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1.
Cell ; 184(1): 194-206.e14, 2021 01 07.
Article in English | MEDLINE | ID: mdl-33357447

ABSTRACT

Wnts are evolutionarily conserved ligands that signal at short range to regulate morphogenesis, cell fate, and stem cell renewal. The first and essential steps in Wnt secretion are their O-palmitoleation and subsequent loading onto the dedicated transporter Wntless/evenness interrupted (WLS/Evi). We report the 3.2 Å resolution cryogenic electron microscopy (cryo-EM) structure of palmitoleated human WNT8A in complex with WLS. This is accompanied by biochemical experiments to probe the physiological implications of the observed association. The WLS membrane domain has close structural homology to G protein-coupled receptors (GPCRs). A Wnt hairpin inserts into a conserved hydrophobic cavity in the GPCR-like domain, and the palmitoleate protrudes between two helices into the bilayer. A conformational switch of highly conserved residues on a separate Wnt hairpin might contribute to its transfer to receiving cells. This work provides molecular-level insights into a central mechanism in animal body plan development and stem cell biology.


Subject(s)
Intracellular Signaling Peptides and Proteins/chemistry , Intracellular Signaling Peptides and Proteins/metabolism , Receptors, G-Protein-Coupled/chemistry , Receptors, G-Protein-Coupled/metabolism , Wnt Proteins/metabolism , Amino Acid Sequence , Animals , Disulfides/metabolism , Glycosylation , Humans , Hydrophobic and Hydrophilic Interactions , Intracellular Signaling Peptides and Proteins/isolation & purification , Models, Molecular , Protein Binding , Protein Domains , Protein Structure, Secondary , Protein Transport , Receptors, G-Protein-Coupled/isolation & purification , Receptors, G-Protein-Coupled/ultrastructure , Structural Homology, Protein , Structure-Activity Relationship , Wnt Proteins/chemistry , Wnt Proteins/isolation & purification , Wnt Proteins/ultrastructure
2.
J Immunol ; 205(1): 153-167, 2020 07 01.
Article in English | MEDLINE | ID: mdl-32404352

ABSTRACT

Tripartite motif-containing proteins (TRIMs) play a variety of recently described roles in innate immunity. Although many TRIMs regulate type I IFN expression following cytosolic nucleic acid sensing of viruses, their contribution to innate immune signaling and gene expression during bacterial infection remains largely unknown. Because Mycobacterium tuberculosis is an activator of cGAS-dependent cytosolic DNA sensing, we set out to investigate a role for TRIM proteins in regulating macrophage responses to M. tuberculosis In this study, we demonstrate that TRIM14, a noncanonical TRIM that lacks an E3 ubiquitin ligase RING domain, is a critical negative regulator of the type I IFN response in Mus musculus macrophages. We show that TRIM14 interacts with both cGAS and TBK1 and that macrophages lacking TRIM14 dramatically hyperinduce IFN stimulated gene (ISG) expression following M. tuberculosis infection, cytosolic nucleic acid transfection, and IFN-ß treatment. Consistent with a defect in resolution of the type I IFN response, Trim14 knockout macrophages have more phospho-Ser754 STAT3 relative to phospho-Ser727 and fail to upregulate the STAT3 target Socs3, which is required to turn off IFNAR signaling. These data support a model whereby TRIM14 acts as a scaffold between TBK1 and STAT3 to promote phosphorylation of STAT3 at Ser727 and resolve ISG expression. Remarkably, Trim14 knockout macrophages hyperinduce expression of antimicrobial genes like Nos2 and are significantly better than control cells at limiting M. tuberculosis replication. Collectively, these data reveal an unappreciated role for TRIM14 in resolving type I IFN responses and controlling M. tuberculosis infection.


Subject(s)
Interferon Type I/metabolism , Intracellular Signaling Peptides and Proteins/metabolism , Mycobacterium tuberculosis/immunology , Signal Transduction/immunology , Tripartite Motif Proteins/metabolism , Tuberculosis/immunology , Animals , Disease Models, Animal , Gene Expression Regulation/immunology , Gene Knockout Techniques , HEK293 Cells , Humans , Intracellular Signaling Peptides and Proteins/genetics , Intracellular Signaling Peptides and Proteins/isolation & purification , Macrophages/immunology , Macrophages/metabolism , Membrane Proteins/metabolism , Mice , Nitric Oxide Synthase Type II/metabolism , Nucleotidyltransferases/genetics , Nucleotidyltransferases/isolation & purification , Nucleotidyltransferases/metabolism , Phosphorylation/immunology , Primary Cell Culture , Protein Serine-Threonine Kinases/genetics , Protein Serine-Threonine Kinases/isolation & purification , Protein Serine-Threonine Kinases/metabolism , RAW 264.7 Cells , Receptor, Interferon alpha-beta/metabolism , Recombinant Proteins/genetics , Recombinant Proteins/isolation & purification , Recombinant Proteins/metabolism , STAT3 Transcription Factor/metabolism , Tripartite Motif Proteins/genetics , Tripartite Motif Proteins/isolation & purification , Tuberculosis/microbiology
3.
J Mol Recognit ; 33(3): e2821, 2020 03.
Article in English | MEDLINE | ID: mdl-31883179

