151
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Xu YZ, Thuraisingam T, Kanagaratham C, Tao S, Radzioch D. c-Src kinase is involved in the tyrosine phosphorylation and activity of SLC11A1 in differentiating macrophages. PLoS One 2018; 13:e0196230. [PMID: 29723216 PMCID: PMC5933793 DOI: 10.1371/journal.pone.0196230] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 04/09/2018] [Indexed: 11/18/2022] Open
Abstract
Studies have demonstrated that the solute carrier family 11 member 1 (SLC11A1) is heavily glycosylated and phosphorylated in macrophages. However, the mechanisms of SLC11A1 phosphorylation, and the effects of phosphorylation on SLC11A1 activity remain largely unknown. Here, the tyrosine phosphorylation of SLC11A1 is observed in SLC11A1-expressing U937 cells when differentiated into macrophages by phorbol myristate acetate (PMA). The phosphorylation of SLC11A1 is almost completely blocked by treatment with PP2, a selective inhibitor of Src family kinases. Furthermore, we found that SLC11A1 is a direct substrate for active c-Src kinase and siRNA-mediated knockdown of cellular Src (c-Src) expression results in a significant decrease in tyrosine phosphorylation. We found that PMA induces the interaction of SLC11A1 with c-Src kinase. We demonstrated that SLC11A1 is phosphorylated by Src family kinases at tyrosine 15 and this type of phosphorylation is required for SLC11A1-mediated modulation of NF-κB activation and nitric oxide (NO) production induced by LPS. Our results demonstrate important roles for c-Src tyrosine kinase in phosphorylation and activation of SLC11A1 in macrophages.
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Affiliation(s)
- Yong Zhong Xu
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Thusanth Thuraisingam
- Division of Dermatology, Faculty of Medicine, McGill University, Montreal, QC, Canada
| | - Cynthia Kanagaratham
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Shao Tao
- Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- Division of Experimental Medicine, Faculty of Medicine, McGill University, Montreal, QC, Canada
| | - Danuta Radzioch
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- Division of Experimental Medicine, Faculty of Medicine, McGill University, Montreal, QC, Canada
- * E-mail:
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152
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Abstract
The third most abundant polypeptide conformation in nature, the polyproline-II helix, is a polar, extended secondary structure with a local organization stabilized by intercarbonyl interactions within the peptide chain. Here we design a hydrophobic polyproline-II helical peptide based on an oligomeric octahydroindole-2-carboxylic acid scaffold and demonstrate its transmembrane alignment in model lipid bilayers by means of solid-state 19F NMR. As result, we provide a first example of a purely artificial transmembrane peptide with a structural organization that is not based on hydrogen-bonding.
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Affiliation(s)
- Vladimir Kubyshkin
- Institute of Chemistry , Technical University of Berlin , Müller-Breslau-Strasse 10 , Berlin 10623 , Germany
| | - Stephan L Grage
- Institute of Biological Interfaces (IBG-2) , Karlsruhe Institute of Technology (KIT) , P.O.B. 3640, Karlsruhe 76021 , Germany
| | - Jochen Bürck
- Institute of Biological Interfaces (IBG-2) , Karlsruhe Institute of Technology (KIT) , P.O.B. 3640, Karlsruhe 76021 , Germany
| | - Anne S Ulrich
- Institute of Biological Interfaces (IBG-2) , Karlsruhe Institute of Technology (KIT) , P.O.B. 3640, Karlsruhe 76021 , Germany
- Institute of Organic Chemistry , KIT , Fritz-Haber-Weg 6 , Karlsruhe 76131 , Germany
| | - Nediljko Budisa
- Institute of Chemistry , Technical University of Berlin , Müller-Breslau-Strasse 10 , Berlin 10623 , Germany
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153
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Carver JA, Ecroyd H, Truscott RJW, Thorn DC, Holt C. Proteostasis and the Regulation of Intra- and Extracellular Protein Aggregation by ATP-Independent Molecular Chaperones: Lens α-Crystallins and Milk Caseins. Acc Chem Res 2018; 51:745-752. [PMID: 29442498 DOI: 10.1021/acs.accounts.7b00250] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Molecular chaperone proteins perform a diversity of roles inside and outside the cell. One of the most important is the stabilization of misfolding proteins to prevent their aggregation, a process that is potentially detrimental to cell viability. Diseases such as Alzheimer's, Parkinson's, and cataract are characterized by the accumulation of protein aggregates. In vivo, many proteins are metastable and therefore under mild destabilizing conditions have an inherent tendency to misfold, aggregate, and hence lose functionality. As a result, protein levels are tightly regulated inside and outside the cell. Protein homeostasis, or proteostasis, describes the network of biological pathways that ensures the proteome remains folded and functional. Proteostasis is a major factor in maintaining cell, tissue, and organismal viability. We have extensively investigated the structure and function of intra- and extracellular molecular chaperones that operate in an ATP-independent manner to stabilize proteins and prevent their misfolding and subsequent aggregation into amorphous particles or highly ordered amyloid fibrils. These types of chaperones are therefore crucial in maintaining proteostasis under normal and stress (e.g., elevated temperature) conditions. Despite their lack of sequence similarity, they exhibit many common features, i.e., extensive structural disorder, dynamism, malleability, heterogeneity, oligomerization, and similar mechanisms of chaperone action. In this Account, we concentrate on the chaperone roles of α-crystallins and caseins, the predominant proteins in the eye lens and milk, respectively. Intracellularly, the principal ATP-independent chaperones are the small heat-shock proteins (sHsps). In vivo, sHsps are the first line of defense in preventing intracellular protein aggregation. The lens proteins αA- and αB-crystallin are sHsps. They play a crucial role in maintaining solubility of the crystallins (including themselves) with age and hence in lens proteostasis and, ultimately, lens transparency. As there is little metabolic activity and no protein turnover in the lens, crystallins are very long lived proteins. Lens proteostasis is therefore very different to that in normal, metabolically active cells. Crystallins undergo extensive post-translational modification (PTM), including deamidation, racemization, phosphorylation, and truncation, which can alter their stability. Despite this, the lens remains transparent for tens of years, implying that lens proteostasis is intimately integrated with crystallin PTMs. Many PTMs do not significantly alter crystallin stability, solubility, and functionality, which thereby facilitates lens transparency. In the long term, however, extensive accumulation of crystallin PTMs leads to large-scale crystallin aggregation, lens opacification, and cataract formation. Extracellularly, various ATP-independent molecular chaperones exist that exhibit sHsp-like structural and functional features. For example, caseins, the major milk proteins, exhibit chaperone ability by inhibiting the amorphous and amyloid fibrillar aggregation of a diversity of destabilized proteins. Caseins maintain proteostasis within milk by preventing deleterious casein amyloid fibril formation via incorporation of thousands of individual caseins into an amorphous structure known as the casein micelle. Hundreds of nanoclusters of calcium phosphate are sequestered within each casein micelle through interactions with short, highly phosphorylated casein sequences. This results in a stable biofluid that contains a high concentration of potentially amyloidogenic caseins and concentrations of calcium and phosphate that can be far in excess of the solubility of calcium phosphate. Casein micelle formation therefore performs vital roles in neonatal nutrition and calcium homeostasis in the mammary gland.
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Affiliation(s)
- John A. Carver
- Research School of Chemistry, The Australian National University, Acton, ACT 2601, Australia
| | - Heath Ecroyd
- Illawarra Health and Medical Research Institute and School of Biological Sciences, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Roger J. W. Truscott
- Illawarra Health and Medical Research Institute and School of Biological Sciences, University of Wollongong, Wollongong, NSW 2522, Australia
| | - David C. Thorn
- Research School of Chemistry, The Australian National University, Acton, ACT 2601, Australia
| | - Carl Holt
- Institute of Molecular, Cell and Systems Biology, University of Glasgow, Glasgow G12 8QQ, United Kingdom
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154
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Wong LE, Maier J, Wienands J, Becker S, Griesinger C. Sensitivity-Enhanced Four-Dimensional Amide–Amide Correlation NMR Experiments for Sequential Assignment of Proline-Rich Disordered Proteins. J Am Chem Soc 2018; 140:3518-3522. [DOI: 10.1021/jacs.8b00215] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Leo E. Wong
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Faßberg 11, 37077 Göttingen, Germany
| | - Joachim Maier
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Faßberg 11, 37077 Göttingen, Germany
| | - Jürgen Wienands
- Institute of Cellular and Molecular Immunology, Georg August University of Göttingen, Humboldtallee 34, 37073 Göttingen, Germany
| | - Stefan Becker
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Faßberg 11, 37077 Göttingen, Germany
| | - Christian Griesinger
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Faßberg 11, 37077 Göttingen, Germany
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155
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Malley KR, Koroleva O, Miller I, Sanishvili R, Jenkins CM, Gross RW, Korolev S. The structure of iPLA 2β reveals dimeric active sites and suggests mechanisms of regulation and localization. Nat Commun 2018; 9:765. [PMID: 29472584 PMCID: PMC5823874 DOI: 10.1038/s41467-018-03193-0] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 01/26/2018] [Indexed: 11/17/2022] Open
Abstract
Calcium-independent phospholipase A2β (iPLA2β) regulates important physiological processes including inflammation, calcium homeostasis and apoptosis. It is genetically linked to neurodegenerative disorders including Parkinson’s disease. Despite its known enzymatic activity, the mechanisms underlying iPLA2β-induced pathologic phenotypes remain poorly understood. Here, we present a crystal structure of iPLA2β that significantly revises existing mechanistic models. The catalytic domains form a tight dimer. They are surrounded by ankyrin repeat domains that adopt an outwardly flared orientation, poised to interact with membrane proteins. The closely integrated active sites are positioned for cooperative activation and internal transacylation. The structure and additional solution studies suggest that both catalytic domains can be bound and allosterically inhibited by a single calmodulin. These features suggest mechanisms of iPLA2β cellular localization and activity regulation, providing a basis for inhibitor development. Furthermore, the structure provides a framework to investigate the role of neurodegenerative mutations and the function of iPLA2β in the brain. Calcium-independent phospholipase A2β (iPLA2β) is involved in many physiological and pathological processes but the underlying mechanisms are largely unknown. Here, the authors present the structure of dimeric iPLA2β, providing insights into the regulation of its activity and cellular localization.
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Affiliation(s)
- Konstantin R Malley
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, 63104, USA
| | - Olga Koroleva
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, 63104, USA
| | - Ian Miller
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, 63104, USA
| | - Ruslan Sanishvili
- GM/CA@APS, Advanced Photon Source, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - Christopher M Jenkins
- Division of Bioorganic Chemistry and Molecular Pharmacology, Department of Medicine, Washington University School of Medicine, 660 South Euclid Avenue, Campus Box 8020, Saint Louis, MO, 63110, USA
| | - Richard W Gross
- Division of Bioorganic Chemistry and Molecular Pharmacology, Department of Medicine, Washington University School of Medicine, 660 South Euclid Avenue, Campus Box 8020, Saint Louis, MO, 63110, USA.,Department of Developmental Biology, Washington University School of Medicine, Saint Louis, MO, 63110, USA.,Department of Medicine, Center for Cardiovascular Research, Washington University School of Medicine, Saint Louis, MO, 63110, USA.,Department of Chemistry, Washington University, Saint Louis, MO, 63130, USA
| | - Sergey Korolev
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, 63104, USA.
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156
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Metelli A, Salem M, Wallace CH, Wu BX, Li A, Li X, Li Z. Immunoregulatory functions and the therapeutic implications of GARP-TGF-β in inflammation and cancer. J Hematol Oncol 2018; 11:24. [PMID: 29458436 PMCID: PMC5819195 DOI: 10.1186/s13045-018-0570-z] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 02/06/2018] [Indexed: 12/12/2022] Open
Abstract
GARP (glycoprotein-A repetitions predominant) is a type I transmembrane cell surface docking receptor for latent transforming growth factor-β (TGF-β) that is abundantly expressed on regulatory T lymphocytes and platelets. GARP regulates the availability of membrane-bound latent TGF-β and modulates its activation. For this reason, GARP expression on immune and non-immune cells is involved in maintaining peripheral tolerance. It plays an important role in preventing inflammatory diseases such as allergy and graft versus host disease (GvHD). GARP is also frequently hijacked by cancer cells to promote oncogenesis. This review summarizes the most important features of GARP biology described to date including gene regulation, protein expression and mechanism in activating latent TGF-β, and the function of GARP in regulatory T cell biology and peripheral tolerance, as well as GARP’s increasingly recognized roles in platelet-mediated cancer immune evasion. The promise for GARP-targeted strategy as a novel immunotherapy of cancer is also highlighted.
