugan C, Steenwyk JL, Goldman GH, Rokas A. The evolution of the gliotoxin biosynthetic gene cluster in Penicillium fungi. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.17.524442. [PMID: 36711793 PMCID: PMC9882216 DOI: 10.1101/2023.01.17.524442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Fungi biosynthesize a diversity of secondary metabolites, small organic bioactive molecules that play diverse roles in fungal ecology. Fungal secondary metabolites are often encoded by physically clustered sets of genes known as biosynthetic gene clusters (BGCs). Fungi in the genus Penicillium produce diverse secondary metabolites that have been both useful (e.g., the antibiotic penicillin and the cholesterol-lowering drug mevastatin) and harmful (e.g., the mycotoxin patulin and the immunosuppressant gliotoxin) to human affairs. BGCs often also encode resistance genes that confer self-protection to the secondary metabolite-producing fungus. Some Penicillium species, such as Penicillium lilacinoechinulatum and Penicillium decumbens, are known to produce gliotoxin, a secondary metabolite with known immunosuppressant activity; however, an evolutionary characterization of the BGC responsible for gliotoxin biosynthesis among Penicillium species is lacking. Here, we examine the conservation of genes involved in gliotoxin biosynthesis and resistance in 35 Penicillium genomes from 23 species. We found homologous, less fragmented gliotoxin BGCs in 12 genomes, mostly fragmented remnants of the gliotoxin BGC in 21 genomes, whereas the remaining two Penicillium genomes lacked the gliotoxin BGC altogether. In contrast, we observed broad conservation of homologs of resistance genes that reside outside the BGC across Penicillium genomes. Evolutionary rate analysis revealed that BGCs with higher numbers of genes evolve slower than BGCs with few genes. Even though the gliotoxin BGC is fragmented to varying degrees in nearly all genomes examined, ancestral state reconstruction suggests that the ancestor of Penicillium species possessed the gliotoxin BGC. Our analyses suggest that genes that are part of BGCs can be retained in genomes long after the loss of secondary metabolite biosynthesis.
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Affiliation(s)
- Charu Balamurugan
- Vanderbilt University, Department of Biological Sciences, VU Station B #35-1634, Nashville, TN 37235, United States of America
- Vanderbilt Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN, United States
| | - Jacob L. Steenwyk
- Vanderbilt University, Department of Biological Sciences, VU Station B #35-1634, Nashville, TN 37235, United States of America
- Vanderbilt Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN, United States
- Howards Hughes Medical Institute and the Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Gustavo H. Goldman
- Faculdade de Ciencias Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Antonis Rokas
- Vanderbilt University, Department of Biological Sciences, VU Station B #35-1634, Nashville, TN 37235, United States of America
- Vanderbilt Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN, United States
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10
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Huber EM. Epipolythiodioxopiperazine-Based Natural Products: Building Blocks, Biosynthesis and Biological Activities. Chembiochem 2022; 23:e202200341. [PMID: 35997236 PMCID: PMC10086836 DOI: 10.1002/cbic.202200341] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 08/19/2022] [Indexed: 01/25/2023]
Abstract
Epipolythiodioxopiperazines (ETPs) are fungal secondary metabolites that share a 2,5-diketopiperazine scaffold built from two amino acids and bridged by a sulfide moiety. Modifications of the core and the amino acid side chains, for example by methylations, acetylations, hydroxylations, prenylations, halogenations, cyclizations, and truncations create the structural diversity of ETPs and contribute to their biological activity. However, the key feature responsible for the bioactivities of ETPs is their sulfide moiety. Over the last years, combinations of genome mining, reverse genetics, metabolomics, biochemistry, and structural biology deciphered principles of ETP production. Sulfurization via glutathione and uncovering of the thiols followed by either oxidation or methylation crystallized as fundamental steps that impact expression of the biosynthesis cluster, toxicity and secretion of the metabolite as well as self-tolerance of the producer. This article showcases structure and activity of prototype ETPs such as gliotoxin and discusses the current knowledge on the biosynthesis routes of these exceptional natural products.
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Affiliation(s)
- Eva M Huber
- Chair of Biochemistry, Center for Protein Assemblies, Technical University of Munich, Ernst-Otto-Fischer-Str. 8, 85748, Garching, Germany
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11
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Vignolle GA, Mach RL, Mach-Aigner AR, Zimmermann C. FunOrder 2.0 - a method for the fully automated curation of co-evolved genes in fungal biosynthetic gene clusters. FRONTIERS IN FUNGAL BIOLOGY 2022; 3:1020623. [PMID: 37746171 PMCID: PMC10512238 DOI: 10.3389/ffunb.2022.1020623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 10/03/2022] [Indexed: 09/26/2023]
Abstract
Coevolution is an important biological process that shapes interacting proteins - may it be physically interacting proteins or consecutive enzymes in a metabolic pathway, such as the biosynthetic pathways for secondary metabolites. Previously, we developed FunOrder, a semi-automated method for the detection of co-evolved genes, and demonstrated that FunOrder can be used to identify essential genes in biosynthetic gene clusters from different ascomycetes. A major drawback of this original method was the need for a manual assessment, which may create a user bias and prevents a high-throughput application. Here we present a fully automated version of this method termed FunOrder 2.0. In the improved version, we use several mathematical indices to determine the optimal number of clusters in the FunOrder output, and a subsequent k-means clustering based on the first three principal components of a principal component analysis of the FunOrder output to automatically detect co-evolved genes. Further, we replaced the BLAST tool with the DIAMOND tool as a prerequisite for using larger proteome databases. Potentially, FunOrder 2.0 may be used for the assessment of complete genomes, which has not been attempted yet. However, the introduced changes slightly decreased the sensitivity of this method, which is outweighed by enhanced overall speed and specificity.
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Affiliation(s)
- Gabriel A. Vignolle
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
- Center for Health & Bioresources, Competence Unit Molecular Diagnostics, AIT Austrian Institute of Technology GmbH, Vienna, Austria
| | - Robert L. Mach
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
| | - Astrid R. Mach-Aigner
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
| | - Christian Zimmermann
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
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12
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Brown A, Mead ME, Steenwyk JL, Goldman GH, Rokas A. Extensive non-coding sequence divergence between the major human pathogen Aspergillus fumigatus and its relatives. FRONTIERS IN FUNGAL BIOLOGY 2022; 3:802494. [PMID: 36866034 PMCID: PMC9977105 DOI: 10.3389/ffunb.2022.802494] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 06/09/2022] [Indexed: 11/13/2022]
Abstract
Invasive aspergillosis is a deadly fungal disease; more than 400,000 patients are infected worldwide each year and the mortality rate can be as high as 50-95%. Of the ~450 species in the genus Aspergillus only a few are known to be clinically relevant, with the major pathogen Aspergillus fumigatus being responsible for ~50% of all invasive mold infections. Genomic comparisons between A. fumigatus and other Aspergillus species have historically focused on protein-coding regions. However, most A. fumigatus genes, including those that modulate its virulence, are also present in other pathogenic and non-pathogenic closely related species. Our hypothesis is that differential gene regulation - mediated through the non-coding regions upstream of genes' first codon - contributes to A. fumigatus pathogenicity. To begin testing this, we compared non-coding regions upstream of the first codon of single-copy orthologous genes from the two A. fumigatus reference strains Af293 and A1163 and eight closely related Aspergillus section Fumigati species. We found that these non-coding regions showed extensive sequence variation and lack of homology across species. By examining the evolutionary rates of both protein-coding and non-coding regions in a subset of orthologous genes with highly conserved non-coding regions across the phylogeny, we identified 418 genes, including 25 genes known to modulate A. fumigatus virulence, whose non-coding regions exhibit a different rate of evolution in A. fumigatus. Examination of sequence alignments of these non-coding regions revealed numerous instances of insertions, deletions, and other types of mutations of at least a few nucleotides in A. fumigatus compared to its close relatives. These results show that closely related Aspergillus species that vary greatly in their pathogenicity exhibit extensive non-coding sequence variation and identify numerous changes in non-coding regions of A. fumigatus genes known to contribute to virulence.
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Affiliation(s)
- Alec Brown
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, United States
- Vanderbilt Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN, United States
| | - Matthew E. Mead
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, United States
- Vanderbilt Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN, United States
| | - Jacob L. Steenwyk
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, United States
- Vanderbilt Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN, United States
| | - Gustavo H. Goldman
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, United States
- Vanderbilt Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN, United States
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Redrado S, Esteban P, Domingo MP, Lopez C, Rezusta A, Ramirez-Labrada A, Arias M, Pardo J, Galvez EM. Integration of In Silico and In Vitro Analysis of Gliotoxin Production Reveals a Narrow Range of Producing Fungal Species. J Fungi (Basel) 2022; 8:jof8040361. [PMID: 35448592 PMCID: PMC9030297 DOI: 10.3390/jof8040361] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/28/2022] [Accepted: 03/29/2022] [Indexed: 02/06/2023] Open
Abstract
Gliotoxin is a fungal secondary metabolite with impact on health and agriculture since it might act as virulence factor and contaminate human and animal food. Homologous gliotoxin (GT) gene clusters are spread across a number of fungal species although if they produce GT or other related epipolythiodioxopiperazines (ETPs) remains obscure. Using bioinformatic tools, we have identified homologous gli gene clusters similar to the A. fumigatus GT gene cluster in several fungal species. In silico study led to in vitro confirmation of GT and Bisdethiobis(methylthio)gliotoxin (bmGT) production in fungal strain cultures by HPLC detection. Despite we selected most similar homologous gli gene cluster in 20 different species, GT and bmGT were only detected in section Fumigati species and in a Trichoderma virens Q strain. Our results suggest that in silico gli homology analyses in different fungal strains to predict GT production might be only informative when accompanied by analysis about mycotoxin production in cell cultures.
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Affiliation(s)
- Sergio Redrado
- Instituto de Carboquımica ICB-CSIC, 50018 Zaragoza, Spain; (S.R.); (M.P.D.)
| | - Patricia Esteban
- Biomedical Research Centre of Aragon (CIBA), Fundacion Instituto de Investigacion Sanitaria Aragon (IIS Aragon), 50009 Zaragoza, Spain; (P.E.); (A.R.-L.); (M.A.); (J.P.)
| | | | - Concepción Lopez
- Department of Microbiology, Hospital Universitario Miguel Servet, IIS Aragón, 50009 Zaragoza, Spain; (C.L.); (A.R.)
| | - Antonio Rezusta
- Department of Microbiology, Hospital Universitario Miguel Servet, IIS Aragón, 50009 Zaragoza, Spain; (C.L.); (A.R.)
| | - Ariel Ramirez-Labrada
- Biomedical Research Centre of Aragon (CIBA), Fundacion Instituto de Investigacion Sanitaria Aragon (IIS Aragon), 50009 Zaragoza, Spain; (P.E.); (A.R.-L.); (M.A.); (J.P.)
| | - Maykel Arias
- Biomedical Research Centre of Aragon (CIBA), Fundacion Instituto de Investigacion Sanitaria Aragon (IIS Aragon), 50009 Zaragoza, Spain; (P.E.); (A.R.-L.); (M.A.); (J.P.)
| | - Julián Pardo
- Biomedical Research Centre of Aragon (CIBA), Fundacion Instituto de Investigacion Sanitaria Aragon (IIS Aragon), 50009 Zaragoza, Spain; (P.E.); (A.R.-L.); (M.A.); (J.P.)
- Department of Microbiology, Pediatrics, Radiology and Public Health, University of Zaragoza, 50009 Zaragoza, Spain
- Aragon I+D Foundation (ARAID), 50018 Zaragoza, Spain
| | - Eva M. Galvez
- Instituto de Carboquımica ICB-CSIC, 50018 Zaragoza, Spain; (S.R.); (M.P.D.)
