1
|
Gao J, Zhong S, Zhou Y, He H, Peng S, Zhu Z, Liu X, Zheng J, Xu B, Zhou H. Comparative Evaluation of Small Molecular Additives and Their Effects on Peptide/Protein Identification. Anal Chem 2017; 89:5784-5792. [PMID: 28530406 DOI: 10.1021/acs.analchem.6b04886] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Detergents and salts are widely used in lysis buffers to enhance protein extraction from biological samples, facilitating in-depth proteomic analysis. However, these detergents and salt additives must be efficiently removed from the digested samples prior to LC-MS/MS analysis to obtain high-quality mass spectra. Although filter-aided sample preparation (FASP), acetone precipitation (AP), followed by in-solution digestion, and strong cation exchange-based centrifugal proteomic reactors (CPRs) are commonly used for proteomic sample processing, little is known about their efficiencies at removing detergents and salt additives. In this study, we (i) developed an integrative workflow for the quantification of small molecular additives in proteomic samples, developing a multiple reaction monitoring (MRM)-based LC-MS approach for the quantification of six additives (i.e., Tris, urea, CHAPS, SDS, SDC, and Triton X-100) and (ii) systematically evaluated the relationships between the level of additive remaining in samples following sample processing and the number of peptides/proteins identified by mass spectrometry. Although FASP outperformed the other two methods, the results were complementary in terms of peptide/protein identification, as well as the GRAVY index and amino acid distributions. This is the first systematic and quantitative study of the effect of detergents and salt additives on protein identification. This MRM-based approach can be used for an unbiased evaluation of the performance of new sample preparation methods. Data are available via ProteomeXchange under identifier PXD005405.
Collapse
Affiliation(s)
- Jing Gao
- Department of Chemistry, College of Sciences, Shanghai University , Shanghai, China 200444.,Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Road, Shanghai, China 201203
| | - Shaoyun Zhong
- Department of Chemistry, College of Sciences, Shanghai University , Shanghai, China 200444.,Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Road, Shanghai, China 201203
| | - Yanting Zhou
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Road, Shanghai, China 201203.,Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology , 130 Meilong Road, Shanghai, China 200237
| | - Han He
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Road, Shanghai, China 201203
| | - Shuying Peng
- Thermo Fisher Scientific (China) Co., Ltd. , No. 6 Building, 27 Xinjinqiao Road, Shanghai, China 201206
| | - Zhenyun Zhu
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Road, Shanghai, China 201203
| | - Xing Liu
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Road, Shanghai, China 201203
| | - Jing Zheng
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology , 130 Meilong Road, Shanghai, China 200237
| | - Bin Xu
- Department of Chemistry, College of Sciences, Shanghai University , Shanghai, China 200444
| | - Hu Zhou
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Road, Shanghai, China 201203.,University of Chinese Academy of Sciences , Beijing, China 100049.,E-institute of Shanghai Municipal Education Committee, Shanghai University of Traditional Chinese Medicine , 1200 Cai Lun Road, Shanghai, China 201203
| |
Collapse
|
2
|
Herrera VLM, Steffen M, Moran AM, Tan GA, Pasion KA, Rivera K, Pappin DJ, Ruiz-Opazo N. Confirmation of translatability and functionality certifies the dual endothelin1/VEGFsp receptor (DEspR) protein. BMC Mol Biol 2016; 17:15. [PMID: 27301377 PMCID: PMC4906906 DOI: 10.1186/s12867-016-0066-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 05/20/2016] [Indexed: 01/16/2023] Open
Abstract
Background In contrast to rat and mouse databases, the NCBI gene database lists the human dual-endothelin1/VEGFsp receptor (DEspR, formerly Dear) as a unitary transcribed pseudogene due to a stop [TGA]-codon at codon#14 in automated DNA and RNA sequences. However, re-analysis is needed given prior single gene studies detected a tryptophan [TGG]-codon#14 by manual Sanger sequencing, demonstrated DEspR translatability and functionality, and since the demonstration of actual non-translatability through expression studies, the standard-of-excellence for pseudogene designation, has not been performed. Re-analysis must meet UNIPROT criteria for demonstration of a protein’s existence at the highest (protein) level, which a priori, would override DNA- or RNA-based deductions. Methods To dissect the nucleotide sequence discrepancy, we performed Maxam–Gilbert sequencing and reviewed 727 RNA-seq entries. To comply with the highest level multiple UNIPROT criteria for determining DEspR’s existence, we performed various experiments using multiple anti-DEspR monoclonal antibodies (mAbs) targeting distinct DEspR epitopes with one spanning the contested tryptophan [TGG]-codon#14, assessing: (a) DEspR protein expression, (b) predicted full-length protein size, (c) sequence-predicted protein-specific properties beyond codon#14: receptor glycosylation and internalization, (d) protein-partner interactions, and (e) DEspR functionality via DEspR-inhibition effects. Results Maxam–Gilbert sequencing and some RNA-seq entries demonstrate