Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Potato ATG8 interactome - N-terminal β-strand underpins biochemical specialization of an ATG8 isoform

ABSTRACT: GFP-IP based interactome of potato ATG8 isoforms following transient expression in Nicotiana benthamiana.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Nicotiana Benthamiana

TISSUE(S): Leaf

SUBMITTER: Richard Imre

LAB HEAD: Yasin Dagdas

PROVIDER: PXD011226 | Pride | 2019-11-12

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	20180807_QExHFX2_RSLC2_Dagdas_Dagdas_GMI_onbead_LysC_try_dig_10per_control_EV_repl_1.raw	Raw
	20180807_QExHFX2_RSLC2_Dagdas_Dagdas_GMI_onbead_LysC_try_dig_10per_control_EV_repl_2.raw	Raw
	20180807_QExHFX2_RSLC2_Dagdas_Dagdas_GMI_onbead_LysC_try_dig_10per_sample_1c1_repl_1.raw	Raw
	20180807_QExHFX2_RSLC2_Dagdas_Dagdas_GMI_onbead_LysC_try_dig_10per_sample_1c1_repl_2.raw	Raw
	20180807_QExHFX2_RSLC2_Dagdas_Dagdas_GMI_onbead_LysC_try_dig_10per_sample_1c2_repl_1.raw	Raw

Items per page:

1 - 5 of 15

Publications

N-terminal β-strand underpins biochemical specialization of an ATG8 isoform.

Zess Erin K EK Jensen Cassandra C Cruz-Mireles Neftaly N De la Concepcion Juan Carlos JC Sklenar Jan J Stephani Madlen M Imre Richard R Roitinger Elisabeth E Hughes Richard R Belhaj Khaoula K Mechtler Karl K Menke Frank L H FLH Bozkurt Tolga T Banfield Mark J MJ Kamoun Sophien S Maqbool Abbas A Dagdas Yasin F YF

PLoS biology 20190722 7

Autophagy-related protein 8 (ATG8) is a highly conserved ubiquitin-like protein that modulates autophagy pathways by binding autophagic membranes and a number of proteins, including cargo receptors and core autophagy components. Throughout plant evolution, ATG8 has expanded from a single protein in algae to multiple isoforms in higher plants. However, the degree to which ATG8 isoforms have functionally specialized to bind distinct proteins remains unclear. Here, we describe a comprehensive prote ...[more]

PMID: 31329577

Similar Datasets

Site-specific ubiquitination of the E3 ligase HOIP regulates apoptosis and immune signaling

Project description:HOIP, the catalytic component of the Linear Ubiquitin chain Assembly Complex (LUBAC), is a critical regulator of inflammation. However, how HOIP itself is regulated to control inflammatory responses is unclear. Here, we discover that site-specific ubiquitination of K784 within HOIP promotes Tumour Necrosis Factor (TNF)-induced inflammatory signalling. A HOIP K784R mutant is catalytically active but shows reduced induction of an NF-B reporter relative to wild type HOIP. HOIP K784 is evolutionarily conserved, equivalent to HOIP K778 in mice. We generated HoipK778R/K778R knockin mice, which show no overt developmental phenotypes; however, in response to TNF, HoipK778R/K778R mouse embryonic fibroblasts display suppressed NF-B activation and increased apoptotic markers. On the other hand, HOIP K778R enhances the TNF-induced formation of TNFR complex II, and an interaction between TNFR complex II and LUBAC. Loss of the LUBAC component SHARPIN leads to embryonic lethality in HoipK778R/K778R mice, which is rescued by knockout of TNFR1. We propose that site-specific ubiquitination of HOIP regulates a LUBAC-dependent switch between survival and apoptosis in TNF-signalling.

