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Arakawa T, Nakagawa M, Sakuma C, Tomioka Y, Kurosawa Y, Ejima D, Akuta T. Electrophoresis, a transport technology that transitioned from moving boundary method to zone method. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2024; 53:1-13. [PMID: 38160206 DOI: 10.1007/s00249-023-01694-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 09/27/2023] [Accepted: 12/02/2023] [Indexed: 01/03/2024]
Abstract
Gel electrophoresis, a transport technology, is one of the most widely used experimental methods in biochemical and pharmaceutical research and development. Transport technologies are used to determine hydrodynamic or electrophoretic properties of macromolecules. Gel electrophoresis is a zone technology, where a small volume of sample is applied to a large separation gel matrix. In contrast, a seldom-used electrophoresis technology is moving boundary electrophoresis, where the sample is present throughout the separation phase or gel matrix. While the zone method gives peaks of separating macromolecular solutes, the moving boundary method gives a boundary between solute-free and solute-containing phases. We will review electrophoresis as a transport technology of zone and moving boundary methods and describe its principles and applications.
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Affiliation(s)
- Tsutomu Arakawa
- Alliance Protein Laboratories, 13380 Pantera Rd., San Diego, CA, 92130, USA.
| | - Masataka Nakagawa
- Research and Development Division, Kyokuto Pharmaceutical Industrial Co., Ltd., 3333-26, Aza-Asayama, Kamitezuna Takahagi-Shi, Ibaraki, 318-0004, Japan
| | - Chiaki Sakuma
- Research and Development Division, Kyokuto Pharmaceutical Industrial Co., Ltd., 3333-26, Aza-Asayama, Kamitezuna Takahagi-Shi, Ibaraki, 318-0004, Japan
| | - Yui Tomioka
- Research and Development Division, Kyokuto Pharmaceutical Industrial Co., Ltd., 3333-26, Aza-Asayama, Kamitezuna Takahagi-Shi, Ibaraki, 318-0004, Japan
| | - Yasunori Kurosawa
- Research and Development Division, Kyokuto Pharmaceutical Industrial Co., Ltd., 3333-26, Aza-Asayama, Kamitezuna Takahagi-Shi, Ibaraki, 318-0004, Japan
| | - Daisuke Ejima
- Sysmex Corporation, Technology Innovation, 1548 Shimo-Okutomi, Sayama, Saitama, 350-1332, Japan
| | - Teruo Akuta
- Research and Development Division, Kyokuto Pharmaceutical Industrial Co., Ltd., 3333-26, Aza-Asayama, Kamitezuna Takahagi-Shi, Ibaraki, 318-0004, Japan
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2
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Cimmino L, Duarte AG, Ni D, Ekundayo BE, Pereira IAC, Stahlberg H, Holliger C, Maillard J. Structure of a membrane-bound menaquinol:organohalide oxidoreductase. Nat Commun 2023; 14:7038. [PMID: 37923808 PMCID: PMC10624902 DOI: 10.1038/s41467-023-42927-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 10/26/2023] [Indexed: 11/06/2023] Open
Abstract
Organohalide-respiring bacteria are key organisms for the bioremediation of soils and aquifers contaminated with halogenated organic compounds. The major players in this process are respiratory reductive dehalogenases, corrinoid enzymes that use organohalides as substrates and contribute to energy conservation. Here, we present the structure of a menaquinol:organohalide oxidoreductase obtained by cryo-EM. The membrane-bound protein was isolated from Desulfitobacterium hafniense strain TCE1 as a PceA2B2 complex catalysing the dechlorination of tetrachloroethene. Two catalytic PceA subunits are anchored to the membrane by two small integral membrane PceB subunits. The structure reveals two menaquinone molecules bound at the interface of the two different subunits, which are the starting point of a chain of redox cofactors for electron transfer to the active site. In this work, the structure elucidates how energy is conserved during organohalide respiration in menaquinone-dependent organohalide-respiring bacteria.
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Affiliation(s)
- Lorenzo Cimmino
- Laboratory for Environmental Biotechnology, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Américo G Duarte
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Oeiras, Portugal
| | - Dongchun Ni
- Laboratory of Biological Electron Microscopy, Ecole Polytechnique Fédérale de Lausanne (EPFL), and Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Babatunde E Ekundayo
- Laboratory of Biological Electron Microscopy, Ecole Polytechnique Fédérale de Lausanne (EPFL), and Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Inês A C Pereira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Oeiras, Portugal
| | - Henning Stahlberg
- Laboratory of Biological Electron Microscopy, Ecole Polytechnique Fédérale de Lausanne (EPFL), and Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland.
| | - Christof Holliger
- Laboratory for Environmental Biotechnology, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
| | - Julien Maillard
- Laboratory for Environmental Biotechnology, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
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Zheng Y, Gibb AA, Xu H, Liu S, Hill BG. The metabolic state of the heart regulates mitochondrial supercomplex abundance in mice. Redox Biol 2023; 63:102740. [PMID: 37210780 DOI: 10.1016/j.redox.2023.102740] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 05/10/2023] [Indexed: 05/23/2023] Open
Abstract
Mitochondrial supercomplexes are observed in mammalian tissues with high energy demand and may influence metabolism and redox signaling. Nevertheless, the mechanisms that regulate supercomplex abundance remain unclear. In this study, we examined the composition of supercomplexes derived from murine cardiac mitochondria and determined how their abundance changes with substrate provision or by genetically induced changes to the cardiac glucose-fatty acid cycle. Protein complexes from digitonin-solubilized cardiac mitochondria were resolved by blue-native polyacrylamide gel electrophoresis and were identified by mass spectrometry and immunoblotting to contain constituents of Complexes I, III, IV, and V as well as accessory proteins involved in supercomplex assembly and stability, cristae architecture, carbohydrate and fat oxidation, and oxidant detoxification. Respiratory analysis of high molecular mass supercomplexes confirmed the presence of intact respirasomes, capable of transferring electrons from NADH to O2. Provision of respiratory substrates to isolated mitochondria augmented supercomplex abundance, with fatty acyl substrate (octanoylcarnitine) promoting higher supercomplex abundance than carbohydrate-derived substrate (pyruvate). Mitochondria isolated from transgenic hearts that express kinase-deficient 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase (GlycoLo), which decreases glucose utilization and increases reliance on fatty acid oxidation for energy, had higher mitochondrial supercomplex abundance and activity compared with mitochondria from wild-type or phosphatase-deficient 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase-expressing hearts (GlycoHi), the latter of which encourages reliance on glucose catabolism for energy. These findings indicate that high energetic reliance on fatty acid catabolism bolsters levels of mitochondrial supercomplexes, supporting the idea that the energetic state of the heart is regulatory factor in supercomplex assembly or stability.
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Affiliation(s)
- Yuting Zheng
- Center for Cardiometabolic Science, Christina Lee Brown Envirome Institute, Department of Medicine, University of Louisville, Louisville, KY, USA
| | - Andrew A Gibb
- Cardiovascular Research Center, Department of Cardiovascular Sciences, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, 19140, USA
| | - Hongkai Xu
- Center of Proteomic Analysis, Beijing Genomics Institute (BGI-Shenzhen), Shenzhen, 518000, China
| | - Siqi Liu
- Center of Proteomic Analysis, Beijing Genomics Institute (BGI-Shenzhen), Shenzhen, 518000, China
| | - Bradford G Hill
- Center for Cardiometabolic Science, Christina Lee Brown Envirome Institute, Department of Medicine, University of Louisville, Louisville, KY, USA.
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Peng M, Zhang Z, Xu X, Zhang H, Zhao Z, Liang Z. Purification and characterization of the enzymes from Brevundimonas naejangsanensis that degrade ochratoxin A and B. Food Chem 2023; 419:135926. [PMID: 37011575 DOI: 10.1016/j.foodchem.2023.135926] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 02/24/2023] [Accepted: 03/08/2023] [Indexed: 04/05/2023]
Abstract
Ochratoxin A (OTA) and Ochratoxin B (OTB) co-contaminate many types of agricultural products. Screening enzymes that degrade both OTA and OTB has significance in food safety. In this study, four novel OTA and OTB degrading enzymes, namely BnOTase1, BnOTase2, BnOTase3, and BnOTase4, were purified from the metabolites of the Brevundimonas naejangsanensis ML17 strain. These four enzymes hydrolyzed OTA into OTα and hydrolyzed OTB into OTβ. BnOTase1, BnOTase2, BnOTase3, and BnOTase4 have the apparent Km values for hydrolyzing OTA of 19.38, 0.92, 12.11, 1.09 μmol/L and for hydrolyzing OTB of 0.76, 2.43, 0.60, 0.64 μmol/L respectively. OTα and OTβ showed no significant cytotoxicity to HEK293 cells, suggesting that these enzymes mitigate the toxicity of OTA and OTB. The discovery of the novel OTA and OTB degrading enzymes enriches the research on ochratoxin control and provides objects for protein rational design.
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Affiliation(s)
- Mengxue Peng
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Zhenzhen Zhang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Xinge Xu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Haoxiang Zhang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Zitong Zhao
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Zhihong Liang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China; The Supervision, Inspection and Testing Center of Genetically Modified Organisms, Ministry of Agriculture, Beijing, China; Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China.
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How hot can mitochondria be? Incubation at temperatures above 43 °C induces the degradation of respiratory complexes and supercomplexes in intact cells and isolated mitochondria. Mitochondrion 2023; 69:83-94. [PMID: 36764502 DOI: 10.1016/j.mito.2023.02.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 01/25/2023] [Accepted: 02/04/2023] [Indexed: 02/11/2023]
Abstract
Mitochondrial function generates an important fraction of the heat that contributes to cellular and organismal temperature maintenance, but the actual values of this parameter reached in the organelles is a matter of debate. The studies addressing this issue have reported divergent results: from detecting in the organelles the same temperature as the cell average or the incubation temperature, to increasing differences of up to 10 degrees above the incubation value. Theoretical calculations based on physical laws exclude the possibility of relevant temperature gradients between mitochondria and their surroundings. These facts have given rise to a conundrum or paradox about hot mitochondria. We have examined by Blue-Native electrophoresis, both in intact cells and in isolated organelles, the stability of respiratory complexes and supercomplexes at different temperatures to obtain information about their tolerance to heat stress. We observe that, upon incubation at values above 43 °C and after relatively short periods, respiratory complexes, and especially complex I and its supercomplexes, are unstable even when the respiratory activity is inhibited. These results support the conclusion that high temperatures (>43 °C) cause damage to mitochondrial structure and function and question the proposal that these organelles can physiologically work at close to 50 °C.
