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This article is part of the Research Topic Retrograde Signaling in Plants

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Original Research ARTICLE

Front. Plant Sci., 24 December 2012 | http://dx.doi.org/10.3389/fpls.2012.00281

Comparison of transcriptional changes to chloroplast and mitochondrial perturbations reveals common and specific responses in Arabidopsis

  • ARC Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, WA, Australia

Throughout the life of a plant, the biogenesis and fine-tuning of energy organelles is essential both under normal growth and stress conditions. Communication from organelle to nucleus is essential to adapt gene regulation and protein synthesis specifically to the current needs of the plant. This organelle-to-nuclear communication is termed retrograde signaling and has been studied extensively over the last decades. In this study we have used large-scale gene expression data sets relating to perturbations of chloroplast and mitochondrial function to gain further insights into plant retrograde signaling and how mitochondrial and chloroplast retrograde pathways interact and differ. Twenty seven studies were included that assess transcript profiles in response to chemical inhibition as well as genetic mutations of organellar proteins. The results show a highly significant overlap between gene expression changes triggered by chloroplast and mitochondrial perturbations. These overlapping gene expression changes appear to be common with general abiotic, biotic, and nutrient stresses. However, retrograde signaling pathways are capable of distinguishing the source of the perturbation as indicated by a statistical overrepresentation of changes in genes encoding proteins of the affected organelle. Organelle-specific overrepresented functional categories among others relate to energy metabolism and protein synthesis. Our analysis also suggests that WRKY transcription factors play a coordinating role on the interface of both organellar signaling pathways. Global comparison of the expression profiles for each experiment revealed that the recently identified chloroplast retrograde pathway using phospho-adenosine phosphate is possibly more related to mitochondrial than chloroplast perturbations. Furthermore, new marker genes have been identified that respond specifically to mitochondrial and/or chloroplast dysfunction.

Keywords: Arabidopsis, mitochondria, chloroplasts, retrograde, stress, microarray

Citation: Van Aken O and Whelan J (2012) Comparison of transcriptional changes to chloroplast and mitochondrial perturbations reveals common and specific responses in Arabidopsis. Front. Plant Sci. 3:281. doi: 10.3389/fpls.2012.00281

Received: 20 November 2012; Accepted: 26 November 2012;
Published online: 24 December 2012.

Edited by:

Tatjana Kleine, Ludwig-Maximilians-Universität München, Germany

Reviewed by:

Rainer E. Häusler, University Cologne, Germany
Iris Finkemeier, Ludwig-Maximilians-Universität München, Germany

Copyright: © 2012 Van Aken and Whelan. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in other forums, provided the original authors and source are credited and subject to any copyright notices concerning any third-party graphics etc.

*Correspondence: James Whelan, ARC Centre of Excellence in Plant Energy Biology, University of Western Australia, 35 Stirling Highway, 6009 Crawley, WA, Australia. e-mail: jim.whelan@uwa.edu.au