ABSTRACT

Gluconeogenesis, the reverse process of glycolysis, is a favorable mechanism at conditions of glucose deprivation. Pck1 is a rate-limiting gluconeogenic enzyme, where its deficiency or mutation contributes to serious clinical situations as neonatal hypoglycemia and liver failure. A recent report confirms that Pck1 is a target for proteasomal degradation through its proline residue at the penultimate position, recognized by Gid4 E3 ligase, but with a lack of informative structural details. In this study, we delineate the localized sequence motif, degron, that specifically interact with Gid4 ligase and unravel the binding mode of Pck1 to the Gid4 ligase by using molecular docking and molecular dynamics. The peptide/protein docking HPEPDOCK web server along with molecular dynamic simulations are applied to demonstrate the binding mode and interactions of a Pck1 wild type (SPSK) and mutant (K4V) with the recently solved structure of Gid4 ligase. Results unveil a distinct binding mode of the mutated peptide compared with the wild type despite having comparable binding affinities to Gid4. Moreover, the four-residue peptide is found insufficient for Gid4 binding, while the seven-residue peptide suffices for binding to Gid4. The amino acids S134, K135, and N137 in the loop L1 (between ß1 and ß2) of the Gid4 are essential for the stabilization of the seven-residue peptide in the binding site of the ligase. The presence of Val4 instead of Lys4 smashes the H-bonds that are formed between Lys4 and Gid4 in the wild type peptide, making the peptide prone to bind with the other side of the binding pocket (L4 loop of Gid4). The dynamics of Gid4 L3 loop is affected dramatically once K4V mutant Pck1 peptide is introduced. This opens the door to explore the mutation effects on the binding mode and smooth the path to target protein degradation by design competitive and non-competitive inhibitors.


Subject(s)
Biosensing Techniques , Gluconeogenesis/genetics , Intracellular Signaling Peptides and Proteins/isolation & purification , Phosphoenolpyruvate Carboxykinase (GTP)/isolation & purification , Ubiquitin-Protein Ligases/chemistry , Binding Sites/genetics , Glucose/chemistry , Humans , Intracellular Signaling Peptides and Proteins/chemistry , Molecular Docking Simulation , Phosphoenolpyruvate Carboxykinase (GTP)/chemistry , Phosphoenolpyruvate Carboxykinase (GTP)/ultrastructure , Proteasome Endopeptidase Complex/chemistry , Proteasome Endopeptidase Complex/genetics , Protein Domains/genetics , Proteolysis , Ubiquitin-Protein Ligases/ultrastructure
4.
Biopolymers ; 111(1): e23339, 2020 Jan.
Article in English | MEDLINE | ID: mdl-31688961

ABSTRACT

Chitin-binding protein 21 (CBP21) from Serratia marcescens is a lytic polysaccharide monooxygenase that contains a copper ion as a cofactor. We aimed to elucidate the unfolding mechanism of CBP21 and the effects of Cu2+ on its structural stability at pH 5.0. Thermal unfolding of both apo- and holoCBP21 was reversible. ApoCBP21 unfolded in a simple two-state transition manner. The peak temperature of the DSC curve, tp , for holoCBP21 (74.4°C) was about nine degrees higher than that for apoCBP21 (65.6°C). The value of tp in the presence of excess Cu2+ was around 75°C, indicating that Cu2+ does not dissociate from the protein molecule during unfolding. The unfolding mechanism of holoCBP21 was considered to be as follows: N∙Cu2+ ⇌ U∙Cu2+ , where N and U represent the native and unfolded states, respectively. Urea-induced equilibrium unfolding analysis showed that holoCBP21 was stabilized by 35 kJ mol-1 in terms of the Gibbs energy change for unfolding (pH 5.0, 25°C), compared with apoCBP21. The increased stability of holoCBP21 was considered to result from the structural stabilization of the protein-Cu2+ complex itself.


Subject(s)
Bacterial Proteins/chemistry , Copper/chemistry , Intracellular Signaling Peptides and Proteins/chemistry , Serratia marcescens/enzymology , Bacterial Proteins/isolation & purification , Calorimetry, Differential Scanning , Circular Dichroism , Coenzymes/chemistry , Hydrogen-Ion Concentration , Intracellular Signaling Peptides and Proteins/isolation & purification , Protein Conformation , Protein Unfolding , Serratia marcescens/chemistry , Spectrometry, Fluorescence , Temperature , Thermodynamics , Urea/chemistry
5.
J Proteome Res ; 16(7): 2339-2358, 2017 07 07.
Article in English | MEDLINE | ID: mdl-28509555

ABSTRACT

Phosphorylation is one of the most important post-translational modifications, playing a crucial role in regulating many cellular processes, including transcription, cytoskeletal rearrangement, cell proliferation, differentiation, apoptosis, and signal transduction. However, to date, little work has been carried out on the phosphoproteome in CHO cells. In this study we have carried out a large scale differential phosphoproteomic analysis of recombinant CHO cells following a reduction of culture temperature (temperature shift). The reduction of culture temperature during the exponential phase of growth is commonly employed by the biopharmaceutical industry to increase product yield; however, the molecular mechanisms of temperature shift in CHO cells remain poorly understood. We have identified 700 differentially expressed phosphopeptides using quantitative label-free LC-MS/MS phosphoproteomic analysis in conjunction with IMAC and TiO2 phosphopeptide enrichment strategies, following a reduction in temperature from 37 to 31 °C. Functional assessment of the phosphoproteomic data using gene ontology analysis showed a significant enrichment of biological processes related to growth (e.g., cell cycle, cell division), ribosomal biogenesis, and cytoskeleton organization, and molecular functions related to RNA binding, transcription factor activity, and protein serine/threonine kinase activity. Differential phosphorylation of two proteins, ATF2 and NDRG1, was confirmed by Western blotting. This data suggests the importance of including the post-translational layer of regulation, such as phosphorylation, in CHO "omics" studies. This study also has the potential to identify phosphoprotein targets that could be modified using cell line engineering approaches to improve the efficiency of recombinant protein production.


