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Li TT, Yang J, Huo YY, Zeng ZY, Huang HY, Xu FR, Dong X. Control of pathogenic fungi on Panax notoginseng by volatile oils from the food ingredients Allium sativum and Foeniculum vulgare. Lett Appl Microbiol 2022; 75:89-102. [PMID: 35334116 DOI: 10.1111/lam.13706] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 03/12/2022] [Accepted: 03/16/2022] [Indexed: 11/28/2022]
Abstract
To screen natural drugs with strong inhibitory effects against pathogenic fungi related to P. notoginseng, the antifungal activities of garlic and fennel EOs were studied by targeting P. notoginseng disease-associated fungi, and the possible action mechanisms of garlic and fennel EOs as plant fungicides were preliminarily discussed. At present, the antifungal mechanism of EOs has not been fully established. Therefore, understanding the antifungal mechanism of plant EOs is helpful to address P. notoginseng diseases continuous cropping disease-related obstacles and other agricultural cultivation problems. First, the Oxford cup method and chessboard were used to confirm that the EOs and oxamyl had a significant inhibitory effect on the growth of Fusarium oxysporum. F. oxysporum is the main pathogen causing root rot of P. notoginseng and the preliminary study on the antifungal mechanisms of the EOs against F. oxysporum showed that the inhibition of EOs mainly affects cell membrane permeability, cell processes, and affects the enzyme activities of microorganism, to achieve antifungal effects. Finally an in vivo model verified that both two EOs could significantly inhibit the occurrence of root rot caused by F. oxysporum.
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Affiliation(s)
- Tian-Tian Li
- School of Chinese Materia Medica, Yunnan University of Chinese Medicine, Kunming, 650500, China
| | - Jing Yang
- School of Chinese Materia Medica, Yunnan University of Chinese Medicine, Kunming, 650500, China
| | - Ying-Ying Huo
- School of Chinese Materia Medica, Yunnan University of Chinese Medicine, Kunming, 650500, China
| | - Zi-Ying Zeng
- School of Chinese Materia Medica, Yunnan University of Chinese Medicine, Kunming, 650500, China
| | - Heng-Yu Huang
- School of Chinese Materia Medica, Yunnan University of Chinese Medicine, Kunming, 650500, China
| | - Fu-Rong Xu
- School of Chinese Materia Medica, Yunnan University of Chinese Medicine, Kunming, 650500, China
| | - Xian Dong
- School of Chinese Materia Medica, Yunnan University of Chinese Medicine, Kunming, 650500, China
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2
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Takino J, Kotani A, Ozaki T, Peng W, Yu J, Guo Y, Mochizuki S, Akimitsu K, Hashimoto M, Ye T, Minami A, Oikawa H. Biochemistry-Guided Prediction of the Absolute Configuration of Fungal Reduced Polyketides. Angew Chem Int Ed Engl 2021; 60:23403-23411. [PMID: 34448341 DOI: 10.1002/anie.202110658] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Indexed: 11/08/2022]
Abstract
Highly reducing polyketide synthases (HR-PKSs) produce structurally diverse polyketides (PKs). The PK diversity is constructed by a variety of factors, including the β-keto processing, chain length, methylation pattern, and relative and absolute configurations of the substituents. We examined the stereochemical course of the PK processing for the synthesis of polyhydroxy PKs such as phialotides, phomenoic acid, and ACR-toxin. Heterologous expression of a HR-PKS gene, a trans-acting enoylreductase gene, and a truncated non-ribosomal peptide synthetase gene resulted in the formation of a linear PK with multiple stereogenic centers. The absolute configurations of the stereogenic centers were determined by chemical degradation followed by comparison of the degradation products with synthetic standards. A stereochemical rule was proposed to explain the absolute configurations of other reduced PKs and highlights an error in the absolute configurations of a reported structure. The present work demonstrates that focused functional analysis of functionally related HR-PKSs leads to a better understanding of the stereochemical course.
