1
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Rashid MA, Lin-Moshier Y, Gunaratne GS, Subramanian S, Marchant JS, Subramanian VS. Vitamin C transport in neurons and epithelia is regulated by secretory carrier-associated membrane protein-2 (SCAMP2). Int J Biol Macromol 2023; 230:123205. [PMID: 36632962 DOI: 10.1016/j.ijbiomac.2023.123205] [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: 11/23/2022] [Revised: 12/28/2022] [Accepted: 01/05/2023] [Indexed: 01/11/2023]
Abstract
The human sodium-dependent vitamin C transporter-1 (hSVCT1) is localized at the apical membrane domain of polarized intestinal and renal epithelial cells to mediate ascorbic acid (AA) uptake. Currently, little is known about the array of interacting proteins that aid hSVCT1 trafficking and functional expression at the cell surface. Here we used an affinity tagging ('One-STrEP') and proteomic approach to identify hSVCT1 interacting proteins, which resolved secretory carrier-associated membrane protein-2 (SCAMP2) as a novel accessary protein partner. SCAMP2 was validated as an accessory protein by co-immunoprecipitation with hSVCT1. Co-expression of hSVCT1 and SCAMP2 in HEK-293 cells revealed both proteins co-localized in intracellular structures and at the plasma membrane. Functionally, over-expression of SCAMP2 potentiated 14C-AA uptake, and reciprocally silencing endogenous SCAMP2 decreased 14C-AA uptake. Finally, knockdown of endogenous hSVCT1 or SCAMP2 impaired differentiation of human-induced pluripotent stem cells (hiPSCs) toward a neuronal fate. These results establish SCAMP2 as a novel hSVCT1 accessary protein partner that regulates AA uptake in absorptive epithelia and during neurogenesis.
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Affiliation(s)
- Mohammad A Rashid
- Department of Cell Biology, Neurobiology & Anatomy, Medical College of Wisconsin, WI 53226, United States
| | - Yaping Lin-Moshier
- Department of Cell Biology, Neurobiology & Anatomy, Medical College of Wisconsin, WI 53226, United States
| | - Gihan S Gunaratne
- Department of Cell Biology, Neurobiology & Anatomy, Medical College of Wisconsin, WI 53226, United States
| | - Sreya Subramanian
- Department of Medicine, University of California, Irvine, CA 92697, United States
| | - Jonathan S Marchant
- Department of Cell Biology, Neurobiology & Anatomy, Medical College of Wisconsin, WI 53226, United States
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2
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Pauwels J, Fijałkowska D, Eyckerman S, Gevaert K. Mass spectrometry and the cellular surfaceome. MASS SPECTROMETRY REVIEWS 2022; 41:804-841. [PMID: 33655572 DOI: 10.1002/mas.21690] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 02/05/2021] [Accepted: 02/09/2021] [Indexed: 06/12/2023]
Abstract
The collection of exposed plasma membrane proteins, collectively termed the surfaceome, is involved in multiple vital cellular processes, such as the communication of cells with their surroundings and the regulation of transport across the lipid bilayer. The surfaceome also plays key roles in the immune system by recognizing and presenting antigens, with its possible malfunctioning linked to disease. Surface proteins have long been explored as potential cell markers, disease biomarkers, and therapeutic drug targets. Despite its importance, a detailed study of the surfaceome continues to pose major challenges for mass spectrometry-driven proteomics due to the inherent biophysical characteristics of surface proteins. Their inefficient extraction from hydrophobic membranes to an aqueous medium and their lower abundance compared to intracellular proteins hamper the analysis of surface proteins, which are therefore usually underrepresented in proteomic datasets. To tackle such problems, several innovative analytical methodologies have been developed. This review aims at providing an extensive overview of the different methods for surfaceome analysis, with respective considerations for downstream mass spectrometry-based proteomics.
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Affiliation(s)
- Jarne Pauwels
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | | | - Sven Eyckerman
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Kris Gevaert
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
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3
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Brown KA, Tucholski T, Alpert AJ, Eken C, Wesemann L, Kyrvasilis A, Jin S, Ge Y. Top-Down Proteomics of Endogenous Membrane Proteins Enabled by Cloud Point Enrichment and Multidimensional Liquid Chromatography-Mass Spectrometry. Anal Chem 2020; 92:15726-15735. [PMID: 33231430 PMCID: PMC7968110 DOI: 10.1021/acs.analchem.0c02533] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Although top-down proteomics has emerged as a powerful strategy to characterize proteins in biological systems, the analysis of endogenous membrane proteins remains challenging due to their low solubility, low abundance, and the complexity of the membrane subproteome. Here, we report a simple but effective enrichment and separation strategy for top-down proteomics of endogenous membrane proteins enabled by cloud point extraction and multidimensional liquid chromatography coupled to high-resolution mass spectrometry (MS). The cloud point extraction efficiently enriched membrane proteins using a single extraction, eliminating the need for time-consuming ultracentrifugation steps. Subsequently, size-exclusion chromatography (SEC) with an MS-compatible mobile phase (59% water, 40% isopropanol, 1% formic acid) was used to remove the residual surfactant and fractionate intact proteins (6-115 kDa). The fractions were separated further by reversed-phase liquid chromatography (RPLC) coupled with MS for protein characterization. This method was applied to human embryonic kidney cells and cardiac tissue lysates to enable the identification of 188 and 124 endogenous integral membrane proteins, respectively, some with as many as 19 transmembrane domains.
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Affiliation(s)
- Kyle A. Brown
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Trisha Tucholski
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Andrew J. Alpert
- PolyLC Inc., Columbia, Maryland 21045, United States
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin, 53705, USA
| | - Christian Eken
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Lucas Wesemann
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin, 53705, USA
| | - Andreas Kyrvasilis
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin, 53705, USA
| | - Song Jin
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin, 53705, USA
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, 53705, USA
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4
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Lee SH, Hadipour-Lakmehsari S, Kim DH, Di Paola M, Kuzmanov U, Shah S, Lee JJH, Kislinger T, Sharma P, Oudit GY, Gramolini AO. Bioinformatic analysis of membrane and associated proteins in murine cardiomyocytes and human myocardium. Sci Data 2020; 7:425. [PMID: 33262348 PMCID: PMC7708497 DOI: 10.1038/s41597-020-00762-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 11/17/2020] [Indexed: 12/13/2022] Open
Abstract
In the current study we examined several proteomic- and RNA-Seq-based datasets of cardiac-enriched, cell-surface and membrane-associated proteins in human fetal and mouse neonatal ventricular cardiomyocytes. By integrating available microarray and tissue expression profiles with MGI phenotypic analysis, we identified 173 membrane-associated proteins that are cardiac-enriched, conserved amongst eukaryotic species, and have not yet been linked to a 'cardiac' Phenotype-Ontology. To highlight the utility of this dataset, we selected several proteins to investigate more carefully, including FAM162A, MCT1, and COX20, to show cardiac enrichment, subcellular distribution and expression patterns in disease. We performed three-dimensional confocal imaging analysis to validate subcellular localization and expression in adult mouse ventricular cardiomyocytes. FAM162A, MCT1, and COX20 were expressed differentially at the transcriptomic and proteomic levels in multiple models of mouse and human heart diseases and may represent potential diagnostic and therapeutic targets for human dilated and ischemic cardiomyopathies. Altogether, we believe this comprehensive cardiomyocyte membrane proteome dataset will prove instrumental to future investigations aimed at characterizing heart disease markers and/or therapeutic targets for heart failure.
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Affiliation(s)
- Shin-Haw Lee
- Translational Biology and Engineering Program, Ted Rogers Centre for Heart Research, Toronto, Ontario, M5G 1M1, Canada
- Department of Physiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, M5S 1M8, Canada
| | - Sina Hadipour-Lakmehsari
- Translational Biology and Engineering Program, Ted Rogers Centre for Heart Research, Toronto, Ontario, M5G 1M1, Canada
- Department of Physiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, M5S 1M8, Canada
| | - Da Hye Kim
- Translational Biology and Engineering Program, Ted Rogers Centre for Heart Research, Toronto, Ontario, M5G 1M1, Canada
- Department of Physiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, M5S 1M8, Canada
| | - Michelle Di Paola
- Translational Biology and Engineering Program, Ted Rogers Centre for Heart Research, Toronto, Ontario, M5G 1M1, Canada
- Department of Physiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, M5S 1M8, Canada
| | - Uros Kuzmanov
- Translational Biology and Engineering Program, Ted Rogers Centre for Heart Research, Toronto, Ontario, M5G 1M1, Canada
- Department of Physiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, M5S 1M8, Canada
| | - Saumya Shah
- Department of Medicine, University of Alberta, Edmonton, Alberta, T6G 2R3, Canada
- Mazankowski Alberta Heart Institute, Edmonton, Alberta, T6G 2B7, Canada
| | - Joseph Jong-Hwan Lee
- Translational Biology and Engineering Program, Ted Rogers Centre for Heart Research, Toronto, Ontario, M5G 1M1, Canada
- Department of Physiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, M5S 1M8, Canada
| | - Thomas Kislinger
- Princess Margaret Cancer Research Centre, Toronto, Ontario, M5G 1L8, Canada
- Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, Ontario, M5G 1L7, Canada
| | - Parveen Sharma
- Department of Physiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, M5S 1M8, Canada
- Department of Cardiovascular & Metabolic Medicine, University of Liverpool, Liverpool, L69 3GE, UK
| | - Gavin Y Oudit
- Department of Medicine, University of Alberta, Edmonton, Alberta, T6G 2R3, Canada
- Mazankowski Alberta Heart Institute, Edmonton, Alberta, T6G 2B7, Canada
| | - Anthony O Gramolini
- Translational Biology and Engineering Program, Ted Rogers Centre for Heart Research, Toronto, Ontario, M5G 1M1, Canada.
- Department of Physiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, M5S 1M8, Canada.
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5
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van der Laarse SAM, van Gelder CAGH, Bern M, Akeroyd M, Olsthoorn MMA, Heck AJR. Targeting proline in (phospho)proteomics. FEBS J 2020; 287:2979-2997. [PMID: 31863553 PMCID: PMC7496877 DOI: 10.1111/febs.15190] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 11/25/2019] [Accepted: 12/19/2019] [Indexed: 01/10/2023]
Abstract
Mass spectrometry-based proteomics experiments typically start with the digestion of proteins using trypsin, chosen because of its high specificity, availability, and ease of use. It has become apparent that the sole use of trypsin may impose certain limits on our ability to grasp the full proteome, missing out particular sites of post-translational modifications, protein segments, or even subsets of proteins. To tackle this problem, alternative proteases have been introduced and shown to lead to an increase in the detectable (phospho)proteome. Here, we argue that there may be further room for improvement and explore the protease EndoPro. For optimal peptide identification rates, we explored multiple peptide fragmentation techniques (HCD, ETD, and EThcD) and employed Byonic as search algorithm. We obtain peptide IDs for about 40% of the MS2 spectra (66% for trypsin). EndoPro cleaves with high specificity at the C-terminal site of Pro and Ala residues and displays activity in a broad pH range, where we focused on its performance at pH = 2 and 5.5. The proteome coverage of EndoPro at these two pH values is rather distinct, and also complementary to the coverage obtained with trypsin. As about 40% of mammalian protein phosphorylations are proline-directed, we also explored the performance of EndoPro in phosphoproteomics. EndoPro extends the coverable phosphoproteome substantially, whereby both the, at pH = 2 and 5.5, acquired phosphoproteomes are complementary to each other and to the phosphoproteome obtained using trypsin. Hence, EndoPro is a powerful tool to exploit in (phospho)proteomics applications.
