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Bielčik M, Schlägel UE, Schäfer M, Aguilar-Trigueros CA, Lakovic M, Sosa-Hernández MA, Hammer EC, Jeltsch F, Rillig MC. Aligning spatial ecological theory with the study of clonal organisms: the case of fungal coexistence. Biol Rev Camb Philos Soc 2024. [PMID: 39073180 DOI: 10.1111/brv.13119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 06/28/2024] [Accepted: 07/02/2024] [Indexed: 07/30/2024]
Abstract
Established ecological theory has focused on unitary organisms, and thus its concepts have matured into a form that often hinders rather than facilitates the ecological study of modular organisms. Here, we use the example of filamentous fungi to develop concepts that enable integration of non-unitary (modular) organisms into the established community ecology theory, with particular focus on its spatial aspects. In doing so, we provide a link between fungal community ecology and modern coexistence theory (MCT). We first show how community processes and predictions made by MCT can be used to define meaningful scales in fungal ecology. This leads to the novel concept of the unit of community interactions (UCI), a promising conceptual tool for applying MCT to communities of modular organisms with indeterminate clonal growth and hierarchical individuality. We outline plausible coexistence mechanisms structuring fungal communities, and show at what spatial scales and in what habitats they are most likely to act. We end by describing challenges and opportunities for empirical and theoretical research in fungal competitive coexistence.
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Affiliation(s)
- Miloš Bielčik
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, Berlin, 14195, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstr.34, Berlin, 14195, Germany
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Center for Agricultural Landscape Research (ZALF), Eberswalder Str.84, Müncheberg, 15374, Germany
| | - Ulrike E Schlägel
- Institute of Biochemistry and Biology, University of Potsdam, Am Mühlenberg 3, House 60, Potsdam-Golm, 14476, Germany
| | - Merlin Schäfer
- Institute of Biochemistry and Biology, University of Potsdam, Am Mühlenberg 3, House 60, Potsdam-Golm, 14476, Germany
- Federal Agency for Nature Conservation, Alte Messe 6, Leipzig, 04103, Germany
| | - Carlos A Aguilar-Trigueros
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, Berlin, 14195, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstr.34, Berlin, 14195, Germany
- Hawkesbury Institute for the Environment, Western Sydney University, Hawkesbury Campus, Building R2, Locked Bag 1797, Penrith, New South Wales, 2751, Australia
- Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35, Seminaarinkatu 15, Jyväskylä, 40014, Finland
| | - Milica Lakovic
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, Berlin, 14195, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstr.34, Berlin, 14195, Germany
| | - Moisés A Sosa-Hernández
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, Berlin, 14195, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstr.34, Berlin, 14195, Germany
| | - Edith C Hammer
- Department of Biology, Microbial Ecology, Lund University, Ekologihuset, Sölvegatan 37, Lund, 22362, Sweden
| | - Florian Jeltsch
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstr.34, Berlin, 14195, Germany
- Institute of Biochemistry and Biology, University of Potsdam, Am Mühlenberg 3, House 60, Potsdam-Golm, 14476, Germany
| | - Matthias C Rillig
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, Berlin, 14195, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstr.34, Berlin, 14195, Germany
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Delcourte L, Berbon M, Rodriguez M, Subban K, Lends A, Grélard A, Morvan E, Habenstein B, Saupe SJ, Delhaes L, Aimanianda V, Daskalov A, Loquet A. Magic-angle spinning NMR spectral editing of polysaccharides in whole cells using the DREAM scheme. Methods 2024; 230:59-67. [PMID: 39047926 DOI: 10.1016/j.ymeth.2024.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Revised: 07/12/2024] [Accepted: 07/15/2024] [Indexed: 07/27/2024] Open
Abstract
Most bacterial, plant and fungal cells possess at their surface a protective layer called the cell wall, conferring strength, plasticity and rigidity to withstand the osmotic pressure. This molecular barrier is crucial for pathogenic microorganisms, as it protects the cell from the local environment and often constitutes the first structural component encountered in the host-pathogen interaction. In pathogenic molds and yeasts, the cell wall constitutes the main target for the development of clinically-relevant antifungal drugs. In the past decade, solid-state NMR has emerged as a powerful analytical technique to investigate the molecular organization of microbial cell walls in the context of intact cells. 13C NMR chemical shift is an exquisite source of information to identify the polysaccharides present in the cell wall, and two-dimensional 13C-13C correlation experiments provide an efficient tool to rapidly access the polysaccharide composition in whole cells. Here we investigate the use of the adiabatic DREAM (for dipolar recoupling enhancement through amplitude modulation) recoupling scheme to improve solid-state NMR analysis of polysaccharides in intact cells. We demonstrate the advantages of two-dimensional 13C-13C experiments using the DREAM recoupling scheme. We report the spectral editing of polysaccharide signals by varying the radio-frequency carrier position. We provide practical considerations for the implementation of DREAM experiments to characterize polysaccharides in whole cells. We demonstrate the approach on intact fungal cells of Neurospora crassa and Aspergillus fumigatus, a model and a pathogenic filamentous fungus, respectively. The approach could be envisioned to efficiently reduce the spectral crowding of more complex cell surfaces, such as cell wall and peptidoglycan in bacteria.
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Affiliation(s)
- Loic Delcourte
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, Pessac, France
| | - Mélanie Berbon
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, Pessac, France
| | - Marion Rodriguez
- CNR des Aspergilloses Chroniques, Mycology-Parasitology Department, CHU Bordeaux, Bordeaux 33000, France
| | - Kamalraj Subban
- ImmunoConcEpT, CNRS, UMR 5164, University of Bordeaux, Bordeaux, France
| | - Alons Lends
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, Pessac, France
| | - Axelle Grélard
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, Pessac, France
| | - Estelle Morvan
- Univ. Bordeaux, CNRS, Inserm, IECB, UAR3033, US01, Pessac, France
| | - Birgit Habenstein
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, Pessac, France
| | - Sven J Saupe
- CNRS, Université de Bordeaux, IBGC, UMR 5095, Bordeaux, France
| | - Laurence Delhaes
- CNR des Aspergilloses Chroniques, Mycology-Parasitology Department, CHU Bordeaux, Bordeaux 33000, France; Centre de Recherche Cardio-Thoracique de Bordeaux, Inserm UMR 1045, Univ Bordeaux, Bordeaux 33000, France
| | - Vishukumar Aimanianda
- Institut Pasteur, Université Paris Cité, Immunobiology of Aspergillus, Mycology Department, Paris, France
| | - Asen Daskalov
- ImmunoConcEpT, CNRS, UMR 5164, University of Bordeaux, Bordeaux, France; State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China.
| | - Antoine Loquet
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, Pessac, France.
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Auxier B, Zhang J, Marquez FR, Senden K, van den Heuvel J, Aanen DK, Snelders E, Debets AJM. The Narrow Footprint of Ancient Balancing Selection Revealed by Heterokaryon Incompatibility Genes in Aspergillus fumigatus. Mol Biol Evol 2024; 41:msae079. [PMID: 38652808 PMCID: PMC11138114 DOI: 10.1093/molbev/msae079] [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: 05/31/2023] [Revised: 04/03/2024] [Accepted: 04/11/2024] [Indexed: 04/25/2024] Open
Abstract
In fungi, fusion between individuals leads to localized cell death, a phenomenon termed heterokaryon incompatibility. Generally, the genes responsible for this incompatibility are observed to be under balancing selection resulting from negative frequency-dependent selection. Here, we assess this phenomenon in Aspergillus fumigatus, a human pathogenic fungus with a very low level of linkage disequilibrium as well as an extremely high crossover rate. Using complementation of auxotrophic mutations as an assay for hyphal compatibility, we screened sexual progeny for compatibility to identify genes involved in this process, called het genes. In total, 5/148 (3.4%) offspring were compatible with a parent and 166/2,142 (7.7%) sibling pairs were compatible, consistent with several segregating incompatibility loci. Genetic mapping identified five loci, four of which could be fine mapped to individual genes, of which we tested three through heterologous expression, confirming their causal relationship. Consistent with long-term balancing selection, trans-species polymorphisms were apparent across several sister species, as well as equal allele frequencies within A. fumigatus. Surprisingly, a sliding window genome-wide population-level analysis of an independent dataset did not show increased Tajima's D near these loci, in contrast to what is often found surrounding loci under balancing selection. Using available de novo assemblies, we show that these balanced polymorphisms are restricted to several hundred base pairs flanking the coding sequence. In addition to identifying the first het genes in an Aspergillus species, this work highlights the interaction of long-term balancing selection with rapid linkage disequilibrium decay.
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Affiliation(s)
- Ben Auxier
- Laboratory of Genetics, Wageningen University & Research, Wageningen, the Netherlands
| | - Jianhua Zhang
- Laboratory of Genetics, Wageningen University & Research, Wageningen, the Netherlands
| | | | - Kira Senden
- Laboratory of Genetics, Wageningen University & Research, Wageningen, the Netherlands
| | - Joost van den Heuvel
- Laboratory of Genetics, Wageningen University & Research, Wageningen, the Netherlands
| | - Duur K Aanen
- Laboratory of Genetics, Wageningen University & Research, Wageningen, the Netherlands
| | - Eveline Snelders
- Laboratory of Genetics, Wageningen University & Research, Wageningen, the Netherlands
| | - Alfons J M Debets
- Laboratory of Genetics, Wageningen University & Research, Wageningen, the Netherlands
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Martin FM, van der Heijden MGA. The mycorrhizal symbiosis: research frontiers in genomics, ecology, and agricultural application. THE NEW PHYTOLOGIST 2024; 242:1486-1506. [PMID: 38297461 DOI: 10.1111/nph.19541] [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: 08/14/2023] [Accepted: 12/07/2023] [Indexed: 02/02/2024]
Abstract
Mycorrhizal symbioses between plants and fungi are vital for the soil structure, nutrient cycling, plant diversity, and ecosystem sustainability. More than 250 000 plant species are associated with mycorrhizal fungi. Recent advances in genomics and related approaches have revolutionized our understanding of the biology and ecology of mycorrhizal associations. The genomes of 250+ mycorrhizal fungi have been released and hundreds of genes that play pivotal roles in regulating symbiosis development and metabolism have been characterized. rDNA metabarcoding and metatranscriptomics provide novel insights into the ecological cues driving mycorrhizal communities and functions expressed by these associations, linking genes to ecological traits such as nutrient acquisition and soil organic matter decomposition. Here, we review genomic studies that have revealed genes involved in nutrient uptake and symbiosis development, and discuss adaptations that are fundamental to the evolution of mycorrhizal lifestyles. We also evaluated the ecosystem services provided by mycorrhizal networks and discuss how mycorrhizal symbioses hold promise for sustainable agriculture and forestry by enhancing nutrient acquisition and stress tolerance. Overall, unraveling the intricate dynamics of mycorrhizal symbioses is paramount for promoting ecological sustainability and addressing current pressing environmental concerns. This review ends with major frontiers for further research.