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6
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Takemori A, Takemori N. Sample preparation for structural mass spectrometry via polyacrylamide gel electrophoresis. Methods Enzymol 2023; 682:187-210. [PMID: 36948702 DOI: 10.1016/bs.mie.2022.08.051] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Mass spectrometry is an analytical technique that can detect protein molecules with high sensitivity. Its use is not limited to the mere identification of protein components in biological samples, but is recently being utilized for large-scale analysis of protein structures in vivo as well. Top-down mass spectrometry with an ultra-high resolution mass spectrometer, for example, ionizes proteins in their intact state and allows rapid analysis of their chemical structure, which is used to determine proteoform profiles. Furthermore, cross-linking mass spectrometry, which analyzes enzyme-digested fragments of chemically cross-linked protein complexes, allows acquisition of conformational information on protein complexes in multimolecular crowding environments. In the analysis workflow of structural mass spectrometry, prior fractionation of crude biological samples is an effective way to obtain more detailed structural information. Polyacrylamide gel electrophoresis (PAGE), known as a simple and reproducible means of protein separation in biochemistry, is one example of an excellent high-resolution sample prefractionation tool for structural mass spectrometry. This chapter describes elemental technologies for PAGE-based sample prefractionation including Passively Eluting Proteins from Polyacrylamide gels as Intact species for Mass Spectrometry (PEPPI-MS), a highly efficient method for intact in-gel protein recovery, and Anion-Exchange disk-assisted Sequential sample Preparation (AnExSP), a rapid enzymatic digestion method using a solid-phase extraction microspin column for gel-recovered proteins, in addition to presenting detailed experimental protocols and examples of their use for structural mass spectrometry.
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Affiliation(s)
- Ayako Takemori
- Advanced Research Support Center, Institute for Promotion of Science and Technology, Ehime University, Toon, Japan
| | - Nobuaki Takemori
- Advanced Research Support Center, Institute for Promotion of Science and Technology, Ehime University, Toon, Japan.
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Defining Two Chemosensory Arrays in Shewanella oneidensis. Biomolecules 2022; 13:biom13010021. [PMID: 36671406 PMCID: PMC9855816 DOI: 10.3390/biom13010021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/15/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022] Open
Abstract
Shewanella oneidensis has 2 functional chemosensory systems named Che1 and Che3, and 27 chemoreceptors. Che3 is dedicated to chemotaxis while Che1 could be involved in RpoS post-translational regulation. In this study, we have shown that two chemoreceptors Aer2so and McpAso, genetically related to the Che1 system, form distinct core-signaling units and signal to Che1 and Che3, respectively. Moreover, we observed that Aer2so is a cytoplasmic dynamic chemoreceptor that, when in complex with CheA1 and CheW1, localizes at the two poles and the centre of the cells. Altogether, the results obtained indicate that Che1 and Che3 systems are interconnected by these two chemoreceptors allowing a global response for bacterial survival.
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8
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Further Evidence of the Melatonin Calmodulin Interaction: Effect on CaMKII Activity. Int J Mol Sci 2022; 23:ijms23052479. [PMID: 35269623 PMCID: PMC8910589 DOI: 10.3390/ijms23052479] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 02/16/2022] [Accepted: 02/17/2022] [Indexed: 02/01/2023] Open
Abstract
Melatonin (MEL) is a pleiotropic indolamine that reaches multiple intracellular targets. Among these, MEL binds to calmodulin (CaM) with high affinity. In presence of Ca2+, CaM binds to CaM-dependent kinase II (CaMKII). The Ca2+-CaM/CaMKII pathway regulates a myriad of brain functions in different cellular compartments. Evidence showing the regulation of this cellular pathway by MEL is scarce. Thus, our main objective was to study the interaction of MEL with CaM and its effects on CaMKII activity in two microenvironments (aqueous and lipidic) naturally occurring within the cell. In addition, colocalization of MEL with CaM in vivo was explored in mice brain hippocampus. In vitro CaM-MEL interaction and the structural conformations of CaM in the presence of this indoleamine were assessed through electrophoretic mobility and isoelectric point. The functional consequence of this interaction was evaluated by measuring CaMKII activity. Ca2+-CaM-MEL increased the activity of CaMKII in aqueous buffer but reduced the kinase activity in lipid buffer. Importantly, MEL colocalizes in vivo with Ca2+-CaM in the hippocampus. Our evidence suggests that MEL regulates the key cellular Ca2+-CaM/CaMKII pathway and might explain why physiological MEL concentrations reduce CaMKII activity in some experimental conditions, while in others it drives biological processes through activation of this kinase.
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Miranda-Astudillo HV, Yadav KNS, Boekema EJ, Cardol P. Supramolecular associations between atypical oxidative phosphorylation complexes of Euglena gracilis. J Bioenerg Biomembr 2021; 53:351-363. [PMID: 33646522 PMCID: PMC8124061 DOI: 10.1007/s10863-021-09882-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 02/11/2021] [Indexed: 11/28/2022]
Abstract
In vivo associations of respiratory complexes forming higher supramolecular structures are generally accepted nowadays. Supercomplexes (SC) built by complexes I, III and IV and the so-called respirasome (I/III2/IV) have been described in mitochondria from several model organisms (yeasts, mammals and green plants), but information is scarce in other lineages. Here we studied the supramolecular associations between the complexes I, III, IV and V from the secondary photosynthetic flagellate Euglena gracilis with an approach that involves the extraction with several mild detergents followed by native electrophoresis. Despite the presence of atypical subunit composition and additional structural domains described in Euglena complexes I, IV and V, canonical associations into III2/IV, III2/IV2 SCs and I/III2/IV respirasome were observed together with two oligomeric forms of the ATP synthase (V2 and V4). Among them, III2/IV SC could be observed by electron microscopy. The respirasome was further purified by two-step liquid chromatography and showed in-vitro oxygen consumption independent of the addition of external cytochrome c.
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Affiliation(s)
- H V Miranda-Astudillo
- InBios/Phytosystems, Institut de Botanique, University of Liège, Liège, Belgium.
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico.
| | - K N S Yadav
- Department of Electron Microscopy, Groningen Biological Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
- School of Biochemistry, University of Bristol, Bristol, BS8 1TD, UK
| | - E J Boekema
- Department of Electron Microscopy, Groningen Biological Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - P Cardol
- InBios/Phytosystems, Institut de Botanique, University of Liège, Liège, Belgium.
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Barbosa KL, Malta VRDS, Machado SS, Leal Junior GA, da Silva APV, Almeida RMRG, da Luz JMR. Bacterial cellulase from the intestinal tract of the sugarcane borer. Int J Biol Macromol 2020; 161:441-448. [PMID: 32526296 DOI: 10.1016/j.ijbiomac.2020.06.042] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 05/01/2020] [Accepted: 06/05/2020] [Indexed: 10/24/2022]
Abstract
Cellulolytic enzymes have wide use in several industrial segments (e.g. biofuels, pulp and paper, food, and cosmetics). However, one of the challenges is their large-scale production with high specific activity to eliminate the dependence of the purchase of enzymatic cocktails produced by commercial parties. The aims of this study were (1) isolation, selection, and partial characterization of bacterial cellulases present in the intestinal tract of the sugarcane borer and (2) to identify cellulase-producing bacteria by analyzing the 16S rDNA gene. Cellulase production and purification assays resulted in similar electrophoretic profiles between four bacterial strains. These strains were identified as Klebsiella pneumoniae, Klebsiella sp., and Bacillus sp. K. pneumoniae was the main cellulase-producing microorganism. Our results show the possibility of finding cellulolytic microorganisms that inhabit the gut of herbivorous animals, especially those that are predators of important crops of economic value. Furthermore, K. pneumoniae cellulase is of medical importance. In hospitals, health professionals, hospital technicians, patients and visitors wear clothes containing cellulose. Thus, K. pneumoniae within hospitals can contaminate these clothes and be spread to the environment. In that case, it would be important for the hospital's chemical sterilization products to have at least one cellulase inhibitor.
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Affiliation(s)
- Kledson Lopes Barbosa
- Federal University of Alagoas, Institute of Chemistry and Biotechnology, Campus Maceió, 57072-900 Maceió, AL, Brazil.
| | | | - Sonia Salgueiro Machado
- Federal University of Alagoas, Institute of Chemistry and Biotechnology, Campus Maceió, 57072-900 Maceió, AL, Brazil
| | | | | | | | - Jose Maria Rodrigues da Luz
- Federal University of Alagoas, Institute of Pharmaceutical Science, Postgraduate Multicenter Program of Biochemistry and Molecular Biology, Campus Maceió, 57072-900 Maceió, AL, Brazil
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Takemori A, Butcher DS, Harman VM, Brownridge P, Shima K, Higo D, Ishizaki J, Hasegawa H, Suzuki J, Yamashita M, Loo JA, Loo RRO, Beynon RJ, Anderson LC, Takemori N. PEPPI-MS: Polyacrylamide-Gel-Based Prefractionation for Analysis of Intact Proteoforms and Protein Complexes by Mass Spectrometry. J Proteome Res 2020; 19:3779-3791. [PMID: 32538093 DOI: 10.1021/acs.jproteome.0c00303] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Prefractionation of complex mixtures of proteins derived from biological samples is indispensable for proteome analysis via top-down mass spectrometry (MS). Polyacrylamide gel electrophoresis (PAGE), which enables high-resolution protein separation based on molecular size, is a widely used technique in biochemical experiments and has the potential to be useful in sample fractionation for top-down MS analysis. However, the lack of a means to efficiently recover the separated proteins in-gel has always been a barrier to its use in sample prefractionation. In this study, we present a novel experimental workflow, called Passively Eluting Proteins from Polyacrylamide gels as Intact species for MS ("PEPPI-MS"), which allows top-down MS of PAGE-separated proteins. The optimization of Coomassie brilliant blue staining followed by the passive extraction step in the PEPPI-MS workflow enabled the efficient recovery of proteins, separated on commercial precast gels, from a wide range of molecular weight regions in under 10 min. Two-dimensional separation combining offline PEPPI-MS with online reversed-phase liquid chromatographic separation resulted in identification of over 1000 proteoforms recovered from the target region of the gel (≤50 kDa). Given the widespread availability and relatively low cost of traditional sodium dodecyl sulfate (SDS)-PAGE equipment, the PEPPI-MS workflow will be a powerful prefractionation strategy for top-down proteomics.
