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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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Clavé C, Dheur S, Ament-Velásquez SL, Granger-Farbos A, Saupe SJ. het-B allorecognition in Podospora anserina is determined by pseudo-allelic interaction of genes encoding a HET and lectin fold domain protein and a PII-like protein. PLoS Genet 2024; 20:e1011114. [PMID: 38346076 PMCID: PMC10890737 DOI: 10.1371/journal.pgen.1011114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 02/23/2024] [Accepted: 01/29/2024] [Indexed: 02/25/2024] Open
Abstract
Filamentous fungi display allorecognition genes that trigger regulated cell death (RCD) when strains of unlike genotype fuse. Podospora anserina is one of several model species for the study of this allorecognition process termed heterokaryon or vegetative incompatibility. Incompatibility restricts transmission of mycoviruses between isolates. In P. anserina, genetic analyses have identified nine incompatibility loci, termed het loci. Here we set out to clone the genes controlling het-B incompatibility. het-B displays two incompatible alleles, het-B1 and het-B2. We find that the het-B locus encompasses two adjacent genes, Bh and Bp that exist as highly divergent allelic variants (Bh1/Bh2 and Bp1/Bp2) in the incompatible haplotypes. Bh encodes a protein with an N-terminal HET domain, a cell death inducing domain bearing homology to Toll/interleukin-1 receptor (TIR) domains and a C-terminal domain with a predicted lectin fold. The Bp product is homologous to PII-like proteins, a family of small trimeric proteins acting as sensors of adenine nucleotides in bacteria. We show that although the het-B system appears genetically allelic, incompatibility is in fact determined by the non-allelic Bh1/Bp2 interaction while the reciprocal Bh2/Bp1 interaction plays no role in incompatibility. The highly divergent C-terminal lectin fold domain of BH determines recognition specificity. Population studies and genome analyses indicate that het-B is under balancing selection with trans-species polymorphism, highlighting the evolutionary significance of the two incompatible haplotypes. In addition to emphasizing anew the central role of TIR-like HET domains in fungal RCD, this study identifies novel players in fungal allorecognition and completes the characterization of the entire het gene set in that species.
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Affiliation(s)
- Corinne Clavé
- IBGC, UMR 5095, CNRS-Université de Bordeaux, Bordeaux, France
| | - Sonia Dheur
- IBGC, UMR 5095, CNRS-Université de Bordeaux, Bordeaux, France
| | | | | | - Sven J. Saupe
- IBGC, UMR 5095, CNRS-Université de Bordeaux, Bordeaux, France
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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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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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Comparative genomic analysis reveals contraction of gene families with putative roles in pathogenesis in the fungal boxwood pathogens Calonectria henricotiae and C. pseudonaviculata. BMC Ecol Evol 2022; 22:79. [PMID: 35725368 PMCID: PMC9210730 DOI: 10.1186/s12862-022-02035-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 06/08/2022] [Indexed: 11/23/2022] Open
Abstract
Background Boxwood blight disease caused by Calonectria henricotiae and C. pseudonaviculata is of ecological and economic significance in cultivated and native ecosystems worldwide. Prior research has focused on understanding the population genetic and genomic diversity of C. henricotiae and C. pseudonaviculata, but gene family evolution in the context of host adaptation, plant pathogenesis, and trophic lifestyle is poorly understood. This study applied bioinformatic and phylogenetic methods to examine gene family evolution in C. henricotiae, C. pseudonaviculata and 22 related fungi in the Nectriaceae that vary in pathogenic and saprobic (apathogenic) lifestyles. Results A total of 19,750 gene families were identified in the 24 genomes, of which 422 were rapidly evolving. Among the six Calonectria species, C. henricotiae and C. pseudonaviculata were the only species to experience high levels of rapid contraction of pathogenesis-related gene families (89% and 78%, respectively). In contrast, saprobic species Calonectria multiphialidica and C. naviculata, two of the closest known relatives of C. henricotiae and C. pseudonaviculata, showed rapid expansion of pathogenesis-related gene families. Conclusions Our results provide novel insight into gene family evolution within C. henricotiae and C. pseudonaviculata and suggest gene family contraction may have contributed to limited host-range expansion of these pathogens within the plant family Buxaceae. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-022-02035-4.
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Ament-Velásquez SL, Vogan AA, Granger-Farbos A, Bastiaans E, Martinossi-Allibert I, Saupe SJ, de Groot S, Lascoux M, Debets AJM, Clavé C, Johannesson H. Allorecognition genes drive reproductive isolation in Podospora anserina. Nat Ecol Evol 2022; 6:910-923. [PMID: 35551248 PMCID: PMC9262711 DOI: 10.1038/s41559-022-01734-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 03/15/2022] [Indexed: 11/09/2022]
Abstract
Allorecognition, the capacity to discriminate self from conspecific non-self, is a ubiquitous organismal feature typically governed by genes evolving under balancing selection. Here, we show that in the fungus Podospora anserina, allorecognition loci controlling vegetative incompatibility (het genes), define two reproductively isolated groups through pleiotropic effects on sexual compatibility. These two groups emerge from the antagonistic interactions of the unlinked loci het-r (encoding a NOD-like receptor) and het-v (encoding a methyltransferase and an MLKL/HeLo domain protein). Using a combination of genetic and ecological data, supported by simulations, we provide a concrete and molecularly defined example whereby the origin and coexistence of reproductively isolated groups in sympatry is driven by pleiotropic genes under balancing selection.
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Affiliation(s)
- S Lorena Ament-Velásquez
- Systematic Biology, Department of Organismal Biology, Uppsala University, Uppsala, Sweden. .,Department of Zoology, Stockholm University, Stockholm, Sweden.
| | - Aaron A Vogan
- Systematic Biology, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Alexandra Granger-Farbos
- Institut de Biochimie et de Génétique Cellulaires, UMR 5095, CNRS, Université de Bordeaux, Bordeaux, France
| | - Eric Bastiaans
- Systematic Biology, Department of Organismal Biology, Uppsala University, Uppsala, Sweden.,Laboratory of Genetics, Wageningen University & Research, Wageningen, the Netherlands
| | - Ivain Martinossi-Allibert
- Systematic Biology, Department of Organismal Biology, Uppsala University, Uppsala, Sweden.,Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Sven J Saupe
- Institut de Biochimie et de Génétique Cellulaires, UMR 5095, CNRS, Université de Bordeaux, Bordeaux, France
| | - Suzette de Groot
- Laboratory of Genetics, Wageningen University & Research, Wageningen, the Netherlands
| | - Martin Lascoux
- Plant Ecology and Evolution, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Alfons J M Debets
- Laboratory of Genetics, Wageningen University & Research, Wageningen, the Netherlands
| | - Corinne Clavé
- Institut de Biochimie et de Génétique Cellulaires, UMR 5095, CNRS, Université de Bordeaux, Bordeaux, France
| | - Hanna Johannesson
- Systematic Biology, Department of Organismal Biology, Uppsala University, Uppsala, Sweden.
