Your browser doesn't support javascript.
loading
Show: 20 | 50 | 100
Results 1 - 20 de 1.141
Filter
1.
Nature ; 627(8003): 437-444, 2024 Mar.
Article in English | MEDLINE | ID: mdl-38383789

ABSTRACT

Stalled ribosomes at the endoplasmic reticulum (ER) are covalently modified with the ubiquitin-like protein UFM1 on the 60S ribosomal subunit protein RPL26 (also known as uL24)1,2. This modification, which is known as UFMylation, is orchestrated by the UFM1 ribosome E3 ligase (UREL) complex, comprising UFL1, UFBP1 and CDK5RAP3 (ref. 3). However, the catalytic mechanism of UREL and the functional consequences of UFMylation are unclear. Here we present cryo-electron microscopy structures of UREL bound to 60S ribosomes, revealing the basis of its substrate specificity. UREL wraps around the 60S subunit to form a C-shaped clamp architecture that blocks the tRNA-binding sites at one end, and the peptide exit tunnel at the other. A UFL1 loop inserts into and remodels the peptidyl transferase centre. These features of UREL suggest a crucial function for UFMylation in the release and recycling of stalled or terminated ribosomes from the ER membrane. In the absence of functional UREL, 60S-SEC61 translocon complexes accumulate at the ER membrane, demonstrating that UFMylation is necessary for releasing SEC61 from 60S subunits. Notably, this release is facilitated by a functional switch of UREL from a 'writer' to a 'reader' module that recognizes its product-UFMylated 60S ribosomes. Collectively, we identify a fundamental role for UREL in dissociating 60S subunits from the SEC61 translocon and the basis for UFMylation in regulating protein homeostasis at the ER.


Subject(s)
Endoplasmic Reticulum , Protein Processing, Post-Translational , Ribosome Subunits, Large, Eukaryotic , Ubiquitin-Protein Ligases , Adaptor Proteins, Signal Transducing/metabolism , Binding Sites , Cell Cycle Proteins/chemistry , Cell Cycle Proteins/metabolism , Cell Cycle Proteins/ultrastructure , Cryoelectron Microscopy , Endoplasmic Reticulum/metabolism , Endoplasmic Reticulum/ultrastructure , Homeostasis , Intracellular Membranes/metabolism , Peptidyl Transferases/chemistry , Peptidyl Transferases/metabolism , Peptidyl Transferases/ultrastructure , Ribosomal Proteins/chemistry , Ribosomal Proteins/metabolism , Ribosomal Proteins/ultrastructure , RNA, Transfer/metabolism , SEC Translocation Channels/chemistry , SEC Translocation Channels/metabolism , SEC Translocation Channels/ultrastructure , Tumor Suppressor Proteins/chemistry , Tumor Suppressor Proteins/metabolism , Tumor Suppressor Proteins/ultrastructure , Ubiquitin-Protein Ligases/chemistry , Ubiquitin-Protein Ligases/metabolism , Ubiquitin-Protein Ligases/ultrastructure , Ribosome Subunits, Large, Eukaryotic/chemistry , Ribosome Subunits, Large, Eukaryotic/metabolism , Ribosome Subunits, Large, Eukaryotic/ultrastructure
2.
Science ; 382(6674): 1042-1050, 2023 12.
Article in English | MEDLINE | ID: mdl-37972196

ABSTRACT

Ephrin type-A receptor 2 (EphA2) is a receptor tyrosine kinase that initiates both ligand-dependent tumor-suppressive and ligand-independent oncogenic signaling. We used time-resolved, live-cell fluorescence spectroscopy to show that the ligand-free EphA2 assembles into multimers driven by two types of intermolecular interactions in the ectodomain. The first type entails extended symmetric interactions required for ligand-induced receptor clustering and tumor-suppressive signaling that inhibits activity of the oncogenic extracellular signal-regulated kinase (ERK) and protein kinase B (AKT) protein kinases and suppresses cell migration. The second type is an asymmetric interaction between the amino terminus and the membrane proximal domain of the neighboring receptors, which supports oncogenic signaling and promotes migration in vitro and tumor invasiveness in vivo. Our results identify the molecular interactions that drive the formation of the EphA2 multimeric signaling clusters and reveal the pivotal role of EphA2 assembly in dictating its opposing functions in oncogenesis.


