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Identification of interacting partners of Hrd1 in Arabidopsis

ABSTRACT: We performed a co-immunoprecipitation using anti-HRD1 antibodies on wild-type Arabidopsis lysates, followed by label-free quantitative mass spectrometry. Mock IPs (beads without antibody) were used to assess background binding.

INSTRUMENT(S):

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

SUBMITTER: Sebastian Hoernstein

LAB HEAD: Pitter F. Huesgen

PROVIDER: PXD065941 | Pride | 2025-09-29

REPOSITORIES: Pride

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			Action	DRS
	EX008220.raw	Raw
	EX008221.raw	Raw
	EX008222.raw	Raw
	EX008223.raw	Raw
	EX008225.raw	Raw

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Publications

ERAD machinery controls the conditional turnover of PIN-LIKES in plants.

Noura Seinab S Ferreira Da Silva Santos Jonathan J Feraru Elena E Hoernstein Sebastian N W SNW Feraru Mugurel I MI Montero-Morales Laura L Rößling Ann-Kathrin AK Scheuring David D Strasser Richard R Huesgen Pitter F PF Waidmann Sascha S Kleine-Vehn Jürgen J

Science advances 20250919 38

Auxin is a crucial phytohormone that regulates plant development and facilitates dynamic responses to environmental changes through subcellular control mechanisms. PIN-LIKES (PILS) are auxin transport facilitators at the endoplasmic reticulum (ER) that mediate nuclear auxin abundance and signaling. Although the posttranslational regulation of PILS is important for acclimating growth responses, the molecular mechanisms involved remain largely unknown. This study demonstrates that components of th ...[more]

PMID: 40971429

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Microarray for transcript expression comparison of normal and Sox18 dominant negative dermal spheres.

Project description:The experiment was designed to identify differential gene expression due to dominant negative mutation of the Sox18 gene in the ragged Opossum spontaneous mouse mutant. Gene expression was analysed after whole RNA isolation in dermal spheres as hair follicle inductive mesenchyme tissue, and was intended to identify gene expression patterns associated with alteration of hair induction post Sox18 mutation.

2017-05-16 | E-MTAB-5673 | biostudies-arrayexpress

DNA-seq of an ELMSeq reporter cassette to study impact of C-terminal sequence variations on protein abundance

Project description:A ELMSeq reporter cassette was created to monitor Dam levels by methylation, and introduced in the genome. The regions of 6 nt upstream and 6 nt downstream the stop codon were randomized to study their effect on gene expression. The ELMSeq reporter cassette was composed of: promoter - dam - random N6 - stop codon TAA - random N6 - spacer - 4xGATC. The amplicon was spanning the C-terminal region. The cassette was introduced in Mycoplasma pneumoniae.

2020-05-04 | E-MTAB-8223 | biostudies-arrayexpress

Impaired exocytosis Weibel-Palade bodies due to biallelic MADD mutations

Project description:The regulated secretion of von Willebrand factor (VWF) from Weibel-Palade bodies (WPB) in endothelial cells is fundamental to hemostasis. This process relies on the recruitment of Rab GTPases and their effectors to the WPB membrane, with the guanine nucleotide exchange factor (GEF) MAP-kinase activating death domain (MADD) playing a central role. Biallelic mutations in MADD lead to a pleiotropic disorder that can include bleeding abnormalities. This study investigates the impact of pathogenic MADD mutations on VWF secretion using patient-derived endothelial cells. We isolated endothelial colony forming cells (ECFCs) from the peripheral blood of three pediatric patients with biallelic MADD mutations, unaffected heterozygous family members, and healthy controls All patients exhibited low VWF plasma levels. Proteomic analysis of patient-derived ECFCs revealed an absence of MADD peptides, reduced VWF, and downregulation of proteins involved in the exocytotic machinery, including Rab3D and the Rab3/27 effector Slp4-a. Functional assays demonstrated diminished Rab27A and Rab3D activity and their failure to localize to WPBs in patient cells. Biochemical and live-imaging studies showed that histamine-induced VWF and VWF propeptide secretion were significantly reduced in patient cells as a result of delayed and reduced degranulation of WPBs. Our findings demonstrate the critical role of MADD in maintaining the secretion competence of WPBs and the magnitude of VWF secretion by regulating the recruitment of the endothelial exocytotic machinery. This study highlights the in vivo significance of WPB exocytosis in maintaining plasma VWF levels and establishes MADD as the first causal gene for quantitative von Willebrand Disease (VWD) in patients without pathogenic VWF variants.