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Affiliation(s)
- Junya Takino
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Akari Kotani
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Taro Ozaki
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Wenquan Peng
- State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Xili, Nanshan District, Shenzhen, 518055, China
| | - Jie Yu
- State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Xili, Nanshan District, Shenzhen, 518055, China.,School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, 529020, China
| | - Yian Guo
- State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Xili, Nanshan District, Shenzhen, 518055, China.,School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, 529020, China
| | - Susumu Mochizuki
- International Institute of Rare Sugar Research and Education & Faculty of Agriculture, Kagawa University, Kagawa, 761-0795, Japan
| | - Kazuya Akimitsu
- International Institute of Rare Sugar Research and Education & Faculty of Agriculture, Kagawa University, Kagawa, 761-0795, Japan
| | - Masaru Hashimoto
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, 036-8561, Japan
| | - Tao Ye
- State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Xili, Nanshan District, Shenzhen, 518055, China
| | - Atsushi Minami
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Hideaki Oikawa
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
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3
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Takino J, Kotani A, Ozaki T, Peng W, Yu J, Guo Y, Mochizuki S, Akimitsu K, Hashimoto M, Ye T, Minami A, Oikawa H. Biochemistry‐Guided Prediction of the Absolute Configuration of Fungal Reduced Polyketides. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202110658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Junya Takino
- Department of Chemistry Faculty of Science Hokkaido University Sapporo 060-0810 Japan
| | - Akari Kotani
- Department of Chemistry Faculty of Science Hokkaido University Sapporo 060-0810 Japan
| | - Taro Ozaki
- Department of Chemistry Faculty of Science Hokkaido University Sapporo 060-0810 Japan
| | - Wenquan Peng
- State Key Laboratory of Chemical Oncogenomics Peking University Shenzhen Graduate School Xili, Nanshan District Shenzhen 518055 China
| | - Jie Yu
- State Key Laboratory of Chemical Oncogenomics Peking University Shenzhen Graduate School Xili, Nanshan District Shenzhen 518055 China
- School of Biotechnology and Health Sciences Wuyi University Jiangmen 529020 China
| | - Yian Guo
- State Key Laboratory of Chemical Oncogenomics Peking University Shenzhen Graduate School Xili, Nanshan District Shenzhen 518055 China
- School of Biotechnology and Health Sciences Wuyi University Jiangmen 529020 China
| | - Susumu Mochizuki
- International Institute of Rare Sugar Research and Education & Faculty of Agriculture Kagawa University Kagawa 761-0795 Japan
| | - Kazuya Akimitsu
- International Institute of Rare Sugar Research and Education & Faculty of Agriculture Kagawa University Kagawa 761-0795 Japan
| | - Masaru Hashimoto
- Faculty of Agriculture and Life Science Hirosaki University Hirosaki 036-8561 Japan
| | - Tao Ye
- State Key Laboratory of Chemical Oncogenomics Peking University Shenzhen Graduate School Xili, Nanshan District Shenzhen 518055 China
| | - Atsushi Minami
- Department of Chemistry Faculty of Science Hokkaido University Sapporo 060-0810 Japan
| | - Hideaki Oikawa
- Department of Chemistry Faculty of Science Hokkaido University Sapporo 060-0810 Japan
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4
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Soyer JL, Clairet C, Gay EJ, Lapalu N, Rouxel T, Stukenbrock EH, Fudal I. Genome-wide mapping of histone modifications during axenic growth in two species of Leptosphaeria maculans showing contrasting genomic organization. Chromosome Res 2021; 29:219-236. [PMID: 34018080 PMCID: PMC8159818 DOI: 10.1007/s10577-021-09658-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 02/16/2021] [Accepted: 03/03/2021] [Indexed: 12/25/2022]
Abstract
Leptosphaeria maculans 'brassicae' (Lmb) and Leptosphaeria maculans 'lepidii' (Lml) are closely related phytopathogenic species that exhibit a large macrosynteny but contrasting genome structure. Lmb has more than 30% of repeats clustered in large repeat-rich regions, while the Lml genome has only a small amount of evenly distributed repeats. Repeat-rich regions of Lmb are enriched in effector genes, expressed during plant infection. The distinct genome structures of Lmb and Lml provide an excellent model for comparing the organization of pathogenicity genes in relation to the chromatin landscape in two closely related phytopathogenic fungi. Here, we performed chromatin immunoprecipitation (ChIP) during axenic culture, targeting histone modifications typical for heterochromatin or euchromatin, combined with transcriptomic analysis to analyze the influence of chromatin organization on gene expression. In both species, we found that facultative heterochromatin is enriched with genes lacking functional annotation, including numerous effector and species-specific genes. Notably, orthologous genes located in H3K27me3 domains are enriched with effector genes. Compared to other fungal species, including Lml, Lmb is distinct in having large H3K9me3 domains associated with repeat-rich regions that contain numerous species-specific effector genes. Discovery of these two distinctive heterochromatin landscapes now raises questions about their involvement in the regulation of pathogenicity, the dynamics of these domains during plant infection and the selective advantage to the fungus to host effector genes in H3K9me3 or H3K27me3 domains.
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Affiliation(s)
- Jessica L Soyer
- Université Paris-Saclay, INRAE, AgroParisTech, UMR BIOGER, 78850, Thiverval-Grignon, France.
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306, Plön, Germany.
