1
|
Coorssen JR, Padula MP. Proteomics-The State of the Field: The Definition and Analysis of Proteomes Should Be Based in Reality, Not Convenience. Proteomes 2024; 12:14. [PMID: 38651373 PMCID: PMC11036260 DOI: 10.3390/proteomes12020014] [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: 03/17/2024] [Revised: 04/17/2024] [Accepted: 04/17/2024] [Indexed: 04/25/2024] Open
Abstract
With growing recognition and acknowledgement of the genuine complexity of proteomes, we are finally entering the post-proteogenomic era. Routine assessment of proteomes as inferred correlates of gene sequences (i.e., canonical 'proteins') cannot provide the necessary critical analysis of systems-level biology that is needed to understand underlying molecular mechanisms and pathways or identify the most selective biomarkers and therapeutic targets. These critical requirements demand the analysis of proteomes at the level of proteoforms/protein species, the actual active molecular players. Currently, only highly refined integrated or integrative top-down proteomics (iTDP) enables the analytical depth necessary to provide routine, comprehensive, and quantitative proteome assessments across the widest range of proteoforms inherent to native systems. Here we provide a broad perspective of the field, taking in historical and current realities, to establish a more balanced understanding of where the field has come from (in particular during the ten years since Proteomes was launched), current issues, and how things likely need to proceed if necessary deep proteome analyses are to succeed. We base this in our firm belief that the best proteomic analyses reflect, as closely as possible, the native sample at the moment of sampling. We also seek to emphasise that this and future analytical approaches are likely best based on the broad recognition and exploitation of the complementarity of currently successful approaches. This also emphasises the need to continuously evaluate and further optimize established approaches, to avoid complacency in thinking and expectations but also to promote the critical and careful development and introduction of new approaches, most notably those that address proteoforms. Above all, we wish to emphasise that a rigorous focus on analytical quality must override current thinking that largely values analytical speed; the latter would certainly be nice, if only proteoforms could thus be effectively, routinely, and quantitatively assessed. Alas, proteomes are composed of proteoforms, not molecular species that can be amplified or that directly mirror genes (i.e., 'canonical'). The problem is hard, and we must accept and address it as such, but the payoff in playing this longer game of rigorous deep proteome analyses is the promise of far more selective biomarkers, drug targets, and truly personalised or even individualised medicine.
Collapse
Affiliation(s)
- Jens R. Coorssen
- Department of Biological Sciences, Faculty of Mathematics and Science, Brock University, St. Catharines, ON L2S 3A1, Canada
- Institute for Globally Distributed Open Research and Education (IGDORE), St. Catharines, ON L2N 4X2, Canada
| | - Matthew P. Padula
- School of Life Sciences and Proteomics, Lipidomics and Metabolomics Core Facility, Faculty of Science, University of Technology Sydney, Sydney, NSW 2007, Australia
| |
Collapse
|
2
|
Ding F, Zhang S, Chen Q, Xie X, Xi Z, Ge Z, Zuo X, Yang X, Willner I, Fan C, Li Q, Xia Q. Programmable Atom-Like Nanoparticle Reporters for High-Precision Urinalysis of In Situ Membrane Proteins. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2310199. [PMID: 38096904 DOI: 10.1002/adma.202310199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 12/09/2023] [Indexed: 12/22/2023]
Abstract
The expression of disease-specific membrane proteins (MPs) is a crucial indicator for evaluating the onset and progression of diseases. Urinalysis of in situ MPs has the potential for point-of-care disease diagnostics, yet remains challenging due to the lack of molecular reporter to transform the expression information of in situ MPs into the measurable urine composition. Herein, a series of tetrahedral DNA frameworks (TDFs) are employed as the cores of programmable atom-like nanoparticles (PANs) to direct the self-assembly of PAN reporters with defined ligand valence and spatial distribution. With the rational spatial organization of ligands, the interaction between PAN reporters and MPs exhibits superior stability on cell-membrane interface under renal tubule-mimic fluid microenvironment, thus enabling high-fidelity conversion of MPs expression level into binding events and reverse assessment of in situ MP levels via measurement of the renal clearance efficiency of PAN reporters. Such PAN reporter-mediated signal transformation mechanism empowers urinalysis of the onset of acute kidney injury at least 6 h earlier than the existing methods with an area under the curve of 100%. This strategy has the potential for urinalysis of a variety of in situ membrane proteins.
Collapse
Affiliation(s)
- Fei Ding
- Department of Liver Surgery, Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Transplantation, Shanghai, 200127, China
| | - Shuangye Zhang
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Qian Chen
- Department of Liver Surgery, Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Transplantation, Shanghai, 200127, China
| | - Xiaodong Xie
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Zhifeng Xi
- Department of Liver Surgery, Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Transplantation, Shanghai, 200127, China
| | - Zhilei Ge
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiaolei Zuo
- Department of Liver Surgery, Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Transplantation, Shanghai, 200127, China
| | - Xiurong Yang
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Itamar Willner
- Institute of Chemistry, Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Qian Li
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
- WLA Laboratories, World Laureates Association, Shanghai, 201203, China
| | - Qiang Xia
- Department of Liver Surgery, Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Transplantation, Shanghai, 200127, China
| |
Collapse
|
3
|
Dowling P, Swandulla D, Ohlendieck K. Mass Spectrometry-Based Proteomic Technology and Its Application to Study Skeletal Muscle Cell Biology. Cells 2023; 12:2560. [PMID: 37947638 PMCID: PMC10649384 DOI: 10.3390/cells12212560] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 10/27/2023] [Accepted: 10/31/2023] [Indexed: 11/12/2023] Open
Abstract
Voluntary striated muscles are characterized by a highly complex and dynamic proteome that efficiently adapts to changed physiological demands or alters considerably during pathophysiological dysfunction. The skeletal muscle proteome has been extensively studied in relation to myogenesis, fiber type specification, muscle transitions, the effects of physical exercise, disuse atrophy, neuromuscular disorders, muscle co-morbidities and sarcopenia of old age. Since muscle tissue accounts for approximately 40% of body mass in humans, alterations in the skeletal muscle proteome have considerable influence on whole-body physiology. This review outlines the main bioanalytical avenues taken in the proteomic characterization of skeletal muscle tissues, including top-down proteomics focusing on the characterization of intact proteoforms and their post-translational modifications, bottom-up proteomics, which is a peptide-centric method concerned with the large-scale detection of proteins in complex mixtures, and subproteomics that examines the protein composition of distinct subcellular fractions. Mass spectrometric studies over the last two decades have decisively improved our general cell biological understanding of protein diversity and the heterogeneous composition of individual myofibers in skeletal muscles. This detailed proteomic knowledge can now be integrated with findings from other omics-type methodologies to establish a systems biological view of skeletal muscle function.
Collapse
Affiliation(s)
- Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland;
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, W23 F2H6 Maynooth, Co. Kildare, Ireland
| | - Dieter Swandulla
- Institute of Physiology, Faculty of Medicine, University of Bonn, D53115 Bonn, Germany;
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland;
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, W23 F2H6 Maynooth, Co. Kildare, Ireland
| |
Collapse
|
4
|
Dowling P, Gargan S, Swandulla D, Ohlendieck K. Fiber-Type Shifting in Sarcopenia of Old Age: Proteomic Profiling of the Contractile Apparatus of Skeletal Muscles. Int J Mol Sci 2023; 24:ijms24032415. [PMID: 36768735 PMCID: PMC9916839 DOI: 10.3390/ijms24032415] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/20/2023] [Accepted: 01/23/2023] [Indexed: 01/28/2023] Open
Abstract
The progressive loss of skeletal muscle mass and concomitant reduction in contractile strength plays a central role in frailty syndrome. Age-related neuronal impairments are closely associated with sarcopenia in the elderly, which is characterized by severe muscular atrophy that can considerably lessen the overall quality of life at old age. Mass-spectrometry-based proteomic surveys of senescent human skeletal muscles, as well as animal models of sarcopenia, have decisively improved our understanding of the molecular and cellular consequences of muscular atrophy and associated fiber-type shifting during aging. This review outlines the mass spectrometric identification of proteome-wide changes in atrophying skeletal muscles, with a focus on contractile proteins as potential markers of changes in fiber-type distribution patterns. The observed trend of fast-to-slow transitions in individual human skeletal muscles during the aging process is most likely linked to a preferential susceptibility of fast-twitching muscle fibers to muscular atrophy. Studies with senescent animal models, including mostly aged rodent skeletal muscles, have confirmed fiber-type shifting. The proteomic analysis of fast versus slow isoforms of key contractile proteins, such as myosin heavy chains, myosin light chains, actins, troponins and tropomyosins, suggests them as suitable bioanalytical tools of fiber-type transitions during aging.
Collapse
Affiliation(s)
- Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, W23 F2H6 Maynooth, Co. Kildare, Ireland
| | - Stephen Gargan
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, W23 F2H6 Maynooth, Co. Kildare, Ireland
| | - Dieter Swandulla
- Institute of Physiology, University of Bonn, D53115 Bonn, Germany
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, W23 F2H6 Maynooth, Co. Kildare, Ireland
- Correspondence: ; Tel.: +353-1-7083842
| |
Collapse
|
5
|
Abstract
The combination of large-scale protein separation techniques, sophisticated mass spectrometry, and systems bioinformatics has led to the establishment of proteomics as a distinct discipline within the wider field of protein biochemistry. Both discovery proteomics and targeted proteomics are widely used in biological and biomedical research, whereby the analytical approaches can be broadly divided into proteoform-centric top-down proteomics versus peptide-centric bottom-up proteomics. This chapter outlines the scientific value of top-down proteomics and describes how fluorescence two-dimensional difference gel electrophoresis can be combined with the systematic analysis of crucial post-translational modifications. The concept of on-membrane digestion following the electrophoretic transfer of proteins and the usefulness of comparative two-dimensional immunoblotting are discussed.
Collapse
Affiliation(s)
- Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland.
| |
Collapse
|
6
|
Di Stefano LH, Saba LJ, Oghbaie M, Jiang H, McKerrow W, Benitez-Guijarro M, Taylor MS, LaCava J. Affinity-Based Interactome Analysis of Endogenous LINE-1 Macromolecules. Methods Mol Biol 2023; 2607:215-256. [PMID: 36449166 DOI: 10.1007/978-1-0716-2883-6_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
During their proliferation and the host's concomitant attempts to suppress it, LINE-1 (L1) retrotransposons give rise to a collection of heterogeneous ribonucleoproteins (RNPs); their protein and RNA compositions remain poorly defined. The constituents of L1-associated macromolecules can differ depending on numerous factors, including, for example, position within the L1 life cycle, whether the macromolecule is productive or under suppression, and the cell type within which the proliferation is occurring. This chapter describes techniques that aid the capture and characterization of protein and RNA components of L1 macromolecules from tissues that natively express them. The protocols described have been applied to embryonal carcinoma cell lines that are popular model systems for L1 molecular biology (e.g., N2102Ep, NTERA-2, and PA-1 cells), as well as colorectal cancer tissues. N2102Ep cells are given as the use case for this chapter; the protocols should be applicable to essentially any tissue exhibiting endogenous L1 expression with minor modifications.
