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Wu J, Zhang H, Yang L, Chen Y, Li J, Yang M, Zhang X, He C, Wang X, Xu X. Syntaxin 7 modulates seizure activity in epilepsy. Neurobiol Dis 2023; 181:106118. [PMID: 37031804 DOI: 10.1016/j.nbd.2023.106118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/18/2023] [Accepted: 04/05/2023] [Indexed: 04/11/2023] Open
Abstract
The exact pathogenesis of epilepsy, one of the most common and devastating diseases of the nervous system, is not fully understood. Syntaxin7 (STX7) is a member of the SNARE superfamily, which mediates membrane fusion events in all cells. However, the role STX7 plays in epilepsy remains unclear. Therefore, this study investigates the role of STX7 in epilepsy. Our study found that the expression of STX7 was reduced in the epileptic brain and that overexpression of STX7 decreased the susceptibility to epileptic seizures and alleviated epileptic activity in a kainic acid-induced model and pentylenetetrazole-induced kindling model of epilepsy, whereas the downregulation of STX7 showed opposite effects. Whole-cell patch-clamp recordings showed that STX7 does not affect the intrinsic excitability of neurons, but rather the excitation/inhibition ratio mediated by affecting the release of presynaptic γ-aminobutyric acid neurotransmitters. Transmission electron microscopy results showed that STX7 did not affect the density of inhibitory synapses but could affect the density of inhibitory vesicles. Taken together, these results reveal a previously unknown function of STX7 in epilepsy and suggest that STX7 may serve as a novel target for epilepsy therapy.
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Affiliation(s)
- Junhong Wu
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Neurology, 1 Youyi Road, Chongqing 400016, China
| | - Hui Zhang
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Neurology, 1 Youyi Road, Chongqing 400016, China; Department of Neurology, The First Hospital of Shanxi Medical University, No.85 Jiefang South Road, Taiyuan, Shanxi Province, China
| | - Liu Yang
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Neurology, 1 Youyi Road, Chongqing 400016, China; Department of Neurology, The First Hospital of Shanxi Medical University, No.85 Jiefang South Road, Taiyuan, Shanxi Province, China
| | - Yuanyuan Chen
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Neurology, 1 Youyi Road, Chongqing 400016, China
| | - Jiyuan Li
- Department of Neurology, The First Hospital of Shanxi Medical University, No.85 Jiefang South Road, Taiyuan, Shanxi Province, China
| | - Min Yang
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Neurology, 1 Youyi Road, Chongqing 400016, China
| | - Xiaogang Zhang
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Neurology, 1 Youyi Road, Chongqing 400016, China; Department of Neurology, Chongqing General Hospital, Chongqing Key Laboratory of Neurodegenerative Diseases, No.118, Xingguang Avenue, Liangjiang New Area, Chongqing 401147, China
| | - Changlong He
- Department of Laboratory Medicine, People's Hospital of Jiulongpo District, Chongqing 40016, China; Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing 400016, China.
| | - Xuefeng Wang
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Neurology, 1 Youyi Road, Chongqing 400016, China.
| | - Xin Xu
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Neurology, 1 Youyi Road, Chongqing 400016, China.
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Mohsin AZ, Sukor R, Selamat J, Meor Hussin AS, Ismail IH, Jambari NN, Jonet A. A highly selective two-way purification method using liquid chromatography for isolating α S2-casein from goat milk of five different breeds. J Chromatogr B Analyt Technol Biomed Life Sci 2020; 1160:122380. [PMID: 32971369 DOI: 10.1016/j.jchromb.2020.122380] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 07/27/2020] [Accepted: 09/07/2020] [Indexed: 12/22/2022]
Abstract
The main challenges in the purification of αS2-casein are due to the low quantity in milk and high homology with other casein subunits, i.e., αS1-casein, β-casein, and κ-casein. To overcome these challenges, the aim of this study was to develop a two-step purification to isolate native αS2-casein in goat milk from five different breeds; British Alpine, Jamnapari, Saanen, Shami, and Toggenburg. The first step of the purification was executed by anion-exchange chromatography under optimal elution conditions followed by size exclusion chromatography. Tryptic peptides from in-gel digestion of purified αS2-casein were sequenced and analyzed by LC-ESI-MS/MS. From 1.05 g of whole casein, the highest yield of αS2-casein (6.7 mg/mL) was obtained from Jamnapari and the lowest yield (2.2 mg/mL) was from Saanen. A single band of pure αS2-casein was observed on SDS-PAGE for all breeds. The αS2-casein showed coverage percentage of amino acid sequence from 76.68 to 92.83%. The two-step purification process developed herein was successfully applied for isolating native αS2-casein from goat milk with high purity, which will allow for future in vitro studies to be conducted on this protein.
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Affiliation(s)
- Aliah Zannierah Mohsin
- Laboratory of Food Safety and Food Integrity, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - Rashidah Sukor
- Laboratory of Food Safety and Food Integrity, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia; Faculty of Food Science and Technology, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia.
| | - Jinap Selamat
- Laboratory of Food Safety and Food Integrity, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia; Faculty of Food Science and Technology, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - Anis Shobirin Meor Hussin
- Faculty of Food Science and Technology, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - Intan Hakimah Ismail
- Faculty of Medicine, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - Nuzul Noorahya Jambari
- Laboratory of Food Safety and Food Integrity, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia; Faculty of Food Science and Technology, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - Anuar Jonet
- Department of Structural Biology and Biophysics, Malaysia Genome Institute, Kajang 43000, Selangor, Malaysia
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Aragón CC, Tafúr RA, Suárez-Avellaneda A, Martínez MDT, Salas ADL, Tobón GJ. Urinary biomarkers in lupus nephritis. J Transl Autoimmun 2020; 3:100042. [PMID: 32743523 PMCID: PMC7388339 DOI: 10.1016/j.jtauto.2020.100042] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 01/07/2020] [Accepted: 02/06/2020] [Indexed: 02/08/2023] Open
Abstract
Systemic lupus erythematosus (SLE) is the prototypical autoimmune disease that can affect any organ of the body. Multiple mechanisms may contribute to the pathophysiology of systemic lupus, including failure to remove apoptotic bodies, hyperactivity of self-reactive B and T lymphocytes, abnormal exposure to autoantigens, and increased levels of B-cell stimulatory cytokines. The involvement of the kidney, called lupus nephritis (LN), during the course of the disease affects between 30% and 60% of adult SLE patients, and up to 70% of children. LN is an immune-mediated glomerulonephritis that is a common and serious finding in patients with SLE. Nowadays, renal biopsy is considered the gold standard for classifying LN, besides its degree of activity or chronicity. Nevertheless, renal biopsy lacks the ability to predict which patients will respond to immunosuppressive therapy and is a costly and risky procedure that is not practical in the monitoring of LN because serial repetitions would be necessary. Consequently, many serum and urinary biomarkers have been studied in SLE patients for the complementary study of LN, existing conventional biomarkers like proteinuria, protein/creatinine ratio in spot urine, 24 h urine proteinuria, creatinine clearance, among others and non-conventional biomarkers, like Monocyte chemoattractant protein-1 (MCP-1), have been correlated with the histological findings of the different types of LN. In this article, we review the advances in lupus nephritis urinary biomarkers. Such markers ideally should be capable of predicting early sub-clinical flares and could be used to follow response to therapy. In addition, some of these markers have been found to be involved in the pathogenesis of lupus nephritis.
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Affiliation(s)
- Cristian C. Aragón
- GIRAT: Grupo de Investigación en Reumatología, Autoinmunidad y Medicina Traslacional, Fundación Valle Del Lili and Universidad Icesi, Cali, Colombia
| | - Raúl-Alejandro Tafúr
- GIRAT: Grupo de Investigación en Reumatología, Autoinmunidad y Medicina Traslacional, Fundación Valle Del Lili and Universidad Icesi, Cali, Colombia
- Universidad Icesi, Medical School, Cali, Colombia
| | - Ana Suárez-Avellaneda
- GIRAT: Grupo de Investigación en Reumatología, Autoinmunidad y Medicina Traslacional, Fundación Valle Del Lili and Universidad Icesi, Cali, Colombia
| | - MD. Tatiana Martínez
- GIRAT: Grupo de Investigación en Reumatología, Autoinmunidad y Medicina Traslacional, Fundación Valle Del Lili and Universidad Icesi, Cali, Colombia
- Universidad Icesi, Medical School, Cali, Colombia
| | - Alejandra de las Salas
- GIRAT: Grupo de Investigación en Reumatología, Autoinmunidad y Medicina Traslacional, Fundación Valle Del Lili and Universidad Icesi, Cali, Colombia
- Universidad Icesi, Medical School, Cali, Colombia
| | - Gabriel J. Tobón
- GIRAT: Grupo de Investigación en Reumatología, Autoinmunidad y Medicina Traslacional, Fundación Valle Del Lili and Universidad Icesi, Cali, Colombia
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Guo C, Sun D, Wang X, Mao S. A Combined Metabolomic and Proteomic Study Revealed the Difference in Metabolite and Protein Expression Profiles in Ruminal Tissue From Goats Fed Hay or High-Grain Diets. Front Physiol 2019; 10:66. [PMID: 30800073 PMCID: PMC6375843 DOI: 10.3389/fphys.2019.00066] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 01/21/2019] [Indexed: 12/23/2022] Open
Abstract
Currently, knowledge about the impact of high-grain (HG) feeding on metabolite and protein expression profiles in ruminal tissue is limited. In this study, a combination of proteomic and metabolomic approaches was applied to evaluate metabolic and proteomic changes of the rumen epithelium in goats fed a hay diet (Hay) or HG diet. At the metabolome level, results from principal component analysis (PCA) and PLS-DA revealed clear differences in the biochemical composition of ruminal tissue of the control (Hay) and the grain-fed groups, demonstrating the evident impact of HG feeding on metabolite profile of ruminal epithelial tissues. As compared with the Hay group, HG feeding increased the levels of eight metabolites and decreased the concentrations of seven metabolites in ruminal epithelial tissues. HG feeding mainly altered starch and sucrose metabolism, purine metabolism, glyoxylate and dicarboxylate metabolism, glycerolipid metabolism, pyruvate metabolism, glycolysis or gluconeogenesis, galactose metabolism, glycine, serine and threonine metabolism, and arginine and proline metabolism in ruminal epithelium. At the proteome level, 35 differentially expressed proteins were found in the rumen epithelium between the Hay and HG groups, with 12 upregulated and 23 downregulated proteins. The downregulated proteins were related to fatty acid metabolism, carbohydrate metabolic processes and nucleoside metabolic processes, while most of upregulated proteins were involved in oxidative stress and detoxification. In general, our findings revealed that HG feeding resulted in differential proteomic and metabolomic profiles in the rumen epithelia of goats, which may contribute to better understanding how rumen epithelium adapt to HG feeding.
