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Zhang B, Zhang N, Li R, Fu Z, Sun Y, Ren Z, Mu F, Han Y, Han Y. Underlying Mechanisms of the Hedgehog-Like Panicle and Filamentous Leaf Tissue Symptoms Caused by Sclerospora graminicola in Foxtail Millet. PHYTOPATHOLOGY 2024; 114:73-83. [PMID: 37535821 DOI: 10.1094/phyto-03-23-0097-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
Downy mildew caused by Sclerospora graminicola is a systemic infectious disease affecting foxtail millet production in Africa and Asia. S. graminicola-infected leaves could be decomposed to a state where only the veins remain, resulting in a filamentous leaf tissue symptom. The aim of the present study was to investigate how S. graminicola influences the formation of the filamentous leaf tissue symptoms in hosts at the morphological and molecular levels. We discovered that vegetative hyphae expanded rapidly, with high biomass accumulated at the early stages of S. graminicola infection. In addition, S. graminicola could affect spikelet morphological development at the panicle branch differentiation stage to the pistil and stamen differentiation stage by interfering with hormones and nutrient metabolism in the host, resulting in hedgehog-like panicle symptoms. S. graminicola could acquire high amounts of nutrients from host tissues through secretion of β-glucosidase, endoglucanase, and pectic enzyme, and destroyed host mesophyll cells by mechanical pressure caused by rapid expansion of hyphae. At the later stages, S. graminicola could rapidly complete sexual reproduction through tryptophan, fatty acid, starch, and sucrose metabolism and subsequently produce numerous oospores. Oospore proliferation and development further damage host leaves via mechanical pressure, resulting in a large number of degraded and extinct mesophyll cells and, subsequently, malformed leaves with only veins left, that is, "filamentous leaf tissue." Our study revealed the S. graminicola expansion characteristics from its asexual to sexual development stages, and the potential mechanisms via which the destructive effects of S. graminicola on hosts occur at different growth stages.
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Affiliation(s)
- Baojun Zhang
- College of Plant Protection, Shanxi Agricultural University, Taigu, 030801, China
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, Taiyuan, 030000, China
| | - Nuo Zhang
- College of Plant Protection, Shanxi Agricultural University, Taigu, 030801, China
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, Taiyuan, 030000, China
| | - Renjian Li
- College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430000, China
| | - Zhenxin Fu
- College of Plant Protection, Shanxi Agricultural University, Taigu, 030801, China
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, Taiyuan, 030000, China
| | - Yurong Sun
- College of Plant Protection, Shanxi Agricultural University, Taigu, 030801, China
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, Taiyuan, 030000, China
| | - Zhixian Ren
- College of Plant Protection, Shanxi Agricultural University, Taigu, 030801, China
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, Taiyuan, 030000, China
| | - Fan Mu
- College of Plant Protection, Shanxi Agricultural University, Taigu, 030801, China
| | - Yuanhuai Han
- College of Plant Protection, Shanxi Agricultural University, Taigu, 030801, China
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, Taiyuan, 030000, China
| | - Yanqing Han
- College of Plant Protection, Shanxi Agricultural University, Taigu, 030801, China
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, Taiyuan, 030000, China
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Hypothetical Protein VDAG_07742 Is Required for Verticillium dahliae Pathogenicity in Potato. Int J Mol Sci 2023; 24:ijms24043630. [PMID: 36835042 PMCID: PMC9965449 DOI: 10.3390/ijms24043630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/09/2023] [Accepted: 02/09/2023] [Indexed: 02/15/2023] Open
Abstract
Verticillium dahliae is a soil-borne pathogenic fungus that causes Verticillium wilt in host plants, a particularly serious problem in potato cultivation. Several pathogenicity-related proteins play important roles in the host infection process, hence, identifying such proteins, especially those with unknown functions, will surely aid in understanding the mechanism responsible for the pathogenesis of the fungus. Here, tandem mass tag (TMT) was used to quantitatively analyze the differentially expressed proteins in V. dahliae during the infection of the susceptible potato cultivar "Favorita". Potato seedlings were infected with V. dahliae and incubated for 36 h, after which 181 proteins were found to be significantly upregulated. Gene ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses showed that most of these proteins were involved in early growth and cell wall degradation. The hypothetical, secretory protein with an unknown function, VDAG_07742, was significantly upregulated during infection. The functional analysis with knockout and complementation mutants revealed that the associated gene was not involved in mycelial growth, conidial production, or germination; however, the penetration ability and pathogenicity of VDAG_07742 deletion mutants were significantly reduced. Therefore, our results strongly indicate that VDAG_07742 is essential in the early stage of potato infection by V. dahliae.
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He T, Ren Z, Muhae-Ud-Din G, Guo Q, Liu T, Chen W, Gao L. Transcriptomics Analysis of Wheat Tassel Response to Tilletia laevis Kühn, Which Causes Common Bunt of Wheat. FRONTIERS IN PLANT SCIENCE 2022; 13:823907. [PMID: 35273625 PMCID: PMC8902468 DOI: 10.3389/fpls.2022.823907] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 01/10/2022] [Indexed: 05/20/2023]
Abstract
Tilletia laevis Kühn [synonym T. foetida (Wallr.) Liro] can lead to a wheat common bunt, which is one of the most serious diseases affecting kernels, a serious reduction in grain yield, and losses can reach up to 80% in favorable environments. To understand how wheat tassels respond to T. laevis, based on an RNA-Seq technology, we analyzed a host transcript accumulation on healthy wheat tassels and on tassels infected by the pathogen. Our results showed that 7,767 out of 15,658 genes were upregulated and 7,891 out of 15,658 genes were downregulated in wheat tassels. Subsequent gene ontology (GO) showed that differentially expressed genes (DEGs) are predominantly involved in biological processes, cellular components, and molecular functions. Additionally, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that 20 pathways were expressed significantly during the infection of wheat with T. laevis, while biosynthesis of amino acids, carbon metabolism, and starch and sucrose metabolism pathways were more highly expressed. Our findings also demonstrated that genes involved in defense mechanisms and myeloblastosis (MYB) transcription factor families were mostly upregulated, and the RNA-seq results were validated by quantitative real-time polymerase chain reaction (qRT-PCR). This is the first report on transcriptomics analysis of wheat tassels in response to T. laevis, which will contribute to understanding the interaction of T. laevis and wheat, and may provide higher efficiency control strategies, including developing new methods to increase the resistance of wheat crops to T. laevis-caused wheat common bunt.
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Affiliation(s)
- Ting He
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- Key Laboratory of Agricultural Integrated Pest Management, Qinghai University, Xining, China
| | - Zhaoyu Ren
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ghulam Muhae-Ud-Din
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qingyun Guo
- Key Laboratory of Agricultural Integrated Pest Management, Qinghai University, Xining, China
| | - Taiguo Liu
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wanquan Chen
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Li Gao
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: Li Gao,
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Wang X, Yang X, Feng Y, Dang P, Wang W, Graze R, Clevenger JP, Chu Y, Ozias-Akins P, Holbrook C, Chen C. Transcriptome Profile Reveals Drought-Induced Genes Preferentially Expressed in Response to Water Deficit in Cultivated Peanut ( Arachis hypogaea L.). FRONTIERS IN PLANT SCIENCE 2021; 12:645291. [PMID: 33995444 PMCID: PMC8120000 DOI: 10.3389/fpls.2021.645291] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 03/12/2021] [Indexed: 05/28/2023]
Abstract
Cultivated peanut (Arachis hypogaea) is one of the most widely grown food legumes in the world, being valued for its high protein and unsaturated oil contents. Drought stress is one of the major constraints that limit peanut production. This study's objective was to identify the drought-responsive genes preferentially expressed under drought stress in different peanut genotypes. To accomplish this, four genotypes (drought tolerant: C76-16 and 587; drought susceptible: Tifrunner and 506) subjected to drought stress in a rainout shelter experiment were examined. Transcriptome sequencing analysis identified that all four genotypes shared a total of 2,457 differentially expressed genes (DEGs). A total of 139 enriched gene ontology terms consisting of 86 biological processes and 53 molecular functions, with defense response, reproductive process, and signaling pathways, were significantly enriched in the common DEGs. In addition, 3,576 DEGs were identified only in drought-tolerant lines in which a total of 74 gene ontology terms were identified, including 55 biological processes and 19 molecular functions, mainly related to protein modification process, pollination, and metabolic process. These terms were also found in shared genes in four genotypes, indicating that tolerant lines adjusted more related genes to respond to drought. Forty-three significantly enriched Kyoto Encyclopedia of Genes and Genomes pathways were also identified, and the most enriched pathways were those processes involved in metabolic pathways, biosynthesis of secondary metabolites, plant circadian rhythm, phenylpropanoid biosynthesis, and starch and sucrose metabolism. This research expands our current understanding of the mechanisms that facilitate peanut drought tolerance and shed light on breeding advanced peanut lines to combat drought stress.
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Affiliation(s)
- Xu Wang
- Department of Crop, Soil and Environmental Sciences, Auburn University, Auburn, AL, United States
| | - Xinlei Yang
- Department of Crop, Soil and Environmental Sciences, Auburn University, Auburn, AL, United States
- State Key Laboratory of North China Crop Improvement and Regulation, Laboratory of Crop Germplasm Resources of Hebei, Hebei Agricultural University, Baoding, China
| | - Yucheng Feng
- Department of Crop, Soil and Environmental Sciences, Auburn University, Auburn, AL, United States
| | - Phat Dang
- United States Department of Agriculture–Agricultural Research Service National Peanut Research Laboratory, Dawson, GA, United States
| | - Wenwen Wang
- Department of Crop, Soil and Environmental Sciences, Auburn University, Auburn, AL, United States
| | - Rita Graze
- Department of Biology, Auburn University, Auburn, AL, United States
| | - Josh P. Clevenger
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
| | - Ye Chu
- Center for Applied Genetic Technologies, University of Georgia, Tifton, GA, United States
| | - Peggy Ozias-Akins
- Center for Applied Genetic Technologies, University of Georgia, Tifton, GA, United States
| | - Corley Holbrook
- United States Department of Agriculture–Agricultural Research Service Crop Genetics and Breeding Research, Tifton, GA, United States
| | - Charles Chen
- Department of Crop, Soil and Environmental Sciences, Auburn University, Auburn, AL, United States
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Tan Y, Yang X, Pei M, Xu X, Wang C, Liu X. A genome-wide survey of interaction between rice and Magnaporthe oryzae via microarray analysis. Bioengineered 2020; 12:108-116. [PMID: 33356807 PMCID: PMC8806351 DOI: 10.1080/21655979.2020.1860479] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
The main aim of the work is to study the regulation of gene expression in the interaction between rice and Magnaporthe oryzae by gene chip technology. In this study, we mainly focused on changes of gene expression at 24, 48, and 72 hours post-inoculation (hpi), through which we could conduct a more comprehensive analysis of rice blast-related genes in the process of infection. The results showed that the experimental groups contained 460, 1227, and 3937 significant differentially expressed genes at 24, 48, and 72 hpi, respectively. Furthermore, 115 significantly differentially expressed genes were identified in response to rice blast infection at all three time points. By annotating these 115 genes, they were divided into three categories: metabolic pathways, proteins or enzymes, and organelle components. As expected, many of these genes were known rice blast-related genes; however, we discovered new genes with high fold changes. Most of them encoded conserved hypothetical proteins, and some were hypothetically conserved genes. Our study may contribute to finding new resistance genes and understanding the mechanism of rice blast development.
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Affiliation(s)
- Yanping Tan
- Hubei Provincia Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, Key Laboratory of State Ethnic Affairs Commission for Biological Technology, College of Life Science, South-Central University for Nationalities , Wuhan, China
| | - Xiaolin Yang
- Hubei Key Laboratory of Crop Disease, Insect Pests and Weeds, Institute of Plant Protection and Soil Science, Hubei Academy of Agricultural Sciences , Wuhan, China
| | - Minghao Pei
- Hubei Provincia Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, Key Laboratory of State Ethnic Affairs Commission for Biological Technology, College of Life Science, South-Central University for Nationalities , Wuhan, China
| | - Xin Xu
- Hubei Provincia Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, Key Laboratory of State Ethnic Affairs Commission for Biological Technology, College of Life Science, South-Central University for Nationalities , Wuhan, China
| | - Chuntai Wang
- Hubei Provincia Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, Key Laboratory of State Ethnic Affairs Commission for Biological Technology, College of Life Science, South-Central University for Nationalities , Wuhan, China
| | - Xinqiong Liu
- Hubei Provincia Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, Key Laboratory of State Ethnic Affairs Commission for Biological Technology, College of Life Science, South-Central University for Nationalities , Wuhan, China
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Tian D, Yang F, Niu Y, Lin Y, Chen Z, Li G, Luo Q, Wang F, Wang M. Loss function of SL (sekiguchi lesion) in the rice cultivar Minghui 86 leads to enhanced resistance to (hemi)biotrophic pathogens. BMC PLANT BIOLOGY 2020; 20:507. [PMID: 33148178 PMCID: PMC7640399 DOI: 10.1186/s12870-020-02724-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 10/26/2020] [Indexed: 05/02/2023]
Abstract
BACKGROUND Serotonin, originally identified as a neurotransmitter in mammals, functions as an antioxidant to scavenge cellular ROS in plants. In rice, the conversion of tryptamine to serotonin is catalyzed by SL (sekiguchi lesion), a member of cytochrome P450 monooxygenase family. The sl mutant, originated from rice cultivar Sekiguchi-asahi, exhibits spontaneous lesions, whereas its immune responses to pathogens have not been clearly characterized. RESULTS Here we identified three allelic mutants of SL in an indica rice restore line Minghui 86 (MH86), named as sl-MH-1, - 2 and - 3, all of which present the typical lesions under normal growth condition. Compared with those in MH86, the serotonin content in sl-MH-1 is dramatically decreased, whereas the levels of tryptamine and L-trytophan are significantly increased. The sl-MH-1 mutant accumulates high H2O2 level at its lesion sites and is more sensitive to exogenous H2O2 treatment than the wild type. When treated with the reductant vitamin C (Vc), the lesion formation on sl-MH-1 leaves could be efficiently suppressed. In addition, sl-MH-1 displayed more resistant to both the blast fungus and blight bacteria, Pyricularia oryzae (P. oryzae, teleomorph: Magnaporthe oryzae) and Xanthomonas oryzae pv. Oryzae (Xoo), respectively. The pathogen-associated molecular patterns (PAMPs)-triggered immunity (PTI) responses, like reactive oxygen species (ROS) burst and callose deposition, were enhanced in sl-MH-1. Moreover, loss function of SL resulted in higher resting levels of the defense hormones, salicylic acid and jasmonic acid. The RNA-seq analysis indicated that after P. oryzae infection, transcription of the genes involved in reduction-oxidation regulation was the most markedly changed in sl-MH-1, compared with MH86. CONCLUSIONS Our results indicate that SL, involving in the final step of serotonin biosynthesis, negatively regulates rice resistance against (hemi)biotrophic pathogens via compromising the PTI responses and defense hormones accumulation.
