1
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Ujcikova H, Lee YS, Roubalova L, Svoboda P. The impact of multifunctional enkephalin analogs and morphine on the protein changes in crude membrane fractions isolated from the rat brain cortex and hippocampus. Peptides 2024; 174:171165. [PMID: 38307418 DOI: 10.1016/j.peptides.2024.171165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/12/2024] [Accepted: 01/29/2024] [Indexed: 02/04/2024]
Abstract
Endogenous opioid peptides serve as potent analgesics through the opioid receptor (OR) activation. However, they often suffer from poor metabolic stability, low lipophilicity, and low blood-brain barrier permeability. Researchers have developed many strategies to overcome the drawbacks of current pain medications and unwanted biological effects produced by the interaction with opioid receptors. Here, we tested multifunctional enkephalin analogs LYS739 (MOR/DOR agonist and KOR partial antagonist) and LYS744 (MOR/DOR agonist and KOR full antagonist) under in vivo conditions in comparison with MOR agonist, morphine. We applied 2D electrophoretic resolution to investigate differences in proteome profiles of crude membrane (CM) fractions isolated from the rat brain cortex and hippocampus exposed to the drugs (10 mg/kg, seven days). Our results have shown that treatment with analog LYS739 induced the most protein changes in cortical and hippocampal samples. The identified proteins were mainly associated with energy metabolism, cell shape and movement, apoptosis, protein folding, regulation of redox homeostasis, and signal transduction. Among these, the isoform of mitochondrial ATP synthase subunit beta (ATP5F1B) was the only protein upregulation in the hippocampus but not in the brain cortex. Contrarily, the administration of analog LYS744 caused a small number of protein alterations in both brain parts. Our results indicate that the KOR full antagonism, together with MOR/DOR agonism of multifunctional opioid ligands, can be beneficial in treating chronic pain states by reducing changes in protein expression levels but retaining analgesic efficacy.
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Affiliation(s)
- Hana Ujcikova
- Laboratory of Neurochemistry, Institute of Physiology of the Czech Academy of Sciences, Videnska 1083, Prague 4 14200, Czech Republic.
| | - Yeon Sun Lee
- Department of Pharmacology, University of Arizona, Tucson, AZ 85724, USA
| | - Lenka Roubalova
- Laboratory of Neurochemistry, Institute of Physiology of the Czech Academy of Sciences, Videnska 1083, Prague 4 14200, Czech Republic
| | - Petr Svoboda
- Laboratory of Neurochemistry, Institute of Physiology of the Czech Academy of Sciences, Videnska 1083, Prague 4 14200, Czech Republic
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2
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Alhazmi HA, Albratty M. Analytical Techniques for the Characterization and Quantification of Monoclonal Antibodies. Pharmaceuticals (Basel) 2023; 16:291. [PMID: 37259434 PMCID: PMC9967501 DOI: 10.3390/ph16020291] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/17/2023] [Accepted: 01/18/2023] [Indexed: 08/12/2023] Open
Abstract
Monoclonal antibodies (mAbs) are a fast-growing class of biopharmaceuticals. They are widely used in the identification and detection of cell makers, serum analytes, and pathogenic agents, and are remarkably used for the cure of autoimmune diseases, infectious diseases, or malignancies. The successful application of therapeutic mAbs is based on their ability to precisely interact with their appropriate target sites. The precision of mAbs rely on the isolation techniques delivering pure, consistent, stable, and safe lots that can be used for analytical, diagnostic, or therapeutic applications. During the creation of a biologic, the key quality features of a particular mAb, such as structure, post-translational modifications, and activities at the biomolecular and cellular levels, must be characterized and profiled in great detail. This implies the requirement of powerful state of the art analytical techniques for quality control and characterization of mAbs. Until now, various analytical techniques have been developed to characterize and quantify the mAbs according to the regulatory guidelines. The present review summarizes the major techniques used for the analyses of mAbs which include chromatographic, electrophoretic, spectroscopic, and electrochemical methods in addition to the modifications in these methods for improving the quality of mAbs. This compilation of major analytical techniques will help students and researchers to have an overview of the methodologies employed by the biopharmaceutical industry for structural characterization of mAbs for eventual release of therapeutics in the drug market.
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Affiliation(s)
- Hassan A. Alhazmi
- Department of Pharmaceutical Chemistry and Pharmacognosy, College of Pharmacy, Jazan University, Jazan 45142, Saudi Arabia
- Substance Abuse and Toxicology Research Centre, Jazan University, Jazan 45142, Saudi Arabia
| | - Mohammed Albratty
- Department of Pharmaceutical Chemistry and Pharmacognosy, College of Pharmacy, Jazan University, Jazan 45142, Saudi Arabia
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3
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Berka M, Kopecká R, Berková V, Brzobohatý B, Černý M. Regulation of heat shock proteins 70 and their role in plant immunity. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:1894-1909. [PMID: 35022724 PMCID: PMC8982422 DOI: 10.1093/jxb/erab549] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 12/10/2021] [Indexed: 05/03/2023]
Abstract
Heat shock proteins 70 (HSP70s) are steadily gaining more attention in the field of plant biotic interactions. Though their regulation and activity in plants are much less well characterized than are those of their counterparts in mammals, accumulating evidence indicates that the role of HSP70-mediated defense mechanisms in plant cells is indispensable. In this review, we summarize current knowledge of HSP70 post-translational control in plants. We comment on the phytohormonal regulation of HSP70 expression and protein abundance, and identify a prominent role for cytokinin in HSP70 control. We outline HSP70s' subcellular localizations, chaperone activity, and chaperone-mediated protein degradation. We focus on the role of HSP70s in plant pathogen-associated molecular pattern-triggered immunity and effector-triggered immunity, and discuss the contribution of different HSP70 subfamilies to plant defense against pathogens.
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Affiliation(s)
- Miroslav Berka
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, CZ-61300 Brno, Czech Republic
| | - Romana Kopecká
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, CZ-61300 Brno, Czech Republic
| | - Veronika Berková
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, CZ-61300 Brno, Czech Republic
| | - Břetislav Brzobohatý
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, CZ-61300 Brno, Czech Republic
| | - Martin Černý
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, CZ-61300 Brno, Czech Republic
- Correspondence:
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4
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Miao H, Chen S, Ding R. Evaluation of the Molecular Mechanisms of Sepsis Using Proteomics. Front Immunol 2021; 12:733537. [PMID: 34745104 PMCID: PMC8566982 DOI: 10.3389/fimmu.2021.733537] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 10/08/2021] [Indexed: 12/12/2022] Open
Abstract
Sepsis is a complex syndrome promoted by pathogenic and host factors; it is characterized by dysregulated host responses and multiple organ dysfunction, which can lead to death. However, its underlying molecular mechanisms remain unknown. Proteomics, as a biotechnology research area in the post-genomic era, paves the way for large-scale protein characterization. With the rapid development of proteomics technology, various approaches can be used to monitor proteome changes and identify differentially expressed proteins in sepsis, which may help to understand the pathophysiological process of sepsis. Although previous reports have summarized proteomics-related data on the diagnosis of sepsis and sepsis-related biomarkers, the present review aims to comprehensively summarize the available literature concerning “sepsis”, “proteomics”, “cecal ligation and puncture”, “lipopolysaccharide”, and “post-translational modifications” in relation to proteomics research to provide novel insights into the molecular mechanisms of sepsis.
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Affiliation(s)
- He Miao
- Department of Intensive Care Unit, The First Hospital of China Medical University, Shenyang, China
| | - Song Chen
- Department of Trauma Intensive Care Unit, The First Affiliated Hospital of Hainan Medical University, Haikou, China.,Key Laboratory of Emergency and Trauma of Ministry of Education, Hainan Medical University, Haikou, China
| | - Renyu Ding
- Department of Intensive Care Unit, The First Hospital of China Medical University, Shenyang, China
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5
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Righetti PG, Boschetti E. Low-abundance plant protein enrichment with peptide libraries to enlarge proteome coverage and related applications. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 290:110302. [PMID: 31779915 DOI: 10.1016/j.plantsci.2019.110302] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 09/15/2019] [Accepted: 10/05/2019] [Indexed: 06/10/2023]
Abstract
In plant tissues proteins are present in low amounts but in a very large number. To this peculiar situation many complex foreign components render protein extraction and purification very difficult. In the last several years interesting technologies have been described to improve the technical situation to the point that some methodologies allow reaching very low-abundance proteins and minor allergens. Among enrichment methods the one documented in this report is based on combinatorial peptide ligand libraries (CPLLs) that emerged in the last decade by contributing to largely improve the knowledge in plant proteomics. It is the aim of this review to describe how this technology allows detecting low-abundance proteins from various plant tissues and to report the dynamics of the proteome components in response to environmental changes and biotic attacks. Typical documented examples with the description of their scientific interest are reported. The described technical approach and selected applications are considered as one of the most advanced approaches for plant proteomics investigations with possibilities not only to enlarge the knowledge of plant proteomes but also to discover novel allergens as well as plant biomarkers subsequent to stressful situations.
