The general stress response (GSR) is an evolutionarily conserved rapid and transient transcriptional reprograming of genes central for transducing environmental signals into cellular responses, leading to metabolic and physiological readjustments to cope with prevailing conditions. Defining the regulatory components of the GSR will provide crucial insight into the design principles of early stressresponse modules and their role in orchestrating master regulators of adaptive responses. Overaccumulation of methylerythritol cyclodiphosphate (MEcPP), a bifunctional chemical entity serving as both a precursor of isoprenoids produced by the plastidial methylerythritol phosphate (MEP) pathway and a stress-specific retrograde signal, in ceh1 (constitutively expressing hydroperoxide lyase1)-mutant plants leads to large-scale transcriptional alterations. Bioinformatic analyses of microarray data in ceh1 plants established the overrepresentation of a stress-responsive cis element and key GSR marker, the rapid stress response element (RSRE), in the promoters of robustly induced genes. ceh1 plants carrying an established 4×RSRE:Luciferase reporter for monitoring the GSR support constitutive activation of the response in this mutant background. Genetics and pharmacological approaches confirmed the specificity of MEcPP in RSRE induction via the transcription factor CALMODULIN-BINDING TRANSCRIPTION ACTIVATOR 3 (CAMTA3), in a calcium-dependent manner. Moreover, CAMTA3-dependent activation of IRE1a (inositol-requiring protein-1) and bZIP60 (basic leucine zipper 60), two RSRE containing unfolded protein-response genes, bridges MEcPP-mediated GSR induction to the potentiation of protein-folding homeostasis in the endoplasmic reticulum. These findings introduce the notion of transcriptional regulation by a key plastidial retrograde signaling metabolite that induces nuclear GSR, thereby offering a window into the role of interorgannellar communication in shaping cellular adaptive responses.S tress-triggered transcriptional reprogramming plays fundamental roles in transducing stress signals and ultimately enabling adaptive responses through readjustments of the appropriate physiological and metabolic processes. The initial transcriptional reprograming known as the "general stress response" (GSR), at times referred to as the "cellular stress response" or "core stress response," is a recognized evolutionarily conserved stress response present across kingdoms (1-5).The GSR, a rapid and transient transcriptional reprogramming, is induced by a wide variety of stresses imposed upon organisms by environmental forces on macromolecules such as membrane lipids, proteins, and/or DNA (6). Bioinformatic analysis of the promoters of the rapid wound-response genes (5 min after mechanical damage) in plants led to the identification of an overrepresented functional cis-element, the rapid stress response element (RSRE), which is analogous to the yeast stress response element (STRE) (4, 7). A reporter line containing luciferase (LUC) driven by a synthet...

Gene transcription is counterbalanced by mRNA decay processes that regulate transcript quality and quantity. We show here that the evolutionarily conserved DHH1/DDX6-like RNA HELICASEs of Arabidopsis thaliana control the ephemerality of a subset of cellular mRNAs.These RNA helicases co-localize with key markers of processing bodies and stress granules and contribute to their subcellular dynamics. These RHs function to limit the precocious accumulation and translation of stress-responsive mRNAs associated with autoimmunity and growth inhibition under non-stress conditions. Given the conservation of this RH subfamily, they may control basal levels of conditionally-regulated mRNAs in diverse eukaryotes, accelerating responses without penalty. XRN1/4 . These 5' and 3' pathways have substrate specificity, but are not mutually exclusive.When decapping-dependent decay is compromised in Arabidopsis, the 3'-to-5' exoribonuclease SOV can compensate to control mRNA abundance and homeostasis 10,11 . Spatiotemporal regulation of mRNA decay is critical for the cellular transcriptome adjustment in response to both developmental and environmental cues in plants 1 . Dysfunction in decapping due to loss-of-function of non-redundant components results in post-embryonic lethality (DCP1, DCP2, VCS, and DCP5) or severe growth alterations (LSM1 and PAT1) [12][13][14][15][16] .The cause of the developmental defects in some decapping mutants is associated with disruption of mRNA quality control and small interfering (si)RNA production 17 . However, there is limited knowledge of the role of the decay machinery in the spatial and temporal turnover of specific mRNAs and the connections between turnover and mRNA translation and mobilization to PBs and SGs. Mutations in the mRNA decay machinery have been identified in genetic screens for altered sensitivity to biotic and abiotic stresses 16,[18][19][20][21][22][23][24] , yet there is poor understanding of the importance of mRNA decay in restricting accumulation of mRNAs that provide stress resilience but constrain growth.The DHH1/DDX6 family of DEAD-box RNA helicases is conserved across eukaryotes 25 .These proteins function at the nexus between mRNA translation, storage and decay, mediating translational repression and initiating mRNA degradation [26][27][28][29][30][31][32][33] . For example, yeast DHH1 can activate mRNA decapping 34 , promote translational repression 35 , and associate with ribosomes to sense the codon-dependent rate of translational elongation to trigger cotranslational decay 36 . However, the transcript-specific role of these helicases is generally understudied. Here we identify the Arabidopsis DHH1/DDX6-like proteins RNA HELICASE 6 (RH6), RH8, and RH12 as additive and functionally redundant mRNA decay factors required for growth and development.Severe deficiency of RH6, RH8 and RH12 function impairs PB and SG formation, and shifts the transcriptome and translatome homeostasis so that defense-and other stress-responsive mRNAs accumulate despite when grown under standar...