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Affiliation(s)
- Dagang Tian
- Biotechnology Research Institute, Fujian Key Laboratory of Genetic Engineering for Agriculture, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, Fujian, China
| | - Fang Yang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Yuqing Niu
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Yan Lin
- Biotechnology Research Institute, Fujian Key Laboratory of Genetic Engineering for Agriculture, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, Fujian, China
| | - Zaijie Chen
- Biotechnology Research Institute, Fujian Key Laboratory of Genetic Engineering for Agriculture, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, Fujian, China
| | - Gang Li
- Biotechnology Research Institute, Fujian Key Laboratory of Genetic Engineering for Agriculture, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, Fujian, China
| | - Qiong Luo
- Ministry of Education Key Laboratory of Agriculture Biodiversity for Plant Disease Management, Yunnan Agricultural University, Kunming, 650201, China
| | - Feng Wang
- Biotechnology Research Institute, Fujian Key Laboratory of Genetic Engineering for Agriculture, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, Fujian, China.
| | - Mo Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
- Fujian University Key Laboratory for Plant-Microbe Interaction, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
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Sruthilaxmi CB, Babu S. Proteome Responses to Individual Pathogens and Abiotic Conditions in Rice Seedlings. PHYTOPATHOLOGY 2020; 110:1326-1341. [PMID: 32175828 DOI: 10.1094/phyto-11-19-0425-r] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Rice plants under field conditions experience various biotic and abiotic stresses and are adapted to survive using a molecular cross-talk of genes and their protein products based on the severity of a given stress. Seedlings of cultivated variety ASD16 (resistant to fungal disease, blast; tolerant to abiotic stress, salinity) were subjected to salt, drought, high temperature and low temperature stress as well as infection by Rhizoctonia solani and Xanthomonas oryzae pv. oryzae (causing reemerging diseases such as sheath blight and leaf blight), respectively, the sheath blight and bacterial leaf blight pathogens. Leaf proteome was analyzed using two-dimensional electrophoresis and differentially expressed proteins were identified using mass spectrometry. In addition to many other differentially expressed proteins, acidic endochitinase was found to be upregulated during fungal infection and drought treatment, and a germin-like protein upregulated during fungal infection and high temperature stress. These two proteins were further validated at the gene expression level using reverse transcription-PCR in dual stress experiments. Pot culture plants were subjected to fungal infection followed by drought and drought followed by fungal infection to validate chitinase gene expression. Similarly, plants subjected to fungal infections followed by high temperature stress and vice versa were used to validate the expression of germin-like protein-coding gene. The results of the present study indicate that chitinase and germin-like protein are potential targets for further exploration to develop rice plants resistant or tolerant to biotic and abiotic stresses.
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Affiliation(s)
| | - Subramanian Babu
- VIT School of Agricultural Innovations and Advanced Learning, Vellore Institute of Technology, Vellore 632014, India
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Ngernmuen A, Suktrakul W, Kate-Ngam S, Jantasuriyarat C. Transcriptome Comparison of Defense Responses in the Rice Variety 'Jao Hom Nin' Regarding Two Blast Resistant Genes, Pish and Pik. PLANTS 2020; 9:plants9060694. [PMID: 32485961 PMCID: PMC7356797 DOI: 10.3390/plants9060694] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 05/21/2020] [Accepted: 05/27/2020] [Indexed: 11/24/2022]
Abstract
Jao Hom Nin (JHN) is a Thai rice variety with broad-spectrum resistant against rice blast fungus. JHN contains two rice blast resistant genes, Pish and Pik, located on chromosome 1 and on chromosome 11, respectively. To understand the blast resistance in JHN, the study of the defense mechanism related to the Pish and Pik genes is crucial. This study aimed to dissect defense response genes between the Pish and Pik genes using the RNA-seq technique. Differentially expressed genes (DEGs) of Pish and Pik backcross inbred lines were identified between 0 and 24 h after inoculation with rice blast spore suspension. The results showed that 1248 and 858 DEGs were unique to the Pish and Pik lines, respectively. The wall-associated kinase gene was unique to the Pish line and the zinc-finger-containing protein gene was unique to the Pik line. Pathogenicity-related proteins PR-4 and PR-10 were commonly found in both Pish and Pik lines. Moreover, DEGs functionally categorized in brassinosteriod, jasmonic acid, and salicylic acid pathways were detected in both Pish and Pik lines. These unique and shared genes in the Pish and Pik rice blast defense responses will help to dissect the mechanisms of plant defense and facilitate rice blast breeding programs.
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Affiliation(s)
- Athipat Ngernmuen
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkhen Campus, Ladyao, Chatuchak, Bangkok 10900, Thailand; (A.N.); (W.S.)
| | - Worrawit Suktrakul
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkhen Campus, Ladyao, Chatuchak, Bangkok 10900, Thailand; (A.N.); (W.S.)
| | - Sureeporn Kate-Ngam
- Department of Agronomy, Faculty of Agriculture, Ubon Ratchathani University, Warinchamrap, Ubon Ratchathani 34190, Thailand;
| | - Chatchawan Jantasuriyarat
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkhen Campus, Ladyao, Chatuchak, Bangkok 10900, Thailand; (A.N.); (W.S.)
- Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University (CASTNAR, NRU-KU), Kasetsart University, Bangkok 10900, Thailand
- Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Kasetsart University, Bangkok 10900, Thailand
- Correspondence: ; Tel.: +662-562-5444
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Niche-specific metabolic adaptation in biotrophic and necrotrophic oomycetes is manifested in differential use of nutrients, variation in gene content, and enzyme evolution. PLoS Pathog 2019; 15:e1007729. [PMID: 31002734 PMCID: PMC6493774 DOI: 10.1371/journal.ppat.1007729] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 05/01/2019] [Accepted: 03/25/2019] [Indexed: 12/12/2022] Open
Abstract
The use of host nutrients to support pathogen growth is central to disease. We addressed the relationship between metabolism and trophic behavior by comparing metabolic gene expression during potato tuber colonization by two oomycetes, the hemibiotroph Phytophthora infestans and the necrotroph Pythium ultimum. Genes for several pathways including amino acid, nucleotide, and cofactor biosynthesis were expressed more by Ph. infestans during its biotrophic stage compared to Py. ultimum. In contrast, Py. ultimum had higher expression of genes for metabolizing compounds that are normally sequestered within plant cells but released to the pathogen upon plant cell lysis, such as starch and triacylglycerides. The transcription pattern of metabolic genes in Ph. infestans during late infection became more like that of Py. ultimum, consistent with the former's transition to necrotrophy. Interspecific variation in metabolic gene content was limited but included the presence of γ-amylase only in Py. ultimum. The pathogens were also found to employ strikingly distinct strategies for using nitrate. Measurements of mRNA, 15N labeling studies, enzyme assays, and immunoblotting indicated that the assimilation pathway in Ph. infestans was nitrate-insensitive but induced during amino acid and ammonium starvation. In contrast, the pathway was nitrate-induced but not amino acid-repressed in Py. ultimum. The lack of amino acid repression in Py. ultimum appears due to the absence of a transcription factor common to fungi and Phytophthora that acts as a nitrogen metabolite repressor. Evidence for functional diversification in nitrate reductase protein was also observed. Its temperature optimum was adapted to each organism's growth range, and its Km was much lower in Py. ultimum. In summary, we observed divergence in patterns of gene expression, gene content, and enzyme function which contribute to the fitness of each species in its niche. A key feature of disease is the pathogen's consumption of host metabolites to support its growth and multiplication. Understanding how host nutrients are used by pathogens may lead to strategies for limiting disease, for example by developing inhibitors of metabolic pathways needed for pathogen growth. Feeding strategies of plant pathogens range between two extremes: necrotrophs kill host cells and consume the released nutrients, while biotrophs do not injure host cells but instead acquire nutrients from extracellular spaces in the plant. In this study, a comparison was made between the metabolism of Phytophthora infestans (the infamous Irish Famine pathogen) and Pythium ultimum during potato tuber colonization. These microbes have close evolutionary histories, but while Py. ultimum is a necrotroph, Ph. infestans is a biotroph for most of the disease cycle. It was discovered that distinct patterns of metabolic gene expression, gene content, and enzyme behavior underlie these lifestyles. For example, genes for utilizing compounds that are normally stored within plant cells were expressed more by Py. ultimum, while Ph. infestans appeared to synthesize more biosubstances from precursors. Several differences in carbon and nitrogen metabolism were linked to variation in enzyme content and gene expression regulators in the two species.
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Dube G, Kadoo N, Prashant R. Exploring the biological roles of Dothideomycetes ABC proteins: Leads from their phylogenetic relationships with functionally-characterized Ascomycetes homologs. PLoS One 2018; 13:e0197447. [PMID: 30071023 PMCID: PMC6071951 DOI: 10.1371/journal.pone.0197447] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 05/02/2018] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The ATP-binding cassette (ABC) superfamily is one of the largest, ubiquitous and diverse protein families in nature. Categorized into nine subfamilies, its members are important to most organisms including fungi, where they play varied roles in fundamental cellular processes, plant pathogenesis or fungicide tolerance. However, these proteins are not yet well-understood in the class Dothideomycetes, which includes several phytopathogens that infect a wide range of food crops including wheat, barley and maize and cause major economic losses. RESULTS We analyzed the genomes of 14 Dothideomycetes fungi (Test set) and seven well-known Ascomycetes fungi (Model set- that possessed gene expression/ functional analysis data about the ABC genes) and predicted 578 and 338 ABC proteins from each set respectively. These proteins were classified into subfamilies A to I, which revealed the distribution of the subfamily members across the Dothideomycetes and Ascomycetes genomes. Phylogenetic analysis of Dothideomycetes ABC proteins indicated evolutionary relationships among the subfamilies within this class. Further, phylogenetic relationships among the ABC proteins from the Model and the Test fungi within each subfamily were analyzed, which aided in classifying these proteins into subgroups. We compiled and curated functional and gene expression information from the previous literature for 118 ABC genes and mapped them on the phylogenetic trees, which suggested possible roles in pathogenesis and/or fungicide tolerance for the newly identified Dothideomycetes ABC proteins. CONCLUSIONS The present analysis is one of the firsts to extensively analyze ABC proteins from Dothideomycetes fungi. Their phylogenetic analysis and annotating the clades with functional information indicated a subset of Dothideomycetes ABC genes that could be considered for experimental validation for their roles in plant pathogenesis and/or fungicide tolerance.
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Affiliation(s)
- Gaurav Dube
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, India
| | - Narendra Kadoo
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, India
- Academy of Scientific and Innovative Research (AcSIR), New Delhi, India
| | - Ramya Prashant
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, India
- MIT School of Bioengineering Sciences & Research, MIT-Art, Design and Technology University, Pune, India
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11
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Bandara YMAY, Weerasooriya DK, Liu S, Little CR. The Necrotrophic Fungus Macrophomina phaseolina Promotes Charcoal Rot Susceptibility in Grain Sorghum Through Induced Host Cell-Wall-Degrading Enzymes. PHYTOPATHOLOGY 2018; 108:948-956. [PMID: 29465007 DOI: 10.1094/phyto-12-17-0404-r] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The cell-wall-degrading enzymes (CWDE) secreted by necrotrophs are important virulence factors. Although not unequivocally demonstrated, it has been suggested that necrotrophs induce hosts to cooperate in disease development through manipulation of host CWDE. The necrotrophic fungus Macrophomina phaseolina causes charcoal rot disease in Sorghum bicolor. An RNA-seq experiment was conducted to investigate the behavior of sorghum CWDE-encoding genes after M. phaseolina inoculation. Results revealed M. phaseolina's ability to significantly upregulate pectin methylesterase-, polygalacturonase-, cellulase-, endoglucanase-, and glycosyl hydrolase-encoding genes in a charcoal rot-susceptible sorghum genotype (Tx7000) but not in a resistant genotype (SC599). For functional validation, crude enzyme mixtures were extracted from M. phaseolina- and mock-inoculated charcoal-rot-resistant (SC599 and SC35) and -susceptible (Tx7000 and BTx3042) sorghum genotype stalks. A gel diffusion assay (pectin substrate) revealed significantly increased pectin methylesterase activity in M. phaseolina-inoculated Tx7000 and BTx3042. Polygalacturonase activity was determined using a ruthenium red absorbance assay (535 nm). Significantly increased polygalacturonase activity was observed in two susceptible genotypes after M. phaseolina inoculation. The activity of cellulose-degrading enzymes was determined using a 2-cyanoacetamide fluorimetric assay (excitation and emission maxima at 331 and 383 nm, respectively). The assay revealed significantly increased cellulose-degrading enzyme activity in M. phaseolina-inoculated Tx7000 and BTx3042. These findings revealed M. phaseolina's ability to promote charcoal rot susceptibility in grain sorghum through induced host CWDE.