Subject(s)
Phosphopeptides/isolation & purification , Phosphoproteins/isolation & purification , Protein Processing, Post-Translational , Proteomics/methods , Activating Transcription Factor 2/isolation & purification , Activating Transcription Factor 2/metabolism , Adsorption , Amino Acid Sequence , Animals , CHO Cells , Cell Cycle/genetics , Cell Cycle Proteins/isolation & purification , Cell Cycle Proteins/metabolism , Cricetulus , Cytoskeleton/genetics , Cytoskeleton/metabolism , Intracellular Signaling Peptides and Proteins/isolation & purification , Intracellular Signaling Peptides and Proteins/metabolism , Molecular Sequence Annotation , Organelle Biogenesis , Phosphopeptides/classification , Phosphopeptides/metabolism , Phosphoproteins/classification , Phosphoproteins/metabolism , Phosphorylation , Protein Serine-Threonine Kinases/isolation & purification , Protein Serine-Threonine Kinases/metabolism , Proteomics/instrumentation , RNA-Binding Proteins/isolation & purification , RNA-Binding Proteins/metabolism , Ribosomes/genetics , Ribosomes/metabolism , Temperature , Titanium/chemistry
6.
Bioorg Med Chem ; 25(17): 4829-4834, 2017 09 01.
Article in English | MEDLINE | ID: mdl-28760530

ABSTRACT

Eurycomanone (1) and 13ß,21-epoxyeurycomanone (2) were isolated from Eurycoma longifolia for studies of lipolytic activity. Compound 1 enhanced lipolysis in adipocytes with an EC50 of 14.6µM, while its epoxy derivate, compound 2, had a stronger activity with an EC50 of 8.6µM. Based on molecular mechanistic study using several specific inhibitors to lipolytic signaling pathways, it was found that PKA inhibitor totally diminished the lipolytic activity of 1 and 2. Further immunoblotting analysis confirmed the activation of phosphorylated PKA by both 1 and 2. With the growing need to develop new anti-obesity agents, eurycomanone and its epoxy derivate can be used as promising lead compounds to target lipid catabolism.


Subject(s)
Anti-Obesity Agents/chemistry , Epoxy Compounds/chemistry , Eurycoma/chemistry , Plant Extracts/chemistry , Quassins/chemistry , Adipocytes/cytology , Adipocytes/drug effects , Adipocytes/metabolism , Animals , Anti-Obesity Agents/isolation & purification , Anti-Obesity Agents/pharmacology , Cell Line , Cell Survival/drug effects , Cyclic AMP-Dependent Protein Kinases/metabolism , Eurycoma/metabolism , Intracellular Signaling Peptides and Proteins/chemistry , Intracellular Signaling Peptides and Proteins/isolation & purification , Intracellular Signaling Peptides and Proteins/pharmacology , Lipolysis/drug effects , Mice , Plant Extracts/isolation & purification , Plant Extracts/pharmacology , Plant Roots/chemistry , Plant Roots/metabolism , Quassins/isolation & purification , Quassins/pharmacology , Signal Transduction/drug effects
7.
Mol Cell Proteomics ; 11(5): 187-201, 2012 May.
Article in English | MEDLINE | ID: mdl-22322096

ABSTRACT

Proteomic studies of post-translational modifications by metal affinity or antibody-based methods often employ data-dependent analysis, providing rich data sets that consist of randomly sampled identified peptides because of the dynamic response of the mass spectrometer. This can complicate the primary goal of programs for drug development, mutational analysis, and kinase profiling studies, which is to monitor how multiple nodes of known, critical signaling pathways are affected by a variety of treatment conditions. Cell Signaling Technology has developed an immunoaffinity-based LC-MS/MS method called PTMScan Direct for multiplexed analysis of these important signaling proteins. PTMScan Direct enables the identification and quantification of hundreds of peptides derived from specific proteins in signaling pathways or specific protein types. Cell lines, tissues, or xenografts can be used as starting material. PTMScan Direct is compatible with both SILAC and label-free quantification. Current PTMScan Direct reagents target key nodes of many signaling pathways (PTMScan Direct: Multipathway), serine/threonine kinases, tyrosine kinases, and the Akt/PI3K pathway. Validation of each reagent includes score filtering of MS/MS assignments, filtering by identification of peptides derived from expected targets, identification of peptides homologous to expected targets, minimum signal intensity of peptide ions, and dependence upon the presence of the reagent itself compared with a negative control. The Multipathway reagent was used to study sensitivity of human cancer cell lines to receptor tyrosine kinase inhibitors and showed consistent results with previously published studies. The Ser/Thr kinase reagent was used to compare relative levels of kinase-derived phosphopeptides in mouse liver, brain, and embryo, showing tissue-specific activity of many kinases including Akt and PKC family members. PTMScan Direct will be a powerful quantitative method for elucidation of changes in signaling in a wide array of experimental systems, combining the specificity of traditional biochemical methods with the high number of data points and dynamic range of proteomic methods.


Subject(s)
Intracellular Signaling Peptides and Proteins/chemistry , Peptide Fragments/chemistry , Protein Processing, Post-Translational , Animals , Brain/metabolism , Cell Line , Chromatography, Affinity , Chromatography, Liquid , Embryo, Mammalian/metabolism , Humans , Immunoprecipitation , Intracellular Signaling Peptides and Proteins/isolation & purification , Intracellular Signaling Peptides and Proteins/metabolism , Liver/metabolism , Mice , Mice, Inbred BALB C , Peptide Fragments/isolation & purification , Peptide Mapping/methods , Phosphoproteins/chemistry , Phosphoproteins/isolation & purification , Phosphoproteins/metabolism , Phosphorylation , Protein Interaction Maps , Receptor Protein-Tyrosine Kinases/chemistry , Receptor Protein-Tyrosine Kinases/isolation & purification , Receptor Protein-Tyrosine Kinases/metabolism , Signal Transduction , Tandem Mass Spectrometry
8.
J Proteome Res ; 12(9): 3969-79, 2013 Sep 06.
Article in English | MEDLINE | ID: mdl-23924207

