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Jin X, Zhu L, Tao C, Xie Q, Xu X, Chang L, Tan Y, Ding G, Li H, Wang X. An improved protein extraction method applied to cotton leaves is compatible with 2-DE and LC-MS. BMC Genomics 2019; 20:285. [PMID: 30975097 PMCID: PMC6458646 DOI: 10.1186/s12864-019-5658-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Accepted: 03/29/2019] [Indexed: 12/16/2022] Open
Abstract
Background Two-dimensional electrophoresis (2-DE) and liquid chromatography-tandem mass spectrometry (LC-MS/MS) are widely used in plant proteomics research. However, these two techniques cannot be simultaneously satisfied by traditional protein extraction methods when investigate cotton leaf proteome. Results Here, we evaluated the efficiency of three different protein extraction methods for 2-DE and LC-MS/MS analyses of total proteins obtained from cotton leaves. The protein yield of the borax/PVPP/phenol (BPP) method (0.14%) was significantly lower than the yields of the trichloroacetic acid/acetone (TCA) precipitation method (1.42%) and optimized TCA combined with BPP (TCA-B) method (0.47%). The BPP method was failed to get a clear 2-DE electrophoretogram. Fifty pairs of protein spots were randomly selected from the 2-DE gels of TCA- and TCA-B-extracted proteins for identification by MALDI TOF/TOF, and the results of 42 pairs were consistent. High-throughput proteomic analysis showed that 6339, 9282 and 9697 unique proteins were identified from the total cotton leaf proteins extracted by the TCA, BPP and TCA-B methods, respectively. Gene Ontology (GO) analysis revealed that the proteins specifically identified by TCA method were primarily distributed in the plasma membrane, while BPP and TCA-B methods specific proteins distributed in the cytosol, indicating the sub-cellular preference of different protein extraction methods. Further, ATP-dependent zinc metalloprotease FTSH 8 could be observed in the 2-DE gels of TCA and TCA-B methods, and could only be detected in the LC-MS/MS results of the BPP and TCA-B methods, showing that TCA-B method might be the optimized choice for both 2-DE and LC-MS/MS. Conclusion Our data provided an improved TCA-B method for protein extraction that is compatible with 2-DE and LC-MS/MS for cotton leaves and similar plant tissues which is rich in polysaccharides and polyphenols. Electronic supplementary material The online version of this article (10.1186/s12864-019-5658-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xiang Jin
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, 571158, China.,College of Life Sciences, Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Shihezi University, Shihezi, 832003, China
| | - Liping Zhu
- College of Life Sciences, Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Shihezi University, Shihezi, 832003, China
| | - Chengcheng Tao
- College of Life Sciences, Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Shihezi University, Shihezi, 832003, China
| | - Quanliang Xie
- College of Life Sciences, Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Shihezi University, Shihezi, 832003, China
| | - Xinyang Xu
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, 571158, China
| | - Lili Chang
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China
| | - Yanhua Tan
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China
| | - Guohua Ding
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, 571158, China
| | - Hongbin Li
- College of Life Sciences, Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Shihezi University, Shihezi, 832003, China.
| | - Xuchu Wang
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, 571158, China. .,College of Life Sciences, Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Shihezi University, Shihezi, 832003, China. .,Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China.
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Exercise Training Impacts Cardiac Mitochondrial Proteome Remodeling in Murine Urothelial Carcinoma. Int J Mol Sci 2018; 20:ijms20010127. [PMID: 30602657 PMCID: PMC6337197 DOI: 10.3390/ijms20010127] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 12/21/2018] [Accepted: 12/24/2018] [Indexed: 12/28/2022] Open
Abstract
Cardiac dysfunction secondary to cancer may exert a negative impact in patients’ tolerance to therapeutics, quality of life, and survival. The aim of this study was to evaluate the potential therapeutic effect of exercise training on the heart in the setting of cancer, after diagnosis. Thus, the molecular pathways harbored in heart mitochondria from a murine model of chemically-induced urothelial carcinoma submitted to 8-weeks of high intensity treadmill exercise were characterized using mass spectrometry-based proteomics. Data highlight the protective effects of high intensity exercise training in preventing left ventricle diastolic dysfunction, fibrosis, and structural derangement observed in tumor-bearing mice. At the mitochondrial level, exercise training counteracted the lower ability to produce ATP observed in the heart of animals with urothelial carcinoma and induced the up-regulation of fatty acid oxidation and down-regulation of the biological process “cardiac morphogenesis”. Taken together, our data support the prescription of exercise training after cancer diagnosis for the management of disease-related cardiac dysfunction.
