Small Glutamine-Rich Tetratricopeptide Repeat
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Nucleocytoplasmic Shuttling of the Glucocorticoid Receptor Is Influenced by Tetratricopeptide Repeat-Containing Proteins Gisela I
© 2020. Published by The Company of Biologists Ltd | Journal of Cell Science (2020) 133, jcs238873. doi:10.1242/jcs.238873 RESEARCH ARTICLE Nucleocytoplasmic shuttling of the glucocorticoid receptor is influenced by tetratricopeptide repeat-containing proteins Gisela I. Mazaira1,*, Pablo C. Echeverria2,* and Mario D. Galigniana1,3,‡ ABSTRACT FKBP52 (also known as FKBP4), FKBP51 (FKBP5) and CyP40 It has been demonstrated that tetratricopeptide-repeat (TPR) domain (PPID), and the immunophilin-like proteins PP5, FKBPL (WISp39) proteins regulate the subcellular localization of glucocorticoid receptor and FKBP37 (ARA9/XAP2/AIP) are counted among the best (GR). This study analyses the influence of the TPR domain of high characterized members of the TPR domain family of proteins molecular weight immunophilins in the retrograde transport and associated with nuclear receptor family members via Hsp90 (Pratt nuclear retention of GR. Overexpression of the TPR peptide et al., 2004a; Storer et al., 2011). TPR domains are composed of prevented efficient nuclear accumulation of the GR by disrupting the loosely conserved 34 amino acid sequence motifs that are found in formation of complexes with the dynein-associated immunophilin arrays comprising between 2 and 20 repeats, wherein the repeats pack FKBP52 (also known as FKBP4), the adaptor transporter importin-β1 against each other giving rise to coiled and superhelical structures (KPNB1), the nuclear pore-associated glycoprotein Nup62 and nuclear (Perez-Riba and Itzhaki, 2019). Originally identified in components of matrix-associated structures. We also show that nuclear import of GR the anaphase-promoting complex (Sikorski et al., 1991), TPR was impaired, whereas GR nuclear export was enhanced. domains are now known to mediate specific protein interactions in Interestingly, the CRM1 (exportin-1) inhibitor leptomycin-B abolished numerous cellular contexts. -
A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus
Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated. -
4-6 Weeks Old Female C57BL/6 Mice Obtained from Jackson Labs Were Used for Cell Isolation
Methods Mice: 4-6 weeks old female C57BL/6 mice obtained from Jackson labs were used for cell isolation. Female Foxp3-IRES-GFP reporter mice (1), backcrossed to B6/C57 background for 10 generations, were used for the isolation of naïve CD4 and naïve CD8 cells for the RNAseq experiments. The mice were housed in pathogen-free animal facility in the La Jolla Institute for Allergy and Immunology and were used according to protocols approved by the Institutional Animal Care and use Committee. Preparation of cells: Subsets of thymocytes were isolated by cell sorting as previously described (2), after cell surface staining using CD4 (GK1.5), CD8 (53-6.7), CD3ε (145- 2C11), CD24 (M1/69) (all from Biolegend). DP cells: CD4+CD8 int/hi; CD4 SP cells: CD4CD3 hi, CD24 int/lo; CD8 SP cells: CD8 int/hi CD4 CD3 hi, CD24 int/lo (Fig S2). Peripheral subsets were isolated after pooling spleen and lymph nodes. T cells were enriched by negative isolation using Dynabeads (Dynabeads untouched mouse T cells, 11413D, Invitrogen). After surface staining for CD4 (GK1.5), CD8 (53-6.7), CD62L (MEL-14), CD25 (PC61) and CD44 (IM7), naïve CD4+CD62L hiCD25-CD44lo and naïve CD8+CD62L hiCD25-CD44lo were obtained by sorting (BD FACS Aria). Additionally, for the RNAseq experiments, CD4 and CD8 naïve cells were isolated by sorting T cells from the Foxp3- IRES-GFP mice: CD4+CD62LhiCD25–CD44lo GFP(FOXP3)– and CD8+CD62LhiCD25– CD44lo GFP(FOXP3)– (antibodies were from Biolegend). In some cases, naïve CD4 cells were cultured in vitro under Th1 or Th2 polarizing conditions (3, 4). -
Loss of Postnatal Quiescence of Neural Stem Cells Through Mtor Activation Upon Genetic Removal of Cysteine String Protein-Α
