Your browser doesn't support javascript.
loading
Show: 20 | 50 | 100
Results 1 - 20 de 21
Filter
Add more filters










Publication year range
1.
Cell Rep ; 42(8): 112960, 2023 08 29.
Article in English | MEDLINE | ID: mdl-37556322

ABSTRACT

The small ubiquitin-like modifier (SUMO) protease SENP6 disassembles SUMO chains from cellular substrate proteins. We use a proteomic method to identify putative SENP6 substrates based on increased apparent molecular weight after SENP6 depletion. Proteins of the lamin family of intermediate filaments show substantially increased SUMO modification after SENP6 depletion. This is accompanied by nuclear structural changes remarkably like those associated with laminopathies. Two SUMO attachment sites on lamin A/C are close to sites of mutations in Emery-Driefuss and limb girdle muscular dystrophy. To establish a direct link between lamin SUMOylation and the observed phenotype, we developed proximity-induced SUMO modification (PISM), which fuses a lamin A/C targeting DARPin to a SUMO E3 ligase domain. This directly targets lamin A/C for SUMO conjugation and demonstrates that enhanced lamin SUMO modification recapitulates the altered nuclear structure manifest after SENP6 depletion. This shows SENP6 activity protects the nucleus against hyperSUMOylation-induced laminopathy-like alterations.


Subject(s)
Lamin Type A , Peptide Hydrolases , Lamin Type A/metabolism , Peptide Hydrolases/metabolism , Small Ubiquitin-Related Modifier Proteins/metabolism , Ubiquitin/metabolism , Cysteine Endopeptidases/metabolism , Proteomics , Sumoylation
2.
Mol Cell ; 79(1): 155-166.e9, 2020 07 02.
Article in English | MEDLINE | ID: mdl-32454028

ABSTRACT

To understand gene function, the encoding DNA or mRNA transcript can be manipulated and the consequences observed. However, these approaches do not have a direct effect on the protein product of the gene, which is either permanently abrogated or depleted at a rate defined by the half-life of the protein. We therefore developed a single-component system that could induce the rapid degradation of the specific endogenous protein itself. A construct combining the RING domain of ubiquitin E3 ligase RNF4 with a protein-specific camelid nanobody mediates target destruction by the ubiquitin proteasome system, a process we describe as antibody RING-mediated destruction (ARMeD). The technique is highly specific because we observed no off-target protein destruction. Furthermore, bacterially produced nanobody-RING fusion proteins electroporated into cells induce degradation of target within minutes. With increasing availability of protein-specific nanobodies, this method will allow rapid and specific degradation of a wide range of endogenous proteins.


Subject(s)
Endopeptidases/metabolism , NEDD8 Protein/metabolism , Nuclear Proteins/metabolism , Proteasome Endopeptidase Complex/metabolism , Single-Domain Antibodies/metabolism , Transcription Factors/metabolism , Ubiquitin/metabolism , Endopeptidases/immunology , HeLa Cells , Humans , NEDD8 Protein/immunology , Nuclear Proteins/immunology , Proteasome Endopeptidase Complex/immunology , Proteolysis , Single-Domain Antibodies/immunology , Transcription Factors/immunology , Ubiquitination
3.
J Invest Dermatol ; 140(6): 1154-1165.e5, 2020 06.
Article in English | MEDLINE | ID: mdl-31705877

ABSTRACT

We performed a small interfering RNA screen to identify targets for cutaneous squamous cell carcinoma (cSCC) therapy in the ubiquitin/ubiquitin-like system. We provide evidence for selective anti-cSCC activity of knockdown of the E3 ubiquitin ligase MARCH4, the ATPase p97/VCP, the deubiquitinating enzyme USP8, the cullin-RING ligase (CRL) 4 substrate receptor CDT2/DTL, and components of the anaphase-promoting complex/cyclosome (APC/C). Specifically attenuating CRL4CDT2 by CDT2 knockdown can be more potent in killing cSCC cells than targeting CRLs or CRL4s in general by RBX1 or DDB1 depletion. Suppression of the APC/C or forced APC/C activation by targeting its repressor EMI1 are both potential therapeutic approaches. We observed that cSCC cells can be selectively killed by small-molecule inhibitors of USP8 (DUBs-IN-3/compound 22c) and the NEDD8 E1 activating enzyme/CRLs (MLN4924/pevonedistat). A substantial proportion of cSCC cell lines are very highly MLN4924-sensitive. Pathways that respond to defects in proteostasis are involved in the anti-cSCC activity of p97 suppression. Targeting USP8 can reduce the expression of growth factor receptors that participate in cSCC development. EMI1 and CDT2 depletion can selectively cause DNA re-replication and DNA damage in cSCC cells.