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Affiliation(s)
- Changzheng Guo
- Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, Laboratory of Gastrointestinal Microbiology, National Experimental Teaching Demonstration Center of Animal Science, National Center for International Research on Animal Gut Nutrition, Joint International Research Laboratory of Animal Health and Food Safety, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Daming Sun
- Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, Laboratory of Gastrointestinal Microbiology, National Experimental Teaching Demonstration Center of Animal Science, National Center for International Research on Animal Gut Nutrition, Joint International Research Laboratory of Animal Health and Food Safety, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Xinfeng Wang
- College of Animal Science and Technology, Shihezi University, Shihezi, China
| | - Shengyong Mao
- Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, Laboratory of Gastrointestinal Microbiology, National Experimental Teaching Demonstration Center of Animal Science, National Center for International Research on Animal Gut Nutrition, Joint International Research Laboratory of Animal Health and Food Safety, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
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Abstract
Significant alterations in gene sequences, expression levels and protein structures have been associated with specific types of thyroid epithelial tumorigenesis. Recent revolutionary changes in molecular biology have spanned the disciplines of genomics and proteomics, which systematically generate and analyze the information about genomes, gene transcripts, proteins and their functions in a global, comprehensive manner. The application of these approaches will better discriminate between thyroid tumor subtypes that are not recognizable when traditional pathological criteria are used.
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Affiliation(s)
- Italia Bongarzone
- Department of Experimental Oncology, National Cancer Institute, Milan, Italy.
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The influence of transcript assembly on the proteogenomics discovery of microproteins. PLoS One 2018; 13:e0194518. [PMID: 29584760 PMCID: PMC5870951 DOI: 10.1371/journal.pone.0194518] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 03/05/2018] [Indexed: 11/19/2022] Open
Abstract
Proteogenomics methods have identified many non-annotated protein-coding genes in the human genome. Many of the newly discovered protein-coding genes encode peptides and small proteins, referred to collectively as microproteins. Microproteins are produced through ribosome translation of small open reading frames (smORFs). The discovery of many smORFs reveals a blind spot in traditional gene-finding algorithms for these genes. Biological studies have found roles for microproteins in cell biology and physiology, and the potential that there exists additional bioactive microproteins drives the interest in detection and discovery of these molecules. A key step in any proteogenomics workflow is the assembly of RNA-Seq data into likely mRNA transcripts that are then used to create a searchable protein database. Here we demonstrate that specific features of the assembled transcriptome impact microprotein detection by shotgun proteomics. By tailoring transcript assembly for downstream mass spectrometry searching, we show that we can detect more than double the number of high-quality microprotein candidates and introduce a novel open-source mRNA assembler for proteogenomics (MAPS) that incorporates all of these features. By integrating our specialized assembler, MAPS, and a popular generalized assembler into our proteogenomics pipeline, we detect 45 novel human microproteins from a high quality proteogenomics dataset of a human cell line. We then characterize the features of the novel microproteins, identifying two classes of microproteins. Our work highlights the importance of specialized transcriptome assembly upstream of proteomics validation when searching for short and potentially rare and poorly conserved proteins.
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Soetkamp D, Raedschelders K, Mastali M, Sobhani K, Bairey Merz CN, Van Eyk J. The continuing evolution of cardiac troponin I biomarker analysis: from protein to proteoform. Expert Rev Proteomics 2017; 14:973-986. [PMID: 28984473 DOI: 10.1080/14789450.2017.1387054] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
INTRODUCTION The troponin complex consists of three proteins that fundamentally couple excitation with contraction. Circulating cardiac-specific Troponin I (cTnI) serves as diagnostic biomarker tools for risk stratification of acute coronary syndromes and acute myocardial infarction (MI). Within the heart, cTnI oscillates between inactive and active conformations to either block or disinhibit actinomyosin formation. This molecular mechanism is fine-tuned through extensive protein modifications whose profiles are maladaptively altered with co-morbidities including hypertrophic cardiomyopathy, diabetes, and heart failure. Technological advances in analytical platforms over the last decade enable routine baseline cTnI analysis in patients without cardiovascular complications, and hold potential to expand cTnI readouts that include modified cTnI proteoforms. Areas covered: This review covers the current state, advances, and prospects of analytical platforms that now enable routine baseline cTnI analysis in patients. In parallel, improved mass spectrometry instrumentation and workflows already reveal an array of modified cTnI proteoforms with promising diagnostic implications. Expert commentary: New analytical capabilities provide clinicians and researchers with an opportunity to address important questions surrounding circulating cTnI in the improved diagnosis of specific patient cohorts. These techniques also hold considerable promise for new predictive and prescriptive applications for individualized profiling and improve patient care.
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Affiliation(s)
- Daniel Soetkamp
- a Heart Institute , Cedars-Sinai Medical Center , Los Angeles , CA , USA
| | - Koen Raedschelders
- a Heart Institute , Cedars-Sinai Medical Center , Los Angeles , CA , USA
| | - Mitra Mastali
- a Heart Institute , Cedars-Sinai Medical Center , Los Angeles , CA , USA
| | - Kimia Sobhani
- b Pathology and Laboratory Medicine , Cedars-Sinai Medical Center , Los Angeles , CA , USA
| | - C Noel Bairey Merz
- c Women's Heart Center , Cedars-Sinai Medical Center , Los Angeles , CA , USA
| | - Jennifer Van Eyk
- a Heart Institute , Cedars-Sinai Medical Center , Los Angeles , CA , USA
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9
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Edwards JE, Forster RJ, Callaghan TM, Dollhofer V, Dagar SS, Cheng Y, Chang J, Kittelmann S, Fliegerova K, Puniya AK, Henske JK, Gilmore SP, O'Malley MA, Griffith GW, Smidt H. PCR and Omics Based Techniques to Study the Diversity, Ecology and Biology of Anaerobic Fungi: Insights, Challenges and Opportunities. Front Microbiol 2017; 8:1657. [PMID: 28993761 PMCID: PMC5622200 DOI: 10.3389/fmicb.2017.01657] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 08/15/2017] [Indexed: 11/25/2022] Open
Abstract
Anaerobic fungi (phylum Neocallimastigomycota) are common inhabitants of the digestive tract of mammalian herbivores, and in the rumen, can account for up to 20% of the microbial biomass. Anaerobic fungi play a primary role in the degradation of lignocellulosic plant material. They also have a syntrophic interaction with methanogenic archaea, which increases their fiber degradation activity. To date, nine anaerobic fungal genera have been described, with further novel taxonomic groupings known to exist based on culture-independent molecular surveys. However, the true extent of their diversity may be even more extensively underestimated as anaerobic fungi continue being discovered in yet unexplored gut and non-gut environments. Additionally many studies are now known to have used primers that provide incomplete coverage of the Neocallimastigomycota. For ecological studies the internal transcribed spacer 1 region (ITS1) has been the taxonomic marker of choice, but due to various limitations the large subunit rRNA (LSU) is now being increasingly used. How the continued expansion of our knowledge regarding anaerobic fungal diversity will impact on our understanding of their biology and ecological role remains unclear; particularly as it is becoming apparent that anaerobic fungi display niche differentiation. As a consequence, there is a need to move beyond the broad generalization of anaerobic fungi as fiber-degraders, and explore the fundamental differences that underpin their ability to exist in distinct ecological niches. Application of genomics, transcriptomics, proteomics and metabolomics to their study in pure/mixed cultures and environmental samples will be invaluable in this process. To date the genomes and transcriptomes of several characterized anaerobic fungal isolates have been successfully generated. In contrast, the application of proteomics and metabolomics to anaerobic fungal analysis is still in its infancy. A central problem for all analyses, however, is the limited functional annotation of anaerobic fungal sequence data. There is therefore an urgent need to expand information held within publicly available reference databases. Once this challenge is overcome, along with improved sample collection and extraction, the application of these techniques will be key in furthering our understanding of the ecological role and impact of anaerobic fungi in the wide range of environments they inhabit.
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Affiliation(s)
- Joan E. Edwards
- Laboratory of Microbiology, Wageningen University & ResearchWageningen, Netherlands
| | - Robert J. Forster
- Lethbridge Research and Development Centre, Agriculture and Agri-Food CanadaLethbridge, AB, Canada
| | - Tony M. Callaghan
- Department for Quality Assurance and Analytics, Bavarian State Research Center for AgricultureFreising, Germany
| | - Veronika Dollhofer
- Department for Quality Assurance and Analytics, Bavarian State Research Center for AgricultureFreising, Germany
| | | | - Yanfen Cheng
- Laboratory of Gastrointestinal Microbiology, Nanjing Agricultural UniversityNanjing, China
| | - Jongsoo Chang
- Department of Agricultural Science, Korea National Open UniversitySeoul, South Korea
| | - Sandra Kittelmann
- Grasslands Research Centre, AgResearch Ltd.Palmerston North, New Zealand
| | - Katerina Fliegerova
- Institute of Animal Physiology and Genetics, Czech Academy of SciencesPrague, Czechia
| | - Anil K. Puniya
- College of Dairy Science and Technology, Guru Angad Dev Veterinary and Animal Sciences UniversityLudhiana, India
- Dairy Microbiology Division, ICAR-National Dairy Research InstituteKarnal, India
| | - John K. Henske
- Department of Chemical Engineering, University of California, Santa BarbaraSanta Barbara, CA, United States
| | - Sean P. Gilmore
- Department of Chemical Engineering, University of California, Santa BarbaraSanta Barbara, CA, United States
| | - Michelle A. O'Malley
- Department of Chemical Engineering, University of California, Santa BarbaraSanta Barbara, CA, United States
| | - Gareth W. Griffith
- Institute of Biological Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, United Kingdom
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & ResearchWageningen, Netherlands
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Wong YK, Zhang J, Hua ZC, Lin Q, Shen HM, Wang J. Recent advances in quantitative and chemical proteomics for autophagy studies. Autophagy 2017; 13:1472-1486. [PMID: 28820289 DOI: 10.1080/15548627.2017.1313944] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Macroautophagy/autophagy is an evolutionarily well-conserved cellular degradative process with important biological functions that is closely implicated in health and disease. In recent years, quantitative mass spectrometry-based proteomics and chemical proteomics have emerged as important tools for the study of autophagy, through large-scale unbiased analysis of the proteome or through highly specific and accurate analysis of individual proteins of interest. At present, a variety of approaches have been successfully applied, including (i) expression and interaction proteomics for the study of protein post-translational modifications, (ii) investigating spatio-temporal dynamics of protein synthesis and degradation, and (iii) direct determination of protein activity and profiling molecular targets in the autophagic process. In this review, we attempted to provide an overview of principles and techniques relevant to the application of quantitative and chemical proteomics methods to autophagy, and outline the current landscape as well as future outlook of these methods in autophagy research.
