Plants require daily coordinated regulation of energy metabolism for optimal growth and survival and therefore need to integrate cellular responses with both mitochondrial and plastid retrograde signaling. Using a forward genetic screen to characterize regulators of alternative oxidase1a (rao) mutants, we identified RAO2/Arabidopsis NAC domain-containing protein17 (ANAC017) as a direct positive regulator of AOX1a. RAO2/ANAC017 is targeted to connections and junctions in the endoplasmic reticulum (ER) and F-actin via a C-terminal transmembrane (TM) domain. A consensus rhomboid protease cleavage site is present in ANAC017 just prior to the predicted TM domain. Furthermore, addition of the rhomboid protease inhibitor N-p-Tosyl-L-Phe chloromethyl abolishes the induction of AOX1a upon antimycin A treatment. Simultaneous fluorescent tagging of ANAC017 with N-terminal red fluorescent protein (RFP) and C-terminal green fluorescent protein (GFP) revealed that the N-terminal RFP domain migrated into the nucleus, while the C-terminal GFP tag remained in the ER. Genome-wide analysis of the transcriptional network regulated by RAO2/ANAC017 under stress treatment revealed that RAO2/ANAC017 function was necessary for >85% of the changes observed as a primary response to cytosolic hydrogen peroxide (H 2 O 2 ), but only ;33% of transcriptional changes observed in response to antimycin A treatment. Plants with mutated rao2/anac017 were more stress sensitive, whereas a gain-of-function mutation resulted in plants that had lower cellular levels of H 2 O 2 under untreated conditions. INTRODUCTIONMitochondria and plastids (chloroplasts) are composed of ;1500 and ;3000 proteins, respectively, with >95% of these proteins encoded by nuclear-located genes (Woodson and Chory, 2008). It has been shown that two-way communication pathways exist between the nucleus and mitochondria and chloroplasts, called anterograde and retrograde signaling pathways (Rhoads and Subbaiah, 2007;Woodson and Chory, 2008). Anterograde regulation refers to a top-down regulatory pathway, where signals have a direct impact on gene expression in the nucleus. Conversely, nuclear gene expression is also influenced by signals that originate from within the organelles, mitochondria, or chloroplasts and is referred to as retrograde regulation.Several components involved in plastid retrograde signaling have been identified, with at least five different pathways characterized: reactive oxygen species (ROS), redox signals, plastidial gene expression, pigment biosynthesis, and specific signaling metabolites (Pfannschmidt, 2010). The most intensively studied retrograde signaling pathway is in the genomes uncoupled (gun) mutants that uncouple the expression of nuclear-encoded chloroplastic proteins from the functional state of chloroplasts (Susek et al., 1993). A recently identified plastid-bound transcription factor, PTM (plant homeodomaintype transcription factor with transmembrane [TM] domains), was also identified as a regulator for plastid retrograde signaling and acts do...

Using rice (Oryza sativa) as a model crop species, we performed an in-depth temporal transcriptome analysis, covering the early and late stages of Pi deprivation as well as Pi recovery in roots and shoots, using next-generation sequencing. Analyses of 126 paired-end RNA sequencing libraries, spanning nine time points, provided a comprehensive overview of the dynamic responses of rice to Pi stress. Differentially expressed genes were grouped into eight sets based on their responses to Pi starvation and recovery, enabling the complex signaling pathways involved in Pi homeostasis to be untangled. A reference annotation-based transcript assembly was also generated, identifying 438 unannotated loci that were differentially expressed under Pi starvation. Several genes also showed induction of unannotated splice isoforms under Pi starvation. Among these, PHOSPHATE2 (PHO2), a key regulator of Pi homeostasis, displayed a Pi starvation-induced isoform, which was associated with increased translation activity. In addition, microRNA (miRNA) expression profiles after long-term Pi starvation in roots and shoots were assessed, identifying 20 miRNA families that were not previously associated with Pi starvation, such as miR6250. In this article, we present a comprehensive spatio-temporal transcriptome analysis of plant responses to Pi stress, revealing a large number of potential key regulators of Pi homeostasis in plants.