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Affiliation(s)
- Ayako Takemori
- Division of Analytical Bio-Medicine, Advanced Research Support Center, Ehime University, Toon 791-0295, Ehime, Japan
| | - David S Butcher
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, United States
| | - Victoria M Harman
- Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, U.K
| | - Philip Brownridge
- Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, U.K
| | - Keisuke Shima
- Shimadzu Corporation, Nakagyo-ku, Kyoto 604-8511, Japan
| | - Daisuke Higo
- Thermo Fisher Scientific K.K., Yokohama 221-0022, Kanagawa, Japan
| | - Jun Ishizaki
- Department of Hematology, Clinical Immunology and Infectious Diseases, Graduate School of Medicine, Ehime University, Toon 791-0295, Ehime, Japan
| | - Hitoshi Hasegawa
- Department of Hematology, Clinical Immunology and Infectious Diseases, Graduate School of Medicine, Ehime University, Toon 791-0295, Ehime, Japan
| | - Junpei Suzuki
- Department of Immunology, Graduate School of Medicine, Ehime University, Toon 791-0295, Ehime, Japan
| | - Masakatsu Yamashita
- Department of Immunology, Graduate School of Medicine, Ehime University, Toon 791-0295, Ehime, Japan
| | - Joseph A Loo
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, California 90095, United States.,Department of Biological Chemistry, UCLA/DOE Institute for Genomics and Proteomics, and UCLA Molecular Biology Institute, University of California-Los Angeles, Los Angeles, California 90095, United States
| | - Rachel R Ogorzalek Loo
- Department of Biological Chemistry, UCLA/DOE Institute for Genomics and Proteomics, and UCLA Molecular Biology Institute, University of California-Los Angeles, Los Angeles, California 90095, United States
| | - Robert J Beynon
- Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, U.K
| | - Lissa C Anderson
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, United States
| | - Nobuaki Takemori
- Division of Analytical Bio-Medicine, Advanced Research Support Center, Ehime University, Toon 791-0295, Ehime, Japan
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Liang S, Fuchs S, Mymrikov EV, Stulz A, Kaiser M, Heerklotz H, Hunte C. Calcium affects CHP1 and CHP2 conformation and their interaction with sodium/proton exchanger 1. FASEB J 2020; 34:3253-3266. [DOI: 10.1096/fj.201902093r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 12/10/2019] [Accepted: 12/23/2019] [Indexed: 01/27/2023]
Affiliation(s)
- Shuo Liang
- Institute for Biochemistry and Molecular Biology ZBMZ, Faculty of Medicine University of Freiburg Freiburg Germany
- Faculty of Biology University of Freiburg Freiburg Germany
| | - Simon Fuchs
- Institute for Biochemistry and Molecular Biology ZBMZ, Faculty of Medicine University of Freiburg Freiburg Germany
- Faculty of Biology University of Freiburg Freiburg Germany
| | - Evgeny V. Mymrikov
- Institute for Biochemistry and Molecular Biology ZBMZ, Faculty of Medicine University of Freiburg Freiburg Germany
- CIBSS ‐ Centre for Integrative Biological Signalling Studies University of Freiburg Freiburg Germany
| | - Anja Stulz
- Department of Pharmaceutical Technology and Biopharmacy University of Freiburg Freiburg Germany
| | - Michael Kaiser
- Department of Pharmaceutical Technology and Biopharmacy University of Freiburg Freiburg Germany
| | - Heiko Heerklotz
- CIBSS ‐ Centre for Integrative Biological Signalling Studies University of Freiburg Freiburg Germany
- Department of Pharmaceutical Technology and Biopharmacy University of Freiburg Freiburg Germany
- Leslie Dan Faculty of Pharmacy University of Toronto Toronto Canada
- BIOSS Centre for Biological Signalling Studies University of Freiburg Freiburg Germany
| | - Carola Hunte
- Institute for Biochemistry and Molecular Biology ZBMZ, Faculty of Medicine University of Freiburg Freiburg Germany
- CIBSS ‐ Centre for Integrative Biological Signalling Studies University of Freiburg Freiburg Germany
- BIOSS Centre for Biological Signalling Studies University of Freiburg Freiburg Germany
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13
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Agarose native gel electrophoresis of proteins. Int J Biol Macromol 2019; 140:668-671. [DOI: 10.1016/j.ijbiomac.2019.08.066] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 08/06/2019] [Accepted: 08/07/2019] [Indexed: 11/18/2022]
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14
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Blanco-Redondo B, Nuwal N, Kneitz S, Nuwal T, Halder P, Liu Y, Ehmann N, Scholz N, Mayer A, Kleber J, Kähne T, Schmitt D, Sadanandappa MK, Funk N, Albertova V, Helfrich-Förster C, Ramaswami M, Hasan G, Kittel RJ, Langenhan T, Gerber B, Buchner E. Implications of the Sap47 null mutation for synapsin phosphorylation, longevity, climbing proficiency and behavioural plasticity in adult Drosophila. ACTA ACUST UNITED AC 2019; 222:jeb.203505. [PMID: 31488622 DOI: 10.1242/jeb.203505] [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: 03/19/2019] [Accepted: 08/29/2019] [Indexed: 12/18/2022]
Abstract
The Sap47 gene of Drosophila melanogaster encodes a highly abundant 47 kDa synaptic vesicle-associated protein. Sap47 null mutants show defects in synaptic plasticity and larval olfactory associative learning but the molecular function of Sap47 at the synapse is unknown. We demonstrate that Sap47 modulates the phosphorylation of another highly abundant conserved presynaptic protein, synapsin. Site-specific phosphorylation of Drosophila synapsin has repeatedly been shown to be important for behavioural plasticity but it was not known where these phospho-synapsin isoforms are localized in the brain. Here, we report the distribution of serine-6-phosphorylated synapsin in the adult brain and show that it is highly enriched in rings of synapses in the ellipsoid body and in large synapses near the lateral triangle. The effects of knockout of Sap47 or synapsin on olfactory associative learning/memory support the hypothesis that both proteins operate in the same molecular pathway. We therefore asked if this might also be true for other aspects of their function. We show that knockout of Sap47 but not synapsin reduces lifespan, whereas knockout of Sap47 and synapsin, either individually or together, affects climbing proficiency, as well as plasticity in circadian rhythms and sleep. Furthermore, electrophysiological assessment of synaptic properties at the larval neuromuscular junction (NMJ) reveals increased spontaneous synaptic vesicle fusion and reduced paired pulse facilitation in Sap47 and synapsin single and double mutants. Our results imply that Sap47 and synapsin cooperate non-uniformly in the control of synaptic properties in different behaviourally relevant neuronal networks of the fruitfly.
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Affiliation(s)
- Beatriz Blanco-Redondo
- Institute of Clinical Neurobiology, University of Würzburg, 97078 Würzburg, Germany .,Department of Neurobiology and Genetics, Biocenter of the University of Würzburg, 97074 Würzburg, Germany.,Rudolf Schönheimer Institute of Biochemistry, Division of General Biochemistry, Leipzig University, 04103 Leipzig, Germany
| | - Nidhi Nuwal
- Department of Neurobiology and Genetics, Biocenter of the University of Würzburg, 97074 Würzburg, Germany
| | - Susanne Kneitz
- Department of Physiological Chemistry, Biocenter of the University of Würzburg, 97074 Würzburg, Germany
| | - Tulip Nuwal
- Department of Neurobiology and Genetics, Biocenter of the University of Würzburg, 97074 Würzburg, Germany
| | - Partho Halder
- Department of Neurobiology and Genetics, Biocenter of the University of Würzburg, 97074 Würzburg, Germany
| | - Yiting Liu
- Department of Neurobiology and Genetics, Biocenter of the University of Würzburg, 97074 Würzburg, Germany
| | - Nadine Ehmann
- Department of Neurophysiology, Institute of Physiology, University of Würzburg, 97070 Würzburg, Germany.,Department of Animal Physiology, Institute of Biology, Leipzig University, 04103 Leipzig, Germany.,Carl-Ludwig-Institute for Physiology, Leipzig University, 04103 Leipzig, Germany
| | - Nicole Scholz
- Rudolf Schönheimer Institute of Biochemistry, Division of General Biochemistry, Leipzig University, 04103 Leipzig, Germany.,Department of Neurophysiology, Institute of Physiology, University of Würzburg, 97070 Würzburg, Germany
| | - Annika Mayer
- Institute of Clinical Neurobiology, University of Würzburg, 97078 Würzburg, Germany
| | - Jörg Kleber
- Leibniz Institute of Neurobiology, 39118 Magdeburg, Germany
| | - Thilo Kähne
- Institute of Experimental Internal Medicine, Otto von Guericke University, 39120 Magdeburg, Germany
| | - Dominique Schmitt
- Institute of Clinical Neurobiology, University of Würzburg, 97078 Würzburg, Germany
| | - Madhumala K Sadanandappa
- Institute of Clinical Neurobiology, University of Würzburg, 97078 Würzburg, Germany.,National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, Karnataka 560065, India
| | - Natalja Funk
- Department of Neurobiology and Genetics, Biocenter of the University of Würzburg, 97074 Würzburg, Germany
| | - Viera Albertova
- Institute of Clinical Neurobiology, University of Würzburg, 97078 Würzburg, Germany.,Department of Neurobiology and Genetics, Biocenter of the University of Würzburg, 97074 Würzburg, Germany
| | - Charlotte Helfrich-Förster
- Department of Neurobiology and Genetics, Biocenter of the University of Würzburg, 97074 Würzburg, Germany
| | - Mani Ramaswami
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, Karnataka 560065, India
| | - Gaiti Hasan
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, Karnataka 560065, India
| | - Robert J Kittel
- Department of Neurophysiology, Institute of Physiology, University of Würzburg, 97070 Würzburg, Germany.,Department of Animal Physiology, Institute of Biology, Leipzig University, 04103 Leipzig, Germany.,Carl-Ludwig-Institute for Physiology, Leipzig University, 04103 Leipzig, Germany
| | - Tobias Langenhan
- Rudolf Schönheimer Institute of Biochemistry, Division of General Biochemistry, Leipzig University, 04103 Leipzig, Germany.,Department of Neurophysiology, Institute of Physiology, University of Würzburg, 97070 Würzburg, Germany
| | - Bertram Gerber
- Leibniz Institute of Neurobiology, 39118 Magdeburg, Germany.,Institute of Biology, University of Magdeburg, 39120 Magdeburg, Germany.,Center for Behavioral Brain Sciences, 39106 Magdeburg, Germany
| | - Erich Buchner
- Institute of Clinical Neurobiology, University of Würzburg, 97078 Würzburg, Germany .,Department of Neurobiology and Genetics, Biocenter of the University of Würzburg, 97074 Würzburg, Germany
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15
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Electrochemical studies of human nAChR a7 subunit phosphorylation by kinases PKA, PKC and Src. Anal Biochem 2019; 574:46-56. [DOI: 10.1016/j.ab.2019.03.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 03/19/2019] [Accepted: 03/19/2019] [Indexed: 12/19/2022]
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16
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Kuthanová Trsková E, Bína D, Santabarbara S, Sobotka R, Kaňa R, Belgio E. Isolation and characterization of CAC antenna proteins and photosystem I supercomplex from the cryptophytic alga Rhodomonas salina. PHYSIOLOGIA PLANTARUM 2019; 166:309-319. [PMID: 30677144 DOI: 10.1111/ppl.12928] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 01/17/2019] [Indexed: 06/09/2023]
Abstract
In the present paper, we report an improved method combining sucrose density gradient with ion-exchange chromatography for the isolation of pure chlorophyll a/c antenna proteins from the model cryptophytic alga Rhodomonas salina. Antennas were used for in vitro quenching experiments in the absence of xanthophylls, showing that protein aggregation is a plausible mechanism behind non-photochemical quenching in R. salina. From sucrose gradient, it was also possible to purify a functional photosystem I supercomplex, which was in turn characterized by steady-state and time-resolved fluorescence spectroscopy. R. salina photosystem I showed a remarkably fast photochemical trapping rate, similar to what recently reported for other red clade algae such as Chromera velia and Phaeodactylum tricornutum. The method reported therefore may also be suitable for other still partially unexplored algae, such as cryptophytes.
