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1.
PLoS Pathog ; 19(7): e1011508, 2023 07.
Article in English | MEDLINE | ID: mdl-37523405

ABSTRACT

Antimicrobial Peptides (AMPs) are immune effectors that are key components of the invertebrate innate immune system providing protection against pathogenic microbes. Parasitic helminths (phylum Nematoda and phylum Platyhelminthes) share complex interactions with their hosts and closely associated microbiota that are likely regulated by a diverse portfolio of antimicrobial immune effectors including AMPs. Knowledge of helminth AMPs has largely been derived from nematodes, whereas the flatworm AMP repertoire has not been described. This study highlights limitations in the homology-based approaches, used to identify putative nematode AMPs, for the characterisation of flatworm AMPs, and reveals that innovative algorithmic AMP prediction approaches provide an alternative strategy for novel helminth AMP discovery. The data presented here: (i) reveal that flatworms do not encode traditional lophotrochozoan AMP groups (Big Defensin, CSαß peptides and Myticalin); (ii) describe a unique integrated computational pipeline for the discovery of novel helminth AMPs; (iii) reveal >16,000 putative AMP-like peptides across 127 helminth species; (iv) highlight that cysteine-rich peptides dominate helminth AMP-like peptide profiles; (v) uncover eight novel helminth AMP-like peptides with diverse antibacterial activities, and (vi) demonstrate the detection of AMP-like peptides from Ascaris suum biofluid. These data represent a significant advance in our understanding of the putative helminth AMP repertoire and underscore a potential untapped source of antimicrobial diversity which may provide opportunities for the discovery of novel antimicrobials. Further, unravelling the role of endogenous worm-derived antimicrobials and their potential to influence host-worm-microbiome interactions may be exploited for the development of unique helminth control approaches.


Subject(s)
Anti-Infective Agents , Nematoda , Animals , Antimicrobial Cationic Peptides , Anti-Bacterial Agents
2.
Sci Data ; 9(1): 335, 2022 06 14.
Article in English | MEDLINE | ID: mdl-35701420

ABSTRACT

The number of mass spectrometry (MS)-based proteomics datasets in the public domain keeps increasing, particularly those generated by Data Independent Acquisition (DIA) approaches such as SWATH-MS. Unlike Data Dependent Acquisition datasets, the re-use of DIA datasets has been rather limited to date, despite its high potential, due to the technical challenges involved. We introduce a (re-)analysis pipeline for public SWATH-MS datasets which includes a combination of metadata annotation protocols, automated workflows for MS data analysis, statistical analysis, and the integration of the results into the Expression Atlas resource. Automation is orchestrated with Nextflow, using containerised open analysis software tools, rendering the pipeline readily available and reproducible. To demonstrate its utility, we reanalysed 10 public DIA datasets from the PRIDE database, comprising 1,278 SWATH-MS runs. The robustness of the analysis was evaluated, and the results compared to those obtained in the original publications. The final expression values were integrated into Expression Atlas, making SWATH-MS experiments more widely available and combining them with expression data originating from other proteomics and transcriptomics datasets.


Subject(s)
Proteomics , Software , Data Analysis , Databases, Protein , Datasets as Topic , Mass Spectrometry/methods , Proteomics/methods
3.
Sci Data ; 8(1): 118, 2021 04 26.
Article in English | MEDLINE | ID: mdl-33903600

ABSTRACT

Murine models are amongst the most widely used systems to study biology and pathology. Targeted quantitative proteomic analysis is a relatively new tool to interrogate such systems. Recently the need for relative quantification on hundreds to thousands of samples has driven the development of Data Independent Acquisition methods. One such technique is SWATH-MS, which in the main requires prior acquisition of mass spectra to generate an assay reference library. In stem cell research, it has been shown pluripotency can be induced starting with a fibroblast population. In so doing major changes in expressed proteins is inevitable. Here we have created a reference library to underpin such studies. This is inclusive of an extensively documented script to enable replication of library generation from the raw data. The documented script facilitates reuse of data and adaptation of the library to novel applications. The resulting library provides deep coverage of the mouse proteome. The library covers 29519 proteins (53% of the proteome) of which 7435 (13%) are supported by a proteotypic peptide.