- Christian-Albrechts University of Kiel, Am Botanischen Garten 1-9, 24118, Kiel, Germany.
| | - Colin Clairet
- Université Paris-Saclay, INRAE, AgroParisTech, UMR BIOGER, 78850, Thiverval-Grignon, France
| | - Elise J Gay
- Université Paris-Saclay, INRAE, AgroParisTech, UMR BIOGER, 78850, Thiverval-Grignon, France
| | - Nicolas Lapalu
- Université Paris-Saclay, INRAE, AgroParisTech, UMR BIOGER, 78850, Thiverval-Grignon, France
| | - Thierry Rouxel
- Université Paris-Saclay, INRAE, AgroParisTech, UMR BIOGER, 78850, Thiverval-Grignon, France
| | - Eva H Stukenbrock
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306, Plön, Germany
- Christian-Albrechts University of Kiel, Am Botanischen Garten 1-9, 24118, Kiel, Germany
| | - Isabelle Fudal
- Université Paris-Saclay, INRAE, AgroParisTech, UMR BIOGER, 78850, Thiverval-Grignon, France
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Gay EJ, Soyer JL, Lapalu N, Linglin J, Fudal I, Da Silva C, Wincker P, Aury JM, Cruaud C, Levrel A, Lemoine J, Delourme R, Rouxel T, Balesdent MH. Large-scale transcriptomics to dissect 2 years of the life of a fungal phytopathogen interacting with its host plant. BMC Biol 2021; 19:55. [PMID: 33757516 PMCID: PMC7986464 DOI: 10.1186/s12915-021-00989-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 02/19/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The fungus Leptosphaeria maculans has an exceptionally long and complex relationship with its host plant, Brassica napus, during which it switches between different lifestyles, including asymptomatic, biotrophic, necrotrophic, and saprotrophic stages. The fungus is also exemplary of "two-speed" genome organisms in the genome of which gene-rich and repeat-rich regions alternate. Except for a few stages of plant infection under controlled conditions, nothing is known about the genes mobilized by the fungus throughout its life cycle, which may last several years in the field. RESULTS We performed RNA-seq on samples corresponding to all stages of the interaction of L. maculans with its host plant, either alive or dead (stem residues after harvest) in controlled conditions or in field experiments under natural inoculum pressure, over periods of time ranging from a few days to months or years. A total of 102 biological samples corresponding to 37 sets of conditions were analyzed. We show here that about 9% of the genes of this fungus are highly expressed during its interactions with its host plant. These genes are distributed into eight well-defined expression clusters, corresponding to specific infection lifestyles or to tissue-specific genes. All expression clusters are enriched in effector genes, and one cluster is specific to the saprophytic lifestyle on plant residues. One cluster, including genes known to be involved in the first phase of asymptomatic fungal growth in leaves, is re-used at each asymptomatic growth stage, regardless of the type of organ infected. The expression of the genes of this cluster is repeatedly turned on and off during infection. Whatever their expression profile, the genes of these clusters are enriched in heterochromatin regions associated with H3K9me3 or H3K27me3 repressive marks. These findings provide support for the hypothesis that part of the fungal genes involved in niche adaptation is located in heterochromatic regions of the genome, conferring an extreme plasticity of expression. CONCLUSION This work opens up new avenues for plant disease control, by identifying stage-specific effectors that could be used as targets for the identification of novel durable disease resistance genes, or for the in-depth analysis of chromatin remodeling during plant infection, which could be manipulated to interfere with the global expression of effector genes at crucial stages of plant infection.
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Affiliation(s)
- Elise J Gay
- Université Paris-Saclay, INRAE, AgroParisTech, UMR BIOGER, 78850, Thiverval-Grignon, France
| | - Jessica L Soyer
- Université Paris-Saclay, INRAE, AgroParisTech, UMR BIOGER, 78850, Thiverval-Grignon, France
| | - Nicolas Lapalu
- Université Paris-Saclay, INRAE, AgroParisTech, UMR BIOGER, 78850, Thiverval-Grignon, France
| | - Juliette Linglin
- Université Paris-Saclay, INRAE, AgroParisTech, UMR BIOGER, 78850, Thiverval-Grignon, France
| | - Isabelle Fudal
- Université Paris-Saclay, INRAE, AgroParisTech, UMR BIOGER, 78850, Thiverval-Grignon, France
| | - Corinne Da Silva
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057, Evry, France
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057, Evry, France
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057, Evry, France
| | - Corinne Cruaud
- Genoscope, Institut François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Anne Levrel
- INRAE, Institut Agro, Univ Rennes, IGEPP, 35653, Le Rheu, France
| | - Jocelyne Lemoine
- INRAE, Institut Agro, Univ Rennes, IGEPP, 35653, Le Rheu, France
| | - Regine Delourme
- INRAE, Institut Agro, Univ Rennes, IGEPP, 35653, Le Rheu, France
| | - Thierry Rouxel
- Université Paris-Saclay, INRAE, AgroParisTech, UMR BIOGER, 78850, Thiverval-Grignon, France
| | - Marie-Hélène Balesdent
- Université Paris-Saclay, INRAE, AgroParisTech, UMR BIOGER, 78850, Thiverval-Grignon, France.
