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

Karrikins are smoke-derived compounds presumed to mimic endogenous signalling molecules (KAI2-ligand, KL), whose signalling pathway is closely related to that of strigolactones (SLs), important regulators of plant development. Both karrikins/KLs and SLs are perceived by closely related α/β hydrolase receptors (KAI2 and D14 respectively), and signalling through both receptors requires the F-box protein MAX2. Furthermore, both pathways trigger proteasome-mediated degradation of related SMAX1-LIKE (SMXL) proteins, to influence development. It has previously been suggested in multiple studies that SLs are important regulators of root and root hair development in Arabidopsis, but these conclusions are based on phenotypes observed in the non-specific max2 mutants and by use of racemic-GR24, a mixture of stereoisomers that activates both D14 and KAI2 signalling pathways. Here, we demonstrate that the majority of the effects on Arabidopsis root development previously attributed to SL signalling are actually mediated by the KAI2 signalling pathway. Using mutants defective in SL or KL synthesis and/or perception, we show that KAI2-mediated signalling alone regulates root hair density and root hair length as well as root skewing, straightness and diameter, while both KAI2 and D14 pathways regulate lateral root density and epidermal cell length. We test the key hypothesis that KAI2 signals by a non-canonical receptor-target mechanism in the context of root development. Our results provide no evidence for this, and we instead show that all effects of KAI2 in the root can be explained by canonical SMAX1/SMXL2 activity. However, we do find evidence for non-canonical GR24 ligand-receptor interactions in D14/KAI2-mediated root hair development. Overall, our results demonstrate that the KAI2 signalling pathway is an important new regulator of root hair and root development in Arabidopsis and lay an important basis for research into a molecular understanding of how very similar and partially overlapping hormone signalling pathways regulate different phenotypic outputs.

Regulatory myeloid immune cells, such as myeloid-derived suppressor cells (MDSCs), populate inflamed or cancer tissue and block immune cell effector functions. Lack of mechanistic insight 54 into MDSC suppressive activity and a marker for their identification hampered attempts to 55 overcome T cell-inhibition and unleash anti-cancer immunity. Here we report that human MDSCs 56 were characterized by strongly reduced metabolism and conferred this compromised metabolic 57 state to CD8 + T cells thereby paralyzing their effector functions. We identified accumulation of the dicarbonyl-radical methylglyoxal, generated by semicarbazide-sensitive amine oxidase (SSAO), to cause the metabolic phenotype of MDSCs and MDSC-mediated paralysis of CD8 + T cells. In a murine cancer model, neutralization of dicarbonyl-activity overcame MDSC-mediated T cell-suppression and together with checkpoint inhibition improved efficacy of cancer immune therapy. Our results identify the dicarbonyl methylglyoxal as marker metabolite for MDSCs that mediates T cell paralysis and can serve as target to improve cancer immune therapy. Results 92 Dormant metabolic phenotype in MDSCs 93Suppressive myeloid cells arise during chronic inflammation in tissues 17 , and tissue stromal cells 94 induce transition of monocytes into monocytic MDSCs 16 . We exploited this capacity of stromal cells to convert human peripheral blood monocytes into MDSCs, which are phenotypically similar 96 to CD14 + HLA-DR -/low suppressive myeloid cells directly isolated from cancer patients 16 , to characterize the mechanism of MDSC-mediated T cell suppression. Transcriptome analysis showed less than 200 differentially expressed genes between MDSCs and monocytes, which did not include surface molecules suitable for phenotypic discrimination or known immune suppressive mediators to explain their suppressive activity (supplementary table I-IV, Extended Data Fig. 1). Consistently, blockade of known immune suppressive mediators did not prevent MDSC-mediated T cell suppression (Extended Data Fig. 2). Surprisingly, we found downregulation of genes encoding glycolysis-related enzymes in MDSCs (Fig. 1a, and Extended Data Table V).Indeed, MDSCs showed reduced glucose uptake and Glut1 surface expression (Fig. 1b), the main transporter mediating glucose uptake in immune cells. As predicted from gene expression analysis, hexokinase activity was lower in MDSCs (Fig. 1c). To validate these results, we isolated CD14 + HLA-DR -/lo cells from tumor tissue of patients with hepatocellular carcinoma by enzymatic digestion followed by density centrifugation and flow cytometric cell sorting. We confirmed reduced glucose uptake and hexokinase activity in CD14 + HLA-DR -/low cells isolated from tumor tissue of cancer patients (Fig. 1d,e, and Extended Data Table VI), which are considered to represent MDSCs. Strikingly, MDSCs failed to utilize glucose for glycolysis and also showed reduced cellular bioenergetics, i.e. lower mitochondrial membrane potential quantified by the potentiometric mitochondrial ...

Arbuscular mycorrhiza (AM) is a widespread symbiosis between roots of the majority of land plants and Glomeromycotina fungi. AM is important for ecosystem health and functioning as the fungi critically support plant performance by providing essential mineral nutrients, particularly the poorly accessible phosphate, in exchange for organic carbon. AM fungi colonize the inside of roots and this is promoted at low but inhibited at high plant phosphate status, while the mechanistic basis for this phosphate-dependence remained obscure. Here we demonstrate that a major transcriptional regulator of phosphate starvation responses in rice PHOSPHATE STARVATION RESPONSE 2 (PHR2) regulates AM. Root colonization of phr2 mutants is drastically reduced, and PHR2 is required for root colonization, mycorrhizal phosphate uptake, and yield increase in field soil. PHR2 promotes AM by targeting genes required for pre-contact signaling, root colonization, and AM function. Thus, this important symbiosis is directly wired to the PHR2-controlled plant phosphate starvation response.

A fatty acid triggers immune responses Plants and animals respond to the microbial communities around them, whether in antagonistic or mutualistic ways. Some of these interactions are mediated by lipopolysaccharide—a large, complex, and irregular molecule on the surface of most Gram-negative bacteria. Studying the small mustard plant Arabidopsis , Kutschera et al. identified a 3-hydroxydecanoyl chain as the structural element sensed by the plant's lectin receptor kinase. Indeed, synthetic 3-hydroxydecanoic acid alone was sufficient to produce a response. A small microbial metabolite may thus suffice to trigger immune responses. Science , this issue p. 178