Collapse
|
7
|
Kim CL, Lim SB, Kim K, Jeong HS, Mo JS. Phosphorylation analysis of the Hippo-YAP pathway using Phos-tag. J Proteomics 2022; 261:104582. [DOI: 10.1016/j.jprot.2022.104582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 03/22/2022] [Accepted: 03/31/2022] [Indexed: 10/18/2022]
|
8
|
Time-Dependent Changes in Protein Composition of Medial Prefrontal Cortex in Rats with Neuropathic Pain. Int J Mol Sci 2022; 23:ijms23020955. [PMID: 35055141 PMCID: PMC8781622 DOI: 10.3390/ijms23020955] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/10/2022] [Accepted: 01/14/2022] [Indexed: 01/03/2023] Open
Abstract
Chronic pain is associated with time-dependent structural and functional reorganization of the prefrontal cortex that may reflect adaptive pain compensatory and/or maladaptive pain-promoting mechanisms. However, the molecular underpinnings of these changes and whether there are time-dependent relationships to pain progression are not well characterized. In this study, we analyzed protein composition in the medial prefrontal cortex (mPFC) of rats at two timepoints after spinal nerve ligation (SNL) using two-dimensional gel electrophoresis (2D-ELFO) and liquid chromatography with tandem mass spectrometry (LC–MS/MS). SNL, but not sham-operated, rats developed persistent tactile allodynia and thermal hyperalgesia, confirming the presence of experimental neuropathic pain. Two weeks after SNL (early timepoint), we identified 11 proteins involved in signal transduction, protein transport, cell homeostasis, metabolism, and apoptosis, as well as heat-shock proteins and chaperones that were upregulated by more than 1.5-fold compared to the sham-operated rats. Interestingly, there were only four significantly altered proteins identified at 8 weeks after SNL (late timepoint). These findings demonstrate extensive time-dependent modifications of protein expression in the rat mPFC under a chronic neuropathic pain state that might underlie the evolution of chronic pain characterized by early pain-compensatory and later aberrant mechanisms.
Collapse
|
9
|
De Vos J, Pereira Aguilar P, Köppl C, Fischer A, Grünwald-Gruber C, Dürkop M, Klausberger M, Mairhofer J, Striedner G, Cserjan-Puschmann M, Jungbauer A, Lingg N. Production of full-length SARS-CoV-2 nucleocapsid protein from Escherichia coli optimized by native hydrophobic interaction chromatography hyphenated to multi-angle light scattering detection. Talanta 2021; 235:122691. [PMID: 34517577 PMCID: PMC8284068 DOI: 10.1016/j.talanta.2021.122691] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 07/02/2021] [Accepted: 07/03/2021] [Indexed: 11/22/2022]
Abstract
The nucleocapsid protein (NP) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is critical for several steps of the viral life cycle, and is abundantly expressed during infection, making it an ideal diagnostic target protein. This protein has a strong tendency for dimerization and interaction with nucleic acids. For the first time, high titers of NP were expressed in E. coli with a CASPON tag, using a growth-decoupled protein expression system. Purification was accomplished by nuclease treatment of the cell homogenate and a sequence of downstream processing (DSP) steps. An analytical method consisting of native hydrophobic interaction chromatography hyphenated to multi-angle light scattering detection (HIC-MALS) was established for in-process control, in particular, to monitor product fragmentation and multimerization throughout the purification process. 730 mg purified NP per liter of fermentation could be produced by the optimized process, corresponding to a yield of 77% after cell lysis. The HIC-MALS method was used to demonstrate that the NP product can be produced with a purity of 95%. The molecular mass of the main NP fraction is consistent with dimerized protein as was verified by a complementary native size-exclusion separation (SEC)-MALS analysis. Peptide mapping mass spectrometry and host cell specific enzyme-linked immunosorbent assay confirmed the high product purity, and the presence of a minor endogenous chaperone explained the residual impurities. The optimized HIC-MALS method enables monitoring of the product purity, and simultaneously access its molecular mass, providing orthogonal information complementary to established SEC-MALS methods. Enhanced resolving power can be achieved over SEC, attributed to the extended variables to tune selectivity in HIC mode.
Collapse
Affiliation(s)
- Jelle De Vos
- Vrije Universiteit Brussel, Department of Chemical Engineering, 1050, Brussels, Belgium; Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna (BOKU), 1190 Vienna, Austria
| | - Patricia Pereira Aguilar
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna (BOKU), 1190 Vienna, Austria; acib - Austrian Centre of Industrial Biotechnology, 1190, Vienna, Austria.
| | - Christoph Köppl
- acib - Austrian Centre of Industrial Biotechnology, 1190, Vienna, Austria
| | - Andreas Fischer
- acib - Austrian Centre of Industrial Biotechnology, 1190, Vienna, Austria
| | - Clemens Grünwald-Gruber
- BOKU Core Facility Mass Spectrometry, University of Natural Resources and Life Sciences, Vienna (BOKU), 1190, Vienna, Austria
| | - Mark Dürkop
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna (BOKU), 1190 Vienna, Austria; Novasign GmbH, 1190, Vienna, Austria
| | - Miriam Klausberger
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna (BOKU), 1190 Vienna, Austria
| | | | - Gerald Striedner
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna (BOKU), 1190 Vienna, Austria; acib - Austrian Centre of Industrial Biotechnology, 1190, Vienna, Austria; enGenes Biotech GmbH, 1190, Vienna, Austria
| | - Monika Cserjan-Puschmann
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna (BOKU), 1190 Vienna, Austria; acib - Austrian Centre of Industrial Biotechnology, 1190, Vienna, Austria
| | - Alois Jungbauer
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna (BOKU), 1190 Vienna, Austria; acib - Austrian Centre of Industrial Biotechnology, 1190, Vienna, Austria
| | - Nico Lingg
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna (BOKU), 1190 Vienna, Austria; acib - Austrian Centre of Industrial Biotechnology, 1190, Vienna, Austria
| |
Collapse
|
10
|
Kassem S, van der Pan K, de Jager AL, Naber BAE, de Laat IF, Louis A, van Dongen JJM, Teodosio C, Díez P. Proteomics for Low Cell Numbers: How to Optimize the Sample Preparation Workflow for Mass Spectrometry Analysis. J Proteome Res 2021; 20:4217-4230. [PMID: 34328739 PMCID: PMC8419858 DOI: 10.1021/acs.jproteome.1c00321] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Indexed: 12/20/2022]
Abstract
Nowadays, massive genomics and transcriptomics data can be generated at the single-cell level. However, proteomics in this setting is still a big challenge. Despite the great improvements in sensitivity and performance of mass spectrometry instruments and the better knowledge on sample preparation processing, it is widely acknowledged that multistep proteomics workflows may lead to substantial sample loss, especially when working with paucicellular samples. Still, in clinical fields, frequently limited sample amounts are available for downstream analysis, thereby hampering comprehensive characterization at protein level. To aim at better protein and peptide recoveries, we compare existing and novel approaches in the multistep sample preparation protocols for mass spectrometry studies, from sample collection, cell lysis, protein quantification, and electrophoresis/staining to protein digestion, peptide recovery, and LC-MS/MS instruments. From this critical evaluation, we conclude that the recent innovations and technologies, together with high quality management of samples, make proteomics on paucicellular samples possible, which will have immediate impact for the proteomics community.
Collapse
Affiliation(s)
- Sara Kassem
- Department
of Immunology, Leiden University Medical
Center (LUMC), Albinusdreef 2, 2333ZA Leiden, Netherlands
| | - Kyra van der Pan
- Department
of Immunology, Leiden University Medical
Center (LUMC), Albinusdreef 2, 2333ZA Leiden, Netherlands
| | - Anniek L. de Jager
- Department
of Immunology, Leiden University Medical
Center (LUMC), Albinusdreef 2, 2333ZA Leiden, Netherlands
| | - Brigitta A. E. Naber
- Department
of Immunology, Leiden University Medical
Center (LUMC), Albinusdreef 2, 2333ZA Leiden, Netherlands
| | - Inge F. de Laat
- Department
of Immunology, Leiden University Medical
Center (LUMC), Albinusdreef 2, 2333ZA Leiden, Netherlands
| | - Alesha Louis
- Department
of Immunology, Leiden University Medical
Center (LUMC), Albinusdreef 2, 2333ZA Leiden, Netherlands
| | - Jacques J. M. van Dongen
- Department
of Immunology, Leiden University Medical
Center (LUMC), Albinusdreef 2, 2333ZA Leiden, Netherlands
| | - Cristina Teodosio
- Department
of Immunology, Leiden University Medical
Center (LUMC), Albinusdreef 2, 2333ZA Leiden, Netherlands
| | - Paula Díez
- Department
of Immunology, Leiden University Medical
Center (LUMC), Albinusdreef 2, 2333ZA Leiden, Netherlands
| |
Collapse
|
11
|
Carbonara K, Andonovski M, Coorssen JR. Proteomes Are of Proteoforms: Embracing the Complexity. Proteomes 2021; 9:38. [PMID: 34564541 PMCID: PMC8482110 DOI: 10.3390/proteomes9030038] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 08/24/2021] [Accepted: 08/29/2021] [Indexed: 12/17/2022] Open
Abstract
Proteomes are complex-much more so than genomes or transcriptomes. Thus, simplifying their analysis does not simplify the issue. Proteomes are of proteoforms, not canonical proteins. While having a catalogue of amino acid sequences provides invaluable information, this is the Proteome-lite. To dissect biological mechanisms and identify critical biomarkers/drug targets, we must assess the myriad of proteoforms that arise at any point before, after, and between translation and transcription (e.g., isoforms, splice variants, and post-translational modifications [PTM]), as well as newly defined species. There are numerous analytical methods currently used to address proteome depth and here we critically evaluate these in terms of the current 'state-of-the-field'. We thus discuss both pros and cons of available approaches and where improvements or refinements are needed to quantitatively characterize proteomes. To enable a next-generation approach, we suggest that advances lie in transdisciplinarity via integration of current proteomic methods to yield a unified discipline that capitalizes on the strongest qualities of each. Such a necessary (if not revolutionary) shift cannot be accomplished by a continued primary focus on proteo-genomics/-transcriptomics. We must embrace the complexity. Yes, these are the hard questions, and this will not be easy…but where is the fun in easy?
Collapse
Affiliation(s)
| | | | - Jens R. Coorssen
- Faculties of Applied Health Sciences and Mathematics & Science, Departments of Health Sciences and Biological Sciences, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, ON L2S 3A1, Canada; (K.C.); (M.A.)
| |
Collapse
|
12
|
Proteomics of Multiple Sclerosis: Inherent Issues in Defining the Pathoetiology and Identifying (Early) Biomarkers. Int J Mol Sci 2021; 22:ijms22147377. [PMID: 34298997 PMCID: PMC8306353 DOI: 10.3390/ijms22147377] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 06/25/2021] [Accepted: 06/29/2021] [Indexed: 02/06/2023] Open
Abstract
Multiple Sclerosis (MS) is a demyelinating disease of the human central nervous system having an unconfirmed pathoetiology. Although animal models are used to mimic the pathology and clinical symptoms, no single model successfully replicates the full complexity of MS from its initial clinical identification through disease progression. Most importantly, a lack of preclinical biomarkers is hampering the earliest possible diagnosis and treatment. Notably, the development of rationally targeted therapeutics enabling pre-emptive treatment to halt the disease is also delayed without such biomarkers. Using literature mining and bioinformatic analyses, this review assessed the available proteomic studies of MS patients and animal models to discern (1) whether the models effectively mimic MS; and (2) whether reasonable biomarker candidates have been identified. The implication and necessity of assessing proteoforms and the critical importance of this to identifying rational biomarkers are discussed. Moreover, the challenges of using different proteomic analytical approaches and biological samples are also addressed.
