Expression data from wildtype and spy-3 roots
Ontology highlight
ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE50952 | GEO | 2015/05/16
SECONDARY ACCESSION(S): PRJNA219416
REPOSITORIES: GEO
Similar Datasets
Project description:SPY is an O-linked N-acetylglucosamine transferase involved in many signaling and developmental processes in Arabidopsis. SPY also has a role in root development. In the spy mutant, a middle cortex is produced prematurely. To understand how SPY regulates root cortex proliferation, we sought to identify the genes affected by the spy mutation in the root. The transciptomes from the root of one-week-old seedlings, Col or spy-3 mutant, were compared. The seedlings were grown on a nylon membrane placed on 1X MS agar medium and the plates are positionally vertically in a Pecival growth chamber with 16 hr light and 8 hr dark. Three biological replicates were performed.
2015-05-16 | E-GEOD-50952 | biostudies-arrayexpress
Project description:Both wild-type and SPY-3 OX A. thaliana plants (Arabidopsis thaliana L. ecotype-Columbia) were grown in GM plates for 3 weeks under a 16 h light/8 h dark regimen (40 M-1 10 umol photons/m2/s) at 22M-0C. Dehydration treatment: The 3-week-old plants were grown for 2 h without watering.
2012-08-24 | E-MEXP-3362 | biostudies-arrayexpress
Project description:The recent discovery of SPY-catalyzed protein O-fucosylation reveals a novel mechanism for regulating nucleocytoplasmic protein functions in plants. Genetic evidence indicates important roles of SPY in diverse developmental and physiological processes, however, the upstream signal controlling SPY activity and the downstream substrate proteins O-fucosylated by SPY remain largely unknown. Here, we demonstrate that SPY mediates sugar-dependent growth. We further identify hundreds of O-fucosylated proteins using lectin affinity chromatography followed by mass spectrometry. All the O-fucosylation events quantified in proteomic analyses are undetectable or decreased in the spy mutants and thus likely catalyzed by SPY. The O-fucosylome includes mostly nuclear and cytosolic proteins. Many O-fucosylated proteins function in essential cellular processes, hormone signaling, and developmental programs, consistent with the genetic functions of SPY. The O-fucosylome also includes many proteins modified by O-linked-N-acetylglucosamine (O-GlcNAc) and by phosphorylation downstream of the target of rapamycin (TOR) kinase, revealing the convergence of these nutrient signaling pathways on key regulatory functions such as post-transcriptional/translational regulation and hormonal responses. Our study identifies numerous targets of SPY/O-fucosylation and potential nodes of crosstalk among sugar/nutrient signaling pathways, enabling future dissection of the signaling network that mediates sugar regulation of plant growth and development.
2023-05-10 | PXD038490 | Pride
Project description:The recent discovery of SPY-catalyzed protein O-fucosylation reveals a novel mechanism for regulating nucleocytoplasmic protein functions in plants. Genetic evidence indicates important roles of SPY in diverse developmental and physiological processes, however, the upstream signal controlling SPY activity and the downstream substrate proteins O-fucosylated by SPY remain largely unknown. Here, we demonstrate that SPY mediates sugar-dependent growth. We further identify hundreds of O-fucosylated proteins using lectin affinity chromatography followed by mass spectrometry. All the O-fucosylation events quantified in proteomic analyses are undetectable or decreased in the spy mutants and thus likely catalyzed by SPY. The O-fucosylome includes mostly nuclear and cytosolic proteins. Many O-fucosylated proteins function in essential cellular processes, hormone signaling, and developmental programs, consistent with the genetic functions of SPY. The O-fucosylome also includes many proteins modified by O-linked-N-acetylglucosamine (O-GlcNAc) and by phosphorylation downstream of the target of rapamycin (TOR) kinase, revealing the convergence of these nutrient signaling pathways on key regulatory functions such as post-transcriptional/translational regulation and hormonal responses. Our study identifies numerous targets of SPY/O-fucosylation and potential nodes of crosstalk among sugar/nutrient signaling pathways, enabling future dissection of the signaling network that mediates sugar regulation of plant growth and development.
2023-05-10 | PXD038491 | Pride
Project description:SPINDLY (SPY) in Arabidopsis thaliana is a novel nucleocytoplasmic protein O-fucosyltransferase (POFUT), which regulates diverse developmental processes. Sequence analysis indicates that AtSPY is distinct from ER-localized POFUTs and contains N-terminal tetratricopeptide-repeats (TPRs) and a C-terminal catalytic domain resembling the O-linked-N-acetylglucosamine (GlcNAc) transferases (OGTs). However, the structural feature that determines the distinct enzymatic selectivity of SPY remains unknown. Here we report the cryo-electron microscopy (cryo-EM) structure of AtSPY and its complex with GDP-fucose, revealing distinct active-site features enabling GDP-fucose instead of UDP-GlcNAc binding. AtSPY forms an antiparallel dimer instead of the X-shaped dimer in human OGT, and its catalytic domain dynamically interconverts among inward, middle, and outward states. The entire eleven TPRs are visible in the middle state, with TPR1 of one subunit touching down on the catalytic domain of the other subunit of the AtSPY dimer, whereas the densities of TPRs 1-5 are absent or severely attenuated in the inward and outward states. Analysis of mass spectrometry, co-IP, in planta fucosylation activity, and cryo-EM data further demonstrates that the N-terminal disordered peptide in SPY contains trans auto-fucosylation sites and inhibits its catalytic activity, whereas TPRs 1-5 regulate SPY activity by interfering with protein substrate binding.
2023-02-28 | PXD040480 | Pride
Project description:Rhizobium deserti strain:SPY-1 Genome sequencing and assembly
| PRJNA526777 | ENA
Project description:Comparison of the proteome of the root outer (epidermis, exodermis) and inner (cortex, vasculature) tissues
| MSV000086166 | MassIVE
Project description:Homeostasis of histone acetylation and the control of transcription. Involvement of histone acetyl transferase HAG4 in the root development.<br> hag4 mutant (with a insertion in HAG4 gene encoding a Histone Acetyl Transferase) and wild-type ecotype (Ws) were grown during 15 days, in vitro. RNA were extrated from roots of seedlings. Each sample (ws or hag4) corresponds to a pool of 3 independant cultures and harvesting. <br>
2007-05-03 | E-MEXP-792 | biostudies-arrayexpress
Project description:Most plant roots have multiple cortex layers that make up the bulk of the organ and play key roles in physiology like flood tolerance and symbiosis. However, little is known about how cortical layers form outside the highly reduced anatomy of the model Arabidopsis. Here we use single-cell RNAseq to rapidly generate a cell-resolution map of the maize root, revealing an alternative configuration of the tissue-formative SHORT-ROOT (SHR) signaling pathway adjacent to the expanded cortex. We show that maize SHR protein is hypermobile, moving at least eight cell layers into the cortex. Higher order SHR mutants in both maize and Setaria have reduced numbers of cortical layers, showing that the SHR pathway controls expansion of cortical tissue in monocots that sets up anatomical complexity and a host of key traits.
2021-07-01 | GSE172277 | GEO