- Correspondence:
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Margalit A, Sheehan D, Carolan JC, Kavanagh K. Exposure to the Pseudomonas aeruginosa secretome alters the proteome and secondary metabolite production of Aspergillus fumigatus. MICROBIOLOGY (READING, ENGLAND) 2022; 168:001164. [PMID: 35333152 PMCID: PMC9558348 DOI: 10.1099/mic.0.001164] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 02/16/2022] [Indexed: 01/09/2023]
Abstract
The fungal pathogen Aspergillus fumigatus is frequently cultured from the sputum of cystic fibrosis (CF) patients along with the bacterium Pseudomonas aeruginosa. A. fumigatus secretes a range of secondary metabolites, and one of these, gliotoxin, has inhibitory effects on the host immune response. The effect of P. aeruginosa culture filtrate (CuF) on fungal growth and gliotoxin production was investigated. Exposure of A. fumigatus hyphae to P. aeruginosa cells induced increased production of gliotoxin and a decrease in fungal growth. In contrast, exposure of A. fumigatus hyphae to P. aeruginosa CuF led to increased growth and decreased gliotoxin production. Quantitative proteomic analysis was used to characterize the proteomic response of A. fumigatus upon exposure to P. aeruginosa CuF. Changes in the profile of proteins involved in secondary metabolite biosynthesis (e.g. gliotoxin, fumagillin, pseurotin A), and changes to the abundance of proteins involved in oxidative stress (e.g. formate dehydrogenase) and detoxification (e.g. thioredoxin reductase) were observed, indicating that the bacterial secretome had a profound effect on the fungal proteome. Alterations in the abundance of proteins involved in detoxification and oxidative stress highlight the ability of A. fumigatus to differentially regulate protein synthesis in response to environmental stresses imposed by competitors such as P. aeruginosa. Such responses may ultimately have serious detrimental effects on the host.
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Affiliation(s)
- Anatte Margalit
- Department of Biology, Maynooth University, Co. Kildare, Ireland
| | - David Sheehan
- Department of Biology, Maynooth University, Co. Kildare, Ireland
| | - James C. Carolan
- Department of Biology, Maynooth University, Co. Kildare, Ireland
| | - Kevin Kavanagh
- Department of Biology, Maynooth University, Co. Kildare, Ireland
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15
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Colabardini AC, Wang F, Dong Z, Pardeshi L, Rocha MC, Costa JH, dos Reis TF, Brown A, Jaber QZ, Fridman M, Fill T, Rokas A, Malavazi I, Wong KH, Goldman GH. Heterogeneity in the transcriptional response of the human pathogen Aspergillus fumigatus to the antifungal agent caspofungin. Genetics 2022; 220:iyab183. [PMID: 34718550 PMCID: PMC8733440 DOI: 10.1093/genetics/iyab183] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 10/07/2021] [Indexed: 01/11/2023] Open
Abstract
Aspergillus fumigatus is the main causative agent of invasive pulmonary aspergillosis (IPA), a severe disease that affects immunosuppressed patients worldwide. The fungistatic drug caspofungin (CSP) is the second line of therapy against IPA but has increasingly been used against clinical strains that are resistant to azoles, the first line antifungal therapy. In high concentrations, CSP induces a tolerance phenotype with partial reestablishment of fungal growth called CSP paradoxical effect (CPE), resulting from a change in the composition of the cell wall. An increasing number of studies has shown that different isolates of A. fumigatus exhibit phenotypic heterogeneity, including heterogeneity in their CPE response. To gain insights into the underlying molecular mechanisms of CPE response heterogeneity, we analyzed the transcriptomes of two A. fumigatus reference strains, Af293 and CEA17, exposed to low and high CSP concentrations. We found that there is a core transcriptional response that involves genes related to cell wall remodeling processes, mitochondrial function, transmembrane transport, and amino acid and ergosterol metabolism, and a variable response related to secondary metabolite (SM) biosynthesis and iron homeostasis. Specifically, we show here that the overexpression of a SM pathway that works as an iron chelator extinguishes the CPE in both backgrounds, whereas iron depletion is detrimental for the CPE in Af293 but not in CEA17. We next investigated the function of the transcription factor CrzA, whose deletion was previously shown to result in heterogeneity in the CPE response of the Af293 and CEA17 strains. We found that CrzA constitutively binds to and modulates the expression of several genes related to processes involved in CSP tolerance and that crzA deletion differentially impacts the SM production and growth of Af293 and CEA17. As opposed to the ΔcrzACEA17 mutant, the ΔcrzAAf293 mutant fails to activate cell wall remodeling genes upon CSP exposure, which most likely severely affects its macrostructure and extinguishes its CPE. This study describes how heterogeneity in the response to an antifungal agent between A. fumigatus strains stems from heterogeneity in the function of a transcription factor and its downstream target genes.
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Affiliation(s)
- Ana Cristina Colabardini
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo CEP 14040-903, Brazil
- Faculty of Health Sciences, University of Macau, Macau 999078, China
| | - Fang Wang
- Faculty of Health Sciences, University of Macau, Macau 999078, China
| | - Zhiqiang Dong
- Faculty of Health Sciences, University of Macau, Macau 999078, China
| | - Lakhansing Pardeshi
- Faculty of Health Sciences, University of Macau, Macau 999078, China
- Genomics, Bioinformatics and Single Cell Analysis Core, Faculty of Health Sciences, University of Macau, Macau, 999078, China
| | - Marina Campos Rocha
- Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, São Carlos CEP 13565-905, Brazil
| | - Jonas Henrique Costa
- Instituto de Química, Universidade Estadual de Campinas, Campinas, São Paulo CEP 13083-970, Brazil
| | - Thaila Fernanda dos Reis
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo CEP 14040-903, Brazil
| | - Alec Brown
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
| | - Qais Z Jaber
- School of Chemistry, Raymond & Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Micha Fridman
- School of Chemistry, Raymond & Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Taicia Fill
- Instituto de Química, Universidade Estadual de Campinas, Campinas, São Paulo CEP 13083-970, Brazil
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
| | - Iran Malavazi
- Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, São Carlos CEP 13565-905, Brazil
| | - Koon Ho Wong
- Faculty of Health Sciences, University of Macau, Macau 999078, China
- Faculty of Health Sciences, Institute of Translational Medicine, University of Macau, Macau 999078, China
- MoE Frontiers Science Center for Precision Oncology, University of Macau, Macau 999078, China
| | - Gustavo Henrique Goldman
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo CEP 14040-903, Brazil
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16
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de Castro PA, Colabardini AC, Moraes M, Horta MAC, Knowles SL, Raja HA, Oberlies NH, Koyama Y, Ogawa M, Gomi K, Steenwyk JL, Rokas A, Gonçales RA, Duarte-Oliveira C, Carvalho A, Ries LNA, Goldman GH. Regulation of gliotoxin biosynthesis and protection in Aspergillus species. PLoS Genet 2022; 18:e1009965. [PMID: 35041649 PMCID: PMC8797188 DOI: 10.1371/journal.pgen.1009965] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/28/2022] [Accepted: 01/04/2022] [Indexed: 02/07/2023] Open
Abstract
Aspergillus fumigatus causes a range of human and animal diseases collectively known as aspergillosis. A. fumigatus possesses and expresses a range of genetic determinants of virulence, which facilitate colonisation and disease progression, including the secretion of mycotoxins. Gliotoxin (GT) is the best studied A. fumigatus mycotoxin with a wide range of known toxic effects that impair human immune cell function. GT is also highly toxic to A. fumigatus and this fungus has evolved self-protection mechanisms that include (i) the GT efflux pump GliA, (ii) the GT neutralising enzyme GliT, and (iii) the negative regulation of GT biosynthesis by the bis-thiomethyltransferase GtmA. The transcription factor (TF) RglT is the main regulator of GliT and this GT protection mechanism also occurs in the non-GT producing fungus A. nidulans. However, the A. nidulans genome does not encode GtmA and GliA. This work aimed at analysing the transcriptional response to exogenous GT in A. fumigatus and A. nidulans, two distantly related Aspergillus species, and to identify additional components required for GT protection. RNA-sequencing shows a highly different transcriptional response to exogenous GT with the RglT-dependent regulon also significantly differing between A. fumigatus and A. nidulans. However, we were able to observe homologs whose expression pattern was similar in both species (43 RglT-independent and 11 RglT-dependent). Based on this approach, we identified a novel RglT-dependent methyltranferase, MtrA, involved in GT protection. Taking into consideration the occurrence of RglT-independent modulated genes, we screened an A. fumigatus deletion library of 484 transcription factors (TFs) for sensitivity to GT and identified 15 TFs important for GT self-protection. Of these, the TF KojR, which is essential for kojic acid biosynthesis in Aspergillus oryzae, was also essential for virulence and GT biosynthesis in A. fumigatus, and for GT protection in A. fumigatus, A. nidulans, and A. oryzae. KojR regulates rglT, gliT, gliJ expression and sulfur metabolism in Aspergillus species. Together, this study identified conserved components required for GT protection in Aspergillus species. A. fumigatus secretes mycotoxins that are essential for its virulence and pathogenicity. Gliotoxin (GT) is a sulfur-containing mycotoxin, which is known to impair several aspects of the human immune response. GT is also toxic to different fungal species, which have evolved several GT protection strategies. To further decipher these responses, we used transcriptional profiling aiming to compare the response to GT in the GT producer A. fumigatus and the GT non-producer A. nidulans. This analysis allowed us to identify additional genes with a potential role in GT protection. We also identified 15 transcription factors (TFs) encoded in the A. fumigatus genome that are important for conferring resistance to exogenous gliotoxin. One of these TFs, KojR, which is essential for A. oryzae kojic acid production, is also important for virulence in A. fumigatus and GT protection in A. fumigatus, A. nidulans and A. oryzae. KojR regulates the expression of genes important for gliotoxin biosynthesis and protection, and sulfur metabolism. Together, this work identified conserved components required for gliotoxin protection in Aspergillus species.
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Affiliation(s)
- Patrícia Alves de Castro
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Ana Cristina Colabardini
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Maísa Moraes
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | | | - Sonja L. Knowles
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, North Carolina United States of America
| | - Huzefa A. Raja
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, North Carolina United States of America
| | - Nicholas H. Oberlies
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, North Carolina United States of America
| | - Yasuji Koyama
- Noda Institute for Scientific Research, 338 Noda, Chiba, Japan
| | - Masahiro Ogawa
- Noda Institute for Scientific Research, 338 Noda, Chiba, Japan
| | - Katsuya Gomi
- Department of Bioindustrial Informatics and Genomics, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Jacob L. Steenwyk
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Relber A. Gonçales
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B’s—PT Government Associate Laboratory, Guimarães/Braga, Portugal
| | - Cláudio Duarte-Oliveira
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B’s—PT Government Associate Laboratory, Guimarães/Braga, Portugal
| | - Agostinho Carvalho
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B’s—PT Government Associate Laboratory, Guimarães/Braga, Portugal
| | - Laure N. A. Ries
- MRC Centre for Medical Mycology at the University of Exeter, Geoffrey Pope Building, Exeter, United Kingdom
- * E-mail: (LNAR); (GHG)
| | - Gustavo H. Goldman
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
- * E-mail: (LNAR); (GHG)
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Complete Genome Sequences and Genome-Wide Characterization of Trichoderma Biocontrol Agents Provide New Insights into their Evolution and Variation in Genome Organization, Sexual Development, and Fungal-Plant Interactions. Microbiol Spectr 2021; 9:e0066321. [PMID: 34908505 PMCID: PMC8672877 DOI: 10.1128/spectrum.00663-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Trichoderma spp. represent one of the most important fungal genera to mankind and in natural environments. The genus harbors prolific producers of wood-decaying enzymes, biocontrol agents against plant pathogens, plant-growth-promoting biofertilizers, as well as model organisms for studying fungal-plant-plant pathogen interactions. Pursuing highly accurate, contiguous, and chromosome-level reference genomes has become a primary goal of fungal research communities. Here, we report the chromosome-level genomic sequences and whole-genome annotation data sets of four strains used as biocontrol agents or biofertilizers (Trichoderma virens Gv29-8, Trichoderma virens FT-333, Trichoderma asperellum FT-101, and Trichoderma atroviride P1). Our results provide comprehensive categorization, correct positioning, and evolutionary detail of both nuclear and mitochondrial genomes, including telomeres, AT-rich blocks, centromeres, transposons, mating-type loci, nuclear-encoded mitochondrial sequences, as well as many new secondary metabolic and carbohydrate-active enzyme gene clusters. We have also identified evolutionarily conserved core genes contributing to plant-fungal interactions, as well as variations potentially linked to key behavioral traits such as sex, genome defense, secondary metabolism, and mycoparasitism. The genomic resources we provide herein significantly extend our knowledge not only of this economically important fungal genus, but also fungal evolution and basic biology in general. IMPORTANCE Telomere-to-telomere and gapless reference genome assemblies are necessary to ensure that all genomic variants are studied and discovered, including centromeres, telomeres, AT-rich blocks, mating type loci, biosynthetic, and metabolic gene clusters. Here, we applied long-range sequencing technologies to determine the near-completed genome sequences of four widely used biocontrol agents or biofertilizers: Trichoderma virens Gv29-8 and FT-333, Trichoderma asperellum FT-101, and Trichoderma atroviride P1. Like those of three Trichoderma reesei wild isolates [QM6a, CBS999.97(MAT1-1) and CBS999.97(MAT1-2)] we reported previously, these four biocontrol agent genomes each contain seven nuclear chromosomes and a circular mitochondrial genome. Substantial intraspecies and intragenus diversities are also discovered, including single nucleotide polymorphisms, chromosome shuffling, as well as genomic relics derived from historical transposition events and repeat-induced point (RIP) mutations.
