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Dölfors F, Ilbäck J, Bejai S, Fogelqvist J, Dixelius C. Nitrate transporter protein NPF5.12 and major latex-like protein MLP6 are important defense factors against Verticillium longisporum. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:4148-4164. [PMID: 38666306 PMCID: PMC11233413 DOI: 10.1093/jxb/erae185] [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: 07/17/2023] [Accepted: 04/23/2024] [Indexed: 07/11/2024]
Abstract
Plant defense responses to the soil-borne fungus Verticillium longisporum causing stem stripe disease on oilseed rape (Brassica napus) are poorly understood. In this study, a population of recombinant inbred lines (RILs) using the Arabidopsis accessions Sei-0 and Can-0 was established. Composite interval mapping, transcriptome data, and T-DNA mutant screening identified the NITRATE/PEPTIDE TRANSPORTER FAMILY 5.12 (AtNPF5.12) gene as being associated with disease susceptibility in Can-0. Co-immunoprecipitation revealed interaction between AtNPF5.12 and the MAJOR LATEX PROTEIN family member AtMLP6, and fluorescence microscopy confirmed this interaction in the plasma membrane and endoplasmic reticulum. CRISPR/Cas9 technology was applied to mutate the NPF5.12 and MLP6 genes in B. napus. Elevated fungal growth in the npf5.12 mlp6 double mutant of both oilseed rape and Arabidopsis demonstrated the importance of these genes in defense against V. longisporum. Colonization of this fungus depends also on available nitrates in the host root. Accordingly, the negative effect of nitrate depletion on fungal growth was less pronounced in Atnpf5.12 plants with impaired nitrate transport. In addition, suberin staining revealed involvement of the NPF5.12 and MLP6 genes in suberin barrier formation. Together, these results demonstrate a dependency on multiple plant factors that leads to successful V. longisporum root infection.
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Affiliation(s)
- Fredrik Dölfors
- Swedish University of Agricultural Sciences, Department of Plant Biology, Uppsala BioCenter, Linnean Center for Plant Biology, P.O. Box 7080, S-75007 Uppsala, Sweden
| | - Jonas Ilbäck
- Swedish University of Agricultural Sciences, Department of Plant Biology, Uppsala BioCenter, Linnean Center for Plant Biology, P.O. Box 7080, S-75007 Uppsala, Sweden
| | - Sarosh Bejai
- Swedish University of Agricultural Sciences, Department of Plant Biology, Uppsala BioCenter, Linnean Center for Plant Biology, P.O. Box 7080, S-75007 Uppsala, Sweden
| | - Johan Fogelqvist
- Swedish University of Agricultural Sciences, Department of Plant Biology, Uppsala BioCenter, Linnean Center for Plant Biology, P.O. Box 7080, S-75007 Uppsala, Sweden
| | - Christina Dixelius
- Swedish University of Agricultural Sciences, Department of Plant Biology, Uppsala BioCenter, Linnean Center for Plant Biology, P.O. Box 7080, S-75007 Uppsala, Sweden
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Rafiei V, Vélëz H, Piombo E, Dubey M, Tzelepis G. Verticillium longisporum phospholipase VlsPLA 2 is a virulence factor that targets host nuclei and modulates plant immunity. MOLECULAR PLANT PATHOLOGY 2023; 24:1078-1092. [PMID: 37171182 PMCID: PMC10423322 DOI: 10.1111/mpp.13352] [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: 02/07/2023] [Revised: 04/13/2023] [Accepted: 04/25/2023] [Indexed: 05/13/2023]
Abstract
Phospholipase A2 (PLA2 ) is a lipolytic enzyme that hydrolyses phospholipids in the cell membrane. In the present study, we investigated the role of secreted PLA2 (VlsPLA2 ) in Verticillium longisporum, a fungal phytopathogen that mostly infects plants belonging to the Brassicaceae family, causing severe annual yield loss worldwide. Expression of the VlsPLA2 gene, which encodes active PLA2 , is highly induced during the interaction of the fungus with the host plant Brassica napus. Heterologous expression of VlsPLA2 in Nicotiana benthamiana resulted in increased synthesis of certain phospholipids compared to plants in which enzymatically inactive PLA2 was expressed (VlsPLA2 ΔCD ). Moreover, VlsPLA2 suppresses the hypersensitive response triggered by the Cf4/Avr4 complex, thereby suppressing the chitin-induced reactive oxygen species burst. VlsPLA2 -overexpressing V. longisporum strains showed increased virulence in Arabidopsis plants, and transcriptomic analysis of this fungal strain revealed that the induction of the gene contributed to increased virulence. VlsPLA2 was initially localized to the host nucleus and then translocated to the chloroplasts at later time points. In addition, VlsPLA2 bound to the vesicle-associated membrane protein A (VAMPA) and was transported to the nuclear membrane. In the nucleus, VlsPLA2 caused major alterations in the expression levels of genes encoding transcription factors and subtilisin-like proteases, which play a role in plant immunity. In conclusion, our study showed that VlsPLA2 acts as a virulence factor, possibly by hydrolysing host nuclear envelope phospholipids, which, through a signal transduction cascade, may suppress basal plant immune responses.
