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Qu HQ, Kao C, Garifallou J, Wang F, Snyder J, Slater DJ, Hou C, March M, Connolly JJ, Glessner JT, Hakonarson H. Single Cell Transcriptome Analysis of Peripheral Blood Mononuclear Cells in Freshly Isolated versus Stored Blood Samples. Genes (Basel) 2023; 14:142. [PMID: 36672883 PMCID: PMC9859202 DOI: 10.3390/genes14010142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 12/27/2022] [Accepted: 01/03/2023] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Peripheral blood mononuclear cells (PBMCs) are widely used as a model in the study of different human diseases. There is often a time delay from blood collection to PBMC isolation during the sampling process, which can result in an experimental bias, particularly when performing single cell RNA-seq (scRNAseq) studies. METHODS This study examined the impact of different time periods from blood draw to PBMC isolation on the subsequent transcriptome profiling of different cell types in PBMCs by scRNAseq using the 10X Chromium Single Cell Gene Expression assay. RESULTS Examining the five major cell types constituting the PBMC cell population, i.e., CD4+ T cells, CD8+ T cells, NK cells, monocytes, and B cells, both common changes and cell-type-specific changes were observed in the single cell transcriptome profiling over time. In particular, the upregulation of genes regulated by NF-kB in response to TNF was observed in all five cell types. Significant changes in key genes involved in AP-1 signaling were also observed. RBC contamination was a major issue in stored blood, whereas RBC adherence had no direct impact on the cell transcriptome. CONCLUSIONS Significant transcriptome changes were observed across different PBMC cell types as a factor of time from blood draw to PBMC isolation and as a consequence of blood storage. This should be kept in mind when interpreting experimental results.
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Affiliation(s)
- Hui-Qi Qu
- The Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Charlly Kao
- The Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - James Garifallou
- The Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Fengxiang Wang
- The Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - James Snyder
- The Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Diana J. Slater
- The Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Cuiping Hou
- The Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Michael March
- The Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - John J. Connolly
- The Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Joseph T. Glessner
- The Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Hakon Hakonarson
- The Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Pulmonary Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland
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E Costa RAP, Granato DC, Trino LD, Yokoo S, Carnielli CM, Kawahara R, Domingues RR, Pauletti BA, Neves LX, Santana AG, Paulo JA, Aragão AZB, Heleno Batista FA, Migliorini Figueira AC, Laurindo FRM, Fernandes D, Hansen HP, Squina F, Gygi SP, Paes Leme AF. ADAM17 cytoplasmic domain modulates Thioredoxin-1 conformation and activity. Redox Biol 2020; 37:101735. [PMID: 33011677 PMCID: PMC7513893 DOI: 10.1016/j.redox.2020.101735] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/26/2020] [Accepted: 09/17/2020] [Indexed: 12/15/2022] Open
Abstract
The activity of Thioredoxin-1 (Trx-1) is adjusted by the balance of its monomeric, active and its dimeric, inactive state. The regulation of this balance is not completely understood. We have previously shown that the cytoplasmic domain of the transmembrane protein A Disintegrin And Metalloprotease 17 (ADAM17cyto) binds to Thioredoxin-1 (Trx-1) and the destabilization of this interaction favors the dimeric state of Trx-1. Here, we investigate whether ADAM17 plays a role in the conformation and activation of Trx-1. We found that disrupting the interacting interface with Trx-1 by a site-directed mutagenesis in ADAM17 (ADAM17cytoF730A) caused a decrease of Trx-1 reductive capacity and activity. Moreover, we observed that ADAM17 overexpressing cells favor the monomeric state of Trx-1 while knockdown cells do not. As a result, there is a decrease of cell oxidant levels and ADAM17 sheddase activity and an increase in the reduced cysteine-containing peptides in intracellular proteins in ADAM17cyto overexpressing cells. A mechanistic explanation that ADAM17cyto favors the monomeric, active state of Trx-1 is the formation of a disulfide bond between Cys824 at the C-terminal of ADAM17cyto with the Cys73 of Trx-1, which is involved in the dimerization site of Trx-1. In summary, we propose that ADAM17 is able to modulate Trx-1 conformation affecting its activity and intracellular redox state, bringing up a novel possibility for positive regulation of thiol isomerase activity in the cell by mammalian metalloproteinases.