The ancient morphoregulatory hormone auxin dynamically realigns dedicated cellular processes that shape plant growth under prevailing environmental conditions. However, the nature of the stress-responsive signal altering auxin homeostasis remains elusive. Here we establish that the evolutionarily conserved plastidial retrograde signaling metabolite methylerythritol cyclodiphosphate (MEcPP) controls adaptive growth by dual transcriptional and post-translational regulatory inputs that modulate auxin levels and distribution patterns in response to stress. We demonstrate that in vivo accumulation or exogenous application of MEcPP alters the expression of two auxin reporters, DR5:GFP and DII-VENUS, and reduces the abundance of the auxin-efflux carrier PIN-FORMED1 (PIN1) at the plasma membrane. However, pharmacological intervention with clathrin-mediated endocytosis blocks the PIN1 reduction. This study provides insight into the interplay between these two indispensable signaling metabolites by establishing the mode of MEcPP action in altering auxin homeostasis, and as such, positioning plastidial function as the primary driver of adaptive growth.

Plant survival necessitates constant monitoring of fluctuating light and balancing growth demands with adaptive responses, tasks mediated via interconnected sensing and signaling networks. Photoreceptor phytochrome B (phyB) and plastidial retrograde signaling metabolite methylerythritol cyclodiphosphate (MEcPP) are evolutionarily conserved sensing and signaling components eliciting responses through unknown connection(s). Here, via a suppressor screen, we identify two phyB mutant alleles that revert the dwarf and high salicylic acid phenotypes of the high MEcPP containing mutant ceh1 . Biochemical analyses show high phyB protein levels in MEcPP-accumulating plants resulting from reduced expression of phyB antagonists and decreased auxin levels. We show that auxin treatment negatively regulates phyB abundance. Additional studies identify CAMTA3, a MEcPP-activated calcium-dependent transcriptional regulator, as critical for maintaining phyB abundance. These studies provide insights into biological organization fundamentals whereby a signal from a single plastidial metabolite is transduced into an ensemble of regulatory networks controlling the abundance of phyB, positioning plastids at the information apex directing adaptive responses.

Plants have evolved tightly regulated signaling networks to respond and adapt to environmental perturbations, but the nature of the signaling hub(s) involved have remained an enigma. We have previously established that methylerythritol cyclodiphosphate (MEcPP), a precursor of plastidial isoprenoids and a stress-specific retrograde signaling metabolite, enables cellular readjustments for high-order adaptive functions. Here, we specifically show that MEcPP promotes two Brassicaceae-specific traits, namely endoplasmic reticulum (ER) body formation and induction of indole glucosinolate (IGs) metabolism selectively, via transcriptional regulation of key regulators NAI1 for ER body formation and MYB51/122 for IGs biosynthesis). The specificity of MEcPP is further confirmed by the lack of induction of wound-inducible ER body genes as well as IGs by other altered methylerythritol phosphate pathway enzymes. Genetic analyses revealed MEcPP-mediated COI1-dependent induction of these traits. Moreover, MEcPP signaling integrates the biosynthesis and hydrolysis of IGs through induction of nitrile-specifier protein1 and reduction of the suppressor, ESM1, and production of simple nitriles as the bioactive end product. The findings position the plastidial metabolite, MEcPP, as the initiation hub, transducing signals to adjust the activity of hard-wired gene circuitry to expand phytochemical diversity and alter the associated subcellular structure required for functionality of the secondary metabolites, thereby tailoring plant stress responses.