Balancing the messages: RNA metabolism mediates stress-signaling and recovery in plants

Abstract

Key to the success of plants is their ability to co-ordinate timely responses to stressful environments using intricate intracellular signaling mechanisms. Most, if not all stress signaling cascades register in the nucleus and trigger transcriptional changes that are fundamental for acclimation to stress. Over the last decade it has also become apparent that chloroplasts operate as sensors of prevailing environmental conditions, perceiving abiotic stress and orchestrating the remodelling of the nuclear transcriptome. Nevertheless, these retrograde signals may also have roles beyond bilateral chloroplast-to-nucleus communication when considered in the context of the broader complexity of a cell. Accordingly, identifying the signaling mechanisms and understanding how intracellular signals are translated into expression changes is essential. Throughout a plant’s life history, stress also alters subsequent plant responses. As a result, the prospect of epigenetic memory is an evocative subject with exciting research and agronomic possibilities. Yet the more common strategy employed by plants is likely to be recovery and resetting, underpinned by post transcriptional processes and RNA metabolism. This thesis demonstrates the existence of the ’SAL1-PAP-XRN’ retrograde signaling pathway in Arabidopsis thaliana (Arabidopsis), providing mechanistic insight into the functions of retrograde signaling during stress. Key to this model is the discovery that the signal is transmitted and interpreted via the nucleotide 3’-phosphoadenosine 5’-phosphate (PAP) and the 5’-3’ exoribonucleases (XRNs) respectively. Evidence that key changes in gene expression are mediated by regulation of RNA Polymerase II read-through and activation of downstream genes is also presented, contributing to our understanding of the transmission and specificity of the PAP signal. Beyond a linear retrograde signaling pathway, it is also demonstrated that PAP-signaling is entwined with other components in the complex networks of the eukaryotic cell. In particular, PAP and the XRNs can regulate stomatal responsiveness and in turn drought tolerance, raising the prospect that PAP is a secondary messenger. Indeed, independent of the XRNs, novel PAP binding proteins are identified including NDPKs, CATs and SOS2 implicating PAP in the regulation of Reactive Oxygen Species (ROS), ABA signaling and cellular energy homeostasis. Characterisation of the PAP-XRN regulon highlights to the importance of RNA metabolism in regulating stress responses, raising questions about how cells recover from stress and the contribution of RNA metabolism and post transcriptional processes. It is argued that elucidating the mechanisms of stress recovery is essential for a complete understanding of stress signaling, tolerance and memory. Consequently, Rapid Recovery Gene Silencing (RRGS) is presented as a new mechanism promoting stress recovery. Consistent with this hypothesis, transcripts are turned-over incredibly fast during stress and recovery establishing RRGS as a prevalent phenomenon in Arabidopsis. The generation of the RRGS time course data set establishes a resource for further investigations into how plants balance recovery and memory at the molecular level, comprising comprehensive profiles of the transcriptome, degradome, sRNAome and DNA methylome.