two guanines, hence a tryptophan [TGG]-codon#14 within a compression site spanning an error-prone compression sequence motif. Western blot analysis using anti-DEspR mAbs targeting distinct DEspR epitopes detect the identical glycosylated 17.5 kDa pull-down protein. Decrease in DEspR-protein size after PNGase-F digest demonstrates post-translational glycosylation, concordant with the consensus-glycosylation site beyond codon#14. Like other small single-transmembrane proteins, mass spectrometry analysis of anti-DEspR mAb pull-down proteins do not detect DEspR, but detect DEspR-protein interactions with proteins implicated in intracellular trafficking and cancer. FACS analyses also detect DEspR-protein in different human cancer stem-like cells (CSCs). DEspR-inhibition studies identify DEspR-roles in CSC survival and growth. Live cell imaging detects fluorescently-labeled anti-DEspR mAb targeted-receptor internalization, concordant with the single internalization-recognition sequence also located beyond codon#14. Conclusions Data confirm translatability of DEspR, the full-length DEspR protein beyond codon#14, and elucidate DEspR-specific functionality. Along with detection of the tryptophan [TGG]-codon#14 within an error-prone compression site, cumulative data demonstrating DEspR protein existence fulfill multiple UNIPROT criteria, thus refuting its pseudogene designation. Electronic supplementary material The online version of this article (doi:10.1186/s12867-016-0066-8) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Victoria L M Herrera
- Whitaker Cardiovascular Institute, Boston University School of Medicine, 700 Albany Street, Boston, MA, 02118, USA.,Department of Medicine, Boston University School of Medicine, 700 Albany Street, Boston, MA, 02118, USA
| | - Martin Steffen
- Department of Pathology and Biomedical Engineering, Boston University, Boston, USA
| | - Ann Marie Moran
- Whitaker Cardiovascular Institute, Boston University School of Medicine, 700 Albany Street, Boston, MA, 02118, USA.,Department of Medicine, Boston University School of Medicine, 700 Albany Street, Boston, MA, 02118, USA
| | - Glaiza A Tan
- Whitaker Cardiovascular Institute, Boston University School of Medicine, 700 Albany Street, Boston, MA, 02118, USA.,Department of Medicine, Boston University School of Medicine, 700 Albany Street, Boston, MA, 02118, USA
| | - Khristine A Pasion
- Whitaker Cardiovascular Institute, Boston University School of Medicine, 700 Albany Street, Boston, MA, 02118, USA.,Department of Medicine, Boston University School of Medicine, 700 Albany Street, Boston, MA, 02118, USA
| | - Keith Rivera
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY, 11724, USA
| | - Darryl J Pappin
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY, 11724, USA
| | - Nelson Ruiz-Opazo
- Whitaker Cardiovascular Institute, Boston University School of Medicine, 700 Albany Street, Boston, MA, 02118, USA. .,Department of Medicine, Boston University School of Medicine, 700 Albany Street, Boston, MA, 02118, USA.
| |
Collapse
|
3
|
Fukuyama Y, Nakajima C, Izumi S, Tanaka K. Membrane Protein Analyses Using Alkylated Trihydroxyacetophenone (ATHAP) as a MALDI Matrix. Anal Chem 2016; 88:1688-95. [DOI: 10.1021/acs.analchem.5b03700] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yuko Fukuyama
- Koichi
Tanaka Laboratory of Advanced Science and Technology, Shimadzu Corporation, 1, Nishinokyo-Kuwabaracho, Nakagyo-ku, Kyoto 604-8511, Japan
- Koichi
Tanaka Mass Spectrometry Research Laboratory, Shimadzu Corporation, 1, Nishinokyo-Kuwabaracho, Nakagyo-ku, Kyoto 604-8511, Japan
| | - Chihiro Nakajima
- Koichi
Tanaka Laboratory of Advanced Science and Technology, Shimadzu Corporation, 1, Nishinokyo-Kuwabaracho, Nakagyo-ku, Kyoto 604-8511, Japan
| | - Shunsuke Izumi
- Department
of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526, Japan
| | - Koichi Tanaka
- Koichi
Tanaka Laboratory of Advanced Science and Technology, Shimadzu Corporation, 1, Nishinokyo-Kuwabaracho, Nakagyo-ku, Kyoto 604-8511, Japan
- Koichi
Tanaka Mass Spectrometry Research Laboratory, Shimadzu Corporation, 1, Nishinokyo-Kuwabaracho, Nakagyo-ku, Kyoto 604-8511, Japan
| |
Collapse
|
4
|
Alfonso-Garrido J, Garcia-Calvo E, Luque-Garcia JL. Sample preparation strategies for improving the identification of membrane proteins by mass spectrometry. Anal Bioanal Chem 2015; 407:4893-905. [PMID: 25967148 DOI: 10.1007/s00216-015-8732-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Revised: 04/15/2015] [Accepted: 04/22/2015] [Indexed: 12/31/2022]
Abstract
Despite enormous advances in the mass spectrometry and proteomics fields during the last two decades, the analysis of membrane proteins still remains a challenge for the proteomic community. Membrane proteins play a wide number of key roles in several cellular events, making them relevant target molecules to study in a significant variety of investigations (e.g., cellular signaling, immune surveillance, drug targets, vaccine candidates, etc.). Here, we critically review the several attempts that have been carried out on the different steps of the sample preparation procedure to improve and modify existing conventional proteomic strategies in order to make them suitable for the study of membrane proteins. We also revise novel techniques that have been designed to tackle the difficult but relevant task of identifying and characterizing membrane proteins.