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The histone H2A isoform Hist2h2ac is a novel regulator of proliferation and epithelial–mesenchymal transition in mammary epithelial and in breast cancer cells. Cancer Lett 2017; 396:42-52. [DOI: 10.1016/j.canlet.2017.03.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 03/01/2017] [Accepted: 03/03/2017] [Indexed: 01/11/2023]
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Di Venere M, Viglio S, Sassera D, Fumagalli M, Bardoni A, Salvini R, Cagnone M, Iadarola P. Do the complementarities of electrokinetic and chromatographic procedures represent the "Swiss knife" in proteomic investigation? An overview of the literature in the past decade. Electrophoresis 2017; 38:1538-1550. [PMID: 28130906 DOI: 10.1002/elps.201600504] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 01/11/2017] [Accepted: 01/11/2017] [Indexed: 12/21/2022]
Abstract
This report reviews the literature of the past decade dealing with the combination of electrokinetic and chromatographic strategies in the proteomic field. Aim of this article is to highlight how the application of complementary techniques may contribute to substantially improve protein identification. Several studies here considered demonstrate that exploring the combination of these approaches can be a strategy to enrich the extent of proteomic information achieved from a sample. The coupling of "top-down" and "bottom-up" proteomics may result in the generation of a hybrid analytical tool, very efficient not only for large-scale profiling of complex proteomes but also for studying specific subproteomes. The range of applications described, while evidencing a continuous boost in the imagination of researchers for developing new combinations of methods for protein separation, also underlines the adaptability of these techniques to a wide variety of samples. This report points out the general usefulness of combining different procedures for proteomic analysis, an approach that allows researchers to go deeper in the proteome of samples under investigation.
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Affiliation(s)
- Monica Di Venere
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Italy
| | - Simona Viglio
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Italy
| | - Davide Sassera
- Department of Biology and Biotechnologies "L. Spallanzani,", Biochemistry Unit, University of Pavia, Italy
| | - Marco Fumagalli
- Department of Biology and Biotechnologies "L. Spallanzani,", Biochemistry Unit, University of Pavia, Italy
| | - Anna Bardoni
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Italy
| | - Roberta Salvini
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Italy
| | - Maddalena Cagnone
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Italy
| | - Paolo Iadarola
- Department of Biology and Biotechnologies "L. Spallanzani,", Biochemistry Unit, University of Pavia, Italy
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Proteomic studies with a novel nano-magnetic chelating system to capture metalloproteins and its application in the preliminary study of monocyte and macrophage sub-secretome. Talanta 2016; 158:110-117. [PMID: 27343584 DOI: 10.1016/j.talanta.2016.05.051] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 05/13/2016] [Accepted: 05/16/2016] [Indexed: 01/18/2023]
Abstract
A new chelating chromatography method was developed based in the use of magnetic iron oxide nanoparticles functionalized with EDTA-TMS ((N-(trimethoxysilylpropyl)ethylenediaminetriacetate trisodium salt). These particles combine a high surface area, biocompatibility and magnetic removal from solution, with the chelating affinity towards metal ions. The particles were used to selectively capture metallo-dependant proteins in secretome obtained from human monocytes and mouse macrophages. Secreted metallo-dependant proteins are highly important sources of information since they are involved in several pathological processes. The identification of secreted proteins involved in these processes is highly important for diagnosis or monitoring the progression of a disease. In this multiple-approach study it was possible to not only selectively capture several secreted metallo-dependant proteins, but also to significantly avoid masking proteins such as the highly abundant albumin form the fetal bovine serum used to supplement the cell culture medium. Overall, the magnetic nanoparticle-based chelating chromatography method developed here has proved to be a sensitive, low cost, and a quick tool for sample treatment in order to selectively enrich metalloproteins while overcoming the contamination of highly abundant proteins.