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Sbaraini N, Bellini R, Penteriche AB, Guedes RLM, Garcia AWA, Gerber AL, Vainstein MH, de Vasconcelos ATR, Schrank A, Staats CC. Genome-wide DNA methylation analysis of Metarhizium anisopliae during tick mimicked infection condition. BMC Genomics 2019; 20:836. [PMID: 31711419 PMCID: PMC6849299 DOI: 10.1186/s12864-019-6220-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 10/24/2019] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND The Metarhizium genus harbors important entomopathogenic fungi. These species have been widely explored as biological control agents, and strategies to improve the fungal virulence are under investigation. Thus, the interaction between Metarhizium species and susceptible hosts have been explored employing different methods in order to characterize putative virulence determinants. However, the impact of epigenetic modulation on the infection cycle of Metarhizium is still an open topic. Among the different epigenetic modifications, DNA methylation of cytosine bases is an important mechanism to control gene expression in several organisms. To better understand if DNA methylation can govern Metarhizium-host interactions, the genome-wide DNA methylation profile of Metarhizium anisopliae was explored in two conditions: tick mimicked infection and a saprophytic-like control. RESULTS Using a genome wide DNA methylation profile based on bisulfite sequencing (BS-Seq), approximately 0.60% of the total cytosines were methylated in saprophytic-like condition, which was lower than the DNA methylation level (0.89%) in tick mimicked infection condition. A total of 670 mRNA genes were found to be putatively methylated, with 390 mRNA genes uniquely methylated in the tick mimicked infection condition. GO terms linked to response to stimuli, cell wall morphogenesis, cytoskeleton morphogenesis and secondary metabolism biosynthesis were over-represented in the tick mimicked infection condition, suggesting that energy metabolism is directed towards the regulation of genes associated with infection. However, recognized virulence determinants known to be expressed at distinct infection steps, such as the destruxin backbone gene and the collagen-like protein gene Mcl1, were found methylated, suggesting that a dynamic pattern of methylation could be found during the infectious process. These results were further endorsed employing RT-qPCR from cultures treated or not with the DNA methyltransferase inhibitor 5-Azacytidine. CONCLUSIONS The set of genes here analyzed focused on secondary metabolites associated genes, known to be involved in several processes, including virulence. The BS-Seq pipeline and RT-qPCR analysis employing 5-Azacytidine led to identification of methylated virulence genes in M. anisopliae. The results provided evidences that DNA methylation in M. anisopliae comprises another layer of gene expression regulation, suggesting a main role of DNA methylation regulating putative virulence determinants during M. anisopliae infection cycle.
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Affiliation(s)
- Nicolau Sbaraini
- Centro de Biotecnologia, UFRGS, Porto Alegre, RS, Brazil.,Rede Avançada em Biologia Computacional, RABICÓ, Petrópolis, RJ, Brazil
| | - Reinaldo Bellini
- Laboratório Nacional de Computação Científica, LNCC, Petrópolis, RJ, Brazil.,Rede Avançada em Biologia Computacional, RABICÓ, Petrópolis, RJ, Brazil
| | | | - Rafael Lucas Muniz Guedes
- Laboratório Nacional de Computação Científica, LNCC, Petrópolis, RJ, Brazil.,Rede Avançada em Biologia Computacional, RABICÓ, Petrópolis, RJ, Brazil
| | | | | | - Marilene Henning Vainstein
- Centro de Biotecnologia, UFRGS, Porto Alegre, RS, Brazil.,Rede Avançada em Biologia Computacional, RABICÓ, Petrópolis, RJ, Brazil
| | - Ana Tereza Ribeiro de Vasconcelos
- Laboratório Nacional de Computação Científica, LNCC, Petrópolis, RJ, Brazil.,Rede Avançada em Biologia Computacional, RABICÓ, Petrópolis, RJ, Brazil
| | - Augusto Schrank
- Centro de Biotecnologia, UFRGS, Porto Alegre, RS, Brazil.,Rede Avançada em Biologia Computacional, RABICÓ, Petrópolis, RJ, Brazil
| | - Charley Christian Staats
- Centro de Biotecnologia, UFRGS, Porto Alegre, RS, Brazil. .,Rede Avançada em Biologia Computacional, RABICÓ, Petrópolis, RJ, Brazil.