2025-07-17 | PXD058221 | Pride

ChIP-nexus analysis of fission yeast transcription factors Cbf11, Cbf11DBM, Cbf12, Cbf12DBM, Mga2 and Fkh2

Project description:Genome-wide identification of transcription factor (TF) binding sites in the genome of the fission yeast Schizosaccharomyces pombe. The ChIP-nexus method was used. TFs included were: Cbf11-TAP and Cbf12-TAP (and their DBM mutants with impaired DNA binding), TAP-Mga2, and Fkh2-TAP (as an irrelevant control TF). IPs from an untagged WT strain were also analyzed. Cbf11-related IPs were performed from exponential cultures, while Cbf12-related IPs were performed from stationary cultures. YES complex medium was used for all cultivations.

2024-04-05 | E-MTAB-13258 | biostudies-arrayexpress

RNA-seq analysis of fission yeast wild type and cbf11∆ mutant in standard and ammonium-supplemented complex media

Project description:Transcriptome analyses of the fission yeast Schizosaccharomyces pombe cells lacking the CSL transcription factor cbf11. Wild-type cells were used as a control. Both genotypes were analyzed when grown to exponential phase in the complex YES medium, or in YES supplemented with ammonium chloride. The aim was to identify Cbf11-regulated genes, and cbf11-associated phenotypes are affected by the presence of a good nitrogen source.

2024-04-05 | E-MTAB-13302 | biostudies-arrayexpress

Distinct interactomes of ADAR1 nuclear and cytoplasmic protein isoforms and their responses to Interferon induction

Project description:Adenosine deaminase acting on RNA 1 (ADAR1), is an enzyme that catalyzes the conversion of adenosine to inosine in double-stranded RNA, a process critical for regulation of innate immune response and distinguishing between ‘self and non-self RNA’. It is expressed as two isoforms: nucleolar p110 and cytoplasmic, interferon (IFN)-inducible, p150. The interactome of the p110 under steady-state conditions is well-studied; however, less is known about the interactions of the p150 isoform, particularly during IFN response. To elucidate ADAR1's protein interactions during IFN stimulation, alongside steady-state conditions, three distinct methods of enrichment were used followed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). These included: immunoprecipitation (IP) of endogenous ADAR1, IP of Strep II-tagged ADAR1, and proximity labeling using BioID. Individual ADAR1 isoforms (p110 and p150) and their respective dsRNA binding-deficient mutants were created to discern isoform-specific and dsRNA-dependent interactions. Altogether, our results reveal a comprehensive ADAR1 interaction map, identifying both known and novel partners, and highlighting the isoform-specific and dsRNA-binding-dependent nature of ADAR1 interactions. Under IFN stimulation, ADAR1's interaction spectrum encompasses viral replication inhibitors and LINE-1 regulators. Mimicking viral infection with HMW poly(I:C) changed the proximal network of proteins for both isoforms. Our findings provide new insights into ADAR1's roles and its dynamic during IFN response.