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Affiliation(s)
- Rute A P E Costa
- Laboratório Nacional de Biociências, LNBio, CNPEM, Campinas, São Paulo, Brazil
| | - Daniela C Granato
- Laboratório Nacional de Biociências, LNBio, CNPEM, Campinas, São Paulo, Brazil
| | - Luciana D Trino
- Laboratório Nacional de Biociências, LNBio, CNPEM, Campinas, São Paulo, Brazil
| | - Sami Yokoo
- Laboratório Nacional de Biociências, LNBio, CNPEM, Campinas, São Paulo, Brazil
| | | | - Rebeca Kawahara
- Laboratório Nacional de Biociências, LNBio, CNPEM, Campinas, São Paulo, Brazil
| | - Romênia R Domingues
- Laboratório Nacional de Biociências, LNBio, CNPEM, Campinas, São Paulo, Brazil
| | | | | | - Aline G Santana
- Laboratório Nacional de Biociências, LNBio, CNPEM, Campinas, São Paulo, Brazil
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, USA
| | - Annelize Z B Aragão
- Laboratório Nacional de Biociências, LNBio, CNPEM, Campinas, São Paulo, Brazil
| | | | | | - Francisco R M Laurindo
- Instituto Do Coração, Faculdade de Medicina, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Denise Fernandes
- Instituto Do Coração, Faculdade de Medicina, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Hinrich P Hansen
- Department of Internal Medicine I, University Hospital Cologne, CECAD Research Center, Cologne, Germany
| | - Fabio Squina
- Universidade de Sorocaba, Departamento de Processos Tecnológicos e Ambientais, São Paulo, Brazil
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, USA
| | - Adriana F Paes Leme
- Laboratório Nacional de Biociências, LNBio, CNPEM, Campinas, São Paulo, Brazil.
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Roskamp KW, Azim S, Kassier G, Norton-Baker B, Sprague-Piercy MA, Miller RJD, Martin RW. Human γS-Crystallin-Copper Binding Helps Buffer against Aggregation Caused by Oxidative Damage. Biochemistry 2020; 59:2371-2385. [PMID: 32510933 DOI: 10.1021/acs.biochem.0c00293] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Divalent metal cations can play a role in protein aggregation diseases, including cataract. Here we compare the aggregation of human γS-crystallin, a key structural protein of the eye lens, via mutagenesis, ultraviolet light damage, and the addition of metal ions. All three aggregation pathways result in globular, amorphous-looking structures that do not elongate into fibers. We also investigate the molecular mechanism underlying copper(II)-induced aggregation. This work was motivated by the observation that zinc(II)-induced aggregation of γS-crystallin is driven by intermolecular bridging of solvent-accessible cysteine residues, while in contrast, copper(II)-induced aggregation of this protein is exacerbated by the removal of solvent-accessible cysteines via mutation. Here we find that copper(II)-induced aggregation results from a complex mechanism involving multiple interactions with the protein. The initial protein-metal interactions result in the reduction of Cu(II) to Cu(I) with concomitant oxidation of γS-crystallin. In addition to the intermolecular disulfides that represent a starting point for aggregation, intramolecular disulfides also occur in the cysteine loop, a region of the N-terminal domain that was previously found to mediate the early stages of cataract formation. This previously unobserved ability of γS-crystallin to transfer disulfides intramolecularly suggests that it may serve as an oxidation sink for the lens after glutathione levels have become depleted during aging. γS-Crystallin thus serves as the last line of defense against oxidation in the eye lens, a result that underscores the chemical functionality of this protein, which is generally considered to play a purely structural role.