ABSTRACT

Improvement in bladder cancer (BC) management requires more effective diagnosis and prognosis of disease recurrence and progression. Urinary biomarkers attract special interest because of the noninvasive means of urine collection. Proteomic analysis of urine entails the adoption of a fractionation methodology to reduce sample complexity. In this study, we applied immobilized metal affinity chromatography in combination with high-resolution LC-MS/MS for the discovery of native urinary peptides potentially associated with BC aggressiveness. This approach was employed toward urine samples from patients with invasive BC, noninvasive BC, and benign urogenital diseases. A total of 1845 peptides were identified, corresponding to a total of 638 precursor proteins. Specific enrichment for proteins involved in nucleosome assembly and for zinc-finger transcription factors was observed. The differential expression of two candidate biomarkers, histone H2B and NIF-1 (zinc finger 335) in BC, was verified in independent sets of urine samples by ELISA and by immunohistochemical analysis of BC tissue. The results collectively support changes in the expression of both of these proteins with tumor progression, suggesting their potential role as markers for discriminating BC stages. In addition, the data indicate a possible involvement of NIF-1 in BC progression, likely as a suppressor and through interactions with Sox9 and HoxA1.


Subject(s)
Biomarkers, Tumor/metabolism , Carcinoma, Transitional Cell/urine , Histones/urine , Intracellular Signaling Peptides and Proteins/urine , Nuclear Proteins/urine , Urinary Bladder Neoplasms/urine , Aged , Aged, 80 and over , Biomarkers, Tumor/chemistry , Biomarkers, Tumor/isolation & purification , Carcinoma, Transitional Cell/pathology , Cell Fractionation , Chromatography, Affinity , DNA-Binding Proteins , Female , Histones/chemistry , Histones/isolation & purification , Humans , Intracellular Signaling Peptides and Proteins/chemistry , Intracellular Signaling Peptides and Proteins/isolation & purification , Male , Middle Aged , Neoplasm Grading , Nuclear Proteins/chemistry , Nuclear Proteins/isolation & purification , Tandem Mass Spectrometry , Transcription Factors , Urinary Bladder Neoplasms/pathology
9.
Blood ; 117(5): 1574-84, 2011 Feb 03.
Article in English | MEDLINE | ID: mdl-21123826

ABSTRACT

B-cell migration into and within lymphoid tissues is not only central to the humoral immune response but also for the development of malignancies and autoimmunity. We previously demonstrated that SWAP-70, an F-actin-binding, Rho GTPase-interacting protein strongly expressed in activated B cells, is necessary for normal B-cell migration in vivo. SWAP-70 regulates integrin-mediated adhesion and cell attachment. Here we show that upon B-cell activation, SWAP-70 is extensively posttranslationally modified and becomes tyrosine phosphorylated by SYK at position 517. This phosphorylation inhibits binding of SWAP-70 to F-actin. Phospho-site mutants of SWAP-70 disrupt B-cell polarization in a dominant-negative fashion in vitro and impair migration in vivo. After CXCL12 stimulation of B cells SYK becomes activated and SWAP-70 is phosphorylated in a SYK-dependent manner. Use of the highly specific SYK inhibitor BAY61-3606 showed SYK activity is necessary for normal chemotaxis and B-cell polarization in vitro and for entry of B cells into lymph nodes in vivo. These findings demonstrate a novel requirement for SYK in migration and polarization of naive recirculating B cells and show that SWAP-70 is an important target of SYK in this pathway.


Subject(s)
Actins/metabolism , B-Lymphocytes/metabolism , Cell Movement , DNA-Binding Proteins/physiology , Guanine Nucleotide Exchange Factors/physiology , Intracellular Signaling Peptides and Proteins/metabolism , Nuclear Proteins/physiology , Protein-Tyrosine Kinases/metabolism , Tyrosine/metabolism , Animals , B-Lymphocytes/cytology , Blotting, Western , Flow Cytometry , Immunoprecipitation , Intracellular Signaling Peptides and Proteins/genetics , Intracellular Signaling Peptides and Proteins/isolation & purification , Mice , Minor Histocompatibility Antigens , Phosphorylation , Protein-Tyrosine Kinases/genetics , Protein-Tyrosine Kinases/isolation & purification , Syk Kinase
10.
Bioorg Khim ; 39(2): 247-52, 2013.
Article in Russian | MEDLINE | ID: mdl-23964527

ABSTRACT

We have developed methods for producing recombinant proteins of Noggin family (Noggin1 and Noggin2 of the Xenopus laevis frog) that can interact with BMP factors of TGF-beta superfamily. The genetic constructs which allow one to effectively obtain Noggin1 and Noggin2 from synthetic mRNA microinjected into Xenopus laevis early embryos, as well as in the prokaryotic expression system, were generated. The obtained proteins contain three Myc-tag epitopes on their N-terminus. This allow one to compare the expression levels of Noggin1 and Noggin 2 constructs, to purify them on the affine immunosorbent and to show the activity of Noggin proteins by analyzing their ability to bind BMP4 factor TGF-beta surperfamily by co-immunoprecipitation.