2024-12-08 | PXD049991 | Pride

Distinct interactomes of ADAR1 nuclear and cytoplasmic protein isoforms and their responses to Interferon induction

Project description:The RNA editing enzyme ADAR1, is essential for correct functioning of innate immune responses. The ADAR1p110 isoform is mainly nuclear and ADAR1p150, which is interferon inducible, is predominately cytoplasmic. Using three different approaches, co-IP with endogenous ADAR1, and Strep-tag co-IP and BioID with individual ADAR1 isoforms, a comprehensive interactome was generated during both homeostasis and the IFN response. Both known and novel interactors and editing regulators were identified. Nuclear proteins were detected as stable interactors with both ADAR1 isoforms. In contrast, BioID identified distinct protein networks for each ADAR1 isoform, with nuclear components observed with ADAR1p110 and components of cytoplasmic cellular condensates with ADAR1p150. RNase A digestion distinguished between distal and proximal interactors, as did a dsRNA-binding mutant of ADAR1 which demonstrated the importance of dsRNA binding for ADAR1 interactions. IFN treatment did not affect the core ADAR1 interactomes but resulted in novel interactions, the majority of which are proximal interactions retained after RNase A treatment. Short treatment with HMW poly(I:C) during the IFN response resulted in dsRNA-binding-dependent changes in the proximal protein network of ADAR1p110 and association of the ADAR1p150 proximal protein network with some components of antiviral stress granules.

2024-12-08 | PXD056080 | Pride

A deeply conserved protease, acylamino acid-releasing enzyme (AARE), acts in aging in Physcomitrella and Arabidopsis

Project description:Protein oxidation results from the reaction of amino-acid side chains with reactive oxygen species (ROS) and is mostly irreversible. In non-photosynthetic tissues, mitochondria are a main source of ROS, whereas plastids are the major source in photosynthetic tissues. Oxidized proteins suffer from decreased structural integrity and even loss of function, and their accumulation ultimately leads to cytotoxic aggregates. In mammals, this correlates with aging and is linked to several age-related pathologies. Mammalian proteolytic pathways for clearance of oxidized proteins are under intensive research, while mechanistic insights into this process in plants is scarce. AARE enzymes are ATP-independent serine proteases presumably acting on oxidized proteins and operating in a dual exo-/endopeptidase mode. They are found in all domains of life. Here, we investigated AARE enzymes in the moss Physcomitrella and the angiosperm Arabidopsis and identified three homologous nuclear genes in Physcomitrella (PpAARE1-3) and a single nuclear gene in Arabidopsis (AtAARE). Surprisingly, we observed triple localization of the proteins AtAARE and PpAARE1 to plastids, mitochondria and the cytosol in vivo, likely conserved across the plant lineage. This represents an ATP-independent possibility for degradation of oxidized proteins in the major source organelles of ROS in plants, which is distinct to mammals. Combinatorial knockout plants and protein interaction analysis revealed specific interactions of the moss AARE isoforms and functions in progressive aging. Analysis of an AtAARE T-DNA mutant further suggests conservation of AARE function in age-related development.

2023-03-11 | PXD033854 | Pride

Detection of Lactococcus lactis contamination in standard and ethanol-washed casein used in mouse diets for microbiome studies

Project description:Casein is a common source of dietary protein in defined diets used to investigate the effect of diet on the gut microbiota. Previously it has been shown that the metagenomes of mice fed with a diet containing casein were contaminated with DNA from the bacterium Lactococcus lactis and that washing the casein with ethanol removed this contamination (https://doi.org/10.1016/j.chom.2019.06.013). We have identified the same phenomenon when identifying proteins from mouse diets with casein However, in contrast to DNA sequencing we did not see a reduction in L. lactis contamination in proteomes. Two lots each of standard casein and ethanol-washed casein were analyzed using proteomics.

2024-12-18 | PXD040649 | Pride

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Project description:We performed high numbers of replicates of CUT&RUN LoV-U against H3K4me3, β-catenin, and the negative control IgG in human colorectal cancer HCT116 cells over two independent rounds of experiments to discover the complete set of binding events.

2023-07-21 | E-MTAB-13143 | biostudies-arrayexpress

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