Frontiers In Plant Science

Autor: Kuan Yang, Haktan Suren, Curtis Klumas, Jason A. Holliday, Ruth Grene, Lenwood S. Heath, Elijah Myers, Eva Collakova
Přispěvatelé: Computer Science, Forest Resources and Environmental Conservation, Fralin Life Sciences Institute, School of Plant and Environmental Sciences
Rok vydání: 2012
Předmět:
Zdroj: Frontiers in Plant Science, Vol 3 (2012)
Frontiers in Plant Science
ISSN: 1664-462X
DOI: 10.3389/fpls.2012.00241
Popis: Microarray gene expression profiling is a powerful technique to understand complex developmental processes, but making biologically meaningful inferences from such studies has always been challenging. We previously reported a microarray study of the freezing acclimation period in Sitka spruce (Picea sitchensis) in which a large number of candidate genes for climatic adaptation were identified. In the current paper, we apply additional systems biology tools to these data to further probe changes in the levels of genes and metabolites and activities of associated pathways that regulate this complex developmental transition. One aspect of this adaptive process that is not well understood is the role of the cell wall. Our data suggest coordinated metabolic and signaling responses leading to cell wall remodeling. Co-expression of genes encoding proteins associated with biosynthesis of structural and non-structural cell wall carbohydrates was observed, which may be regulated by ethylene signaling components. At the same time, numerous genes, whose products are putatively localized to the endomembrane system and involved in both the synthesis and trafficking of cell wall carbohydrates, were up-regulated. Taken together, these results suggest a link between ethylene signaling and biosynthesis, and targeting of cell wall related gene products during the period of winter hardening. Automated Layout Pipeline for Inferred NEtworks (ALPINE), an in-house plugin for the Cytoscape visualization environment that utilizes the existing GeneMANIA and Mosaic plugins, together with the use of visualization tools, provided images of proposed signaling processes that became active over the time course of winter hardening, particularly at later time points in the process. The resulting visualizations have the potential to reveal novel, hypothesis generating, gene association patterns in the context of targeted subcellular location. National Science Foundation iPlant Collaborative [DBI-0735191] NSF [ABI1062472] This work was supported by the National Science Foundation iPlant Collaborative (DBI-0735191) and NSF ABI1062472.
Databáze: OpenAIRE
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