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Affiliation(s)
- Pier Giorgio Righetti
- Department of Chemistry Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, 20131, Milan, Italy.
| | - Egisto Boschetti
- Scientific Consultant, JAM Conseil, 92200, Neuilly-sur-Seine, France
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6
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Klein R, Kretzschmar A, Unden G. Control of the bifunctional O
2
‐sensor kinase NreB of
Staphylococcus carnosus
by the nitrate sensor NreA: Switching from kinase to phosphatase state. Mol Microbiol 2019; 113:369-380. [DOI: 10.1111/mmi.14425] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 11/05/2019] [Accepted: 11/12/2019] [Indexed: 12/13/2022]
Affiliation(s)
- Robin Klein
- Microbiology and Wine Research, Institute for Molecular Physiology Johannes Gutenberg‐University Mainz Germany
| | - Ann‐Katrin Kretzschmar
- Microbiology and Wine Research, Institute for Molecular Physiology Johannes Gutenberg‐University Mainz Germany
| | - Gottfried Unden
- Microbiology and Wine Research, Institute for Molecular Physiology Johannes Gutenberg‐University Mainz Germany
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7
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Rhode H, Muckova P, Büchler R, Wendler S, Tautkus B, Vogel M, Moore T, Grosskreutz J, Klemm A, Nabity M. A next generation setup for pre-fractionation of non-denatured proteins reveals diverse albumin proteoforms each carrying several post-translational modifications. Sci Rep 2019; 9:11733. [PMID: 31409882 PMCID: PMC6692309 DOI: 10.1038/s41598-019-48278-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 07/29/2019] [Indexed: 02/07/2023] Open
Abstract
Proteomic biomarker search requires the greatest analytical reproducibility and detailed information on altered proteoforms. Our protein pre-fractionation applies orthogonal native chromatography and conserves important features of protein variants such as native molecular weight, charge and major glycans. Moreover, we maximized reproducibility of sample pre-fractionation and preparation before mass spectrometry by parallelization and automation. In blood plasma and cerebrospinal fluid (CSF), most proteins, including candidate biomarkers, distribute into a multitude of chromatographic clusters. Plasma albumin, for example, divides into 15-17 clusters. As an example of our technique, we analyzed these albumin clusters from healthy volunteers and from dogs and identified cluster-typical modification patterns. Renal disease further modifies these patterns. In human CSF, we found only a subset of proteoforms with fewer modifications than in plasma. We infer from this example that our method can be used to identify and characterize distinct proteoforms and, optionally, enrich them, thereby yielding the characteristics of proteoform-selective biomarkers.
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Affiliation(s)
- Heidrun Rhode
- Institute of Biochemistry I, Nonnenplan 2-4, University Hospital Jena, 07740, Jena, Germany.
| | - Petra Muckova
- Institute of Biochemistry I, Nonnenplan 2-4, University Hospital Jena, 07740, Jena, Germany
| | - Rita Büchler
- Institute of Biochemistry I, Nonnenplan 2-4, University Hospital Jena, 07740, Jena, Germany.,Pharmachem Straße 1, Pharmachem Pößneck GmbH & Co. KG, 07381, Pößneck, Germany
| | - Sindy Wendler
- Institute of Biochemistry I, Nonnenplan 2-4, University Hospital Jena, 07740, Jena, Germany.,Institute of Microbiology, Am Klinikum 1, University Hospital Jena, 07747, Jena, Germany
| | - Bärbel Tautkus
- Institute of Biochemistry I, Nonnenplan 2-4, University Hospital Jena, 07740, Jena, Germany
| | - Michaela Vogel
- Institute of Biochemistry I, Nonnenplan 2-4, University Hospital Jena, 07740, Jena, Germany
| | - Thomas Moore
- Analytik Jena, Konrad-Zuse-Str.1, 07745, Jena, Germany
| | - Julian Grosskreutz
- Department of Neurology, Am Klinikum 1, University Hospital Jena, 07747, Jena, Germany
| | - Andree Klemm
- KfH Kuratorium für Dialyse und Nierentransplantation e.V., Ernst-Ruska-Ring 19, 07745, Jena, Germany
| | - Mary Nabity
- Department of Veterinary Pathobiology, College of Veterinary Medicine, 4467 TAMU, Texas A&M University, College Station, TX, 77843-4467, Texas, USA
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8
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Černý M, Habánová H, Berka M, Luklová M, Brzobohatý B. Hydrogen Peroxide: Its Role in Plant Biology and Crosstalk with Signalling Networks. Int J Mol Sci 2018; 19:E2812. [PMID: 30231521 PMCID: PMC6163176 DOI: 10.3390/ijms19092812] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 09/13/2018] [Accepted: 09/15/2018] [Indexed: 12/30/2022] Open
Abstract
Hydrogen peroxide (H₂O₂) is steadily gaining more attention in the field of molecular biology research. It is a major REDOX (reduction⁻oxidation reaction) metabolite and at high concentrations induces oxidative damage to biomolecules, which can culminate in cell death. However, at concentrations in the low nanomolar range, H₂O₂ acts as a signalling molecule and in many aspects, resembles phytohormones. Though its signalling network in plants is much less well characterized than are those of its counterparts in yeast or mammals, accumulating evidence indicates that the role of H₂O₂-mediated signalling in plant cells is possibly even more indispensable. In this review, we summarize hydrogen peroxide metabolism in plants, the sources and sinks of this compound and its transport via peroxiporins. We outline H₂O₂ perception, its direct and indirect effects and known targets in the transcriptional machinery. We focus on the role of H₂O₂ in plant growth and development and discuss the crosstalk between it and phytohormones. In addition to a literature review, we performed a meta-analysis of available transcriptomics data which provided further evidence for crosstalk between H₂O₂ and light, nutrient signalling, temperature stress, drought stress and hormonal pathways.
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Affiliation(s)
- Martin Černý
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences Mendel University in Brno, 613 00 Brno, Czech Republic.
- Phytophthora Research Centre, Faculty of AgriSciences, Mendel University in Brno, 613 00 Brno, Czech Republic.
| | - Hana Habánová
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences Mendel University in Brno, 613 00 Brno, Czech Republic.
- CEITEC-Central European Institute of Technology, Faculty of AgriSciences Mendel University in Brno, 613 00 Brno, Czech Republic.
- Brno Ph.D. Talent, South Moravian Centre for International Mobility, 602 00 Brno, Czech Republic.
| | - Miroslav Berka
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences Mendel University in Brno, 613 00 Brno, Czech Republic.
| | - Markéta Luklová
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences Mendel University in Brno, 613 00 Brno, Czech Republic.
- CEITEC-Central European Institute of Technology, Faculty of AgriSciences Mendel University in Brno, 613 00 Brno, Czech Republic.
| | - Břetislav Brzobohatý
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences Mendel University in Brno, 613 00 Brno, Czech Republic.
- CEITEC-Central European Institute of Technology, Faculty of AgriSciences Mendel University in Brno, 613 00 Brno, Czech Republic.
- Institute of Biophysics AS CR, 613 00 Brno, Czech Republic.
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9
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Pavlů J, Novák J, Koukalová V, Luklová M, Brzobohatý B, Černý M. Cytokinin at the Crossroads of Abiotic Stress Signalling Pathways. Int J Mol Sci 2018; 19:ijms19082450. [PMID: 30126242 PMCID: PMC6121657 DOI: 10.3390/ijms19082450] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 08/14/2018] [Accepted: 08/17/2018] [Indexed: 01/13/2023] Open
Abstract
Cytokinin is a multifaceted plant hormone that plays major roles not only in diverse plant growth and development processes, but also stress responses. We summarize knowledge of the roles of its metabolism, transport, and signalling in responses to changes in levels of both macronutrients (nitrogen, phosphorus, potassium, sulphur) and micronutrients (boron, iron, silicon, selenium). We comment on cytokinin's effects on plants' xenobiotic resistance, and its interactions with light, temperature, drought, and salinity signals. Further, we have compiled a list of abiotic stress-related genes and demonstrate that their expression patterns overlap with those of cytokinin metabolism and signalling genes.
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Affiliation(s)
- Jaroslav Pavlů
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, 613 00 Brno, Czech Republic.
- CEITEC-Central European Institute of Technology, Faculty of AgriSciences, Mendel University in Brno, 613 00 Brno, Czech Republic.
| | - Jan Novák
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, 613 00 Brno, Czech Republic.
| | - Vladěna Koukalová
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, 613 00 Brno, Czech Republic.
| | - Markéta Luklová
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, 613 00 Brno, Czech Republic.