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Affiliation(s)
- Yin-Kwan Wong
- a Department of Physiology, Yong Loo Lin School of Medicine , National University of Singapore , Singapore
| | - Jianbin Zhang
- b Department of Oncology, Clinical Research Institute , Zhejiang Provincial People's Hospital , Hangzhou , China
| | - Zi-Chun Hua
- c Changzhou High-Tech Research Institute of Nanjing University and the State Key Laboratory of Pharmaceutical Biotechnology, College of Life Sciences , Nanjing University , Nanjing , China
| | - Qingsong Lin
- d Department of Biological Sciences , National University of Singapore , Singapore
| | - Han-Ming Shen
- a Department of Physiology, Yong Loo Lin School of Medicine , National University of Singapore , Singapore.,e NUS Graduate School for Integrative Sciences and Engineering , National University of Singapore , Singapore
| | - Jigang Wang
- a Department of Physiology, Yong Loo Lin School of Medicine , National University of Singapore , Singapore.,c Changzhou High-Tech Research Institute of Nanjing University and the State Key Laboratory of Pharmaceutical Biotechnology, College of Life Sciences , Nanjing University , Nanjing , China
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11
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Trenchevska O, Nelson RW, Nedelkov D. Mass Spectrometric Immunoassays in Characterization of Clinically Significant Proteoforms. Proteomes 2016; 4:proteomes4010013. [PMID: 28248223 PMCID: PMC5217360 DOI: 10.3390/proteomes4010013] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 03/10/2016] [Accepted: 03/14/2016] [Indexed: 02/07/2023] Open
Abstract
Proteins can exist as multiple proteoforms in vivo, as a result of alternative splicing and single-nucleotide polymorphisms (SNPs), as well as posttranslational processing. To address their clinical significance in a context of diagnostic information, proteoforms require a more in-depth analysis. Mass spectrometric immunoassays (MSIA) have been devised for studying structural diversity in human proteins. MSIA enables protein profiling in a simple and high-throughput manner, by combining the selectivity of targeted immunoassays, with the specificity of mass spectrometric detection. MSIA has been used for qualitative and quantitative analysis of single and multiple proteoforms, distinguishing between normal fluctuations and changes related to clinical conditions. This mini review offers an overview of the development and application of mass spectrometric immunoassays for clinical and population proteomics studies. Provided are examples of some recent developments, and also discussed are the trends and challenges in mass spectrometry-based immunoassays for the next-phase of clinical applications.
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Affiliation(s)
- Olgica Trenchevska
- The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA.
| | - Randall W Nelson
- The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA.
| | - Dobrin Nedelkov
- The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA.
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Butyrylcholinesterase identification in a phenylvalerate esterase-enriched fraction sensitive to low mipafox concentrations in chicken brain. Arch Toxicol 2016; 91:909-919. [DOI: 10.1007/s00204-016-1670-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2015] [Accepted: 01/13/2016] [Indexed: 10/22/2022]
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13
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Sghaier-Hammami B, Redondo-López I, Valero-Galvàn J, Jorrín-Novo JV. Protein profile of cotyledon, tegument, and embryonic axis of mature acorns from a non-orthodox plant species: Quercus ilex. PLANTA 2016; 243:369-96. [PMID: 26424229 DOI: 10.1007/s00425-015-2404-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 09/03/2015] [Indexed: 05/24/2023]
Abstract
Contrary to the orthodox seeds, recalcitrant Holm oak seeds possess the enzymatic machinery to start germination during the maturation phase. The protein profile of the different parts, mature seeds, of the Holm oak, a non-orthodox plant species, has been characterized using one- and two-dimensional gel electrophoresis coupled to matrix-assisted laser desorption ionization-time of flight mass spectrometry. Protein content and profiles of the three seed tissues (cotyledon, embryonic axis and tegument) were quite different. The embryonic axis showed 4-fold and 20-fold higher protein content than the cotyledon and the tegument, respectively. Two hundred and twenty-six variable proteins among the three seed parts were identified, being classified according to their function into eight main groups. The cotyledon presented the highest number of metabolic and storage proteins (89% of them are legumin) compared to the embryonic axis and tegument. The embryonic axis had the highest number of the species within the protein fate group. The tegument presented the largest number of the defense-/stress-related and cytoskeleton proteins. This distribution is in good agreement with the biological role of the tissues. The study of the seed tissue proteome demonstrated a compartmentalization of pathways and a division of metabolic tasks between embryonic axis, cotyledon and tegument. This compartmentalization uncovered in our study should provide a starting point for understanding, at the molecular level, the particularities of the recalcitrant seeds.
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Affiliation(s)
- Besma Sghaier-Hammami
- Laboratory of Extremophile Plants, Biotechnology Centre of Borj Cedria, P. O. Box 901, 2050, Hammam-Lif, Tunisia.
- Agroforestry and Plant Biochemistry and Proteomics Research Group, Department of Biochemistry and Molecular Biology, University of Cordoba-CeiA3, Cordoba, Spain.
| | - Inmaculada Redondo-López
- Agroforestry and Plant Biochemistry and Proteomics Research Group, Department of Biochemistry and Molecular Biology, University of Cordoba-CeiA3, Cordoba, Spain
| | - José Valero-Galvàn
- Agroforestry and Plant Biochemistry and Proteomics Research Group, Department of Biochemistry and Molecular Biology, University of Cordoba-CeiA3, Cordoba, Spain
- Department of Chemistry-Biology, Biomedical Sciences Institute, Autonomous University of Ciudad Juárez, Ciudad Juárez, Chihuahua, Mexico
| | - Jesús V Jorrín-Novo
- Agroforestry and Plant Biochemistry and Proteomics Research Group, Department of Biochemistry and Molecular Biology, University of Cordoba-CeiA3, Cordoba, Spain
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14
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Abstract
Compared to genomics or transcriptomics, proteomics is often regarded as an "emerging technology," i.e., as not having reached the same level of maturity. While the successful implementation of proteomics workflows and technology still requires significant levels of expertise and specialization, great strides have been made to make the technology more powerful, streamlined and accessible. In 2014, two landmark studies published the first draft versions of the human proteome.We aim to provide an introduction specifically into the background of mass spectrometry (MS)-based proteomics. Within the field, mass spectrometry has emerged as a core technology. Coupled to increasingly powerful separations and data processing and bioinformatics solution, it allows the quantitative analysis of whole proteomes within a matter of days, a timescale that has made global comparative proteome studies feasible at last. We present and discuss the basic concepts behind proteomics mass spectrometry and the accompanying topic of protein and peptide separations, with a focus on the properties of datasets emerging from such studies.
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15
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Zhang SF, Zhang Y, Xie ZX, Zhang H, Lin L, Wang DZ. iTRAQ-based quantitative proteomic analysis of a toxigenic dinoflagellate Alexandrium catenella and its non-toxic mutant. Proteomics 2015; 15:4041-50. [PMID: 26417864 DOI: 10.1002/pmic.201500156] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 09/01/2015] [Accepted: 09/22/2015] [Indexed: 11/06/2022]
Abstract
Paralytic shellfish toxins (PSTs) are a group of potent neurotoxic alkaloids produced by cyanobacteria and dinoflagellates. The PST biosynthesis gene cluster and several toxin-related proteins have been unveiled in cyanobacteria, yet little is known about dinoflagellates. Here, we compared the protein profiles of a toxin-producing dinoflagellate Alexandrium catenella (ACHK-T) and its non-toxic mutant (ACHK-NT), and characterized differentially displayed proteins using a combination of the iTRAQ-based proteomic approach and the transcriptomic database. Totally 3488 proteins were identified from A. catenella, and proteins involved in carbohydrate, amino acid and energy metabolism were the most abundant. Among them, 185 proteins were differentially displayed: proteins involved in amino acid biosynthesis, protein and carbohydrate metabolism and bioluminescence were more abundant in ACHK-T, while proteins participating in photosynthesis, fatty acid biosynthesis, and the processes occurring in peroxisome displayed higher abundances in ACHK-NT. Seven toxin-related proteins were identified but they varied insignificantly between the two strains. Different carbon and energy utilization strategies were potentially related to the toxin producing ability, and the regulation mechanism of PST biosynthesis was more complex in dinoflagellates. Our study provides the first comprehensive dataset on the dinoflagellate proteome and lays the groundwork for future proteomic study.
