Towards a temporal modeling of the genetic network controlling Systemic Acquired Resistance in Arabidopsis thaliana

We studied defense mechanism of the Arabidopsis thaliana subjected to Salicylic Acid (SA) treatment for 0, 1, and 8 hours using a broader application of the frequent itemset approach. Four genotypes of the plant were used in this study, Columbia wild type, mutant npr1-3, double mutant tga1 tga4 and triple mutant tga2 tga5 tga6. We defined the major patterns of transcription regulation governing pathogen defense mechanism, thereby creating a model of the Systemic Acquired Resistance (SAR) at three time points. The temporal model describes the relationships among the regulators and defines groups of genes that are subject to similar regulation. The results obtained offered a first glimpse into the temporal pattern of the transcription regulatory network during SAR in Arabidopsis thaliana. We found that most of the genes that responded to SA challenge are in fact dependent on one or more of the NPR1 and TGA factors tested in this study.

[1]  M. Kesarwani,et al.  Genetic Interactions of TGA Transcription Factors in the Regulation of Pathogenesis-Related Genes and Disease Resistance in Arabidopsis1[W] , 2007, Plant Physiology.

[2]  Fumiaki Katagiri,et al.  The genetic network controlling the Arabidopsis transcriptional response to Pseudomonas syringae pv. maculicola: roles of major regulators and the phytotoxin coronatine. , 2008, Molecular plant-microbe interactions : MPMI.

[3]  Ruggero G. Pensa,et al.  Assessment of discretization techniques for relevant pattern discovery from gene expression data , 2004, BIOKDD.

[4]  Cyril Zipfel,et al.  News from the frontline: recent insights into PAMP-triggered immunity in plants. , 2008, Current opinion in plant biology.

[5]  Murray Grant,et al.  Type III effectors orchestrate a complex interplay between transcriptional networks to modify basal defence responses during pathogenesis and resistance. , 2006, The Plant journal : for cell and molecular biology.

[6]  C. Pieterse,et al.  NPR1: the spider in the web of induced resistance signaling pathways. , 2004, Current opinion in plant biology.

[7]  F. Parcy,et al.  bZIP transcription factors in Arabidopsis. , 2002, Trends in plant science.

[8]  Erik Andreasson,et al.  Arabidopsis MAP Kinase 4 Negatively Regulates Systemic Acquired Resistance , 2000, Cell.

[9]  Timothy S Gardner,et al.  Reverse-engineering transcription control networks. , 2005, Physics of life reviews.

[10]  Andrew B. Nobel,et al.  Mining Approximate Frequent Itemsets In the Presence of Noise: Algorithm and Analysis , 2006, SDM.

[11]  Anthony K. H. Tung,et al.  FARMER: finding interesting rule groups in microarray datasets , 2004, SIGMOD '04.

[12]  Darrell Desveaux,et al.  The Arabidopsis NPR1 Disease Resistance Protein Is a Novel Cofactor That Confers Redox Regulation of DNA Binding Activity to the Basic Domain/Leucine Zipper Transcription Factor TGA1 Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.012849. , 2003, The Plant Cell Online.

[13]  Jonathan D. G. Jones,et al.  The plant immune system , 2006, Nature.

[14]  Xinnian Dong,et al.  NPR1, all things considered. , 2004, Current opinion in plant biology.

[15]  Chad Creighton,et al.  Mining gene expression databases for association rules , 2003, Bioinform..

[16]  J. Ryals,et al.  Arabidopsis signal transduction mutant defective in chemically and biologically induced disease resistance. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[17]  H. Signer,et al.  Increase in Salicylic Acid at the Onset of Systemic Acquired Resistance in Cucumber , 1990, Science.

[18]  Heikki Mannila,et al.  Fast Discovery of Association Rules , 1996, Advances in Knowledge Discovery and Data Mining.

[19]  Edward R. Dougherty,et al.  Probabilistic Boolean networks: a rule-based uncertainty model for gene regulatory networks , 2002, Bioinform..

[20]  C. Becquet,et al.  Strong-association-rule mining for large-scale gene-expression data analysis: a case study on human SAGE data , 2002, Genome Biology.

[21]  Sieu Phan,et al.  GOAL: A software tool for assessing biological significance of genes groups , 2009, BMC Bioinformatics.

[22]  E. Grotewold,et al.  MYB transcription factors in Arabidopsis. , 2002, Trends in plant science.

[23]  Tomasz Imielinski,et al.  Mining association rules between sets of items in large databases , 1993, SIGMOD Conference.

[24]  Ahmed H. Tewfik,et al.  DNA Microarray Data Analysis: A Novel Biclustering Algorithm Approach , 2006, EURASIP J. Adv. Signal Process..

[25]  Christopher Johnson,et al.  Salicylic Acid and NPR1 Induce the Recruitment of trans-Activating TGA Factors to a Defense Gene Promoter in Arabidopsis Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.012211. , 2003, The Plant Cell Online.

[26]  R. Laubenbacher,et al.  A computational algebra approach to the reverse engineering of gene regulatory networks. , 2003, Journal of theoretical biology.

[27]  Thomas Eulgem,et al.  Regulation of the Arabidopsis defense transcriptome. , 2005, Trends in plant science.

[28]  Leslie Friedrich,et al.  Requirement of Salicylic Acid for the Induction of Systemic Acquired Resistance , 1993, Science.

[29]  L. C. Loon,et al.  The families of pathogenesis-related proteins, their activities, and comparative analysis of PR-1 type proteins , 1999 .

[30]  Fazel Famili,et al.  Discovery of Functional Genes for Systemic Acquired Resistance in arabidopsis Thaliana through Integrated Data Mining , 2004, J. Bioinform. Comput. Biol..

[31]  Monica Stein,et al.  Loss of a Callose Synthase Results in Salicylic Acid-Dependent Disease Resistance , 2003, Science.

[32]  E. Lam,et al.  DNA-binding properties, genomic organization and expression pattern of TGA6, a new member of the TGA family of bZIP transcription factors in Arabidopsis thaliana , 1997, Plant Molecular Biology.

[33]  D F Klessig,et al.  Salicylic Acid: A Likely Endogenous Signal in the Resistance Response of Tobacco to Viral Infection , 1990, Science.

[34]  Enwu Liu,et al.  The Arabidopsis NPR1/NIM1 Protein Enhances the DNA Binding Activity of a Subgroup of the TGA Family of bZIP Transcription Factors , 2000, Plant Cell.