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Rico-Ramírez AM, Pedro Gonçalves A, Louise Glass N. Fungal Cell Death: The Beginning of the End. Fungal Genet Biol 2022; 159:103671. [PMID: 35150840 DOI: 10.1016/j.fgb.2022.103671] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 01/04/2022] [Accepted: 01/29/2022] [Indexed: 11/04/2022]
Abstract
Death is an important part of an organism's existence and also marks the end of life. On a cellular level, death involves the execution of complex processes, which can be classified into different types depending on their characteristics. Despite their "simple" lifestyle, fungi carry out highly specialized and sophisticated mechanisms to regulate the way their cells die, and the pathways underlying these mechanisms are comparable with those of plants and metazoans. This review focuses on regulated cell death in fungi and discusses the evidence for the occurrence of apoptotic-like, necroptosis-like, pyroptosis-like death, and the role of the NLR proteins in fungal cell death. We also describe recent data on meiotic drive elements involved in "spore killing" and the molecular basis of allorecognition-related cell death during cell fusion of genetically dissimilar cells. Finally, we discuss how fungal regulated cell death can be relevant in developing strategies to avoid resistance and tolerance to antifungal agents.
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Affiliation(s)
- Adriana M Rico-Ramírez
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720
| | - A Pedro Gonçalves
- Department of Cell Biology and Anatomy, College of Medicine, National Cheng Kung University, Tainan City, 701, Taiwan
| | - N Louise Glass
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720.
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Dyrka W, Coustou V, Daskalov A, Lends A, Bardin T, Berbon M, Kauffmann B, Blancard C, Salin B, Loquet A, Saupe SJ. Identification of NLR-associated Amyloid Signaling Motifs in Bacterial Genomes. J Mol Biol 2020; 432:6005-6027. [PMID: 33058872 DOI: 10.1016/j.jmb.2020.10.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 10/05/2020] [Accepted: 10/05/2020] [Indexed: 02/06/2023]
Abstract
In filamentous fungi, amyloid signaling sequences allow Nod-like receptors (NLRs) to activate downstream cell-death inducing proteins with HeLo and HeLo-like (HELL) domains and amyloid RHIM and RHIM-related motifs control immune defense pathways in mammals and flies. Herein, we show bioinformatically that analogous amyloid signaling motifs exist in bacteria. These short motifs are found at the N terminus of NLRs and at the C terminus of proteins with a domain we term BELL. The corresponding NLR and BELL proteins are encoded by adjacent genes. We identify 10 families of such bacterial amyloid signaling sequences (BASS), one of which (BASS3) is homologous to RHIM and a fungal amyloid motif termed PP. BASS motifs occur nearly exclusively in bacteria forming multicellular structures (mainly in Actinobacteria and Cyanobacteria). We analyze experimentally a subset of seven of these motifs (from the most common BASS1 family and the RHIM-related BASS3 family) and find that these sequences form fibrils in vitro. Using a fungal in vivo model, we show that all tested BASS-motifs form prions and that the NLR-side motifs seed prion-formation of the corresponding BELL-side motif. We find that BASS3 motifs show partial prion cross-seeding with mammalian RHIM and fungal PP-motifs and that proline mutations on key positions of the BASS3 core motif, conserved in RHIM and PP-motifs, abolish prion formation. This work expands the paradigm of prion amyloid signaling to multicellular prokaryotes and suggests a long-term evolutionary conservation of these motifs from bacteria, to fungi and animals.
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Affiliation(s)
- Witold Dyrka
- Politechnika Wrocławska, Wydział Podstawowych Problemów Techniki, Katedra Inżynierii Biomedycznej, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Virginie Coustou
- Non-self Recognition in Fungi, Institut de Biochimie et de Génétique Cellulaire, UMR 5095 CNRS, Université de Bordeaux, 1 Rue Camille Saint Saëns, 33077 Bordeaux CEDEX, France
| | - Asen Daskalov
- Institute of Chemistry & Biology of Membranes & Nanoobjects, UMR5248 CBMN, IECB, CNRS, Université de Bordeaux, Allee Geoffroy Saint-Hilaire, 33607 Pessac, France
| | - Alons Lends
- Institute of Chemistry & Biology of Membranes & Nanoobjects, UMR5248 CBMN, IECB, CNRS, Université de Bordeaux, Allee Geoffroy Saint-Hilaire, 33607 Pessac, France
| | - Thierry Bardin
- Non-self Recognition in Fungi, Institut de Biochimie et de Génétique Cellulaire, UMR 5095 CNRS, Université de Bordeaux, 1 Rue Camille Saint Saëns, 33077 Bordeaux CEDEX, France
| | - Mélanie Berbon
- Institut de Biochimie et de Génétique Cellulaire, UMR 5095 CNRS, Université de Bordeaux, 1 Rue Camille Saint Saëns, 33077 Bordeaux CEDEX, France
| | - Brice Kauffmann
- IECB, UMS 3033, US 001, CNRS, Université de Bordeaux, 2 Rue Robert Escarpit, 33607 Pessac, France
| | - Corinne Blancard
- Institut de Biochimie et de Génétique Cellulaire, UMR 5095 CNRS, Université de Bordeaux, 1 Rue Camille Saint Saëns, 33077 Bordeaux CEDEX, France
| | - Bénédicte Salin
- Institut de Biochimie et de Génétique Cellulaire, UMR 5095 CNRS, Université de Bordeaux, 1 Rue Camille Saint Saëns, 33077 Bordeaux CEDEX, France
| | - Antoine Loquet
- Institute of Chemistry & Biology of Membranes & Nanoobjects, UMR5248 CBMN, IECB, CNRS, Université de Bordeaux, Allee Geoffroy Saint-Hilaire, 33607 Pessac, France
| | - Sven J Saupe
- Non-self Recognition in Fungi, Institut de Biochimie et de Génétique Cellulaire, UMR 5095 CNRS, Université de Bordeaux, 1 Rue Camille Saint Saëns, 33077 Bordeaux CEDEX, France.