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Affiliation(s)
- Y M A Y Bandara
- First third, and fourth authors: Department of Plant Pathology, and second author: Department of Agronomy, Kansas State University, Manhattan 66506
| | - D K Weerasooriya
- First third, and fourth authors: Department of Plant Pathology, and second author: Department of Agronomy, Kansas State University, Manhattan 66506
| | - S Liu
- First third, and fourth authors: Department of Plant Pathology, and second author: Department of Agronomy, Kansas State University, Manhattan 66506
| | - C R Little
- First third, and fourth authors: Department of Plant Pathology, and second author: Department of Agronomy, Kansas State University, Manhattan 66506
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Pham J, Stam R, Heredia VM, Csukai M, Huitema E. An NMRA-Like Protein Regulates Gene Expression in Phytophthora capsici to Drive the Infection Cycle on Tomato. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2018; 31:665-677. [PMID: 29419371 DOI: 10.1094/mpmi-07-17-0193-r] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Phytophthora spp. cause devastating disease epidemics on important crop plants and pose a grave threat to global crop production. Critically, Phytophthora pathogens represent a distinct evolutionary lineage in which pathogenicity has been acquired independently. Therefore, there is an urgent need to understand and disrupt the processes that drive infection if we aspire to defeat oomycete pathogens in the field. One area that has received little attention thus far in this respect is the regulation of Phytophthora gene expression during infection. Here, we characterize PcNMRAL1 (Phyca11_505845), a homolog of the Aspergillus nidulans nitrogen metabolite repression regulator NMRA and demonstrate a role for this protein in progression of the Phytophthora capsici infection cycle. PcNmrAL1 is coexpressed with the biotrophic marker gene PcHmp1 (haustorial membrane protein 1) and, when overexpressed, extends the biotrophic infection stage. Microarray analyses revealed that PcNmrAL1 overexpression in P. capsici leads to large-scale transcriptional changes during infection and in vitro. Importantly, detailed analysis reveals that PcNmrAL1 overexpression induces biotrophy-associated genes while repressing those associated with necrotrophy. In addition to factors controlling transcription, translation, and nitrogen metabolism, PcNMRAL1 helps regulate the expression of a considerable effector repertoire in P. capsici. Our data suggests that PcNMRAL1 is a transcriptional regulator that mediates the biotrophy to necrotrophy transition. PcNMRAL1 represents a novel factor that may drive the Phytophthora disease cycle on crops. This study provides the first insight into mechanisms that regulate infection-related processes in Phytophthora spp. and provides a platform for further studies aimed at disabling pathogenesis and preventing crop losses.
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Affiliation(s)
- Jasmine Pham
- 1 Division of Plant Sciences, University of Dundee, Dundee DD2 5DA, U.K
- 2 Dundee Effector Consortium, James Hutton Institute, Invergowrie, Dundee DD2 5DA, U.K
| | - Remco Stam
- 3 School for Life Sciences, Weihenstephan Technische Universität München, Freising, Germany; and
| | | | - Michael Csukai
- 4 Syngenta, Jealott's Hill International Research Centre, Bracknell, U.K
| | - Edgar Huitema
- 1 Division of Plant Sciences, University of Dundee, Dundee DD2 5DA, U.K
- 2 Dundee Effector Consortium, James Hutton Institute, Invergowrie, Dundee DD2 5DA, U.K
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13
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Basenko EY, Pulman JA, Shanmugasundram A, Harb OS, Crouch K, Starns D, Warrenfeltz S, Aurrecoechea C, Stoeckert CJ, Kissinger JC, Roos DS, Hertz-Fowler C. FungiDB: An Integrated Bioinformatic Resource for Fungi and Oomycetes. J Fungi (Basel) 2018; 4:jof4010039. [PMID: 30152809 PMCID: PMC5872342 DOI: 10.3390/jof4010039] [Citation(s) in RCA: 194] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 03/07/2018] [Accepted: 03/15/2018] [Indexed: 02/06/2023] Open
Abstract
FungiDB (fungidb.org) is a free online resource for data mining and functional genomics analysis for fungal and oomycete species. FungiDB is part of the Eukaryotic Pathogen Genomics Database Resource (EuPathDB, eupathdb.org) platform that integrates genomic, transcriptomic, proteomic, and phenotypic datasets, and other types of data for pathogenic and nonpathogenic, free-living and parasitic organisms. FungiDB is one of the largest EuPathDB databases containing nearly 100 genomes obtained from GenBank, Aspergillus Genome Database (AspGD), The Broad Institute, Joint Genome Institute (JGI), Ensembl, and other sources. FungiDB offers a user-friendly web interface with embedded bioinformatics tools that support custom in silico experiments that leverage FungiDB-integrated data. In addition, a Galaxy-based workspace enables users to generate custom pipelines for large-scale data analysis (e.g., RNA-Seq, variant calling, etc.). This review provides an introduction to the FungiDB resources and focuses on available features, tools, and queries and how they can be used to mine data across a diverse range of integrated FungiDB datasets and records.
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Affiliation(s)
- Evelina Y Basenko
- Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
| | - Jane A Pulman
- Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
| | - Achchuthan Shanmugasundram
- Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
| | - Omar S Harb
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Kathryn Crouch
- Wellcome Trust Centre for Molecular Parasitology, Glasgow G12 8TA, UK.
| | - David Starns
- Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
| | - Susanne Warrenfeltz
- Center for Tropical and Emerging Global Diseases, Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA.
| | - Cristina Aurrecoechea
- Center for Tropical and Emerging Global Diseases, Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA.
| | | | - Jessica C Kissinger
- Center for Tropical and Emerging Global Diseases, Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA.
| | - David S Roos
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Christiane Hertz-Fowler
- Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
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14
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Hernández C, Milagres AMF, Vázquez-Marrufo G, Muñoz-Páez KM, García-Pérez JA, Alarcón E. An ascomycota coculture in batch bioreactor is better than polycultures for cellulase production. Folia Microbiol (Praha) 2018; 63:467-478. [PMID: 29423709 DOI: 10.1007/s12223-018-0588-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 01/24/2018] [Indexed: 01/23/2023]
Abstract
Efficient hydrolysis of holocellulose depends on a proper balance between cellulase (endoglucanase, exoglucanase, β-glucosidase) and xylanase activities. The present study aimed to induce the production of cellulases and xylanases using liquid cultures (one, two, three, and four fungal strains on the same bioreactor) of wild strains of Trichoderma harzianum, Aspergillus niger, and Fusarium oxysporum. The strains were identified by amplification and analysis of the ITS rDNA region and the obtained sequences were deposited in Genbank. Enzymes (endoglucanase, exoglucansae, β-glucosidase, and xylanase activities) and the profile of extracellular protein isoforms (SDS-PAGE) produced by different fungal combinations (N = 14) were analyzed by Pearson's correlation matrix and principal component analysis (PCA). According to our results, induction of endoglucanase (19.02%) and β-glucosidase (6.35%) were obtained after 4 days when A. niger and F. oxysporum were cocultured. The combination of A. niger-T. harzianum produced higher endoglucanase in a shorter time than monocultures. On the contrary, when more than two strains were cultured in the same reactor, the relationships of competition were established, trending to diminish the amount of enzymes and the extracellular protein isoforms produced. The xylanase production was sensible to stress produced by mixed cultures, decreasing their activity. This is important when the aim is to produce cellulase-free xylanase. In addition, exoglucanase activity did not change in the combinations tested.
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Affiliation(s)
- Christian Hernández
- Instituto de Biotecnología y Ecología Aplicada (INBIOTECA), Universidad Veracruzana, Avenida de las culturas veracruzanas no. 101, colonia Emiliano Zapata, 91090, Xalapa, Veracruz, Mexico
| | - Adriane M F Milagres
- Departamento de Biotecnología, Escola de engenharia de Lorena (EEL), Universidade de São Paulo, Estrada Municipal do Campinho s/n - Pte Nova, Lorena, SP, 12602-810, Brazil
| | - Gerardo Vázquez-Marrufo
- Centro Multidisciplinario de Estudios en Biotecnología (CMEB), Facultad de Medicina Veterinaria y Zootecnia, Universidad Michoacana de San Nicolás de Hidalgo, Calle Morelia-Zinapecuaro Km 9.5, colonia La Palma, 58262, Tarímbaro, Michoacán, Mexico
| | - Karla María Muñoz-Páez
- Laboratorio de Investigación en Procesos Avanzados de Tratamiento de Aguas, Unidad Académica Juriquilla, Instituto de Ingeniería, Universidad Nacional Autónoma de México, Blvd. Juriquilla 3001, 76230, Querétaro, Mexico
| | - José Antonio García-Pérez
- Facultad de Biología, Universidad Veracruzana, Circuito Gonzalo Aguirre Beltrán, Zona Universitaria, 91090, Xalapa, Veracruz, Mexico
| | - Enrique Alarcón
- Instituto de Biotecnología y Ecología Aplicada (INBIOTECA), Universidad Veracruzana, Avenida de las culturas veracruzanas no. 101, colonia Emiliano Zapata, 91090, Xalapa, Veracruz, Mexico.
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15
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Saijo Y, Loo EPI, Yasuda S. Pattern recognition receptors and signaling in plant-microbe interactions. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 93:592-613. [PMID: 29266555 DOI: 10.1111/tpj.13808] [Citation(s) in RCA: 232] [Impact Index Per Article: 38.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 12/09/2017] [Accepted: 12/14/2017] [Indexed: 05/20/2023]
Abstract
Plants solely rely on innate immunity of each individual cell to deal with a diversity of microbes in the environment. Extracellular recognition of microbe- and host damage-associated molecular patterns leads to the first layer of inducible defenses, termed pattern-triggered immunity (PTI). In plants, pattern recognition receptors (PRRs) described to date are all membrane-associated receptor-like kinases or receptor-like proteins, reflecting the prevalence of apoplastic colonization of plant-infecting microbes. An increasing inventory of elicitor-active patterns and PRRs indicates that a large number of them are limited to a certain range of plant groups/species, pointing to dynamic and convergent evolution of pattern recognition specificities. In addition to common molecular principles of PRR signaling, recent studies have revealed substantial diversification between PRRs in their functions and regulatory mechanisms. This serves to confer robustness and plasticity to the whole PTI system in natural infections, wherein different PRRs are simultaneously engaged and faced with microbial assaults. We review the functional significance and molecular basis of PRR-mediated pathogen recognition and disease resistance, and also an emerging role for PRRs in homeostatic association with beneficial or commensal microbes.
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Affiliation(s)
- Yusuke Saijo
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, 630-0192, Japan
| | - Eliza Po-Iian Loo
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, 630-0192, Japan
| | - Shigetaka Yasuda
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, 630-0192, Japan
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16
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Zhao X, Li C, Wan S, Zhang T, Yan C, Shan S. Transcriptomic analysis and discovery of genes in the response of Arachis hypogaea to drought stress. Mol Biol Rep 2018; 45:119-131. [PMID: 29330721 DOI: 10.1007/s11033-018-4145-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 01/05/2018] [Indexed: 12/17/2022]
Abstract
The peanut (Arachis hypogaea) is an important crop species that is threatened by drought stress. The genome sequences of peanut, which was officially released in 2016, may help explain the molecular mechanisms that underlie drought tolerance in this species. We report here a gene expression profiling of A. hypogaea to gain a global view of its drought resistance. Using whole-transcriptome sequencing, we analysed differential gene expression in response to drought stress in the drought-resistant peanut cultivar J11. Pooled samples obtained at 6, 12, 18, 24, and 48 h were compared with control samples at 0 h. In total, 51,554 genes were found, including 49,289 known genes and 2265 unknown genes. We identified 224 differentially expressed transcription factors, 296,335 SNPs and 28,391 InDELs. In addition, we detected significant differences in the gene expression profiles of the treatment and control groups. After comparing the two groups, 4648 genes were identified. An in-depth analysis of the data revealed that a large number of genes were associated with drought stress, including transcription factors and genes involved in photosynthesis-antenna proteins, carbon metabolism and the citrate cycle. The results of this study provide insights into the diverse mechanisms that underlie the successful establishment of drought resistance in the peanut, thereby facilitating the identification of important genes in the peanut related to drought management. Transcriptome analysis based on RNA-Seq is a powerful approach for gene discovery and molecular marker development for this species.
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Affiliation(s)
- Xiaobo Zhao
- Laboratory of Genetics and Breeding, Shandong Peanut Research Institute, Qingdao, 266100, Shandong Province, People's Republic of China
| | - Chunjuan Li
- Laboratory of Genetics and Breeding, Shandong Peanut Research Institute, Qingdao, 266100, Shandong Province, People's Republic of China
| | - Shubo Wan
- Shandong Academy of Agricultural Sciences, Jinan, 250100, Shandong Province, People's Republic of China
| | - Tingting Zhang
- Laboratory of Genetics and Breeding, Shandong Peanut Research Institute, Qingdao, 266100, Shandong Province, People's Republic of China
| | - Caixia Yan
- Laboratory of Genetics and Breeding, Shandong Peanut Research Institute, Qingdao, 266100, Shandong Province, People's Republic of China
| | - Shihua Shan
- Laboratory of Genetics and Breeding, Shandong Peanut Research Institute, Qingdao, 266100, Shandong Province, People's Republic of China.
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17
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Nayak SN, Agarwal G, Pandey MK, Sudini HK, Jayale AS, Purohit S, Desai A, Wan L, Guo B, Liao B, Varshney RK. Aspergillus flavus infection triggered immune responses and host-pathogen cross-talks in groundnut during in-vitro seed colonization. Sci Rep 2017; 7:9659. [PMID: 28851929 PMCID: PMC5574979 DOI: 10.1038/s41598-017-09260-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 07/19/2017] [Indexed: 11/25/2022] Open
Abstract
Aflatoxin contamination, caused by fungal pathogen Aspergillus flavus, is a major quality and health problem delimiting the trade and consumption of groundnut (Arachis hypogaea L.) worldwide. RNA-seq approach was deployed to understand the host-pathogen interaction by identifying differentially expressed genes (DEGs) for resistance to in-vitro seed colonization (IVSC) at four critical stages after inoculation in J 11 (resistant) and JL 24 (susceptible) genotypes of groundnut. About 1,344.04 million sequencing reads have been generated from sixteen libraries representing four stages in control and infected conditions. About 64% and 67% of quality filtered reads (1,148.09 million) were mapped onto A (A. duranensis) and B (A. ipaёnsis) subgenomes of groundnut respectively. About 101 million unaligned reads each from J 11 and JL 24 were used to map onto A. flavus genome. As a result, 4,445 DEGs including defense-related genes like senescence-associated proteins, resveratrol synthase, 9s-lipoxygenase, pathogenesis-related proteins were identified. In A. flavus, about 578 DEGs coding for growth and development of fungus, aflatoxin biosynthesis, binding, transport, and signaling were identified in compatible interaction. Besides identifying candidate genes for IVSC resistance in groundnut, the study identified the genes involved in host-pathogen cross-talks and markers that can be used in breeding resistant varieties.
