1
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Deng X, Yao Q, Horvath A, Jiang Z, Zhao J, Fischer T, Sugiyama T. The fission yeast ortholog of Coilin, Mug174, forms Cajal body-like nuclear condensates and is essential for cellular quiescence. Nucleic Acids Res 2024:gkae463. [PMID: 38828770 DOI: 10.1093/nar/gkae463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 05/08/2024] [Accepted: 05/16/2024] [Indexed: 06/05/2024] Open
Abstract
The Cajal body, a nuclear condensate, is crucial for ribonucleoprotein assembly, including small nuclear RNPs (snRNPs). While Coilin has been identified as an integral component of Cajal bodies, its exact function remains unclear. Moreover, no Coilin ortholog has been found in unicellular organisms to date. This study unveils Mug174 (Meiosis-upregulated gene 174) as the Coilin ortholog in the fission yeast Schizosaccharomyces pombe. Mug174 forms phase-separated condensates in vitro and is often associated with the nucleolus and the cleavage body in vivo. The generation of Mug174 foci relies on the trimethylguanosine (TMG) synthase Tgs1. Moreover, Mug174 interacts with Tgs1 and U snRNAs. Deletion of the mug174+ gene in S. pombe causes diverse pleiotropic phenotypes, encompassing defects in vegetative growth, meiosis, pre-mRNA splicing, TMG capping of U snRNAs, and chromosome segregation. In addition, we identified weak homology between Mug174 and human Coilin. Notably, human Coilin expressed in fission yeast colocalizes with Mug174. Critically, Mug174 is indispensable for the maintenance of and transition from cellular quiescence. These findings highlight the Coilin ortholog in fission yeast and suggest that the Cajal body is implicated in cellular quiescence, thereby preventing human diseases.
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Affiliation(s)
- Xiaoling Deng
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Qinglian Yao
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Attila Horvath
- The John Curtin School of Medical Research, The Australian National University, Canberra 2601, Australia
| | - Ziling Jiang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Junjie Zhao
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Tamás Fischer
- The John Curtin School of Medical Research, The Australian National University, Canberra 2601, Australia
| | - Tomoyasu Sugiyama
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
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2
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Helbing DL, Böhm L, Oraha N, Stabenow LK, Cui Y. A Ponceau S Staining-Based Dot Blot Assay for Rapid Protein Quantification of Biological Samples. Gels 2022; 8:gels8010043. [PMID: 35049578 PMCID: PMC8775029 DOI: 10.3390/gels8010043] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 12/20/2021] [Accepted: 01/01/2022] [Indexed: 02/01/2023] Open
Abstract
Despite the availability of a wide range of commercial kits, protein quantification is often unreliable, especially for tissue-derived samples, leading to uneven loading in subsequent experiments. Here we show that the widely used Bicinchoninic Acid (BCA) assay tends to underestimate protein concentrations of tissue samples. We present a Ponceau S staining-based dot-blot assay as an alternative for protein quantification. This method is simple, rapid, more reliable than the BCA assay, compatible with biological samples lysed in RIPA or 2x SDS gel-loading buffer, and also inexpensive.
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Affiliation(s)
- Dario Lucas Helbing
- Leibniz Institute on Aging—Fritz Lipmann Institute, 07745 Jena, Germany; (L.B.); (N.O.)
- Faculty of Medicine, Friedrich-Schiller-University Jena, 07743 Jena, Germany;
- Institute of Molecular Cell Biology, University Hospital Jena, Friedrich-Schiller-University, 07745 Jena, Germany
- Correspondence: (D.L.H.); (Y.C.)
| | - Leopold Böhm
- Leibniz Institute on Aging—Fritz Lipmann Institute, 07745 Jena, Germany; (L.B.); (N.O.)
- Faculty of Medicine, Friedrich-Schiller-University Jena, 07743 Jena, Germany;
- Institute of Molecular Cell Biology, University Hospital Jena, Friedrich-Schiller-University, 07745 Jena, Germany
| | - Nova Oraha
- Leibniz Institute on Aging—Fritz Lipmann Institute, 07745 Jena, Germany; (L.B.); (N.O.)
- Faculty of Medicine, Friedrich-Schiller-University Jena, 07743 Jena, Germany;
- Institute of Molecular Cell Biology, University Hospital Jena, Friedrich-Schiller-University, 07745 Jena, Germany
| | - Leonie Karoline Stabenow
- Faculty of Medicine, Friedrich-Schiller-University Jena, 07743 Jena, Germany;
- Institute of Molecular Cell Biology, University Hospital Jena, Friedrich-Schiller-University, 07745 Jena, Germany
| | - Yan Cui
- Leibniz Institute on Aging—Fritz Lipmann Institute, 07745 Jena, Germany; (L.B.); (N.O.)
- International Center for Aging and Cancer, Hainan Medical University, Haikou 571199, China
- Correspondence: (D.L.H.); (Y.C.)
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3
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Holthaus D, Delgado-Betancourt E, Aebischer T, Seeber F, Klotz C. Harmonization of Protocols for Multi-Species Organoid Platforms to Study the Intestinal Biology of Toxoplasma gondii and Other Protozoan Infections. Front Cell Infect Microbiol 2021; 10:610368. [PMID: 33692963 PMCID: PMC7937733 DOI: 10.3389/fcimb.2020.610368] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 12/30/2020] [Indexed: 12/20/2022] Open
Abstract
The small intestinal epithelium is the primary route of infection for many protozoan parasites. Understanding the mechanisms of infection, however, has been hindered due to the lack of appropriate models that recapitulate the complexity of the intestinal epithelium. Here, we describe an in vitro platform using stem cell-derived intestinal organoids established for four species that are important hosts of Apicomplexa and other protozoa in a zoonotic context: human, mouse, pig and chicken. The focus was set to create organoid-derived monolayers (ODMs) using the transwell system amenable for infection studies, and we provide straightforward guidelines for their generation and differentiation from organ-derived intestinal crypts. To this end, we reduced medium variations to an absolute minimum, allowing generation and differentiation of three-dimensional organoids for all four species and the subsequent generation of ODMs. Quantitative RT-PCR, immunolabeling with antibodies against marker proteins as well as transepithelial-electrical resistance (TEER) measurements were used to characterize ODM's integrity and functional state. These experiments show an overall uniform generation of monolayers suitable for Toxoplasma gondii infection, although robustness in terms of generation of stable TEER levels and cell differentiation status varies from species to species. Murine duodenal ODMs were then infected with T. gondii and/or Giardia duodenalis, two parasites that temporarily co-inhabit the intestinal niche but have not been studied previously in cellular co-infection models. T. gondii alone did not alter TEER values, integrity and transcriptional abundance of tight junction components. In contrast, in G. duodenalis-infected ODMs all these parameters were altered and T. gondii had no apparent influence on the G. duodenalis-triggered phenotype. In conclusion, we provide robust protocols for the generation, differentiation and characterization of intestinal organoids and ODMs from four species. We show their applications for comparative studies on parasite-host interactions during the early phase of a T. gondii infection but also its use for co-infections with other relevant intestinal protozoans.
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Affiliation(s)
| | | | | | | | - Christian Klotz
- FG 16: Mycotic and Parasitic Agents and Mycobacteria, Robert Koch-Institute, Berlin, Germany
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4
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Han S, Cui Y, Helbing DL. Inactivation of Horseradish Peroxidase by Acid for Sequential Chemiluminescent Western Blot. Biotechnol J 2019; 15:e1900397. [PMID: 31647189 DOI: 10.1002/biot.201900397] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Indexed: 11/11/2022]
Abstract
Chemiluminescent western blot (WB) is often performed sequentially for detection of overlapping proteins; in between, prior antibodies must be stripped or the conjugated horseradish peroxidase (HRP) inactivated. However, often, stripping either is insufficient to remove all the bound antibodies or causes protein loss, whereas treatment with hydrogen peroxide, a popular way to inactivate HRP, may affect epitope recognition as the authors previously reported. To date, an ideal method for sequential chemiluminescent WB is still missing. Here it is demonstrated that acid equivalent to 10% acetic acid can efficiently inactivate HRP, allowing sequential probing without protein loss or epitope damage.