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Affiliation(s)
- Eliška Kuthanová Trsková
- Institute of Microbiology, Academy of Sciences of the Czech Republic, 379 81, Třeboň, Czech Republic
- Faculty of Science, University of South Bohemia in České Budějovice, 370 05, České Budějovice, Czech Republic
| | - David Bína
- Faculty of Science, University of South Bohemia in České Budějovice, 370 05, České Budějovice, Czech Republic
- Institute of Plant Molecular Biology, Biology Centre CAS, 370 05, České Budějovice, Czech Republic
| | - Stefano Santabarbara
- Photosynthesis Research Unit, Centro Studi sulla Biologia Cellulare e Molecolare delle Piante, 20133, Milan, Italy
| | - Roman Sobotka
- Institute of Microbiology, Academy of Sciences of the Czech Republic, 379 81, Třeboň, Czech Republic
- Faculty of Science, University of South Bohemia in České Budějovice, 370 05, České Budějovice, Czech Republic
| | - Radek Kaňa
- Institute of Microbiology, Academy of Sciences of the Czech Republic, 379 81, Třeboň, Czech Republic
- Faculty of Science, University of South Bohemia in České Budějovice, 370 05, České Budějovice, Czech Republic
| | - Erica Belgio
- Institute of Microbiology, Academy of Sciences of the Czech Republic, 379 81, Třeboň, Czech Republic
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17
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Gong H, Li J, Xu A, Tang Y, Ji W, Gao R, Wang S, Yu L, Tian C, Li J, Yen HY, Man Lam S, Shui G, Yang X, Sun Y, Li X, Jia M, Yang C, Jiang B, Lou Z, Robinson CV, Wong LL, Guddat LW, Sun F, Wang Q, Rao Z. An electron transfer path connects subunits of a mycobacterial respiratory supercomplex. Science 2018; 362:science.aat8923. [PMID: 30361386 DOI: 10.1126/science.aat8923] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 10/10/2018] [Indexed: 11/02/2022]
Abstract
We report a 3.5-angstrom-resolution cryo-electron microscopy structure of a respiratory supercomplex isolated from Mycobacterium smegmatis. It comprises a complex III dimer flanked on either side by individual complex IV subunits. Complex III and IV associate so that electrons can be transferred from quinol in complex III to the oxygen reduction center in complex IV by way of a bridging cytochrome subunit. We observed a superoxide dismutase-like subunit at the periplasmic face, which may be responsible for detoxification of superoxide formed by complex III. The structure reveals features of an established drug target and provides a foundation for the development of treatments for human tuberculosis.
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Affiliation(s)
- Hongri Gong
- State Key Laboratory of Medicinal Chemical Biology and College of Life Science, Nankai University, Tianjin 300353, China
| | - Jun Li
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China.,CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences (CAS), 320 Yueyang Road, Shanghai 200031, China
| | - Ao Xu
- State Key Laboratory of Medicinal Chemical Biology and College of Life Science, Nankai University, Tianjin 300353, China.,National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, CAS, Beijing 100101, China
| | - Yanting Tang
- State Key Laboratory of Medicinal Chemical Biology and College of Life Science, Nankai University, Tianjin 300353, China
| | - Wenxin Ji
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, CAS, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Ruogu Gao
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, CAS, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Shuhui Wang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China.,CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences (CAS), 320 Yueyang Road, Shanghai 200031, China
| | - Lu Yu
- High Magnetic Field Laboratory, CAS, Hefei 230031, China
| | - Changlin Tian
- High Magnetic Field Laboratory, CAS, Hefei 230031, China.,Hefei National Laboratory of Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Jingwen Li
- Department of Chemistry, University of Oxford, Physical and Theoretical Chemistry Laboratory, South Parks Rd, Oxford, OX1 3QZ, UK
| | - Hsin-Yung Yen
- Department of Chemistry, University of Oxford, Physical and Theoretical Chemistry Laboratory, South Parks Rd, Oxford, OX1 3QZ, UK.,OMass Technologies, Begbroke Science Park, Woodstock Rd, Yarnton, Kidlington OX5 1PF, UK
| | - Sin Man Lam
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, CAS, Beijing 100101, China
| | - Guanghou Shui
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, CAS, Beijing 100101, China
| | - Xiuna Yang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China.,CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences (CAS), 320 Yueyang Road, Shanghai 200031, China
| | - Yuna Sun
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, CAS, Beijing 100101, China
| | - Xuemei Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, CAS, Beijing 100101, China
| | - Minze Jia
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, CAS, Beijing 100101, China
| | - Cheng Yang
- State Key Laboratory of Medicinal Chemical Biology and College of Life Science, Nankai University, Tianjin 300353, China
| | - Biao Jiang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China
| | - Zhiyong Lou
- Laboratory of Structural Biology, Tsinghua University, Beijing 100084, China
| | - Carol V Robinson
- Department of Chemistry, University of Oxford, Physical and Theoretical Chemistry Laboratory, South Parks Rd, Oxford, OX1 3QZ, UK
| | - Luet-Lok Wong
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Road, Oxford OX1 3QR, UK
| | - Luke W Guddat
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072 Queensland, Australia
| | - Fei Sun
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, CAS, Beijing 100101, China. .,University of Chinese Academy of Sciences, Beijing, China
| | - Quan Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, CAS, Beijing 100101, China.
| | - Zihe Rao
- State Key Laboratory of Medicinal Chemical Biology and College of Life Science, Nankai University, Tianjin 300353, China. .,Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China.,CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences (CAS), 320 Yueyang Road, Shanghai 200031, China.,National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, CAS, Beijing 100101, China.,Laboratory of Structural Biology, Tsinghua University, Beijing 100084, China
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18
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Chen Z, Gu J, El Ayadi A, Oberhauser AF, Zhou J, Sousse LE, Finnerty CC, Herndon DN, Boor PJ. Effect of N-(2-aminoethyl) ethanolamine on hypertrophic scarring changes in vitro: Finding novel anti-fibrotic therapies. Toxicol Appl Pharmacol 2018; 362:9-19. [PMID: 30248415 DOI: 10.1016/j.taap.2018.09.026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 08/29/2018] [Accepted: 09/20/2018] [Indexed: 01/21/2023]
Abstract
Hypertrophic scars (HS) limit movement, decrease quality of life, and remain a major impediment to rehabilitation from burns. However, no effective pharmacologic therapies for HS exist. Here we tested the in vitro anti-fibrotic effects of the novel chemical N-(2-aminoethyl) ethanolamine (AEEA) at non-toxic concentrations. Scanning electron microscopy showed that AEEA markedly altered the structure of the extracellular matrix (ECM) produced by primary dermal fibroblasts isolated from a HS of a burn patient (HTS). Compression atomic force microscopy revealed that AEEA stiffened the 3D nanostructure of ECM formed by HTS fibroblasts. Western blot analysis in three separate types of primary human dermal fibroblasts (including HTS) showed that AEEA exposure increased the extractability of type I collagen in a dose- and time-dependent fashion, while not increasing collagen synthesis. A comparison of the electrophoretic behavior of the same set of samples under native and denaturing conditions suggested that AEEA alters the 3D structure of type I collagen. The antagonization effect of AEEA to TGF-β1 on ECM formation was also observed. Furthermore, analyses of the anti-fibrotic effects of analogs of AEEA (with modified pharmacophores) suggest the existence of a chemical structure-activity relationship. Thus, AEEA and its analogs may inhibit HS development; further study and optimization of analogs may be a promising strategy for the discovery for effective HS therapies.
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Affiliation(s)
- Zhenping Chen
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA; Department of Surgery, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Jianhua Gu
- AFM/SEM Core Facility, The Houston Methodist Hospital Research Institute, Houston, TX 77030, USA
| | - Amina El Ayadi
- Department of Surgery, University of Texas Medical Branch, Galveston, TX 77555, USA; Shriners Hospitals for Children, Galveston, TX 77550, USA
| | - Andres F Oberhauser
- Department of Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, TX 77555, USA; Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Jia Zhou
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Linda E Sousse
- Department of Surgery, University of Texas Medical Branch, Galveston, TX 77555, USA; Shriners Hospitals for Children, Galveston, TX 77550, USA
| | - Celeste C Finnerty
- Department of Surgery, University of Texas Medical Branch, Galveston, TX 77555, USA; Shriners Hospitals for Children, Galveston, TX 77550, USA
| | - David N Herndon
- Department of Surgery, University of Texas Medical Branch, Galveston, TX 77555, USA; Shriners Hospitals for Children, Galveston, TX 77550, USA
| | - Paul J Boor
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA; Shriners Hospitals for Children, Galveston, TX 77550, USA.
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19
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Miranda-Astudillo HV, Yadav KNS, Colina-Tenorio L, Bouillenne F, Degand H, Morsomme P, Boekema EJ, Cardol P. The atypical subunit composition of respiratory complexes I and IV is associated with original extra structural domains in Euglena gracilis. Sci Rep 2018; 8:9698. [PMID: 29946152 PMCID: PMC6018760 DOI: 10.1038/s41598-018-28039-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 06/14/2018] [Indexed: 11/10/2022] Open
Abstract
In mitochondrial oxidative phosphorylation, electron transfer from NADH or succinate to oxygen by a series of large protein complexes in the inner mitochondrial membrane (complexes I-IV) is coupled to the generation of an electrochemical proton gradient, the energy of which is utilized by complex V to generate ATP. In Euglena gracilis, a non-parasitic secondary green alga related to trypanosomes, these respiratory complexes totalize more than 40 Euglenozoa-specific subunits along with about 50 classical subunits described in other eukaryotes. In the present study the Euglena proton-pumping complexes I, III, and IV were purified from isolated mitochondria by a two-steps liquid chromatography approach. Their atypical subunit composition was further resolved and confirmed using a three-steps PAGE analysis coupled to mass spectrometry identification of peptides. The purified complexes were also observed by electron microscopy followed by single-particle analysis. Even if the overall structures of the three oxidases are similar to the structure of canonical enzymes (e.g. from mammals), additional atypical domains were observed in complexes I and IV: an extra domain located at the tip of the peripheral arm of complex I and a "helmet-like" domain on the top of the cytochrome c binding region in complex IV.
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Affiliation(s)
- H V Miranda-Astudillo
- Laboratoire de Génétique et Physiologie des microalgues, InBioS/Phytosystems, Institut de Botanique, Université de Liège, Liege, Belgium
| | - K N S Yadav
- Department of Electron Microscopy, Groningen Biological Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - L Colina-Tenorio
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico, Mexico
| | - F Bouillenne
- InBioS/Center for Protein Engineering, Université de Liège, Liege, Belgium
| | - H Degand
- Institut des Sciences de la Vie, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - P Morsomme
- Institut des Sciences de la Vie, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - E J Boekema
- Department of Electron Microscopy, Groningen Biological Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - P Cardol
- Laboratoire de Génétique et Physiologie des microalgues, InBioS/Phytosystems, Institut de Botanique, Université de Liège, Liege, Belgium.
