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...

Germination represents a rapid transition from dormancy to a high level of metabolic activity. In-depth transcriptomic profiling at 10 time points in Arabidopsis (Arabidopsis thaliana), including fresh seed, ripened seed, during stratification, germination, and postgermination per se, revealed specific temporal expression patterns that to our knowledge have not previously been identified. Over 10,000 transcripts were differentially expressed during cold stratification, with subequal numbers up-regulated as down-regulated, revealing an active period in preparing seeds for germination, where transcription and RNA degradation both play important roles in regulating the molecular sequence of events. A previously unidentified transient expression pattern was observed for a group of genes, whereby a significant rise in expression was observed at the end of stratification and significantly lower expression was observed 6 h later. These genes were further defined as germination specific, as they were most highly expressed at this time in germination, in comparison with all developmental tissues in the AtGenExpress data set. Functional analysis of these genes using genetic inactivation revealed that they displayed a significant enrichment for embryo-defective or -arrested phenotype. This group was enriched in genes encoding mitochondrial and nuclear RNA-processing proteins, including more than 45% of all pentatricopeptide domain-containing proteins expressed during germination. The presence of mitochondrial DNA replication factors and RNA-processing functions in this germination-specific subset represents the earliest events in organelle biogenesis, preceding any changes associated with energy metabolism. Green fluorescent protein analysis also confirmed organellar localization for 65 proteins, largely showing germination-specific expression. These results suggest that mitochondrial biogenesis involves a two-step process to produce energetically active organelles: an initial phase at the end of stratification involving mitochondrial DNA synthesis and RNA processing, and a later phase for building the better-known energetic functions. This also suggests that signals with a mitochondrial origin and retrograde signals may be crucial for successful germination.