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Affiliation(s)
- Shu-Fei Zhang
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, P. R. China
| | - Yong Zhang
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, P. R. China
| | - Zhang-Xian Xie
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, P. R. China
| | - Hao Zhang
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, P. R. China
| | - Lin Lin
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, P. R. China
| | - Da-Zhi Wang
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, P. R. China
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16
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Complementary PTM Profiling of Drug Response in Human Gastric Carcinoma by Immunoaffinity and IMAC Methods with Total Proteome Analysis. Proteomes 2015; 3:160-183. [PMID: 28248267 PMCID: PMC5217380 DOI: 10.3390/proteomes3030160] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Revised: 07/21/2015] [Accepted: 07/22/2015] [Indexed: 01/14/2023] Open
Abstract
Gaining insight into normal cellular signaling and disease biology is a critical goal of proteomic analyses. The ability to perform these studies successfully to extract the maximum value and discovery of biologically relevant candidate biomarkers is therefore of primary importance. Many successful studies in the past have focused on total proteome analysis (changes at the protein level) combined with phosphorylation analysis by metal affinity enrichment (changes at the PTM level). Here, we use the gastric carcinoma cell line MKN-45 treated with the c-Met inhibitor SU11274 and PKC inhibitor staurosporine to investigate the most efficient and most comprehensive strategies for both total protein and PTM analysis. Under the conditions used, total protein analysis yielded few changes in response to either compound, while analysis of phosphorylation identified thousands of sites that changed differentially between the two treatments. Both metal affinity and antibody-based enrichments were used to assess phosphopeptide changes, and the data generated by the two methods was largely complementary (non-overlapping). Label-free quantitation of peptide peak abundances was used to accurately determine fold-changes between control and treated samples. Protein interaction network analysis allowed the data to be placed in a biologically relevant context, and follow-up validation of selected findings confirmed the accuracy of the proteomic data. Together, this study provides a framework for start-to-finish proteomic analysis of any experimental system under investigation to maximize the value of the proteomic study and yield the best chance for uncovering actionable target candidates.
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17
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Lindsey ML, Mayr M, Gomes AV, Delles C, Arrell DK, Murphy AM, Lange RA, Costello CE, Jin YF, Laskowitz DT, Sam F, Terzic A, Van Eyk J, Srinivas PR. Transformative Impact of Proteomics on Cardiovascular Health and Disease: A Scientific Statement From the American Heart Association. Circulation 2015. [PMID: 26195497 DOI: 10.1161/cir.0000000000000226] [Citation(s) in RCA: 111] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The year 2014 marked the 20th anniversary of the coining of the term proteomics. The purpose of this scientific statement is to summarize advances over this period that have catalyzed our capacity to address the experimental, translational, and clinical implications of proteomics as applied to cardiovascular health and disease and to evaluate the current status of the field. Key successes that have energized the field are delineated; opportunities for proteomics to drive basic science research, facilitate clinical translation, and establish diagnostic and therapeutic healthcare algorithms are discussed; and challenges that remain to be solved before proteomic technologies can be readily translated from scientific discoveries to meaningful advances in cardiovascular care are addressed. Proteomics is the result of disruptive technologies, namely, mass spectrometry and database searching, which drove protein analysis from 1 protein at a time to protein mixture analyses that enable large-scale analysis of proteins and facilitate paradigm shifts in biological concepts that address important clinical questions. Over the past 20 years, the field of proteomics has matured, yet it is still developing rapidly. The scope of this statement will extend beyond the reaches of a typical review article and offer guidance on the use of next-generation proteomics for future scientific discovery in the basic research laboratory and clinical settings.
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18
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Rees JC, Pierce CL, Schieltz DM, Barr JR. Simultaneous Identification and Susceptibility Determination to Multiple Antibiotics of Staphylococcus aureus by Bacteriophage Amplification Detection Combined with Mass Spectrometry. Anal Chem 2015; 87:6769-77. [PMID: 26016659 PMCID: PMC5713475 DOI: 10.1021/acs.analchem.5b00959] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The continued advance of antibiotic resistance in clinically relevant bacterial strains necessitates the development and refinement of assays that can rapidly and cost-effectively identify bacteria and determine their susceptibility to a panel of antibiotics. A methodology is described herein that exploits the specificity and physiology of the Staphylococci bacteriophage K to identify Staphylococcus aureus (S. aureus) and determine its susceptibility to clindamycin and cefoxitin. The method uses liquid chromatography-mass spectrometry to monitor the replication of bacteriophage after it is used to infect samples thought to contain S. aureus. Amplification of bacteriophage K indicates the sample contains S. aureus, for it is only in the presence of a suitable host that bacteriophage K can amplify. If bacteriophage amplification is detected in samples containing the antibiotics clindamycin or cefoxitin, the sample is deemed to be resistant to these antibiotics, respectively, for bacteriophage can only amplify in a viable host. Thus, with a single work flow, S. aureus can be detected in an unknown sample and susceptibility to clindamycin and cefoxitin can be ascertained. This Article discusses implications for the use of bacteriophage amplification in the clinical laboratory.
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Affiliation(s)
- Jon C. Rees
- Division of Laboratory Sciences, National Center for Environmental Health, Centers for Disease Control and Prevention, Chamblee, Georgia 30341, United States
| | - Carrie L. Pierce
- Division of Laboratory Sciences, National Center for Environmental Health, Centers for Disease Control and Prevention, Chamblee, Georgia 30341, United States
| | - David M. Schieltz
- Division of Laboratory Sciences, National Center for Environmental Health, Centers for Disease Control and Prevention, Chamblee, Georgia 30341, United States
| | - John R. Barr
- Division of Laboratory Sciences, National Center for Environmental Health, Centers for Disease Control and Prevention, Chamblee, Georgia 30341, United States
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19
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Theophilou G, Paraskevaidi M, Lima KMG, Kyrgiou M, Martin-Hirsch PL, Martin FL. Extracting biomarkers of commitment to cancer development: potential role of vibrational spectroscopy in systems biology. Expert Rev Mol Diagn 2015; 15:693-713. [DOI: 10.1586/14737159.2015.1028372] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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20
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Tripković T, Charvy C, Alves S, Lolić AĐ, Baošić RM, Nikolić-Mandić SD, Tabet JC. Electrospray ionization linear trap quadrupole Orbitrap in analysis of old tempera paintings: application to nineteenth-century Orthodox icons. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2015; 21:679-692. [PMID: 26353990 DOI: 10.1255/ejms.1346] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Proteomic approach in combination with mass spectrometry demonstrates a great potential for identification of proteinaceous materials in works of art. In this study we used a linear trap quadrupole Orbitrap (LTQ-Orbitrap), a state-of-the-art mass spectrometer for parts per million accuracy analyses of peptides behind tryptic hydrolysis. After the efficiency of the proteomic method was confirmed for reference and model samples, micro-samples from historical paintings were for the first time analysed using this technique. Superior performances of the liquid chromatography-mass spectrometry approach using a LTQ-Orbitrap mass spectrometer allowed identification of egg yolk peptides in two samples from nineteenth-century Orthodox icons, indicating egg tempera as the painting technique. Accurate precursor ion masses, in the range of ±2 ppm, and retention times of tryptic peptides strengthen protein identification. Additionally, in all historical samples the presence of animal glues suggested that the ground layer was likely bound using bovine collagen. Comparing to results acquired using matrix-assisted laser desorption/ionization time-of-flight tandem mass spectrometry in our previous study, here we achieved higher ion scores and protein scores, better sequence coverage and more identified proteins. In fact, a combination of the two mass spectrometric techniques provided overlapping and complementary data, related to the detection of peptides with different physicochemical properties.
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Affiliation(s)
- T Tripković
- Institute for the Protection of Cultural Monuments of Serbia, Radoslava Grujića 11, 11000 Belgrade, Serbia.
| | - C Charvy
- Universite Pierre et Marie Curie-Paris 6, Institut Parisien de Chimie Moleculaire, UMR 7201, 4 place Jussieu, 75252 Paris Cedex 05, France.
| | - S Alves
- Universite Pierre et Marie Curie-Paris 6, Institut Parisien de Chimie Moleculaire, UMR 7201, 4 place Jussieu, 75252 Paris Cedex 05, France.
| | - A Đ Lolić
- University of Belgrade, Faculty of Chemistry, Studentski trg 12, 11000 Belgrade, Serbia.
| | - R M Baošić
- University of Belgrade, Faculty of Chemistry, Studentski trg 12, 11000 Belgrade, Serbia.
| | - S D Nikolić-Mandić
- University of Belgrade, Faculty of Chemistry, Studentski trg 12, 11000 Belgrade, Serbia.
| | - J C Tabet
- Universite Pierre et Marie Curie-Paris 6, Institut Parisien de Chimie Moleculaire, UMR 7201, 4 place Jussieu, 75252 Paris Cedex 05, France.
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21
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Randall EC, Bunch J, Cooper HJ. Direct analysis of intact proteins from Escherichia coli colonies by liquid extraction surface analysis mass spectrometry. Anal Chem 2014; 86:10504-10. [PMID: 25333355 DOI: 10.1021/ac503349d] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Top-down identification of proteins by liquid extraction surface analysis (LESA) mass spectrometry has previously been reported for tissue sections and dried blood spot samples. Here, we present a modified "contact" LESA method for top-down analysis of proteins directly from living bacterial colonies grown in Petri dishes, without any sample pretreatment. It was possible to identify a number of proteins by use of collision-induced dissociation tandem mass spectrometry followed by searches of the data against an E. coli protein database. The proteins identified suggest that the method may provide insight into the bacterial response to environmental conditions. Moreover, the results show that the "contact" LESA approach results in a smaller sampling area than typical LESA, which may have implications for spatial profiling.
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Affiliation(s)
- Elizabeth C Randall
- School of Biosciences, University of Birmingham , Edgbaston, Birmingham, B15 2TT, United Kingdom
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22
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Samson M, Jow MM, Wong CCL, Fitzpatrick C, Aslanian A, Saucedo I, Estrada R, Ito T, Park SKR, Yates JR, Chu DS. The specification and global reprogramming of histone epigenetic marks during gamete formation and early embryo development in C. elegans. PLoS Genet 2014; 10:e1004588. [PMID: 25299455 PMCID: PMC4191889 DOI: 10.1371/journal.pgen.1004588] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Accepted: 07/09/2014] [Indexed: 11/18/2022] Open
Abstract
In addition to the DNA contributed by sperm and oocytes, embryos receive parent-specific epigenetic information that can include histone variants, histone post-translational modifications (PTMs), and DNA methylation. However, a global view of how such marks are erased or retained during gamete formation and reprogrammed after fertilization is lacking. To focus on features conveyed by histones, we conducted a large-scale proteomic identification of histone variants and PTMs in sperm and mixed-stage embryo chromatin from C. elegans, a species that lacks conserved DNA methylation pathways. The fate of these histone marks was then tracked using immunostaining. Proteomic analysis found that sperm harbor ∼2.4 fold lower levels of histone PTMs than embryos and revealed differences in classes of PTMs between sperm and embryos. Sperm chromatin repackaging involves the incorporation of the sperm-specific histone H2A variant HTAS-1, a widespread erasure of histone acetylation, and the retention of histone methylation at sites that mark the transcriptional history of chromatin domains during spermatogenesis. After fertilization, we show HTAS-1 and 6 histone PTM marks distinguish sperm and oocyte chromatin in the new embryo and characterize distinct paternal and maternal histone remodeling events during the oocyte-to-embryo transition. These include the exchange of histone H2A that is marked by ubiquitination, retention of HTAS-1, removal of the H2A variant HTZ-1, and differential reprogramming of histone PTMs. This work identifies novel and conserved features of paternal chromatin that are specified during spermatogenesis and processed in the embryo. Furthermore, our results show that different species, even those with diverged DNA packaging and imprinting strategies, use conserved histone modification and removal mechanisms to reprogram epigenetic information.