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Affiliation(s)
- Alessandra Metelli
- Department of Microbiology and Immunology, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Mohammad Salem
- Department of Microbiology and Immunology, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Caroline H Wallace
- Department of Microbiology and Immunology, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Bill X Wu
- Department of Microbiology and Immunology, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Anqi Li
- Department of Microbiology and Immunology, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Xue Li
- Children's Hospital Boston, Harvard Medical School, Boston, MA, 02115, USA
| | - Zihai Li
- Department of Microbiology and Immunology, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, 29425, USA. .,The First Affiliated Hospital, Zhengzhou University School of Medicine, Zhengzhou, 450052, China.
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157
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Zhou T, Erber L, Liu B, Gao Y, Ruan HB, Chen Y. Proteomic analysis reveals diverse proline hydroxylation-mediated oxygen-sensing cellular pathways in cancer cells. Oncotarget 2018; 7:79154-79169. [PMID: 27764789 PMCID: PMC5346705 DOI: 10.18632/oncotarget.12632] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 09/25/2016] [Indexed: 12/28/2022] Open
Abstract
Proline hydroxylation is a critical cellular mechanism regulating oxygen-response pathways in tumor initiation and progression. Yet, its substrate diversity and functions remain largely unknown. Here, we report a system-wide analysis to characterize proline hydroxylation substrates in cancer cells using an immunoaffinity-purification assisted proteomics strategy. We identified 562 sites from 272 proteins in HeLa cells. Bioinformatic analysis revealed that proline hydroxylation substrates are significantly enriched with mRNA processing and stress-response cellular pathways with canonical and diverse flanking sequence motifs. Structural analysis indicates a significant enrichment of proline hydroxylation participating in the secondary structure of substrate proteins. Our study identified and validated Brd4, a key transcription factor, as a novel proline hydroxylation substrate. Functional analysis showed that the inhibition of proline hydroxylation pathway significantly reduced the proline hydroxylation abundance on Brd4 and affected Brd4-mediated transcriptional activity as well as cell proliferation in AML leukemia cells. Taken together, our study identified a broad regulatory role of proline hydroxylation in cellular oxygen-sensing pathways and revealed potentially new targets that dynamically respond to hypoxia microenvironment in tumor cells.
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Affiliation(s)
- Tong Zhou
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota at Twin Cities, Minneapolis, MN 55455, USA
| | - Luke Erber
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota at Twin Cities, Minneapolis, MN 55455, USA
| | - Bing Liu
- Department of Integrative Biology and Physiology, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Yankun Gao
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota at Twin Cities, Minneapolis, MN 55455, USA
| | - Hai-Bin Ruan
- Department of Integrative Biology and Physiology, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Yue Chen
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota at Twin Cities, Minneapolis, MN 55455, USA
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158
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Oue Y, Murakami S, Isshiki K, Tsuji A, Yuasa K. Intracellular localization and binding partners of death associated protein kinase-related apoptosis-inducing protein kinase 1. Biochem Biophys Res Commun 2018; 496:1222-1228. [DOI: 10.1016/j.bbrc.2018.01.175] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 01/29/2018] [Indexed: 10/18/2022]
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159
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Structural and functional characterization of shaft, anchor, and tip proteins of the Mfa1 fimbria from the periodontal pathogen Porphyromonas gingivalis. Sci Rep 2018; 8:1793. [PMID: 29379120 PMCID: PMC5789003 DOI: 10.1038/s41598-018-20067-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 01/12/2018] [Indexed: 12/23/2022] Open
Abstract
Very little is known about how fimbriae of Bacteroidetes bacteria are assembled. To shed more light on this process, we solved the crystal structures of the shaft protein Mfa1, the regulatory protein Mfa2, and the tip protein Mfa3 from the periodontal pathogen Porphyromonas gingivalis. Together these build up part of the Mfa1 fimbria and represent three of the five proteins, Mfa1-5, encoded by the mfa1 gene cluster. Mfa1, Mfa2 and Mfa3 have the same overall fold i.e., two β-sandwich domains. Upon polymerization, the first β-strand of the shaft or tip protein is removed by indigenous proteases. Although the resulting void is expected to be filled by a donor-strand from another fimbrial protein, the mechanism by which it does so is still not established. In contrast, the first β-strand in Mfa2, the anchoring protein, is firmly attached by a disulphide bond and is not cleaved. Based on the structural information, we created multiple mutations in P. gingivalis and analysed their effect on fimbrial polymerization and assembly in vivo. Collectively, these data suggest an important role for the C-terminal tail of Mfa1, but not of Mfa3, affecting both polymerization and maturation of downstream fimbrial proteins.
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160
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Cronin JC, Loftus SK, Baxter LL, Swatkoski S, Gucek M, Pavan WJ. Identification and functional analysis of SOX10 phosphorylation sites in melanoma. PLoS One 2018; 13:e0190834. [PMID: 29315345 PMCID: PMC5760019 DOI: 10.1371/journal.pone.0190834] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 12/20/2017] [Indexed: 12/17/2022] Open
Abstract
The transcription factor SOX10 plays an important role in vertebrate neural crest development, including the establishment and maintenance of the melanocyte lineage. SOX10 is also highly expressed in melanoma tumors, and SOX10 expression increases with tumor progression. The suppression of SOX10 in melanoma cells activates TGF-β signaling and can promote resistance to BRAF and MEK inhibitors. Since resistance to BRAF/MEK inhibitors is seen in the majority of melanoma patients, there is an immediate need to assess the underlying biology that mediates resistance and to identify new targets for combinatorial therapeutic approaches. Previously, we demonstrated that SOX10 protein is required for tumor initiation, maintenance and survival. Here, we present data that support phosphorylation as a mechanism employed by melanoma cells to tightly regulate SOX10 expression. Mass spectrometry identified eight phosphorylation sites contained within SOX10, three of which (S24, S45 and T240) were selected for further analysis based on their location within predicted MAPK/CDK binding motifs. SOX10 mutations were generated at these phosphorylation sites to assess their impact on SOX10 protein function in melanoma cells, including transcriptional activation on target promoters, subcellular localization, and stability. These data further our understanding of SOX10 protein regulation and provide critical information for identification of molecular pathways that modulate SOX10 protein levels in melanoma, with the ultimate goal of discovering novel targets for more effective combinatorial therapeutic approaches for melanoma patients.
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Affiliation(s)
- Julia C. Cronin
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States of America
| | - Stacie K. Loftus
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States of America
| | - Laura L. Baxter
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States of America
| | - Steve Swatkoski
- Proteomics Core, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, United States of America
| | - Marjan Gucek
- Proteomics Core, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, United States of America
| | - William J. Pavan
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States of America
- * E-mail:
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161
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Kubyshkin V, Pridma S, Budisa N. Comparative effects of trifluoromethyl- and methyl-group substitutions in proline. NEW J CHEM 2018. [DOI: 10.1039/c8nj02631a] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
What is the outcome of trifluoromethyl-/methyl-substitution in each position of the proline ring? Look inside to find out.
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Affiliation(s)
- Vladimir Kubyshkin
- Biocatalysis Group
- Institute of Chemistry
- Technical University of Berlin
- Berlin 10623
- Germany
| | | | - Nediljko Budisa
- Biocatalysis Group
- Institute of Chemistry
- Technical University of Berlin
- Berlin 10623
- Germany
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162
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PFN2a, a new partner of RARα in the cytoplasm. Biochem Biophys Res Commun 2018; 495:846-853. [PMID: 29158086 DOI: 10.1016/j.bbrc.2017.11.096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 11/15/2017] [Indexed: 11/23/2022]
Abstract
Retinoic acid receptors (RARs) are classically considered as nuclear ligand-dependent regulators of transcription. Here we highlighted a novel face of the RARα subtype: RARα is present in low amounts in the cytoplasm of mouse embryonic fibroblasts (MEFs) where it interacts with profilin2a (PFN2A), a small actin-binding protein involved in filaments polymerization. The interaction involves the N-terminal proline-rich motif (PRM) of RARα and the SH3-like domain of PFN2a. When increased in the cytoplasm, RARα competes with other PFN2a-binding proteins bearing PRMs and involved in actin filaments elongation. Consequently, the actin filament network is altered and MEFs adhesion is decreased. This novel role opens novel avenues for the understanding of pathologies characterized by increased levels of cytoplasmic RARα.
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163
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Blüher D, Laha D, Thieme S, Hofer A, Eschen-Lippold L, Masch A, Balcke G, Pavlovic I, Nagel O, Schonsky A, Hinkelmann R, Wörner J, Parvin N, Greiner R, Weber S, Tissier A, Schutkowski M, Lee J, Jessen H, Schaaf G, Bonas U. A 1-phytase type III effector interferes with plant hormone signaling. Nat Commun 2017; 8:2159. [PMID: 29255246 PMCID: PMC5735085 DOI: 10.1038/s41467-017-02195-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 11/13/2017] [Indexed: 11/16/2022] Open
Abstract
Most Gram-negative phytopathogenic bacteria inject type III effector (T3E) proteins into plant cells to manipulate signaling pathways to the pathogen's benefit. In resistant plants, specialized immune receptors recognize single T3Es or their biochemical activities, thus halting pathogen ingress. However, molecular function and mode of recognition for most T3Es remains elusive. Here, we show that the Xanthomonas T3E XopH possesses phytase activity, i.e., dephosphorylates phytate (myo-inositol-hexakisphosphate, InsP6), the major phosphate storage compound in plants, which is also involved in pathogen defense. A combination of biochemical approaches, including a new NMR-based method to discriminate inositol polyphosphate enantiomers, identifies XopH as a naturally occurring 1-phytase that dephosphorylates InsP6 at C1. Infection of Nicotiana benthamiana and pepper by Xanthomonas results in a XopH-dependent conversion of InsP6 to InsP5. 1-phytase activity is required for XopH-mediated immunity of plants carrying the Bs7 resistance gene, and for induction of jasmonate- and ethylene-responsive genes in N. benthamiana.
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Affiliation(s)
- Doreen Blüher
- Institute for Biology, Department of Genetics, Martin-Luther University Halle-Wittenberg, Weinbergweg 10, 06120, Halle (Saale), Germany
| | - Debabrata Laha
- Institute of Crop Science and Resource Conservation, Department of Plant Nutrition, University of Bonn, Karlrobert-Kreiten-Strasse 13, 53115, Bonn, Germany
- Center for Plant Molecular Biology, Department of Plant Physiology, Eberhard Karls University Tübingen, Auf der Morgenstelle 32, 72076, Tübingen, Germany
| | - Sabine Thieme
- Institute for Biology, Department of Genetics, Martin-Luther University Halle-Wittenberg, Weinbergweg 10, 06120, Halle (Saale), Germany
| | - Alexandre Hofer
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Lennart Eschen-Lippold
- Department of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle (Saale), Germany
| | - Antonia Masch
- Institute for Biochemistry and Biotechnology, Department of Enzymology, Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Strasse 3, 06120, Halle (Saale), Germany
| | - Gerd Balcke
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle (Saale), Germany
| | - Igor Pavlovic
- Institute of Organic Chemistry, Albert-Ludwigs University Freiburg, Albertstrasse 21, 79104, Freiburg, Germany
| | - Oliver Nagel
- Institute for Biology, Department of Genetics, Martin-Luther University Halle-Wittenberg, Weinbergweg 10, 06120, Halle (Saale), Germany
| | - Antje Schonsky
- Institute for Biology, Department of Genetics, Martin-Luther University Halle-Wittenberg, Weinbergweg 10, 06120, Halle (Saale), Germany
| | - Rahel Hinkelmann
- Institute of Organic Chemistry, Albert-Ludwigs University Freiburg, Albertstrasse 21, 79104, Freiburg, Germany
| | - Jakob Wörner
- Institute of Physical Chemistry, Albert-Ludwigs University Freiburg, Albertstrasse 21, 79104, Freiburg, Germany
| | - Nargis Parvin
- Center for Plant Molecular Biology, Department of Plant Physiology, Eberhard Karls University Tübingen, Auf der Morgenstelle 32, 72076, Tübingen, Germany
| | - Ralf Greiner
- Department of Food Technology and Bioprocess Engineering, Max-Rubner-Institut, Federal Research Institute of Nutrition and Food, Haid-und-Neu-Straße 9, 76131, Karlsruhe, Germany
| | - Stefan Weber
- Institute of Physical Chemistry, Albert-Ludwigs University Freiburg, Albertstrasse 21, 79104, Freiburg, Germany
| | - Alain Tissier
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle (Saale), Germany
| | - Mike Schutkowski
- Institute for Biochemistry and Biotechnology, Department of Enzymology, Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Strasse 3, 06120, Halle (Saale), Germany
| | - Justin Lee
- Department of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle (Saale), Germany
| | - Henning Jessen
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.