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20
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Bassett B, Waibel B, White A, Hansen H, Stephens D, Koelper A, Larsen EM, Kim C, Glanzer A, Lavis LD, Hoops GC, Johnson RJ. Measuring the Global Substrate Specificity of Mycobacterial Serine Hydrolases Using a Library of Fluorogenic Ester Substrates. ACS Infect Dis 2018; 4:904-911. [PMID: 29648787 PMCID: PMC5993602 DOI: 10.1021/acsinfecdis.7b00263] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Among the proteins required for lipid metabolism in Mycobacterium tuberculosis are a significant number of uncharacterized serine hydrolases, especially lipases and esterases. Using a streamlined synthetic method, a library of immolative fluorogenic ester substrates was expanded to better represent the natural lipidomic diversity of Mycobacterium. This expanded fluorogenic library was then used to rapidly characterize the global structure activity relationship (SAR) of mycobacterial serine hydrolases in M. smegmatis under different growth conditions. Confirmation of fluorogenic substrate activation by mycobacterial serine hydrolases was performed using nonspecific serine hydrolase inhibitors and reinforced the biological significance of the SAR. The hydrolases responsible for the global SAR were then assigned using gel-resolved activity measurements, and these assignments were used to rapidly identify the relative substrate specificity of previously uncharacterized mycobacterial hydrolases. These measurements provide a global SAR of mycobacterial hydrolase activity, a picture of cycling hydrolase activity, and a detailed substrate specificity profile for previously uncharacterized hydrolases.
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Affiliation(s)
- Braden Bassett
- Department of Chemistry and Biochemistry, Butler University, 4600 Sunset Ave., Indianapolis, IN 46208-3443 (USA)
| | - Brent Waibel
- Department of Chemistry and Biochemistry, Butler University, 4600 Sunset Ave., Indianapolis, IN 46208-3443 (USA)
| | - Alex White
- Department of Chemistry and Biochemistry, Butler University, 4600 Sunset Ave., Indianapolis, IN 46208-3443 (USA)
| | - Heather Hansen
- Department of Chemistry and Biochemistry, Butler University, 4600 Sunset Ave., Indianapolis, IN 46208-3443 (USA)
| | - Dominique Stephens
- Department of Chemistry and Biochemistry, Butler University, 4600 Sunset Ave., Indianapolis, IN 46208-3443 (USA)
| | - Andrew Koelper
- Department of Chemistry and Biochemistry, Butler University, 4600 Sunset Ave., Indianapolis, IN 46208-3443 (USA)
| | - Erik M. Larsen
- Department of Chemistry and Biochemistry, Butler University, 4600 Sunset Ave., Indianapolis, IN 46208-3443 (USA)
| | - Charles Kim
- Howard Hughes Medical Institute, Janelia Research Campus, 19700 Helix Dr., Ashburn, VA 20147-2439 (USA)
| | - Adam Glanzer
- Department of Chemistry and Biochemistry, Butler University, 4600 Sunset Ave., Indianapolis, IN 46208-3443 (USA)
| | - Luke D. Lavis
- Howard Hughes Medical Institute, Janelia Research Campus, 19700 Helix Dr., Ashburn, VA 20147-2439 (USA)
| | - Geoffrey C. Hoops
- Department of Chemistry and Biochemistry, Butler University, 4600 Sunset Ave., Indianapolis, IN 46208-3443 (USA)
| | - R. Jeremy Johnson
- Department of Chemistry and Biochemistry, Butler University, 4600 Sunset Ave., Indianapolis, IN 46208-3443 (USA)
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21
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Kielkopf CS, Low JKK, Mok YF, Bhatia S, Palasovski T, Oakley AJ, Whitten AE, Garner B, Brown SHJ. Identification of a novel tetrameric structure for human apolipoprotein-D. J Struct Biol 2018; 203:205-218. [PMID: 29885491 DOI: 10.1016/j.jsb.2018.05.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 05/18/2018] [Accepted: 05/30/2018] [Indexed: 10/14/2022]
Abstract
Apolipoprotein-D is a 25 kDa glycosylated member of the lipocalin family that folds into an eight-stranded β-barrel with a single adjacent α-helix. Apolipoprotein-D specifically binds a range of small hydrophobic ligands such as progesterone and arachidonic acid and has an antioxidant function that is in part due to the reduction of peroxidised lipids by methionine-93. Therefore, apolipoprotein-D plays multiple roles throughout the body and is protective in Alzheimer's disease, where apolipoprotein-D overexpression reduces the amyloid-β burden in Alzheimer's disease mouse models. Oligomerisation is a common feature of lipocalins that can influence ligand binding. The native structure of apolipoprotein-D, however, has not been conclusively defined. Apolipoprotein-D is generally described as a monomeric protein, although it dimerises when reducing peroxidised lipids. Here, we investigated the native structure of apolipoprotein-D derived from plasma, breast cyst fluid (BCF) and cerebrospinal fluid. In plasma and cerebrospinal fluid, apolipoprotein-D was present in high-molecular weight complexes, potentially in association with lipoproteins. In contrast, apolipoprotein-D in BCF formed distinct oligomeric species. We assessed apolipoprotein-D oligomerisation using native apolipoprotein-D purified from BCF and a suite of complementary methods, including multi-angle laser light scattering, analytical ultracentrifugation and small-angle X-ray scattering. Our analyses showed that apolipoprotein-D predominantly forms a ∼95 to ∼100 kDa tetramer. Small-angle X-ray scattering analysis confirmed these findings and provided a structural model for apolipoprotein-D tetramer. These data indicate apolipoprotein-D rarely exists as a free monomer under physiological conditions and provide insights into novel native structures of apolipoprotein-D and into oligomerisation behaviour in the lipocalin family.
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Affiliation(s)
- Claudia S Kielkopf
- Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW, Australia; School of Biological Sciences, University of Wollongong, Wollongong, NSW, Australia; Molecular Horizons, University of Wollongong, Wollongong, NSW, Australia.
| | - Jason K K Low
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia.
| | - Yee-Foong Mok
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, Australia.
| | - Surabhi Bhatia
- Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW, Australia; School of Biological Sciences, University of Wollongong, Wollongong, NSW, Australia.
| | - Tony Palasovski
- Illawarra and Shoalhaven Local Health District (ISLHD), Wollongong, NSW, Australia; Specialist Breast Clinic Sutherland Shire and Wollongong, NSW, Australia; Integrated Specialist Health Care Sutherland Shire, NSW, Australia
| | - Aaron J Oakley
- Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW, Australia; Molecular Horizons, University of Wollongong, Wollongong, NSW, Australia; School of Chemistry, University of Wollongong, Wollongong, NSW, Australia.
| | - Andrew E Whitten
- Australian Nuclear Science and Technology Organisation, Lucas Heights, NSW, Australia.
| | - Brett Garner
- Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW, Australia; School of Biological Sciences, University of Wollongong, Wollongong, NSW, Australia; Molecular Horizons, University of Wollongong, Wollongong, NSW, Australia.
| | - Simon H J Brown
- Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW, Australia; School of Biological Sciences, University of Wollongong, Wollongong, NSW, Australia; Molecular Horizons, University of Wollongong, Wollongong, NSW, Australia.
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22
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Wong CW, Lam KKW, Lee CL, Yeung WSB, Zhao WE, Ho PC, Ou JP, Chiu PCN. The roles of protein disulphide isomerase family A, member 3 (ERp57) and surface thiol/disulphide exchange in human spermatozoa-zona pellucida binding. Hum Reprod 2017; 32:733-742. [PMID: 28175305 DOI: 10.1093/humrep/dex007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 01/16/2017] [Indexed: 12/28/2022] Open
Abstract
Study question Are multimeric sperm plasma membrane protein complexes, ERp57 and sperm surface thiol content involved in human spermatozoa-zona pellucida (ZP) interaction? Summary answer ERp57 is a component of a multimeric spermatozoa-ZP receptor complex involved in regulation of human spermatozoa-ZP binding via up-regulation of sperm surface thiol content. What is known already A spermatozoon acquires its fertilization capacity within the female reproductive tract by capacitation. Spermatozoa-ZP receptor is suggested to be a composite structure that is assembled into a functional complex during capacitation. Sperm surface thiol content is elevated during capacitation. ERp57 is a protein disulphide isomerase that modulates the thiol-disulphide status of proteins. Study design, size, duration The binding ability and components of protein complexes in extracted membrane protein fractions of spermatozoa were studied. The roles of capacitation, thiol-disulphide reagent treatments and ERp57 on sperm functions and sperm surface thiol content were assessed. Participants/materials, setting, methods Spermatozoa were obtained from semen samples from normozoospermic men. Human oocytes were obtained from an assisted reproduction programme. Blue native polyacrylamide gel electrophoresis, western ligand blotting and mass spectrometry were used to identify the components of solubilized ZP/ZP3-binding complexes. The localization and expression of sperm surface thiol and ERp57 were studied by immunostaining and sperm surface protein biotinylation followed by western blotting. Sperm functions were assessed by standard assays. Main results and the role of chance Several ZP-binding complexes were isolated from the cell membrane of capacitated spermatozoa. ERp57 was a component of one of these complexes. Capacitation significantly increased the sperm surface thiol content, acrosomal thiol distribution and ERp57 expression on sperm surface. Sperm surface thiol and ERp57 immunoreactivity were localized to the acrosomal region of spermatozoa, a region responsible for ZP-binding. Up-regulation of the surface thiol content or ERp57 surface expression in vitro stimulated ZP-binding capacity of human spermatozoa. Blocking of ERp57 function by specific antibody or inhibitors against ERp57 reduced the surface thiol content and ZP-binding capacity of human spermatozoa. Large scale data N/A. Limitations, reasons for caution The mechanisms by which up-regulation of surface thiol content stimulates spermatozoa-ZP binding have not been depicted. Wider implications of the findings Thiol-disulphide exchange is a crucial event in capacitation. ERp57 modulates the event and the subsequent fertilization process. Modulation of the surface thiol content of the spermatozoa of subfertile men may help to increase fertilization rate in assisted reproduction. Study funding/competing interest(s) This work was supported by The Hong Kong Research Grant Council Grant HKU764611 and HKU764512M to P.C.N.C. The authors have no competing interests.
