基于RNA-Seq的稻瘟病菌Δznf1突变体的表达谱分析

doi:10.3864/j.issn.0578-1752.2016.17.009

Abstract

Abstract: 【Objective】Magnaporthe oryzae is the causal agent of rice blast, which is one of the most important disease threatening the production of cultivated rice worldwide. Appressorium-mediated penetration is a key step in the disease cycle of the fungus. Previously, it was reported that a C₂H₂ zinc finger transcription factor encoded by ZNF1 is essential for appressorium development, penetration and pathogenicity in the rice blast fungus. The objective of this study is to understand the regulatory mechanism of Znf1 and reveal the genes transcriptionally regulated by Znf1, thus providing new clues for further investigating molecular mechanism of pathogenicity in this fungus. 【Method】The transcriptome profiles of vegetative mycelia of the wild-type strain Guy11 and a Δznf1 mutant were assayed with the RNA-Seq technique. The gene expression levels were calculated using the FPKM method. The criteria of false discovery rate (FDR)≤0.001 and absolute value of log₂ ratio≥1 were used to identify differentially expressed genes (DEGs). The sequences of the DEGs were subjected to BLAST queries against the gene ontology (GO) database and KEGG pathway database to predict their biological function and pathways. In order to define in more detail about the sub-set of genes regulated by Znf1, transcriptome profiles of a mutant lacking the PMK1 MAP kinase-encoding gene was also analyzed based on the RNA-Seq technique. To identify the genes regulated by both Znf1 and Pmk1, the DEGs between Δznf1 and Δpmk1 were compared. In addition, the genes highly expressed during appressorium formation but down-regulated in either Δznf1 or Δpmk1 were obtained by comparison with the previous transcriptional profile data. 【Result】 Totally, 709 DEGs in the Δznf1 mutant, including 299 up-regulated and 410 down-regulated genes, were identified by comparison with the wild-type strain Guy11. Gene ontology enrichment analysis showed that 118, 299 and 308 DEGs were classified into cellular component, molecular function and biological process, respectively. KEGG pathway enrichment analysis revealed that the DEGs were mainly involved in metabolic pathways, biosynthesis of secondary metabolites and glycerophospholipid metabolism. Several known pathogenicity-related genes, including LPP3, HOX7, PBS2 and MPG1, were found down-regulated in Δznf1. The comparison of DEGs showed that about 56% DEGs in Δznf1 shared identical to those in Δpmk1. Three isotrichodermin C-15 hydroxylase encoding genes, MGG_03825, MGG_02329 and MGG_08498, were significantly down-regulated in both Δznf1 and Δpmk1. In addition, 48 genes up-regulated during appressorium formation were down-regulated in the two mutants, indicating that these putative appressorium-associated genes were regulated directly or indirectly by Znf1 and Pmk1. To confirm the reliability of the RNA-Seq data, 10 DEGs were randomly selected for qRT-PCR. The results showed that the expression patterns in qRT-PCR were consistent with those in RNA-Seq.【Conclusion】 The expression profiling data and predicted molecular function of Znf1-dependent DEGs were obtained by RNA-Seq technique. Several pathogenicity-associated genes were regulated by Znf1. Additionally, several genes highly expressed during appressoria formation were also regulated by Znf1 as well as Pmk1. This study provided valuable information for further research on Znf1 downstream gene regulatory network.

Key words: rice, Magnaporthe oryzae, appressorium, Δznf1, RNA-Seq, differentially expressed genes

YUE Xiao-feng, QUE Ya-wei, WANG Zheng-yi. Analysis of RNA-Seq-Based Expression Profiles of Δznf1 Mutants in Magnaporthe oryzae[J].Scientia Agricultura Sinica, 2016, 49(17): 3347-3358.

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References

[1] Talbot N J. On the trail of a cereal killer: Exploring the biology of Magnaporthe grisea. Annual Review of Microbiology, 2003, 57: 177-202.

[2] Ebbole D J. Magnaporthe as a model for understanding host-pathogen interactions. Annual Review of Phytopathology, 2007, 45: 437-456.

[3] Wilson R A, Talbot N J. Under pressure: investigating the biology of plant infection by Magnaporthe oryzae. Nature Reviews Microbiology, 2009, 7: 185-195.

[4] Tucker S L, Talbot N J. Surface attachment and pre-penetration stage development by plant pathogenic fungi. Annual Review of Phytopathology, 2001, 39: 385-417.

[5] de Jong J C, McCormack B J, Smirnoff N, Talbot N J. Glycerol generates turgor in rice blast. Nature,1997, 389: 244-245.

[6] 李杨, 王耀雯, 王育荣, 于洁. 水稻稻瘟病菌研究进展. 广西农业科学, 2010, 41(8): 789-792.

LI Y, Wang Y W, Wang Y R, Yu J. Research progress on rice blast fungus. Guangxi Agricultural Sciences, 2010, 41(8): 789-792. (in Chinese)

[7] Lee Y H, Dean R A. cAMP regulates infection structure formation in the plant pathogenic fungus Magnaporthe grisea. The Plant Cell, 1993, 5(6): 693-700.