2020-08-31 | PXD021217 | Pride

A heterochromatin-dependent transcription machinery drives piRNA expression

Project description:Nuclear small RNA pathways safeguard genome integrity by establishing transcription-repressing heterochromatin at transposable elements. This inevitably also targets the transposon-rich source loci of the small RNAs themselves. How small RNA source loci are efficiently transcribed while transposon promoters are potently silenced, is not understood. Here, we show that transcription of Drosophila piRNA clusters—small RNA source loci in animal gonads—is enforced through RNA Polymerase II pre-initiation complex formation within repressive heterochromatin. This is accomplished through the TFIIA-L paralog Moonshiner, which is recruited to piRNA clusters via the Heterochromatin Protein-1 variant Rhino. Moonshiner triggers transcription initiation within piRNA clusters by recruiting the TATA box-binding protein (TBP)-related factor TRF2, an animal TFIID core variant. Thus, transcription of heterochromatic small RNA source loci relies on direct recruitment of the core transcriptional machinery to DNA via histone marks rather than sequence motifs, a concept that we argue is a recurring theme in evolution.

2017-08-07 | PXD005026 | Pride

LSD1 inhibition induces differentiation and cell death in Merkel cell carcinoma

Project description:Merkel cell carcinoma (MCC) is a highly aggressive, neuroendocrine skin cancer that lacks actionable mutations, which could be utilized for targeted therapies. Epigenetic regulators governing cell identity may represent unexplored therapeutic entry points. Here, we targeted epigenetic regulators in a pharmacological screen and discovered that the lysine-specific histone demethylase 1A (LSD1/KDM1A) is required for MCC growth in vitro and in vivo. We show that LSD1 inhibition in MCC disrupts the LSD1-CoREST complex leading to displacement and degradation of HMG20B (BRAF35), a poorly characterized complex member that is essential for MCC proliferation. Inhibition of LSD1 causes derepression of transcriptional master regulators of the neuronal lineage, activates a gene expression signature resembling normal Merkel cells, and induces cell cycle arrest and cell death. Our study unveils the importance of LSD1 for proliferation and maintaining cell identity in MCC. There is growing evidence that cancer cells exploit cellular plasticity and dedifferentiation programs to evade destruction by the immune system. The combination of LSD1 inhibitors with checkpoint inhibitors may thus represent a promising treatment strategy for MCC patients.

2020-11-03 | PXD020590 | Pride

in vitro ubiquitination by E3 ligase Cbl-b

Project description:Fungal infections claim an estimated 1.5 million lives every year. Mechanisms that protect from fungal infections are still elusive. Recognition of fungal pathogens relies on C-type lectin receptors (CLR) and their downstream signaling kinase SYK. Here we report that the E3-ubiquitin-ligase CBL-B controls proximal C-type lectin receptor signaling in macrophages and dendritic cells. We show that CBL-B associates with SYK and ubiquitinates SYK, Dectin-1, and Dectin-2 upon fungal recognition. Functionally, CBL-B deficiency results in increased inflammasome activation, enhanced reactive oxygen species production, and increased fungal killing. Genetic deletion of Cblb protects mice from morbidity caused by cutaneous infection and markedly improves survival upon a lethal systemic infection with Candida albicans. Based on these findings, we engineered a cell-permeable CBL-B inhibitory peptide that protects mice from lethal C. albicans infections. We thus describe a key role for Cblb in the regulation of innate anti-fungal immunity and establish a novel paradigm for the treatment of fungal sepsis.

2016-06-17 | PXD004256 | Pride

Drosophila Schneider S2 cell TFIIA-L Immunoprecipitation

Project description:In order to identify interaction partner of the Drosophila melanogaster TFIIA protein, we have immunoprecipitated an endogenously 3xFLAG-AID tagged TFIIA-L from Drosophila Schneider S2 cells

2023-02-16 | PXD028094 | Pride

A nuclear RNA export factor variant licenses piRNA-guided heterochromatin formation