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Affiliation(s)
- Saar A. M. van der Laarse
- Biomolecular Mass Spectrometry and ProteomicsBijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical SciencesUtrecht UniversityThe Netherlands
- Netherlands Proteomics CenterUtrechtThe Netherlands
| | - Charlotte A. G. H. van Gelder
- Biomolecular Mass Spectrometry and ProteomicsBijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical SciencesUtrecht UniversityThe Netherlands
- Netherlands Proteomics CenterUtrechtThe Netherlands
| | | | | | | | - Albert J. R. Heck
- Biomolecular Mass Spectrometry and ProteomicsBijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical SciencesUtrecht UniversityThe Netherlands
- Netherlands Proteomics CenterUtrechtThe Netherlands
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6
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Wu Q, Tian Y, Yang C, Liang Z, Shan Y, Zhang L, Zhang Y. Sequential amidation of peptide C-termini for improving fragmentation efficiency. JOURNAL OF MASS SPECTROMETRY : JMS 2020; 56:e4529. [PMID: 32419269 DOI: 10.1002/jms.4529] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 03/23/2020] [Accepted: 04/09/2020] [Indexed: 06/11/2023]
Abstract
Owing to the poor fragmentation efficiency caused by the lack of a positively charged basic group at the C-termini of peptides, the identification of nontryptic peptides in classical proteomics is known to be less efficient. Particularly, attaching positively charged basic groups to C-termini via chemical derivatizations is known to be able to enhance their fragmentation efficiency. In this study, we introduced a novel strategy, C-termini sequential amidation reaction (CSAR), to improve peptide fragmentation efficiency. By this strategy, C-terminal and side-chain carboxyl groups were firstly amidated by neutral methylamine (MA), and then C-terminal amide bonds were selectively deamidated through peptide amidase while side-chain amide bonds remained unchanged, followed by the secondary amidation of C-termini via basic agmatine (AG). We optimized the amidation reaction conditions to achieve the MA derivatization efficiency of >99% for side-chain carboxyl groups and AG derivatization efficiency of 80% for the hydrolytic C-termini. We applied CSAR strategy to identify bovine serum albumin (BSA) chymotryptic digests, resulting in the increased fragmentation efficiencies (improvement by 9-32%) and charge states (improvement by 39-52%) under single or multiple dissociation modes. The strategy described here might be a promising approach for the identification of peptides that suffered from poor fragmentation efficiency.
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Affiliation(s)
- Qiong Wu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, 116023, China
| | - Yu'e Tian
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Chao Yang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, 116023, China
| | - Zhen Liang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, 116023, China
| | - Yichu Shan
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, 116023, China
| | - Lihua Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, 116023, China
| | - Yukui Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, 116023, China
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7
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Milman BL, Solov’eva AV, Lugovkina NV, Zhurkovich IK. Features of Tryptic Peptides Providing Their Detection and Identification by MALDI Mass Spectrometry. JOURNAL OF ANALYTICAL CHEMISTRY 2019. [DOI: 10.1134/s1061934819130094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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8
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Vit O, Harant K, Klener P, Man P, Petrak J. A three-pronged "Pitchfork" strategy enables an extensive description of the human membrane proteome and the identification of missing proteins. J Proteomics 2019; 204:103411. [PMID: 31176011 DOI: 10.1016/j.jprot.2019.103411] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 05/14/2019] [Accepted: 06/03/2019] [Indexed: 11/28/2022]
Abstract
Integral membrane proteins are under-represented in standard proteomic analyses, mostly because of their low expression and absence of trypsin-cleavage sites in their hydrophobic transmembrane segments. Novel and effective strategies for membrane proteomic analysis aim at soluble N-glycosylated segments of integral membrane proteins (CSC, SPEG, N-glyco-FASP) or selectively target the hydrophobic transmembrane alpha-helical segments employing chemical peptide cleavage by CNBr (hpTC). We combined a solid phase enrichment of glycopeptides (SPEG) with a transmembrane segment-oriented hpTC method and a standard "detergent and trypsin" approach into a three-pronged "Pitchfork" strategy to maximize the membrane proteome coverage in human lymphoma cells. This strategy enabled the identification of >1200 integral membrane proteins from all cellular compartments, including 105 CD antigens, 24 G protein-coupled receptors, and 141 solute carrier transporters. The advantage of the combination lies in the complementarity of the methods. SPEG and hpTC target different sets of membrane proteins. HpTC provided identifications of proteins and peptides with significantly higher hydrophobicity compared to SPEG and detergent-trypsin approaches. Among all identified proteins, we observed 32 so-called "missing proteins". The Pitchfork strategy presented here is universally applicable and enables deep and fast description of membrane proteomes in only 3 LC-MS/MS runs per replicate. SIGNIFICANCE: Integral membrane proteins (IMPs) are encoded by roughly a quarter of human coding genes. Their functions and their specific localization makes IMPs highly attractive drug targets. In fact, roughly half of the currently approved drugs in medicine target IMPs. Our knowledge of membrane proteomes is, however, limited. We present a new strategy for the membrane proteome analysis that combines three complementary methods targeting different features of IMPs. Using the combined strategy, we identified over 1200 IMPs in human lymphoma tissue from all sub-cellular compartments in only 3 LC-MS/MS runs per replicate. The three-pronged "Pitchfork" strategy is universally applicable, and offers a fast way toward a reasonably concise description of membrane proteomes in multiple samples.
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Affiliation(s)
- Ondrej Vit
- BIOCEV, First Faculty of Medicine, Charles University, Czech Republic
| | - Karel Harant
- Laboratory of Mass Spectrometry - Service Laboratory of Biology Section, BIOCEV, Faculty of Science, Charles University, Prague, Czech Republic
| | - Pavel Klener
- Institute of Pathological Physiology, First Faculty of Medicine, Charles University, Czech Republic
| | - Petr Man
- BIOCEV, Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic; Department of Biochemistry, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jiri Petrak
- BIOCEV, First Faculty of Medicine, Charles University, Czech Republic.
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9
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Adhikari S, Sharma S, Ahn SB, Baker MS. In Silico Peptide Repertoire of Human Olfactory Receptor Proteomes on High-Stringency Mass Spectrometry. J Proteome Res 2019; 18:4117-4123. [PMID: 31046287 DOI: 10.1021/acs.jproteome.8b00494] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Human olfactory receptors (ORs) are seven-pass transmembrane G-protein coupled receptors (GPCR) involved in smell perception and many other signaling pathways. They are primarily expressed in the olfactory epithelium and ectopically expressed in several other organs and tissues. neXtProt contains 4 PE1 (protein existence 1, evidenced at the protein level) ORs, determined on the basis of either protein interaction data (i.e., OR1D4 and OR2AG1) or convincing genetic, haplotype, or biochemical data (i.e., OR1D2 and OR2J3). Not a single OR currently qualifies for neXtProt PE1 status based on mass spectrometry (MS) evidence. Many reasons for this absence of MS-based identification have been proposed, including (i) confined or spatiotemporal or developmental expression, (ii) low copy number, (iii) OR repertoire gene silencing, and (iv) limited tissue availability. OR transmembrane domains (TMDs) inherently limit MS identification because the hydrophobic nature restricts the access of trypsin to potential cleavage sites. Equally, the extremely low frequency or lack of accessible arginine and lysine residues in TMDs renders trypsin cleavage ineffective. Here, we demonstrate an analytical approach specifically focused on the hydrophilic (trypsin-accessible) domains of ORs [i.e., with all transmembrane segments and anchored peptides excluded). We predicted the ability of OR soluble (hydrophilic) domains to yield 2 or more >9 amino acids (aa) length unique mapping (unique to a protein only), non-nested (peptides with varying length at the N or C terminal but containing the same core sequence), leucine/isoleucine (I/L) switch examined (I and L have same mass and cannot be distinguished by MS) tryptic peptides. Our analysis showed that ∼58% of the human OR proteome could potentially generate tryptic peptides that satisfy current the Human Proteome Project data interpretation guidelines (version 2.1) when no missed cleavages are allowed and increases to ∼78% when one missed cleavage is allowed. The utilization of current biological data (adjuvant genomics, expression profile, transcriptomics, epigenome silencing data, etc.) and the adoption of a non-conventional proteomics approach (e.g., Confetti multiprotease digestion, CNBr cleavage of TMDs, and more-extreme chromatographic and MS methods) could aid in the detection of the remaining ORs.
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Affiliation(s)
- Subash Adhikari
- Department of Biomedical Sciences, Faculty of Medicine & Health Sciences , Macquarie University , Sydney , New South Wales 2109 , Australia
| | - Samridhi Sharma
- Department of Biomedical Sciences, Faculty of Medicine & Health Sciences , Macquarie University , Sydney , New South Wales 2109 , Australia
| | - Seong Beom Ahn
- Department of Biomedical Sciences, Faculty of Medicine & Health Sciences , Macquarie University , Sydney , New South Wales 2109 , Australia
| | - Mark S Baker
- Department of Biomedical Sciences, Faculty of Medicine & Health Sciences , Macquarie University , Sydney , New South Wales 2109 , Australia
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10
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Sun J, Shi J, Wang Y, Chen Y, Li Y, Kong D, Chang L, Liu F, Lv Z, Zhou Y, He F, Zhang Y, Xu P. Multiproteases Combined with High-pH Reverse-Phase Separation Strategy Verified Fourteen Missing Proteins in Human Testis Tissue. J Proteome Res 2018; 17:4171-4177. [PMID: 30280576 DOI: 10.1021/acs.jproteome.8b00397] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Subsequent to conducting the Chromosome-Centric Human Proteome Project, we have focused on human testis-enriched missing proteins (MPs) since 2015. For protein coverage to be enhanced, a multiprotease strategy was used for separation of samples by 10% SDS-PAGE. For the separating efficiency to be improved, a high-pH reverse phase (RP) separation strategy was applied to fractionate complex samples in this study. A total of 11,558 proteins was identified, which is the largest proteome data set for single human tissue sample so far. On the basis of this large-scale data set, we verified 14 MPs (PE2) in neXtProt (2018-01) after spectrum quality analysis, isobaric post-translational modification, and single amino acid variant filtering, and synthesized peptide matching. Tissue expression analysis showed that 3 of 14 MPs were testis-specific proteins. Functional analysis showed that 10 of 14 MPs were closely related to liver tumor, liver carcinoma, and hepatocellular carcinoma. Another 100 MPs were listed as candidates but required additional verification information. All MS data sets have been deposited into the ProteomeXchange with the identifier PXD009737.