[8] Mitchell T K, Dean R A. The cAMP-dependent protein kinase catalytic subunit is required for appressorium formation and pathogenesis by the rice blast pathogen Magnaporthe grisea. The Plant Cell, 1995, 7(11): 1869-1878.

[9] Xu J R, Urban M, Sweigard J A, Hamer J E. The CPKA gene of Magnaporthe grisea is essential for appressorial penetration. Molecular Plant-Microbe Interactions, 1997, 10(2): 187-194.

[10] Choi W, Dean R A. The adenylate cyclase gene MAC1 of Magnaporthe grisea controls appressorium formation and other aspects of growth and development. The Plant Cell, 1997, 9(11): 1973-1983.

[11] 李德葆, 金庆超, 董海涛. 稻瘟病菌附着胞发育相关信号传递研究进展. 浙江大学学报 (农业与生命科学版), 2006, 32(3): 257-264.

Li D B, Jin Q C, Dong H T. Research advances of cell signaling involved in appressorium development of Magnaporthe grisea. Journal of Zhejiang University (Agricultural & Life Science), 2006, 32(3): 257-264. (in Chinese)

[12] 贺春萍, 郑服丛. 稻瘟菌附着胞分化相关基因研究进展. 热带农业科学, 2006, 26(1): 47-59.

He C P, Zheng F C. Research progress on the related genes in appressorium differentiation of Magnaporthe grisea. Chinese Journal of Tropical Agriculture, 2006, 26(1): 47-59. (in Chinese)

[13] Xu J R, Hamer J E. MAP kinase and cAMP signaling regulate infection structure formation and pathogenic growth in the rice blast fungus Magnaporthe grisea. Genes & Development, 1996, 10(21): 2696-2706.

[14] Zhao X, Kim Y, Park G, Xu J R. A mitogen-activated protein kinase cascade regulating infection-related morphogenesis in Magnaporthe grisea. The Plant Cell, 2005, 17(4): 1317-1329.

[15] Park G, Xue C, Zheng L, Lam S, Xu J R. MST12 regulates infectious growth but not appressorium formation in the rice blast fungus Magnaporthe grisea. Molecular Plant-Microbe Interactions, 2002, 15(3): 183-192.

[16] Kim S, Park S Y, Kim K S, Rho H S, Chi M-H, Choi J, Park J, Kong S, Park J, Goh J, Lee Y H. Homeobox transcription factors are required for conidiation and appressorium development in the rice blast fungus Magnaporthe oryzae. PLoS Genetics, 2009, 5(12): e1000757.

[17] Park G, Kenneth S B, Christopher J S, Talbot N J, Xu J R. Independent genetic mechanisms mediate turgor generation and penetration peg formation during plant infection in the rice blast fungus. Molecular Microbiology, 2004, 53(6): 1695-1707.

[18] Yue X F, Que Y W, Xu L, Deng S Z, Peng Y L, Talbot N J, Wang Z Y. ZNF1 encodes a putative C₂H₂ zinc-finger protein essential for appressorium differentiation by the rice blast fungus Magnaporthe oryzae. Molecular Plant-Microbe Interactions, 2016, 29(1): 22-35.

[19] Mortazavi A, Williams B A, McCueK, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature Methods, 2008, 5(7): 621-628.

[20] Ye J, Fang L, Zheng H K, Zhang Y, Chen J, Zhang Z, Wang J, Li S, Li R, Bolund L, Wang J. WEGO: a web tool for plotting GO annotations. Nucleic Acids Research, 2006, 34(Web Server issue): W293-W297.

[21] Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, Katayama T, Kawashima S, Okuda S, Tokimatsu Y. KEGG for linking genomes to life and the environment. Nucleic Acids Research, 2008, 36(Database issue): D480-D484.and T, Yamanishi

[22] Livak K J, Schmittgen T D. Analysis of relative gene expression data using real-time quantitative PCR and the 2^-^DD^CT method. Methods, 2001, 25(4): 402-408.

[23] Xie C, Mao X, Huang J, Ding Y, Wu J, Dong S, Kong L, Gao G, Li C, Wei L. Kobas 2.0: A web server for annotation and identification of enriched pathways and diseases. Nucleic Acids Research, 2011, 39(Web Server issue): W316-W322.

[24] Sadat M A, Jeon J, Mir A A, Choi J Y, Lee Y H. Regulation of cellular diacylglycerol through lipid phosphate phosphatases is required for pathogenesis of the rice blast fungus, Magnaporthe oryzae. Plos One, 2014, 9(6): e100726.

[25] Cao H J, Huang P Y, Zhang L L, Shi Y K, Sun D D, Yan Y X, Liu X H, Dong B, Chen G Q, Snyder J H, Lin F C, Lu J P. Characterization of 47 Cys2-His2 zinc finger proteins required for the development and pathogenicity of the rice blast fungus Magnaporthe oryzae. New Phytologist, 2016, 211(3): 1035-1051.

[26] Xu J R, Staiger C J, Hamer J E. Inactivation of the mitogen-activated protein kinase Mps1 from the rice blast fungus prevents penetration of host cells but allows activation of plant defense responses. Proceedings of the National Academy of Sciences of the United States of America, 1998, 95(21): 12713-12718.