- Institute of Organic Chemistry, Albert-Ludwigs University Freiburg, Albertstrasse 21, 79104, Freiburg, Germany.
| | - Gabriel Schaaf
- Institute of Crop Science and Resource Conservation, Department of Plant Nutrition, University of Bonn, Karlrobert-Kreiten-Strasse 13, 53115, Bonn, Germany.
- Center for Plant Molecular Biology, Department of Plant Physiology, Eberhard Karls University Tübingen, Auf der Morgenstelle 32, 72076, Tübingen, Germany.
| | - Ulla Bonas
- Institute for Biology, Department of Genetics, Martin-Luther University Halle-Wittenberg, Weinbergweg 10, 06120, Halle (Saale), Germany.
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164
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Tien JF, Mazloomian A, Cheng SWG, Hughes CS, Chow CCT, Canapi LT, Oloumi A, Trigo-Gonzalez G, Bashashati A, Xu J, Chang VCD, Shah SP, Aparicio S, Morin GB. CDK12 regulates alternative last exon mRNA splicing and promotes breast cancer cell invasion. Nucleic Acids Res 2017; 45:6698-6716. [PMID: 28334900 PMCID: PMC5499812 DOI: 10.1093/nar/gkx187] [Citation(s) in RCA: 117] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 03/09/2017] [Indexed: 12/31/2022] Open
Abstract
CDK12 (cyclin-dependent kinase 12) is a regulatory kinase with evolutionarily conserved roles in modulating transcription elongation. Recent tumor genome studies of breast and ovarian cancers highlighted recurrent CDK12 mutations, which have been shown to disrupt DNA repair in cell-based assays. In breast cancers, CDK12 is also frequently co-amplified with the HER2 (ERBB2) oncogene. The mechanisms underlying functions of CDK12 in general and in cancer remain poorly defined. Based on global analysis of mRNA transcripts in normal and breast cancer cell lines with and without CDK12 amplification, we demonstrate that CDK12 primarily regulates alternative last exon (ALE) splicing, a specialized subtype of alternative mRNA splicing, that is both gene- and cell type-specific. These are unusual properties for spliceosome regulatory factors, which typically regulate multiple forms of alternative splicing in a global manner. In breast cancer cells, regulation by CDK12 modulates ALE splicing of the DNA damage response activator ATM and a DNAJB6 isoform that influences cell invasion and tumorigenesis in xenografts. We found that there is a direct correlation between CDK12 levels, DNAJB6 isoform levels and the migration capacity and invasiveness of breast tumor cells. This suggests that CDK12 gene amplification can contribute to the pathogenesis of the cancer.
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Affiliation(s)
- Jerry F Tien
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver V5Z 1L3, Canada
| | - Alborz Mazloomian
- Graduate Bioinformatics Training Program, University of British Columbia, Vancouver V5Z 4S6, Canada.,Department of Molecular Oncology, BC Cancer Agency, Vancouver V5Z 1L3, Canada
| | - S-W Grace Cheng
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver V5Z 1L3, Canada
| | - Christopher S Hughes
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver V5Z 1L3, Canada
| | - Christalle C T Chow
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver V5Z 1L3, Canada
| | - Leanna T Canapi
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver V5Z 1L3, Canada
| | - Arusha Oloumi
- Department of Molecular Oncology, BC Cancer Agency, Vancouver V5Z 1L3, Canada
| | - Genny Trigo-Gonzalez
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver V5Z 1L3, Canada
| | - Ali Bashashati
- Department of Molecular Oncology, BC Cancer Agency, Vancouver V5Z 1L3, Canada
| | - James Xu
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver V6T 2B5, Canada
| | - Vicky C-D Chang
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver V5Z 1L3, Canada
| | - Sohrab P Shah
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver V5Z 1L3, Canada.,Department of Molecular Oncology, BC Cancer Agency, Vancouver V5Z 1L3, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver V6T 2B5, Canada
| | - Samuel Aparicio
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver V5Z 1L3, Canada.,Department of Molecular Oncology, BC Cancer Agency, Vancouver V5Z 1L3, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver V6T 2B5, Canada
| | - Gregg B Morin
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver V5Z 1L3, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver V6H 3N1, Canada
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165
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Large G protein α-subunit XLαs limits clathrin-mediated endocytosis and regulates tissue iron levels in vivo. Proc Natl Acad Sci U S A 2017; 114:E9559-E9568. [PMID: 29078380 DOI: 10.1073/pnas.1712670114] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Alterations in the activity/levels of the extralarge G protein α-subunit (XLαs) are implicated in various human disorders, such as perinatal growth retardation. Encoded by GNAS, XLαs is partly identical to the α-subunit of the stimulatory G protein (Gsα), but the cellular actions of XLαs remain poorly defined. Following an initial proteomic screen, we identified sorting nexin-9 (SNX9) and dynamins, key components of clathrin-mediated endocytosis, as binding partners of XLαs. Overexpression of XLαs in HEK293 cells inhibited internalization of transferrin, a process that depends on clathrin-mediated endocytosis, while its ablation by CRISPR/Cas9 in an osteocyte-like cell line (Ocy454) enhanced it. Similarly, primary cardiomyocytes derived from XLαs knockout (XLKO) pups showed enhanced transferrin internalization. Early postnatal XLKO mice showed a significantly higher degree of cardiac iron uptake than wild-type littermates following iron dextran injection. In XLKO neonates, iron and ferritin levels were elevated in heart and skeletal muscle, where XLαs is normally expressed abundantly. XLKO heart and skeletal muscle, as well as XLKO Ocy454 cells, showed elevated SNX9 protein levels, and siRNA-mediated knockdown of SNX9 in XLKO Ocy454 cells prevented enhanced transferrin internalization. In transfected cells, XLαs also inhibited internalization of the parathyroid hormone and type 2 vasopressin receptors. Internalization of transferrin and these G protein-coupled receptors was also inhibited in cells expressing an XLαs mutant missing the Gα portion, but not Gsα or an N-terminally truncated XLαs mutant unable to interact with SNX9 or dynamin. Thus, XLαs restricts clathrin-mediated endocytosis and plays a critical role in iron/transferrin uptake in vivo.
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166
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Ettelaie C, Collier MEW, Featherby S, Greenman J, Maraveyas A. Peptidyl-prolyl isomerase 1 (Pin1) preserves the phosphorylation state of tissue factor and prolongs its release within microvesicles. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2017; 1865:12-24. [PMID: 28962834 DOI: 10.1016/j.bbamcr.2017.09.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 08/07/2017] [Accepted: 09/24/2017] [Indexed: 01/23/2023]
Abstract
The exposure and release of TF is regulated by post-translational modifications of its cytoplasmic domain. Here, the potential of Pin1 to interact with the cytoplasmic domain of TF, and the outcome on TF function was examined. MDA-MB-231 and transfected-primary endothelial cells were incubated with either Pin1 deactivator Juglone, or its control Plumbagin, as well as transfected with Pin1-specific or control siRNA. TF release into microvesicles following activation, and also phosphorylation and ubiquitination states of cellular-TF were then assessed. Furthermore, the ability of Pin1 to bind wild-type and mutant forms of overexpressed TF-tGFP was investigated by co-immunoprecipitation. Additionally, the ability of recombinant or cellular Pin1 to bind to peptides of the C-terminus of TF, synthesised in different phosphorylation states was examined by binding assays and spectroscopically. Finally, the influence of recombinant Pin1 on the ubiquitination and dephosphorylation of the TF-peptides was examined. Pre-incubation of Pin1 with Juglone but not Plumbagin, reduced TF release as microvesicles and was also achievable following transfection with Pin1-siRNA. This was concurrent with early ubiquitination and dephosphorylation of cellular TF at Ser253. Pin1 co-immunoprecipitated with overexpressed wild-type TF-tGFP but not Ser258→Ala or Pro259→Ala substituted mutants. Pin1 did interact with Ser258-phosphorylated and double-phosphorylated TF-peptides, with the former having higher affinity. Finally, recombinant Pin1 was capable of interfering with the ubiquitination and dephosphorylation of TF-derived peptides. In conclusion, Pin1 is a fast-acting enzyme which may be utilised by cells to protect the phosphorylation state of TF in activated cells prolonging TF activity and release, and therefore ensuring adequate haemostasis.
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Affiliation(s)
- Camille Ettelaie
- Biomedical Section, Department of Biological Sciences, University of Hull, Cottingham Road, Hull HU6 7RX, UK.
| | - Mary E W Collier
- Department of Cardiovascular Sciences, University of Leicester, Clinical Sciences Wing, Glenfield General Hospital, Leicester LE3 9QP, UK
| | - Sophie Featherby
- Biomedical Section, Department of Biological Sciences, University of Hull, Cottingham Road, Hull HU6 7RX, UK
| | - John Greenman
- Biomedical Section, Department of Biological Sciences, University of Hull, Cottingham Road, Hull HU6 7RX, UK
| | - Anthony Maraveyas
- Division of Cancer, Hull York Medical School University of Hull, Cottingham Road, Hull HU6 7RX, UK
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167
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Berglund LL, Hao X, Liu B, Grantham J, Nyström T. Differential effects of soluble and aggregating polyQ proteins on cytotoxicity and type-1 myosin-dependent endocytosis in yeast. Sci Rep 2017; 7:11328. [PMID: 28900136 PMCID: PMC5595923 DOI: 10.1038/s41598-017-11102-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 08/17/2017] [Indexed: 11/19/2022] Open
Abstract
Huntington’s disease develops when the polyglutamine (polyQ) repeat in the Huntingtin (Htt) protein is expanded to over 35 glutamines rendering it aggregation-prone. Here, using Htt exon-1 as a polyQ model protein in a genome-wide screen in yeast, we show that the normal and soluble Htt exon-1 is toxic in cells with defects in type-1 myosin-dependent endocytosis. The toxicity of Htt is linked to physical interactions with type-1 myosins, which occur via the Htt proline-rich region, leading to a reduction in actin patch polarization and clathrin-dependent endocytosis. An expansion of the polyQ stretch from 25 to 103 glutamines, which causes Htt aggregation, alleviated Htt toxicity in cells lacking Myo5 or other components involved in early endocytosis. The data suggest that the proline-rich stretch of Htt interacts with type-1 myosin/clathrin-dependent processes and demonstrate that a reduction in the activity of such processes may result in a positive selection for polyQ expansions.