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Affiliation(s)
- Jinshuai Sun
- Hebei Province Key Lab of Research and Application on Microbial Diversity, College of Life Sciences , Hebei University , Baoding , Hebei 071002 , China.,State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing) , Beijing Institute of Lifeomics , Beijing 102206 , China
| | - Jiahui Shi
- Hebei Province Key Lab of Research and Application on Microbial Diversity, College of Life Sciences , Hebei University , Baoding , Hebei 071002 , China.,State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing) , Beijing Institute of Lifeomics , Beijing 102206 , China
| | - Yihao Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing) , Beijing Institute of Lifeomics , Beijing 102206 , China
| | - Yang Chen
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing) , Beijing Institute of Lifeomics , Beijing 102206 , China
| | - Yanchang Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing) , Beijing Institute of Lifeomics , Beijing 102206 , China
| | - Degang Kong
- Department of Hepatopancreatobiliary Surgery , The Second Affiliated Hospital of Tianjin Medical University , Tianjin 300211 , China
| | - Lei Chang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing) , Beijing Institute of Lifeomics , Beijing 102206 , China
| | - Fengsong Liu
- Hebei Province Key Lab of Research and Application on Microbial Diversity, College of Life Sciences , Hebei University , Baoding , Hebei 071002 , China
| | - Zhitang Lv
- Hebei Province Key Lab of Research and Application on Microbial Diversity, College of Life Sciences , Hebei University , Baoding , Hebei 071002 , China
| | - Yue Zhou
- Demo Laboratory of Thermofisher Scientific China , Shanghai 200120 , China
| | - Fuchu He
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing) , Beijing Institute of Lifeomics , Beijing 102206 , China
| | - Yao Zhang
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences , Sun Yat-Sen University , Guangzhou 510275 , China
| | - Ping Xu
- Hebei Province Key Lab of Research and Application on Microbial Diversity, College of Life Sciences , Hebei University , Baoding , Hebei 071002 , China.,State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing) , Beijing Institute of Lifeomics , Beijing 102206 , China.,Key Laboratory of Combinational Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, School of Pharmaceutical Science , Wuhan University , Wuhan 430072 , China
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11
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Zhang Y, Lin Z, Hao P, Hou K, Sui Y, Zhang K, He Y, Li H, Yang H, Liu S, Ren Y. Improvement of Peptide Separation for Exploring the Missing Proteins Localized on Membranes. J Proteome Res 2018; 17:4152-4159. [DOI: 10.1021/acs.jproteome.8b00409] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yuanliang Zhang
- BGI-Shenzhen, Beishan Industrial Zone 11th building, Yantian District, Shenzhen, Guangdong 518083, China
- China National GeneBank, BGI-Shenzhen, Jinsha Road, Shenzhen 518120, China
| | - Zhilong Lin
- BGI-Shenzhen, Beishan Industrial Zone 11th building, Yantian District, Shenzhen, Guangdong 518083, China
- China National GeneBank, BGI-Shenzhen, Jinsha Road, Shenzhen 518120, China
| | - Piliang Hao
- School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, China
| | - Kexia Hou
- The Second Maternal and Child Health Care Center of Huangdao District, 236 Fuchunjiang Road, Qingdao 266555, Shandong, China
| | - Yuanyuan Sui
- The Second Maternal and Child Health Care Center of Huangdao District, 236 Fuchunjiang Road, Qingdao 266555, Shandong, China
| | - Keren Zhang
- BGI-Shenzhen, Beishan Industrial Zone 11th building, Yantian District, Shenzhen, Guangdong 518083, China
- China National GeneBank, BGI-Shenzhen, Jinsha Road, Shenzhen 518120, China
| | - Yanbin He
- BGI-Shenzhen, Beishan Industrial Zone 11th building, Yantian District, Shenzhen, Guangdong 518083, China
- China National GeneBank, BGI-Shenzhen, Jinsha Road, Shenzhen 518120, China
| | - Hong Li
- Pulmonary Function Room, Shenzhen Seventh People’s Hospital, 2010 Wutong Road, Yantian District, Shenzhen, Guangdong 518081, China
| | - Huanming Yang
- BGI-Shenzhen, Beishan Industrial Zone 11th building, Yantian District, Shenzhen, Guangdong 518083, China
- James D. Watson Institute of Genome Sciences, Hangzhou 310058, China
| | - Siqi Liu
- BGI-Shenzhen, Beishan Industrial Zone 11th building, Yantian District, Shenzhen, Guangdong 518083, China
- China National GeneBank, BGI-Shenzhen, Jinsha Road, Shenzhen 518120, China
| | - Yan Ren
- BGI-Shenzhen, Beishan Industrial Zone 11th building, Yantian District, Shenzhen, Guangdong 518083, China
- China National GeneBank, BGI-Shenzhen, Jinsha Road, Shenzhen 518120, China
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12
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Weldemariam MM, Han CL, Shekari F, Kitata RB, Chuang CY, Hsu WT, Kuo HC, Choong WK, Sung TY, He FC, Chung MCM, Salekdeh GH, Chen YJ. Subcellular Proteome Landscape of Human Embryonic Stem Cells Revealed Missing Membrane Proteins. J Proteome Res 2018; 17:4138-4151. [DOI: 10.1021/acs.jproteome.8b00407] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Mehari Muuz Weldemariam
- Institute of Chemistry, Academia Sinica, Taipei 115, Taiwan
- Department of Chemistry, National Taiwan University, Taipei 112, Taiwan
| | - Chia-Li Han
- Master Program in Clinical Pharmacogenomics and Pharmacoproteomics, College of Pharmacy, Taipei Medical University, Taipei 110, Taiwan
| | - Faezeh Shekari
- Department of Molecular Systems Biology at Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | | | - Ching-Yu Chuang
- Genomics Research Center, Academia Sinica, Taiepei 115, Taiwan
| | | | | | | | | | - Fu-Chu He
- Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing, 102206 China
| | - Maxey Ching Ming Chung
- Department of Biochemistry, Yong Loo Lin School of Medicine, NUS, 14 Science Drive 4, singapore, 117543 Singpore
| | - Ghasem Hosseini Salekdeh
- Department of Molecular Systems Biology at Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
- Department of Molecular Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
- Department of Systems and Synthetic Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education, and Extension Organization, Karaj, Iran
| | - Yu-Ju Chen
- Institute of Chemistry, Academia Sinica, Taipei 115, Taiwan
- Department of Chemistry, National Taiwan University, Taipei 112, Taiwan
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13
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Glisovic-Aplenc T, Gill S, Spruce LA, Smith IR, Fazelinia H, Shestova O, Ding H, Tasian SK, Aplenc R, Seeholzer SH. Improved surfaceome coverage with a label-free nonaffinity-purified workflow. Proteomics 2017; 17. [PMID: 28116781 DOI: 10.1002/pmic.201600344] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 01/05/2017] [Accepted: 01/19/2017] [Indexed: 01/17/2023]
Abstract
The proteins of the cellular plasma membrane (PM) perform important functions relating to homeostasis and intercellular communication. Due to its overall low cellular abundance, amphipathic character, and low membrane-to-cytoplasm ratio, the PM proteome has been challenging to isolate and characterize, and is poorly represented in standard LC-MS/MS analyses. In this study, we employ sucrose gradient ultracentrifugation for the enrichment of the PM proteome, without chemical labeling and affinity purification, together with GeLCMS and use subsequent bioinformatics tools to select proteins associated with the PM/cell surface, herein referred to as the surfaceome. Using this methodology, we identify over 1900 cell surface associated proteins in a human acute myeloid leukemia cell line. These surface proteins comprise almost 50% of all detected cellular proteins, a number that substantially exceeds the depth of coverage in previously published studies describing the leukemia surfaceome.
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Affiliation(s)
- Tina Glisovic-Aplenc
- Division of Oncology, Center for Childhood Cancer Research, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Saar Gill
- Center for Cellular Immunotherapies, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Lynn A Spruce
- Protein and Proteomics Core Facility, The Children's Hospital of Philadelphia Research Institute, Philadelphia, PA, USA
| | - Ian R Smith
- Protein and Proteomics Core Facility, The Children's Hospital of Philadelphia Research Institute, Philadelphia, PA, USA
| | - Hossein Fazelinia
- Protein and Proteomics Core Facility, The Children's Hospital of Philadelphia Research Institute, Philadelphia, PA, USA
| | - Olga Shestova
- Center for Cellular Immunotherapies, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Hua Ding
- Protein and Proteomics Core Facility, The Children's Hospital of Philadelphia Research Institute, Philadelphia, PA, USA
| | - Sarah K Tasian
- Division of Oncology, Center for Childhood Cancer Research, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Richard Aplenc
- Division of Oncology, Center for Childhood Cancer Research, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Steven H Seeholzer
- Protein and Proteomics Core Facility, The Children's Hospital of Philadelphia Research Institute, Philadelphia, PA, USA
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14
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Membrane-bound electron transport systems of an anammox bacterium: A complexome analysis. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:1694-704. [DOI: 10.1016/j.bbabio.2016.07.006] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 07/14/2016] [Accepted: 07/19/2016] [Indexed: 11/24/2022]
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15
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Vit O, Petrak J. Integral membrane proteins in proteomics. How to break open the black box? J Proteomics 2016; 153:8-20. [PMID: 27530594 DOI: 10.1016/j.jprot.2016.08.006] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 06/30/2016] [Accepted: 08/09/2016] [Indexed: 12/22/2022]
Abstract
Integral membrane proteins (IMPs) are coded by 20-30% of human genes and execute important functions - transmembrane transport, signal transduction, cell-cell communication, cell adhesion to the extracellular matrix, and many other processes. Due to their hydrophobicity, low expression and lack of trypsin cleavage sites in their transmembrane segments, IMPs have been generally under-represented in routine proteomic analyses. However, the field of membrane proteomics has changed markedly in the past decade, namely due to the introduction of filter assisted sample preparation (FASP), the establishment of cell surface capture (CSC) protocols, and the development of methods that enable analysis of the hydrophobic transmembrane segments. This review will summarize the recent developments in the field and outline the most successful strategies for the analysis of integral membrane proteins. SIGNIFICANCE Integral membrane proteins (IMPs) are attractive therapeutic targets mostly due to their many important functions. However, our knowledge of the membrane proteome is severely limited to effectively exploit their potential. This is mostly due to the lack of appropriate techniques or methods compatible with the typical features of IMPs, namely hydrophobicity, low expression and lack of trypsin cleavage sites. This review summarizes the most recent development in membrane proteomics and outlines the most successful strategies for their large-scale analysis.
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Affiliation(s)
- O Vit
- BIOCEV, First Faculty of Medicine, Charles University in Prague, Czech Republic.
| | - J Petrak
- BIOCEV, First Faculty of Medicine, Charles University in Prague, Czech Republic
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16
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Proteomic analysis of drug-resistant Mycobacterium tuberculosis by one-dimensional gel electrophoresis and charge chromatography. Arch Microbiol 2016; 199:9-15. [PMID: 27417316 DOI: 10.1007/s00203-016-1267-8] [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] [Received: 09/13/2015] [Revised: 06/20/2016] [Accepted: 06/22/2016] [Indexed: 02/03/2023]
Abstract
Multidrug-resistant tuberculosis (MDR-TB) is a form of TB caused by Mycobacterium tuberculosis (M. tuberculosis) that do not respond to, at least, isoniazid and rifampicin, the two most powerful, first-line (or standard) anti-TB drugs. Novel intervention strategies for eliminating this disease were based on finding proteins that can be used for designing new drugs or new and reliable kits for diagnosis. The aim of this study was to compare the protein profiles of MDR-TB with sensitive isolates. Proteomic analysis of M. tuberculosis MDR-TB and sensitive isolates was obtained with ion exchange chromatography coupled with MALDI-TOF-TOF (matrix-assisted laser desorption/ionization) in order to identify individual proteins that have different expression in MDR-TB to be used as a drug target or diagnostic marker for designing valuable TB vaccines or TB rapid tests. We identified eight proteins in MDR-TB isolates, and analyses showed that these proteins are absent in M. tuberculosis-sensitive isolates: (Rv2140c, Rv0009, Rv1932, Rv0251c, Rv2558, Rv1284, Rv3699 and MMP major membrane proteins). These data will provide valuable clues in further investigation for suitable TB rapid tests or drug targets against drug-resistant and sensitive M. tuberculosis isolates.