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Affiliation(s)
- Vahideh Rafiei
- Department of Forest Mycology and Plant PathologySwedish University of Agricultural Sciences, Uppsala BiocenterUppsalaSweden
| | - Heriberto Vélëz
- Department of Forest Mycology and Plant PathologySwedish University of Agricultural Sciences, Uppsala BiocenterUppsalaSweden
| | - Edoardo Piombo
- Department of Forest Mycology and Plant PathologySwedish University of Agricultural Sciences, Uppsala BiocenterUppsalaSweden
| | - Mukesh Dubey
- Department of Forest Mycology and Plant PathologySwedish University of Agricultural Sciences, Uppsala BiocenterUppsalaSweden
| | - Georgios Tzelepis
- Department of Forest Mycology and Plant PathologySwedish University of Agricultural Sciences, Uppsala BiocenterUppsalaSweden
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3
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Tuveng TR, Østby H, Tamburrini KC, Bissaro B, Hegnar OA, Stepnov AA, Várnai A, Berrin JG, Eijsink VGH. Revisiting the AA14 family of lytic polysaccharide monooxygenases and their catalytic activity. FEBS Lett 2023; 597:2086-2102. [PMID: 37418595 DOI: 10.1002/1873-3468.14694] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 06/08/2023] [Accepted: 06/26/2023] [Indexed: 07/09/2023]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) belonging to the AA14 family are believed to contribute to the enzymatic degradation of lignocellulosic biomass by specifically acting on xylan in recalcitrant cellulose-xylan complexes. Functional characterization of an AA14 LPMO from Trichoderma reesei, TrAA14A, and a re-evaluation of the properties of the previously described AA14 from Pycnoporus coccineus, PcoAA14A, showed that these proteins have oxidase and peroxidase activities that are common for LPMOs. However, we were not able to detect activity on cellulose-associated xylan or any other tested polysaccharide substrate, meaning that the substrate of these enzymes remains unknown. Next to raising questions regarding the true nature of AA14 LPMOs, the present data illustrate possible pitfalls in the functional characterization of these intriguing enzymes.
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Affiliation(s)
- Tina R Tuveng
- Faculty of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Heidi Østby
- Faculty of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Ketty C Tamburrini
- INRAE, Aix Marseille Univ, UMR1163 Biodiversité et Biotechnologie Fongiques, Marseille, France
| | - Bastien Bissaro
- INRAE, Aix Marseille Univ, UMR1163 Biodiversité et Biotechnologie Fongiques, Marseille, France
| | - Olav A Hegnar
- Faculty of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Anton A Stepnov
- Faculty of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Anikó Várnai
- Faculty of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Jean-Guy Berrin
- INRAE, Aix Marseille Univ, UMR1163 Biodiversité et Biotechnologie Fongiques, Marseille, France
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
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Gostinčar C, Sun X, Černoša A, Fang C, Gunde-Cimerman N, Song Z. Clonality, inbreeding, and hybridization in two extremotolerant black yeasts. Gigascience 2022; 11:giac095. [PMID: 36200832 PMCID: PMC9535773 DOI: 10.1093/gigascience/giac095] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 07/29/2022] [Accepted: 09/12/2022] [Indexed: 11/04/2022] Open
Abstract
BACKGROUND The great diversity of lifestyles and survival strategies observed in fungi is reflected in the many ways in which they reproduce and recombine. Although a complete absence of recombination is rare, it has been reported for some species, among them 2 extremotolerant black yeasts from Dothideomycetes: Hortaea werneckii and Aureobasidium melanogenum. Therefore, the presence of diploid strains in these species cannot be explained as the product of conventional sexual reproduction. RESULTS Genome sequencing revealed that the ratio of diploid to haploid strains in both H. werneckii and A. melanogenum is about 2:1. Linkage disequilibrium between pairs of polymorphic loci and a high degree of concordance between the phylogenies of different genomic regions confirmed that both species are clonal. Heterozygosity of diploid strains is high, with several hybridizing genome pairs reaching the intergenomic distances typically seen between different fungal species. The origin of diploid strains collected worldwide can be traced to a handful of hybridization events that produced diploids, which were stable over long periods of time and distributed over large geographic areas. CONCLUSIONS Our results, based on the genomes of over 100 strains of 2 black yeasts, show that although they are clonal, they occasionally form stable and highly heterozygous diploid intraspecific hybrids. The mechanism of these apparently rare hybridization events, which are not followed by meiosis or haploidization, remains unknown. Both extremotolerant yeasts, H. werneckii and even more so A. melanogenum, a close relative of the intensely recombining and biotechnologically relevant Aureobasidium pullulans, provide an attractive model for studying the role of clonality and ploidy in extremotolerant fungi.