Subject(s)
Carrier Proteins/genetics , Embryonic Development/genetics , Intracellular Signaling Peptides and Proteins/genetics , RNA, Messenger/genetics , Recombinant Proteins/genetics , Xenopus Proteins/genetics , Amino Acid Sequence , Animals , Bone Morphogenetic Protein 4/metabolism , Carrier Proteins/isolation & purification , Carrier Proteins/metabolism , Gene Expression Regulation, Developmental , Intracellular Signaling Peptides and Proteins/isolation & purification , Protein Binding , RNA, Messenger/chemical synthesis , RNA, Messenger/metabolism , Recombinant Proteins/isolation & purification , Recombinant Proteins/metabolism , Signal Transduction , Transforming Growth Factor beta/genetics , Transforming Growth Factor beta/metabolism , Xenopus Proteins/isolation & purification , Xenopus laevis/genetics , Xenopus laevis/metabolism
11.
J Proteome Res ; 11(7): 3520-32, 2012 Jul 06.
Article in English | MEDLINE | ID: mdl-22578083

ABSTRACT

The prevalence of diabetes mellitus is increasing dramatically throughout the world, and the disease has become a major public health issue. The most common form of the disease, type 2 diabetes, is characterized by insulin resistance and insufficient insulin production from the pancreatic beta-cell. Since glucose is the most potent regulator of beta-cell function under physiological conditions, identification of the insulin secretory defect underlying type 2 diabetes requires a better understanding of glucose regulation of human beta-cell function. To this aim, a bottom-up LC-MS/MS-based proteomics approach was used to profile pooled islets from multiple donors under basal (5 mM) or high (15 mM) glucose conditions. Our analysis discovered 256 differentially abundant proteins (∼p < 0.05) after 24 h of high glucose exposure from more than 4500 identified in total. Several novel glucose-regulated proteins were elevated under high glucose conditions, including regulators of mRNA splicing (pleiotropic regulator 1), processing (retinoblastoma binding protein 6), and function (nuclear RNA export factor 1), in addition to neuron navigator 1 and plasminogen activator inhibitor 1. Proteins whose abundances markedly decreased during incubation at 15 mM glucose included Bax inhibitor 1 and synaptotagmin-17. Up-regulation of dicer 1 and SLC27A2 and down-regulation of phospholipase Cß4 were confirmed by Western blots. Many proteins found to be differentially abundant after high glucose stimulation are annotated as uncharacterized or hypothetical. These findings expand our knowledge of glucose regulation of the human islet proteome and suggest many hitherto unknown responses to glucose that require additional studies to explore novel functional roles.


Subject(s)
Glucose/physiology , Islets of Langerhans/metabolism , Proteome/metabolism , Acetyltransferases/genetics , Acetyltransferases/isolation & purification , Acetyltransferases/metabolism , Chromatography, Ion Exchange , Chromatography, Reverse-Phase , Cluster Analysis , Coenzyme A Ligases/metabolism , DEAD-box RNA Helicases/metabolism , Fatty Acid Elongases , Gene Expression Regulation , Humans , Intracellular Signaling Peptides and Proteins/genetics , Intracellular Signaling Peptides and Proteins/isolation & purification , Intracellular Signaling Peptides and Proteins/metabolism , Mitochondria/enzymology , Peptide Mapping , Phospholipase C beta/metabolism , Proteome/genetics , Proteome/isolation & purification , Proteomics , Ribonuclease III/metabolism , Tandem Mass Spectrometry , Tissue Culture Techniques
12.
J Proteome Res ; 11(10): 4863-72, 2012 Oct 05.
Article in English | MEDLINE | ID: mdl-22909348

ABSTRACT

Human nonintegrin laminin receptor is a multifunctional protein acting as an integral component of the ribosome and a cell surface receptor for laminin-1. The laminin receptor is overexpressed in several human cancers and is also the cell surface receptor for several viruses and pathogenic prion proteins, making it a pathologically significant protein. This study focused on the proteomic characterization of laminin receptor interacting proteins from Mus musculus. The use of affinity chromatography with immobilized recombinant laminin receptor coupled with mass spectrometry analysis identified 45 proteins with high confidence. Following validation through coimmunoprecipitation, the proteins were classified based on predicted function into ribosomal, RNA processing, signal transduction/metabolism, protein processing, cytoskeleton/cell anchorage, DNA/chromatin, and unknown functions. A significant portion of the identified proteins is related to functions or localizations previously described for laminin receptor. This work represents a comprehensive proteomic approach to studying laminin receptor and provides an essential stepping stone to a better mechanistic understanding of this protein's diverse functions.


Subject(s)
Proteome/chemistry , Animals , Chaperonin Containing TCP-1/chemistry , Chaperonin Containing TCP-1/isolation & purification , Chromatography, Affinity , Cytoskeletal Proteins/chemistry , Cytoskeletal Proteins/isolation & purification , Hexosyltransferases , Histones/chemistry , Histones/isolation & purification , Humans , Intracellular Signaling Peptides and Proteins/chemistry , Intracellular Signaling Peptides and Proteins/isolation & purification , Mice , NIH 3T3 Cells , Proteasome Endopeptidase Complex/chemistry , Proteasome Endopeptidase Complex/isolation & purification , Protein Binding , Proteome/isolation & purification , Proteomics , RNA-Binding Proteins/chemistry , RNA-Binding Proteins/isolation & purification , Receptors, Laminin/chemistry , Ribosomal Proteins/chemistry , Ribosomal Proteins/isolation & purification , Transcription Factors/chemistry , Transcription Factors/isolation & purification
13.
Glycobiology ; 22(3): 379-88, 2012 Mar.
Article in English | MEDLINE | ID: mdl-21868414

ABSTRACT

In recent years, sugars with a unique chemical handle have been used to detect and elucidate the function of glycoconjugates. Such chemical handles have generally been part of an N-acetyl moiety of a sugar. We have previously developed several applications using the single mutant Y289L-ß1,4-galactosyltransferase I (Y289L-ß4Gal-T1) and the wild-type polypeptide-α-GalNAc-T enzymes with UDP-C2-keto-Gal. Here, we describe for the first time that the GlcNAc-transferring enzymes-R228K-Y289L-ß4Gal-T1 mutant enzyme, the wild-type human ß1,3-N-acetylglucosaminyltransferase-2 and human Maniac Fringe-can also transfer the GlcNAc analog C2-keto-Glc molecule from UDP-C2-keto-Glc to their respective acceptor substrates. Although the R228K-Y289L-ß4Gal-T1 mutant enzyme transfers the donor sugar substrate GlcNAc or its analog C2-keto-Glc only to its natural acceptor substrate, GlcNAc, it does not transfer to its analog C2-keto-Glc. Thus, these observations suggest that the GlcNAc-transferring glycosyltransferases can generally accommodate a chemical handle in the N-acetyl-binding cavity of the donor sugar substrate, but not in the N-acetyl-binding cavity of the acceptor sugar.