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Affiliation(s)
- Mark Samson
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Margaret M. Jow
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Catherine C. L. Wong
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California, United States of America
- Mass Spectrometry Division, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Science, Shanghai, China
| | - Colin Fitzpatrick
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Aaron Aslanian
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Israel Saucedo
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Rodrigo Estrada
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Takashi Ito
- Department of Biochemistry, Nagasaki University School of Medicine, Nagasaki, Japan
| | - Sung-kyu Robin Park
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California, United States of America
| | - John R. Yates
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Diana S. Chu
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
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23
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Zhang S, Van Pelt CK. Chip-based nanoelectrospray mass spectrometry for protein characterization. Expert Rev Proteomics 2014; 1:449-68. [PMID: 15966841 DOI: 10.1586/14789450.1.4.449] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
In the last several years, significant progress has been made in the development of microfluidic-based analytical technologies for proteomic and drug discovery applications. Chip-based nanoelectrospray coupled to a mass spectrometer detector is one of the recently developed analytical microscale technologies. This technology offers unique advantages for automated nanoelectrospray including reduced sample consumption, improved detection sensitivity and enhanced data quality for proteomic studies. This review presents an overview and introduction of recent developments in chip devices coupled to electrospray mass spectrometers including the development of the automated nanoelectrospray ionization chip device for protein characterization. Applications using automated chip-based nanoelectrospray ionization technology in proteomic and bioanalytical studies are also extensively reviewed in the fields of high-throughput protein identification, protein post-translational modification studies, top-down proteomics, biomarker screening by pattern recognition, noncovalent protein-ligand binding for drug discovery and lipid analysis. Additionally, future trends in chip-based nanoelectrospray technology are discussed.
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Affiliation(s)
- Sheng Zhang
- Cornell University, 135 Biotechnology Building, Ithaca, NY 14853, USA.
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24
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Chen G, Pramanik BN. LC-MS for protein characterization: current capabilities and future trends. Expert Rev Proteomics 2014; 5:435-44. [DOI: 10.1586/14789450.5.3.435] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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25
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Abstract
Proteomic analysis of membrane proteins is a promising approach for the identification of novel drug targets and/or disease biomarkers. Despite notable technological developments, obstacles related to extraction and solublization of membrane proteins are encountered. A critical discussion of the different preparative methods of membrane proteins is offered in relation to downstream proteomic applications, mainly gel-based analyses and mass spectrometry. Frequently, unknown proteins are identified by high-throughput profiling of membrane proteins. In search for novel membrane proteins, analysis of protein sequences using computational tools is performed to predict the presence of transmembrane domains. This review also presents these bioinformatic tools with the human proteome as a case study. Along with technological innovations, advancements in the areas of sample preparation and computational prediction of membrane proteins will lead to exciting discoveries.
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Affiliation(s)
- Mamoun Ahram
- Biological Sciences Division, Pacific Northwest National Laboratory, Battelle, PO Box 999, Richland, WA 99352, USA.
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26
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Affiliation(s)
- Shengwen Shen
- Department
of Laboratory Medicine
and Pathology, 10-102 Clinical Sciences Building, University
of Alberta, Edmonton, Alberta, Canada, T6G 2G3
| | - Xing-Fang Li
- Department
of Laboratory Medicine
and Pathology, 10-102 Clinical Sciences Building, University
of Alberta, Edmonton, Alberta, Canada, T6G 2G3
| | - William R. Cullen
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver,
British Columbia, Canada, V6T 1Z1
| | - Michael Weinfeld
- Department of Oncology, Cross
Cancer Institute, University of Alberta, 11560 University Avenue, Edmonton, Alberta, Canada, T6G 1Z2
| | - X. Chris Le
- Department
of Laboratory Medicine
and Pathology, 10-102 Clinical Sciences Building, University
of Alberta, Edmonton, Alberta, Canada, T6G 2G3
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27
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Ciechanover A, Stanhill A. The complexity of recognition of ubiquitinated substrates by the 26S proteasome. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2013; 1843:86-96. [PMID: 23872423 DOI: 10.1016/j.bbamcr.2013.07.007] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Revised: 07/02/2013] [Accepted: 07/08/2013] [Indexed: 02/03/2023]
Abstract
The Ubiquitin Proteasome System (UPS) was discovered in two steps. Initially, APF-1 (ATP-dependent proteolytic Factor 1) later identified as ubiquitin (Ub), a hitherto known protein of unknown function, was found to covalently modify proteins. This modification led to degradation of the tagged protein by - at that time - an unknown protease. This was followed later by the identification of the 26S proteasome complex which is composed of a previously identified Multi Catalytic Protease (MCP) and an additional regulatory complex, as the protease that degrades Ub-tagged proteins. While Ub conjugation and proteasomal degradation are viewed as a continued process responsible for most of the regulated proteolysis in the cell, the two processes have also independent roles. In parallel and in the years that followed, the hallmark signal that links the substrate to the proteasome was identified as an internal Lys48-based polyUb chain. However, since these initial findings were described, our understanding of both ends of the process (i.e. Ub-conjugation to proteins, and their recognition and degradation), have advanced significantly. This enabled us to start bridging the ends of this continuous process which suffered until lately from limited structural data regarding the 26S proteasomal architecture and the structure and diversity of the Ub chains. These missing pieces are of great importance because the link between ubiquitination and proteasomal processing is subject to numerous regulatory steps and are found to function improperly in several pathologies. Recently, the molecular architecture of the 26S proteasome was resolved in great detail, enabling us to address mechanistic questions regarding the various molecular events that polyubiquitinated (polyUb) substrates undergo during binding and processing by the 26S proteasome. In addition, advancement in analytical and synthetic methods enables us to better understand the structure and diversity of the degradation signal. The review summarizes these recent findings and addresses the extrapolated meanings in light of previous reports. Finally, it addresses some of the still remaining questions to be solved in order to obtain a continuous mechanistic view of the events that a substrate undergoes from its initial ubiquitination to proteasomal degradation. This article is part of a Special Issue entitled: Ubiquitin-Proteasome System. Guest Editors: Thomas Sommer and Dieter H. Wolf.
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Affiliation(s)
- Aaron Ciechanover
- The David and Janet Polak Cancer and Vascular Biology Research Center, The Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Haifa 31096, Israel
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28
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Mechanism exploration of adsorption-immobilized enzymatic reactor using polymer-coated silica microbeads. Talanta 2013; 110:101-7. [DOI: 10.1016/j.talanta.2013.02.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Revised: 02/04/2013] [Accepted: 02/08/2013] [Indexed: 11/22/2022]
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29
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Swigonska S, Weidner S. Proteomic analysis of response to long-term continuous stress in roots of germinating soybean seeds. JOURNAL OF PLANT PHYSIOLOGY 2013; 170:470-9. [PMID: 23394790 DOI: 10.1016/j.jplph.2012.11.020] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Revised: 10/12/2012] [Accepted: 11/16/2012] [Indexed: 05/27/2023]
Abstract
Germination is a complex process, highly dependent on various environmental factors, including temperature and water availability. Germinating soybean seeds are especially vulnerable to unfavorable environmental conditions and exposure to long-term abiotic stresses may result in diminishing much of the yield and most importantly - restrained germination. In the present study, a proteomic approach was employed to analyze influence of cold and osmotic stress on roots of germinated soybean (Glycine max, L.) seeds. Seeds were germinating under continuous conditions of cold stress (+10°C/H2O), osmotic stress (+25°C/-0.2MPa) as well as cold and osmotic stress combined (+10°C/-0.2MPa). Proteome maps established for control samples and stress-treated samples displayed 1272 CBB-stained spots. A total of 59 proteins, present in both control and stress-treated samples and showing significant differences in volume, were identified with LC/nanoESI-MS. Identified proteins divided into functional categories, revealed 9 proteins involved in plant defense, 8 proteins responsible for plant destination and storage and 10 proteins involved in various tracks of carbohydrate metabolism. Furthermore, a number of proteins were assigned to electron transport, range of metabolic pathways, secondary metabolism, protein synthesis, embryogenesis and development, signal transduction, cellular transport, translocation and storage. By analyzing differences in expression patterns, it was possible to trace the soybean response to long-term abiotic stress as well as to distinguish similarities and differences between response to cold and osmotic stress.
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Affiliation(s)
- Sylwia Swigonska
- Department of Biochemistry, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Oczapowskiego Street 1a, 10-957 Olsztyn, Poland.
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30
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Kravtsova-Ivantsiv Y, Sommer T, Ciechanover A. The lysine48-based polyubiquitin chain proteasomal signal: not a single child anymore. Angew Chem Int Ed Engl 2012; 52:192-8. [PMID: 23124625 DOI: 10.1002/anie.201205656] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Indexed: 11/07/2022]
Abstract
The conjugation of ubiquitin (Ub) to proteins is involved in the regulation of many processes. The modification serves as a recognition element in trans, in which downstream effectors bind to the modified protein and determine its fate and/or function. A polyUb chain that is linked through internal lysine (Lys)-48 of Ub and anchored to an internal Lys residue of the substrate has become the accepted "canonical" signal for proteasomal targeting and degradation. However, recent studies show that the signal is far more diverse and that chains based on other internal linkages, as well as linear or heterologous chains made of Ub and Ub-like proteins and even monoUb, are recognized by the proteasome. In addition, chains linked to residues other than internal Lys were described, all challenging the current paradigm.