Collapse
|
13
|
Itze-Mayrhofer C, Brem G. Quantitative proteomic strategies to study reproduction in farm animals: Female reproductive fluids. J Proteomics 2020; 225:103884. [PMID: 32593762 DOI: 10.1016/j.jprot.2020.103884] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 06/10/2020] [Accepted: 06/21/2020] [Indexed: 02/06/2023]
Abstract
Reproductive fluids from the female reproductive tract are gaining attention for their potential to support and optimize reproductive processes, including gamete maturation and embryo culture in vitro. Quantitative proteomics is a powerful way to decipher the proteome of reproductive tract fluids and to identify biologically relevant proteins. The present review describes proteomic strategies for analysing female reproductive fluid proteins. In addition, it considers the strategies for the preparation of oviductal, uterine and follicular fluid samples. Finally, it highlights the main results of quantitative proteomic studies, providing insights into the biological processes related to reproductive biology in farm animals. SIGNIFICANCE: Assisted reproductive technologies (ARTs) have become vitally important for farm animal breeding and much effort is going into the optimization and refinement of the techniques. There are also attempts to imitate physiological conditions by adding reproductive fluids or individual fluid proteins to improve in vitro procedures. A detailed knowledge of the reproductive fluid proteomes is indispensable. The present review summarizes the most widely used quantitative proteomic approaches for the analysis of fluids from the female reproductive tract and highlights the potential of quantitative proteomics to delineate reproductive processes and identify candidate proteins for ARTs in farm animals.
Collapse
Affiliation(s)
- Corina Itze-Mayrhofer
- Institute of Animal Breeding and Genetics, Group Molecular Reproduction IFA-Tulln, University of Veterinary Medicine, Vienna, Austria.
| | - Gottfried Brem
- Institute of Animal Breeding and Genetics, Department of Biomedical Sciences, University of Veterinary Medicine, Vienna, Austria
| |
Collapse
|
14
|
Karu K, Swanwick RS, Novejarque-Gadea A, Antunes-Martins A, Thomas B, Yoshimi E, Foster W, Fang M, McMahon SB, Bennett DLH, Rice ASC, Okuse K. Quantitative Proteomic Analysis of the Central Amygdala in Neuropathic Pain Model Rats. J Proteome Res 2020; 19:1592-1619. [DOI: 10.1021/acs.jproteome.9b00805] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Kersti Karu
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, U.K
| | - Richard S. Swanwick
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, U.K
| | - Amparo Novejarque-Gadea
- Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London SW10 9NH, U.K
| | - Ana Antunes-Martins
- The Wolfson Centre for Age-Related Diseases, King’s College London, Guy’s Campus, London SE1 1UL, U.K
| | - Benjamin Thomas
- Central Proteomics Facility, Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, U.K
| | - Eiji Yoshimi
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, U.K
| | - William Foster
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, U.K
| | - Min Fang
- Public Health England, London SE1 8UG, U.K
| | - Stephen B. McMahon
- The Wolfson Centre for Age-Related Diseases, King’s College London, Guy’s Campus, London SE1 1UL, U.K
| | - David L. H. Bennett
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DU, U.K
| | - Andrew S. C. Rice
- Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London SW10 9NH, U.K
| | - Kenji Okuse
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, U.K
| |
Collapse
|
15
|
Hooijberg EH, Cray C, Miller M, Buss P, Steenkamp G, Goddard A. Bias between two methods of albumin measurement in the white rhinoceros, Ceratotherium simum. Vet Clin Pathol 2020; 49:91-94. [PMID: 31925822 DOI: 10.1111/vcp.12820] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 05/03/2019] [Accepted: 05/05/2019] [Indexed: 11/30/2022]
Abstract
BACKGROUND The bromocresol green (BCG) method has been reported to overestimate serum albumin concentration in several species due to non-specific binding to globulins. As the white rhinoceros has high concentrations of serum globulins, significant differences in albumin measured by the BCG method, and the field method of agarose gel serum protein electrophoresis (SPE) are expected. OBJECTIVES We aimed to compare the BCG and SPE methods for albumin determination in the serum of white rhinoceroses. METHODS SPE and BCG albumin were measured in 82 white rhinoceros serum samples. Results were compared using Bland-Altman difference plots and Passing-Bablok regression analysis. RESULTS BCG albumin showed a significant mean constant positive bias of 7 g/L, or 36%, which was more than the total allowable error of 15% and was clinically significant. Methods were not comparable within the inherent imprecision of each method. CONCLUSIONS The BCG method overestimated albumin concentrations in this species compared with agarose gel SPE, and method-specific reference intervals should be used.
Collapse
Affiliation(s)
- Emma H Hooijberg
- Department of Companion Animal Clinical Studies and Centre for Veterinary Wildlife Studies, Faculty of Veterinary Science, University of Pretoria, Pretoria, South Africa
| | - Carolyn Cray
- Department of Pathology & Laboratory Medicine, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Michele Miller
- Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical TB Research/Medical Research, Council Centre for Tuberculosis Research, Stellenbosch University, Stellenbosch, South Africa
| | - Peter Buss
- Veterinary Wildlife Services, South African National Parks, Kruger National Park, Skukuza, South Africa
| | - Gerhard Steenkamp
- Department of Companion Animal Clinical Studies and Centre for Veterinary Wildlife Studies, Faculty of Veterinary Science, University of Pretoria, Pretoria, South Africa
| | - Amelia Goddard
- Department of Companion Animal Clinical Studies and Centre for Veterinary Wildlife Studies, Faculty of Veterinary Science, University of Pretoria, Pretoria, South Africa
| |
Collapse
|
16
|
Innovating the Concept and Practice of Two-Dimensional Gel Electrophoresis in the Analysis of Proteomes at the Proteoform Level. Proteomes 2019; 7:proteomes7040036. [PMID: 31671630 PMCID: PMC6958347 DOI: 10.3390/proteomes7040036] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 09/15/2019] [Accepted: 10/28/2019] [Indexed: 12/21/2022] Open
Abstract
Two-dimensional gel electrophoresis (2DE) is an important and well-established technical platform enabling extensive top-down proteomic analysis. However, the long-held but now largely outdated conventional concepts of 2DE have clearly impacted its application to in-depth investigations of proteomes at the level of protein species/proteoforms. It is time to popularize a new concept of 2DE for proteomics. With the development and enrichment of the proteome concept, any given “protein” is now recognized to consist of a series of proteoforms. Thus, it is the proteoform, rather than the canonical protein, that is the basic unit of a proteome, and each proteoform has a specific isoelectric point (pI) and relative mass (Mr). Accordingly, using 2DE, each proteoform can routinely be resolved and arrayed according to its different pI and Mr. Each detectable spot contains multiple proteoforms derived from the same gene, as well as from different genes. Proteoforms derived from the same gene are distributed into different spots in a 2DE pattern. High-resolution 2DE is thus actually an initial level of separation to address proteome complexity and is effectively a pre-fractionation method prior to analysis using mass spectrometry (MS). Furthermore, stable isotope-labeled 2DE coupled with high-sensitivity liquid chromatography-tandem MS (LC-MS/MS) has tremendous potential for the large-scale detection, identification, and quantification of the proteoforms that constitute proteomes.
Collapse
|
17
|
Dowling P, Zweyer M, Swandulla D, Ohlendieck K. Characterization of Contractile Proteins from Skeletal Muscle Using Gel-Based Top-Down Proteomics. Proteomes 2019; 7:proteomes7020025. [PMID: 31226838 PMCID: PMC6631179 DOI: 10.3390/proteomes7020025] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 06/14/2019] [Accepted: 06/17/2019] [Indexed: 12/22/2022] Open
Abstract
The mass spectrometric analysis of skeletal muscle proteins has used both peptide-centric and protein-focused approaches. The term 'top-down proteomics' is often used in relation to studying purified proteoforms and their post-translational modifications. Two-dimensional gel electrophoresis, in combination with peptide generation for the identification and characterization of intact proteoforms being present in two-dimensional spots, plays a critical role in specific applications of top-down proteomics. A decisive bioanalytical advantage of gel-based and top-down approaches is the initial bioanalytical focus on intact proteins, which usually enables the swift identification and detailed characterisation of specific proteoforms. In this review, we describe the usage of two-dimensional gel electrophoretic top-down proteomics and related approaches for the systematic analysis of key components of the contractile apparatus, with a special focus on myosin heavy and light chains and their associated regulatory proteins. The detailed biochemical analysis of proteins belonging to the thick and thin skeletal muscle filaments has decisively improved our biochemical understanding of structure-function relationships within the contractile apparatus. Gel-based and top-down proteomics has clearly established a variety of slow and fast isoforms of myosin, troponin and tropomyosin as excellent markers of fibre type specification and dynamic muscle transition processes.
Collapse
Affiliation(s)
- Paul Dowling
- Department of Biology, Maynooth University, Maynooth, W23F2H6 Co. Kildare, Ireland.
- MU Human Health Research Institute, Maynooth University, Maynooth, W23F2H6 Co. Kildare, Ireland.
| | - Margit Zweyer
- Institute of Physiology II, University of Bonn, D-53115 Bonn, Germany.
| | - Dieter Swandulla
- Institute of Physiology II, University of Bonn, D-53115 Bonn, Germany.
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, Maynooth, W23F2H6 Co. Kildare, Ireland.