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Affiliation(s)
- Shuting Han
- Leibniz Institute on Aging, Fritz Lipmann Institute, 07745, Jena, Germany.,Department of Medical Oncology, Sir Run Run Shaw Hospital, Medical School of Zhejiang University, 310016, Hangzhou, China
| | - Yan Cui
- Leibniz Institute on Aging, Fritz Lipmann Institute, 07745, Jena, Germany
| | - Dario L Helbing
- Leibniz Institute on Aging, Fritz Lipmann Institute, 07745, Jena, Germany.,Faculty of Medicine, Friedrich-Schiller-University Jena, 07743, Jena, Germany
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5
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Vanacloig-Pedros E, Lozano-Pérez C, Alarcón B, Pascual-Ahuir A, Proft M. Live-cell assays reveal selectivity and sensitivity of the multidrug response in budding yeast. J Biol Chem 2019; 294:12933-12946. [PMID: 31296662 DOI: 10.1074/jbc.ra119.009291] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 07/04/2019] [Indexed: 11/06/2022] Open
Abstract
Pleiotropic drug resistance arises by the enhanced extrusion of bioactive molecules and is present in a wide range of organisms, ranging from fungi to human cells. A key feature of this adaptation is the sensitive detection of intracellular xenobiotics by transcriptional activators, activating expression of multiple drug exporters. Here, we investigated the selectivity and sensitivity of the budding yeast (Saccharomyces cerevisiae) multidrug response to better understand how differential drug recognition leads to specific activation of drug exporter genes and to drug resistance. Applying live-cell luciferase reporters, we demonstrate that the SNQ2, PDR5, PDR15, and YOR1 transporter genes respond to different mycotoxins, menadione, and hydrogen peroxide in a distinguishable manner and with characteristic amplitudes, dynamics, and sensitivities. These responses correlated with differential sensitivities of the respective transporter mutants to the specific xenobiotics. We further establish a binary vector system, enabling quantitative determination of xenobiotic-transcription factor (TF) interactions in real time. Applying this system we found that the TFs Pdr1, Pdr3, Yrr1, Stb5, and Pdr8 have largely different drug recognition patterns. We noted that Pdr1 is the most promiscuous activator, whereas Yrr1 and Stb5 are selective for ochratoxin A and hydrogen peroxide, respectively. We also show that Pdr1 is rapidly degraded after xenobiotic exposure, which leads to a desensitization of the Pdr1-specific response upon repeated activation. The findings of our work indicate that in the yeast multidrug system, several transcriptional activators with distinguishable selectivities trigger differential activation of the transporter genes.
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Affiliation(s)
- Elena Vanacloig-Pedros
- Department of Biotechnology, Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València, 46022 Valencia, Spain
| | - Carlos Lozano-Pérez
- Department of Molecular and Cellular Pathology and Therapy, Instituto de Biomedicina de Valencia IBV-CSIC, 46010 Valencia, Spain
| | - Benito Alarcón
- Department of Molecular and Cellular Pathology and Therapy, Instituto de Biomedicina de Valencia IBV-CSIC, 46010 Valencia, Spain
| | - Amparo Pascual-Ahuir
- Department of Biotechnology, Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València, 46022 Valencia, Spain.
| | - Markus Proft
- Department of Molecular and Cellular Pathology and Therapy, Instituto de Biomedicina de Valencia IBV-CSIC, 46010 Valencia, Spain.
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6
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Poliner E, Takeuchi T, Du ZY, Benning C, Farré EM. Nontransgenic Marker-Free Gene Disruption by an Episomal CRISPR System in the Oleaginous Microalga, Nannochloropsis oceanica CCMP1779. ACS Synth Biol 2018; 99:112-127. [PMID: 29518315 PMCID: PMC6616531 DOI: 10.1111/tpj.14314] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 02/18/2019] [Accepted: 02/26/2019] [Indexed: 04/25/2023]
Abstract
Utilization of microalgae has been hampered by limited tools for creating loss-of-function mutants. Furthermore, modified strains for deployment into the field must be free of antibiotic resistance genes and face fewer regulatory hurdles if they are transgene free. The oleaginous microalga, Nannochloropsis oceanica CCMP1779, is an emerging model for microalgal lipid metabolism. We present a one-vector episomal CRISPR/Cas9 system for N. oceanica that enables the generation of marker-free mutant lines. The CEN/ARS6 region from Saccharomyces cerevisiae was included in the vector to facilitate its maintenance as circular extrachromosal DNA. The vector utilizes a bidirectional promoter to produce both Cas9 and a ribozyme flanked sgRNA. This system efficiently generates targeted mutations, and allows the loss of episomal DNA after the removal of selection pressure, resulting in marker-free nontransgenic engineered lines. To test this system, we disrupted the nitrate reductase gene ( NR) and subsequently removed the CRISPR episome to generate nontransgenic marker-free nitrate reductase knockout lines (NR-KO).
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Affiliation(s)
- Eric Poliner
- Cell and Molecular Biology Program, Michigan State University, East Lansing, Michigan
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan
| | - Tomomi Takeuchi
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan
- Biochemistry and Molecular Department, Michigan State University, East Lansing, Michigan
| | - Zhi-Yan Du
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan
- Biochemistry and Molecular Department, Michigan State University, East Lansing, Michigan
| | - Christoph Benning
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan
- Biochemistry and Molecular Department, Michigan State University, East Lansing, Michigan
- Plant Biology Department, Michigan State University, East Lansing, Michigan
| | - Eva M. Farré
- Plant Biology Department, Michigan State University, East Lansing, Michigan
- Corresponding Author: Eva M. Farré (), Phone: +1-517-353-5215
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7
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Timón-Gómez A, Sanfeliu-Redondo D, Pascual-Ahuir A, Proft M. Regulation of the Stress-Activated Degradation of Mitochondrial Respiratory Complexes in Yeast. Front Microbiol 2018; 9:106. [PMID: 29441058 PMCID: PMC5797626 DOI: 10.3389/fmicb.2018.00106] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 01/17/2018] [Indexed: 02/05/2023] Open
Abstract
Repair and removal of damaged mitochondria is a key process for eukaryotic cell homeostasis. Here we investigate in the yeast model how different protein complexes of the mitochondrial electron transport chain are subject to specific degradation upon high respiration load and organelle damage. We find that the turnover of subunits of the electron transport complex I equivalent and complex III is preferentially stimulated upon high respiration rates. Particular mitochondrial proteases, but not mitophagy, are involved in this activated degradation. Further mitochondrial damage by valinomycin treatment of yeast cells triggers the mitophagic removal of the same respiratory complexes. This selective protein degradation depends on the mitochondrial fusion and fission apparatus and the autophagy adaptor protein Atg11, but not on the mitochondrial mitophagy receptor Atg32. Loss of autophagosomal protein function leads to valinomycin sensitivity and an overproduction of reactive oxygen species upon mitochondrial damage. A specific event in this selective turnover of electron transport chain complexes seems to be the association of Atg11 with the mitochondrial network, which can be achieved by overexpression of the Atg11 protein even in the absence of Atg32. Furthermore, the interaction of various Atg11 molecules via the C-terminal coil domain is specifically and rapidly stimulated upon mitochondrial damage and could therefore be an early trigger of selective mitophagy in response to the organelles dysfunction. Our work indicates that autophagic quality control upon mitochondrial damage operates in a selective manner.
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Affiliation(s)
- Alba Timón-Gómez
- Department of Molecular and Cellular Pathology and Therapy, Instituto de Biomedicina de Valencia-CSIC, Valencia, Spain.,Department of Biotechnology, Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València, Valencia, Spain
| | - David Sanfeliu-Redondo
- Department of Biotechnology, Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València, Valencia, Spain
| | - Amparo Pascual-Ahuir
- Department of Biotechnology, Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València, Valencia, Spain
| | - Markus Proft
- Department of Molecular and Cellular Pathology and Therapy, Instituto de Biomedicina de Valencia-CSIC, Valencia, Spain
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8
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Moritz CP. Tubulin or Not Tubulin: Heading Toward Total Protein Staining as Loading Control in Western Blots. Proteomics 2018; 17. [PMID: 28941183 DOI: 10.1002/pmic.201600189] [Citation(s) in RCA: 110] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 09/13/2017] [Indexed: 12/30/2022]
Abstract
Western blotting is an analytical method widely used for detecting and (semi-)quantifying specific proteins in given samples. Western blots are continuously applied and developed by the protein community. This review article focuses on a significant, but not yet well-established, improvement concerning the internal loading control as a prerequisite to accurately quantifying Western blots. Currently, housekeeping proteins (HKPs) like actin, tubulin, or GAPDH are often used to check for equal loading or to compensate potential loading differences. However, this loading control has multiple drawbacks. Staining of the total protein on the blotting membrane has emerged as a better loading control. Total protein staining (TPS) represents the actual loading amount more accurately than HKPs due to minor technical and biological variation. Further, the broad dynamic range of TPS solves the issue of HKPs that commonly fail to show loading differences above small loading amounts of 0.5-10 μg. Although these and further significant advantages have been demonstrated over the past 10 years, only a small percentage of laboratories take advantage of it. The objective of this review article is to collect and compare information about TPS options and to invite users to reconsider their applied loading control. Nine benefits of TPS are discussed and seven different variants are critically evaluated by comparing technical details. Consequently, this review article offers an orientation in selecting the appropriate staining type. I conclude that TPS should be the preferred loading control in future Western blot approaches.