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Affiliation(s)
- Francis M Martin
- Université de Lorraine, INRAE, UMR IAM, Champenoux, 54280, France
- Institute of Applied Mycology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Marcel G A van der Heijden
- Department of Agroecology & Environment, Plant-Soil Interactions, Agroscope, Zürich, 8046, Switzerland
- Department of Plant and Microbial Biology, University of Zürich, Zürich, 8057, Switzerland
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5
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Naumann TA, Dowling NV, Price NPJ, Rose DR. In vitro functional analysis and in silico structural modelling of pathogen-secreted polyglycine hydrolases. Biochem Biophys Res Commun 2024; 706:149746. [PMID: 38461646 DOI: 10.1016/j.bbrc.2024.149746] [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: 11/29/2023] [Revised: 02/16/2024] [Accepted: 03/01/2024] [Indexed: 03/12/2024]
Abstract
Polyglycine hydrolases are fungal effectors composed of an N-domain with unique sequence and structure and a C-domain that resembles β-lactamases, with serine protease activity. These secreted fungal proteins cleave Gly-Gly bonds within a polyglycine sequence in corn ChitA chitinase. The polyglycine hydrolase N-domain (PND) function is unknown. In this manuscript we provide evidence that the PND does not directly participate in ChitA cleavage. In vitro analysis of site-directed mutants in conserved residues of the PND of polyglycine hydrolase Es-cmp did not specifically impair protease activity. Furthermore, in silico structural models of three ChitA-bound polyglycine hydrolases created by High Ambiguity Driven protein-protein DOCKing (HADDOCK) did not predict significant interactions between the PND and ChitA. Together these results suggest that the PND has another function. To determine what types of PND-containing proteins exist in nature we performed a computational analysis of Foldseek-identified PND-containing proteins. The analysis showed that proteins with PNDs are present throughout biology as either single domain proteins or fused to accessory domains that are diverse but are usually proteases or kinases.
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Affiliation(s)
- Todd A Naumann
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit, 1815 N. University, Peoria, IL, 61604, USA.
| | - Nicole V Dowling
- Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
| | - Neil P J Price
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Renewable Product Technologies Research Unit, 1815 N. University, Peoria, IL, 61604, USA
| | - David R Rose
- Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
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6
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Wang S, Ma T, Xia X, Zhang L. Evolutionary insights and functional diversity of gasdermin family proteins and homologs in microorganisms. Front Immunol 2024; 15:1371611. [PMID: 38571940 PMCID: PMC10989679 DOI: 10.3389/fimmu.2024.1371611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 03/07/2024] [Indexed: 04/05/2024] Open
Abstract
The gasdermin protein family and its homologs in microorganisms have gained significant attention due to their roles in programmed cell death, immune defense, and microbial infection. This review summarizes the current research status of gasdermin proteins, their structural features, and functional roles in fungi, bacteria, and viruses. The review presents evolutionary parallels between mammalian and microbial defense systems, highlighting the conserved role of gasdermin proteins in regulating cell death processes and immunity. Additionally, the structural and functional characteristics of gasdermin homologs in microorganisms are summarized, shedding light on their potential as targets for therapeutic interventions. Future research directions in this field are also discussed to provide a roadmap for further investigation.
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Affiliation(s)
- Shule Wang
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, Shandong, China
- School of Clinical Medicine, Shandong Second Medical University, Weifang, Shandong, China
| | - Tingbo Ma
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, Shandong, China
- School of Clinical Medicine, Shandong Second Medical University, Weifang, Shandong, China
| | - Xiaoyi Xia
- Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Leiliang Zhang
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, Shandong, China
- Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, China
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Arshed S, Cox MP, Beever RE, Parkes SL, Pearson MN, Bowen JK, Templeton MD. The Bcvic1 and Bcvic2 vegetative incompatibility genes in Botrytis cinerea encode proteins with domain architectures involved in allorecognition in other filamentous fungi. Fungal Genet Biol 2023; 169:103827. [PMID: 37640199 DOI: 10.1016/j.fgb.2023.103827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 07/19/2023] [Accepted: 08/24/2023] [Indexed: 08/31/2023]
Abstract
Vegetative incompatibility is a fungal allorecognition system characterised by the inability of genetically distinct conspecific fungal strains to form a viable heterokaryon and is controlled by multiple polymorphic loci termed vic (vegetative incompatibility) or het (heterokaryon incompatibility). We have genetically identified and characterised the first vic locus in the economically important, plant-pathogenic, necrotrophic fungus Botrytis cinerea. A bulked segregant approach coupled with whole genome Illumina sequencing of near-isogenic lines of B. cinerea was used to map a vic locus to a 60-kb region of the genome. Within that locus, we identified two adjacent, highly polymorphic open reading frames, Bcvic1 and Bcvic2, which encode predicted proteins that contain domain architectures implicated in vegetative incompatibility in other filamentous fungi. Bcvic1 encodes a predicted protein containing a putative serine esterase domain, a NACHT family of NTPases domain, and several Ankyrin repeats. Bcvic2 encodes a putative syntaxin protein containing a SNARE domain; such proteins typically function in vesicular transport. Deletion of Bcvic1 and Bcvic2 individually had no effect on vegetative incompatibility. However, deletion of the region containing both Bcvic1 and Bcvic2 resulted in mutant lines that were severely restricted in growth and showed loss of vegetative incompatibility. Complementation of these mutants by ectopic expression restored the growth and vegetative incompatibility phenotype, indicating that Bcvic1 and Bcvic2 are controlling vegetative incompatibility at this vic locus.
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Affiliation(s)
- Saadiah Arshed
- Bioprotection, New Zealand Institute of Plant and Food Research, Auckland, New Zealand; School of Biological Sciences, University of Auckland, Auckland, New Zealand; Bioprotection Aotearoa Centre of Research Excellence, New Zealand
| | - Murray P Cox
- Bioprotection Aotearoa Centre of Research Excellence, New Zealand; School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Ross E Beever
- Manaaki Whenua Landcare Research, Auckland, New Zealand
| | | | - Michael N Pearson
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Joanna K Bowen
- Bioprotection, New Zealand Institute of Plant and Food Research, Auckland, New Zealand.
| | - Matthew D Templeton
- Bioprotection, New Zealand Institute of Plant and Food Research, Auckland, New Zealand; School of Biological Sciences, University of Auckland, Auckland, New Zealand; Bioprotection Aotearoa Centre of Research Excellence, New Zealand.
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Zheng Q, Daskalov A. Microbial gasdermins: More than a billion years of pyroptotic-like cell death. Semin Immunol 2023; 69:101813. [PMID: 37480832 DOI: 10.1016/j.smim.2023.101813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 07/16/2023] [Accepted: 07/17/2023] [Indexed: 07/24/2023]
Abstract
In the recent past, the concept of immunity has been extended to eukaryotic and prokaryotic microorganisms, like fungi and bacteria. The latest findings have drawn remarkable evolutionary parallels between metazoan and microbial defense-related genes, unveiling a growing number of shared transkingdom components of immune systems. One such component is the gasdermin family of pore-forming proteins - executioners of a highly inflammatory immune cell death program in mammals, termed pyroptosis. Pyroptotic cell death limits the spread of intracellular pathogens by eliminating infected cells and coordinates the broader inflammatory response to infection. The microbial gasdermins have similarly been implicated in defense-related cell death reactions in fungi, bacteria and archaea. Moreover, the discovery of the molecular regulators of gasdermin cytotoxicity in fungi and bacteria, has established additional evolutionary links to mammalian pyroptotic pathways. Here, we focus on the gasdermin proteins in microorganisms and their role in organismal defense and provide perspective on this remarkable case study in comparative immunology.
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Affiliation(s)
- Qi Zheng
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Asen Daskalov
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China; ImmunoConcEpT, CNRS UMR 5164, University of Bordeaux, Bordeaux, France.
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Dijksterhuis J. Endosymbionts: Bacterial hijacking of fungi? Curr Biol 2023; 33:R765-R767. [PMID: 37490862 DOI: 10.1016/j.cub.2023.06.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
Bacteria inside fungal hyphae allow the fungus Rhizopus microsporus to form spores and operate via effectors in 'stealth' mode. When the functionality of one effector is taken away, bacteria are captured in septated cells and die.
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Affiliation(s)
- Jan Dijksterhuis
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.
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10
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Popović M, Nuskern L, Peranić K, Vuković R, Katanić Z, Krstin L, Ćurković-Perica M, Leigh DM, Poljak I, Idžojtić M, Rigling D, Ježić M. Physiological variations in hypovirus-infected wild and model long-term laboratory strains of Cryphonectria parasitica. Front Microbiol 2023; 14:1192996. [PMID: 37426020 PMCID: PMC10324583 DOI: 10.3389/fmicb.2023.1192996] [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: 03/24/2023] [Accepted: 05/25/2023] [Indexed: 07/11/2023] Open
Abstract
Introduction Forest ecosystems are highly threatened by the simultaneous effects of climate change and invasive pathogens. Chestnut blight, caused by the invasive phytopathogenic fungus Cryphonectria parasitica, has caused severe damage to European chestnut groves and catastrophic dieback of American chestnut in North America. Within Europe, the impacts of the fungus are widely mitigated through biological control that utilizes the RNA mycovirus: Cryphonectria hypovirus 1 (CHV1). Viral infections, similarly to abiotic factors, can cause oxidative stress in their hosts leading to physiological attrition through stimulating ROS (reactive oxygen species) and NOx production. Methods To fully understand the interactions leading to the biocontrol of chestnut blight, it is vital to determine oxidative stress damage arising during CHV1 infection, especially considering that other abiotic factors, like long-term cultivation of model fungal strains, can also impact oxidative stress. Our study compared CHV1-infected C. parasitica isolates from two Croatian wild populations with CHV1-infected model strains (EP713, Euro7 and CR23) that have experienced long-term laboratory cultivation. Results and Discussion We determined the level of oxidative stress in the samples by measuring stress enzymes' activity and oxidative stress biomarkers. Furthermore, for the wild populations, we studied the activity of fungal laccases, expression of the laccase gene lac1, and a possible effect of CHV1 intra-host diversity on the observed biochemical responses. Relative to the wild isolates, the long-term model strains had lower enzymatic activities of superoxide dismutase (SOD) and glutathione S-transferase (GST), and higher content of malondialdehyde (MDA) and total non-protein thiols. This indicated generally higher oxidative stress, likely arising from their decades-long history of subculturing and freeze-thaw cycles. When comparing the two wild populations, differences between them in stress resilience and levels of oxidative stress were also observed, as evident from the different MDA content. The intra-host genetic diversity of the CHV1 had no discernible effect on the stress levels of the virus-infected fungal cultures. Our research indicated that an important determinant modulating both lac1 expression and laccase enzyme activity is intrinsic to the fungus itself, possibly related to the vc type of the fungus, i.e., vegetative incompatibility genotype.
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Affiliation(s)
- Maja Popović
- Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Lucija Nuskern
- Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Karla Peranić
- Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Rosemary Vuković
- Department of Biology, Josip Juraj Strossmayer University of Osijek, Osijek, Croatia
| | - Zorana Katanić
- Department of Biology, Josip Juraj Strossmayer University of Osijek, Osijek, Croatia
| | - Ljiljana Krstin
- Department of Biology, Josip Juraj Strossmayer University of Osijek, Osijek, Croatia
| | | | | | - Igor Poljak
- Faculty of Forestry and Wood Technology, University of Zagreb, Zagreb, Croatia
| | - Marilena Idžojtić
- Faculty of Forestry and Wood Technology, University of Zagreb, Zagreb, Croatia
| | - Daniel Rigling
- Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Marin Ježić
- Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
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Abstract
Investigation of fungal biology has been frequently motivated by the fact that many fungal species are important plant and animal pathogens. Such efforts have contributed significantly toward our understanding of fungal pathogenic lifestyles (virulence factors and strategies) and the interplay with host immune systems. In parallel, work on fungal allorecognition systems leading to the characterization of fungal regulated cell death determinants and pathways, has been instrumental for the emergent concept of fungal immunity. The uncovered evolutionary trans-kingdom parallels between fungal regulated cell death pathways and innate immune systems incite us to reflect further on the concept of a fungal immune system. Here, I briefly review key findings that have shaped the fungal immunity paradigm, providing a perspective on what I consider its most glaring knowledge gaps. Undertaking to fill such gaps would establish firmly the fungal immune system inside the broader field of comparative immunology.
