Plants are indispensable for life on earth and represent organisms of extreme biological diversity with unique molecular capabilities 1. Here, we present a quantitative atlas of the transcriptomes, proteomes and phosphoproteomes of 30 tissues of the model plant Arabidopsis thaliana. It provides initial answers to how many genes exist as proteins (>18,000), where they are expressed, in which approximate quantities (>6 orders of magnitude dynamic range) and to what extent they are phosphorylated (>43,000 sites). We present examples for how the data may be used, for instance, to discover proteins translated from short open reading frames, to uncover sequence motifs involved in protein expression regulation, to identify tissue-specific protein complexes or phosphorylation-mediated signaling events to name a few. Interactive access to this unique resource for the plant community is provided via ProteomicsDB and ATHENA which include powerful bioinformatics tools to explore and characterize Arabidopsis proteins, their modifications and interplay. Main The plant model organism Arabidopsis thaliana (AT) has revolutionized our understanding of plant biology and influenced many other areas of the life sciences 1. Knowledge derived from Arabidopsis has also provided mechanistic understanding of important agronomic traits in crop species 2. The Arabidopsis genome was sequenced 20 years ago and hundreds of natural variants have since been analyzed at the genome and epigenome level 3,4. In contrast, the Arabidopsis proteome as the main executer of most biological processes is far less comprehensively characterized. To address this gap, we used state-of-the-art mass spectrometry and RNA sequencing (RNA-seq) to provide the first integrated proteomic, phosphoproteomic and transcriptomic atlas of Arabidopsis. Illustrated by selected examples, we show how this rich molecular resource can be used to explore the function of single proteins or entire pathways across multiple omics levels. Multi-omics atlas of Arabidopsis We generated an expression atlas covering, on average, 17,603 ± 1,317 transcripts, 14,430 ± 911 proteins and 14,689 ± 2,509 phosphorylation sites (p-sites) per tissue, using a reproducible biochemical and analytical approach (Fig. 1a,b; Extended Data Fig. 1a-c; Supplementary Data 1,2). In total, the protein expression data covers 18,210 of the 27,655 protein-coding genes (66%) annotated in Araport11 5. This is a substantial increase compared to the percentage of genes with protein level evidence reported in UniProt (27%) 6 and more than double the number of proteins identified in an earlier tissue proteome analysis 7 (Fig. 1c, Extended Data Fig. 1d-f). In addition, we report tissue-resolved quantitative evidence for a total of 43,903 p-sites making this study the most comprehensive single Arabidopsis phosphoproteome published to date (Fig. 1c). 47% of the expressed proteome was found to be phosphorylated in at least one instance, confirming earlier analyses of individual