Subject(s)
Carcinoma, Squamous Cell/drug therapy , Skin Neoplasms/drug therapy , Carcinoma, Squamous Cell/pathology , Cell Cycle Proteins/antagonists & inhibitors , Cell Cycle Proteins/genetics , Cell Cycle Proteins/metabolism , Cell Line, Tumor , Cyclopentanes/pharmacology , Cyclopentanes/therapeutic use , Drug Screening Assays, Antitumor , Endopeptidases/genetics , Endopeptidases/metabolism , Endosomal Sorting Complexes Required for Transport/antagonists & inhibitors , Endosomal Sorting Complexes Required for Transport/genetics , Endosomal Sorting Complexes Required for Transport/metabolism , F-Box Proteins/antagonists & inhibitors , F-Box Proteins/genetics , F-Box Proteins/metabolism , Gene Knockdown Techniques , Humans , Molecular Targeted Therapy/methods , Nuclear Proteins/antagonists & inhibitors , Nuclear Proteins/genetics , Nuclear Proteins/metabolism , Pyrimidines/pharmacology , Pyrimidines/therapeutic use , RNA, Small Interfering/metabolism , Skin Neoplasms/pathology , Ubiquitin Thiolesterase/antagonists & inhibitors , Ubiquitin Thiolesterase/genetics , Ubiquitin Thiolesterase/metabolism , Ubiquitin-Activating Enzymes/antagonists & inhibitors , Ubiquitin-Activating Enzymes/genetics , Ubiquitin-Activating Enzymes/metabolism
4.
Mol Cell ; 75(3): 483-497.e9, 2019 08 08.
Article in English | MEDLINE | ID: mdl-31253574

ABSTRACT

In mammals, ∼100 deubiquitinases act on ∼20,000 intracellular ubiquitination sites. Deubiquitinases are commonly regarded as constitutively active, with limited regulatory and targeting capacity. The BRCA1-A and BRISC complexes serve in DNA double-strand break repair and immune signaling and contain the lysine-63 linkage-specific BRCC36 subunit that is functionalized by scaffold subunits ABRAXAS and ABRO1, respectively. The molecular basis underlying BRCA1-A and BRISC function is currently unknown. Here we show that in the BRCA1-A complex structure, ABRAXAS integrates the DNA repair protein RAP80 and provides a high-affinity binding site that sequesters the tumor suppressor BRCA1 away from the break site. In the BRISC structure, ABRO1 binds SHMT2α, a metabolic enzyme enabling cancer growth in hypoxic environments, which we find prevents BRCC36 from binding and cleaving ubiquitin chains. Our work explains modularity in the BRCC36 DUB family, with different adaptor subunits conferring diversified targeting and regulatory functions.


Subject(s)
BRCA1 Protein/genetics , DNA Repair/genetics , DNA-Binding Proteins/genetics , Deubiquitinating Enzymes/genetics , Histone Chaperones/genetics , Neoplasms/genetics , Binding Sites/genetics , Carrier Proteins/genetics , Cell Nucleus/genetics , Cell Nucleus/immunology , Cytoplasm/genetics , Cytoplasm/immunology , DNA Breaks, Double-Stranded , DNA Repair/immunology , Deubiquitinating Enzymes/immunology , HeLa Cells , Humans , Immunity, Cellular/genetics , Multiprotein Complexes/chemistry , Multiprotein Complexes/genetics , Neoplasms/immunology , Nuclear Matrix-Associated Proteins/genetics , Protein Binding/genetics , Ubiquitin/genetics , Ubiquitin-Specific Proteases/genetics , Ubiquitination/genetics
5.
Nat Protoc ; 10(9): 1374-88, 2015 Sep.
Article in English | MEDLINE | ID: mdl-26292070

ABSTRACT

The protein called 'small ubiquitin-like modifier' (SUMO) is post-translationally linked to target proteins at the ɛ-amino group of lysine residues. This 'SUMOylation' alters the behavior of the target protein, a change that is utilized to regulate diverse cellular processes. Understanding the target-specific consequences of SUMO modification requires knowledge of the location of conjugation sites, and we have developed a straightforward protocol for the proteome-wide identification of SUMO modification sites using mass spectrometry (MS). The approach described herein requires the expression of a mutant form of SUMO, in which the residue preceding the C-terminal Gly-Gly (diGly) is replaced with a lysine (SUMO(KGG)). Digestion of SUMO(KGG) protein conjugates with endoproteinase Lys-C yields a diGly motif attached to target lysines. Peptides containing this adduct are enriched using a diGly-Lys (K-ɛ-GG)-specific antibody and identified by MS. This diGly signature is characteristic of SUMO(KGG) conjugation alone, as no other ubiquitin-like protein (Ubl) yields this adduct upon Lys-C digestion. We have demonstrated the utility of the approach in SUMOylation studies, but, in principle, it may be adapted for the site-specific identification of proteins modified by any Ubl. Starting from cell lysis, this protocol can be completed in ∼5 d.