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Affiliation(s)
- Asen Daskalov
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- ImmunoConcEpT, CNRS UMR 5164, University of Bordeaux, Bordeaux, France
- Corresponding author
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12
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Richter I, Wein P, Uzum Z, Stanley CE, Krabbe J, Molloy EM, Moebius N, Ferling I, Hillmann F, Hertweck C. Transcription activator-like effector protects bacterial endosymbionts from entrapment within fungal hyphae. Curr Biol 2023:S0960-9822(23)00623-1. [PMID: 37301202 DOI: 10.1016/j.cub.2023.05.028] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 03/30/2023] [Accepted: 05/12/2023] [Indexed: 06/12/2023]
Abstract
As an endosymbiont of the ecologically and medically relevant fungus Rhizopus microsporus, the toxin-producing bacterium Mycetohabitans rhizoxinica faces myriad challenges, such as evading the host's defense mechanisms. However, the bacterial effector(s) that facilitate the remarkable ability of M. rhizoxinica to freely migrate within fungal hyphae have thus far remained unknown. Here, we show that a transcription activator-like (TAL) effector released by endobacteria is an essential symbiosis factor. By combining microfluidics with fluorescence microscopy, we observed enrichment of TAL-deficient M. rhizoxinica in side hyphae. High-resolution live imaging showed the formation of septa at the base of infected hyphae, leading to the entrapment of endobacteria. Using a LIVE/DEAD stain, we demonstrate that the intracellular survival of trapped TAL-deficient bacteria is significantly reduced compared with wild-type M. rhizoxinica, indicative of a protective host response in the absence of TAL proteins. Subversion of host defense in TAL-competent endobacteria represents an unprecedented function of TAL effectors. Our data illustrate an unusual survival strategy of endosymbionts in the host and provide deeper insights into the dynamic interactions between bacteria and eukaryotes.
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Affiliation(s)
- Ingrid Richter
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Philipp Wein
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Zerrin Uzum
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Claire E Stanley
- Department of Bioengineering, Imperial College, South Kensington, London SW7 2AZ, UK
| | - Jana Krabbe
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Evelyn M Molloy
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Nadine Moebius
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Iuliia Ferling
- Junior Research Group Evolution of Microbial Interactions, Leibniz Institute for Natural Product Research and Infection Biology, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Falk Hillmann
- Junior Research Group Evolution of Microbial Interactions, Leibniz Institute for Natural Product Research and Infection Biology, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745 Jena, Germany; Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743 Jena, Germany.
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13
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Beeson W, Gabriel K, Cornelison C. Fungi as a source of eumelanin: current understanding and prospects. J Ind Microbiol Biotechnol 2023; 50:kuad014. [PMID: 37336591 PMCID: PMC10569377 DOI: 10.1093/jimb/kuad014] [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: 12/21/2022] [Accepted: 06/15/2023] [Indexed: 06/21/2023]
Abstract
Melanins represent a diverse collection of pigments with a variety of structures and functions. One class of melanin, eumelanin, is recognizable to most as the source of the dark black color found in cephalopod ink. Sepia officinalis is the most well-known and sought-after source of non-synthetic eumelanin, but its harvest is limited by the availability of cuttlefish, and its extraction from an animal source brings rise to ethical concerns. In recent years, these limitations have become more pressing as more applications for eumelanin are developed-particularly in medicine and electronics. This surge in interest in the applications of eumelanin has also fueled a rise in the interest of alternative, bio-catalyzed production methods. Many culinarily-utilized fungi are ideal candidates in this production scheme, as examples exist which have been shown to produce eumelanin, their growth at large scales is well understood, and they can be cultivated on recaptured waste streams. However, much of the current research on the fungal production of eumelanin focuses on pathogenic fungi and eumelanin's role in virulence. In this paper, we will review the potential for culinary fungi to produce eumelanin and provide suggestions for new research areas that would be most impactful in the search for improved fungal eumelanin producers.
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Affiliation(s)
- William Beeson
- Department of Molecular and Cellular Biology, Kennesaw State
University, 1000 Chastain Road NW, Kennesaw, GA
30144, USA
| | - Kyle Gabriel
- Department of Molecular and Cellular Biology, Kennesaw State
University, 1000 Chastain Road NW, Kennesaw, GA
30144, USA
| | - Christopher Cornelison
- Department of Molecular and Cellular Biology, Kennesaw State
University, 1000 Chastain Road NW, Kennesaw, GA
30144, USA
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14
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Wojciechowski JW, Tekoglu E, Gąsior-Głogowska M, Coustou V, Szulc N, Szefczyk M, Kopaczyńska M, Saupe SJ, Dyrka W. Exploring a diverse world of effector domains and amyloid signaling motifs in fungal NLR proteins. PLoS Comput Biol 2022; 18:e1010787. [PMID: 36542665 PMCID: PMC9815663 DOI: 10.1371/journal.pcbi.1010787] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 01/05/2023] [Accepted: 12/02/2022] [Indexed: 12/24/2022] Open
Abstract
NLR proteins are intracellular receptors constituting a conserved component of the innate immune system of cellular organisms. In fungi, NLRs are characterized by high diversity of architectures and presence of amyloid signaling. Here, we explore the diverse world of effector and signaling domains of fungal NLRs using state-of-the-art bioinformatic methods including MMseqs2 for fast clustering, probabilistic context-free grammars for sequence analysis, and AlphaFold2 deep neural networks for structure prediction. In addition to substantially improving the overall annotation, especially in basidiomycetes, the study identifies novel domains and reveals the structural similarity of MLKL-related HeLo- and Goodbye-like domains forming the most abundant superfamily of fungal NLR effectors. Moreover, compared to previous studies, we found several times more amyloid motif instances, including novel families, and validated aggregating and prion-forming properties of the most abundant of them in vitro and in vivo. Also, through an extensive in silico search, the NLR-associated amyloid signaling was identified in basidiomycetes. The emerging picture highlights similarities and differences in the NLR architectures and amyloid signaling in ascomycetes, basidiomycetes and other branches of life.
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Affiliation(s)
- Jakub W. Wojciechowski
- Katedra Inżynierii Biomedycznej, Wydział Podstawowych Problemów Techniki, Politechnika Wrocławska, Wrocław, Poland
| | - Emirhan Tekoglu
- Biyomühendislik Bölümü, Yıldız Teknik Üniversitesi, İstanbul, Turkey
- Wydział Chemiczny, Politechnika Wrocławska, Poland
| | - Marlena Gąsior-Głogowska
- Katedra Inżynierii Biomedycznej, Wydział Podstawowych Problemów Techniki, Politechnika Wrocławska, Wrocław, Poland
| | - Virginie Coustou
- Institut de Biochimie et de Génétique Cellulaire, UMR 5095 CNRS, Université de Bordeaux, Bordeaux, France
| | - Natalia Szulc
- Katedra Inżynierii Biomedycznej, Wydział Podstawowych Problemów Techniki, Politechnika Wrocławska, Wrocław, Poland
| | - Monika Szefczyk
- Katedra Chemii Bioorganicznej, Wydział Chemiczny, Politechnika Wrocławska, Wrocław, Poland
| | - Marta Kopaczyńska
- Katedra Inżynierii Biomedycznej, Wydział Podstawowych Problemów Techniki, Politechnika Wrocławska, Wrocław, Poland
| | - Sven J. Saupe
- Institut de Biochimie et de Génétique Cellulaire, UMR 5095 CNRS, Université de Bordeaux, Bordeaux, France
- * E-mail: (SJS); (WD)
| | - Witold Dyrka
- Katedra Inżynierii Biomedycznej, Wydział Podstawowych Problemów Techniki, Politechnika Wrocławska, Wrocław, Poland
- * E-mail: (SJS); (WD)
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15
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Chai H, Liu P, Ma Y, Chen W, Tao N, Zhao Y. Characterization of Vegetative Incompatibility in Morchella importuna and Location of the Related-Genes by Bulk Segregant Analysis. Front Microbiol 2022; 13:828514. [PMID: 35330770 PMCID: PMC8940278 DOI: 10.3389/fmicb.2022.828514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 01/31/2022] [Indexed: 12/04/2022] Open
Abstract
Vegetative incompatibility (VI) is a widespread phenomenon developed in Morchella importuna, a species of ascomycete fungus that is cultivated on a rapidly expanding scale in China. Understanding the genetic bases of this nonself-recognition phenomenon is beneficial for resolving some problems that are associated with the production of this highly prized edible fungus, such as crossbreeding, strain classification, and pathogen transmission. VI is genetically controlled by het genes, organized in two different systems, namely allelic and nonallelic. These het genes have been well characterized in Podospora anserina and Neurospora crassa. In this work, putative het-homologs were identified in the genome of M. importuna, but their low allelic polymorphism in different vegetative compatibility groups (VCGs) suggested that VI in this fungus might not be regulated by these het genes. The progeny derived from vegetative compatible parents became a VCG, while the single-ascospore strains from vegetative incompatible parents were divided into four VCGs, and the interaction between the inter-group strains led to the formation of two types of barrages, viz., thin dark line and raised aggregate of hyphae. The Bulk Segregant Analysis confirmed that the genes mimpvic32 and mimpvic33 were linked to VI reactions in M. importuna; nevertheless, the formation of barrages also occurred between the pairs carrying the same allele of these two genes. In sum, the VI control system in M. importuna was complicated, and there were more other allelic or non-allelic VI-related genes.
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Affiliation(s)
- Hongmei Chai
- Biotechnology and Germplasmic Resource Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China.,Yunnan Provincial Key Laboratory of Agricultural Biotechnology, Kunming, China.,Key Laboratory of Southwestern Crop Resource Germplasm Innovation, Ministry of Agriculture and Rural Affairs, Kunming, China
| | - Ping Liu
- Biotechnology and Germplasmic Resource Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China.,Yunnan Provincial Key Laboratory of Agricultural Biotechnology, Kunming, China.,Key Laboratory of Southwestern Crop Resource Germplasm Innovation, Ministry of Agriculture and Rural Affairs, Kunming, China
| | - Yuanhao Ma
- Biotechnology and Germplasmic Resource Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China.,Yunnan Provincial Key Laboratory of Agricultural Biotechnology, Kunming, China.,Key Laboratory of Southwestern Crop Resource Germplasm Innovation, Ministry of Agriculture and Rural Affairs, Kunming, China
| | - Weimin Chen
- Biotechnology and Germplasmic Resource Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China.,Yunnan Provincial Key Laboratory of Agricultural Biotechnology, Kunming, China.,Key Laboratory of Southwestern Crop Resource Germplasm Innovation, Ministry of Agriculture and Rural Affairs, Kunming, China
| | - Nan Tao
- Biotechnology and Germplasmic Resource Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China.,Yunnan Provincial Key Laboratory of Agricultural Biotechnology, Kunming, China.,Key Laboratory of Southwestern Crop Resource Germplasm Innovation, Ministry of Agriculture and Rural Affairs, Kunming, China
| | - Yongchang Zhao
- Biotechnology and Germplasmic Resource Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China.,Yunnan Provincial Key Laboratory of Agricultural Biotechnology, Kunming, China.,Key Laboratory of Southwestern Crop Resource Germplasm Innovation, Ministry of Agriculture and Rural Affairs, Kunming, China
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16
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A dialogue-like cell communication mechanism is conserved in filamentous ascomycete fungi and mediates interspecies interactions. Proc Natl Acad Sci U S A 2022; 119:e2112518119. [PMID: 35286209 PMCID: PMC8944665 DOI: 10.1073/pnas.2112518119] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
This study reveals that a dialogue-like communication mechanism, which mediates cell–cell fusion in filamentous fungi, is a conserved complex trait. It allows the communication and behavioral coordination of cells of distantly related species and mediates their mutual attraction and subsequent physical contact, although interspecies fusion does not occur. Through the activation of this signaling machinery, one species can reprogram the developmental program of the other fungus. These data promote our understanding of microbial communication, illustrate the mechanism of repurposing of existing building blocks in cellular evolution, revive the hypothesis of vegetative fusion as an avenue of horizontal gene transfer in fungi, and establish the idea of developmental reprogramming as a tool for controlling fungi. In many filamentous fungi, germinating spores cooperate by fusing into supracellular structures, which develop into the mycelial colony. In the model fungus Neurospora crassa, this social behavior is mediated by an intriguing mode of communication, in which two fusing cells take turns in signal sending and receiving. Here we show that this dialogue-like cell communication mechanism is highly conserved in distantly related fungal species and mediates interspecies interactions. In mixed populations, cells of N. crassa and the phytopathogenic gray mold Botrytis cinerea coordinate their behavior over a spatial distance and establish physical contact. Subsequent cell–cell fusion is, however, restricted to germlings of the same species, indicating that species specificity of germling fusion has evolved not on the level of the signal/receptor but at subsequent levels of the fusion process. In B. cinerea, fusion and infectious growth are mutually exclusive cellular programs. Remarkably, the presence of N. crassa can reprogram this behavior and induce fusion of the gray mold on plant surfaces, potentially weakening its pathogenic potential. In a third fungal species, the nematode-trapping fungus Arthrobotrys flagrans, the conserved signaling mechanism mediates vegetative fusion within mycelial colonies but has also been repurposed for the formation of nematode-catching traps. In summary, this study identified the cell dialogue mechanism as a conserved complex trait and revealed that even distantly related fungi possess a common molecular language, which promotes cellular contact formation across species borders.