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The Toxic Mechanism of Gliotoxins and Biosynthetic Strategies for Toxicity Prevention. Int J Mol Sci 2021; 22:ijms222413510. [PMID: 34948306 PMCID: PMC8705807 DOI: 10.3390/ijms222413510] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/09/2021] [Accepted: 12/13/2021] [Indexed: 12/13/2022] Open
Abstract
Gliotoxin is a kind of epipolythiodioxopiperazine derived from different fungi that is characterized by a disulfide bridge. Gliotoxins can be biosynthesized by a gli gene cluster and regulated by a positive GliZ regulator. Gliotoxins show cytotoxic effects via the suppression the function of macrophage immune function, inflammation, antiangiogenesis, DNA damage by ROS production, peroxide damage by the inhibition of various enzymes, and apoptosis through different signal pathways. In the other hand, gliotoxins can also be beneficial with different doses. Low doses of gliotoxin can be used as an antioxidant, in the diagnosis and treatment of HIV, and as an anti-tumor agent in the future. Gliotoxins have also been used in the control of plant pathogens, including Pythium ultimum and Sclerotinia sclerotiorum. Thus, it is important to elucidate the toxic mechanism of gliotoxins. The toxic mechanism of gliotoxins and biosynthetic strategies to reduce the toxicity of gliotoxins and their producing strains are summarized in this review.
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Traynor AM, Owens RA, Coughlin CM, Holton MC, Jones GW, Calera JA, Doyle S. At the metal-metabolite interface in Aspergillus fumigatus: towards untangling the intersecting roles of zinc and gliotoxin. MICROBIOLOGY (READING, ENGLAND) 2021; 167. [PMID: 34738889 PMCID: PMC8743625 DOI: 10.1099/mic.0.001106] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Cryptic links between apparently unrelated metabolic systems represent potential new drug targets in fungi. Evidence of such a link between zinc and gliotoxin (GT) biosynthesis in Aspergillus fumigatus is emerging. Expression of some genes of the GT biosynthetic gene cluster gli is influenced by the zinc-dependent transcription activator ZafA, zinc may relieve GT-mediated fungal growth inhibition and, surprisingly, GT biosynthesis is influenced by zinc availability. In A. fumigatus, dithiol gliotoxin (DTG), which has zinc-chelating properties, is converted to either GT or bis-dethiobis(methylthio)gliotoxin (BmGT) by oxidoreductase GliT and methyltransferase GtmA, respectively. A double deletion mutant lacking both GliT and GtmA was previously observed to be hypersensitive to exogenous GT exposure. Here we show that compared to wild-type exposure, exogenous GT and the zinc chelator N,N,N',N'-tetrakis(2-pyridinylmethyl)-1,2-ethanediamine (TPEN) inhibit A. fumigatus ΔgliTΔgtmA growth, specifically under zinc-limiting conditions, which can be reversed by zinc addition. While GT biosynthesis is evident in zinc-depleted medium, addition of zinc (1 µM) suppressed GT and activated BmGT production. In addition, secretion of the unferrated siderophore, triacetylfusarinine C (TAFC), was evident by A. fumigatus wild-type (at >5 µM zinc) and ΔgtmA (at >1 µM zinc) in a low-iron medium. TAFC secretion suggests that differential zinc-sensing between both strains may influence fungal Fe3+ requirement. Label-free quantitative proteomic analysis of both strains under equivalent differential zinc conditions revealed protein abundance alterations in accordance with altered metabolomic observations, in addition to increased GliT abundance in ΔgtmA at 5 µM zinc, compared to wild-type, supporting a zinc-sensing deficiency in the mutant strain. The relative abundance of a range of oxidoreductase- and secondary metabolism-related enzymes was also evident in a zinc- and strain-dependent manner. Overall, we elaborate new linkages between zinc availability, natural product biosynthesis and oxidative stress homeostasis in A. fumigatus.
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Affiliation(s)
- Aimee M Traynor
- Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland
| | - Rebecca A Owens
- Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland
| | - Claudia M Coughlin
- Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland
| | - Maeve C Holton
- Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland
| | - Gary W Jones
- Centre for Biomedical Science Research, School of Clinical and Applied Sciences, Leeds Beckett University, Leeds, UK
| | - José A Calera
- Instituto de Biología Funcional y Genómica (IBFG-CSIC), Universidad de Salamanca, Salamanca, Spain
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
| | - Sean Doyle
- Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland
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20
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Beyond the Biosynthetic Gene Cluster Paradigm: Genome-Wide Coexpression Networks Connect Clustered and Unclustered Transcription Factors to Secondary Metabolic Pathways. Microbiol Spectr 2021; 9:e0089821. [PMID: 34523946 PMCID: PMC8557879 DOI: 10.1128/spectrum.00898-21] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Fungal secondary metabolites are widely used as therapeutics and are vital components of drug discovery programs. A major challenge hindering discovery of novel secondary metabolites is that the underlying pathways involved in their biosynthesis are transcriptionally silent under typical laboratory growth conditions, making it difficult to identify the transcriptional networks that they are embedded in. Furthermore, while the genes participating in secondary metabolic pathways are typically found in contiguous clusters on the genome, known as biosynthetic gene clusters (BGCs), this is not always the case, especially for global and pathway-specific regulators of pathways’ activities. To address these challenges, we used 283 genome-wide gene expression data sets of the ascomycete cell factory Aspergillus niger generated during growth under 155 different conditions to construct two gene coexpression networks based on Spearman’s correlation coefficients (SCCs) and on mutual rank-transformed Pearson’s correlation coefficients (MR-PCCs). By mining these networks, we predicted six transcription factors, named MjkA to MjkF, to regulate secondary metabolism in A. niger. Overexpression of each transcription factor using the Tet-On cassette modulated the production of multiple secondary metabolites. We found that the SCC and MR-PCC approaches complemented each other, enabling the delineation of putative global (SCC) and pathway-specific (MR-PCC) transcription factors. These results highlight the potential of coexpression network approaches to identify and activate fungal secondary metabolic pathways and their products. More broadly, we argue that drug discovery programs in fungi should move beyond the BGC paradigm and focus on understanding the global regulatory networks in which secondary metabolic pathways are embedded. IMPORTANCE There is an urgent need for novel bioactive molecules in both agriculture and medicine. The genomes of fungi are thought to contain vast numbers of metabolic pathways involved in the biosynthesis of secondary metabolites with diverse bioactivities. Because these metabolites are biosynthesized only under specific conditions, the vast majority of the fungal pharmacopeia awaits discovery. To discover the genetic networks that regulate the activity of secondary metabolites, we examined the genome-wide profiles of gene activity of the cell factory Aspergillus niger across hundreds of conditions. By constructing global networks that link genes with similar activities across conditions, we identified six putative global and pathway-specific regulators of secondary metabolite biosynthesis. Our study shows that elucidating the behavior of the genetic networks of fungi under diverse conditions harbors enormous promise for understanding fungal secondary metabolism, which ultimately may lead to novel drug candidates.
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21
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Vignolle GA, Schaffer D, Zehetner L, Mach RL, Mach-Aigner AR, Derntl C. FunOrder: A robust and semi-automated method for the identification of essential biosynthetic genes through computational molecular co-evolution. PLoS Comput Biol 2021; 17:e1009372. [PMID: 34570757 PMCID: PMC8476034 DOI: 10.1371/journal.pcbi.1009372] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 08/23/2021] [Indexed: 11/24/2022] Open
Abstract
Secondary metabolites (SMs) are a vast group of compounds with different structures and properties that have been utilized as drugs, food additives, dyes, and as monomers for novel plastics. In many cases, the biosynthesis of SMs is catalysed by enzymes whose corresponding genes are co-localized in the genome in biosynthetic gene clusters (BGCs). Notably, BGCs may contain so-called gap genes, that are not involved in the biosynthesis of the SM. Current genome mining tools can identify BGCs, but they have problems with distinguishing essential genes from gap genes. This can and must be done by expensive, laborious, and time-consuming comparative genomic approaches or transcriptome analyses. In this study, we developed a method that allows semi-automated identification of essential genes in a BGC based on co-evolution analysis. To this end, the protein sequences of a BGC are blasted against a suitable proteome database. For each protein, a phylogenetic tree is created. The trees are compared by treeKO to detect co-evolution. The results of this comparison are visualized in different output formats, which are compared visually. Our results suggest that co-evolution is commonly occurring within BGCs, albeit not all, and that especially those genes that encode for enzymes of the biosynthetic pathway are co-evolutionary linked and can be identified with FunOrder. In light of the growing number of genomic data available, this will contribute to the studies of BGCs in native hosts and facilitate heterologous expression in other organisms with the aim of the discovery of novel SMs. The discovery and description of novel fungal secondary metabolites promises novel antibiotics, pharmaceuticals, and other useful compounds. A way to identify novel secondary metabolites is to express the corresponding genes in a suitable expression host. Consequently, a detailed knowledge or an accurate prediction of these genes is necessary. In fungi, the genes are co-localized in so-called biosynthetic gene clusters. Notably, the clusters may also contain genes that are not necessary for the biosynthesis of the secondary metabolites, so-called gap genes. We developed a method to detect co-evolved genes within the clusters and demonstrated that essential genes are co-evolving and can thus be differentiated from the gap genes. This adds an additional layer of information, which can support researchers with their decisions on which genes to study and express for the discovery of novel secondary metabolites.