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Abstract
Numerous cell death-controlling genes have been identified in fungi, especially in the context of conspecific nonself discrimination (allorecognition). However, our understanding of the molecular mechanisms by which these genes trigger programmed cell death (PCD) is limited, as is our knowledge about their relation to PCD pathways in other major eukaryotic kingdoms. Here, we show that the cell death-inducing RCD-1 protein from Neurospora crassa is related to the cytotoxic N-terminal domain of gasdermin, which is the executioner of inflammatory cell death reaction in mammals termed pyroptosis. Our work documents an evolutionary transkingdom relationship of cell death execution proteins between fungi and animals. Programmed cell death (PCD) in filamentous fungi prevents cytoplasmic mixing following fusion between conspecific genetically distinct individuals (allorecognition) and serves as a defense mechanism against mycoparasitism, genome exploitation, and deleterious cytoplasmic elements (i.e., senescence plasmids). Recently, we identified regulatorof cell death-1 (rcd-1), a gene controlling PCD in germinated asexual spores in the filamentous fungus Neurospora crassa. rcd-1 alleles are highly polymorphic and fall into two haplogroups in N. crassa populations. Coexpression of alleles from the two haplogroups, rcd-1–1 and rcd-1–2, is necessary and sufficient to trigger a cell death reaction. Here, we investigated the molecular bases of rcd-1-dependent cell death. Based on in silico analyses, we found that RCD-1 is a remote homolog of the N-terminal pore-forming domain of gasdermin, the executioner protein of a highly inflammatory cell death reaction termed pyroptosis, which plays a key role in mammalian innate immunity. We show that RCD-1 localizes to the cell periphery and that cellular localization of RCD-1 was correlated with conserved positively charged residues on predicted amphipathic α-helices, as shown for murine gasdermin-D. Similar to gasdermin, RCD-1 binds acidic phospholipids in vitro, notably, cardiolipin and phosphatidylserine, and interacts with liposomes containing such lipids. The RCD-1 incompatibility system was reconstituted in human 293T cells, where coexpression of incompatible rcd-1–1/rcd-1–2 alleles triggered pyroptotic-like cell death. Oligomers of RCD-1 were associated with the cell death reaction, further supporting the evolutionary relationship between gasdermin and rcd-1. This report documents an ancient transkingdom relationship of cell death execution modules involved in organismal defense.
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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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12
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Kubicek CP, Steindorff AS, Chenthamara K, Manganiello G, Henrissat B, Zhang J, Cai F, Kopchinskiy AG, Kubicek EM, Kuo A, Baroncelli R, Sarrocco S, Noronha EF, Vannacci G, Shen Q, Grigoriev IV, Druzhinina IS. Evolution and comparative genomics of the most common Trichoderma species. BMC Genomics 2019; 20:485. [PMID: 31189469 PMCID: PMC6560777 DOI: 10.1186/s12864-019-5680-7] [Citation(s) in RCA: 121] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Accepted: 04/09/2019] [Indexed: 12/31/2022] Open
Abstract
Background The growing importance of the ubiquitous fungal genus Trichoderma (Hypocreales, Ascomycota) requires understanding of its biology and evolution. Many Trichoderma species are used as biofertilizers and biofungicides and T. reesei is the model organism for industrial production of cellulolytic enzymes. In addition, some highly opportunistic species devastate mushroom farms and can become pathogens of humans. A comparative analysis of the first three whole genomes revealed mycoparasitism as the innate feature of Trichoderma. However, the evolution of these traits is not yet understood. Results We selected 12 most commonly occurring Trichoderma species and studied the evolution of their genome sequences. Trichoderma evolved in the time of the Cretaceous-Palaeogene extinction event 66 (±15) mya, but the formation of extant sections (Longibrachiatum, Trichoderma) or clades (Harzianum/Virens) happened in Oligocene. The evolution of the Harzianum clade and section Trichoderma was accompanied by significant gene gain, but the ancestor of section Longibrachiatum experienced rapid gene loss. The highest number of genes gained encoded ankyrins, HET domain proteins and transcription factors. We also identified the Trichoderma core genome, completely curated its annotation, investigated several gene families in detail and compared the results to those of other fungi. Eighty percent of those genes for which a function could be predicted were also found in other fungi, but only 67% of those without a predictable function. Conclusions Our study presents a time scaled pattern of genome evolution in 12 Trichoderma species from three phylogenetically distant clades/sections and a comprehensive analysis of their genes. The data offer insights in the evolution of a mycoparasite towards a generalist. Electronic supplementary material The online version of this article (10.1186/s12864-019-5680-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Christian P Kubicek
- Microbiology and Applied Genomics Group, Research Area Biochemical Technology, Institute of Chemical, Environmental & Bioscience Engineering (ICEBE), TU Wien, Vienna, Austria.,, Vienna, Austria
| | - Andrei S Steindorff
- Departamento de Biologia Celular, Universidade de Brasília, Brasíla, DF, Brazil.,US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Komal Chenthamara
- Microbiology and Applied Genomics Group, Research Area Biochemical Technology, Institute of Chemical, Environmental & Bioscience Engineering (ICEBE), TU Wien, Vienna, Austria
| | - Gelsomina Manganiello
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA.,Dipartimento di Agraria, Università degli Studi di Napoli "Federico II", Naples, Portici, Italy
| | - Bernard Henrissat
- CNRS, Aix-Marseille Université, Marseille, France.,INRA, Marseille, France.,Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Jian Zhang
- Jiangsu Provincial Key Lab of Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - Feng Cai
- Jiangsu Provincial Key Lab of Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - Alexey G Kopchinskiy
- Microbiology and Applied Genomics Group, Research Area Biochemical Technology, Institute of Chemical, Environmental & Bioscience Engineering (ICEBE), TU Wien, Vienna, Austria
| | | | - Alan Kuo
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Riccardo Baroncelli
- Centro Hispano-Luso de Investigaciones Agrarias (CIALE), Departamento de Microbiología y Genética, Universidad de Salamanca, Campus de Villamayor, Calle Del Duero, Villamayor, España
| | - Sabrina Sarrocco
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | | | - Giovanni Vannacci
- Centro Hispano-Luso de Investigaciones Agrarias (CIALE), Departamento de Microbiología y Genética, Universidad de Salamanca, Campus de Villamayor, Calle Del Duero, Villamayor, España
| | - Qirong Shen
- Jiangsu Provincial Key Lab of Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing, China.
