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Mayer HK, Lenz K, Halbauer EM. "A2 milk" authentication using isoelectric focusing and different PCR techniques. Food Res Int 2021; 147:110523. [PMID: 34399501 DOI: 10.1016/j.foodres.2021.110523] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 06/01/2021] [Accepted: 06/09/2021] [Indexed: 12/17/2022]
Abstract
Genetic variants of milk proteins have attracted great interest for decades as they are related to important issues such as the composition and technological properties of milk. More recently, an "A1/A2 hypothesis" was developed saying that β-casein variant A1 may be a dietary risk factor for cardiovascular diseases, type 1 diabetes, sudden infant death syndrome and neurological disorders due to the release of β-casomorphin-7, whereas no evidence for such adverse effects was assumed for β-casein A2. Thus, the aim of this study was to adapt and establish analytical methods for the identification of genetic variants of β-casein using isoelectric focusing of milk proteins as well as appropriate PCR techniques. Allele-specific polymerase chain reaction (AS-PCR) proved to be a reliable method for differentiating most common β-casein variants (A1, A2, B, C), amplification-created restriction site (ACRS)-PCR using three different restriction enzymes allowed also the detection of variant A3, and the restriction fragment length polymorphism (RFLP)-PCR method enabled the reliable discrimination between A2 (homozygote/heterozygote) and non-A2 animals. Since traces of β-casein A1 were also found in commercial "A2 milk" in Austria, the authentication of such expensive dairy products is urgently recommended, both by genotyping of all dairy cows at farm level (to confirm that all cows are homozygous β-casein A2A2) and by screening commercial products on the market (to confirm the absence of β-casein variants A1, B, and C in dairy products labelled "A2 milk") to protect consumers from this unexpected fraud.
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Affiliation(s)
- Helmut K Mayer
- Department of Food Science and Technology, Food Chemistry Laboratory, BOKU - University of Natural Resources and Life Sciences Vienna, Muthgasse 11, A-1190 Vienna, Austria.
| | - Kathrin Lenz
- Department of Food Science and Technology, Food Chemistry Laboratory, BOKU - University of Natural Resources and Life Sciences Vienna, Muthgasse 11, A-1190 Vienna, Austria
| | - Eva-Maria Halbauer
- Department of Food Science and Technology, Food Chemistry Laboratory, BOKU - University of Natural Resources and Life Sciences Vienna, Muthgasse 11, A-1190 Vienna, Austria
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2
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Wang K, Zhao X, Pang C, Zhou S, Qian X, Tang N, Yang N, Xu P, Xu X, Gao J. IMPERFECTIVE EXINE FORMATION ( IEF) is required for exine formation and male fertility in Arabidopsis. Plant Mol Biol 2021; 105:625-635. [PMID: 33481140 DOI: 10.1007/s11103-020-01114-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Accepted: 12/30/2020] [Indexed: 06/12/2023]
Abstract
KEY MESSAGE IEF, a novel plasma plasma membrane protein, is important for exine formation in Arabidopsis. Exine, an important part of pollen wall, is crucial for male fertility. The major component of exine is sporopollenin which are synthesized and secreted by tapetum. Although sporopollenin synthesis has been well studied, the transportation of it remains elusive. To understand it, we analyzed the gene expression pattern in tapetal microdissection data, and investigated the potential transporter genes that are putatively regulated by ABORTED MICROSPORES (AMS). Among these genes, we identified IMPERFECTIVE EXINE FORMATION (IEF) that is important for exine formation. Compared to the wild type, ief mutants exhibit severe male sterility and pollen abortion, suggesting IEF is crucial for pollen development and male fertility. Using both scanning and transmission electron microscopes, we showed that exine structure was not well defined in ief mutant. The transient expression of IEF-GFP driven by the 35S promoter indicated that IEF-GFP was localized in plasma membrane. Furthermore, AMS can specifically activate the expression of promoterIEF:LUC in vitro, which suggesting AMS regulates IEF for exine formation. The expression of ATP-BINDING CASSETTE TRANSPORTER G26 (AGCB26) was not affected in ief mutants. In addition, SEM and TEM data showed that the sporopollenin deposition is more defective in abcg26/ief-2 than that of in abcg26, which suggesting that IEF is involved in an independent sporopollenin transportation pathway. This work reveal a novel gene, IEF regulated by AMS that is essential for exine formation.
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Affiliation(s)
- Kaiqi Wang
- School of Environmental and Geographical Sciences, Shanghai Normal University, Shanghai, 200234, China
- College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Xin Zhao
- College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Chaoting Pang
- College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Sida Zhou
- College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Xuexue Qian
- College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Nan Tang
- College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Naiying Yang
- College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Ping Xu
- College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Xiaofeng Xu
- College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China.
| | - Jufang Gao
- College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China.
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3
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Frömmel C. Newborn Screening for Sickle Cell Disease and Other Hemoglobinopathies: A Short Review on Classical Laboratory Methods-Isoelectric Focusing, HPLC, and Capillary Electrophoresis. Int J Neonatal Screen 2018; 4:39. [PMID: 33072959 DOI: 10.3390/ijns4040039] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Accepted: 11/01/2018] [Indexed: 12/04/2022] Open
Abstract
Sickle cell disease (SCD) and other hemoglobinopathies are a major health concern with a high burden of disease worldwide. Since the implementation of newborn screening (NBS) for SCD and other hemoglobinopathies in several regions of the world, technical progress of laboratory methods was achieved. This short review aims to summarize the current practice of classical laboratory methods for the detection of SCD and other hemoglobinopathies. This includes the newborn screening technologies of high-performance liquid chromatography (HPLC), capillary electrophoresis (CE), and isoelectric focusing (IEF).
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4
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Abstract
Two-dimensional gel electrophoresis is one of the most powerful tools for separating proteins based on their size and charge. Two-dimensional gel electrophoresis (2-DE) is very useful to separate two proteins with identical molecular weights but different charges, which cannot be achieved with just sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). Here, a simpler and easier version of 2-DE is presented which is also faster than all the currently available techniques. In this modified version of 2-DE, isoelectric focusing is carried out in the first dimension using a vertical sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) apparatus. Following the first-dimensional IEF, each individual lane is excised from the IEF gel and after a 90° rotation, is inserted into a second-dimensional SDS-PAGE, which can be stained with Coomassie Brilliant Blue for protein analysis or immunoblotted for further analysis. This version of IEF can be run in less than 2 h compared to the overnight run required by O'Farrell's method. Difficult tube gel casting and gel extrusion as well as tube gel distortion are eliminated in our method. This method is simpler, faster, and inexpensive. Both dimensions can be done on the same SDS-PAGE apparatus, and up to ten samples can be run simultaneously using one gel.