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Affiliation(s)
- Chi-Wai Wong
- Department of Obstetrics and Gynaecology, The University of Hong Kong, Queen Mary Hospital, Pokfulam Road, Hong Kong, Hong Kong SAR, China
| | - Kevin K W Lam
- Department of Obstetrics and Gynaecology, The University of Hong Kong, Queen Mary Hospital, Pokfulam Road, Hong Kong, Hong Kong SAR, China.,Centre of Reproduction, Development and Growth, The University of Hong Kong, Queen Mary Hospital, Pokfulam Road, Hong Kong, Hong Kong SAR, China.,Shenzhen Key Laboratory of Fertility Regulation, Department of Obstetrics and Gynecology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Hong Kong SAR, P.R. China
| | - Cheuk-Lun Lee
- Department of Obstetrics and Gynaecology, The University of Hong Kong, Queen Mary Hospital, Pokfulam Road, Hong Kong, Hong Kong SAR, China.,Centre of Reproduction, Development and Growth, The University of Hong Kong, Queen Mary Hospital, Pokfulam Road, Hong Kong, Hong Kong SAR, China.,Shenzhen Key Laboratory of Fertility Regulation, Department of Obstetrics and Gynecology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Hong Kong SAR, P.R. China
| | - William S B Yeung
- Department of Obstetrics and Gynaecology, The University of Hong Kong, Queen Mary Hospital, Pokfulam Road, Hong Kong, Hong Kong SAR, China.,Centre of Reproduction, Development and Growth, The University of Hong Kong, Queen Mary Hospital, Pokfulam Road, Hong Kong, Hong Kong SAR, China.,Shenzhen Key Laboratory of Fertility Regulation, Department of Obstetrics and Gynecology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Hong Kong SAR, P.R. China
| | - Wei E Zhao
- The Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, P.R. China
| | - Pak-Chung Ho
- Department of Obstetrics and Gynaecology, The University of Hong Kong, Queen Mary Hospital, Pokfulam Road, Hong Kong, Hong Kong SAR, China.,Centre of Reproduction, Development and Growth, The University of Hong Kong, Queen Mary Hospital, Pokfulam Road, Hong Kong, Hong Kong SAR, China.,Shenzhen Key Laboratory of Fertility Regulation, Department of Obstetrics and Gynecology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Hong Kong SAR, P.R. China
| | - Jian-Ping Ou
- Center for Reproductive Medicine, The Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, P.R. China
| | - Philip C N Chiu
- Department of Obstetrics and Gynaecology, The University of Hong Kong, Queen Mary Hospital, Pokfulam Road, Hong Kong, Hong Kong SAR, China.,Centre of Reproduction, Development and Growth, The University of Hong Kong, Queen Mary Hospital, Pokfulam Road, Hong Kong, Hong Kong SAR, China.,Shenzhen Key Laboratory of Fertility Regulation, Department of Obstetrics and Gynecology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Hong Kong SAR, P.R. China
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23
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Extensive gain and loss of photosystem I subunits in chromerid algae, photosynthetic relatives of apicomplexans. Sci Rep 2017; 7:13214. [PMID: 29038514 PMCID: PMC5643376 DOI: 10.1038/s41598-017-13575-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 09/26/2017] [Indexed: 12/16/2022] Open
Abstract
In oxygenic photosynthesis the initial photochemical processes are carried out by photosystem I (PSI) and II (PSII). Although subunit composition varies between cyanobacterial and plastid photosystems, the core structures of PSI and PSII are conserved throughout photosynthetic eukaryotes. So far, the photosynthetic complexes have been characterised in only a small number of organisms. We performed in silico and biochemical studies to explore the organization and evolution of the photosynthetic apparatus in the chromerids Chromera velia and Vitrella brassicaformis, autotrophic relatives of apicomplexans. We catalogued the presence and location of genes coding for conserved subunits of the photosystems as well as cytochrome b6f and ATP synthase in chromerids and other phototrophs and performed a phylogenetic analysis. We then characterised the photosynthetic complexes of Chromera and Vitrella using 2D gels combined with mass-spectrometry and further analysed the purified Chromera PSI. Our data suggest that the photosynthetic apparatus of chromerids underwent unique structural changes. Both photosystems (as well as cytochrome b6f and ATP synthase) lost several canonical subunits, while PSI gained one superoxide dismutase (Vitrella) or two superoxide dismutases and several unknown proteins (Chromera) as new regular subunits. We discuss these results in light of the extraordinarily efficient photosynthetic processes described in Chromera.
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24
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Alvarez-Paggi D, Hannibal L, Castro MA, Oviedo-Rouco S, Demicheli V, Tórtora V, Tomasina F, Radi R, Murgida DH. Multifunctional Cytochrome c: Learning New Tricks from an Old Dog. Chem Rev 2017; 117:13382-13460. [DOI: 10.1021/acs.chemrev.7b00257] [Citation(s) in RCA: 135] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Damián Alvarez-Paggi
- Departamento
de Química Inorgánica, Analítica y Química
Física and INQUIMAE (CONICET-UBA), Facultad de Ciencias Exactas
y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2, piso 1, Buenos Aires C1428EHA, Argentina
| | - Luciana Hannibal
- Department
of Pediatrics, Universitätsklinikum Freiburg, Mathildenstrasse 1, Freiburg 79106, Germany
- Departamento
de Bioquímica and Center for Free Radical and Biomedical Research,
Facultad de Medicina, Universidad de la República, Av.
Gral. Flores 2125, Montevideo 11800, Uruguay
| | - María A. Castro
- Departamento
de Química Inorgánica, Analítica y Química
Física and INQUIMAE (CONICET-UBA), Facultad de Ciencias Exactas
y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2, piso 1, Buenos Aires C1428EHA, Argentina
| | - Santiago Oviedo-Rouco
- Departamento
de Química Inorgánica, Analítica y Química
Física and INQUIMAE (CONICET-UBA), Facultad de Ciencias Exactas
y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2, piso 1, Buenos Aires C1428EHA, Argentina
| | - Veronica Demicheli
- Departamento
de Bioquímica and Center for Free Radical and Biomedical Research,
Facultad de Medicina, Universidad de la República, Av.
Gral. Flores 2125, Montevideo 11800, Uruguay
| | - Veronica Tórtora
- Departamento
de Bioquímica and Center for Free Radical and Biomedical Research,
Facultad de Medicina, Universidad de la República, Av.
Gral. Flores 2125, Montevideo 11800, Uruguay
| | - Florencia Tomasina
- Departamento
de Bioquímica and Center for Free Radical and Biomedical Research,
Facultad de Medicina, Universidad de la República, Av.
Gral. Flores 2125, Montevideo 11800, Uruguay
| | - Rafael Radi
- Departamento
de Bioquímica and Center for Free Radical and Biomedical Research,
Facultad de Medicina, Universidad de la República, Av.
Gral. Flores 2125, Montevideo 11800, Uruguay
| | - Daniel H. Murgida
- Departamento
de Química Inorgánica, Analítica y Química
Física and INQUIMAE (CONICET-UBA), Facultad de Ciencias Exactas
y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2, piso 1, Buenos Aires C1428EHA, Argentina
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25
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Jang S, Lewis TS, Powers C, Khuchua Z, Baines CP, Wipf P, Javadov S. Elucidating Mitochondrial Electron Transport Chain Supercomplexes in the Heart During Ischemia-Reperfusion. Antioxid Redox Signal 2017; 27:57-69. [PMID: 27604998 PMCID: PMC5488255 DOI: 10.1089/ars.2016.6635] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
AIMS Mitochondrial supercomplexes (SCs) are the large supramolecular assembly of individual electron transport chain (ETC) complexes that apparently provide highly efficient ATP synthesis and reduce electron leakage and reactive oxygen species (ROS) production. Oxidative stress during cardiac ischemia-reperfusion (IR) can result in degradation of SCs through oxidation of cardiolipin (CL). Also, IR induces calcium overload and enhances reactive oxygen species (mitROS) in mitochondria that result in the opening of the nonselective permeability transition pores (PTP). The opening of the PTP further compromises cellular energetics and increases mitROS ultimately leading to cell death. Here, we examined the role of PTP-induced mitROS in disintegration of SCs during cardiac IR. The relationship between mitochondrial PTP, ROS, and SCs was investigated using Langendorff-perfused rat hearts subjected to global ischemia (25 min) followed by short-time (5 min) or long-time (60 min) reperfusion in the presence or absence of the PTP inhibitor, sanglifehrin A (SfA), and the mitochondrial targeted ROS and electron scavenger, XJB-5-131. Also, the effects of CL deficiency on SC degradation, PTP, and mitROS were investigated in tafazzin knockdown (TazKD) mice. RESULTS Cardiac IR induced PTP opening and mitROS generation, inhibited by SfA. Percent distributions of SCs were significantly affected by IR, and the effects were dependent on the reperfusion time and reversed by SfA and XJB-5-131. TazKD mice demonstrated a 40% lower SC I + III+IV with reduced basal mitochondrial PTP, ROS, and ETC complex activity. Innovation and Conclusion: Sustained reperfusion after cardiac ischemia induces disintegration of mitochondrial SCs, and PTP-induced ROS presumably play a causal role in SC disassembly. Antioxid. Redox Signal. 27, 57-69.
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Affiliation(s)
- Sehwan Jang
- Department of Physiology, University of Puerto Rico School of Medicine, San Juan, Puerto Rico
| | - Taber S. Lewis
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Corey Powers
- The Heart Institute, Cincinnati Children's Medical Center and University of Cincinnati, Cincinnati, Ohio
| | - Zaza Khuchua
- The Heart Institute, Cincinnati Children's Medical Center and University of Cincinnati, Cincinnati, Ohio
| | - Christopher P. Baines
- Department of Biomedical Sciences, University of Missouri-Columbia, Columbia, Missouri
| | - Peter Wipf
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Sabzali Javadov
- Department of Physiology, University of Puerto Rico School of Medicine, San Juan, Puerto Rico
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26
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Takabayashi A, Takabayashi S, Takahashi K, Watanabe M, Uchida H, Murakami A, Fujita T, Ikeuchi M, Tanaka A. PCoM-DB Update: A Protein Co-Migration Database for Photosynthetic Organisms. PLANT & CELL PHYSIOLOGY 2017; 58:e10. [PMID: 28011869 DOI: 10.1093/pcp/pcw219] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 12/01/2016] [Indexed: 05/29/2023]
Abstract
The identification of protein complexes is important for the understanding of protein structure and function and the regulation of cellular processes. We used blue-native PAGE and tandem mass spectrometry to identify protein complexes systematically, and built a web database, the protein co-migration database (PCoM-DB, http://pcomdb.lowtem.hokudai.ac.jp/proteins/top), to provide prediction tools for protein complexes. PCoM-DB provides migration profiles for any given protein of interest, and allows users to compare them with migration profiles of other proteins, showing the oligomeric states of proteins and thus identifying potential interaction partners. The initial version of PCoM-DB (launched in January 2013) included protein complex data for Synechocystis whole cells and Arabidopsis thaliana thylakoid membranes. Here we report PCoM-DB version 2.0, which includes new data sets and analytical tools. Additional data are included from whole cells of the pelagic marine picocyanobacterium Prochlorococcus marinus, the thermophilic cyanobacterium Thermosynechococcus elongatus, the unicellular green alga Chlamydomonas reinhardtii and the bryophyte Physcomitrella patens. The Arabidopsis protein data now include data for intact mitochondria, intact chloroplasts, chloroplast stroma and chloroplast envelopes. The new tools comprise a multiple-protein search form and a heat map viewer for protein migration profiles. Users can compare migration profiles of a protein of interest among different organelles or compare migration profiles among different proteins within the same sample. For Arabidopsis proteins, users can compare migration profiles of a protein of interest with putative homologous proteins from non-Arabidopsis organisms. The updated PCoM-DB will help researchers find novel protein complexes and estimate their evolutionary changes in the green lineage.