Subject(s)
Galactose/analogs & derivatives , Galactose/chemistry , Hexosyltransferases/chemistry , Intracellular Signaling Peptides and Proteins/chemistry , Membrane Proteins/chemistry , N-Acetylglucosaminyltransferases/chemistry , Acetylglucosamine/chemistry , Amino Acid Substitution , Binding Sites , Carbohydrate Conformation , Carbohydrate Sequence , Chromatography, Affinity , Cloning, Molecular , Escherichia coli , Factor VII/chemistry , Glucosyltransferases , Glycosylation , Hexosyltransferases/biosynthesis , Hexosyltransferases/genetics , Hexosyltransferases/isolation & purification , Humans , Hydrogen Bonding , Hydrophobic and Hydrophilic Interactions , Intracellular Signaling Peptides and Proteins/genetics , Intracellular Signaling Peptides and Proteins/isolation & purification , Membrane Proteins/biosynthesis , Membrane Proteins/genetics , Membrane Proteins/isolation & purification , Models, Molecular , Molecular Sequence Data , Mutant Proteins/chemistry , N-Acetylglucosaminyltransferases/biosynthesis , N-Acetylglucosaminyltransferases/genetics , N-Acetylglucosaminyltransferases/isolation & purification , Oligosaccharides/chemistry , Protein Binding , Recombinant Fusion Proteins/biosynthesis , Recombinant Fusion Proteins/chemistry , Recombinant Fusion Proteins/genetics , Recombinant Fusion Proteins/isolation & purification , Surface Properties
14.
J Immunol ; 184(4): 1990-2000, 2010 Feb 15.
Article in English | MEDLINE | ID: mdl-20061403

ABSTRACT

Nucleotide-binding oligomerization domain-like receptors (NLRs) are a group of intracellular proteins that mediate recognition of pathogen-associated molecular patterns or other cytosolic danger signals. Mutations in NLR genes have been linked to a variety of inflammatory diseases, underscoring their pivotal role in host defense and immunity. This report describes the genomic organization and regulation of the human NLR family member NLRC5 and aspects of cellular function of the encoded protein. We have analyzed the tissue-specific expression of NLRC5 and have characterized regulatory elements in the NLRC5 promoter region that are responsive to IFN-gamma. We show that NLRC5 is upregulated in human fibroblasts postinfection with CMV and demonstrate the role of a JAK/STAT-mediated autocrine signaling loop involving IFN-gamma. We demonstrate that overexpression and enforced oligomerization of NLRC5 protein results in activation of the IFN-responsive regulatory promoter elements IFN-gamma activation sequence and IFN-specific response element and upregulation of antiviral target genes (e.g., IFN-alpha, OAS1, and PRKRIR). Finally, we demonstrate the effect of small interfering RNA-mediated knockdown of NLRC5 on a target gene level in the context of viral infection. We conclude that NLRC5 may represent a molecular switch of IFN-gamma activation sequence/IFN-specific response element signaling pathways contributing to antiviral defense mechanisms.


Subject(s)
Cytomegalovirus/immunology , Interferon-gamma/physiology , Intracellular Signaling Peptides and Proteins/physiology , Oligodeoxyribonucleotides/metabolism , Amino Acid Sequence , Caco-2 Cells , Cell Line, Tumor , Cells, Cultured , Fibroblasts/immunology , Fibroblasts/virology , HT29 Cells , HeLa Cells , Humans , Interferon-gamma/chemistry , Interferon-gamma/metabolism , Intracellular Signaling Peptides and Proteins/genetics , Intracellular Signaling Peptides and Proteins/isolation & purification , Molecular Sequence Data , Oligodeoxyribonucleotides/genetics , Protein Binding/immunology , Protein Structure, Tertiary/genetics , Response Elements/immunology , Signal Transduction/immunology
15.
Protein Expr Purif ; 79(1): 44-8, 2011 Sep.
Article in English | MEDLINE | ID: mdl-21575723

ABSTRACT

UL16-binding proteins (ULBPs) are markers of cellular stress which are upregulated on the surface of virus-infected and tumor cells. Recognition of ULBP1 by the activating receptor NKG2D on the surface of cytotoxic natural killer (NK) and T cells promotes lysis of cells expressing ULBP1 and is an important mechanism of immune surveillance. We report a robust method for the generation of large quantities of crystal-grade recombinant ULBP1 protein. The extracellular portion of human ULBP1 was cloned into a T7 expression vector for expression in Escherichia coli. Unpaired cysteines in the sequence which are predicted not to be involved in the intramolecular disulfide bond formation were mutated to serine. ULBP1 was expressed in E. coli BL21 (DE3) pLysS cells as inclusion bodies. Purified inclusion bodies were solubilized by denaturation in guanidine, and refolded by slow dilution. The refolded protein was purified by size exclusion gel filtration and anion exchange chromatography. Furthermore, we have identified conditions optimal for the crystallization of this protein and have obtained initial diffraction data to 4.6Å from these crystals.