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Affiliation(s)
- Gabriel A. Vignolle
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
| | - Denise Schaffer
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
| | - Leopold Zehetner
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
| | - Robert L. Mach
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
| | - Astrid R. Mach-Aigner
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
| | - Christian Derntl
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
- * E-mail:
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22
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Wang W, Yu Y, Keller NP, Wang P. Presence, Mode of Action, and Application of Pathway Specific Transcription Factors in Aspergillus Biosynthetic Gene Clusters. Int J Mol Sci 2021; 22:ijms22168709. [PMID: 34445420 PMCID: PMC8395729 DOI: 10.3390/ijms22168709] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 08/10/2021] [Accepted: 08/10/2021] [Indexed: 01/21/2023] Open
Abstract
Fungal secondary metabolites are renowned toxins as well as valuable sources of antibiotics, cholesterol-lowering drugs, and immunosuppressants; hence, great efforts were levied to understand how these compounds are genetically regulated. The genes encoding for the enzymes required for synthesizing secondary metabolites are arranged in biosynthetic gene clusters (BGCs). Often, BGCs contain a pathway specific transcription factor (PSTF), a valuable tool in shutting down or turning up production of the BGC product. In this review, we present an in-depth view of PSTFs by examining over 40 characterized BGCs in the well-studied fungal species Aspergillus nidulans and Aspergillus fumigatus. Herein, we find BGC size is a predictor for presence of PSTFs, consider the number and the relative location of PSTF in regard to the cluster(s) regulated, discuss the function and the evolution of PSTFs, and present application strategies for pathway specific activation of cryptic BGCs.
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Affiliation(s)
- Wenjie Wang
- Ocean College, Zhejiang University, Zhoushan 316021, China; (W.W.); (Y.Y.)
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Yuchao Yu
- Ocean College, Zhejiang University, Zhoushan 316021, China; (W.W.); (Y.Y.)
| | - Nancy P. Keller
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
- Correspondence: (N.P.K.); (P.W.)
| | - Pinmei Wang
- Ocean College, Zhejiang University, Zhoushan 316021, China; (W.W.); (Y.Y.)
- Correspondence: (N.P.K.); (P.W.)
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23
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Ye W, Li S, Liu S, Kong Y, Zhang W, Liu S, Liu T, Zhang W. Characterization of novel gliotoxin biosynthesis-related genes from deep-sea-derived fungus Geosmithia pallida FS140. Biochimie 2021; 191:1-10. [PMID: 34364944 DOI: 10.1016/j.biochi.2021.08.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 07/24/2021] [Accepted: 08/03/2021] [Indexed: 11/15/2022]
Abstract
Gliotoxins are epipolythiodioxopiperazine toxins produced by the filamentous fungi, which show great potential in the treatment of liver and lung cancer because of its cytotoxicity. In this study, three novel genes related to gliotoxin biosynthesis, gliT, gliM and gliK encoding thioredoxin reductase, O-methyltransferase and gamma-glutamyl cyclotransferase, respectively, from the deep-sea-derived fungus Geosmithia pallida were cloned from G. pallida and expressed in Escherichia coli. The recombinant GliT, GliM and GliK proteins were expressed and purified by Ni affinity column, which was demonstrated by SDS-PAGE and Western blot analysis. The inclusion bodies of GliT were renatured and the corresponding enzymatic properties of the two enzymes were further investigated. Using DTNB as a substrate, GliT showed the highest enzymatic activity of 11041 mU/L at pH 7.0, and the optimal reaction temperature was 40 °C. Using EGCG as a substrate, GliM showed the highest enzymatic activity of 239.19 mU/mg at pH 7.0, the optimum temperature was 35 °C. GliK from G. pallida was firstly reported to show bi-function of glutymal cyclotransferase and acetyltransfearse actvity with highest enzymatic activity of 615.5 U/mg in this study. The results suggested the important enzymatic function of GliT, GliM and GliK in the gliotoxin biosynthesis in G. pallida, which would lay a foundation for the mechanism elucidation of the gliotoxin biosynthesis in G. pallida and the exploitation of novel gliotoxin derivaties.
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Affiliation(s)
- Wei Ye
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, China
| | - Saini Li
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, China
| | - Shuai Liu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, China
| | - Yali Kong
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, China
| | - Weiyang Zhang
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, China
| | - Shan Liu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, China
| | - Taomei Liu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, China
| | - Weimin Zhang
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, China.
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24
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Boysen JM, Saeed N, Hillmann F. Natural products in the predatory defence of the filamentous fungal pathogen Aspergillus fumigatus. Beilstein J Org Chem 2021; 17:1814-1827. [PMID: 34394757 PMCID: PMC8336654 DOI: 10.3762/bjoc.17.124] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 07/14/2021] [Indexed: 11/30/2022] Open
Abstract
The kingdom of fungi comprises a large and highly diverse group of organisms that thrive in diverse natural environments. One factor to successfully confront challenges in their natural habitats is the capability to synthesize defensive secondary metabolites. The genetic potential for the production of secondary metabolites in fungi is high and numerous potential secondary metabolite gene clusters have been identified in sequenced fungal genomes. Their production may well be regulated by specific ecological conditions, such as the presence of microbial competitors, symbionts or predators. Here we exemplarily summarize our current knowledge on identified secondary metabolites of the pathogenic fungus Aspergillus fumigatus and their defensive function against (microbial) predators.
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Affiliation(s)
- Jana M Boysen
- Junior Research Group Evolution of Microbial Interactions, Leibniz-Institute for Natural Product Research and Infection Biology – Hans Knöll Institute (HKI), Beutenbergstr. 11a, 07745 Jena, Germany
- Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Nauman Saeed
- Junior Research Group Evolution of Microbial Interactions, Leibniz-Institute for Natural Product Research and Infection Biology – Hans Knöll Institute (HKI), Beutenbergstr. 11a, 07745 Jena, Germany
- Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Falk Hillmann
- Junior Research Group Evolution of Microbial Interactions, Leibniz-Institute for Natural Product Research and Infection Biology – Hans Knöll Institute (HKI), Beutenbergstr. 11a, 07745 Jena, Germany
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25
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Scherlach K, Kuttenlochner W, Scharf DH, Brakhage AA, Hertweck C, Groll M, Huber EM. Strukturelle und mechanistische Einblicke in die Bildung der C‐S‐Bindungen in Gliotoxin. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202104372] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Kirstin Scherlach
- Abteilung Biomolekulare Chemie Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie (HKI) Beutenbergstraße 11a 07745 Jena Deutschland
| | - Wolfgang Kuttenlochner
- Technische Universität München Zentrum für Proteinforschung (CPA) Ernst-Otto-Fischer-Straße 8 85747 Garching Deutschland
| | - Daniel H. Scharf
- Abteilung Molekulare und Angewandte Mikrobiologie Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie (HKI) Beutenbergstraße 11a 07745 Jena Deutschland
- Abteilung Mikrobiologie und Kinderkrankenhaus Zhejiang Universität Fakultät für Medizin Hangzhou 310058 Zhejiang V.R. China
| | - Axel A. Brakhage
- Abteilung Molekulare und Angewandte Mikrobiologie Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie (HKI) Beutenbergstraße 11a 07745 Jena Deutschland
- Fakultät für Biowissenschaften Friedrich Schiller Universität Jena 07743 Jena Deutschland
| | - Christian Hertweck
- Abteilung Biomolekulare Chemie Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie (HKI) Beutenbergstraße 11a 07745 Jena Deutschland
- Fakultät für Biowissenschaften Friedrich Schiller Universität Jena 07743 Jena Deutschland
| | - Michael Groll
- Technische Universität München Zentrum für Proteinforschung (CPA) Ernst-Otto-Fischer-Straße 8 85747 Garching Deutschland
| | - Eva M. Huber
- Technische Universität München Zentrum für Proteinforschung (CPA) Ernst-Otto-Fischer-Straße 8 85747 Garching Deutschland
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26
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Scherlach K, Kuttenlochner W, Scharf DH, Brakhage AA, Hertweck C, Groll M, Huber EM. Structural and Mechanistic Insights into C-S Bond Formation in Gliotoxin. Angew Chem Int Ed Engl 2021; 60:14188-14194. [PMID: 33909314 PMCID: PMC8251611 DOI: 10.1002/anie.202104372] [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: 03/29/2021] [Indexed: 12/01/2022]
Abstract
Glutathione‐S‐transferases (GSTs) usually detoxify xenobiotics. The human pathogenic fungus Aspergillus fumigatus however uses the exceptional GST GliG to incorporate two sulfur atoms into its virulence factor gliotoxin. Because these sulfurs are essential for biological activity, glutathionylation is a key step of gliotoxin biosynthesis. Yet, the mechanism of carbon−sulfur linkage formation from a bis‐hydroxylated precursor is unresolved. Here, we report structures of GliG with glutathione (GSH) and its reaction product cyclo[‐l‐Phe‐l‐Ser]‐bis‐glutathione, which has been purified from a genetically modified A. fumigatus strain. The structures argue for stepwise processing of first the Phe and second the Ser moiety. Enzyme‐mediated dehydration of the substrate activates GSH and a helix dipole stabilizes the resulting anion via a water molecule for the nucleophilic attack. Activity assays with mutants validate the interactions of GliG with the ligands and enrich our knowledge about enzymatic C−S bond formation in gliotoxin and epipolythiodioxopiperazine (ETP) natural compounds in general.
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Affiliation(s)
- Kirstin Scherlach
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Wolfgang Kuttenlochner
- Technical University of Munich, Center for Protein Assemblies, Ernst-Otto-Fischer-Strasse 8, 85747, Garching, Germany
| | - Daniel H Scharf
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstrasse 11a, 07745, Jena, Germany.,Department of Microbiology and The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, Zhejiang, P.R. China
| | - Axel A Brakhage
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstrasse 11a, 07745, Jena, Germany.,Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743, Jena, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstrasse 11a, 07745, Jena, Germany.,Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743, Jena, Germany
| | - Michael Groll
- Technical University of Munich, Center for Protein Assemblies, Ernst-Otto-Fischer-Strasse 8, 85747, Garching, Germany
| | - Eva M Huber
- Technical University of Munich, Center for Protein Assemblies, Ernst-Otto-Fischer-Strasse 8, 85747, Garching, Germany
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27
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Understanding the fundamental role of virulence determinants to combat Aspergillus fumigatus infections: exploring beyond cell wall. Mycol Prog 2021. [DOI: 10.1007/s11557-021-01677-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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28
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Owens RA, Doyle S. Effects of antifungal agents on the fungal proteome: informing on mechanisms of sensitivity and resistance. Expert Rev Proteomics 2021; 18:185-199. [PMID: 33797307 DOI: 10.1080/14789450.2021.1912601] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
INTRODUCTION Antifungal agents are essential in the fight against serious fungal disease, however emerging resistance is threatening an already limited collection of therapeutics. Proteomic analyses of effects of antifungal agents can expand our understanding of multifactorial mechanisms of action and have also proven valuable to elucidate proteomic changes associated with antifungal resistance. AREAS COVERED This review covers the application of proteomic techniques to examine sensitivity and resistance to antifungals including commonly used therapeutics, amphotericin B, echinocandins and the azoles, based predominantly on studies involving Aspergillus fumigatus, Candida albicans and Candida glabrata from the last 10 years. In addition, non-clinical antimicrobial agents are also discussed, which highlight the potential of proteomics to identify new antifungal targets. EXPERT COMMENTARY Fungal proteomics has evolved in the last decade with increased genome availability and developments in mass spectrometry. Collectively, these have led to the advancement of proteomic techniques, allowing increased coverage of the proteome. Gel-based proteomics laid the foundation for these types of studies, which has now shifted to the more powerful gel-free proteomics. This has resulted in the identification of key mediators and potential biomarkers of antifungal resistance, as well as elucidating the mechanisms of action of novel and established antifungal agents.
