Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Proximity labeling of trans-cinnamic acid 4-hydroxylase in Petunia inflata petal protoplasts

ABSTRACT: Proximity-dependent labeling allows untargeted determination of both direct and indirect protein interactions in vivo, and therefore stands as an attractive alternative to targeted binary assays for determining global proteinprotein interaction networks. We used TurboID-based proximity labeling to study protein interaction networks of the core phenylpropanoid and anthocyanin pathways in petunia. To do so, we coupled the endoplasmic reticulum (ER) membrane anchored cytochrome P450 cinnamic acid 4-hydroxylase (C4H, CYP73A412) from Petunia inflata to TurboID and expressed it in protoplasts derived from anthocyanin-rich petunia petals. We identified multiple soluble enzymes from the late anthocyanin pathway among enriched proteins, along with other C4H isoforms, and other ER membrane anchored CYPs. Several of these interactions were subsequently confirmed by bimolecular fluorescence complementation (BiFC).

INSTRUMENT(S): timsTOF Pro

ORGANISM(S): Petunia Integrifolia Subsp. Inflata

TISSUE(S): Flower

SUBMITTER: Silas Mellor

LAB HEAD: Tomas Laursen

PROVIDER: PXD055778 | Pride | 2024-09-11

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	20220808_TIMS6_EVO3_PRI_P0155_R0536_44min_DDA_S10_S2-G10_1_581.d.zip	Other
	20220808_TIMS6_EVO3_PRI_P0155_R0536_44min_DDA_S11_S2-G11_1_582.d.zip	Other
	20220808_TIMS6_EVO3_PRI_P0155_R0536_44min_DDA_S12_S2-G12_1_583.d.zip	Other
	20220808_TIMS6_EVO3_PRI_P0155_R0536_44min_DDA_S13_S2-H1_1_584.d.zip	Other
	20220808_TIMS6_EVO3_PRI_P0155_R0536_44min_DDA_S14_S2-H2_1_585.d.zip	Other

Items per page:

1 - 5 of 20

Similar Datasets

Global proteome of mid- and late-development Petunia inflata flower petal protoplasts

Project description:Establishing the global proteomes of Petunia inflata flower protoplasts at S3 and S5 developmental stages to assess the presence of anthocyanin biosynthetic enzymes and determine the suitability of flowers in different developmental stages as material for transient expression of TurboID-tagged bait proteins for proximity labeling.

2024-09-11 | PXD055749 | Pride

Spatial Proteomics of a human brain tumour

Project description:The spatial organisation of Cellular protein expression profiles within tissues determines cellular function and are key to understanding disease pathology. To define molecular phenotypes in the spatial context of tissue, there is a need for unbiased, quantitative technology capable of mapping proteomes within tissue structures. Here, we present a workflow for spatially resolved, quantitative proteomics of tissue that generates maps of protein expression across a tissue slice derived from a human atypical teratoid-rhabdoid tumour (AT/RT). We employ spatially-aware statistical methods that do not require prior knowledge of the fine tissue structure to detect proteins and pathways with varying spatial abundance patterns. We identified PYGL, ASPH and CD45 as spatial markers for tumour boundary and reveal immune response driven, spatially organized protein networks of the extracellular tumour matrix. Overall, this work informs on methods for spatially resolved deep proteo-phenotyping of tissue heterogeneity, which will push the boundaries of understanding tissue biology and pathology at the molecular level.

2023-10-10 | PXD039159 | Pride

Activation of an endogenous pararetrovirus, petunia vein clearing virus, during long-term cultivation of host plants is associated with disturbance of star-type floral color pattern in Petunia hybrida

Project description:White areas of star-type bicolor petals of petunia (Petunia hybrida) are caused by post-transcriptional gene silencing (PTGS) of the key enzyme of anthocyanin biosynthesis. We observed blotched flowers and vein-clearing symptom in leaves in 3- to 4-month-old petunia plants. In order to determine the cause of blotched flowers, we examined an endogenous pararetrovirus, petunia vein clearing virus (PVCV), because this virus causes vein-clearing symptom and may have a suppressor of PTGS. Transcripts and episomal DNA derived from proviral PVCV loci highly accumulated in 3- to 4-month-old plants, indicating that PVCV was activated as the host plant ages. Furthermore, CG and CHG sites of the promoter region of PVCV were highly methylated in 1-month-old plants but these cytosines were not methylated in 3- to 4-month-old plants, suggesting that poor maintenance of DNA methylation activates propagation of PVCV. In parallel, de novo methylation at CHH sites and 24-nt small RNAs were detected on the promoter region of PVCV, indicating that RNA-directed DNA methylation was induced by PVCV activation. Detections of transcripts and episomal DNA of PVCV in blotched regions and suppressor activity of PTGS support the mechanism that suppression of PTGS by activated PVCV causes blotched flowers.

