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The plant hormone auxin triggers an ultra-fast proteome-wide response.

ABSTRACT: The plant signaling molecule auxin controls growth and development through a simple nuclear pathway that regulates the expression of numerous genes. There are however several cellular and physiological responses to auxin that occur within seconds, far too rapid to be mediated by gene expression changes, for which no molecular mechanism has yet been identified. Using a phosphoproteomic strategy in Arabidopsis thaliana roots, an ultra-rapid auxin response system that targets >2000 proteins of which many within 30 seconds was identified.

INSTRUMENT(S): Q Exactive HF-X, Orbitrap Exploris 480

ORGANISM(S): Arabidopsis Thaliana (mouse-ear Cress)

TISSUE(S): Root

SUBMITTER: Sjef Boeren

LAB HEAD: Dolf Weijers

PROVIDER: PXD038369 | Pride | 2024-01-26

REPOSITORIES: Pride

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RAF-like protein kinases mediate a deeply conserved, rapid auxin response.

Kuhn Andre A Roosjen Mark M Mutte Sumanth S Dubey Shiv Mani SM Carrillo Carrasco Vanessa Polet VP Boeren Sjef S Monzer Aline A Koehorst Jasper J Kohchi Takayuki T Nishihama Ryuichi R Fendrych Matyáš M Sprakel Joris J Friml Jiří J Weijers Dolf D

Cell 20231220 1

The plant-signaling molecule auxin triggers fast and slow cellular responses across land plants and algae. The nuclear auxin pathway mediates gene expression and controls growth and development in land plants, but this pathway is absent from algal sister groups. Several components of rapid responses have been identified in Arabidopsis, but it is unknown if these are part of a conserved mechanism. We recently identified a fast, proteome-wide phosphorylation response to auxin. Here, we show that t ...[more]

PMID: 38128538

Similar Datasets

The central mediator of auxin-triggered phosphorylation in plants is a RAF-like kinase.

Project description:The plant signaling molecule auxin triggers both fast and slow cellular responses across the plant lineage, including both land plants and algae. We discovered an ultra-fast proteome-wide phosphorylation response to auxin across 5 land plant and algal species, converging on a core group of shared target proteins. We find conserved rapid physiological responses to auxin in the same species and identified a RAF-like protein kinase as a central mediator of auxin-triggered phosphorylation across species.

2024-01-26 | PXD038363 | Pride

ABP1-TMK auxin perception mediates rapid phosphorylation for regeneration and auxin canalization

Project description:The phytohormone auxin triggers transcriptional reprograming utilizing a well-characterized nuclear perception machinery. In contrast, mechanisms underlying other auxin effects, such as auxin feed-back on its transport, rapid regulation of ion fluxes or ultrafast global phospho-response, remain enigmatic. Auxin Binding Protein 1 (ABP1) has been contested as an auxin receptor candidate since decades. Here we show that a fraction of Arabidopsis thaliana ABP1 is secreted and binds auxin specifically at the acidic pH typical for the apoplast. ABP1 and its plasma membrane-localized partner, Transmembrane Kinase 1 (TMK1) are required for auxin-induced phosphorylation of about thousand proteins. Loss-of-function abp1 alleles but not complemented lines show defects in in vitro shoot regeneration and formation of auxin-transporting channels for vasculature formation and regeneration. These results support a role of ABP1-TMK1 in cell surface auxin perception mediating global auxin phospho-response and regenerative development.

2022-08-25 | PXD031063 | Pride

Auxin profiling in Arabidopsis endoplasmic reticulum.

Project description:Endoplasmic reticulum (ER) is an intracellular extensive network of membranes. Among major ER functions belong proteosynthesis, protein folding, their post-transcriptional modification and sorting within the cell and last but not least lipid anabolism. Moreover, several recent studies have indicated involvement of plant ER in regulation of intracellular auxin homeostasis by modulation of its metabolism. Therefore, in order to study auxin metabolome in ER, it is necessary to obtain highly enriched and, if possible, pure ER fraction. The separation of ER is troublesome due to similar biochemical properties with other cellular endomembranes. The majority of published protocols for ER isolation utilise density gradient ultracentrifugation despite the suboptimal resolving power of this approach. This work aims to optimize the isolation of ER from Arabidopsis thaliana for the subsequent determination of ER-specific auxin metabolite profiles by mass spectrometry. Following auxin metabolite determination showed a high increase of active auxin form within ER compared to whole plant. Moreover, our optimized isolation of ER may be further followed by multiple “omics” technologies including analysis of macromolecular as well as low molecular-weight compound from same sample.

2021-11-09 | PXD027522 | Pride

Transcription profiling of Acanthamoeba polyphaga mimivirus infecting Acanthamoeba castellanii for different lengths of time

Project description:A culture of Acanthamoeba castellanii cells was infected with mimivirus. At specified times after infection, infected cells aliquots were subjected to total RNA extraction. Cy3 labeled cDNA was hybridized on custom designed Agilent oligonucleotide tiling microarrays covering both strands of the mimivirus genome.