Subject(s)
Protein Multimerization , Receptor, EphA2 , Tumor Suppressor Proteins , Humans , Ligands , Neoplasm Invasiveness , Phosphorylation , Receptor, EphA2/chemistry , Receptor, EphA2/metabolism , Signal Transduction , Spectrometry, Fluorescence , Tumor Suppressor Proteins/chemistry , Tumor Suppressor Proteins/metabolism
3.
Nature ; 619(7970): 650-657, 2023 Jul.
Article in English | MEDLINE | ID: mdl-37344587

ABSTRACT

Homologous recombination is a fundamental process of life. It is required for the protection and restart of broken replication forks, the repair of chromosome breaks and the exchange of genetic material during meiosis. Individuals with mutations in key recombination genes, such as BRCA2 (also known as FANCD1), or the RAD51 paralogues RAD51B, RAD51C (also known as FANCO), RAD51D, XRCC2 (also known as FANCU) and XRCC3, are predisposed to breast, ovarian and prostate cancers1-10 and the cancer-prone syndrome Fanconi anaemia11-13. The BRCA2 tumour suppressor protein-the product of BRCA2-is well characterized, but the cellular functions of the RAD51 paralogues remain unclear. Genetic knockouts display growth defects, reduced RAD51 focus formation, spontaneous chromosome abnormalities, sensitivity to PARP inhibitors and replication fork defects14,15, but the precise molecular roles of RAD51 paralogues in fork stability, DNA repair and cancer avoidance remain unknown. Here we used cryo-electron microscopy, AlphaFold2 modelling and structural proteomics to determine the structure of the RAD51B-RAD51C-RAD51D-XRCC2 complex (BCDX2), revealing that RAD51C-RAD51D-XRCC2 mimics three RAD51 protomers aligned within a nucleoprotein filament, whereas RAD51B is highly dynamic. Biochemical and single-molecule analyses showed that BCDX2 stimulates the nucleation and extension of RAD51 filaments-which are essential for recombinational DNA repair-in reactions that depend on the coupled ATPase activities of RAD51B and RAD51C. Our studies demonstrate that BCDX2 orchestrates RAD51 assembly on single stranded DNA for replication fork protection and double strand break repair, in reactions that are critical for tumour avoidance.


Subject(s)
Cryoelectron Microscopy , DNA-Binding Proteins , Multiprotein Complexes , Rad51 Recombinase , Tumor Suppressor Proteins , Humans , DNA Repair , DNA Replication , DNA-Binding Proteins/chemistry , DNA-Binding Proteins/metabolism , DNA-Binding Proteins/ultrastructure , Homologous Recombination , Rad51 Recombinase/chemistry , Rad51 Recombinase/metabolism , Rad51 Recombinase/ultrastructure , Tumor Suppressor Proteins/chemistry , Tumor Suppressor Proteins/metabolism , Tumor Suppressor Proteins/ultrastructure , Poly(ADP-ribose) Polymerase Inhibitors , Neoplasms/genetics , Neoplasms/prevention & control , Proteomics , Computer Simulation , Multiprotein Complexes/chemistry , Multiprotein Complexes/metabolism , Multiprotein Complexes/ultrastructure , DNA Breaks, Double-Stranded
4.
Biophys Chem ; 300: 107070, 2023 09.
Article in English | MEDLINE | ID: mdl-37339533

ABSTRACT

The BRCA1-BARD1 complex is a crucial tumor suppressor E3 ubiquitin ligase involved in DNA double-stranded break repair. The BRCA1-BARD1 RING domains interact with UBE2D3 through the BRCA1 interface and this complex flexibly tether to the nucleosome core particle (NCP), where BRCA1 and BARD1 interacts with histone H2A and H2B of NCP. Mutations in the BRCA1-BARD1 RING domains have been linked to familial breast and ovarian cancer. Seven mutations were analyzed to understand their effect on the binding interface of protein partners and changes in conformational dynamics. Molecular dynamics simulations revealed that mutant complexes were less conformationally flexible than the wildtype complex. Protein-protein interaction profiling showed the importance of specific molecular interactions, hotspot and hub residues, and some of these were lost in the mutant complexes. Two mutations (BRCA1L51W-K65R and BARD1C53W) hindered significant interaction between protein partners and may prevent signaling for ubiquitination of histones in NCP and other cellular targets. The structural compactness and reduced significant interaction in mutant complexes may be the possible reason of preventing ubiquitination and hinder DNA repair, resulting cancer.


Subject(s)
Nucleosomes , Tumor Suppressor Proteins , Tumor Suppressor Proteins/genetics , Tumor Suppressor Proteins/chemistry , Tumor Suppressor Proteins/metabolism , Ubiquitin/genetics , Ubiquitination , Ubiquitin-Protein Ligases/genetics , Ubiquitin-Protein Ligases/chemistry , Ubiquitin-Protein Ligases/metabolism , Histones/genetics
5.
Biochemistry ; 62(11): 1631-1642, 2023 06 06.
Article in English | MEDLINE | ID: mdl-37167199