Loss of postnatal quiescence of neural stem cells through mTOR activation upon genetic removal of cysteine string protein-α Jose L. Nieto-Gonzáleza,b,c,1,2, Leonardo Gómez-Sáncheza,b,c,1, Fabiola Mavillarda,b,c, Pedro Linares-Clementea,b,c, María C. Riveroa,b,c, Marina Valenzuela-Villatoroa,b,c, José L. Muñoz-Bravoa,b,c, Ricardo Pardala,b,c, and Rafael Fernández-Chacóna,b,c,2 aInstituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/Consejo Superior de Investigaciones Científicas/Universidad de Sevilla, 41013 Sevilla, Spain; bDepartamento de Fisiología Médica y Biofísica, Universidad de Sevilla, 41009 Sevilla, Spain; and cCentro Investigación Biomédica en Red Enfermedades Neurodegenerativas, 41013 Sevilla, Spain Edited by Thomas C. Südhof, Stanford University School of Medicine, Stanford, CA, and approved March 4, 2019 (received for review October 9, 2018) Neural stem cells continuously generate newborn neurons that protein-A (SGTA) (13). Interestingly, CSP-α is required to maintain integrate into and modify neural circuitry in the adult hippocam- the stability of the SNARE protein SNAP25 at synaptic termi- pus. The molecular mechanisms that regulate or perturb neural nals (14–16). SNAP25 cannot maintain its function without a stem cell proliferation and differentiation, however, remain poorly chaperone, which is probably due to the molecular stress induced understood. Here, we have found that mouse hippocampal radial during cycles of assembly and disassembly of the SNARE com- glia-like (RGL) neural stem cells express the synaptic cochaperone plex (15, 17). Remarkably, knockout (KO) mice lacking CSP-α cysteine string protein-α (CSP-α). Remarkably, in CSP-α knockout suffer from a devastating and early synaptic degeneration (18) mice, RGL stem cells lose quiescence postnatally and enter into a that is particularly evident in highly active neurons (19). -
Consensus Tetratricopeptide Repeat Proteins Are Complex Superhelical 2 Nanosprings
bioRxiv preprint doi: https://doi.org/10.1101/2021.03.27.437344; this version posted August 30, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Consensus tetratricopeptide repeat proteins are complex superhelical 2 nanosprings 1, ∗ 1 1 2 2 3 Marie Synakewicz, Rohan S. Eapen, Albert Perez-Riba, Daniela Bauer, Andreas Weißl, 3 3 2 1, ∗ 4, ∗ 4 Gerhard Fischer, Marko Hyv¨onen, Matthias Rief, Laura S. Itzhaki, and Johannes Stigler 1 5 Department of Pharmacology, University of Cambridge, 6 Tennis Court Road, Cambridge, CB2 1PD, United Kingdom 2 7 Physik-Department, Technische Universit¨atM¨unchen, 8 James-Franck-Straße 1, 85748 Garching, Germany 3 9 Department of Biochemistry, University of Cambridge, 10 Tennis Court Road, Cambridge, CB2 1GA, United Kingdom 4 11 Gene Center Munich, Ludwig-Maximilians-Universit¨atM¨unchen, 12 Feodor-Lynen-Straße 25, 81377 M¨unchen,Germany 13 (Dated: August 20, 2021) Abstract. Tandem-repeat proteins comprise small secondary structure motifs that stack to form one- dimensional arrays with distinctive mechanical properties that are proposed to direct their cellular functions. Here, we use single-molecule optical tweezers to study the folding of consensus-designed tetratricopeptide repeats (CTPRs) | superhelical arrays of short helix-turn-helix motifs. We find that CTPRs display a spring-like mechanical response in which individual repeats undergo rapid equilibrium fluctuations between folded and unfolded conformations. We rationalise the force response using Ising models and dissect the folding pathway of CTPRs under mechanical load, revealing how the repeat arrays form from the centre towards both termini simultaneously. -
Supplementary Table S4. FGA Co-Expressed Gene List in LUAD