Subject(s)
Proteomics/methods , Sumoylation , Amino Acid Sequence , HEK293 Cells , Humans , Mass Spectrometry , Molecular Sequence Data
6.
J Vis Exp ; (87)2014 May 24.
Article in English | MEDLINE | ID: mdl-24893647

ABSTRACT

Post-translational modification of proteins with ubiquitin and ubiquitin-like molecules (UBLs) is emerging as a dynamic cellular signaling network that regulates diverse biological pathways including the hypoxia response, proteostasis, the DNA damage response and transcription. To better understand how UBLs regulate pathways relevant to human disease, we have compiled a human siRNA "ubiquitome" library consisting of 1,186 siRNA duplex pools targeting all known and predicted components of UBL system pathways. This library can be screened against a range of cell lines expressing reporters of diverse biological pathways to determine which UBL components act as positive or negative regulators of the pathway in question. Here, we describe a protocol utilizing this library to identify ubiquitome-regulators of the HIF1A-mediated cellular response to hypoxia using a transcription-based luciferase reporter. An initial assay development stage is performed to establish suitable screening parameters of the cell line before performing the screen in three stages: primary, secondary and tertiary/deconvolution screening. The use of targeted over whole genome siRNA libraries is becoming increasingly popular as it offers the advantage of reporting only on members of the pathway with which the investigators are most interested. Despite inherent limitations of siRNA screening, in particular false-positives caused by siRNA off-target effects, the identification of genuine novel regulators of the pathways in question outweigh these shortcomings, which can be overcome by performing a series of carefully undertaken control experiments.


Subject(s)
Proteomics/methods , RNA, Small Interfering/genetics , Ubiquitin/metabolism , Ubiquitination , Bone Neoplasms , Cell Hypoxia , Cell Line, Tumor , Gene Expression Regulation , Humans , Hypoxia-Inducible Factor 1, alpha Subunit/genetics , Hypoxia-Inducible Factor 1, alpha Subunit/metabolism , Osteosarcoma , Response Elements , Signal Transduction , Ubiquitin/analysis , Ubiquitin/genetics
7.
Sci Signal ; 7(323): rs2, 2014 Apr 29.
Article in English | MEDLINE | ID: mdl-24782567

ABSTRACT

Posttranslational modification with small ubiquitin-like modifiers (SUMOs) alters the function of proteins involved in diverse cellular processes. SUMO-specific enzymes conjugate SUMOs to lysine residues in target proteins. Although proteomic studies have identified hundreds of sumoylated substrates, methods to identify the modified lysines on a proteomic scale are lacking. We developed a method that enabled proteome-wide identification of sumoylated lysines that involves the expression of polyhistidine (6His)-tagged SUMO2 with Thr(90) mutated to Lys. Endoproteinase cleavage with Lys-C of 6His-SUMO2(T90K)-modified proteins from human cell lysates produced a diGly remnant on SUMO2(T90K)-conjugated lysines, enabling immunoprecipitation of SUMO2(T90K)-modified peptides and producing a unique mass-to-charge signature. Mass spectrometry analysis of SUMO-enriched peptides revealed more than 1000 sumoylated lysines in 539 proteins, including many functionally related proteins involved in cell cycle, transcription, and DNA repair. Not only can this strategy be used to study the dynamics of sumoylation and other potentially similar posttranslational modifications, but also, these data provide an unprecedented resource for future research on the role of sumoylation in cellular physiology and disease.


Subject(s)
Protein Processing, Post-Translational , Proteome/metabolism , Proteomics/methods , Small Ubiquitin-Related Modifier Proteins/metabolism , Amino Acid Sequence , Blotting, Western , HEK293 Cells , Histidine/genetics , Humans , Lysine/genetics , Lysine/metabolism , Mass Spectrometry , Molecular Sequence Data , Mutation , Peptides/metabolism , Proteome/genetics , Sequence Homology, Amino Acid , Signal Transduction/genetics , Small Ubiquitin-Related Modifier Proteins/genetics , Sumoylation , Threonine/genetics , Threonine/metabolism
8.
Cancer Res ; 74(8): 2246-2257, 2014 Apr 15.
Article in English | MEDLINE | ID: mdl-24686174

ABSTRACT

The genotoxin cisplatin is commonly used in chemotherapy to treat solid tumors, yet our understanding of the mechanism underlying the drug response is limited. In a focused siRNA screen, using an siRNA library targeting genes involved in ubiquitin and ubiquitin-like signaling, we identified the E3 ubiquitin ligase HOIP as a key regulator of cisplatin-induced genotoxicity. HOIP forms, with SHARPIN and HOIL-1L, the linear ubiquitin assembly complex (LUBAC). We show that cells deficient in the HOIP ligase complex exhibit hypersensitivity to cisplatin. This is due to a dramatic increase in caspase-8/caspase-3-mediated apoptosis that is strictly dependent on ATM-, but not ATR-mediated DNA damage checkpoint activation. Moreover, basal and cisplatin-induced activity of the stress response kinase JNK is enhanced in HOIP-depleted cells and, conversely, JNK inhibition can increase cellular resistance to cisplatin and reverse the apoptotic hyperactivation in HOIP-depleted cells. Furthermore, we show that HOIP depletion sensitizes cancer cells, derived from carcinomas of various origins, through an enhanced apoptotic cell death response. We also provide evidence that ovarian cancer cells classified as cisplatin-resistant can regain sensitivity following HOIP downregulation. Cumulatively, our study identifies a HOIP-regulated antiapoptotic signaling pathway, and we envisage HOIP as a potential target for the development of combinatorial chemotherapies to potentiate the efficacy of platinum-based anticancer drugs.