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Affiliation(s)
- Christian P Moritz
- Synaptopathies and Autoantibodies, Faculty of Medicine, University Jean Monnet, Saint-Étienne, France.,Institut NeuroMyoGène, Team Synaptopathies and Autoantibodies, Lyon/Saint-Étienne, France
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9
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Chung HS, Murray CI, Van Eyk JE. A Proteomics Workflow for Dual Labeling Biotin Switch Assay to Detect and Quantify Protein S-Nitroylation. Methods Mol Biol 2018; 1747:89-101. [PMID: 29600453 DOI: 10.1007/978-1-4939-7695-9_8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
S-nitrosylation (or S-nitrosation, SNO) is an oxidative posttranslational modification to the thiol group of a cysteine amino acid residue. There are several methods to detect SNO modifications, mostly based on the classic biotin-switch assay, where the labile SNO sites are replaced with a stable biotin moiety to facilitate enrichment of the modified proteins. As the technique has evolved, new and more advanced thiol-reactive reagents have been introduced in the protocol to improve the identification of modified peptides or to quantify the level of modification at individual cysteine residues. However, the growing diversity of thiol-reactive affinity tags has not produced a consistent set of protein modifications, suggesting incomplete coverage using a single tag. Here, we present a parallel dual labeling strategy followed by an optimized proteomics workflow, which maximizes the overall detection of SNO by reducing the labeling bias derived from the use of a single tag-capture approach.
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Affiliation(s)
| | | | - Jennifer E Van Eyk
- Medicine and Heart Institute, Cedars Sinai Medical Center, Los Angeles, CA, USA.
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10
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Partial Immunoblotting of 2D-Gels: A Novel Method to Identify Post-Translationally Modified Proteins Exemplified for the Myelin Acetylome. Proteomes 2017; 5:proteomes5010003. [PMID: 28248254 PMCID: PMC5372224 DOI: 10.3390/proteomes5010003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 12/23/2016] [Accepted: 01/04/2017] [Indexed: 11/17/2022] Open
Abstract
Post-translational modifications (PTMs) play a key role in regulating protein function, yet their identification is technically demanding. Here, we present a straightforward workflow to systematically identify post-translationally modified proteins based on two-dimensional gel electrophoresis. Upon colloidal Coomassie staining the proteins are partially transferred, and the investigated PTMs are immunodetected. This strategy allows tracking back the immunopositive antigens to the corresponding spots on the original gel, from which they are excised and mass spectrometrically identified. Candidate proteins are validated on the same membrane by immunodetection using a second fluorescence channel. We exemplify the power of partial immunoblotting with the identification of lysine-acetylated proteins in myelin, the oligodendroglial membrane that insulates neuronal axons. The excellent consistency of the detected fluorescence signals at all levels allows the differential comparison of PTMs across multiple conditions. Beyond PTM screening, our multi-level workflow can be readily adapted to clinical applications such as identifying auto-immune antigens or host-pathogen interactions.
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11
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Fujioka H, Sakai A, Tanaka S, Kimura K, Miyamoto A, Iwamoto M, Uchiyama K. Comparative proteomic analysis of paclitaxel resistance-related proteins in human breast cancer cell lines. Oncol Lett 2016; 13:289-295. [PMID: 28123557 DOI: 10.3892/ol.2016.5455] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 10/06/2016] [Indexed: 11/06/2022] Open
Abstract
Paclitaxel is widely used to treat various cancers; however, resistance to this drug is a major obstacle to breast cancer chemotherapy. To identify the proteins involved in paclitaxel resistance, the present study compared the proteomes of MCF-7 human breast cancer cells and its paclitaxel-resistant subclone MCF-7/PTX. Using two-dimensional gel electrophoresis and matrix-assisted laser desorption/ionization time of flight mass spectrometry, 11 upregulated and 12 downregulated proteins were identified in MCF-7/PTX cells compared with the parental cell line. These 23 proteins were functionally classified as stress-induced chaperones, metabolic enzymes and cytoskeletal proteins. The anti-apoptotic proteins, stress-70 protein, 78-kD glucose-regulated protein, peptidyl-prolyl cis-trans isomerase A (PPIA) and heterogeneous nuclear ribonucleoprotein H3, were also upregulated in MCF-7/PTX cells. Notably, knockdown of the stress-response chaperone PPIA using small interfering RNA in MCF-7/PTX cells restored their sensitivity to paclitaxel. These findings indicated that PPIA may have an important role in paclitaxel resistance in MCF-7/PTX cells.
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Affiliation(s)
- Hiroya Fujioka
- Section of Breast and Endocrine Surgery, Department of General and Gastroenterological Surgery, Osaka Medical College, Takatsuki, Osaka 569-8686, Japan
| | - Akiko Sakai
- Department of Chemistry, Osaka Medical College, Takatsuki, Osaka 569-8686, Japan
| | - Satoru Tanaka
- Section of Breast and Endocrine Surgery, Department of General and Gastroenterological Surgery, Osaka Medical College, Takatsuki, Osaka 569-8686, Japan
| | - Kosei Kimura
- Section of Breast and Endocrine Surgery, Department of General and Gastroenterological Surgery, Osaka Medical College, Takatsuki, Osaka 569-8686, Japan
| | - Akiko Miyamoto
- Section of Breast and Endocrine Surgery, Department of General and Gastroenterological Surgery, Osaka Medical College, Takatsuki, Osaka 569-8686, Japan
| | - Mitsuhiko Iwamoto
- Section of Breast and Endocrine Surgery, Department of General and Gastroenterological Surgery, Osaka Medical College, Takatsuki, Osaka 569-8686, Japan
| | - Kazuhisa Uchiyama
- Section of Breast and Endocrine Surgery, Department of General and Gastroenterological Surgery, Osaka Medical College, Takatsuki, Osaka 569-8686, Japan
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12
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Skjolding AD, Holst AV, Broholm H, Laursen H, Juhler M. Differences in distribution and regulation of astrocytic aquaporin-4 in human and rat hydrocephalic brain. Neuropathol Appl Neurobiol 2015; 39:179-91. [PMID: 22497211 DOI: 10.1111/j.1365-2990.2012.01275.x] [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] [Indexed: 11/28/2022]
Abstract
AIMS Aquaporin-4 (AQP4) is the most abundant cellular water channel in brain and could be a molecular basis for a cerebrospinal fluid absorption route additional to the arachnoid villi. In the search for 'alternative' cerebrospinal fluid absorption pathways it is important to compare experimental findings with human pathophysiology. This study compares expression of AQP4 in hydrocephalic human brain with human controls and hydrocephalic rat brain. METHODS Cortical biopsies from patients with chronic hydrocephalus (n = 29) were sampled secondary to planned surgical intervention. AQP4 in human hydrocephalic cortex relative to controls was quantified by Western blotting (n = 28). A second biopsy (n = 13) was processed for immunohistochemistry [glial fibrillary acidic protein (GFAP), CD68, CD34 and AQP4] and double immunofluorescence (AQP4 + GFAP and AQP4 + CD34). Brain tissue from human controls and kaolin-induced hydrocephalic rats was processed in parallel. Immunohistochemistry and immunofluorescence were assessed qualitatively. RESULTS Western blotting showed that AQP4 abundance was significantly increased (P < 0.05) in hydrocephalic human brain compared with controls. AQP4 immunoreactivity was present in both white and grey matter. In human brain (hydrocephalic and controls) AQP4 immunoreactivity was found on the entire astrocyte membrane, unlike hydrocephalic rat brain where pronounced endfeet polarization was present. Endothelial AQP4 immunoreactivity was not observed. CONCLUSIONS This study shows a significant increase in astrocytic AQP4 in human hydrocephalic cortex compared with control. Cell type specific expression in astrocytes is conserved between rat and human, although differences of expression in specific membrane domains are seen. This study addresses direct translational aspects from rat to human, hereby emphasizing the relevance and use of models in hydrocephalus research.