Collapse
Affiliation(s)
- Javier Alfonso-Garrido
- Department of Analytical Chemistry, Faculty of Chemistry, Complutense University of Madrid, Av. Complutense s/n, 28004, Madrid, Spain
| | | | | |
Collapse
|
5
|
Jeanson L, Guerrera IC, Papon JF, Chhuon C, Zadigue P, Prulière-Escabasse V, Amselem S, Escudier E, Coste A, Edelman A. Proteomic analysis of nasal epithelial cells from cystic fibrosis patients. PLoS One 2014; 9:e108671. [PMID: 25268127 PMCID: PMC4182543 DOI: 10.1371/journal.pone.0108671] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Accepted: 08/24/2014] [Indexed: 11/21/2022] Open
Abstract
The pathophysiology of cystic fibrosis (CF) lung disease remains incompletely understood. New explanations for the pathogenesis of CF lung disease may be discovered by studying the patterns of protein expression in cultured human nasal epithelial cells (HNEC). To that aim, we compared the level of protein expressions in primary cultures of HNEC from nasal polyps secondary to CF (CFNP, n = 4), primary nasal polyps (NP, n = 8) and control mucosa (CTRL, n = 4) using isobaric tag for relative and absolute quantification (iTRAQ) labeling coupled with liquid chromatography (LC)-MS-MS. The analysis of the data revealed 42 deregulated protein expressions in CFNP compared to NP and CTRL, suggesting that these alterations are related to CF. Overall, AmiGo analysis highlighted six major pathways important for cell functions that seem to be impaired: metabolism, G protein process, inflammation and oxidative stress response, protein folding, proteolysis and structural proteins. Among them, glucose and fatty acid metabolic pathways could be impaired in CF with nine deregulated proteins. Our proteomic study provides a reproducible set of differentially expressed proteins in airway epithelial cells from CF patients and reveals many novel deregulated proteins that could lead to further studies aiming to clarify the involvement of such proteins in CF pathophysiology.
Collapse
Affiliation(s)
- Ludovic Jeanson
- Service de Génétique et Embryologie Médicales, Unité Mixte de Recherche_Scientifique 933, Institut National de la Santé et de la Recherche Médicale, Université Pierre et Marie Curie – Paris 6, and Assistance Publique – Hôpitaux de Paris, Hôpital Armand Trousseau, Paris, France
- Unité_1151, Institut National de la Santé et de la Recherche Médicale, Université Paris Descartes, Paris, France
| | - Ida Chiara Guerrera
- Unité_1151, Institut National de la Santé et de la Recherche Médicale, Université Paris Descartes, Paris, France
- Plateau Proteome Necker, Structure Fédérative de Recherche de Necker, Université Paris Descartes, Paris, France
| | - Jean-François Papon
- Unité Mixte de Recherche_Scientifique 855, Institut National de la Santé et de la Recherche Médicale, Université Paris 12, Faculté de Médecine, Créteil, France
- Service d’Otorhinolaryngologie et de chirurgie cervico-faciale, Assistance Publique – Hôpitaux de Paris, Hôpital inter-communal et Groupe Hospitalier Henri Mondor-Albert Chenevier, Créteil, France
| | - Cerina Chhuon
- Unité_1151, Institut National de la Santé et de la Recherche Médicale, Université Paris Descartes, Paris, France
- Plateau Proteome Necker, Structure Fédérative de Recherche de Necker, Université Paris Descartes, Paris, France
| | - Patricia Zadigue
- Unité Mixte de Recherche_Scientifique 855, Institut National de la Santé et de la Recherche Médicale, Université Paris 12, Faculté de Médecine, Créteil, France
| | - Virginie Prulière-Escabasse
- Service d’Otorhinolaryngologie et de chirurgie cervico-faciale, Assistance Publique – Hôpitaux de Paris, Hôpital inter-communal et Groupe Hospitalier Henri Mondor-Albert Chenevier, Créteil, France
| | - Serge Amselem
- Service de Génétique et Embryologie Médicales, Unité Mixte de Recherche_Scientifique 933, Institut National de la Santé et de la Recherche Médicale, Université Pierre et Marie Curie – Paris 6, and Assistance Publique – Hôpitaux de Paris, Hôpital Armand Trousseau, Paris, France
| | - Estelle Escudier
- Service de Génétique et Embryologie Médicales, Unité Mixte de Recherche_Scientifique 933, Institut National de la Santé et de la Recherche Médicale, Université Pierre et Marie Curie – Paris 6, and Assistance Publique – Hôpitaux de Paris, Hôpital Armand Trousseau, Paris, France
| | - André Coste
- Unité Mixte de Recherche_Scientifique 855, Institut National de la Santé et de la Recherche Médicale, Université Paris 12, Faculté de Médecine, Créteil, France
- Service d’Otorhinolaryngologie et de chirurgie cervico-faciale, Assistance Publique – Hôpitaux de Paris, Hôpital inter-communal et Groupe Hospitalier Henri Mondor-Albert Chenevier, Créteil, France
| | - Aleksander Edelman
- Unité_1151, Institut National de la Santé et de la Recherche Médicale, Université Paris Descartes, Paris, France
- Plateau Proteome Necker, Structure Fédérative de Recherche de Necker, Université Paris Descartes, Paris, France
| |
Collapse
|
6
|
Bagag A, Jault JM, Sidahmed-Adrar N, Réfrégiers M, Giuliani A, Le Naour F. Characterization of hydrophobic peptides in the presence of detergent by photoionization mass spectrometry. PLoS One 2013; 8:e79033. [PMID: 24236085 PMCID: PMC3827311 DOI: 10.1371/journal.pone.0079033] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Accepted: 09/18/2013] [Indexed: 12/18/2022] Open
Abstract
The characterization of membrane proteins is still challenging. The major issue is the high hydrophobicity of membrane proteins that necessitates the use of detergents for their extraction and solubilization. The very poor compatibility of mass spectrometry with detergents remains a tremendous obstacle in studies of membrane proteins. Here, we investigated the potential of atmospheric pressure photoionization (APPI) for mass spectrometry study of membrane proteins. This work was focused on the tetraspanin CD9 and the multidrug transporter BmrA. A set of peptides from CD9, exhibiting a broad range of hydropathicity, was investigated using APPI as compared to electrospray ionization (ESI). Mass spectrometry experiments revealed that the most hydrophobic peptides were hardly ionized by ESI whereas all peptides, including the highly hydrophobic one that corresponds to the full sequence of the first transmembrane domain of CD9, were easily ionized by APPI. The native protein BmrA purified in the presence of the non-ionic detergent beta-D-dodecyl maltoside (DDM) was digested in-solution using trypsin. The resulting peptides were investigated by flow injection analysis of the mixture followed by mass spectrometry. Upon ESI, only detergent ions were detected and the ionic signals from the peptides were totally suppressed. In contrast, APPI allowed many peptides distributed along the sequence of the protein to be detected. Furthermore, the parent ion corresponding to the first transmembrane domain of the protein BmrA was detected under APPI conditions. Careful examination of the APPI mass spectrum revealed a-, b-, c- and y- fragment ions generated by in-source fragmentation. Those fragment ions allowed unambiguous structural characterization of the transmembrane domain. In conclusion, APPI-MS appears as a versatile method allowing the ionization and fragmentation of hydrophobic peptides in the presence of detergent.