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Affiliation(s)
- Kyle W Roskamp
- Department of Chemistry, University of California, Irvine, California 92697-2025, United States
| | - Sana Azim
- Max Planck Institute for the Structure and Dynamics of Matter, Center for Free Electron Laser Science, Luruper Chaussee 149, Hamburg 22761, Germany
| | - Günther Kassier
- Max Planck Institute for the Structure and Dynamics of Matter, Center for Free Electron Laser Science, Luruper Chaussee 149, Hamburg 22761, Germany
| | - Brenna Norton-Baker
- Department of Chemistry, University of California, Irvine, California 92697-2025, United States.,Max Planck Institute for the Structure and Dynamics of Matter, Center for Free Electron Laser Science, Luruper Chaussee 149, Hamburg 22761, Germany
| | - Marc A Sprague-Piercy
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3900, United States
| | - R J Dwyane Miller
- Max Planck Institute for the Structure and Dynamics of Matter, Center for Free Electron Laser Science, Luruper Chaussee 149, Hamburg 22761, Germany.,Departments of Chemistry and Physics, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada
| | - Rachel W Martin
- Department of Chemistry, University of California, Irvine, California 92697-2025, United States.,Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3900, United States
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He H, Wu S, Mei M, Ning J, Li C, Ma L, Zhang G, Yi L. A Combinational Strategy for Effective Heterologous Production of Functional Human Lysozyme in Pichia pastoris. Front Bioeng Biotechnol 2020; 8:118. [PMID: 32211388 PMCID: PMC7075855 DOI: 10.3389/fbioe.2020.00118] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Accepted: 02/06/2020] [Indexed: 11/13/2022] Open
Abstract
Human lysozyme (hLYZ), known for its bacteriolytic activity, is widely applied in the food and pharmaceutical industries as an antimicrobial agent. However, its extensive application was limited by its low large-scale production efficiency. In this study, a combinational method of integrating codon optimization, multiple gene copies, and ER molecular chaperone co-expression was developed to improve the heterologous production of hLYZ in Pichia pastoris GS115. Our results showed that increasing the copy number of the optimized hLYZ gene in P. pastoris could enhance its secretory production level up to 1.57-fold. The recombinant opt-hLYZ-6C strain that contains six copies of opt-hLYZ gene exhibited the highest mRNA transcription levels, giving the highest production of 0.22 ± 0.02 mg/mL of hLYZ in the medium supernatant with a bacteriolytic activity of 14,680 ± 300 U/mL against Micrococcus lysodeikticus in the shaking flask experiment. Moreover, co-overexpression of ER retention molecular chaperones, such as Pdi1 or Ero1, in the recombinant opt-hLYZ-6C strain both presented positive effects on the secretory production of hLYZ. Our further characterization indicated that tandem co-expression of Ero1 and Pdi1 together presented an added-up effect. The secretory production of hLYZ in the medium supernatant reached 0.34 ± 0.02 mg/mL of the recombinant opt-hLYZ-6C-EP strain in the shaking flask experiment, with a bacteriolytic activity of 21,200 ± 400 U/mL. Compared to the recombinant opt-hLYZ-1C strain, these final improvements were calculated as 2.43-fold and 2.30-fold on secretory protein levels and antibacterial activity, respectively. Finally, the recombinant opt-hLYZ-6C-EP strain was applied for high-density cultivation in 5 L of fermenter, in which the secretory yield of hLYZ reached 2.34 ± 0.02 mg/mL in the medium supernatant, with a bacteriolytic activity of 1.76 ± 0.02 × 105 U/mL against M. lysodeikticus. All these numbers presented the highest heterologous production levels of hLYZ in microbial systems.