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17
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Fungal gasdermin-like proteins are controlled by proteolytic cleavage. Proc Natl Acad Sci U S A 2022; 119:2109418119. [PMID: 35135876 PMCID: PMC8851545 DOI: 10.1073/pnas.2109418119] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/04/2022] [Indexed: 12/11/2022] Open
Abstract
Gasdermins are a family of pore-forming proteins controlling an inflammatory cell death reaction in the mammalian immune system. The pore-forming ability of the gasdermin proteins is released by proteolytic cleavage with the removal of their inhibitory C-terminal domain. Recently, gasdermin-like proteins have been discovered in fungi and characterized as cell death-inducing toxins in the context of conspecific non-self-discrimination (allorecognition). Although functional analogies have been established between mammalian and fungal gasdermins, the molecular pathways regulating gasdermin activity in fungi remain largely unknown. Here, we characterize a gasdermin-based cell death reaction controlled by the het-Q allorecognition genes in the filamentous fungus Podospora anserina We show that the cytotoxic activity of the HET-Q1 gasdermin is controlled by proteolysis. HET-Q1 loses a ∼5-kDa C-terminal fragment during the cell death reaction in the presence of a subtilisin-like serine protease termed HET-Q2. Mutational analyses and successful reconstitution of the cell death reaction in heterologous hosts (Saccharomyces cerevisiae and human 293T cells) suggest that HET-Q2 directly cleaves HET-Q1 to induce cell death. By analyzing the genomic landscape of het-Q1 homologs in fungi, we uncovered that the vast majority of the gasdermin genes are clustered with protease-encoding genes. These HET-Q2-like proteins carry either subtilisin-like or caspase-related proteases, which, in some cases, correspond to the N-terminal effector domain of nucleotide-binding and oligomerization-like receptor proteins. This study thus reveals the proteolytic regulation of gasdermins in fungi and establishes evolutionary parallels between fungal and mammalian gasdermin-dependent cell death pathways.
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18
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Atriztán-Hernández K, Herrera-Estrella A. Drosophila attack inhibits hyphal regeneration and defense mechanisms activation for the fungus Trichoderma atroviride. THE ISME JOURNAL 2022; 16:149-158. [PMID: 34282283 PMCID: PMC8692604 DOI: 10.1038/s41396-021-01068-9] [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: 01/14/2021] [Revised: 06/30/2021] [Accepted: 07/09/2021] [Indexed: 02/07/2023]
Abstract
The capability to respond to wounding is a process shared by organisms of different kingdoms that can result in the regeneration of whole-body parts or lost structures or organs. Filamentous fungi constitute a rich food source that ensures survival and reproduction of their predators and are therefore continuously exposed to mechanical damage. Nevertheless, our understanding of how fungi respond to wounding and predators is scarce. Fungi like plants and animals respond to injury recognizing Damage- and Microbe-Associated Molecular Patterns (DAMPs/MAMPs) that activate Ca2+ and Mitogen-Activated Protein Kinase dependent signaling for the activation of defense mechanisms. During herbivory, plants, in addition to activating pathways related to injury, activate specific responses to combat their predators. Using a transcriptional approach, we studied the capacity of the filamentous fungus Trichoderma atroviride to activate specific responses to injury and attack by different arthropods. Attack by Drosophila melanogaster inhibited the transcriptional activation of genes required for hyphal regeneration, and the fungal innate immune and chemical defense responses. We also provide mechanistic insight of this inhibition involving components of the D. melanogaster salivary glands that repress the expression of a set of genes and block hyphal regeneration.
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19
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Wu Q, Wang Y, Liu LN, Shi K, Li CY. Comparative Genomics and Gene Pool Analysis Reveal the Decrease of Genome Diversity and Gene Number in Rice Blast Fungi by Stable Adaption with Rice. J Fungi (Basel) 2021; 8:jof8010005. [PMID: 35049945 PMCID: PMC8778285 DOI: 10.3390/jof8010005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 12/12/2021] [Accepted: 12/17/2021] [Indexed: 11/16/2022] Open
Abstract
Magnaporthe oryzae caused huge losses in rice and wheat production worldwide. Comparing to long-term co-evolution history with rice, wheat-infecting isolates were new-emerging. To reveal the genetic differences between rice and wheat blast on global genomic scale, 109 whole-genome sequences of M. oryzae from rice, wheat, and other hosts were reanalyzed in this study. We found that the rice lineage had gone through stronger selective sweep and fewer conserved genes than those of Triticum and Lolium lineages, which indicated that rice blast fungi adapted to rice by gene loss and rapid evolution of specific loci. Furthermore, 228 genes associated with host adaptation of M. oryzae were found by presence/absence variation (PAV) analyses. The functional annotation of these genes found that the fine turning of genes gain/loss involved with transport and transcription factor, thiol metabolism, and nucleotide metabolism respectively are major mechanisms for rice adaption. This result implies that genetic base of specific host plant may lead to gene gain/loss variation of pathogens, so as to enhance their adaptability to host. Further characterization of these specific loci and their roles in adaption and evaluation of the fungi may eventually lead to understanding of interaction mechanism and develop new strategies of the disease management.
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Affiliation(s)
- Qi Wu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China; (Q.W.); (Y.W.); (L.-N.L.)
- College of Science, Yunnan Agricultural University, Kunming 650201, China
- Yunnan Organic Tea Industry Intelligent Engineering Research Center, Key Laboratory of Intelligent Organic Tea Garden Construction in Universities of Yunnan Province, Key Laboratory for Crop Production and Smart Agriculture of Yunnan Province, Yunnan Agricultural University, Kunming 650201, China
| | - Yi Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China; (Q.W.); (Y.W.); (L.-N.L.)
| | - Li-Na Liu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China; (Q.W.); (Y.W.); (L.-N.L.)
- Key Laboratory of Green Prevention and Control of Agricultural Transboundary Pests of Yunnan Province, Agricultural Environment and Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming 650201, China
| | - Kai Shi
- School of Foreign Language, Yunnan Agricultural University, Kunming 650201, China;
| | - Cheng-Yun Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China; (Q.W.); (Y.W.); (L.-N.L.)
- Correspondence:
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20
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Interactions among Escovopsis, Antagonistic Microfungi Associated with the Fungus-Growing Ant Symbiosis. J Fungi (Basel) 2021; 7:jof7121007. [PMID: 34946990 PMCID: PMC8703566 DOI: 10.3390/jof7121007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 11/12/2021] [Accepted: 11/13/2021] [Indexed: 11/17/2022] Open
Abstract
Fungi in the genus Escovopsis (Ascomycota: Hypocreales) are prevalent associates of the complex symbiosis between fungus-growing ants (Tribe Attini), the ants' cultivated basidiomycete fungi and a consortium of both beneficial and harmful microbes found within the ants' garden communities. Some Escovopsis spp. have been shown to attack the ants' cultivated fungi, and co-infections by multiple Escovopsis spp. are common in gardens in nature. Yet, little is known about how Escovopsis strains impact each other. Since microbe-microbe interactions play a central role in microbial ecology and evolution, we conducted experiments to assay the types of interactions that govern Escovopsis-Escovopsis relationships. We isolated Escovopsis strains from the gardens of 10 attine ant genera representing basal (lower) and derived groups in the attine ant phylogeny. We conducted in vitro experiments to determine the outcome of both intraclonal and interclonal Escovopsis confrontations. When paired with self (intraclonal interactions), Escovopsis isolated from lower attine colonies exhibited antagonistic (inhibitory) responses, while strains isolated from derived attine colonies exhibited neutral or mutualistic interactions, leading to a clear phylogenetic pattern of interaction outcome. Interclonal interactions were more varied, exhibiting less phylogenetic signal. These results can serve as the basis for future studies on the costs and benefits of Escovopsis coinfection, and on the genetic and chemical mechanisms that regulate the compatibility and incompatibility observed here.
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21
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A New Double-Stranded RNA Mycovirus in Cryphonectria naterciae Is Able to Cross the Species Barrier and Is Deleterious to a New Host. J Fungi (Basel) 2021; 7:jof7100861. [PMID: 34682282 PMCID: PMC8538617 DOI: 10.3390/jof7100861] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/07/2021] [Accepted: 10/12/2021] [Indexed: 12/25/2022] Open
Abstract
Cryphonectria is a fungal genus associated with economically significant disease of trees. Herein we characterized a novel double-stranded RNA virus from the fungal species Cryphonectria naterciae, a species unexplored as a virus host. De novo assembly of RNA-seq data and Sanger sequencing of RACE (rapid amplification of cDNA ends) clones gave the complete, non-segmented genome (10,164 bp) of the virus termed Cryphonectria naterciae fusagravirus (CnFGV1) that was phylogenetically placed within the previously proposed viral family Fusagraviridae. Of 31 field-collected strains of C. naterciae, 40% tested CnFGV1-positive. Cocultivation resulted in within-species transmission of CnFGV1 to virus-free strains of C. naterciae. Comparison of the mycelium phenotype and the growth rate of CnFGV1-infected and virus-free isogenic strains revealed frequent sectoring and growth reduction in C. naterciae upon virus infection. Co-culturing also led to cross-species transmission of CnFGV1 to Cryphonectria carpinicola and Cryphonectria radicalis, but not to Cryphonectria parasitica. The virus-infected C. naterciae and the experimentally infected Cryphonectria spp. readily transmitted CnFGV1 through asexual spores to the next generation. CnFGV1 strongly reduced conidiation and in some cases vegetative growth of C. carpinicola, which is involved in the European hornbeam disease. This study is the first report of a fusagravirus in the family Cryphonectriaceae and lays the groundwork for assessing a hypovirulence effect of CnFGV1 against the hornbeam decline in Europe.