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Affiliation(s)
- Spurthi N Nayak
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, India
| | - Gaurav Agarwal
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Crop Protection and Management Research Unit, USDA-Agricultural Research Service, Tifton, GA, USA
- University of Georgia, Department of Plant Pathology, Tifton, GA, USA
| | - Manish K Pandey
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Hari K Sudini
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Ashwin S Jayale
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Shilp Purohit
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Aarthi Desai
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Liyun Wan
- Oil Crops Research Institute (OCRI), Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Baozhu Guo
- Crop Protection and Management Research Unit, USDA-Agricultural Research Service, Tifton, GA, USA
| | - Boshou Liao
- Oil Crops Research Institute (OCRI), Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
- The University of Western Australia, Crawley, WA, Australia.
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18
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van der Does HC, Rep M. Adaptation to the Host Environment by Plant-Pathogenic Fungi. ANNUAL REVIEW OF PHYTOPATHOLOGY 2017; 55:427-450. [PMID: 28645233 DOI: 10.1146/annurev-phyto-080516-035551] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Many fungi can live both saprophytically and as endophyte or pathogen inside a living plant. In both environments, complex organic polymers are used as sources of nutrients. Propagation inside a living host also requires the ability to respond to immune responses of the host. We review current knowledge of how plant-pathogenic fungi do this. First, we look at how fungi change their global gene expression upon recognition of the host environment, leading to secretion of effectors, enzymes, and secondary metabolites; changes in metabolism; and defense against toxic compounds. Second, we look at what is known about the various cues that enable fungi to sense the presence of living plant cells. Finally, we review literature on transcription factors that participate in gene expression in planta or are suspected to be involved in that process because they are required for the ability to cause disease.
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Affiliation(s)
| | - Martijn Rep
- Molecular Plant Pathology, University of Amsterdam, 1098XH Amsterdam, The Netherlands;
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19
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Xu X, Li G, Li L, Su Z, Chen C. Genome-wide comparative analysis of putative Pth11-related G protein-coupled receptors in fungi belonging to Pezizomycotina. BMC Microbiol 2017; 17:166. [PMID: 28743231 PMCID: PMC5526305 DOI: 10.1186/s12866-017-1076-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 07/18/2017] [Indexed: 01/23/2023] Open
Abstract
Background G-protein coupled receptors (GPCRs) are the largest family of transmembrane receptors in fungi, where they play important roles in signal transduction. Among them, the Pth11-related GPCRs form a large and divergent protein family, and are only found in fungi in Pezizomycotina. However, the evolutionary process and potential functions of Pth11-related GPCRs remain largely unknown. Results Twenty genomes of fungi in Pezizomycotina covering different nutritional strategies were mined for putative Pth11-related GPCRs. Phytopathogens encode much more putative Pth11-related GPCRs than symbionts, saprophytes, or entomopathogens. Based on the phylogenetic tree, these GPCRs can be divided into nine clades, with each clade containing fungi in different taxonomic orders. Instead of fungi from the same order, those fungi with similar nutritional strategies were inclined to share orthologs of putative Pth11-related GPCRs. Most of the CFEM domain-containing Pth11-related GPCRs, which were only included in two clades, were detected in phytopathogens. Furthermore, many putative Pth11-related GPCR genes of phytopathogens were upregulated during invasive plant infection, but downregulated under biotic stress. The expressions of putative Pth11-related GPCR genes of saprophytes and entomopathogens could be affected by nutrient conditions, especially the carbon source. The gene expressions revealed that Pth11-related GPCRs could respond to biotic/abiotic stress and invasive plant infection with different expression patterns. Conclusion Our results indicated that the Pth11-related GPCRs existed before the diversification of Pezizomycotina and have been gained and/or lost several times during the evolutionary process. Tandem duplications and trophic variations have been important factors in this evolution. Electronic supplementary material The online version of this article (doi:10.1186/s12866-017-1076-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xihui Xu
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Guopeng Li
- Agricultural Product Processing Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, 524001, China
| | - Lu Li
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhenzhu Su
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Chen Chen
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China.
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20
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Ah-Fong AMV, Kim KS, Judelson HS. RNA-seq of life stages of the oomycete Phytophthora infestans reveals dynamic changes in metabolic, signal transduction, and pathogenesis genes and a major role for calcium signaling in development. BMC Genomics 2017; 18:198. [PMID: 28228125 PMCID: PMC5322657 DOI: 10.1186/s12864-017-3585-x] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2016] [Accepted: 02/13/2017] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND The oomycete Phytophthora infestans causes the devastating late blight diseases of potato and tomato. P. infestans uses spores for dissemination and infection, like many other filamentous eukaryotic plant pathogens. The expression of a subset of its genes during spore formation and germination were studied previously, but comprehensive genome-wide data have not been available. RESULTS RNA-seq was used to profile hyphae, sporangia, sporangia undergoing zoosporogenesis, motile zoospores, and germinated cysts of P. infestans. Parallel studies of two isolates generated robust expression calls for 16,000 of 17,797 predicted genes, with about 250 transcribed in one isolate but not the other. The largest changes occurred in the transition from hyphae to sporangia, when >4200 genes were up-regulated. More than 1350 of these were induced >100-fold, accounting for 26% of total mRNA. Genes encoding calcium-binding proteins, cation channels, signaling proteins, and flagellar proteins were over-represented in genes up-regulated in sporangia. Proteins associated with pathogenicity were transcribed in waves with subclasses induced during zoosporogenesis, in zoospores, or in germinated cysts. Genes involved in most metabolic pathways were down-regulated upon sporulation and reactivated during cyst germination, although there were exceptions such as DNA replication, where transcripts peaked in zoospores. Inhibitor studies indicated that the transcription of two-thirds of genes induced during zoosporogenesis relied on calcium signaling. A sporulation-induced protein kinase was shown to bind a constitutive Gβ-like protein, which contributed to fitness based on knock-down analysis. CONCLUSIONS Spore formation and germination involves the staged expression of a large subset of the transcriptome, commensurate with the importance of spores in the life cycle. A comparison of the RNA-seq results with the older microarray data indicated that information is now available for about twice the number of genes than before. Analyses based on function revealed dynamic changes in genes involved in pathogenicity, metabolism, and signaling, with diversity in expression observed within members of multigene families and between isolates. The effects of calcium signaling, a spore-induced protein kinase, and an interacting Gβ-like protein were also demonstrated experimentally. The results reveal aspects of oomycete biology that underly their success as pathogens and potential targets for crop protection chemicals.
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Affiliation(s)
- Audrey M. V. Ah-Fong
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA 92521 USA
| | - Kyoung Su Kim
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA 92521 USA
- Present address: Department of Applied Biology, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, Korea
| | - Howard S. Judelson
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA 92521 USA
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Zhu L, Ni W, Liu S, Cai B, Xing H, Wang S. Transcriptomics Analysis of Apple Leaves in Response to Alternaria alternata Apple Pathotype Infection. FRONTIERS IN PLANT SCIENCE 2017; 8:22. [PMID: 28163714 PMCID: PMC5248534 DOI: 10.3389/fpls.2017.00022] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 01/04/2017] [Indexed: 05/03/2023]
Abstract
Alternaria blotch disease of apple (Malus × domestica Borkh.), caused by the apple pathotype of Alternaria alternata, is one of the most serious fungal diseases to affect apples. To develop an understanding of how apples respond to A. alternata apple pathotype (AAAP) infection, we examined the host transcript accumulation over the period between 0 and 72 h post AAAP inoculation. Large-scale gene expression analysis was conducted of the compatible interaction between "Starking Delicious" apple cultivar and AAAP using RNA-Seq and digital gene expression (DGE) profiling methods. Our results show that a total of 9080 differentially expressed genes (DEGs) were detected (>two-fold and FDR < 0.001) by RNA-Seq. During the early phase of infection, 12 h post inoculation (HPI), AAAP exhibited limited fungal development and little change in the transcript accumulation status (950 DEGs). During the intermediate phase of infection, the period between 18 and 36 HPI, increased fungal development, active infection, and increased transcript accumulation were detected (4111 and 3838 DEGs detected at each time point, respectively). The majority of DEGs were detected by 72 HPI, suggesting that this is an important time point in the response of apples' AAAP infection. Subsequent gene ontology (GO) and pathway enrichment analyses showed that DEGs are predominately involved in biological processes and metabolic pathways; results showed that almost gene associated with photosynthesis, oxidation-reduction were down-regulated, while transcription factors (i.e., WRKY, MYB, NAC, and Hsf) and DEGs involved in cell wall modification, defense signaling, the synthesis of defense-related metabolites, including pathogenesis-related (PRs) genes and phenylpropanoid/cyanoamino acid /flavonoid biosynthesis, were activated during this process. Our study also suggested that the cell wall defensive vulnerability and the down-regulation of most PRs and HSP70s in "Starking Delicious" following AAAP infection might interpret its susceptible to AAAP.
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Affiliation(s)
- Longming Zhu
- Department of Horticulture, Nanjing Agricultural UniversityNanjing, China
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Department of Agricultural, Nanjing Agricultural UniversityNanjing, China
| | - Weichen Ni
- Department of Horticulture, Nanjing Agricultural UniversityNanjing, China
| | - Shuai Liu
- Department of Horticulture, Nanjing Agricultural UniversityNanjing, China
| | - Binhua Cai
- Department of Horticulture, Nanjing Agricultural UniversityNanjing, China
| | - Han Xing
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Department of Agricultural, Nanjing Agricultural UniversityNanjing, China
| | - Sanhong Wang
- Department of Horticulture, Nanjing Agricultural UniversityNanjing, China
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Using Network Extracted Ontologies to Identify Novel Genes with Roles in Appressorium Development in the Rice Blast Fungus Magnaporthe oryzae. Microorganisms 2017; 5:microorganisms5010003. [PMID: 28106722 PMCID: PMC5374380 DOI: 10.3390/microorganisms5010003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 01/04/2017] [Accepted: 01/07/2017] [Indexed: 11/17/2022] Open
Abstract
Magnaporthe oryzae is the causal agent of rice blast disease, the most important infection of rice worldwide. Half the world's population depends on rice for its primary caloric intake and, as such, rice blast poses a serious threat to food security. The stages of M. oryzae infection are well defined, with the formation of an appressorium, a cell type that allows penetration of the plant cuticle, particularly well studied. However, many of the key pathways and genes involved in this disease stage are yet to be identified. In this study, I have used network-extracted ontologies (NeXOs), hierarchical structures inferred from RNA-Seq data, to identify pathways involved in appressorium development, which in turn highlights novel genes with potential roles in this process. This study illustrates the use of NeXOs for pathway identification from large-scale genomics data and also identifies novel genes with potential roles in disease. The methods presented here will be useful to study disease processes in other pathogenic species and these data represent predictions of novel targets for intervention in M. oryzae.
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Huang H, Nguyen Thi Thu T, He X, Gravot A, Bernillon S, Ballini E, Morel JB. Increase of Fungal Pathogenicity and Role of Plant Glutamine in Nitrogen-Induced Susceptibility (NIS) To Rice Blast. FRONTIERS IN PLANT SCIENCE 2017; 8:265. [PMID: 28293247 PMCID: PMC5329020 DOI: 10.3389/fpls.2017.00265] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 02/13/2017] [Indexed: 05/20/2023]
Abstract
Highlight Modifications in glutamine synthetase OsGS1-2 expression and fungal pathogenicity underlie nitrogen-induced susceptibility to rice blast. Understanding why nitrogen fertilization increase the impact of many plant diseases is of major importance. The interaction between Magnaporthe oryzae and rice was used as a model for analyzing the molecular mechanisms underlying Nitrogen-Induced Susceptibility (NIS). We show that our experimental system in which nitrogen supply strongly affects rice blast susceptibility only slightly affects plant growth. In order to get insights into the mechanisms of NIS, we conducted a dual RNA-seq experiment on rice infected tissues under two nitrogen fertilization regimes. On the one hand, we show that enhanced susceptibility was visible despite an over-induction of defense gene expression by infection under high nitrogen regime. On the other hand, the fungus expressed to high levels effectors and pathogenicity-related genes in plants under high nitrogen regime. We propose that in plants supplied with elevated nitrogen fertilization, the observed enhanced induction of plant defense is over-passed by an increase in the expression of the fungal pathogenicity program, thus leading to enhanced susceptibility. Moreover, some rice genes implicated in nitrogen recycling were highly induced during NIS. We further demonstrate that the OsGS1-2 glutamine synthetase gene enhances plant resistance to M. oryzae and abolishes NIS and pinpoint glutamine as a potential key nutrient during NIS.
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Affiliation(s)
- Huichuan Huang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural UniversityKunming, China
| | | | - Xiahong He
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural UniversityKunming, China
| | | | - Stéphane Bernillon
- INRA, UMR1332, Biologie du Fruit et Pathologie, Plateforme Métabolome de BordeauxVillenave d'Ornon, France
| | - Elsa Ballini
- SupAgro, UMR BGPI Institut National de la Recherche Agronomique/CIRAD/SupAgro, Campus International de BaillarguetMontpellier, France
| | - Jean-Benoit Morel
- Institut National de la Recherche Agronomique, UMR BGPI Institut National de la Recherche Agronomique/CIRAD/SupAgro, Campus International de BaillarguetMontpellier, France
- *Correspondence: Jean-Benoit Morel
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Chen JY, Xiao HL, Gui YJ, Zhang DD, Li L, Bao YM, Dai XF. Characterization of the Verticillium dahliae Exoproteome Involves in Pathogenicity from Cotton-Containing Medium. Front Microbiol 2016; 7:1709. [PMID: 27840627 PMCID: PMC5083787 DOI: 10.3389/fmicb.2016.01709] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 10/12/2016] [Indexed: 12/31/2022] Open
Abstract
Verticillium wilt, caused by the Verticillium dahliae phytopathogen, is a devastating disease affecting many economically important crops. Previous studies have shown that the exoproteome of V. dahliae plays a significant role in this pathogenic process, but the components and mechanisms that underlie this remain unclear. In this study, the exoproteome of V. dahliae was induced in a cotton-containing C’zapek-Dox (CCD) medium and quantified using the high-throughput isobaric tag technique for relative and absolute quantification (iTRAQ). Results showed that the abundance of 271 secreted proteins was affected by the CCD medium, of which 172 contain typical signal peptides generally produced by the Golgi/endoplasmic reticulum (ER). These enhanced abundance proteins were predominantly enriched in carbohydrate hydrolases; 126 were classified as carbohydrate-active (CAZymes) and almost all were significantly up-regulated in the CCD medium. Results showed that CAZymes proteins 30 and 22 participate in pectin and cellulose degradation pathways, corresponding with the transcription levels of several genes encoded plant cell wall degradation enzyme activated significantly during cotton infection. In addition, targeted deletion of two pectin lyase genes (VdPL3.1 and VdPL3.3) impaired wilt virulence to cotton. This study demonstrates that the V. dahliae exoproteome plays a crucial role in the development of symptoms of wilting and necrosis, predominantly via the pathogenic mechanisms of plant cell wall degradation as part of host plant infection.