Supplementary Table S4. FGA co-expressed gene list in LUAD tumors Symbol R Locus Description FGG 0.919 4q28 fibrinogen gamma chain FGL1 0.635 8p22 fibrinogen-like 1 SLC7A2 0.536 8p22 solute carrier family 7 (cationic amino acid transporter, y+ system), member 2 DUSP4 0.521 8p12-p11 dual specificity phosphatase 4 HAL 0.51 12q22-q24.1histidine ammonia-lyase PDE4D 0.499 5q12 phosphodiesterase 4D, cAMP-specific FURIN 0.497 15q26.1 furin (paired basic amino acid cleaving enzyme) CPS1 0.49 2q35 carbamoyl-phosphate synthase 1, mitochondrial TESC 0.478 12q24.22 tescalcin INHA 0.465 2q35 inhibin, alpha S100P 0.461 4p16 S100 calcium binding protein P VPS37A 0.447 8p22 vacuolar protein sorting 37 homolog A (S. cerevisiae) SLC16A14 0.447 2q36.3 solute carrier family 16, member 14 PPARGC1A 0.443 4p15.1 peroxisome proliferator-activated receptor gamma, coactivator 1 alpha SIK1 0.435 21q22.3 salt-inducible kinase 1 IRS2 0.434 13q34 insulin receptor substrate 2 RND1 0.433 12q12 Rho family GTPase 1 HGD 0.433 3q13.33 homogentisate 1,2-dioxygenase PTP4A1 0.432 6q12 protein tyrosine phosphatase type IVA, member 1 C8orf4 0.428 8p11.2 chromosome 8 open reading frame 4 DDC 0.427 7p12.2 dopa decarboxylase (aromatic L-amino acid decarboxylase) TACC2 0.427 10q26 transforming, acidic coiled-coil containing protein 2 MUC13 0.422 3q21.2 mucin 13, cell surface associated C5 0.412 9q33-q34 complement component 5 NR4A2 0.412 2q22-q23 nuclear receptor subfamily 4, group A, member 2 EYS 0.411 6q12 eyes shut homolog (Drosophila) GPX2 0.406 14q24.1 glutathione peroxidase -
Supplementary Material
BMJ Publishing Group Limited (BMJ) disclaims all liability and responsibility arising from any reliance Supplemental material placed on this supplemental material which has been supplied by the author(s) J Neurol Neurosurg Psychiatry Page 1 / 45 SUPPLEMENTARY MATERIAL Appendix A1: Neuropsychological protocol. Appendix A2: Description of the four cases at the transitional stage. Table A1: Clinical status and center proportion in each batch. Table A2: Complete output from EdgeR. Table A3: List of the putative target genes. Table A4: Complete output from DIANA-miRPath v.3. Table A5: Comparison of studies investigating miRNAs from brain samples. Figure A1: Stratified nested cross-validation. Figure A2: Expression heatmap of miRNA signature. Figure A3: Bootstrapped ROC AUC scores. Figure A4: ROC AUC scores with 100 different fold splits. Figure A5: Presymptomatic subjects probability scores. Figure A6: Heatmap of the level of enrichment in KEGG pathways. Kmetzsch V, et al. J Neurol Neurosurg Psychiatry 2021; 92:485–493. doi: 10.1136/jnnp-2020-324647 BMJ Publishing Group Limited (BMJ) disclaims all liability and responsibility arising from any reliance Supplemental material placed on this supplemental material which has been supplied by the author(s) J Neurol Neurosurg Psychiatry Appendix A1. Neuropsychological protocol The PREV-DEMALS cognitive evaluation included standardized neuropsychological tests to investigate all cognitive domains, and in particular frontal lobe functions. The scores were provided previously (Bertrand et al., 2018). Briefly, global cognitive efficiency was evaluated by means of Mini-Mental State Examination (MMSE) and Mattis Dementia Rating Scale (MDRS). Frontal executive functions were assessed with Frontal Assessment Battery (FAB), forward and backward digit spans, Trail Making Test part A and B (TMT-A and TMT-B), Wisconsin Card Sorting Test (WCST), and Symbol-Digit Modalities test. -
Augmented Expression of Ki-67 Is Correlated with Clinicopathological
Wei et al. Respiratory Research (2018) 19:150 https://doi.org/10.1186/s12931-018-0843-7 REVIEW Open Access Augmented expression of Ki-67 is correlated with clinicopathological characteristics and prognosis for lung cancer patients: an up-dated systematic review and meta-analysis with 108 studies and 14,732 patients Dan-ming Wei, Wen-jie Chen, Rong-mei Meng, Na Zhao, Xiang-yu Zhang, Dan-yu Liao and Gang Chen* Abstract Background: Lung cancer ranks as the leading cause of cancer-related deaths worldwide and we performed this meta-analysis to investigate eligible studies and determine the prognostic effect of Ki-67. Methods: In total, 108 studies in 95 articles with 14,732 patients were found to be eligible, of which 96 studies reported on overall survival (OS) and 19 studies reported on disease-free survival (DFS) with relation to Ki-67 