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Genome-wide prediction and functional validation of promoter motifs regulating gene expression in spore and infection stages of Phytophthora infestans.
PLoS Pathog. 2013 Mar; 9(3):e1003182.PP

Abstract

Most eukaryotic pathogens have complex life cycles in which gene expression networks orchestrate the formation of cells specialized for dissemination or host colonization. In the oomycete Phytophthora infestans, the potato late blight pathogen, major shifts in mRNA profiles during developmental transitions were identified using microarrays. We used those data with search algorithms to discover about 100 motifs that are over-represented in promoters of genes up-regulated in hyphae, sporangia, sporangia undergoing zoosporogenesis, swimming zoospores, or germinated cysts forming appressoria (infection structures). Most of the putative stage-specific transcription factor binding sites (TFBSs) thus identified had features typical of TFBSs such as position or orientation bias, palindromy, and conservation in related species. Each of six motifs tested in P. infestans transformants using the GUS reporter gene conferred the expected stage-specific expression pattern, and several were shown to bind nuclear proteins in gel-shift assays. Motifs linked to the appressoria-forming stage, including a functionally validated TFBS, were over-represented in promoters of genes encoding effectors and other pathogenesis-related proteins. To understand how promoter and genome architecture influence expression, we also mapped transcription patterns to the P. infestans genome assembly. Adjacent genes were not typically induced in the same stage, including genes transcribed in opposite directions from small intergenic regions, but co-regulated gene pairs occurred more than expected by random chance. These data help illuminate the processes regulating development and pathogenesis, and will enable future attempts to purify the cognate transcription factors.

Authors+Show Affiliations

Department of Plant Pathology and Microbiology, University of California, Riverside, CA, USA.No affiliation info availableNo affiliation info available

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

Language

eng

PubMed ID

23516354

Citation

Roy, Sourav, et al. "Genome-wide Prediction and Functional Validation of Promoter Motifs Regulating Gene Expression in Spore and Infection Stages of Phytophthora Infestans." PLoS Pathogens, vol. 9, no. 3, 2013, pp. e1003182.
Roy S, Kagda M, Judelson HS. Genome-wide prediction and functional validation of promoter motifs regulating gene expression in spore and infection stages of Phytophthora infestans. PLoS Pathog. 2013;9(3):e1003182.
Roy, S., Kagda, M., & Judelson, H. S. (2013). Genome-wide prediction and functional validation of promoter motifs regulating gene expression in spore and infection stages of Phytophthora infestans. PLoS Pathogens, 9(3), e1003182. https://doi.org/10.1371/journal.ppat.1003182
Roy S, Kagda M, Judelson HS. Genome-wide Prediction and Functional Validation of Promoter Motifs Regulating Gene Expression in Spore and Infection Stages of Phytophthora Infestans. PLoS Pathog. 2013;9(3):e1003182. PubMed PMID: 23516354.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Genome-wide prediction and functional validation of promoter motifs regulating gene expression in spore and infection stages of Phytophthora infestans. AU - Roy,Sourav, AU - Kagda,Meenakshi, AU - Judelson,Howard S, Y1 - 2013/03/14/ PY - 2012/09/08/received PY - 2012/12/20/accepted PY - 2013/3/22/entrez PY - 2013/3/22/pubmed PY - 2015/4/4/medline SP - e1003182 EP - e1003182 JF - PLoS pathogens JO - PLoS Pathog. VL - 9 IS - 3 N2 - Most eukaryotic pathogens have complex life cycles in which gene expression networks orchestrate the formation of cells specialized for dissemination or host colonization. In the oomycete Phytophthora infestans, the potato late blight pathogen, major shifts in mRNA profiles during developmental transitions were identified using microarrays. We used those data with search algorithms to discover about 100 motifs that are over-represented in promoters of genes up-regulated in hyphae, sporangia, sporangia undergoing zoosporogenesis, swimming zoospores, or germinated cysts forming appressoria (infection structures). Most of the putative stage-specific transcription factor binding sites (TFBSs) thus identified had features typical of TFBSs such as position or orientation bias, palindromy, and conservation in related species. Each of six motifs tested in P. infestans transformants using the GUS reporter gene conferred the expected stage-specific expression pattern, and several were shown to bind nuclear proteins in gel-shift assays. Motifs linked to the appressoria-forming stage, including a functionally validated TFBS, were over-represented in promoters of genes encoding effectors and other pathogenesis-related proteins. To understand how promoter and genome architecture influence expression, we also mapped transcription patterns to the P. infestans genome assembly. Adjacent genes were not typically induced in the same stage, including genes transcribed in opposite directions from small intergenic regions, but co-regulated gene pairs occurred more than expected by random chance. These data help illuminate the processes regulating development and pathogenesis, and will enable future attempts to purify the cognate transcription factors. SN - 1553-7374 UR - https://www.unboundmedicine.com/medline/citation/23516354/Genome_wide_prediction_and_functional_validation_of_promoter_motifs_regulating_gene_expression_in_spore_and_infection_stages_of_Phytophthora_infestans_ L2 - http://dx.plos.org/10.1371/journal.ppat.1003182 DB - PRIME DP - Unbound Medicine ER -