Collapse
Affiliation(s)
- Aïcha Bagag
- Inserm, U785, Villejuif, France
- Université Paris-Sud 11, Institut André Lwoff, Villejuif, France
| | - Jean-Michel Jault
- Université Joseph Fourier-Grenoble 1, Institut de Biologie Structurale, Grenoble, France
- CNRS, UMR 5075, Grenoble, France
- CEA, Institut de Biologie Structurale, Grenoble, France
| | - Nazha Sidahmed-Adrar
- Inserm, U785, Villejuif, France
- Université Paris-Sud 11, Institut André Lwoff, Villejuif, France
| | | | - Alexandre Giuliani
- Synchrotron SOLEIL, Gif-sur-Yvette, France
- INRA, UAR 1008 CEPIA, Nantes, France
| | - François Le Naour
- Inserm, U785, Villejuif, France
- Université Paris-Sud 11, Institut André Lwoff, Villejuif, France
| |
Collapse
|
7
|
Miranda HV, Xiang W, de Oliveira RM, Simões T, Pimentel J, Klucken J, Penque D, Outeiro TF. Heat-mediated enrichment of α-synuclein from cells and tissue for assessing post-translational modifications. J Neurochem 2013; 126:673-84. [DOI: 10.1111/jnc.12251] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Revised: 03/12/2013] [Accepted: 03/25/2013] [Indexed: 01/06/2023]
Affiliation(s)
- Hugo Vicente Miranda
- Cell and Molecular Neuroscience Unit; Instituto de Medicina Molecular; Lisboa Portugal
| | - Wei Xiang
- Institut für Biochemie (Emil-Fischer-Zentrum); Friedrich-Alexander Universität Erlangen-Nürnberg; Erlangen Germany
| | - Rita M. de Oliveira
- Cell and Molecular Neuroscience Unit; Instituto de Medicina Molecular; Lisboa Portugal
| | - Tânia Simões
- Laboratório de Proteómica; Departamento de Genética; Instituto Nacional de Saúde Dr. Ricardo Jorge; Lisboa Portugal
| | - José Pimentel
- Laboratory of Neuropathology; Department of Neurosciences; Serviço de Neurologia; CHLN EPE-Hospital de Santa Maria; Lisboa Portugal
- Neurological Clinical Research Unit; Instituto de Medicina Molecular; Lisboa Portugal
| | - Jochen Klucken
- Department of Molecular Neurology; University Hospital Erlangen; Erlangen Germany
| | - Deborah Penque
- Laboratório de Proteómica; Departamento de Genética; Instituto Nacional de Saúde Dr. Ricardo Jorge; Lisboa Portugal
| | - Tiago F. Outeiro
- Cell and Molecular Neuroscience Unit; Instituto de Medicina Molecular; Lisboa Portugal
- Instituto de Fisiologia; Faculdade de Medicina de Lisboa; Lisboa Portugal
- Department of Neurodegeneration and Restorative Research; Center for Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB); University Medical Center Göttingen; Göttingen Germany
| |
Collapse
|
8
|
Pacheco SA, Torres VM, Louro H, Gomes F, Lopes C, Marçal N, Fragoso E, Martins C, Oliveira CL, Hagenfeldt M, Bugalho-Almeida A, Penque D, Simões T. Effects of occupational exposure to tobacco smoke: is there a link between environmental exposure and disease? JOURNAL OF TOXICOLOGY AND ENVIRONMENTAL HEALTH. PART A 2013; 76:311-327. [PMID: 23514073 DOI: 10.1080/15287394.2013.757269] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
In a previous study, evidence was provided that indoor secondhand tobacco smoke (SHS) air pollution remains high in Lisbon restaurants where smoking is allowed, regardless of the protective measures used. The aim of this study was to determine in these locations the levels of polycyclic aromatic hydrocarbons (PAH) associated with the particulate phase of SHS (PPAH), a fraction that contains recognized carginogens, such as benzo[a]pyrene (BaP). Data showed that restaurant smoking areas might contain PPAH levels as high as 110 ng/m(3), a value significantly higher than that estimated for nonsmoking areas (30 ng/m(3)) or smoke-free restaurants (22 ng/m(3)). The effective exposure to SHS components in restaurant smoking rooms was confirmed as cotinine levels found in workers' urine. Considering that all workers exhibited normal lung function, eventual molecular changes in blood that might be associated with occupational exposure to SHS and SHS-associated PPAH were investigated by measurement of two oxidative markers, total antioxidant status (TAS) and 8-hydroxyguanosine (8-OHdG) in plasma and serum, respectively. SHS-exposed workers exhibited higher mean levels of serum 8-OHdG than nonexposed workers, regardless of smoking status. By using a proteomics approach based on 2D-DIGE-MS, it was possible to identify nine differentially expressed proteins in the plasma of SHS-exposed nonsmoker workers. Two acute-phase inflammation proteins, ceruloplasmin and inter-alpha-trypsin inhibitor heavy chain 4 (ITIH4), were predominant. These two proteins presented a high number of isoforms modulated by SHS