- CEITEC-Central European Institute of Technology, Faculty of AgriSciences, Mendel University in Brno, 613 00 Brno, Czech Republic.
| | - Břetislav Brzobohatý
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, 613 00 Brno, Czech Republic.
- CEITEC-Central European Institute of Technology, Faculty of AgriSciences, Mendel University in Brno, 613 00 Brno, Czech Republic.
- Institute of Biophysics AS CR, 612 00 Brno, Czech Republic.
| | - Martin Černý
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, 613 00 Brno, Czech Republic.
- Phytophthora Research Centre, Faculty of AgriSciences, Mendel University in Brno, 613 00 Brno, Czech Republic.
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10
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2013-2014. MASS SPECTROMETRY REVIEWS 2018; 37:353-491. [PMID: 29687922 DOI: 10.1002/mas.21530] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 11/29/2016] [Indexed: 06/08/2023]
Abstract
This review is the eighth update of the original article published in 1999 on the application of Matrix-assisted laser desorption/ionization mass spectrometry (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2014. Topics covered in the first part of the review include general aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, fragmentation, and arrays. The second part of the review is devoted to applications to various structural types such as oligo- and poly- saccharides, glycoproteins, glycolipids, glycosides, and biopharmaceuticals. Much of this material is presented in tabular form. The third part of the review covers medical and industrial applications of the technique, studies of enzyme reactions, and applications to chemical synthesis. © 2018 Wiley Periodicals, Inc. Mass Spec Rev 37:353-491, 2018.
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Affiliation(s)
- David J Harvey
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom
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11
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Tan BC, Lim YS, Lau SE. Proteomics in commercial crops: An overview. J Proteomics 2017; 169:176-188. [PMID: 28546092 DOI: 10.1016/j.jprot.2017.05.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Revised: 04/21/2017] [Accepted: 05/19/2017] [Indexed: 02/06/2023]
Abstract
Proteomics is a rapidly growing area of biological research that is positively affecting plant science. Recent advances in proteomic technology, such as mass spectrometry, can now identify a broad range of proteins and monitor their modulation during plant growth and development, as well as during responses to abiotic and biotic stresses. In this review, we highlight recent proteomic studies of commercial crops and discuss the advances in understanding of the proteomes of these crops. We anticipate that proteomic-based research will continue to expand and contribute to crop improvement. SIGNIFICANCE Plant proteomics study is a rapidly growing area of biological research that is positively impacting plant science. With the recent advances in new technologies, proteomics not only allows us to comprehensively analyses crop proteins, but also help us to understand the functions of the genes. In this review, we highlighted recent proteomic studies in commercial crops and updated the advances in our understanding of the proteomes of these crops. We believe that proteomic-based research will continue to grow and contribute to the improvement of crops.
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Affiliation(s)
- Boon Chin Tan
- Centre for Research in Biotechnology for Agriculture, University of Malaya, Lembah Pantai, 50603 Kuala Lumpur, Malaysia.
| | - Yin Sze Lim
- School of Biosciences, Faculty of Science, University of Nottingham Malaysia Campus, Jalan Broga, 43500 Semenyih, Selangor, Malaysia
| | - Su-Ee Lau
- Centre for Research in Biotechnology for Agriculture, University of Malaya, Lembah Pantai, 50603 Kuala Lumpur, Malaysia
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12
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Liu Y, Perez L, Mettry M, Gill AD, Byers SR, Easley CJ, Bardeen CJ, Zhong W, Hooley RJ. Site selective reading of epigenetic markers by a dual-mode synthetic receptor array. Chem Sci 2017; 8:3960-3970. [PMID: 28553538 PMCID: PMC5433514 DOI: 10.1039/c7sc00865a] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 03/21/2017] [Indexed: 12/13/2022] Open
Abstract
Variably functionalized self-folding deep cavitands form an arrayed, fluorescent indicator displacement assay system for the detection of post-translationally modified (PTM) histone peptides. The hosts bind trimethyllysine (KMe3) groups, and use secondary upper rim interactions to provide more sensitive discrimination between targets with identical KMe3 binding handles. The sensor array uses multiple different recognition modes to distinguish between miniscule differences in target, such as identical lysine modifications at different sites of histone peptides. In addition, the sensor is affected by global changes in structure, so it is capable of discriminating between identical PTMs, at identical positions on amino acid fragments that vary only in peptide backbone length, and can be applied to detect non-methylation modifications such as acetylation and phosphorylations located multiple residues away from the targeted binding site. The synergistic application of multiple variables allows dual-mode deep cavitands to approach levels of recognition selectivity usually only seen with antibodies.
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Affiliation(s)
- Yang Liu
- Environmental Toxicology Program , University of California - Riverside , Riverside , CA 92521 , USA
| | - Lizeth Perez
- Department of Chemistry , University of California - Riverside , Riverside , CA 92521 , USA . ;
| | - Magi Mettry
- Department of Chemistry , University of California - Riverside , Riverside , CA 92521 , USA . ;
| | - Adam D Gill
- Department of Biochemistry and Molecular Biology , University of California - Riverside , Riverside , CA 92521 , USA
| | - Samantha R Byers
- Department of Chemistry , University of California - Riverside , Riverside , CA 92521 , USA . ;
| | - Connor J Easley
- Department of Chemistry , University of California - Riverside , Riverside , CA 92521 , USA . ;
| | - Christopher J Bardeen
- Department of Chemistry , University of California - Riverside , Riverside , CA 92521 , USA . ;
| | - Wenwan Zhong
- Department of Chemistry , University of California - Riverside , Riverside , CA 92521 , USA . ;
- Environmental Toxicology Program , University of California - Riverside , Riverside , CA 92521 , USA
| | - Richard J Hooley
- Department of Chemistry , University of California - Riverside , Riverside , CA 92521 , USA . ;
- Department of Biochemistry and Molecular Biology , University of California - Riverside , Riverside , CA 92521 , USA
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13
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Qing G, Lu Q, Xiong Y, Zhang L, Wang H, Li X, Liang X, Sun T. New Opportunities and Challenges of Smart Polymers in Post-Translational Modification Proteomics. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2017; 29:1604670. [PMID: 28112833 DOI: 10.1002/adma.201604670] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 11/13/2016] [Indexed: 06/06/2023]
Abstract
Protein post-translational modifications (PTMs), which denote covalent additions of various functional groups (e.g., phosphate, glycan, methyl, or ubiquitin) to proteins, significantly increase protein complexity and diversity. PTMs play crucial roles in the regulation of protein functions and numerous cellular processes. However, in a living organism, native PTM proteins are typically present at substoichiometric levels, considerably impeding mass-spectrometry-based analyses and identification. Over the past decade, the demand for in-depth PTM proteomics studies has spawned a variety of selective affinity materials capable of capturing trace amounts of PTM peptides from highly complex biosamples. However, novel design ideas or strategies are urgently required for fulfilling the increasingly complex and accurate requirements of PTM proteomics analysis, which can hardly be met by using conventional enrichment materials. Considering two typical types of protein PTMs, phosphorylation and glycosylation, an overview of polymeric enrichment materials is provided here, with an emphasis on the superiority of smart-polymer-based materials that can function in intelligent modes. Moreover, some smart separation materials are introduced to demonstrate the enticing prospects and the challenges of smart polymers applied in PTM proteomics.
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Affiliation(s)
- Guangyan Qing
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, 122 Luoshi Road, Wuhan, 430070, P. R. China
| | - Qi Lu
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, 122 Luoshi Road, Wuhan, 430070, P. R. China
| | - Yuting Xiong
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, 122 Luoshi Road, Wuhan, 430070, P. R. China
| | - Lei Zhang
- Institute of Biomedical and Pharmaceutical Sciences, College of Bioengineering, Hubei University of Technology, 28 Nanli Road, Wuhan, 430068, P. R. China
| | - Hongxi Wang
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, 122 Luoshi Road, Wuhan, 430070, P. R. China
| | - Xiuling Li
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, P. R. China
| | - Xinmiao Liang
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, P. R. China
| | - Taolei Sun
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, 122 Luoshi Road, Wuhan, 430070, P. R. China
- International School of Materials Science and Engineering, Wuhan University of Technology, 122 Luoshi Road, Wuhan, 430070, P. R. China
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14
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Morbioli GG, Mazzu-Nascimento T, Aquino A, Cervantes C, Carrilho E. Recombinant drugs-on-a-chip: The usage of capillary electrophoresis and trends in miniaturized systems – A review. Anal Chim Acta 2016; 935:44-57. [DOI: 10.1016/j.aca.2016.06.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 06/07/2016] [Accepted: 06/10/2016] [Indexed: 01/09/2023]
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15
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Wessels HJCT, de Almeida NM, Kartal B, Keltjens JT. Bacterial Electron Transfer Chains Primed by Proteomics. Adv Microb Physiol 2016; 68:219-352. [PMID: 27134025 DOI: 10.1016/bs.ampbs.2016.02.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Electron transport phosphorylation is the central mechanism for most prokaryotic species to harvest energy released in the respiration of their substrates as ATP. Microorganisms have evolved incredible variations on this principle, most of these we perhaps do not know, considering that only a fraction of the microbial richness is known. Besides these variations, microbial species may show substantial versatility in using respiratory systems. In connection herewith, regulatory mechanisms control the expression of these respiratory enzyme systems and their assembly at the translational and posttranslational levels, to optimally accommodate changes in the supply of their energy substrates. Here, we present an overview of methods and techniques from the field of proteomics to explore bacterial electron transfer chains and their regulation at levels ranging from the whole organism down to the Ångstrom scales of protein structures. From the survey of the literature on this subject, it is concluded that proteomics, indeed, has substantially contributed to our comprehending of bacterial respiratory mechanisms, often in elegant combinations with genetic and biochemical approaches. However, we also note that advanced proteomics offers a wealth of opportunities, which have not been exploited at all, or at best underexploited in hypothesis-driving and hypothesis-driven research on bacterial bioenergetics. Examples obtained from the related area of mitochondrial oxidative phosphorylation research, where the application of advanced proteomics is more common, may illustrate these opportunities.