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Affiliation(s)
- Lisa L Berglund
- Institute of Biomedicine - Department of Microbiology & Immunology, Sahlgrenska Academy, University of Gothenburg, Medicinaregatan 7A, 405 30, Göteborg, Sweden
| | - Xinxin Hao
- Institute of Biomedicine - Department of Microbiology & Immunology, Sahlgrenska Academy, University of Gothenburg, Medicinaregatan 7A, 405 30, Göteborg, Sweden
| | - Beidong Liu
- Department of Chemistry and Molecular Biology, University of Gothenburg, Medicinaregatan 9C, 405 30, Göteborg, Sweden
| | - Julie Grantham
- Department of Chemistry and Molecular Biology, University of Gothenburg, Medicinaregatan 9C, 405 30, Göteborg, Sweden
| | - Thomas Nyström
- Institute of Biomedicine - Department of Microbiology & Immunology, Sahlgrenska Academy, University of Gothenburg, Medicinaregatan 7A, 405 30, Göteborg, Sweden.
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168
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Hausrath AC, Kingston RL. Conditionally disordered proteins: bringing the environment back into the fold. Cell Mol Life Sci 2017; 74:3149-3162. [PMID: 28597298 PMCID: PMC11107710 DOI: 10.1007/s00018-017-2558-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 06/01/2017] [Indexed: 12/19/2022]
Abstract
For many proteins, biological function requires the folding of the polypeptide chain into a unique and persistent tertiary structure. This review concerns proteins that adopt a specific tertiary structure to function, but are otherwise partially or completely disordered. The biological cue for protein folding is environmental perturbation or minor post-translational modification. Hence, we term these proteins conditionally disordered. Many of these proteins recognize and bind other molecules, and conditional disorder has been hypothesized to allow for more nuanced control and regulation of binding processes. However, this remains largely unproven. The sequences of conditionally disordered proteins suggest their propensity to fold; yet, under the standard laboratory conditions, they do not do so, which may appear surprising. We argue that the surprise results from the failure to consider the role of the environment in protein structure formation and that conditional disorder arises as a natural consequence of the marginal stability of the folded state.
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Affiliation(s)
- Andrew C Hausrath
- School of Biological Sciences, The University of Auckland, Auckland, 1010, New Zealand
| | - Richard L Kingston
- School of Biological Sciences, The University of Auckland, Auckland, 1010, New Zealand.
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169
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The PPII-to-α-helix transition of poly- l -lysine in methanol/water solvent mixtures accompanied by fibrillar self-aggregation: An influence of fluphenazine molecules. Biophys Chem 2017; 227:14-20. [DOI: 10.1016/j.bpc.2017.05.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 05/23/2017] [Accepted: 05/23/2017] [Indexed: 11/19/2022]
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170
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Tsiatsiani L, Akeroyd M, Olsthoorn M, Heck AJR. Aspergillus niger Prolyl Endoprotease for Hydrogen-Deuterium Exchange Mass Spectrometry and Protein Structural Studies. Anal Chem 2017; 89:7966-7973. [PMID: 28657298 PMCID: PMC5541327 DOI: 10.1021/acs.analchem.7b01161] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 06/28/2017] [Indexed: 12/30/2022]
Abstract
To monitor the structural integrity of therapeutic proteins, hydrogen-deuterium exchange mass spectrometry (HDX-MS) is increasingly utilized in the pharmaceutical industry. The successful outcome of HDX-MS analyses depends on the sample preparation conditions, which involve the rapid digestion of proteins at 0 °C and pH 2.5. Very few proteases are able to withstand such harsh conditions, with pepsin being the best-known exception, even though its activity is also strongly reduced at 0 °C. Here, we evaluate the usage of a prolyl endopeptidase from Aspergillus niger (An-PEP) for HDX-MS. What makes this protease very attractive is that it cleaves preferentially the hardest to digest amino acid, proline. To our surprise, and in contrast to previous reports, An-PEP activity was found optimal around pH 2.5 and could be further enhanced by urea up to 40%. Under typical HDX-MS conditions and using small amounts of enzyme, An-PEP generated an equivalent number of peptides as pepsin, as exemplified by using the two model systems tetrameric human hemoglobin (Hb) and human IgG4. Interestingly, because An-PEP peptides are shorter than pepsin-generated peptides, higher sequence resolution could be achieved, especially for Pro-containing protein regions in the alpha subunit of Hb, revealing new protected Hb regions that were not observed with pepsin. Due to its Pro-preference and resistance to low pH, we conclude that An-PEP is an archetype enzyme for HDX-MS, highly complementary to pepsin, and especially promising for structural studies on Pro-rich proteins or proteins containing Pro-rich binding domains involved in cellular signaling.
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Affiliation(s)
- Liana Tsiatsiani
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for
Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences and Netherlands Proteomics
Centre, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Michiel Akeroyd
- DSM
Biotechnology Center, PO Box 1, 2600 MA Delft, The Netherlands
| | | | - Albert J. R. Heck
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for
Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences and Netherlands Proteomics
Centre, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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171
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Zhu K, Shan Z, Chen X, Cai Y, Cui L, Yao W, Wang Z, Shi P, Tian C, Lou J, Xie Y, Wen W. Allosteric auto-inhibition and activation of the Nedd4 family E3 ligase Itch. EMBO Rep 2017; 18:1618-1630. [PMID: 28747490 DOI: 10.15252/embr.201744454] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 07/07/2017] [Accepted: 07/07/2017] [Indexed: 11/09/2022] Open
Abstract
The Nedd4 family E3 ligases are key regulators of cell growth and proliferation and are often misregulated in human cancers and other diseases. The ligase activities of Nedd4 E3s are tightly controlled via auto-inhibition. However, the molecular mechanism underlying Nedd4 E3 auto-inhibition and activation is poorly understood. Here, we show that the WW domains proceeding the catalytic HECT domain play an inhibitory role by binding directly to HECT in the Nedd4 E3 family member Itch. Our structural and biochemical analyses of Itch reveal that the WW2 domain and a following linker allosterically lock HECT in an inactive state inhibiting E2-E3 transthiolation. Binding of the Ndfip1 adaptor or JNK1-mediated phosphorylation relieves the auto-inhibition of Itch in a WW2-dependent manner. Aberrant activation of Itch leads to migration defects of cortical neurons during development. Our study provides a new mechanism governing the regulation of Itch.
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Affiliation(s)
- Kang Zhu
- Department of Neurosurgery, Huashan Hospital, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Zelin Shan
- Department of Neurosurgery, Huashan Hospital, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Xing Chen
- Department of Neurosurgery, Huashan Hospital, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Yuqun Cai
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and Collaborative Innovation Center for Brain Science, Fudan University, Shanghai, China
| | - Lei Cui
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Weiyi Yao
- Department of Neurosurgery, Huashan Hospital, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Zhen Wang
- Department of Neurosurgery, Huashan Hospital, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Pan Shi
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Changlin Tian
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Jizhong Lou
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yunli Xie
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and Collaborative Innovation Center for Brain Science, Fudan University, Shanghai, China
| | - Wenyu Wen
- Department of Neurosurgery, Huashan Hospital, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
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172
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Jeong J, Park S, An HT, Kang M, Ko J. Small leucine zipper protein functions as a negative regulator of estrogen receptor α in breast cancer. PLoS One 2017; 12:e0180197. [PMID: 28662179 PMCID: PMC5491147 DOI: 10.1371/journal.pone.0180197] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 06/12/2017] [Indexed: 01/15/2023] Open
Abstract
The nuclear transcription factor estrogen receptor α (ERα) plays a critical role in breast cancer progression. ERα acts as an important growth stimulatory protein in breast cancer and the expression level of ERα is tightly related to the prognosis and treatment of patients. Small leucine zipper protein (sLZIP) functions as a transcriptional cofactor by binding to various nuclear receptors, including glucocorticoid receptor, androgen receptor, and peroxisome proliferator-activated receptor γ. However, the role of sLZIP in the regulation of ERα and its involvement in breast cancer progression is unknown. We found that sLZIP binds to ERα and represses the transcriptional activity of ERα in ERα-positive breast cancer cells. sLZIP also suppressed the expression of ERα target genes. sLZIP disrupted the binding of ERα to the estrogen response element of the target gene promoter, resulting in suppression of cell proliferation. sLZIP is a novel co-repressor of ERα, and plays a negative role in ERα-mediated cell proliferation in breast cancer.
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Affiliation(s)
- Juyeon Jeong
- Division of Life Sciences, Korea University, Seoul, South Korea
| | - Sodam Park
- Division of Life Sciences, Korea University, Seoul, South Korea
| | - Hyoung-Tae An
- Division of Life Sciences, Korea University, Seoul, South Korea
| | - Minsoo Kang
- Division of Life Sciences, Korea University, Seoul, South Korea
| | - Jesang Ko
- Division of Life Sciences, Korea University, Seoul, South Korea
- * E-mail:
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173
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C-terminal tail of NADPH oxidase organizer 1 (Noxo1) mediates interaction with NADPH oxidase activator (Noxa1) in the NOX1 complex. Biochem Biophys Res Commun 2017. [PMID: 28625920 DOI: 10.1016/j.bbrc.2017.06.083] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
NOX1 (NADPH oxidase) similar to phagocyte NADPH oxidase, is expressed mainly in the colon epithelium and it is responsible for host defense against microbial infections by generating ROS (reactive oxygen species). NOX1 is activated by two regulatory cytosolic proteins that form a hetero-dimer, Noxo1 (NOX organizer 1) and Noxa1 (NOX activator 1). The interaction between Noxa1 and Noxo1 is critical for activating NOX1. However no structural studies for interaction between Noxa1 and Noxo1 has not been reported till date. Here, we studied the inter-molecular interaction between the SH3 domain of Noxa1 and Noxo1 using pull-down assay and NMR spectroscopy. 15N/13C-labeled SH3 domain of Noxa1 has been purified for hetero-nuclear NMR experiments (HNCACB, CBCACONH, HNCA, HNCO, and HSQC). TALOS analysis using backbone assignment data of the Noxa1 SH3 domain showed that the structure primarily consists of β-sheets. Data from pull-down assay between the Noxo1 and Noxa1 showed that the SH3 domains (Noxa1) is responsible for interaction with Noxo1 C-terminal tail harboring proline rich region (PRR). The concentration-dependent titration of the Noxo1 C-terminal tail to Noxa1 shows that Noxo1 particularly in the RT loop: Q407*, H408, S409, A412*, G414*, E416, D417, L418, and F420; n-Src loop: C430, E431*, V432*, A435, W436, and L437; and terminal region: I447; F448*, F452* and V454 interact with Noxa1. Our results will provide a detailed understanding for interaction between Noxa1 and Noxo1 at the molecular level, providing insights into their cytoplasmic activity-mediated functioning as well as regulatory role of C-terminal tail of Noxo1 in the NOX1 complex.
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174
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Baker EG, Williams C, Hudson KL, Bartlett GJ, Heal JW, Porter Goff KL, Sessions RB, Crump MP, Woolfson DN. Engineering protein stability with atomic precision in a monomeric miniprotein. Nat Chem Biol 2017; 13:764-770. [PMID: 28530710 DOI: 10.1038/nchembio.2380] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 02/27/2017] [Indexed: 02/04/2023]
Abstract
Miniproteins simplify the protein-folding problem, allowing the dissection of forces that stabilize protein structures. Here we describe PPα-Tyr, a designed peptide comprising an α-helix buttressed by a polyproline II helix. PPα-Tyr is water soluble and monomeric, and it unfolds cooperatively with a midpoint unfolding temperature (TM) of 39 °C. NMR structures of PPα-Tyr reveal proline residues docked between tyrosine side chains, as designed. The stability of PPα is sensitive to modifications in the aromatic residues: replacing tyrosine with phenylalanine, i.e., changing three solvent-exposed hydroxyl groups to protons, reduces the TM to 20 °C. We attribute this result to the loss of CH-π interactions between the aromatic and proline rings, which we probe by substituting the aromatic residues with nonproteinogenic side chains. In analyses of natural protein structures, we find a preference for proline-tyrosine interactions over other proline-containing pairs, and observe abundant CH-π interactions in biologically important complexes between proline-rich ligands and SH3 and similar domains.