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Affiliation(s)
- Jie-Yin Chen
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences Beijing, China
| | - Hong-Li Xiao
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences Beijing, China
| | - Yue-Jing Gui
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences Beijing, China
| | - Dan-Dan Zhang
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences Beijing, China
| | - Lei Li
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences Beijing, China
| | - Yu-Ming Bao
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences Beijing, China
| | - Xiao-Feng Dai
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences Beijing, China
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Lakshmanan V, Cottone J, Bais HP. Killing Two Birds with One Stone: Natural Rice Rhizospheric Microbes Reduce Arsenic Uptake and Blast Infections in Rice. FRONTIERS IN PLANT SCIENCE 2016; 7:1514. [PMID: 27790229 PMCID: PMC5062539 DOI: 10.3389/fpls.2016.01514] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Accepted: 09/26/2016] [Indexed: 05/13/2023]
Abstract
Our recent work has shown that a rice thizospheric natural isolate, a Pantoea sp (hereafter EA106) attenuates Arsenic (As) uptake in rice. In parallel, yet another natural rice rhizospheric isolate, a Pseudomonas chlororaphis (hereafter EA105), was shown to inhibit rice blast pathogen Magnaporthe oryzae. Considering the above, we envisaged to evaluate the importance of mixed stress regime in rice plants subjected to both As toxicity and blast infections. Plants subjected to As regime showed increased susceptibility to blast infections compared to As-untreated plants. Rice blast pathogen M. oryzae showed significant resistance against As toxicity compared to other non-host fungal pathogens. Interestingly, plants treated with EA106 showed reduced susceptibility against blast infections in plants pre-treated with As. This data also corresponded with lower As uptake in plants primed with EA106. In addition, we also evaluated the expression of defense related genes in host plants subjected to As treatment. The data showed that plants primed with EA106 upregulated defense-related genes with or without As treatment. The data shows the first evidence of how rice plants cope with mixed stress regimes. Our work highlights the importance of natural association of plant microbiome which determines the efficacy of benign microbes to promote the development of beneficial traits in plants.
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Affiliation(s)
- Venkatachalam Lakshmanan
- Department of Plant and Soil Sciences, University of DelawareNewark, DE, USA
- Delaware Biotechnology InstituteNewark, DE, USA
| | - Jonathon Cottone
- Department of Plant and Soil Sciences, University of DelawareNewark, DE, USA
- Delaware Biotechnology InstituteNewark, DE, USA
| | - Harsh P. Bais
- Department of Plant and Soil Sciences, University of DelawareNewark, DE, USA
- Delaware Biotechnology InstituteNewark, DE, USA
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Validation of Reference Genes for Robust qRT-PCR Gene Expression Analysis in the Rice Blast Fungus Magnaporthe oryzae. PLoS One 2016; 11:e0160637. [PMID: 27560664 PMCID: PMC4999194 DOI: 10.1371/journal.pone.0160637] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 07/23/2016] [Indexed: 11/19/2022] Open
Abstract
The rice blast fungus causes significant annual harvest losses. It also serves as a genetically-tractable model to study fungal ingress. Whilst pathogenicity determinants have been unmasked and changes in global gene expression described, we know little about Magnaporthe oryzae cell wall remodelling. Our interests, in wall remodelling genes expressed during infection, vegetative growth and under exogenous wall stress, demand robust choice of reference genes for quantitative Real Time-PCR (qRT-PCR) data normalisation. We describe the expression stability of nine candidate reference genes profiled by qRT-PCR with cDNAs derived during asexual germling development, from sexual stage perithecia and from vegetative mycelium grown under various exogenous stressors. Our Minimum Information for Publication of qRT-PCR Experiments (MIQE) compliant analysis reveals a set of robust reference genes used to track changes in the expression of the cell wall remodelling gene MGG_Crh2 (MGG_00592). We ranked nine candidate reference genes by their expression stability (M) and report the best gene combination needed for reliable gene expression normalisation, when assayed in three tissue groups (Infective, Vegetative, and Global) frequently used in M. oryzae expression studies. We found that MGG_Actin (MGG_03982) and the 40S 27a ribosomal subunit MGG_40s (MGG_02872) proved to be robust reference genes for the Infection group and MGG_40s and MGG_Ef1 (Elongation Factor1-α) for both Vegetative and Global groups. Using the above validated reference genes, M. oryzae MGG_Crh2 expression was found to be significantly (p<0.05) elevated three-fold during vegetative growth as compared with dormant spores and two fold higher under cell wall stress (Congo Red) compared to growth under optimal conditions. We recommend the combinatorial use of two reference genes, belonging to the cytoskeleton and ribosomal synthesis functional groups, MGG_Actin, MGG_40s, MGG_S8 (Ribosomal subunit 40S S8) or MGG_Ef1, which demonstrated low M values across heterogeneous tissues. By contrast, metabolic pathway genes MGG_Fad (FAD binding domain-containing protein) and MGG_Gapdh (Glyceraldehyde-3-phosphate dehydrogenase) performed poorly, due to their lack of expression stability across samples.
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Magnesium Uptake by CorA Transporters Is Essential for Growth, Development and Infection in the Rice Blast Fungus Magnaporthe oryzae. PLoS One 2016; 11:e0159244. [PMID: 27416318 PMCID: PMC4945025 DOI: 10.1371/journal.pone.0159244] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 06/29/2016] [Indexed: 11/29/2022] Open
Abstract
Magnaporthe oryzae, the causative organism of rice blast, infects cereal crops and grasses at various stages of plant development. A comprehensive understanding of its metabolism and the implications on pathogenesis is necessary for countering this devastating crop disease. We present the role of the CorA magnesium transporters, MoAlr2 and MoMnr2, in development and pathogenicity of M. oryzae. The MoALR2 and MoMNR2 genes individually complement the Mg2+ uptake defects of a S. cerevisiae CorA transporter double mutant. MoALR2 and MoMNR2 respond to extracellular Mg2+ and Ca2+ levels and their expression is elevated under Mg2+ scarce conditions. RNA silencing mediated knockdown of MoALR2 (WT+siALR2, Δmnr2+siALR2 and ALR2+MNR2 simultaneous silencing) drastically alters intracellular cation concentrations and sensitivity to metal ions. MoALR2 silencing is detrimental to vegetative growth and surface hydrophobicity of mycelia, and the transformants display loss of cell wall integrity. MoALR2 is required for conidiogenesis and appressorium development, and is essential for infection. Investigation of knockdown transformants reveal low cAMP levels and altered expression of genes encoding proteins involved in MoMps1 cell wall integrity and cAMP MoPmk1 driven MAP Kinase signaling pathways. In contrast to MoALR2 knockdowns, the MoMNR2 deletion (Δmnr2) shows increased sensitivity to CorA inhibitors as well as altered cation sensitivity, but has limited effect on surface hydrophobicity and severity of plant infection. Interestingly, MoALR2 expression is elevated in Δmnr2. Impairment of development and infectivity of knockdown transformants and altered intracellular cation composition suggest that CorA transporters are essential for Mg2+ homeostasis within the cell, and are crucial to maintaining normal gene expression associated with cell structure, signal transduction and surface hydrophobicity in M. oryzae. We suggest that CorA transporters, and especially MoALR2, constitute an attractive target for the development of antifungal agents against this pathogen.
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Mogga V, Delventhal R, Weidenbach D, Langer S, Bertram PM, Andresen K, Thines E, Kroj T, Schaffrath U. Magnaporthe oryzae effectors MoHEG13 and MoHEG16 interfere with host infection and MoHEG13 counteracts cell death caused by Magnaporthe-NLPs in tobacco. PLANT CELL REPORTS 2016; 35:1169-85. [PMID: 26883226 DOI: 10.1007/s00299-016-1943-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 01/24/2016] [Indexed: 05/21/2023]
Abstract
KEY MESSAGE Adapted pathogens are able to modulate cell responses of their hosts most likely due to the activity of secreted effector molecules thereby enabling colonisation by ostensible nonhost pathogens. It is postulated that host and nonhost pathogens of a given plant species differ in their repertoire of secreted effector molecules that are able to suppress plant resistance. We pursued the strategy of identifying novel effectors of Magnaporthe oryzae, the causal agent of blast disease, by comparing the infection process of closely related host vs. nonhost Magnaporthe species on barley (Hordeum vulgare L.). When both types of pathogen simultaneously attacked the same cell, the nonhost isolate became a successful pathogen possibly due to potent effectors secreted by the host isolate. Microarray studies led to a set of M. oryzae Hypothetical Effector Genes (MoHEGs) which were classified as Early- and LateMoHEGs according to the maximal transcript abundance during colonization of barley. Interestingly, orthologs of these MoHEGs from a nonhost pathogen were similarly regulated when investigated in a host situation, suggesting evolutionary conserved functions. Knockout mutants of MoHEG16 from the group of EarlyMoHEGs were less virulent on barley and microscopic studies revealed an attenuated transition from epidermal to mesophyll colonization. MoHEG13, a LateMoHEG, was shown to antagonize cell death induced by M. oryzae Necrosis-and ethylene-inducing-protein-1 (Nep1)-like proteins in Nicotiana benthamiana. MoHEG13 has a virulence function as a knockout mutant showed attenuated disease progression when inoculated on barley.
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Affiliation(s)
- Valerie Mogga
- Department of Plant Physiology, RWTH Aachen University, 52056, Aachen, Germany
| | - Rhoda Delventhal
- Department of Plant Physiology, RWTH Aachen University, 52056, Aachen, Germany
| | - Denise Weidenbach
- Department of Plant Physiology, RWTH Aachen University, 52056, Aachen, Germany
| | - Samantha Langer
- Department of Plant Physiology, RWTH Aachen University, 52056, Aachen, Germany
| | - Philipp M Bertram
- Department of Plant Physiology, RWTH Aachen University, 52056, Aachen, Germany
| | - Karsten Andresen
- Institute of Biotechnology and Drug Research, Erwin-Schrödinger-Strasse 56, 67663, Kaiserslautern, Germany
| | - Eckhard Thines
- Institute of Biotechnology and Drug Research, Erwin-Schrödinger-Strasse 56, 67663, Kaiserslautern, Germany
- Biotechnology, Johannes Gutenberg-University, 55099, Mainz, Germany
| | - Thomas Kroj
- INRA, UMR BGPI, Campus International de Baillarguet, TA A-54/K, 34398, Montpellier Cedex 5, France
| | - Ulrich Schaffrath
- Department of Plant Physiology, RWTH Aachen University, 52056, Aachen, Germany.
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Vega A, Canessa P, Hoppe G, Retamal I, Moyano TC, Canales J, Gutiérrez RA, Rubilar J. Transcriptome analysis reveals regulatory networks underlying differential susceptibility to Botrytis cinerea in response to nitrogen availability in Solanum lycopersicum. FRONTIERS IN PLANT SCIENCE 2015; 6:911. [PMID: 26583019 PMCID: PMC4631835 DOI: 10.3389/fpls.2015.00911] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 10/12/2015] [Indexed: 05/20/2023]
Abstract
Nitrogen (N) is one of the main limiting nutrients for plant growth and crop yield. It is well documented that changes in nitrate availability, the main N source found in agricultural soils, influences a myriad of developmental programs and processes including the plant defense response. Indeed, many agronomical reports indicate that the plant N nutritional status influences their ability to respond effectively when challenged by different pathogens. However, the molecular mechanisms involved in N-modulation of plant susceptibility to pathogens are poorly characterized. In this work, we show that Solanum lycopersicum defense response to the necrotrophic fungus Botrytis cinerea is affected by plant N availability, with higher susceptibility in nitrate-limiting conditions. Global gene expression responses of tomato against B. cinerea under contrasting nitrate conditions reveals that plant primary metabolism is affected by the fungal infection regardless of N regimes. This result suggests that differential susceptibility to pathogen attack under contrasting N conditions is not only explained by a metabolic alteration. We used a systems biology approach to identify the transcriptional regulatory network implicated in plant response to the fungus infection under contrasting nitrate conditions. Interestingly, hub genes in this network are known key transcription factors involved in ethylene and jasmonic acid signaling. This result positions these hormones as key integrators of nitrate and defense against B. cinerea in tomato plants. Our results provide insights into potential crosstalk mechanisms between necrotrophic defense response and N status in plants.