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Affiliation(s)
- Yelena Kravtsova-Ivantsiv
- Cancer and Vascular Biology Research Center, Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel.
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31
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Ghosh SK, Yohannes E, Bebek G, Weinberg A, Jiang B, Willard B, Chance MR, Kinter MT, McCormick TS. Proteomic and bioinformatic profile of primary human oral epithelial cells. J Proteome Res 2012; 11:5492-502. [PMID: 23035736 DOI: 10.1021/pr3007254] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Wounding of the oral mucosa occurs frequently in a highly septic environment. Remarkably, these wounds heal quickly and the oral cavity, for the most part, remains healthy. Deciphering the normal human oral epithelial cell (NHOEC) proteome is critical for understanding the mechanism(s) of protection elicited when the mucosal barrier is intact, as well as when it is breached. Combining 2D gel electrophoresis with shotgun proteomics resulted in identification of 1662 NHOEC proteins. Proteome annotations were performed based on protein classes, molecular functions, disease association and membership in canonical and metabolic signaling pathways. Comparing the NHOEC proteome with a database of innate immunity-relevant interactions (InnateDB) identified 64 common proteins associated with innate immunity. Comparison with published salivary proteomes revealed that 738/1662 NHOEC proteins were common, suggesting that significant numbers of salivary proteins are of epithelial origin. Gene ontology analysis showed similarities in the distributions of NHOEC and saliva proteomes with regard to biological processes, and molecular functions. We also assessed the interindividual variability of the NHOEC proteome and observed it to be comparable with other primary cells. The baseline proteome described in this study should serve as a resource for proteome studies of the oral mucosa, especially in relation to disease processes.
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Affiliation(s)
- Santosh K Ghosh
- Department of Biological Sciences, Case Western Reserve University, Cleveland, Ohio 44106, USA.
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Cunsolo V, Muccilli V, Saletti R, Foti S. Mass spectrometry in the proteome analysis of mature cereal kernels. MASS SPECTROMETRY REVIEWS 2012; 31:448-465. [PMID: 22711440 DOI: 10.1002/mas.20347] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Revised: 07/07/2011] [Accepted: 07/07/2011] [Indexed: 06/01/2023]
Abstract
In the last decade, the improved performance and versatility of the mass spectrometers together with the increasing availability of gene and genomic sequence database, led the mass spectrometry to become an indispensable tool for either protein and proteome analyses in cereals. Mass spectrometric works on prolamins have rapidly evolved from the determination of the molecular masses of proteins to the proteomic approaches aimed to a large-scale protein identification and study of functional and regulatory aspects of proteins. Mass spectrometry coupled with electrophoresis, chromatographic methods, and bioinformatics tools is currently making significant contributions to a better knowledge of the composition and structure of the cereal proteins and their structure-function relationships. Results obtained using mass spectrometry, including characterization of prolamins, investigation of the gluten toxicity for coeliac patients, identification of proteins responsible of cereal allergies, determination of the protein pattern and its modification under environmental or stress effects, investigation of genetically modified varieties by proteomic approaches, are summarized here, to illustrate current trends, analytical troubles and challenges, and suggest possible future perspectives.
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Affiliation(s)
- Vincenzo Cunsolo
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Italy
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Ngara R, Ndimba R, Borch-Jensen J, Jensen ON, Ndimba B. Identification and profiling of salinity stress-responsive proteins in Sorghum bicolor seedlings. J Proteomics 2012; 75:4139-50. [DOI: 10.1016/j.jprot.2012.05.038] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2012] [Revised: 05/18/2012] [Accepted: 05/21/2012] [Indexed: 11/27/2022]
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Liu H, Yang Z, Yang M, Shen S. The differential proteome of endosperm and embryo from mature seed of Jatropha curcas. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2011; 181:660-6. [PMID: 21958708 DOI: 10.1016/j.plantsci.2011.03.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2010] [Revised: 01/24/2011] [Accepted: 03/18/2011] [Indexed: 05/23/2023]
Abstract
Jatrpha curcas L., a non-model woody plant belonging to Euphorbiaceae family, is a promising economic plant due to the high oil content in seed and high tolerance to drought and salt stress. The embryo and endosperm of J. curcas seed differ in morphology, function and ploidy. To characterize the protein profiles of these two tissues, we have performed proteomic analysis with the dry mature J. curcas seeds. The data showed that the 2-DE profiles of endosperm and embryo were similar to each other. There are 66 differential proteins between the two seed tissues, in which 28 proteins distributed in 9 distinct functional classes, have been identified successfully in endosperm or embryo. The major groups of differential proteins are associated with metabolism (25%) and disease/defence (18%). Our results demonstrated that in the dry mature J. curcas seeds, the proteins involved in oil mobilization, signal transduction, transcription, protein synthesis, and cell cycle which are essential for the seed germination have occurred in endosperm and embryo, reflecting the fact that proteins required for germination are already present in the dry mature seed.
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Affiliation(s)
- Hui Liu
- Key Laboratory of Research and Development for Resource Plant, Institute of Botany, The Chinese Academy of Sciences, Beijing, China
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Zhou Z, Gu J, Du YL, Li YQ, Wang Y. The -omics Era- Toward a Systems-Level Understanding of Streptomyces. Curr Genomics 2011; 12:404-16. [PMID: 22379394 PMCID: PMC3178909 DOI: 10.2174/138920211797248556] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2011] [Revised: 06/28/2011] [Accepted: 07/03/2011] [Indexed: 11/22/2022] Open
Abstract
Streptomyces is a group of soil bacteria of medicinal, economic, ecological, and industrial importance. It is renowned for its complex biology in gene regulation, antibiotic production, morphological differentiation, and stress response. In this review, we provide an overview of the recent advances in Streptomyces biology inspired by -omics based high throughput technologies. In this post-genomic era, vast amounts of data have been integrated to provide significant new insights into the fundamental mechanisms of system control and regulation dynamics of Streptomyces.
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Affiliation(s)
- Zhan Zhou
- College of Life Sciences, Zhejiang University, Hangzhou 310058, P.R. China
- Department of Biology, University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Jianying Gu
- Department of Biology, College of Staten Island, City University of New York, Staten Island, NY 10314, USA
| | - Yi-Ling Du
- College of Life Sciences, Zhejiang University, Hangzhou 310058, P.R. China
| | - Yong-Quan Li
- College of Life Sciences, Zhejiang University, Hangzhou 310058, P.R. China
| | - Yufeng Wang
- Department of Biology, University of Texas at San Antonio, San Antonio, TX 78249, USA
- South Texas Center for Emerging Infectious Diseases, University of Texas at San Antonio, San Antonio, TX 78249, USA
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Schieltz DM, McGrath SC, McWilliams LG, Rees J, Bowen MD, Kools JJ, Dauphin LA, Gomez-Saladin E, Newton BN, Stang HL, Vick MJ, Thomas J, Pirkle JL, Barr JR. Analysis of active ricin and castor bean proteins in a ricin preparation, castor bean extract, and surface swabs from a public health investigation. Forensic Sci Int 2011; 209:70-9. [PMID: 21251774 DOI: 10.1016/j.forsciint.2010.12.013] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2010] [Revised: 11/29/2010] [Accepted: 12/15/2010] [Indexed: 11/20/2022]
Abstract
In late February 2008, law enforcement officials in Las Vegas, Nevada, discovered in a hotel room, a copy of The Anarchist Cookbook, suspected castor beans and a "white powder" thought to be a preparation of ricin. Ricin is a deadly toxin from the seed of the castor bean plant (Ricinus communis). The United States regulates the possession, use, and transfer of ricin and it is the only substance considered a warfare agent in both the Chemical and the Biological Weapons Conventions. Six samples obtained from the hotel room were analyzed by laboratories at the Centers for Disease Control and Prevention using a panel of biological and mass spectrometric assays. The biological assays (real time-PCR, time resolved fluorescence and cytotoxicity) provided presumptive evidence of active ricin in each of the samples. This initial screen was followed by an in-depth analysis using a novel, state-of-the-art mass spectrometry-based ricin functional assay and high sensitivity tandem mass spectrometry for protein identification. Mass spectrometric analysis positively identified ricin and confirmed that in each of the samples it was enzymatically active. The tandem mass spectrometry analysis used here is the most selective method available to detect ricin toxin. In each sample, ricin was unequivocally identified along with other R. communis plant proteins, including the highly homologous protein RCA120. Although database searches using tandem mass spectra acquired from the samples indicated that additional controlled substances were not present in these samples, the mass spectrometric results did provide extensive detail about the sample contents. To the best of our knowledge following a review of the available literature, this report describes the most detailed analysis of a white powder for a public health or forensic investigation involving ricin.
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Affiliation(s)
- David M Schieltz
- Emergency Response and Air Toxicants Branch, Division of Laboratory Sciences, National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, GA 30341, USA
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Rozenbrand J, de Jong GJ, van Bennekom WP. Comparison of monolithic and 1.8-μm RP-18 silica capillary columns using chromatographic data and mass spectrometric identification scores for proteins. J Sep Sci 2011; 34:2199-205. [DOI: 10.1002/jssc.201100151] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2011] [Revised: 04/20/2011] [Accepted: 04/20/2011] [Indexed: 11/09/2022]
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38
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Complete genome sequence and immunoproteomic analyses of the bacterial fish pathogen Streptococcus parauberis. J Bacteriol 2011; 193:3356-66. [PMID: 21531805 DOI: 10.1128/jb.00182-11] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Although Streptococcus parauberis is known as a bacterial pathogen associated with bovine udder mastitis, it has recently become one of the major causative agents of olive flounder (Paralichthys olivaceus) streptococcosis in northeast Asia, causing massive mortality resulting in severe economic losses. S. parauberis contains two serotypes, and it is likely that capsular polysaccharide antigens serve to differentiate the serotypes. In the present study, the complete genome sequence of S. parauberis (serotype I) was determined using the GS-FLX system to investigate its phylogeny, virulence factors, and antigenic proteins. S. parauberis possesses a single chromosome of 2,143,887 bp containing 1,868 predicted coding sequences (CDSs), with an average GC content of 35.6%. Whole-genome dot plot analysis and phylogenetic analysis of a 60-kDa chaperonin-encoding gene and the glyceraldehyde-3-phosphate dehydrogenase (GAPDH)-encoding gene showed that the strain was evolutionarily closely related to Streptococcus uberis. S. parauberis antigenic proteins were analyzed using an immunoproteomic technique. Twenty-one antigenic protein spots were identified in S. parauberis, by reaction with an antiserum obtained from S. parauberis-challenged olive flounder. This work provides the foundation needed to understand more clearly the relationship between pathogen and host and develops new approaches toward prophylactic and therapeutic strategies to deal with streptococcosis in fish. The work also provides a better understanding of the physiology and evolution of a significant representative of the Streptococcaceae.