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Affiliation(s)
- Emily G Baker
- School of Chemistry, University of Bristol, Bristol, UK
| | - Christopher Williams
- School of Chemistry, University of Bristol, Bristol, UK.,BrisSynBio, University of Bristol, Bristol, UK
| | | | | | - Jack W Heal
- School of Chemistry, University of Bristol, Bristol, UK
| | | | - Richard B Sessions
- BrisSynBio, University of Bristol, Bristol, UK.,School of Biochemistry, University of Bristol, Bristol, UK
| | - Matthew P Crump
- School of Chemistry, University of Bristol, Bristol, UK.,BrisSynBio, University of Bristol, Bristol, UK
| | - Derek N Woolfson
- School of Chemistry, University of Bristol, Bristol, UK.,BrisSynBio, University of Bristol, Bristol, UK.,School of Biochemistry, University of Bristol, Bristol, UK
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175
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García-Villegas R, Camacho-Villasana Y, Shingú-Vázquez MÁ, Cabrera-Orefice A, Uribe-Carvajal S, Fox TD, Pérez-Martínez X. The Cox1 C-terminal domain is a central regulator of cytochrome c oxidase biogenesis in yeast mitochondria. J Biol Chem 2017; 292:10912-10925. [PMID: 28490636 DOI: 10.1074/jbc.m116.773077] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 05/09/2017] [Indexed: 12/21/2022] Open
Abstract
Cytochrome c oxidase (CcO) is the last electron acceptor in the respiratory chain. The CcO core is formed by mitochondrial DNA-encoded Cox1, Cox2, and Cox3 subunits. Cox1 synthesis is highly regulated; for example, if CcO assembly is blocked, Cox1 synthesis decreases. Mss51 activates translation of COX1 mRNA and interacts with Cox1 protein in high-molecular-weight complexes (COA complexes) to form the Cox1 intermediary assembly module. Thus, Mss51 coordinates both Cox1 synthesis and assembly. We previously reported that the last 15 residues of the Cox1 C terminus regulate Cox1 synthesis by modulating an interaction of Mss51 with Cox14, another component of the COA complexes. Here, using site-directed mutagenesis of the mitochondrial COX1 gene from Saccharomyces cerevisiae, we demonstrate that mutations P521A/P522A and V524E disrupt the regulatory role of the Cox1 C terminus. These mutations, as well as C terminus deletion (Cox1ΔC15), reduced binding of Mss51 and Cox14 to COA complexes. Mss51 was enriched in a translationally active form that maintains full Cox1 synthesis even if CcO assembly is blocked in these mutants. Moreover, Cox1ΔC15, but not Cox1-P521A/P522A and Cox1-V524E, promoted formation of aberrant supercomplexes in CcO assembly mutants lacking Cox2 or Cox4 subunits. The aberrant supercomplex formation depended on the presence of cytochrome b and Cox3, supporting the idea that supercomplex assembly factors associate with Cox3 and demonstrating that supercomplexes can be formed even if CcO is inactive and not fully assembled. Our results indicate that the Cox1 C-terminal end is a key regulator of CcO biogenesis and that it is important for supercomplex formation/stability.
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Affiliation(s)
- Rodolfo García-Villegas
- From the Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, 04510, Mexico
| | - Yolanda Camacho-Villasana
- From the Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, 04510, Mexico
| | - Miguel Ángel Shingú-Vázquez
- the Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
| | - Alfredo Cabrera-Orefice
- the Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands, and
| | - Salvador Uribe-Carvajal
- From the Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, 04510, Mexico
| | - Thomas D Fox
- the Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853
| | - Xochitl Pérez-Martínez
- From the Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, 04510, Mexico,
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176
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Randell A, Daneshtalab N. Elastin microfibril interface-located protein 1, transforming growth factor beta, and implications on cardiovascular complications. ACTA ACUST UNITED AC 2017; 11:437-448. [PMID: 28545768 DOI: 10.1016/j.jash.2017.04.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 03/07/2017] [Accepted: 04/20/2017] [Indexed: 01/12/2023]
Abstract
Elastin microfibril interface-located protein 1 (EMILIN1), a glycoprotein, is associated with elastin in the extracellular matrix (ECM) of arteries, lymph vasculature, and other tissues. EMILIN1 particularly has a niche role in elastin fiber biogenesis (elastogenesis) by aiding with the fusion of elastin fibers, rendering them more ordered. In addition to elastogenesis, EMILIN1 has been shown to have roles in maintenance of vascular cell morphology, smooth muscle cell adhesion to elastic fibers, and transforming growth factor (TGFβ) regulation, by inhibiting TGFβ activation via blocking the proteolytic production of the latency-associated peptide/active TGFβ complex. The increased TGFβ signaling induced during EMILIN1 deficiency alters TGFβ activity, resulting in vascular smooth muscle cell growth and vascular remodeling. The increasing systemic blood pressure associated with TGFβ signaling may be closely linked to the activity of other mediators that affect cardiovascular homeostasis, such as angiotensin II. The increase in prevalence of hypertension and other cardiovascular diseases in other disease states likely involve a complex activation of TGFβ signaling and ECM dysfunction. Thus, the interaction of TGFβ and ECM components appears to be integrative involving both structural alterations to vessels through EMILIN1 and changes in TGFβ signaling processes. This review summarizes the current knowledge on the EMILIN1-TGFβ relationship; the specific roles of EMILIN1 and TGFβ in blood pressure regulation, their synergistic interaction, and in particular the role of TGFβ (in conjunction with ECM proteins) in other disease states altering cardiovascular homeostasis.
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Affiliation(s)
- Amy Randell
- Health Sciences Center, School of Pharmacy, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
| | - Noriko Daneshtalab
- Health Sciences Center, School of Pharmacy, Memorial University of Newfoundland, St. John's, Newfoundland, Canada.
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177
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Graham LA, Dominiczak AF, Ferreri NR. Role of renal transporters and novel regulatory interactions in the TAL that control blood pressure. Physiol Genomics 2017; 49:261-276. [PMID: 28389525 PMCID: PMC5451551 DOI: 10.1152/physiolgenomics.00017.2017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 03/27/2017] [Accepted: 04/05/2017] [Indexed: 12/31/2022] Open
Abstract
Hypertension (HTN), a major public health issue is currently the leading factor in the global burden of disease, where associated complications account for 9.4 million deaths worldwide every year. Excessive dietary salt intake is among the environmental factors that contribute to HTN, known as salt sensitivity. The heterogeneity of salt sensitivity and the multiple mechanisms that link high salt intake to increases in blood pressure are of upmost importance for therapeutic application. A continual increase in the kidney's reabsorption of sodium (Na+) relies on sequential actions at various segments along the nephron. When the distal segments of the nephron fail to regulate Na+, the effects on Na+ homeostasis are unfavorable. We propose that the specific nephron region where increased active uptake occurs as a result of variations in Na+ reabsorption is at the thick ascending limb of the loop of Henle (TAL). The purpose of this review is to urge the consideration of the TAL as contributing to the pathophysiology of salt-sensitive HTN. Further research in this area will enable development of a therapeutic application for targeted treatment.
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Affiliation(s)
- Lesley A Graham
- BHF Glasgow Cardiovascular Research Centre, University of Glasgow Cardiovascular and Medical Sciences, Glasgow, United Kingdom; and
| | - Anna F Dominiczak
- BHF Glasgow Cardiovascular Research Centre, University of Glasgow Cardiovascular and Medical Sciences, Glasgow, United Kingdom; and
| | - Nicholas R Ferreri
- Department of Pharmacology, New York Medical College, Valhalla, New York
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178
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Guo T, Noble W, Hanger DP. Roles of tau protein in health and disease. Acta Neuropathol 2017; 133:665-704. [PMID: 28386764 PMCID: PMC5390006 DOI: 10.1007/s00401-017-1707-9] [Citation(s) in RCA: 642] [Impact Index Per Article: 80.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 03/26/2017] [Accepted: 03/26/2017] [Indexed: 01/18/2023]
Abstract
Tau is well established as a microtubule-associated protein in neurons. However, under pathological conditions, aberrant assembly of tau into insoluble aggregates is accompanied by synaptic dysfunction and neural cell death in a range of neurodegenerative disorders, collectively referred to as tauopathies. Recent advances in our understanding of the multiple functions and different locations of tau inside and outside neurons have revealed novel insights into its importance in a diverse range of molecular pathways including cell signalling, synaptic plasticity, and regulation of genomic stability. The present review describes the physiological and pathophysiological properties of tau and how these relate to its distribution and functions in neurons. We highlight the post-translational modifications of tau, which are pivotal in defining and modulating tau localisation and its roles in health and disease. We include discussion of other pathologically relevant changes in tau, including mutation and aggregation, and how these aspects impinge on the propensity of tau to propagate, and potentially drive neuronal loss, in diseased brain. Finally, we describe the cascade of pathological events that may be driven by tau dysfunction, including impaired axonal transport, alterations in synapse and mitochondrial function, activation of the unfolded protein response and defective protein degradation. It is important to fully understand the range of neuronal functions attributed to tau, since this will provide vital information on its involvement in the development and pathogenesis of disease. Such knowledge will enable determination of which critical molecular pathways should be targeted by potential therapeutic agents developed for the treatment of tauopathies.
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Affiliation(s)
- Tong Guo
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, SE5 9NU, UK
| | - Wendy Noble
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, SE5 9NU, UK
| | - Diane P Hanger
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, SE5 9NU, UK.
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179
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Fecher-Trost C, Wissenbach U, Weissgerber P. TRPV6: From identification to function. Cell Calcium 2017; 67:116-122. [PMID: 28501141 DOI: 10.1016/j.ceca.2017.04.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 04/26/2017] [Accepted: 04/26/2017] [Indexed: 12/20/2022]
Affiliation(s)
- Claudia Fecher-Trost
- Institute of Experimental and Clinical Pharmacology and Toxicology, Saarland University, Building 46, 66421 Homburg, Germany.
| | - Ulrich Wissenbach
- Institute of Experimental and Clinical Pharmacology and Toxicology, Saarland University, Building 46, 66421 Homburg, Germany
| | - Petra Weissgerber
- Institute of Experimental and Clinical Pharmacology and Toxicology, Saarland University, Building 46, 66421 Homburg, Germany.
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180
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Jennek S, Mittag S, Reiche J, Westphal JK, Seelk S, Dörfel MJ, Pfirrmann T, Friedrich K, Schütz A, Heinemann U, Huber O. Tricellulin is a target of the ubiquitin ligase Itch. Ann N Y Acad Sci 2017; 1397:157-168. [DOI: 10.1111/nyas.13349] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 03/08/2017] [Accepted: 03/14/2017] [Indexed: 01/05/2023]
Affiliation(s)
- Susanne Jennek
- Department of Biochemistry II; Jena University Hospital, Friedrich Schiller University Jena; Jena Germany
| | - Sonnhild Mittag
- Department of Biochemistry II; Jena University Hospital, Friedrich Schiller University Jena; Jena Germany
| | - Juliane Reiche
- Department of Biochemistry II; Jena University Hospital, Friedrich Schiller University Jena; Jena Germany
| | - Julie K. Westphal
- Department of Biochemistry II; Jena University Hospital, Friedrich Schiller University Jena; Jena Germany
| | - Stefanie Seelk
- Department of Biochemistry II; Jena University Hospital, Friedrich Schiller University Jena; Jena Germany
| | - Max J. Dörfel
- Department of Biochemistry II; Jena University Hospital, Friedrich Schiller University Jena; Jena Germany
| | - Thorsten Pfirrmann
- Institute of Physiological Chemistry, University Hospital Halle; Martin Luther University Halle-Wittenberg; Halle/Saale Germany
| | - Karlheinz Friedrich
- Department of Biochemistry II; Jena University Hospital, Friedrich Schiller University Jena; Jena Germany
| | - Anja Schütz
- Helmholtz Protein Sample Production Facility; Max-Delbrück-Center for Molecular Medicine; Berlin Germany
| | - Udo Heinemann
- Helmholtz Protein Sample Production Facility; Max-Delbrück-Center for Molecular Medicine; Berlin Germany
- Crystallography; Max Delbrück Center for Molecular Medicine; Berlin Germany
- Chemistry and Biochemistry Institute; Freie Universität Berlin; Berlin Germany
| | - Otmar Huber
- Department of Biochemistry II; Jena University Hospital, Friedrich Schiller University Jena; Jena Germany
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181
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Miyamoto T, Minase G, Shin T, Ueda H, Okada H, Sengoku K. Human male infertility and its genetic causes. Reprod Med Biol 2017; 16:81-88. [PMID: 29259455 PMCID: PMC5661822 DOI: 10.1002/rmb2.12017] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 12/16/2016] [Indexed: 01/11/2023] Open
Abstract
Background Infertility affects about 15% of couples who wish to have children and half of these cases are associated with male factors. Genetic causes of azoospermia include chromosomal abnormalities, Y chromosome microdeletions, and specific mutations/deletions of several Y chromosome genes. Many researchers have analyzed genes in the AZF region on the Y chromosome; however, in 2003 the SYCP3 gene on chromosome 12 (12q23) was identified as causing azoospermia by meiotic arrest through a point mutation. Methods We mainly describe the SYCP3 and PLK4 genes that we have studied in our laboratory, and add comments on other genes associated with human male infertility. Results Up to now, The 17 genes causing male infertility by their mutation have been reported in human. Conclusions Infertility caused by nonobstructive azoospermia (NOA) is very important in the field of assisted reproductive technology. Even with the aid of chromosomal analysis, ultrasonography of the testis, and detailed endocrinology, only MD‐TESE can confirm the presence of immature spermatozoa in the testes. We strongly hope that these studies help clinics avoid ineffective MD‐TESE procedures.