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Affiliation(s)
- H J C T Wessels
- Nijmegen Center for Mitochondrial Disorders, Radboud Proteomics Centre, Translational Metabolic Laboratory, Radboud University Medical Center, Nijmegen, The Netherlands
| | - N M de Almeida
- Institute of Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - B Kartal
- Institute of Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands; Laboratory of Microbiology, Ghent University, Ghent, Belgium
| | - J T Keltjens
- Institute of Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands.
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16
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Bochi GV, Torbitz VD, de Campos LP, Sangoi MB, Fernandes NF, Gomes P, Moretto MB, Barbisan F, da Cruz IBM, Moresco RN. In Vitro Oxidation of Collagen Promotes the Formation of Advanced Oxidation Protein Products and the Activation of Human Neutrophils. Inflammation 2016; 39:916-27. [DOI: 10.1007/s10753-016-0325-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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17
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Johnová P, Skalák J, Saiz-Fernández I, Brzobohatý B. Plant responses to ambient temperature fluctuations and water-limiting conditions: A proteome-wide perspective. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:916-31. [PMID: 26861773 DOI: 10.1016/j.bbapap.2016.02.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Revised: 12/26/2015] [Accepted: 02/04/2016] [Indexed: 12/24/2022]
Abstract
BACKGROUND Every year, environmental stresses such as limited water and nutrient availability, salinity, and temperature fluctuations inflict significant losses on crop yields across the globe. Recently, developments in analytical techniques, e.g. mass spectrometry, have led to great advances towards understanding how plants respond to environmental stresses. These processes are mediated by many molecular pathways and, at least partially, via proteome-environment interactions. SCOPE OF REVIEW This review focuses on the current state of knowledge about interactions between the plant proteome and the environment, with a special focus on drought and temperature responses of plant proteome dynamics, and subcellular and organ-specific compartmentalization, in Arabidopsis thaliana and crop species. MAJOR CONCLUSIONS Correct plant development under non-optimal conditions requires complex self-protection mechanisms, many of them common to different abiotic stresses. Proteome analyses of plant responses to temperature and drought stresses have revealed an intriguing interplay of modifications, mainly affecting the photosynthetic machinery, carbohydrate metabolism, and ROS activation and scavenging. Imbalances between transcript-level and protein-level regulation observed during adaptation to abiotic stresses suggest that many of the regulatory processes are controlled at translational and post-translational levels; proteomics is thus essential in revealing important regulatory networks. GENERAL SIGNIFICANCE Because information from proteomic data extends far beyond what can be deduced from transcriptome analysis, the results of proteome studies have substantially deepened our understanding of stress adaptation in plants; this is clearly a prerequisite for designing strategies to improve the yield and quality of crops grown under unfavorable conditions brought about by ongoing climatic change. This article is part of a Special Issue entitled: Plant Proteomics--a bridge between fundamental processes and crop production, edited by Dr. Hans-Peter Mock.
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Affiliation(s)
- Patricie Johnová
- Laboratory of Plant Molecular Biology, Institute of Biophysics AS CR, v.v.i. and, Mendel University in Brno, CEITEC - Central European Institute of Technology, Mendel University in Brno, Zemědělská 1, CZ-613 00 Brno, Czech Republic.
| | - Jan Skalák
- Laboratory of Plant Molecular Biology, Institute of Biophysics AS CR, v.v.i. and, Mendel University in Brno, CEITEC - Central European Institute of Technology, Mendel University in Brno, Zemědělská 1, CZ-613 00 Brno, Czech Republic.
| | - Iñigo Saiz-Fernández
- Laboratory of Plant Molecular Biology, Institute of Biophysics AS CR, v.v.i. and, Mendel University in Brno, CEITEC - Central European Institute of Technology, Mendel University in Brno, Zemědělská 1, CZ-613 00 Brno, Czech Republic.
| | - Břetislav Brzobohatý
- Laboratory of Plant Molecular Biology, Institute of Biophysics AS CR, v.v.i. and, Mendel University in Brno, CEITEC - Central European Institute of Technology, Mendel University in Brno, Zemědělská 1, CZ-613 00 Brno, Czech Republic.
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18
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Abstract
Proteins are acylated by a variety of metabolites that regulates many important cellular pathways in all kingdoms of life. Acyl groups in cells can vary in structure from the smallest unit, acetate, to modified long-chain fatty acids, all of which can be activated and covalently attached to diverse amino acid side chains and consequently modulate protein function. For example, acetylation of Lys residues can alter the charge state of proteins and generate new recognition elements for protein-protein interactions. Alternatively, long-chain fatty-acylation targets proteins to membranes and enables spatial control of cell signalling. To facilitate the analysis of protein acylation in biology, acyl analogues bearing alkyne or azide tags have been developed that enable fluorescent imaging and proteomic profiling of modified proteins using bioorthogonal ligation methods. Herein, we summarize the currently available acylation chemical reporters and highlight their utility to discover and quantify the roles of protein acylation in biology.
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19
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Černý M, Novák J, Habánová H, Cerna H, Brzobohatý B. Role of the proteome in phytohormonal signaling. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1864:1003-15. [PMID: 26721743 DOI: 10.1016/j.bbapap.2015.12.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 11/30/2015] [Accepted: 12/16/2015] [Indexed: 02/07/2023]
Abstract
Phytohormones are orchestrators of plant growth and development. A lot of time and effort has been invested in attempting to comprehend their complex signaling pathways but despite success in elucidating some key components, molecular mechanisms in the transduction pathways are far from being resolved. The last decade has seen a boom in the analysis of phytohormone-responsive proteins. Abscisic acid, auxin, brassinosteroids, cytokinin, ethylene, gibberellins, nitric oxide, oxylipins, strigolactones, salicylic acid--all have been analyzed to various degrees. For this review, we collected data from proteome-wide analyses resulting in a list of over 2000 annotated proteins from Arabidopsis proteomics and nearly 500 manually filtered protein families merged from all the data available from different species. We present the currently accepted model of phytohormone signaling, highlight the contributions made by proteomic-based research and describe the key nodes in phytohormone signaling networks, as revealed by proteome analysis. These include ubiquitination and proteasome mediated degradation, calcium ion signaling, redox homeostasis, and phosphoproteome dynamics. Finally, we discuss potential pitfalls and future perspectives in the field. This article is part of a Special Issue entitled: Plant Proteomics--a bridge between fundamental processes and crop production, edited by Dr. Hans-Peter Mock.
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Affiliation(s)
- Martin Černý
- Laboratory of Plant Molecular Biology, Institute of Biophysics AS CR, v.v.i. and CEITEC - Central European Institute of Technology, Mendel University in Brno, Zemědělská 1, CZ-613 00 Brno, Czech Republic.
| | - Jan Novák
- Laboratory of Plant Molecular Biology, Institute of Biophysics AS CR, v.v.i. and CEITEC - Central European Institute of Technology, Mendel University in Brno, Zemědělská 1, CZ-613 00 Brno, Czech Republic.
| | - Hana Habánová
- Laboratory of Plant Molecular Biology, Institute of Biophysics AS CR, v.v.i. and CEITEC - Central European Institute of Technology, Mendel University in Brno, Zemědělská 1, CZ-613 00 Brno, Czech Republic.
| | - Hana Cerna
- Laboratory of Plant Molecular Biology, Institute of Biophysics AS CR, v.v.i. and CEITEC - Central European Institute of Technology, Mendel University in Brno, Zemědělská 1, CZ-613 00 Brno, Czech Republic.
| | - Břetislav Brzobohatý
- Laboratory of Plant Molecular Biology, Institute of Biophysics AS CR, v.v.i. and CEITEC - Central European Institute of Technology, Mendel University in Brno, Zemědělská 1, CZ-613 00 Brno, Czech Republic.