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Affiliation(s)
- A D Skjolding
- University Clinic of NeurosurgeryLaboratory of Neuropathology, Copenhagen University Hospital, RigshopitaletDepartment of Neuroscience and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - A V Holst
- University Clinic of NeurosurgeryLaboratory of Neuropathology, Copenhagen University Hospital, RigshopitaletDepartment of Neuroscience and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - H Broholm
- University Clinic of NeurosurgeryLaboratory of Neuropathology, Copenhagen University Hospital, RigshopitaletDepartment of Neuroscience and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - H Laursen
- University Clinic of NeurosurgeryLaboratory of Neuropathology, Copenhagen University Hospital, RigshopitaletDepartment of Neuroscience and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - M Juhler
- University Clinic of NeurosurgeryLaboratory of Neuropathology, Copenhagen University Hospital, RigshopitaletDepartment of Neuroscience and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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13
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Poliner E, Panchy N, Newton L, Wu G, Lapinsky A, Bullard B, Zienkiewicz A, Benning C, Shiu SH, Farré EM. Transcriptional coordination of physiological responses in Nannochloropsis oceanica CCMP1779 under light/dark cycles. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015. [PMID: 26216534 DOI: 10.1111/tpj.12944] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Nannochloropsis oceanica CCMP1779 is a marine unicellular stramenopile and an emerging reference species for basic research on oleogenic microalgae with biotechnological relevance. We investigated its physiology and transcriptome under light/dark cycles. We observed oscillations in lipid content and a predominance of cell division in the first half of the dark phase. Globally, more than 60% of the genes cycled in N. oceanica CCMP1779, with gene expression peaking at different times of the day. Interestingly, the phase of expression of genes involved in certain biological processes was conserved across photosynthetic lineages. Furthermore, in agreement with our physiological studies we found the processes of lipid metabolism and cell division enriched in cycling genes. For example, there was tight coordination of genes involved in the lower part of glycolysis, fatty acid synthesis and lipid production at dawn preceding lipid accumulation during the day. Our results suggest that diel lipid storage plays a key role for N. oceanica CCMP1779 growth under natural conditions making this alga a promising model to gain a basic mechanistic understanding of triacylglycerol production in photosynthetic cells. Our data will help the formulation of new hypotheses on the role of cyclic gene expression in cell growth and metabolism in Nannochloropsis.
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Affiliation(s)
- Eric Poliner
- Cell and Molecular Biology Program, Michigan State University, East Lansing, MI, 48824, USA
| | - Nicholas Panchy
- Genetics Program, Michigan State University, East Lansing, MI, 48824, USA
| | - Linsey Newton
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Guangxi Wu
- Cell and Molecular Biology Program, Michigan State University, East Lansing, MI, 48824, USA
| | - Andrew Lapinsky
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Blair Bullard
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Agnieszka Zienkiewicz
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Christoph Benning
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Shin-Han Shiu
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Eva M Farré
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
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14
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Burniston JG, Kenyani J, Gray D, Guadagnin E, Jarman IH, Cobley JN, Cuthbertson DJ, Chen YW, Wastling JM, Lisboa PJ, Koch LG, Britton SL. Conditional independence mapping of DIGE data reveals PDIA3 protein species as key nodes associated with muscle aerobic capacity. J Proteomics 2014; 106:230-45. [PMID: 24769234 PMCID: PMC4150023 DOI: 10.1016/j.jprot.2014.04.015] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2014] [Revised: 04/03/2014] [Accepted: 04/09/2014] [Indexed: 12/11/2022]
Abstract
Profiling of protein species is important because gene polymorphisms, splice variations and post-translational modifications may combine and give rise to multiple protein species that have different effects on cellular function. Two-dimensional gel electrophoresis is one of the most robust methods for differential analysis of protein species, but bioinformatic interrogation is challenging because the consequences of changes in the abundance of individual protein species on cell function are unknown and cannot be predicted. We conducted DIGE of soleus muscle from male and female rats artificially selected as either high- or low-capacity runners (HCR and LCR, respectively). In total 696 protein species were resolved and LC–MS/MS identified proteins in 337 spots. Forty protein species were differentially (P < 0.05, FDR < 10%) expressed between HCR and LCR and conditional independence mapping found distinct networks within these data, which brought insight beyond that achieved by functional annotation. Protein disulphide isomerase A3 emerged as a key node segregating with differences in aerobic capacity and unsupervised bibliometric analysis highlighted further links to signal transducer and activator of transcription 3, which were confirmed by western blotting. Thus, conditional independence mapping is a useful technique for interrogating DIGE data that is capable of highlighting latent features.
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Affiliation(s)
- Jatin G Burniston
- Research Institute for Sport and Exercise Sciences, Liverpool John Moores University, Liverpool L3 3AF, UK.
| | - Jenna Kenyani
- Department of Cellular and Molecular Physiology, University of Liverpool, Nuffield Building, Liverpool L69 3BX, UK
| | - Donna Gray
- Department of Obesity and Endocrinology, Clinical Sciences Center, University Hospital Anitree, Liverpool L9 7AL, UK
| | - Eleonora Guadagnin
- Center for Genetic Medicine Research, Children's National Medical Center, Washington, DC 20010, USA
| | - Ian H Jarman
- Department of Mathematics and Statistics, Liverpool John Moores University, Liverpool L3 3AF, UK
| | - James N Cobley
- Research Institute for Sport and Exercise Sciences, Liverpool John Moores University, Liverpool L3 3AF, UK
| | - Daniel J Cuthbertson
- Department of Obesity and Endocrinology, Clinical Sciences Center, University Hospital Anitree, Liverpool L9 7AL, UK
| | - Yi-Wen Chen
- Center for Genetic Medicine Research, Children's National Medical Center, Washington, DC 20010, USA; Department of Integrative Systems Biology, George Washington University, Washington DC, USA
| | - Jonathan M Wastling
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool Science Park IC2, L3 5RF, UK
| | - Paulo J Lisboa
- Department of Mathematics and Statistics, Liverpool John Moores University, Liverpool L3 3AF, UK
| | - Lauren G Koch
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109-2200, USA; Department of Anesthesiology, University of Michigan, Ann Arbor, MI 48109-2200, USA
| | - Steven L Britton
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109-2200, USA; Department of Anesthesiology, University of Michigan, Ann Arbor, MI 48109-2200, USA
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15
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Edogawa S, Sakai A, Inoue T, Harada S, Takeuchi T, Umegaki E, Hayashi H, Higuchi K. Down-regulation of collagen I biosynthesis in intestinal epithelial cells exposed to indomethacin: a comparative proteome analysis. J Proteomics 2014; 103:35-46. [PMID: 24698663 DOI: 10.1016/j.jprot.2014.03.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Revised: 03/07/2014] [Accepted: 03/19/2014] [Indexed: 01/16/2023]
Abstract
UNLABELLED In contrast to accumulated knowledge about gastroduodenal injury associated with nonsteroidal antiinflammatory drugs (NSAIDs) such as indomethacin, small intestinal mucosal injuries have been noticed only recently, and the precise mechanism remains to be elucidated. To clarify the mechanism, we performed 2-DE on IEC-6 rat normal intestinal cells that were treated with indomethacin (200μΜ, 24h) or a vehicle control and identified 18 up-regulated and 8 down-regulated proteins through MALDI-TOF/TOF mass spectrometry. Among these proteins, collagen I and proteins involved in collagen I biosynthesis and maturation, including prolyl 4-hydroxylase subunit α1, protein disulfide isomerase A3 (PDIA3), calreticulin, and endoplasmin, were all down-regulated by indomethacin. Immunohistochemical staining of the intestinal mucosa of indomethacin-administered rats showed a decrease of collagen I on the apical surface of intestinal cells. Cell death induced by indomethacin was prominently suppressed when IEC-6 cells were grown on collagen I-coated plates. cis-4-Hydroxy-l-proline, a proline analog that inhibits collagen synthesis, depressed IEC-6 cell viability in a concentration-dependent manner. Cell death was also induced by short interfering RNA knockdown of endogenous collagen I in IEC-6 cells. In conclusion, by comparative proteome analysis, we identified down-regulation of collagen I as an important mechanism in NSAID-induced intestinal injury. BIOLOGICAL SIGNIFICANCE Small intestinal lesions induced by NSAIDs are of great concern in clinical settings. Various hypotheses have been proposed for the origin of these inflammatory responses, such as reduction in the blood flow, intestinal hypermotility, abnormal intestinal mucosal permeability, mitochondrial dysfunction, and reactive oxygen species, many of which are related to the inhibition of prostaglandin synthesis. However, the precise mechanism is yet to be known. The cellular process of the lesions must involve up- and down-regulations of a large number of proteins and complex interactions between them. To elucidate it, global and systematic identification of the proteins in intestinal cells affected by NSAIDs is essential. We found that the proteins exhibiting reduced expression by indomethacin treatment are collagen I and the proteins involved in collagen I synthesis and maturation. Consistent with this, immunohistochemical analysis showed that the indomethacin-treated rat intestinal mucosal cells exhibits decreased collagen I expression on its apical surface. Furthermore, the cell-protective effect of collagen on intestinal mucosal cells was demonstrated by the use of a collagen-synthesis inhibitor, short interfering RNA (siRNA) knockdown of endogenous collagen I, and cell cultivation on collagen I-coated plates versus uncoated plates. These results give important information on the role of the collagen synthesis in intestinal mucosa in the mechanism of NSAID-induced small intestinal lesions.