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17
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Yari S, Tasbiti AH, Ghanei M, Shokrgozar MA, Vaziri B, Mahdian R, Yari F, Bahrmand A. Proteomic analysis of sensitive and multi drug resistant Mycobacterium tuberculosis strains. Microbiology (Reading) 2016. [DOI: 10.1134/s0026261716030164] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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18
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Yacoub HA, Al-Maghrabi OA, Ahmed ES, Uversky VN. Abundance and functional roles of intrinsic disorder in the antimicrobial peptides of the NK-lysin family. J Biomol Struct Dyn 2016; 35:836-856. [DOI: 10.1080/07391102.2016.1164077] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Haitham A. Yacoub
- Faculty of Science, Department of Biological Sciences, University of Jeddah, Jeddah, Saudi Arabia
- Department of Cell Biology, Genetic Engineering and Biotechnology Division, National Research Centre, P.O. Box 12622, Gizza, Egypt
| | - Omar A. Al-Maghrabi
- Faculty of Science, Department of Biological Sciences, University of Jeddah, Jeddah, Saudi Arabia
| | - Ekram S. Ahmed
- Department of Cell Biology, Genetic Engineering and Biotechnology Division, National Research Centre, P.O. Box 12622, Gizza, Egypt
| | - Vladimir N. Uversky
- Faculty of Sciences, Department of Biological Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah, Saudi Arabia
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
- Department of Molecular Medicine and USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
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19
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Wessels HJCT, de Almeida NM, Kartal B, Keltjens JT. Bacterial Electron Transfer Chains Primed by Proteomics. Adv Microb Physiol 2016; 68:219-352. [PMID: 27134025 DOI: 10.1016/bs.ampbs.2016.02.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Electron transport phosphorylation is the central mechanism for most prokaryotic species to harvest energy released in the respiration of their substrates as ATP. Microorganisms have evolved incredible variations on this principle, most of these we perhaps do not know, considering that only a fraction of the microbial richness is known. Besides these variations, microbial species may show substantial versatility in using respiratory systems. In connection herewith, regulatory mechanisms control the expression of these respiratory enzyme systems and their assembly at the translational and posttranslational levels, to optimally accommodate changes in the supply of their energy substrates. Here, we present an overview of methods and techniques from the field of proteomics to explore bacterial electron transfer chains and their regulation at levels ranging from the whole organism down to the Ångstrom scales of protein structures. From the survey of the literature on this subject, it is concluded that proteomics, indeed, has substantially contributed to our comprehending of bacterial respiratory mechanisms, often in elegant combinations with genetic and biochemical approaches. However, we also note that advanced proteomics offers a wealth of opportunities, which have not been exploited at all, or at best underexploited in hypothesis-driving and hypothesis-driven research on bacterial bioenergetics. Examples obtained from the related area of mitochondrial oxidative phosphorylation research, where the application of advanced proteomics is more common, may illustrate these opportunities.
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Affiliation(s)
- H J C T Wessels
- Nijmegen Center for Mitochondrial Disorders, Radboud Proteomics Centre, Translational Metabolic Laboratory, Radboud University Medical Center, Nijmegen, The Netherlands
| | - N M de Almeida
- Institute of Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - B Kartal
- Institute of Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands; Laboratory of Microbiology, Ghent University, Ghent, Belgium
| | - J T Keltjens
- Institute of Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands.
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20
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MCLIP Detection of Novel Protein–Protein Interactions at the Nuclear Envelope. Methods Enzymol 2016; 569:503-15. [DOI: 10.1016/bs.mie.2015.08.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
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21
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Paul P, Chaturvedi P, Selymesi M, Ghatak A, Mesihovic A, Scharf KD, Weckwerth W, Simm S, Schleiff E. The membrane proteome of male gametophyte in Solanum lycopersicum. J Proteomics 2016; 131:48-60. [DOI: 10.1016/j.jprot.2015.10.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2015] [Revised: 09/21/2015] [Accepted: 10/08/2015] [Indexed: 12/11/2022]
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22
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Papanastasiou M, Orfanoudaki G, Kountourakis N, Koukaki M, Sardis MF, Aivaliotis M, Tsolis KC, Karamanou S, Economou A. Rapid label-free quantitative analysis of the E. coli
BL21(DE3) inner membrane proteome. Proteomics 2015; 16:85-97. [DOI: 10.1002/pmic.201500304] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Revised: 09/05/2015] [Accepted: 10/12/2015] [Indexed: 12/12/2022]
Affiliation(s)
- Malvina Papanastasiou
- Institute of Molecular Biology and Biotechnology; Foundation for Research & Technology; Iraklio Greece
- Department Pathology & Laboratory Medicine, Perelman School of Medicine; University of Pennsylvania; Philadelphia USA
| | - Georgia Orfanoudaki
- Institute of Molecular Biology and Biotechnology; Foundation for Research & Technology; Iraklio Greece
- Department of Biology; University of Crete; Iraklio Greece
| | - Nikos Kountourakis
- Institute of Molecular Biology and Biotechnology; Foundation for Research & Technology; Iraklio Greece
| | - Marina Koukaki
- Institute of Molecular Biology and Biotechnology; Foundation for Research & Technology; Iraklio Greece
| | - Marios Frantzeskos Sardis
- Institute of Molecular Biology and Biotechnology; Foundation for Research & Technology; Iraklio Greece
- Laboratory of Molecular Bacteriology, Rega Institute, Department of Microbiology and Immunology; Katholieke Universiteit Leuven; Leuven Belgium
| | - Michalis Aivaliotis
- Institute of Molecular Biology and Biotechnology; Foundation for Research & Technology; Iraklio Greece
| | - Konstantinos C. Tsolis
- Institute of Molecular Biology and Biotechnology; Foundation for Research & Technology; Iraklio Greece
- Department of Biology; University of Crete; Iraklio Greece
- Laboratory of Molecular Bacteriology, Rega Institute, Department of Microbiology and Immunology; Katholieke Universiteit Leuven; Leuven Belgium
| | - Spyridoula Karamanou
- Institute of Molecular Biology and Biotechnology; Foundation for Research & Technology; Iraklio Greece
- Laboratory of Molecular Bacteriology, Rega Institute, Department of Microbiology and Immunology; Katholieke Universiteit Leuven; Leuven Belgium
| | - Anastassios Economou
- Institute of Molecular Biology and Biotechnology; Foundation for Research & Technology; Iraklio Greece
- Department of Biology; University of Crete; Iraklio Greece
- Laboratory of Molecular Bacteriology, Rega Institute, Department of Microbiology and Immunology; Katholieke Universiteit Leuven; Leuven Belgium
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23
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Dimayacyac-Esleta BRT, Tsai CF, Kitata RB, Lin PY, Choong WK, Lin TD, Wang YT, Weng SH, Yang PC, Arco SD, Sung TY, Chen YJ. Rapid High-pH Reverse Phase StageTip for Sensitive Small-Scale Membrane Proteomic Profiling. Anal Chem 2015; 87:12016-23. [PMID: 26554430 DOI: 10.1021/acs.analchem.5b03639] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Membrane proteins are crucial targets for cancer biomarker discovery and drug development. However, in addition to the inherent challenges of hydrophobicity and low abundance, complete membrane proteome coverage of clinical specimen is usually hindered by the requirement of large amount of starting materials. Toward comprehensive membrane proteomic profiling for small amounts of samples (10 μg), we developed high-pH reverse phase (Hp-RP) combined with stop-and-go extraction tip (StageTip) technique, as a fast (∼15 min.), sensitive, reproducible, high-resolution and multiplexed fractionation method suitable for accurate quantification of the membrane proteome. This approach provided almost 2-fold enhanced detection of peptides encompassing transmembrane helix (TMH) domain, as compared with strong anion exchange (SAX) and strong cation exchange (SCX) StageTip techniques. Almost 5000 proteins (∼60% membrane proteins) can be identified in only 10 μg of membrane protein digests, showing the superior sensitivity of the Hp-RP StageTip approach. The method allowed up to 9- and 6-fold increase in the identification of unique hydrophobic and hydrophilic peptides, respectively. The Hp-RP StageTip method enabled in-depth membrane proteome profiling of 11 lung cancer cell lines harboring different EGFR mutation status, which resulted in the identification of 3983 annotated membrane proteins. This provides the largest collection of reference peptide spectral data for lung cancer membrane subproteome. Finally, relative quantification of membrane proteins between Gefitinib-resistant and -sensitive lung cancer cell lines revealed several up-regulated membrane proteins with key roles in lung cancer progression.