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Kiyonami R, Schoen A, Prakash A, Peterman S, Zabrouskov V, Picotti P, Aebersold R, Huhmer A, Domon B. Increased selectivity, analytical precision, and throughput in targeted proteomics. Mol Cell Proteomics 2010; 10:M110.002931. [PMID: 20664071 PMCID: PMC3033677 DOI: 10.1074/mcp.m110.002931] [Citation(s) in RCA: 132] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Proteomics is gradually complementing large shotgun qualitative studies with hypothesis-driven quantitative experiments. Targeted analyses performed on triple quadrupole instruments in selected reaction monitoring mode are characterized by a high degree of selectivity and low limit of detection; however, the concurrent analysis of multiple analytes occurs at the expense of sensitivity because of reduced dwell time and/or selectivity due to limitation to a few transitions. A new data acquisition paradigm is presented in which selected reaction monitoring is performed in two ways to simultaneously quantify and confirm the identity of the targeted peptides. A first set of primary transitions is continuously monitored during a predetermined elution time window to precisely quantify each peptide. In addition, a set of six to eight transitions is acquired in a data-dependent event, triggered when all the primary transitions exceed a preset threshold. These additional transitions are used to generate composite tandem mass spectra to formally confirm the identity of the targeted peptides. This technique was applied to analyze the tryptic digest of a yeast lysate to demonstrate the performance of the technique. We showed a limit of detection down to tens of attomoles injected and a throughput exceeding 6000 transitions in one 60-min experiment. The technique was integrated into a linear work flow, including experimental design, data acquisition, and data evaluation, enabling large scale proteomic studies.
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Affiliation(s)
- Reiko Kiyonami
- ThermoFisher Scientific, San Jose, California 95134, USA
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40
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Protein identification from two-dimensional gel electrophoresis by connecting ZipTip with a home-assembled nanoflow system. Mikrochim Acta 2010. [DOI: 10.1007/s00604-010-0399-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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41
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Knyazev VD, Stein SE. Monte Carlo/RRKM/Classical Trajectories Modeling of Collisional Excitation and Dissociation of n-Butylbenzene Ion in Multipole Collision Cells of Tandem Mass Spectrometers. J Phys Chem A 2010; 114:6384-93. [DOI: 10.1021/jp101526m] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Vadim D. Knyazev
- Chemical and Biochemical Reference Data Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, and Research Center for Chemical Kinetics, Department of Chemistry, The Catholic University of America, Washington, D.C. 20064
| | - Stephen E. Stein
- Chemical and Biochemical Reference Data Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, and Research Center for Chemical Kinetics, Department of Chemistry, The Catholic University of America, Washington, D.C. 20064
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42
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Knyazev VD, Stein SE. Classical trajectories and RRKM modeling of collisional excitation and dissociation of benzylammonium and tert-butyl benzylammonium ions in a quadrupole-hexapole-quadrupole tandem mass spectrometer. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2010; 21:425-439. [PMID: 20060316 DOI: 10.1016/j.jasms.2009.11.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2009] [Revised: 11/24/2009] [Accepted: 11/24/2009] [Indexed: 05/28/2023]
Abstract
Collision-induced dissociation of the benzylammonium and the 4-tert-butyl benzylammonium ions was studied experimentally in an electrospray ionization quadrupole-hexapole-quadrupole tandem mass spectrometer. Ion fragmentation efficiencies were determined as functions of the kinetic energy of ions and the collider gas (argon) pressure. A theoretical Monte Carlo model of ion collisional excitation, scattering, and decomposition was developed. The model includes simulation of the trajectories of the parent and the product ions flight through the hexapole collision cell, quasiclassical trajectory modeling of collisional activation and scattering of ions, and Rice-Ramsperger-Kassel-Marcus (RRKM) modeling of the parent ion decomposition. The results of modeling demonstrate a general agreement between calculations and experiment. Calculated values of ion fragmentation efficiency are sensitive to initial vibrational excitation of ions, scattering of product ions from the collision cell, and distribution of initial ion velocities orthogonal to the axis of the collision cell. Three critical parameters of the model were adjusted to reproduce the experimental data on the dissociation of the benzylammonium ion: reaction enthalpy and initial internal and translational temperatures of the ions. Subsequent application of the model to decomposition of the t-butyl benzylammonium ion required adjustment of the internal ion temperature only. Energy distribution functions obtained in modeling depend on the average numbers of collisions between the ion and the atoms of the collider gas and, in general, have non-Boltzmann shapes.
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Affiliation(s)
- Vadim D Knyazev
- National Institute of Standards and Technology, Physical and Chemical Properties Division, Gaithersburg, Maryland, USA.
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43
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Hodgkinson VC, Eagle GL, Drew PJ, Lind MJ, Cawkwell L. Biomarkers of chemotherapy resistance in breast cancer identified by proteomics: current status. Cancer Lett 2010; 294:13-24. [PMID: 20176436 DOI: 10.1016/j.canlet.2010.01.036] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2009] [Revised: 01/26/2010] [Accepted: 01/29/2010] [Indexed: 11/26/2022]
Abstract
This review describes and discusses the advantages and limitations of proteomic approaches in the identification of biomarkers associated with chemotherapy resistance. Both gel-based (two-dimensional polyacrylamide gel electrophoresis) and gel-free (shotgun and quantitative) mass spectrometry approaches are discussed. Non-mass spectrometry approaches including antibody microarray platforms are described as complementary proteomic strategies. Methods for technical confirmation and clinical validation of putative biomarkers are presented. Use of this proteomic toolbox in the quest for biomarkers of chemotherapy resistance in breast cancer is reviewed. Technical aspects of sample selection, acquisition, storage and analysis are discussed and putative biomarkers identified through proteomic approaches are presented.
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Affiliation(s)
- Victoria C Hodgkinson
- Cancer Biology Proteomics Group, Postgraduate Medical Institute of the University of Hull, Hull, UK
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44
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Abstract
The review describes methods of de novo sequencing of peptides by mass spectrometry. De novo methods utilize computational approaches to deduce the sequence or partial sequence of peptides directly from the experimental MS/MS spectra. The concepts behind a number of de novo sequencing methods are discussed. The other approach to identify peptides by tandem mass spectrometry is to match the fragment ions with virtual peptide ions generated from a genomic or protein database. De novo methods are essential to identify proteins when the genomes are not known but they are also extremely useful even when the genomes are known since they are not affected by errors in a search database. Another advantage of de novo methods is that the partial sequence can be used to search for posttranslation modifications or for the identification of mutations by homology based software.
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Affiliation(s)
- Christopher Hughes
- Department of Biochemistry, University of Western Ontario, London, ON, Canada
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45
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Volchenboum SL, Kristjansdottir K, Wolfgeher D, Kron SJ. Rapid validation of Mascot search results via stable isotope labeling, pair picking, and deconvolution of fragmentation patterns. Mol Cell Proteomics 2009; 8:2011-22. [PMID: 19435713 DOI: 10.1074/mcp.m800472-mcp200] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Conventional LC-MS/MS data analysis matches each precursor ion and fragmentation pattern to their best fit within databases of theoretical spectra, yielding a peptide identification. Confidence is estimated by a score but can be validated by statistics, false discovery rates, and/or manual validation. A weakness is that each ion is evaluated independently, discarding potentially useful cross-correlations. In a classical approach to de novo sequence analysis, mixtures of peptides differing only in a carboxyl-terminal isotopic label yield fragmentation spectra with single, unlabeled b-type ions but pairs of isotope-labeled y-type ions, facilitating confident assignments. To apply this principle to identification by fragmentation pattern matching, we developed Validator, software that recognizes isotopic peptide pairs and compares their identifications and fragmentation patterns. Testing Validator 1 on a Mascot results file from FT-ICR LC-MS/MS of (16)O/(18)O-labeled yeast cell lysate peptides yielded 2,775 peptide pairs sharing a common identification but differing in carboxyl-terminal label. Comparing observed b- and y-ions with the predicted fragmentation pattern improved the threshold Mascot score for 5% false discovery from 36 to 22, significantly increasing both sensitivity and specificity. Validator 2, which identifies pairs by precursor mass difference alone before comparing observed fragmentation with that predicted by Mascot, found 2,021 isotopic pairs, similarly achieving improved sensitivity and specificity. Finally Validator 3, which finds pairs based on mass difference alone and then deconvolutes fragmentation patterns independently of Mascot, found 964 predicted peptides. Validator 3 allowed raw mass spectrometry data to be mined not only to validate Mascot results but also to discover peptides missed by Mascot. Using standard desktop hardware, the Validator 1-3 software processed the 11,536 spectra in the 93-MB Mascot .DAT file in less than 6 min (32 spectra/s), revealing high confidence peptide identifications without regard to Mascot score, far faster than manual or other independent validation methods.
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Affiliation(s)
- Samuel L Volchenboum
- Department of Pediatrics, The University of Chicago, Chicago, Illinois 60637, USA.