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22
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Daskalov A, Glass NL. Gasdermin and Gasdermin-Like Pore-Forming Proteins in Invertebrates, Fungi and Bacteria. J Mol Biol 2021; 434:167273. [PMID: 34599942 DOI: 10.1016/j.jmb.2021.167273] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 09/22/2021] [Accepted: 09/22/2021] [Indexed: 10/20/2022]
Abstract
The gasdermin family of pore-forming proteins (PFPs) has recently emerged as key molecular players controlling immune-related cell death in mammals. Characterized mammalian gasdermins are activated through proteolytic cleavage by caspases or serine proteases, which remove an inhibitory carboxy-terminal domain, allowing the pore-formation process. Processed gasdermins form transmembrane pores permeabilizing the plasma membrane, which often results in lytic and inflammatory cell death. While the gasdermin-dependent cell death (pyroptosis) has been predominantly characterized in mammals, it now has become clear that gasdermins also control cell death in early vertebrates (teleost fish) and invertebrate animals such as corals (Cnidaria). Moreover, gasdermins and gasdermin-like proteins have been identified and characterized in taxa outside of animals, notably Fungi and Bacteria. Fungal and bacterial gasdermins share many features with mammalian gasdermins including their mode of activation through proteolysis. It has been shown that in some cases the proteolytic activation is executed by evolutionarily related proteases acting downstream of proteins resembling immune receptors controlling pyroptosis in mammals. Overall, these findings establish gasdermins and gasdermin-regulated cell death as an extremely ancient mechanism of cellular suicide and build towards an understanding of the evolution of regulated cell death in the context of immunology. Here, we review the broader gasdermin family, focusing on recent discoveries in invertebrates, fungi and bacteria.
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Affiliation(s)
- Asen Daskalov
- Institut de Biochimie et Génétique Cellulaires, University of Bordeaux, France.
| | - N Louise Glass
- The Plant and Microbial Biology Department, The University of California, Berkeley, CA 94720-3102, United States
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23
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Dauphin B, de Freitas Pereira M, Kohler A, Grigoriev IV, Barry K, Na H, Amirebrahimi M, Lipzen A, Martin F, Peter M, Croll D. Cryptic genetic structure and copy-number variation in the ubiquitous forest symbiotic fungus Cenococcum geophilum. Environ Microbiol 2021; 23:6536-6556. [PMID: 34472169 PMCID: PMC9293092 DOI: 10.1111/1462-2920.15752] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 08/27/2021] [Accepted: 08/30/2021] [Indexed: 01/22/2023]
Abstract
Ectomycorrhizal (ECM) fungi associated with plants constitute one of the most successful symbiotic interactions in forest ecosystems. ECM support trophic exchanges with host plants and are important factors for the survival and stress resilience of trees. However, ECM clades often harbour morpho-species and cryptic lineages, with weak morphological differentiation. How this relates to intraspecific genome variability and ecological functioning is poorly known. Here, we analysed 16 European isolates of the ascomycete Cenococcum geophilum, an extremely ubiquitous forest symbiotic fungus with no known sexual or asexual spore-forming structures but with a massively enlarged genome. We carried out whole-genome sequencing to identify single-nucleotide polymorphisms. We found no geographic structure at the European scale but divergent lineages within sampling sites. Evidence for recombination was restricted to specific cryptic lineages. Lineage differentiation was supported by extensive copy-number variation. Finally, we confirmed heterothallism with a single MAT1 idiomorph per genome. Synteny analyses of the MAT1 locus revealed substantial rearrangements and a pseudogene of the opposite MAT1 idiomorph. Our study provides the first evidence for substantial genome-wide structural variation, lineage-specific recombination and low continent-wide genetic differentiation in C. geophilum. Our study provides a foundation for targeted analyses of intra-specific functional variation in this major symbiosis.
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Affiliation(s)
| | - Maíra de Freitas Pereira
- Swiss Federal Research Institute WSL, Birmensdorf, Switzerland.,INRAE, UMR 1136 INRAE-University of Lorraine, Interactions Arbres/Microorganismes, Laboratory of Excellence ARBRE, INRAE-Grand Est, Champenoux, France
| | - Annegret Kohler
- INRAE, UMR 1136 INRAE-University of Lorraine, Interactions Arbres/Microorganismes, Laboratory of Excellence ARBRE, INRAE-Grand Est, Champenoux, France
| | - Igor V Grigoriev
- Department of Plant and Microbial Biology, University of California, Berkeley, USA.,U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, USA
| | - Kerrie Barry
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, USA
| | - Hyunsoo Na
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, USA
| | - Mojgan Amirebrahimi
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, USA
| | - Anna Lipzen
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, USA
| | - Francis Martin
- INRAE, UMR 1136 INRAE-University of Lorraine, Interactions Arbres/Microorganismes, Laboratory of Excellence ARBRE, INRAE-Grand Est, Champenoux, France
| | - Martina Peter
- Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
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24
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Vangalis V, Likhotkin I, Knop M, Typas MA, Papaioannou IA. Starvation-induced cell fusion and heterokaryosis frequently escape imperfect allorecognition systems in an asexual fungal pathogen. BMC Biol 2021; 19:169. [PMID: 34429100 PMCID: PMC8385987 DOI: 10.1186/s12915-021-01101-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Accepted: 07/16/2021] [Indexed: 01/02/2023] Open
Abstract
Background Asexual fungi include important pathogens of plants and other organisms, and their effective management requires understanding of their evolutionary dynamics. Genetic recombination is critical for adaptability and could be achieved via heterokaryosis — the co-existence of genetically different nuclei in a cell resulting from fusion of non-self spores or hyphae — and the parasexual cycle in the absence of sexual reproduction. Fusion between different strains and establishment of viable heterokaryons are believed to be rare due to non-self recognition systems. Here, we investigate the extent and mechanisms of cell fusion and heterokaryosis in the important asexual plant pathogen Verticillium dahliae. Results We used live-cell imaging and genetic complementation assays of tagged V. dahliae strains to analyze the extent of non-self vegetative fusion, heterokaryotic cell fate, and nuclear behavior. An efficient CRISPR/Cas9-mediated system was developed to investigate the involvement of autophagy in heterokaryosis. Under starvation, non-self fusion of germinating spores occurs frequently regardless of the previously assessed vegetative compatibility of the partners. Supposedly “incompatible” fusions often establish viable heterokaryotic cells and mosaic mycelia, where nuclei can engage in fusion or transfer of genetic material. The molecular machinery of autophagy has a protective function against the destruction of “incompatible” heterokaryons. Conclusions We demonstrate an imperfect function of somatic incompatibility systems in V. dahliae. These systems frequently tolerate the establishment of heterokaryons and potentially the initiation of the parasexual cycle even between strains that were previously regarded as “incompatible.” Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01101-5.
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Affiliation(s)
- Vasileios Vangalis
- Department of Genetics and Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Ilya Likhotkin
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
| | - Michael Knop
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany.,German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Milton A Typas
- Department of Genetics and Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
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25
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Interspecific hybridization as a driver of fungal evolution and adaptation. Nat Rev Microbiol 2021; 19:485-500. [PMID: 33767366 DOI: 10.1038/s41579-021-00537-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/22/2021] [Indexed: 02/01/2023]
Abstract
Cross-species gene transfer is often associated with bacteria, which have evolved several mechanisms that facilitate horizontal DNA exchange. However, the increased availability of whole-genome sequences has revealed that fungal species also exchange DNA, leading to intertwined lineages, blurred species boundaries or even novel species. In contrast to prokaryotes, fungal DNA exchange originates from interspecific hybridization, where two genomes are merged into a single, often highly unstable, polyploid genome that evolves rapidly into stabler derivatives. The resulting hybrids can display novel combinations of genetic and phenotypic variation that enhance fitness and allow colonization of new niches. Interspecific hybridization led to the emergence of important pathogens of humans and plants (for example, various Candida and 'powdery mildew' species, respectively) and industrially important yeasts, such as Saccharomyces hybrids that are important in the production of cold-fermented lagers or cold-cellared Belgian ales. In this Review, we discuss the genetic processes and evolutionary implications of fungal interspecific hybridization and highlight some of the best-studied examples. In addition, we explain how hybrids can be used to study molecular mechanisms underlying evolution, adaptation and speciation, and serve as a route towards development of new variants for industrial applications.
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26
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Huene AL, Chen T, Nicotra ML. New binding specificities evolve via point mutation in an invertebrate allorecognition gene. iScience 2021; 24:102811. [PMID: 34296075 PMCID: PMC8282982 DOI: 10.1016/j.isci.2021.102811] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 06/16/2021] [Accepted: 06/28/2021] [Indexed: 01/04/2023] Open
Abstract
Many organisms use genetic self-recognition systems to distinguish themselves from conspecifics. In the cnidarian, Hydractinia symbiolongicarpus, self-recognition is partially controlled by allorecognition 2 (Alr2). Alr2 encodes a highly polymorphic transmembrane protein that discriminates self from nonself by binding in trans to other Alr2 proteins with identical or similar sequences. Here, we focused on the N-terminal domain of Alr2, which can determine its binding specificity. We pair ancestral sequence reconstruction and experimental assays to show that amino acid substitutions can create sequences with novel binding specificities either directly (via one mutation) or via sequential mutations and intermediates with relaxed specificities. We also show that one side of the domain has experienced positive selection and likely forms the binding interface. Our results provide direct evidence that point mutations can generate Alr2 proteins with novel binding specificities. This provides a plausible mechanism for the generation and maintenance of functional variation in nature.
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Affiliation(s)
- Aidan L. Huene
- Thomas E. Starzl Transplantation Institute, Department of Surgery, University of Pittsburgh, Pittsburgh, PA 15260, USA
- Center for Evolutionary Biology and Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Traci Chen
- Thomas E. Starzl Transplantation Institute, Department of Surgery, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Matthew L. Nicotra
- Thomas E. Starzl Transplantation Institute, Department of Surgery, University of Pittsburgh, Pittsburgh, PA 15260, USA
- Center for Evolutionary Biology and Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15260, USA
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27
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Daskalov A, El Mammeri N, Lends A, Shenoy J, Lamon G, Fichou Y, Saad A, Martinez D, Morvan E, Berbon M, Grélard A, Kauffmann B, Ferber M, Bardiaux B, Habenstein B, Saupe SJ, Loquet A. Structures of Pathological and Functional Amyloids and Prions, a Solid-State NMR Perspective. Front Mol Neurosci 2021; 14:670513. [PMID: 34276304 PMCID: PMC8280340 DOI: 10.3389/fnmol.2021.670513] [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] [Received: 02/21/2021] [Accepted: 05/26/2021] [Indexed: 12/20/2022] Open
Abstract
Infectious proteins or prions are a remarkable class of pathogens, where pathogenicity and infectious state correspond to conformational transition of a protein fold. The conformational change translates into the formation by the protein of insoluble amyloid aggregates, associated in humans with various neurodegenerative disorders and systemic protein-deposition diseases. The prion principle, however, is not limited to pathogenicity. While pathological amyloids (and prions) emerge from protein misfolding, a class of functional amyloids has been defined, consisting of amyloid-forming domains under natural selection and with diverse biological roles. Although of great importance, prion amyloid structures remain challenging for conventional structural biology techniques. Solid-state nuclear magnetic resonance (SSNMR) has been preferentially used to investigate these insoluble, morphologically heterogeneous aggregates with poor crystallinity. SSNMR methods have yielded a wealth of knowledge regarding the fundamentals of prion biology and have helped to solve the structures of several prion and prion-like fibrils. Here, we will review pathological and functional amyloid structures and will discuss some of the obtained structural models. We will finish the review with a perspective on integrative approaches combining solid-state NMR, electron paramagnetic resonance and cryo-electron microscopy, which can complement and extend our toolkit to structurally explore various facets of prion biology.