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PK study of octreotide based on LC–MS/MS combining protein precipitation and impurity extraction technique. Bioanalysis 2015; 7:885-94. [DOI: 10.4155/bio.15.22] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Aim: To establish a robust methodology for quantitative analysis of therapeutic peptide in biological samples. Materials & Methods: Octreotide was chosen as a model therapeutic peptide, and oxidized-octreotide was synthesized as internal standard. Protein precipitation combining liquid-liquid extraction technique was adopted to enhance the recovery and reduce the endogenous interferences effectively. A LC–MS/MS method for the quantification of octreotide in plasma has been optimized and validated according to FDA guidelines. Results: Linearity, selectivity, accuracy, precision, stability, matrix effect and recovery were within bioanalytical method validation acceptance criteria as FDA guidelines. The methodology was then successfully applied into the studies for octreotide. Conclusion: This robust methodology would be useful for the PK studies for octreotide and other therapeutic peptides.
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Oliveira-Silva R, Pinto da Costa J, Vitorino R, Daniel-da-Silva AL. Magnetic chelating nanoprobes for enrichment and selective recovery of metalloproteases from human saliva. J Mater Chem B 2015; 3:238-249. [DOI: 10.1039/c4tb01189a] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Magnetic nanoparticles effective in the selective recovery of metalloproteases from human saliva were fabricated by surface modification of Fe3O4@SiO2nanoparticles with EDTA-TMS.
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Affiliation(s)
- Rui Oliveira-Silva
- Organic Chemistry
- Natural and Agro-Food Products Research Unit (QOPNA)
- Department of Chemistry
- University of Aveiro
- 3810-193 Aveiro
| | - João Pinto da Costa
- Organic Chemistry
- Natural and Agro-Food Products Research Unit (QOPNA)
- Department of Chemistry
- University of Aveiro
- 3810-193 Aveiro
| | - Rui Vitorino
- Organic Chemistry
- Natural and Agro-Food Products Research Unit (QOPNA)
- Department of Chemistry
- University of Aveiro
- 3810-193 Aveiro
| | - Ana L. Daniel-da-Silva
- CICECO
- Department of Chemistry
- Aveiro Institute of Nanotechnology
- University of Aveiro
- 3810-193 Aveiro
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Tun AW, Chaiyarit S, Kaewsutthi S, Katanyoo W, Chuenkongkaew W, Kuwano M, Tomonaga T, Peerapittayamongkol C, Thongboonkerd V, Lertrit P. Profiling the mitochondrial proteome of Leber's Hereditary Optic Neuropathy (LHON) in Thailand: down-regulation of bioenergetics and mitochondrial protein quality control pathways in fibroblasts with the 11778G>A mutation. PLoS One 2014; 9:e106779. [PMID: 25215595 PMCID: PMC4162555 DOI: 10.1371/journal.pone.0106779] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 08/08/2014] [Indexed: 12/24/2022] Open
Abstract
Leber's Hereditary Optic Neuropathy (LHON) is one of the commonest mitochondrial diseases. It causes total blindness, and predominantly affects young males. For the disease to develop, it is necessary for an individual to carry one of the primary mtDNA mutations 11778G>A, 14484T>C or 3460G>A. However these mutations are not sufficient to cause disease, and they do not explain the characteristic features of LHON such as the higher prevalence in males, incomplete penetrance, and relatively later age of onset. In order to explore the roles of nuclear encoded mitochondrial proteins in development of LHON, we applied a proteomic approach to samples from affected and unaffected individuals from 3 pedigrees and from 5 unrelated controls. Two-dimensional electrophoresis followed by MS/MS analysis in the mitochondrial lysate identified 17 proteins which were differentially expressed between LHON cases and unrelated controls, and 24 proteins which were differentially expressed between unaffected relatives and unrelated controls. The proteomic data were successfully validated by western blot analysis of 3 selected proteins. All of the proteins identified in the study were mitochondrial proteins and most of them were down regulated in 11778G>A mutant fibroblasts. These proteins included: subunits of OXPHOS enzyme complexes, proteins involved in intermediary metabolic processes, nucleoid related proteins, chaperones, cristae remodelling proteins and an anti-oxidant enzyme. The protein profiles of both the affected and unaffected 11778G>A carriers shared many features which differed from those of unrelated control group, revealing similar proteomic responses to 11778G>A mutation in both affected and unaffected individuals. Differentially expressed proteins revealed two broad groups: a cluster of bioenergetic pathway proteins and a cluster involved in protein quality control system. Defects in these systems are likely to impede the function of retinal ganglion cells, and may lead to the development of LHON in synergy with the primary mtDNA mutation.