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Koelsch KA. Single-Cell High-Resolution Detection and Quantification of Protein Isoforms Differing by a Single Charge Unit. Methods Mol Biol 2019; 1855:501-9. [PMID: 30426445 DOI: 10.1007/978-1-4939-8793-1_44] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Isoelectric focusing (IEF) is an electrophoretic technique that enables the separation of proteins based on their isoelectric points. Until recently, this valuable method was not feasible for single-cell applications, which are necessary to interrogate heterogeneous cell populations. Herein we highlight a recently published method enabling the analysis of single-cell proteomics, which utilizes microfluidics coupled with IEF, photocapture, and immunoprobing of the protein in the same micro-gel, which can be stripped and reprobed multiple times.
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Xue CY, Zhou RJ, Li YJ, Xiao D, Fu JF. Cell-wall-degrading enzymes produced in vitro and in vivo by Rhizoctonia solani, the causative fungus of peanut sheath blight. PeerJ 2018; 6:e5580. [PMID: 30202660 PMCID: PMC6129149 DOI: 10.7717/peerj.5580] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Accepted: 08/14/2018] [Indexed: 11/20/2022] Open
Abstract
Rhizoctonia solani causes the disease peanut sheath blight, involving symptoms of maceration and necrosis of infected tissue, mainly caused by cell-wall-degrading enzymes (CWDEs). This study investigated the production of CWDEs including polygalacturonase (PG), polymethyl-galacturonase (PMG), cellulase (Cx) and β-glucosidase by R. solani in vitro (in liquid culture) and in vivo (in peanut plants). Significant PG, PMG, Cx and β-glucosidase activities were detected in infected tissues including stalk and leaves of Baisha and Silihong peanut cultivars. Extracts of healthy tissue showed little or no such activities. In shaken liquid cultures of R. solani in medium containing pectin or pectin plus carboxymethyl cellulose (CMC) as the carbon source(s), PG and PMG were notably active. Significant Cx activity was detected in cultures with CMC or pectin plus CMC as the carbon source(s). However, only a very low level of β-glucosidase activity was observed in cultures with any of the tested carbon sources. An increase of pH was recorded in decayed peanut tissues and liquid culture filtrates; the filtrate pH and fungal growth positively correlated. The fungal growth and/or pH were important factors for the production of PG, PMG and Cx in culture with pectin plus CMC as the carbon source. A single active PG isozyme with isoelectric point around 9.2 was detected in culture filtrates and in infected peanut tissues by the method of isoelectric focusing electrophoresis. The crude enzymes extracted from liquid culture of R. solani induced decay of healthy peanut leaves.
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Affiliation(s)
- Cai Yun Xue
- Department of Plant Protection, Shenyang Agriculture University, Shenyang, Liaoning, China
| | - Ru Jun Zhou
- Department of Plant Protection, Shenyang Agriculture University, Shenyang, Liaoning, China
| | - Yuan Jie Li
- Department of Plant Protection, Shenyang Agriculture University, Shenyang, Liaoning, China
| | - Di Xiao
- Department of Plant Protection, Shenyang Agriculture University, Shenyang, Liaoning, China
| | - Jun Fan Fu
- Department of Plant Protection, Shenyang Agriculture University, Shenyang, Liaoning, China
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Sonet J, Mounicou S, Chavatte L. Detection of Selenoproteins by Laser Ablation Inductively Coupled Plasma Mass Spectrometry (LA-ICP MS) in Immobilized pH Gradient (IPG) Strips. Methods Mol Biol 2018; 1661:205-217. [PMID: 28917047 DOI: 10.1007/978-1-4939-7258-6_15] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
In contrast to other trace elements that are cofactors of enzymes and removed from proteins under denaturing conditions, Se is covalently bound to proteins when incorporated into selenoproteins, since it is a component of selenocysteine aminoacid. It implies that selenoproteins can undergo several biochemical separation methods in stringent and chaotropic conditions and still maintain the presence of selenium in the primary sequence. This feature has been used to develop a method for the detection of trace levels of human selenoproteins in cell extracts without the use of radioactive isotopes. The selenoproteins are separated as a function of their isoelectric point (pI) using iso-electrofocusing (IEF) electrophoretic strips and detected by laser ablation-inductively coupled plasma mass spectrometry (LA-ICP MS). This method, therefore referred to as IEF-LA-ICP MS, allowed the detection of several selenoproteins in human cell lines, including Gpx1, Gpx4, TXNRD1, TXNRD2, and SELENOF.
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Affiliation(s)
- Jordan Sonet
- Laboratoire de Chimie Analytique Bio-Inorganique et Environnement, LCABIE, CNRS/Univ Pau & Pays Adour, Institut des Sciences Analytiques et de Physico-Chimie Pour l'Environnement et Les Matériaux, UMR5254, Pau, 64000, France
| | - Sandra Mounicou
- Laboratoire de Chimie Analytique Bio-Inorganique et Environnement, LCABIE, CNRS/Univ Pau & Pays Adour, Institut des Sciences Analytiques et de Physico-Chimie Pour l'Environnement et Les Matériaux, UMR5254, Pau, 64000, France
| | - Laurent Chavatte
- Laboratoire de Chimie Analytique Bio-Inorganique et Environnement, LCABIE, CNRS/Univ Pau & Pays Adour, Institut des Sciences Analytiques et de Physico-Chimie Pour l'Environnement et Les Matériaux, UMR5254, Pau, 64000, France. .,Centre International de Recherche en Infectiologie, CIRI, Lyon, 69007, France. .,INSERM U1111, Lyon, 69007, France. .,CNRS/ENS/UCBL1 UMR5308, Lyon, 69007, France.