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Darma R, Lutz A, Elliott CE, Idnurm A. Identification of a gene cluster for the synthesis of the plant hormone abscisic acid in the plant pathogen Leptosphaeria maculans. Fungal Genet Biol 2019; 130:62-71. [DOI: 10.1016/j.fgb.2019.04.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 04/10/2019] [Accepted: 04/25/2019] [Indexed: 12/30/2022]
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8
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Botcinic acid biosynthesis in Botrytis cinerea relies on a subtelomeric gene cluster surrounded by relics of transposons and is regulated by the Zn2Cys6 transcription factor BcBoa13. Curr Genet 2019; 65:965-980. [DOI: 10.1007/s00294-019-00952-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 02/26/2019] [Accepted: 03/02/2019] [Indexed: 01/11/2023]
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Condon BJ, Elliott C, González JB, Yun SH, Akagi Y, Wiesner-Hanks T, Kodama M, Turgeon BG. Clues to an Evolutionary Mystery: The Genes for T-Toxin, Enabler of the Devastating 1970 Southern Corn Leaf Blight Epidemic, Are Present in Ancestral Species, Suggesting an Ancient Origin. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2018; 31:1154-1165. [PMID: 29792566 DOI: 10.1094/mpmi-03-18-0070-r] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The Southern corn leaf blight (SCLB) epidemic of 1970 devastated fields of T-cytoplasm corn planted in monoculture throughout the eastern United States. The epidemic was driven by race T, a previously unseen race of Cochliobolus heterostrophus. A second fungus, Phyllosticta zeae-maydis, with the same biological specificity, appeared coincidentally. Race T produces T-toxin, while Phyllosticta zeae-maydis produces PM-toxin, both host-selective polyketide toxins necessary for supervirulence. The present abundance of genome sequences offers an opportunity to tackle the evolutionary origins of T- and PM- toxin biosynthetic genes, previously thought unique to these species. Using the C. heterostrophus genes as probes, we identified orthologs in six additional Dothideomycete and three Eurotiomycete species. In stark contrast to the genetically fragmented race T Tox1 locus that encodes these genes, all newly found Tox1-like genes in other species reside at a single collinear locus. This compact arrangement, phylogenetic analyses, comparisons of Tox1 protein tree topology to a species tree, and Tox1 gene characteristics suggest that the locus is ancient and that some species, including C. heterostrophus, gained Tox1 by horizontal gene transfer. C. heterostrophus and Phyllosticta zeae-maydis did not exchange Tox1 DNA at the time of the SCLB epidemic, but how they acquired Tox1 remains uncertain. The presence of additional genes in Tox1-like clusters of other species, although not in C. heterostrophus and Phyllosticta zeae-maydis, suggests that the metabolites produced differ from T- and PM-toxin.
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Affiliation(s)
- Bradford J Condon
- 1 Section of Plant Pathology & Plant-Microbe Biology, School of Integrative Plant Science, 334 Plant Science Building, Cornell University, Ithaca, NY 14853, U.S.A
| | - Candace Elliott
- 2 School of Biosciences, Building 122 Rm 121, The University of Melbourne, Parkville 3010 VIC Australia
| | - Jonathan B González
- 1 Section of Plant Pathology & Plant-Microbe Biology, School of Integrative Plant Science, 334 Plant Science Building, Cornell University, Ithaca, NY 14853, U.S.A
| | - Sung Hwan Yun
- 3 Department of Medical Biotechnology, Soonchunhyang University, Asan 31538, South Korea
| | - Yasunori Akagi
- 4 The United Graduate School of Agricultural Sciences, Tottori University, 4-101 Koyama-Minami, Tottori 680-8553, Japan; and
| | - Tyr Wiesner-Hanks
- 5 Section of Plant Breeding, School of Integrative Plant Science, 240 Emerson Hall, Cornell University, Ithaca, NY 14853
| | - Motochiro Kodama
- 4 The United Graduate School of Agricultural Sciences, Tottori University, 4-101 Koyama-Minami, Tottori 680-8553, Japan; and
| | - B Gillian Turgeon
- 1 Section of Plant Pathology & Plant-Microbe Biology, School of Integrative Plant Science, 334 Plant Science Building, Cornell University, Ithaca, NY 14853, U.S.A
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10
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Sbaraini N, Guedes RLM, Andreis FC, Junges Â, de Morais GL, Vainstein MH, de Vasconcelos ATR, Schrank A. Secondary metabolite gene clusters in the entomopathogen fungus Metarhizium anisopliae: genome identification and patterns of expression in a cuticle infection model. BMC Genomics 2016; 17:736. [PMID: 27801295 PMCID: PMC5088523 DOI: 10.1186/s12864-016-3067-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Background The described species from the Metarhizium genus are cosmopolitan fungi that infect arthropod hosts. Interestingly, while some species infect a wide range of hosts (host-generalists), other species infect only a few arthropods (host-specialists). This singular evolutionary trait permits unique comparisons to determine how pathogens and virulence determinants emerge. Among the several virulence determinants that have been described, secondary metabolites (SMs) are suggested to play essential roles during fungal infection. Despite progress in the study of pathogen-host relationships, the majority of genes related to SM production in Metarhizium spp. are uncharacterized, and little is known about their genomic organization, expression and regulation. To better understand how infection conditions may affect SM production in Metarhizium anisopliae, we have performed a deep survey and description