Subject(s)
Antineoplastic Agents/pharmacology , Apoptosis/drug effects , Cisplatin/pharmacology , Ubiquitin-Protein Ligases/metabolism , Apoptosis/physiology , Cell Cycle Checkpoints/physiology , Cell Death/drug effects , Cell Death/physiology , DNA Damage , Female , HCT116 Cells , HEK293 Cells , HeLa Cells , Humans , MAP Kinase Kinase 4/metabolism , Ovarian Neoplasms/drug therapy , Ovarian Neoplasms/enzymology , Ovarian Neoplasms/pathology , RNA, Small Interfering/administration & dosage , RNA, Small Interfering/genetics , Signal Transduction , Ubiquitin-Protein Ligases/genetics
9.
PLoS One ; 9(2): e89547, 2014.
Article in English | MEDLINE | ID: mdl-24586861

ABSTRACT

The System L1-type amino acid transporter mediates transport of large neutral amino acids (LNAA) in many mammalian cell-types. LNAA such as leucine are required for full activation of the mTOR-S6K signalling pathway promoting protein synthesis and cell growth. The SLC7A5 (LAT1) catalytic subunit of high-affinity System L1 functions as a glycoprotein-associated heterodimer with the multifunctional protein SLC3A2 (CD98). We generated a floxed Slc7a5 mouse strain which, when crossed with mice expressing Cre driven by a global promoter, produced Slc7a5 heterozygous knockout (Slc7a5+/-) animals with no overt phenotype, although homozygous global knockout of Slc7a5 was embryonically lethal. Muscle-specific (MCK Cre-mediated) Slc7a5 knockout (MS-Slc7a5-KO) mice were used to study the role of intracellular LNAA delivery by the SLC7A5 transporter for mTOR-S6K pathway activation in skeletal muscle. Activation of muscle mTOR-S6K (Thr389 phosphorylation) in vivo by intraperitoneal leucine injection was blunted in homozygous MS-Slc7a5-KO mice relative to wild-type animals. Dietary intake and growth rate were similar for MS-Slc7a5-KO mice and wild-type littermates fed for 10 weeks (to age 120 days) with diets containing 10%, 20% or 30% of protein. In MS-Slc7a5-KO mice, Leu and Ile concentrations in gastrocnemius muscle were reduced by ∼40% as dietary protein content was reduced from 30 to 10%. These changes were associated with >50% decrease in S6K Thr389 phosphorylation in muscles from MS-Slc7a5-KO mice, indicating reduced mTOR-S6K pathway activation, despite no significant differences in lean tissue mass between groups on the same diet. MS-Slc7a5-KO mice on 30% protein diet exhibited mild insulin resistance (e.g. reduced glucose clearance, larger gonadal adipose depots) relative to control animals. Thus, SLC7A5 modulates LNAA-dependent muscle mTOR-S6K signalling in mice, although it appears non-essential (or is sufficiently compensated by e.g. SLC7A8 (LAT2)) for maintenance of normal muscle mass.


Subject(s)
Dietary Proteins/administration & dosage , Insulin/metabolism , Large Neutral Amino Acid-Transporter 1/physiology , Leucine/administration & dosage , Muscle, Skeletal/metabolism , Ribosomal Protein S6 Kinases, 70-kDa/metabolism , TOR Serine-Threonine Kinases/metabolism , Animals , Blotting, Western , Cells, Cultured , Glucose Tolerance Test , Insulin Resistance , Integrases/metabolism , Mice , Mice, Knockout , Mice, Transgenic , Muscle, Skeletal/cytology , Phosphorylation , RNA, Messenger/genetics , Real-Time Polymerase Chain Reaction , Reverse Transcriptase Polymerase Chain Reaction , Ribosomal Protein S6 Kinases, 70-kDa/genetics , Signal Transduction , TOR Serine-Threonine Kinases/genetics
10.
Biosci Rep ; 33(5)2013 Sep 04.
Article in English | MEDLINE | ID: mdl-23844980

ABSTRACT

Aspergillus fumigatus is the causative agent of IA (invasive aspergillosis) in immunocompromised patients. It possesses a cell wall composed of chitin, glucan and galactomannan, polymeric carbohydrates synthesized by processive glycosyltransferases from intracellular sugar nucleotide donors. Here we demonstrate that A. fumigatus possesses an active AfAGM1 (A. fumigatus N-acetylphosphoglucosamine mutase), a key enzyme in the biosynthesis of UDP (uridine diphosphate)-GlcNAc (N-acetylglucosamine), the nucleotide sugar donor for chitin synthesis. A conditional agm1 mutant revealed the gene to be essential. Reduced expression of agm1 resulted in retarded cell growth and altered cell wall ultrastructure and composition. The crystal structure of AfAGM1 revealed an amino acid change in the active site compared with the human enzyme, which could be exploitable in the design of selective inhibitors. AfAGM1 inhibitors were discovered by high-throughput screening, inhibiting the enzyme with IC50s in the low µM range. Together, these data provide a platform for the future development of AfAGM1 inhibitors with antifungal activity.