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Affiliation(s)
- Rebecca A Owens
- Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland.,The Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, Co. Kildare, Ireland
| | - Sean Doyle
- Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland
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29
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Abreu SC, Hampton TH, Hoffman E, Dearborn J, Ashare A, Singh Sidhu K, Matthews DE, McKenna DH, Amiel E, Barua J, Krasnodembskaya A, English K, Mahon B, Dos Santos C, Cruz FF, Chambers DC, Liu KD, Matthay MA, Cramer RA, Stanton BA, Rocco PRM, Wargo MJ, Weiss DJ, Rolandsson Enes S. Differential effects of the cystic fibrosis lung inflammatory environment on mesenchymal stromal cells. Am J Physiol Lung Cell Mol Physiol 2020; 319:L908-L925. [PMID: 32901521 PMCID: PMC7792680 DOI: 10.1152/ajplung.00218.2020] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 08/14/2020] [Accepted: 08/23/2020] [Indexed: 12/23/2022] Open
Abstract
Growing evidence demonstrates that human mesenchymal stromal cells (MSCs) modify their in vivo anti-inflammatory actions depending on the specific inflammatory environment encountered. Understanding this better is crucial to refine MSC-based cell therapies for lung and other diseases. Using acute exacerbations of cystic fibrosis (CF) lung disease as a model, the effects of ex vivo MSC exposure to clinical bronchoalveolar lavage fluid (BALF) samples, as a surrogate for the in vivo clinical lung environment, on MSC viability, gene expression, secreted cytokines, and mitochondrial function were compared with effects of BALF collected from healthy volunteers. CF BALF samples that cultured positive for Aspergillus sp. (Asp) induced rapid MSC death, usually within several hours of exposure. Further analyses suggested the fungal toxin gliotoxin as a potential mediator contributing to CF BALF-induced MSC death. RNA sequencing analyses of MSCs exposed to either Asp+ or Asp- CF BALF samples identified a number of differentially expressed transcripts, including those involved in interferon signaling, antimicrobial gene expression, and cell death. Toxicity did not correlate with bacterial lung infections. These results suggest that the potential use of MSC-based cell therapies for CF or other lung diseases may not be warranted in the presence of Aspergillus.
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Affiliation(s)
- Soraia C Abreu
- Department of Medicine, Larner College of Medicine, University of Vermont, Burlington, Vermont
- Laboratory of Pulmonary Investigation, Carlos Chagas Filho Institute of Biophysics, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Thomas H Hampton
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
| | - Evan Hoffman
- Department of Medicine, Larner College of Medicine, University of Vermont, Burlington, Vermont
| | - Jacob Dearborn
- Department of Medicine, Larner College of Medicine, University of Vermont, Burlington, Vermont
| | - Alix Ashare
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
- Section of Pulmonary and Critical Care Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire
| | | | - Dwight E Matthews
- Department of Medicine, Larner College of Medicine, University of Vermont, Burlington, Vermont
- Department of Chemistry, University of Vermont, Burlington, Vermont
| | - David H McKenna
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota
| | - Eyal Amiel
- Department of Biomedical and Health Sciences, College of Nursing and Health Sciences, University of Vermont, Burlington, Vermont
| | - Jayita Barua
- Division of Pulmonary Disease and Critical Care, University of Vermont, and The Vermont Lung Center, Burlington, Vermont
| | - Anna Krasnodembskaya
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University of Belfast, Belfast, United Kingdom
| | - Karen English
- Cellular Immunology Laboratory, Biology Department, Human Health Research Institute, Maynooth University, Maynooth, Ireland
| | - Bernard Mahon
- Immunology & Cell Biology Laboratory, Biology Department, Human Health Research Institute, Maynooth University, Maynooth, Ireland
| | - Claudia Dos Santos
- Departments of Medicine and Critical Care Medicine and the Keenan Research Center for Biomedical Science, St. Michael's Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Fernanda F Cruz
- Laboratory of Pulmonary Investigation, Carlos Chagas Filho Institute of Biophysics, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- National Institute of Science and Technology for Regenerative Medicine, Rio de Janeiro, Brazil
| | - Daniel C Chambers
- School of Medicine, University of Queensland, Brisbane, Queensland, Australia
- Queenland Lung Transplant Service, The Prince Charles Hospital, Brisbane, Queensland, Australia
| | - Kathleen D Liu
- Departments of Medicine and Anesthesiology and the Cardiovascular Research Institute, University of California, San Francisco, California
| | - Michael A Matthay
- Departments of Medicine and Anesthesiology and the Cardiovascular Research Institute, University of California, San Francisco, California
| | - Robert A Cramer
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
| | - Bruce A Stanton
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
| | - Patricia R M Rocco
- Laboratory of Pulmonary Investigation, Carlos Chagas Filho Institute of Biophysics, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- National Institute of Science and Technology for Regenerative Medicine, Rio de Janeiro, Brazil
| | - Matthew J Wargo
- Department of Microbiology & Molecular Genetics, Larner College of Medicine, University of Vermont, Burlington, Vermont
| | - Daniel J Weiss
- Department of Medicine, Larner College of Medicine, University of Vermont, Burlington, Vermont
| | - Sara Rolandsson Enes
- Department of Medicine, Larner College of Medicine, University of Vermont, Burlington, Vermont
- Department of Experimental Medical Science, Lung Biology Unit, Lund University, Lund, Sweden
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The sino-nasal warzone: transcriptomic and genomic studies on sino-nasal aspergillosis in dogs. NPJ Biofilms Microbiomes 2020; 6:51. [PMID: 33184275 PMCID: PMC7665010 DOI: 10.1038/s41522-020-00163-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 10/16/2020] [Indexed: 12/21/2022] Open
Abstract
We previously showed that each dog with chronic non-invasive sino-nasal aspergillosis (SNA) was infected with a single genotype of Aspergillus fumigatus. Here, we studied the transcriptome of this fungal pathogen and the canine host within the biofilm resulting from the infection. We describe here transcriptomes resulting from natural infections in animal species with A. fumigatus. The host transcriptome showed high expression of IL-8 and alarmins, uncontrolled inflammatory reaction and dysregulation of the Th17 response. The fungal transcriptome showed in particular expression of genes involved in secondary metabolites and nutrient acquisition. Single-nucleotide polymorphism analysis of fungal isolates from the biofilms showed large genetic variability and changes related with adaptation to host environmental factors. This was accompanied with large phenotypic variability in in vitro stress assays, even between isolates from the same canine patient. Our analysis provides insights in genetic and phenotypic variability of Aspergillus fumigatus in biofilms of naturally infected dogs reflecting in-host adaptation. Absence of a Th17 response and dampening of the Th1 response contributes to the formation of a chronic sino-nasal warzone.
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Hagee D, Abu Hardan A, Botero J, Arnone JT. Genomic clustering within functionally related gene families in Ascomycota fungi. Comput Struct Biotechnol J 2020; 18:3267-3277. [PMID: 33209211 PMCID: PMC7653285 DOI: 10.1016/j.csbj.2020.10.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 10/15/2020] [Accepted: 10/17/2020] [Indexed: 12/17/2022] Open
Abstract
Multiple mechanisms collaborate for proper regulation of gene expression. One layer of this regulation is through the clustering of functionally related genes at discrete loci throughout the genome. This phenomenon occurs extensively throughout Ascomycota fungi and is an organizing principle for many gene families whose proteins participate in diverse molecular functions throughout the cell. Members of this phylum include organisms that serve as model systems and those of interest medically, pharmaceutically, and for industrial and biotechnological applications. In this review, we discuss the prevalence of functional clustering through a broad range of organisms within the phylum. Position effects on transcription, genomic locations of clusters, transcriptional regulation of clusters, and selective pressures contributing to the formation and maintenance of clusters are addressed, as are common methods to identify and characterize clusters.
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Affiliation(s)
- Danielle Hagee
- Department of Biology, William Paterson University, Wayne, NJ 07470, USA
| | - Ahmad Abu Hardan
- Department of Biology, William Paterson University, Wayne, NJ 07470, USA
| | - Juan Botero
- Department of Biology, William Paterson University, Wayne, NJ 07470, USA
| | - James T. Arnone
- Department of Biology, William Paterson University, Wayne, NJ 07470, USA
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Ries LNA, Pardeshi L, Dong Z, Tan K, Steenwyk JL, Colabardini AC, Ferreira Filho JA, de Castro PA, Silva LP, Preite NW, Almeida F, de Assis LJ, dos Santos RAC, Bowyer P, Bromley M, Owens RA, Doyle S, Demasi M, Hernández DCR, Netto LES, Pupo MT, Rokas A, Loures FV, Wong KH, Goldman GH. The Aspergillus fumigatus transcription factor RglT is important for gliotoxin biosynthesis and self-protection, and virulence. PLoS Pathog 2020; 16:e1008645. [PMID: 32667960 PMCID: PMC7384679 DOI: 10.1371/journal.ppat.1008645] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 07/27/2020] [Accepted: 05/19/2020] [Indexed: 12/21/2022] Open
Abstract
Aspergillus fumigatus is an opportunistic fungal pathogen that secretes an array of immune-modulatory molecules, including secondary metabolites (SMs), which contribute to enhancing fungal fitness and growth within the mammalian host. Gliotoxin (GT) is a SM that interferes with the function and recruitment of innate immune cells, which are essential for eliminating A. fumigatus during invasive infections. We identified a C6 Zn cluster-type transcription factor (TF), subsequently named RglT, important for A. fumigatus oxidative stress resistance, GT biosynthesis and self-protection. RglT regulates the expression of several gli genes of the GT biosynthetic gene cluster, including the oxidoreductase-encoding gene gliT, by directly binding to their respective promoter regions. Subsequently, RglT was shown to be important for virulence in a chemotherapeutic murine model of invasive pulmonary aspergillosis (IPA). Homologues of RglT and GliT are present in eurotiomycete and sordariomycete fungi, including the non-GT-producing fungus A. nidulans, where a conservation of function was described. Phylogenetically informed model testing led to an evolutionary scenario in which the GliT-based resistance mechanism is ancestral and RglT-mediated regulation of GliT occurred subsequently. In conclusion, this work describes the function of a previously uncharacterised TF in oxidative stress resistance, GT biosynthesis and self-protection in both GT-producing and non-producing Aspergillus species.
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Affiliation(s)
- Laure N. A. Ries
- Faculty of Medicine of Ribeirao Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Lakhansing Pardeshi
- Genomics and Bioinformatics Core, Faculty of Health Sciences, University of Macau, Macau SAR, China
- Faculty of Health Sciences, University of Macau, Macau SAR, China
| | - Zhiqiang Dong
- Faculty of Health Sciences, University of Macau, Macau SAR, China
| | - Kaeling Tan
- Genomics and Bioinformatics Core, Faculty of Health Sciences, University of Macau, Macau SAR, China
- Faculty of Health Sciences, University of Macau, Macau SAR, China
- Centre for Precision Medicine and Research and Training, University of Macau, Macau SAR, China
| | - Jacob L. Steenwyk
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, United States of America
| | - Ana Cristina Colabardini
- Faculty of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Jaire A. Ferreira Filho
- Faculty of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Patricia A. de Castro
- Faculty of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Lilian P. Silva
- Faculty of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Nycolas W. Preite
- Institute of Science and Technology, Federal University of São Paulo, São José dos Campos, Brazil
| | - Fausto Almeida
- Faculty of Medicine of Ribeirao Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Leandro J. de Assis
- Faculty of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Renato A. C. dos Santos
- Faculty of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Paul Bowyer
- Manchester Fungal Infection Group, Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Michael Bromley
- Manchester Fungal Infection Group, Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | | | - Sean Doyle
- Department of Biology, Maynooth University, Maynooth, Ireland
| | - Marilene Demasi
- Institute Butantan, Laboratory of Biochemistry and Biophysics, São Paulo, Brazil
| | - Diego C. R. Hernández
- Faculty of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, Ribeirão Preto, Brazil
| | | | - Monica T. Pupo
- Faculty of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, United States of America
| | - Flavio V. Loures
- Institute of Science and Technology, Federal University of São Paulo, São José dos Campos, Brazil
| | - Koon H. Wong
- Genomics and Bioinformatics Core, Faculty of Health Sciences, University of Macau, Macau SAR, China
- Institute of Translational Medicine, University of Macau, Macau SAR, China
| | - Gustavo H. Goldman
- Faculty of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, Ribeirão Preto, Brazil
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Coleine C, Gevi F, Fanelli G, Onofri S, Timperio AM, Selbmann L. Specific adaptations are selected in opposite sun exposed Antarctic cryptoendolithic communities as revealed by untargeted metabolomics. PLoS One 2020; 15:e0233805. [PMID: 32460306 PMCID: PMC7253227 DOI: 10.1371/journal.pone.0233805] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 05/12/2020] [Indexed: 12/18/2022] Open
Abstract
Antarctic cryptoendolithic communities are self-supporting borderline ecosystems spreading across the extreme conditions of the Antarctic desert and represent the predominant life-form in the ice-free areas of McMurdo Dry Valleys, accounted as the closest terrestrial Martian analogue. Components of these communities are highly adapted extremophiles and extreme-tolerant microorganisms, among the most resistant known to date. Recently, studies investigated biodiversity and community composition in these ecosystems but the metabolic activity of the metacommunity has never been investigated. Using an untargeted metabolomics, we explored stress-response of communities spreading in two sites of the same location, subjected to increasing environmental pressure due to opposite sun exposure, accounted as main factor influencing the diversity and composition of these ecosystems. Overall, 331 altered metabolites (206 and 125 unique for north and south, respectively), distinguished the two differently exposed communities. We also selected 10 metabolites and performed two-stage Receiver Operating Characteristic (ROC) analysis to test them as potential biomarkers. We further focused on melanin and allantoin as protective substances; their concentration was highly different in the community in the shadow or in the sun. These results clearly indicate that opposite insolation selected organisms in the communities with different adaptation strategies in terms of key metabolites produced.