expression in lung cancer patients. Results: The pooled hazard ratio (HR) indicated that a high Ki-67 level could be a valuable prognostic factor for lung cancer (HR = 1.122 for OS, P < 0.001 and HR = 1.894 for DFS, P < 0.001). Subsequently, the results revealed that a high Ki-67 level was significantly associated with clinical parameters of lung cancer including age (odd ratio, OR = 1.246 for older patients, P = 0.018), gender (OR = 1.874 for males, P < 0.001) and smoking status (OR = 3.087 for smokers, P < 0.001). Additionally, significant positive correlations were found between Ki-67 overexpression and poorer differentiation (OR = 1.993, P = 0.003), larger tumor size (OR = 1.436, P = 0.003), and higher pathologic stages (OR = 1.867 for III-IV, P < 0.001). -
Appendix 2. Significantly Differentially Regulated Genes in Term Compared with Second Trimester Amniotic Fluid Supernatant
Appendix 2. Significantly Differentially Regulated Genes in Term Compared With Second Trimester Amniotic Fluid Supernatant Fold Change in term vs second trimester Amniotic Affymetrix Duplicate Fluid Probe ID probes Symbol Entrez Gene Name 1019.9 217059_at D MUC7 mucin 7, secreted 424.5 211735_x_at D SFTPC surfactant protein C 416.2 206835_at STATH statherin 363.4 214387_x_at D SFTPC surfactant protein C 295.5 205982_x_at D SFTPC surfactant protein C 288.7 1553454_at RPTN repetin solute carrier family 34 (sodium 251.3 204124_at SLC34A2 phosphate), member 2 238.9 206786_at HTN3 histatin 3 161.5 220191_at GKN1 gastrokine 1 152.7 223678_s_at D SFTPA2 surfactant protein A2 130.9 207430_s_at D MSMB microseminoprotein, beta- 99.0 214199_at SFTPD surfactant protein D major histocompatibility complex, class II, 96.5 210982_s_at D HLA-DRA DR alpha 96.5 221133_s_at D CLDN18 claudin 18 94.4 238222_at GKN2 gastrokine 2 93.7 1557961_s_at D LOC100127983 uncharacterized LOC100127983 93.1 229584_at LRRK2 leucine-rich repeat kinase 2 HOXD cluster antisense RNA 1 (non- 88.6 242042_s_at D HOXD-AS1 protein coding) 86.0 205569_at LAMP3 lysosomal-associated membrane protein 3 85.4 232698_at BPIFB2 BPI fold containing family B, member 2 84.4 205979_at SCGB2A1 secretoglobin, family 2A, member 1 84.3 230469_at RTKN2 rhotekin 2 82.2 204130_at HSD11B2 hydroxysteroid (11-beta) dehydrogenase 2 81.9 222242_s_at KLK5 kallikrein-related peptidase 5 77.0 237281_at AKAP14 A kinase (PRKA) anchor protein 14 76.7 1553602_at MUCL1 mucin-like 1 76.3 216359_at D MUC7 mucin 7, -
Exploring the Folding Energy Landscape of a Series of Designed Consensus Tetratricopeptide Repeat Proteins
PHYSICS, BIOPHYSICS AND COMPUTATIONAL BIOLOGY BIOPHYSICS AND COMPUTATIONAL BIOLOGY Correction for ‘‘The role of fluctuations and stress on the Correction for ‘‘Exploring the folding energy landscape of a effective viscosity of cell aggregates,’’ by Philippe Marmottant, series of designed consensus tetratricopeptide repeat proteins,’’ Abbas Mgharbel, Jos Ka¨fer,Benjamin Audren, Jean-Paul Rieu, by Yalda Javadi and Ewan R. G. Main, which appeared in issue Jean-Claude Vial, Boudewijn van der Sanden, Athanasius F. M. 41, October 13, 2009, of Proc Natl Acad Sci USA (106:17383– Mare´e, Franc¸ois Graner, and He´le`ne Delanoe¨-Ayari, which 17388; first published October 1, 2009; 10.1073/pnas. appeared in issue 41, October 13, 2009, of Proc Natl Acad Sci 0907455106). USA (106:17271–17275; first published September 25, 2009; The authors note that, due to a printer’s error, some text 10.1073/pnas.0902085106). appeared incorrectly on page 17384. In the left column, the The authors note that, due to a printer’s error, the affiliation second sentence in the third full paragraph, ‘‘This yielded [D]50% for Abbas Mgharbel, Benjamin Audren, Jean-Paul Rieu, and (midpoint of unfolding) and mD-N (change in solvent-accessible ⌬ H2O ⌬ H2O He´le`ne Delanoe¨-Ayari at Universite´ de Lyon appeared incor- surface area upon protein unfolding) from which GD–N/ G03j rectly in part. The name of the authors’ laboratory, Laboratoire (free energy of unfolding in water) was calculated (Table S1),’’ Mate´riaux et Phe´nome`nes Quantiques, should instead have should instead have appeared as ‘‘This yielded [D]50% (midpoint appeared as Laboratoire de Physique de la Matie`re Condense´e of unfolding) and mD-N (change in solvent-accessible surface ⌬ H2O et Nanostructures. -