ABSTRACT

An increase in phosphorylation of the Tau protein is associated with Alzheimer's disease (AD) progression through unclear molecular mechanisms. In general, phosphorylation modifies the interaction of intrinsically disordered proteins, such as Tau, with other proteins; however, elucidating the structural basis of this regulation mechanism remains challenging. The bridging integrator-1 gene is an AD genetic determinant whose gene product, BIN1, directly interacts with Tau. The proline-rich motif recognized within a Tau(210-240) peptide by the SH3 domain of BIN1 (BIN1 SH3) is defined as 216PTPP219, and this interaction is modulated by phosphorylation. Phosphorylation of T217 within the Tau(210-240) peptide led to a 6-fold reduction in the affinity, while single phosphorylation at either T212, T231, or S235 had no effect on the interaction. Nonetheless, combined phosphorylation of T231 and S235 led to a 3-fold reduction in the affinity, although these phosphorylations are not within the BIN1 SH3-bound region of the Tau peptide. Using nuclear magnetic resonance (NMR) spectroscopy, these phosphorylations were shown to affect the local secondary structure and dynamics of the Tau(210-240) peptide. Models of the (un)phosphorylated peptides were obtained from molecular dynamics (MD) simulation validated by experimental data and showed compaction of the phosphorylated peptide due to increased salt bridge formation. This dynamic folding might indirectly impact the BIN1 SH3 binding by a decreased accessibility of the binding site. Regulation of the binding might thus not only be due to local electrostatic or steric effects from phosphorylation but also to the modification of the conformational properties of Tau.


Subject(s)
Alzheimer Disease , tau Proteins , Humans , tau Proteins/metabolism , Phosphorylation , src Homology Domains , Protein Binding , Alzheimer Disease/metabolism , Peptides/chemistry , Binding Sites , Proline/metabolism , Nuclear Proteins/metabolism , Tumor Suppressor Proteins/chemistry , Adaptor Proteins, Signal Transducing/metabolism
6.
Biomol NMR Assign ; 17(1): 151-157, 2023 06.
Article in English | MEDLINE | ID: mdl-37155029

ABSTRACT

SASH1 is a scaffold protein with context-dependent biological functions in cell adhesion, tumor metastasis, lung development, and pigmentation. As a member of the SLy protein family, it contains the conserved SLY, SH3, and SAM domains. The 19 kDa SLY domain harbors over 70% of the SASH1 variants associated with pigmentation disorders. However, its solution structure or dynamics have not been investigated yet, and its exact position in the sequence is not clearly defined. Based on the bioinformatic and experimental evidence, we propose renaming this region to the SLy Proteins Associated Disordered Region (SPIDER) and defining the exact position to be amino acids 400-554 of SASH1. We have previously identified a variant in this region linked to a pigmentation disorder, S519N. Here, we used a novel deuteration technique, a suite of TROSY-based 3D NMR experiments, and a high-quality HNN to obtain near complete solution backbone assignment of SASH1's SPIDER. A comparison with the chemical shifts of non-variant (S519) SPIDER shows that the S519N substitution does not alter the free form solution structural propensities of SPIDER. This assignment is the first step to characterize the role of SPIDER in SASH1-mediated cellular functions and provides a model for the future study of sister SPIDER domains in the SLy protein family.


Subject(s)
Tumor Suppressor Proteins , Cell Line, Tumor , Cell Movement , Magnetic Resonance Spectroscopy , Nuclear Magnetic Resonance, Biomolecular , Tumor Suppressor Proteins/chemistry , Tumor Suppressor Proteins/metabolism
7.
Nat Commun ; 14(1): 891, 2023 02 16.
Article in English | MEDLINE | ID: mdl-36797229

ABSTRACT

The atypical cadherins Fat and Dachsous are key regulators of cell growth and animal development. In contrast to classical cadherins, which form homophilic interactions to segregate cells, Fat and Dachsous cadherins form heterophilic interactions to induce cell polarity within tissues. Here, we determine the co-crystal structure of the human homologs Fat4 and Dachsous1 (Dchs1) to establish the molecular basis for Fat-Dachsous interactions. The binding domains of Fat4 and Dchs1 form an extended interface along extracellular cadherin (EC) domains 1-4 of each protein. Biophysical measurements indicate that Fat4-Dchs1 affinity is among the highest reported for cadherin superfamily members, which is attributed to an extensive network of salt bridges not present in structurally similar protocadherin homodimers. Furthermore, modeling suggests that unusual extracellular phosphorylation modifications directly modulate Fat-Dachsous binding by introducing charged contacts across the interface. Collectively, our analyses reveal how the molecular architecture of Fat4-Dchs1 enables them to form long-range, high-affinity interactions to maintain planar cell polarity.


Subject(s)
Cadherins , Cell Polarity , Tumor Suppressor Proteins , Humans , Cadherins/chemistry , Tumor Suppressor Proteins/chemistry , Cadherin Related Proteins/chemistry
8.
J Biomol Struct Dyn ; 41(22): 12734-12752, 2023.
Article in English | MEDLINE | ID: mdl-36775657