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Affiliation(s)
- Cene Gostinčar
- Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, Qingdao 266555, China
| | - Xiaohuan Sun
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen 518083, China
| | - Anja Černoša
- Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Chao Fang
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen 518083, China
| | - Nina Gunde-Cimerman
- Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Zewei Song
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen 518083, China
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Rafiei V, Ruffino A, Persson Hodén K, Tornkvist A, Mozuraitis R, Dubey M, Tzelepis G. A Verticillium longisporum pleiotropic drug transporter determines tolerance to the plant host β-pinene monoterpene. MOLECULAR PLANT PATHOLOGY 2022; 23:291-303. [PMID: 34825755 PMCID: PMC8743018 DOI: 10.1111/mpp.13162] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 10/19/2021] [Accepted: 11/01/2021] [Indexed: 05/05/2023]
Abstract
Terpenes constitute a major part of secondary metabolites secreted by plants in the rhizosphere. However, their specific functions in fungal-plant interactions have not been investigated thoroughly. In this study we investigated the role of monoterpenes in interactions between oilseed rape (Brassica napus) and the soilborne pathogen Verticillium longisporum. We identified seven monoterpenes produced by B. napus, and production of α-pinene, β-pinene, 3-carene, and camphene was significantly increased upon fungal infection. Among them, β-pinene was chosen for further analysis. Transcriptome analysis of V. longisporum on exposure to β-pinene resulted in identification of two highly expressed pleotropic drug transporters paralog genes named VlAbcG1a and VlAbcG1b. Overexpression of VlAbcG1a in Saccharomyces cerevisiae increased tolerance to β-pinene, while deletion of the VlAbcG1a homologous gene in Verticillium dahliae resulted in mutants with increased sensitivity to certain monoterpenes. Furthermore, the VlAbcG1a overexpression strain displayed an increased tolerance to β-pinene and increased virulence in tomato plants. Data from this study give new insights into the roles of terpenes in plant-fungal pathogen interactions and the mechanisms fungi deploy to cope with the toxicity of these secondary metabolites.
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Affiliation(s)
- Vahideh Rafiei
- Department of Forest Mycology and Plant PathologyUppsala BiocenterSwedish University of Agricultural SciencesUppsalaSweden
| | - Alessandra Ruffino
- Department of Plant BiologyUppsala BiocenterSwedish University of Agricultural SciencesLinnean Center for Plant BiologyUppsalaSweden
| | - Kristian Persson Hodén
- Department of Plant BiologyUppsala BiocenterSwedish University of Agricultural SciencesLinnean Center for Plant BiologyUppsalaSweden
| | - Anna Tornkvist
- Department of Plant BiologyUppsala BiocenterSwedish University of Agricultural SciencesLinnean Center for Plant BiologyUppsalaSweden
| | | | - Mukesh Dubey
- Department of Forest Mycology and Plant PathologyUppsala BiocenterSwedish University of Agricultural SciencesUppsalaSweden
| | - Georgios Tzelepis
- Department of Forest Mycology and Plant PathologyUppsala BiocenterSwedish University of Agricultural SciencesUppsalaSweden
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Harting R, Starke J, Kusch H, Pöggeler S, Maurus I, Schlüter R, Landesfeind M, Bulla I, Nowrousian M, de Jonge R, Stahlhut G, Hoff KJ, Aßhauer KP, Thürmer A, Stanke M, Daniel R, Morgenstern B, Thomma BPHJ, Kronstad JW, Braus‐Stromeyer SA, Braus GH. A 20-kb lineage-specific genomic region tames virulence in pathogenic amphidiploid Verticillium longisporum. MOLECULAR PLANT PATHOLOGY 2021; 22:939-953. [PMID: 33955130 PMCID: PMC8295516 DOI: 10.1111/mpp.13071] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 03/30/2021] [Indexed: 05/04/2023]
Abstract
Amphidiploid fungal Verticillium longisporum strains Vl43 and Vl32 colonize the plant host Brassica napus but differ in their ability to cause disease symptoms. These strains represent two V. longisporum lineages derived from different hybridization events of haploid parental Verticillium strains. Vl32 and Vl43 carry same-sex mating-type genes derived from both parental lineages. Vl32 and Vl43 similarly colonize and penetrate plant roots, but asymptomatic Vl32 proliferation in planta is lower than virulent Vl43. The highly conserved Vl43 and Vl32 genomes include less than 1% unique genes, and the karyotypes of 15 or 16 chromosomes display changed genetic synteny due to substantial genomic reshuffling. A 20 kb Vl43 lineage-specific (LS) region apparently originating from the Verticillium dahliae-related ancestor is specific for symptomatic Vl43 and encodes seven genes, including two putative transcription factors. Either partial or complete deletion of this LS region in Vl43 did not reduce virulence but led to induction of even more severe disease symptoms in rapeseed. This suggests that the LS insertion in the genome of symptomatic V. longisporum Vl43 mediates virulence-reducing functions, limits damage on the host plant, and therefore tames Vl43 from being even more virulent.