Subject(s)
Intracellular Signaling Peptides and Proteins/chemistry , Intracellular Signaling Peptides and Proteins/genetics , Cloning, Molecular , Crystallization , Crystallography, X-Ray , Escherichia coli/genetics , GPI-Linked Proteins/chemistry , GPI-Linked Proteins/genetics , GPI-Linked Proteins/isolation & purification , Humans , Intracellular Signaling Peptides and Proteins/isolation & purification , Protein Refolding , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/isolation & purification
16.
Article in English | MEDLINE | ID: mdl-34182125

ABSTRACT

Shell matrix proteins have important roles in the biomineralization of shells. In this study, we isolated and identified a novel shell matrix protein gene, hic7, from the mussel Hyriopsis cumingii. The cDNA of hic7 was 459 bp long, including a 240-bp open reading frame. It encoded a 79 amino acid-long protein, with amino acids 1-19 constituting the signal peptide. The resulting hic7 is rich in cysteine (16.5%). After removing the signal peptide, the molecular weight was 8.85 kDa and the theoretical isoelectric point was 6.34, indicating that hic7 is a weakly acidic shell matrix protein. Hic7 is mainly expressed in the mantle tissue of H. cumingii. In situ hybridization showed hic7 signals at the edge and dorsal region of the mantle outer fold, indicating that it is related to the formation of the prismatic and nacreous layer of the shell. RNA interference indicated that when hic7 was inhibited by 80%, the crystal morphology of the prism and nacre layers of the shell were irregular and disordered. In addition, the expression of hic7 during the early development of the pearl sac indicated that it has an important role in the transformation of calcium carbonate crystals from a disordered to an orderly deposition pattern. These results suggest that matrix protein hic7 take part in constructing the framework of crystal nucleation and regulating the calcium carbonate crystal morphology of the nacreous and prismatic layers of shells and pearls.


Subject(s)
Animal Shells/growth & development , Extracellular Matrix Proteins/metabolism , Intracellular Signaling Peptides and Proteins/metabolism , Nacre/biosynthesis , Unionidae/growth & development , Amino Acid Sequence , Animals , Base Sequence , Extracellular Matrix Proteins/genetics , Extracellular Matrix Proteins/isolation & purification , Intracellular Signaling Peptides and Proteins/genetics , Intracellular Signaling Peptides and Proteins/isolation & purification , Unionidae/genetics , Unionidae/metabolism
17.
Protein Sci ; 30(3): 650-662, 2021 03.
Article in English | MEDLINE | ID: mdl-33433908

ABSTRACT

Efficient production of large quantities of soluble, properly folded proteins is of high demand in modern structural and functional genomics. Despite much advancement toward improving recombinant protein expression, many eukaryotic proteins especially small peptides often fail to be recovered due to rapid proteolytic degradation. Here we show that the sandwiched-fusion strategy, which is based on two protein tags incorporated both at the amino- and carboxyl-terminus of target protein, could be employed to overcome this obstacle. We have exploited this strategy on heterologous expression in Escherichia coli of eight small degradation-prone eukaryotic proteins, whose successful recombinant productions have yet to be achieved. These include seven mitochondria-derived peptides (MDPS), a class of unique metabolic regulators of human body, and a labile mosquito transcription factor, Guy1. We show here that the sandwiched-fusion strategy, which provides robust protection against proteolysis, affords an economical method to obtain large quantities of pure five MDPs and the transcription factor Guy1, in sharp contrast to otherwise unsuccessful recovery using the traditional amino-fusion method. Further biophysical characterization and interaction studies by NMR spectroscopy confirmed that the proteins produced by this novel approach are properly folded into their biologically active structures. We anticipate this strategy could be widely utilized in production of other labile protein systems.


Subject(s)
Recombinant Fusion Proteins , Animals , Culicidae , Escherichia coli/genetics , Insect Proteins/chemistry , Insect Proteins/genetics , Insect Proteins/metabolism , Intracellular Signaling Peptides and Proteins/chemistry , Intracellular Signaling Peptides and Proteins/genetics , Intracellular Signaling Peptides and Proteins/isolation & purification , Intracellular Signaling Peptides and Proteins/metabolism , Mitochondrial Proteins/chemistry , Mitochondrial Proteins/genetics , Mitochondrial Proteins/metabolism , Protein Stability , Recombinant Fusion Proteins/chemistry , Recombinant Fusion Proteins/genetics , Recombinant Fusion Proteins/metabolism
18.
Biochim Biophys Acta ; 1791(12): 1114-24, 2009 Dec.
Article in English | MEDLINE | ID: mdl-19615464

ABSTRACT

Tazarotene-induced protein 3 (TIG3) and HRAS-like suppressor family 2 (HRASLS2) exhibit tumor-suppressing activities and belong to the lecithin retinol acyltransferase (LRAT) protein family. Since Ca(2+)-independent N-acyltransferase and H-rev107 (another tumor suppressor), both of which are members of the LRAT family, have been recently reported to possess catalytic activities related to phospholipid metabolism, we examined possible enzyme activities of human TIG3 and HRASLS2 together with human H-rev107. The purified recombinant proteins of TIG3, HRASLS2, and H-rev107 functioned as phospholipase (PL) A(1/2) in a Ca(2+)-independent manner with maximal activities of 0.53, 0.67, and 2.57 micromol/min/mg of protein, respectively. The proteins were active with various phosphatidylcholines (PCs) and phosphatidylethanolamines (PEs), and for most of substrates the PLA(1) activity was much higher than the PLA(2) activity. In addition, HRASLS2 catalyzed N-acylation of PE to form N-acyl-PE and O-acylation of lyso PC to form PC. TIG3 and H-rev107 catalyzed the N-acylation and O-acylation at relatively low rates. Moreover, these three proteins showed different expression profiles in human tissues. These results suggest that the tumor suppressors TIG3, HRASLS2 and H-rev107 are involved in the phospholipid metabolism with different physiological roles.