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Affiliation(s)
- Claudia Coleine
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
| | - Federica Gevi
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
- Department of Science and Technology for Agriculture, Forestry, Nature and Energy, University of Tuscia, Viterbo, Italy
| | - Giuseppina Fanelli
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
- Department of Science and Technology for Agriculture, Forestry, Nature and Energy, University of Tuscia, Viterbo, Italy
| | - Silvano Onofri
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
| | - Anna Maria Timperio
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
- Department of Science and Technology for Agriculture, Forestry, Nature and Energy, University of Tuscia, Viterbo, Italy
- * E-mail: (AMT); (LS)
| | - Laura Selbmann
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
- Italian National Antarctic Museum (MNA), Mycological Section, Genoa, Italy
- * E-mail: (AMT); (LS)
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Bulgari D, Fiorini L, Gianoncelli A, Bertuzzi M, Gobbi E. Enlightening Gliotoxin Biological System in Agriculturally Relevant Trichoderma spp. Front Microbiol 2020; 11:200. [PMID: 32226413 PMCID: PMC7080844 DOI: 10.3389/fmicb.2020.00200] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 01/28/2020] [Indexed: 01/29/2023] Open
Abstract
Gliotoxin (GT) is a dual fungal secondary metabolite (SM). It displays pleiotropic activities and possesses medicinal properties and biocontrol abilities but, unfortunately, has toxic properties in humans. Various Trichoderma species are used as fungal biological control agents (BCAs), as a sustainable alternative for crop protection worldwide. Among them is Trichoderma virens, a GT-producing fungus. Since no information was available on the genetically coded prerequisites for the production of GT in other Trichoderma spp., genome analyses were carried out in 10 Trichoderma spp. genomes. Moreover, a real-time PCR assay setup ad hoc and high-performance liquid chromatography (HPLC) analyses were employed to understand the GT-producing biological systems in T. virens GV29-8 (TvGv29-8) and Trichoderma afroharzianum T6776 (TaT6776), two relevant biocontrol fungi. The structure of the GT biosynthesis genes (GT-BG) is polymorphic, with two distinct types associated with the ability to produce GT. GliH, a key protein for GT synthesis, is absent in most of the Trichoderma GT biosynthetic pathways, which may be the reason for their inability to produce GT. The GT-BG are expressed in TvGv29-8 as expected, while they are silent in TaT6776. Interestingly, in the GT-non-producing TaT6776, only gliA (putative GT transporter) and gtmA (putative GT S-methyltransferase) were induced by exogenous GT, underlining the ability of this strain to reduce the deleterious effect of the toxin. This ability is confirmed by growth assays and by the detection of the bis-thiomethylated form of GT catalyzed by GtmA in the culture medium supplemented with GT. To the best of our knowledge, this is the first general description of the GT biological system in different Trichoderma spp. as far as the GT-BG content and organization is concerned and a preliminary insight into their functionality.
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Affiliation(s)
- Daniela Bulgari
- Piattaforma di Microbiologia Agroalimentare ed Ambientale (Pi.Mi.A.A.), AgroFood Lab, Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Lisa Fiorini
- Piattaforma di Microbiologia Agroalimentare ed Ambientale (Pi.Mi.A.A.), AgroFood Lab, Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Alessandra Gianoncelli
- Piattaforma di Proteomica, AgroFood Lab, Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Michela Bertuzzi
- Piattaforma di Proteomica, AgroFood Lab, Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Emanuela Gobbi
- Piattaforma di Microbiologia Agroalimentare ed Ambientale (Pi.Mi.A.A.), AgroFood Lab, Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
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Pfliegler WP, Pócsi I, Győri Z, Pusztahelyi T. The Aspergilli and Their Mycotoxins: Metabolic Interactions With Plants and the Soil Biota. Front Microbiol 2020; 10:2921. [PMID: 32117074 PMCID: PMC7029702 DOI: 10.3389/fmicb.2019.02921] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 12/04/2019] [Indexed: 01/06/2023] Open
Abstract
Species of the highly diverse fungal genus Aspergillus are well-known agricultural pests, and, most importantly, producers of various mycotoxins threatening food safety worldwide. Mycotoxins are studied predominantly from the perspectives of human and livestock health. Meanwhile, their roles are far less known in nature. However, to understand the factors behind mycotoxin production, the roles of the toxins of Aspergilli must be understood from a complex ecological perspective, taking mold-plant, mold-microbe, and mold-animal interactions into account. The Aspergilli may switch between saprophytic and pathogenic lifestyles, and the production of secondary metabolites, such as mycotoxins, may vary according to these fungal ways of life. Recent studies highlighted the complex ecological network of soil microbiotas determining the niches that Aspergilli can fill in. Interactions with the soil microbiota and soil macro-organisms determine the role of secondary metabolite production to a great extent. While, upon infection of plants, metabolic communication including fungal secondary metabolites like aflatoxins, gliotoxin, patulin, cyclopiazonic acid, and ochratoxin, influences the fate of both the invader and the host. In this review, the role of mycotoxin producing Aspergillus species and their interactions in the ecosystem are discussed. We intend to highlight the complexity of the roles of the main toxic secondary metabolites as well as their fate in natural environments and agriculture, a field that still has important knowledge gaps.
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Affiliation(s)
- Walter P. Pfliegler
- Department of Molecular Biotechnology and Microbiology, Institute of Biotechnology, Faculty of Science and Technology, University of Debrecen, Debrecen, Hungary
| | - István Pócsi
- Department of Molecular Biotechnology and Microbiology, Institute of Biotechnology, Faculty of Science and Technology, University of Debrecen, Debrecen, Hungary
| | - Zoltán Győri
- Institute of Nutrition, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Debrecen, Hungary
| | - Tünde Pusztahelyi
- Central Laboratory of Agricultural and Food Products, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Debrecen, Hungary
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Knowles SL, Mead ME, Silva LP, Raja HA, Steenwyk JL, Goldman GH, Oberlies NH, Rokas A. Gliotoxin, a Known Virulence Factor in the Major Human Pathogen Aspergillus fumigatus, Is Also Biosynthesized by Its Nonpathogenic Relative Aspergillus fischeri. mBio 2020; 11:e03361-19. [PMID: 32047138 PMCID: PMC7018655 DOI: 10.1128/mbio.03361-19] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 01/03/2020] [Indexed: 11/20/2022] Open
Abstract
Aspergillus fumigatus is a major opportunistic human pathogen. Multiple traits contribute to A. fumigatus pathogenicity, including its ability to produce specific secondary metabolites, such as gliotoxin. Gliotoxin is known to inhibit the host immune response, and genetic mutants that inactivate gliotoxin biosynthesis (or secondary metabolism in general) attenuate A. fumigatus virulence. The genome of Aspergillus fischeri, a very close nonpathogenic relative of A. fumigatus, contains a biosynthetic gene cluster that is homologous to the A. fumigatus gliotoxin cluster. However, A. fischeri is not known to produce gliotoxin. To gain further insight into the similarities and differences between the major pathogen A. fumigatus and the nonpathogen A. fischeri, we examined whether A. fischeri strain NRRL 181 biosynthesizes gliotoxin and whether the production of secondary metabolites influences the virulence profile of A. fischeri We found that A. fischeri biosynthesizes gliotoxin under the same conditions as A. fumigatus However, whereas loss of laeA, a master regulator of secondary metabolite production (including gliotoxin biosynthesis), has previously been shown to reduce A. fumigatus virulence, we found that laeA loss (and loss of secondary metabolite production) in A. fischeri does not influence its virulence. These results suggest that LaeA-regulated secondary metabolites are virulence factors in the genomic and phenotypic background of the major pathogen A. fumigatus but are much less important in the background of the nonpathogen A. fischeri Understanding the observed spectrum of pathogenicity across closely related pathogenic and nonpathogenic Aspergillus species will require detailed characterization of their biological, chemical, and genomic similarities and differences.IMPORTANCEAspergillus fumigatus is a major opportunistic fungal pathogen of humans, but most of its close relatives are nonpathogenic. Why is that so? This important, yet largely unanswered, question can be addressed by examining how A. fumigatus and its close nonpathogenic relatives are similar or different with respect to virulence-associated traits. We investigated whether Aspergillus fischeri, a nonpathogenic close relative of A. fumigatus, can produce gliotoxin, a mycotoxin known to contribute to A. fumigatus virulence. We discovered that the nonpathogenic A. fischeri produces gliotoxin under the same conditions as those of the major pathogen A. fumigatus However, we also discovered that, in contrast to what has previously been observed in A. fumigatus, the loss of secondary metabolite production in A. fischeri does not alter its virulence. Our results are consistent with the "cards of virulence" model of opportunistic fungal disease, in which the ability to cause disease stems from the combination ("hand") of virulence factors ("cards") but not from individual factors per se.
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Affiliation(s)
- Sonja L Knowles
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, North Carolina, USA
| | - Matthew E Mead
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | - Lilian Pereira Silva
- Faculdade de Ciencias Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - Huzefa A Raja
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, North Carolina, USA
| | - Jacob L Steenwyk
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | - Gustavo H Goldman
- Faculdade de Ciencias Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - Nicholas H Oberlies
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, North Carolina, USA
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
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Choi YH, Lee MW, Igbalajobi OA, Yu JH, Shin KS. Transcriptomic and Functional Studies of the RGS Protein Rax1 in Aspergillus fumigatus. Pathogens 2019; 9:pathogens9010036. [PMID: 31906167 PMCID: PMC7168642 DOI: 10.3390/pathogens9010036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 12/26/2019] [Accepted: 12/30/2019] [Indexed: 12/24/2022] Open
Abstract
In the comparative transcriptomic studies of wild type (WT) and rax1 null mutant strains, we obtained an average of 22,222,727 reads of 101 bp per sample and found that 183 genes showed greater than 2.0-fold differential expression, where 92 and 91 genes were up-and down-regulated in Δrax1 compared to WT, respectively. In accordance with the significantly reduced levels of gliM and casB transcripts in the absence of rax1, the Δrax1 mutant exhibited increased sensitivity to exogenous gliotoxin (GT) without affecting levels of GT production. Moreover, Δrax1 resulted in significantly restricted colony growth and reduced viability under endoplasmic reticulum stress condition. In summary, Rax1 positively affects expression of gliM and metacaspase genes.