ABSTRACT

The N-terminal RING-RING domain of BRCA1-BARD1 is an E3 ubiquitin ligase complex that plays a critical role in tumor suppression through DNA double stranded repair mechanism. Mutations in the BRCA1-BARD1 heterodimer RING domains were found to have an association with breast and ovarian cancer by a way of hampering the E3 ubiquitin ligase activity. Herein, the molecular mechanism of interaction, conformational change due to the specific mutations on the BRCA1-BARD1 complex at atomic level has been examined by employing molecular modeling techniques. Sixteen mutations have been selected for the study. Molecular dynamics simulation results reveal that the mutant complexes have more local perturbation with a high residual fluctuation in the zinc binding sites and central helix. A few of the BRCA1 (V11A, I21V, I42V, R71G, I31M and L51W) mutants have been experimentally identified that do not impair E3 ligase activity, display an enhanced number of H-bonds and non-bonded contacts at the interacting interface as revealed by MD simulation. The mutation of BRCA1 (C61G, C64Y, C39Y and C24R) and BARD1 (C53W, C71Y and C83R) zinc binding residues displayed a smaller number of significant H-bonds, other interactions and also loss of some of the hotspot residues. Additionally, most of the mutant complexes display relatively lower electrostatic energy, H-bonding and total stabilizing energy as compared to wild-type. The current study attempts to unravel the role of BRCA1-BARD1 mutations and delineates the structural and conformational dynamics in the progression of breast cancer.Communicated by Ramaswamy H. Sarma.


Subject(s)
Breast Neoplasms , Humans , Female , Breast Neoplasms/genetics , Breast Neoplasms/metabolism , Tumor Suppressor Proteins/chemistry , Ubiquitin-Protein Ligases/genetics , Ubiquitin-Protein Ligases/chemistry , Ubiquitin-Protein Ligases/metabolism , Molecular Dynamics Simulation , BRCA1 Protein/genetics , BRCA1 Protein/chemistry , Mutation , Zinc
9.
J Mol Biol ; 434(14): 167662, 2022 07 30.
Article in English | MEDLINE | ID: mdl-35640718

ABSTRACT

Degradation of cytoplasmic mRNA in eukaryotes involves the shortening and removal of the mRNA poly(A) tail by poly(A)-selective ribonuclease (deadenylase) enzymes. In human cells, BTG2 can stimulate deadenylation of poly(A) bound by cytoplasmic poly(A)-binding protein PABPC1. This involves the concurrent binding by BTG2 of PABPC1 and the Caf1/CNOT7 nuclease subunit of the Ccr4-Not deadenylase complex. To understand in molecular detail how PABPC1 and BTG2 interact, we set out to identify amino acid residues of PABPC1 and BTG2 contributing to the interaction. To this end, we first used algorithms to predict PABPC1 interaction surfaces. Comparison of the predicted interaction surface with known residues involved in the binding to poly(A) resulted in the identification of a putative interaction surface for BTG2. Subsequently, we used pulldown assays to confirm the requirement of PABPC1 residues for the interaction with BTG2. Analysis of RNA-binding by PABPC1 variants indicated that PABPC1 residues required for interaction with BTG2 do not interfere with poly(A) binding. After further defining residues of BTG2 that are required for the interaction with PABPC1, we used information from published NMR chemical shift perturbation experiments to guide docking and generate a structural model of the BTG2-PABPC1 complex. A quaternary poly(A)-PABPC1-BTG2-Caf1/CNOT7 model showed that the 3' end of poly(A) RNA is directed towards the catalytic centre of Caf1/CNOT7, thereby providing a rationale for enhanced deadenylation by Caf1/CNOT7 in the presence of BTG2 and PABPC1.


Subject(s)
Immediate-Early Proteins , Poly(A)-Binding Proteins , Tumor Suppressor Proteins , Humans , Immediate-Early Proteins/chemistry , Immediate-Early Proteins/genetics , Models, Structural , Molecular Docking Simulation , Mutagenesis , Poly A/chemistry , Poly A/metabolism , Poly(A)-Binding Proteins/chemistry , Poly(A)-Binding Proteins/genetics , Protein Conformation , RNA, Messenger/chemistry , RNA, Messenger/metabolism , Tumor Suppressor Proteins/chemistry , Tumor Suppressor Proteins/genetics
10.
J Mol Biol ; 434(9): 167553, 2022 05 15.
Article in English | MEDLINE | ID: mdl-35317997

ABSTRACT

BRAC1 associated protein-1 (BAP1) is a major tumor suppressor involved in many cancers. The deubiquitinase (DUB) activity of BAP1 is essential for its nuclear localization, histone remodeling and proteostasis associated with mitochondrial calcium flux. Loss of the DUB activity due to catalytic mutations within the ubiquitin C-terminal hydrolase (UCH) domain of BAP1 (BAP1-UCH) directly contributes to oncogenesis. Nevertheless, it is non-trivial to rationalize how the other high-frequency but non-catalytic mutations within the BAP1-UCH lead to malignancies. Here we used multiplex spectroscopic, thermodynamic and biophysical analyses to investigate the impacts of eleven high-occurrence mutations within BAP1-UCH on the structure, folding and function. Several mutations significantly destabilize BAP1-UCH and increase its aggregation propensity. Hydrogen-deuterium exchange mass spectrometry data revealed allosteric destabilizations caused by mutations distant from the catalytic site. Our findings gave a comprehensive and multiscale account of the molecular basis of how these non-catalytic mutations within BAP1-UCH may be implicated in oncogenesis.