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA. .,Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA.
| | - Irina S Druzhinina
- Microbiology and Applied Genomics Group, Research Area Biochemical Technology, Institute of Chemical, Environmental & Bioscience Engineering (ICEBE), TU Wien, Vienna, Austria. .,Jiangsu Provincial Key Lab of Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing, China.
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Loquet A, Saupe SJ. Diversity of Amyloid Motifs in NLR Signaling in Fungi. Biomolecules 2017; 7:biom7020038. [PMID: 28406433 PMCID: PMC5485727 DOI: 10.3390/biom7020038] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 04/10/2017] [Accepted: 04/10/2017] [Indexed: 01/11/2023] Open
Abstract
Amyloid folds not only represent the underlying cause of a large class of human diseases but also display a variety of functional roles both in prokaryote and eukaryote organisms. Among these roles is a recently-described activity in signal transduction cascades functioning in host defense and programmed cell death and involving Nod-like receptors (NLRs). In different fungal species, prion amyloid folds convey activation signals from a receptor protein to an effector domain by an amyloid templating and propagation mechanism. The discovery of these amyloid signaling motifs derives from the study of [Het-s], a fungal prion of the species Podospora anserina. These signaling pathways are typically composed of two basic components encoded by adjacent genes, the NLR receptor bearing an amyloid motif at the N-terminal end and a cell death execution protein with a HeLo pore-forming domain bearing a C-terminal amyloid motif. Activation of the NLR receptor allows for amyloid folding of the N-terminal amyloid motifs which then template trans-conformation of the homologous motif in the cell death execution protein. A variety of such motifs, which differ by their sequence signature, have been described in fungi. Among them, the PP-motif bears resemblance with the RHIM amyloid motif involved in the necroptosis pathway in mammals suggesting an evolutionary conservation of amyloid signaling from fungi to mammals.
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Affiliation(s)
- Antoine Loquet
- Institute of Chemistry and Biology of Membranes and Nanoobjects, UMR 5248 CBMN-CNRS Université de Bordeaux, Allée Geoffroy Saint-Hillaire, 33600 Pessac, France.
| | - Sven J Saupe
- Non-Self Recognition in Fungi, Institut de Biochimie et de Génétique Cellulaire, UMR 5095 CNRS Université de Bordeaux, 1 rue Camille Saint Saëns, 33077 Bordeaux CEDEX, France.
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Abstract
ABSTRACT
For the majority of fungal species, the somatic body of an individual is a network of interconnected cells sharing a common cytoplasm and organelles. This syncytial organization contributes to an efficient distribution of resources, energy, and biochemical signals. Cell fusion is a fundamental process for fungal development, colony establishment, and habitat exploitation and can occur between hyphal cells of an individual colony or between colonies of genetically distinct individuals. One outcome of cell fusion is the establishment of a stable heterokaryon, culminating in benefits for each individual via shared resources or being of critical importance for the sexual or parasexual cycle of many fungal species. However, a second outcome of cell fusion between genetically distinct strains is formation of unstable heterokaryons and the induction of a programmed cell death reaction in the heterokaryotic cells. This reaction of nonself rejection, which is termed heterokaryon (or vegetative) incompatibility, is widespread in the fungal kingdom and acts as a defense mechanism against genome exploitation and mycoparasitism. Here, we review the currently identified molecular players involved in the process of somatic cell fusion and its regulation in filamentous fungi. Thereafter, we summarize the knowledge of the molecular determinants and mechanism of heterokaryon incompatibility and place this phenomenon in the broader context of biotropic interactions and immunity.
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15
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Vegetative incompatibility in fungi: From recognition to cell death, whatever does the trick. FUNGAL BIOL REV 2016. [DOI: 10.1016/j.fbr.2016.08.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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16
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Daskalov A, Habenstein B, Martinez D, Debets AJM, Sabaté R, Loquet A, Saupe SJ. Signal transduction by a fungal NOD-like receptor based on propagation of a prion amyloid fold. PLoS Biol 2015; 13:e1002059. [PMID: 25671553 PMCID: PMC4344463 DOI: 10.1371/journal.pbio.1002059] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Accepted: 12/29/2014] [Indexed: 01/09/2023] Open
Abstract
In the fungus Podospora anserina, the [Het-s] prion induces programmed cell death by activating the HET-S pore-forming protein. The HET-s β-solenoid prion fold serves as a template for converting the HET-S prion-forming domain into the same fold. This conversion, in turn, activates the HET-S pore-forming domain. The gene immediately adjacent to het-S encodes NWD2, a Nod-like receptor (NLR) with an N-terminal motif similar to the elementary repeat unit of the β-solenoid fold. NLRs are immune receptors controlling cell death and host defense processes in animals, plants and fungi. We have proposed that, analogously to [Het-s], NWD2 can activate the HET-S pore-forming protein by converting its prion-forming region into the β-solenoid fold. Here, we analyze the ability of NWD2 to induce formation of the β-solenoid prion fold. We show that artificial NWD2 variants induce formation of the [Het-s] prion, specifically in presence of their cognate ligands. The N-terminal motif is responsible for this prion induction, and mutations predicted to affect the β-solenoid fold abolish templating activity. In vitro, the N-terminal motif assembles into infectious prion amyloids that display a structure resembling the β-solenoid fold. In vivo, the assembled form of the NWD2 N-terminal region activates the HET-S pore-forming protein. This study documenting the role of the β-solenoid fold in fungal NLR function further highlights the general importance of amyloid and prion-like signaling in immunity-related cell fate pathways. The fungus Podospora anserina uses a prion amyloid fold as a signal transduction device between a Nod-like receptor and a downstream cell death execution protein. Although amyloids are best known as protein aggregates that are responsible for fatal neurodegenerative diseases, amyloid structures can also fulfill functional roles in cells. In particular, the controlled formation of amyloid structures appears to be involved in different signaling processes in the context of programmed cell death and host defense. The [Het-s] prion of the filamentous fungus Podospora anserina is a model system in which the 3-D structure of the prion form has been solved. The [Het-s] prion works as an activation switch for a second protein termed HET-S. HET-S is a pore-forming protein that is activated when the [Het-s] prion causes its C-terminal domain to adopt an amyloid-like fold. The protein encoded by the gene adjacent to het-S is a Nod-like receptor (NLR) called NWD2. NLRs are immune receptors that control host defense and cell death processes in plants, animals, and fungi. We show that NWD2 can template the formation of the [Het-s] prion fold in a ligand-controlled manner. NWD2 has an N-terminal motif homologous to the HET-S/s prion-forming region; we find that this region is both necessary and sufficient for its prion-inducing activity, and our functional and structural approaches reveal that the N-terminal region of NWD2 adopts a fold closely related to that of the HET-S/s prion. This study illustrates how the controlled formation of a prion amyloid fold can be used in a signaling process whereby a Nod-like receptor protein activates a downstream cell death execution domain.