of SM biosynthetic gene clusters (BGCs) in M. anisopliae, analyzed RNA-seq data from fungi grown on cattle-tick cuticles, evaluated the differential expression of BGCs, and assessed conservation among the Metarhizium genus. Furthermore, our analysis extended to the construction of a phylogeny for the following three BGCs: a tropolone/citrinin-related compound (MaPKS1), a pseurotin-related compound (MaNRPS-PKS2), and a putative helvolic acid (MaTERP1). Results Among 73 BGCs identified in M. anisopliae, 20 % were up-regulated during initial tick cuticle infection and presumably possess virulence-related roles. These up-regulated BGCs include known clusters, such as destruxin, NG39x and ferricrocin, together with putative helvolic acid and, pseurotin and tropolone/citrinin-related compound clusters as well as uncharacterized clusters. Furthermore, several previously characterized and putative BGCs were silent or down-regulated in initial infection conditions, indicating minor participation over the course of infection. Interestingly, several up-regulated BGCs were not conserved in host-specialist species from the Metarhizium genus, indicating differences in the metabolic strategies employed by generalist and specialist species to overcome and kill their host. These differences in metabolic potential may have been partially shaped by horizontal gene transfer (HGT) events, as our phylogenetic analysis provided evidence that the putative helvolic acid cluster in Metarhizium spp. originated from an HGT event. Conclusions Several unknown BGCs are described, and aspects of their organization, regulation and origin are discussed, providing further support for the impact of SM on the Metarhizium genus lifestyle and infection process. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3067-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nicolau Sbaraini
- Rede Avançada em Biologia Computacional, RABICÓ, Petrópolis, RJ, Brazil.,Centro de Biotecnologia, Programa de Pós-graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Rafael Lucas Muniz Guedes
- Rede Avançada em Biologia Computacional, RABICÓ, Petrópolis, RJ, Brazil.,Laboratório Nacional de Computação Científica, LNCC, Petrópolis, RJ, Brazil
| | - Fábio Carrer Andreis
- Rede Avançada em Biologia Computacional, RABICÓ, Petrópolis, RJ, Brazil.,Centro de Biotecnologia, Programa de Pós-graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Ângela Junges
- Rede Avançada em Biologia Computacional, RABICÓ, Petrópolis, RJ, Brazil.,Centro de Biotecnologia, Programa de Pós-graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Guilherme Loss de Morais
- Rede Avançada em Biologia Computacional, RABICÓ, Petrópolis, RJ, Brazil.,Centro de Biotecnologia, Programa de Pós-graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.,Laboratório Nacional de Computação Científica, LNCC, Petrópolis, RJ, Brazil
| | - Marilene Henning Vainstein
- Rede Avançada em Biologia Computacional, RABICÓ, Petrópolis, RJ, Brazil.,Centro de Biotecnologia, Programa de Pós-graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Ana Tereza Ribeiro de Vasconcelos
- Rede Avançada em Biologia Computacional, RABICÓ, Petrópolis, RJ, Brazil.,Laboratório Nacional de Computação Científica, LNCC, Petrópolis, RJ, Brazil
| | - Augusto Schrank
- Rede Avançada em Biologia Computacional, RABICÓ, Petrópolis, RJ, Brazil. .,Centro de Biotecnologia, Programa de Pós-graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.
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11
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Haddadi P, Ma L, Wang H, Borhan MH. Genome-wide transcriptomic analyses provide insights into the lifestyle transition and effector repertoire of Leptosphaeria maculans during the colonization of Brassica napus seedlings. MOLECULAR PLANT PATHOLOGY 2016; 17:1196-210. [PMID: 26679637 PMCID: PMC6638455 DOI: 10.1111/mpp.12356] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 11/18/2015] [Accepted: 12/11/2015] [Indexed: 05/08/2023]
Abstract
Molecular interaction between the causal agent of blackleg disease, Leptosphaeria maculans (Lm), and its host, Brassica napus, is largely unknown. We applied a deep RNA-sequencing approach to gain insight into the pathogenicity mechanisms of Lm and the defence response of B. napus. RNA from the infected susceptible B. napus cultivar Topas DH16516, sampled at 2-day intervals (0-8 days), was sequenced and used for gene expression profiling. Patterns of gene expression regulation in B. napus showed multifaceted defence responses evident by the differential expression of genes encoding the pattern recognition receptor CERK1 (chitin elicitor receptor kinase 1), receptor like proteins and WRKY transcription factors. The up-regulation of genes related to salicylic acid and jasmonic acid at the initial and late stages of infection, respectively, provided evidence for the biotrophic and necrotrophic life stages of Lm during the infection of B. napus cotyledons. Lm transition from biotrophy to necrotropy was also supported by the expression function of Lm necrosis and ethylene-inducing (Nep-1)-like peptide. Genes encoding polyketide synthases and non-ribosomal peptide synthetases, with potential roles in pathogenicity, were up-regulated at 6-8 days after inoculation. Among other plant defence-related genes differentially regulated in response to Lm infection were genes involved in the reinforcement of the cell wall and the production of glucosinolates. Dual RNA-sequencing allowed us to define the Lm candidate effectors expressed during the infection of B. napus. Several candidate effectors suppressed Bax-induced cell death when transiently expressed in Nicotiana benthamaina leaves.