Subject(s)
Cellular Reprogramming , Databases, Protein , Mice , Proteome , Animals , Mass Spectrometry/methods , Mice/genetics , Mice/metabolism , Mice/physiology , Protein Array Analysis/methods , Proteomics/methods
4.
Elife ; 82019 10 09.
Article in English | MEDLINE | ID: mdl-31596236

ABSTRACT

Differentiating cells tailor their metabolism to fulfill their specialized functions. We examined whether mitochondrial fusion is important for metabolic tailoring during spermatogenesis. Acutely after depletion of mitofusins Mfn1 and Mfn2, spermatogenesis arrests due to failure to accomplish a metabolic shift during meiosis. This metabolic shift includes increased mitochondrial content, mitochondrial elongation, and upregulation of oxidative phosphorylation (OXPHOS). With long-term mitofusin loss, all differentiating germ cell types are depleted, but proliferation of stem-like undifferentiated spermatogonia remains unaffected. Thus, compared with undifferentiated spermatogonia, differentiating spermatogonia and meiotic spermatocytes have cell physiologies that require high levels of mitochondrial fusion. Proteomics in fibroblasts reveals that mitofusin-null cells downregulate respiratory chain complexes and mitochondrial ribosomal subunits. Similarly, mitofusin depletion in immortalized spermatocytes or germ cells in vivo results in reduced OXPHOS subunits and activity. We reveal that by promoting OXPHOS, mitofusins enable spermatogonial differentiation and a metabolic shift during meiosis.


Subject(s)
Cell Differentiation , Meiosis , Mitochondrial Dynamics , Spermatogonia/physiology , Animals , GTP Phosphohydrolases/metabolism , Male , Mice
5.
Br J Cancer ; 121(6): 483-489, 2019 09.
Article in English | MEDLINE | ID: mdl-31388184

ABSTRACT

BACKGROUND: An early detection tool for EOC was constructed from analysis of biomarker expression data from serum collected during the UKCTOCS. METHODS: This study included 49 EOC cases (19 Type I and 30 Type II) and 31 controls, representing 482 serial samples spanning seven years pre-diagnosis. A logit model was trained by analysis of dysregulation of expression data of four putative biomarkers, (CA125, phosphatidylcholine-sterol acyltransferase, vitamin K-dependent protein Z and C-reactive protein); by scoring the specificity associated with dysregulation from the baseline expression for each individual. RESULTS: The model is discriminatory, passes k-fold and leave-one-out cross-validations and was further validated in a Type I EOC set. Samples were analysed as a simulated annual screening programme, the algorithm diagnosed cases with >30% PPV 1-2 years pre-diagnosis. For Type II cases (~80% were HGS) the algorithm classified 64% at 1 year and 28% at 2 years tDx as severe. CONCLUSIONS: The panel has the potential to diagnose EOC one-two years earlier than current diagnosis. This analysis provides a tangible worked example demonstrating the potential for development as a screening tool and scrutiny of its properties. Limits on interpretation imposed by the number of samples available are discussed.


Subject(s)
Biomarkers, Tumor/blood , Blood Proteins/analysis , C-Reactive Protein/analysis , CA-125 Antigen/blood , Carcinoma, Ovarian Epithelial/diagnosis , Early Detection of Cancer/methods , Phosphatidylcholine-Sterol O-Acyltransferase/blood , Algorithms , Carcinoma, Ovarian Epithelial/blood , Female , Follow-Up Studies , Humans , Prognosis , Prospective Studies , Retrospective Studies
6.
Biochem Biophys Res Commun ; 503(3): 1599-1604, 2018 09 10.
Article in English | MEDLINE | ID: mdl-30049443

ABSTRACT

SynGAP is a Ras and Rap GTPase-activating protein (GAP) found in high concentration in the postsynaptic density (PSD) fraction from mammalian forebrain where it binds to PDZ domains of PSD-95. Phosphorylation of pure recombinant synGAP by Ca2+/calmodulin-dependent protein kinase II (CaMKII) shifts the balance of synGAP's GAP activity toward inactivation of Rap1; whereas phosphorylation by cyclin-dependent kinase 5 (CDK5) has the opposite effect, shifting the balance toward inactivation of HRas. These shifts in balance contribute to regulation of the numbers of surface AMPA receptors, which rise during synaptic potentiation (CaMKII) and fall during synaptic scaling (CDK5). Polo-like kinase 2 (Plk2/SNK), like CDK5, contributes to synaptic scaling. These two kinases act in concert to reduce the number of surface AMPA receptors following elevated neuronal activity by tagging spine-associated RapGAP protein (SPAR) for degradation, thus raising the level of activated Rap. Here we show that Plk2 also phosphorylates and regulates synGAP. Phosphorylation of synGAP by Plk2 stimulates its GAP activity toward HRas by 65%, and toward Rap1 by 16%. Simultaneous phosphorylation of synGAP by Plk2 and CDK5 at distinct sites produces an additive increase in GAP activity toward HRas (∼230%) and a smaller, non-additive increase in activity toward Rap1 (∼15%). Dual phosphorylation also produces an increase in GAP activity toward Rap2 (∼40-50%), an effect not produced by either kinase alone. As we previously observed for CDK5, addition of Ca2+/CaM causes a substrate-directed doubling of the rate and stoichiometry of phosphorylation of synGAP by Plk2, targeting residues also phosphorylated by CaMKII. In summary, phosphorylation by Plk2, like CDK5, shifts the ratio of GAP activity of synGAP to produce a greater decrease in active Ras than in active Rap, which would produce a shift toward a decrease in the number of surface AMPA receptors in neuronal dendrites.