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Affiliation(s)
- Asen Daskalov
- Non-self recognition in Fungi, Institut de Biochimie et de Génétique Cellulaire, UMR 5095, CNRS—Université de Bordeaux, Bordeaux, France
| | - Birgit Habenstein
- Institute of Chemistry & Biology of Membranes & Nanoobjects, CNRS, CBMN, UMR 5248, Pessac, France
| | - Denis Martinez
- Institute of Chemistry & Biology of Membranes & Nanoobjects, CNRS, CBMN, UMR 5248, Pessac, France
| | - Alfons J. M. Debets
- Laboratory of Genetics, Wageningen University, Droevendaalsesteeg, Wageningen, The Netherlands
| | - Raimon Sabaté
- Institut de Nanociència i nanotecnologia, Departament Fisicoquímica, Universitat de Barcelona, Joan XXIII s/n, Barcelona, Spain
| | - Antoine Loquet
- Institute of Chemistry & Biology of Membranes & Nanoobjects, CNRS, CBMN, UMR 5248, Pessac, France
| | - Sven J. Saupe
- Non-self recognition in Fungi, Institut de Biochimie et de Génétique Cellulaire, UMR 5095, CNRS—Université de Bordeaux, Bordeaux, France
- * E-mail:
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Comeau AM, Dufour J, Bouvet GF, Jacobi V, Nigg M, Henrissat B, Laroche J, Levesque RC, Bernier L. Functional annotation of the Ophiostoma novo-ulmi genome: insights into the phytopathogenicity of the fungal agent of Dutch elm disease. Genome Biol Evol 2014; 7:410-30. [PMID: 25539722 PMCID: PMC4350166 DOI: 10.1093/gbe/evu281] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/09/2014] [Indexed: 12/18/2022] Open
Abstract
The ascomycete fungus Ophiostoma novo-ulmi is responsible for the pandemic of Dutch elm disease that has been ravaging Europe and North America for 50 years. We proceeded to annotate the genome of the O. novo-ulmi strain H327 that was sequenced in 2012. The 31.784-Mb nuclear genome (50.1% GC) is organized into 8 chromosomes containing a total of 8,640 protein-coding genes that we validated with RNA sequencing analysis. Approximately 53% of these genes have their closest match to Grosmannia clavigera kw1407, followed by 36% in other close Sordariomycetes, 5% in other Pezizomycotina, and surprisingly few (5%) orphans. A relatively small portion (∼3.4%) of the genome is occupied by repeat sequences; however, the mechanism of repeat-induced point mutation appears active in this genome. Approximately 76% of the proteins could be assigned functions using Gene Ontology analysis; we identified 311 carbohydrate-active enzymes, 48 cytochrome P450s, and 1,731 proteins potentially involved in pathogen-host interaction, along with 7 clusters of fungal secondary metabolites. Complementary mating-type locus sequencing, mating tests, and culturing in the presence of elm terpenes were conducted. Our analysis identified a specific genetic arsenal impacting the sexual and vegetative growth, phytopathogenicity, and signaling/plant-defense-degradation relationship between O. novo-ulmi and its elm host and insect vectors.
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Affiliation(s)
- André M Comeau
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada Centre d'Étude de la Forêt (CEF), Université Laval, Québec, Québec, Canada Present address: Department of Pharmacology, Dalhousie University, Halifax, NS, Canada
| | - Josée Dufour
- Centre d'Étude de la Forêt (CEF), Université Laval, Québec, Québec, Canada
| | - Guillaume F Bouvet
- Institut de Recherches Cliniques de Montréal (IRCM), Montréal, Québec, Canada
| | - Volker Jacobi
- Centre d'Étude de la Forêt (CEF), Université Laval, Québec, Québec, Canada
| | - Martha Nigg
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada Centre d'Étude de la Forêt (CEF), Université Laval, Québec, Québec, Canada
| | - Bernard Henrissat
- Centre National de la Recherche Scientifique (CNRS), UMR7257, Université Aix-Marseille, France Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Jérôme Laroche
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
| | - Roger C Levesque
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada Département de Microbiologie-Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec, Québec, Canada
| | - Louis Bernier
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada Centre d'Étude de la Forêt (CEF), Université Laval, Québec, Québec, Canada
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18
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Dyrka W, Lamacchia M, Durrens P, Kobe B, Daskalov A, Paoletti M, Sherman DJ, Saupe SJ. Diversity and variability of NOD-like receptors in fungi. Genome Biol Evol 2014; 6:3137-58. [PMID: 25398782 PMCID: PMC4986451 DOI: 10.1093/gbe/evu251] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Nucleotide-binding oligomerization domain (NOD)-like receptors (NLRs) are intracellular receptors that control innate immunity and other biotic interactions in animals and plants. NLRs have been characterized in plant and animal lineages, but in fungi, this gene family has not been systematically described. There is however previous indications of the involvement of NLR-like genes in nonself recognition and programmed cell death in fungi. We have analyzed 198 fungal genomes for the presence of NLRs and have annotated a total of 5,616 NLR candidates. We describe their phylogenetic distribution, domain organization, and evolution. Fungal NLRs are characterized by a great diversity of domain organizations, suggesting frequently occurring combinatorial assortments of different effector, NOD and repeat domains. The repeat domains are of the WD, ANK, and TPR type; no LRR motifs were found. As previously documented for WD-repeat domains of fungal NLRs, TPR, and ANK repeats evolve under positive selection and show highly conserved repeats and repeat length polymorphism, suggesting the possibility of concerted evolution of these repeats. We identify novel effector domains not previously found associated with NLRs, whereas others are related to effector domains of plant or animals NLRs. In particular, we show that the HET domain found in fungal NLRs may be related to Toll/interleukin-1 receptor domains found in animal and plant immune receptors. This description of fungal NLR repertoires reveals both similarities and differences with plant and animals NLR collections, highlights the importance of domain reassortment and repeat evolution and provides a novel entry point to explore the evolution of NLRs in eukaryotes.