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20
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Berry IJ, Steele JR, Padula MP, Djordjevic SP. The application of terminomics for the identification of protein start sites and proteoforms in bacteria. Proteomics 2015; 16:257-72. [DOI: 10.1002/pmic.201500319] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 09/21/2015] [Accepted: 09/30/2015] [Indexed: 01/11/2023]
Affiliation(s)
- Iain J. Berry
- The ithree Institute; University of Technology Sydney; Broadway NSW Australia
- Proteomics Core Facility; University of Technology Sydney; Broadway NSW Australia
| | - Joel R. Steele
- Proteomics Core Facility; University of Technology Sydney; Broadway NSW Australia
| | - Matthew P. Padula
- The ithree Institute; University of Technology Sydney; Broadway NSW Australia
- Proteomics Core Facility; University of Technology Sydney; Broadway NSW Australia
| | - Steven P. Djordjevic
- The ithree Institute; University of Technology Sydney; Broadway NSW Australia
- Proteomics Core Facility; University of Technology Sydney; Broadway NSW Australia
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21
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Chicooree N, Unwin RD, Griffiths JR. The application of targeted mass spectrometry-based strategies to the detection and localization of post-translational modifications. MASS SPECTROMETRY REVIEWS 2015; 34:595-626. [PMID: 24737647 DOI: 10.1002/mas.21421] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2013] [Accepted: 12/10/2013] [Indexed: 06/03/2023]
Abstract
This review describes some of the more interesting and imaginative ways in which mass spectrometry has been utilized to study a number of important post-translational modifications over the past two decades; from circa 1990 to 2013. A diverse range of modifications is covered, including citrullination, sulfation, hydroxylation and sumoylation. A summary of the biological role of each modification described, along with some brief mechanistic detail, is also included. Emphasis has been placed on strategies specifically aimed at detecting target modifications, as opposed to more serendipitous modification discovery approaches, which rely upon straightforward product ion scanning methods. The authors have intentionally excluded from this review both phosphorylation and glycosylation since these major modifications have been extensively reviewed elsewhere.
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Affiliation(s)
- Navin Chicooree
- CRUK Manchester Institute, University of Manchester, Wilmslow Road, Manchester, M20 4BX, UK
- School of Chemistry, University of Manchester, Brunswick Street, Manchester, M13 9SU, UK
| | - Richard D Unwin
- Centre for Advanced Discovery and Experimental Therapeutics (CADET), Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester, M13 9WL, UK
- Institute of Human Development, Faculty of Medical and Human Sciences, University of Manchester, Manchester, UK
| | - John R Griffiths
- CRUK Manchester Institute, University of Manchester, Wilmslow Road, Manchester, M20 4BX, UK
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22
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Lorenzatto KR, Kim K, Ntai I, Paludo GP, Camargo de Lima J, Thomas PM, Kelleher NL, Ferreira HB. Top Down Proteomics Reveals Mature Proteoforms Expressed in Subcellular Fractions of the Echinococcus granulosus Preadult Stage. J Proteome Res 2015; 14:4805-14. [PMID: 26465659 DOI: 10.1021/acs.jproteome.5b00642] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Echinococcus granulosus is the causative agent of cystic hydatid disease, a neglected zoonosis responsible for high morbidity and mortality. Several molecular mechanisms underlying parasite biology remain poorly understood. Here, E. granulosus subcellular fractions were analyzed by top down and bottom up proteomics for protein identification and characterization of co-translational and post-translational modifications (CTMs and PTMs, respectively). Nuclear and cytosolic extracts of E. granulosus protoscoleces were fractionated by 10% GELFrEE and proteins under 30 kDa were analyzed by LC-MS/MS. By top down analysis, 186 proteins and 207 proteoforms were identified, of which 122 and 52 proteoforms were exclusively detected in nuclear and cytosolic fractions, respectively. CTMs were evident as 71% of the proteoforms had methionine excised and 47% were N-terminal acetylated. In addition, in silico internal acetylation prediction coupled with top down MS allowed the characterization of 9 proteins differentially acetylated, including histones. Bottom up analysis increased the overall number of identified proteins in nuclear and cytosolic fractions to 154 and 112, respectively. Overall, our results provided the first description of the low mass proteome of E. granulosus subcellular fractions and highlighted proteoforms with CTMs and PTMS whose characterization may lead to another level of understanding about molecular mechanisms controlling parasitic flatworm biology.
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Affiliation(s)
- Karina R Lorenzatto
- Laboratório de Genômica Estrutural e Funcional, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul , Avenida Bento Gonçalves, 9500 Porto Alegre, Rio Grande do Sul, Brazil
| | - Kyunggon Kim
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University , 2145 North Sheridan Road, Evanston, Illinois 60208, United States
| | - Ioanna Ntai
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University , 2145 North Sheridan Road, Evanston, Illinois 60208, United States
| | - Gabriela P Paludo
- Laboratório de Genômica Estrutural e Funcional, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul , Avenida Bento Gonçalves, 9500 Porto Alegre, Rio Grande do Sul, Brazil
| | - Jeferson Camargo de Lima
- Laboratório de Genômica Estrutural e Funcional, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul , Avenida Bento Gonçalves, 9500 Porto Alegre, Rio Grande do Sul, Brazil
| | - Paul M Thomas
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University , 2145 North Sheridan Road, Evanston, Illinois 60208, United States
| | - Neil L Kelleher
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University , 2145 North Sheridan Road, Evanston, Illinois 60208, United States
| | - Henrique B Ferreira
- Laboratório de Genômica Estrutural e Funcional, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul , Avenida Bento Gonçalves, 9500 Porto Alegre, Rio Grande do Sul, Brazil
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23
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Olszowy P, Donnelly MR, Lee C, Ciborowski P. Profiling post-translational modifications of histones in human monocyte-derived macrophages. Proteome Sci 2015; 13:24. [PMID: 26412985 PMCID: PMC4582717 DOI: 10.1186/s12953-015-0080-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 09/17/2015] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Histones and their post-translational modifications impact cellular function by acting as key regulators in the maintenance and remodeling of chromatin, thus affecting transcription regulation either positively (activation) or negatively (repression). In this study we describe a comprehensive, bottom-up proteomics approach to profiling post-translational modifications (acetylation, mono-, di- and tri-methylation, phosphorylation, biotinylation, ubiquitination, citrullination and ADP-ribosylation) in human macrophages, which are primary cells of the innate immune system. As our knowledge expands, it becomes more evident that macrophages are a heterogeneous population with potentially subtle differences in their responses to various stimuli driven by highly complex epigenetic regulatory mechanisms. METHODS To profile post-translational modifications (PTMs) of histones in macrophages we used two platforms of liquid chromatography and mass spectrometry. One platform was based on Sciex5600 TripleTof and the second one was based on VelosPro Orbitrap Elite ETD mass spectrometers. RESULTS We provide side-by-side comparison of profiling using two mass spectrometric platforms, ion trap and qTOF, coupled with the application of collisional induced and electron transfer dissociation. We show for the first time methylation of a His residue in macrophages and demonstrate differences in histone PTMs between those currently reported for macrophage cell lines and what we identified in primary cells. We have found a relatively low level of histone PTMs in differentiated but resting human primary monocyte derived macrophages. CONCLUSIONS This study is the first comprehensive profiling of histone PTMs in primary human MDM. Our study implies that epigenetic regulatory mechanisms operative in transformed cell lines and primary cells are overlapping to a limited extent. Our mass spectrometric approach provides groundwork for the investigation of how histone PTMs contribute to epigenetic regulation in primary human macrophages.