Subject(s)
Carcinogenesis , Tumor Suppressor Proteins , Ubiquitin Thiolesterase , Carcinogenesis/genetics , Humans , Mutation , Protein Domains , Structure-Activity Relationship , Tumor Suppressor Proteins/chemistry , Tumor Suppressor Proteins/genetics , Tumor Suppressor Proteins/metabolism , Ubiquitin Thiolesterase/chemistry , Ubiquitin Thiolesterase/genetics , Ubiquitin Thiolesterase/metabolism
11.
Biochem Biophys Res Commun ; 599: 57-62, 2022 04 09.
Article in English | MEDLINE | ID: mdl-35176625

ABSTRACT

Deubiquitinating enzymes (DUBs) form a large protease family involved in a myriad of biological and pathological processes, including ROS sensors. ROS-mediated inhibition of their DUB activities is critical for fine-tuning the stress-activated signaling pathways. Here, we demonstrate that the ubiquitin C-terminal hydrolase (UCH) domain of BAP1 (BAP1-UCH) is highly sensitive to moderate oxidative stress. Oxidation of the catalytic C91 significantly destabilizes BAP1-UCH and increases the population of partially unfolded form, which is prone to aggregation. Unlike other DUBs, the oxidation-induced structural and functional loss of BAP1-UCH cannot be fully reversed by reducing agents. The oligomerization of oxidized BAP1-UCH is attributed to inter-molecular disulfide bond formation. Hydrogen-deuterium mass exchange spectrometry (HDX-MS) reveals increased fluctuations of the central ß-sheet upon oxidation. Our findings suggest that oxidation-mediated functional loss and increased aggregation propensity may contribute to oncogenesis associated with BAP1.


Subject(s)
Cysteine/metabolism , Tumor Suppressor Proteins/chemistry , Tumor Suppressor Proteins/metabolism , Ubiquitin Thiolesterase/chemistry , Ubiquitin Thiolesterase/metabolism , Carcinogenesis , Circular Dichroism , Disulfides/chemistry , Humans , Hydrogen Deuterium Exchange-Mass Spectrometry , Hydrogen Peroxide/chemistry , Oxidation-Reduction , Oxidative Stress , Protein Aggregation, Pathological/metabolism , Protein Domains , Protein Folding , Spectrometry, Fluorescence , Tumor Suppressor Proteins/genetics , Ubiquitin Thiolesterase/genetics
12.
eNeuro ; 9(2)2022.
Article in English | MEDLINE | ID: mdl-35165201

ABSTRACT

Genetic mutations in nitrogen permease regulator-like 2 (NPRL2) are associated with a wide spectrum of familial focal epilepsies, autism, and sudden unexpected death of epileptics (SUDEP), but the mechanisms by which NPRL2 contributes to these effects are not well known. NPRL2 is a requisite subunit of the GAP activity toward Rags 1 (GATOR1) complex, which functions as a negative regulator of mammalian target of rapamycin complex 1 (mTORC1) kinase when intracellular amino acids are low. Here, we show that loss of NPRL2 expression in mouse excitatory glutamatergic neurons causes seizures before death, consistent with SUDEP in humans with epilepsy. Additionally, the absence of NPRL2 expression increases mTORC1-dependent signal transduction and significantly alters amino acid homeostasis in the brain. Loss of NPRL2 reduces dendritic branching and increases the strength of electrically stimulated action potentials (APs) in neurons. The increased AP strength is consistent with elevated expression of epilepsy-linked, voltage-gated sodium channels in the NPRL2-deficient brain. Targeted deletion of NPRL2 in primary neurons increases the expression of sodium channel Scn1A, whereas treatment with the pharmacological mTORC1 inhibitor called rapamycin prevents Scn1A upregulation. These studies demonstrate a novel role of NPRL2 and mTORC1 signaling in the regulation of sodium channels, which can contribute to seizures and early lethality.


Subject(s)
Membrane Transport Proteins , Tumor Suppressor Proteins , Amino Acids , Animals , Brain/metabolism , Homeostasis , Mammals/metabolism , Mechanistic Target of Rapamycin Complex 1/metabolism , Membrane Transport Proteins/metabolism , Mice , NAV1.1 Voltage-Gated Sodium Channel/metabolism , Nitrogen/metabolism , Sodium Channels/metabolism , Tumor Suppressor Proteins/chemistry , Tumor Suppressor Proteins/genetics , Tumor Suppressor Proteins/metabolism
13.
Biochim Biophys Acta Gen Subj ; 1866(5): 130099, 2022 05.
Article in English | MEDLINE | ID: mdl-35134491