2020-02-18 | GSE145373 | GEO

Shared behavioural impairments in visual perception and place avoidance across different autism models are driven by periaqueductal grey hypoexcitability in Setd5 haploinsufficient mice.

Project description:Despite the diverse genetic origins of autism spectrum disorders (ASDs), affected individuals share strikingly similar and correlated behavioural traits that include perceptual and sensory processing challenges. Notably, the severity of these sensory symptoms is often predictive of the expression of other autistic traits. However, the origin of these perceptual deficits remains largely elusive. Here, we show a recurrent impairment in visual threat perception that is similarly impaired in three independent models of ASD with different molecular aetiologies. Interestingly, this deficit is associated with reduced avoidance of threatening environments - a non-perceptual trait. Focusing on a common cause of ASDs, the Setd5 gene mutation, we define the molecular mechanism. We show that the perceptual impairment is caused by a potassium channel (Kv1) mediated hypoexcitability in a subcortical node essential for the initiation of escape responses, the dorsal periaqueductal grey (dPAG). Proteomic profiling of tissue samples across different brain regions didn't show a perturbation in Kv1 levels in mutant mice. Targeted pharmacological Kv1 blockade rescued both perceptual and place avoidance deficits, causally linking seemingly unrelated trait deficits to the dPAG. Furthermore, we show that different molecular mechanisms converge on similar behavioural phenotypes by demonstrating that the autism models Cul3 and Ptchd1, despite having similar behavioural phenotypes, differ in their functional and molecular alteration. Our findings reveal a link between rapid perception controlled by subcortical pathways and appropriate learned interactions with the environment, and define a non-developmental source of such deficits in ASD.

2024-05-15 | PXD051022 | Pride

Interactome of the Autophagy Receptor TAX1BP1 (T6BP)

Project description:CD4+ T lymphocytes play a major role in the establishment and maintenance of immunity. They are activated by antigenic peptides derived from extracellular or newly synthesized (endogenous) proteins presented on the surface of antigen presenting cells (APCs) by the MHC-II molecules. The pathways leading to endogenous MHC-II presentation remain poorly characterized. We demonstrate here that the autophagy receptor, T6BP, influences both autophagy-dependent and -independent endogenous presentation of HIV- and HCMV-derived peptides. By studying the immunopeptidome of MHC-II molecules, we show that T6BP affects both the quantity and quality of peptides presented. T6BP silencing induces mislocalization of the MHC-II-loading compartments and a rapid degradation of the invariant chain (CD74) without altering the expression and internalization kinetics of MHC-II molecules. T6BP also controls the ER localization of the chaperone calnexin that we identified as a T6BP partner. Remarkably, calnexin silencing in APCs replicates the functional consequences of T6BP silencing: decreased CD4+ T cell activation and exacerbated CD74 degradation. Altogether, we unravel T6BP as a key player of the MHC-II-restricted endogenous presentation pathway and we propose one potential mechanism of action.

2022-09-22 | PXD024330 | Pride

The effects of PhACL silencing on protein acetylation in petunia the effects of acetyl-CoA

Project description:Acetyl-coenzyme A (acetyl-CoA) is a central metabolite and the acetyl source for protein acetylation. The formation of cytosolic acetyl-CoA is catalyzed by ATP-citrate lyase (ACL) from citrate. However, the effects of acetyl-CoA on protein acetylation were not well known. In this study, four genes, PhACLA1, PhACLA2, PhACLB1, PhACLB2, encoding ACLA and ACLB submits in petunia (Petunia hybrida) were identified. VIGS-mediated PhACLA1-A2 and PhACLB1-B2 silencing leads to abnormal leave and flower development and reduced total anthocyanins content, while silencing of any single PhACL gene did not result in visible phenotype change. We quantitatively investigated the petunia proteome, acetylome, and the association between them in petunia corollas treated with pTRV2-PhACLB1-B2 and pTRV2. In total, 6200 protein groups were identified from petunia, among which 5343 proteins were quantified. A total of 345 proteins were up-regulated and 182 proteins were down-regulated (with a threshold of 1.2-fold) in PhACLB1-B2-silenced plant compared with the control (P <0.05). A total of 2210 lysine acetylation sites in 1148 protein groups were identified, among which 1744 sites in 921 proteins were accurately quantified (Additional file 2: Table S7). We subsequently used the quantification results of the global proteome to normalize the acetylome quantification data. From these, 68 sites in 54 lysine acetylation proteins were quantified as up-regulated targets and 40 sites in 38 lysine acetylation proteins were quantified as down-regulated targets at a threshold of 1.2 (P < 0.05). The global proteome and acetylome were negatively correlated, implying that proteome expression levels were negatively regulated by acetylation in PhACLB1-B2-silenced plants compared with the control.