Subject(s)
GTPase-Activating Proteins/metabolism , Protein Serine-Threonine Kinases/metabolism , Proto-Oncogene Proteins p21(ras)/metabolism , rap GTP-Binding Proteins/metabolism , rap1 GTP-Binding Proteins/metabolism , Animals , COS Cells , Chlorocebus aethiops , Humans , Mass Spectrometry , Phosphorylation
7.
Br J Cancer ; 117(5): 666-674, 2017 Aug 22.
Article in English | MEDLINE | ID: mdl-28664912

ABSTRACT

BACKGROUND: There is an urgent need for biomarkers for the early detection of ovarian cancer (OC). The purpose of this study was to assess whether changes in serum levels of lecithin-cholesterol acyltransferase (LCAT), sex hormone-binding globulin (SHBG), glucose-regulated protein, 78 kDa (GRP78), calprotectin and insulin-like growth factor-binding protein 2 (IGFBP2) are observed before clinical presentation and to assess the performance of these markers alone and in combination with CA125 for early detection. METHODS: This nested case-control study used samples from the United Kingdom Collaborative Trial of Ovarian Cancer Screening trial. The sample set consisted of 482 serum samples from 49 OC subjects and 31 controls, with serial samples spanning up to 7 years pre-diagnosis. The set was divided into the following: (I) a discovery set, which included all women with only two samples from each woman, the first at<14 months and the second at >32 months to diagnosis; and (ii) a corroboration set, which included all the serial samples from the same women spanning the 7-year period. Lecithin-cholesterol acyltransferase, SHBG, GRP78, calprotectin and IGFBP2 were measured using ELISA. The performance of the markers to detect cancers pre-diagnosis was assessed. RESULTS: A combined threshold model IGFBP2 >78.5 ng ml-1 : LCAT <8.831 µg ml-1 : CA125 >35 U ml-1 outperformed CA125 alone for the earlier detection of OC. The threshold model was able to identify the most aggressive Type II cancers. In addition, it increased the lead time by 5-6 months and identified 26% of Type I subjects and 13% of Type II subjects that were not identified by CA125 alone. CONCLUSIONS: Combined biomarker panels (IGFBP2, LCAT and CA125) outperformed CA125 up to 3 years pre-diagnosis, identifying cancers missed by CA125, providing increased diagnostic lead times for Type I and Type II OC. The model identified more aggressive Type II cancers, with women crossing the threshold dying earlier, indicating that these markers can improve on the sensitivity of CA125 alone for the early detection of OC.


Subject(s)
Biomarkers, Tumor/blood , CA-125 Antigen/blood , Early Detection of Cancer/methods , Insulin-Like Growth Factor Binding Protein 2/blood , Ovarian Neoplasms/blood , Ovarian Neoplasms/diagnosis , Phosphatidylcholine-Sterol O-Acyltransferase/blood , Case-Control Studies , Endoplasmic Reticulum Chaperone BiP , Female , Heat-Shock Proteins/blood , Humans , Leukocyte L1 Antigen Complex/blood , Ovarian Neoplasms/pathology , Sex Hormone-Binding Globulin/metabolism , Time Factors
8.
Oncotarget ; 8(1): 785-797, 2017 Jan 03.
Article in English | MEDLINE | ID: mdl-27903971

ABSTRACT

PURPOSE: Ovarian cancer (OC) is the most lethal gynaecological cancer. Early detection is required to improve patient survival. Risk estimation models were constructed for Type I (Model I) and Type II (Model II) OC from analysis of Protein Z, Fibronectin, C-reactive protein and CA125 levels in prospectively collected samples from the United Kingdom Collaborative Trial of Ovarian Cancer Screening (UKCTOCS). RESULTS: Model I identifies cancers earlier than CA125 alone, with a potential lead time of 3-4 years. Model II detects a number of high grade serous cancers at an earlier stage (Stage I/II) than CA125 alone, with a potential lead time of 2-3 years and assigns high risk to patients that the ROCA Algorithm classified as normal. MATERIALS AND METHODS: This nested case control study included 418 individual serum samples serially collected from 49 OC cases and 31 controls up to six years pre-diagnosis. Discriminatory logit models were built combining the ELISA results for candidate proteins with CA125 levels. CONCLUSIONS: These models have encouraging sensitivities for detecting pre-clinical ovarian cancer, demonstrating improved sensitivity compared to CA125 alone. In addition we demonstrate how the models improve on ROCA for some cases and outline their potential future use as clinical tools.