[27] Shi Z, Leung H. Genetic analysis and rapid mapping of a sporulation mutation in Magnaporthe grisea. Molecular Plant- Microbe Interactions, 1994, 7(1): 113-120.

[28] Talbot N J, Ebbole D J, Hamer J E. Identification and characterization of MPG1, a gene involved in pathogenicity from the rice blast fungus Magnaporthe grisea. The Plant Cell, 1993, 5(11): 1575-1590.

[29] DeZwaan T M, Carroll A M, Valent B, Sweigard J A. Magnaporthe grisea pth11p is a novel plasma membrane protein that mediates appressorium differentiation in response to inductive substrate cues. The Plant Cell, 1999, 11(10): 2013-2030.

[30] Kong L A, Yang J, Li G T, Qi L L, Zhang Y J, Wang C F, Zhao W S, Xu J R, Peng Y L. Different chitin synthase genes are required for various developmental and plant infection processes in the rice blast fungus Magnaporthe oryzae. PLoS Pathogens, 2012, 8(2): e1002526.

[31] Dixon K P, Xu J R, Smirnoff N, Talbot N J. Independent signaling pathways regulate cellular turgor during hyperosmotic stress and appressorium-mediated plant infection by Magnaporthe grisea. The Plant Cell, 1999, 11: 2045-2058.

[32] Fujikawa T, Kuga Y, Yano S, Yoshimi A, Tachiki T, Abe K, Nishimura M. Dynamics of cell wall components of Magnaporthe grisea during infectious structure development. Molecular Microbiology, 2009, 73(4): 553-570.

[33] Yang J, Kong L A, Chen X L, Wang D W, Qi L L, Zhao W S, Zhang Y, Liu X Z, Peng Y L. A carnitine-acylcarnitine carrier protein, MoCrc1, is essential for pathogenicity in Magnaporthe oryzae. Current Genetics, 2012, 58(3): 139-148.

[34] Samalova M, Johnson J, Illes M, Kelly S, Fricker M, Gurr S. Nitric oxide generated by the rice blast fungus Magnaporthe oryzae drives plant infection. New Phytologist, 2013, 197(1): 207-222.

[35] Chumley F G, Valent B. Genetic analysis of melanin-deficient, nonpathogenic mutants of Magnaporthe grisea. Molecular Plant-Microbe Interactions, 1990, 3(3): 135-143.

[36] Howard R J, Valent B. Breaking and entering: host penetration by the fungal rice blast pathogen Magnaporthe grisea. Annual Review of Microbiology, 1996, 50: 491-512.

[37] Yi M, Lee Y H. Identification of genes encoding heat shock protein 40 family and the functional characterization of two Hsp40s, MHF16 and MHF21, in Magnaporthe oryzae. Journal of Plant Pathology, 2008, 24(2): 131-142.

[38] Kong S, Park S Y, Lee Y H. Systematic characterization of the bZIP transcription factor gene family in the rice blast fungus, Magnaporthe oryzae. Environment Microbiology, 2015, 17(4): 1425-1443.

[39] Mortazavi A, Williams B A, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature Methods, 2008, 5(7): 621-628.

[40] Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nature Reviews Genetics, 2009, 10(1): 57-63.

[41] 张春兰, 秦孜娟, 王桂芝, 纪志宾, 王建民. 转录组与RNA-Seq技术. 生物技术通报, 2012(12): 51-56.

Zhang C L, Qin Z J, Wang G Z, Ji Z B, Wang J M. Transcriptome and RNA-Seq technology. Biotechnology Bulletin, 2012(12): 51-56. (in Chinese)

[42] Soanes D M, Chakrabarti A, Paszkiewicz K H, Dawe A L, Talbot N J. Genome-wide transcriptional profiling of appressorium development by the rice blast fungus Magnaporthe oryzae. PLoS Pathogens, 2012, 8(2): e1002514.

[43] Li X Y, Han X X, Liu Z Q, He C Z. The function and properties of the transcriptional regulator COS1 in Magnaporthe oryzae. Fungal biology, 2013, 117(4): 239-249.

[44] Pham K T, Inoue Y, Vu B V, Nguyen H H, Nakayashiki T, Ikeda K, Nakayashiki H. MoSET1 (Histone H3K4 methyltransferase in Magnaporthe oryzae) regulates global gene expression during infection-related morphogenesis. PLoS Genetics, 2015, 11(7): e1005385.

[45] Brown D W, Dyer R B, McCormick S P, Kendra D F, Plattner R D. Functional demarcation of the Fusarium core trichothecene gene cluster. Fungal Genetics and Biology, 2004, 41(4): 454-462.

[46] Alexander N J, Hohn T M, McCormick S P. The TRI11 gene of Fusarium sporotrichioides encodes a cytochrome P-450 monooxygenase required for C-15 hydroxylation in trichothecene biosynthesis. Applied and Environmental Microbiology, 1998, 64(1): 221-225.

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Analysis of RNA-Seq-Based Expression Profiles of Δznf1 Mutants in Magnaporthe oryzae

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