ABSTRACT

OLA1 is a P-loop ATPase, implicated in centrosome duplication through the interactions with tumor suppressors BRCA1 and BARD1. Disruption of the interaction of OLA1 with BARD1 results in centrosome amplification. However, the molecular interplay and mechanism of the OLA1-BARD1 complex remain elusive. Here, we use a battery of biophysical, biochemical, and structural analyses to elucidate the molecular basis of the OLA1-BARD1 interaction. Our structural and enzyme kinetics analyses show this nucleotide-dependent interaction enhances the ATPase activity of OLA1 by increasing the turnover number (kcat). Unlike canonical GTPase activating proteins that act directly on the catalytic G domain, the BARD1 BRCT domain binds to the OLA1 TGS domain via a highly conserved BUDR motif. A cancer related mutation V695L on BARD1 is known to associate with centrosome abnormality. The V695L mutation reduces the BARD1 BRCT-mediated activation of OLA1. Crystallographic snapshot of the BRCT V695L mutant at 1.88 Å reveals this mutation perturbs the OLA1 binding site, resulting in reduced interaction. Altogether, our findings suggest the BARD1 BRCT domain serves as an ATPase activating protein to control OLA1 allosterically.


Subject(s)
Adenosine Triphosphatases , Tumor Suppressor Proteins , Adenosine Triphosphatases/metabolism , Cell Cycle , Centrosome/metabolism , Tumor Suppressor Proteins/chemistry , Ubiquitin-Protein Ligases/metabolism
14.
Proc Natl Acad Sci U S A ; 119(4)2022 01 25.
Article in English | MEDLINE | ID: mdl-35046037

ABSTRACT

SAMD9 and SAMD9L (SAMD9/9L) are antiviral factors and tumor suppressors, playing a critical role in innate immune defense against poxviruses and the development of myeloid tumors. SAMD9/9L mutations with a gain-of-function (GoF) in inhibiting cell growth cause multisystem developmental disorders including many pediatric myelodysplastic syndromes. Predicted to be multidomain proteins with an architecture like that of the NOD-like receptors, SAMD9/9L molecular functions and domain structures are largely unknown. Here, we identified a SAMD9/9L effector domain that functions by binding to double-stranded nucleic acids (dsNA) and determined the crystal structure of the domain in complex with DNA. Aided with precise mutations that differentially perturb dsNA binding, we demonstrated that the antiviral and antiproliferative functions of the wild-type and GoF SAMD9/9L variants rely on dsNA binding by the effector domain. Furthermore, we showed that GoF variants inhibit global protein synthesis, reduce translation elongation, and induce proteotoxic stress response, which all require dsNA binding by the effector domain. The identification of the structure and function of a SAMD9/9L effector domain provides a therapeutic target for SAMD9/9L-associated human diseases.


Subject(s)
Intracellular Signaling Peptides and Proteins/chemistry , Models, Molecular , Protein Conformation , Protein Interaction Domains and Motifs , Tumor Suppressor Proteins/chemistry , Binding Sites , DNA-Binding Proteins/chemistry , DNA-Binding Proteins/metabolism , Humans , Intracellular Signaling Peptides and Proteins/metabolism , Mutation , Protein Binding , Stress, Physiological , Structure-Activity Relationship , Tumor Suppressor Proteins/metabolism
15.
Int J Mol Sci ; 23(2)2022 Jan 17.
Article in English | MEDLINE | ID: mdl-35055180

ABSTRACT

Pyridine Nucleotide-Disulfide Oxidoreductase Domain 2 (PYROXD2; previously called YueF) is a mitochondrial inner membrane/matrix-residing protein and is reported to regulate mitochondrial function. The clinical importance of PYROXD2 has been unclear, and little is known of the protein's precise biological function. In the present paper, we report biallelic variants in PYROXD2 identified by genome sequencing in a patient with suspected mitochondrial disease. The child presented with acute neurological deterioration, unresponsive episodes, and extreme metabolic acidosis, and received rapid genomic testing. He died shortly after. Magnetic resonance imaging (MRI) brain imaging showed changes resembling Leigh syndrome, one of the more common childhood mitochondrial neurological diseases. Functional studies in patient fibroblasts showed a heightened sensitivity to mitochondrial metabolic stress and increased mitochondrial superoxide levels. Quantitative proteomic analysis demonstrated decreased levels of subunits of the mitochondrial respiratory chain complex I, and both the small and large subunits of the mitochondrial ribosome, suggesting a mitoribosomal defect. Our findings support the critical role of PYROXD2 in human cells, and suggest that the biallelic PYROXD2 variants are associated with mitochondrial dysfunction, and can plausibly explain the child's clinical presentation.


