1
|
Noel D, Hallsworth JE, Gelhaye E, Darnet S, Sormani R, Morel-Rouhier M. Modes-of-action of antifungal compounds: Stressors and (target-site-specific) toxins, toxicants, or Toxin-stressors. Microb Biotechnol 2023. [PMID: 37191200 DOI: 10.1111/1751-7915.14242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/11/2023] [Accepted: 02/16/2023] [Indexed: 05/17/2023] Open
Abstract
Fungi and antifungal compounds are relevant to the United Nation's Sustainable Development Goals. However, the modes-of-action of antifungals-whether they are naturally occurring substances or anthropogenic fungicides-are often unknown or are misallocated in terms of their mechanistic category. Here, we consider the most effective approaches to identifying whether antifungal substances are cellular stressors, toxins/toxicants (that are target-site-specific), or have a hybrid mode-of-action as Toxin-stressors (that induce cellular stress yet are target-site-specific). This newly described 'toxin-stressor' category includes some photosensitisers that target the cell membrane and, once activated by light or ultraviolet radiation, cause oxidative damage. We provide a glossary of terms and a diagrammatic representation of diverse types of stressors, toxic substances, and Toxin-stressors, a classification that is pertinent to inhibitory substances not only for fungi but for all types of cellular life. A decision-tree approach can also be used to help differentiate toxic substances from cellular stressors (Curr Opin Biotechnol 2015 33: 228-259). For compounds that target specific sites in the cell, we evaluate the relative merits of using metabolite analyses, chemical genetics, chemoproteomics, transcriptomics, and the target-based drug-discovery approach (based on that used in pharmaceutical research), focusing on both ascomycete models and the less-studied basidiomycete fungi. Chemical genetic methods to elucidate modes-of-action currently have limited application for fungi where molecular tools are not yet available; we discuss ways to circumvent this bottleneck. We also discuss ecologically commonplace scenarios in which multiple substances act to limit the functionality of the fungal cell and a number of as-yet-unresolved questions about the modes-of-action of antifungal compounds pertaining to the Sustainable Development Goals.
Collapse
Affiliation(s)
| | - John E Hallsworth
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast, UK
| | - Eric Gelhaye
- Université de Lorraine, INRAE, IAM, Nancy, France
| | | | | | | |
Collapse
|
2
|
Miyauchi S, Hage H, Drula E, Lesage-Meessen L, Berrin JG, Navarro D, Favel A, Chaduli D, Grisel S, Haon M, Piumi F, Levasseur A, Lomascolo A, Ahrendt S, Barry K, LaButti KM, Chevret D, Daum C, Mariette J, Klopp C, Cullen D, de Vries RP, Gathman AC, Hainaut M, Henrissat B, Hildén KS, Kües U, Lilly W, Lipzen A, Mäkelä MR, Martinez AT, Morel-Rouhier M, Morin E, Pangilinan J, Ram AFJ, Wösten HAB, Ruiz-Dueñas FJ, Riley R, Record E, Grigoriev IV, Rosso MN. Conserved white-rot enzymatic mechanism for wood decay in the Basidiomycota genus Pycnoporus. DNA Res 2021; 27:5856740. [PMID: 32531032 PMCID: PMC7406137 DOI: 10.1093/dnares/dsaa011] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 06/05/2020] [Indexed: 12/12/2022] Open
Abstract
White-rot (WR) fungi are pivotal decomposers of dead organic matter in forest ecosystems and typically use a large array of hydrolytic and oxidative enzymes to deconstruct lignocellulose. However, the extent of lignin and cellulose degradation may vary between species and wood type. Here, we combined comparative genomics, transcriptomics and secretome proteomics to identify conserved enzymatic signatures at the onset of wood-decaying activity within the Basidiomycota genus Pycnoporus. We observed a strong conservation in the genome structures and the repertoires of protein-coding genes across the four Pycnoporus species described to date, despite the species having distinct geographic distributions. We further analysed the early response of P. cinnabarinus, P. coccineus and P. sanguineus to diverse (ligno)-cellulosic substrates. We identified a conserved set of enzymes mobilized by the three species for breaking down cellulose, hemicellulose and pectin. The co-occurrence in the exo-proteomes of H2O2-producing enzymes with H2O2-consuming enzymes was a common feature of the three species, although each enzymatic partner displayed independent transcriptional regulation. Finally, cellobiose dehydrogenase-coding genes were systematically co-regulated with at least one AA9 lytic polysaccharide monooxygenase gene, indicative of enzymatic synergy in vivo. This study highlights a conserved core white-rot fungal enzymatic mechanism behind the wood-decaying process.