Subject(s)
Models, Statistical , Ovarian Neoplasms/epidemiology , Algorithms , Biomarkers, Tumor , Early Detection of Cancer/methods , Epidemiologic Factors , Female , Humans , Mass Screening , Neoplasm Staging , Ovarian Neoplasms/diagnosis , ROC Curve , Reproducibility of Results , Risk
9.
Int J Cancer ; 138(12): 2984-92, 2016 Jun 15.
Article in English | MEDLINE | ID: mdl-26815306

ABSTRACT

Ovarian cancer (OC) has the highest mortality of all gynaecological cancers. Early diagnosis offers an approach to achieving better outcomes. We conducted a blinded-evaluation of prospectively collected preclinical serum from participants in the multimodal group of the United Kingdom Collaborative Trial of Ovarian Cancer Screening. Using isobaric tags (iTRAQ) we identified 90 proteins differentially expressed between OC cases and controls. A second targeted mass spectrometry analysis of twenty of these candidates identified Protein Z as a potential early detection biomarker for OC. This was further validated by ELISA analysis in 482 serial serum samples, from 80 individuals, 49 OC cases and 31 controls, spanning up to 7 years prior to diagnosis. Protein Z was significantly down-regulated up to 2 years pre-diagnosis (p = 0.000000411) in 8 of 19 Type I patients whilst in 5 Type II individuals, it was significantly up-regulated up to 4 years before diagnosis (p = 0.01). ROC curve analysis for CA-125 and CA-125 combined with Protein Z showed a statistically significant (p = 0.00033) increase in the AUC from 77 to 81% for Type I and a statistically significant (p= 0.00003) increase in the AUC from 76 to 82% for Type II. Protein Z is a novel independent early detection biomarker for Type I and Type II ovarian cancer; which can discriminate between both types. Protein Z also adds to CA-125 and potentially the Risk of Ovarian Cancer algorithm in the detection of both subtypes.


Subject(s)
Biomarkers, Tumor/blood , Blood Proteins/metabolism , Neoplasms, Glandular and Epithelial/diagnosis , Ovarian Neoplasms/diagnosis , Aged , Early Detection of Cancer , Female , Humans , Middle Aged , Neoplasms, Glandular and Epithelial/blood , Ovarian Neoplasms/blood , ROC Curve
10.
Proc Natl Acad Sci U S A ; 112(9): 2705-10, 2015 Mar 03.
Article in English | MEDLINE | ID: mdl-25691744

ABSTRACT

Proteomic analysis of rare cells in heterogeneous environments presents difficult challenges. Systematic methods are needed to enrich, identify, and quantify proteins expressed in specific cells in complex biological systems including multicellular plants and animals. Here, we have engineered a Caenorhabditis elegans phenylalanyl-tRNA synthetase capable of tagging proteins with the reactive noncanonical amino acid p-azido-L-phenylalanine. We achieved spatiotemporal selectivity in the labeling of C. elegans proteins by controlling expression of the mutant synthetase using cell-selective (body wall muscles, intestinal epithelial cells, neurons, and pharyngeal muscle) or state-selective (heat-shock) promoters in several transgenic lines. Tagged proteins are distinguished from the rest of the protein pool through bioorthogonal conjugation of the azide side chain to probes that permit visualization and isolation of labeled proteins. By coupling our methodology with stable-isotope labeling of amino acids in cell culture (SILAC), we successfully profiled proteins expressed in pharyngeal muscle cells, and in the process, identified proteins not previously known to be expressed in these cells. Our results show that tagging proteins with spatiotemporal selectivity can be achieved in C. elegans and illustrate a convenient and effective approach for unbiased discovery of proteins expressed in targeted subsets of cells.


Subject(s)
Caenorhabditis elegans Proteins/biosynthesis , Caenorhabditis elegans/cytology , Caenorhabditis elegans/metabolism , Gene Expression Regulation/physiology , Proteome/biosynthesis , Proteomics/methods , Animals , Caenorhabditis elegans/genetics , Caenorhabditis elegans Proteins/genetics , Isotope Labeling/methods , Mutation , Proteome/genetics
11.
J Biol Chem ; 290(8): 4908-4927, 2015 Feb 20.
Article in English | MEDLINE | ID: mdl-25533468

ABSTRACT

synGAP is a neuron-specific Ras and Rap GTPase-activating protein (GAP) found in high concentrations in the postsynaptic density (PSD) fraction from the mammalian forebrain. We have previously shown that, in situ in the PSD fraction or in recombinant form in Sf9 cell membranes, synGAP is phosphorylated by Ca(2+)/calmodulin-dependent protein kinase II (CaMKII), another prominent component of the PSD. Here, we show that recombinant synGAP (r-synGAP), lacking 102 residues at the N terminus, can be purified in soluble form and is phosphorylated by cyclin-dependent kinase 5 (CDK5) as well as by CaMKII. Phosphorylation of r-synGAP by CaMKII increases its HRas GAP activity by 25% and its Rap1 GAP activity by 76%. Conversely, phosphorylation by CDK5 increases r-synGAP's HRas GAP activity by 98% and its Rap1 GAP activity by 20%. Thus, phosphorylation by both kinases increases synGAP activity; CaMKII shifts the relative GAP activity toward inactivation of Rap1, and CDK5 shifts the relative activity toward inactivation of HRas. GAP activity toward Rap2 is not altered by phosphorylation by either kinase. CDK5 phosphorylates synGAP primarily at two sites, Ser-773 and Ser-802. Phosphorylation at Ser-773 inhibits r-synGAP activity, and phosphorylation at Ser-802 increases it. However, the net effect of concurrent phosphorylation of both sites, Ser-773 and Ser-802, is an increase in GAP activity. synGAP is phosphorylated at Ser-773 and Ser-802 in the PSD fraction, and its phosphorylation by CDK5 and CaMKII is differentially regulated by activation of NMDA-type glutamate receptors in cultured neurons.