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Affiliation(s)
- Pawel Olszowy
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198-5880 USA ; Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, Gagarin 7 Street, 87-100 Torun, Poland
| | - Maire Rose Donnelly
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198-5880 USA
| | - Chanho Lee
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198-5880 USA
| | - Pawel Ciborowski
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198-5880 USA
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24
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Schubert M, Walczak MJ, Aebi M, Wider G. Posttranslational Modifications of Intact Proteins Detected by NMR Spectroscopy: Application to Glycosylation. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201502093] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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25
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Szabo Z, Janaky T. Challenges and developments in protein identification using mass spectrometry. Trends Analyt Chem 2015. [DOI: 10.1016/j.trac.2015.03.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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26
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Novák J, Černý M, Pavlů J, Zemánková J, Skalák J, Plačková L, Brzobohatý B. Roles of proteome dynamics and cytokinin signaling in root to hypocotyl ratio changes induced by shading roots of Arabidopsis seedlings. PLANT & CELL PHYSIOLOGY 2015; 56:1006-18. [PMID: 25700275 DOI: 10.1093/pcp/pcv026] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Indexed: 05/20/2023]
Abstract
In nature, root systems of most terrestrial plants are protected from light exposure by growing in a dark soil environment. Hence, in vitro cultivation in transparent Petri dishes leads to physiological perturbations, but the mechanisms underlying root-mediated light perception and responses have not been fully elucidated. Thus, we compared Arabidopsis thaliana seedling development in transparent and darkened Petri dishes at low light intensity (20 µmol m(-2) s(-1)), allowing us to follow (inter alia) hypocotyl elongation, which is an excellent process for studying interactions of signals involved in the regulation of growth and developmental responses. To obtain insights into molecular events underlying differences in seedling growth under these two conditions, we employed liquid chromatography-mass spectrometry (LC-MS) shotgun proteomics (available via the PRIDE deposit PXD001612). In total, we quantified the relative abundances of peptides representing 1,209 proteins detected in all sample replicates of LC-MS analyses. Comparison of MS spectra after manual validation revealed 48 differentially expressed proteins. Functional classification, analysis of available gene expression data and literature searches revealed alterations associated with root illumination (inter alia) in autotrophic CO2 fixation, C compound and carbohydrate metabolism, and nitrogen metabolism. The results also indicate a previously unreported role for cytokinin plant hormones in the escape-tropism response to root illumination. We complemented these results with reverse transcription followed by quantitative PCR (RT-qPCR), chlorophyll fluorescence and detailed cytokinin signaling analyses, detecting in the latter a significant increase in the activity of the cytokinin two-component signaling cascade in roots and implicating the cytokinin receptor AHK3 as the major mediator of root to hypocotyl signaling in responses to root illumination.
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Affiliation(s)
- Jan Novák
- Laboratory of Plant Molecular Biology, Institute of Biophysics AS CR, v.v.i. and CEITEC-Central European Institute of Technology, Mendel University in Brno, Zemědělská 1, CZ-613 00 Brno, Czech Republic These authors contributed equally to this work
| | - Martin Černý
- Laboratory of Plant Molecular Biology, Institute of Biophysics AS CR, v.v.i. and CEITEC-Central European Institute of Technology, Mendel University in Brno, Zemědělská 1, CZ-613 00 Brno, Czech Republic These authors contributed equally to this work
| | - Jaroslav Pavlů
- Laboratory of Plant Molecular Biology, Institute of Biophysics AS CR, v.v.i. and CEITEC-Central European Institute of Technology, Mendel University in Brno, Zemědělská 1, CZ-613 00 Brno, Czech Republic
| | - Jana Zemánková
- Laboratory of Plant Molecular Biology, Institute of Biophysics AS CR, v.v.i. and CEITEC-Central European Institute of Technology, Mendel University in Brno, Zemědělská 1, CZ-613 00 Brno, Czech Republic
| | - Jan Skalák
- Laboratory of Plant Molecular Biology, Institute of Biophysics AS CR, v.v.i. and CEITEC-Central European Institute of Technology, Mendel University in Brno, Zemědělská 1, CZ-613 00 Brno, Czech Republic
| | - Lenka Plačková
- Laboratory of Growth Regulators & Department of Chemical Biology and Genetics, Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany AS CR & Faculty of Science of Palacký University, Šlechtitelů 11, CZ-78371 Olomouc, Czech Republic
| | - Břetislav Brzobohatý
- Laboratory of Plant Molecular Biology, Institute of Biophysics AS CR, v.v.i. and CEITEC-Central European Institute of Technology, Mendel University in Brno, Zemědělská 1, CZ-613 00 Brno, Czech Republic
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27
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Schubert M, Walczak MJ, Aebi M, Wider G. Posttranslational modifications of intact proteins detected by NMR spectroscopy: application to glycosylation. Angew Chem Int Ed Engl 2015; 54:7096-100. [PMID: 25924827 DOI: 10.1002/anie.201502093] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Indexed: 02/02/2023]
Abstract
Posttranslational modifications (PTMs) are an integral part of the majority of proteins. The characterization of structure and function of PTMs can be very challenging especially for glycans. Existing methods to analyze PTMs require complicated sample preparations and suffer from missing certain modifications, the inability to identify linkage types and thus chemical structure. We present a direct, robust, and simple NMR spectroscopy method for the detection and identification of PTMs in proteins. No isotope labeling is required, nor does the molecular weight of the studied protein limit the application. The method can directly detect modifications on intact proteins without sophisticated sample preparation. This approach is well suited for diagnostics of proteins derived from native organisms and for the quality control of biotechnologically produced therapeutic proteins.
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Affiliation(s)
- Mario Schubert
- Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich (Switzerland). .,Present address: Department of Molecular Biology, University of Salzburg, Billrothstrasse 11, 5020 Salzburg (Austria).
| | - Michal J Walczak
- Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich (Switzerland).
| | - Markus Aebi
- Institute of Microbiology, ETH Zürich, 8093 Zürich (Switzerland)
| | - Gerhard Wider
- Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich (Switzerland)
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28
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Fiorentino F, Angelini GD, Suleiman MS, Rahman A, Anderson J, Bryan AJ, Culliford LA, Moscarelli M, Punjabi PP, Reeves BC. Investigating the effect of remote ischaemic preconditioning on biomarkers of stress and injury-related signalling in patients having isolated coronary artery bypass grafting or aortic valve replacement using cardiopulmonary bypass: study protocol for a randomized controlled trial. Trials 2015; 16:181. [PMID: 25899533 PMCID: PMC4425928 DOI: 10.1186/s13063-015-0696-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 03/30/2015] [Indexed: 01/14/2023] Open
Abstract
Background Ischaemia-reperfusion injury occurs during heart surgery that uses cardiopulmonary bypass (CPB) and cardioplegic arrest. It is hypothesised that remote ischaemic preconditioning (RIPC) protects the heart against such injury. Despite the numerous studies investigating the protective effects of RIPC, there is still uncertainty about the interpretation of the findings as well as conflicting results between studies. The objective of this trial is to investigate the cardioprotective effect of RIPC in patients having coronary artery bypass grafting (CABG) or aortic valve replacement surgery. This will be achieved by estimating the effect of the intervention in the two groups of pathologies and by investigating the signalling mechanisms that may underpin the cardioprotective effect. Methods/Design A two-centre randomised controlled trial will be used to investigate the effects of RIPC in two pathologies: patients having isolated CABG and those having aortic valve replacement surgery (AVR) with CPB. Participants will be randomised to RIPC or control (sham RIPC), stratified by surgical stratum. The intervention will be delivered by a research nurse. Data will be collected by a research nurse blinded to the intervention. The patient and the theatre staff are also blinded to the allocation. Markers of myocardial injury and inflammation will be measured in myocardial biopsies and in blood samples at different times. Discussion This trial is designed to investigate whether RIPC will reduce myocardial injury and inflammation following heart surgery and whether there is a difference in effect between participants having CABG or AVR. This trial is a unique opportunity to study the mechanisms associated with RIPC using human myocardial tissue and blood, and to relate these to the extent of myocardial injury/protection. Trial registration Current Controlled Trials ISRCTN33084113 (25 March 2013). Electronic supplementary material The online version of this article (doi:10.1186/s13063-015-0696-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Francesca Fiorentino
- National Heart and Lung Institute, Cardiothoracic Surgery Department, Imperial College London, Du Cane Road, W12 0NN, London, UK.
| | - Gianni D Angelini
- National Heart and Lung Institute, Cardiothoracic Surgery Department, Imperial College London, Du Cane Road, W12 0NN, London, UK. .,Bristol Heart Institute, University of Bristol, Bristol Royal Infirmary, Marlborough Street, BS2 8HW, Bristol, UK.
| | - M-Saadeh Suleiman
- Bristol Heart Institute, University of Bristol, Bristol Royal Infirmary, Marlborough Street, BS2 8HW, Bristol, UK.
| | - Alima Rahman
- National Heart and Lung Institute, Cardiothoracic Surgery Department, Imperial College London, Du Cane Road, W12 0NN, London, UK.
| | - Jon Anderson
- National Heart and Lung Institute, Cardiothoracic Surgery Department, Imperial College London, Du Cane Road, W12 0NN, London, UK.
| | - Alan J Bryan
- Bristol Heart Institute, University of Bristol, Bristol Royal Infirmary, Marlborough Street, BS2 8HW, Bristol, UK.
| | - Lucy A Culliford
- Bristol Heart Institute, University of Bristol, Bristol Royal Infirmary, Marlborough Street, BS2 8HW, Bristol, UK.
| | - Marco Moscarelli
- National Heart and Lung Institute, Cardiothoracic Surgery Department, Imperial College London, Du Cane Road, W12 0NN, London, UK.
| | - Prakash P Punjabi
- National Heart and Lung Institute, Cardiothoracic Surgery Department, Imperial College London, Du Cane Road, W12 0NN, London, UK.
| | - Barnaby C Reeves
- Bristol Heart Institute, University of Bristol, Bristol Royal Infirmary, Marlborough Street, BS2 8HW, Bristol, UK.
