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Input control proteome analysis of EPEC infection (LFQ)

ABSTRACT: Total proteome analysis to complement phosphoproteomic study aimed at identifying the substrate of NleH1

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Homo Sapiens (human) Escherichia Coli

TISSUE(S): Epithelial Cell

SUBMITTER: Nichollas Scott

LAB HEAD: Elizabeth Hartland

PROVIDER: PXD008481 | Pride | 2022-08-07

REPOSITORIES: Pride

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NleH1/2 proteomic analysis scripts

Project description:Combined script for the generation of images within paper. Three experiments in total 1) Phosphopeptide enrichment of Three biological replicates of each condition (uninfected, WT infected , detla NleH1 NleH2 infected, pNleH1 infected and pNleH2 infection) 2) Total proteome analysis to complement phosphoproteomic study aimed at identifying the substrate of NleH1/2 3) In vitro assays of EPS8 with catalytically active and inactive NleH1 and NleH2.

2022-08-07 | PXD031117 | Pride

NleH LFQ phoshoproteome analysis

Project description:Using Phosphopeptide enrichment and MS analysis the effect of NleH1 and NleH2 on the phosphoproteome of host cells was investigated

2022-08-07 | PXD008480 | Pride

NleH LFQ phoshoproteome analysis (EThcD runs)

Project description:Using Phosphopeptide enrichment and MS analysis the effect of NleH1 and NleH2 on the phosphoproteome of host cells was investigated - EThcD runs of samples

2022-08-07 | PXD031090 | Pride

identification of the endogenous host targets of the Salmonella effectors SSeK1 and 3

Project description:Strains of Salmonella utilise two distinct type three secretion systems to deliver effector proteins directly into host cells. The Salmonella effectors SseK1 and SseK3 are arginine glycosyltransferases that modify mammalian death domain containing proteins with N-acetyl glucosamine (GlcNAc) when overexpressed ectopically or as recombinant protein fusions. Here, we combined Arg-GlcNAc glycopeptide immunoprecipitation and mass spectrometry to identify host proteins GlcNAcylated by endogenous levels of SseK1 and SseK3 during Salmonella infection. We observed that SseK1 modified the mammalian signaling protein TRADD, but not FADD as previously reported. Overexpression of SseK1 greatly broadened substrate specificity, while ectopic co-expression of SseK1 and TRADD increased the range of modified arginine residues within the death domain of TRADD. In contrast, endogenous levels of SseK3 resulted in modification of the death domains of receptors of the mammalian TNF superfamily, TNFR1 and TRAILR, at residues Arg376 and Arg293 respectively. Structural studies on SseK3 showed that the enzyme displays a classic GT-A glycosyltransferase fold and binds UDP-GlcNAc in a narrow and deep cleft with the GlcNAc facing the surface. Together our data suggests that Salmonellae carrying sseK1 and sseK3 employ the glycosyltransferase effectors to antagonise different components of death receptor signaling.

2019-03-27 | PXD010769 | Pride

Scanned optogenetic control of mammalian somatosensory input to map input-specific behavioral outputs.

Project description: Not available

| S-EPMC8428846 | biostudies-literature

Diverse two-dimensional input functions control bacterial sugar genes.

Project description: Not available

| S-EPMC2366073 | biostudies-literature

Asparagine hydroxylation of the UBA domain in Cezanne (OTUD7B)

Project description:by DUBs need to be tightly controlled. Here, we identify asparagine hydroxylation as a novel posttranslational modification involved in the regulation of Cezanne (OTUD7B), a DUB that controls key cellular functions and signaling pathways. We demonstrate that Cezanne is a substrate for FIH1- and oxygen-dependent asparagine hydroxylation. FIH1 modifies Asn35 within the uncharacterized N-terminal ubiquitin-associated (UBA)-like domain of Cezanne (UBACez), which lacks conserved UBA domain properties. We show for the first time that UBACez binds Lys11-, Lys48-, Lys63- and Met1-linked ubiquitin chains in vitro, and thereby establish UBACez as a functional ubiquitin-binding domain. We reveal that interaction of UBACez with ubiquitin is mediated via a non-canonical surface, and that hydroxylation of Asn35 inhibits ubiquitin binding. Recently, it has been suggested that recruitment of Cezanne to specific target proteins depends on UBACez. Our data show that UBACez can indeed fulfil this role as regulatory domain by binding differently linked ubiquitin chains and that this interaction with ubiquitin, and thus modified substrates, can be modulated by asparagine hydroxylation.

2020-01-24 | PXD015216 | Pride

Efficient human-machine control with asymmetric marginal reliability input devices.

Project description: Not available

| S-EPMC7263597 | biostudies-literature

NleB host targets - The bacterial arginine glycosyltransferase effector NleB preferentially modifies Fas-associated death domain protein (FADD)

Project description:The inhibition of host innate immunity pathways is essential for the survival of attaching and effacing (A/E) pathogens such as enteropathogenic Escherichia coli (EPEC) and Citrobacter rodentium during mammalian infections. To subvert these pathways, A/E pathogens utilize a type III secretion system (T3SS) to introduce effectors that target key signaling pathways thereby suppressing the anti-microbial response. One effector used by A/E pathogens is the arginine glycosyltransferase NleB1 (NleBCR in C. rodentium) that modifies conserved arginine residues with N-acetylglucosamine (GlcNAc) in death-domain containing host proteins thereby blocking extrinsic apoptosis signaling. When expressed ectopically, NleB1 modifies the host proteins, FADD, TRADD and RIPK1. However, the true repertoire of arginine-GlcNAcylation during infection with endogenous levels of NleB delivered by the pathogen is unknown. Here we explored the effects of arginine-GlcNAcylation by NleB on the global host proteome. Utilizing an affinity proteomic approach for Arginine-GlcNAcylated glycopeptide, we compared the global repertoire of arginine-GlcNAcylation during ectopic expression of NleB, EPEC infection in vitro or C. rodentium infection in vivo. When NleB was overexpressed, multiple host proteins were arginine-GlcNAcylated. However, when endogenous levels of NleB were delivered during EPEC and C. rodentium infection, R117of FADD was rapidly and preferentially modified. The arginine-GlcNAcylation modification of FADD was extremely stable and insensitive to environmental or host cell degradation. Despite its stability and effect on the inhibition of apoptosis, arginine-GlcNAcylation did not illicit any proteomic changes, even in response to prolonged expression of NleB. Thus, under wild type levels of expression, NleB1/NleBCR antagonizes death-receptor-induced apoptosis of infected cells by modifying FADD in an irreversible and silent manner.

2017-09-11 | PXD006810 | Pride

identification of the endogenous insoluble host targets of the Salmonella effectors SSeK3

Project description:Strains of Salmonella utilise two distinct type three secretion systems to deliver effector proteins directly into host cells. The Salmonella effector SseK3 is a arginine glycosyltransferase that modify mammalian proteins with N-acetyl glucosamine (GlcNAc). Here, we used Arg-GlcNAc glycopeptide immunoprecipitation and mass spectrometry appraoch to identify host proteins GlcNAcylated by endogenous levels of SseK3 during Salmonella infection. Focusing on the insoluble proteome we demostrate multiple typically insoluble proteins are targetted by SseK3 during infections. Surpisingly unlike SseK1 and the EPEC homologue NleB1 which target death domain contain proteins SseK3 appears to modify a number of proteins lacking death domains. These results demostrate that under endogenous infection non-death domain containing proteins can be modified by Salmonella.

2020-07-28 | PXD015082 | Pride

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