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Affiliation(s)
- Rebekka Harting
- Department of Molecular Microbiology and GeneticsInstitute of Microbiology and Genetics and Göttingen Center for Molecular BiosciencesUniversity of GöttingenGöttingenGermany
| | - Jessica Starke
- Department of Molecular Microbiology and GeneticsInstitute of Microbiology and Genetics and Göttingen Center for Molecular BiosciencesUniversity of GöttingenGöttingenGermany
| | - Harald Kusch
- Department of Molecular Microbiology and GeneticsInstitute of Microbiology and Genetics and Göttingen Center for Molecular BiosciencesUniversity of GöttingenGöttingenGermany
| | - Stefanie Pöggeler
- Department of Genetics of Eukaryotic MicroorganismsInstitute of Microbiology and Genetics and Göttingen Center for Molecular BiosciencesUniversity of GöttingenGöttingenGermany
| | - Isabel Maurus
- Department of Molecular Microbiology and GeneticsInstitute of Microbiology and Genetics and Göttingen Center for Molecular BiosciencesUniversity of GöttingenGöttingenGermany
| | - Rabea Schlüter
- Imaging Center of the Department of BiologyUniversity of GreifswaldGreifswaldGermany
| | - Manuel Landesfeind
- Department of BioinformaticsInstitute of Microbiology and Genetics and Göttingen Center for Molecular BiosciencesUniversity of GöttingenGöttingenGermany
| | - Ingo Bulla
- Institute for Mathematics and Computer ScienceUniversity of GreifswaldGreifswaldGermany
| | - Minou Nowrousian
- Department of Molecular and Cellular BotanyRuhr‐Universität BochumBochumGermany
| | - Ronnie de Jonge
- Plant–Microbe Interactions, Department of Biology, Science4LifeUtrecht UniversityUtrechtNetherlands
- Laboratory of PhytopathologyWageningen UniversityWageningenNetherlands
| | - Gertrud Stahlhut
- Department of Genetics of Eukaryotic MicroorganismsInstitute of Microbiology and Genetics and Göttingen Center for Molecular BiosciencesUniversity of GöttingenGöttingenGermany
| | - Katharina J. Hoff
- Institute for Mathematics and Computer ScienceUniversity of GreifswaldGreifswaldGermany
- Center for Functional Genomics of MicrobesUniversity of GreifswaldGreifswaldGermany
| | - Kathrin P. Aßhauer
- Department of BioinformaticsInstitute of Microbiology and Genetics and Göttingen Center for Molecular BiosciencesUniversity of GöttingenGöttingenGermany
| | - Andrea Thürmer
- Department of Genomic and Applied MicrobiologyInstitute of Microbiology and Genetics and Göttingen Center for Molecular BiosciencesUniversity of GöttingenGöttingenGermany
| | - Mario Stanke
- Institute for Mathematics and Computer ScienceUniversity of GreifswaldGreifswaldGermany
- Center for Functional Genomics of MicrobesUniversity of GreifswaldGreifswaldGermany
| | - Rolf Daniel
- Department of Genomic and Applied MicrobiologyInstitute of Microbiology and Genetics and Göttingen Center for Molecular BiosciencesUniversity of GöttingenGöttingenGermany
| | - Burkhard Morgenstern
- Department of BioinformaticsInstitute of Microbiology and Genetics and Göttingen Center for Molecular BiosciencesUniversity of GöttingenGöttingenGermany
| | | | - James W. Kronstad
- Michael Smith Laboratories, Department of Microbiology and ImmunologyUniversity of British ColumbiaVancouverBCCanada
| | - Susanna A. Braus‐Stromeyer
- Department of Molecular Microbiology and GeneticsInstitute of Microbiology and Genetics and Göttingen Center for Molecular BiosciencesUniversity of GöttingenGöttingenGermany
| | - Gerhard H. Braus
- Department of Molecular Microbiology and GeneticsInstitute of Microbiology and Genetics and Göttingen Center for Molecular BiosciencesUniversity of GöttingenGöttingenGermany
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Harting R, Nagel A, Nesemann K, Höfer AM, Bastakis E, Kusch H, Stanley CE, Stöckli M, Kaever A, Hoff KJ, Stanke M, deMello AJ, Künzler M, Haney CH, Braus-Stromeyer SA, Braus GH. Pseudomonas Strains Induce Transcriptional and Morphological Changes and Reduce Root Colonization of Verticillium spp. Front Microbiol 2021; 12:652468. [PMID: 34108946 PMCID: PMC8180853 DOI: 10.3389/fmicb.2021.652468] [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: 01/12/2021] [Accepted: 04/26/2021] [Indexed: 11/13/2022] Open
Abstract
Phytopathogenic Verticillia cause Verticillium wilt on numerous economically important crops. Plant infection begins at the roots, where the fungus is confronted with rhizosphere inhabiting bacteria. The effects of different fluorescent pseudomonads, including some known biocontrol agents of other plant pathogens, on fungal growth of the haploid Verticillium dahliae and/or the amphidiploid Verticillium longisporum were compared on pectin-rich medium, in microfluidic interaction channels, allowing visualization of single hyphae, or on Arabidopsis thaliana roots. We found that the potential for formation of bacterial lipopeptide syringomycin resulted in stronger growth reduction effects on saprophytic Aspergillus nidulans compared to Verticillium spp. A more detailed analyses on bacterial-fungal co-cultivation in narrow interaction channels of microfluidic devices revealed that the strongest inhibitory potential was found for Pseudomonas protegens CHA0, with its inhibitory potential depending on the