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Affiliation(s)
- Atsushi Takabayashi
- Institute of Low Temperature Science, Hokkaido University, Kita-ku, Sapporo, Japan
- CREST, JST, Kita-ku, Sapporo, Japan
| | - Saeka Takabayashi
- Institute of Low Temperature Science, Hokkaido University, Kita-ku, Sapporo, Japan
- Department of Public Health, Graduate School of Medicine Hokkaido University, Kita-ku, Sapporo, Japan
| | - Kaori Takahashi
- Institute of Low Temperature Science, Hokkaido University, Kita-ku, Sapporo, Japan
| | - Mai Watanabe
- Department of Life Sciences, Graduate School of Arts and Sciences, University of Tokyo, Tokyo, Japan
| | - Hiroko Uchida
- Kobe University Research Center for Inland Seas, Awaji, Japan
| | - Akio Murakami
- Kobe University Research Center for Inland Seas, Awaji, Japan
| | - Tomomichi Fujita
- Faculty of Science, Hokkaido University, N10 W8 Kita-ku, Sapporo 060-0810, Japan Tokyo, Tokyo, Japan
| | - Masahiko Ikeuchi
- Department of Life Sciences, Graduate School of Arts and Sciences, University of Tokyo, Tokyo, Japan
| | - Ayumi Tanaka
- Institute of Low Temperature Science, Hokkaido University, Kita-ku, Sapporo, Japan
- CREST, JST, Kita-ku, Sapporo, Japan
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27
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Gerber S, Ding MG, Gérard X, Zwicker K, Zanlonghi X, Rio M, Serre V, Hanein S, Munnich A, Rotig A, Bianchi L, Amati-Bonneau P, Elpeleg O, Kaplan J, Brandt U, Rozet JM. Compound heterozygosity for severe and hypomorphic NDUFS2 mutations cause non-syndromic LHON-like optic neuropathy. J Med Genet 2016; 54:346-356. [PMID: 28031252 DOI: 10.1136/jmedgenet-2016-104212] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 11/29/2016] [Accepted: 12/01/2016] [Indexed: 11/03/2022]
Abstract
BACKGROUND Non-syndromic hereditary optic neuropathy (HON) has been ascribed to mutations in mitochondrial fusion/fission dynamics genes, nuclear and mitochondrial DNA-encoded respiratory enzyme genes or nuclear genes of poorly known mitochondrial function. However, the disease causing gene remains unknown in many families. The objective of the present study was to identify the molecular cause of non-syndromic LHON-like disease in siblings born to non-consanguineous parents of French origin. METHODS We used a combination of genetic analysis (gene mapping and whole-exome sequencing) in a multiplex family of non-syndromic HON and of functional analyses in patient-derived cultured skin fibroblasts and the yeast Yarrowia lipolytica. RESULTS We identified compound heterozygote NDUFS2 disease-causing mutations (p.Tyr53Cys; p.Tyr308Cys). Studies using patient-derived cultured skin fibroblasts revealed mildly decreased NDUFS2 and complex I abundance but apparently normal respiratory chain activity. In the yeast Y. lipolytica ortholog NUCM, the mutations resulted in absence of complex I and moderate reduction in nicotinamide adenine dinucleotide-ubiquinone oxidoreductase activity, respectively. CONCLUSIONS Biallelism for NDUFS2 mutations causing severe complex I deficiency has been previously reported to cause Leigh syndrome with optic neuropathy. Our results are consistent with the view that compound heterozygosity for severe and hypomorphic NDUFS2 mutations can cause non-syndromic HON. This observation suggests a direct correlation between the severity of NDUFS2 mutations and that of the disease and further support that there exist a genetic overlap between non-syndromic and syndromic HON due to defective mitochondrial function.
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Affiliation(s)
- Sylvie Gerber
- Laboratory of Genetics in Ophthalmology (LGO), INSERM UMR1163, Institute of Genetic Diseases, Imagine, Paris Descartes University, Paris, France
| | - Martina G Ding
- Molecular Bioenergetics Group, Goethe-University Medical School, Frankfurt am Main, Germany
| | - Xavier Gérard
- Laboratory of Genetics in Ophthalmology (LGO), INSERM UMR1163, Institute of Genetic Diseases, Imagine, Paris Descartes University, Paris, France
| | - Klaus Zwicker
- Institute of Biochemistry I, Goethe-University Medical School, Frankfurt am Main, Germany
| | | | - Marlène Rio
- Department of Genetics, Necker Hospital, Paris, France
| | - Valérie Serre
- UMR7592 CNRS, Jacques Monod Institute, Paris Diderot University, Paris, France.,Laboratory of Genetics in Mitochondrial Diseases, INSERM UMR1163, Institute of Genetic Diseases, Imagine, Paris Descartes University, Paris, France
| | - Sylvain Hanein
- Laboratory of Genetics in Ophthalmology (LGO), INSERM UMR1163, Institute of Genetic Diseases, Imagine, Paris Descartes University, Paris, France
| | | | - Agnès Rotig
- Laboratory of Genetics in Mitochondrial Diseases, INSERM UMR1163, Institute of Genetic Diseases, Imagine, Paris Descartes University, Paris, France
| | - Lucas Bianchi
- Laboratory of Genetics in Mitochondrial Diseases, INSERM UMR1163, Institute of Genetic Diseases, Imagine, Paris Descartes University, Paris, France
| | - Patrizia Amati-Bonneau
- Department of Biochemistry and Genetics, UMR CNRS 6214-INSERM U1083, CHU Angers, Angers, France
| | - Orly Elpeleg
- Monique and Jacques Roboh Department of Genetic Research, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Josseline Kaplan
- Laboratory of Genetics in Ophthalmology (LGO), INSERM UMR1163, Institute of Genetic Diseases, Imagine, Paris Descartes University, Paris, France
| | - Ulrich Brandt
- Radboud Center for Mitochondrial Medicine (RCMM), Radboud University Medical Center, Nijmegen, The Netherlands.,Cluster of Excellence Frankfurt Macromolecular Complexes, Goethe-University, Frankfurt am Main, Germany
| | - Jean-Michel Rozet
- Laboratory of Genetics in Ophthalmology (LGO), INSERM UMR1163, Institute of Genetic Diseases, Imagine, Paris Descartes University, Paris, France
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28
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Wöhlbrand L, Ruppersberg HS, Feenders C, Blasius B, Braun HP, Rabus R. Analysis of membrane-protein complexes of the marine sulfate reducer Desulfobacula toluolica Tol2 by 1D blue native-PAGE complexome profiling and 2D blue native-/SDS-PAGE. Proteomics 2016; 16:973-88. [PMID: 26792001 DOI: 10.1002/pmic.201500360] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 12/16/2015] [Accepted: 12/30/2015] [Indexed: 02/03/2023]
Abstract
Sulfate-reducing bacteria (SRB) obtain energy from cytoplasmic reduction of sulfate to sulfide involving APS-reductase (AprAB) and dissimilatory sulfite reductase (DsrAB). These enzymes are predicted to obtain electrons from membrane redox complexes, i.e. the quinone-interacting membrane-bound oxidoreductase (QmoABC) and DsrMKJOP complexes. In addition to these conserved complexes, the genomes of SRB encode a large number of other (predicted) membrane redox complexes, the function and actual formation of which is unknown. This study reports the establishment of 1D Blue Native-PAGE complexome profiling and 2D BN-/SDS-PAGE for analysis of the membrane protein complexome of the marine sulfate reducer Desulfobacula toluolica Tol2. Analysis of normalized score profiles of >800 proteins in combination with hierarchical clustering and identification of 2D BN-/SDS-PAGE separated spots demonstrated separation of membrane complexes in their native form, e.g. ATP synthase. In addition to the QmoABC and DsrMKJOP complexes, other complexes were detected that constitute the basic membrane complexome of D. toluolica Tol2, e.g. transport proteins (e.g. sodium/sulfate symporters) or redox complexes involved in Na(+) -based bioenergetics (RnfABCDEG). Notably, size estimation indicates dimer and quadruple formation of the DsrMKJOP complex in vivo. Furthermore, cluster analysis suggests interaction of this complex with a rhodanese-like protein (Tol2_C05230) possibly representing a periplasmic electron transfer partner for DsrMKJOP.
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Affiliation(s)
- Lars Wöhlbrand
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Oldenburg, Germany
| | - Hanna S Ruppersberg
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Oldenburg, Germany
| | - Christoph Feenders
- Mathematical Modelling, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Oldenburg, Germany
| | - Bernd Blasius
- Mathematical Modelling, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Oldenburg, Germany
| | - Hans-Peter Braun
- Plant Proteomics, Institute of Plant Genetics, Leibniz University Hannover, Hannover, Germany
| | - Ralf Rabus
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Oldenburg, Germany
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29
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Moreno-Loshuertos R, Enríquez JA. Respiratory supercomplexes and the functional segmentation of the CoQ pool. Free Radic Biol Med 2016; 100:5-13. [PMID: 27105951 DOI: 10.1016/j.freeradbiomed.2016.04.018] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Revised: 04/15/2016] [Accepted: 04/17/2016] [Indexed: 12/14/2022]
Abstract
The evidence accumulated during the last fifteen years on the existence of respiratory supercomplexes and their proposed functional implications has changed our understanding of the OXPHOS system complexity and regulation. The plasticity model is a point of encounter accounting for the apparently contradictory experimental observations claimed to support either the solid or the fluid models. It allows the explanation of previous observations such as the dependence between respiratory complexes, supercomplex assembly dynamics or the existence of different functional ubiquinone pools. With the general acceptation of respiratory supercomplexes as true entities, this review evaluates the supporting evidences in favor or against the existence of different ubiquinone pools and the relationship between supercomplexes, ROS production and pathology.
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Affiliation(s)
- Raquel Moreno-Loshuertos
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Pedro Cerbuna, 12, Zaragoza 50009, Spain
| | - José Antonio Enríquez
- Centro Nacional de Investigaciones Cardiovasculares Carlos III, Melchor Fernández Almagro, 3, 28029 Madrid, Spain; Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Pedro Cerbuna, 12, Zaragoza 50009, Spain.