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The phytohormone abscisic acid (ABA) is induced in response to abiotic stress to mediate plant acclimation to environmental challenge. Key players of the ABA-signaling pathway are the ABA-binding receptors (RCAR/PYR1/PYL), which, together with a plant-specific subclade of protein phosphatase 2C (PP2C), form functional holoreceptors. The Arabidopsis genome encodes nine PP2C coreceptors and 14 different RCARs, which can be divided into three subfamilies. The presence of these gene families in higher plants points to the existence of an intriguing regulatory network and poses questions as to the functional compatibility and specificity of receptor-coreceptor interactions. Here, we analyzed all RCAR-PP2C combinations for their capacity to regulate ABA signaling by transient expression in Arabidopsis protoplasts. Of 126 possible RCAR-PP2C pairings, 113 were found to be functional. The three subfamilies within the RCAR family showed different sensitivities to regulating the ABA response at basal ABA levels when efficiently expressed. At exogenous high ABA levels, the RCARs regulated most PP2Cs and activated the ABA response to a similar extent. The PP2C AHG1 was regulated only by RCAR1/PYL9, RCAR2/ PYL7, and RCAR3/PYL8, which are characterized by a unique tyrosine residue. Site-directed mutagenesis of RCAR1 showed that its tyrosine residue is critical for AHG1 interaction and regulation. Furthermore, the PP2Cs HAI1 to HAI3 were regulated by all RCARs, and the ABA receptor RCAR4/PYL10 showed ABA-dependent PP2C regulation. The findings unravel the interaction network of possible RCAR-PP2C pairings and their different potentials to serve a rheostat function for integrating fluctuating hormone levels into the ABA-response pathway.BA regulates a plethora of responses associated with plant growth and the homeostatic control of water relations. ABA controls root extension and branching, stomatal opening and density, and tolerance to water deficit during seed maturation and drought (1, 2). Core ABA signaling can be considered as a threestep regulatory process involving the receptor complex, protein kinases as intermediate signaling components, and downstream targets such as ion channels and transcription factors (1). The heteromeric receptor complex consists of the ABA-binding RCAR/PYR1/PYL receptor and the PP2C coreceptor. The protein phosphatase activity is regulated by ABA that stabilizes the PP2C-RCAR interaction, which blocks substrate access and thereby inhibits the catalytic activity of the coreceptor (3, 4).The clade A of Arabidopsis PP2Cs comprises nine members and forms a plant-specific subgroup among the large family of PP2Cs, which are Mg 2+ -and Mn 2+-dependent serine-threonine protein phosphatases (5). The ABA-mediated inactivation of PP2C activity releases SNF1-related kinase 2 (SnRK2) from inhibition, and it subsequently targets downstream components such as transcription factors and ion channels (6-12). The 14 different RCARs of Arabidopsis can be divided into three subfamilies according to their sequence hom...

The phytohormone abscisic acid (ABA) regulates plant responses to abiotic stress, such as drought and high osmotic conditions. The multitude of functionally redundant components involved in ABA signaling poses a major challenge for elucidating individual contributions to the response selectivity and sensitivity of the pathway. Here, we reconstructed single ABA signaling pathways in yeast for combinatorial analysis of ABA receptors and coreceptors, downstream‐acting SnRK2 protein kinases, and transcription factors. The analysis shows that some ABA receptors stimulate the pathway even in the absence of ABA and that SnRK2s are major determinants of ABA responsiveness by differing in the ligand‐dependent control. Five SnRK2s, including SnRK2.4 known to be active under osmotic stress in plants, activated ABA‐responsive transcription factors and were regulated by ABA receptor complexes in yeast. In the plant tissue, SnRK2.4 and ABA receptors competed for coreceptor interaction in an ABA‐dependent manner consistent with a tight integration of SnRK2.4 into the ABA signaling pathway. The study establishes the suitability of the yeast system for the dissection of core signaling cascades and opens up future avenues of research on ligand‐receptor regulation.

Background and Aims Water deficit is the single most important factor limiting plant productivity in the field. Poplar is a crop used for second-generation bioenergy production that can be cultivated on marginal land without competing for land use in food production. Poplar has a high demand for water, which makes improving its water use efficiency (WUE) an attractive goal. Recently, we showed that enhanced expression of specific receptors of arabidopsis for the phytohormone abscisic acid (ABA) can improve WUE in arabidopsis and water productivity, i.e. more biomass is formed per unit of water over time. In this study, we examined whether ABA receptors from poplar can enhance WUE and water productivity in arabidopsis. Methods ABA receptors from poplar were stably introduced into arabidopsis for analysis of their effect on water use efficiency. Physiological analysis included growth assessment and gas exchange measurements. Key Results The data presented here are in agreement with the functionality of poplar ABA receptors in arabidopsis, which led to ABA-hypersensitive seed germination and root growth. In addition, arabidopsis lines expressing poplar RCAR10, but not RCAR9, showed increased WUE by up to 26 % compared with the wild type with few trade-offs in growth that also resulted in higher water productivity during drought. The improved WUE was mediated by reduced stomatal conductance, a steeper CO2 gradient at the leaf boundary and sustained photosynthesis resulting in an increased intrinsic WUE (iWUE). Conclusions The analysis is a case study supporting the use of poplar ABA receptors for improving WUE and showing the feasibility of using a heterologous expression strategy for generating plants with improved water productivity.