The COP9 signalosome is an evolutionary conserved multiprotein complex of unknown function that acts as a negative regulator of photomorphogenic seedling development in Arabidopsis. Here, we show that plants with reduced COP9 signalosome levels had decreased auxin response similar to loss-of-function mutants of the E3 ubiquitin ligase SCFTIR1. Furthermore, we found that the COP9 signalosome and SCFTIR1 interacted in vivo and that the COP9 signalosome was required for efficient degradation of PSIAA6, a candidate substrate of SCFTIR1. Thus, the COP9 signalosome may play an important role in mediating E3 ubiquitin ligase-mediated responses.

Gibberellic acid (GA) promotes seed germination, elongation growth, and flowering time in plants. GA responses are repressed by DELLA proteins, which contain an N-terminal DELLA domain essential for GA-dependent proteasomal degradation of DELLA repressors. Mutations of or within the DELLA domain of DELLA repressors have been described for species including Arabidopsis thaliana, wheat (Triticum aestivum), maize (Zea mays), and barley (Hordeum vulgare), and we show that these mutations confer GA insensitivity when introduced into the Arabidopsis GA INSENSITIVE (GAI) DELLA repressor. We also demonstrate that Arabidopsis mutants lacking the three GA INSENSITIVE DWARF1 (GID1) GA receptor genes are GA insensitive with respect to GA-promoted growth responses, GA-promoted DELLA repressor degradation, and GA-regulated gene expression. Our genetic interaction studies indicate that GAI and its close homolog REPRESSOR OF ga1-3 are the major growth repressors in a GA receptor mutant background. We further demonstrate that the GA insensitivity of the GAI DELLA domain mutants is explained in all cases by the inability of the mutant proteins to interact with the GID1A GA receptor. Since we found that the GAI DELLA domain alone can mediate GA-dependent GID1A interactions, we propose that the DELLA domain functions as a receiver domain for activated GA receptors.

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

The phytohormone gibberellin (GA) regulates various developmental processes in plants such as germination, greening, elongation growth, and flowering time. DELLA proteins, which are degraded in response to GA, repress GA signaling by inhibitory interactions with PHYTOCHROME-INTERACTING FACTOR (PIF) family transcription factors. How GA signaling is controlled downstream from the DELLA and PIF regulators is, at present, unclear. Here, we characterize GNC (GATA, NITRATE-INDUCIBLE, CARBON-METABOLISM INVOLVED) and GNL/CGA1 (GNC-LIKE/CYTOKININ-RESPONSIVE GATA FACTOR1), two homologous GATA-type transcription factors from Arabidopsis thaliana that we initially identified as GA-regulated genes. Our genetic analyses of loss-of-function mutants and overexpression lines establish that GNC and GNL are functionally redundant regulators of germination, greening, elongation growth and flowering time. We further show by chromatin immunoprecipitation that both genes are potentially direct transcription targets of PIF transcription factors, and that their expression is up-regulated in pif mutant backgrounds. In line with a key role of GNC or GNL downstream from DELLA and PIF signaling, we find that their overexpression leads to gene expression changes that largely resemble those observed in a ga1 biosynthesis mutant or a pif quadruple mutant. These findings, together with the fact that gnc and gnl loss-of-function mutations suppress ga1 phenotypes, support the hypothesis that GNC and GNL are important repressors of GA signaling downstream from the DELLA and PIF regulators.[Keywords: Arabidopsis thaliana; DELLA protein; GATA factor; gibberellin; LLM domain; phytochrome-interacting factor; PIF] Supplemental material is available at http://www.genesdev.org.

The development and morphology of vascular plants is critically determined by synthesis and proper distribution of the phytohormone auxin. The directed cell-to-cell distribution of auxin is achieved through a system of auxin influx and efflux transporters. PIN-FORMED (PIN) proteins are proposed auxin efflux transporters, and auxin fluxes can seemingly be predicted based on the—in many cells—asymmetric plasma membrane distribution of PINs. Here, we show in a heterologous Xenopus oocyte system as well as in Arabidopsis thaliana inflorescence stems that PIN-mediated auxin transport is directly activated by D6 PROTEIN KINASE (D6PK) and PINOID (PID)/WAG kinases of the Arabidopsis AGCVIII kinase family. At the same time, we reveal that D6PKs and PID have differential phosphosite preferences. Our study suggests that PIN activation by protein kinases is a crucial component of auxin transport control that must be taken into account to understand auxin distribution within the plant.DOI: http://dx.doi.org/10.7554/eLife.02860.001