presence of the GacS/GacA system controlling several bacterial metabolites. Hyphal tip polarity was altered when V. longisporum was confronted with pseudomonads in narrow interaction channels, resulting in a curly morphology instead of straight hyphal tip growth. These results support the hypothesis that the fungus attempts to evade the bacterial confrontation. Alterations due to co-cultivation with bacteria could not only be observed in fungal morphology but also in fungal transcriptome. P. protegens CHA0 alters transcriptional profiles of V. longisporum during 2 h liquid media co-cultivation in pectin-rich medium. Genes required for degradation of and growth on the carbon source pectin were down-regulated, whereas transcripts involved in redox processes were up-regulated. Thus, the secondary metabolite mediated effect of Pseudomonas isolates on Verticillium species results in a complex transcriptional response, leading to decreased growth with precautions for self-protection combined with the initiation of a change in fungal growth direction. This interplay of bacterial effects on the pathogen can be beneficial to protect plants from infection, as shown with A. thaliana root experiments. Treatment of the roots with bacteria prior to infection with V. dahliae resulted in a significant reduction of fungal root colonization. Taken together we demonstrate how pseudomonads interfere with the growth of Verticillium spp. and show that these bacteria could serve in plant protection.
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Affiliation(s)
- Rebekka Harting
- Institute of Microbiology and Genetics, Göttingen Center for Molecular Biosciences, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Alexandra Nagel
- Institute of Microbiology and Genetics, Göttingen Center for Molecular Biosciences, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Kai Nesemann
- Institute of Microbiology and Genetics, Göttingen Center for Molecular Biosciences, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Annalena M Höfer
- Institute of Microbiology and Genetics, Göttingen Center for Molecular Biosciences, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Emmanouil Bastakis
- Institute of Microbiology and Genetics, Göttingen Center for Molecular Biosciences, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Harald Kusch
- Institute of Microbiology and Genetics, Göttingen Center for Molecular Biosciences, Georg-August-Universität Göttingen, Göttingen, Germany.,Department of Medical Informatics, University Medical Center, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Claire E Stanley
- Institute of Chemical and Bioengineering, ETH Zürich, Zurich, Switzerland
| | | | - Alexander Kaever
- Institute of Microbiology and Genetics, Göttingen Center for Molecular Biosciences, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Katharina J Hoff
- Institute of Mathematics and Computer Science, Universität Greifswald, Greifswald, Germany
| | - Mario Stanke
- Institute of Mathematics and Computer Science, Universität Greifswald, Greifswald, Germany
| | - Andrew J deMello
- Institute of Chemical and Bioengineering, ETH Zürich, Zurich, Switzerland
| | - Markus Künzler
- Institute of Microbiology, ETH Zürich, Zurich, Switzerland
| | - Cara H Haney
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, BC, Canada
| | - Susanna A Braus-Stromeyer
- Institute of Microbiology and Genetics, Göttingen Center for Molecular Biosciences, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Gerhard H Braus
- Institute of Microbiology and Genetics, Göttingen Center for Molecular Biosciences, Georg-August-Universität Göttingen, Göttingen, Germany
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Evolutionary and genomic comparisons of hybrid uninucleate and nonhybrid Rhizoctonia fungi. Commun Biol 2021; 4:201. [PMID: 33589695 PMCID: PMC7884421 DOI: 10.1038/s42003-021-01724-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 01/19/2021] [Indexed: 01/30/2023] Open
Abstract
The basidiomycetous fungal genus, Rhizoctonia, can cause severe damage to many plants and is composed of multinucleate, binucleate, and uninucleate species differing in pathogenicity. Here we generated chromosome-scale genome assemblies of the three nuclear types of Rhizoctonia isolates. The genomic comparisons revealed that the uninucleate JN strain likely arose by somatic hybridization of two binucleate isolates, and maintained a diploid nucleus. Homeolog gene pairs in the JN genome have experienced both decelerated or accelerated evolution. Homeolog expression dominance occurred between JN subgenomes, in which differentially expressed genes show potentially less evolutionary constraint than the genes without. Analysis of mating-type genes suggested that Rhizoctonia maintains the ancestral tetrapolarity of the Basidiomycota. Long terminal repeat-retrotransposons displayed a reciprocal correlation with the chromosomal GC content in the three chromosome-scale genomes. The more aggressive multinucleate XN strain had more genes encoding enzymes for host cell wall decomposition. These findings demonstrate some evolutionary changes of a recently derived hybrid and in multiple nuclear types of Rhizoctonia.