Subject(s)
Calcium-Calmodulin-Dependent Protein Kinase Type 2 , Cyclin-Dependent Kinase 5 , GTPase-Activating Proteins , Oncogene Proteins , Proto-Oncogene Proteins p21(ras) , Synapses/enzymology , rap GTP-Binding Proteins , rap1 GTP-Binding Proteins , ras GTPase-Activating Proteins , ras Proteins , Animals , Calcium-Calmodulin-Dependent Protein Kinase Type 2/chemistry , Calcium-Calmodulin-Dependent Protein Kinase Type 2/genetics , Calcium-Calmodulin-Dependent Protein Kinase Type 2/metabolism , Cells, Cultured , Cyclin-Dependent Kinase 5/chemistry , Cyclin-Dependent Kinase 5/genetics , Cyclin-Dependent Kinase 5/metabolism , GTPase-Activating Proteins/chemistry , GTPase-Activating Proteins/genetics , GTPase-Activating Proteins/metabolism , Humans , Neurons/cytology , Neurons/enzymology , Oncogene Proteins/chemistry , Oncogene Proteins/genetics , Oncogene Proteins/metabolism , Phosphorylation , Proto-Oncogene Proteins p21(ras)/chemistry , Proto-Oncogene Proteins p21(ras)/genetics , Proto-Oncogene Proteins p21(ras)/metabolism , Rats , Receptors, N-Methyl-D-Aspartate/chemistry , Receptors, N-Methyl-D-Aspartate/genetics , Receptors, N-Methyl-D-Aspartate/metabolism , rap1 GTP-Binding Proteins/chemistry , rap1 GTP-Binding Proteins/genetics , rap1 GTP-Binding Proteins/metabolism , ras GTPase-Activating Proteins/chemistry , ras GTPase-Activating Proteins/genetics , ras GTPase-Activating Proteins/metabolism , ras Proteins/chemistry , ras Proteins/genetics , ras Proteins/metabolism
12.
PLoS One ; 9(2): e88960, 2014.
Article in English | MEDLINE | ID: mdl-24586458

ABSTRACT

Clostridium difficile is considered to be the most frequent cause of infectious bacterial diarrhoea in hospitals worldwide yet its adaptive ability remains relatively uncharacterised. Here, we used GeLC/MS and the exponentially modified protein abundance index (emPAI) calculation to determine proteomic changes in response to a clinically relevant heat stress. Reproducibility between both biological and technical replicates was good, and a 37°C proteome of 224 proteins was complemented by a 41°C proteome of 202 proteins at a 1% false discovery rate. Overall, 236 C. difficile proteins were identified and functionally categorised, of which 178 were available for comparative purposes. A total of 65 proteins (37%) were modulated by 1.5-fold or more at 41°C compared to 37°C and we noted changes in the majority of proteins associated with amino acid metabolism, including upregulation of the reductive branch of the leucine fermentation pathway. Motility was reduced at 41°C as evidenced by a 2.7 fold decrease in the flagellar filament protein, FliC, and a global increase in proteins associated with detoxification and adaptation to atypical conditions was observed, concomitant with decreases in proteins mediating transcriptional elongation and the initiation of protein synthesis. Trigger factor was down regulated by almost 5-fold. We propose that under heat stress, titration of the GroESL and dnaJK/grpE chaperones by misfolded proteins will, in the absence of trigger factor, prevent nascent chains from emerging efficiently from the ribosome causing translational stalling and also an increase in secretion. The current work has thus allowed development of a heat stress model for the key cellular processes of protein folding and export.