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Affiliation(s)
- Witold Dyrka
- INRIA-Université Bordeaux-CNRS, MAGNOME, Talence, France
| | - Marina Lamacchia
- Institut de Biochimie et de Génétique Cellulaire, UMR 5095, CNRS-Université de Bordeaux, France
| | - Pascal Durrens
- INRIA-Université Bordeaux-CNRS, MAGNOME, Talence, France
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Centre for Infectious Disease Research, University of Queensland, Brisbane, Queensland, Australia
| | - Asen Daskalov
- Institut de Biochimie et de Génétique Cellulaire, UMR 5095, CNRS-Université de Bordeaux, France
| | - Matthieu Paoletti
- Institut de Biochimie et de Génétique Cellulaire, UMR 5095, CNRS-Université de Bordeaux, France
| | | | - Sven J Saupe
- Institut de Biochimie et de Génétique Cellulaire, UMR 5095, CNRS-Université de Bordeaux, France
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Bastiaans E, Debets AJM, Aanen DK, van Diepeningen AD, Saupe SJ, Paoletti M. Natural variation of heterokaryon incompatibility gene het-c in Podospora anserina reveals diversifying selection. Mol Biol Evol 2014; 31:962-74. [PMID: 24448643 PMCID: PMC3969566 DOI: 10.1093/molbev/msu047] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
In filamentous fungi, allorecognition takes the form of heterokaryon incompatibility, a cell death reaction triggered when genetically distinct hyphae fuse. Heterokaryon incompatibility is controlled by specific loci termed het-loci. In this article, we analyzed the natural variation in one such fungal allorecognition determinant, the het-c heterokaryon incompatibility locus of the filamentous ascomycete Podospora anserina. The het-c locus determines an allogenic incompatibility reaction together with two unlinked loci termed het-d and het-e. Each het-c allele is incompatible with a specific subset of the het-d and het-e alleles. We analyzed variability at the het-c locus in a population of 110 individuals, and in additional isolates from various localities. We identified a total of 11 het-c alleles, which define 7 distinct incompatibility specificity classes in combination with the known het-d and het-e alleles. We found that the het-c allorecognition gene of P. anserina is under diversifying selection. We find a highly unequal allele distribution of het-c in the population, which contrasts with the more balanced distribution of functional groups of het-c based on their allorecognition function. One explanation for the observed het-c diversity in the population is its function in allorecognition. However, alleles that are most efficient in allorecognition are rare. An alternative and not exclusive explanation for the observed diversity is that het-c is involved in pathogen recognition. In Arabidopsis thaliana, a homolog of het-c is a pathogen effector target, supporting this hypothesis. We hypothesize that the het-c diversity in P. anserina results from both its functions in pathogen-defense, and allorecognition.
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Affiliation(s)
- Eric Bastiaans
- Laboratory of Genetics, Wageningen University, Droevendaalsesteeg, Wageningen, The Netherlands
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Van der Nest MA, Olson A, Lind M, Vélëz H, Dalman K, Brandström Durling M, Karlsson M, Stenlid J. Distribution and evolution of het gene homologs in the basidiomycota. Fungal Genet Biol 2013; 64:45-57. [PMID: 24380733 DOI: 10.1016/j.fgb.2013.12.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Revised: 12/04/2013] [Accepted: 12/20/2013] [Indexed: 12/24/2022]
Abstract
In filamentous fungi a system known as somatic incompatibility (SI) governs self/non-self recognition. SI is controlled by a regulatory signaling network involving proteins encoded at the het (heterokaryon incompatible) loci. Despite the wide occurrence of SI, the molecular identity and structure of only a small number of het genes and their products have been characterized in the model fungi Neurospora crassa and Podospora anserina. Our aim was to identify and study the distribution and evolution of putative het gene homologs in the Basidiomycota. For this purpose we used the information available for the model fungi to identify homologs of het genes in other fungi, especially the Basidiomycota. Putative het-c, het-c2 and un-24 homologs, as well as sequences containing the NACHT, HET or WD40 domains present in the het-e, het-r, het-6 and het-d genes were identified in certain members of the Ascomycota and Basidiomycota. The widespread phylogenetic distribution of certain het genes may reflect the fact that the encoded proteins are involved in fundamental cellular processes other than SI. Although homologs of het-S were previously known only from the Sordariomycetes (Ascomycota), we also identified a putative homolog of this gene in Gymnopus luxurians (Basidiomycota, class Agaricomycetes). Furthermore, with the exception of un-24, all of the putative het genes identified occurred mostly in a multi-copy fashion, some with lineage and species-specific expansions. Overall our results indicated that gene duplication followed by gene loss and/or gene family expansion, as well as multiple events of domain fusion and shuffling played an important role in the evolution of het gene homologs of Basidiomycota and other filamentous fungi.
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Affiliation(s)
- M A Van der Nest
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala SE-750 07, Sweden.
| | - A Olson
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala SE-750 07, Sweden
| | - M Lind
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala SE-750 07, Sweden
| | - H Vélëz
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala SE-750 07, Sweden
| | - K Dalman
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala SE-750 07, Sweden
| | - M Brandström Durling
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala SE-750 07, Sweden
| | - M Karlsson
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala SE-750 07, Sweden
| | - J Stenlid
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala SE-750 07, Sweden
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Abstract
In fungi, heterokaryon incompatibility is a nonself recognition process occurring when filaments of different isolates of the same species fuse. Compatibility is controlled by so-called het loci and fusion of strains of unlike het genotype triggers a complex incompatibility reaction that leads to the death of the fusion cell. Herein, we analyze the transcriptional changes during the incompatibility reaction in Podospora anserina. The incompatibility response was found to be associated with a massive transcriptional reprogramming: 2231 genes were up-regulated by a factor 2 or more during incompatibility. In turn, 2441 genes were down-regulated. HET, NACHT, and HeLo domains previously found to be involved in the control of heterokaryon incompatibility were enriched in the up-regulated gene set. In addition, incompatibility was characterized by an up-regulation of proteolytic and other hydrolytic activities, of secondary metabolism clusters and toxins and effector-like proteins. The up-regulated set was found to be enriched for proteins lacking orthologs in other species and chromosomal distribution of the up-regulated genes was uneven with up-regulated genes residing preferentially in genomic islands and on chromosomes IV and V. There was a significant overlap between regulated genes during incompatibility in P. anserina and Neurospora crassa, indicating similarities in the incompatibility responses in these two species. Globally, this study illustrates that the expression changes occurring during cell fusion incompatibility in P. anserina are in several aspects reminiscent of those described in host-pathogen or symbiotic interactions in other fungal species.