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Affiliation(s)
- Baby Rorielyn T Dimayacyac-Esleta
- Institute of Chemistry, University of the Philippines , Diliman Quezon City 1101, Philippines.,Institute of Chemistry, Academia Sinica , Taipei 115, Taiwan
| | - Chia-Feng Tsai
- Institute of Chemistry, Academia Sinica , Taipei 115, Taiwan
| | - Reta Birhanu Kitata
- Institute of Chemistry, Academia Sinica , Taipei 115, Taiwan.,Department of Chemistry, National Tsing Hua University , Hsinchu 30013, Taiwan.,Molecular Science and Technology Program, Taiwan International Graduate Program, Academia Sinica , Taipei 115, Taiwan
| | - Pei-Yi Lin
- Institute of Chemistry, Academia Sinica , Taipei 115, Taiwan
| | - Wai-Kok Choong
- Institute of Information Science, Academia Sinica , Taipei 115, Taiwan
| | - Tai-Du Lin
- Institute of Chemistry, Academia Sinica , Taipei 115, Taiwan.,Department of Biochemical Sciences, National Taiwan University , Taipei 10617, Taiwan
| | - Yi-Ting Wang
- Institute of Chemistry, Academia Sinica , Taipei 115, Taiwan
| | - Shao-Hsing Weng
- Institute of Chemistry, Academia Sinica , Taipei 115, Taiwan.,Genome and Systems Biology Degree Program, National Taiwan University , Taipei 10617, Taiwan
| | - Pan-Chyr Yang
- Department of Internal Medicine, National Taiwan University Hospital , Taipei 10617, Taiwan.,National Taiwan University College of Medicine , Taipei 10051, Taiwan.,Institute of Biomedical Science, Academia Sinica , Taipei 115, Taiwan
| | - Susan D Arco
- Institute of Chemistry, University of the Philippines , Diliman Quezon City 1101, Philippines
| | - Ting-Yi Sung
- Institute of Information Science, Academia Sinica , Taipei 115, Taiwan
| | - Yu-Ju Chen
- Institute of Chemistry, Academia Sinica , Taipei 115, Taiwan.,Department of Chemistry, National Tsing Hua University , Hsinchu 30013, Taiwan.,Molecular Science and Technology Program, Taiwan International Graduate Program, Academia Sinica , Taipei 115, Taiwan
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24
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Quan Q, Szeto SSW, Law HCH, Zhang Z, Wang Y, Chu IK. Fully Automated Multidimensional Reversed-Phase Liquid Chromatography with Tandem Anion/Cation Exchange Columns for Simultaneous Global Endogenous Tyrosine Nitration Detection, Integral Membrane Protein Characterization, and Quantitative Proteomics Mapping in Cerebral Infarcts. Anal Chem 2015; 87:10015-24. [DOI: 10.1021/acs.analchem.5b02619] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Quan Quan
- Department
of Chemistry, The University of Hong Kong, Hong Kong 999077, China
| | - Samuel S. W. Szeto
- Department
of Chemistry, The University of Hong Kong, Hong Kong 999077, China
| | - Henry C. H. Law
- Department
of Chemistry, The University of Hong Kong, Hong Kong 999077, China
| | - Zaijun Zhang
- Institute
of New Drug Research and Guangdong Province Key Laboratory of Pharmacodynamic
Constituents of Traditional Chinese Medicine, College of Pharmacy, Jinan University, Guangzhou, Guangdong 510632, China
| | - Yuqiang Wang
- Institute
of New Drug Research and Guangdong Province Key Laboratory of Pharmacodynamic
Constituents of Traditional Chinese Medicine, College of Pharmacy, Jinan University, Guangzhou, Guangdong 510632, China
| | - Ivan K. Chu
- Department
of Chemistry, The University of Hong Kong, Hong Kong 999077, China
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25
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Lin Y, Wang K, Liu Z, Lin H, Yu L. Enhanced SDC-assisted digestion coupled with lipid chromatography-tandem mass spectrometry for shotgun analysis of membrane proteome. J Chromatogr B Analyt Technol Biomed Life Sci 2015; 1002:144-51. [PMID: 26319803 DOI: 10.1016/j.jchromb.2015.08.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2015] [Revised: 07/07/2015] [Accepted: 08/14/2015] [Indexed: 01/09/2023]
Abstract
Despite the biological importance of membrane proteins, their analysis has lagged behind that of soluble proteins and still presents a great challenge mainly because of their highly hydrophobic nature and low abundance. Sodium deoxycholate (SDC)-assisted digestion strategy has been introduced in our previous papers, which cleverly circumvents many of the challenges in shotgun membrane proteomics. However, it is associated with significant sample loss due to the slightly weaker extraction/solubilization ability of 1% SDC. In this study, an enhanced SDC-assisted digestion method (ESDC method) was developed that incorporates the almost strongest ability of SDC with a high concentration (5%) to lyse membrane and extract/solubilize hydrophobic membrane proteins, and then dilution to 1% for more efficient digestion. The comparative study using rat liver membrane-enriched sample showed that, compared with previous SDC-assisted method and the "universal" filter-aided sample preparation (FASP) method, the ESDC method not only increased the identified number of total proteins, membrane proteins, hydrophobic proteins, integral membrane proteins (IMPs) and IMPs with more than 5 transmembrane domains (TMDs) by an average of 10.8%, 13.2%, 17.8%, 17.9% and 52.9%, respectively, but also enhanced the identified number of total peptides and hydrophobic peptides by averagely 12.5% and 14.2%. These results demonstrated that the ESDC method provides a substantial improvement in the recovery and identification of membrane proteins, especially those with high hydrophobicity and multiple TMDs, and thereby displaying more potential for shotgun membrane proteomics.
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Affiliation(s)
- Yong Lin
- National Research Center of Engineering & Technology for Utilization of Botanical Functional Ingredients, College of Horticulture and Landscape, Hunan Agricultural University, Changsha 410128, PR China; Hunan Collaborative Innovation Center for Utilization of Functional Ingredients from Botanicals, Hunan Agricultural University, Changsha 410128, PR China.
| | - Kunbo Wang
- National Research Center of Engineering & Technology for Utilization of Botanical Functional Ingredients, College of Horticulture and Landscape, Hunan Agricultural University, Changsha 410128, PR China; Key Laboratory of Tea Science of Ministry of Education, College of Horticulture and Landscape, Hunan Agricultural University, Changsha 410128, PR China
| | - Zhonghua Liu
- National Research Center of Engineering & Technology for Utilization of Botanical Functional Ingredients, College of Horticulture and Landscape, Hunan Agricultural University, Changsha 410128, PR China; Key Laboratory of Tea Science of Ministry of Education, College of Horticulture and Landscape, Hunan Agricultural University, Changsha 410128, PR China; Hunan Collaborative Innovation Center for Utilization of Functional Ingredients from Botanicals, Hunan Agricultural University, Changsha 410128, PR China.
| | - Haiyan Lin
- National Research Center of Engineering & Technology for Utilization of Botanical Functional Ingredients, College of Horticulture and Landscape, Hunan Agricultural University, Changsha 410128, PR China
| | - Lijun Yu
- Key Laboratory of Tea Science of Ministry of Education, College of Horticulture and Landscape, Hunan Agricultural University, Changsha 410128, PR China
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26
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Kitata RB, Dimayacyac-Esleta BRT, Choong WK, Tsai CF, Lin TD, Tsou CC, Weng SH, Chen YJ, Yang PC, Arco SD, Nesvizhskii AI, Sung TY, Chen YJ. Mining Missing Membrane Proteins by High-pH Reverse-Phase StageTip Fractionation and Multiple Reaction Monitoring Mass Spectrometry. J Proteome Res 2015. [PMID: 26202522 DOI: 10.1021/acs.jproteome.5b00477] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Despite significant efforts in the past decade toward complete mapping of the human proteome, 3564 proteins (neXtProt, 09-2014) are still "missing proteins". Over one-third of these missing proteins are annotated as membrane proteins, owing to their relatively challenging accessibility with standard shotgun proteomics. Using nonsmall cell lung cancer (NSCLC) as a model study, we aim to mine missing proteins from disease-associated membrane proteome, which may be still largely under-represented. To increase identification coverage, we employed Hp-RP StageTip prefractionation of membrane-enriched samples from 11 NSCLC cell lines. Analysis of membrane samples from 20 pairs of tumor and adjacent normal lung tissue was incorporated to include physiologically expressed membrane proteins. Using multiple search engines (X!Tandem, Comet, and Mascot) and stringent evaluation of FDR (MAYU and PeptideShaker), we identified 7702 proteins (66% membrane proteins) and 178 missing proteins (74 membrane proteins) with PSM-, peptide-, and protein-level FDR of 1%. Through multiple reaction monitoring using synthetic peptides, we provided additional evidence of eight missing proteins including seven with transmembrane helix domains. This study demonstrates that mining missing proteins focused on cancer membrane subproteome can greatly contribute to map the whole human proteome. All data were deposited into ProteomeXchange with the identifier PXD002224.
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Affiliation(s)
- Reta Birhanu Kitata
- Institute of Chemistry, Academia Sinica , No. 128, Academia Road Sec. 2, Taipei 115, Taiwan.,Department of Chemistry, National Tsing Hua University , 101, Sec 2, Kuang-Fu Road, Hsinchu 30013, Taiwan.,Molecular Science and Technology Program, Taiwan International Graduate Program, Academia Sinica , No. 1, Roosevelt Road, Sec. 4, Taipei 10617, Taiwan
| | - Baby Rorielyn T Dimayacyac-Esleta
- Institute of Chemistry, Academia Sinica , No. 128, Academia Road Sec. 2, Taipei 115, Taiwan.,Institute of Chemistry, University of the Philippines , Diliman Quezon City, Philippines
| | - Wai-Kok Choong
- Institute of Information Science, Academia Sinica , 128 Academia Road, Section 2, Taipei 115, Taiwan
| | - Chia-Feng Tsai
- Institute of Chemistry, Academia Sinica , No. 128, Academia Road Sec. 2, Taipei 115, Taiwan
| | - Tai-Du Lin
- Institute of Chemistry, Academia Sinica , No. 128, Academia Road Sec. 2, Taipei 115, Taiwan.,Department of Biochemical Sciences, National Taiwan University , 1 Roosevelt Road, Sec. 4, Taipei 106, Taiwan
| | - Chih-Chiang Tsou
- Department of Computational Medicine and Bioinformatics and Department of Pathology, University of Michigan Medical School , 1301 Catherine, Ann Arbor, Michigan 48109, United States
| | - Shao-Hsing Weng
- Institute of Chemistry, Academia Sinica , No. 128, Academia Road Sec. 2, Taipei 115, Taiwan.,Genome and Systems Biology Degree Program, National Taiwan University , 1, Roosevelt Road, Section 4, Taipei 10617, Taiwan
| | - Yi-Ju Chen
- Institute of Chemistry, Academia Sinica , No. 128, Academia Road Sec. 2, Taipei 115, Taiwan
| | - Pan-Chyr Yang
- Department of Internal Medicine, National Taiwan University Hospital , 1 Jen-Ai Road, Section 1, Taipei 10051, Taiwan.,National Taiwan University College of Medicine , No. 1, Section 1, Ren'ai Road, Taipei 100, Taiwan.,Institute of Biomedical Science, Academia Sinica , 128 Academia Road, Section 2, Taipei 115, Taiwan
| | - Susan D Arco
- Institute of Chemistry, University of the Philippines , Diliman Quezon City, Philippines
| | - Alexey I Nesvizhskii
- Department of Computational Medicine and Bioinformatics and Department of Pathology, University of Michigan Medical School , 1301 Catherine, Ann Arbor, Michigan 48109, United States
| | - Ting-Yi Sung
- Institute of Information Science, Academia Sinica , 128 Academia Road, Section 2, Taipei 115, Taiwan
| | - Yu-Ju Chen
- Institute of Chemistry, Academia Sinica , No. 128, Academia Road Sec. 2, Taipei 115, Taiwan.,Department of Chemistry, National Tsing Hua University , 101, Sec 2, Kuang-Fu Road, Hsinchu 30013, Taiwan.,Molecular Science and Technology Program, Taiwan International Graduate Program, Academia Sinica , No. 1, Roosevelt Road, Sec. 4, Taipei 10617, Taiwan
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Min L, Choe LH, Lee KH. Improved protease digestion conditions for membrane protein detection. Electrophoresis 2015; 36:1690-8. [PMID: 25884272 DOI: 10.1002/elps.201400579] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Revised: 03/03/2015] [Accepted: 04/08/2015] [Indexed: 01/16/2023]
Abstract
This work presents improved protease digestion conditions for membrane protein detection. The enzymatic digest of bacteriorhodopsin (BR), a model membrane protein with seven transmembrane domains (TMDs) was investigated. An initial in-gel digestion identified 17% BR sequence coverage, including part of the seventh TMD. To improve sequence coverage, BR digest was tested with different concentrations of RapiGest, methanol (MeOH) and SDS using either trypsin or chymotrypsin. Two improved conditions, 0.01% SDS or the combination of 10% MeOH and 0.01% RapiGest, were chosen. Trypsin digestions in both conditions achieved more than 40% BR sequence coverage compared to 0% using standard digestion conditions. Peptides detected from trypsin and chymotrypsin digestions in the same condition were combined to maximize sequence coverage. The same conditions were applied to a different membrane protein with one TMD, Selenoprotein S, and proteins from Escherichia coli. For Selenoprotein S, a higher sequence coverage, including a peptide from the TMD, was detected from the improved condition compared to the typical condition. The application of both improved conditions to a membrane protein fraction of Escherichia coli resulted in the identification of 309 (SDS) and 329 (MeOH/RapiGest) unique proteins of which 140/309 and 148/329 were membrane proteins.