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Affiliation(s)
- Shoko Edogawa
- 2nd Department of Internal Medicine, Osaka Medical College, Osaka, Japan.
| | - Akiko Sakai
- Department of Chemistry, Osaka Medical College, Osaka, Japan
| | - Takuya Inoue
- 2nd Department of Internal Medicine, Osaka Medical College, Osaka, Japan
| | - Satoshi Harada
- 2nd Department of Internal Medicine, Osaka Medical College, Osaka, Japan
| | - Toshihisa Takeuchi
- 2nd Department of Internal Medicine, Osaka Medical College, Osaka, Japan
| | - Eiji Umegaki
- 2nd Department of Internal Medicine, Osaka Medical College, Osaka, Japan
| | | | - Kazuhide Higuchi
- 2nd Department of Internal Medicine, Osaka Medical College, Osaka, Japan
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16
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Zeng L, Guo J, Xu HB, Huang R, Shao W, Yang L, Wang M, Chen J, Xie P. Direct Blue 71 staining as a destaining-free alternative loading control method for Western blotting. Electrophoresis 2014; 34:2234-9. [PMID: 23712695 DOI: 10.1002/elps.201300140] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2013] [Revised: 04/10/2013] [Accepted: 04/10/2013] [Indexed: 11/07/2022]
Abstract
In Western blotting, a suitable loading control is indispensable for correcting errors in the total amount of loaded protein. Immunodetection of housekeeping proteins and total protein staining have traditionally been used as loading control methods. Direct Blue 71 (DB71) staining-a novel, sensitive, dye-binding staining method compatible with immunodetection-may offer advantages over these traditional loading control methods. Three common neuroscientific samples (human plasma, human oligodendrocytes, and rat brain) were employed to assess DB71 staining as a loading control method for Western blotting. DB71, CBB, one traditional housekeeping protein, and one protein of interest were comparatively assessed for reliability and repeatability and linear dynamic range over 2.5-40 μg of protein loaded. DB71's effect on the reliability and repeatability and linear dynamic range of immunoreaction were also assessed. Across all three sample types, DB71 was either equivalent or superior to CBB and housekeeping protein-based methods in terms of reliability and repeatability and linear dynamic range. Across all three sample types, DB71 staining did not impair the reliability and repeatability or linear dynamic range of immunoreaction. Our results demonstrate that the DB71 staining can be used as a destaining-free alternative loading control method for Western blotting.
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Affiliation(s)
- Li Zeng
- Department of Neurology, First Affiliated Hospital, Chongqing Medical University, Chongqing, PR China
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17
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Epicocconone staining: A powerful loading control for Western blots. Proteomics 2014; 14:162-8. [DOI: 10.1002/pmic.201300089] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Revised: 11/18/2013] [Accepted: 11/25/2013] [Indexed: 02/06/2023]
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18
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Timón-Gómez A, Proft M, Pascual-Ahuir A. Differential regulation of mitochondrial pyruvate carrier genes modulates respiratory capacity and stress tolerance in yeast. PLoS One 2013; 8:e79405. [PMID: 24244496 PMCID: PMC3828368 DOI: 10.1371/journal.pone.0079405] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Accepted: 09/30/2013] [Indexed: 12/13/2022] Open
Abstract
Mpc proteins are highly conserved from yeast to humans and are necessary for the uptake of pyruvate at the inner mitochondrial membrane, which is used for leucine and valine biosynthesis and as a fuel for respiration. Our analysis of the yeast MPC gene family suggests that amino acid biosynthesis, respiration rate and oxidative stress tolerance are regulated by changes in the Mpc protein composition of the mitochondria. Mpc2 and Mpc3 are highly similar but functionally different: Mpc2 is most abundant under fermentative non stress conditions and important for amino acid biosynthesis, while Mpc3 is the most abundant family member upon salt stress or when high respiration rates are required. Accordingly, expression of the MPC3 gene is highly activated upon NaCl stress or during the transition from fermentation to respiration, both types of regulation depend on the Hog1 MAP kinase. Overexpression experiments show that gain of Mpc2 function leads to a severe respiration defect and ROS accumulation, while Mpc3 stimulates respiration and enhances tolerance to oxidative stress. Our results identify the regulated mitochondrial pyruvate uptake as an important determinant of respiration rate and stress resistance.
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Affiliation(s)
- Alba Timón-Gómez
- Department of Biotechnology, Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia, Valencia, Spain
| | - Markus Proft
- Department of Mechanisms of Plant Stress Responses, Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Valencia, Spain
- * E-mail: (APA); (MP)
| | - Amparo Pascual-Ahuir
- Department of Biotechnology, Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia, Valencia, Spain
- * E-mail: (APA); (MP)
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19
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Dong W, Matsuno YK, Kameyama A. Serum protein fractionation using supported molecular matrix electrophoresis. Electrophoresis 2013; 34:2432-9. [DOI: 10.1002/elps.201300154] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Revised: 04/24/2013] [Accepted: 04/29/2013] [Indexed: 11/11/2022]
Affiliation(s)
- Weijie Dong
- Bioproduction Research Institute; National Institute of Advanced Industrial Science and Technology (AIST); Open Space Laboratory C-2; Tsukuba; Ibaraki; Japan
| | - Yu-ki Matsuno
- Bioproduction Research Institute; National Institute of Advanced Industrial Science and Technology (AIST); Open Space Laboratory C-2; Tsukuba; Ibaraki; Japan
| | - Akihiko Kameyama
- Bioproduction Research Institute; National Institute of Advanced Industrial Science and Technology (AIST); Open Space Laboratory C-2; Tsukuba; Ibaraki; Japan
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20
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Hugo LE, Monkman J, Dave KA, Wockner LF, Birrell GW, Norris EL, Kienzle VJ, Sikulu MT, Ryan PA, Gorman JJ, Kay BH. Proteomic biomarkers for ageing the mosquito Aedes aegypti to determine risk of pathogen transmission. PLoS One 2013; 8:e58656. [PMID: 23536806 PMCID: PMC3594161 DOI: 10.1371/journal.pone.0058656] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Accepted: 02/05/2013] [Indexed: 11/18/2022] Open
Abstract
Biomarkers of the age of mosquitoes are required to determine the risk of transmission of various pathogens as each pathogen undergoes a period of extrinsic incubation in the mosquito host. Using the 2-D Difference Gel Electrophoresis (2-D DIGE) procedure, we investigated the abundance of up to 898 proteins from the Yellow Fever and dengue virus vector, Aedes aegypti, during ageing. By applying a mixed-effects model of protein expression, we identified five common patterns of abundance change during ageing and demonstrated an age-related decrease in variance for four of these. This supported a search for specific proteins with abundance changes that remain tightly associated with ageing for use as ageing biomarkers. Using MALDI-TOF/TOF mass spectrometry we identified ten candidate proteins that satisfied strict biomarker discovery criteria (identified in two out of three multivariate analysis procedures and in two cohorts of mosquitoes). We validated the abundances of the four most suitable candidates (Actin depolymerising factor; ADF, Eukaryotic initiation factor 5A; eIF5A, insect cuticle protein Q17LN8, and Anterior fat body protein; AFP) using semi-quantitative Western analysis of individual mosquitoes of six ages. The redox-response protein Manganese superoxide dismutase (SOD2) and electron shuttling protein Electron transfer oxidoreductase (ETO) were subject to post-translational modifications affecting their charge states with potential effects on function. For the four candidates we show remarkably consistent decreases in abundance during ageing, validating initial selections. In particular, the abundance of AFP is an ideal biomarker candidate for whether a female mosquito has lived long enough to be capable of dengue virus transmission. We have demonstrated proteins to be a suitable class of ageing biomarkers in mosquitoes and have identified candidates for epidemiological studies of dengue and the evaluation of new disease reduction projects targeting mosquito longevity.
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Affiliation(s)
- Leon E Hugo
- Mosquito Control Laboratory, Queensland Institute of Medical Research, Brisbane, Queensland, Australia.
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21
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Murray CI, Chung HS, Uhrigshardt H, Van Eyk JE. Quantification of mitochondrial S-nitrosylation by CysTMT⁶ switch assay. Methods Mol Biol 2013; 1005:169-179. [PMID: 23606257 DOI: 10.1007/978-1-62703-386-2_14] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
S-nitrosylation (SNO) is an important oxidative posttranslational modification in the regulation of cardiac mitochondria. SNO modification of several mitochondrial proteins has been associated with cardiac preconditioning and improved cell survival following ischemia/reperfusion injury. Due to their labile nature, SNO modifications are challenging to study using traditional biochemical techniques; particularly, the identification of individual modified cysteine residues. Here, we describe the details of the cysTMT(6) switch assay, a variation of the classic biotin switch protocol. The cysTMT(6) reagent provides a simplified and powerful approach to SNO detection by combining unambiguous identification of the modified cysteine residue and relative quantification of up to six samples by mass spectrometry analysis.