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8
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Yamauchi KA, Tentori AM, Herr AE. Arrayed isoelectric focusing using photopatterned multi-domain hydrogels. Electrophoresis 2018; 39:1040-1047. [PMID: 29385243 PMCID: PMC6106862 DOI: 10.1002/elps.201700386] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Revised: 01/11/2018] [Accepted: 01/12/2018] [Indexed: 01/23/2023]
Abstract
Isoelectric focusing (IEF) is a powerful separation method, useful for resolving subtle changes in the isoelectric point of unlabeled proteins. While microfluidic IEF has reduced the separation times from hours in traditional benchtop IEF to minutes, the enclosed devices hinder post-separation access to the sample for downstream analysis. The two-layer open IEF device presented here comprises a photopatterned hydrogel lid layer containing the chemistries required for IEF and a thin polyacrylamide bottom layer in which the analytes are separated. The open IEF device produces comparable minimum resolvable difference in isoelectric point and gradient stability to enclosed microfluidic devices while providing post-separation sample access by simple removal of the lid layer. Further, using simulations, we determine that the material properties and the length of the separation lanes are the primary factors that affect the electric field magnitude in the separation region. Finally, we demonstrate self-indexed photomasks for alignment-free fabrication of multi-domain hydrogels. We leverage this approach to generate arrayed pH gradients with a total of 80 concurrent separation lanes, which to our knowledge is the first demonstration of multiple IEF separations in series addressed by a single pair of electrodes.
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Affiliation(s)
- Kevin A. Yamauchi
- The UC Berkeley/UCSF Graduate Program in Bioengineering, Berkeley, CA, USA
| | - Augusto M. Tentori
- The UC Berkeley/UCSF Graduate Program in Bioengineering, Berkeley, CA, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Amy E. Herr
- The UC Berkeley/UCSF Graduate Program in Bioengineering, Berkeley, CA, USA
- Department of Bioengineering, UC Berkeley, Berkeley, CA, USA
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9
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Naryzhny S, Zgoda V, Kopylov A, Petrenko E, Archakov А. A semi-virtual two dimensional gel electrophoresis: IF-ESI LC-MS/MS. MethodsX 2017; 4:260-264. [PMID: 28913169 PMCID: PMC5587868 DOI: 10.1016/j.mex.2017.08.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 08/25/2017] [Indexed: 01/30/2023] Open
Abstract
A method for increasing the productivity of ESI LC-MS/MS (electrospray ionization-liquid chromatography-tandem mass spectrometry) was proposed and applied. After IF (isoelectric focusing) of the sample using IPG (immobilized pH gradient) strip, the strip was cut to sections, and every section was treated according to trypsinolysis protocol for MS/MS analysis. The peptides produced were further analyzed by ESI LC-MS/MS. The procedure allows to: identify many more proteins and proteoforms compared to shotgun analysis of extracts. build a semi-virtual 2DE map of identified proteins.
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Affiliation(s)
- Stanislav Naryzhny
- Orekhovich Institute of Biomedical Chemistry of Russian Academy of Medical Sciences, Pogodinskaya 10, Moscow, 119121, Russia.,B.P. Konstantinov Petersburg Nuclear Physics Institute, National Research Center "Kurchatov Institute", Orlova roscha, Gatchina, Leningrad region, 188300, Russia
| | - Victor Zgoda
- Orekhovich Institute of Biomedical Chemistry of Russian Academy of Medical Sciences, Pogodinskaya 10, Moscow, 119121, Russia
| | - Artur Kopylov
- Orekhovich Institute of Biomedical Chemistry of Russian Academy of Medical Sciences, Pogodinskaya 10, Moscow, 119121, Russia
| | - Elena Petrenko
- Orekhovich Institute of Biomedical Chemistry of Russian Academy of Medical Sciences, Pogodinskaya 10, Moscow, 119121, Russia
| | - Аlexander Archakov
- Orekhovich Institute of Biomedical Chemistry of Russian Academy of Medical Sciences, Pogodinskaya 10, Moscow, 119121, Russia
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10
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Akbas N, Gonzalez G, Buffone GJ, Grenache DG, Devaraj S. A Library of Rare α1-Antitrypsin (AAT) Variant Phenotypes to Aid in the Diagnosis of AAT Deficiency. Am J Clin Pathol 2016; 146:289-93. [PMID: 27543976 DOI: 10.1093/ajcp/aqw112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES α1-Antitrypsin (AAT) deficiency is a hereditary disorder due to defective production of the serine protease inhibitor, AAT, which can cause lung and liver diseases. Severity of disease depends particularly on the phenotypic representation of AAT variants in the patient. METHODS In this study, we present determination of seven common and nine rare variant phenotypes of AAT using pediatric samples collected in Texas Children's Hospital to address the knowledge gap in the identification of rare variants. We tested 16 different AAT variants that had been stored in a -80 °C freezer over the years to add to the reference library of AAT variants. The gold-standard isoelectric focusing electrophoresis method was used for analysis and interpretation of AAT variants. Each variant was inspected visually by comparing multiple bands, unique to phenotypic identity, with a previously identified pattern. RESULTS Seven common M, S, and Z variants were identified as M1M1, M2M2, M1M2, MS, SS, SZ, and ZZ. Nine rare variants were identified as FM, FS, FZ, PM, XM, YM, IM, TS, and EP. These were interpreted independently and in a blinded manner by an experienced technologist and two clinical chemists from two different institutions. CONCLUSIONS Our results add to the reference library to identify the rare variant phenotypes of AAT protein. This report will guide clinical laboratories for proper assessment of rare variants and in turn contribute to accurate diagnosis and management of AAT deficiency.
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Affiliation(s)
- Neval Akbas
- From the Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX Texas Children's Hospital, Houston
| | | | - Gregory J Buffone
- From the Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX Texas Children's Hospital, Houston
| | - David G Grenache
- Department of Pathology, University of Utah School of Medicine, Salt Lake City
| | - Sridevi Devaraj
- From the Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX Texas Children's Hospital, Houston
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11
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Ishihara T, Ifuku K, Yamashita E, Fukunaga Y, Nishino Y, Miyazawa A, Kashino Y, Inoue-Kashino N. Utilization of light by fucoxanthin-chlorophyll-binding protein in a marine centric diatom, Chaetoceros gracilis. Photosynth Res 2015; 126:437-47. [PMID: 26149177 DOI: 10.1007/s11120-015-0170-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Accepted: 06/20/2015] [Indexed: 05/23/2023]
Abstract
The major light-harvesting pigment protein complex (fucoxanthin-chlorophyll-binding protein complex; FCP) was purified from a marine centric diatom, Chaetoceros gracilis, by mild solubilization followed by sucrose density gradient centrifugation, and then characterized. The dynamic light scattering measurement showed unimodality, indicating that the complex was highly purified. The amount of chlorophyll a (Chl a) bound to the purified FCP accounted for more than 60 % of total cellular Chl a. The complex was composed of three abundant polypeptides, although there are nearly 30 FCP-related genes. The two major components were identified as Fcp3 (Lhcf3)- and Fcp4 (Lhcf4)-equivalent proteins based on their internal amino acid sequences and a two-dimensional isoelectric focusing electrophoresis analysis developed in this work. Compared with the thylakoids, the FCP complex showed higher contents of fucoxanthin and chlorophyll c but lower contents of the xanthophyll cycle pigments diadinoxanthin and diatoxanthin. Fluorescence excitation spectra analyses indicated that light harvesting, rather than photosystem protection, is the major function of the purified FCP complex, which is associated with more than 60 % of total cellular Chl a. These findings suggest that the huge amount of Chl bound to the FCP complex composed of Lhcf3, Lhcf4, and an unidentified minor protein has a light-harvesting function to allow efficient photosynthesis under the dim-light conditions in the ocean.