- MU Human Health Research Institute, Maynooth University, Maynooth, W23F2H6 Co. Kildare, Ireland.
| |
Collapse
|
18
|
Refinement of two-dimensional electrophoresis for vitreous proteome profiling using an artificial neural network. Anal Bioanal Chem 2019; 411:5115-5126. [DOI: 10.1007/s00216-019-01887-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 04/18/2019] [Accepted: 04/30/2019] [Indexed: 01/07/2023]
|
19
|
Krause RG, Goldring JD. Crystal violet stains proteins in SDS-PAGE gels and zymograms. Anal Biochem 2019; 566:107-115. [DOI: 10.1016/j.ab.2018.11.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 11/15/2018] [Accepted: 11/16/2018] [Indexed: 11/28/2022]
|
20
|
Murphy S, Henry M, Meleady P, Ohlendieck K. Utilization of dried and long-term stored polyacrylamide gels for the advanced proteomic profiling of mitochondrial contact sites from rat liver. Biol Methods Protoc 2018; 3:bpy008. [PMID: 32161802 PMCID: PMC6994098 DOI: 10.1093/biomethods/bpy008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 06/07/2018] [Accepted: 07/24/2018] [Indexed: 11/25/2022] Open
Abstract
Following subcellular fractionation, the complexity of proteins derived from a particular cellular compartment is often evaluated by gel electrophoretic analysis. For the proteomic cataloguing of these distinct protein populations and their biochemical characterization, gel electrophoretic protein separation can be conveniently combined with liquid chromatography mass spectrometry. Here we describe a gel-enhanced liquid chromatography mass spectrometry (GeLC-MS)/MS approach with a new bioanalytical focus on the proteomic profiling of mitochondrial contact sites from rat liver using the highly sensitive Orbitrap Fusion Tribrid mass spectrometer for optimum protein identification following extraction from dried and long-term stored gels. Mass spectrometric analysis identified 964 protein species in the mitochondrial contact site fraction, whereby 459 proteins were identified by ≥3 unique peptides. This included mitochondrial components of the supramolecular complexes that form the ATP synthase, the respiratory chain, ribosomal subunits and the cytochrome P450 system, as well as crucial components of the translocase complexes translocase of the inner membrane (TIM) and translocase of the outer membrane (TOM) of the two mitochondrial membranes. Proteomics also identified contact site markers, such as glutathione transferase, monoamine oxidase and the pore protein voltage dependent anion channel (VDAC)-1. Hence, this report demonstrates that the GeLC-MS/MS method can be used to study complex mixtures of proteins that have been embedded and stored in dried polyacrylamide gels for a long period of time. Careful re-swelling and standard in-gel digestion is suitable to produce peptide profiles from old gels that can be used to extract sophisticated proteomic maps and enable the subsequent bioinformatics analysis of the distribution of protein function and the determination of potential protein clustering within the contact site system.
Collapse
Affiliation(s)
- Sandra Murphy
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland
| | - Michael Henry
- National Institute for Cellular Biotechnology, Dublin City University, Dublin 9, Ireland
| | - Paula Meleady
- National Institute for Cellular Biotechnology, Dublin City University, Dublin 9, Ireland
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland
| |
Collapse
|
21
|
Gel-based proteomics in disease research: Is it still valuable? BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1867:9-16. [PMID: 30392562 DOI: 10.1016/j.bbapap.2018.08.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 06/30/2018] [Accepted: 08/09/2018] [Indexed: 12/17/2022]
Abstract
Gel electrophoresis had been the primary method in proteomics. In the early era of proteomics, gel electrophoresis was a dominant technique of sample preparation for mass spectrometry analysis. Particularly, two-dimensional electrophoresis provided high-resolution proteome separation, and was regarded as the standard methodology for the separation of wide-range proteomes. However, gel electrophoresis turned downwards due to the progress of other separations including liquid chromatography and ionization techniques, resulting gel-free proteomics finally becoming dominant players at present. There are numerous advantages in gel-free approach in aspects of current trends of disease research. Interestingly, gel-free approaches are still advanced, it seems that gel electrophoresis will not be disappeared. The unique features of gel electrophoresis can be complementary for gel-free and it is suitable for the new wave of top-down functional proteomics.
Collapse
|
22
|
Xie S, Wong AYH, Kwok RTK, Li Y, Su H, Lam JWY, Chen S, Tang BZ. Fluorogenic Ag + -Tetrazolate Aggregation Enables Efficient Fluorescent Biological Silver Staining. Angew Chem Int Ed Engl 2018; 57:5750-5753. [PMID: 29575702 PMCID: PMC5969303 DOI: 10.1002/anie.201801653] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Indexed: 01/08/2023]
Abstract
Silver staining, which exploits the special bioaffinity and the chromogenic reduction of silver ions, is an indispensable visualization method in biology. It is a most popular method for in-gel protein detection. However, it is limited by run-to-run variability, background staining, inability for protein quantification, and limited compatibility with mass spectroscopic (MS) analysis; limitations that are largely attributed to the tricky chromogenic visualization. Herein, we reported a novel water-soluble fluorogenic Ag+ probe, the sensing mechanism of which is based on an aggregation-induced emission (AIE) process driven by tetrazolate-Ag+ interactions. The fluorogenic sensing can substitute the chromogenic reaction, leading to a new fluorescence silver staining method. This new staining method offers sensitive detection of total proteins in polyacrylamide gels with a broad linear dynamic range and robust operations that rival the silver nitrate stain and the best fluorescent stains.
Collapse
Affiliation(s)
- Sheng Xie
- Department of ChemistryHong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and ReconstructionInstitute of Molecular Functional MaterialsState Key Laboratory of NeuroscienceDivision of Biomedical Engineering, and Division of Life Science.The Hong Kong University of Science and TechnologyKowloonHong KongChina
- Ming Wai Lau Centre for Reparative MedicineKarolinska InstitutetHong KongChina
| | - Alex Y. H. Wong
- Ming Wai Lau Centre for Reparative MedicineKarolinska InstitutetHong KongChina
| | - Ryan T. K. Kwok
- Department of ChemistryHong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and ReconstructionInstitute of Molecular Functional MaterialsState Key Laboratory of NeuroscienceDivision of Biomedical Engineering, and Division of Life Science.The Hong Kong University of Science and TechnologyKowloonHong KongChina
| | - Ying Li
- Department of ChemistryHong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and ReconstructionInstitute of Molecular Functional MaterialsState Key Laboratory of NeuroscienceDivision of Biomedical Engineering, and Division of Life Science.The Hong Kong University of Science and TechnologyKowloonHong KongChina
| | - Huifang Su
- Department of ChemistryHong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and ReconstructionInstitute of Molecular Functional MaterialsState Key Laboratory of NeuroscienceDivision of Biomedical Engineering, and Division of Life Science.The Hong Kong University of Science and TechnologyKowloonHong KongChina
| | - Jacky W. Y. Lam
- Department of ChemistryHong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and ReconstructionInstitute of Molecular Functional MaterialsState Key Laboratory of NeuroscienceDivision of Biomedical Engineering, and Division of Life Science.The Hong Kong University of Science and TechnologyKowloonHong KongChina
| | - Sijie Chen
- Ming Wai Lau Centre for Reparative MedicineKarolinska InstitutetHong KongChina
| | - Ben Zhong Tang
- Department of ChemistryHong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and ReconstructionInstitute of Molecular Functional MaterialsState Key Laboratory of NeuroscienceDivision of Biomedical Engineering, and Division of Life Science.The Hong Kong University of Science and TechnologyKowloonHong KongChina
- Guangdong Provincial Key Laboratory of Brain ScienceDisease and Drug DevelopmentHKUST-Shenzhen Research InstituteNanshanShenzhenChina
- Guangdong Innovative Research Team, SCUT-HKUST Joint Research LaboratoryState Key Laboratory of Luminescent Materials and DevicesSouth China University of TechnologyGuangzhouChina
| |
Collapse
|
23
|
Xie S, Wong AYH, Kwok RTK, Li Y, Su H, Lam JWY, Chen S, Tang BZ. Fluorogenic Ag+
-Tetrazolate Aggregation Enables Efficient Fluorescent Biological Silver Staining. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201801653] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Sheng Xie
- Department of Chemistry; Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction; Institute of Molecular Functional Materials; State Key Laboratory of Neuroscience; Division of Biomedical Engineering, and Division of Life Science.; The Hong Kong University of Science and Technology; Kowloon Hong Kong China
- Ming Wai Lau Centre for Reparative Medicine; Karolinska Institutet; Hong Kong China
| | - Alex Y. H. Wong
- Ming Wai Lau Centre for Reparative Medicine; Karolinska Institutet; Hong Kong China
| | - Ryan T. K. Kwok
- Department of Chemistry; Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction; Institute of Molecular Functional Materials; State Key Laboratory of Neuroscience; Division of Biomedical Engineering, and Division of Life Science.; The Hong Kong University of Science and Technology; Kowloon Hong Kong China
| | - Ying Li
- Department of Chemistry; Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction; Institute of Molecular Functional Materials; State Key Laboratory of Neuroscience; Division of Biomedical Engineering, and Division of Life Science.; The Hong Kong University of Science and Technology; Kowloon Hong Kong China
| | - Huifang Su
- Department of Chemistry; Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction; Institute of Molecular Functional Materials; State Key Laboratory of Neuroscience; Division of Biomedical Engineering, and Division of Life Science.; The Hong Kong University of Science and Technology; Kowloon Hong Kong China
| | - Jacky W. Y. Lam
- Department of Chemistry; Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction; Institute of Molecular Functional Materials; State Key Laboratory of Neuroscience; Division of Biomedical Engineering, and Division of Life Science.; The Hong Kong University of Science and Technology; Kowloon Hong Kong China
| | - Sijie Chen
- Ming Wai Lau Centre for Reparative Medicine; Karolinska Institutet; Hong Kong China
| | - Ben Zhong Tang
- Department of Chemistry; Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction; Institute of Molecular Functional Materials; State Key Laboratory of Neuroscience; Division of Biomedical Engineering, and Division of Life Science.; The Hong Kong University of Science and Technology; Kowloon Hong Kong China
- Guangdong Provincial Key Laboratory of Brain Science; Disease and Drug Development; HKUST-Shenzhen Research Institute; Nanshan Shenzhen China
- Guangdong Innovative Research Team, SCUT-HKUST Joint Research Laboratory; State Key Laboratory of Luminescent Materials and Devices; South China University of Technology; Guangzhou China
| |
Collapse
|
24
|
Fluorescent Protein Visualization Immediately After Gel Electrophoresis Using an In-Gel Trichloroethanol Photoreaction with Tryptophan. Methods Mol Biol 2018; 1853:179-190. [PMID: 30097944 DOI: 10.1007/978-1-4939-8745-0_22] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
SDS-polyacrylamide gel electrophoresis (SDS-PAGE) is one of the essential techniques in molecular biology and biochemistry laboratories and requires rapid visualization methods for efficient sample analysis. Proteins on polyacrylamide gels can be visualized within 5 min via the photoreaction of tryptophan with trichloroethanol. This process does not require protein fixation, staining, or destaining. In this method polyacrylamide gels are prepared by adding trichloroethanol before polymerization. After electrophoresis, the gel is immediately activated on a standard UV transilluminator and the fluorescently labeled proteins are imaged. The reaction is based on the photoreaction of trichloroethanol with tryptophan residues within the protein. This generates a visible blue-green fluorescence (∼500 nm) that is accurately imaged. Here we describe the preparation of Tris-glycine and Tris-tricine SDS-polyacrylamide gels with trichloroethanol and the photoreaction and visualization of tryptophan containing proteins.