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Affiliation(s)
- Andrea Vega
- Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de ChileSantiago, Chile
- Millennium Nucleus Center for Plant Systems and Synthetic BiologySantiago, Chile
| | - Paulo Canessa
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de ChileSantiago, Chile
- Millennium Nucleus for Fungal Integrative and Synthetic BiologySantiago, Chile
| | - Gustavo Hoppe
- Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de ChileSantiago, Chile
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de ChileSantiago, Chile
| | - Ignacio Retamal
- Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de ChileSantiago, Chile
| | - Tomas C. Moyano
- Millennium Nucleus Center for Plant Systems and Synthetic BiologySantiago, Chile
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de ChileSantiago, Chile
| | - Javier Canales
- Facultad de Ciencias, Instituto de Bioquímica y Microbiología, Universidad Austral de ChileValdivia, Chile
| | - Rodrigo A. Gutiérrez
- Millennium Nucleus Center for Plant Systems and Synthetic BiologySantiago, Chile
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de ChileSantiago, Chile
| | - Joselyn Rubilar
- Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de ChileSantiago, Chile
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Pham KTM, Inoue Y, Vu BV, Nguyen HH, Nakayashiki T, Ikeda KI, Nakayashiki H. MoSET1 (Histone H3K4 Methyltransferase in Magnaporthe oryzae) Regulates Global Gene Expression during Infection-Related Morphogenesis. PLoS Genet 2015; 11:e1005385. [PMID: 26230995 PMCID: PMC4521839 DOI: 10.1371/journal.pgen.1005385] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2014] [Accepted: 06/23/2015] [Indexed: 12/18/2022] Open
Abstract
Here we report the genetic analyses of histone lysine methyltransferase (KMT) genes in the phytopathogenic fungus Magnaporthe oryzae. Eight putative M. oryzae KMT genes were targeted for gene disruption by homologous recombination. Phenotypic assays revealed that the eight KMTs were involved in various infection processes at varying degrees. Moset1 disruptants (Δmoset1) impaired in histone H3 lysine 4 methylation (H3K4me) showed the most severe defects in infection-related morphogenesis, including conidiation and appressorium formation. Consequently, Δmoset1 lost pathogenicity on wheat host plants, thus indicating that H3K4me is an important epigenetic mark for infection-related gene expression in M. oryzae. Interestingly, appressorium formation was greatly restored in the Δmoset1 mutants by exogenous addition of cAMP or of the cutin monomer, 16-hydroxypalmitic acid. The Δmoset1 mutants were still infectious on the super-susceptible barley cultivar Nigrate. These results suggested that MoSET1 plays roles in various aspects of infection, including signal perception and overcoming host-specific resistance. However, since Δmoset1 was also impaired in vegetative growth, the impact of MoSET1 on gene regulation was not infection specific. ChIP-seq analysis of H3K4 di- and tri-methylation (H3K4me2/me3) and MoSET1 protein during infection-related morphogenesis, together with RNA-seq analysis of the Δmoset1 mutant, led to the following conclusions: 1) Approximately 5% of M. oryzae genes showed significant changes in H3K4-me2 or -me3 abundance during infection-related morphogenesis. 2) In general, H3K4-me2 and -me3 abundance was positively associated with active transcription. 3) Lack of MoSET1 methyltransferase, however, resulted in up-regulation of a significant portion of the M. oryzae genes in the vegetative mycelia (1,491 genes), and during infection-related morphogenesis (1,385 genes), indicating that MoSET1 has a role in gene repression either directly or more likely indirectly. 4) Among the 4,077 differentially expressed genes (DEGs) between mycelia and germination tubes, 1,201 and 882 genes were up- and down-regulated, respectively, in a Moset1-dependent manner. 5) The Moset1-dependent DEGs were enriched in several gene categories such as signal transduction, transport, RNA processing, and translation. This paper provides two major contributions to the field of genetics. First, we systematically studied the biological roles of eight histone lysine methyltransferase (KMT) genes in the phytopathogenic fungus Magnaporthe oryzae. We investigated their roles, especially focusing on their involvement in infection-related morphogenesis and pathogenicity. The results showed that the eight KMTs were involved in various infection processes to varying degrees, and that MoSET1, one of the KMTs catalyzing methylation at histone H3 lysine 4 (H3K4), had the largest impact on the pathogenicity of the fungus. Second, we focused on the role of MoSET1 in global gene regulation. H3K4 methylation is generally believed to be an epigenetic mark for gene activation in higher eukaryotes. However, in Saccharomyces cerevisiae, SET1 was originally characterized as being required for transcriptional silencing of silent mating-type loci. We addressed this apparent discrepancy by examining genome-wide gene expression and H3K4 methylation during infection-related morphogenesis in M. oryzae. RNA-seq analysis of a MoSET1 deletion mutant revealed that MoSET1 was indeed required for proper gene activation and repression. ChIP-seq analyses of H3K4 methylation and MoSET1 suggested that MoSET1 could directly play a role in gene activation while MoSET1-dependent gene repression may be caused by indirect effects.
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Affiliation(s)
- Kieu Thi Minh Pham
- Laboratory of Cell Function and Structure, Graduate School of Agricultural Science, Kobe University, Nada Kobe, Japan
| | - Yoshihiro Inoue
- Laboratory of Cell Function and Structure, Graduate School of Agricultural Science, Kobe University, Nada Kobe, Japan
| | - Ba Van Vu
- Laboratory of Cell Function and Structure, Graduate School of Agricultural Science, Kobe University, Nada Kobe, Japan
| | - Hanh Hieu Nguyen
- Laboratory of Cell Function and Structure, Graduate School of Agricultural Science, Kobe University, Nada Kobe, Japan
| | - Toru Nakayashiki
- Laboratory of Cell Function and Structure, Graduate School of Agricultural Science, Kobe University, Nada Kobe, Japan
| | - Ken-ichi Ikeda
- Laboratory of Cell Function and Structure, Graduate School of Agricultural Science, Kobe University, Nada Kobe, Japan
| | - Hitoshi Nakayashiki
- Laboratory of Cell Function and Structure, Graduate School of Agricultural Science, Kobe University, Nada Kobe, Japan
- * E-mail:
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31
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Eaton CJ, Dupont PY, Solomon P, Clayton W, Scott B, Cox MP. A Core Gene Set Describes the Molecular Basis of Mutualism and Antagonism in Epichloë spp. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2015; 28:218-31. [PMID: 25496592 DOI: 10.1094/mpmi-09-14-0293-fi] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Beneficial plant-fungal interactions play an important role in the ability of plants to survive changing environmental conditions. In contrast, phytopathogenic fungi fall at the opposite end of the symbiotic spectrum, causing reduced host growth or even death. In order to exploit beneficial interactions and prevent pathogenic ones, it is essential to understand the molecular differences underlying these alternative states. The association between the endophyte Epichloë festucae and Lolium perenne (perennial ryegrass) is an excellent system for studying these molecular patterns due to the existence of several fungal mutants that have an antagonistic rather than a mutualistic interaction with the host plant. By comparing gene expression in a wild-type beneficial association with three mutant antagonistic associations disrupted in key signaling genes, we identified a core set of 182 genes that show common differential expression patterns between these two states. These gene expression changes are indicative of a nutrient-starvation response, as supported by the upregulation of genes encoding degradative enzymes, transporters, and primary metabolism, and downregulation of genes encoding putative small-secreted proteins and secondary metabolism. These results suggest that disruption of a mutualistic symbiotic interaction may lead to an elevated uptake and degradation of host-derived nutrients and cell-wall components, reminiscent of phytopathogenic interactions.
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Meijueiro ML, Santoyo F, Ramirez L, Pisabarro AG. Transcriptome characteristics of filamentous fungi deduced using high-throughput analytical technologies. Brief Funct Genomics 2014; 13:440-50. [DOI: 10.1093/bfgp/elu033] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
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Micallef L, Rodgers P. eulerAPE: drawing area-proportional 3-Venn diagrams using ellipses. PLoS One 2014; 9:e101717. [PMID: 25032825 PMCID: PMC4102485 DOI: 10.1371/journal.pone.0101717] [Citation(s) in RCA: 342] [Impact Index Per Article: 34.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2014] [Accepted: 06/10/2014] [Indexed: 12/22/2022] Open
Abstract
Venn diagrams with three curves are used extensively in various medical and scientific disciplines to visualize relationships between data sets and facilitate data analysis. The area of the regions formed by the overlapping curves is often directly proportional to the cardinality of the depicted set relation or any other related quantitative data. Drawing these diagrams manually is difficult and current automatic drawing methods do not always produce appropriate diagrams. Most methods depict the data sets as circles, as they perceptually pop out as complete distinct objects due to their smoothness and regularity. However, circles cannot draw accurate diagrams for most 3-set data and so the generated diagrams often have misleading region areas. Other methods use polygons to draw accurate diagrams. However, polygons are non-smooth and non-symmetric, so the curves are not easily distinguishable and the diagrams are difficult to comprehend. Ellipses are more flexible than circles and are similarly smooth, but none of the current automatic drawing methods use ellipses. We present eulerAPE as the first method and software that uses ellipses for automatically drawing accurate area-proportional Venn diagrams for 3-set data. We describe the drawing method adopted by eulerAPE and we discuss our evaluation of the effectiveness of eulerAPE and ellipses for drawing random 3-set data. We compare eulerAPE and various other methods that are currently available and we discuss differences between their generated diagrams in terms of accuracy and ease of understanding for real world data.
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Affiliation(s)
- Luana Micallef
- School of Computing, University of Kent, Canterbury, Kent, United Kingdom
- * E-mail:
| | - Peter Rodgers
- School of Computing, University of Kent, Canterbury, Kent, United Kingdom
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Chadha S, Sharma M. Transposable elements as stress adaptive capacitors induce genomic instability in fungal pathogen Magnaporthe oryzae. PLoS One 2014; 9:e94415. [PMID: 24709911 PMCID: PMC3978060 DOI: 10.1371/journal.pone.0094415] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 03/16/2014] [Indexed: 12/13/2022] Open
Abstract
A fundamental problem in fungal pathogenesis is to elucidate the evolutionary forces responsible for genomic rearrangements leading to races with fitter genotypes. Understanding the adaptive evolutionary mechanisms requires identification of genomic components and environmental factors reshaping the genome of fungal pathogens to adapt. Herein, Magnaporthe oryzae, a model fungal plant pathogen is used to demonstrate the impact of environmental cues on transposable elements (TE) based genome dynamics. For heat shock and copper stress exposed samples, eight TEs belonging to class I and II family were employed to obtain DNA profiles. Stress induced mutant bands showed a positive correlation with dose/duration of stress and provided evidences of TEs role in stress adaptiveness. Further, we demonstrate that genome dynamics differ for the type/family of TEs upon stress exposition and previous reports of stress induced MAGGY transposition has underestimated the role of TEs in M. oryzae. Here, we identified Pyret, MAGGY, Pot3, MINE, Mg-SINE, Grasshopper and MGLR3 as contributors of high genomic instability in M. oryzae in respective order. Sequencing of mutated bands led to the identification of LTR-retrotransposon sequences within regulatory regions of psuedogenes. DNA transposon Pot3 was identified in the coding regions of chromatin remodelling protein containing tyrosinase copper-binding and PWWP domains. LTR-retrotransposons Pyret and MAGGY are identified as key components responsible for the high genomic instability and perhaps these TEs are utilized by M. oryzae for its acclimatization to adverse environmental conditions. Our results demonstrate how common field stresses change genome dynamics of pathogen and provide perspective to explore the role of TEs in genome adaptability, signalling network and its impact on the virulence of fungal pathogens.
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Affiliation(s)
- Sonia Chadha
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Mradul Sharma
- Astrophysical Sciences Division, Bhabha Atomic Research Centre, Mumbai, India
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Spence CA, Raman V, Donofrio NM, Bais HP. Global gene expression in rice blast pathogen Magnaporthe oryzae treated with a natural rice soil isolate. PLANTA 2014; 239:171-85. [PMID: 24126723 DOI: 10.1007/s00425-013-1974-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Accepted: 10/03/2013] [Indexed: 05/08/2023]
Abstract
The rhizospheric microbiome is comprised of many microbes, some of which reduce the virulence of their phytopathogenic neighbors; however, the mechanisms underlying these interactions are largely unknown. Rice soil isolate Pseudomonas chlororaphis EA105 strongly inhibits Magnaporthe oryzae's in vitro growth by restricting fungal diameter as well as inhibiting the formation of the appressorium, required for penetration. We were interested in elucidating M. oryzae's response to EA105 treatment, and utilized a microarray approach to obtain a global perspective of EA105 elicited changes in this pathogen. Based on this analysis, three genes of interest were knocked out in M. oryzae 70-15, and their sensitivity to EA105 treatment as well as their ability to infect rice was determined. Priming rice plants with EA105 prior to M. oryzae infection decreased lesion size, and the mutants were tested to see if this effect was retained. A null 70-15 mutant in a trichothecene biosynthesis gene showed less susceptibility to bacterial treatment, forming more appressoria than the parental type 70-15. A similar pattern was seen in a null mutant for a stress-inducible protein, MGG_03098. In addition, when this mutant was inoculated onto the leaves of EA105-primed rice plants, lesions were reduced to a greater extent than in 70-15, implicating the lack of this gene with an increased ISR response in rice. Understanding the global effect of biocontrol bacteria on phytopathogens is a key for developing successful and lasting solutions to crop loss caused by plant diseases and has the potential to greatly increase food supply.
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Affiliation(s)
- Carla A Spence
- Department of Biological Sciences, University of Delaware, Newark, DE, 19716, USA,
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Samalova M, Meyer AJ, Gurr SJ, Fricker MD. Robust anti-oxidant defences in the rice blast fungus Magnaporthe oryzae confer tolerance to the host oxidative burst. THE NEW PHYTOLOGIST 2014; 201:556-573. [PMID: 24117971 DOI: 10.1111/nph.12530] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 08/20/2013] [Indexed: 05/22/2023]
Abstract
Plants respond to pathogen attack via a rapid burst of reactive oxygen species (ROS). However, ROS are also produced by fungal metabolism and are required for the development of infection structures in Magnaporthe oryzae. To obtain a better understanding of redox regulation in M. oryzae, we measured the amount and redox potential of glutathione (E(GSH)), as the major cytoplasmic anti-oxidant, the rates of ROS production, and mitochondrial activity using multi-channel four-dimensional (x,y,z,t) confocal imaging of Grx1-roGFP2 and fluorescent reporters during spore germination, appressorium formation and infection. High levels of mitochondrial activity and ROS were localized to the growing germ tube and appressorium, but E(GSH) was highly reduced and tightly regulated during development. Furthermore, germlings were extremely resistant to external H2O2 exposure ex planta. EGSH remained highly reduced during successful infection of the susceptible rice cultivar CO39. By contrast, there was a dramatic reduction in the infection of resistant (IR68) rice, but the sparse hyphae that did form also maintained a similar reduced E(GSH). We conclude that M. oryzae has a robust anti-oxidant defence system and maintains tight control of EGSH despite substantial oxidative challenge. Furthermore, the magnitude of the host oxidative burst alone does not stress the pathogen sufficiently to prevent infection in this pathosystem.