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Affiliation(s)
- Tomoko Ishihara
- Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Kohto, Kamigohri, Ako-gun, Hyogo, 678-1297, Japan
| | - Kentaro Ifuku
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502, Japan
| | - Eiki Yamashita
- Institute of Protein Research, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Yuko Fukunaga
- Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Kohto, Kamigohri, Ako-gun, Hyogo, 678-1297, Japan
| | - Yuri Nishino
- Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Kohto, Kamigohri, Ako-gun, Hyogo, 678-1297, Japan
| | - Atsuo Miyazawa
- Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Kohto, Kamigohri, Ako-gun, Hyogo, 678-1297, Japan
| | - Yasuhiro Kashino
- Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Kohto, Kamigohri, Ako-gun, Hyogo, 678-1297, Japan.
| | - Natsuko Inoue-Kashino
- Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Kohto, Kamigohri, Ako-gun, Hyogo, 678-1297, Japan
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12
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Roudeau S, Chevreux S, Carmona A, Ortega R. Reduced net charge and heterogeneity of pI isoforms in familial amyotrophic lateral sclerosis mutants of copper/zinc superoxide dismutase. Electrophoresis 2015; 36:2482-8. [PMID: 26084641 DOI: 10.1002/elps.201500187] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 05/23/2015] [Accepted: 05/25/2015] [Indexed: 01/20/2023]
Abstract
Familial cases of amyotrophic lateral sclerosis (fALS) are related to mutations of copper/zinc superoxide dismutase 1 (SOD1). Aggregation of SOD1 plays a central role in the pathogenesis of fALS and altered metallation of SOD1 mutants could be involved in this process. Using IEF gel electrophoresis under non-denaturating conditions and particle induced X-ray emission (PIXE) analysis, we studied the pI distribution and metallation status of fALS SOD1 mutants (A4V, G93A, D125H) compared to human wild-type (hWT). SOD1 fALS mutants are characterized by a variable number of isoforms and higher pI compared to hWT, reflecting a reduced net charge that might explain their greater propensity to precipitation and aggregation. Cu/Zn ratios were slightly different for the predominant expressed isoforms of A4V, G93A, and D125H mutants compared to hWT. Differences in metallation were observed within each genotype, the more basic isoforms exhibiting lower Cu/Zn ratios. Moreover, we revealed the existence of a pool of fALS mutants SOD1 pI isoforms, slightly expressed (<10%), with a low Cu/Zn ratio and high pI values. Overall, IEF-PIXE results suggest that the toxicity of SOD1 mutants should be studied at the pI isoform level with a particular attention to the species with the lowest charges.
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Affiliation(s)
- Stéphane Roudeau
- University of Bordeaux, CENBG, UMR 5797, Gradignan, France.,CNRS, IN2P3, CENBG, UMR 5797, Gradignan, France
| | - Sylviane Chevreux
- University of Bordeaux, CENBG, UMR 5797, Gradignan, France.,CNRS, IN2P3, CENBG, UMR 5797, Gradignan, France
| | - Asuncion Carmona
- University of Bordeaux, CENBG, UMR 5797, Gradignan, France.,CNRS, IN2P3, CENBG, UMR 5797, Gradignan, France
| | - Richard Ortega
- University of Bordeaux, CENBG, UMR 5797, Gradignan, France.,CNRS, IN2P3, CENBG, UMR 5797, Gradignan, France
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13
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Meisrimler CN, Schwendke A, Lüthje S. Two-dimensional phos-tag zymograms for tracing phosphoproteins by activity in-gel staining. Front Plant Sci 2015; 6:230. [PMID: 25926840 PMCID: PMC4396385 DOI: 10.3389/fpls.2015.00230] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 03/23/2015] [Indexed: 06/04/2023]
Abstract
Protein phosphorylation is one of the most common post-translational modifications regulating many cellular processes. The phos-tag technology was combined with two-dimensional zymograms, which consisted of non-reducing IEF PAGE or NEPHGE in the first dimension and high resolution clear native electrophoresis (hrCNE) in the second dimension. The combination of these electrophoresis methods was mild enough to accomplish in-gel activity staining for Fe(III)-reductases by NADH/Fe(III)-citrate/ferrozine, 3,3'-Diaminobenzidine/H2O2 or TMB/H2O2 in the second dimension. The phos-tag zymograms can be used to investigate phosphorylation-dependent changes in enzyme activity. Phos-tag zymograms can be combined with further downstream analysis like mass spectrometry. Non-reducing IEF will resolve proteins with a pI of 3-10, whereas non-reducing NEPHGE finds application for alkaline proteins with a pI higher than eight. Advantages and disadvantages of these new methods will be discussed in detail.
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Affiliation(s)
- Claudia-Nicole Meisrimler
- Plant Physiology, Biocenter Klein Flottbek and Botanical Garden, University of HamburgHamburg, Germany
- Laboratoire de Biologie du Développement des Plantes, Commissariat à l'Energie Atomique et aux Energies Alternatives, Institut de Biologie, Environnementale et de BiotechnologieSaint-Paul-lez-Durance, France
| | - Alexandra Schwendke
- Plant Physiology, Biocenter Klein Flottbek and Botanical Garden, University of HamburgHamburg, Germany
| | - Sabine Lüthje
- Plant Physiology, Biocenter Klein Flottbek and Botanical Garden, University of HamburgHamburg, Germany
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Gallego P, Martin L, Blazquez A, Guerra H, Villalobos N. Involvement of peroxidase activity in developing somatic embryos of Medicago arborea L. Identification of an isozyme peroxidase as biochemical marker of somatic embryogenesis. J Plant Physiol 2014; 171:78-84. [PMID: 24331422 DOI: 10.1016/j.jplph.2013.09.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2013] [Revised: 09/08/2013] [Accepted: 09/24/2013] [Indexed: 06/03/2023]
Abstract
The legume Medicago arborea L. is very interesting as regards the regeneration of marginal arid soils. The problem is that it does not have a good germinative yield. It was therefore decided to regenerate via somatic embryogenesis and find a marker of embryogenic potential. In this study, peroxidase activity was evaluated in non-embryogenic and embryogenic calli from M. arborea L. A decrease in soluble peroxidase activity is observed in its embryonic calli at the time at which the somatic embryos begin to appear. This activity is always lower in embryonic calli than in non-embryonic ones (unlike what happens in the case of wall-bound peroxidases). These results suggest that peroxidases can be considered to be enzymes involved in somatic embryogenesis in M. arborea. In addition, isozyme analyses were carried out on protein extracts using polyacrylamide gel electrophoresis. The band called P5 was detected only in embryogenic cultures at very early stages of development. This band was digested with trypsin and analyzed using linear ion trap (LTQ) mass spectrometer. In P5 isoform a peroxidase-L-ascorbate peroxidase was identified. It can be used as a marker that allows the identification of embryological potential.
