title: Protein-protein interaction and gene co-expression maps of ARFs and Aux/IAAs in Arabidopsis.
abstract: The phytohormone auxin regulates nearly all aspects of plant growth and development. Based on the current model in Arabidopsis thaliana, Auxin/indole-3-acetic acid (Aux/IAA) proteins repress auxin-inducible genes by inhibiting auxin response transcription factors (ARFs). Experimental evidence suggests that heterodimerization between Aux/IAA and ARF proteins are related to their unique biological functions. The objective of this study was to generate the Aux/IAA-ARF protein-protein interaction map using full length sequences and locate the interacting protein pairs to specific gene co-expression networks in order to define tissue-specific responses of the Aux/IAA-ARF interactome. Pairwise interactions between 19 ARFs and 29 Aux/IAAs resulted in the identification of 213 specific interactions of which 79 interactions were previously unknown. The incorporation of co-expression profiles with protein-protein interaction data revealed a strong correlation of gene co-expression for 70% of the ARF-Aux/IAA interacting pairs in at least one tissue/organ, indicative of the biological significance of these interactions. Importantly, ARF4-8 and 19, which were found to interact with almost all Aux-Aux/IAA showed broad co-expression relationships with Aux/IAA genes, thus, formed the central hubs of the co-expression network. Our analyses provide new insights into the biological significance of ARF-Aux/IAA associations in the morphogenesis and development of various plant tissues and organs.
authors.affiliation: Department of Plant Sciences, University of Tennessee Knoxville, TN, USA.
authors.forename: Sarbottam
authors.initials: S
authors.lastname: Piya
authors.affiliation: Department of Entomology and Plant Pathology, University of Tennessee Knoxville, TN, USA.
authors.forename: Sandesh K
authors.initials: SK
authors.lastname: Shrestha
authors.affiliation: Department of Biochemistry, Cellular, and Molecular Biology, University of Tennessee Knoxville, TN, USA.
authors.forename: Brad
authors.initials: B
authors.lastname: Binder
authors.affiliation: Department of Plant Sciences, University of Tennessee Knoxville, TN, USA.
authors.forename: C Neal
authors.initials: CN
authors.lastname: Stewart
authors.affiliation: Department of Plant Sciences, University of Tennessee Knoxville, TN, USA.
authors.forename: Tarek
authors.initials: T
authors.lastname: Hewezi
keywords: Arabidopsis; auxin; auxin response transcription factors; auxin/indole-3-acetic acid proteins; co-expression network; protein-protein interactions