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Affiliation(s)
- Parham Haddadi
- Agriculture and Agri-Food Canada, Saskatoon Research Centre, 107 Science Place, Saskatoon, SK, Canada, S7N 0X2
| | - Lisong Ma
- Agriculture and Agri-Food Canada, Saskatoon Research Centre, 107 Science Place, Saskatoon, SK, Canada, S7N 0X2
| | - Haiyan Wang
- Agriculture and Agri-Food Canada, Saskatoon Research Centre, 107 Science Place, Saskatoon, SK, Canada, S7N 0X2
- Center of Plant Disease and Plant Pests of Hebei Province, College of Plant Protection, Agricultural University of Hebei, Baoding, China, 071001
| | - M Hossein Borhan
- Agriculture and Agri-Food Canada, Saskatoon Research Centre, 107 Science Place, Saskatoon, SK, Canada, S7N 0X2.
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12
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Naseeb S, Carter Z, Minnis D, Donaldson I, Zeef L, Delneri D. Widespread Impact of Chromosomal Inversions on Gene Expression Uncovers Robustness via Phenotypic Buffering. Mol Biol Evol 2016; 33:1679-96. [PMID: 26929245 PMCID: PMC4915352 DOI: 10.1093/molbev/msw045] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The nonrandom gene organization in eukaryotes plays a significant role in genome evolution and function. Chromosomal structural changes impact meiotic fitness and, in several organisms, are associated with speciation and rapid adaptation to different environments. Small sized chromosomal inversions, encompassing few genes, are pervasive in Saccharomyces “sensu stricto” species, while larger inversions are less common in yeasts compared with higher eukaryotes. To explore the effect of gene order on phenotype, reproductive isolation, and gene expression, we engineered 16 Saccharomyces cerevisiae strains carrying all possible paracentric and pericentric inversions between Ty1 elements, a natural substrate for rearrangements. We found that 4 inversions were lethal, while the other 12 did not show any fitness advantage or disadvantage in rich and minimal media. At meiosis, only a weak negative correlation with fitness was seen with the size of the inverted region. However, significantly lower fertility was seen in heterozygote invertant strains carrying recombination hotspots within the breakpoints. Altered transcription was observed throughout the genome rather than being overrepresented within the inversions. In spite of the large difference in gene expression in the inverted strains, mitotic fitness was not impaired in the majority of the 94 conditions tested, indicating that the robustness of the expression network buffers the deleterious effects of structural changes in several environments. Overall, our results support the notion that transcriptional changes may compensate for Ty-mediated rearrangements resulting in the maintenance of a constant phenotype, and suggest that large inversions in yeast are unlikely to be a selectable trait during vegetative growth.
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Affiliation(s)
- Samina Naseeb
- Computational and Evolutionary Biology Research Theme, Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Zorana Carter
- Computational and Evolutionary Biology Research Theme, Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - David Minnis
- Computational and Evolutionary Biology Research Theme, Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Ian Donaldson
- Computational and Evolutionary Biology Research Theme, Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Leo Zeef
- Computational and Evolutionary Biology Research Theme, Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Daniela Delneri
- Computational and Evolutionary Biology Research Theme, Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
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13
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Donzelli B, Krasnoff S. Molecular Genetics of Secondary Chemistry in Metarhizium Fungi. GENETICS AND MOLECULAR BIOLOGY OF ENTOMOPATHOGENIC FUNGI 2016; 94:365-436. [DOI: 10.1016/bs.adgen.2016.01.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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14
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Muria-Gonzalez MJ, Chooi YH, Breen S, Solomon PS. The past, present and future of secondary metabolite research in the Dothideomycetes. MOLECULAR PLANT PATHOLOGY 2015; 16:92-107. [PMID: 24889519 PMCID: PMC6638331 DOI: 10.1111/mpp.12162] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The Dothideomycetes represents a large and diverse array of fungi in which prominent plant pathogens are over-represented. Species within the Cochliobolus, Alternaria, Pyrenophora and Mycosphaerella (amongst others) all cause diseases that threaten food security in many parts of the world. Significant progress has been made over the past decade in understanding how some of these pathogens cause disease at a molecular level. It is reasonable to suggest that much of this progress can be attributed to the increased availability of genome sequences. However, together with revealing mechanisms of pathogenicity, these genome sequences have also highlighted the capacity of the Dothideomycetes to produce an extensive array of secondary metabolites, far greater than originally thought. Indeed, it is now clear that we appear to have only scratched the surface to date in terms of the identification of secondary metabolites produced by these fungi. In the first half of this review, we examine the current status of secondary metabolite research in the Dothideomycetes and highlight the diversity of the molecules discovered thus far, in terms of both structure and biological activity. In the second part of this review, we survey the emerging techniques and technologies that will be required to shed light on the vast array of secondary metabolite potential that is encoded within these genomes. Experimental design, analytical chemistry and synthetic biology are all discussed in the context of how they will contribute to this field.