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Trnková L, Dršata J, Boušová I. Oxidation as an important factor of protein damage: Implications for Maillard reaction. J Biosci 2015; 40:419-39. [DOI: 10.1007/s12038-015-9523-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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Affiliation(s)
- He Huang
- Ben May Department of Cancer Research, The University of Chicago, Chicago, Illinois 60637, United States
| | - Shu Lin
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Benjamin A. Garcia
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Yingming Zhao
- Ben May Department of Cancer Research, The University of Chicago, Chicago, Illinois 60637, United States
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Arabidopsis proteome responses to the smoke-derived growth regulator karrikin. J Proteomics 2015; 120:7-20. [PMID: 25746380 DOI: 10.1016/j.jprot.2015.02.011] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2014] [Revised: 02/19/2015] [Accepted: 02/23/2015] [Indexed: 12/19/2022]
Abstract
UNLABELLED Karrikins are butenolide plant growth regulators in smoke from burning plant material that have proven ability to promote germination and seedling photomorphogenesis. However, the molecular mechanisms underlying these processes are unclear. Here we provide the first proteome-wide analysis of early responses to karrikin in plants (Arabidopsis seedlings). Image analysis of two-dimensionally separated proteins, Rubisco-depleted proteomes and phosphoproteomes, together with LC-MS profiling, detected >1900 proteins, 113 of which responded to karrikin treatment. All the differentially abundant proteins (except HSP70-3) are novel karrikin-responders, and most are involved in photosynthesis, carbohydrate metabolism, redox homeostasis, transcription control, proteosynthesis, protein transport and processing, or protein degradation. Our data provide functionally complementary information to previous identifications of karrikin-responsive genes and evidence for a novel karrikin signalling pathway originating in chloroplasts. We present an updated model of karrikin signalling that integrates proteomic data and is supported by growth response observations. BIOLOGICAL SIGNIFICANCE Karrikin has shown promising potential in agricultural applications, yet this process is poorly understood at the molecular level. To the best of our knowledge, this is the first survey of early global proteomic responses to karrikin in plants (Arabidopsis seedlings). The combination of label-free LC-MS profiling and 2-DE analyses provided highly sensitive snapshots of protein abundance and quantitative information on proteoform-level changes. These results present evidence of proteasome-independent karrikin signalling pathways and provide novel targets for detailed mechanistic studies using, e.g., mutants and transgenic plants.
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Samperi R, Capriotti AL, Cavaliere C, Colapicchioni V, Chiozzi RZ, Laganà A. Food Proteins and Peptides. ADVANCED MASS SPECTROMETRY FOR FOOD SAFETY AND QUALITY 2015. [DOI: 10.1016/b978-0-444-63340-8.00006-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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Almeida AM, Bassols A, Bendixen E, Bhide M, Ceciliani F, Cristobal S, Eckersall PD, Hollung K, Lisacek F, Mazzucchelli G, McLaughlin M, Miller I, Nally JE, Plowman J, Renaut J, Rodrigues P, Roncada P, Staric J, Turk R. Animal board invited review: advances in proteomics for animal and food sciences. Animal 2015; 9:1-17. [PMID: 25359324 PMCID: PMC4301196 DOI: 10.1017/s1751731114002602] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 09/27/2014] [Indexed: 01/15/2023] Open
Abstract
Animal production and health (APH) is an important sector in the world economy, representing a large proportion of the budget of all member states in the European Union and in other continents. APH is a highly competitive sector with a strong emphasis on innovation and, albeit with country to country variations, on scientific research. Proteomics (the study of all proteins present in a given tissue or fluid - i.e. the proteome) has an enormous potential when applied to APH. Nevertheless, for a variety of reasons and in contrast to disciplines such as plant sciences or human biomedicine, such potential is only now being tapped. To counter such limited usage, 6 years ago we created a consortium dedicated to the applications of Proteomics to APH, specifically in the form of a Cooperation in Science and Technology (COST) Action, termed FA1002--Proteomics in Farm Animals: www.cost-faproteomics.org. In 4 years, the consortium quickly enlarged to a total of 31 countries in Europe, as well as Israel, Argentina, Australia and New Zealand. This article has a triple purpose. First, we aim to provide clear examples on the applications and benefits of the use of proteomics in all aspects related to APH. Second, we provide insights and possibilities on the new trends and objectives for APH proteomics applications and technologies for the years to come. Finally, we provide an overview and balance of the major activities and accomplishments of the COST Action on Farm Animal Proteomics. These include activities such as the organization of seminars, workshops and major scientific conferences, organization of summer schools, financing Short-Term Scientific Missions (STSMs) and the generation of scientific literature. Overall, the Action has attained all of the proposed objectives and has made considerable difference by putting proteomics on the global map for animal and veterinary researchers in general and by contributing significantly to reduce the East-West and North-South gaps existing in the European farm animal research. Future activities of significance in the field of scientific research, involving members of the action, as well as others, will likely be established in the future.
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Affiliation(s)
- A. M. Almeida
- Instituto de Investigação Científica Tropical, CVZ – Centro de Veterinária e Zootecnia, Av. Univ. Técnica, 1300-477 Lisboa, Portugal
- CIISA – Centro Interdisciplinar de Investigação em Sanidade Animal, 1300-477 Lisboa, Portugal
- ITQB – Instituto de Tecnologia Química e Biológica da UNL, 2780-157 Oeiras, Portugal
- IBET – Instituto de Biologia Experimental e Tecnológica, 2780-157 Oeiras, Portugal
| | - A. Bassols
- Departament de Bioquímica i Biologia Molecular, Facultat de Veterinària, Universitat Autònoma de Barcelona,08193 Cerdanyola del Vallès, Spain
| | - E. Bendixen
- Institute of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - M. Bhide
- Laboratory of Biomedical Microbiology and Immunology, University of Veterinary Medicine and Pharmacy, Komenskeho-73 Kosice, Slovakia
| | - F. Ceciliani
- Department of Veterinary Science and Public Health, Università di Milano, Via Celoria 10, 20133 Milano, Italy
| | - S. Cristobal
- Department of Clinical and Experimental Medicine, Division of Cell Biology, Faculty of Health Science, Linköping University, SE-581 85 Linköping, Sweden
- IKERBASQUE, Basque Foundation for Science, Department of Physiology, Faculty of Medicine and Dentistry, University of Basque Country,48940 Leioa, Bizkaia, Spain
| | - P. D. Eckersall
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Garscube Estate, Glasgow G61 1QH, UK
| | - K. Hollung
- Nofima AS, PO Box 210, NO-1431 Aas, Norway
| | - F. Lisacek
- Swiss Institute of Bioinformatics, CMU – Rue Michel-Servet 1, 1211 Geneva 4, Switzerland
| | - G. Mazzucchelli
- Mass Spectrometry Laboratory, GIGA-Research, Department of Chemistry, University of Liège, 4000 Liège, Belgium
| | - M. McLaughlin
- Division of Veterinary Bioscience, School of Veterinary Medicine, University of Glasgow, Garscube Estate, Glasgow G61 1QH, UK
| | - I. Miller
- Institute of Medical Biochemistry, University of Veterinary Medicine, Veterinaerplatz 1, A-1210 Vienna, Austria
| | - J. E. Nally
- National Animal Disease Center, Bacterial Diseases of Livestock Research Unit, Agricultural Research Service, United States Department of Agriculture, Ames, IA 50010, USA
| | - J. Plowman
- Food & Bio-Based Products, AgResearch, Lincoln Research Centre, Christchurch 8140, New Zealand
| | - J. Renaut
- Department of Environment and Agrobiotechnologies, Centre de Recherche Public – Gabriel Lippmann, 41 rue du Brill, L-4422 Belvaux, Luxembourg
| | - P. Rodrigues
- CCMAR – Centre of Marine Sciences of Algarve, University of Algarve, Campus de Gambelas, 8005-139 Faro, Portugal
| | - P. Roncada
- Department of Veterinary Science and Public Health, Istituto Sperimentale Italiano L. Spallanzani Milano, University of Milano, 20133 Milano, Italy
| | - J. Staric
- Clinic for Ruminants with Ambulatory Clinic, Veterinary Faculty, University of Ljubljana, Gerbičeva 60, 1000 Ljubljana, Slovenia
| | - R. Turk
- Department of Pathophysiology, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, 10000 Zagreb, Croatia
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Huang J, Wang F, Ye M, Zou H. Enrichment and separation techniques for large-scale proteomics analysis of the protein post-translational modifications. J Chromatogr A 2014; 1372C:1-17. [DOI: 10.1016/j.chroma.2014.10.107] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 10/31/2014] [Accepted: 10/31/2014] [Indexed: 12/16/2022]
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Chen F, Wan D, Chang Z, Pu H, Jin M. Highly efficient separation, enrichment, and recovery of peptides by silica-supported polyethylenimine. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:12250-12257. [PMID: 25262957 DOI: 10.1021/la502093k] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Highly efficient and charge-selective adsorption and desorption of peptides at trace level by a solid-phase adsorbent is described. The adsorbent of SiO2@PEI is synthesized by covalent immobilization of branched polyethylenimines (PEI) exclusively on the outer surface of the porous silica particles (∼300 μm). For aqueous peptides (Mw = 600-3000 Da), SiO2@PEI can capture the negatively charged ones and leave the positively charged ones intact, and by adjusting pH of the system peptides with different isoelectric points (pIs) can be well separated. Targeted peptide at low abundance (at least as low as 0.1 mol % with respect to the highest one) can be well separated. The association constants of K > 10(12) M(-1) at pH > pI and K < 10(4) M(-1) at pH < pI are found; that is, selectivity > 10(8) is generally available. Thus, a peptide even at sub-femtomolar level can be extracted and eluted for analysis, and efficient recovery (79-92%) of the peptides is found. The extraction is mainly promoted by multisite electrostatic interaction, and the hydrophilic and cationic properties of PEI at low pH play a unique role in desorption efficiency and selectivity. The unbiased nature of this method renders the adsorbent applicable to the efficient separation of a broad spectrum of peptides, including those with similar pIs.