Subject(s)
Aspergillus fumigatus/enzymology , Fungal Proteins/chemistry , Phosphotransferases (Phosphomutases)/chemistry , Antifungal Agents/chemistry , Aspergillus fumigatus/ultrastructure , Catalytic Domain , Cell Wall/enzymology , Crystallography, X-Ray , Fungal Proteins/antagonists & inhibitors , Fungal Proteins/genetics , Humans , Inhibitory Concentration 50 , Kinetics , Magnesium , Microbial Sensitivity Tests , Microbial Viability , Models, Molecular , Phosphotransferases (Phosphomutases)/antagonists & inhibitors , Phosphotransferases (Phosphomutases)/genetics , Protein Structure, Secondary
11.
Mol Microbiol ; 89(3): 479-93, 2013 Aug.
Article in English | MEDLINE | ID: mdl-23750903

ABSTRACT

The sugar nucleotide UDP-N-acetylglucosamine (UDP-GlcNAc) is an essential metabolite in both prokaryotes and eukaryotes. In fungi, it is the precursor for the synthesis of chitin, an essential component of the fungal cell wall. UDP-N-acetylglucosamine pyrophosphorylase (UAP) is the final enzyme in eukaryotic UDP-GlcNAc biosynthesis, converting UTP and N-acetylglucosamine-1-phosphate (GlcNAc-1P) to UDP-GlcNAc. As such, this enzyme may provide an attractive target against pathogenic fungi. Here, we demonstrate that the fungal pathogen Aspergillus fumigatus possesses an active UAP (AfUAP1) that shows selectivity for GlcNAc-1P as the phosphosugar substrate. A conditional mutant, constructed by replacing the native promoter of the A. fumigatus uap1 gene with the Aspergillus nidulans alcA promoter, revealed that uap1 is essential for cell survival and important for cell wall synthesis and morphogenesis. The crystal structure of AfUAP1 was determined and revealed exploitable differences in the active site compared with the human enzyme. Thus AfUAP1 could represent a novel antifungal target and this work will assist the future discovery of small molecule inhibitors against this enzyme.


Subject(s)
Aspergillus fumigatus/enzymology , Fungal Proteins/chemistry , Nucleotidyltransferases/chemistry , Acetylglucosamine/analogs & derivatives , Acetylglucosamine/chemistry , Aspergillus fumigatus/genetics , Aspergillus fumigatus/ultrastructure , Cell Wall/ultrastructure , Cloning, Molecular , Fungal Proteins/genetics , Genes, Essential , Mutation , Nucleotidyltransferases/genetics , Promoter Regions, Genetic , Protein Structure, Tertiary , Substrate Specificity
12.
Biochem J ; 451(2): 185-94, 2013 Apr 15.
Article in English | MEDLINE | ID: mdl-23398456

ABSTRACT

HIF1A (hypoxia-inducible factor 1α) is the master regulator of the cellular response to hypoxia and is implicated in cancer progression. Whereas the regulation of HIF1A protein in response to oxygen is well characterized, less is known about the fate of HIF1A mRNA. In the present study, we have identified the pseudo-DUB (deubiquitinating enzyme)/deadenylase USP52 (ubiquitin-specific protease 52)/PAN2 [poly(A) nuclease 2] as an important regulator of the HIF1A-mediated hypoxic response. Depletion of USP52 reduced HIF1A mRNA and protein levels and resulted in reduced expression of HIF1A-regulated hypoxic targets due to a 3'-UTR (untranslated region)-dependent poly(A)-tail-length-independent destabilization in HIF1A mRNA. MS analysis revealed an association of USP52 with several P-body (processing body) components and we confirmed further that USP52 protein and HIF1A mRNA co-localized with cytoplasmic P-bodies. Importantly, P-body dispersal by knockdown of GW182 or LSM1 resulted in a reduction of HIF1A mRNA levels. These data uncover a novel role for P-bodies in regulating HIF1A mRNA stability, and demonstrate that USP52 is a key component of P-bodies required to prevent HIF1A mRNA degradation.