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Affiliation(s)
- Marketa Samalova
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Andreas J Meyer
- INRES, Universität Bonn, Friedrich-Ebert-Allee 144, D-53113, Bonn, Germany
| | - Sarah J Gurr
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
- Biosciences, University of Exeter, Devon, EX4 4QD, UK
| | - Mark D Fricker
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
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Kubicek CP, Starr TL, Glass NL. Plant cell wall-degrading enzymes and their secretion in plant-pathogenic fungi. ANNUAL REVIEW OF PHYTOPATHOLOGY 2014; 52:427-51. [PMID: 25001456 DOI: 10.1146/annurev-phyto-102313-045831] [Citation(s) in RCA: 426] [Impact Index Per Article: 42.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Approximately a tenth of all described fungal species can cause diseases in plants. A common feature of this process is the necessity to pass through the plant cell wall, an important barrier against pathogen attack. To this end, fungi possess a diverse array of secreted enzymes to depolymerize the main structural polysaccharide components of the plant cell wall, i.e., cellulose, hemicellulose, and pectin. Recent advances in genomic and systems-level studies have begun to unravel this diversity and have pinpointed cell wall-degrading enzyme (CWDE) families that are specifically present or enhanced in plant-pathogenic fungi. In this review, we discuss differences between the CWDE arsenal of plant-pathogenic and non-plant-pathogenic fungi, highlight the importance of individual enzyme families for pathogenesis, illustrate the secretory pathway that transports CWDEs out of the fungal cell, and report the transcriptional regulation of expression of CWDE genes in both saprophytic and phytopathogenic fungi.
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38
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Lehtonen MT, Takikawa Y, Rönnholm G, Akita M, Kalkkinen N, Ahola-Iivarinen E, Somervuo P, Varjosalo M, Valkonen JPT. Protein secretome of moss plants (Physcomitrella patens) with emphasis on changes induced by a fungal elicitor. J Proteome Res 2013; 13:447-59. [PMID: 24295333 DOI: 10.1021/pr400827a] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Studies on extracellular proteins (ECPs) contribute to understanding of the multifunctional nature of apoplast. Unlike vascular plants (tracheophytes), little information about ECPs is available from nonvascular plants, such as mosses (bryophytes). In this study, moss plants (Physcomitrella patens) were grown in liquid culture and treated with chitosan, a water-soluble form of chitin that occurs in cell walls of fungi and insects and elicits pathogen defense in plants. ECPs released to the culture medium were compared between chitosan-treated and nontreated control cultures using quantitative mass spectrometry (Orbitrap) and 2-DE-LC-MS/MS. Over 400 secreted proteins were detected, of which 70% were homologous to ECPs reported in tracheophyte secretomes. Bioinformatics analyses using SignalP and SecretomeP predicted classical signal peptides for secretion (37%) or leaderless secretion (27%) for most ECPs of P. patens, but secretion of the remaining proteins (36%) could not be predicted using bioinformatics. Cultures treated with chitosan contained 72 proteins not found in untreated controls, whereas 27 proteins found in controls were not detected in chitosan-treated cultures. Pathogen defense-related proteins dominated in the secretome of P. patens, as reported in tracheophytes. These results advance knowledge on protein secretomes of plants by providing a comprehensive account of ECPs of a bryophyte.
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Affiliation(s)
- Mikko T Lehtonen
- Department of Agricultural Sciences, University of Helsinki , PO Box 27, FI-00014 Helsinki, Finland
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Rebollar A, López-García B. PAF104, a synthetic peptide to control rice blast disease by blocking appressorium formation in Magnaporthe oryzae. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2013; 26:1407-1416. [PMID: 23902261 DOI: 10.1094/mpmi-04-13-0110-r] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Magnaporthe oryzae is the most devastating pathogen of rice and the main cause of crop losses worldwide. The successful management of blast disease caused by this fungus is a clear necessity. The synthetic peptide PAF104 has been characterized by its inhibition of M. oryzae appressorium formation on hydrophobic surfaces. Growth and the ability of conidia to germinate was not affected by PAF104, indicating the lack of toxicity on fungal conidia. The addition of the cutin monomer 1,16-hexadecanediol does not interfere with the inhibitory effect of PAF104 on in vitro hydrophobic surfaces. On the other hand, inhibition of appressorium formation by PAF104 was nullified by the exogenous addition of cAMP. Our results suggest that PAF104 affects the Pmk1 pathway by repression of the gene expression of MoMSB2, which encodes a sensing surface protein, and the mitogen-activated protein/extracellular signal-regulated kinase kinase kinase MST11. The pathogenicity of M. oryzae was reduced after PAF104 treatment specifically blocking appressorium formation. Our results support PAF104 as a promising compound to control rice blast disease by blocking a specific target related to appressorium formation, a process essential for infection of rice leaves. Moreover, PAF104 is proposed as a lead compound to develop novel specific fungicides with improved properties.
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Mathioni SM, Patel N, Riddick B, Sweigard JA, Czymmek KJ, Caplan JL, Kunjeti SG, Kunjeti S, Raman V, Hillman BI, Kobayashi DY, Donofrio NM. Transcriptomics of the rice blast fungus Magnaporthe oryzae in response to the bacterial antagonist Lysobacter enzymogenes reveals candidate fungal defense response genes. PLoS One 2013; 8:e76487. [PMID: 24098512 PMCID: PMC3789685 DOI: 10.1371/journal.pone.0076487] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 08/28/2013] [Indexed: 12/15/2022] Open
Abstract
Plants and animals have evolved a first line of defense response to pathogens called innate or basal immunity. While basal defenses in these organisms are well studied, there is almost a complete lack of understanding of such systems in fungal species, and more specifically, how they are able to detect and mount a defense response upon pathogen attack. Hence, the goal of the present study was to understand how fungi respond to biotic stress by assessing the transcriptional profile of the rice blast pathogen, Magnaporthe oryzae, when challenged with the bacterial antagonist Lysobacter enzymogenes. Based on microscopic observations of interactions between M. oryzae and wild-type L. enzymogenes strain C3, we selected early and intermediate stages represented by time-points of 3 and 9 hours post-inoculation, respectively, to evaluate the fungal transcriptome using RNA-seq. For comparative purposes, we also challenged the fungus with L. enzymogenes mutant strain DCA, previously demonstrated to be devoid of antifungal activity. A comparison of transcriptional data from fungal interactions with the wild-type bacterial strain C3 and the mutant strain DCA revealed 463 fungal genes that were down-regulated during attack by C3; of these genes, 100 were also found to be up-regulated during the interaction with DCA. Functional categorization of genes in this suite included those with roles in carbohydrate metabolism, cellular transport and stress response. One gene in this suite belongs to the CFEM-domain class of fungal proteins. Another CFEM class protein called PTH11 has been previously characterized, and we found that a deletion in this gene caused advanced lesion development by C3 compared to its growth on the wild-type fungus. We discuss the characterization of this suite of 100 genes with respect to their role in the fungal defense response.
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Affiliation(s)
- Sandra M. Mathioni
- Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware, United States of America
| | - Nrupali Patel
- Department of Plant Biology and Pathology, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Bianca Riddick
- Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware, United States of America
| | - James A. Sweigard
- DuPont Stine Haskell Research Center, Newark, Delaware, United States of America
| | - Kirk J. Czymmek
- Delaware Biotechnology Institute BioImaging Center, University of Delaware, Newark, Delaware, United States of America
- Department of Biological Sciences, University of Delaware, Newark, Delaware, United States of America
| | - Jeffrey L. Caplan
- Delaware Biotechnology Institute BioImaging Center, University of Delaware, Newark, Delaware, United States of America
| | - Sridhara G. Kunjeti
- Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware, United States of America
| | - Saritha Kunjeti
- Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware, United States of America
| | - Vidhyavathi Raman
- Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware, United States of America
| | - Bradley I. Hillman
- Department of Plant Biology and Pathology, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Donald Y. Kobayashi
- Department of Plant Biology and Pathology, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Nicole M. Donofrio
- Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware, United States of America
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Franck WL, Gokce E, Oh Y, Muddiman DC, Dean RA. Temporal analysis of the magnaporthe oryzae proteome during conidial germination and cyclic AMP (cAMP)-mediated appressorium formation. Mol Cell Proteomics 2013; 12:2249-65. [PMID: 23665591 PMCID: PMC3734583 DOI: 10.1074/mcp.m112.025874] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Revised: 04/09/2013] [Indexed: 11/06/2022] Open
Abstract
Rice blast disease caused by Magnaporthe oryzae is one of the most serious threats to global rice production. During the earliest stages of rice infection, M. oryzae conidia germinate on the leaf surface and form a specialized infection structure termed the appressorium. The development of the appressorium represents the first critical stage of infectious development. A total of 3200 unique proteins were identified by nanoLC-MS/MS in a temporal study of conidial germination and cAMP-induced appressorium formation in M. oryzae. Using spectral counting based label free quantification, observed changes in relative protein abundance during the developmental process revealed changes in the cell wall biosynthetic machinery, transport functions, and production of extracellular proteins in developing appressoria. One hundred and sixty-six up-regulated and 208 down-regulated proteins were identified in response to cAMP treatment. Proteomic analysis of a cAMP-dependent protein kinase A mutant that is compromised in the ability to form appressoria identified proteins whose developmental regulation is dependent on cAMP signaling. Selected reaction monitoring was used for absolute quantification of four regulated proteins to validate the global proteomics data and confirmed the germination or appressorium specific regulation of these proteins. Finally, a comparison of the proteome and transcriptome was performed and revealed little correlation between transcript and protein regulation. A subset of regulated proteins were identified whose transcripts show similar regulation patterns and include many of the most strongly regulated proteins indicating a central role in appressorium formation. A temporal quantitative RT-PCR analysis confirmed a strong correlation between transcript and protein abundance for some but not all genes. Collectively, the data presented here provide the first comprehensive view of the M. oryzae proteome during early infection-related development and highlight biological processes important for pathogenicity.
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Affiliation(s)
| | - Emine Gokce
- §W.M. Keck Fourier Transform-ICR Mass Spectrometry Laboratory, Department of Chemistry, North Carolina State University, Raleigh, North Carolina, 27606
| | - Yeonyee Oh
- From the ‡Center for Integrated Fungal Research
| | - David C. Muddiman
- §W.M. Keck Fourier Transform-ICR Mass Spectrometry Laboratory, Department of Chemistry, North Carolina State University, Raleigh, North Carolina, 27606
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Song Z, Yin Y, Jiang S, Liu J, Chen H, Wang Z. Comparative transcriptome analysis of microsclerotia development in Nomuraea rileyi. BMC Genomics 2013; 14:411. [PMID: 23777366 PMCID: PMC3698084 DOI: 10.1186/1471-2164-14-411] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Accepted: 06/07/2013] [Indexed: 12/02/2022] Open
Abstract
Background Nomuraea rileyi is used as an environmental-friendly biopesticide. However, mass production and commercialization of this organism are limited due to its fastidious growth and sporulation requirements. When cultured in amended medium, we found that N. rileyi could produce microsclerotia bodies, replacing conidiophores as the infectious agent. However, little is known about the genes involved in microsclerotia development. In the present study, the transcriptomes were analyzed using next-generation sequencing technology to find the genes involved in microsclerotia development. Results A total of 4.69 Gb of clean nucleotides comprising 32,061 sequences was obtained, and 20,919 sequences were annotated (about 65%). Among the annotated sequences, only 5928 were annotated with 34 gene ontology (GO) functional categories, and 12,778 sequences were mapped to 165 pathways by searching against the Kyoto Encyclopedia of Genes and Genomes pathway (KEGG) database. Furthermore, we assessed the transcriptomic differences between cultures grown in minimal and amended medium. In total, 4808 sequences were found to be differentially expressed; 719 differentially expressed unigenes were assigned to 25 GO classes and 1888 differentially expressed unigenes were assigned to 161 KEGG pathways, including 25 enrichment pathways. Subsequently, we examined the up-regulation or uniquely expressed genes following amended medium treatment, which were also expressed on the enrichment pathway, and found that most of them participated in mediating oxidative stress homeostasis. To elucidate the role of oxidative stress in microsclerotia development, we analyzed the diversification of unigenes using quantitative reverse transcription-PCR (RT-qPCR). Conclusion Our findings suggest that oxidative stress occurs during microsclerotia development, along with a broad metabolic activity change. Our data provide the most comprehensive sequence resource available for the study of N. rileyi. We believe that the transcriptome datasets will serve as an important public information platform to accelerate studies on N. rileyi microsclerotia.
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Affiliation(s)
- Zhangyong Song
- Genetic Engineering Research Centre, School of Life Science, Chongqing University, Chongqing 400030, China
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Park SY, Choi J, Lim SE, Lee GW, Park J, Kim Y, Kong S, Kim SR, Rho HS, Jeon J, Chi MH, Kim S, Khang CH, Kang S, Lee YH. Global expression profiling of transcription factor genes provides new insights into pathogenicity and stress responses in the rice blast fungus. PLoS Pathog 2013; 9:e1003350. [PMID: 23762023 PMCID: PMC3675110 DOI: 10.1371/journal.ppat.1003350] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Accepted: 03/25/2013] [Indexed: 11/19/2022] Open
Abstract
Because most efforts to understand the molecular mechanisms underpinning fungal pathogenicity have focused on studying the function and role of individual genes, relatively little is known about how transcriptional machineries globally regulate and coordinate the expression of a large group of genes involved in pathogenesis. Using quantitative real-time PCR, we analyzed the expression patterns of 206 transcription factor (TF) genes in the rice blast fungus Magnaporthe oryzae under 32 conditions, including multiple infection-related developmental stages and various abiotic stresses. The resulting data, which are publicly available via an online platform, provided new insights into how these TFs are regulated and potentially work together to control cellular responses to a diverse array of stimuli. High degrees of differential TF expression were observed under the conditions tested. More than 50% of the 206 TF genes were up-regulated during conidiation and/or in conidia. Mutations in ten conidiation-specific TF genes caused defects in conidiation. Expression patterns in planta were similar to those under oxidative stress conditions. Mutants of in planta inducible genes not only exhibited sensitive to oxidative stress but also failed to infect rice. These experimental validations clearly demonstrated the value of TF expression patterns in predicting the function of individual TF genes. The regulatory network of TF genes revealed by this study provides a solid foundation for elucidating how M. oryzae regulates its pathogenesis, development, and stress responses.