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Affiliation(s)
- Lie Min
- Department of Chemical and Biomolecular Engineering and Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA
| | - Leila H Choe
- Department of Chemical and Biomolecular Engineering and Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA
| | - Kelvin H Lee
- Department of Chemical and Biomolecular Engineering and Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA
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28
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Landreh M, Robinson CV. A new window into the molecular physiology of membrane proteins. J Physiol 2014; 593:355-62. [PMID: 25630257 PMCID: PMC4303381 DOI: 10.1113/jphysiol.2014.283150] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 10/14/2014] [Indexed: 12/18/2022] Open
Abstract
Integral membrane proteins comprise ∼25% of the human proteome. Yet, our understanding of their molecular physiology is still in its infancy. This can be attributed to two factors: the experimental challenges that arise from the difficult chemical nature of membrane proteins, and the unclear relationship between their activity and their native environment. New approaches are therefore required to address these challenges. Recent developments in mass spectrometry have shown that it is possible to study membrane proteins in a solvent-free environment and provide detailed insights into complex interactions, ligand binding and folding processes. Interestingly, not only detergent micelles but also lipid bilayer nanodiscs or bicelles can serve as a means for the gentle desolvation of membrane proteins in the gas phase. In this manner, as well as by direct addition of lipids, it is possible to study the effects of different membrane components on the structure and function of the protein components allowing us to add functional data to the least accessible part of the proteome.
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Affiliation(s)
- Michael Landreh
- Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 5QY, UK
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29
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Tanca A, Abbondio M, Pisanu S, Pagnozzi D, Uzzau S, Addis MF. Critical comparison of sample preparation strategies for shotgun proteomic analysis of formalin-fixed, paraffin-embedded samples: insights from liver tissue. Clin Proteomics 2014; 11:28. [PMID: 25097466 PMCID: PMC4115481 DOI: 10.1186/1559-0275-11-28] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 07/03/2014] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND The growing field of formalin-fixed paraffin-embedded (FFPE) tissue proteomics holds promise for improving translational research. Direct tissue trypsinization (DT) and protein extraction followed by in solution digestion (ISD) or filter-aided sample preparation (FASP) are the most common workflows for shotgun analysis of FFPE samples, but a critical comparison of the different methods is currently lacking. EXPERIMENTAL DESIGN DT, FASP and ISD workflows were compared by subjecting to the same label-free quantitative approach three independent technical replicates of each method applied to FFPE liver tissue. Data were evaluated in terms of method reproducibility and protein/peptide distribution according to localization, MW, pI and hydrophobicity. RESULTS DT showed lower reproducibility, good preservation of high-MW proteins, a general bias towards hydrophilic and acidic proteins, much lower keratin contamination, as well as higher abundance of non-tryptic peptides. Conversely, FASP and ISD proteomes were depleted in high-MW proteins and enriched in hydrophobic and membrane proteins; FASP provided higher identification yields, while ISD exhibited higher reproducibility. CONCLUSIONS These results highlight that diverse sample preparation strategies provide significantly different proteomic information, and present typical biases that should be taken into account when dealing with FFPE samples. When a sufficient amount of tissue is available, the complementary use of different methods is suggested to increase proteome coverage and depth.
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Affiliation(s)
- Alessandro Tanca
- Porto Conte Ricerche, S.P. 55 Porto Conte/Capo Caccia Km 8.400, Tramariglio, 07041 Alghero, Italy
| | - Marcello Abbondio
- Porto Conte Ricerche, S.P. 55 Porto Conte/Capo Caccia Km 8.400, Tramariglio, 07041 Alghero, Italy
| | - Salvatore Pisanu
- Porto Conte Ricerche, S.P. 55 Porto Conte/Capo Caccia Km 8.400, Tramariglio, 07041 Alghero, Italy
| | - Daniela Pagnozzi
- Porto Conte Ricerche, S.P. 55 Porto Conte/Capo Caccia Km 8.400, Tramariglio, 07041 Alghero, Italy
| | - Sergio Uzzau
- Porto Conte Ricerche, S.P. 55 Porto Conte/Capo Caccia Km 8.400, Tramariglio, 07041 Alghero, Italy ; Dipartimento di Scienze Biomediche, Università di Sassari, Viale San Pietro 43/B, 07100, Sassari, Italy
| | - Maria Filippa Addis
- Porto Conte Ricerche, S.P. 55 Porto Conte/Capo Caccia Km 8.400, Tramariglio, 07041 Alghero, Italy
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30
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Burkhart JM, Gambaryan S, Watson SP, Jurk K, Walter U, Sickmann A, Heemskerk JWM, Zahedi RP. What can proteomics tell us about platelets? Circ Res 2014; 114:1204-19. [PMID: 24677239 DOI: 10.1161/circresaha.114.301598] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
More than 130 years ago, it was recognized that platelets are key mediators of hemostasis. Nowadays, it is established that platelets participate in additional physiological processes and contribute to the genesis and progression of cardiovascular diseases. Recent data indicate that the platelet proteome, defined as the complete set of expressed proteins, comprises >5000 proteins and is highly similar between different healthy individuals. Owing to their anucleate nature, platelets have limited protein synthesis. By implication, in patients experiencing platelet disorders, platelet (dys)function is almost completely attributable to alterations in protein expression and dynamic differences in post-translational modifications. Modern platelet proteomics approaches can reveal (1) quantitative changes in the abundance of thousands of proteins, (2) post-translational modifications, (3) protein-protein interactions, and (4) protein localization, while requiring only small blood donations in the range of a few milliliters. Consequently, platelet proteomics will represent an invaluable tool for characterizing the fundamental processes that affect platelet homeostasis and thus determine the roles of platelets in health and disease. In this article we provide a critical overview on the achievements, the current possibilities, and the future perspectives of platelet proteomics to study patients experiencing cardiovascular, inflammatory, and bleeding disorders.
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Affiliation(s)
- Julia M Burkhart
- From the Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Dortmund, Germany (J.M.B., A.S., R.P.Z); Institut für Klinische Biochemie und Pathobiochemie, Universitätsklinikum Würzburg, Würzburg, Germany (S.G.); Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, St. Petersburg, Russia (S.G.); Centre for Cardiovascular Sciences, Institute for Biomedical Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom (S.P.W.); Center for Thrombosis and Hemostasis, Universitätsklinikum der Johannes Gutenberg-Universität Mainz, Mainz, Germany (K.J., U.W.); Medizinisches Proteom Center, Ruhr Universität Bochum, Bochum, Germany (A.S.); Department of Chemistry, College of Physical Sciences, University of Aberdeen, Aberdeen, Scotland, United Kingdom (A.S.); and Department of Biochemistry, CARIM, Maastricht University, Maastricht, The Netherlands (J.W.M.H.)
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31
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Valeriano VD, Parungao-Balolong MM, Kang DK. In vitro evaluation of the mucin-adhesion ability and probiotic potential of Lactobacillus mucosae LM1. J Appl Microbiol 2014; 117:485-97. [PMID: 24807045 DOI: 10.1111/jam.12539] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Revised: 03/23/2014] [Accepted: 03/28/2014] [Indexed: 11/28/2022]
Abstract
AIMS In this report, we characterized the probiotic potential of Lactobacillus mucosae LM1, focusing on its in vitro mucin-adhesion abilities. METHODS AND RESULTS Screening assays were used to evaluate LM1. Previous studies on Lact. mucosae species have been performed, but few have examined the ability of this species to adhere to and colonize the intestinal mucosa. Thus, adhesion, aggregation and pathogen inhibition assays of LM1 along with microbial adhesion to solvents (MATS) assay were carried out in comparison with another putative probiotic, Lactobacillus johnsonii PF01, and the commercial strain, Lactobacillus rhamnosus GG. Based on MATS assay, the cell surfaces of the lactobacilli strains were found to be hydrophobic and highly electron-donating, but the average hydropathy (GRAVY) index of predicted surface-exposed proteins in the LM1 genome indicated that most were hydrophilic. LM1 showed the highest adhesion, aggregation and hydrophobicity among the strains tested and significantly inhibited the adhesion of Escherichia coli K88 and Salmonella enterica serovar Typhimurium KCCM 40253. Correlations among adhesion, aggregation and hydrophobicity, as well as between coaggregation and displacement of E. coli, were observed. CONCLUSIONS Increased adhesion may not always correlate with increased pathogen inhibition due to various strain-specific mechanisms. Nevertheless, LM1 has promising probiotic properties that can be explored further using a genomics approach. SIGNIFICANCE AND IMPACT OF THE STUDY Our data on adhesion of LM1 strain showed a significant correlation between adhesion, hydrophobicity of cell surface and autoaggregation. This study gives basic knowledge for the elucidation of the adhesion mechanism of Lactobacillus sp. and prediction of its adherence in specific host models.
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Affiliation(s)
- V D Valeriano
- Department of Animal Resources Science, Dankook University, Cheonan, Korea
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32
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Guo X, Trudgian DC, Lemoff A, Yadavalli S, Mirzaei H. Confetti: a multiprotease map of the HeLa proteome for comprehensive proteomics. Mol Cell Proteomics 2014; 13:1573-84. [PMID: 24696503 DOI: 10.1074/mcp.m113.035170] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Bottom-up proteomics largely relies on tryptic peptides for protein identification and quantification. Tryptic digestion often provides limited coverage of protein sequence because of issues such as peptide length, ionization efficiency, and post-translational modification colocalization. Unfortunately, a region of interest in a protein, for example, because of proximity to an active site or the presence of important post-translational modifications, may not be covered by tryptic peptides. Detection limits, quantification accuracy, and isoform differentiation can also be improved with greater sequence coverage. Selected reaction monitoring (SRM) would also greatly benefit from being able to identify additional targetable sequences. In an attempt to improve protein sequence coverage and to target regions of proteins that do not generate useful tryptic peptides, we deployed a multiprotease strategy on the HeLa proteome. First, we used seven commercially available enzymes in single, double, and triple enzyme combinations. A total of 48 digests were performed. 5223 proteins were detected by analyzing the unfractionated cell lysate digest directly; with 42% mean sequence coverage. Additional strong-anion exchange fractionation of the most complementary digests permitted identification of over 3000 more proteins, with improved mean sequence coverage. We then constructed a web application (https://proteomics.swmed.edu/confetti) that allows the community to examine a target protein or protein isoform in order to discover the enzyme or combination of enzymes that would yield peptides spanning a certain region of interest in the sequence. Finally, we examined the use of nontryptic digests for SRM. From our strong-anion exchange fractionation data, we were able to identify three or more proteotypic SRM candidates within a single digest for 6056 genes. Surprisingly, in 25% of these cases the digest producing the most observable proteotypic peptides was neither trypsin nor Lys-C. SRM analysis of Asp-N versus tryptic peptides for eight proteins determined that Asp-N yielded higher signal in five of eight cases.