Subject(s)
Cytoplasmic Structures/metabolism , Exoribonucleases/metabolism , Hypoxia-Inducible Factor 1, alpha Subunit/genetics , RNA Stability , 3' Untranslated Regions , AU Rich Elements , Autoantigens/genetics , Autoantigens/metabolism , Cell Hypoxia/genetics , Cell Line , Cytoplasmic Structures/genetics , Exoribonucleases/genetics , Gene Knockdown Techniques , Humans , Hypoxia-Inducible Factor 1, alpha Subunit/metabolism , Poly A , Proto-Oncogene Proteins/genetics , Proto-Oncogene Proteins/metabolism , RNA-Binding Proteins/genetics , RNA-Binding Proteins/metabolism
13.
PLoS Pathog ; 8(1): e1002373, 2012 Jan.
Article in English | MEDLINE | ID: mdl-22253590

ABSTRACT

Vibrio cholerae is a bacterial pathogen that colonizes the chitinous exoskeleton of zooplankton as well as the human gastrointestinal tract. Colonization of these different niches involves an N-acetylglucosamine binding protein (GbpA) that has been reported to mediate bacterial attachment to both marine chitin and mammalian intestinal mucin through an unknown molecular mechanism. We report structural studies that reveal that GbpA possesses an unusual, elongated, four-domain structure, with domains 1 and 4 showing structural homology to chitin binding domains. A glycan screen revealed that GbpA binds to GlcNAc oligosaccharides. Structure-guided GbpA truncation mutants show that domains 1 and 4 of GbpA interact with chitin in vitro, whereas in vivo complementation studies reveal that domain 1 is also crucial for mucin binding and intestinal colonization. Bacterial binding studies show that domains 2 and 3 bind to the V. cholerae surface. Finally, mouse virulence assays show that only the first three domains of GbpA are required for colonization. These results explain how GbpA provides structural/functional modular interactions between V. cholerae, intestinal epithelium and chitinous exoskeletons.


Subject(s)
Fimbriae Proteins/chemistry , Fimbriae Proteins/metabolism , Host-Pathogen Interactions , Protein Interaction Domains and Motifs/physiology , Receptors, Cell Surface/metabolism , Vibrio cholerae , Animals , Chitin/chemistry , Chitin/metabolism , Crystallography, X-Ray , Fimbriae Proteins/genetics , Host-Pathogen Interactions/genetics , Mice , Mice, Inbred BALB C , Models, Biological , Models, Molecular , Organisms, Genetically Modified , Protein Binding , Protein Interaction Domains and Motifs/genetics , Protein Structure, Tertiary , Rabbits , Receptors, Cell Surface/chemistry , Sequence Homology, Amino Acid , Vibrio cholerae/genetics , Vibrio cholerae/growth & development , Vibrio cholerae/pathogenicity , Vibrio cholerae/physiology
14.
Chem Biol ; 17(12): 1275-81, 2010 Dec 22.
Article in English | MEDLINE | ID: mdl-21168763

ABSTRACT

Natural products are often large, synthetically intractable molecules, yet frequently offer surprising inroads into previously unexplored chemical space for enzyme inhibitors. Argifin is a cyclic pentapeptide that was originally isolated as a fungal natural product. It competitively inhibits family 18 chitinases by mimicking the chitooligosaccharide substrate of these enzymes. Interestingly, argifin is a nanomolar inhibitor of the bacterial-type subfamily of fungal chitinases that possess an extensive chitin-binding groove, but does not inhibit the much smaller, plant-type enzymes from the same family that are involved in fungal cell division and are thought to be potential drug targets. Here we show that a small, highly efficient, argifin-derived, nine-atom fragment is a micromolar inhibitor of the plant-type chitinase ChiA1 from the opportunistic pathogen Aspergillus fumigatus. Evaluation of the binding mode with the first crystal structure of an A. fumigatus plant-type chitinase reveals that the compound binds the catalytic machinery in the same manner as observed for argifin with the bacterial-type chitinases. The structure of the complex was used to guide synthesis of derivatives to explore a pocket near the catalytic machinery. This work provides synthetically tractable plant-type family 18 chitinase inhibitors from the repurposing of a natural product.


Subject(s)
Biological Products/chemistry , Chitinases/antagonists & inhibitors , Enzyme Inhibitors/chemistry , Peptides, Cyclic/chemistry , Aspergillus fumigatus/drug effects , Binding Sites , Biological Products/pharmacology , Catalytic Domain , Chitinases/metabolism , Crystallography, X-Ray , Drug Evaluation, Preclinical , Enzyme Inhibitors/pharmacology , Fungi/enzymology , Peptides, Cyclic/pharmacology , Protein Binding
15.
Cell Metab ; 12(5): 456-66, 2010 Nov 03.
Article in English | MEDLINE | ID: mdl-21035757

ABSTRACT

Glycogen synthase (GS), a key enzyme in glycogen synthesis, is activated by the allosteric stimulator glucose-6-phosphate (G6P) and by dephosphorylation through inactivation of GS kinase-3 with insulin. The relative importance of these two regulatory mechanisms in controlling GS is not established, mainly due to the complex interplay between multiple phosphorylation sites and allosteric effectors. Here we identify a residue that plays an important role in the allosteric activation of GS by G6P. We generated knockin mice in which wild-type muscle GS was replaced by a mutant that could not be activated by G6P but could still be activated normally by dephosphorylation. We demonstrate that knockin mice expressing the G6P-insensitive mutant display an ∼80% reduced muscle glycogen synthesis by insulin and markedly reduced glycogen levels. Our study provides genetic evidence that allosteric activation of GS is the primary mechanism by which insulin promotes muscle glycogen accumulation in vivo.