Subject(s)
Clostridioides difficile/genetics , Clostridioides difficile/metabolism , Proteome/genetics , Proteome/metabolism , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Chromatography, Liquid/methods , Down-Regulation/genetics , Hot Temperature , Proteomics/methods , Reproducibility of Results , Tandem Mass Spectrometry , Up-Regulation/genetics , Workflow
13.
J Proteomics ; 98: 90-8, 2014 Feb 26.
Article in English | MEDLINE | ID: mdl-24382552

ABSTRACT

Gram-negative bacteria constitutively release outer membrane vesicles (OMVs) during cell growth that play significant roles in bacterial survival, virulence and pathogenesis. In this study, comprehensive proteomic analysis of OMVs from a human gastrointestinal pathogen Campylobacter jejuni NCTC11168 was performed using high-resolution mass spectrometry. The OMVs of C. jejuni NCTC11168 were isolated from culture supernatants then characterized using electron microscopy and dynamic light scattering revealing spherical OMVs of an average diameter of 50nm. We then identified 134 vesicular proteins using high-resolution LTQ-Orbitrap mass spectrometry. Subsequent functional analysis of the genes revealed the relationships of the vesicular proteins. Furthermore, known N-glycoproteins were identified from the list of the vesicular proteome, implying the potential role of the OMVs as a delivery means for biologically relevant bacterial glycoproteins. These results enabled us to elucidate the overall proteome profile of pathogenic bacterium C. jejuni and to speculate on the function of OMVs in bacterial infections and communication. BIOLOGICAL SIGNIFICANCE: This work demonstrates the importance of understanding vesicular proteomes from a human pathogen Campylobacter jejuni. From the secreted outer membrane vesicles (OMVs) of C. jejuni NCTC11168, we found a variety of virulence factors and essential proteins for bacterial survival. Bioinformatics analysis of these proteins predicted functional enrichment and localization. The most highly enriched were redox enzymes, which are considered to be essential for survival in oxygen-limiting environments and are predicted to be on the twin-arginine translocation (Tat) pathway suggesting a role for this pathway in the biogenesis of OMVs. This study additionally implicates a biological role for N-linked glycoproteins in OMVs. These approaches allow for a better understanding of the physiology of this important human pathogen.


Subject(s)
Bacterial Outer Membrane Proteins/metabolism , Campylobacter jejuni/metabolism , Proteome/metabolism , Proteomics , Bacterial Outer Membrane Proteins/genetics , Campylobacter jejuni/pathogenicity , Humans , Mass Spectrometry , Proteome/genetics
14.
Mol Cell Proteomics ; 13(3): 780-91, 2014 Mar.
Article in English | MEDLINE | ID: mdl-24390425

ABSTRACT

The programmed formation of specific tissues from embryonic stem cells is a major goal of regenerative medicine. To identify points of intervention in cardiac tissue formation, we performed an siRNA screen in murine embryonic stem cells to identify ubiquitin system genes that repress cardiovascular tissue formation. Our screen uncovered an F-box protein, Fbxl16, as a repressor of one of the earliest steps in the cardiogenic lineage: FLK1+ progenitor formation. Whereas F-box proteins typically form SCF ubiquitin ligases, shotgun mass spectrometry revealed that FBXL16 instead binds protein phosphatase 2A (PP2A) containing a B55 specificity subunit (PP2A(B55)). Phosphoproteomic analyses indicate that FBXL16 negatively regulates phosphorylation of the established PP2A(B55) substrate, vimentin. We suggest that FBXL16 negatively regulates the activity of B55α-PP2A to modulate the genesis of FLK1+ progenitor cells.


Subject(s)
Cell Differentiation , Cell Lineage , Embryonic Stem Cells/cytology , Embryonic Stem Cells/microbiology , F-Box Proteins/metabolism , Protein Phosphatase 2/metabolism , Vascular Endothelial Growth Factor Receptor-2/metabolism , 3T3 Cells , Animals , Biocatalysis , Cullin Proteins/metabolism , Holoenzymes/metabolism , Humans , Immunoprecipitation , Mass Spectrometry , Mice , Myocytes, Cardiac/cytology , Myocytes, Cardiac/metabolism , Phosphoproteins/metabolism , Phosphorylation , Protein Binding , Proteomics , SKP Cullin F-Box Protein Ligases/metabolism
15.
Proc Natl Acad Sci U S A ; 111(1): 433-8, 2014 Jan 07.
Article in English | MEDLINE | ID: mdl-24347637

ABSTRACT

Pathogenic microbes have evolved complex secretion systems to deliver virulence factors into host cells. Identification of these factors is critical for understanding the infection process. We report a powerful and versatile approach to the selective labeling and identification of secreted pathogen proteins. Selective labeling of microbial proteins is accomplished via translational incorporation of azidonorleucine (Anl), a methionine surrogate that requires a mutant form of the methionyl-tRNA synthetase for activation. Secreted pathogen proteins containing Anl can be tagged by azide-alkyne cycloaddition and enriched by affinity purification. Application of the method to analysis of the type III secretion system of the human pathogen Yersinia enterocolitica enabled efficient identification of secreted proteins, identification of distinct secretion profiles for intracellular and extracellular bacteria, and determination of the order of substrate injection into host cells. This approach should be widely useful for the identification of virulence factors in microbial pathogens and the development of potential new targets for antimicrobial therapy.