Structural Basis for Regulation of the Nucleo-Cytoplasmic Distribution of Bag6 by TRC35
Structural basis for regulation of the nucleo-cytoplasmic distribution of Bag6 by TRC35 Jee-Young Mocka, Yue Xub, Yihong Yeb, and William M. Clemons Jr.a,1 aDivision of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125; and bLaboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institute of Health, Bethesda, MD 75534 Edited by Jeffrey L. Brodsky, University of Pittsburgh, Pittsburgh, PA, and accepted by Editorial Board Member F. Ulrich Hartl, September 20, 2017 (received for review February 23, 2017) The metazoan protein BCL2-associated athanogene cochaperone 6 heterotetrameric Get4–Get5 complex (3, 13), but the addition of (Bag6) forms a hetero-trimeric complex with ubiquitin-like 4A and Bag6 leads to different interactions. transmembrane domain recognition complex 35 (TRC35). This Crystal structures of fungal Get4 revealed 14 α-helices that can Bag6 complex is involved in tail-anchored protein targeting and be divided into N-terminal domains (NTD) and C-terminal do- various protein quality-control pathways in the cytosol as well as mains (CTD) (Fig. 1A and Fig. S1A)(14–16). The NTD contains regulating transcription and histone methylation in the nucleus. conserved residues (Fig. S1C) involved in binding and regulating Here we present a crystal structure of Bag6 and its cytoplasmic Get3 (13, 15), while the CTD forms a stable interaction with the retention factor TRC35, revealing that TRC35 is remarkably Get5 N terminus (Get5-N) (15). The Get5 interface includes a conserved throughout the opisthokont lineage except at the hydrophobic cleft in Get4 formed by a β-hairpin between α13 and C-terminal Bag6-binding groove, which evolved to accommodate α14 that binds the helix in Get5-N (15). -
Crystal Structures of the Tetratricopeptide Repeat Domains of Kinesin Light Chains: Insight Into Cargo Recognition Mechanisms
Crystal Structures of the Tetratricopeptide Repeat Domains of Kinesin Light Chains: Insight into Cargo Recognition Mechanisms Haizhong Zhu1., Han Youl Lee2., Yufeng Tong1, Bum-Soo Hong1, Kyung-Phil Kim2, Yang Shen1, Kyung Jik Lim3, Farrell Mackenzie1, Wolfram Tempel1, Hee-Won Park1,2* 1 Structural Genomics Consortium, Toronto, Ontario, Canada, 2 Department of Pharmacology, University of Toronto, Toronto, Ontario, Canada, 3 Philip Pocock Catholic Secondary School, Mississauga, Ontario, Canada Abstract Kinesin-1 transports various cargos along the axon by interacting with the cargos through its light chain subunit. Kinesin light chains (KLC) utilize its tetratricopeptide repeat (TPR) domain to interact with over 10 different cargos. Despite a high sequence identity between their TPR domains (87%), KLC1 and KLC2 isoforms exhibit differential binding properties towards some cargos. We determined the structures of human KLC1 and KLC2 tetratricopeptide repeat (TPR) domains using X-ray crystallography and investigated the different mechanisms by which KLCs interact with their cargos. Using isothermal titration calorimetry, we attributed the specific interaction between KLC1 and JNK-interacting protein 1 (JIP1) cargo to residue N343 in the fourth TRP repeat. Structurally, the N343 residue is adjacent to other asparagines and lysines, creating a positively charged polar patch within the groove of the TPR domain. Whereas, KLC2 with the corresponding residue S328 did not interact with JIP1. Based on these finding, we propose that N343 of KLC1 can form ‘‘a carboxylate clamp’’ with its neighboring asparagine to interact with JIP1, similar to that of HSP70/HSP90 organizing protein-1’s (HOP1) interaction with heat shock proteins. For the binding of cargos shared by KLC1 and KLC2, we propose a different site located within the groove but not involving N343.