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Affiliation(s)
- Huahua He
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Engineering Research Center for Bio-enzyme Catalysis, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, China
| | - Shijie Wu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Engineering Research Center for Bio-enzyme Catalysis, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, China
| | - Meng Mei
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Engineering Research Center for Bio-enzyme Catalysis, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, China
| | - Jiali Ning
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Engineering Research Center for Bio-enzyme Catalysis, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, China
| | - Chaoyin Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Engineering Research Center for Bio-enzyme Catalysis, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, China
| | - Lixin Ma
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Engineering Research Center for Bio-enzyme Catalysis, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, China
| | - Guimin Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Engineering Research Center for Bio-enzyme Catalysis, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, China
| | - Li Yi
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Engineering Research Center for Bio-enzyme Catalysis, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, China
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Di Girolamo M, Fabrizio G. Overview of the mammalian ADP-ribosyl-transferases clostridia toxin-like (ARTCs) family. Biochem Pharmacol 2019; 167:86-96. [PMID: 31283932 DOI: 10.1016/j.bcp.2019.07.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 07/03/2019] [Indexed: 01/22/2023]
Abstract
Mono-ADP-ribosylation is a reversible post-translational protein modification that modulates the function of proteins involved in different cellular processes, including signal transduction, protein transport, transcription, cell cycle regulation, DNA repair and apoptosis. In mammals, mono-ADP-ribosylation is mainly catalyzed by members of two different classes of enzymes: ARTCs and ARTDs. The human ARTC family is composed of four structurally related ecto-mono-ARTs, expressed at the cell surface or secreted into the extracellular compartment that are either active mono-ARTs (hARTC1, hARTC5) or inactive proteins (hARTC3, hARTC4). The human ARTD enzyme family consists of 17 multidomain proteins that can be divided on the basis of their catalytic activity into polymerases (ARTD1-6), mono-ART (ARTD7-17), and the inactive ARTD13. In recent years, ADP-ribosylation was intensively studied, and research was dominated by studies focusing on the role of this modification and its implication on various cellular processes. The aim of this review is to provide a general overview of the ARTC enzymes. In the following sections, we will report the mono-ADP-ribosylation reactions that are catalysed by the active ARTC enzymes, with a particular focus on hARTC1 that recently has been intensively studied with the discovery of new targets and functions.
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Affiliation(s)
- Maria Di Girolamo
- SoL&Pharma s.r.l. Biotechnology Research, Registered Office, Via Brasile 13, 66030 Mozzagrogna, CH, Italy.
| | - Gaia Fabrizio
- SoL&Pharma s.r.l. Biotechnology Research, Registered Office, Via Brasile 13, 66030 Mozzagrogna, CH, Italy
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6
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Biosynthesis of human myeloperoxidase. Arch Biochem Biophys 2018; 642:1-9. [PMID: 29408362 DOI: 10.1016/j.abb.2018.02.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 01/31/2018] [Accepted: 02/02/2018] [Indexed: 01/30/2023]
Abstract
Members of Chordata peroxidase subfamily [1] expressed in mammals, including myeloperoxidase (MPO), eosinophil peroxidase (EPO), lactoperoxidase (LPO), and thyroid peroxidase (TPO), express conserved motifs around the heme prosthetic group essential for their activity, a calcium-binding site, and at least two covalent bonds linking the heme group to the protein backbone. Although most studies of the biosynthesis of these peroxidases have focused on MPO, many of the features described occur during biosynthesis of other members of the protein subfamily. Whereas MPO biosynthesis includes events typical for proteins generated in the secretory pathway, the importance and consequences of heme insertion are events uniquely associated with peroxidases. This Review summarizes decades of work elucidating specific steps in the biosynthetic pathway of human MPO. Discussion includes cotranslational glycosylation and subsequent modifications of the N-linked carbohydrate sidechains, contributions by molecular chaperones in the endoplasmic reticulum, cleavage of the propeptide from proMPO, and proteolytic processing of protomers and dimerization to yield mature MPO. Parallels between the biosynthesis of MPO and TPO as well as the impact of inherited mutations in the MPO gene on normal biosynthesis will be summarized. Lastly, specific gaps in our knowledge revealed by this review of our current understanding will be highlighted.