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Affiliation(s)
- Mariano Jordi Muria-Gonzalez
- Plant Sciences Division, Research School of Biology, The Australian National University, Canberra, 0200, Australia
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15
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Schwenk D, Nett M, Dahse HM, Horn U, Blanchette RA, Hoffmeister D. Injury-induced biosynthesis of methyl-branched polyene pigments in a white-rotting basidiomycete. JOURNAL OF NATURAL PRODUCTS 2014; 77:2658-2663. [PMID: 25420175 DOI: 10.1021/np500552a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
A stereaceous basidiomycete was investigated with regard to its capacity to produce yellow pigments after physical injury of the mycelium. Two pigments were isolated from mycelial extracts, and their structures were elucidated by ESIMS and one- and two-dimensional NMR methods. The structures were identified as the previously undescribed polyenes (3Z,5E,7E,9E,11E,13Z,15E,17E)-18-methyl-19-oxoicosa-3,5,7,9,11,13,15,17-octaenoic acid (1) and (3E,5Z,7E,9E,11E,13E,15Z,17E,19E)-20-methyl-21-oxodocosa-3,5,7,9,11,13,15,17,19-nonaenoic acid (2). Stable-isotope feeding with [1-(13)C]acetate and l-[methyl-(13)C]methionine demonstrated a polyketide backbone and that the introduction of the sole methyl branch is most likely S-adenosyl-l-methionine-dependent. Dose-dependent inhibition of Drosophila melanogaster larval development was observed with both polyenes in concentrations between 12.5 and 100 μM. GI50 values for 1 and 2 against HUVEC (K-562 cells) were 71.6 and 17.4 μM (15.4 and 1.1 μM), respectively, whereas CC50 values for HeLa cells were virtually identical (44.1 and 45.1 μM).
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Affiliation(s)
- Daniel Schwenk
- Department of Pharmaceutical Microbiology at the Hans-Knöll-Institute, Friedrich-Schiller-Universität , Beutenbergstrasse 11a, 07745 Jena, Germany
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16
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Chooi YH, Solomon PS. A chemical ecogenomics approach to understand the roles of secondary metabolites in fungal cereal pathogens. Front Microbiol 2014; 5:640. [PMID: 25477876 PMCID: PMC4237128 DOI: 10.3389/fmicb.2014.00640] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 11/06/2014] [Indexed: 11/19/2022] Open
Abstract
Secondary metabolites (SMs) are known to play important roles in the virulence and lifestyle of fungal plant pathogens. The increasing availability of fungal pathogen genome sequences and next-generation genomic tools have allowed us to survey the SM gene cluster inventory in individual fungi. Thus, there is immense opportunity for SM discovery in these plant pathogens. Comparative genomics and transcriptomics have been employed to obtain insights on the genetic features that enable fungal pathogens to adapt in individual ecological niches and to adopt the different pathogenic lifestyles. Here, we will discuss how we can use these tools to search for ecologically important SM gene clusters in fungi, using cereal pathogens as models. This ecological genomics approach, combined with genome mining and chemical ecology tools, is likely to advance our understanding of the natural functions of SMs and accelerate bioactive molecule discovery.
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Affiliation(s)
- Yit-Heng Chooi
- Plant Sciences Division, Research School of Biology, The Australian National University Canberra, ACT, Australia
| | - Peter S Solomon
- Plant Sciences Division, Research School of Biology, The Australian National University Canberra, ACT, Australia
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17
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Chooi YH, Muria-Gonzalez MJ, Solomon PS. A genome-wide survey of the secondary metabolite biosynthesis genes in the wheat pathogen Parastagonospora nodorum.. Mycology 2014; 5:192-206. [PMID: 25379341 PMCID: PMC4205913 DOI: 10.1080/21501203.2014.928386] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Accepted: 05/22/2014] [Indexed: 12/02/2022] Open
Abstract
The model pathogen Parastagonospora nodorum is a necrotroph and the causal agent of the wheat disease Septoria nodorum blotch (SNB). The sequenced P. nodorum genome has revealed that the fungus harbours a large number of secondary metabolite genes. Secondary metabolites are known to play important roles in the virulence of plant pathogens, but limited knowledge is available about the SM repertoire of this wheat pathogen. Here, we review the secondary metabolites that have been isolated from P. nodorum and related species of the same genus and provide an in-depth genome-wide overview of the secondary metabolite gene clusters encoded in the P. nodorum genome. The secondary metabolite gene survey reveals that P. nodorum is capable of producing a diverse range of small molecules and exciting prospects exist for discovery of novel virulence factors and bioactive molecules.
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Affiliation(s)
- Yit-Heng Chooi
- Plant Sciences Division, Research School of Biology, The Australian National University , Canberra , 0200 , Australia
| | - Mariano Jordi Muria-Gonzalez
- Plant Sciences Division, Research School of Biology, The Australian National University , Canberra , 0200 , Australia
| | - Peter S Solomon
- Plant Sciences Division, Research School of Biology, The Australian National University , Canberra , 0200 , Australia
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