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Affiliation(s)
- Christopher I Murray
- Department of Biological Chemistry, Johns Hopkins University, Baltimore, MD, USA
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22
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Zgheib C, Kurdi M, Zouein FA, Gunter BW, Stanley BA, Zgheib J, Romero DG, King SB, Paolocci N, Booz GW. Acyloxy nitroso compounds inhibit LIF signaling in endothelial cells and cardiac myocytes: evidence that STAT3 signaling is redox-sensitive. PLoS One 2012; 7:e43313. [PMID: 22905257 PMCID: PMC3419695 DOI: 10.1371/journal.pone.0043313] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2012] [Accepted: 07/19/2012] [Indexed: 12/31/2022] Open
Abstract
We previously showed that oxidative stress inhibits leukemia inhibitory factor (LIF) signaling by targeting JAK1, and the catalytic domains of JAK 1 and 2 have a cysteine-based redox switch. Thus, we postulated that the NO sibling and thiophylic compound, nitroxyl (HNO), would inhibit LIF-induced JAK-STAT3 activation. Pretreatment of human microvascular endothelial cells (HMEC-1) or neonatal rat cardiomyocytes with the HNO donors Angeli’s salt or nitrosocyclohexyl acetate (NCA) inhibited LIF-induced STAT3 activation. NCA pretreatment also blocked the induction of downstream inflammatory genes (e.g. intercellular adhesion molecule 1, CCAAT/enhancer binding protein delta). The related 1-nitrosocyclohexyl pivalate (NCP; not a nitroxyl donor) was equally effective in inhibiting STAT3 activation, suggesting that these compounds act as thiolate targeting electrophiles. The JAK1 redox switch is likely not a target of acyloxy nitroso compounds, as NCA had no effect on JAK1 catalytic activity and only modestly affected JAK1-induced phosphorylation of the LIF receptor. However, pretreatment of recombinant human STAT3 with NCA or NCP reduced labeling of free sulfhydryl residues. We show that NCP in the presence of diamide enhanced STAT3 glutathionylation and dimerization in adult mouse cardiac myocytes and altered STAT3 under non-reducing conditions. Finally, we show that monomeric STAT3 levels are decreased in the Gαq model of heart failure in a redox-sensitive manner. Altogether, our evidence indicates that STAT3 has redox-sensitive cysteines that regulate its activation and are targeted by HNO donors and acyloxy nitroso compounds. These findings raise the possibility of new therapeutic strategies to target STAT3 signaling via a redox-dependent manner, particularly in the context of cardiac and non-cardiac diseases with prominent pro-inflammatory signaling.
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Affiliation(s)
- Carlos Zgheib
- Departments of Pharmacology and Toxicology, School of Medicine, and Center for Excellence in Cardiovascular-Renal Research, The University of Mississippi Medical Center, Jackson, Mississippi, United States of America
| | - Mazen Kurdi
- Department of Chemistry and Biochemistry, Faculty of Sciences, Lebanese University, Rafic Hariri Educational Campus, Hadath, Lebanon
| | - Fouad A. Zouein
- Departments of Pharmacology and Toxicology, School of Medicine, and Center for Excellence in Cardiovascular-Renal Research, The University of Mississippi Medical Center, Jackson, Mississippi, United States of America
| | - Barak W. Gunter
- Departments of Pharmacology and Toxicology, School of Medicine, and Center for Excellence in Cardiovascular-Renal Research, The University of Mississippi Medical Center, Jackson, Mississippi, United States of America
| | - Brian A. Stanley
- Division of Cardiology, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
| | - Joe Zgheib
- Department of Medicine, Division of Cardiology, Centre Hospitalier Universitaire de Nancy, Brabois, France
| | - Damian G. Romero
- Department of Biochemistry, School of Medicine, and Center for Excellence in Cardiovascular-Renal Research, The University of Mississippi Medical Center, Jackson, Mississippi, United States of America
| | - S. Bruce King
- Department of Chemistry, Wake Forest University, Winston-Salem, North Carolina, United States of America
| | - Nazareno Paolocci
- Division of Cardiology, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
- Clinical Medicine Department, Section of General Pathology, University of Perugia, Perugia, Italy
| | - George W. Booz
- Departments of Pharmacology and Toxicology, School of Medicine, and Center for Excellence in Cardiovascular-Renal Research, The University of Mississippi Medical Center, Jackson, Mississippi, United States of America
- * E-mail:
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23
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Garcia-Segura S, Centellas F, Arias C, Garrido JA, Rodríguez RM, Cabot PL, Brillas E. Comparative decolorization of monoazo, diazo and triazo dyes by electro-Fenton process. Electrochim Acta 2011. [DOI: 10.1016/j.electacta.2011.09.049] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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24
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Martínez-Pastor M, Proft M, Pascual-Ahuir A. Adaptive Changes of the Yeast Mitochondrial Proteome in Response to Salt Stress. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2010; 14:541-52. [DOI: 10.1089/omi.2010.0020] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Mar Martínez-Pastor
- Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia (UPV)—Consejo Superior de Investigaciones Científicas (CSIC), Ciudad Politécnica de la Innovación, Ingeniero Fausto Elio, Valencia, Spain
| | - Markus Proft
- Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia (UPV)—Consejo Superior de Investigaciones Científicas (CSIC), Ciudad Politécnica de la Innovación, Ingeniero Fausto Elio, Valencia, Spain
| | - Amparo Pascual-Ahuir
- Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia (UPV)—Consejo Superior de Investigaciones Científicas (CSIC), Ciudad Politécnica de la Innovación, Ingeniero Fausto Elio, Valencia, Spain
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25
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Stefanyk LE, Coverdale N, Roy BD, Peters SJ, LeBlanc PJ. Skeletal Muscle Type Comparison of Subsarcolemmal Mitochondrial Membrane Phospholipid Fatty Acid Composition in Rat. J Membr Biol 2010; 234:207-15. [DOI: 10.1007/s00232-010-9247-4] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2009] [Accepted: 03/04/2010] [Indexed: 12/22/2022]
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26
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Evans IM, Rus AM, Belanger EM, Kimoto M, Brusslan JA. Dismantling of Arabidopsis thaliana mesophyll cell chloroplasts during natural leaf senescence. PLANT BIOLOGY (STUTTGART, GERMANY) 2010; 12:1-12. [PMID: 20653883 PMCID: PMC4383266 DOI: 10.1111/j.1438-8677.2009.00206.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
One of the earliest events in the process of leaf senescence is dismantling of chloroplasts. Mesophyll cell chloroplasts from rosette leaves were studied in Arabidopsis thaliana undergoing natural senescence. The number of chloroplasts decreased by only 17% in fully yellow leaves, and chloroplasts were found to undergo progressive photosynthetic and ultrastructural changes as senescence proceeded. In ultrastructural studies, an intact tonoplast could not be visualized, thus, a 35S-GFP::delta-TIP line with a GFP-labeled tonoplast was used to demonstrate that chloroplasts remain outside of the tonoplast even at late stages of senescence. Chloroplast DNA was measured by real-time PCR at four different chloroplast loci, and a fourfold decrease in chloroplast DNA per chloroplast was noted in yellow senescent leaves when compared to green leaves from plants of the same age. Although chloroplast DNA did decrease, the chloroplast/nuclear gene copy ratio was still 31:1 in yellow leaves. Interestingly, mRNA levels for the four loci differed: psbA and ndhB mRNAs remained abundant late into senescence, while rpoC1 and rbcL mRNAs decreased in parallel to chloroplast DNA. Together, these data demonstrate that, during senescence, chloroplasts remain outside of the vacuole as distinct organelles while the thylakoid membranes are dismantled internally. As thylakoids were dismantled, Rubisco large subunit, Lhcb1, and chloroplast DNA levels declined, but variable levels of mRNA persisted.