Subject(s)
Amino Acids/chemistry , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Microbiological Techniques , Anti-Bacterial Agents/chemistry , HeLa Cells , Humans , Mass Spectrometry , Methionine-tRNA Ligase/chemistry , Microscopy, Confocal , Microscopy, Fluorescence , Models, Biological , Mutation , Norleucine/chemistry , Proteome , Proteomics/methods , Time Factors , Virulence Factors , Yersinia enterocolitica/metabolism
16.
Mol Cell Proteomics ; 12(10): 2791-803, 2013 Oct.
Article in English | MEDLINE | ID: mdl-23793018

ABSTRACT

Yeast Cdc48 (p97/VCP in human cells) is a hexameric AAA ATPase that is thought to use ATP hydrolysis to power the segregation of ubiquitin-conjugated proteins from tightly bound partners. Current models posit that Cdc48 is linked to its substrates through adaptor proteins, including a family of seven proteins (13 in human) that contain a Cdc48-binding UBX domain. However, few substrates for specific UBX proteins are known, and hence the generality of this hypothesis remains untested. Here, we use mass spectrometry to identify ubiquitin conjugates that accumulate in cdc48 and ubx mutants. Different ubx mutants exhibit unique patterns of conjugate accumulation that point to functional specialization of individual Ubx proteins. To validate our findings, we examined in detail the endoplasmic reticulum-bound transcription factor Spt23, which we identified as a putative Ubx2 substrate. Mutant ubx2Δ cells are deficient in both cleaving the ubiquitinated 120 kDa precursor of Spt23 to form active p90 and in localizing p90 to the nucleus, resulting in reduced expression of the target gene OLE1, which encodes fatty acid desaturase. Our findings provide a resource for future investigations on Cdc48, illustrate the utility of proteomics to identify ligands for specific ubiquitin receptor pathways, and uncover Ubx2 as a key player in the regulation of membrane lipid biosynthesis.


Subject(s)
Adenosine Triphosphatases/metabolism , Carrier Proteins/metabolism , Cell Cycle Proteins/metabolism , Membrane Lipids/metabolism , Saccharomyces cerevisiae Proteins/metabolism , Ubiquitin/metabolism , Carrier Proteins/genetics , Membrane Proteins/metabolism , Mutation , Proteome , Saccharomyces cerevisiae/metabolism , Saccharomyces cerevisiae Proteins/genetics , Transcription Factors/metabolism , Valosin Containing Protein
17.
Cell ; 153(1): 206-15, 2013 Mar 28.
Article in English | MEDLINE | ID: mdl-23453757

ABSTRACT

The modular SCF (Skp1, cullin, and F box) ubiquitin ligases feature a large family of F box protein substrate receptors that enable recognition of diverse targets. However, how the repertoire of SCF complexes is sustained remains unclear. Real-time measurements of formation and disassembly indicate that SCF(Fbxw7) is extraordinarily stable, but, in the Nedd8-deconjugated state, the cullin-binding protein Cand1 augments its dissociation by one-million-fold. Binding and ubiquitylation assays show that Cand1 is a protein exchange factor that accelerates the rate at which Cul1-Rbx1 equilibrates with multiple F box protein-Skp1 modules. Depletion of Cand1 from cells impedes recruitment of new F box proteins to pre-existing Cul1 and profoundly alters the cellular landscape of SCF complexes. We suggest that catalyzed protein exchange may be a general feature of dynamic macromolecular machines and propose a hypothesis for how substrates, Nedd8, and Cand1 collaborate to regulate the cellular repertoire of SCF complexes.


Subject(s)
SKP Cullin F-Box Protein Ligases/metabolism , Transcription Factors/metabolism , Animals , Cell Line , Cullin Proteins/metabolism , Escherichia coli/genetics , F-Box Proteins/metabolism , Humans , Mass Spectrometry , SKP Cullin F-Box Protein Ligases/chemistry
18.
Nucleic Acids Res ; 41(6): 3924-36, 2013 Apr 01.
Article in English | MEDLINE | ID: mdl-23396443

ABSTRACT

Lens epithelium-derived growth factor (LEDGF/p75) tethers lentiviral preintegration complexes (PICs) to chromatin and is essential for effective HIV-1 replication. LEDGF/p75 interactions with lentiviral integrases are well characterized, but the structural basis for how LEDGF/p75 engages chromatin is unknown. We demonstrate that cellular LEDGF/p75 is tightly bound to mononucleosomes (MNs). Our proteomic experiments indicate that this interaction is direct and not mediated by other cellular factors. We determined the solution structure of LEDGF PWWP and monitored binding to the histone H3 tail containing trimethylated Lys36 (H3K36me3) and DNA by NMR. Results reveal two distinct functional interfaces of LEDGF PWWP: a well-defined hydrophobic cavity, which selectively interacts with the H3K36me3 peptide and adjacent basic surface, which non-specifically binds DNA. LEDGF PWWP exhibits nanomolar binding affinity to purified native MNs, but displays markedly lower affinities for the isolated H3K36me3 peptide and DNA. Furthermore, we show that LEDGF PWWP preferentially and tightly binds to in vitro reconstituted MNs containing a tri-methyl-lysine analogue at position 36 of H3 and not to their unmodified counterparts. We conclude that cooperative binding of the hydrophobic cavity and basic surface to the cognate histone peptide and DNA wrapped in MNs is essential for high-affinity binding to chromatin.