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Affiliation(s)
- Asen Daskalov
- CNRS, CBMN UMR 5348, IECB, University of Bordeaux, Pessac, France
| | - Nadia El Mammeri
- CNRS, CBMN UMR 5348, IECB, University of Bordeaux, Pessac, France
| | - Alons Lends
- CNRS, CBMN UMR 5348, IECB, University of Bordeaux, Pessac, France
| | | | - Gaelle Lamon
- CNRS, CBMN UMR 5348, IECB, University of Bordeaux, Pessac, France
| | - Yann Fichou
- CNRS, CBMN UMR 5348, IECB, University of Bordeaux, Pessac, France
| | - Ahmad Saad
- CNRS, CBMN UMR 5348, IECB, University of Bordeaux, Pessac, France
| | - Denis Martinez
- CNRS, CBMN UMR 5348, IECB, University of Bordeaux, Pessac, France
| | - Estelle Morvan
- CNRS, INSERM, IECB, UMS 3033, University of Bordeaux, Pessac, France
| | - Melanie Berbon
- CNRS, CBMN UMR 5348, IECB, University of Bordeaux, Pessac, France
| | - Axelle Grélard
- CNRS, CBMN UMR 5348, IECB, University of Bordeaux, Pessac, France
| | - Brice Kauffmann
- CNRS, INSERM, IECB, UMS 3033, University of Bordeaux, Pessac, France
| | | | | | | | - Sven J. Saupe
- CNRS, IBGC UMR 5095, University of Bordeaux, Bordeaux, France
| | - Antoine Loquet
- CNRS, CBMN UMR 5348, IECB, University of Bordeaux, Pessac, France
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28
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Auxier B, Scholtmeijer K, van Peer AF, Baars JJP, Debets AJM, Aanen DK. Cytoplasmic Mixing, Not Nuclear Coexistence, Can Explain Somatic Incompatibility in Basidiomycetes. Microorganisms 2021; 9:1248. [PMID: 34201361 PMCID: PMC8229728 DOI: 10.3390/microorganisms9061248] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 06/03/2021] [Accepted: 06/04/2021] [Indexed: 12/03/2022] Open
Abstract
Nonself recognition leading to somatic incompatibility (SI) is commonly used by mycologists to distinguish fungal individuals. Despite this, the process remains poorly understood in basidiomycetes as all current models of SI are based on genetic and molecular research in ascomycete fungi. Ascomycete fungi are mainly found in a monokaryotic stage, with a single type of haploid nuclei, and only briefly during mating do two genomes coexist in heterokaryotic cells. The sister phylum, Basidiomycota, differs in several relevant aspects. Basidiomycete fungi have an extended heterokaryotic stage, and SI is generally observed between heterokaryons instead of between homokaryons. Additionally, considerable nuclear migration occurs during a basidiomycete mating reaction, introducing a nucleus into a resident homokaryon with cytoplasmic mixing limited to the fused or neighboring cells. To accommodate these differences, we describe a basidiomycete model for nonself recognition using post-translational modification, based on a reader-writer system as found in other organisms. This post-translational modification combined with nuclear migration allows for the coexistence of two genomes in one individual while maintaining nonself recognition during all life stages. Somewhat surprisingly, this model predicts localized cell death during mating, which is consistent with previous observations but differs from the general assumptions of basidiomycete mating. This model will help guide future research into the mechanisms behind basidiomycete nonself recognition.
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Affiliation(s)
- Ben Auxier
- Laboratory of Genetics, Wageningen University and Research, 6708 PB Wageningen, The Netherlands;
| | - Karin Scholtmeijer
- Mushroom Group, Plant Breeding Department, Wageningen University and Research, 6708 PB Wageningen, The Netherlands; (K.S.); (A.F.v.P.); (J.J.P.B.)
| | - Arend F. van Peer
- Mushroom Group, Plant Breeding Department, Wageningen University and Research, 6708 PB Wageningen, The Netherlands; (K.S.); (A.F.v.P.); (J.J.P.B.)
| | - Johan J. P. Baars
- Mushroom Group, Plant Breeding Department, Wageningen University and Research, 6708 PB Wageningen, The Netherlands; (K.S.); (A.F.v.P.); (J.J.P.B.)
- CNC Grondstoffen, P.O. Box 13, 6590 AA Gennep, The Netherlands
| | - Alfons J. M. Debets
- Laboratory of Genetics, Wageningen University and Research, 6708 PB Wageningen, The Netherlands;
| | - Duur K. Aanen
- Laboratory of Genetics, Wageningen University and Research, 6708 PB Wageningen, The Netherlands;
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29
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Paganini J, Pontarotti P. Search for MHC/TCR-Like Systems in Living Organisms. Front Immunol 2021; 12:635521. [PMID: 34017326 PMCID: PMC8129030 DOI: 10.3389/fimmu.2021.635521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 04/07/2021] [Indexed: 12/02/2022] Open
Abstract
Highly polymorphic loci evolved many times over the history of species. These polymorphic loci are involved in three types of functions: kind recognition, self-incompatibility, and the jawed vertebrate adaptive immune system (AIS). In the first part of this perspective, we reanalyzed and described some cases of polymorphic loci reported in the literature. There is a convergent evolution within each functional category and between functional categories, suggesting that the emergence of these self/non-self recognition loci has occurred multiple times throughout the evolutionary history. Most of the highly polymorphic loci are coding for proteins that have a homophilic interaction or heterophilic interaction between linked loci, leading to self or non-self-recognition. The highly polymorphic MHCs, which are involved in the AIS have a different functional mechanism, as they interact through presented self or non-self-peptides with T cell receptors, whose diversity is generated by somatic recombination. Here we propose a mechanism called “the capacity of recognition competition mechanism” that might contribute to the evolution of MHC polymorphism. We propose that the published cases corresponding to these three biological categories represent a small part of what can be found throughout the tree of life, and that similar mechanisms will be found many times, including the one where polymorphic loci interact with somatically generated loci.
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Affiliation(s)
| | - Pierre Pontarotti
- XEGEN, Gemenos, France.,Aix Marseille Université, IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France.,SNC5039 CNRS, Marseille, France
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30
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Vangalis V, Papaioannou IA, Markakis EA, Knop M, Typas MA. Hex1, the Major Component of Woronin Bodies, Is Required for Normal Development, Pathogenicity, and Stress Response in the Plant Pathogenic Fungus Verticillium dahliae. J Fungi (Basel) 2020; 6:jof6040344. [PMID: 33297524 PMCID: PMC7762394 DOI: 10.3390/jof6040344] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 11/27/2020] [Accepted: 12/03/2020] [Indexed: 12/31/2022] Open
Abstract
Woronin bodies are membrane-bound organelles of filamentous ascomycetes that mediate hyphal compartmentalization by plugging septal pores upon hyphal damage. Their major component is the peroxisomal protein Hex1, which has also been implicated in additional cellular processes in fungi. Here, we analyzed the Hex1 homolog of Verticillium dahliae, an important asexual plant pathogen, and we report its pleiotropic involvement in fungal growth, physiology, stress response, and pathogenicity. Alternative splicing of the Vdhex1 gene can lead to the production of two Hex1 isoforms, which are structurally similar to their Neurospora crassa homolog. We show that VdHex1 is targeted to the septum, consistently with its demonstrated function in sealing hyphal compartments to prevent excessive cytoplasmic bleeding upon injury. Furthermore, our investigation provides direct evidence for significant contributions of Hex1 in growth and morphogenesis, as well as in asexual reproduction capacity. We discovered that Hex1 is required both for normal responses to osmotic stress and factors that affect the cell wall and plasma-membrane integrity, and for normal resistance to oxidative stress and reactive oxygen species (ROS) homeostasis. The Vdhex1 mutant exhibited diminished ability to colonize and cause disease on eggplant. Overall, we show that Hex1 has fundamentally important multifaceted roles in the biology of V. dahliae.
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Affiliation(s)
- Vasileios Vangalis
- Department of Genetics & Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, 15784 Athens, Greece;
| | - Ioannis A. Papaioannou
- Center for Molecular Biology, Heidelberg University (ZMBH), 69120 Heidelberg, Germany; (I.A.P.); (M.K.)
| | - Emmanouil A. Markakis
- Laboratory of Mycology, Department of Viticulture, Vegetable Crops, Floriculture and Plant Protection, Institute of Olive Tree, Subtropical Crops and Viticulture, N.A.G.R.E.F., Hellenic Agricultural Organization—DEMETER, 71307 Heraklion, Crete, Greece;
| | - Michael Knop
- Center for Molecular Biology, Heidelberg University (ZMBH), 69120 Heidelberg, Germany; (I.A.P.); (M.K.)
- German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Milton A. Typas
- Department of Genetics & Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, 15784 Athens, Greece;
- Correspondence:
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31
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Jacquat AG, Theumer MG, Cañizares MC, Debat HJ, Iglesias J, García Pedrajas MD, Dambolena JS. A Survey of Mycoviral Infection in Fusarium spp. Isolated from Maize and Sorghum in Argentina Identifies the First Mycovirus from Fusarium verticillioides. Viruses 2020; 12:v12101161. [PMID: 33066620 PMCID: PMC7602464 DOI: 10.3390/v12101161] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 09/28/2020] [Accepted: 10/09/2020] [Indexed: 12/30/2022] Open
Abstract
Mycoviruses appear to be widespread in Fusarium species worldwide. The aim of this work was to identify mycoviral infections in Fusarium spp., isolated from maize and sorghum grown in Argentina, and to estimate their potential effects on the pathogenicity and toxigenesis of the host fungus towards maize. Mycoviruses were identified in 2 out of 105 isolates analyzed; Fusarium verticillioides strain Sec505 and Fusarium andiyazi strain 162. They were characterized as members of the genus Mitovirus by high-throughput sequencing and sequence analysis. The F. verticillioides mitovirus was a novel mycovirus whereas the F. andiyazi mitovirus was found to be a new strain of a previously identified mitovirus. We have named these mitoviruses, Fusarium verticillioides mitovirus 1 (FvMV1) and Fusarium andiyazi mitovirus 1 strain 162 (FaMV1-162). To our knowledge, FvMV1 is the first mycovirus reported as naturally infecting F. verticillioides, the major causal agent of ear rot and fumonisin producer in corn. Both mitoviruses exhibited 100% vertical transmission rate to microconidia. The Fa162 strain infected with FaMV1-162 did not show phenotypic alterations. In contract, F. verticillioides Sec505 infected with FvMV1 showed increased virulence as well as microconidia and fumonisin-B1 production, compared with two uninfected strains. These results suggest that FvMV1 could have a role in modulating F. verticillioides pathogenicity and toxin production worth further exploring.