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Affiliation(s)
- Toshinobu Miyamoto
- Department of Obstetrics and Gynecology Asahikawa Medical University Asahikawa Japan
| | - Gaku Minase
- Department of Obstetrics and Gynecology Asahikawa Medical University Asahikawa Japan
| | - Takeshi Shin
- Department of Urology Dokkyo Medical University Koshigaya Hospital Koshigaya City Japan
| | - Hiroto Ueda
- Department of Obstetrics and Gynecology Asahikawa Medical University Asahikawa Japan
| | - Hiroshi Okada
- Department of Urology Dokkyo Medical University Koshigaya Hospital Koshigaya City Japan
| | - Kazuo Sengoku
- Department of Obstetrics and Gynecology Asahikawa Medical University Asahikawa Japan
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182
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Bianco PR, Lyubchenko YL. SSB and the RecG DNA helicase: an intimate association to rescue a stalled replication fork. Protein Sci 2017; 26:638-649. [PMID: 28078722 DOI: 10.1002/pro.3114] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 12/26/2016] [Accepted: 12/28/2016] [Indexed: 12/27/2022]
Abstract
In E. coli, the regression of stalled DNA replication forks is catalyzed by the DNA helicase RecG. One means of gaining access to the fork is by binding to the single strand binding protein or SSB. This interaction occurs via the wedge domain of RecG and the intrinsically disordered linker (IDL) of SSB, in a manner similar to that of SH3 domains binding to PXXP motif-containing ligands in eukaryotic cells. During loading, SSB remodels the wedge domain so that the helicase domains bind to the parental, duplex DNA, permitting the helicase to translocate using thermal energy. This translocation may be used to clear the fork of obstacles, prior to the initiation of fork regression.
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Affiliation(s)
- Piero R Bianco
- SUNY Microbiology and Immunology, Center for Single Molecule Biophysics, University at Buffalo, 321 Cary Hall, 3435 Main St, Buffalo, New York 14214.,Department of Microbiology and Immunology, University at Buffalo, Buffalo, New York.,Department of Biochemistry, University at Buffalo, Buffalo, New York
| | - Yuri L Lyubchenko
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, Nebraska, 68198-6025
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183
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Park M, Liu RW, An H, Geczy CL, Thomas PS, Tedla N. A dual positive and negative regulation of monocyte activation by leukocyte Ig-like receptor B4 depends on the position of the tyrosine residues in its ITIMs. Innate Immun 2017; 23:381-391. [PMID: 28409541 DOI: 10.1177/1753425917699465] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The leukocyte Ig-like receptor B4 (LILRB4) is an inhibitory cell surface receptor, primarily expressed on mono-myeloid cells. It contains 2 C-type Ig-like extracellular domains and a long cytoplasmic domain that contains three intracellular immunoreceptor tyrosine-based inhibitory motifs (ITIMs). Data suggest that LILRB4 suppresses Fc receptor-dependent monocyte functions via its ITIMs, but relative contributions of the three ITIMs are not characterised. To address this, tyrosine (Tyr) residues at positions 337, 389 and 419 were single, double or triple mutated to phenylalanine and stably transfected into a human monocytic cell line, THP-1. Intact Tyr389 was sufficient to maximally inhibit FcγRI-mediated TNF-α production in THP-1 cells, but, paradoxically, Tyr337 significantly enhanced TNF-α production. In contrast, bactericidal activity was significantly enhanced in mutants containing Tyr419, while Tyr337 markedly inhibited bacteria killing. Taken together, these results indicate that LILRB4 might have dual inhibitory and activating functions, depending on the position of the functional tyrosine residues in its ITIMs and/or the nature of the stimuli.
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Affiliation(s)
- Mijeong Park
- 1 Mechanisms of Diseases Translational Research, University of New South Wales, School of Medical Sciences, Department of Pathology, Sydney, Australia
| | - Robert W Liu
- 2 Stanford University School of Medicine, Department of Medicine, Stanford, CA, USA
| | - Hongyan An
- 1 Mechanisms of Diseases Translational Research, University of New South Wales, School of Medical Sciences, Department of Pathology, Sydney, Australia
| | - Carolyn L Geczy
- 1 Mechanisms of Diseases Translational Research, University of New South Wales, School of Medical Sciences, Department of Pathology, Sydney, Australia
| | - Paul S Thomas
- 1 Mechanisms of Diseases Translational Research, University of New South Wales, School of Medical Sciences, Department of Pathology, Sydney, Australia.,3 Department of Respiratory Medicine, Prince of Wales Hospital, Sydney, Australia
| | - Nicodemus Tedla
- 1 Mechanisms of Diseases Translational Research, University of New South Wales, School of Medical Sciences, Department of Pathology, Sydney, Australia
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184
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Tan HY, Wilczek LA, Pottinger S, Manosas M, Yu C, Nguyenduc T, Bianco PR. The intrinsically disordered linker of E. coli SSB is critical for the release from single-stranded DNA. Protein Sci 2017; 26:700-717. [PMID: 28078720 DOI: 10.1002/pro.3115] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 12/28/2016] [Indexed: 11/08/2022]
Abstract
The Escherichia coli single stranded DNA binding protein (SSB) is crucial for DNA replication, recombination and repair. Within each process, it has two seemingly disparate roles: it stabilizes single-stranded DNA (ssDNA) intermediates generated during DNA processing and, forms complexes with a group of proteins known as the SSB-interactome. Key to both roles is the C-terminal, one-third of the protein, in particular the intrinsically disordered linker (IDL). Previously, they have shown using a series of linker deletion mutants that the IDL links both ssDNA and target protein binding by mediating interactions with the oligosaccharide/oligonucleotide binding fold in the target. In this study, they examine the role of the linker region in SSB function in a variety of DNA metabolic processes in vitro. Using the same linker mutants, the results show that in addition to association reactions (either DNA or protein), the IDL is critical for the release of SSB from DNA. This release can be under conditions of ssDNA competition or active displacement by a DNA helicase or recombinase. Consistent with their previous work these results indicate that SSB linker mutants are defective for SSB-SSB interactions, and when the IDL is removed a terminal SSB-DNA complex results. Formation of this complex inhibits downstream processing of DNA by helicases such as RecG or PriA as well as recombination, mediated by RecA. A model, based on the evidence herein, is presented to explain how the IDL acts in SSB function.
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Affiliation(s)
- Hui Yin Tan
- Department of Microbiology and Immunology, Center for Single Molecule Biophysics, University at Buffalo, Buffalo, New York
| | - Luke A Wilczek
- Department of Microbiology and Immunology, Center for Single Molecule Biophysics, University at Buffalo, Buffalo, New York
| | - Sasheen Pottinger
- Department of Microbiology and Immunology, Center for Single Molecule Biophysics, University at Buffalo, Buffalo, New York
| | - Maria Manosas
- Departament de Física Fonamental, Facultat de Física, Universitat de Barcelona, Diagonal 647, 08028, Barcelona, Spain.,CIBER-BBN de Bioingenieria, Biomateriales y Nanomedicina, Instituto de Sanidad Carlos III, Madrid, Spain
| | - Cong Yu
- Department of Microbiology and Immunology, Center for Single Molecule Biophysics, University at Buffalo, Buffalo, New York
| | - Trong Nguyenduc
- Department of Microbiology and Immunology, Center for Single Molecule Biophysics, University at Buffalo, Buffalo, New York
| | - Piero R Bianco
- Department of Microbiology and Immunology, Center for Single Molecule Biophysics, University at Buffalo, Buffalo, New York
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185
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186
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Desrochers G, Cappadocia L, Lussier-Price M, Ton AT, Ayoubi R, Serohijos A, Omichinski JG, Angers A. Molecular basis of interactions between SH3 domain-containing proteins and the proline-rich region of the ubiquitin ligase Itch. J Biol Chem 2017; 292:6325-6338. [PMID: 28235806 DOI: 10.1074/jbc.m116.754440] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 02/07/2017] [Indexed: 11/06/2022] Open
Abstract
The ligase Itch plays major roles in signaling pathways by inducing ubiquitylation-dependent degradation of several substrates. Substrate recognition and binding are critical for the regulation of this reaction. Like closely related ligases, Itch can interact with proteins containing a PPXY motif via its WW domains. In addition to these WW domains, Itch possesses a proline-rich region (PRR) that has been shown to interact with several Src homology 3 (SH3) domain-containing proteins. We have previously established that despite the apparent surface uniformity and conserved fold of SH3 domains, they display different binding mechanisms and affinities for their interaction with the PRR of Itch. Here, we attempt to determine the molecular bases underlying the wide range of binding properties of the Itch PRR. Using pulldown assays combined with mass spectrometry analysis, we show that the Itch PRR preferentially forms complexes with endophilins, amphyphisins, and pacsins but can also target a variety of other SH3 domain-containing proteins. In addition, we map the binding sites of these proteins using a combination of PRR sub-sequences and mutants. We find that different SH3 domains target distinct proline-rich sequences overlapping significantly. We also structurally analyze these protein complexes using crystallography and molecular modeling. These structures depict the position of Itch PRR engaged in a 1:2 protein complex with β-PIX and a 1:1 complex with the other SH3 domain-containing proteins. Taken together, these results reveal the binding preferences of the Itch PRR toward its most common SH3 domain-containing partners and demonstrate that the PRR region is sufficient for binding.