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Affiliation(s)
- Yong-Ho Choi
- Department of Microbiology, Graduate School, Daejeon University, Daejeon 34520, Korea;
| | - Min-Woo Lee
- Soonchunhyang Institute of Medi-bio Science, Soonchunhyang University, Chungcheongnam-do 31151, Korea;
| | - Olumuyiwa Ayokunle Igbalajobi
- Department of Microbiology, Institute for Applied Biosciences, Karlsruhe Institute of Technology, Fritz-Haber Weg 4, D-76131 Karlsruhe, Germany;
| | - Jae-Hyuk Yu
- Departments of Bacteriology and Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Systems Biotechnology, Konkuk University, Seoul 05029, Korea
- Correspondence: (J.-H.Y.); (K.-S.S.)
| | - Kwang-Soo Shin
- Department of Microbiology, Graduate School, Daejeon University, Daejeon 34520, Korea;
- Correspondence: (J.-H.Y.); (K.-S.S.)
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Traynor AM, Sheridan KJ, Jones GW, Calera JA, Doyle S. Involvement of Sulfur in the Biosynthesis of Essential Metabolites in Pathogenic Fungi of Animals, Particularly Aspergillus spp.: Molecular and Therapeutic Implications. Front Microbiol 2019; 10:2859. [PMID: 31921039 PMCID: PMC6923255 DOI: 10.3389/fmicb.2019.02859] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 11/25/2019] [Indexed: 12/13/2022] Open
Abstract
Fungal sulfur uptake is required for incorporation into the sidechains of the amino acids cysteine and methionine, and is also essential for the biosynthesis of the antioxidant glutathione (GSH), S-adenosylmethionine (SAM), the key source of methyl groups in cellular transmethylation reactions, and S-adenosylhomocysteine (SAH). Biosynthesis of redox-active gliotoxin in the opportunistic fungal pathogen Aspergillus fumigatus has been elucidated over the past 10 years. Some fungi which produce gliotoxin-like molecular species have undergone unexpected molecular rewiring to accommodate this high-risk biosynthetic process. Specific disruption of gliotoxin biosynthesis, via deletion of gliK, which encodes a γ-glutamyl cyclotransferase, leads to elevated intracellular antioxidant, ergothioneine (EGT), levels, and confirms crosstalk between the biosynthesis of both sulfur-containing moieties. Gliotoxin is ultimately formed by gliotoxin oxidoreductase GliT-mediated oxidation of dithiol gliotoxin (DTG). In fact, DTG is a substrate for both GliT and a bis-thiomethyltransferase, GtmA. GtmA converts DTG to bisdethiobis(methylthio)gliotoxin (BmGT), using 2 mol SAM and resultant SAH must be re-converted to SAM via the action of the Methyl/Met cycle. In the absence of GliT, DTG fluxes via GtmA to BmGT, which results in both SAM depletion and SAH overproduction. Thus, the negative regulation of gliotoxin biosynthesis via GtmA must be counter-balanced by GliT activity to avoid Methyl/Met cycle dysregulation, SAM depletion and trans consequences on global cellular biochemistry in A. fumigatus. DTG also possesses potent Zn2+ chelation properties which positions this sulfur-containing metabolite as a putative component of the Zn2+ homeostasis system within fungi. EGT plays an essential role in high-level redox homeostasis and its presence requires significant consideration in future oxidative stress studies in pathogenic filamentous fungi. In certain filamentous fungi, sulfur is additionally indirectly required for the formation of EGT and the disulfide-bridge containing non-ribosomal peptide, gliotoxin, and related epipolythiodioxopiperazines. Ultimately, interference with emerging sulfur metabolite functionality may represent a new strategy for antifungal drug development.
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Affiliation(s)
- Aimee M Traynor
- Department of Biology, Maynooth University, Maynooth, Ireland
| | | | - Gary W Jones
- Centre for Biomedical Science Research, School of Clinical and Applied Sciences, Leeds Beckett University, Leeds, United Kingdom
| | - José A Calera
- Instituto de Biología Funcional y Genómica (IBFG-CSIC), Universidad de Salamanca, Salamanca, Spain.,Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
| | - Sean Doyle
- Department of Biology, Maynooth University, Maynooth, Ireland
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Lwin HP, Choi YH, Lee MW, Yu JH, Shin KS. RgsA Attenuates the PKA Signaling, Stress Response, and Virulence in the Human Opportunistic Pathogen Aspergillus fumigatus. Int J Mol Sci 2019; 20:ijms20225628. [PMID: 31717953 PMCID: PMC6888639 DOI: 10.3390/ijms20225628] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 11/05/2019] [Accepted: 11/07/2019] [Indexed: 12/14/2022] Open
Abstract
The regulator of G-protein signaling (RGS) proteins play an important role in upstream control of heterotrimeric G-protein signaling pathways. In the genome of the human opportunistic pathogenic fungus Aspergillus fumigatus, six RGS protein-encoding genes are present. To characterize the rgsA gene predicted to encode a protein with an RGS domain, we generated an rgsA null mutant and observed the phenotypes of the mutant. The deletion (Δ) of rgsA resulted in increased radial growth and enhanced asexual sporulation in both solid and liquid culture conditions. Accordingly, transcripts levels of the key asexual developmental regulators abaA, brlA, and wetA are elevated in the ΔrgsA mutant. Moreover, ΔrgsA resulted in elevated spore germination rates in the absence of a carbon source. The activity of cAMP-dependent protein kinase A (PKA) and mRNA levels of genes encoding PKA signaling elements are elevated by ΔrgsA. In addition, mRNA levels of genes associated with stress-response signaling increased with the lack of rgsA, and the ΔrgsA spores showed enhanced tolerance against oxidative stressors. Comparative transcriptomic analyses revealed that the ΔrgsA mutant showed higher mRNA levels of gliotoxin (GT) biosynthetic genes. Accordingly, the rgsA null mutant exhibited increased production of GT and elevated virulence in the mouse. Conversely, the majority of genes encoding glucan degrading enzymes were down-regulated by ΔrgsA, and endoglucanase activities were reduced. In summary, RgsA plays multiple roles, governing growth, development, stress responses, virulence, and external polymer degradation-likely by attenuating PKA signaling.
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Affiliation(s)
- Hnin Phyu Lwin
- Department of Microbiology, Graduate School, Daejeon University, Daejeon 34520, Korea; (H.P.L.); (Y.-H.C.)
| | - Yong-Ho Choi
- Department of Microbiology, Graduate School, Daejeon University, Daejeon 34520, Korea; (H.P.L.); (Y.-H.C.)
| | - Min-Woo Lee
- Soonchunhyang Institute of Medi-bio Science, Soonchunhyang University, Chungcheongnam-do 31151, Korea;
| | - Jae-Hyuk Yu
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Systems Biotechnology, Konkuk University, Seoul 05029, Korea
- Correspondence: (J.-H.Y.); (K.-S.S.); Tel.: +1-608-262-4696 (J.-H.Y.); +82-42-280-2439 (K.-S.S.); Fax: +1-608-262-2976 (J.-H.Y.); +82-42-280-2608 (K.-S.S.)
| | - Kwang-Soo Shin
- Department of Microbiology, Graduate School, Daejeon University, Daejeon 34520, Korea; (H.P.L.); (Y.-H.C.)
- Correspondence: (J.-H.Y.); (K.-S.S.); Tel.: +1-608-262-4696 (J.-H.Y.); +82-42-280-2439 (K.-S.S.); Fax: +1-608-262-2976 (J.-H.Y.); +82-42-280-2608 (K.-S.S.)
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Baccile JA, Le HH, Pfannenstiel BT, Bok JW, Gomez C, Brandenburger E, Hoffmeister D, Keller NP, Schroeder FC. Diketopiperazine Formation in Fungi Requires Dedicated Cyclization and Thiolation Domains. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201909052] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Joshua A. Baccile
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology Cornell University Ithaca NY USA
- Present Address: Division of Chemistry and Chemical Engineering California Institute of Technology Pasadena CA USA
| | - Henry H. Le
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology Cornell University Ithaca NY USA
| | - Brandon T. Pfannenstiel
- Departments of Bacteriology Medical Microbiology and Immunology University of Wisconsin-Madison Madison WI USA
| | - Jin Woo Bok
- Departments of Bacteriology Medical Microbiology and Immunology University of Wisconsin-Madison Madison WI USA
| | - Christian Gomez
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology Cornell University Ithaca NY USA
| | - Eileen Brandenburger
- Department of Pharmaceutical Microbiology Hans-Knöll-Institute Friedrich Schiller University Jena Germany
| | - Dirk Hoffmeister
- Department of Pharmaceutical Microbiology Hans-Knöll-Institute Friedrich Schiller University Jena Germany
| | - Nancy P. Keller
- Departments of Bacteriology Medical Microbiology and Immunology University of Wisconsin-Madison Madison WI USA
| | - Frank C. Schroeder
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology Cornell University Ithaca NY USA
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Bosnjak N, Smith KM, Asaria I, Lahola-Chomiak A, Kishore N, Todd AT, Freitag M, Nargang FE. Involvement of a G Protein Regulatory Circuit in Alternative Oxidase Production in Neurospora crassa. G3 (BETHESDA, MD.) 2019; 9:3453-3465. [PMID: 31444295 PMCID: PMC6778808 DOI: 10.1534/g3.119.400522] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 08/19/2019] [Indexed: 12/12/2022]
Abstract
The Neurospora crassa nuclear aod-1 gene encodes an alternative oxidase that functions in mitochondria. The enzyme provides a branch from the standard electron transport chain by transferring electrons directly from ubiquinol to oxygen. In standard laboratory strains, aod-1 is transcribed at very low levels under normal growth conditions. However, if the standard electron transport chain is disrupted, aod-1 mRNA expression is induced and the AOD1 protein is produced. We previously identified a strain of N. crassa, that produces high levels of aod-1 transcript under non-inducing conditions. Here we have crossed this strain to a standard lab strain and determined the genomic sequences of the parents and several progeny. Analysis of the sequence data and the levels of aod-1 mRNA in uninduced cultures revealed that a frameshift mutation in the flbA gene results in the high uninduced expression of aod-1 The flbA gene encodes a regulator of G protein signaling that decreases the activity of the Gα subunit of heterotrimeric G proteins. Our data suggest that strains with a functional flbA gene prevent uninduced expression of aod-1 by inactivating a G protein signaling pathway, and that this pathway is activated in cells grown under conditions that induce aod-1 Induced cells with a deletion of the gene encoding the Gα protein still have a partial increase in aod-1 mRNA levels, suggesting a second pathway for inducing transcription of the gene in N. crassa We also present evidence that a translational control mechanism prevents production of AOD1 protein in uninduced cultures.
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Affiliation(s)
- Natasa Bosnjak
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada T6G 2E9 and
| | - Kristina M Smith
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331-4003
| | - Iman Asaria
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada T6G 2E9 and
| | - Adrian Lahola-Chomiak
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada T6G 2E9 and
| | - Nishka Kishore
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada T6G 2E9 and
| | - Andrea T Todd
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada T6G 2E9 and
| | - Michael Freitag
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331-4003
| | - Frank E Nargang
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada T6G 2E9 and
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43
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Baccile JA, Le HH, Pfannenstiel BT, Bok JW, Gomez C, Brandenburger E, Hoffmeister D, Keller NP, Schroeder FC. Diketopiperazine Formation in Fungi Requires Dedicated Cyclization and Thiolation Domains. Angew Chem Int Ed Engl 2019; 58:14589-14593. [PMID: 31342608 PMCID: PMC6764874 DOI: 10.1002/anie.201909052] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Indexed: 01/08/2023]
Abstract
Cyclization of linear dipeptidyl precursors derived from nonribosomal peptide synthetases (NRPSs) into 2,5-diketopiperazines (DKPs) is a crucial step in the biosynthesis of a large number of bioactive natural products. However, the mechanism of DKP formation in fungi has remained unclear, despite extensive studies of their biosyntheses. Here we show that DKP formation en route to the fungal virulence factor gliotoxin requires a seemingly extraneous couplet of condensation (C) and thiolation (T) domains in the NRPS GliP. In vivo truncation of GliP to remove the CT couplet or just the T domain abrogated production of gliotoxin and all other gli pathway metabolites. Point mutation of conserved active sites in the C and T domains diminished cyclization activity of GliP in vitro and abolished gliotoxin biosynthesis in vivo. Verified NRPSs of other fungal DKPs terminate with similar CT domain couplets, suggesting a conserved strategy for DKP biosynthesis by fungal NRPSs.