exposure with the high-molecular-weight (high-MW) isoforms decreased in abundance while low-MW isoforms were increased in abundance. Whether these expression profiles are due to (1) a specific proteolytic cleavage, (2) a change on protein stability, or (3) alterations on post-translational modification pattern of these proteins remains to be investigated. Considering that these events seem to precede the first symptoms of tobacco-related diseases, our findings might contribute to elucidation of early SHS-induced pathogenic mechanisms and constitute a useful tool for monitoring the effects of SHS on occupationally exposed individuals such as those working in the hospitality industry.
Collapse
Affiliation(s)
- Solange A Pacheco
- Laboratório de Proteómica, Departamento de Genética Humana, Lisboa, Portugal
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
9
|
Pedroso N, Gomes-Alves P, Marinho HS, Brito VB, Boada C, Antunes F, Herrero E, Penque D, Cyrne L. The plasma membrane-enriched fraction proteome response during adaptation to hydrogen peroxide in Saccharomyces cerevisiae. Free Radic Res 2012; 46:1267-79. [PMID: 22712517 DOI: 10.3109/10715762.2012.704997] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In Saccharomyces cerevisiae, adaptation to hydrogen peroxide (H₂O₂) decreases plasma membrane permeability to H₂O₂, changes its lipid composition and reorganizes ergosterol-rich microdomains by a still unknown mechanism. Here we show, by a quantitative analysis of the H₂O₂-induced adaptation effect on the S. cerevisiae plasma membrane-enriched fraction proteome, using two-dimensional gel electrophoresis, that 44 proteins are differentially expressed. Most of these proteins were regulated at a post-transcriptional level. Fourteen of these proteins contain redox-sensitive cysteine residues and nine proteins are associated with lipid and vesicle traffic. In particular, three proteins found in eisosomes and in the eisosome-associated membrane compartment occupied by Can1p were up-regulated (Pil1p, Rfs1p and Pst2p) during adaptation to H₂O₂. Survival studies after exposure to lethal H₂O₂ doses using yeast strains bearing a gene deletion corresponding to proteins associated to lipid and vesicle traffic demonstrated for the first time that down-regulation of Kes1p, Vps4p and Ynl010wp and up-regulation of Atp1 and Atp2 increases resistance to H₂O₂. Moreover, for the pil1Δ strain, H₂O₂ at low levels produces a hormetic effect by increasing proliferation. In conclusion, these data further confirms the plasma membrane as an active cellular site during adaptation to H₂O₂ and shows that proteins involved in lipid and vesicle traffic are important mediators of H₂O₂ adaptation.
Collapse
Affiliation(s)
- Nuno Pedroso
- Departamento de Química e Bioquímica & Centro de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Portugal
| | | | | | | | | | | | | | | | | |
Collapse
|
10
|
Bagag A, Giuliani A, Canon F, Réfrégiers M, Le Naour F. Separation of peptides from detergents using ion mobility spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2011; 25:3436-3440. [PMID: 22002698 DOI: 10.1002/rcm.5242] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Mass spectrometry (MS) has dramatically evolved in the last two decades and has been the driving force of the spectacular expansion of proteomics during this period. However, the very poor compatibility of MS with detergents is still a technical obstacle in some studies, in particular on membrane proteins. Indeed, the high hydrophobicity of membrane proteins necessitates the use of detergents for their extraction and solubilization. Here, we address the analytical potential of high-field asymmetric waveform ion mobility spectrometry (FAIMS) for separating peptides from detergents. The study was focused on peptides from the human integral membrane protein CD9. A tryptic peptide was mixed with the non-ionic detergents Triton X-100 or beta-D-dodecyl maltoside (DDM) as well as with the ionic detergents sodium dodecyl sulfate (SDS) or sodium deoxycholate (SDC). Although electrospray ionization (ESI) alone led to a total suppression of the peptide ion signal on mass spectra with only detection of the detergents, use of FAIMS allowed separation and clear identification of the peptide with any of the detergents studied. The detection and identification of the target compound in the presence of an excess of detergents are then feasible. FAIMS should prove especially useful in the structural and proteomic analysis of membrane proteins.