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Fabrizio G, Di Paola S, Stilla A, Giannotta M, Ruggiero C, Menzel S, Koch-Nolte F, Sallese M, Di Girolamo M. ARTC1-mediated ADP-ribosylation of GRP78/BiP: a new player in endoplasmic-reticulum stress responses. Cell Mol Life Sci 2015; 72:1209-25. [PMID: 25292337 PMCID: PMC11113179 DOI: 10.1007/s00018-014-1745-6] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 09/23/2014] [Accepted: 09/25/2014] [Indexed: 12/12/2022]
Abstract
Protein mono-ADP-ribosylation is a reversible post-translational modification of cellular proteins. This scheme of amino-acid modification is used not only by bacterial toxins to attack host cells, but also by endogenous ADP-ribosyltransferases (ARTs) in mammalian cells. These latter ARTs include members of three different families of proteins: the well characterised arginine-specific ecto-enzymes (ARTCs), two sirtuins, and some members of the poly(ADP-ribose) polymerase (PARP/ARTD) family. In the present study, we demonstrate that human ARTC1 is localised to the endoplasmic reticulum (ER), in contrast to the previously characterised ARTC proteins, which are typical GPI-anchored ecto-enzymes. Moreover, using the "macro domain" cognitive binding module to identify ADP-ribosylated proteins, we show here that the ER luminal chaperone GRP78/BiP (glucose-regulated protein of 78 kDa/immunoglobulin heavy-chain-binding protein) is a cellular target of human ARTC1 and hamster ARTC2. We further developed a procedure to visualise ADP-ribosylated proteins using immunofluorescence. With this approach, in cells overexpressing ARTC1, we detected staining of the ER that co-localises with GRP78/BiP, thus confirming that this modification occurs in living cells. In line with the key role of GRP78/BiP in the ER stress response system, we provide evidence here that ARTC1 is activated during the ER stress response, which results in acute ADP-ribosylation of GRP78/BiP paralleling translational inhibition. Thus, this identification of ARTC1 as a regulator of GRP78/BiP defines a novel, previously unsuspected, player in GRP78-mediated ER stress responses.
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Affiliation(s)
- Gaia Fabrizio
- Laboratory of G-Protein-mediated Signalling, Department of Cellular and Translational Pharmacology, Mario Negri Sud Foundation, Via Nazionale 8/A, 66030 Santa Maria Imbaro, CH Italy
| | - Simone Di Paola
- Laboratory of G-Protein-mediated Signalling, Department of Cellular and Translational Pharmacology, Mario Negri Sud Foundation, Via Nazionale 8/A, 66030 Santa Maria Imbaro, CH Italy
- Present Address: Telethon Institute of Genetics and Medicine, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Annalisa Stilla
- Laboratory of G-Protein-mediated Signalling, Department of Cellular and Translational Pharmacology, Mario Negri Sud Foundation, Via Nazionale 8/A, 66030 Santa Maria Imbaro, CH Italy
| | - Monica Giannotta
- Genomic Approaches to Membrane Traffic Unit, Department of Cellular and Translational Pharmacology, Mario Negri Sud Foundation, Via Nazionale, 8/A, 66030 Santa Maria Imbaro, CH Italy
- Present Address: Unit of Vascular Biology, The FIRC Institute of Molecular Oncology Foundation, Milan, Italy
| | - Carmen Ruggiero
- Genomic Approaches to Membrane Traffic Unit, Department of Cellular and Translational Pharmacology, Mario Negri Sud Foundation, Via Nazionale, 8/A, 66030 Santa Maria Imbaro, CH Italy
- Present Address: Associated International Laboratory (LIA) NEOGENEX CNRS, University of Nice Sophia Antipolis, Institut de Pharmacologie Moléculaire et Cellulaire, CNRS, 660 route des Lucioles, Sophia Antipolis, 06560 Valbonne, France
| | - Stephan Menzel
- Institute of Immunology, University Medical Centre Hamburg-Eppendorf, Martinist 52, 20246 Hamburg, Germany
| | - Friedrich Koch-Nolte
- Institute of Immunology, University Medical Centre Hamburg-Eppendorf, Martinist 52, 20246 Hamburg, Germany
| | - Michele Sallese
- Genomic Approaches to Membrane Traffic Unit, Department of Cellular and Translational Pharmacology, Mario Negri Sud Foundation, Via Nazionale, 8/A, 66030 Santa Maria Imbaro, CH Italy
| | - Maria Di Girolamo
- Laboratory of G-Protein-mediated Signalling, Department of Cellular and Translational Pharmacology, Mario Negri Sud Foundation, Via Nazionale 8/A, 66030 Santa Maria Imbaro, CH Italy
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Fizil Á, Gáspári Z, Barna T, Marx F, Batta G. "Invisible" conformers of an antifungal disulfide protein revealed by constrained cold and heat unfolding, CEST-NMR experiments, and molecular dynamics calculations. Chemistry 2015; 21:5136-44. [PMID: 25676351 PMCID: PMC4464532 DOI: 10.1002/chem.201404879] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Indexed: 12/12/2022]
Abstract
Transition between conformational states in proteins is being recognized as a possible key factor of function. In support of this, hidden dynamic NMR structures were detected in several cases up to populations of a few percent. Here, we show by two- and three-state analysis of thermal unfolding, that the population of hidden states may weight 20-40 % at 298 K in a disulfide-rich protein. In addition, sensitive (15) N-CEST NMR experiments identified a low populated (0.15 %) state that was in slow exchange with the folded PAF protein. Remarkably, other techniques failed to identify the rest of the NMR "dark matter". Comparison of the temperature dependence of chemical shifts from experiments and molecular dynamics calculations suggests that hidden conformers of PAF differ in the loop and terminal regions and are most similar in the evolutionary conserved core. Our observations point to the existence of a complex conformational landscape with multiple conformational states in dynamic equilibrium, with diverse exchange rates presumably responsible for the completely hidden nature of a considerable fraction.