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Affiliation(s)
| | - Laurent Cappadocia
- Biochemistry and Molecular Medicine, University of Montreal, Montreal, Quebec H3C 3J7, Canada
| | - Mathieu Lussier-Price
- Biochemistry and Molecular Medicine, University of Montreal, Montreal, Quebec H3C 3J7, Canada
| | - Anh-Tien Ton
- Biochemistry and Molecular Medicine, University of Montreal, Montreal, Quebec H3C 3J7, Canada
| | | | - Adrian Serohijos
- Biochemistry and Molecular Medicine, University of Montreal, Montreal, Quebec H3C 3J7, Canada
| | - James G Omichinski
- Biochemistry and Molecular Medicine, University of Montreal, Montreal, Quebec H3C 3J7, Canada
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187
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Sheu MJ, Hsieh MJ, Chou YE, Wang PH, Yeh CB, Yang SF, Lee HL, Liu YF. Effects of ADAMTS14 genetic polymorphism and cigarette smoking on the clinicopathologic development of hepatocellular carcinoma. PLoS One 2017; 12:e0172506. [PMID: 28231306 PMCID: PMC5322915 DOI: 10.1371/journal.pone.0172506] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 02/05/2017] [Indexed: 01/12/2023] Open
Abstract
Background ADAMTS14 is a member of the ADAMTS (adisintegrin and metalloproteinase with thrombospondin motifs), which are proteolytic enzymes with a variety of further ancillary domain in the C-terminal region for substrate specificity and enzyme localization via extracellular matrix association. However, whether ADAMTS14 genetic variants play a role in hepatocellular carcinoma (HCC) susceptibility remains unknown. Methodology/Principal findings Four non-synonymous single-nucleotide polymorphisms (nsSNPs) of the ADAMTS14 gene were examined from 680 controls and 340 patients with HCC. Among 141 HCC patients with smoking behaviour, we found significant associations of the rs12774070 (CC+AA vs CC) and rs61573157 (CT+TT vs CC) variants with a clinical stage of HCC (OR: 2.500 and 2.767; 95% CI: 1.148–5.446 and 1.096–6.483; P = 0.019 and 0.026, respectively) and tumour size (OR: 2.387 and 2.659; 95% CI: 1.098–5.188 and 1.055–6.704; P = 0.026 and 0.034, respectively), but not with lymph node metastasis or other clinical statuses. Moreover, an additional integrated in silico analysis proposed that rs12774070 and rs61573157 affected essential post-translation O-glycosylation site within the 3rd thrombospondin type 1 repeat and a novel proline-rich region embedded within the C-terminal extension, respectively. Conclusions Taken together, our results suggest an involvement of ADAMTS14 SNP rs12774070 and rs61573157 in the liver tumorigenesis and implicate the ADAMTS14 gene polymorphism as a predict factor during the progression of HCC.
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Affiliation(s)
- Ming-Jen Sheu
- Department of Gastroenterology and Hepatology, Chi Mei Medical Center, Tainan, Taiwan
| | - Ming-Ju Hsieh
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan
- Cancer Research Center, Changhua Christian Hospital, Changhua, Taiwan
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
| | - Ying-Erh Chou
- School of Medicine, Chung Shan Medical University, Taichung, Taiwan
- Department of Medical Research, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Po-Hui Wang
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan
- Department of Obstetrics and Gynecology, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Chao-Bin Yeh
- School of Medicine, Chung Shan Medical University, Taichung, Taiwan
- Department of Emergency Medicine, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Shun-Fa Yang
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan
- Department of Medical Research, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Hsiang-Lin Lee
- School of Medicine, Chung Shan Medical University, Taichung, Taiwan
- Deptartment of Surgery, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Yu-Fan Liu
- Department of Biomedical Sciences, College of Medicine Sciences and Technology, Chung Shan Medical University, Taichung, Taiwan
- Division of Allergy, Department of Pediatrics, Chung-Shan Medical University Hospital, Taichung, Taiwan
- * E-mail:
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188
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Zeng D, Shen Q, Cho JH. Thermodynamic contribution of backbone conformational entropy in the binding between SH3 domain and proline-rich motif. Biochem Biophys Res Commun 2017; 484:21-26. [DOI: 10.1016/j.bbrc.2017.01.089] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 01/18/2017] [Indexed: 01/08/2023]
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189
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Bansode ND, Madhanagopal B, Sonar MV, Ganesh KN. Stereodependent and solvent-specific formation of unusual β-structure through side chain-backbone H-bonding in C4(S)-(NH2/OH/NHCHO)-L-prolyl polypeptides. Biopolymers 2017; 108. [DOI: 10.1002/bip.22981] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2016] [Revised: 08/08/2016] [Accepted: 08/25/2016] [Indexed: 01/10/2023]
Affiliation(s)
- Nitin D. Bansode
- Chemical Biology Unit, Chemistry Discipline, Indian Institute of Science Education and Research; Dr. Homi Bhabha Road Pashan, Pune 411008
| | - B. Madhanagopal
- Chemical Biology Unit, Chemistry Discipline, Indian Institute of Science Education and Research; Dr. Homi Bhabha Road Pashan, Pune 411008
| | - Mahesh V. Sonar
- Chemical Biology Unit, Chemistry Discipline, Indian Institute of Science Education and Research; Dr. Homi Bhabha Road Pashan, Pune 411008
| | - Krishna N. Ganesh
- Chemical Biology Unit, Chemistry Discipline, Indian Institute of Science Education and Research; Dr. Homi Bhabha Road Pashan, Pune 411008
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190
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Bianco PR, Pottinger S, Tan HY, Nguyenduc T, Rex K, Varshney U. The IDL of E. coli SSB links ssDNA and protein binding by mediating protein-protein interactions. Protein Sci 2017; 26:227-241. [PMID: 28127816 DOI: 10.1002/pro.3072] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 10/17/2016] [Indexed: 11/10/2022]
Abstract
The E. coli single strand DNA binding protein (SSB) is essential to viability where it functions in two seemingly disparate roles: it binds to single stranded DNA (ssDNA) and to target proteins that comprise the SSB interactome. The link between these roles resides in a previously under-appreciated region of the protein known as the intrinsically disordered linker (IDL). We present a model wherein the IDL is responsible for mediating protein-protein interactions critical to each role. When interactions occur between SSB tetramers, cooperative binding to ssDNA results. When binding occurs between SSB and an interactome partner, storage or loading of that protein onto the DNA takes place. The properties of the IDL that facilitate these interactions include the presence of repeats, a putative polyproline type II helix and, PXXP motifs that may facilitate direct binding to the OB-fold in a manner similar to that observed for SH3 domain binding of PXXP ligands in eukaryotic systems.
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Affiliation(s)
- Piero R Bianco
- Department of Microbiology and Immunology, Center for Single Molecule Biophysics, University at Buffalo, Buffalo, New York, 14214
| | - Sasheen Pottinger
- Department of Microbiology and Immunology, Center for Single Molecule Biophysics, University at Buffalo, Buffalo, New York, 14214
| | - Hui Yin Tan
- Department of Microbiology and Immunology, Center for Single Molecule Biophysics, University at Buffalo, Buffalo, New York, 14214
| | - Trong Nguyenduc
- Department of Microbiology and Immunology, Center for Single Molecule Biophysics, University at Buffalo, Buffalo, New York, 14214
| | - Kervin Rex
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Umesh Varshney
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
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191
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Dufayard JF, Bettembourg M, Fischer I, Droc G, Guiderdoni E, Périn C, Chantret N, Diévart A. New Insights on Leucine-Rich Repeats Receptor-Like Kinase Orthologous Relationships in Angiosperms. FRONTIERS IN PLANT SCIENCE 2017; 8:381. [PMID: 28424707 PMCID: PMC5380761 DOI: 10.3389/fpls.2017.00381] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 03/06/2017] [Indexed: 05/18/2023]
Abstract
Leucine-Rich Repeats Receptor-Like Kinase (LRR-RLK) genes represent a large and complex gene family in plants, mainly involved in development and stress responses. These receptors are composed of an LRR-containing extracellular domain (ECD), a transmembrane domain (TM) and an intracellular kinase domain (KD). To provide new perspectives on functional analyses of these genes in model and non-model plant species, we performed a phylogenetic analysis on 8,360 LRR-RLK receptors in 31 angiosperm genomes (8 monocots and 23 dicots). We identified 101 orthologous groups (OGs) of genes being conserved among almost all monocot and dicot species analyzed. We observed that more than 10% of these OGs are absent in the Brassicaceae species studied. We show that the ECD structural features are not always conserved among orthologs, suggesting that functions may have diverged in some OG sets. Moreover, we looked at targets of positive selection footprints in 12 pairs of OGs and noticed that depending on the subgroups, positive selection occurred more frequently either in the ECDs or in the KDs.
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Affiliation(s)
| | | | | | | | | | | | - Nathalie Chantret
- INRA, UMR AGAPMontpellier, France
- *Correspondence: Anne Diévart, Nathalie Chantret,
| | - Anne Diévart
- CIRAD, UMR AGAPMontpellier, France
- *Correspondence: Anne Diévart, Nathalie Chantret,
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192
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Jami-Alahmadi Y, Linford BD, Fridgen TD. Distinguishing Isomeric Peptides: The Unimolecular Reactivity and Structures of (LeuPro)M+ and (ProLeu)M+ (M = Alkali Metal). J Phys Chem B 2016; 120:13039-13046. [DOI: 10.1021/acs.jpcb.6b09588] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Yasaman Jami-Alahmadi
- Department of Chemistry, Memorial University, St. John’s, Newfoundland A1N 4T8, Canada
| | - Bryan D. Linford
- Department of Chemistry, Memorial University, St. John’s, Newfoundland A1N 4T8, Canada
| | - Travis D. Fridgen
- Department of Chemistry, Memorial University, St. John’s, Newfoundland A1N 4T8, Canada
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193
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Margolis HC, Beniash E, Fowler CE. Role of Macromolecular Assembly of Enamel Matrix Proteins in Enamel Formation. J Dent Res 2016; 85:775-93. [PMID: 16931858 DOI: 10.1177/154405910608500902] [Citation(s) in RCA: 207] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Unlike other mineralized tissues, mature dental enamel is primarily (> 95% by weight) composed of apatitic crystals and has a unique hierarchical structure. Due to its high mineral content and organized structure, enamel has exceptional functional properties and is the hardest substance in the human body. Enamel formation (amelogenesis) is the result of highly orchestrated extracellular processes that regulate the nucleation, growth, and organization of forming mineral crystals. However, major aspects of the mechanism of enamel formation are not well-understood, although substantial evidence suggests that protein-protein and protein-mineral interactions play crucial roles in this process. The purpose of this review is a critical evaluation of the present state of knowledge regarding the potential role of the assembly of enamel matrix proteins in the regulation of crystal growth and the structural organization of the resulting enamel tissue. This review primarily focuses on the structure and function of amelogenin, the predominant enamel matrix protein. This review also provides a brief description of novel in vitro approaches that have used synthetic macromolecules ( i.e., surfactants and polymers) to regulate the formation of hierarchical inorganic (composite) structures in a fashion analogous to that believed to take place in biological systems, such as enamel. Accordingly, this review illustrates the potential for developing bio-inspired approaches to mineralized tissue repair and regeneration. In conclusion, the authors present a hypothesis, based on the evidence presented, that the full-length amelogenin uniquely regulates proper enamel formation through a process of cooperative mineralization, and not as a pre-formed matrix.
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Affiliation(s)
- H C Margolis
- Department of Biomineralization, The Forsyth Institute, 140 The Fenway, Boston, MA 02115, USA.
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194
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A dual inhibition mechanism of herpesviral ICP47 arresting a conformationally thermostable TAP complex. Sci Rep 2016; 6:36907. [PMID: 27845362 PMCID: PMC5109273 DOI: 10.1038/srep36907] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 10/24/2016] [Indexed: 11/09/2022] Open
Abstract
As a centerpiece of antigen processing, the ATP-binding cassette transporter associated with antigen processing (TAP) became a main target for viral immune evasion. The herpesviral ICP47 inhibits TAP function, thereby suppressing an adaptive immune response. Here, we report on a thermostable ICP47-TAP complex, generated by fusion of different ICP47 fragments. These fusion complexes allowed us to determine the direction and positioning in the central cavity of TAP. ICP47-TAP fusion complexes are arrested in a stable conformation, as demonstrated by MHC I surface expression, melting temperature, and the mutual exclusion of herpesviral TAP inhibitors. We unveiled a conserved region next to the active domain of ICP47 as essential for the complete stabilization of the TAP complex. Binding of the active domain of ICP47 arrests TAP in an open inward facing conformation rendering the complex inaccessible for other viral factors. Based on our findings, we propose a dual interaction mechanism for ICP47. A per se destabilizing active domain inhibits the function of TAP, whereas a conserved C-terminal region additionally stabilizes the transporter. These new insights into the ICP47 inhibition mechanism can be applied for future structural analyses of the TAP complex.