Subject(s)
Phospholipids/metabolism , Receptors, Retinoic Acid/metabolism , Tumor Suppressor Proteins/metabolism , Acylation , Amino Acid Sequence , Animals , Biocatalysis , COS Cells , Cell Line, Tumor , Chlorocebus aethiops , Gene Expression Profiling , Gene Expression Regulation, Neoplastic , Genome, Human/genetics , Humans , Intracellular Signaling Peptides and Proteins/chemistry , Intracellular Signaling Peptides and Proteins/genetics , Intracellular Signaling Peptides and Proteins/isolation & purification , Intracellular Signaling Peptides and Proteins/metabolism , Lysophosphatidylcholines/metabolism , Models, Biological , Molecular Sequence Data , Phosphatidylethanolamines/metabolism , Phospholipases A2/metabolism , Phospholipases A2, Calcium-Independent , Receptors, Retinoic Acid/chemistry , Receptors, Retinoic Acid/genetics , Receptors, Retinoic Acid/isolation & purification , Recombinant Proteins/metabolism , Stereoisomerism , Substrate Specificity , Tumor Suppressor Proteins/chemistry , Tumor Suppressor Proteins/genetics , Tumor Suppressor Proteins/isolation & purification
19.
Mol Syst Biol ; 5: 269, 2009.
Article in English | MEDLINE | ID: mdl-19455133

ABSTRACT

The molecular complexity of mammalian proteomes demands new methods for mapping the organization of multiprotein complexes. Here, we combine mouse genetics and proteomics to characterize synapse protein complexes and interaction networks. New tandem affinity purification (TAP) tags were fused to the carboxyl terminus of PSD-95 using gene targeting in mice. Homozygous mice showed no detectable abnormalities in PSD-95 expression, subcellular localization or synaptic electrophysiological function. Analysis of multiprotein complexes purified under native conditions by mass spectrometry defined known and new interactors: 118 proteins comprising crucial functional components of synapses, including glutamate receptors, K+ channels, scaffolding and signaling proteins, were recovered. Network clustering of protein interactions generated five connected clusters, with two clusters containing all the major ionotropic glutamate receptors and one cluster with voltage-dependent K+ channels. Annotation of clusters with human disease associations revealed that multiple disorders map to the network, with a significant correlation of schizophrenia within the glutamate receptor clusters. This targeted TAP tagging strategy is generally applicable to mammalian proteomics and systems biology approaches to disease.


Subject(s)
Gene Targeting/methods , Intracellular Signaling Peptides and Proteins , Membrane Proteins , Multiprotein Complexes/isolation & purification , Nerve Tissue Proteins/isolation & purification , Schizophrenia/metabolism , Animals , Brain/metabolism , Chromatography, Affinity , Disks Large Homolog 4 Protein , Gene Expression , Guanylate Kinases , Humans , Immunohistochemistry , Intracellular Signaling Peptides and Proteins/genetics , Intracellular Signaling Peptides and Proteins/isolation & purification , Intracellular Signaling Peptides and Proteins/metabolism , Membrane Proteins/genetics , Membrane Proteins/isolation & purification , Membrane Proteins/metabolism , Mice , Multiprotein Complexes/metabolism , Nerve Tissue Proteins/metabolism , Neuronal Plasticity , Protein Interaction Mapping/methods , Recombinant Fusion Proteins/genetics , Recombinant Fusion Proteins/isolation & purification , Recombinant Fusion Proteins/metabolism , Synapses/metabolism , Synaptic Potentials , Tandem Mass Spectrometry
20.
Protein Expr Purif ; 71(1): 103-7, 2010 May.
Article in English | MEDLINE | ID: mdl-20100577

ABSTRACT

Tarzarotene-induced gene 3 (TIG3) and HRAS-like suppressor (HRASLS3) are members of the HREV107 family of class II tumor suppressors, which are down-regulated in various cancer cells. TIG3 and HRASLS3 also exhibit phospholipase activities. Both proteins share a common domain architecture with hydrophilic N-terminal and hydrophobic C-terminal regions. The hydrophobic C-terminal region is important for tumor suppression. However, the function of the hydrophilic N-terminal region remains elusive. To facilitate biochemical characterizations of TIG3 and HRASLS3, we expressed and purified the N-terminal regions of TIG3 and HRASLS3, designated TIG3 (1-134) and HRASLS3 (1-133), in a bacterial system. We found that the N-terminal regions of TIG3 and HRASLS3 have calcium-independent phospholipase A(2) activities. Limited proteolysis revealed that TIG3 (1-132) is a structural domain in the N-terminal region of TIG3. Our data suggest that the hydrophobic C-terminal regions might be crucial for cellular localization, while the hydrophilic N-terminal regions are sufficient for the enzymatic activity of both TIG3 and HRASLS3.


Subject(s)
Biochemistry/methods , Intracellular Signaling Peptides and Proteins/chemistry , Intracellular Signaling Peptides and Proteins/isolation & purification , Receptors, Retinoic Acid/chemistry , Receptors, Retinoic Acid/isolation & purification , Tumor Suppressor Proteins/chemistry , Tumor Suppressor Proteins/isolation & purification , Amino Acid Sequence , Humans , Intracellular Signaling Peptides and Proteins/metabolism , Molecular Sequence Data , Phospholipases A2/metabolism , Phospholipases A2, Calcium-Independent , Protein Structure, Tertiary , Receptors, Retinoic Acid/metabolism , Recombinant Proteins/chemistry , Recombinant Proteins/isolation & purification , Recombinant Proteins/metabolism , Tumor Suppressor Proteins/metabolism
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