2010-03-18 | E-MTAB-187 | biostudies-arrayexpress

ABLs and TMKs are co-receptors for extracellular auxin

Project description:Extracellular perception of auxin, an essential phytohormone in plants, has been debated for decades. Auxin binding protein 1 (ABP1) physically interacts with quintessential transmembrane kinases (TMKs) and was proposed to act as an extracellular auxin receptor, but its role was disputed because abp1 knockout mutants lack obvious morphological phenotypes. Here we identified two new auxin-binding proteins, ABL1 and ABL2, that are localized to the apoplast and directly interact with the extracellular domain of TMKs in an auxin-dependent manner. Furthermore, functionally redundant ABL1 and ABL2 genetically interact with TMKs and exhibit functions that are overlapping with those of ABP1 as well as independent of ABP1. Importantly, the extracellular domain of TMK1 itself binds auxin and synergizes with either ABP1 or ABL1 in auxin binding. Thus, our findings discovered new auxin receptors ABL1 and ABL2 having functions overlapping with but distinct from ABP1 and acting together with TMKs as co-receptors for extracellular auxin.

2023-11-25 | PXD044623 | Pride

Phosphoproteomics of MEFs with loss-of-function PTEN mutations

Project description:The PTEN tumor suppressor controls cell death and survival by regulating functions of various molecular targets. Whilst the role of PTEN lipid-phosphatase activity on PtdIns(3,4,5)P3 and inhibition of PI3K pathway is well characterized, the biological relevance of PTEN protein-phosphatase activity remains undefined. Using knock-in (KI) mice harbouring cancer-associated and functionally relevant missense mutations, we show that although loss of PTEN lipid-phosphatase function cooperates with oncogenic PI3K to promote rapid mammary tumorigenesis, the additional loss of PTEN protein-phosphatase activity triggered an extensive cell death response evident in early and advanced mammary tumors. Omics and drug-targeting studies revealed that PI3Ks act to reduce glucocorticoid receptor (GR) levels, which are rescued by loss of PTEN protein-phosphatase activity to restrain cell survival. The dual regulation of GR by PI3K and PTEN functions as a rheostat that can be exploited for the treatment of PTEN-loss driven cancers.

2020-10-15 | PXD016184 | Pride

Fractionation of phosphopeptides using reversed phase microcolumn prior to LC-MS analysis

Project description:A protocol for an improved phosphopeptide identification in tryptically digested complex peptide samples is described. The common TiO2 based phoshopeptide enrichment is coupled to a simple peptide fractionation protocol with following LC-MS analysis of the obtained fractions and proteomic identification of phosphorylated peptides. The fractions are obtained by an optimized protocol for peptide fractionation using a home-made capillary column coupled to a microgradient elution using a gastight microsyringe. The protocol leads to a substantially increased number of phosphopeptides (more than twice).

2020-08-31 | PXD018663 | Pride

Flavonol-mediated stabilization of efflux complexes regulates polar auxin transport

Project description:The transport of auxin controls the rate, direction and localization of plant growth and development. The course of auxin transport is defined by the polar subcellular localization of the PIN proteins, a family of auxin efflux transporters. Using blue native PAGE and quantitative mass spectrometry, we identify native PIN core transport units as homo- and heteromers assembled from PIN1, 2, 3, 4 and 7 subunits only. To identify the protein composition of the larger, low stringency-solubilized PIN assembly we affinity-purified GFP-fused PIN proteins from Arabidopsis roots after expression from their native promoters and after the induction of discrete lateral roots, and analyzed the captured proteins by label-free quantitative mass spectrometry (LC-MS/MS).

2020-10-08 | PXD021543 | Pride

ChIPseq for histone marks in WT and Hdac3 knock-out clones of TNG-A derived mESCs in 2iLIF and SL differentiation conditions

Project description:H3K27ac and H4K5ac ChIPseq in WT and Hdac3-/- mESCs in order to determine the role of Hdac3 on the activity of cis-regulatory elements during differentiation.<br>This experiment is part of the study: "Mechanistic framework of lineage restriction in embryonic stem cells" by Olivieri et al.

2021-03-15 | E-MTAB-9450 | biostudies-arrayexpress

A Broad Network of Dysregulated Protein Phosphorylation Underlies Muscle Insulin Resistance in Type 2 Diabetes

Project description:Skeletal muscle insulin resistance is the earliest defect in type 2 diabetes (T2D), preceding and predicting disease development. Whether this represents the underlying primary defect in T2D or effects of changes in hormones or circulating metabolites is unknown. To address this question, we have developed a “disease-in-a-dish” model by differentiating iPS cells from T2D patients and controls into myoblasts (iMyo) and studied their function in vitro. We find that T2D iMyos exhibit multiple defects mirroring human disease including altered insulin signaling through the IRS/AKT pathway, decreased insulin-stimulated glucose uptake, and reduced mitochondrial oxidation. In addition, using global phosphoproteomics we find that T2D alters phosphorylation of a large network of targets of mTOR, S6K, PKC and other kinases including proteins involved in regulation of Rho-GTPases, mRNA splicing/processing, vesicular trafficking, gene transcription and chromatin remodeling. This cell-autonomous dysregulated phosphorylation network reveals a new dimension in the mechanism underlying insulin resistance in T2D.

2020-08-27 | PXD015430 | Pride

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