Collapse
Affiliation(s)
- Shingo Miyauchi
- INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France.,INRAE, UMR1136, Interactions Arbres/Microorganismes, Université de Lorraine, Nancy, France
| | - Hayat Hage
- INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France
| | - Elodie Drula
- INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France
| | - Laurence Lesage-Meessen
- INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France.,INRAE, CIRM-CF, UMR1163, Aix Marseille University, Marseille, France
| | - Jean-Guy Berrin
- INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France
| | - David Navarro
- INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France.,INRAE, CIRM-CF, UMR1163, Aix Marseille University, Marseille, France
| | - Anne Favel
- INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France.,INRAE, CIRM-CF, UMR1163, Aix Marseille University, Marseille, France
| | - Delphine Chaduli
- INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France.,INRAE, CIRM-CF, UMR1163, Aix Marseille University, Marseille, France
| | - Sacha Grisel
- INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France
| | - Mireille Haon
- INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France
| | - François Piumi
- INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France
| | | | - Anne Lomascolo
- INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France
| | - Steven Ahrendt
- US Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Kerrie Barry
- US Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Kurt M LaButti
- US Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Didier Chevret
- INRAE, UMR1319, Micalis, Plateforme d'Analyse Protéomique de Paris Sud-Ouest, Jouy-en-Josas, France
| | - Chris Daum
- US Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Jérôme Mariette
- INRAE, Genotoul Bioinfo, UR875, Mathématiques et Informatique Appliquées de Toulouse, Castanet-Tolosan, France
| | - Christophe Klopp
- INRAE, Genotoul Bioinfo, UR875, Mathématiques et Informatique Appliquées de Toulouse, Castanet-Tolosan, France
| | | | - Ronald P de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute and Fungal Molecular Physiology, Utrecht University, Utrecht, The Netherlands.,Department of Microbiology, University of Helsinki, Helsinki, Finland
| | - Allen C Gathman
- Department of Biology, Southeast Missouri State University, Cape Girardeau, MI, USA
| | - Matthieu Hainaut
- CNRS, UMR7257, AFMB, Aix Marseille University, Marseille, France.,INRAE, USC1408, AFMB, Marseille, France
| | - Bernard Henrissat
- CNRS, UMR7257, AFMB, Aix Marseille University, Marseille, France.,INRAE, USC1408, AFMB, Marseille, France
| | | | - Ursula Kües
- Department of Molecular Wood Biotechnology and Technical Mycology, Büsgen-Institute, Georg-August-University Göttingen, Göttingen, Germany.,Center for Molecular Biosciences (GZMB), Georg-August-University Göttingen, Göttingen, Germany
| | - Walt Lilly
- Department of Biology, Southeast Missouri State University, Cape Girardeau, MI, USA
| | - Anna Lipzen
- US Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Miia R Mäkelä
- Department of Microbiology, University of Helsinki, Helsinki, Finland
| | | | - Mélanie Morel-Rouhier
- INRAE, UMR1136, Interactions Arbres/Microorganismes, Université de Lorraine, Nancy, France
| | - Emmanuelle Morin
- INRAE, UMR1136, Interactions Arbres/Microorganismes, Université de Lorraine, Nancy, France
| | - Jasmyn Pangilinan
- US Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Arthur F J Ram
- Molecular Microbiology and Biotechnology, Institute of Biology Leiden, Leiden University, Leiden, The Netherlands
| | - Han A B Wösten
- Microbiology, Utrecht University, Utrecht, The Netherlands
| | | | - Robert Riley
- US Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Eric Record
- INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France
| | - Igor V Grigoriev
- US Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA.,Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Marie-Noëlle Rosso
- INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France
| |
Collapse
|
3
|
Valette N, Renou J, Boutilliat A, Fernández-González AJ, Gautier V, Silar P, Guyeux C, Charr JC, Cuenot S, Rose C, Gelhaye E, Morel-Rouhier M. OSIP1 is a self-assembling DUF3129 protein required to protect fungal cells from toxins and stressors. Environ Microbiol 2021; 23:1594-1607. [PMID: 33393164 DOI: 10.1111/1462-2920.15381] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 12/28/2020] [Indexed: 11/28/2022]
Abstract
Secreted proteins are key players in fungal physiology and cell protection against external stressing agents and antifungals. Oak stress-induced protein 1 (OSIP1) is a fungal-specific protein with unknown function. By using Podospora anserina and Phanerochaete chrysosporium as models, we combined both in vivo functional approaches and biophysical characterization of OSIP1 recombinant protein. The P. anserina OSIP1Δ mutant showed an increased sensitivity to the antifungal caspofungin compared to the wild type. This correlated with the production of a weakened extracellular exopolysaccharide/protein matrix (ECM). Since the recombinant OSIP1 from P. chrysosporium self-assembled as fibers and was capable of gelation, it is likely that OSIP1 is linked to ECM formation that acts as a physical barrier preventing drug toxicity. Moreover, compared to the wild type, the OSIP1Δ mutant was more sensitive to oak extractives including chaotropic phenols and benzenes. It exhibited a strongly modified secretome pattern and an increased production of proteins associated to the cell-wall integrity signalling pathway, when grown on oak sawdust. This demonstrates that OSIP1 has also an important role in fungal resistance to extractive-induced stress.