Collapse
|
25
|
Felczak MM, Chodavarapu S, Kaguni JM. DnaC, the indispensable companion of DnaB helicase, controls the accessibility of DnaB helicase by primase. J Biol Chem 2017; 292:20871-20882. [PMID: 29070678 DOI: 10.1074/jbc.m117.807644] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 10/11/2017] [Indexed: 11/06/2022] Open
Abstract
Former studies relying on hydrogen/deuterium exchange analysis suggest that DnaC bound to DnaB alters the conformation of the N-terminal domain (NTD) of DnaB to impair the ability of this DNA helicase to interact with primase. Supporting this idea, the work described herein based on biosensor experiments and enzyme-linked immunosorbent assays shows that the DnaB-DnaC complex binds poorly to primase in comparison with DnaB alone. Using a structural model of DnaB complexed with the C-terminal domain of primase, we found that Ile-85 is located at the interface in the NTD of DnaB that contacts primase. An alanine substitution for Ile-85 specifically interfered with this interaction and impeded DnaB function in DNA replication, but not its activity as a DNA helicase or its ability to bind to ssDNA. By comparison, substitutions of Asn for Ile-136 (I136N) and Thr for Ile-142 (I142T) in a subdomain previously named the helical hairpin in the NTD of DnaB altered the conformation of the helical hairpin and/or compromised its pairwise arrangement with the companion subdomain in each brace of protomers of the DnaB hexamer. In contrast with the I85A mutant, the latter were defective in DNA replication due to impaired binding to both ssDNA and primase. In view of these findings, we propose that DnaC controls the ability of DnaB to interact with primase by modifying the conformation of the NTD of DnaB.
Collapse
Affiliation(s)
- Magdalena M Felczak
- From the Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824-1319
| | - Sundari Chodavarapu
- From the Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824-1319
| | - Jon M Kaguni
- From the Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824-1319
| |
Collapse
|
26
|
Noaman N, Abbineni PS, Withers M, Coorssen JR. Coomassie staining provides routine (sub)femtomole in-gel detection of intact proteoforms: Expanding opportunities for genuine Top-down Proteomics. Electrophoresis 2017; 38:3086-3099. [PMID: 28872692 DOI: 10.1002/elps.201700190] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 07/11/2017] [Accepted: 08/25/2017] [Indexed: 01/22/2023]
Abstract
Modified colloidal Coomassie Brilliant Blue (cCBB) staining utilising a novel destain protocol and near-infrared fluorescence detection (nIRFD) rivals the in-gel protein detection sensitivity (DS) of SYPRO Ruby. However, established DS estimates are likely inaccurate in terms of 2DE-resolved proteoform 'spots' since DS is routinely measured from comparatively diffuse protein 'bands' following wide-well 1DE. Here, cCBB DS for 2DE-based proteomics was more accurately determined using narrow-well 1DE. As precise estimates of protein standard monomer concentrations are essential for accurate quantitation, coupling UV absorbance with gel-based purity assessments is described. Further, as cCBB is compatible with both nIRFD and densitometry, the impacts of imaging method (and image resolution) on DS were assessed. Narrow-well 1DE enabled more accurate quantitation of cCBB DS for 2DE, achieving (sub)femtomole DS with either nIRFD or densitometry. While densitometry offers comparative simplicity and affordability, nIRFD has the unique potential for enhanced DS with Deep Imaging. Higher-resolution nIRFD also improved analysis of a 2DE-resolved proteome, surpassing the DS of standard nIRFD and densitometry, with nIRFD Deep Imaging further maximising proteome coverage. cCBB DS for intact proteins rivals that of mass spectrometry (MS) for peptides in complex mixtures, reaffirming that 2DE-MS currently provides the most routine, broadly applicable, robust, and information-rich Top-down approach to Discovery Proteomics.
Collapse
Affiliation(s)
- Nour Noaman
- Department of Molecular Physiology, and the WSU Molecular Medicine Research Group, School of Medicine, Western Sydney University, Campbelltown, New South Wales, Australia
| | - Prabhodh S Abbineni
- Department of Pharmacology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Michael Withers
- Department of Molecular Physiology, and the WSU Molecular Medicine Research Group, School of Medicine, Western Sydney University, Campbelltown, New South Wales, Australia
| | - Jens R Coorssen
- Departments of Health Sciences and Biological Sciences, Brock University, St Catharines, Ontario, Canada
| |
Collapse
|
27
|
Feng K, Wang LY, Liao DJ, Lu XP, Hu DJ, Liang X, Zhao J, Mo ZY, Li SP. Potential molecular mechanisms for fruiting body formation of Cordyceps illustrated in the case of Cordyceps sinensis. Mycology 2017; 8:231-258. [PMID: 30123644 PMCID: PMC6059060 DOI: 10.1080/21501203.2017.1365314] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 08/04/2017] [Indexed: 11/30/2022] Open
Abstract
The fruiting body formation mechanisms of Cordyceps sinensis are still unclear. To explore the mechanisms, proteins potentially related to the fruiting body formation, proteins from fruiting bodies, and mycelia of Cordyceps species were assessed by using two-dimensional fluorescence difference gel electrophoresis, and the differential expression proteins were identified by matrix-assisted laser desorption/ionisation tandem time of flight mass spectrometry. The results showed that 198 differential expression proteins (252 protein spots) were identified during the fruiting body formation of Cordyceps species, and 24 of them involved in fruiting body development in both C. sinensis and other microorganisms. Especially, enolase and malate dehydrogenase were first found to play an important role in fruiting body development in macro-fungus. The results implied that cAMP signal pathway involved in fruiting body development of C. sinensis, meanwhile glycometabolism, protein metabolism, energy metabolism, and cell reconstruction were more active during fruiting body development. It has become evident that fruiting body formation of C. sinensis is a highly complex differentiation process and requires precise integration of a number of fundamental biological processes. Although the fruiting body formation mechanisms for all these activities remain to be further elucidated, the possible mechanism provides insights into the culture of C. sinensis.
Collapse
Affiliation(s)
- Kun Feng
- State Key Laboratory of Quality Research in Chinese Medicine, University of Macau, Macao, China
| | - Lan-Ying Wang
- State Key Laboratory of Quality Research in Chinese Medicine, University of Macau, Macao, China.,Department of Chemistry and Pharmacy, Zhuhai College of Jilin University, Zhuhai, China
| | - Dong-Jiang Liao
- The State Key Laboratory of Respiratory Diseases, Guangzhou Medical University, Guangzhou, China
| | - Xin-Peng Lu
- The State Key Laboratory of Respiratory Diseases, Guangzhou Medical University, Guangzhou, China
| | - De-Jun Hu
- State Key Laboratory of Quality Research in Chinese Medicine, University of Macau, Macao, China
| | | | - Jing Zhao
- State Key Laboratory of Quality Research in Chinese Medicine, University of Macau, Macao, China
| | - Zi-Yao Mo
- The State Key Laboratory of Respiratory Diseases, Guangzhou Medical University, Guangzhou, China
| | - Shao-Ping Li
- State Key Laboratory of Quality Research in Chinese Medicine, University of Macau, Macao, China
| |
Collapse
|
28
|
Proteomic analysis of protein phosphatase Z1 from Candida albicans. PLoS One 2017; 12:e0183176. [PMID: 28837603 PMCID: PMC5570430 DOI: 10.1371/journal.pone.0183176] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 07/31/2017] [Indexed: 11/19/2022] Open
Abstract
Protein phosphatase Z is a "novel type" fungus specific serine/threonine protein phosphatase. Previously our research group identified the CaPPZ1 gene in the opportunistic pathogen Candida albicans and reported that the gene deletion had several important physiological consequences. In order to reveal the protein targets and the associated mechanisms behind the functions of the phosphatase a proteomic method was adopted for the comparison of the cappz1 deletion mutant and the genetically matching QMY23 control strain. Proteins extracted from the control and deletion mutant strains were separated by two-dimensional gel electrophoresis and the protein spots were stained with RuBPS and Pro-Q Diamond in order to visualize the total proteome and the phosphoproteome, respectively. The alterations in spot intensities were determined by densitometry and were analysed with the Delta2D (Decodon) software. Spots showing significantly different intensities between the mutant and control strains were excised from the gels and were digested with trypsin. The resulting peptides were identified by LC-MS/MS mass spectrometry. As many as 15 protein spots were found that exhibited significant changes in their intensity upon the deletion of the phosphatase and 20 phosphoproteins were identified in which the level of phosphorylation was modified significantly in the mutant. In agreement with previous findings we found that the affected proteins function in protein synthesis, oxidative stress response, regulation of morphology and metabolism. Among these proteins we identified two potential CaPpz1 substrates (Eft2 and Rpp0) that may regulate the elongation step of translation. RT-qPCR experiments revealed that the expression of the genes coding for the affected proteins was not altered significantly. Thus, the absence of CaPpz1 exerted its effects via protein synthesis/degradation and phosphorylation/dephosphorylation. In addition, our proteomics data strongly suggested a role for CaPpz1 in biofilm formation, was confirmed experimentally. Thus our unbiased proteomic approach lead to the discovery of a novel function for this phosphatase in C. albicans.
Collapse
|
29
|
Identification of a host cell protein impurity in therapeutic protein, P1. J Pharm Biomed Anal 2017; 141:32-38. [DOI: 10.1016/j.jpba.2017.03.065] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 03/15/2017] [Accepted: 03/31/2017] [Indexed: 11/20/2022]
|
30
|
A Routine 'Top-Down' Approach to Analysis of the Human Serum Proteome. Proteomes 2017; 5:proteomes5020013. [PMID: 28587287 PMCID: PMC5489773 DOI: 10.3390/proteomes5020013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 05/30/2017] [Accepted: 05/30/2017] [Indexed: 12/21/2022] Open
Abstract
Serum provides a rich source of potential biomarker proteoforms. One of the major obstacles in analysing serum proteomes is detecting lower abundance proteins owing to the presence of hyper-abundant species (e.g., serum albumin and immunoglobulins). Although depletion methods have been used to address this, these can lead to the concomitant removal of non-targeted protein species, and thus raise issues of specificity, reproducibility, and the capacity for meaningful quantitative analyses. Altering the native stoichiometry of the proteome components may thus yield a more complex series of issues than dealing directly with the inherent complexity of the sample. Hence, here we targeted method refinements so as to ensure optimum resolution of serum proteomes via a top down two-dimensional gel electrophoresis (2DE) approach that enables the routine assessment of proteoforms and is fully compatible with subsequent mass spectrometric analyses. Testing included various fractionation and non-fractionation approaches. The data show that resolving 500 µg protein on 17 cm 3–10 non-linear immobilised pH gradient strips in the first dimension followed by second dimension resolution on 7–20% gradient gels with a combination of lithium dodecyl sulfate (LDS) and sodium dodecyl sulfate (SDS) detergents markedly improves the resolution and detection of proteoforms in serum. In addition, well established third dimension electrophoretic separations in combination with deep imaging further contributed to the best available resolution, detection, and thus quantitative top-down analysis of serum proteomes.
Collapse
|
31
|
Global Proteomic Profiling and Identification of Stress-Responsive Proteins Using Two-Dimensional Gel Electrophoresis. Methods Mol Biol 2017; 1631:163-179. [PMID: 28735397 DOI: 10.1007/978-1-4939-7136-7_10] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Global proteome profiling is a direct representation of the protein set in an organism, organ, tissues, or an organelle. One of the main objectives of proteomic analysis is the comparison and relative quantitation of proteins under a defined set of conditions. Two-dimensional gel electrophoresis (2-DE) has gained prominence over the last 4 decades for successfully aiding differential proteomics, providing visual confirmation of changes in protein abundance, which otherwise cannot be predicted from genome analysis. Each protein spot on 2-DE gel can be analyzed by its abundance, location, or even its presence or absence. This versatile gel-based method combines and utilizes the finest principle for separation of protein complexes by virtue of their charge and mass, visual mapping coupled with successful mass spectrometric identification of individual proteins.
