Transcriptional networks that control root developmental responses to ethylene
Elevated levels of the plant hormone ethylene modulate root development, leading to shorter primary roots, fewer lateral roots, and greater numbers of root hairs. Genetic approaches have identified the ethylene signaling machinery, which includes a family of 5 receptors that modulate distinct developmental processes.1 We have identified the roles of these receptors in root architecture in collaboration with the laboratory of Brad Binder.2 The early ethylene signaling pathway has been studied in detail, but downstream transcriptional effects have not been as well-studied, especially in roots and in light grown seedlings.
To identify the root transcriptional responses to ethylene we examined the kinetics of changes in transcript abundance and overlaid these on the kinetics of developmental changes.2 Current work is using this time course transcriptomic data to uncover the transcription factor networks controlling ethylene-dependent developmental changes. We are using computational approaches to identify transcription factor targets and for Bayesian modeling of time course transcriptomics in collaboration with David John, James Norris, and William Turkett from Computer Science and Mathematics at Wake Forest.
1. Shakeel SN, Wang X, Binder BM & Schaller GE (2013) Mechanisms of signal transduction by ethylene: Overlapping and non-overlapping signalling roles in a receptor family. AoB Plants 5: plt010-plt010
2. Harkey, AF, Watkins, JR, Olex, AL, DiNapoli, KT, Lewis, DR, Fetrow, JS, Binder, BMc, and Muday, GK (In press) Identification of transcriptional and receptor networks that control root responses to ethylene using time course transcriptomics. Plant Physiology.
Norris, JN, Patton, KL, Huang, S, John, D, and Muday, GK (2015) First and Second Order Markov Posterior Probabilities on Multiple Time-Course Data Sets. In Proceedings of Southeast Congress 2015. Publisher IEEE, pp1-8
Patton, KL, John, DJ, Norris, JL, Lewis, DR, and Muday, GK (2014) Hierarchical Bayesian system network modeling of multiple related replicates. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 11: 336-346.
Lewis, DR, Negi, S, Sukumar, P, Muday, GK (2011) Ethylene inhibits lateral root development and enhances IAA transport by altered expression and localization of auxin transport proteins. Development 138: 3485-3495.
Lewis, DR, Ramirez, MV, Valbuena, P, Miller, ND, Keith, R, Helm, R, Winkel, BSJ, Muday, GK (2011) Auxin and ethylene induce distinct flavonol accumulation patterns through independent transcriptional networks: Plant Physiol. 156: 144-164
Negi, S, Sukumar, P, Liu, X, Cohen, JD, and Muday, GK (2010) Genetic dissection of the role of ethylene in regulating auxin dependent lateral and adventitious root formation in tomato. Plant Journal 61: 3-15
This work is supported by the National Science Foundation Molecular and Cellular Biosciences Division: Systems and Synthetic Biology Program.