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Affiliation(s)
- Piedad Gallego
- Departamento de Fisiología Vegetal, Facultad de Biología, Universidad de Salamanca, Plaza de los Doctores de la Reina s/n, E-37007 Salamanca, Spain
| | - Luisa Martin
- Departamento de Fisiología Vegetal, Facultades de Biología, Universidad Complutense de Madrid, Madrid, Spain
| | - Antonio Blazquez
- Departamento de Estadística, Facultad de Economía y Empresa, Universidad de Salamanca, Plaza de los Doctores de la Reina s/n, E-37007 Salamanca, Spain
| | - Hilario Guerra
- Departamento de Fisiología Vegetal, Facultad de Biología, Universidad de Salamanca, Plaza de los Doctores de la Reina s/n, E-37007 Salamanca, Spain
| | - Nieves Villalobos
- Departamento de Fisiología Vegetal, Facultad de Biología, Universidad de Salamanca, Plaza de los Doctores de la Reina s/n, E-37007 Salamanca, Spain.
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Uaprasert N, Settapiboon R, Amornsiriwat S, Sarnthammakul P, Thanapat T, Rojnuckarin P, Sutcharitchan P. Diagnostic utility of isoelectric focusing and high performance liquid chromatography in neonatal cord blood screening for thalassemia and non-sickling hemoglobinopathies. Clin Chim Acta 2014; 427:23-6. [PMID: 24095765 DOI: 10.1016/j.cca.2013.09.041] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Revised: 09/23/2013] [Accepted: 09/24/2013] [Indexed: 11/22/2022]
Abstract
BACKGROUND Thalassemia syndromes are highly prevalent in Southeast Asia. In Thailand, high performance liquid chromatography (HPLC) is the most common technique routinely performed in diagnosis of thalassemia and hemoglobinopathies, while isoelectric focusing (IEF) is rarely employed. We compared the diagnostic utility of IEF and HPLC in neonatal screening for thalassemia and non-sickling hemoglobinopathies. METHODS Two-hundred and forty-one cord blood samples were analyzed using IEF and HPLC, β-thalassemia short program. The results were correlated with red cell indices and molecular analyses. Hemoglobin (Hb) Bart's was quantified only on IEF. RESULTS Of 241 newborns, IEF and HPLC yielded 85.4% and 76.4% sensitivity to identify α-thalassemia syndrome, respectively. HbBart's≥2% yielded 100% sensitivity to identify 2 α-globin gene deletions and/or mutations, while MCV≤95fl and MCH≤30pg yielded 100% sensitivity to identify 2 α-globin gene deletions. DNA analysis revealed HbE mutation in all 61 subjects with HbA2>1% on both IEF and HPLC. CONCLUSION IEF is an effective method in neonatal screening for thalassemia and non-sickling hemoglobinopathies. The HbBart's level, MCV and MCH are helpful for identifying α-thalassemia. The presence of HbA2 higher than 1% in cord blood indicates HbE carriers in Southeast Asian newborns.
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16
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Mazzeo MF, Cacace G, Ferriello F, Puopolo G, Zoina A, Ercolano MR, Siciliano RA. Proteomic investigation of response to FORL infection in tomato roots. Plant Physiol Biochem 2014; 74:42-9. [PMID: 24262994 DOI: 10.1016/j.plaphy.2013.10.031] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Accepted: 10/24/2013] [Indexed: 05/07/2023]
Abstract
Fusarium oxysporum f. sp. radicis-lycopersici (FORL) leading to fusarium crown and root rot is considered one of the most destructive tomato soilborne diseases occurring in greenhouse and field crops. In this study, response to FORL infection in tomato roots was investigated by differential proteomics in susceptible (Monalbo) and resistant (Momor) isogenic tomato lines, thus leading to identify 33 proteins whose amount changed depending on the pathogen infection, and/or on the two genotypes. FORL infection induced accumulation of pathogen-related proteins (PR proteins) displaying glucanase and endochitinases activity or involved in redox processes in the Monalbo genotype. Interestingly, the level of the above mentioned PR proteins was not influenced by FORL infection in the resistant tomato line, while other proteins involved in general response mechanisms to biotic and/or abiotic stresses showed significant quantitative differences. In particular, the increased level of proteins participating to arginine metabolism and glutathione S-transferase (GST; EC 2.5.1.18) as well as that of protein LOC544002 and phosphoprotein ECPP44-like, suggested their key role in pathogen defence.
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Affiliation(s)
- Maria Fiorella Mazzeo
- Proteomic and Biomolecular Mass Spectrometry Center, Institute of Food Sciences, Italian National Research Council (CNR), Via Roma 64 a/c, 83100 Avellino, Italy
| | - Giuseppina Cacace
- Proteomic and Biomolecular Mass Spectrometry Center, Institute of Food Sciences, Italian National Research Council (CNR), Via Roma 64 a/c, 83100 Avellino, Italy
| | - Francesca Ferriello
- Department of Agricultural Sciences, University of Naples 'Federico II', Via Università 100, 80055 Portici, NA, Italy
| | - Gerardo Puopolo
- Department of Sustainable Agro-Ecosystems and Bioresources, Fondazione Edmund Mach, Via E. Mach 1, 38010 S. Michele all'Adige, TN, Italy
| | - Astolfo Zoina
- Department of Agricultural Sciences, University of Naples 'Federico II', Via Università 100, 80055 Portici, NA, Italy
| | - Maria Raffaella Ercolano
- Department of Agricultural Sciences, University of Naples 'Federico II', Via Università 100, 80055 Portici, NA, Italy
| | - Rosa Anna Siciliano
- Proteomic and Biomolecular Mass Spectrometry Center, Institute of Food Sciences, Italian National Research Council (CNR), Via Roma 64 a/c, 83100 Avellino, Italy.