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Genomic clustering and homology between HET-S and the NWD2 STAND protein in various fungal genomes. PLoS One 2012; 7:e34854. [PMID: 22493719 PMCID: PMC3321046 DOI: 10.1371/journal.pone.0034854] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2011] [Accepted: 03/08/2012] [Indexed: 12/23/2022] Open
Abstract
Background Prions are infectious proteins propagating as self-perpetuating amyloid polymers. The [Het-s] prion of Podospora anserina is involved in a cell death process associated with non-self recognition. The prion forming domain (PFD) of HET-s adopts a β-solenoid amyloid structure characterized by the two fold repetition of an elementary triangular motif. [Het-s] induces cell death when interacting with HET-S, an allelic variant of HET-s. When templated by [Het-s], HET-S undergoes a trans-conformation, relocates to the cell membrane and induces toxicity. Methodology/Principal Findings Here, comparing HET-s homologs from different species, we devise a consensus for the HET-s elementary triangular motif. We use this motif to screen genomic databases and find a match to the N-terminus of NWD2, a STAND protein, encoded by the gene immediately adjacent to het-S. STAND proteins are signal transducing ATPases which undergo ligand-induced oligomerisation. Homology modelling predicts that the NWD2 N-terminal region adopts a HET-s-like fold. We propose that upon NWD2 oligomerisation, these N-terminal extensions adopt the β-solenoid fold and template HET-S to adopt the amyloid fold and trigger toxicity. We extend this model to a putative prion, the σ infectious element in Nectria haematococca, because the s locus controlling propagation of σ also encodes a STAND protein and displays analogous features. Comparative genomic analyses indicate evolutionary conservation of these STAND/prion-like gene pairs, identify a number of novel prion candidates and define, in addition to the HET-s PFD motif, two distinct, novel putative PFD-like motifs. Conclusions/Significance We suggest the existence, in the fungal kingdom, of a widespread and evolutionarily conserved mode of signal transduction based on the transmission of an amyloid-fold from a NOD-like STAND receptor protein to an effector protein.
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Iotti M, Rubini A, Tisserant E, Kholer A, Paolocci F, Zambonelli A. Self/nonself recognition in Tuber melanosporum is not mediated by a heterokaryon incompatibility system. Fungal Biol 2011; 116:261-75. [PMID: 22289772 DOI: 10.1016/j.funbio.2011.11.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2011] [Revised: 11/17/2011] [Accepted: 11/21/2011] [Indexed: 11/26/2022]
Abstract
Vegetative incompatibility is a widespread phenomenon in filamentous ascomycetes, which limits formation of viable heterokaryons. Whether this phenomenon plays a role in maintaining the homokaryotic state of the hyphae during the vegetative growth of Tuber spp. Gene expression, polymorphism analysis as well as targeted in vitro experiments allowed us to test whether a heterokaryon incompatibility (HI) system operates in Tuber melanosporum. HI is controlled by different genetic systems, often involving HET domain genes and their partners whose interaction can trigger a cell death reaction. Putative homologues to HI-related genes previously characterized in Neurospora crassa and Podospora anserina were identified in the T. melanosporum genome. However, only two HET domain genes were found. In many other ascomycetes HET domains have been found within different genes including some members of the NWD (NACHT and WD-repeat associated domains) gene family of P. anserina. More than 50 NWD homologues were found in T. melanosporum but none of these contain a HET domain. All these T. melanosporum paralogs showed a conserved gene organization similar to the microexon genes only recently characterized in Schistosoma mansoni. Expression data of the annotated HI-like genes along with low allelic polymorphism suggest that they have cellular functions unrelated to HI. Moreover, morphological analyses did not provide evidence for HI reactions between pairs of genetically different T. melanosporum strains. Thus, the maintenance of the genetic integrity during the vegetative growth of this species likely depends on mechanisms that act before hyphal fusion.
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Affiliation(s)
- Mirco Iotti
- Dipartimento di Protezione e Valorizzazione Agroalimentare, University of Bologna, Via Fanin 46, 40127 Bologna, Italy
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Lafontaine DL, Smith ML. Diverse interactions mediate asymmetric incompatibility by the het-6 supergene complex in Neurospora crassa. Fungal Genet Biol 2011; 49:65-73. [PMID: 22094057 DOI: 10.1016/j.fgb.2011.11.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2011] [Revised: 10/20/2011] [Accepted: 11/02/2011] [Indexed: 11/28/2022]
Abstract
Heterokaryon incompatibility (HI) in filamentous fungi is a form of nonself recognition that operates during the vegetative phase of the life cycle. One HI gene complex in Neurospora crassa, the het-6 locus, comprises two incompatibility genes, het-6 and un-24, each having two allelic variants, Oak Ridge (OR) and Panama (PA). The un-24 gene also encodes the large subunit of ribonucleotide reductase while het-6 appears to be a member of a repetitive gene family with no other known function aside from HI. These two genes are in severe linkage disequilibrium such that only un-24(OR)het-6(OR) and un-24(PA)het-6(PA) haplotypes occur in nature. In this study we unravel several genetic interactions that govern the HI functions of this gene complex. We use novel un-24(PA)het-6(OR) strains and het-6 deletion strains to demonstrate that nonallelic interactions occur between un-24 and het-6 and reveal an allelic incompatibility interaction between the OR and PA forms of un-24 that is asymmetrically enhanced by the presence of het-6(OR) or het-6(PA). We also show how two allelic forms of vib-1, a suppressor of het-c- and mat-associated incompatibility, differentially act as recessive suppressors of HI associated with nonallelic interactions between un-24(PA) and het-6(OR). In contrast, vib-1 is a dominant suppressor of HI associated with allelic differences at un-24 and a dominant partial suppressor of the un-24(OR) and het-6(PA) nonallelic interaction. The range of suppressor activities is largely explained by an interesting differential effect on het-6(OR) and het-6(PA) transcript levels by VIB-1.