Collapse
|
11
|
Colas J, Faure G, Saussereau E, Trudel S, Rabeh WM, Bitam S, Guerrera IC, Fritsch J, Sermet-Gaudelus I, Davezac N, Brouillard F, Lukacs GL, Herrmann H, Ollero M, Edelman A. Disruption of cytokeratin-8 interaction with F508del-CFTR corrects its functional defect. Hum Mol Genet 2011; 21:623-34. [PMID: 22038833 DOI: 10.1093/hmg/ddr496] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We have previously reported an increased expression of cytokeratins 8/18 (K8/K18) in cells expressing the F508del mutation of cystic fibrosis transmembrane conductance regulator (CFTR). This is associated with increased colocalization of CFTR and K18 in the vicinity of the endoplasmic reticulum, although this is reversed by treating cells with curcumin, resulting in the rescue of F508del-CFTR. In the present work, we hypothesized that (i) the K8/K18 network may interact physically with CFTR, and that (ii) this interaction may modify CFTR function. CFTR was immunoprecipitated from HeLa cells transfected with either wild-type (WT) CFTR or F508del-CFTR. Precipitates were subjected to 2D-gel electrophoresis and differential spots identified by mass spectrometry. K8 and K18 were found significantly increased in F508del-CFTR precipitates. Using surface plasmon resonance, we demonstrate that K8, but not K18, binds directly and preferentially to the F508del over the WT human NBD1 (nucleotide-binding domain-1). In vivo K8 interaction with F508del-CFTR was confirmed by proximity ligation assay in HeLa cells and in primary cultures of human respiratory epithelial cells. Ablation of K8 expression by siRNA in F508del-expressing HeLa cells led to the recovery of CFTR-dependent iodide efflux. Moreover, F508del-expressing mice topically treated with K8-siRNA showed restored nasal potential difference, equivalent to that of WT mice. These results show that disruption of F508del-CFTR and K8 interaction leads to the correction of the F508del-CFTR processing defect, suggesting a novel potential therapeutic target in CF.
Collapse
Affiliation(s)
- Julien Colas
- Faculté de Médecine Paris-Descartes, INSERM, U845, Paris, France
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
12
|
Signaling pathways of proteostasis network unraveled by proteomic approaches on the understanding of misfolded protein rescue. Methods Enzymol 2011. [PMID: 21329803 DOI: 10.1016/b978-0-12-385928-0.00013-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Attempts to promote normal processing and function of F508del-CFTR, the most common mutant in cystic fibrosis (CF), have been described as potential therapeutic strategies in the management of this disease. Here we described the proteomic approaches, namely two-dimensional electrophoresis (2DE), mass spectrometry (MS), and bioinformatics tools used in our recent studies to gain insight into the proteins potentially involved in low-temperature or mutagenic treatment-induced rescue process of F508del-CFTR. The proteins identified are part of the proteostasis network, such as the unfolded protein response (UPR) signaling pathways that may regulate the processing of CF transmembrane conductance regulator (CFTR) through the folding and trafficking progression. The complete characterization of these signaling pathways and their regulators in CF will certainly contribute to the development of novel therapeutic strategies against CF.
Collapse
|
13
|
Supramolecular organizations in the aerobic respiratory chain of Escherichia coli. Biochimie 2010; 93:418-25. [PMID: 21040753 DOI: 10.1016/j.biochi.2010.10.014] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2010] [Accepted: 10/20/2010] [Indexed: 12/26/2022]
Abstract
The organization of respiratory chain complexes in supercomplexes has been shown in the mitochondria of several eukaryotes and in the cell membranes of some bacteria. These supercomplexes are suggested to be important for oxidative phosphorylation efficiency and to prevent the formation of reactive oxygen species. Here we describe, for the first time, the identification of supramolecular organizations in the aerobic respiratory chain of Escherichia coli, including a trimer of succinate dehydrogenase. Furthermore, two heterooligomerizations have been shown: one resulting from the association of the NADH:quinone oxidoreductases NDH-1 and NDH-2, and another composed by the cytochrome bo(3) quinol:oxygen reductase, cytochrome bd quinol:oxygen reductase and formate dehydrogenase (fdo). These results are supported by blue native-electrophoresis, mass spectrometry and kinetic data of wild type and mutant E . coli strains.
Collapse
|
14
|
Charro N, Hood BL, Faria D, Pacheco P, Azevedo P, Lopes C, de Almeida AB, Couto FM, Conrads TP, Penque D. Serum proteomics signature of cystic fibrosis patients: a complementary 2-DE and LC-MS/MS approach. J Proteomics 2010; 74:110-26. [PMID: 20950718 DOI: 10.1016/j.jprot.2010.10.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2010] [Revised: 09/17/2010] [Accepted: 10/05/2010] [Indexed: 01/01/2023]
Abstract
Complementary 2D-PAGE and 'shotgun' LC-MS/MS approaches were combined to identify medium and low-abundant proteins in sera of Cystic Fibrosis (CF) patients (mild or severe pulmonary disease) in comparison with healthy CF-carrier and non-CF carrier individuals aiming to gain deeper insights into the pathogenesis of this multifactorial genetic disease. 78 differentially expressed spots were identified from 2D-PAGE proteome profiling yielding 28 identifications and postulating the existence of post-translation modifications (PTM). The 'shotgun' approach highlighted altered levels of proteins actively involved in CF: abnormal tissue/airway remodeling, protease/antiprotease imbalance, innate immune dysfunction, chronic inflammation, nutritional imbalance and Pseudomonas aeruginosa colonization. Members of the apolipoproteins family (VDBP, ApoA-I, and ApoB) presented gradually lower expression from non-CF to CF-carrier individuals and from those to CF patients, results validated by an independent assay. The multifunctional enzyme NDKB was identified only in the CF group and independently validated by WB. Its functions account for ion sensor in epithelial cells, pancreatic secretion, neutrophil-mediated inflammation and energy production, highlighting its physiological significance in the context of CF. Complementary proteomics-based approaches are reliable tools to reveal pathways and circulating proteins actively involved in a heterogeneous disease such as CF.