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Affiliation(s)
- Andrés Gustavo Jacquat
- Facultad de Ciencias Exactas Físicas y Naturales (FCEFyN), Universidad Nacional de Córdoba (UNC), Córdoba 5000, Argentina;
- Instituto Multidisciplinario de Biología Vegetal (IMBIV), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Avenida Vélez Sarsfield 1611, Córdoba X5016GCA, Argentina
| | - Martín Gustavo Theumer
- Departamento de Bioquímica Clínica, Facultad de Ciencias Químicas (FCQ), Universidad Nacional de Córdoba (UNC), Córdoba 5000, Argentina;
- Centro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Haya de la Torre y Medina Allende—Ciudad Universitaria, Córdoba X5000HUA, Argentina
| | - María Carmen Cañizares
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM—UMA—CSIC), Estación Experimental “La Mayora”, Avenida Dr. Wienberg s/n, 29750 Algarrobo-Costa, Málaga, Spain;
| | - Humberto Julio Debat
- Instituto de Patología Vegetal, Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnología Agropecuaria (IPAVE—CIAP—INTA), Camino 60 Cuadras Km 5.5, Córdoba X5020ICA, Argentina;
| | - Juliana Iglesias
- Estación Experimental Pergamino, (EEA) INTA Pergamino, Universidad Nacional Noroeste (UNNOBA), Pergamino (Buenos Aires) B2700, Argentina;
| | - María Dolores García Pedrajas
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM—UMA—CSIC), Estación Experimental “La Mayora”, Avenida Dr. Wienberg s/n, 29750 Algarrobo-Costa, Málaga, Spain;
- Correspondence: (M.D.G.P.); (J.S.D.)
| | - José Sebastián Dambolena
- Facultad de Ciencias Exactas Físicas y Naturales (FCEFyN), Universidad Nacional de Córdoba (UNC), Córdoba 5000, Argentina;
- Instituto Multidisciplinario de Biología Vegetal (IMBIV), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Avenida Vélez Sarsfield 1611, Córdoba X5016GCA, Argentina
- Correspondence: (M.D.G.P.); (J.S.D.)
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32
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Abstract
Amyloids are implicated in many protein misfolding diseases. Amyloid folds, however, also display a range of functional roles particularly in the microbial world. The templating ability of these folds endows them with specific properties allowing their self-propagation and protein-to-protein transmission in vivo. This property, the prion principle, is exploited by specific signaling pathways that use transmission of the amyloid fold as a way to convey information from a receptor to an effector protein. I describe here amyloid signaling pathways involving fungal nucleotide binding and oligomerization domain (NOD)-like receptors that were found to control nonself recognition and programmed cell death processes. Studies on these fungal amyloid signaling motifs stem from the characterization of the fungal [Het-s] prion protein and have led to the identification in fungi but also in multicellular bacteria of several distinct families of signaling motifs, one of which is related to RHIM [receptor-interacting protein (RIP) homotypic interaction motif], an amyloid motif regulating mammalian necroptosis.
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Affiliation(s)
- Sven J. Saupe
- Institut de Biochimie et de Génétique Cellulaire, UMR 5095 CNRS, Université de Bordeaux, 33077 Bordeaux CEDEX, France
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33
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Gonçalves AP, Heller J, Rico-Ramírez AM, Daskalov A, Rosenfield G, Glass NL. Conflict, Competition, and Cooperation Regulate Social Interactions in Filamentous Fungi. Annu Rev Microbiol 2020; 74:693-712. [PMID: 32689913 DOI: 10.1146/annurev-micro-012420-080905] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Social cooperation impacts the development and survival of species. In higher taxa, kin recognition occurs via visual, chemical, or tactile cues that dictate cooperative versus competitive interactions. In microbes, the outcome of cooperative versus competitive interactions is conferred by identity at allorecognition loci, so-called kind recognition. In syncytial filamentous fungi, the acquisition of multicellularity is associated with somatic cell fusion within and between colonies. However, such intraspecific cooperation entails risks, as fusion can transmit deleterious genotypes or infectious components that reduce fitness, or give rise to cheaters that can exploit communal goods without contributing to their production. Allorecognition mechanisms in syncytial fungi regulate somatic cell fusion by operating precontact during chemotropic interactions, during cell adherence, and postfusion by triggering programmed cell death reactions. Alleles at fungal allorecognition loci are highly polymorphic, fall into distinct haplogroups, and show evolutionary signatures of balancing selection, similar to allorecognition loci across the tree of life.
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Affiliation(s)
- A Pedro Gonçalves
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA.,Current Affiliation: Institute of Molecular Biology, Academia Sinica, Nangang District, Taipei 115, Taiwan
| | - Jens Heller
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA.,Current Affiliation: Perfect Day, Inc., Emeryville, California 94608, USA
| | - Adriana M Rico-Ramírez
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
| | - Asen Daskalov
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA.,Current Affiliation: Institut Européen de Chimie et Biologie, 33600 Pessac, France
| | - Gabriel Rosenfield
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA.,Current Affiliation: Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - N Louise Glass
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
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Tsakou-Ngouafo L, Paganini J, Kaufman J, Pontarotti P. Origins of the RAG Transposome and the MHC. Trends Immunol 2020; 41:561-571. [PMID: 32467030 DOI: 10.1016/j.it.2020.05.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 05/04/2020] [Accepted: 05/06/2020] [Indexed: 01/12/2023]
Abstract
How innate immunity gave rise to adaptive immunity in vertebrates remains unknown. We propose an evolutionary scenario beginning with pathogen-associated molecular pattern(s) (PAMPs) being presented by molecule(s) on one cell to specific receptor(s) on other cells, much like MHC molecules and T cell receptors (TCRs). In this model, mutations in MHC-like molecule(s) that bound new PAMP(s) would not be recognized by original TCR-like molecule(s), and new MHC-like gene(s) would be lost by neutral drift. Integrating recombination activating gene (RAG) transposon(s) in a TCR-like gene would result in greater recognition diversity, with new MHC-like variants recognized and selected, along with a new RAG/TCR-like system. MHC genes would be selected to present many peptides, through multigene families, allelic polymorphism, and peptide-binding promiscuity.
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Affiliation(s)
- Louis Tsakou-Ngouafo
- Aix Marseille University IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille France 3, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
| | | | - Jim Kaufman
- University of Cambridge, Department of Pathology, Tennis Court Road, Cambridge CB2 1QP, UK; University of Cambridge, Department of Veterinary Medicine, Madingley Road, Cambridge CB2 0ES, UK; University of Edinburgh, Institute for Immunology and Infection Research, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK.
| | - Pierre Pontarotti
- Aix Marseille University IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille France 3, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; SNC5039 CNRS, 19-21 Boulevard Jean Moulin, 13005 Marseilles, France.
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Plaumann PL, Koch C. The Many Questions about Mini Chromosomes in Colletotrichum spp. PLANTS 2020; 9:plants9050641. [PMID: 32438596 PMCID: PMC7284448 DOI: 10.3390/plants9050641] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/08/2020] [Accepted: 05/14/2020] [Indexed: 11/16/2022]
Abstract
Many fungal pathogens carry accessory regions in their genome, which are not required for vegetative fitness. Often, although not always, these regions occur as relatively small chromosomes in different species. Such mini chromosomes appear to be a typical feature of many filamentous plant pathogens. Since these regions often carry genes coding for effectors or toxin-producing enzymes, they may be directly related to virulence of the respective pathogen. In this review, we outline the situation of small accessory chromosomes in the genus Colletotrichum, which accounts for ecologically important plant diseases. We summarize which species carry accessory chromosomes, their gene content, and chromosomal makeup. We discuss the large variation in size and number even between different isolates of the same species, their potential roles in host range, and possible mechanisms for intra- and interspecies exchange of these interesting genetic elements.
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Daskalov A, Gladieux P, Heller J, Glass NL. Programmed Cell Death in Neurospora crassa Is Controlled by the Allorecognition Determinant rcd-1. Genetics 2019; 213:1387-1400. [PMID: 31636083 PMCID: PMC6893366 DOI: 10.1534/genetics.119.302617] [Citation(s) in RCA: 29] [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: 08/11/2019] [Accepted: 10/17/2019] [Indexed: 12/31/2022] Open
Abstract
Nonself recognition following cell fusion between genetically distinct individuals of the same species in filamentous fungi often results in a programmed cell death (PCD) reaction, where the heterokaryotic fusion cell is compartmentalized and rapidly killed. The allorecognition process plays a key role as a defense mechanism that restricts genome exploitation, resource plundering, and the spread of deleterious senescence plasmids and mycoviruses. Although a number of incompatibility systems have been described that function in mature hyphae, less is known about the PCD pathways in asexual spores, which represent the main infectious unit in various human and plant fungal pathogens. Here, we report the identification of regulator of cell death-1 (rcd-1), a novel allorecognition gene, controlling PCD in germinating asexual spores of Neurospora crassa; rcd-1 is one of the most polymorphic genes in the genomes of wild N. crassa isolates. The coexpression of two antagonistic rcd-1-1 and rcd-1-2 alleles was necessary and sufficient to trigger cell death in fused germlings and in hyphae. Based on analysis of wild populations of N. crassa and N. discreta, rcd-1 alleles appeared to be under balancing selection and associated with trans-species polymorphisms. We shed light on genomic rearrangements that could have led to the emergence of the incompatibility system in Neurospora and show that rcd-1 belongs to a much larger gene family in fungi. Overall, our work contributes toward a better understanding of allorecognition and PCD in an underexplored developmental stage of filamentous fungi.
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Affiliation(s)
- Asen Daskalov
- Plant and Microbial Biology Department, The University of California, Berkeley, California 94720
| | - Pierre Gladieux
- UMR BGPI, INRA, CIRAD, Montpellier SupAgro, University Montpellier, 34060, France
| | - Jens Heller
- Plant and Microbial Biology Department, The University of California, Berkeley, California 94720
- Environmental Genomics and Systems Biology Division, The Lawrence Berkeley National Laboratory, California 94720
| | - N Louise Glass
- Plant and Microbial Biology Department, The University of California, Berkeley, California 94720
- Environmental Genomics and Systems Biology Division, The Lawrence Berkeley National Laboratory, California 94720
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37
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Abstract
Fungi can fuse with other individuals to enable cooperative growth, although this process is restricted by certain self/non-self recognition systems. A novel layer of compatibility has now been discovered, acting at the stage of germling cell wall fusion, showing the remarkable complexity of allorecognition in fungi.
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Affiliation(s)
- Paul S Dyer
- School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK.
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38
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Allorecognition upon Fungal Cell-Cell Contact Determines Social Cooperation and Impacts the Acquisition of Multicellularity. Curr Biol 2019; 29:3006-3017.e3. [PMID: 31474536 DOI: 10.1016/j.cub.2019.07.060] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Revised: 07/16/2019] [Accepted: 07/19/2019] [Indexed: 12/18/2022]
Abstract
Somatic cell fusion and conspecific cooperation are crucial social traits for microbial unicellular-to-multicellular transitions, colony expansion, and substrate foraging but are also associated with risks of parasitism. We identified a cell wall remodeling (cwr) checkpoint that acts upon cell contact to assess genetic compatibility and regulate cell wall dissolution during somatic cell fusion in a wild population of the filamentous fungus Neurospora crassa. Non-allelic interactions between two linked loci, cwr-1 and cwr-2, were necessary and sufficient to block cell fusion: cwr-1 encodes a polysaccharide monooxygenase (PMO), a class of enzymes associated with extracellular degradative capacities, and cwr-2 encodes a predicted transmembrane protein. Mutations of sites in CWR-1 essential for PMO catalytic activity abolished the block in cell fusion between formerly incompatible strains. In Neurospora, alleles cwr-1 and cwr-2 were highly polymorphic, fell into distinct haplogroups, and showed trans-species polymorphisms. Distinct haplogroups and trans-species polymorphisms at cwr-1 and cwr-2 were also identified in the distantly related genus Fusarium, suggesting convergent evolution. Proteins involved in chemotropic processes showed extended localization at contact sites, suggesting that cwr regulates the transition between chemotropic growth and cell wall dissolution. Our work revealed an allorecognition surveillance system based on kind discrimination that inhibits cooperative behavior in fungi by blocking cell fusion upon contact, contributing to fungal immunity by preventing formation of chimeras between genetically non-identical colonies.