Collapse
|
32
|
Hussain S, Dutta A, Sarkar A, Singh A, Gupta ML, Biswas S. Proteomic analysis of irradiated lung tissue of mice using gel-based proteomic approach. Int J Radiat Biol 2016; 93:373-380. [PMID: 28000521 DOI: 10.1080/09553002.2016.1266058] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
PURPOSE Exposure to radiation causes severe alterations of protein expression level inside the cell, thus it may influence the biological events and stress response. In the present investigation, we have demonstrated the effect of radiation on mice lung tissues. MATERIALS AND METHODS Two-dimensional gel electrophoresis (2-DE) coupled with MALDI-TOF/TOF was used to check the expression changes in lung proteome profile of strain 'A' female mice after exposure to lethal doses of gamma irradiation at different time periods (24 and 48 h). Identified proteins were analysed for their altered expression and were further validated by Western blotting and enzyme-linked immunosorbent assay (ELISA). RESULTS Nine significant differentially expressed proteins were identified from irradiated lungs tissues. The expression level of zinc finger protein was found to be up regulated at 24 h irradiation in comparison to 48 h irradiation. CONCLUSIONS Zinc finger protein may be considered as a radiation responsive protein. Alteration in its expression pattern may primarily affect binding specificity of the protein that can further result in the interference in transcriptional control of multiple stress responsive genes.
Collapse
Affiliation(s)
- Shabir Hussain
- a Department of Genomics & Molecular Medicine , CSIR - Institute of Genomics & Integrative Biology (IGIB), Delhi University Campus , Delhi , India
| | - Ajaswrata Dutta
- b Division of Radioprotective Drug Development Research , Institute of Nuclear Medicine and Allied Sciences , Delhi , India
| | - Ashish Sarkar
- a Department of Genomics & Molecular Medicine , CSIR - Institute of Genomics & Integrative Biology (IGIB), Delhi University Campus , Delhi , India
| | - Abhinav Singh
- b Division of Radioprotective Drug Development Research , Institute of Nuclear Medicine and Allied Sciences , Delhi , India
| | - Manju Lata Gupta
- b Division of Radioprotective Drug Development Research , Institute of Nuclear Medicine and Allied Sciences , Delhi , India
| | - Sagarika Biswas
- a Department of Genomics & Molecular Medicine , CSIR - Institute of Genomics & Integrative Biology (IGIB), Delhi University Campus , Delhi , India
| |
Collapse
|
33
|
Naryzhny S. Towards the Full Realization of 2DE Power. Proteomes 2016; 4:proteomes4040033. [PMID: 28248243 PMCID: PMC5260966 DOI: 10.3390/proteomes4040033] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Revised: 11/03/2016] [Accepted: 11/09/2016] [Indexed: 01/29/2023] Open
Abstract
Here, approaches that allow disclosure of the information hidden inside and outside of two-dimensional gel electrophoresis (2DE) are described. Experimental identification methods, such as mass spectrometry of high resolution and sensitivity (MALDI-TOF MS and ESI LC-MS/MS) and immunodetection (Western and Far-Western) in combination with bioinformatics (collection of all information about proteoforms), move 2DE to the next level of power. The integration of these technologies will promote 2DE as a powerful methodology of proteomics technology.
Collapse
Affiliation(s)
- Stanislav Naryzhny
- Institute of Biomedical Chemistry, Pogodinskaya 10, Moscow 119121, Russia.
- B. P. Konstantinov Petersburg Nuclear Physics Institute, National Research Center "Kurchatov Institute", Leningrad region, Gatchina 188300, Russia.
| |
Collapse
|
34
|
Murphy S, Dowling P, Ohlendieck K. Comparative Skeletal Muscle Proteomics Using Two-Dimensional Gel Electrophoresis. Proteomes 2016; 4:proteomes4030027. [PMID: 28248237 PMCID: PMC5217355 DOI: 10.3390/proteomes4030027] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 08/31/2016] [Accepted: 09/07/2016] [Indexed: 12/16/2022] Open
Abstract
The pioneering work by Patrick H. O’Farrell established two-dimensional gel electrophoresis as one of the most important high-resolution protein separation techniques of modern biochemistry (Journal of Biological Chemistry1975, 250, 4007–4021). The application of two-dimensional gel electrophoresis has played a key role in the systematic identification and detailed characterization of the protein constituents of skeletal muscles. Protein changes during myogenesis, muscle maturation, fibre type specification, physiological muscle adaptations and natural muscle aging were studied in depth by the original O’Farrell method or slightly modified gel electrophoretic techniques. Over the last 40 years, the combined usage of isoelectric focusing in the first dimension and sodium dodecyl sulfate polyacrylamide slab gel electrophoresis in the second dimension has been successfully employed in several hundred published studies on gel-based skeletal muscle biochemistry. This review focuses on normal and physiologically challenged skeletal muscle tissues and outlines key findings from mass spectrometry-based muscle proteomics, which was instrumental in the identification of several thousand individual protein isoforms following gel electrophoretic separation. These muscle-associated protein species belong to the diverse group of regulatory and contractile proteins of the acto-myosin apparatus that forms the sarcomere, cytoskeletal proteins, metabolic enzymes and transporters, signaling proteins, ion-handling proteins, molecular chaperones and extracellular matrix proteins.
Collapse
Affiliation(s)
- Sandra Murphy
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland.
| | - Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland.
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland.
| |
Collapse
|
35
|
Dechtawewat T, Paemanee A, Roytrakul S, Songprakhon P, Limjindaporn T, Yenchitsomanus PT, Saitornuang S, Puttikhunt C, Kasinrerk W, Malasit P, Noisakran S. Mass spectrometric analysis of host cell proteins interacting with dengue virus nonstructural protein 1 in dengue virus-infected HepG2 cells. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:1270-1280. [PMID: 27108190 DOI: 10.1016/j.bbapap.2016.04.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 03/26/2016] [Accepted: 04/19/2016] [Indexed: 01/09/2023]
Abstract
Dengue virus (DENV) infection is a leading cause of the mosquito-borne infectious diseases that affect humans worldwide. Virus-host interactions appear to play significant roles in DENV replication and the pathogenesis of DENV infection. Nonstructural protein 1 (NS1) of DENV is likely involved in these processes; however, its associations with host cell proteins in DENV infection remain unclear. In this study, we used a combination of techniques (immunoprecipitation, in-solution trypsin digestion, and LC-MS/MS) to identify the host cell proteins that interact with cell-associated NS1 in an in vitro model of DENV infection in the human hepatocyte HepG2 cell line. Thirty-six novel host cell proteins were identified as potential DENV NS1-interacting partners. A large number of these proteins had characteristic binding or catalytic activities, and were involved in cellular metabolism. Coimmunoprecipitation and colocalization assays confirmed the interactions of DENV NS1 and human NIMA-related kinase 2 (NEK2), thousand and one amino acid protein kinase 1 (TAO1), and component of oligomeric Golgi complex 1 (COG1) proteins in virus-infected cells. This study reports a novel set of DENV NS1-interacting host cell proteins in the HepG2 cell line and proposes possible roles for human NEK2, TAO1, and COG1 in DENV infection.
Collapse
Affiliation(s)
- Thanyaporn Dechtawewat
- Division of Molecular Medicine, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Atchara Paemanee
- Proteomics Research Unit, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani 12120, Thailand
| | - Sittiruk Roytrakul
- Proteomics Research Unit, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani 12120, Thailand
| | - Pucharee Songprakhon
- Division of Molecular Medicine, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Thawornchai Limjindaporn
- Department of Anatomy, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Pa-Thai Yenchitsomanus
- Division of Molecular Medicine, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Sawanan Saitornuang
- Division of Dengue Hemorrhagic Fever Unit, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; Medical Biotechnology Research Unit, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Bangkok 10700, Thailand
| | - Chunya Puttikhunt
- Division of Dengue Hemorrhagic Fever Unit, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; Medical Biotechnology Research Unit, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Bangkok 10700, Thailand
| | - Watchara Kasinrerk
- Biomedical Technology Research Center, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Chiang Mai 50200, Thailand; Division of Clinical Immunology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Prida Malasit
- Division of Dengue Hemorrhagic Fever Unit, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; Medical Biotechnology Research Unit, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Bangkok 10700, Thailand
| | - Sansanee Noisakran
- Division of Dengue Hemorrhagic Fever Unit, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; Medical Biotechnology Research Unit, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Bangkok 10700, Thailand.
| |
Collapse
|
36
|
Golshaei R, Guler Z, Sarac SA. (Au/PANA/PVAc) nanofibers as a novel composite matrix for albumin and streptavidin immobilization. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2016; 60:260-275. [DOI: 10.1016/j.msec.2015.11.046] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 10/27/2015] [Accepted: 11/16/2015] [Indexed: 12/30/2022]
|
37
|
Abstract
The LINE-1 retrotransposon (L1) encodes two proteins, ORF1p and ORF2p, which bind to the L1 RNA in cis, forming a ribonucleoprotein (RNP) complex that is critical for retrotransposition. Interactions with both permissive and repressive host factors pervade every step of the L1 life cycle. Until recently, limitations in detection and production precluded in-depth characterization of L1 RNPs. Inducible expression and recombinant engineering of epitope tags have made detection of both L1 ORFs routine. Here, we describe large-scale production of L1-expressing HEK-293T cells in suspension cell culture, cryomilling and affinity capture of L1 RNP complexes, sample preparation for analysis by mass spectrometry, and assay using the L1 element amplification protocol (LEAP) and qRT-PCR.