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Affiliation(s)
- Aung Win Tun
- Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Sakdithep Chaiyarit
- Medical Proteomics Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Supannee Kaewsutthi
- Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Wanphen Katanyoo
- Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Wanicha Chuenkongkaew
- Department of Ophthalmology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Masayoshi Kuwano
- Laboratory of Proteome Research, National Institute of Biomedical Innovation, Osaka, Japan
| | - Takeshi Tomonaga
- Laboratory of Proteome Research, National Institute of Biomedical Innovation, Osaka, Japan
| | | | - Visith Thongboonkerd
- Medical Proteomics Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Center for Research in Complex Systems Science, Mahidol University, Bangkok, Thailand
- * E-mail: (PL); (VT)
| | - Patcharee Lertrit
- Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- * E-mail: (PL); (VT)
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Qiao X, Qin X, She D, Wang R, Zhang X, Zhang L, Zhang Y. Mass spectrometry-based tag and its application to high efficient peptide analysis – A review. Talanta 2014; 126:91-102. [DOI: 10.1016/j.talanta.2014.03.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Revised: 02/27/2014] [Accepted: 03/10/2014] [Indexed: 12/16/2022]
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Giorgianni F, Koirala D, Weber KT, Beranova-Giorgianni S. Proteome analysis of subsarcolemmal cardiomyocyte mitochondria: a comparison of different analytical platforms. Int J Mol Sci 2014; 15:9285-301. [PMID: 24865490 PMCID: PMC4100094 DOI: 10.3390/ijms15069285] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Revised: 05/09/2014] [Accepted: 05/16/2014] [Indexed: 01/05/2023] Open
Abstract
Mitochondria are complex organelles that play critical roles in diverse aspects of cellular function. Heart disease and a number of other pathologies are associated with perturbations in the molecular machinery of the mitochondria. Therefore, comprehensive, unbiased examination of the mitochondrial proteome represents a powerful approach toward system-level insights into disease mechanisms. A crucial aspect in proteomics studies is design of bioanalytical strategies that maximize coverage of the complex repertoire of mitochondrial proteins. In this study, we evaluated the performance of gel-based and gel-free multidimensional platforms for profiling of the proteome in subsarcolemmal mitochondria harvested from rat heart. We compared three different multidimensional proteome fractionation platforms: polymeric reversed-phase liquid chromatography at high pH (PLRP), sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), and isoelectric focusing (IEF) separations combined with liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS), and bioinformatics for protein identification. Across all three platforms, a total of 1043 proteins were identified. Among the three bioanalytical strategies, SDS-PAGE followed by LC-MS/MS provided the best coverage of the mitochondrial proteome. With this platform, 890 proteins with diverse physicochemical characteristics were identified; the mitochondrial protein panel encompassed proteins with various functional roles including bioenergetics, protein import, and mitochondrial fusion. Taken together, results of this study provide a large-scale view of the proteome in subsarcolemmal mitochondria from the rat heart, and aid in the selection of optimal bioanalytical platforms for differential protein expression profiling of mitochondria in health and disease.
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Affiliation(s)
- Francesco Giorgianni
- Department of Pharmaceutical Sciences, the University of Tennessee Health Science Center, Memphis, TN 38163, USA.
| | - Diwa Koirala
- Department of Pharmaceutical Sciences, the University of Tennessee Health Science Center, Memphis, TN 38163, USA.
| | - Karl T Weber
- Division of Cardiology, Department of Medicine, the University of Tennessee Health Science Center, Memphis, TN 38163, USA.
| | - Sarka Beranova-Giorgianni
- Department of Pharmaceutical Sciences, the University of Tennessee Health Science Center, Memphis, TN 38163, USA.
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