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46
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Satoh M, Tokoro M, Ikegami H, Nagai K, Sono Y, Shin SW, Nishikawa S, Saeki K, Hosoi Y, Iritani A, Fukuda A, Morimoto Y, Matsumoto K. Proteomic analysis of the mouse ovary in response to two gonadotropins, follicle-stimulating hormone and luteinizing hormone. J Reprod Dev 2009; 55:316-26. [PMID: 19325216 DOI: 10.1262/jrd.20217] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Functional and structural changes in the mammalian ovary are coordinately regulated by the pituitary glycoprotein hormones, follicle-stimulating hormone (FSH) and luteinizing hormone (LH), leading to follicular development, ovulation and transformation of follicles into corpus lutea. To investigate protein profiles during these processes of the mouse ovarian cycle, we applied combined methods (two-dimensional gel electrophoresis [2-DE] for separation and visualization of proteins plus matrix laser desorption/ionization time-of-flight mass spectrometry [MALDI-TOF/MS] analysis for protein identification) for comparative proteomic analysis using immature mice at 3 weeks of age. Protein profiles were obtained from proteins extracted from intact ovaries that had been collected from pregnant mare serum gonadotropin (PMSG)/human chorionic gonadotropin (hCG)-primed immature mice at 0 (no PMSG), 24 and 48 h post PMSG, as well as at 10 and 20 h post hCG. The results showed that 1028 common protein spots were found in representative gels that had been separated in the 3 to 11 pH range and the 15-200 kDa range, 253 protein spots (24.6%) of which were differentially expressed (p<0.05) during the mouse ovarian cycle. Of these 253 protein spots, 99 were identified by MALDI-TOF/MS. This comparative proteomic approach to identifying proteins that were potentially involved in the complex process of the ovarian cycle could contribute to our understanding of the molecular basis of functional and structural changes in the ovary in response to gonadotropins. Furthermore, the interesting ovarian proteins identified in this study may eventually serve as diagnostic biomarker candidates of ovarian function.
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Affiliation(s)
- Manabu Satoh
- The Centre for Reproductive Medicine and Infertility, IVF Namba Clinic
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47
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Ndimba BK, Thomas LA. Proteomics in South Africa: current status, challenges and prospects. Biotechnol J 2009; 3:1368-74. [PMID: 19016510 DOI: 10.1002/biot.200800236] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Proteomics is a biotechnology research area that is generally defined as the large-scale study of protein expression, structure and functions. Primarily, proteomics is used to study relative cellular, subcellular and extracellular abundances of proteins expressed at a defined physiological state on a large scale. In contrast to the analysis of mRNA expression studies, generally referred to as transcriptomics, proteomics approaches take into consideration the post-transcriptional, translational and post-translational modifications of polypeptides. Over the past 10 years, the proteomics field has been growing tremendously and contributing positively to biotechnology, particularly in North America, Europe and Asia. Research output in Africa is still very low in comparison. This article reviews proteomics capacity as well as research activities in South Africa. We highlight, with examples, the potential that this technology has in the acceleration of disease biomarker discovery and its role in drug design. Our ultimate objective is to promote further developments, research and applications of proteomics in South Africa, aiming for the generation of new scientific knowledge for our continent and for the rest of the world.
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Affiliation(s)
- Bongani K Ndimba
- Proteomics Research Group, Department of Biotechnology, University of the Western Cape, Bellville, South Africa.
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48
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Tuytten R, Ruttens B, Gheysen K, Sandra K, De Cremer K, Vlieghe D, Van Landuyt N, Thomas G, Martins JC, Sandra P, Kas K, Verleysen K. Application of a Combined Weak Cation-Exchange/Crown Ether Column: First Demonstrations of a Versatile Tool for Proteome Subselection. Anal Chem 2009; 81:2456-69. [DOI: 10.1021/ac801975b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Robin Tuytten
- Pronota NV, VIB Bioincubator, Technologiepark 4, B-9052 Zwijnaarde Ghent, Belgium; NMR and Structural Analysis Unit, Department of Organic Chemistry, Krijgslaan 281 S4, Ghent University, B-9000 Ghent, Belgium, and Research Institute for Chromatography (RIC), B-8510 Kortrijk, Belgium
| | - Bart Ruttens
- Pronota NV, VIB Bioincubator, Technologiepark 4, B-9052 Zwijnaarde Ghent, Belgium; NMR and Structural Analysis Unit, Department of Organic Chemistry, Krijgslaan 281 S4, Ghent University, B-9000 Ghent, Belgium, and Research Institute for Chromatography (RIC), B-8510 Kortrijk, Belgium
| | - Katelijne Gheysen
- Pronota NV, VIB Bioincubator, Technologiepark 4, B-9052 Zwijnaarde Ghent, Belgium; NMR and Structural Analysis Unit, Department of Organic Chemistry, Krijgslaan 281 S4, Ghent University, B-9000 Ghent, Belgium, and Research Institute for Chromatography (RIC), B-8510 Kortrijk, Belgium
| | - Koen Sandra
- Pronota NV, VIB Bioincubator, Technologiepark 4, B-9052 Zwijnaarde Ghent, Belgium; NMR and Structural Analysis Unit, Department of Organic Chemistry, Krijgslaan 281 S4, Ghent University, B-9000 Ghent, Belgium, and Research Institute for Chromatography (RIC), B-8510 Kortrijk, Belgium
| | - Koen De Cremer
- Pronota NV, VIB Bioincubator, Technologiepark 4, B-9052 Zwijnaarde Ghent, Belgium; NMR and Structural Analysis Unit, Department of Organic Chemistry, Krijgslaan 281 S4, Ghent University, B-9000 Ghent, Belgium, and Research Institute for Chromatography (RIC), B-8510 Kortrijk, Belgium
| | - Dominique Vlieghe
- Pronota NV, VIB Bioincubator, Technologiepark 4, B-9052 Zwijnaarde Ghent, Belgium; NMR and Structural Analysis Unit, Department of Organic Chemistry, Krijgslaan 281 S4, Ghent University, B-9000 Ghent, Belgium, and Research Institute for Chromatography (RIC), B-8510 Kortrijk, Belgium
| | - Natalie Van Landuyt
- Pronota NV, VIB Bioincubator, Technologiepark 4, B-9052 Zwijnaarde Ghent, Belgium; NMR and Structural Analysis Unit, Department of Organic Chemistry, Krijgslaan 281 S4, Ghent University, B-9000 Ghent, Belgium, and Research Institute for Chromatography (RIC), B-8510 Kortrijk, Belgium
| | - Grégoire Thomas
- Pronota NV, VIB Bioincubator, Technologiepark 4, B-9052 Zwijnaarde Ghent, Belgium; NMR and Structural Analysis Unit, Department of Organic Chemistry, Krijgslaan 281 S4, Ghent University, B-9000 Ghent, Belgium, and Research Institute for Chromatography (RIC), B-8510 Kortrijk, Belgium
| | - José C. Martins
- Pronota NV, VIB Bioincubator, Technologiepark 4, B-9052 Zwijnaarde Ghent, Belgium; NMR and Structural Analysis Unit, Department of Organic Chemistry, Krijgslaan 281 S4, Ghent University, B-9000 Ghent, Belgium, and Research Institute for Chromatography (RIC), B-8510 Kortrijk, Belgium
| | - Pat Sandra
- Pronota NV, VIB Bioincubator, Technologiepark 4, B-9052 Zwijnaarde Ghent, Belgium; NMR and Structural Analysis Unit, Department of Organic Chemistry, Krijgslaan 281 S4, Ghent University, B-9000 Ghent, Belgium, and Research Institute for Chromatography (RIC), B-8510 Kortrijk, Belgium
| | - Koen Kas
- Pronota NV, VIB Bioincubator, Technologiepark 4, B-9052 Zwijnaarde Ghent, Belgium; NMR and Structural Analysis Unit, Department of Organic Chemistry, Krijgslaan 281 S4, Ghent University, B-9000 Ghent, Belgium, and Research Institute for Chromatography (RIC), B-8510 Kortrijk, Belgium
| | - Katleen Verleysen
- Pronota NV, VIB Bioincubator, Technologiepark 4, B-9052 Zwijnaarde Ghent, Belgium; NMR and Structural Analysis Unit, Department of Organic Chemistry, Krijgslaan 281 S4, Ghent University, B-9000 Ghent, Belgium, and Research Institute for Chromatography (RIC), B-8510 Kortrijk, Belgium
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Jiang X, Dong J, Wang F, Feng S, Ye M, Zou H. Automation of nanoflow liquid chromatography-tandem mass spectrometry for proteome and peptide profiling analysis by using a monolithic analytical capillary column. Electrophoresis 2008; 29:1612-8. [DOI: 10.1002/elps.200700513] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Wang J, Wei Y, Wang D, Chan LL, Dai J. Proteomic study of the effects of complex environmental stresses in the livers of goldfish (Carassius auratus) that inhabit Gaobeidian Lake in Beijing, China. ECOTOXICOLOGY (LONDON, ENGLAND) 2008; 17:213-220. [PMID: 18080750 DOI: 10.1007/s10646-007-0187-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2007] [Accepted: 12/04/2007] [Indexed: 05/25/2023]
Abstract
Recent advances in proteomics have provided an excellent opportunity to understand biological adaptation under complex environmental stress at the protein level. Gaobeidian Lake, located in Beijing, China, is characterized by complex environmental stresses by serving as both the effluent of a wastewater treatment plant and a coolant of a nearby thermal power plant. Liver is the primary organ of energy metabolism and xenobiotic detoxification. To further our understanding of how organisms that live in Gaobeidian Lake acclimatize themselves to these complex environmental stresses, hepatic protein expression patterns were examined in goldfish Carassius auratus that inhabit the lake. Huairou Reservoir, a drinking water source, was used as a reference site. Twenty four protein spots, which were differently expressed in the two sites, were further digested with trypsin and analyzed by matrix-assisted laser desorption/ionization (MALDI) tandem time of flight mass spectrometry (TOF/TOF). The expression of several energy metabolism and oxidative stress proteins, such as glutathione peroxidase (GPx), ferritin H3, and liver basic fatty acid-binding protein (Lb-FABP) were found to be altered in this stressful environment. In addition to the up-regulation of GPx translation, both the mRNA levels and enzymatic activity of GPx protein were elevated in goldfish living in Gaobeidian Lake. The expression of both peroxisome proliferator activated receptor (PPAR), one of the most important metabolism and stress regulation genes as well as cytochrome P450 1A1 (CYP1A1), a detoxification gene, was also detected by real-time PCR at the two sites. Increased expression levels of both PPAR-beta and CYP1A1 (P < 0.1) were observed in Gaobeidian Lake. Our study provides an integrative view of the expression levels of hepatic proteins and genes in goldfish under complex environmental stress that live in Gaobeidian Lake. Our results showed that anthropogenic environmental stresses in Gaobeidian Lake activated the regulation gene of lipid metabolism PPAR, elevated the lipid metabolism levels, and activated the anti-oxidative adaptation mechanism of organisms in the lake.
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Affiliation(s)
- Jianshe Wang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, P.R. China
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