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9
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Hessenauer P, Feau N, Gill U, Schwessinger B, Brar GS, Hamelin RC. Evolution and Adaptation of Forest and Crop Pathogens in the Anthropocene. PHYTOPATHOLOGY 2021; 111:49-67. [PMID: 33200962 DOI: 10.1094/phyto-08-20-0358-fi] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Anthropocene marks the era when human activity is making a significant impact on earth, its ecological and biogeographical systems. The domestication and intensification of agricultural and forest production systems have had a large impact on plant and tree health. Some pathogens benefitted from these human activities and have evolved and adapted in response to the expansion of crop and forest systems, resulting in global outbreaks. Global pathogen genomics data including population genomics and high-quality reference assemblies are crucial for understanding the evolution and adaptation of pathogens. Crops and forest trees have remarkably different characteristics, such as reproductive time and the level of domestication. They also have different production systems for disease management with more intensive management in crops than forest trees. By comparing and contrasting results from pathogen population genomic studies done on widely different agricultural and forest production systems, we can improve our understanding of pathogen evolution and adaptation to different selection pressures. We find that in spite of these differences, similar processes such as hybridization, host jumps, selection, specialization, and clonal expansion are shaping the pathogen populations in both crops and forest trees. We propose some solutions to reduce these impacts and lower the probability of global pathogen outbreaks so that we can envision better management strategies to sustain global food production as well as ecosystem services.
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Affiliation(s)
- Pauline Hessenauer
- Faculty of Forestry, Geography and Geomatics, Laval University, Quebec City, QC, G1V 0A6 Canada
| | - Nicolas Feau
- Faculty of Forestry, The University of British Columbia, Vancouver, BC, V6T 1Z4 Canada
| | - Upinder Gill
- College of Agriculture, Food Systems, and Natural Resources, North Dakota State University, Fargo, ND 58102, U.S.A
| | - Benjamin Schwessinger
- Research School of Biology, Australian National University, Acton, ACT 2601 Australia
| | - Gurcharn S Brar
- Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC, V6T 1Z4 Canada
| | - Richard C Hamelin
- Faculty of Forestry, Geography and Geomatics, Laval University, Quebec City, QC, G1V 0A6 Canada
- Faculty of Forestry, The University of British Columbia, Vancouver, BC, V6T 1Z4 Canada
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de Vries S, Stukenbrock EH, Rose LE. Rapid evolution in plant-microbe interactions - an evolutionary genomics perspective. THE NEW PHYTOLOGIST 2020; 226:1256-1262. [PMID: 31997351 DOI: 10.1111/nph.16458] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 01/13/2020] [Indexed: 05/22/2023]
Abstract
Access to greater genomic resolution through new sequencing technologies is transforming the field of plant pathology. As scientists embrace these new methods, some overarching patterns and observations come into focus. Evolutionary genomic studies are used to determine not only the origins of pathogen lineages and geographic patterns of genetic diversity, but also to discern how natural selection structures genetic variation across the genome. With greater and greater resolution, we can now pinpoint the targets of selection on a large scale. At multiple levels, crypsis and convergent evolution are evident. Host jumps and shifts may be more pervasive than once believed, and hybridization and horizontal gene transfer (HGT) likely play important roles in the emergence of genetic novelty.