Subject(s)
Intercellular Signaling Peptides and Proteins/chemistry , Nucleosomes/chemistry , DNA/chemistry , DNA/metabolism , Histones/chemistry , Histones/metabolism , Hydrophobic and Hydrophilic Interactions , Intercellular Signaling Peptides and Proteins/metabolism , Models, Molecular , Nucleosomes/metabolism , Protein Binding , Protein Structure, Tertiary
19.
J Proteome Res ; 12(1): 248-59, 2013 Jan 04.
Article in English | MEDLINE | ID: mdl-23205564

ABSTRACT

The adenocarcinoma cell line HeLa serves as a model system for cancer research in general and cervical cancer in particular. In this study, hydrazide enrichment in combination with state-of-the art nanoLC-MS/MS analysis was used to profile N-linked glycosites in HeLa cells. N-Linked glycoproteins were selectively enriched in HeLa cells by the hydrazide capture method, which isolates all glycoproteins independent of their glycans. Nonglycosylated proteins were removed by extensive washing. N-Linked glycoproteins were identified with the specific NXT/S motif and deamidated asparagine (N). Deglycosylation was carried out in both H(2)(16)O and H(2)(18)O to confirm the deamidation. NanoLC-MS/MS analysis indicated that the method selectively enriched at least 100 fold N-linked glycosites in HeLa cells. When both the membrane and cytosolic fractions were used, a total of 268 unique N-glycosylation sites were identified corresponding to 106 glycoproteins. Bioinformatic analysis revealed that most of the glycoproteins identified are known to have an impact on cancer and have been proposed as biomarkers.


Subject(s)
Biomarkers, Tumor , Glycoproteins , Uterine Cervical Neoplasms , Asparagine/metabolism , Biomarkers, Tumor/genetics , Biomarkers, Tumor/metabolism , Chromatography, Liquid , Female , Glycoproteins/genetics , Glycoproteins/metabolism , Glycosylation , HeLa Cells/metabolism , HeLa Cells/pathology , Humans , Peptide-N4-(N-acetyl-beta-glucosaminyl) Asparagine Amidase/metabolism , Polysaccharides/metabolism , Tandem Mass Spectrometry , Uterine Cervical Neoplasms/genetics , Uterine Cervical Neoplasms/metabolism
20.
Anal Chem ; 84(6): 2662-9, 2012 Mar 20.
Article in English | MEDLINE | ID: mdl-22339618

ABSTRACT

We present novel homobifunctional amine-reactive clickable cross-linkers (CXLs) for investigation of three-dimensional protein structures and protein-protein interactions (PPIs). CXLs afford consolidated advantages not previously available in a simple cross-linker, including (1) their small size and cationic nature at physiological pH, resulting in good water solubility and cell-permeability, (2) an alkyne group for bio-orthogonal conjugation to affinity tags via the click reaction for enrichment of cross-linked peptides, (3) a nucleophilic displacement reaction involving the 1,2,3-triazole ring formed in the click reaction, yielding a lock-mass reporter ion for only clicked peptides, and (4) higher charge states of cross-linked peptides in the gas-phase for augmented electron transfer dissociation (ETD) yields. Ubiquitin, a lysine-abundant protein, is used as a model system to demonstrate structural studies using CXLs. To validate the sensitivity of our approach, biotin-azide labeling and subsequent enrichment of cross-linked peptides are performed for cross-linked ubiquitin digests mixed with yeast cell lysates. Cross-linked peptides are detected and identified by collision induced dissociation (CID) and ETD with linear quadrupole ion trap (LTQ)-Fourier transform ion cyclotron resonance (FTICR) and LTQ-Orbitrap mass spectrometers. The application of CXLs to more complex systems (e.g., in vivo cross-linking) is illustrated by Western blot detection of Cul1 complexes including known binders, Cand1 and Skp2, in HEK 293 cells, confirming good water solubility and cell-permeability.


Subject(s)
Cross-Linking Reagents/chemistry , Mass Spectrometry/methods , Proteins/chemistry , Proteomics/methods , Amino Acid Sequence , Avidin/chemistry , Chromatography, Affinity , HEK293 Cells , Humans , Models, Molecular , Molecular Sequence Data , Peptides/chemistry , Ubiquitin/chemistry
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