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Affiliation(s)
- Feng Chen
- Institute of Functional Polymers, School of Materials Science and Engineering, Tongji University , 4800 Cao-an Road, Shanghai 201804, PR China
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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.
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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,
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Littlejohns B, Heesom K, Angelini GD, Suleiman MS. The effect of disease on human cardiac protein expression profiles in paired samples from right and left ventricles. Clin Proteomics 2014; 11:34. [PMID: 25249829 PMCID: PMC4158351 DOI: 10.1186/1559-0275-11-34] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Accepted: 07/28/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cardiac diseases (e.g. coronary and valve) are associated with ventricular cellular remodeling. However, ventricular biopsies from left and right ventricles from patients with different pathologies are rare and thus little is known about disease-induced cellular remodeling in both sides of the heart and between different diseases. We hypothesized that the protein expression profiles between right and left ventricles of patients with aortic valve stenosis (AVS) and patients with coronary artery disease (CAD) are different and that the protein profile is different between the two diseases. Left and right ventricular biopsies were collected from patients with either CAD or AVS. The biopsies were processed for proteomic analysis using isobaric tandem mass tagging and analyzed by reverse phase nano-LC-MS/MS. Western blot for selected proteins showed strong correlation with proteomic analysis. RESULTS Proteomic analysis between ventricles of the same disease (intra-disease) and between ventricles of different diseases (inter-disease) identified more than 500 proteins detected in all relevant ventricular biopsies. Comparison between ventricles and disease state was focused on proteins with relatively high fold (±1.2 fold difference) and significant (P < 0.05) differences. Intra-disease protein expression differences between left and right ventricles were largely structural for AVS patients and largely signaling/metabolism for CAD. Proteins commonly associated with hypertrophy were also different in the AVS group but with lower fold difference. Inter-disease differences between left ventricles of AVS and CAD were detected in 9 proteins. However, inter-disease differences between the right ventricles of CAD and AVS patients were associated with differences in 73 proteins. The majority of proteins which had a significant difference in one ventricle compared to the other pathology also had a similar trend in the adjacent ventricle. CONCLUSIONS This work demonstrates for the first time that left and right ventricles have a different proteome and that the difference is dependent on the type of disease. Inter-disease differential expression was more prominent for right ventricles. The finding that a protein change in one ventricle was often associated with a similar trend in the adjacent ventricle for a large number of proteins suggests cross-talk proteome remodeling between adjacent ventricles.
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Affiliation(s)
- Ben Littlejohns
- Bristol Heart Institute, School of Clinical Sciences, Faculty of Medicine & Dentistry, University of Bristol, Bristol, UK
| | - Kate Heesom
- Proteomics Facility, Faculty of Medical and Veterinary Sciences, University of Bristol, Bristol, UK
| | - Gianni D Angelini
- Bristol Heart Institute, School of Clinical Sciences, Faculty of Medicine & Dentistry, University of Bristol, Bristol, UK
| | - M-Saadeh Suleiman
- Bristol Heart Institute, School of Clinical Sciences, Faculty of Medicine & Dentistry, University of Bristol, Bristol, UK
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da Costa JP, Oliveira-Silva R, Daniel-da-Silva AL, Vitorino R. Bionanoconjugation for Proteomics applications — An overview. Biotechnol Adv 2014; 32:952-70. [DOI: 10.1016/j.biotechadv.2014.04.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 03/15/2014] [Accepted: 04/26/2014] [Indexed: 12/29/2022]
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Wang ST, Huang W, Deng YF, Gao Q, Yuan BF, Feng YQ. “Old” metal oxide affinity chromatography as “novel” strategy for specific capture of cis-diol-containing compounds. J Chromatogr A 2014; 1361:100-7. [DOI: 10.1016/j.chroma.2014.07.091] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2014] [Revised: 07/24/2014] [Accepted: 07/29/2014] [Indexed: 11/30/2022]
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Cerný M, Jedelský PL, Novák J, Schlosser A, Brzobohatý B. Cytokinin modulates proteomic, transcriptomic and growth responses to temperature shocks in Arabidopsis. PLANT, CELL & ENVIRONMENT 2014; 37:1641-55. [PMID: 24393122 DOI: 10.1111/pce.12270] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Revised: 12/27/2013] [Accepted: 12/30/2013] [Indexed: 05/18/2023]
Abstract
As sessile organisms, plants must sense environmental conditions and adjust their growth and development processes accordingly, through adaptive responses regulated by various internal factors, including hormones. A key environmental factor is temperature, but temperature-sensing mechanisms are not fully understood despite intense research. We investigated proteomic responses to temperature shocks (15 min cold or heat treatments) with and without exogenous applications of cytokinin in Arabidopsis. Image and mass spectrometric analysis of the two-dimensionally separated proteins detected 139 differentially regulated spots, in which 148 proteins were identified, most of which have not been previously linked to temperature perception. More than 70% of the temperature-shock response proteins were modulated by cytokinin, mostly in a similar manner as heat shock. Data mining of previous transcriptomic datasets supported extensive interactions between temperature and cytokinin signalling. The biological significance of this finding was tested by assaying an independent growth response of Arabidopsis seedlings to heat stress: hypocotyl elongation. This response was strongly inhibited in mutants with deficiencies in cytokinin signalling or endogenous cytokinin levels. Thus, cytokinins may directly participate in heat signalling in plants. Finally, large proportions of both temperature-shock and cytokinin responsive proteomes co-localize to the chloroplast, which might therefore host a substantial proportion of the temperature response machinery.
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Affiliation(s)
- Martin Cerný
- Laboratory of Plant Molecular Biology, Institute of Biophysics AS CR, v.v.i and CEITEC - Central European Institute of Technology, Mendel University in Brno, CZ-613 00, Brno, Czech Republic
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Huang BY, Yang CK, Liu CP, Liu CY. Stationary phases for the enrichment of glycoproteins and glycopeptides. Electrophoresis 2014; 35:2091-107. [PMID: 24729282 DOI: 10.1002/elps.201400034] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2013] [Revised: 03/25/2014] [Accepted: 04/04/2014] [Indexed: 12/20/2022]
Abstract
The analysis of protein glycosylation is important for biomedical and biopharmaceutical research. Recent advances in LC-MS analysis have enabled the identification of glycosylation sites, the characterisation of glycan structures and the identification and quantification of glycoproteins and glycopeptides. However, this type of analysis remains challenging due to the low abundance of glycopeptides in complex protein digests, the microheterogeneity at glycosylation sites, ion suppression effects and the competition for ionisation by co-eluting peptides. Specific sample preparation is necessary for comprehensive and site-specific glycosylation analyses using MS. Therefore, researchers continue to pursue new columns to broaden their applications. The current manuscript covers recent literature published from 2008 to 2013. The stationary phases containing various chemical bonding methods or ligands immobilisation strategies on solid supports that selectively enrich N-linked or sialylated N-glycopeptides are categorised with either physical or chemical modes of binding. These categories include lectin affinity, hydrophilic interactions, boronate affinity, titanium dioxide affinity, hydrazide chemistry and other separation techniques. This review should aid in better understanding the syntheses and physicochemical properties of each type of stationary phases for enriching glycoproteins and glycopeptides.
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Affiliation(s)
- Bao-Yu Huang
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
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Lichti CF, Wildburger NC, Emmett MR, Mostovenko E, Shavkunov AS, Strain SK, Nilsson CL. Post-translational Modifications in the Human Proteome. TRANSLATIONAL BIOINFORMATICS 2014. [DOI: 10.1007/978-94-017-9202-8_6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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