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Affiliation(s)
- Sophie de Vries
- Institute of Population Genetics, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Eva H Stukenbrock
- Environmental Genomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
- The Botanical Institute, Christian-Albrechts University of Kiel, Am Botanischen Garden 9-11, 24118, Kiel, Germany
| | - Laura E Rose
- Institute of Population Genetics, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
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11
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Depotter JRL, Doehlemann G. Target the core: durable plant resistance against filamentous plant pathogens through effector recognition. PEST MANAGEMENT SCIENCE 2020; 76:426-431. [PMID: 31713986 DOI: 10.1002/ps.5677] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 10/23/2019] [Accepted: 11/04/2019] [Indexed: 06/10/2023]
Abstract
Plant pathogens colonize their host through the secretion of effector proteins that modulate plant metabolism and immune responses to their benefit. Plants evolve towards effector recognition, leading to host immunity. Typically, pathogen effectors are targets for recognition through plant receptors that are encoded by resistance genes. Resistance gene mediated crop immunity puts a tremendous pressure on pathogens to adapt and alter their effector repertoire to overcome recognition. We argue that the type of effector that is recognized by the host may have considerable implications on the durability of resistance against filamentous plant pathogens. Effector genes that are conserved among pathogens and reside in core genome regions are most likely to hold indispensable virulence functions. Consequently, the cost for the pathogen to overcome recognition by the host is higher than for diversified, host-specific effectors with a quantitative impact on virulence. Consequently, resistance genes that directly target conserved effector proteins without the interception of other effector proteins are potentially excellent resistance resources. © 2019 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- Jasper R L Depotter
- Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, BioCenter, Cologne, Germany
| | - Gunther Doehlemann
- Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, BioCenter, Cologne, Germany
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12
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Hybridization Facilitates Adaptive Evolution in Two Major Fungal Pathogens. Genes (Basel) 2020; 11:genes11010101. [PMID: 31963231 PMCID: PMC7017293 DOI: 10.3390/genes11010101] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 01/02/2020] [Accepted: 01/14/2020] [Indexed: 01/13/2023] Open
Abstract
Hybridization is increasingly recognized as an important force impacting adaptation and evolution in many lineages of fungi. During hybridization, divergent genomes and alleles are brought together into the same cell, potentiating adaptation by increasing genomic plasticity. Here, we review hybridization in fungi by focusing on two fungal pathogens of animals. Hybridization is common between the basidiomycete yeast species Cryptococcus neoformans × Cryptococcus deneoformans, and hybrid genotypes are frequently found in both environmental and clinical settings. The two species show 10-15% nucleotide divergence at the genome level, and their hybrids are highly heterozygous. Though largely sterile and unable to mate, these hybrids can propagate asexually and generate diverse genotypes by nondisjunction, aberrant meiosis, mitotic recombination, and gene conversion. Under stress conditions, the rate of such genetic changes can increase, leading to rapid adaptation. Conversely, in hybrids formed between lineages of the chytridiomycete frog pathogen Batrachochytrium dendrobatidis (Bd), the parental genotypes are considerably less diverged (0.2% divergent). Bd hybrids are formed from crosses between lineages that rarely undergo sex. A common theme in both species is that hybrids show genome plasticity via aneuploidy or loss of heterozygosity and leverage these mechanisms as a rapid way to generate genotypic/phenotypic diversity. Some hybrids show greater fitness and survival in both virulence and virulence-associated phenotypes than parental lineages under certain conditions. These studies showcase how experimentation in model species such as Cryptococcus can be a powerful tool in elucidating the genotypic and phenotypic consequences of hybridization.
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13
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Zalar P, Zupančič J, Gostinčar C, Zajc J, de Hoog GS, De Leo F, Azua-Bustos A, Gunde-Cimerman N. The extremely halotolerant black yeast Hortaea werneckii - a model for intraspecific hybridization in clonal fungi. IMA Fungus 2019; 10:10. [PMID: 32647617 PMCID: PMC7325687 DOI: 10.1186/s43008-019-0007-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 04/03/2019] [Indexed: 12/22/2022] Open
Abstract
The polymorphic black yeast Hortaea werneckii (Capnodiales, Ascomycota) is extremely halotolerant (growth from 0 to 30% [w/v] NaCl) and has been extensively studied as a model for halotolerance in Eukaryotes for over two decades. Its most frequent sources are hypersaline environments and adjacent sea-water habitats in temperate, subtropical and tropical climates. Although typically saprobic, H. werneckii can also act as a commensal coloniser on human skin, causing tinea nigra on hands and soles. Here, we report that addition of NaCl to culture media expands the growth range of H. werneckii to 37 °C, which explains its colonisation of human skin, with its increased salinity. The morphological and physiological plasticity/ versatility of H. werneckii indicate that a species complex might be involved. This was investigated in this polyphasic taxonomic analysis based on the global diversity of H. werneckii strains collected from hypersaline environments, and from humans and animals. Analysis of D1/D2domains of 28S and internal transcribed spacer rDNA revealed 10 and 17 genotypes, respectively, that were not always compliant. The genotypes have global distributions. Human and environmental strains with the same genotypes are intermingled. Due to the limited number of phylogenetically informative characters in the ribosomal DNA dataset, the partial genes encoding for β-tubulin (BTB) and mini-chromosome maintenance protein (MCM7) were also sequenced. The use of these genes was hampered by ambiguous sequences obtained by Sanger sequencing, as a consequence of the diploid and highly heterozygous genome of many H. werneckii strains. Analysis of the BTB and MCM7 genes showed that in some cases two copies of the gene from the same genome are positioned in distant phylogenetic clusters of the intraspecific gene tree. Analysis of whole-genome sequences of selected H. werneckii strains generally confirmed the phylogenetic distances estimated on the basis of ribosomal genes, but also showed substantial reticulation within the phylogenetic history of the strains. This is in line with the hypothesis that the diploid genomes of H. werneckii were formed by hybridizations, which have sometimes occurred between relatively divergent strains.