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Affiliation(s)
- Ádám Fizil
- Department of Organic Chemistry, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, 4032 Debrecen (Hungary)
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Mitropoulos V, Mütze A, Fischer P. Mechanical properties of protein adsorption layers at the air/water and oil/water interface: a comparison in light of the thermodynamical stability of proteins. Adv Colloid Interface Sci 2014; 206:195-206. [PMID: 24332621 DOI: 10.1016/j.cis.2013.11.004] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Revised: 09/07/2013] [Accepted: 11/06/2013] [Indexed: 01/18/2023]
Abstract
Over the last decades numerous studies on the interfacial rheological response of protein adsorption layers have been published. The comparison of these studies and the retrieval of a common parameter to compare protein interfacial activity are hampered by the fact that different boundary conditions (e.g. physico-chemical, instrumental, interfacial) were used. In the present work we review previous studies and attempt a unifying approach for the comparison between bulk protein properties and their adsorption films. Among many common food grade proteins we chose bovine serum albumin, β-lactoglobulin and lysozyme for their difference in thermodynamic stability and studied their adsorption at the air/water and limonene/water interface. In order to achieve this we have i) systematically analyzed protein adsorption kinetics in terms of surface pressure rise using a drop profile analysis tensiometer and ii) we addressed the interfacial layer properties under shear stress using an interfacial shear rheometer under the same experimental conditions. We could show that thermodynamically less stable proteins adsorb generally faster and yield films with higher shear rheological properties at air/water interface. The same proteins showed an analog behavior when adsorbing at the limonene/water interface but at slower rates.
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Che P, Tang H, Li Q. The interaction between claudin-1 and dengue viral prM/M protein for its entry. Virology 2013; 446:303-13. [PMID: 24074594 DOI: 10.1016/j.virol.2013.08.009] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Revised: 07/18/2013] [Accepted: 08/09/2013] [Indexed: 02/04/2023]
Abstract
Dengue disease is becoming a huge public health concern around the world as more than one-third of the world's population living in areas at risk of infection. In an effort to assess host factors interacting with dengue virus, we identified claudin-1, a major tight junction component, as an essential cell surface protein for dengue virus entry. When claudin-1 was knocked down in Huh 7.5 cells via shRNA, the amount of dengue virus entering host cells was reduced. Consequently, the progeny virus productions were decreased and dengue virus-induced CPE was prevented. Furthermore, restoring the expression of claudin-1 in the knockdown cells facilitated dengue virus entry. The interaction between claudin-1 and dengue viral prM protein was further demonstrated using the pull-down assay. Deletion of the extracellular loop 1 (ECL1) of claudin-1 abolished such interaction, so did point mutations C54A, C64A and I32M on ECL1. These results suggest that the interaction between viral protein prM and host protein claudin-1 was essential for dengue entry. Since host and viral factors involved in virus entry are promising therapeutic targets, determining the essential role of claudin-1 could lead to the discovery of entry inhibitors with attractive therapeutic potential against dengue disease.