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Affiliation(s)
- I M Evans
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
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27
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Shimazaki Y, Kodama A. Production of immunoaffinity membranes for direct analysis of antigen after antibody separation and blotting under non-denaturing conditions. Anal Chim Acta 2009; 643:61-6. [DOI: 10.1016/j.aca.2009.04.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2009] [Revised: 04/03/2009] [Accepted: 04/04/2009] [Indexed: 11/15/2022]
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28
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LeBlanc PJ, Mulligan M, Antolić A, MacPherson L, Inglis JG, Martin D, Roy BD, Peters SJ. Skeletal muscle type comparison of pyruvate dehydrogenase phosphatase activity and isoform expression: effects of obesity and endurance training. Am J Physiol Regul Integr Comp Physiol 2008; 295:R1224-30. [DOI: 10.1152/ajpregu.90320.2008] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Pyruvate dehydrogenase (PDH) plays an important role in regulating carbohydrate metabolism in skeletal muscle. PDH is activated by PDH phosphatase (PDP) and deactivated by PDH kinase (PDK). Obesity has a large negative impact on skeletal muscle carbohydrate metabolism, whereas endurance training has been shown to improve regulatory control of skeletal muscle carbohydrate metabolism, more so when coupled with obesity. A majority of this literature has focused on PDK, with little information available on PDP. To determine the relative role of PDP in regulating skeletal muscle PDH activity with obesity and endurance training, obese and lean Zucker rats remained sedentary or were endurance trained (1 h/day, 5 days/wk) for a period of 8 wk. Soleus, red gastrocnemius, (RG), and white gastrocnemius (WG) muscles were sampled after the training period. The main findings were 1) obesity resulted in a 46% decrease in PDP activity expressed per milligram extracted mitochondrial protein only in RG, while PDP isoform content was unchanged; 2) 8 wk of endurance training led to a significant 1.4–2.2-fold increase in PDP activity of all muscle examined from obese rats, and the concomitant increase in PDP1 protein was only seen in soleus and RG; 3) 8 wk of endurance training led to a trending 1.4–2.2-fold increase in PDP activity of all muscle examined from obese rats, and the concomitant increase in PDP1 protein was only seen in soleus and RG; and 4) PDP2 protein content was not affected by obesity or training. These results suggest that decreased PDP activity in oxidative skeletal muscles may play a role in the impairment of carbohydrate metabolism in obese rats, which is reversible with endurance training.
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Kumar SA, Lo PH, Chen SM. Electrochemical selective determination of ascorbic acid at redox active polymer modified electrode derived from direct blue 71. Biosens Bioelectron 2008; 24:518-23. [PMID: 18586483 DOI: 10.1016/j.bios.2008.05.007] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2008] [Revised: 05/01/2008] [Accepted: 05/20/2008] [Indexed: 11/19/2022]
Abstract
A simple selective method for determination of ascorbic acid using polymerized direct blue 71 (DB71) is described. Anodic polymerization of the azo dye DB71 on glassy carbon (GC) electrode in 0.1M H(2)SO(4) acidic medium was found to yield thin and stable polymeric films. The poly(DB71) films were electroactive in wide pH range (1-13). A pair of symmetrical redox peaks at a formal redox potential, E('0)=-0.02V vs. Ag/AgCl (pH 7.0) was observed with a Nernstian slope -0.058V, is attributed to a 1:1 proton+electron involving polymer redox reactions at the modified electrode. Scanning electron microscope (SEM), atomic force microscope (AFM) and electrochemical impedance spectroscopy (EIS) measurements were used for surface studies of polymer modified electrode. Poly(DB71) modified GC electrode showed excellent electrocatalytic activity towards ascorbic acid in neutral buffer solution. Using amperometric method, linear range (1x10(-6)-2x10(-3)M), dynamic range (1x10(-6)-0.01M) and detection limit (1x10(-6)M, S/N=3) were estimated for measurement of ascorbic acid in pH 7.0 buffer solution. Major interferences such as dopamine and uric acid are tested at this modified electrode and found that selective detection of ascorbic acid can be achieved. This new method successfully applied for determination of ascorbic acid in commercial tablets with satisfactory results.
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Affiliation(s)
- S Ashok Kumar
- Department of Chemical Engineering and Biotechnology, National Taipei University of Technology, No. 1, Section 3, Chung-Hsiao East Road, Taipei, 106, Taiwan, ROC
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30
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Glenn KA, Nelson RF, Wen HM, Mallinger AJ, Paulson HL. Diversity in tissue expression, substrate binding, and SCF complex formation for a lectin family of ubiquitin ligases. J Biol Chem 2008; 283:12717-29. [PMID: 18203720 DOI: 10.1074/jbc.m709508200] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Post-translational modification of proteins regulates many cellular processes. Some modifications, including N-linked glycosylation, serve multiple functions. For example, the attachment of N-linked glycans to nascent proteins in the endoplasmic reticulum facilitates proper folding, whereas retention of high mannose glycans on misfolded glycoproteins serves as a signal for retrotranslocation and ubiquitin-mediated proteasomal degradation. Here we examine the substrate specificity of the only family of ubiquitin ligase subunits thought to target glycoproteins through their attached glycans. The five proteins comprising this FBA family (FBXO2, FBXO6, FBXO17, FBXO27, and FBXO44) contain a conserved G domain that mediates substrate binding. Using a variety of complementary approaches, including glycan arrays, we show that each family member has differing specificity for glycosylated substrates. Collectively, the F-box proteins in the FBA family bind high mannose and sulfated glycoproteins, with one FBA protein, FBX044, failing to bind any glycans on the tested arrays. Site-directed mutagenesis of two aromatic amino acids in the G domain demonstrated that the hydrophobic pocket created by these amino acids is necessary for high affinity glycan binding. All FBA proteins co-precipitated components of the canonical SCF complex (Skp1, Cullin1, and Rbx1), yet FBXO2 bound very little Cullin1, suggesting that FBXO2 may exist primarily as a heterodimer with Skp1. Using subunit-specific antibodies, we further demonstrate marked divergence in tissue distribution and developmental expression. These differences in substrate recognition, SCF complex formation, and tissue distribution suggest that FBA proteins play diverse roles in glycoprotein quality control.
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Affiliation(s)
- Kevin A Glenn
- Veterans Affairs Medical Center, Iowa City, Iowa 52242, USA.
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31
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March TJ, Able JA, Schultz CJ, Able AJ. A novel late embryogenesis abundant protein and peroxidase associated with black point in barley grains. Proteomics 2007; 7:3800-8. [PMID: 17853513 DOI: 10.1002/pmic.200700456] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Black point of barley grain is a disorder characterised by a brown-black discolouration at the embryo end of the grain. Black point is undesirable to the malting industry and results in significant economic loss annually. To identify proteins associated with barley black point we utilised a proteomic approach with 2-DE to compare proteins from whole grain samples of black pointed and healthy grain. From this comparison two condition-specific proteins were identified: a novel 75 kDa late embryogenesis abundant (LEA) protein and a barley grain peroxidase 1 (BP1) that were specifically more abundant in healthy grain and black pointed grain, respectively. Although LEA protein was less abundant in black pointed grain, LEA gene expression was greater suggesting protein degradation had possibly occurred in black pointed grain. Similarly, the increase in BP1 in black pointed grain could not be explained by gene expression. Western blot analysis also revealed that the identified LEA protein is biotinylated in vivo. The role that each of these proteins might have in black point development is discussed.
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Affiliation(s)
- Timothy J March
- School of Agriculture, Food & Wine, The University of Adelaide, Waite Campus, Glen Osmond, South Australia, Australia
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32
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Shimazaki Y, Kuroda T. Direct analysis of retinal dehydrogenase activity on an electroblotting membrane following separation by non-denaturing two-dimensional electrophoresis. J Chromatogr B Analyt Technol Biomed Life Sci 2007; 860:180-4. [PMID: 17997140 DOI: 10.1016/j.jchromb.2007.10.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2007] [Revised: 10/10/2007] [Accepted: 10/18/2007] [Indexed: 10/22/2022]
Abstract
The reaction from retinal to retinoic acid catalyzed by retinal dehydrogenase on a polyvinylidene difluoride (PVDF) membrane was examined using laser desorption ionization time of flight mass spectrometry (LDI-TOF MS) when the enzyme was separated by non-denaturing two-dimensional electrophoresis (2-DE), transferred onto the membrane, and stained without impairing the enzyme activity. Furthermore, the enzyme was analyzed by de novo sequencing using electrospray ionization tandem mass spectrometry (ESI-MS/MS) after proteins from mouse liver were separated by non-denaturing 2-DE, blotted onto the membrane, and stained. The results indicated that the reported methods could be applied for the direct examination of changes in retinoid catalyzed by enzymes on such membranes.
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Affiliation(s)
- Youji Shimazaki
- Graduate school of Science and Engineering (Science section) and Venture Business Laboratory, Ehime University, Matsuyama, Japan.
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Farré EM, Kay SA. PRR7 protein levels are regulated by light and the circadian clock in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2007; 52:548-60. [PMID: 17877705 DOI: 10.1111/j.1365-313x.2007.03258.x] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Interlocking transcriptional loops and regulated protein degradation are the principal mechanisms involved in the generation of self-sustaining circadian rhythms in many organisms. In Arabidopsis the first proposed regulatory transcriptional loop involved the transcription factors CIRCADIAN CLOCK ASSOCIATED (CCA1) and LATE ELONGATED HYPOCOTYL (LHY) and the pseudo-response regulator TIMING OF CHLOROPHYLL A/B BINDING PROTEIN (TOC1/PRR1). Recent findings indicate that the TOC1 homologues PRR7 and PRR9 might also be involved in transcriptional regulatory loops with CCA1 and LHY. In this study we show that the overexpression of PRR7 in Arabidopsis leads to severely compromised circadian rhythms. These transgenic lines display significantly reduced levels of CCA1 and LHY RNA, providing further evidence for a transcriptional feedback loop between PRR7 and these transcription factors. In addition, we show that the PRR7 protein is phosphorylated in a circadian regulated manner and that its levels are post-translationally regulated by both diurnal and circadian mechanisms. The Arabidopsis circadian oscillator is therefore likely to be entrained to light/dark cycles both through transcriptional and post-transcriptional mechanisms.