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Affiliation(s)
- Polona Zalar
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, SI-1000 Ljubljana, Slovenia
| | - Jerneja Zupančič
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, SI-1000 Ljubljana, Slovenia
| | - Cene Gostinčar
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, SI-1000 Ljubljana, Slovenia
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, Qingdao, 266555 China
| | - Janja Zajc
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
| | - G. Sybren de Hoog
- Westerdijk Fungal Biodiversity Institute, P.O. Box 85167, Utrecht, 3508 AD The Netherlands
- Centre of Expertise in Mycology of RadboudUMC, Canisius Wilhelmina Hospital, Nijmegen, The Netherlands
| | - Filomena De Leo
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences (ChiBioFarAm), University of Messina, Viale F. Stagno d’Alcontres, 31 98166 Messina, Italy
| | - Armando Azua-Bustos
- Centro de Astrobiología (CSIC-INTA), Madrid, Spain
- Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, 8910060 Santiago, Chile
| | - Nina Gunde-Cimerman
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, SI-1000 Ljubljana, Slovenia
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Malarczyk D, Panek J, Frąc M. Alternative Molecular-Based Diagnostic Methods of Plant Pathogenic Fungi Affecting Berry Crops-A Review. Molecules 2019; 24:molecules24071200. [PMID: 30934757 PMCID: PMC6479758 DOI: 10.3390/molecules24071200] [Citation(s) in RCA: 5] [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: 02/13/2019] [Revised: 03/14/2019] [Accepted: 03/23/2019] [Indexed: 01/01/2023] Open
Abstract
Increasing consumer awareness of potentially harmful pesticides used in conventional agriculture has prompted organic farming to become notably more prevalent in recent decades. Central European countries are some of the most important producers of blueberries, raspberries and strawberries in the world and organic cultivation methods for these fruits have a significant market share. Fungal pathogens are considered to be the most significant threat to organic crops of berries, causing serious economic losses and reducing yields. In order to ameliorate the harmful effects of pathogenic fungi on cultivations, the application of rapid and effective identification methods is essential. At present, various molecular methods are applied for fungal species recognition, such as PCR, qPCR, LAMP and NGS.
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Affiliation(s)
- Dominika Malarczyk
- Institute of Agrophysics, Polish Academy of Sciences, 20-290 Lublin, Poland.
| | - Jacek Panek
- Institute of Agrophysics, Polish Academy of Sciences, 20-290 Lublin, Poland.
| | - Magdalena Frąc
- Institute of Agrophysics, Polish Academy of Sciences, 20-290 Lublin, Poland.
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Feurtey A, Stukenbrock EH. Interspecific Gene Exchange as a Driver of Adaptive Evolution in Fungi. Annu Rev Microbiol 2018; 72:377-398. [DOI: 10.1146/annurev-micro-090817-062753] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Throughout evolutionary history in the kingdom Fungi, taxa have exchanged genetic information among species, as revealed in particular by analyses of genome sequences. In fungi, hybridization can occur by sexual mating or by fusion of vegetative structures giving rise to new species or leaving traces of introgression in the genome. Furthermore, gene exchange can occur by horizontal gene transfer between species and can even include organisms outside the kingdom Fungi. In several cases, interspecific gene exchange has been instrumental in rapid adaptive evolution of fungal species and has notably played a role in the emergence of new pathogens. Here we summarize mechanisms and examples of gene exchange in fungi with a particular focus on the genomic context. We emphasize the need for and potential of applying population genetic approaches to better understand the processes and the impact of interspecific gene exchange in rapid adaptive evolution and species diversification. The broad occurrence of gene exchange among fungal species challenges our species concepts in the kingdom Fungi.
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Affiliation(s)
- Alice Feurtey
- Environmental Genomics, Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany;,
| | - Eva H. Stukenbrock
- Environmental Genomics, Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany;,
- Environmental Genomics, Christian-Albrechts University of Kiel, 24118 Kiel, Germany
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