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Affiliation(s)
- Sook-Young Park
- Department of Agricultural Biotechnology, Fungal Bioinformatics Laboratory, Center for Fungal Genetic Resources, and Center for Fungal Pathogenesis, Seoul National University, Seoul, Korea
| | - Jaeyoung Choi
- Department of Agricultural Biotechnology, Fungal Bioinformatics Laboratory, Center for Fungal Genetic Resources, and Center for Fungal Pathogenesis, Seoul National University, Seoul, Korea
| | - Se-Eun Lim
- Department of Agricultural Biotechnology, Fungal Bioinformatics Laboratory, Center for Fungal Genetic Resources, and Center for Fungal Pathogenesis, Seoul National University, Seoul, Korea
| | - Gir-Won Lee
- Department of Agricultural Biotechnology, Fungal Bioinformatics Laboratory, Center for Fungal Genetic Resources, and Center for Fungal Pathogenesis, Seoul National University, Seoul, Korea
| | - Jongsun Park
- Department of Agricultural Biotechnology, Fungal Bioinformatics Laboratory, Center for Fungal Genetic Resources, and Center for Fungal Pathogenesis, Seoul National University, Seoul, Korea
| | - Yang Kim
- Center for Food and Bioconvergence, Seoul National University, Seoul, Korea
| | - Sunghyung Kong
- Department of Agricultural Biotechnology, Fungal Bioinformatics Laboratory, Center for Fungal Genetic Resources, and Center for Fungal Pathogenesis, Seoul National University, Seoul, Korea
| | - Se Ryun Kim
- Department of Agricultural Biotechnology, Fungal Bioinformatics Laboratory, Center for Fungal Genetic Resources, and Center for Fungal Pathogenesis, Seoul National University, Seoul, Korea
| | - Hee-Sool Rho
- Department of Agricultural Biotechnology, Fungal Bioinformatics Laboratory, Center for Fungal Genetic Resources, and Center for Fungal Pathogenesis, Seoul National University, Seoul, Korea
| | - Junhyun Jeon
- Department of Agricultural Biotechnology, Fungal Bioinformatics Laboratory, Center for Fungal Genetic Resources, and Center for Fungal Pathogenesis, Seoul National University, Seoul, Korea
| | - Myung-Hwan Chi
- Department of Agricultural Biotechnology, Fungal Bioinformatics Laboratory, Center for Fungal Genetic Resources, and Center for Fungal Pathogenesis, Seoul National University, Seoul, Korea
| | - Soonok Kim
- National Institute of Biological Resources, Ministry of Environment, Incheon, Korea
| | - Chang Hyun Khang
- Department of Plant Biology, University of Georgia, Athens, Georgia, United States of America
| | - Seogchan Kang
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Yong-Hwan Lee
- Department of Agricultural Biotechnology, Fungal Bioinformatics Laboratory, Center for Fungal Genetic Resources, and Center for Fungal Pathogenesis, Seoul National University, Seoul, Korea
- * E-mail:
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44
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Raman V, Simon SA, Romag A, Demirci F, Mathioni SM, Zhai J, Meyers BC, Donofrio NM. Physiological stressors and invasive plant infections alter the small RNA transcriptome of the rice blast fungus, Magnaporthe oryzae. BMC Genomics 2013; 14:326. [PMID: 23663523 PMCID: PMC3658920 DOI: 10.1186/1471-2164-14-326] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Accepted: 05/02/2013] [Indexed: 11/21/2022] Open
Abstract
Background The rice blast fungus, Magnaporthe oryzae is a destructive pathogen of rice and other related crops, causing significant yield losses worldwide. Endogenous small RNAs (sRNAs), including small interfering RNAs (siRNAs) and microRNAs (miRNAs) are critical components of gene regulation in many eukaryotic organisms. Recently several new species of sRNAs have been identified in fungi. This fact along with the availability of genome sequence makes M. oryzae a compelling target for sRNA profiling. We have examined sRNA species and their biosynthetic genes in M. oryzae, and the degree to which these elements regulate fungal stress responses. To this end, we have characterized sRNAs under different physiological stress conditions, which had not yet been examined in this fungus. Results The resulting libraries are composed of more than 37 million total genome matched reads mapping to intergenic regions, coding sequences, retrotransposons, inverted, tandem, and other repeated regions of the genome with more than half of the small RNAs arising from intergenic regions. The 24 nucleotide (nt) size class of sRNAs was predominant. A comparison to transcriptional data of M. oryzae undergoing the same physiological stresses indicates that sRNAs play a role in transcriptional regulation for a small subset of genes. Support for this idea comes from generation and characterization of mutants putatively involved in sRNAs biogenesis; our results indicate that the deletion of Dicer-like genes and an RNA-Dependent RNA Polymerase gene increases the transcriptional regulation of this subset of genes, including one involved in virulence. Conclusions Various physiological stressors and in planta conditions alter the small RNA profile of the rice blast fungus. Characterization of sRNA biosynthetic mutants helps to clarify the role of sRNAs in transcriptional control.
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Affiliation(s)
- Vidhyavathi Raman
- Department of Plant & Soil Sciences, University of Delaware, Newark, DE 19716, USA
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Kim SG, Wang Y, Lee KH, Park ZY, Park J, Wu J, Kwon SJ, Lee YH, Agrawal GK, Rakwal R, Kim ST, Kang KY. In-depth insight into in vivo apoplastic secretome of rice-Magnaporthe oryzae interaction. J Proteomics 2013; 78:58-71. [DOI: 10.1016/j.jprot.2012.10.029] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Revised: 10/04/2012] [Accepted: 10/26/2012] [Indexed: 12/22/2022]
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Simultaneous RNA-seq analysis of a mixed transcriptome of rice and blast fungus interaction. PLoS One 2012; 7:e49423. [PMID: 23139845 PMCID: PMC3490861 DOI: 10.1371/journal.pone.0049423] [Citation(s) in RCA: 163] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Accepted: 10/08/2012] [Indexed: 11/29/2022] Open
Abstract
A filamentous fungus, Magnaporthe oryzae, is a causal agent of rice blast disease, which is one of the most serious diseases affecting cultivated rice, Oryza sativa. However, the molecular mechanisms underlying both rice defense and fungal attack are not yet fully understood. Extensive past studies have characterized many infection-responsive genes in the pathogen and host plant, separately. To understand the plant-pathogen interaction comprehensively, it is valuable to monitor the gene expression profiles of both interacting organisms simultaneously in the same infected plant tissue. Although the host-pathogen interaction during the initial infection stage is important for the establishment of infection, the detection of fungal gene expression in infected leaves at the stage has been difficult because very few numbers of fungal cells are present. Using the emerging RNA-Seq technique, which has a wide dynamic range for expression analyses, we analyzed the mixed transcriptome of rice and blast fungus in infected leaves at 24 hours post-inoculation, which is the point when the primary infection hyphae penetrate leaf epidermal cells. We demonstrated that our method detected the gene expression of both the host plant and pathogen simultaneously in the same infected leaf blades in natural infection conditions without any artificial treatments. The upregulation of 240 fungal transcripts encoding putative secreted proteins was observed, suggesting that these candidates of fungal effector genes may play important roles in initial infection processes. The upregulation of transcripts encoding glycosyl hydrolases, cutinases and LysM domain-containing proteins were observed in the blast fungus, whereas pathogenesis-related and phytoalexin biosynthetic genes were upregulated in rice. Furthermore, more drastic changes in expression were observed in the incompatible interactions compared with the compatible ones in both rice and blast fungus at this stage. Our mixed transcriptome analysis is useful for the simultaneous elucidation of the tactics of host plant defense and pathogen attack.
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Towards defining nutrient conditions encountered by the rice blast fungus during host infection. PLoS One 2012; 7:e47392. [PMID: 23071797 PMCID: PMC3468542 DOI: 10.1371/journal.pone.0047392] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Accepted: 09/13/2012] [Indexed: 11/29/2022] Open
Abstract
Fungal diseases cause enormous crop losses, but defining the nutrient conditions encountered by the pathogen remains elusive. Here, we generated a mutant strain of the devastating rice pathogen Magnaporthe oryzae impaired for de novo methionine biosynthesis. The resulting methionine-requiring strain grew strongly on synthetic minimal media supplemented with methionine, aspartate or complex mixtures of partially digested proteins, but could not establish disease in rice leaves. Live-cell-imaging showed the mutant could produce normal appressoria and enter host cells but failed to develop, indicating the availability or accessibility of aspartate and methionine is limited in the plant. This is the first report to demonstrate the utility of combining biochemical genetics, plate growth tests and live-cell-imaging to indicate what nutrients might not be readily available to the fungal pathogen in rice host cells.
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Zhang Z, Chen J, Lin S, Li Z, Cheng R, Fang C, Chen H, Lin W. Proteomic and phosphoproteomic determination of ABA's effects on grain-filling of Oryza sativa L. inferior spikelets. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2012; 185-186:259-73. [PMID: 22325889 DOI: 10.1016/j.plantsci.2011.11.012] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2011] [Revised: 11/16/2011] [Accepted: 11/19/2011] [Indexed: 05/08/2023]
Abstract
Cultivars of rice (Oryza sativa L.), especially the large-spikelet-type, often fail to achieve the high yield potential due to poor grain-filling of their inferior (late-flowering) spikelets. The superior (early-flowering) spikelets normally contain more abscisic acid (ABA) than the inferior spikelets. It was speculated that ABA might play a pivotal role in the grain-filling of inferior spikelets. To understand the molecular regulation involved in this process, we employed the 2-D gel-based comparative proteomic and phosphoproteomic analyses to search for differentially expressed proteins in the inferior spikelets under exogenous ABA treatment. A total of 111 significantly differential proteins and 31 phosphoproteins were found in the inferior spikelets after treatment. Among them, 100 proteins and 23 phosphoproteins were identified by using MALDI-TOF/TOF MS. In addition, the gene expression patterns of the inferior spikelets were confirmed with RT-PCR. These differentially expressed proteins are active in defense response, carbohydrate, protein, amino acid, energy and secondary metabolisms, as well as cell development and photosynthesis. The results suggest that the grain-filling of rice inferior spikelets is regulated by ABA through some proteins and phosphoproteins participating in carbon, nitrogen and energy metabolisms.
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Affiliation(s)
- Zhixing Zhang
- Institute of Agricultural Ecology, Fujian Agricultural and Forestry University, Fuzhou, Fujian 35002, People's Republic of China
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Singh K, Nizam S, Sinha M, Verma PK. Comparative transcriptome analysis of the necrotrophic fungus Ascochyta rabiei during oxidative stress: insight for fungal survival in the host plant. PLoS One 2012; 7:e33128. [PMID: 22427966 PMCID: PMC3299738 DOI: 10.1371/journal.pone.0033128] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2011] [Accepted: 02/10/2012] [Indexed: 11/18/2022] Open
Abstract
Localized cell death, known as the hypersensitive response (HR), is an important defense mechanism for neutralizing phytopathogens. The hallmark of the HR is an oxidative burst produced by the host plant. We aimed to identify genes of the necrotrophic chickpea blight fungus Ascochyta rabiei that are involved in counteracting oxidative stress. A subtractive cDNA library was constructed after menadione treatment, which resulted in the isolation of 128 unigenes. A reverse northern blot was used to compare transcript profiles after H(2)O(2), menadione and sodium nitroprusside treatments. A total of 70 unigenes were found to be upregulated by more than two-fold following menadione treatment at different time intervals. A large number of genes not previously associated with oxidative stress were identified, along with many stress-responsive genes. Differential expression patterns of several genes were validated by quantitative real-time PCR (qRT-PCR) and northern blotting. In planta qRT-PCR of several selected genes also showed differential expression patterns during infection and disease progression. These data shed light on the molecular responses of the phytopathogen A. rabiei to overcome oxidative and nitrosative stresses and advance the understanding of necrotrophic fungal pathogen survival mechanisms.
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Affiliation(s)
- Kunal Singh
- Plant Immunity Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Shadab Nizam
- Plant Immunity Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Manisha Sinha
- Plant Immunity Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Praveen K. Verma
- Plant Immunity Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
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Soanes DM, Chakrabarti A, Paszkiewicz KH, Dawe AL, Talbot NJ. Genome-wide transcriptional profiling of appressorium development by the rice blast fungus Magnaporthe oryzae. PLoS Pathog 2012; 8:e1002514. [PMID: 22346750 PMCID: PMC3276559 DOI: 10.1371/journal.ppat.1002514] [Citation(s) in RCA: 125] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Accepted: 12/16/2011] [Indexed: 11/19/2022] Open
Abstract
The rice blast fungus Magnaporthe oryzae is one of the most significant pathogens affecting global food security. To cause rice blast disease the fungus elaborates a specialised infection structure called an appressorium. Here, we report genome wide transcriptional profile analysis of appressorium development using next generation sequencing (NGS). We performed both RNA-Seq and High-Throughput SuperSAGE analysis to compare the utility of these procedures for identifying differential gene expression in M. oryzae. We then analysed global patterns of gene expression during appressorium development. We show evidence for large-scale gene expression changes, highlighting the role of autophagy, lipid metabolism and melanin biosynthesis in appressorium differentiation. We reveal the role of the Pmk1 MAP kinase as a key global regulator of appressorium-associated gene expression. We also provide evidence for differential expression of transporter-encoding gene families and specific high level expression of genes involved in quinate uptake and utilization, consistent with pathogen-mediated perturbation of host metabolism during plant infection. When considered together, these data provide a comprehensive high-resolution analysis of gene expression changes associated with cellular differentiation that will provide a key resource for understanding the biology of rice blast disease.
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Affiliation(s)
- Darren M. Soanes
- College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Apratim Chakrabarti
- College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Konrad H. Paszkiewicz
- College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Angus L. Dawe
- College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
- Department of Biology, New Mexico State University, Las Cruces, New Mexico, United States of America
| | - Nicholas J. Talbot
- College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
- * E-mail:
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