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Affiliation(s)
- Eva M Farré
- Department of Biochemistry, The Scripps Research Institute 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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34
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Nakanishi T, Ando E, Furuta M, Tsunasawa S, Nishimura O. Direct on-membrane peptide mass fingerprinting with MALDI–MS of tyrosine-phosphorylated proteins detected by immunostaining. J Chromatogr B Analyt Technol Biomed Life Sci 2007; 847:24-9. [PMID: 16959554 DOI: 10.1016/j.jchromb.2006.08.024] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2006] [Revised: 08/01/2006] [Accepted: 08/06/2006] [Indexed: 11/23/2022]
Abstract
We have identified tyrosine-phosphorylated proteins on membrane from A-431 human epidermoid carcinoma cells by using detection with anti-phosphotyrosine antibody followed by PMF analysis. In there, on-membrane digestion for these protein spots was carried out on microscale region using chemical inkjet technology and the resulting tryptic digests were directly analyzed by MALDI-TOF MS. Proteins identified by a database search included phosphoproteins that are known to be markedly phosphorylated on tyrosine sites after the cells are treated with epidermal growth factor (EGF). This procedure is a rapid and easily handled approach that enables both detection and identification of phosphoproteins on a single blot membrane.
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Affiliation(s)
- Tsuyoshi Nakanishi
- Life Science Laboratory, Analytical & Measuring Instruments Division, Shimadzu Corporation, 1 Nishinokyo-Kuwabaracho, Nakagyo-ku, Kyoto 604-8511, Japan
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35
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Miller I, Crawford J, Gianazza E. Protein stains for proteomic applications: which, when, why? Proteomics 2007; 6:5385-408. [PMID: 16991193 DOI: 10.1002/pmic.200600323] [Citation(s) in RCA: 142] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
This review recollects literature data on sensitivity and dynamic range for the most commonly used colorimetric and fluorescent dyes for general protein staining, and summarizes procedures for the most common PTM-specific detection methods. It also compiles some important points to be considered in imaging and evaluation. In addition to theoretical considerations, examples are provided to illustrate differential staining of specific proteins with different detection methods. This includes a large body of original data on the comparative evaluation of several pre- and post-electrophoresis stains used in parallel on a single specimen, horse serum run in 2-DE (IPG-DALT). A number of proteins/protein spots are found to be over- or under-revealed with some of the staining procedures.
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Affiliation(s)
- Ingrid Miller
- Institut für Medizinische Chemie, Department für Naturwissenschaften, Veterinärmedizinische Universität Wien, Wien, Austria.
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36
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Shimazaki Y, Miyamoto M. Analysis of lipid hydrolytic activity by esterase on blotting membrane followed by separation using non-denaturing two-dimensional gel electrophoresis. Biotechnol Bioeng 2007; 98:732-6. [PMID: 17385750 DOI: 10.1002/bit.21437] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
After separation by microscale non-denaturing two-dimensional gel electrophoresis (2DE) and transferring to a blotting membrane, major proteins are detected by a staining of direct blue 71 in a neutral solution. The carboxylesterase on the membrane hydrolyzes phosphatidylcholine after the spot of carboxylesterase is excised from the membrane, and incubated with phosphatidylcholine. Lipids of human serum proteins and the purified human high density lipoprotein (HDL) are removed by enzymatic hydrolysis when human serum proteins and the purified HDL are respectively incubated with the spot of carboxylesterase on the membrane. These results indicate that carboxylesterase on the membrane hydrolyzes not only lipids such as phosphatidylcholine but also lipids of lipoproteins such as HDL after separation by the 2DE, transferring to the membrane and staining without impairing the activity. These results also indicate that a micro-immobilized enzyme reactor on the membrane can be produced when biological enzymes are separated by microscale 2DE, transferred to the membrane and stained without impairing their activities.
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Affiliation(s)
- Youji Shimazaki
- Graduate School of Science and Engineering (Science Section), Venture Business Laboratory, Ehime University, Matsuyama City 790-8577, Japan.
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37
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SHIMMA S, FURUTA M, ICHIMURA K, YOSHIDA Y, SETOU M. A Novel Approach to in situ Proteome Analysis Using Chemical Inkjet Printing Technology and MALDI-QIT-TOF Tandem Mass Spectrometer. ACTA ACUST UNITED AC 2006. [DOI: 10.5702/massspec.54.133] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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38
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LeBlanc PJ, Peters SJ, Tunstall RJ, Cameron-Smith D, Heigenhauser GJF. Effects of aerobic training on pyruvate dehydrogenase and pyruvate dehydrogenase kinase in human skeletal muscle. J Physiol 2004; 557:559-70. [PMID: 15020699 PMCID: PMC1665109 DOI: 10.1113/jphysiol.2003.058263] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
This study examined the effects of short- and long-term aerobic training on the stable up-regulation of pyruvate dehydrogenase (PDH) and PDH kinase (PDK) in human skeletal muscle. We hypothesized that 8 weeks, but not 1 week, of aerobic training would increase total PDH (PDHt) and PDK activities compared to pretraining, and this would be detectable at the level of gene transcription (mRNA) and/or gene translation (protein). Resting muscle biopsies were taken before and after 1 and 8 weeks of aerobic cycle exercise training. PDHt and PDK activities, and their respective protein and mRNA expression, did not differ after 1 week of aerobic training. PDHt activity increased 31% after 8 weeks and this may be partially due to a 1.3-fold increase in PDH-E(1)alpha protein expression. PDK activity approximately doubled after 8 weeks of aerobic training and this was attributed to a 1.3-fold increase in PDK2 isoform protein expression. Similar to 1 week, no changes were observed at the mRNA level after 8 weeks of training. These findings suggest that aerobically trained human skeletal muscle has an increased maximal capacity to utilize carbohydrates, evident by increased PDHt, but increased metabolic control sensitivity to pyruvate through increased contribution of PDK2 to total PDK activity.
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Affiliation(s)
- Paul J LeBlanc
- Department Medicine, McMaster University, Hamilton, Ontario, Canada.
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Yatsuda AP, Krijgsveld J, Cornelissen AWCA, Heck AJR, de Vries E. Comprehensive analysis of the secreted proteins of the parasite Haemonchus contortus reveals extensive sequence variation and differential immune recognition. J Biol Chem 2003; 278:16941-51. [PMID: 12576473 DOI: 10.1074/jbc.m212453200] [Citation(s) in RCA: 164] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Haemonchus contortus is a nematode that infects small ruminants. It releases a variety of molecules, designated excretory/secretory products (ESP), into the host. Although the composition of ESP is largely unknown, it is a source of potential vaccine components because ESP are able to induce up to 90% protection in sheep. We used proteomic tools to analyze ESP proteins and determined the recognition of these individual proteins by hyperimmune sera. Following two-dimensional electrophoresis of ESP, matrix-assisted laser desorption ionization time-of-flight and liquid chromatography-tandem mass spectrometry were used for protein identification. Few sequences of H. contortus have been determined. Therefore, the data base of expressed sequence tags (dbEST) and a data base consisting of contigs from Haemonchus ESTs were also consulted for identification. Approximately 200 individual spots were observed in the two-dimensional gel. Comprehensive proteomics analysis, combined with bioinformatic search tools, identified 107 proteins in 102 spots. The data include known as well as novel proteins such as serine, metallo- and aspartyl proteases, in addition to H. contortus ESP components like Hc24, Hc40, Hc15, and apical gut GA1 proteins. Novel proteins were identified from matches with H. contortus ESTs displaying high similarity with proteins like cyclophilins, nucleoside diphosphate kinase, OV39 antigen, and undescribed homologues of Caenorhabditis elegans. Of special note is the finding of microsomal peptidase H11, a vaccine candidate previously regarded as a "hidden antigen" because it was not found in ESP. Extensive sequence variation is present in the abundant Hc15 proteins. The Hc15 isoforms are differentially recognized by hyperimmune sera, pointing to a possible specific role of Hc15 in the infectious process and/or in immune evasion. This concept and the identification of multiple novel immune-recognized components in ESP should assist future vaccine development strategies.
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Affiliation(s)
- Ana P Yatsuda
- Department of Infectious Diseases and Immunology, Utrecht University, PO Box 80165, 3508 TD, Utrecht, The Netherlands
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