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17
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Wong CM, Marcocci L, Das D, Wang X, Luo H, Zungu-Edmondson M, Suzuki YJ. Mechanism of protein decarbonylation. Free Radic Biol Med 2013; 65:1126-1133. [PMID: 24044890 PMCID: PMC3859829 DOI: 10.1016/j.freeradbiomed.2013.09.005] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2013] [Revised: 09/08/2013] [Accepted: 09/10/2013] [Indexed: 12/21/2022]
Abstract
Ligand/receptor stimulation of cells promotes protein carbonylation that is followed by the decarbonylation process, which might involve thiol-dependent reduction (C.M. Wong et al., Circ. Res. 102:301-318; 2008). This study further investigated the properties of this protein decarbonylation mechanism. We found that the thiol-mediated reduction of protein carbonyls is dependent on heat-labile biologic components. Cysteine and glutathione were efficient substrates for decarbonylation. Thiols decreased the protein carbonyl content, as detected by 2,4-dinitrophenylhydrazine, but not the levels of malondialdehyde or 4-hydroxynonenal protein adducts. Mass spectrometry identified proteins that undergo thiol-dependent decarbonylation, which include peroxiredoxins. Peroxiredoxin-2 and -6 were carbonylated and subsequently decarbonylated in response to the ligand/receptor stimulation of cells. siRNA knockdown of glutaredoxin inhibited the decarbonylation of peroxiredoxin. These results strengthen the concept that thiol-dependent decarbonylation defines the kinetics of protein carbonylation signaling.
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Affiliation(s)
- Chi-Ming Wong
- Department of Pharmacology and Physiology, Georgetown University Medical Center, Washington, DC 20057, USA
| | - Lucia Marcocci
- Department of Biochemical Sciences "A. Rossi Fanelli," Sapienza University of Rome, Rome, Italy
| | - Dividutta Das
- Department of Pharmacology and Physiology, Georgetown University Medical Center, Washington, DC 20057, USA
| | - Xinhong Wang
- Department of Pharmacology and Physiology, Georgetown University Medical Center, Washington, DC 20057, USA; Department of Physiology and Pathophysiology, Fudan University Shanghai Medical College, Shanghai 200032, China
| | - Haibei Luo
- Department of Pharmacology and Physiology, Georgetown University Medical Center, Washington, DC 20057, USA
| | | | - Yuichiro J Suzuki
- Department of Pharmacology and Physiology, Georgetown University Medical Center, Washington, DC 20057, USA.
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18
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Keeney JTR, Förster S, Sultana R, Brewer LD, Latimer CS, Cai J, Klein JB, Porter NM, Butterfield DA. Dietary vitamin D deficiency in rats from middle to old age leads to elevated tyrosine nitration and proteomics changes in levels of key proteins in brain: implications for low vitamin D-dependent age-related cognitive decline. Free Radic Biol Med 2013; 65:324-334. [PMID: 23872023 PMCID: PMC3859828 DOI: 10.1016/j.freeradbiomed.2013.07.019] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Revised: 07/10/2013] [Accepted: 07/11/2013] [Indexed: 12/22/2022]
Abstract
In addition to the well-known effects of vitamin D (VitD) in maintaining bone health, there is increasing appreciation that this vitamin may serve important roles in other organs and tissues, including the brain. Given that VitD deficiency is especially widespread among the elderly, it is important to understand how the range of serum VitD levels that mimic those found in humans (from low to high) affects the brain during aging from middle age to old age. To address this issue, 27 male F344 rats were split into three groups and fed isocaloric diets containing low (100 IU/kg food), control (1000 IU/kg food), or high (10,000 IU/kg food) VitD beginning at middle age (12 months) and continued for a period of 4-5 months. We compared the effects of these dietary VitD manipulations on oxidative and nitrosative stress measures in posterior brain cortices. The low-VitD group showed global elevation of 3-nitrotyrosine compared to control and high-VitD-treated groups. Further investigation showed that this elevation may involve dysregulation of the nuclear factor κ-light-chain enhancer of activated B cells (NF-κB) pathway and NF-κB-mediated transcription of inducible nitric oxide synthase (iNOS) as indicated by translocation of NF-κB to the nucleus and elevation of iNOS levels. Proteomics techniques were used to provide insight into potential mechanisms underlying these effects. Several brain proteins were found at significantly elevated levels in the low-VitD group compared to the control and high-VitD groups. Three of these proteins, 6-phosphofructokinase, triose phosphate isomerase, and pyruvate kinase, are involved directly in glycolysis. Two others, peroxiredoxin-3 and DJ-1/PARK7, have peroxidase activity and are found in mitochondria. Peptidyl-prolyl cis-trans isomerase A (cyclophilin A) has been shown to have multiple roles, including protein folding, regulation of protein kinases and phosphatases, immunoregulation, cell signaling, and redox status. Together, these results suggest that dietary VitD deficiency contributes to significant nitrosative stress in brain and may promote cognitive decline in middle-aged and elderly adults.
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Affiliation(s)
- Jeriel T R Keeney
- Department of Chemistry, Center of Membrane Sciences, Sanders Brown Center on Aging, University of Kentucky, Lexington, KY 40506, USA
| | - Sarah Förster
- Department of Chemistry, Center of Membrane Sciences, Sanders Brown Center on Aging, University of Kentucky, Lexington, KY 40506, USA
| | - Rukhsana Sultana
- Department of Chemistry, Center of Membrane Sciences, Sanders Brown Center on Aging, University of Kentucky, Lexington, KY 40506, USA
| | - Lawrence D Brewer
- Department of Molecular and Biomedical Pharmacology, University of Kentucky College of Medicine, Lexington, KY 40536, USA
| | - Caitlin S Latimer
- Department of Molecular and Biomedical Pharmacology, University of Kentucky College of Medicine, Lexington, KY 40536, USA
| | - Jian Cai
- Division of Nephrology, Department of Medicine and Proteomics Center, University of Louisville, Louisville, KY 40292, USA
| | - Jon B Klein
- Division of Nephrology, Department of Medicine and Proteomics Center, University of Louisville, Louisville, KY 40292, USA
| | - Nada M Porter
- Department of Molecular and Biomedical Pharmacology, University of Kentucky College of Medicine, Lexington, KY 40536, USA
| | - D Allan Butterfield
- Department of Chemistry, Center of Membrane Sciences, Sanders Brown Center on Aging, University of Kentucky, Lexington, KY 40506, USA.