Collapse
Affiliation(s)
- Nuno Charro
- Laboratório de Proteómica, Departamento de Genética, INSA, I.P., Lisboa, Portugal
| | | | | | | | | | | | | | | | | | | |
Collapse
|
15
|
Gomes-Alves P, Couto F, Pesquita C, Coelho AV, Penque D. Rescue of F508del-CFTR by RXR motif inactivation triggers proteome modulation associated with the unfolded protein response. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1804:856-65. [DOI: 10.1016/j.bbapap.2009.12.013] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2009] [Revised: 12/17/2009] [Accepted: 12/18/2009] [Indexed: 12/17/2022]
|
16
|
Helbig AO, Heck AJR, Slijper M. Exploring the membrane proteome--challenges and analytical strategies. J Proteomics 2010; 73:868-78. [PMID: 20096812 DOI: 10.1016/j.jprot.2010.01.005] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2009] [Revised: 01/08/2010] [Accepted: 01/08/2010] [Indexed: 12/22/2022]
Abstract
The analysis of proteins in biological membranes forms a major challenge in proteomics. Despite continuous improvements and the development of more sensitive analytical methods, the analysis of membrane proteins has always been hampered by their hydrophobic properties and relatively low abundance. In this review, we describe recent successful strategies that have led to in-depth analyses of the membrane proteome. To facilitate membrane proteome analysis, it is essential that biochemical enrichment procedures are combined with special analytical workflows that are all optimized to cope with hydrophobic polypeptides. These include techniques for protein solubilization, and also well-matched developments in protein separation and protein digestion procedures. Finally, we discuss approaches to target membrane-protein complexes and lipid-protein interactions, as such approaches offer unique insights into function and architecture of cellular membranes.
Collapse
Affiliation(s)
- Andreas O Helbig
- Biomolecular Mass Spectrometry and Proteomics Group, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | | | | |
Collapse
|
17
|
Gomes-Alves P, Neves S, Coelho AV, Penque D. Low temperature restoring effect on F508del-CFTR misprocessing: A proteomic approach. J Proteomics 2009; 73:218-30. [PMID: 19775599 DOI: 10.1016/j.jprot.2009.09.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2009] [Accepted: 09/02/2009] [Indexed: 01/22/2023]
Abstract
To gain insight into the proteins potentially involved in the low temperature-induced F508del-CFTR rescue process, we have explored by two-dimensional electrophoresis (2DE) the proteome of BHK cell lines expressing wt or F508del-CFTR, grown at 37 degrees C or 26 degrees C/24h or 26 degrees C/48h followed by 3h of metabolic labelling with [(35)S]-methionine. A set of 139 protein spots (yielding 125 mass spectrometry identifications) was identified as differentially expressed (p ANOVA<0.05) among the six phenotypic groups analysed. The data analysis suggests that the unfolded protein response (UPR) induction and some cell-metabolism repression are the major cold-shock responses that may generate a favourable cellular environment to promote F508del-CFTR rescue. Down-regulation of proteasome regulatory PA28 and/or COP9 signalosome subunit, both involved in CFTR degradation, could also be a relevant cold-shock-induced condition for F508de-CFTR rescue. Moreover, cold-shock may promote the reestablishment of some proteostasis imbalance associated with over-expression of F508del-CFTR. In BHK-F508del cells, the deregulation of RACK1, a protein described to be important for stable expression of CFTR in the plasma membrane, is partially repaired after low temperature treatment. Together these findings give new insights about F508del-CFTR rescue by low temperature treatment and the proteins involved could ultimately constitute potential therapeutic targets in CF disease.