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Hall C, Welch J, Kowbel DJ, Glass NL. Evolution and diversity of a fungal self/nonself recognition locus. PLoS One 2010; 5:e14055. [PMID: 21124910 PMCID: PMC2988816 DOI: 10.1371/journal.pone.0014055] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2010] [Accepted: 10/25/2010] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Self/nonself discrimination is an essential feature for pathogen recognition and graft rejection and is a ubiquitous phenomenon in many organisms. Filamentous fungi, such as Neurospora crassa, provide a model for analyses of population genetics/evolution of self/nonself recognition loci due to their haploid nature, small genomes and excellent genetic/genomic resources. In N. crassa, nonself discrimination during vegetative growth is determined by 11 heterokaryon incompatibility (het) loci. Cell fusion between strains that differ in allelic specificity at any of these het loci triggers a rapid programmed cell death response. METHODOLOGY/PRINCIPAL FINDINGS In this study, we evaluated the evolution, population genetics and selective mechanisms operating at a nonself recognition complex consisting of two closely linked loci, het-c (NCU03493) and pin-c (NCU03494). The genomic position of pin-c next to het-c is unique to Neurospora/Sordaria species, and originated by gene duplication after divergence from other species within the Sordariaceae. The het-c pin-c alleles in N. crassa are in severe linkage disequilibrium and consist of three haplotypes, het-c1/pin-c1, het-c2/pin-c2 and het-c3/pin-c3, which are equally frequent in population samples and exhibit trans-species polymorphisms. The absence of recombinant haplotypes is correlated with divergence of the het-c/pin-c intergenic sequence. Tests for positive and balancing selection at het-c and pin-c support the conclusion that both of these loci are under non-neutral balancing selection; other regions of both genes appear to be under positive selection. Our data show that the het-c2/pin-c2 haplotype emerged by a recombination event between the het-c1/pin-c1 and het-c3/pin-c3 approximately 3-12 million years ago. CONCLUSIONS/SIGNIFICANCE These results support models by which loci that confer nonself discrimination form by the association of polymorphic genes with genes containing HET domains. Distinct allele classes can emerge by recombination and positive selection and are subsequently maintained by balancing selection and divergence of intergenic sequence resulting in recombination blocks between haplotypes.
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Affiliation(s)
- Charles Hall
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
| | - Juliet Welch
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
| | - David J. Kowbel
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
| | - N. Louise Glass
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
- * E-mail:
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Chevanne D, Saupe SJ, Clavé C, Paoletti M. WD-repeat instability and diversification of the Podospora anserina hnwd non-self recognition gene family. BMC Evol Biol 2010; 10:134. [PMID: 20459612 PMCID: PMC2873952 DOI: 10.1186/1471-2148-10-134] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2009] [Accepted: 05/06/2010] [Indexed: 01/07/2023] Open
Abstract
Background Genes involved in non-self recognition and host defence are typically capable of rapid diversification and exploit specialized genetic mechanism to that end. Fungi display a non-self recognition phenomenon termed heterokaryon incompatibility that operates when cells of unlike genotype fuse and leads to the cell death of the fusion cell. In the fungus Podospora anserina, three genes controlling this allorecognition process het-d, het-e and het-r are paralogs belonging to the same hnwd gene family. HNWD proteins are STAND proteins (signal transduction NTPase with multiple domains) that display a WD-repeat domain controlling recognition specificity. Based on genomic sequence analysis of different P. anserina isolates, it was established that repeat regions of all members of the gene family are extremely polymorphic and undergoing concerted evolution arguing for frequent recombination within and between family members. Results Herein, we directly analyzed the genetic instability and diversification of this allorecognition gene family. We have constituted a collection of 143 spontaneous mutants of the het-R (HNWD2) and het-E (hnwd5) genes with altered recognition specificities. The vast majority of the mutants present rearrangements in the repeat arrays with deletions, duplications and other modifications as well as creation of novel repeat unit variants. Conclusions We investigate the extreme genetic instability of these genes and provide a direct illustration of the diversification strategy of this eukaryotic allorecognition gene family.
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Affiliation(s)
- Damien Chevanne
- Laboratoire de Génétique Moléculaire des Champignons, IBGC, UMR 5095 Université Victor Segalen Bordeaux 2, 1 rue Camille Saint-Saëns, Bordeaux Cedex, France
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Development of a conditional gene expression system using a zearalenone-inducible promoter for the ascomycete fungus Gibberella zeae. Appl Environ Microbiol 2010; 76:3089-96. [PMID: 20348311 DOI: 10.1128/aem.02999-09] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The ascomycete fungus Gibberella zeae is an important plant pathogen that causes fusarium head blight on small grains. Molecular studies of this fungus have been performed extensively to uncover the biological mechanisms related to pathogenicity, toxin production, and sexual reproduction. Molecular methods, such as targeted gene deletion, gene overexpression, and gene fusion to green fluorescent protein (GFP), are relatively easy to perform with this fungus; however, conditional expression systems have not been developed. The purpose of this study was to identify a promoter that could be induced by zearalenone (ZEA) for the development of a conditional expression system in G. zeae. Through microarray analysis, we isolated one zearalenone response gene (ZEAR) whose expression was increased more than 50 times after ZEA treatment. Northern blot analysis showed that the ZEAR transcript dramatically increased after 1 h of ZEA treatment. To determine the utility of the ZEAR promoter, called Pzear, in a conditional expression system, we transformed a Pzear::GFP fusion construct into G. zeae. Our data showed a ZEA concentration-dependent increase in GFP expression. We also replaced the promoter of G. zeae metE (GzmetE), an essential gene for methionine biosynthesis, with the Pzear promoter. The growth of the Pzear-GzmetE mutant on minimal medium was dependent on the ZEA concentration supplemented in the medium and showed that GzMetE expression was induced by ZEA. This study is the first report of an inducible promoter in G. zeae. Our system will be useful for the characterization of essential gene functions in this fungus through differential and ZEA-dependent gene expression. In addition, the Pzear promoter may be applicable as a biosensor for the detection of ZEA contamination in agricultural products.
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Abstract
In fungi, cell fusion between genetically unlike individuals triggers a cell death reaction known as the incompatibility reaction. In Podospora anserina, the genes controlling this process belong to a gene family encoding STAND proteins with an N-terminal cell death effector domain, a central NACHT domain and a C-terminal WD-repeat domain. These incompatibility genes are extremely polymorphic, subject to positive Darwinian selection and display a remarkable genetic plasticity allowing for constant diversification of the WD-repeat domain responsible for recognition of non-self. Remarkably, the architecture of these proteins is related to pathogen-recognition receptors ensuring innate immunity in plants and animals. Here, we hypothesize that these P. anserina incompatibility genes could be components of a yet-unidentified innate immune system of fungi. As already proposed in the case of plant hybrid necrosis or graft rejection in mammals, incompatibility could be a by-product of pathogen-driven divergence in host defense genes.
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Affiliation(s)
- Mathieu Paoletti
- Laboratoire de Génétique Moléculaire des Champignons, Institut de Biochimie et de Génétique Cellulaires, UMR 5095 CNRS-Université de Bordeaux 2, 1 rue Camille St Saëns, 33077 Bordeaux Cedex, France
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