Subject(s)
Leigh Disease/diagnostic imaging , Mutation, Missense , Tumor Suppressor Proteins/genetics , Fatal Outcome , Humans , Infant , Leigh Disease/genetics , Magnetic Resonance Imaging , Male , Mitochondrial Proteins/metabolism , Models, Molecular , Proteomics , Sequence Analysis, RNA , Tumor Suppressor Proteins/chemistry , Whole Genome Sequencing
16.
J Hum Genet ; 67(2): 79-85, 2022 Feb.
Article in English | MEDLINE | ID: mdl-34376795

ABSTRACT

NPRL2 (nitrogen permease regulator like 2) is a component of the GATOR1(GAP activity towards rags complex 1) proteins, which is an inhibitor of the amino acid-sensing branch of the mTORC1 pathway. GATOR1 complex variations were reported to correlate with familial focal epilepsy with variable foci (FFEVF). However, FFEVF caused by NPRL2 variants has not been widely explored. Here, we describe a variant, 339+2T>C, in NPRL2 identified by trio whole-exome sequencing (WES) in a family. This splicing variant that occurred at the 5' end of exon 3 was confirmed by minigene assays, which affected alternative splicing and led to exon 3 skipping in NPRL2. Our cases presented multiple seizure types (febrile seizures, infantile spasms, focal seizures, or focal to generalized tonic-clonic seizures). Electroencephalogram (EEG) showed frequent discharges in the left frontal and central regions. A favorable prognosis was achieved in response to vitamin B6 and topiramate when the patient was seven months old. Our study expands the phenotype and genotype spectrum of FFEVF and provides solid diagnostic evidence for FFEVF.


Subject(s)
Epilepsies, Partial/genetics , Mutation , RNA Splicing , Tumor Suppressor Proteins/genetics , Amino Acid Sequence , Base Sequence , Electroencephalography/methods , Epilepsies, Partial/diagnosis , Epilepsies, Partial/physiopathology , Family Health , Female , HEK293 Cells , HeLa Cells , Humans , Infant , Male , Pedigree , Protein Conformation , Sequence Homology, Amino Acid , Tumor Suppressor Proteins/chemistry , Tumor Suppressor Proteins/metabolism , Exome Sequencing/methods
17.
Molecules ; 26(24)2021 Dec 14.
Article in English | MEDLINE | ID: mdl-34946663

ABSTRACT

Zinc finger proteins play pivotal roles in health and disease and exert critical functions in various cellular processes. A majority of zinc finger proteins bind DNA and act as transcription factors. B-cell lymphoma/leukemia 11B (BCL11B) represents one member of the large family of zinc finger proteins. The N-terminal domain of BCL11B was shown to be crucial for BCL11B to exert its proper function by homodimerization. Here, we describe an easy and fast preparation protocol to yield the fluorescently tagged protein of the recombinant N-terminal BCL11B zinc finger domain (BCL11B42-94) for in vitro studies. First, we expressed fluorescently tagged BCL11B42-94 in E. coli and described the subsequent purification utilizing immobilized metal ion affinity chromatography to achieve very high yields of a purified fusion protein of 200 mg/L culture. We proceeded with characterizing the atypical zinc finger domain using circular dichroism and size exclusion chromatography. Validation of the functional fluorescent pair CyPet-/EYFP-BCL11B42-94 was achieved with Förster resonance energy transfer. Our protocol can be utilized to study other zinc finger domains to expand the knowledge in this field.


Subject(s)
Escherichia coli/metabolism , Gene Expression , Green Fluorescent Proteins , Recombinant Fusion Proteins , Repressor Proteins , Tumor Suppressor Proteins , Escherichia coli/genetics , Green Fluorescent Proteins/biosynthesis , Green Fluorescent Proteins/chemistry , Green Fluorescent Proteins/genetics , Green Fluorescent Proteins/isolation & purification , Humans , Protein Domains , Recombinant Fusion Proteins/biosynthesis , Recombinant Fusion Proteins/chemistry , Recombinant Fusion Proteins/genetics , Recombinant Fusion Proteins/isolation & purification , Repressor Proteins/biosynthesis , Repressor Proteins/chemistry , Repressor Proteins/genetics , Repressor Proteins/isolation & purification , Tumor Suppressor Proteins/biosynthesis , Tumor Suppressor Proteins/chemistry , Tumor Suppressor Proteins/genetics , Tumor Suppressor Proteins/isolation & purification , Zinc Fingers
18.
Genes (Basel) ; 12(11)2021 10 28.
Article in English | MEDLINE | ID: mdl-34828321

ABSTRACT

Tumor mutational burden (TMB) is considered a potential biomarker for predicting the response and effect of immune checkpoint inhibitors (ICIs). To find specific gene mutations related to TMB and the prognosis of patients, the frequently mutated genes in gastric cancer patients from TCGA and ICGC were obtained and the correlation between gene mutation, TMB, and prognosis was analyzed. Furthermore, to clarify whether specific gene mutations can be used as predictive biomarkers of ICIs, a gene set enrichment analysis (GSEA) for immune pathways and an immune infiltration analysis were conducted. The results showed that CUB and Sushi multiple domains 1 (CSMD1) mutation (CSMD1-mut) were associated with higher TMB and better prognosis in patients. The genetic map showed that, compared with wild-type samples, the loss of chromosomes 4q, 5q, 8p, and 9p decreased and the status of microsatellite instability increased in the CSMD1-mut samples. The GSEA analysis showed that immune-related pathways were enriched in the CSMD1-mut samples. The immune infiltration analysis showed that the anti-tumor immune cells were upregulated and that the tumor-promoting immune cells were downregulated in the CSMD1-mut samples. The gene co-expression analysis showed that PD-L1 expression was higher in the CSMD1-mut samples. In summary, CSMD1-mut in gastric cancer was associated with increased TMB and favorable survival and may have potential significance in predicting the efficacy of anti-PD-L1.