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Mori N, Katayama T, Saito R, Iwashita K, Maruyama JI. Inter-strain expression of sequence-diverse HET domain genes severely inhibits growth of Aspergillus oryzae. Biosci Biotechnol Biochem 2019; 83:1557-1569. [DOI: 10.1080/09168451.2019.1580138] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
ABSTRACT
In the Pezizomycotina (filamentous ascomycete) species, genes that encode proteins with an HET domain (Pfam: PF06985) are reportedly involved in heterokaryon incompatibility (HI) in which cell death or growth defects are induced after fusion of cells that are genetically incompatible owing to diversities in their nucleotide sequence. HET domain genes are commonly found in Pezizomycotina genomes and are functionally characterized in only a few species. Here, we compared 44 HET domain genes between an incompatible strain pair of Aspergillus oryzae RIB40 and RIB128 and performed inter-strain expression of 37 sequence-diverse genes for mimicking HI. Four HET domain genes were identified to cause severe growth inhibition in a strain- or sequence-specific manner. Furthermore, SNPs responsible for the inhibition of cell growth were identified. This study provides an important insight into the physiological significance of sequence diversity of HET domain genes and their potential functions in HI of A. oryzae.
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Affiliation(s)
- Noriko Mori
- Department of Biotechnology, The University of Tokyo, Tokyo, Japan
| | - Takuya Katayama
- Department of Biotechnology, The University of Tokyo, Tokyo, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
| | - Ryota Saito
- Division of Fundamental Research, National Research Institute of Brewing (NRIB), Hiroshima, Japan
| | - Kazuhiro Iwashita
- Division of Fundamental Research, National Research Institute of Brewing (NRIB), Hiroshima, Japan
| | - Jun-ichi Maruyama
- Department of Biotechnology, The University of Tokyo, Tokyo, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
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40
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The mitochondrial translocase of the inner membrane PaTim54 is involved in defense response and longevity in Podospora anserina. Fungal Genet Biol 2019; 132:103257. [PMID: 31351193 DOI: 10.1016/j.fgb.2019.103257] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 06/26/2019] [Accepted: 07/22/2019] [Indexed: 11/20/2022]
Abstract
Fungi are very successful microorganisms capable of colonizing virtually any ecological niche where they must constantly cope with competitors including fungi, bacteria and nematodes. We have shown previously that the ascomycete Podopora anserina exhibits Hyphal Interference (HI), an antagonistic response triggered by direct contact of competing fungal hyphae. When challenged with Penicillium chrysogenum, P. anserina produces hydrogen peroxide at the confrontation and kills the hyphae of P. chrysogenum. Here, we report the characterization of the PDC2218 mutant affected in HI. When challenged with P. chrysogenum, the PDC2218 mutant produces a massive oxidative burst at the confrontation. However, this increased production of hydrogen peroxide is not correlated to increased cell death in P. chrysogenum. Hence, the oxidative burst and cell death in the challenger are uncoupled in PDC2218. The gene affected in PDC2218 is PaTim54, encoding the homologue of the budding yeast mitochondrial inner membrane import machinery component Tim54p. We show that PaTim54 is essential in P. anserina and that the phenotypes displayed by the PDC2218 mutant, renamed PaTim542218, are the consequence of a drastic reduction in the expression of PaTim54. Among these pleiotropic phenotypes, PDC2218-PaTim542218- displays increased lifespan, a phenotype in line with the observed mitochondrial defects in the mutant.
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Bertazzoni S, Williams AH, Jones DA, Syme RA, Tan KC, Hane JK. Accessories Make the Outfit: Accessory Chromosomes and Other Dispensable DNA Regions in Plant-Pathogenic Fungi. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2018; 31:779-788. [PMID: 29664319 DOI: 10.1094/mpmi-06-17-0135-fi] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Fungal pathogen genomes can often be divided into core and accessory regions. Accessory regions ARs) may be comprised of either ARs (within core chromosomes (CCs) or wholly dispensable (accessory) chromosomes (ACs). Fungal ACs and ARs typically accumulate mutations and structural rearrangements more rapidly over time than CCs and many harbor genes relevant to host-pathogen interactions. These regions are of particular interest in plant pathology and include host-specific virulence factors and secondary metabolite synthesis gene clusters. This review outlines known ACs and ARs in fungal genomes, methods used for their detection, their common properties that differentiate them from the core genome, and what is currently known of their various roles in pathogenicity. Reports on the evolutionary processes generating and shaping AC and AR compartments are discussed, including repeat induced point mutation and breakage fusion bridge cycles. Previously ACs have been studied extensively within key genera, including Fusarium, Zymoseptoria, and Alternaria, but are growing in frequency of observation and perceived importance across a wider range of fungal species. Recent advances in sequencing technologies permit affordable genome assembly and resequencing of populations that will facilitate further discovery and routine screening of ACs.
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Affiliation(s)
- Stefania Bertazzoni
- 1 Centre for Crop & Disease Management, Curtin University, Perth, Western Australia, Australia; and
| | - Angela H Williams
- 1 Centre for Crop & Disease Management, Curtin University, Perth, Western Australia, Australia; and
| | - Darcy A Jones
- 1 Centre for Crop & Disease Management, Curtin University, Perth, Western Australia, Australia; and
| | - Robert A Syme
- 1 Centre for Crop & Disease Management, Curtin University, Perth, Western Australia, Australia; and
| | - Kar-Chun Tan
- 1 Centre for Crop & Disease Management, Curtin University, Perth, Western Australia, Australia; and
| | - James K Hane
- 1 Centre for Crop & Disease Management, Curtin University, Perth, Western Australia, Australia; and
- 2 Curtin Institute for Computation, Curtin University, Perth, Western Australia, Australia
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Sbrana C, Strani P, Pepe A, de Novais CB, Giovannetti M. Divergence of Funneliformis mosseae populations over 20 years of laboratory cultivation, as revealed by vegetative incompatibility and molecular analysis. MYCORRHIZA 2018; 28:329-341. [PMID: 29574495 DOI: 10.1007/s00572-018-0830-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 03/13/2018] [Indexed: 06/08/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) are widespread, important plant symbionts. They absorb and translocate mineral nutrients from the soil to host plants through an extensive extraradical mycelium, consisting of indefinitely large networks of nonseptate, multinucleated hyphae which may be interconnected by hyphal fusions (anastomoses). This work investigated whether different lineages of the same isolate may lose the ability to establish successful anastomoses, becoming vegetatively incompatible, when grown separately. The occurrence of hyphal incompatibility among five lineages of Funneliformis mosseae, originated from the same ancestor isolate and grown in vivo for more than 20 years in different European locations, was assessed by systematic detection of anastomosis frequency and cytological studies. Anastomosis frequencies ranged from 60 to 80% within the same lineage and from 17 to 44% among different lineages. The consistent detection of protoplasm continuity and nuclei in perfect fusions showed active protoplasm flow both within and between lineages. In pairings between different lineages, post-fusion incompatible reactions occurred in 6-48% of hyphal contacts and pre-fusion incompatibility in 2-17%. Molecular fingerprinting profiles showed genetic divergence among lineages, with overall Jaccard similarity indices ranging from 0.85 to 0.95. Here, phenotypic divergence among the five F. mosseae lineages was demonstrated by the reduction of their ability to form anastomosis and the detection of high levels of vegetative incompatibility. Our data suggest that potential genetic divergence may occur in AMF over only 20 years and represent the basis for detailed studies on the relationship between genes regulating anastomosis formation and hyphal compatibility in AMF.
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Affiliation(s)
- Cristiana Sbrana
- CNR-Institute of Agricultural Biology and Biotechnology, UOS Pisa, Pisa, Italy.
| | - Patrizia Strani
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Alessandra Pepe
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Candido Barreto de Novais
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
- Forestry Institute, Federal Rural University of Rio de Janeiro, Seropédica, Brazil
| | - Manuela Giovannetti
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
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BiFC-based visualisation system reveals cell fusion morphology and heterokaryon incompatibility in the filamentous fungus Aspergillus oryzae. Sci Rep 2018; 8:2922. [PMID: 29440689 PMCID: PMC5811552 DOI: 10.1038/s41598-018-21323-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 02/01/2018] [Indexed: 12/13/2022] Open
Abstract
Aspergillus oryzae is an industrially important filamentous fungus used for Japanese traditional food fermentation and heterologous protein production. Although cell fusion is important for heterokaryon formation and sexual/parasexual reproduction required for cross breeding, knowledge on cell fusion and heterokaryon incompatibility in A. oryzae is limited because of low cell fusion frequency. Therefore, we aimed to develop a BiFC system to specifically visualise fused cells and facilitate the analysis of cell fusion in A. oryzae. The cell fusion ability and morphology of 15 A. oryzae strains were investigated using heterodimerising proteins LZA and LZB fused with split green fluorescence protein. Morphological investigation of fused cells revealed that cell fusion occurred mainly as conidial anastomosis during the early growth stage. Self-fusion abilities were detected in most industrial A. oryzae strains, but only a few strain pairs showed non-self fusion. Protoplast fusion assay demonstrated that almost all the pairs capable of non-self fusion were capable of heterokaryon formation and vice versa, thus providing the first evidence of heterokaryon incompatibility in A. oryzae. The BiFC system developed in this study provides an effective method in studying morphology of fused cells and heterokaryon incompatibility in the filamentous fungal species with low cell fusion efficiency.
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Sahin E, Akata I. Viruses infecting macrofungi. Virusdisease 2018; 29:1-18. [PMID: 29607353 DOI: 10.1007/s13337-018-0434-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 01/25/2018] [Indexed: 11/26/2022] Open
Abstract
Ever since their discovery just about 56 years ago in the cultivated mushroom Agaricus bisporus, many more viruses infecting fungi have been identified in a wide range of fungal taxa. With mostly being asymptomatic, especially the ones that are detrimental to their phytopathogenic hosts are intensively studied due to their considerable importance in developing novel plant protection measures. Contrary to the rapid accumulation of notable data on viruses of plant pathogenic microfungi, much less information have hitherto been obtained in regards to the viruses whose hosts are macrofungi. According to the current literature, only more than 80 distinct viruses bearing either linear dsRNA or linear positive sense ssRNA genome and infecting a total number of 34 macrofungal species represented with four Ascomycota and 30 Basidiomycota have been identified so far. Among these 34 macrofungal species, 14 are cultivated edible and wild edible mushroom species. According to the 10th ICTV (International Committee on Taxonomy of Viruses) Report, macrofungal viruses with linear dsRNA genome are classified into five families (Partitiviridae, Totiviridae, Chrysoviridae, Endornaviridae and Hypoviridae) and macrofungal viruses with linear positive sense ssRNA genome are classified into seven families (Betaflexiviridae, Gammaflexiviridae, Barnaviridae, Narnaviridae, Virgaviridae, Benyviridae and Tymoviridae). In this review, following a brief overview of some general characteristics of fungal viruses, an up to date knowledge on viruses infecting macrofungal hosts were presented by summarizing the previous, recent and prospective studies of the field.
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Affiliation(s)
- Ergin Sahin
- Faculty of Science, Department of Biology, Ankara University, Ankara, Turkey
| | - Ilgaz Akata
- Faculty of Science, Department of Biology, Ankara University, Ankara, Turkey
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Do fungi have an innate immune response? An NLR-based comparison to plant and animal immune systems. PLoS Pathog 2017; 13:e1006578. [PMID: 29073287 PMCID: PMC5658179 DOI: 10.1371/journal.ppat.1006578] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
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