Global Expression Profiling of Transcription Factor Genes Provides New Insights into Pathogenicity and Stress Responses in the Rice Blast Fungus Sook-Young Park 1 , Jaeyoung Choi 1 , Se-Eun Lim 1 , Gir-Won Lee 1 , Jongsun Park 1 , Yang Kim 2 , Sunghyung Kong 1 , Se Ryun Kim 1 , Hee-Sool Rho 1 , Junhyun Jeon 1 , Myung-Hwan Chi 1 , Soonok Kim 3 , Chang Hyun Khang 4 , Seogchan Kang 5 , Yong-Hwan Lee 1 * 1 Department of Agricultural Biotechnology, Fungal Bioinformatics Laboratory, Center for Fungal Genetic Resources, and Center for Fungal Pathogenesis, Seoul National University, Seoul, Korea, 2 Center for Food and Bioconvergence, Seoul National University, Seoul, Korea, 3 National Institute of Biological Resources, Ministry of Environment, Incheon, Korea, 4 Department of Plant Biology, University of Georgia, Athens, Georgia, United States of America, 5 Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, Pennsylvania, United States of America 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. Citation: Park SY, Choi J, Lim SE, Lee GW, Park J, et al. (2013) Global Expression Profiling of Transcription Factor Genes Provides New Insights into Pathogenicity and Stress Responses in the Rice Blast Fungus. PLoS Pathog 9(6): e1003350. doi:10.1371/journal.ppat.1003350 Editor: Leah E. Cowen, University of Toronto, Canada Received July 4, 2012; Accepted March 25, 2013; Published June 6, 2013 Copyright: ß 2013 Park et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: This work was supported by National Research Foundation of Korea grants funded by the Korean government (Grant number: 2012-0001149 and 2012- 0000141; http://www.nrf.re.kr), The Technology Development Program for Agriculture and Forestry (TDPAF) of the MIFAFF of the Korean government (Grant number: 309015-04-SB020; http://www.mifaff.go.kr), and The Next-Generation BioGreen 21 Program of Rural Development Administration in Korea (Grant number: PJ00821201; www.rda.go.kr). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. * E-mail: yonglee@snu.ac.kr Introduction Fungal pathogenesis requires well-orchestrated regulation of multiple cellular and developmental processes in response to diverse stimuli from the host and the environment. Transcription factors (TFs) function as key regulators of such processes. Identification of TF genes, which typically represent 3–6% of the predicted genes in eukaryotic genomes, has been greatly facilitated by genome sequencing [1]. High-throughput methods for gene expression analysis have enabled studies on how TF genes are globally regulated under diverse conditions [2–4]. A combi- nation of these approaches has uncovered putative roles and potential interactions of TFs in animals and plants [3,5]. Although DNA microarrays have been successfully used to study global gene expression patterns, this approach may not be sensitive enough to accurately analyze low-abundance transcripts, including those from many TF genes [6]. Quantitative RT-PCR (qRT-PCR) has been shown to be five times more sensitive than microarrays [4], serving as an effective means for accurate quantification of TF transcripts. The rice blast fungus Magnaporthe oryzae, one of the most devastating pathogens of rice and related grass species, undergoes sequential developmental changes to successfully infect host plants and complete the disease cycles. These processes include conidiogenesis, conidial germination, appressorium formation, penetration peg formation and infectious growth. Extensive studies have been performed to identify and characterize the genes that participate in these developmental changes and pathogenicity in M. oryzae [7–11]. Recent functional analyses of several M. oryzae TF genes demonstrated their critical roles in processes such as conidiation (COS1, MoHOX2, MoHOX4, and COM1; [12–14]), appressorium formation (MoHOX7, MoLDB1, and Con7p; [12,15,16]), infectious growth (Mig1, Mstu1, MoHOX8, and MoMCM1; [12,17–19]), oxidative stress (Moatf1; [20]), and light PLOS Pathogens | www.plospathogens.org 1 June 2013 | Volume 9 | Issue 6 | e1003350