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Affiliation(s)
- Xiaofeng Guo
- From the ‡Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas 75390
| | - David C Trudgian
- From the ‡Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas 75390
| | - Andrew Lemoff
- From the ‡Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas 75390
| | | | - Hamid Mirzaei
- From the ‡Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas 75390
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33
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Waas M, Bhattacharya S, Chuppa S, Wu X, Jensen DR, Omasits U, Wollscheid B, Volkman BF, Noon KR, Gundry RL. Combine and conquer: surfactants, solvents, and chaotropes for robust mass spectrometry based analyses of membrane proteins. Anal Chem 2014; 86:1551-9. [PMID: 24392666 PMCID: PMC4007983 DOI: 10.1021/ac403185a] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
![]()
Mass spectrometry
(MS) based proteomic technologies enable the identification and quantification
of membrane proteins as well as their post-translational modifications.
A prerequisite for their quantitative and reliable MS-based bottom-up
analysis is the efficient digestion into peptides by proteases, though
digestion of membrane proteins is typically challenging due to their
inherent properties such as hydrophobicity. Here, we investigated
the effect of eight commercially available MS-compatible surfactants,
two organic solvents, and two chaotropes on the enzymatic digestion
efficiency of membrane protein-enriched complex mixtures in a multiphase
study using a gelfree approach. Multiple parameters, including the
number of peptides and proteins identified, total protein sequence
coverage, and digestion specificity were used to evaluate transmembrane
protein digestion performance. A new open-source software tool was
developed to allow for the specific assessment of transmembrane domain
sequence coverage. Results demonstrate that while Progenta anionic
surfactants outperform other surfactants when tested alone, combinations
of guanidine and acetonitrile improve performance of all surfactants
to near similar levels as well as enhance trypsin specificity to >90%,
which has critical implications for future quantitative and qualitative
proteomic studies.
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Affiliation(s)
- Matthew Waas
- Milwaukee School of Engineering , Milwaukee, Wisconsin 53202, United States
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Schliekelman P, Liu S. Quantifying the effect of competition for detection between coeluting peptides on detection probabilities in mass-spectrometry-based proteomics. J Proteome Res 2013; 13:348-61. [PMID: 24313442 DOI: 10.1021/pr400034z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
There are many factors that contribute to the variation in detection probabilities of proteins in LC-MS/MS experiments, and currently little is known about their relative importance. In this study, we analyze the effect of competition for detection between coeluting peptides on peptide detection probability. Using a novel method for estimating peptide detection probabilities, we show that these probabilities can vary by an order of magnitude between peptides that elute from the liquid chromatograph at the same time as many other peptides and those that elute with fewer other peptides. To explore these results, we use a mathematical model to show that competition for detection between peptides is expected to be a major source of missed detections in complex mixtures because there will be many MS/MS scanning intervals that contain more coeluting peptides than can be subjected to MS/MS analysis. Our data and simulation results show that the number of coeluting peptides is a primary determinant of whether a peptide will be detected. In our data, this had a several-fold larger effect on peptide detection probability than did peptide abundance. Furthermore, the distribution of elution times for the most frequently detected peptides was strongly shifted toward values where there were few coeluting peptides, indicating that the number of coeluting peptides is a major determinant of whether a peptide is proteotypic.
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Affiliation(s)
- Paul Schliekelman
- Department of Statistics, University of Georgia , 204 Statistics Building, Athens, Georgia 30602, United States
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35
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Barasa B, Slijper M. Challenges for red blood cell biomarker discovery through proteomics. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1844:1003-10. [PMID: 24129076 DOI: 10.1016/j.bbapap.2013.10.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Revised: 09/11/2013] [Accepted: 10/01/2013] [Indexed: 12/23/2022]
Abstract
Red blood cells are rather unique body cells, since they have lost all organelles when mature, which results in lack of potential to replace proteins that have lost their function. They maintain only a few pathways for obtaining energy and reducing power for the key functions they need to fulfill. This makes RBCs highly sensitive to any aberration. If so, these RBCs are quickly removed from circulation, but if the RBC levels reduce extremely fast, this results in hemolytic anemia. Several causes of HA exist, and proteome analysis is the most straightforward way to obtain deeper insight into RBC functioning under the stress of disease. This should result in discovery of biomarkers, typical for each source of anemia. In this review, several challenges to generate in-depth RBC proteomes are described, like to obtain pure RBCs, to overcome the wide dynamic range in protein expression, and to establish which of the identified/quantified proteins are active in RBCs. The final challenge is to acquire and validate suited biomarkers unique for the changes that occur for each of the clinical questions; in red blood cell aging (also important for transfusion medicine), for thalassemias or sickle cell disease. Biomarkers for other hemolytic anemias that are caused by dysfunction of RBC membrane proteins (the RBC membrane defects) or RBC cytosolic proteins (the enzymopathies) are sometimes even harder to discover, in particular for the patients with RBC rare diseases with unknown cause. This article is part of a Special Issue entitled: Biomarkers: A Proteomic Challenge.
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Affiliation(s)
- Benjamin Barasa
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; Netherlands Proteomics Centre, Padualaan 8, 3584 CH, The Netherlands
| | - Monique Slijper
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; Netherlands Proteomics Centre, Padualaan 8, 3584 CH, The Netherlands.
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Kort JC, Esser D, Pham TK, Noirel J, Wright PC, Siebers B. A cool tool for hot and sour Archaea: Proteomics of Sulfolobus solfataricus. Proteomics 2013; 13:2831-50. [DOI: 10.1002/pmic.201300088] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Revised: 04/23/2013] [Accepted: 05/03/2013] [Indexed: 11/10/2022]
Affiliation(s)
- Julia Christin Kort
- Molecular Enzyme Technology and Biochemistry; Biofilm Centre, Faculty of Chemistry, University of Duisburg-Essen; Essen Germany
| | - Dominik Esser
- Molecular Enzyme Technology and Biochemistry; Biofilm Centre, Faculty of Chemistry, University of Duisburg-Essen; Essen Germany
| | - Trong Khoa Pham
- Department of Chemical and Biological Engineering; ChELSI Institute, The University of Sheffield; Sheffield UK
| | - Josselin Noirel
- Department of Chemical and Biological Engineering; ChELSI Institute, The University of Sheffield; Sheffield UK
| | - Phillip C. Wright
- Department of Chemical and Biological Engineering; ChELSI Institute, The University of Sheffield; Sheffield UK
| | - Bettina Siebers
- Molecular Enzyme Technology and Biochemistry; Biofilm Centre, Faculty of Chemistry, University of Duisburg-Essen; Essen Germany
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37
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Cao L, Clifton JG, Reutter W, Josic D. Mass spectrometry-based analysis of rat liver and hepatocellular carcinoma Morris hepatoma 7777 plasma membrane proteome. Anal Chem 2013; 85:8112-20. [PMID: 23909495 PMCID: PMC3840720 DOI: 10.1021/ac400774g] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The gel-based proteomic analysis of plasma membranes from rat liver and chemically induced, malignant hepatocellular carcinoma Morris hepatoma 7777 was systematically optimized to yield the maximum number of proteins containing transmembrane domains (TMDs). Incorporation of plasma membrane proteins into a polyacrylamide "tube gel" followed by in-gel digestion of "tube gel" pieces significantly improved detection by electrospray ionization-liquid chromatography-tandem mass spectrometry. Removal of less hydrophobic proteins by washing isolated plasma membranes with 0.1 M sodium carbonate enables detection of a higher number of hydrophobic proteins containing TMDs in both tissues. Subsequent treatment of plasma membranes by a proteolytic enzyme (trypsin) causes the loss of some of the proteins that are detected after washing with sodium carbonate, but it enables the detection of other hydrophobic proteins containing TMDs. Introduction of mass spectrometers with higher sensitivity, higher mass resolution and mass accuracy, and a faster scan rate significantly improved detection of membrane proteins, but the improved sample preparation is still useful and enables detection of additional hydrophobic proteins. Proteolytic predigestion of plasma membranes enables detection of additional hydrophobic proteins and better sequence coverage of TMD-containing proteins in plasma membranes from both tissues.
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Affiliation(s)
- Lulu Cao
- Proteomics Core, COBRE Center for Cancer Research Development, Rhode Island Hospital, Providence, RI 02903 USA
| | - James G. Clifton
- Department of Molecular Pharmacology, Physiology and Biotechnology, Brown University, Providence, RI 02903, USA
| | - Werner Reutter
- Institut für Laboratoriumsmedizin und Klinische Chemie, Charité-Universitätsmedizin Campus Benjamin Franklin, D-14195 Berlin, Germany
| | - Djuro Josic
- Department of Medicine, Warren Alpert Medical School, Brown University, Providence, RI 02903, USA
- Department of Biotechnology, University of Rijeka, HR-51000 Rijeka, Croatia
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38
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Lin Y, Wang K, Yan Y, Lin H, Peng B, Liu Z. Evaluation of the combinative application of SDS and sodium deoxycholate to the LC-MS-based shotgun analysis of membrane proteomes. J Sep Sci 2013; 36:3026-34. [DOI: 10.1002/jssc.201300413] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2013] [Revised: 06/06/2013] [Accepted: 06/21/2013] [Indexed: 12/17/2022]
Affiliation(s)
- Yong Lin
- National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients; Hunan Agricultural University; Changsha P. R. China
- Key Laboratory of Tea Science of Ministry of Education; College of Horticulture and Landscape; Hunan Agricultural University; Changsha P. R. China
| | - Kunbo Wang
- National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients; Hunan Agricultural University; Changsha P. R. China
- Key Laboratory of Tea Science of Ministry of Education; College of Horticulture and Landscape; Hunan Agricultural University; Changsha P. R. China
| | - Yujun Yan
- National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients; Hunan Agricultural University; Changsha P. R. China
| | - Haiyan Lin
- National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients; Hunan Agricultural University; Changsha P. R. China
- Key Laboratory of Tea Science of Ministry of Education; College of Horticulture and Landscape; Hunan Agricultural University; Changsha P. R. China
| | - Bin Peng
- Key Laboratory of Tea Science of Ministry of Education; College of Horticulture and Landscape; Hunan Agricultural University; Changsha P. R. China
| | - Zhonghua Liu
- National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients; Hunan Agricultural University; Changsha P. R. China
- Key Laboratory of Tea Science of Ministry of Education; College of Horticulture and Landscape; Hunan Agricultural University; Changsha P. R. China
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39
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Balogh LM, Lai Y. Applications of Targeted Proteomics in ADME for IVIVE. TRANSPORTERS IN DRUG DEVELOPMENT 2013. [DOI: 10.1007/978-1-4614-8229-1_5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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40
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Lin Y, Liu H, Liu Z, Liu Y, He Q, Chen P, Wang X, Liang S. Development and evaluation of an entirely solution-based combinative sample preparation method for membrane proteomics. Anal Biochem 2013; 432:41-8. [DOI: 10.1016/j.ab.2012.09.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Revised: 08/31/2012] [Accepted: 09/17/2012] [Indexed: 10/27/2022]
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Simm S, Papasotiriou DG, Ibrahim M, Leisegang MS, Müller B, Schorge T, Karas M, Mirus O, Sommer MS, Schleiff E. Defining the core proteome of the chloroplast envelope membranes. FRONTIERS IN PLANT SCIENCE 2013; 4:11. [PMID: 23390424 PMCID: PMC3565376 DOI: 10.3389/fpls.2013.00011] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Accepted: 01/15/2013] [Indexed: 05/20/2023]
Abstract
High-throughput protein localization studies require multiple strategies. Mass spectrometric analysis of defined cellular fractions is one of the complementary approaches to a diverse array of cell biological methods. In recent years, the protein content of different cellular (sub-)compartments was approached. Despite of all the efforts made, the analysis of membrane fractions remains difficult, in that the dissection of the proteomes of the envelope membranes of chloroplasts or mitochondria is often not reliable because sample purity is not always warranted. Moreover, proteomic studies are often restricted to single (model) species, and therefore limited in respect to differential individual evolution. In this study we analyzed the chloroplast envelope proteomes of different plant species, namely, the individual proteomes of inner and outer envelope (OE) membrane of Pisum sativum and the mixed envelope proteomes of Arabidopsis thaliana and Medicago sativa. The analysis of all three species yielded 341 identified proteins in total, 247 of them being unique. 39 proteins were genuine envelope proteins found in at least two species. Based on this and previous envelope studies we defined the core envelope proteome of chloroplasts. Comparing the general overlap of the available six independent studies (including ours) revealed only a number of 27 envelope proteins. Depending on the stringency of applied selection criteria we found 231 envelope proteins, while less stringent criteria increases this number to 649 putative envelope proteins. Based on the latter we provide a map of the outer and inner envelope core proteome, which includes many yet uncharacterized proteins predicted to be involved in transport, signaling, and response. Furthermore, a foundation for the functional characterization of yet unidentified functions of the inner and OE for further analyses is provided.