2020-06-24 | PXD015480 | Pride

Interactome of P21 Activated Kinase 1 (PAK1) in oligodendrocytes

Project description:In the central nervous system (CNS), myelin formation by oligodendrocytes (OLs) relies on actin dynamics. Actin polymerization supports the ensheathment step, when the OL process contacts and surrounds a selected portion of axon. While a drastic shift to actin depolymerization is then required to enable the wrapping process and the formation of a multilayered myelin sheath. Molecular mechanisms regulating this switch to actin depolymerization are not fully elucidated. P21-activated kinase 1 (PAK1), a downstream effector of Rho GTPases Rac1 and Cdc42, highly expressed in OLs, can regulate actin dynamics through its kinase activity. We found that PAK1 loss-of-function in OLs, in vivo, stimulates the wrapping and the thickening of myelin sheaths. We showed that PAK1 is highly expressed in myelinating OLs, yet in its inactive form, the one with the ability to trigger actin disassembly. Interestingly, we found that modulations of PAK1 kinase activity control actin dynamics in OLs, thereby myelin formation. Our data demonstrate that PAK1 inactivation in OLs is required for actin depolymerization and proper myelin formation, suggesting the presence of an endogenous PAK1 inhibitor in myelinating OLs. Proteomic analysis of PAK1 binding partners enabled us to identify several proteins likely to regulate its activity.

2024-06-03 | PXD044344 | Pride

HNF1A, H3K4me3 and H3K27ac ChIP-seq in control and Haster-deficient mouse livers

Project description:The HASTER promoter region is a cis-regulatory element that stabilizes the transcription of HNF1A, preventing silencing or overexpression. We have generated a mouse model where the promoter of Haster has been specifically deleted in liver (Haster loxP/loxP; AlbCre). In liver the prevailing consequence is upregulation of HNF1A. We performed HNF1A, H3K4me3 and H3K27ac ChIP-seq to assess the impact of HNF1A upregulation on the chromatin landscape of Haster KO liver.

2022-05-01 | E-MTAB-11471 | biostudies-arrayexpress

Crotonylation versus acetylation in PaACL-silenced corollas in petunia

Project description:Protein acetylation and crotonylation are important post-translational modifications (PTMs) of lysine. In animal cells, histone lysines are crotonylated or acetylated depends on the relative intracellular concentrations of crotonyl-CoA and acetyl-CoA, and adding crotonate to cell cultures, or reducing the intracellular levels of acetyl-CoA, leads to an increase in histone crotonylation through the direct production of crotonyl-CoA. However, in plant the relationship of acetylation and crotonylation and the effect of the concentration of acetyl-CoA on protein crotonylation were not well known. Our previous study showed that PhACL silencing changed the content of acetyl CoA in petunia corollas. In this study, we performed a global crotonylation proteome analysis of petunia (Petunia hybrida) and found that protein crotonylation have close relationship with protein acetylation and the protein with more crotonylation sites often had more acetylation sites. Crotonylated proteins and acetylated proteins enriched in many common KEGG pathway. However, PhACL silencing resulted in different KEGG pathway enrichment of proteins with different level of crotonylated sites and acetylated sites. Cytoplasm non-histone lysine crotonylation may not depend on the concentrations of acetyl-CoA in petunia corollas. There was a positive correlation between crotonylome and acetylome expression levels in corollas of PhACL-silenced plants and control.

2022-10-12 | PXD023270 | Pride

Transcription profiling of Arabidopsis protoplasts transfected with TCV or HCRSV and their coat protein mutants

Project description:Common transcriptional responses of Arabidopsis thaliana protoplasts transfected with turnip crinkle virus (TCV) , hibiscus chlorotic ringspot virus (HCRSV) and their coat protein mutants.

2009-07-07 | E-MEXP-1218 | biostudies-arrayexpress