Subject(s)
B7-H1 Antigen/genetics , Chromosome Deletion , Computational Biology/methods , Membrane Proteins/genetics , Microsatellite Instability , Mutation , Stomach Neoplasms/genetics , Tumor Suppressor Proteins/genetics , Biomarkers, Tumor/genetics , Databases, Genetic , Gene Expression Regulation, Neoplastic , Humans , Immune Checkpoint Inhibitors/pharmacology , Immune Checkpoint Inhibitors/therapeutic use , Membrane Proteins/chemistry , Prognosis , Protein Domains , Stomach Neoplasms/drug therapy , Survival Analysis , Tumor Suppressor Proteins/chemistry
19.
Proc Natl Acad Sci U S A ; 118(48)2021 11 30.
Article in English | MEDLINE | ID: mdl-34815344

ABSTRACT

Carriers of heterozygous germline BAP1 mutations (BAP1+/-) are affected by the "BAP1 cancer syndrome." Although they can develop almost any cancer type, they are unusually susceptible to asbestos carcinogenesis and mesothelioma. Here we investigate why among all carcinogens, BAP1 mutations cooperate with asbestos. Asbestos carcinogenesis and mesothelioma have been linked to a chronic inflammatory process promoted by the extracellular release of the high-mobility group box 1 protein (HMGB1). We report that BAP1+/- cells secrete increased amounts of HMGB1, and that BAP1+/- carriers have detectable serum levels of acetylated HMGB1 that further increase when they develop mesothelioma. We linked these findings to our discovery that BAP1 forms a trimeric protein complex with HMGB1 and with histone deacetylase 1 (HDAC1) that modulates HMGB1 acetylation and its release. Reduced BAP1 levels caused increased ubiquitylation and degradation of HDAC1, leading to increased acetylation of HMGB1 and its active secretion that in turn promoted mesothelial cell transformation.


Subject(s)
Asbestos , HMGB1 Protein/chemistry , Histone Deacetylase 1/chemistry , Tumor Suppressor Proteins/chemistry , Ubiquitin Thiolesterase/chemistry , Animals , Biomarkers, Tumor/metabolism , Carcinogenesis , Cell Nucleus/metabolism , Female , Gene-Environment Interaction , Germ-Line Mutation , HMGB1 Protein/genetics , Heterozygote , Histone Deacetylase 1/genetics , Incidence , Inflammation , Male , Mesothelioma/metabolism , Mice , Mutation , Prognosis , Protein Binding , Tumor Suppressor Proteins/metabolism , Ubiquitin/chemistry , Ubiquitin Thiolesterase/metabolism
20.
Nat Commun ; 12(1): 6653, 2021 11 17.
Article in English | MEDLINE | ID: mdl-34789768

ABSTRACT

BRCA1-BARD1 heterodimers act in multiple steps during homologous recombination (HR) to ensure the prompt repair of DNA double strand breaks. Dysfunction of the BRCA1 pathway enhances the therapeutic efficiency of poly-(ADP-ribose) polymerase inhibitors (PARPi) in cancers, but the molecular mechanisms underlying this sensitization to PARPi are not fully understood. Here, we show that cancer cell sensitivity to PARPi is promoted by the ring between ring fingers (RBR) protein RNF19A. We demonstrate that RNF19A suppresses HR by ubiquitinating BARD1, which leads to dissociation of BRCA1-BARD1 complex and exposure of a nuclear export sequence in BARD1 that is otherwise masked by BRCA1, resulting in the export of BARD1 to the cytoplasm. We provide evidence that high RNF19A expression in breast cancer compromises HR and increases sensitivity to PARPi. We propose that RNF19A modulates the cancer cell response to PARPi by negatively regulating the BRCA1-BARD1 complex and inhibiting HR-mediated DNA repair.


Subject(s)
BRCA1 Protein/metabolism , Homologous Recombination , Tumor Suppressor Proteins/metabolism , Ubiquitin-Protein Ligases/metabolism , Ubiquitination , BRCA1 Protein/chemistry , Breast Neoplasms/drug therapy , Breast Neoplasms/genetics , Breast Neoplasms/metabolism , Carcinogenesis , DNA Damage , Female , Humans , Poly(ADP-ribose) Polymerase Inhibitors/pharmacology , Poly(ADP-ribose) Polymerase Inhibitors/therapeutic use , Protein Binding , Protein Multimerization , RING Finger Domains , Tumor Suppressor Proteins/chemistry , Ubiquitin-Protein Ligases/chemistry
SELECTION OF CITATIONS
SEARCH DETAIL
...