Collapse
|
38
|
Chavez-Dozal A, Gorman C, Nishiguchi MK. Proteomic and metabolomic profiles demonstrate variation among free-living and symbiotic vibrio fischeri biofilms. BMC Microbiol 2015; 15:226. [PMID: 26494154 PMCID: PMC4619220 DOI: 10.1186/s12866-015-0560-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2015] [Accepted: 10/08/2015] [Indexed: 11/11/2022] Open
Abstract
Background A number of bacterial species are capable of growing in various life history modes that enable their survival and persistence in both planktonic free-living stages as well as in biofilm communities. Mechanisms contributing to either planktonic cell or biofilm persistence and survival can be carefully delineated using multiple differential techniques (e.g., genomics and transcriptomics). In this study, we present both proteomic and metabolomic analyses of Vibrio fischeri biofilms, demonstrating the potential for combined differential studies for elucidating life-history switches important for establishing the mutualism through biofilm formation and host colonization. Methods The study used a metabolomics/proteomics or “meta-proteomics” approach, referring to the combined protein and metabolic data analysis that bridges the gap between phenotypic changes (planktonic cell to biofilm formation) with genotypic changes (reflected in protein/metabolic profiles). Our methods used protein shotgun construction, followed by liquid chromatography coupled with mass spectrometry (LC-MS) detection and quantification for both free-living and biofilm forming V. fischeri. Results We present a time-resolved picture of approximately 100 proteins (2D-PAGE and shotgun proteomics) and 200 metabolites that are present during the transition from planktonic growth to community biofilm formation. Proteins involved in stress response, DNA repair damage, and transport appeared to be highly expressed during the biofilm state. In addition, metabolites detected in biofilms correspond to components of the exopolysaccharide (EPS) matrix (sugars and glycerol-derived). Alterations in metabolic enzymes were paralleled by more pronounced changes in concentration of intermediates from the glycolysis pathway as well as several amino acids. Conclusions This combined analysis of both types of information (proteins, metabolites) has provided a more complete picture of the biochemical processes of biofilm formation and what determines the switch between the two life history strategies. The reported findings have broad implications for Vibrio biofilm ecology, and mechanisms for successful survival in the host and environment. Electronic supplementary material The online version of this article (doi:10.1186/s12866-015-0560-z) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Alba Chavez-Dozal
- Department of Biology, New Mexico State University, Box 30001, MSC 3AF, Las Cruces, NM, 88003-8001, USA.
| | - Clayton Gorman
- Department of Biology, New Mexico State University, Box 30001, MSC 3AF, Las Cruces, NM, 88003-8001, USA.
| | - Michele K Nishiguchi
- Department of Biology, New Mexico State University, Box 30001, MSC 3AF, Las Cruces, NM, 88003-8001, USA.
| |
Collapse
|
39
|
Zhao WJ, Song Q, Zhang ZJ, Mao L, Zheng WJ, Hu X, Lian HZ. The Kinetic Response of the Proteome in A549 Cells Exposed to ZnSO4 Stress. PLoS One 2015; 10:e0133451. [PMID: 26196515 PMCID: PMC4510299 DOI: 10.1371/journal.pone.0133451] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 06/25/2015] [Indexed: 11/29/2022] Open
Abstract
Zinc, an essential trace element, is involved in many important physiological processes. Cell responses to zinc stress show time-dependent effects besides concentration-dependence and tissue-specificity. Herein, we investigated the time-dependent differential expression of the proteome in A549 cells after administered with ZnSO4 for both 9 and 24 h using 2DE. 123 differentially expressed protein spots were detected, most of which were up-regulated by Zn2+ treatment. Interestingly, 49 proteins exhibited significant differential expression repeatedly during these two treatment periods, and moreover showed a conserved change with different ratios and four time-dependent expression patterns. Pattern 1 (up-regulated with rapid initial induction and subsequent repression) and pattern 4 (down-regulated with steady repression) were the predominant expression patterns. The abundances of the proteins in patterns 1 and 4 after 24 h of zinc treatment are always lower than that after 9 h, indicating that exogenous zinc reduced the expression of proteins in cells after 24 h or longer. Importantly, these findings could also reflect the central challenge in detecting zinc homeostasis proteins by 2DE or other high throughput analytical methods resulting from slight variation in protein expression after certain durations of exogenous zinc treatment and/or low inherent protein content in cells. These time-dependent proteome expression patterns were further validated by measuring dynamic changes in protein content in cells and in expression of two proteins using the Bradford method and western blotting, respectively. The time-dependent changes in total zinc and free Zn2+ ion contents in cells were measured using ICP-MS and confocal microscopy, respectively. The kinetic process of zinc homeostasis regulated by muffling was further revealed. In addition, we identified 50 differentially expressed proteins which are predominantly involved in metabolic process, cellular process or developmental process, and function as binding, catalytic activity or structural molecule activity. This study further elucidates our understanding of dynamic nature of the cellular response to zinc stress and the mechanism of zinc homeostasis.
Collapse
Affiliation(s)
- Wen-jie Zhao
- State Key Laboratory of Analytical Chemistry for Life Science, Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry & Chemical Engineering and Center of Materials Analysis, Nanjing University, Nanjing, Jiangsu, PR China
| | - Qun Song
- State Key Laboratory of Analytical Chemistry for Life Science, Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry & Chemical Engineering and Center of Materials Analysis, Nanjing University, Nanjing, Jiangsu, PR China
| | - Zi-jin Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry & Chemical Engineering and Center of Materials Analysis, Nanjing University, Nanjing, Jiangsu, PR China
| | - Li Mao
- MOE Key Laboratory of Modern Toxicology, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, PR China
| | - Wei-juan Zheng
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science, Nanjing University, Nanjing, Jiangsu, PR China
| | - Xin Hu
- State Key Laboratory of Analytical Chemistry for Life Science, Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry & Chemical Engineering and Center of Materials Analysis, Nanjing University, Nanjing, Jiangsu, PR China
| | - Hong-zhen Lian
- State Key Laboratory of Analytical Chemistry for Life Science, Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry & Chemical Engineering and Center of Materials Analysis, Nanjing University, Nanjing, Jiangsu, PR China
| |
Collapse
|
40
|
Impact of the antifungal protein PgAFP from Penicillium chrysogenum on the protein profile in Aspergillus flavus. Appl Microbiol Biotechnol 2015; 99:8701-15. [DOI: 10.1007/s00253-015-6731-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Revised: 05/24/2015] [Accepted: 05/27/2015] [Indexed: 12/20/2022]
|
41
|
Hakhverdyan Z, Domanski M, Hough LE, Oroskar AA, Oroskar AR, Keegan S, Dilworth DJ, Molloy KR, Sherman V, Aitchison JD, Fenyö D, Chait BT, Jensen TH, Rout MP, LaCava J. Rapid, optimized interactomic screening. Nat Methods 2015; 12:553-60. [PMID: 25938370 PMCID: PMC4449307 DOI: 10.1038/nmeth.3395] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Accepted: 03/03/2015] [Indexed: 12/25/2022]
Abstract
We must reliably map the interactomes of cellular macromolecular
complexes in order to fully explore and understand biological systems. However,
there are no methods to accurately predict how to capture a given macromolecular
complex with its physiological binding partners. Here, we present a screen that
comprehensively explores the parameters affecting the stability of interactions
in affinity-captured complexes, enabling the discovery of physiological binding
partners and the elucidation of their functional interactions in unparalleled
detail. We have implemented this screen on several macromolecular complexes from
a variety of organisms, revealing novel profiles even for well-studied proteins.
Our approach is robust, economical and automatable, providing an inroad to the
rigorous, systematic dissection of cellular interactomes.
Collapse
Affiliation(s)
- Zhanna Hakhverdyan
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York, USA
| | - Michal Domanski
- 1] Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York, USA. [2] Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Loren E Hough
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York, USA
| | | | | | - Sarah Keegan
- 1] Center for Health Informatics and Bioinformatics, New York University School of Medicine, New York, New York, USA. [2] Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York, USA
| | - David J Dilworth
- 1] Institute for Systems Biology, Seattle, Washington, USA. [2] Seattle Biomedical Research Institute, Seattle, Washington, USA
| | - Kelly R Molloy
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, New York, USA
| | - Vadim Sherman
- High Energy Physics Instrument Shop, The Rockefeller University, New York, New York, USA
| | - John D Aitchison
- 1] Institute for Systems Biology, Seattle, Washington, USA. [2] Seattle Biomedical Research Institute, Seattle, Washington, USA
| | - David Fenyö
- 1] Center for Health Informatics and Bioinformatics, New York University School of Medicine, New York, New York, USA. [2] Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York, USA
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, New York, USA
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Michael P Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York, USA
| | - John LaCava
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York, USA
| |
Collapse
|
42
|
LaCava J, Molloy KR, Taylor MS, Domanski M, Chait BT, Rout MP. Affinity proteomics to study endogenous protein complexes: pointers, pitfalls, preferences and perspectives. Biotechniques 2015; 58:103-19. [PMID: 25757543 PMCID: PMC4465938 DOI: 10.2144/000114262] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 02/17/2015] [Indexed: 01/13/2023] Open
Abstract
Dissecting and studying cellular systems requires the ability to specifically isolate distinct proteins along with the co-assembled constituents of their associated complexes. Affinity capture techniques leverage high affinity, high specificity reagents to target and capture proteins of interest along with specifically associated proteins from cell extracts. Affinity capture coupled to mass spectrometry (MS)-based proteomic analyses has enabled the isolation and characterization of a wide range of endogenous protein complexes. Here, we outline effective procedures for the affinity capture of protein complexes, highlighting best practices and common pitfalls.
Collapse
Affiliation(s)
- John LaCava
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York
- Institute for Systems Genetics, New York University School of Medicine, New York, NY
| | - Kelly R. Molloy
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY
| | - Martin S. Taylor
- High Throughput Biology Center and Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Michal Domanski
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York
- Centre for mRNP Biogenesis and Metabolism, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Brian T. Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY
| | - Michael P. Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York
| |
Collapse
|
43
|
Jauchem JR, Cerna CZ, Lim TY, Seaman RL. Exposures of Sus scrofa to a TASER(®) conducted electrical weapon: no effects on 2-dimensional gel electrophoresis patterns of plasma proteins. Forensic Sci Med Pathol 2014; 10:526-34. [PMID: 25319243 DOI: 10.1007/s12024-014-9606-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/25/2014] [Indexed: 11/25/2022]
Abstract
In an earlier study, we found significant changes in red-blood-cell, leukocyte, and platelet counts, and in red-blood-cell membrane proteins, following exposures of anesthetized pigs to a conducted electrical weapon. In the current study, we examined potential changes in plasma proteins [analyzed via two-dimensional gel electrophoresis (2-DGE)] following two 30 s exposures of anesthetized pigs (Sus scrofa) to a TASER (®) C2 conducted electrical weapon. Patterns of proteins, separated by 2-DGE, were consistent and reproducible between animals and between times of sampling. We determined that the blood plasma collection, handling, storage, and processing techniques we used are suitable for swine blood. There were no statistically significant changes in plasma proteins following the conducted-electrical-weapon exposures. Overall gel patterns of fibrinogen were similar to results of other studies of both pigs and humans (in control settings, not exposed to conducted electrical weapons). The lack of significant changes in plasma proteins may be added to the body of evidence regarding relative safety of TASER C2 device exposures.