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Rohlfing AK, Rust S, Reunert J, Tirre M, Du Chesne I, Wemhoff S, Meinhardt F, Hartmann H, Das AM, Marquardt T. ALG1-CDG: a new case with early fatal outcome. Gene 2014; 534:345-51. [PMID: 24157261 DOI: 10.1016/j.gene.2013.10.013] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Revised: 10/02/2013] [Accepted: 10/08/2013] [Indexed: 11/20/2022]
Abstract
Congenital disorders of glycosylation (CDG) are a growing group of inherited metabolic disorders where enzymatic defects in the formation or processing of glycolipids and/or glycoproteins lead to variety of different diseases. The deficiency of GDP-Man:GlcNAc2-PP-dolichol mannosyltransferase, encoded by the human ortholog of ALG1 from yeast, is known as ALG1-CDG (CDG-Ik). The phenotypical, molecular and biochemical analysis of a severely affected ALG1-CDG patient is the focus of this paper. The patient's main symptoms were feeding problems and diarrhea, profound hypoproteinemia with massive ascites, muscular hypertonia, seizures refractory to treatment, recurrent episodes of apnoea, cardiac and hepatic involvement and coagulation anomalies. Compound heterozygosity for the mutations c.1145T>C (M382T) and c.1312C>T (R438W) was detected in the patient's ALG1-coding sequence. In contrast to a previously reported speculation on R438W we confirmed both mutations as disease-causing in ALG1-CDG.
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20
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Gharechahi J, Khalili M, Hasanloo T, Salekdeh GH. An integrated proteomic approach to decipher the effect of methyl jasmonate elicitation on the proteome of Silybum marianum L. hairy roots. Plant Physiol Biochem 2013; 70:115-22. [PMID: 23771036 DOI: 10.1016/j.plaphy.2013.05.031] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Accepted: 05/21/2013] [Indexed: 06/02/2023]
Abstract
Jasmonate and its methyl derivative, methyl jasmonate (MeJA), are naturally occurring compounds that mediate several plant physiological processes in response to pathogen attack, wounding, and ozone. Exogenous application of jasmonates triggers defense responses that resemble those initiated by pathogen infection and also modulates the production of certain secondary metabolites in a variety of plant species. In this study, we treated the hairy root cultures of Silybum marianum L. with 100 μM MeJA and then measured the content of Silymarin (SLM). We observed that the SLM content increased significantly after 48 h of MeJA treatment and remained constant for 120 h. However, MeJA treatment caused a significant growth reduction after 96 h incubation. The activity of lipoxygenase as a key enzyme in the jasmonate biosynthesis pathway and anti-oxidative enzymes; peroxidase and ascorbate peroxidase was also significantly increased after MeJA treatment. To elucidate the global effect of jasmonate on gene expression of S. marianum, we employed high resolution two-dimensional gel electrophoresis coupled with tandem mass spectrometry. Out of 670 reproducibly detected protein spots which were analyzed on each given gel, 32 spots were up- or down regulated upon MeJA treatment. Of them, ten proteins such as ER binding protein, glutamine synthetase, pathogenesis-related protein, caffeoyl CoA O-methyltransferase, and profilin-1 could be identified by mass spectrometry analysis. The possible implications of the identified proteins on physiological outcome of MeJA application in S. marianum hairy root culture will be discussed.
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Affiliation(s)
- Javad Gharechahi
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Karaj, Iran.
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21
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DalCorso G, Fasani E, Furini A. Recent advances in the analysis of metal hyperaccumulation and hypertolerance in plants using proteomics. Front Plant Sci 2013; 4:280. [PMID: 23898342 PMCID: PMC3724048 DOI: 10.3389/fpls.2013.00280] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Accepted: 07/09/2013] [Indexed: 05/22/2023]
Abstract
Hyperaccumulator/hypertolerant plant species have evolved strategies allowing them to grow in metal-contaminated soils, where they accumulate high concentrations of heavy metals in their shoots without signs of toxicity. The mechanisms that allow enhanced metal uptake, root-to-shoot translocation and detoxification in these species are not fully understood. Complementary approaches such as transcriptomic-based DNA microarrays and proteomics have recently been used to gain insight into the molecular pathways evolved by metal hyperaccumulator/hypertolerant species. Proteomics has the advantage of focusing on the translated portion of the genome and it allows to analyze complex networks of proteins. This review discusses the recent analysis of metal hyperaccumulator/hypertolerant plant species using proteomics. Changes in photosynthetic proteins, sulfur, and glutathione metabolism, transport, biotic and xenobiotic defenses as well as the differential regulation of proteins involved in signaling and secondary metabolism are discussed in relation to metal hyperaccumulation. We also consider the potential contribution of several proteins to the hyperaccumulation phenotype.
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22
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Alfadda AA, Benabdelkamel H, Masood A, Moustafa A, Sallam R, Bassas A, Duncan M. Proteomic analysis of mature adipocytes from obese patients in relation to aging. Exp Gerontol 2013; 48:1196-203. [PMID: 23886751 DOI: 10.1016/j.exger.2013.07.008] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Revised: 07/03/2013] [Accepted: 07/15/2013] [Indexed: 01/08/2023]
Abstract
Obesity and aging are interrelated conditions that both cause changes in adipocyte metabolism and affect the distribution of fat in both subcutaneous and visceral depots. In addition, both weight gain and aging can lead to similar clinical outcomes such as insulin resistance, cardiovascular disease, type 2 diabetes mellitus, atherosclerosis and stroke. Our objective was to examine the changes in protein expression within the subcutaneous adipose tissue of obese patients, matched for BMI, in relation to age. Mature adipocytes were isolated from liposuction samples of abdominal subcutaneous adipose tissue collected from both young (26.2±4.3 (mean age±SD); n=7) and old (52.2±4.7 (mean age±SD); n=7) obese individuals. Total protein extracts were then compared by two-dimensional difference in gel electrophoresis (2D DIGE). Thirty differentially expressed protein spots (ANOVA test, p≤0.05; fold-change ≥1.8) were detected, of which, 15 were identified by MALDI-TOF mass spectrometry. These were comprised of a total of thirteen unique protein sequences. Nine proteins were more abundant in the adipocytes isolated from old vs. young individuals. These proteins included prohibitin 1, protein disulphide isomerase A3, beta actin, profilin, aldo-ketoreductase 1 C2, alpha crystallin B and the annexins A1, A5 and A6. Four other proteins were less abundant in the adipocytes from old, obese subjects and these included keratin type 2 cytoskeletal 1, keratin type 2 cytoskeletal 10 and hemoglobins A and B. The differentially abundant proteins were investigated by Ingenuity Pathway Analysis (IPA) to reveal their associations with known biological functions. This analysis identified signal transducer and activator of transcription 3 as the central molecule in the connectivity map and the apoptotic pathway as the pathway with the highest score. Differences in the abundances of several proteins were confirmed by immunoblotting: i.e., prohibitin 1, protein disulphide isomerase A3, beta actin, profilin and signal transducer and activator of transcription 3 proteins. In conclusion, proteomic analysis of subcutaneous adipose tissue reveals differences in the abundance of proteins in adipocytes isolated from young vs. old individuals. These differentially abundant proteins are involved in the regulation of apoptosis, cellular senescence and inflammatory response. All these are common pathologic events in both obesity and aging.