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195
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Bianco PR. The tale of SSB. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2016; 127:111-118. [PMID: 27838363 DOI: 10.1016/j.pbiomolbio.2016.11.001] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 11/04/2016] [Indexed: 01/07/2023]
Abstract
The E. coli single stranded DNA binding protein (SSB) is essential to all aspects of DNA metabolism. Here, it has two seemingly disparate but equally important roles: it binds rapidly and cooperatively to single stranded DNA (ssDNA) and it binds to partner proteins that constitute the SSB interactome. These two roles are not disparate but are instead, intimately linked. A model is presented wherein the intrinsically disordered linker (IDL) is directly responsible for mediating protein-protein interactions. It does this by binding, via PXXP motifs, to the OB-fold (aka SH3 domain) of a nearby protein. When the nearby protein is another SSB tetramer, this leads to a highly efficient ssDNA binding reaction that rapidly and cooperatively covers and protects the exposed nucleic acid from degradation. Alternatively, when the nearby protein is a member of the SSB interactome, loading of the enzyme onto the DNA takes places.
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Affiliation(s)
- Piero R Bianco
- Center for Single Molecule Biophysics, Department of Biochemistry, University at Buffalo, Buffalo, NY, 14214, USA; Department of Microbiology and Immunology, University at Buffalo, Buffalo, NY, 14214, USA.
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196
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Tisdale EJ, Talati NK, Artalejo CR, Shisheva A. GAPDH binds Akt to facilitate cargo transport in the early secretory pathway. Exp Cell Res 2016; 349:310-319. [PMID: 27818247 DOI: 10.1016/j.yexcr.2016.10.025] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 10/12/2016] [Accepted: 10/31/2016] [Indexed: 01/12/2023]
Abstract
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) undergoes numerous post-translational modifications, which impart new function and influence intracellular location. For example, atypical PKC ι/λ phosphorylates GAPDH that locates to vesicular tubular clusters and is required for retrograde membrane trafficking in the early secretory pathway. GAPDH is also required in the endocytic pathway; substitution of Pro234 to Ser (Pro234Ser) rendered CHO cells defective in endocytosis. To determine if GAPDH (Pro234Ser) could inhibit endoplasmic reticulum to Golgi trafficking, we introduced the recombinant mutant enzyme into several biochemical and morphological transport assays. The mutant protein efficiently blocked vesicular stomatitis virus-G protein transport. Because GAPDH binds to microtubules (MTs), we evaluated MT binding and MT intracellular distribution in the presence of the mutant. Although these properties were not changed relative to wild-type, GAPDH (Pro234Ser) altered Golgi complex morphology. We determined that the GAPDH point mutation disrupted association between the enzyme and the serine/threonine kinase Akt. Interestingly Rab1, which functions in anterograde-directed trafficking, stimulates GAPDH-Akt association with membranes in a quantitative binding assay. In contrast, Rab2 does not stimulate GAPDH-Akt membrane binding but instead recruits GAPDH-aPKC. We propose a mechanism whereby the association of GAPDH with Akt or with aPKC serves as a switch to discriminate between anterograde directed cargo and recycling cargo retrieved back to the ER, respectively.
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Affiliation(s)
- Ellen J Tisdale
- Department of Pharmacology, Wayne State University School of Medicine, 540 E. Canfield Ave., 6374 Scott Hall, Detroit, MI 48201, USA.
| | - Nikunj K Talati
- Department of Pharmacology, Wayne State University School of Medicine, 540 E. Canfield Ave., 6374 Scott Hall, Detroit, MI 48201, USA
| | - Cristina R Artalejo
- Department of Pharmacology, Wayne State University School of Medicine, 540 E. Canfield Ave., 6374 Scott Hall, Detroit, MI 48201, USA
| | - Assia Shisheva
- Department of Physiology, Wayne State University School of Medicine, 540 E. Canfield Ave., 6374 Scott Hall, Detroit, MI 48201, USA
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197
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Samipillai M, Bhatt N, Kruger HG, Govender T, Naicker T. Diverse supramolecular arrangement of substituted oxopyrrolidine analogues influenced by weak intermolecular interactions (CH⋯O/CH⋯π/H⋯H). J Mol Struct 2016. [DOI: 10.1016/j.molstruc.2016.05.042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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198
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Benz PM, Laban H, Zink J, Günther L, Walter U, Gambaryan S, Dib K. Vasodilator-Stimulated Phosphoprotein (VASP)-dependent and -independent pathways regulate thrombin-induced activation of Rap1b in platelets. Cell Commun Signal 2016; 14:21. [PMID: 27620165 PMCID: PMC5020514 DOI: 10.1186/s12964-016-0144-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 09/06/2016] [Indexed: 11/13/2022] Open
Abstract
Background Vasodilator-Stimulated Phosphoprotein (VASP) is involved in the inhibition of agonist-induced platelet aggregation by cyclic nucleotides and the adhesion of platelets to the vascular wall. αIIbβ3 is the main integrin responsible for platelet activation and Rap1b plays a key role in integrin signalling. We investigated whether VASP is involved in the regulation of Rap1b in platelets since VASP-null platelets exhibit augmented adhesion to endothelial cells in vivo. Methods Washed platelets from wild type and VASP-deficient mice were stimulated with thrombin, the purinergic receptors agonist ADP, or the thromboxane A2 receptor agonist U46619 and Rap1b activation was measured using the GST-RalGDS-RBD binding assay. Interaction of VASP and Crkl was investigated by co-immunoprecipitation, confocal microscopy, and pull-down assays using Crkl domains expressed as GST-fusion proteins. Results Surprisingly, we found that activation of Rap1b in response to thrombin, ADP, or U46619 was significantly reduced in platelets from VASP-null mice compared to platelets from wild type mice. However, inhibition of thrombin-induced activation of Rap1b by nitric oxide (NO) was similar in platelets from wild type and VASP-null mice indicating that the NO/cGMP/PKG pathway controls inhibition of Rap1b independently from VASP. To understand how VASP regulated Rap1b, we investigated association between VASP and the Crk-like protein (Crkl), an adapter protein which activates the Rap1b guanine nucleotide exchange factor C3G. We demonstrated the formation of a Crkl/VASP complex by showing that: 1) Crkl co-immunoprecipitated VASP from platelet lysates; 2) Crkl and VASP dynamically co-localized at actin-rich protrusions reminiscent of focal adhesions, filopodia, and lamellipodia upon platelet spreading on fibronectin; 3) recombinant VASP bound directly to the N-terminal SH3 domain of Crkl; 4) Protein Kinase A (PKA) -mediated VASP phosphorylation on Ser157 abrogated the binding of Crkl. Conclusions We identified Crkl as a novel protein interacting with VASP in platelets. We propose that the C3G/Crkl/VASP complex plays a role in the regulation of Rap1b and this explains, at least in part, the reduced agonist-induced activation of Rap1b in VASP-null platelets. In addition, the fact that PKA-dependent VASP phosphorylation abrogated its interaction with Crkl may provide, at least in part, a rationale for the PKA-dependent inhibition of Rap1b and platelet aggregation.
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Affiliation(s)
- Peter M Benz
- Institute for Vascular Signalling, Centre for Molecular Medicine, Johann Wolfgang Goethe University and DZHK (German Centre for Cardiovascular Research) partner site Rhine-Main, 60590, Frankfurt, Germany
| | - Hebatullah Laban
- Institute for Vascular Signalling, Centre for Molecular Medicine, Johann Wolfgang Goethe University and DZHK (German Centre for Cardiovascular Research) partner site Rhine-Main, 60590, Frankfurt, Germany
| | - Joana Zink
- Institute for Vascular Signalling, Centre for Molecular Medicine, Johann Wolfgang Goethe University and DZHK (German Centre for Cardiovascular Research) partner site Rhine-Main, 60590, Frankfurt, Germany
| | - Lea Günther
- Institute for Vascular Signalling, Centre for Molecular Medicine, Johann Wolfgang Goethe University and DZHK (German Centre for Cardiovascular Research) partner site Rhine-Main, 60590, Frankfurt, Germany
| | - Ulrich Walter
- Centre for Thrombosis and Hemostasis (CTH), University Medical Center Mainz, Mainz, Germany
| | - Stepan Gambaryan
- Department of Cytology and Histology, St. Petersburg State University, St. Petersburg, Russia.,Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, St. Petersburg, Russia
| | - Karim Dib
- Centre for Experimental Medicine, Medical Biology Center (MBC) building, Queen's University of Belfast, Third floor, 97 Lisburn Road, BT9 7BL, Belfast, Northern Ireland, UK.
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199
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Kumar P, Bansal M. Structural and functional analyses of PolyProline-II helices in globular proteins. J Struct Biol 2016; 196:414-425. [PMID: 27637571 DOI: 10.1016/j.jsb.2016.09.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 09/01/2016] [Accepted: 09/12/2016] [Indexed: 11/18/2022]
Abstract
PolyProline-II (PPII) helices are defined as a continuous stretch of a protein chain in which the constituent residues have backbone torsion angle (φ, ψ) values of (-75°, 145°) and take up an extended left handed helical conformation, without any intra-chain hydrogen bonds. They are found to occur quite frequently in protein structures, with their number exceeding that of π-helices, though it is considerably less than that of α-helices and β-strands. A relatively new procedure, ASSP, for the identification of regular secondary structures using Cα trace identifies 3597 PPII-helices in 3582 protein chains, solved at resolution ⩽2.0Å. Taking advantage of this significantly expanded database of PPII-helices, we have analyzed their structural and functional roles as well as determined the amino acid propensity within and around them. Though Pro residues are highly preferred, their presence is not a mandatory requirement for the formation of PPII-helices, since ∼40% PPII-helices were found to contain no Pro residues. Aromatic amino acids are avoided within this helix, while Gly, Asn and Asp residues are preferred in the proximal flanking regions. The PPII-helices range from 3 to 13 residues in length with the average twist and rise being -121.2°±9.2° and 3.0ű0.1Å respectively. A majority (∼72%) of PPII-helices were found to occur in conjunction with α-helices and β-strands, and serve as linkers as well. The analysis of various intra-helical non-bonded interactions revealed frequent presence of CH⋯O H-bonds. PPII-helices participate in maintaining the three-dimensional structure of proteins and are important constituents of binding motifs involved in various biological functions.
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Affiliation(s)
- Prasun Kumar
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Manju Bansal
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India.
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200
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Immunogenic peptide mimotopes from an epitope of Escherichia coli O157 LPS. Biochem J 2016; 473:3791-3804. [PMID: 27623774 DOI: 10.1042/bcj20160687] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 09/13/2016] [Indexed: 11/17/2022]
Abstract
Escherichia coli O157:H7 is a subtype of Shiga toxin-producing E. coli that is associated with haemorrhagic colitis and haemolytic uremic syndrome (HUS). Studies of populations in endemic areas have reported that the presence of specific antibodies against the O157 lipopolysaccharide (LPS) is associated with a lower incidence of diarrhoea and HUS. Phage display and IgG anti-O157 LPS antibodies were used in the present study to select peptide mimotopes of O157 LPS expressed in protein III of the M13 phage. Synthetic peptides (SP) were designed using the derived amino acid sequences obtained from DNA nucleotides of 63 selected phagotopes. The LxP/YP/SxL motif was identified in five of the phagotope amino acid sequences. Antibody responses against the phagotopes and their corresponding SPs were evaluated. SP12, one of the designed SP, induced the production of antibodies against the homologous peptide (1:800) and O157 LPS (1:200). The specificity of anti-SP12 antiserum was confirmed by analyzing its response to SP3, an SP with a different amino acid sequence than that of SP12, as well as against an E. coli LPS different from O157. Competitive studies with SP12 and O157 LPS showed a significant decrease in anti-SP12 and anti-LPS O157 antiserum responses against SP12 and O157 LPS, respectively. Eighteen (82%) of the 22 human serum samples with positive reactivity against E coli O157 LPS reacted with SP12 SP (cut-off >0.4). These results support the idea that SP12 is an immunogenic mimotope of O157 LPS.
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