Collapse
Affiliation(s)
- Patricia Gomes-Alves
- Departamento de Genética, Instituto Nacional de Saúde Dr Ricardo Jorge, Lisboa, Portugal
| | | | | | | |
Collapse
|
18
|
Carvalho-Oliveira IM, Charro N, Aarbiou J, Buijs-Offerman RM, Wilke M, Schettgen T, Kraus T, Titulaer MK, Burgers P, Luider TM, Penque D, Scholte BJ. Proteomic Analysis of Naphthalene-Induced Airway Epithelial Injury and Repair in a Cystic Fibrosis Mouse Model. J Proteome Res 2009; 8:3606-16. [DOI: 10.1021/pr900021m] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Isabel M. Carvalho-Oliveira
- Department of Cell Biology, Erasmus Medical Centre, Rotterdam, The Netherlands, Laboratório de Proteómica, Departamento de Genética, Instituto Nacional de Saúde Dr Ricardo Jorge, Lisboa, Portugal, Department of Biochemistry, Erasmus University Medical Centre, Rotterdam, The Netherlands, Institut für Arbeitsmedizin und Sozialmedizin Universitätsklinikum Aachen, and Department of Neurology, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Nuno Charro
- Department of Cell Biology, Erasmus Medical Centre, Rotterdam, The Netherlands, Laboratório de Proteómica, Departamento de Genética, Instituto Nacional de Saúde Dr Ricardo Jorge, Lisboa, Portugal, Department of Biochemistry, Erasmus University Medical Centre, Rotterdam, The Netherlands, Institut für Arbeitsmedizin und Sozialmedizin Universitätsklinikum Aachen, and Department of Neurology, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Jamil Aarbiou
- Department of Cell Biology, Erasmus Medical Centre, Rotterdam, The Netherlands, Laboratório de Proteómica, Departamento de Genética, Instituto Nacional de Saúde Dr Ricardo Jorge, Lisboa, Portugal, Department of Biochemistry, Erasmus University Medical Centre, Rotterdam, The Netherlands, Institut für Arbeitsmedizin und Sozialmedizin Universitätsklinikum Aachen, and Department of Neurology, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Ruvalic M. Buijs-Offerman
- Department of Cell Biology, Erasmus Medical Centre, Rotterdam, The Netherlands, Laboratório de Proteómica, Departamento de Genética, Instituto Nacional de Saúde Dr Ricardo Jorge, Lisboa, Portugal, Department of Biochemistry, Erasmus University Medical Centre, Rotterdam, The Netherlands, Institut für Arbeitsmedizin und Sozialmedizin Universitätsklinikum Aachen, and Department of Neurology, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Martina Wilke
- Department of Cell Biology, Erasmus Medical Centre, Rotterdam, The Netherlands, Laboratório de Proteómica, Departamento de Genética, Instituto Nacional de Saúde Dr Ricardo Jorge, Lisboa, Portugal, Department of Biochemistry, Erasmus University Medical Centre, Rotterdam, The Netherlands, Institut für Arbeitsmedizin und Sozialmedizin Universitätsklinikum Aachen, and Department of Neurology, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Thomas Schettgen
- Department of Cell Biology, Erasmus Medical Centre, Rotterdam, The Netherlands, Laboratório de Proteómica, Departamento de Genética, Instituto Nacional de Saúde Dr Ricardo Jorge, Lisboa, Portugal, Department of Biochemistry, Erasmus University Medical Centre, Rotterdam, The Netherlands, Institut für Arbeitsmedizin und Sozialmedizin Universitätsklinikum Aachen, and Department of Neurology, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Thomas Kraus
- Department of Cell Biology, Erasmus Medical Centre, Rotterdam, The Netherlands, Laboratório de Proteómica, Departamento de Genética, Instituto Nacional de Saúde Dr Ricardo Jorge, Lisboa, Portugal, Department of Biochemistry, Erasmus University Medical Centre, Rotterdam, The Netherlands, Institut für Arbeitsmedizin und Sozialmedizin Universitätsklinikum Aachen, and Department of Neurology, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Mark K. Titulaer
- Department of Cell Biology, Erasmus Medical Centre, Rotterdam, The Netherlands, Laboratório de Proteómica, Departamento de Genética, Instituto Nacional de Saúde Dr Ricardo Jorge, Lisboa, Portugal, Department of Biochemistry, Erasmus University Medical Centre, Rotterdam, The Netherlands, Institut für Arbeitsmedizin und Sozialmedizin Universitätsklinikum Aachen, and Department of Neurology, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Peter Burgers
- Department of Cell Biology, Erasmus Medical Centre, Rotterdam, The Netherlands, Laboratório de Proteómica, Departamento de Genética, Instituto Nacional de Saúde Dr Ricardo Jorge, Lisboa, Portugal, Department of Biochemistry, Erasmus University Medical Centre, Rotterdam, The Netherlands, Institut für Arbeitsmedizin und Sozialmedizin Universitätsklinikum Aachen, and Department of Neurology, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Theo M. Luider
- Department of Cell Biology, Erasmus Medical Centre, Rotterdam, The Netherlands, Laboratório de Proteómica, Departamento de Genética, Instituto Nacional de Saúde Dr Ricardo Jorge, Lisboa, Portugal, Department of Biochemistry, Erasmus University Medical Centre, Rotterdam, The Netherlands, Institut für Arbeitsmedizin und Sozialmedizin Universitätsklinikum Aachen, and Department of Neurology, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Deborah Penque
- Department of Cell Biology, Erasmus Medical Centre, Rotterdam, The Netherlands, Laboratório de Proteómica, Departamento de Genética, Instituto Nacional de Saúde Dr Ricardo Jorge, Lisboa, Portugal, Department of Biochemistry, Erasmus University Medical Centre, Rotterdam, The Netherlands, Institut für Arbeitsmedizin und Sozialmedizin Universitätsklinikum Aachen, and Department of Neurology, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Bob J. Scholte
- Department of Cell Biology, Erasmus Medical Centre, Rotterdam, The Netherlands, Laboratório de Proteómica, Departamento de Genética, Instituto Nacional de Saúde Dr Ricardo Jorge, Lisboa, Portugal, Department of Biochemistry, Erasmus University Medical Centre, Rotterdam, The Netherlands, Institut für Arbeitsmedizin und Sozialmedizin Universitätsklinikum Aachen, and Department of Neurology, Erasmus Medical Centre, Rotterdam, The Netherlands
| |
Collapse
|
19
|
Wenge B, Bönisch H, Grabitzki J, Lochnit G, Schmitz B, Ahrend MHJ. Separation of membrane proteins by two-dimensional electrophoresis using cationic rehydrated strips. Electrophoresis 2008; 29:1511-7. [DOI: 10.1002/elps.200700546] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|