Subject(s)
Glucose-6-Phosphate/metabolism , Glycogen Synthase/metabolism , Glycogen/metabolism , Muscles/metabolism , Allosteric Regulation , Animals , Cell Line , Gene Knock-In Techniques , Glucose/metabolism , Glycogen Synthase/genetics , Humans , Insulin/metabolism , Mice , Mutation
16.
Biochem J ; 426(3): 281-92, 2010 Feb 24.
Article in English | MEDLINE | ID: mdl-20030628

ABSTRACT

Legionnaires' disease is caused by a lethal colonization of alveolar macrophages with the Gram-negative bacterium Legionella pneumophila. LpGT (L. pneumophila glucosyltransferase; also known as Lgt1) has recently been identified as a virulence factor, shutting down protein synthesis in the human cell by specific glucosylation of EF1A (elongation factor 1A), using an unknown mode of substrate recognition and a retaining mechanism for glycosyl transfer. We have determined the crystal structure of LpGT in complex with substrates, revealing a GT-A fold with two unusual protruding domains. Through structure-guided mutagenesis of LpGT, several residues essential for binding of the UDP-glucose-donor and EF1A-acceptor substrates were identified, which also affected L. pneumophila virulence as demonstrated by microinjection studies. Together, these results suggested that a positively charged EF1A loop binds to a negatively charged conserved groove on the LpGT structure, and that two asparagine residues are essential for catalysis. Furthermore, we showed that two further L. pneumophila glycosyltransferases possessed the conserved UDP-glucose-binding sites and EF1A-binding grooves, and are, like LpGT, translocated into the macrophage through the Icm/Dot (intracellular multiplication/defect in organelle trafficking) system.


Subject(s)
Bacterial Proteins/metabolism , Glycosyltransferases/metabolism , Legionella pneumophila/enzymology , Peptide Elongation Factor 1/metabolism , Amino Acid Sequence , Apoptosis , Asparagine/chemistry , Asparagine/genetics , Asparagine/metabolism , Bacterial Proteins/chemistry , Bacterial Proteins/genetics , Binding Sites/genetics , Catalysis , Catalytic Domain , Cell Line , Crystallography, X-Ray , Glycosyltransferases/chemistry , Glycosyltransferases/genetics , HL-60 Cells , HeLa Cells , Humans , Isoenzymes/chemistry , Isoenzymes/genetics , Isoenzymes/metabolism , Microscopy, Confocal , Models, Molecular , Molecular Sequence Data , Mutation , Peptide Elongation Factor 1/genetics , Protein Binding , Protein Folding , Protein Structure, Tertiary , Sequence Homology, Amino Acid , Uridine Diphosphate Glucose/chemistry , Uridine Diphosphate Glucose/metabolism
17.
J Biol Chem ; 284(13): 8461-9, 2009 Mar 27.
Article in English | MEDLINE | ID: mdl-19097997

ABSTRACT

Yeast cell wall remodeling is controlled by the equilibrium between glycoside hydrolases, glycosyltransferases, and transglycosylases. Family 72 glycoside hydrolases (GH72) are ubiquitous in fungal organisms and are known to possess significant transglycosylase activity, producing elongated beta(1-3) glucan chains. However, the molecular mechanisms that control the balance between hydrolysis and transglycosylation in these enzymes are not understood. Here we present the first crystal structure of a glucan transglycosylase, Saccharomyces cerevisiae Gas2 (ScGas2), revealing a multidomain fold, with a (betaalpha)(8) catalytic core and a separate glucan binding domain with an elongated, conserved glucan binding groove. Structures of ScGas2 complexes with different beta-glucan substrate/product oligosaccharides provide "snapshots" of substrate binding and hydrolysis/transglycosylation giving the first insights into the mechanisms these enzymes employ to drive beta(1-3) glucan elongation. Together with mutagenesis and analysis of reaction products, the structures suggest a "base occlusion" mechanism through which these enzymes protect the covalent protein-enzyme intermediate from a water nucleophile, thus controlling the balance between hydrolysis and transglycosylation and driving the elongation of beta(1-3) glucan chains in the yeast cell wall.


Subject(s)
Cell Wall/enzymology , Glucan Endo-1,3-beta-D-Glucosidase/chemistry , Glucans/chemistry , Protein Folding , Saccharomyces cerevisiae Proteins/chemistry , Saccharomyces cerevisiae/enzymology , Crystallography, X-Ray , Glucan Endo-1,3-beta-D-Glucosidase/metabolism , Glucans/metabolism , Protein Structure, Tertiary/physiology , Saccharomyces cerevisiae Proteins/metabolism
18.
EMBO J ; 27(20): 2780-8, 2008 Oct 22.
Article in English | MEDLINE | ID: mdl-18818698