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Affiliation(s)
- Assim A Alfadda
- Obesity Research Center, College of Medicine, King Saud University, P.O. Box 2925 (98), Riyadh 11461, Saudi Arabia; Department of Medicine, College of Medicine, King Saud University, P.O. Box 2925 (38), Riyadh 11461, Saudi Arabia.
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Vaudel M, Sickmann A, Martens L. Introduction to opportunities and pitfalls in functional mass spectrometry based proteomics. Biochim Biophys Acta 2013; 1844:12-20. [PMID: 23845992 DOI: 10.1016/j.bbapap.2013.06.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Revised: 06/05/2013] [Accepted: 06/25/2013] [Indexed: 10/26/2022]
Abstract
With the advent of mass spectrometry based proteomics, the identification of thousands of proteins has become commonplace in biology nowadays. Increasingly, efforts have also been invested toward the detection and localization of posttranslational modifications. It is furthermore common practice to quantify the identified entities, a task supported by a panel of different methods. Finally, the results can also be enriched with functional knowledge gained on the proteins, detecting for instance differentially expressed gene ontology terms or biological pathways. In this study, we review the resources, methods and tools available for the researcher to achieve such a quantitative functional analysis. These include statistics for the post-processing of identification and quantification results, online resources and public repositories. With a focus on free but user-friendly software, preferably also open-source, we provide a list of tools designed to help the researcher manage the vast amount of data generated. We also indicate where such applications currently remain lacking. Moreover, we stress the eventual pitfalls of every step of such studies. This article is part of a Special Issue entitled: Computational Proteomics in the Post-Identification Era. Guest Editors: Martin Eisenacher and Christian Stephan.
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Affiliation(s)
- Marc Vaudel
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Dortmund, Germany; Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway.
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24
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Rizzello CG, Curiel JA, Nionelli L, Vincentini O, Di Cagno R, Silano M, Gobbetti M, Coda R. Use of fungal proteases and selected sourdough lactic acid bacteria for making wheat bread with an intermediate content of gluten. Food Microbiol 2013; 37:59-68. [PMID: 24230474 DOI: 10.1016/j.fm.2013.06.017] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Revised: 05/07/2013] [Accepted: 06/27/2013] [Indexed: 11/17/2022]
Abstract
This study was aimed at combining the highest degradation of gluten during wheat flour fermentation with good structural and sensory features of the related bread. As estimated by R5-ELISA, the degree of degradation of immune reactive gluten was ca. 28%. Two-dimensional electrophoresis and RP-FPLC analyses showed marked variations of the protein fractions compared to the untreated flour. The comparison was also extended to in vitro effect of the peptic/tryptic-digests towards K562 and T84 cells. The flour with the intermediate content of gluten (ICG) was used for bread making, and compared to whole gluten (WG) bread. The chemical, structural and sensory features of the ICG bread approached those of the bread made with WG flour. The protein digestibility of the ICG bread was higher than that from WG flour. Also the nutritional quality, as estimated by different indexes, was the highest for ICG bread.
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Wu C, Parrott AM, Liu T, Beuve A, Li H. Functional proteomics approaches for the identification of transnitrosylase and denitrosylase targets. Methods 2013; 62:151-60. [PMID: 23428400 DOI: 10.1016/j.ymeth.2013.02.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Revised: 05/16/2012] [Accepted: 02/06/2013] [Indexed: 10/27/2022] Open
Abstract
Protein S-nitrosylation is a dynamic post-translational modification (PTM) of specific cysteines within a target protein. Both proteins and small molecules are known to regulate the attachment and removal of this PTM, and proteins exhibiting such a function are transnitrosylase or denitrosylase candidates. With the advent of the biotin switch technique coupled to high-throughput proteomics workflows, the identification and quantification of large numbers of S-nitrosylated proteins and peptides is now possible. Proper analysis and interpretation of high throughout and quantitative proteomics data will help identify specific transnitrosylase and denitrosylase target peptide sequences and contribute to an understanding of the function and regulation of specific S-nitrosylation events. Here we describe the application of a quantitative proteomics approach using isotope-coded affinity tags (ICAT) in the biotin switch approach for the identification of transnitrosylation and denitrosylation targets of thioredoxin 1, an enigmatic protein with both reported transnitrosylase and denitrosylase activities.
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Affiliation(s)
- Changgong Wu
- Center for Advanced Proteomics Research and Department of Biochemistry and Molecular Biology, UMDNJ-New Jersey Medical School Cancer Center, Newark, NJ 07103, United States
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Sayyed RZ, Chincholkar SB, Meyer JM, Kale SP. Chemical Characterization, Crossfeeding and Uptake Studies on Hydroxamate Siderophore of Alcaligenes faecalis. Indian J Microbiol 2012; 51:176-81. [PMID: 22654161 DOI: 10.1007/s12088-011-0129-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2009] [Accepted: 07/16/2009] [Indexed: 11/26/2022] Open
Abstract
We report the production of two types of siderophores namely catecholate and hydroxamate in modified succinic acid medium (SM) from Alcaligenes faecalis. Two fractions of siderophores were purified on amberlite XAD, major fraction was hydroxamate type having a λ(max) at 224 nm and minor fraction appeared as catecholate with a λ(max) of 264 nm. The recovery yield obtained from major and minor fractions was 297 and 50 mg ml(-1) respectively. The IEF pattern of XAD-4 purified siderophore suggested the pI value of 6.5. Cross feeding studies revealed that A. faecalis accepts heterologous as well as self (hydroxamate) siderophore in both free and iron complexed forms however; the rate of siderophore uptake was more in case of siderophores complexed to iron. Siderophore iron uptake studies indicated the differences between hydroxamate siderophore of A. faecalis and Alc E, a siderophore of Alcaligenes eutrophus.
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