Collapse
Affiliation(s)
- Nicolas Valette
- Université de Lorraine, INRAE, Interactions Arbres/Micro-organismes (IAM), UMR 1136, Nancy, 54000, France
| | - Julien Renou
- Université de Lorraine, INRAE, Interactions Arbres/Micro-organismes (IAM), UMR 1136, Nancy, 54000, France
| | - Alexis Boutilliat
- Université de Lorraine, INRAE, Interactions Arbres/Micro-organismes (IAM), UMR 1136, Nancy, 54000, France
| | | | - Valérie Gautier
- Université Paris Diderot, Sorbonne Paris Cité, Laboratoire Interdisciplinaire des Energies de Demain (LIED), Paris, 75205, France
| | - Philippe Silar
- Université Paris Diderot, Sorbonne Paris Cité, Laboratoire Interdisciplinaire des Energies de Demain (LIED), Paris, 75205, France
| | - Christophe Guyeux
- Computer Science Department, FEMTO-ST Institute, UMR 6174 CNRS, Université de Bourgogne Franche-Comté, 16 route de Gray, Besançon, 25030, France
| | - Jean-Claude Charr
- Computer Science Department, FEMTO-ST Institute, UMR 6174 CNRS, Université de Bourgogne Franche-Comté, 16 route de Gray, Besançon, 25030, France
| | - Stéphane Cuenot
- Institut des Matériaux Jean Rouxel, Université de Nantes, 2 rue de la Houssinière, Nantes Cedex 3, 44322, France
| | - Christophe Rose
- Université de Lorraine, AgroParisTech, INRAE, UMR Silva, Nancy, 54000, France
| | - Eric Gelhaye
- Université de Lorraine, INRAE, Interactions Arbres/Micro-organismes (IAM), UMR 1136, Nancy, 54000, France
| | - Mélanie Morel-Rouhier
- Université de Lorraine, INRAE, Interactions Arbres/Micro-organismes (IAM), UMR 1136, Nancy, 54000, France
| |
Collapse
|
5
|
Feldman D, Yarden O, Hadar Y. Seeking the Roles for Fungal Small-Secreted Proteins in Affecting Saprophytic Lifestyles. Front Microbiol 2020; 11:455. [PMID: 32265881 PMCID: PMC7105643 DOI: 10.3389/fmicb.2020.00455] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 03/03/2020] [Indexed: 11/24/2022] Open
Abstract
Small secreted proteins (SSPs) comprise 40–60% of the total fungal secretome and are present in fungi of all phylogenetic groups, representing the entire spectrum of lifestyles. They are characteristically shorter than 300 amino acids in length and have a signal peptide. The majority of SSPs are coded by orphan genes, which lack known domains or similarities to known protein sequences. Effectors are a group of SSPs that have been investigated extensively in fungi that interact with living hosts, either pathogens or mutualistic systems. They are involved in suppressing the host defense response and altering its physiology. Here, we aim to delineate some of the potential roles of SSPs in saprotrophic fungi, that have been bioinformatically predicted as effectors, and termed in this mini-review as “effector-like” proteins. The effector-like Ssp1 from the white-rot fungus Pleurotus ostreatus is presented as a case study, and its potential role in regulating the ligninolytic system, secondary metabolism, development, and fruiting body initiation are discussed. We propose that deciphering the nature of effector-like SSPs will contribute to our understanding of development and communication in saprophytic fungi, as well as help, to elucidate the origin, regulation, and mechanisms of fungal-host, fungal-fungal, and fungal-bacterial interactions.
Collapse
Affiliation(s)
- Daria Feldman
- Department of Plant Pathology and Microbiology, The R.H. Smith Faculty Agriculture, Food and Environment, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Oded Yarden
- Department of Plant Pathology and Microbiology, The R.H. Smith Faculty Agriculture, Food and Environment, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yitzhak Hadar
- Department of Plant Pathology and Microbiology, The R.H. Smith Faculty Agriculture, Food and Environment, The Hebrew University of Jerusalem, Jerusalem, Israel
| |
Collapse
|