Project description:Small RNA silencing pathways protect genome integrity in part through establishing heterochromatin at transposon loci. In animals, this process requires piRNA-guided targeting of nuclear PIWI proteins to nascent transcripts. The molecular events contributing to heterochromatin formation upon PIWI binding to nascent RNA, a transient molecule at chromatin, are unknown. Here, we identify SFINX, a protein complex that is required for Piwi-mediated co-transcriptional silencing in Drosophila. It consists of Nxf2—a variant of the nuclear RNA export factor Nxf1/Tap, the mRNA export co-factor Nxt1/p15, and the Piwi-associated protein Panoramix. In the absence of Nxf2, Panoramix is targeted for degradation and piRNA-loaded Piwi is unable to establish heterochromatin. Consequently, nxf2 mutants exhibit severe transposon de-repression and are sterile. We show that within SFINX, Panoramix connects to the heterochromatin machinery while Nxf2 enables target silencing via nascent RNA. Thus, the Nxf2-Nxt1 heterodimer—despite having originated from core mRNA export machinery—has been repurposed for heterochromatin formation. Our data establish an unexpected link between nuclear small RNA biology and NXF-variants, which are widespread in animal lineages, but mostly lack ascribed functions.

2019-06-12 | PXD011201 | Pride

Generation of a C3a-specific monoclonal antibody and immunoapheresis of C3a/C3 and its associates

Project description:A high affine murine monoclonal antibody was generated against complement factor C3 and selected for binding to the C3a region to serve as immunoaffinity reagent. Subsequently, a C3a/C3 specific immunoaffinity column was developed and apheresis of C3a/C3 and its associates was performed. A proteomic analysis was carried out for identification of apheresis products.

2019-11-27 | PXD009829 | Pride

Shuffled ATG8 interacting motifs form an ancestral bridge between UFMylation and C53-mediated autophagy

Project description:UFMylation mediates the covalent modification of substrate proteins with UFM1 (Ubiquitin- fold modifier 1) and regulates the selective degradation of endoplasmic reticulum (ER) via autophagy (ER-phagy) to maintain ER homeostasis. Specifically, collisions of the ER-bound ribosomes trigger ribosome UFMylation, which in turn activates C53-mediated autophagy that clears the toxic incomplete polypeptides. C53 has evolved non-canonical shuffled ATG8 interacting motifs (sAIMs) that are essential for ATG8 interaction and autophagy initiation. Why these non-canonical motifs were selected during evolution, instead of canonical ATG8 interacting motifs remains unknown. Here, using a phylogenomics approach, we show that UFMylation is conserved across the eukaryotes and secondarily lost in fungi and some other species. Further biochemical assays have confirmed those results and showed that the unicellular algae, Chlamydomonas reinhardtii has a functional UFMylation machinery, overturning the assumption that this process is linked to multicellularity. Our conservation analysis also revealed that UFM1 co-evolves with the sAIMs in C53, reflecting a functional link between UFM1 and the sAIMs. Using biochemical and structural approaches, we confirmed the interaction of UFM1 with the C53 sAIMs and found that UFM1 and ATG8 bound to the sAIMs in a different mode. Conversion of sAIMs into canonical AIMs prevented binding of UFM1 to C53, while strengthening ATG8 interaction. This led to the autoactivation of the C53 pathway and sensitized Arabidopsis thaliana to ER stress. Altogether, our findings reveal an ancestral toggle switch embodied in the sAIMs that regulates C53- mediated autophagy to maintain ER homeostasis.

2022-11-22 | PXD038157 | Pride

Promoter DNA-affinity purification

Project description:We have identified the protein binders of functionally distinct promoters from the Drosophila melanogaster genome using nuclear extracts prepared from Schneider S2 cells

2023-02-16 | PXD028090 | Pride

Quantitative proteomics to systematically assess protein changes after HUWE1 knockout in SW620 and A375 cell line

Project description:Quantitative proteomics to systematically assess protein changes after HUWE1 knockout in SW620 and A375 cell line

2023-03-23 | PXD038892 | Pride