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Affiliation(s)
- Stefan Simm
- Institute of Molecular Cell Biology of Plants, Goethe UniversityFrankfurt, Germany
| | | | - Mohamed Ibrahim
- Institute of Molecular Cell Biology of Plants, Goethe UniversityFrankfurt, Germany
| | | | - Bernd Müller
- Department of Biology I, Ludwig-Maximilians-UniversityMunich, Germany
| | - Tobias Schorge
- Institute of Pharmaceutical Chemistry, Goethe UniversityFrankfurt, Germany
| | - Michael Karas
- Institute of Pharmaceutical Chemistry, Goethe UniversityFrankfurt, Germany
- Center of Membrane Proteomics, Goethe UniversityFrankfurt, Germany
- Cluster of Excellence ‘Macromolecular Complexes’, Goethe UniversityFrankfurt, Germany
| | - Oliver Mirus
- Institute of Molecular Cell Biology of Plants, Goethe UniversityFrankfurt, Germany
| | - Maik S. Sommer
- Institute of Molecular Cell Biology of Plants, Goethe UniversityFrankfurt, Germany
| | - Enrico Schleiff
- Institute of Molecular Cell Biology of Plants, Goethe UniversityFrankfurt, Germany
- Center of Membrane Proteomics, Goethe UniversityFrankfurt, Germany
- Cluster of Excellence ‘Macromolecular Complexes’, Goethe UniversityFrankfurt, Germany
- *Correspondence: Enrico Schleiff, Center of Membrane Proteomics, Cluster of Excellence ’Macromolecular Complexes’, Institute of Molecular Cell Biology of Plants, Goethe University, Max-von-Laue Strasse 9, Frankfurt 60438, Germany. e-mail:
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42
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Wang X, Liang S. Sample preparation for the analysis of membrane proteomes by mass spectrometry. Protein Cell 2012; 3:661-8. [PMID: 22926766 DOI: 10.1007/s13238-012-2062-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Accepted: 07/18/2012] [Indexed: 11/27/2022] Open
Abstract
The low abundance and highly hydrophobic nature of most membrane proteins make their analysis more difficult than that for common soluble proteins. Successful membrane protein identification is largely dependent on the sample preparation including the enrichment and dissolution of the membrane proteins. A series of conventional and newly developed methods has been applied to the enrichment of low-abundance membrane proteins at membrane and/or protein levels and to the dissolution of hydrophobic membrane proteins. However, all the existing methods have inherent advantages and limitations. Up to now, there has been no unique method that can universally be employed to solve all the problems and more efforts are needed in improving sample preparation for the analysis of membrane proteomes.
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Affiliation(s)
- Xianchun Wang
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
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43
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Bosman GJCGM, Lasonder E, Groenen-Döpp YAM, Willekens FLA, Werre JM. The proteome of erythrocyte-derived microparticles from plasma: new clues for erythrocyte aging and vesiculation. J Proteomics 2012; 76 Spec No.:203-10. [PMID: 22669077 DOI: 10.1016/j.jprot.2012.05.031] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2012] [Revised: 05/15/2012] [Accepted: 05/18/2012] [Indexed: 01/09/2023]
Abstract
Vesicle formation is an integral part of the physiological erythrocyte aging process. Recent biophysical and immunochemical data have suggested that vesicles originate by the extrusion of membrane patches that, during aging, have become damaged and simultaneously enriched in removal signals. Thereby, vesiculation may serve to postpone the untimely removal of functional cells. As a first step toward the identification of the underlying mechanisms, we isolated erythrocyte-derived vesicles from plasma by fluorescence-activated cell sorting, analyzed their proteome by mass spectrometry, and compared this with the membrane proteomes of erythrocytes that were separated according to cell age. The presence of band 3 and actin in the vesicles together with the absence of almost all other integral membrane and cytoskeletal proteins, and the specific, aging-associated alterations in band 3 aggregation and degradation shown by proteomics as well as immunochemistry, all suggest that the erythrocyte aging process harbors a specific, band 3-centered mechanism for vesicle generation. The age-related recruitment of plasma proteins, proteins of the ubiquitin-proteasome system, and small G proteins to the erythrocyte membrane supports the hypothesis that modification of band 3 and/or degradation initiate vesiculation, and the subsequent recognition and fast removal of vesicles by the immune system. This article is part of a Special Issue entitled: Integrated omics.
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Affiliation(s)
- Giel J C G M Bosman
- Department of Biochemistry, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands.
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44
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Perfusion reversed-phase high-performance liquid chromatography for protein separation from detergent-containing solutions: An alternative to gel-based approaches. Anal Biochem 2012; 424:97-107. [DOI: 10.1016/j.ab.2012.02.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2011] [Revised: 02/15/2012] [Accepted: 02/16/2012] [Indexed: 11/19/2022]
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45
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Barrera NP, Robinson CV. Advances in the mass spectrometry of membrane proteins: from individual proteins to intact complexes. Annu Rev Biochem 2011; 80:247-71. [PMID: 21548785 DOI: 10.1146/annurev-biochem-062309-093307] [Citation(s) in RCA: 127] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Rapid advances in structural genomics and in large-scale proteomic projects have yielded vast amounts of data on soluble proteins and their complexes. Despite these advances, progress in studying membrane proteins using mass spectrometry (MS) has been slow. This is due in part to the inherent solubility and dynamic properties of these proteins, but also to their low abundance and the absence of polar side chains in amino acid residues. Considerable progress in overcoming these challenges is, however, now being made for all levels of structural characterization. This progress includes MS studies of the primary structure of membrane proteins, wherein sophisticated enrichment and trapping procedures are allowing multiple posttranslational modifications to be defined through to the secondary structure level in which proteins and peptides have been probed using hydrogen exchange, covalent, or radiolytic labeling methods. Exciting possibilities now exist to go beyond primary and secondary structure to reveal the tertiary and quaternary interactions of soluble and membrane subunits within intact assemblies of more than 700 kDa.
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Affiliation(s)
- Nelson P Barrera
- Department of Physiology, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile.
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46
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Maddalo G, Chovanec P, Stenberg-Bruzell F, Nielsen HV, Jensen-Seaman MI, Ilag LL, Kline KA, Daley DO. A reference map of the membrane proteome of Enterococcus faecalis. Proteomics 2011; 11:3935-41. [PMID: 21800426 DOI: 10.1002/pmic.201100103] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2011] [Revised: 06/08/2011] [Accepted: 07/11/2011] [Indexed: 11/06/2022]
Abstract
Enterococcus faecalis is a gram-positive bacterium that is part of the indigenous microbiotica of humans and animals as well as an opportunistic pathogen. In this study, we have fractionated the membrane proteome of E. faecalis and identified many of its constituents by mass spectrometry. We present blue native-/SDS-PAGE reference maps that contain 102 proteins. These proteins are important for cellular homeostasis, virulence, and antibiotic intervention. Intriguingly, many proteins with no known function were also identified, indicating that there are substantial gaps in the knowledge of this organism's biology. On a more limited scale, we also provide insight into the composition of membrane protein complexes. This study is a first step toward elucidating the membrane proteome of E. faecalis, which is critical for a better understanding of how this bacterium interacts with a host and with the extracellular milieu.
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Affiliation(s)
- Gianluca Maddalo
- Department of Analytical Chemistry, Stockholm University, Stockholm, Sweden
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47
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Mass spectrometry accelerates membrane protein analysis. Trends Biochem Sci 2011; 36:388-96. [PMID: 21616670 DOI: 10.1016/j.tibs.2011.04.005] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2011] [Revised: 04/19/2011] [Accepted: 04/19/2011] [Indexed: 12/25/2022]
Abstract
Cellular membranes are composed of proteins and glyco- and phospholipids and play an indispensible role in maintaining cellular integrity and homeostasis, by physically restricting biochemical processes within cells and providing protection. Membrane proteins perform many essential functions, which include operating as transporters, adhesion-anchors, receptors, and enzymes. Recent advancements in proteomic mass spectrometry have resulted in substantial progress towards the determination of the plasma membrane (PM) proteome, resolution of membrane protein topology, establishment of numerous receptor protein complexes, identification of ligand-receptor pairs, and the elucidation of signaling networks originating at the PM. Here, we discuss the recent accelerated success of discovery-based proteomic pipelines for the establishment of a complete membrane proteome.
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48
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Improved gel electrophoresis matrix for hydrophobic protein separation and identification. Anal Biochem 2011; 410:98-109. [DOI: 10.1016/j.ab.2010.11.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2010] [Revised: 11/06/2010] [Accepted: 11/08/2010] [Indexed: 12/26/2022]
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49
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Actinoporins from the sea anemones, tropical Radianthus macrodactylus and northern Oulactis orientalis: Comparative analysis of structure–function relationships. Toxicon 2010; 56:1299-314. [DOI: 10.1016/j.toxicon.2010.07.011] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2009] [Revised: 07/16/2010] [Accepted: 07/19/2010] [Indexed: 11/24/2022]
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50
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Heinz E, Pichler P, Heinz C, op den Camp HJM, Toenshoff ER, Ammerer G, Mechtler K, Wagner M, Horn M. Proteomic analysis of the outer membrane of Protochlamydia amoebophila elementary bodies. Proteomics 2010; 10:4363-76. [DOI: 10.1002/pmic.201000302] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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