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Affiliation(s)
- Joshua A Baccile
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
- Present Address: Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Henry H Le
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Brandon T Pfannenstiel
- Departments of Bacteriology, Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
| | - Jin Woo Bok
- Departments of Bacteriology, Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
| | - Christian Gomez
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Eileen Brandenburger
- Department of Pharmaceutical Microbiology, Hans-Knöll-Institute, Friedrich Schiller University, Jena, Germany
| | - Dirk Hoffmeister
- Department of Pharmaceutical Microbiology, Hans-Knöll-Institute, Friedrich Schiller University, Jena, Germany
| | - Nancy P Keller
- Departments of Bacteriology, Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
| | - Frank C Schroeder
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
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Sarkar D, Rovenich H, Jeena G, Nizam S, Tissier A, Balcke GU, Mahdi LK, Bonkowski M, Langen G, Zuccaro A. The inconspicuous gatekeeper: endophytic Serendipita vermifera acts as extended plant protection barrier in the rhizosphere. THE NEW PHYTOLOGIST 2019; 224:886-901. [PMID: 31074884 DOI: 10.1111/nph.15904] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 04/26/2019] [Indexed: 05/21/2023]
Abstract
In nature, beneficial and pathogenic fungi often simultaneously colonise plants. Despite substantial efforts to understand the composition of natural plant-microbe communities, the mechanisms driving such multipartite interactions remain largely unknown. Here we address how the interaction between the beneficial root endophyte Serendipita vermifera and the pathogen Bipolaris sorokiniana affects fungal behaviour and determines barley host responses using a gnotobiotic soil-based split-root system. Fungal confrontation in soil resulted in induction of B. sorokiniana genes involved in secondary metabolism and a significant repression of genes encoding putative effectors. In S. vermifera, genes encoding hydrolytic enzymes were strongly induced. This antagonistic response was not activated during the tripartite interaction in barley roots. Instead, we observed a specific induction of S. vermifera genes involved in detoxification and redox homeostasis. Pathogen infection but not endophyte colonisation resulted in substantial host transcriptional reprogramming and activation of defence. In the presence of S. vermifera, pathogen infection and disease symptoms were significantly reduced despite no marked alterations of the plant transcriptional response. The activation of stress response genes and concomitant repression of putative effector gene expression in B. sorokiniana during confrontation with the endophyte suggest a reduction of the pathogen's virulence potential before host plant infection.
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Affiliation(s)
- Debika Sarkar
- Botanical Institute, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, 50674, Cologne, Germany
| | - Hanna Rovenich
- Botanical Institute, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, 50674, Cologne, Germany
| | - Ganga Jeena
- Botanical Institute, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, 50674, Cologne, Germany
| | - Shadab Nizam
- Botanical Institute, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, 50674, Cologne, Germany
| | - Alain Tissier
- Department of Cell and Metabolic Biology, Institute of Plant Biochemistry, 06120, Halle (Saale), Germany
| | - Gerd U Balcke
- Department of Cell and Metabolic Biology, Institute of Plant Biochemistry, 06120, Halle (Saale), Germany
| | - Lisa K Mahdi
- Botanical Institute, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, 50674, Cologne, Germany
| | - Michael Bonkowski
- Institute of Zoology, Terrestrial Ecology, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, 50674, Cologne, Germany
| | - Gregor Langen
- Botanical Institute, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, 50674, Cologne, Germany
| | - Alga Zuccaro
- Botanical Institute, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, 50674, Cologne, Germany
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RgsD negatively controls development, toxigenesis, stress response, and virulence in Aspergillus fumigatus. Sci Rep 2019; 9:811. [PMID: 30692551 PMCID: PMC6349852 DOI: 10.1038/s41598-018-37124-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 11/28/2018] [Indexed: 12/19/2022] Open
Abstract
The regulator of G protein signaling (RGS) domain proteins generally attenuate heterotrimeric G protein signaling, thereby fine-tune the duration and strength of signal transduction. In this study, we characterize the functions of RgsD, one of the six RGS domain proteins present in the human pathogenic fungus Aspergillus fumigatus. The deletion (Δ) of rgsD results in enhanced asexual sporulation coupled with increased mRNA levels of key developmental activators. Moreover, ΔrgsD leads to increased spore tolerance to UV and oxidative stress, which might be associated with the enhanced expression of melanin biosynthetic genes and increased amount of melanin. Yeast two-hybrid assays reveal that RgsD can interact with the three Gα proteins GpaB, GanA, and GpaA, showing the highest interaction potential with GpaB. Importantly, the ΔrgsD mutant shows elevated expression of genes in the cAMP-dependent protein kinase A (PKA) pathway and PKA catalytic activity. The ΔrgsD mutant also display increased gliotoxin production and elevated virulence toward Galleria mellonella wax moth larvae. Transcriptomic analyses using RNA-seq reveal the expression changes associated with the diverse phenotypic outcomes caused by ΔrgsD. Collectively, we conclude that RgsD attenuates cAMP-PKA signaling pathway and negatively regulates asexual development, toxigenesis, melanin production, and virulence in A. fumigatus.
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Doyle AA, Krämer T, Kavanagh K, Stephens JC. Cinnamaldehydes: Synthesis, antibacterial evaluation, and the effect of molecular structure on antibacterial activity. RESULTS IN CHEMISTRY 2019. [DOI: 10.1016/j.rechem.2019.100013] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
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Abstract
In bacteria, more than half of the genes in the genome are organized in operons. In contrast, in eukaryotes, functionally related genes are usually dispersed across the genome. There are, however, numerous examples of functional clusters of nonhomologous genes for metabolic pathways in fungi and plants. Despite superficial similarities with operons (physical clustering, coordinate regulation), these clusters have not usually originated by horizontal gene transfer from bacteria, and (unlike operons) the genes are typically transcribed separately rather than as a single polycistronic message. This clustering phenomenon raises intriguing questions about the origins of clustered metabolic pathways in eukaryotes and the significance of clustering for pathway function. Here we review metabolic gene clusters from fungi and plants, highlight commonalities and differences, and consider how these clusters form and are regulated. We also identify opportunities for future research in the areas of large-scale genomics, synthetic biology, and experimental evolution.
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Affiliation(s)
- Hans-Wilhelm Nützmann
- Department of Metabolic Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom; .,Current affiliation: Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, United Kingdom;
| | - Claudio Scazzocchio
- Department of Microbiology, Imperial College, London SW7 2AZ, United Kingdom; .,Institute for Integrative Biology of the Cell, 91190 Gif-sur-Yvette, France
| | - Anne Osbourn
- Department of Metabolic Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom;
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Genome-based deletion analysis in Aspergillus terreus reveals the acetylaranotin bis-thiomethyltransferase gene. Fungal Genet Biol 2018; 119:1-6. [PMID: 30096370 DOI: 10.1016/j.fgb.2018.08.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 08/03/2018] [Accepted: 08/06/2018] [Indexed: 11/22/2022]
Abstract
Acetylaranotin is an epipolythiodiketopiperazine (ETP) secondary metabolite with a broad range of bioactivities. We demonstrated that ATEG_01465.1 located outside of acetylaranotin gene cluster is responsible for catalyzing the S-methylation of its biosynthetic pathway. Combining the previous characterization of acetylaranotin biosynthetic gene cluster together with the identification of its S-methyltransferase provides a means to obtain second-generation acetylaranotin derivatives previously inaccessible. By permutations of targeted deletions of ATEG_01465.1, acetyltransferase (AtaH), and benzoate hydroxylase (AtaY), three novel acetylaranotin derivatives were produced by Aspergillus terreus.
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49
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Identification of Antifungal Targets Based on Computer Modeling. J Fungi (Basel) 2018; 4:jof4030081. [PMID: 29973534 PMCID: PMC6162656 DOI: 10.3390/jof4030081] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 06/24/2018] [Accepted: 06/29/2018] [Indexed: 01/07/2023] Open
Abstract
Aspergillus fumigatus is a saprophytic, cosmopolitan fungus that attacks patients with a weak immune system. A rational solution against fungal infection aims to manipulate fungal metabolism or to block enzymes essential for Aspergillus survival. Here we discuss and compare different bioinformatics approaches to analyze possible targeting strategies on fungal-unique pathways. For instance, phylogenetic analysis reveals fungal targets, while domain analysis allows us to spot minor differences in protein composition between the host and fungi. Moreover, protein networks between host and fungi can be systematically compared by looking at orthologs and exploiting information from host⁻pathogen interaction databases. Further data—such as knowledge of a three-dimensional structure, gene expression data, or information from calculated metabolic fluxes—refine the search and rapidly put a focus on the best targets for antimycotics. We analyzed several of the best targets for application to structure-based drug design. Finally, we discuss general advantages and limitations in identification of unique fungal pathways and protein targets when applying bioinformatics tools.
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50
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Ye W, Zhang W, Liu T, Huang Z, Zhu M, Chen Y, Li H, Li S. De Novo Transcriptome Sequencing of the Deep-Sea-Derived Fungus Dichotomomyces cejpii and Analysis of Gliotoxin Biosynthesis Genes. Int J Mol Sci 2018; 19:E1910. [PMID: 29966253 PMCID: PMC6073683 DOI: 10.3390/ijms19071910] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 06/17/2018] [Accepted: 06/26/2018] [Indexed: 12/03/2022] Open
Abstract
Gliotoxin, produced by fungi, is an epipolythiodioxopiperazine (ETP) toxin with bioactivities such as anti-liver fibrosis, antitumor, antifungus, antivirus, antioxidation, and immunoregulation. Recently, cytotoxic gliotoxins were isolated from a deep-sea-derived fungus, Dichotomomyces cejpii. However, the biosynthetic pathway for gliotoxins in D. cejpii remains unclear. In this study, the transcriptome of D. cejpii was sequenced using an Illumina Hiseq 2000. A total of 19,125 unigenes for D. cejpii were obtained from 9.73 GB of clean reads. Ten genes related to gliotoxin biosynthesis were annotated. The expression levels of gliotoxin-related genes were detected through quantitative real-time polymerase chain reaction (qRT-PCR). The GliG gene, encoding a glutathione S-transferase (DC-GST); GliI, encoding an aminotransferase (DC-AI); and GliO, encoding an aldehyde reductase (DC-AR), were cloned and expressed, purified, and characterized. The results suggested the important roles of DC-GST, DC-AT, and DC-AR in the biosynthesis of gliotoxins. Our study on the genes related to gliotoxin biosynthesis establishes a molecular foundation for the wider application of gliotoxins from D. cejpii in the biomedical industry in the future.
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Affiliation(s)
- Wei Ye
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, 100 Central Xianlie Road, Yuexiu District, Guangzhou 510070, China.
| | - Weimin Zhang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, 100 Central Xianlie Road, Yuexiu District, Guangzhou 510070, China.
| | - Taomei Liu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, 100 Central Xianlie Road, Yuexiu District, Guangzhou 510070, China.
| | - Zilei Huang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, 100 Central Xianlie Road, Yuexiu District, Guangzhou 510070, China.
| | - Muzi Zhu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, 100 Central Xianlie Road, Yuexiu District, Guangzhou 510070, China.
| | - Yuchan Chen
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, 100 Central Xianlie Road, Yuexiu District, Guangzhou 510070, China.
| | - Haohua Li
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, 100 Central Xianlie Road, Yuexiu District, Guangzhou 510070, China.
| | - Saini Li
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, 100 Central Xianlie Road, Yuexiu District, Guangzhou 510070, China.
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