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Affiliation(s)
- Pulin Che
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, United States; University of Alabama at Birmingham, Department of Medicine, Division of Infectious Diseases, BBRB 562, 845 19th Street South, Birmingham, AL 35294, United States
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Venketesh S, Dayananda C. Properties, Potentials, and Prospects of Antifreeze Proteins. Crit Rev Biotechnol 2008; 28:57-82. [DOI: 10.1080/07388550801891152] [Citation(s) in RCA: 120] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Abstract
In prokaryotes, disulfides are generated by the DsbA-DsbB system. DsbB functions to generate disulfides by quinone reduction. These disulfides are passed to the DsbA protein and then to folding proteins. To investigate the DsbA-DsbB catalytic system, we performed an in vivo selection for chromosomal dsbA and dsbB mutants. We rediscovered many residues previously shown to be important for the activity of these proteins. In addition, we obtained one novel DsbA mutant (M153R) and four novel DsbB mutants (L43P, H91Y, R133C, and L146R). We also mutated residues that are highly conserved within the DsbB family in an effort to identify residues important for DsbB function. We found classes of mutants that specifically affect the apparent K(m) of DsbB for either DsbA or quinones, suggesting that quinone and DsbA may interact with different regions of the DsbB protein. Our results are consistent with the interpretation that the residues Q33 and Y46 of DsbB interact with DsbA, Q95 and R48 interact with quinones, and that residue M153 of DsbA interacts with DsbB. All of these interactions could be due to direct amino acid interactions or could be indirect through, for instance, their effect on protein structure. In addition, we find that the DsbB H91Y mutant severely affects the k(cat) of the reaction between DsbA and DsbB and that the DsbB L43P mutant is inactive, suggesting that both L43 and H91 are important for the activity of DsbB. These experiments help to better define the residues important for the function of these two protein-folding catalysts.
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Affiliation(s)
- Jacqueline Tan
- Department of Molecular and Cellular Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
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13
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Affiliation(s)
- Jacqueline T Tan
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, 830 North University, Ann Arbor, MI 48109, USA
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Hayano T, Hirose M, Kikuchi M. Protein disulfide isomerase mutant lacking its isomerase activity accelerates protein folding in the cell. FEBS Lett 1995; 377:505-11. [PMID: 8549786 DOI: 10.1016/0014-5793(95)01410-1] [Citation(s) in RCA: 75] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
We investigated the effect of protein disulfide isomerase (PDI) on in vivo protein folding of human lysozyme (h-LZM) in a specially constructed yeast coexpression system. Coexpression with PDI increased the amounts of intracellular h-LZM with the native conformation, leading to an increase in h-LZM secretion. The results indicated that PDI is a real catalyst of protein folding in the cell. The secretion of h-LZM increased even when both active sites of PDI were disrupted, suggesting that the effect of PDI resulted from a function other than the formation of disulfide bonds. This is the first finding that PDI without isomerase activity accelerates protein folding in vivo.
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Affiliation(s)
- T Hayano
- Protein Engineering Research Institute, Osaka, Japan
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15
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Svensson L, Dormitzer PR, von Bonsdorff CH, Maunula L, Greenberg HB. Intracellular manipulation of disulfide bond formation in rotavirus proteins during assembly. J Virol 1994; 68:5204-15. [PMID: 8035518 PMCID: PMC236464 DOI: 10.1128/jvi.68.8.5204-5215.1994] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Rotavirus undergoes a unique mode of assembly in the rough endoplasmic reticulum (RER) of infected cells. Luminal RER proteins undergo significant cotranslational and posttranslational modifications, including disulfide bond formation. Addition of a reducing agent (dithiothreitol [DTT]) to rotavirus-infected cells did not significantly inhibit translation or disrupt established disulfide bonds in rotavirus proteins but prevented the formation of new disulfide bonds and infectious viral progeny. In DTT-treated, rotavirus-infected cells, all vp4, vp6, and ns28 epitopes but no vp7 epitopes were detected by immunohistochemical staining with a panel of monoclonal antibodies. When oxidizing conditions were reestablished in DTT-treated cells, intramolecular disulfide bonds in vp7 were rapidly and correctly established with the restoration of antigenicity, although prolonged DTT treatment led to the accumulation of permanently misfolded vp7. Electron microscopy revealed that cytosolic assembly of single-shelled particles and budding into the ER was not affected by DTT treatment but that outer capsid assembly was blocked, leading to the accumulation of single-shelled and enveloped intermediate subviral particles in the RER lumen.
