Mapping active serine hydrolases during infection in fly models
Ontology highlight
ABSTRACT:
INSTRUMENT(S):
ORGANISM(S): Drosophila Melanogaster (fruit Fly)
TISSUE(S): Whole Body
SUBMITTER: 
Siddhesh Kamat
LAB HEAD: Siddhesh Kamat
PROVIDER: PXD055116 | Pride | 2025-06-24
REPOSITORIES: Pride
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| WT_Treated_vs_Control_1.group | Other | |||
| WT_Treated_vs_Control_1.wiff | Wiff | |||
| WT_Treated_vs_Control_1.wiff.scan | Wiff | |||
| WT_Treated_vs_Control_2.group | Other | |||
| WT_Treated_vs_Control_2.wiff | Wiff |
Items per page: 5 1 - 5 of 7 |
Similar Datasets
Project description:Here we aim to characterize the palmitic acid diazirine alkyne (PA-DA) probe using chemical proteomics approaches in mammalian cell and mouse brain lysates.
2025-06-24 | PXD051775 | Pride
Project description:Here we aim to characterize the 1-palmitoyl-glycerol diazirine alkyne (PGDA) probe using chemical proteomics approaches in mammalian cell and mouse brain lysates.
2025-06-24 | PXD051332 | Pride
Project description:The serine hydrolase (SH) superfamily is perhaps, one of the largest functional enzyme classes in all forms of life, and consists of proteases/peptidases, lipases, and carboxylesterases as representative members. Consistent with the name of this superfamily, all members, without any exception to date, use a nucleophilic serine residue in the enzyme active site to perform hydrolytic-type reactions via a two-step ping-pong mechanism involving a covalent enzyme intermediate. Given the highly conserved catalytic mechanism, this superfamily has served as a classical prototype in the development of several platforms of the chemical proteomics technique, activity-based protein profiling (ABPP), to globally interrogate the functions of its different members in various native, yet complex, biological settings. While ABPP-based proteome-wide activity atlas’ for SH activities are available in numerous organisms, including humans, to the best of our knowledge, such an analysis for this superfamily is lacking in any insect model. To address this, here, we first report a bioinformatics analysis towards the identification and classification of non-redundant SHs in Drosophila melanogaster. Following up on this in silico analysis, leveraging discovery chemoproteomics, we identify and globally map the activities of the SH superfamily during various developmental stages and in different adult tissues of Drosophila. Finally, as proof of concept of the utility of this activity atlas, we highlight sexual dimorphism in SH activities across different tissues in adult Drosophila melanogaster, and together, we prospect new research directions, resources and tools that this study can provide to the fly community.
2021-04-08 | PXD024321 | Pride
Project description:Here we aim to find the protein targets of monoacylglyerol lipids by competing the 1-palmitoyl-glycerol diazirine alkyne (PGDA) vs palmitic acid diazirine alkyne (PGDA) the probe usinc chemical proteomics approaches in mammalian cell and mouse brain lysates.
2025-06-23 | PXD051399 | Pride
Project description:Recent advances in “omics” technologies have opened the possibilities to discover novel biomarkers of meat quality, including the early detection of quality defects such as dark-cutting beef, also known as DFD (dark, firm, and dry) beef characterized by a high ultimate pH. The available studies characterized very few numbers of animals and using mostly gel-based proteomics. The present study uses for the first time a Sequential Window Acquisition of All Theoretical Mass Spectra (SWATH-MS) proteomics approach to characterize and comprehensively quantify the post-mortem muscle proteomes of DFD (pH24 ≥ 6.2) compared to CONTROL beef samples (5.4 ≤ pH24 ≤ 5.6) within the largest database of DFD/CONTROL beef samples to date (26 pairs of samples of the young Asturiana de los Valles bulls, n=52). The statistical comparison yielded 35 putative protein biomarkers that significantly differed in their abundances between the DFD and CONTROL samples. Chemometrics methods using both PLS-DA and OPLS-DA applied on the proteome data revealed 31 and 36 proteins with VIP > 2 respectively. The combination of these findings identified 16 common proteins linked with DFD beef, irrespective of the statistical method. These proteins are associated with interconnected biochemical pathways related to energy metabolism (DHRS7B and CYB5R3), binding and signaling (RABGGTA, MIA3, BPIFA2B, CAP2, APOBEC2, UBE2V1, KIR2DL1), muscle contraction, structure and associated proteins (DMD, PFN2), proteolysis, hydrolases, and activity regulation (AGT, C4A, GLB1, CAND2), and calcium homeostasis (ANXA6). These results evidenced the potential of SWATH-MS and chemometrics to accurately identify novel biomarkers for meat quality defects, providing a deeper understanding of the molecular mechanisms underlying dark-cutting beef.
2025-07-31 | PXD059876 | Pride
Project description:This project aims to characterize the proteomic profile of human entorhinal cortex regarding Alzheimer's disease by SWATH-MS technique.