ABSTRACT

Post-translational modification of protein serines/threonines with N-acetylglucosamine (O-GlcNAc) is dynamic, inducible and abundant, regulating many cellular processes by interfering with protein phosphorylation. O-GlcNAcylation is regulated by O-GlcNAc transferase (OGT) and O-GlcNAcase, both encoded by single, essential, genes in metazoan genomes. It is not understood how OGT recognises its sugar nucleotide donor and performs O-GlcNAc transfer onto proteins/peptides, and how the enzyme recognises specific cellular protein substrates. Here, we show, by X-ray crystallography and mutagenesis, that OGT adopts the (metal-independent) GT-B fold and binds a UDP-GlcNAc analogue at the bottom of a highly conserved putative peptide-binding groove, covered by a mobile loop. Strikingly, the tetratricopeptide repeats (TPRs) tightly interact with the active site to form a continuous 120 A putative interaction surface, whereas the previously predicted phosphatidylinositide-binding site locates to the opposite end of the catalytic domain. On the basis of the structure, we identify truncation/point mutants of the TPRs that have differential effects on activity towards proteins/peptides, giving first insights into how OGT may recognise its substrates.


Subject(s)
N-Acetylglucosaminyltransferases/chemistry , Amino Acid Sequence , Animals , Crystallography, X-Ray , Humans , Models, Biological , Molecular Conformation , Molecular Sequence Data , N-Acetylglucosaminyltransferases/metabolism , Phosphorylation , Protein Binding , Protein Processing, Post-Translational , Sequence Homology, Amino Acid , Signal Transduction , Substrate Specificity , Xenopus
19.
Biochem J ; 415(2): 217-23, 2008 Oct 15.
Article in English | MEDLINE | ID: mdl-18601654

ABSTRACT

Aspergillus fumigatus is the causative agent of aspergillosis, a frequently invasive colonization of the lungs of immunocompromised patients. GNA1 (D-glucosamine-6-phosphate N-acetyltransferase) catalyses the acetylation of GlcN-6P (glucosamine-6-phosphate) to GlcNAc-6P (N-acetylglucosamine-6-phosphate), a key intermediate in the UDP-GlcNAc biosynthetic pathway. Gene disruption of gna1 in yeast and Candida albicans has provided genetic validation of the enzyme as a potential target. An understanding of potential active site differences between the human and A. fumigatus enzymes is required to enable further work aimed at identifying selective inhibitors for the fungal enzyme. In the present study, we describe crystal structures of both human and A. fumigatus GNA1, as well as their kinetic characterization. The structures show significant differences in the sugar-binding site with, in particular, several non-conservative substitutions near the phosphate-binding pocket. Mutagenesis targeting these differences revealed drastic effects on steady-state kinetics, suggesting that the differences could be exploitable with small-molecule inhibitors.


Subject(s)
Aspergillus fumigatus/enzymology , Fungal Proteins/metabolism , Glucosamine 6-Phosphate N-Acetyltransferase/metabolism , Amino Acid Sequence , Aspergillus fumigatus/genetics , Binding Sites/genetics , Crystallography, X-Ray , Fungal Proteins/chemistry , Fungal Proteins/genetics , Glucosamine 6-Phosphate N-Acetyltransferase/chemistry , Glucosamine 6-Phosphate N-Acetyltransferase/genetics , Humans , Kinetics , Models, Molecular , Molecular Sequence Data , Protein Structure, Secondary , Protein Structure, Tertiary , Sequence Homology, Amino Acid
20.
Biochem J ; 405(3): 513-22, 2007 Aug 01.
Article in English | MEDLINE | ID: mdl-17461779

ABSTRACT

The mTOR (mammalian target of rapamycin) protein kinase is an important regulator of cell growth. Two complexes of mTOR have been identified: complex 1, consisting of mTOR-Raptor (regulatory associated protein of mTOR)-mLST8 (termed mTORC1), and complex 2, comprising mTOR-Rictor (rapamycininsensitive companion of mTOR)-mLST8-Sin1 (termed mTORC2). mTORC1 phosphorylates the p70 ribosomal S6K (S6 kinase) at its hydrophobic motif (Thr389), whereas mTORC2 phosphorylates PKB (protein kinase B) at its hydrophobic motif (Ser473). In the present study, we report that widely expressed isoforms of unstudied proteins termed Protor-1 (protein observed with Rictor-1) and Protor-2 interact with Rictor and are components of mTORC2. We demonstrate that immunoprecipitation of Protor-1 or Protor-2 results in the co-immunoprecipitation of other mTORC2 subunits, but not Raptor, a specific component of mTORC1. We show that detergents such as Triton X-100 or n-octylglucoside dissociate mTOR and mLST8 from a complex of Protor-1, Sin1 and Rictor. We also provide evidence that Rictor regulates the expression of Protor-1, and that Protor-1 is not required for the assembly of other mTORC2 subunits into a complex. Protor-1 is a novel Rictor-binding subunit of mTORC2, but further work is required to establish its role.


Subject(s)
Carrier Proteins/metabolism , Protein Kinases/metabolism , Cell Line , Gene Silencing , Humans , Protein Binding , Protein Isoforms , Rapamycin-Insensitive Companion of mTOR Protein , TOR Serine-Threonine Kinases
SELECTION OF CITATIONS
SEARCH DETAIL
...