Collapse
Affiliation(s)
- James R Jauchem
- Bio-Effects Division, Human Effectiveness Directorate, 711th Human Performance Wing, US Air Force Research Laboratory, 711 HPW/RHDR, 4141 Petroleum Road, Fort Sam Houston, TX, 78234, USA,
| | | | | | | |
Collapse
|
44
|
Colombo G, Clerici M, Giustarini D, Portinaro NM, Aldini G, Rossi R, Milzani A, Dalle-Donne I. Pathophysiology of tobacco smoke exposure: recent insights from comparative and redox proteomics. MASS SPECTROMETRY REVIEWS 2014; 33:183-218. [PMID: 24272816 DOI: 10.1002/mas.21392] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2013] [Revised: 05/23/2013] [Accepted: 05/23/2013] [Indexed: 06/02/2023]
Abstract
First-hand and second-hand tobacco smoke are causally linked to a huge number of deaths and are responsible for a broad spectrum of pathologies such as cancer, cardiovascular, respiratory, and eye diseases as well as adverse effects on female reproductive function. Cigarette smoke is a complex mixture of thousands of different chemical species, which exert their negative effects on macromolecules and biochemical pathways, both directly and indirectly. Many compounds can act as oxidants, pro-inflammatory agents, carcinogens, or a combination of these. The redox behavior of cigarette smoke has many implications for smoke related diseases. Reactive oxygen and nitrogen species (both radicals and non-radicals), reactive carbonyl compounds, and other species may induce oxidative damage in almost all the biological macromolecules, compromising their structure and/or function. Different quantitative and redox proteomic approaches have been applied in vitro and in vivo to evaluate, respectively, changes in protein expression and specific oxidative protein modifications induced by exposure to cigarette smoke and are overviewed in this review. Many gel-based and gel-free proteomic techniques have already been used successfully to obtain clues about smoke effects on different proteins in cell cultures, animal models, and humans. The further implementation with other sensitive screening techniques could be useful to integrate the comprehension of cigarette smoke effects on human health. In particular, the redox proteomic approach may also help identify biomarkers of exposure to tobacco smoke useful for preventing these effects or potentially predictive of the onset and/or progression of smoking-induced diseases as well as potential targets for therapeutic strategies.
Collapse
Affiliation(s)
- Graziano Colombo
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy
| | | | | | | | | | | | | | | |
Collapse
|
45
|
Oliveira BM, Coorssen JR, Martins-de-Souza D. 2DE: the phoenix of proteomics. J Proteomics 2014; 104:140-50. [PMID: 24704856 DOI: 10.1016/j.jprot.2014.03.035] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Revised: 03/21/2014] [Accepted: 03/24/2014] [Indexed: 12/22/2022]
Abstract
UNLABELLED Given the rapid developments in mass spectrometry (MS) in terms of sensitivity, mass accuracy, and throughput, some have suggested that two-dimensional gel electrophoresis (2DE) may no longer be a method of choice for proteomic analyses. However, as recognition of issues with these newer shotgun-MS approaches grows, there is a fresh and growing regard for the maturity of 2DE-MS as a genuine top-down analytical approach, particularly as it resolves thousands of intact protein species in a single run, enabling the simultaneous analysis of total protein complement, including isoforms and post-translational modifications. Given the strengths of both, it is most appropriate to view these as complementary or at least parallel approaches: as proteins encompass a myriad of physico-chemical properties, and the real aim is to explore proteomes as deeply as possible, all available resolving strategies must be considered in terms of the complexity encountered. It is time to critically and constructively focus on the optimization and integration of existing techniques rather than simplistically suggesting that one should replace the other. Our intention here is thus to present an overview of protein resolving techniques, focusing on milestones associated with 2DE, including pros, cons, advances and variations, in particular relative to shotgun proteomic approaches. BIOLOGICAL SIGNIFICANCE Proteomic researchers recognize the importance of 2DE in the history of proteomics. But the latest developments in mass spectrometry-based techniques have led some researchers to retire 2DE in their labs. However, we argue here that 2DE-MS is a genuine top-down analytical approach. The significance of this discussion is to make proteomic researchers aware of the importance of this technique in a proteomic pipeline. This article is part of a Special Issue entitled: Environmental and structural proteomics.
Collapse
Affiliation(s)
- Bruno M Oliveira
- Catarinense Federal Institute, Videira Campus, Videira, SC, Brazil
| | - Jens R Coorssen
- Dept. of Molecular Physiology, School of Medicine, University of Western Sydney, Australia; UWS Molecular Medicine Research Group, University of Western Sydney, Australia.
| | - Daniel Martins-de-Souza
- Laboratory of Neuroproteomics, Department of Biochemistry, Institute of Biology, State University of Campinas (UNICAMP), Campinas, Sao Paulo, Brazil; Laboratory of Neuroscience (LIM-27), Department and Institute of Psychiatry, Faculty of Medicine, University of São Paulo, Brazil; Dept. of Psychiatry and Psychotherapy, Ludwig Maximilians University (LMU), Munich, Germany.
| |
Collapse
|
46
|
Wright EP, Partridge MA, Padula MP, Gauci VJ, Malladi CS, Coorssen JR. Top-down proteomics: enhancing 2D gel electrophoresis from tissue processing to high-sensitivity protein detection. Proteomics 2014; 14:872-89. [PMID: 24452924 DOI: 10.1002/pmic.201300424] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Revised: 12/01/2013] [Accepted: 12/16/2013] [Indexed: 02/04/2023]
Abstract
The large-scale resolution and detection of proteins from complex native mixtures is fundamental to quantitative proteomic analyses. Comprehensive analyses depend on careful tissue handling and quantitative protein extraction and assessment. To most effectively link these analyses with an understanding of underlying molecular mechanisms, it is critical that all protein types - isoforms, splice variants and those with functionally important PTMs - are quantitatively extracted with high reproducibility. Methodological details concerning protein extraction and resolution using 2DE are discussed with reference to current in-gel protein detection limits. We confirm a significant increase in total protein, and establish that extraction, resolution and detection of phospho- and glycoproteins are improved following automated frozen disruption relative to manual homogenisation. The quality of 2DE protein resolution is established using third-dimension separations and 'deep imaging'; substantially more proteins/protein species than previously realised are actually resolved by 2DE. Thus, the key issue for effective proteome analyses is most likely to be detection, not resolution. Thus, these systematic methodological and technical advances further solidify the role of 2DE in top-down proteomics. By routinely assessing as much proteomic data from a sample as possible, 2DE enables more detailed and critical insights into molecular mechanisms underlying different physiological states.
Collapse
Affiliation(s)
- Elise P Wright
- Department of Molecular Physiology, Molecular Medicine Research Group, School of Medicine, University of Western Sydney, Penrith, NSW, Australia
| | | | | | | | | | | |
Collapse
|
47
|
Wright EP, Prasad KAG, Padula MP, Coorssen JR. Deep imaging: how much of the proteome does current top-down technology already resolve? PLoS One 2014; 9:e86058. [PMID: 24489691 PMCID: PMC3904854 DOI: 10.1371/journal.pone.0086058] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Accepted: 12/10/2013] [Indexed: 11/21/2022] Open
Abstract
Effective proteome analyses are based on interplay between resolution and detection. It had been claimed that resolution was the main factor limiting the use of two-dimensional gel electrophoresis. Improved protein detection now indicates that this is unlikely to be the case. Using a highly refined protocol, the rat brain proteome was extracted, resolved, and detected. In order to overcome the stain saturation threshold, high abundance protein species were excised from the gel following standard imaging. Gels were then imaged again using longer exposure times, enabling detection of lower abundance, less intensely stained protein species. This resulted in a significant enhancement in the detection of resolved proteins, and a slightly modified digestion protocol enabled effective identification by standard mass spectrometric methods. The data indicate that the resolution required for comprehensive proteome analyses is already available, can assess multiple samples in parallel, and preserve critical information concerning post-translational modifications. Further optimization of staining and detection methods promises additional improvements to this economical, widely accessible and effective top-down approach to proteome analysis.
Collapse
Affiliation(s)
- Elise P. Wright
- Molecular Physiology, and the UWS Molecular Medicine Research Group, School of Medicine, University of Western Sydney, Campbelltown, NSW, Australia
| | - Kali A. G. Prasad
- Molecular Physiology, and the UWS Molecular Medicine Research Group, School of Medicine, University of Western Sydney, Campbelltown, NSW, Australia
| | - Matthew P. Padula
- Proteomics Core Facility, Faculty of Science, University of Technology, Sydney, NSW, Australia
| | - Jens R. Coorssen
- Molecular Physiology, and the UWS Molecular Medicine Research Group, School of Medicine, University of Western Sydney, Campbelltown, NSW, Australia
- * E-mail:
| |
Collapse
|
48
|
Syzgantseva OA, Tognetti V, Boulangé A, Peixoto PA, Leleu S, Franck X, Joubert L. Evaluating Charge Transfer in Epicocconone Analogues: Toward a Targeted Design of Fluorophores. J Phys Chem A 2014; 118:757-64. [DOI: 10.1021/jp410407u] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Olga A. Syzgantseva
- Normandy University, COBRA UMR 6014 & FR 3038, Université de Rouen, INSA Rouen, CNRS, 1 rue Tesniére 76821 Mont St Aignan, Cedex, France
| | - Vincent Tognetti
- Normandy University, COBRA UMR 6014 & FR 3038, Université de Rouen, INSA Rouen, CNRS, 1 rue Tesniére 76821 Mont St Aignan, Cedex, France
| | - Agathe Boulangé
- Normandy University, COBRA UMR 6014 & FR 3038, Université de Rouen, INSA Rouen, CNRS, 1 rue Tesniére 76821 Mont St Aignan, Cedex, France
| | - Philippe A. Peixoto
- Normandy University, COBRA UMR 6014 & FR 3038, Université de Rouen, INSA Rouen, CNRS, 1 rue Tesniére 76821 Mont St Aignan, Cedex, France
| | - Stéphane Leleu
- Normandy University, COBRA UMR 6014 & FR 3038, Université de Rouen, INSA Rouen, CNRS, 1 rue Tesniére 76821 Mont St Aignan, Cedex, France
| | - Xavier Franck
- Normandy University, COBRA UMR 6014 & FR 3038, Université de Rouen, INSA Rouen, CNRS, 1 rue Tesniére 76821 Mont St Aignan, Cedex, France
| | - Laurent Joubert
- Normandy University, COBRA UMR 6014 & FR 3038, Université de Rouen, INSA Rouen, CNRS, 1 rue Tesniére 76821 Mont St Aignan, Cedex, France
| |
Collapse
|
49
|
Panfoli I, Calzia D, Santucci L, Ravera S, Bruschi M, Candiano G. A blue dive: from ‘blue fingers’ to ‘blue silver’. A comparative overview of staining methods for in-gel proteomics. Expert Rev Proteomics 2014; 9:627-34. [DOI: 10.1586/epr.12.63] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
|
50
|
Mayne J, Starr AE, Ning Z, Chen R, Chiang CK, Figeys D. Fine Tuning of Proteomic Technologies to Improve Biological Findings: Advancements in 2011–2013. Anal Chem 2013; 86:176-95. [DOI: 10.1021/ac403551f] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Janice Mayne
- Ottawa Institute of
Systems Biology, Department of Biochemistry, Microbiology
and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON, Canada K1H8M5
| | - Amanda E. Starr
- Ottawa Institute of
Systems Biology, Department of Biochemistry, Microbiology
and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON, Canada K1H8M5
| | - Zhibin Ning
- Ottawa Institute of
Systems Biology, Department of Biochemistry, Microbiology
and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON, Canada K1H8M5
| | - Rui Chen
- Ottawa Institute of
Systems Biology, Department of Biochemistry, Microbiology
and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON, Canada K1H8M5
| | - Cheng-Kang Chiang
- Ottawa Institute of
Systems Biology, Department of Biochemistry, Microbiology
and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON, Canada K1H8M5
| | - Daniel Figeys
- Ottawa Institute of
Systems Biology, Department of Biochemistry, Microbiology
and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON, Canada K1H8M5
| |
Collapse
|