Protein-protein interaction and gene co-expression maps of ARFs and Aux/IAAs in Arabidopsis
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 sugges...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2014-12-01
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| Series: | Frontiers in Plant Science |
| Subjects: | |
| Online Access: | http://journal.frontiersin.org/Journal/10.3389/fpls.2014.00744/full |
| _version_ | 1818133299379306496 |
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| author | Sarbottam ePiya Sandesh K. Shrestha Brad eBinder C. Neal eStewart Jr Tarek eHewezi |
| author_facet | Sarbottam ePiya Sandesh K. Shrestha Brad eBinder C. Neal eStewart Jr Tarek eHewezi |
| author_sort | Sarbottam ePiya |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-11T08:50:31Z |
| format | Article |
| id | doaj.art-942476c49c874e63aa82d1ba20af4bf6 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-12-11T08:50:31Z |
| publishDate | 2014-12-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-942476c49c874e63aa82d1ba20af4bf62022-12-22T01:14:01ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2014-12-01510.3389/fpls.2014.00744122289Protein-protein interaction and gene co-expression maps of ARFs and Aux/IAAs in ArabidopsisSarbottam ePiya0Sandesh K. Shrestha1Brad eBinder2C. Neal eStewart Jr3Tarek eHewezi4The University of TennesseeUniversity of TennesseeThe University of TennesseeThe University of TennesseeThe University of TennesseeThe 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.http://journal.frontiersin.org/Journal/10.3389/fpls.2014.00744/fullArabidopsisauxinprotein-protein interactionsco-expression networksAuxin/indole-3-acetic acid proteinsAuxin response transcription factors |
| spellingShingle | Sarbottam ePiya Sandesh K. Shrestha Brad eBinder C. Neal eStewart Jr Tarek eHewezi Protein-protein interaction and gene co-expression maps of ARFs and Aux/IAAs in Arabidopsis Frontiers in Plant Science Arabidopsis auxin protein-protein interactions co-expression networks Auxin/indole-3-acetic acid proteins Auxin response transcription factors |
| title | Protein-protein interaction and gene co-expression maps of ARFs and Aux/IAAs in Arabidopsis |
| title_full | Protein-protein interaction and gene co-expression maps of ARFs and Aux/IAAs in Arabidopsis |
| title_fullStr | Protein-protein interaction and gene co-expression maps of ARFs and Aux/IAAs in Arabidopsis |
| title_full_unstemmed | Protein-protein interaction and gene co-expression maps of ARFs and Aux/IAAs in Arabidopsis |
| title_short | Protein-protein interaction and gene co-expression maps of ARFs and Aux/IAAs in Arabidopsis |
| title_sort | protein protein interaction and gene co expression maps of arfs and aux iaas in arabidopsis |
| topic | Arabidopsis auxin protein-protein interactions co-expression networks Auxin/indole-3-acetic acid proteins Auxin response transcription factors |
| url | http://journal.frontiersin.org/Journal/10.3389/fpls.2014.00744/full |
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