2023-06-20 | PXD029359 | Pride
Project description:Methods were investigated that would deliver rapid and semi-quantitative analysis of the subcellular composition of Arabidopsis samples, as the standard technique for this i.e. immunoblotting is difficult to quantify and relies on a very few protein targets, whose responses to developmental or environmental cues are often not known. Spectral counts from shotgun analysis of different Arabidopsis tissues, cells or growth stages were compared to selected reaction monitoring (SRM) analyses of the same samples. Results were further compared to a novel protein abundance scoring method, MASCP Gator scoring, described in this study for the first time. The latter is reliant on previously collated public proteomics data and so provides an estimate of protein abundance even in the absence of de-novo experimentation. This scoring method is presented as an online tool, Multiple Marker Abundance Profiling (MMAP), available at http:SUBA.live. This submission comprises the shotgun data from this study. SRM results are available in a separate submission: http://www.peptideatlas.org/PASS/PASS00906
2022-03-02 | PXD004576 | Pride
Project description:PTCs cause a multitude of human diseases and there are no established therapeutic options for their therapeutic management. Herein, we report the high-throughput cloning and identification, characterization and functional analysis of anticodon-edited tRNA which display efficacious PTC reversion in eukaryotic cells and mouse skeletal muscle. Notably, our screen identifies ACE-tRNA, in total, with the potential to repair a vast majority of known human disease-causing PTC, but this therapeutic will require overcoming tissue and delivery specific challenges. However, the engineered tRNA, once delivered, faithfully encode their cognate amino acid, thus abrogating spurious effects on downstream protein stability, folding, and trafficking, and consequently negating the need for tandem therapies involving protein folding or trafficking agents. When transfected as cDNA, ACE-tRNAs rescued multiple full-length proteins via PTC suppression; a NLuc luciferase reporter, a model protein HDH, and two disease nonsense mutations in CFTR.
2019-02-11 | PXD012581 | Pride
Project description:Background - Strongyloidiasis is a neglected tropical disease affecting an estimated 600 million people, particularly in resource-limited settings. The infection can persist lifelong due to Strongyloides stercoralis peculiar auto-infective cycle. The cumbersome diagnosis and the limited knowledge of the mechanisms underpinning this chronic infection are key issues in the disease management. To date, only a few proteomics studies have been conducted to elucidate the molecular mechanisms associated with Strongyloides parasitism or to highlight novel immunological markers and our knowledge of S. stercoralis proteome still limited. Methods - S. stercoralis infective larvae (iL3) we isolated from a faecal sample from an infected subject and analysed by high-throughput tandem mass spectrometry. To achieve a more comprehensive characterisation of iL3 proteome the experimental dataset was analysed through an automatic search strategy combined with manual annotation, which included gene ontology (GO) analysis, InterPro annotation, assessment of the homology with Homo sapiens and other pathogens of clinical importance and B-cell epitope prediction. Results – Our pipeline identified 430 S. stercoralis proteins, 187 (43%) of which corresponded to uncharacterized proteins. Oxidoreductases and peptidases were amongst the most represented protein categories as highlighted by GO analyses (molecular function terms); while membrane and mitochondrial proteins were the most represented cellular component GO categories. In our dataset we also identified a high proportion of proteins bearing CAP, SCP or thioredoxin domain or belonging to cysteine-rich secretory, transthyretin-like or peptidase protein families, confirming previous data on the most represented proteins associated with S. stercoralis parasitism, as inferred from genomic and transcriptomic data. Finally, we also highlighted 9 proteins bearing amino acid sequences with immunogenic properties that might represent novel candidates for serological tests. Conclusions – Here we provide a comprehensive description and annotation of S. stercoralis iL3 proteome and propose some proteins as potentially immunogenic, to be evaluated as novel serological diagnostic markers. In order to highlight novel targets to improve current serodiagnosis and treatment, it is in fact fundamental to expand the molecular understanding derived from ‘omics studies beyond the current state of the art.
2023-03-11 | PXD037243 | Pride
Project description:Bacterial genomes are shaped by cryptic prophages, which are viral genomes integrated into the bacterial chromosome. Escherichia coli genomes have 10 prophages on average. Though usually inactive, prophage genes can profoundly impact host cell physiology. Among the phage genes in the E. coli chromosome, there are several putative transcription factors (TFs). These prophage TFs are predicted to control only phage promoters, however their regulatory functions are not well characterized. The co-habitation of prophages and bacteria has led to conditions under which the majority of prophage genes are unexpressed, at least under normal growth conditions. We characterized a Rac prophage TF, YdaT, expression of which is normally inhibited by Rac TFs and, surprisingly, by the host global regulator OxyR. YdaT, when expressed, leads to a toxic phenotype manifested by drastic cell filamentation and cell death. We determined the binding sites and regulatory action for YdaT, finding two sites within the Rac locus, and one upstream of the host rcsA gene, which codes for the global regulator RcsA. The resulting increase in RcsA strongly impacts the bacterial RcsA/B regulon, which includes operons related to motility, capsule biosynthesis, colanic acid production, biofilm formation and cell division. Our results provide novel insights into the host’s genetic network, which appears to integrate YdaT in a complex manner, favoring its maintenance in the silenced state. The fact that the potentially-toxic YdaT locus remains unmutated suggests its importance and potential benefits for the host, which may appear under stress conditions that are not yet known.
2025-05-07 | PXD059580 | Pride