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Affiliation(s)
- L Svensson
- Division of Gastroenterology, Stanford University Medical Center, California 94305
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16
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Absence of intramolecular disulfides in the structure and function of native rat glucocorticoid receptors. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(17)42378-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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17
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Schatten H. Dithiothreitol prevents membrane fusion but not centrosome or microtubule organization during the first cell cycles in sea urchins. CELL MOTILITY AND THE CYTOSKELETON 1994; 27:59-68. [PMID: 8194110 DOI: 10.1002/cm.970270107] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Dithiothreitol (DTT), a disulfide reducing agent, inhibits the fusion of male and female pronuclei within the activated cytoplasm of sea urchin eggs. The migrations of the pronuclei are not affected by DTT, indicating that microtubule function is not impaired. Centrosomal antigens are detected in the sperm aster and in all subsequent microtubule-based configurations. Nuclear membranes never fuse and the chromatin of male and female pronuclei never mix in the DTT-treated cells. During prophase, when nuclear envelopes break down to undergo mitosis, both sets of chromosomes undergo condensation cycles independent from each other. Both pronuclei initially stain for centrosomal material and surrounding microtubules. With time, the female's centrosomal material as well as the microtubules disappear while the male forms a bipolar spindle. Interestingly, one pole of the paternal mitotic apparatus communicates with the separate maternal chromatin, forming a half spindle which moves the egg-derived chromatin towards its pole. At the time for cell division, the individual karyomeres are not able to fuse their nuclear membranes to reconstitute the blastomere nuclei. When DTT is applied at prometaphase of the first cell cycle, the chromosome cycle continues until next metaphase. Centrosomes also continue their cycle and undergo somewhat atypical splitting during the time for second telophase. Division furrows are initiated but aborted. These results support the hypothesis that disulfide groups are required for membrane fusion of the pronuclei, for membrane fusion of the karyomeres, and for the completion of the division furrow to achieve successful cell division.
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Affiliation(s)
- H Schatten
- Department of Zoology, University of Wisconsin, Madison 53706
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18
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Lodish H, Kong N. The secretory pathway is normal in dithiothreitol-treated cells, but disulfide-bonded proteins are reduced and reversibly retained in the endoplasmic reticulum. J Biol Chem 1993. [DOI: 10.1016/s0021-9258(20)80767-4] [Citation(s) in RCA: 58] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
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19
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Kanaya E, Kikuchi M. Folding of human lysozyme in vivo by the formation of an alternative disulfide bond. J Biol Chem 1992. [DOI: 10.1016/s0021-9258(18)42153-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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20
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Huang H, Breslow E. Identification of the unstable neurophysin disulfide and localization to the hormone-binding site. Relationship to folding-unfolding pathways. J Biol Chem 1992. [DOI: 10.1016/s0021-9258(19)50489-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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21
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Abstract
We describe a mutation (dsbA) that renders Escherichia coli severely defective in disulfide bond formation. In dsbA mutant cells, pulse-labeled beta-lactamase, alkaline phosphatase, and OmpA are secreted but largely lack disulfide bonds. These disulfideless proteins may represent in vivo folding intermediates, since they are protease sensitive and chase slowly into stable oxidized forms. The dsbA gene codes for a 21,000 Mr periplasmic protein containing the sequence cys-pro-his-cys, which resembles the active sites of certain disulfide oxidoreductases. The purified DsbA protein is capable of reducing the disulfide bonds of insulin, an activity that it shares with these disulfide oxidoreductases. Our results suggest that disulfide bond formation is facilitated by DsbA in vivo.
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Affiliation(s)
- J C Bardwell
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, Massachusetts 02115
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