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30
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Rijal R, Arhzaouy K, Strucksberg KH, Cross M, Hofmann A, Schröder R, Clemen CS, Eichinger L. Mutant p97 exhibits species-specific changes of its ATPase activity and compromises the UBXD9-mediated monomerisation of p97 hexamers. Eur J Cell Biol 2016; 95:195-207. [PMID: 27132113 DOI: 10.1016/j.ejcb.2016.03.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 03/22/2016] [Accepted: 03/29/2016] [Indexed: 11/17/2022] Open
Abstract
p97 (VCP) is a homo-hexameric triple-A ATPase that exerts a plethora of cellular processes. Heterozygous missense mutations of p97 cause at least five human neurodegenerative disorders. However, the specific molecular consequences of p97 mutations are hitherto widely unknown. Our in silico structural models of human and Dictyostelium p97 showed that the disease-causing human R93C, R155H, and R155C as well as Dictyostelium R154C, E219K, R154C/E219K p97 mutations constitute variations in surface-exposed locations. In-gel ATPase activity measurements of p97 monomers and hexamers revealed significant mutation- and species-specific differences. While all human p97 mutations led to an increase in ATPase activity, no changes could be detected for the Dictyostelium R154C mutant, which is orthologous to human R155C. The E219K mutation led to an almost complete loss of activity, which was partially recuperated in the R154C/E219K double-mutant indicating p97 inter-domain communication. By means of co-immunoprecipitation experiments we identified an UBX-domain containing Dictyostelium protein as a novel p97 interaction partner. We categorized all UBX-domain containing Dictyostelium proteins and named the interaction partner UBXD9. Pull-down assays and surface plasmon resonance analyses of Dictyostelium UBXD9 or the human orthologue TUG/ASPL/UBXD9 demonstrated direct interactions with p97 as well as species-, mutation- and ATP-dependent differences in the binding affinities. Sucrose density gradient assays revealed that both human and Dictyostelium UBXD9 proteins very efficiently disassembled wild-type, but to a lesser extent mutant p97 hexamers into monomers. Our results are consistent with a scenario in which p97 point mutations lead to differences in enzymatic activities and molecular interactions, which in the long-term result in a late-onset and progressive multisystem disease.
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Affiliation(s)
- Ramesh Rijal
- Centre for Biochemistry, Institute of Biochemistry I, Medical Faculty, University of Cologne, 50931 Cologne, Germany
| | - Khalid Arhzaouy
- Centre for Biochemistry, Institute of Biochemistry I, Medical Faculty, University of Cologne, 50931 Cologne, Germany
| | - Karl-Heinz Strucksberg
- Centre for Biochemistry, Institute of Biochemistry I, Medical Faculty, University of Cologne, 50931 Cologne, Germany
| | - Megan Cross
- Structural Chemistry Program, Eskitis Institute, Griffith University, Brisbane, Queensland 4111, Australia
| | - Andreas Hofmann
- Structural Chemistry Program, Eskitis Institute, Griffith University, Brisbane, Queensland 4111, Australia; Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3030, Australia
| | - Rolf Schröder
- Institute of Neuropathology, University Hospital Erlangen, 91054 Erlangen, Germany
| | - Christoph S Clemen
- Centre for Biochemistry, Institute of Biochemistry I, Medical Faculty, University of Cologne, 50931 Cologne, Germany.
| | - Ludwig Eichinger
- Centre for Biochemistry, Institute of Biochemistry I, Medical Faculty, University of Cologne, 50931 Cologne, Germany.
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Wessels HJCT, de Almeida NM, Kartal B, Keltjens JT. Bacterial Electron Transfer Chains Primed by Proteomics. Adv Microb Physiol 2016; 68:219-352. [PMID: 27134025 DOI: 10.1016/bs.ampbs.2016.02.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Electron transport phosphorylation is the central mechanism for most prokaryotic species to harvest energy released in the respiration of their substrates as ATP. Microorganisms have evolved incredible variations on this principle, most of these we perhaps do not know, considering that only a fraction of the microbial richness is known. Besides these variations, microbial species may show substantial versatility in using respiratory systems. In connection herewith, regulatory mechanisms control the expression of these respiratory enzyme systems and their assembly at the translational and posttranslational levels, to optimally accommodate changes in the supply of their energy substrates. Here, we present an overview of methods and techniques from the field of proteomics to explore bacterial electron transfer chains and their regulation at levels ranging from the whole organism down to the Ångstrom scales of protein structures. From the survey of the literature on this subject, it is concluded that proteomics, indeed, has substantially contributed to our comprehending of bacterial respiratory mechanisms, often in elegant combinations with genetic and biochemical approaches. However, we also note that advanced proteomics offers a wealth of opportunities, which have not been exploited at all, or at best underexploited in hypothesis-driving and hypothesis-driven research on bacterial bioenergetics. Examples obtained from the related area of mitochondrial oxidative phosphorylation research, where the application of advanced proteomics is more common, may illustrate these opportunities.
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Affiliation(s)
- H J C T Wessels
- Nijmegen Center for Mitochondrial Disorders, Radboud Proteomics Centre, Translational Metabolic Laboratory, Radboud University Medical Center, Nijmegen, The Netherlands
| | - N M de Almeida
- Institute of Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - B Kartal
- Institute of Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands; Laboratory of Microbiology, Ghent University, Ghent, Belgium
| | - J T Keltjens
- Institute of Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands.
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Killinger BA, Moszczynska A. Characterization of α-Synuclein Multimer Stoichiometry in Complex Biological Samples by Electrophoresis. Anal Chem 2016; 88:4071-84. [PMID: 26937787 PMCID: PMC4898865 DOI: 10.1021/acs.analchem.6b00419] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
![]()
The
aberrant aggregation of α-synuclein in the brain is a
hallmark of Parkinson’s disease (PD). In vivo soluble α-synuclein
occurs as a monomer and several multimers, the latter of which may
be important for the biological function of α-synuclein. Currently,
there is a lack of reproducible methods to compare α-synuclein
multimer abundance between complex biological samples. Here we developed
a method, termed “multimer-PAGE,” that combines in-gel
chemical cross-linking with several common electrophoretic techniques
to measure the stoichiometry of soluble α-synuclein multimers
in brain tissue lysates. Results show that soluble α-synuclein
from the rat brain exists as several high molecular weight species
of approximately 56 kDa (αS56), 80 kDa (αS80), and 100
kDa (αS100) that comigrate with endogenous lipids, detergents,
and/or micelles during blue native gel electrophoresis (BN-PAGE).
Co-extraction of endogenous lipids with α-synuclein was essential
for the detection of soluble α-synuclein multimers. Homogenization
of brain tissue in small buffer volumes (>50 mg tissue per 1 mL
buffer)
increased relative lipid extraction and subsequently resulted in abundant
soluble multimer detection via multimer-PAGE. α-Synuclein multimers
captured by directly cross-linking soluble lysates resembled those
observed following multimer-PAGE. The ratio of multimer (αS80)
to monomer (αS17) increased linearly with protein input into
multimer-PAGE, suggesting to some extent, multimers were also formed
during electrophoresis. Overall, soluble α-synuclein maintains
lipid interactions following tissue disruption and readily forms multimers
when this lipid–protein complex is preserved. Once the multimer-PAGE
technique was validated, relative stoichiometric comparisons could
be conducted simultaneously between 14 biological samples. Multimer-PAGE
provides a simple inexpensive biochemical technique to study the molecular
factors influencing α-synuclein multimerization.
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Affiliation(s)
- Bryan A Killinger
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University , 259 Mack Avenue, Detroit, Michigan 48201, United States
| | - Anna Moszczynska
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University , 259 Mack Avenue, Detroit, Michigan 48201, United States
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Michaud M, Gros V, Tardif M, Brugière S, Ferro M, Prinz WA, Toulmay A, Mathur J, Wozny M, Falconet D, Maréchal E, Block MA, Jouhet J. AtMic60 Is Involved in Plant Mitochondria Lipid Trafficking and Is Part of a Large Complex. Curr Biol 2016; 26:627-39. [PMID: 26898467 DOI: 10.1016/j.cub.2016.01.011] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 12/08/2015] [Accepted: 01/04/2016] [Indexed: 12/22/2022]
Abstract
The mitochondrion is an organelle originating from an endosymbiotic event and playing a role in several fundamental processes such as energy production, metabolite syntheses, and programmed cell death. This organelle is delineated by two membranes whose synthesis requires an extensive exchange of phospholipids with other cellular organelles such as endoplasmic reticulum (ER) and vacuolar membranes in yeast. These transfers of phospholipids are thought to occur by a non-vesicular pathway at contact sites between two closely apposed membranes. In plants, little is known about the biogenesis of mitochondrial membranes. Contact sites between ER and mitochondria are suspected to play a similar role in phospholipid trafficking as in yeast, but this has never been demonstrated. In contrast, it has been shown that plastids are able to transfer lipids to mitochondria during phosphate starvation. However, the proteins involved in such transfer are still unknown. Here, we identified in Arabidopsis thaliana a large lipid-enriched complex called the mitochondrial transmembrane lipoprotein (MTL) complex. The MTL complex contains proteins located in the two mitochondrial membranes and conserved in all eukaryotic cells, such as the TOM complex and AtMic60, a component of the MICOS complex. We demonstrate that AtMic60 contributes to the export of phosphatidylethanolamine from mitochondria and the import of galactoglycerolipids from plastids during phosphate starvation. Furthermore, AtMic60 promotes lipid desorption from membranes, likely as an initial step for lipid transfer, and binds to Tom40, suggesting that AtMic60 could regulate the tethering between the inner and outer membranes of mitochondria.
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Affiliation(s)
- Morgane Michaud
- Laboratoire de Physiologie Cellulaire et Végétale, UMR 5168 CNRS-CEA-INRA-Université Grenoble Alpes, 38000 Grenoble, France.
| | - Valérie Gros
- Laboratoire de Physiologie Cellulaire et Végétale, UMR 5168 CNRS-CEA-INRA-Université Grenoble Alpes, 38000 Grenoble, France
| | - Marianne Tardif
- Laboratoire de Biologie à Grande Echelle, U1038 CEA-INSERM-Université Grenoble Alpes, 38000 Grenoble, France
| | - Sabine Brugière
- Laboratoire de Biologie à Grande Echelle, U1038 CEA-INSERM-Université Grenoble Alpes, 38000 Grenoble, France
| | - Myriam Ferro
- Laboratoire de Biologie à Grande Echelle, U1038 CEA-INSERM-Université Grenoble Alpes, 38000 Grenoble, France
| | - William A Prinz
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD 20892, USA
| | - Alexandre Toulmay
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD 20892, USA
| | - Jaideep Mathur
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Michael Wozny
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Denis Falconet
- Laboratoire de Physiologie Cellulaire et Végétale, UMR 5168 CNRS-CEA-INRA-Université Grenoble Alpes, 38000 Grenoble, France
| | - Eric Maréchal
- Laboratoire de Physiologie Cellulaire et Végétale, UMR 5168 CNRS-CEA-INRA-Université Grenoble Alpes, 38000 Grenoble, France
| | - Maryse A Block
- Laboratoire de Physiologie Cellulaire et Végétale, UMR 5168 CNRS-CEA-INRA-Université Grenoble Alpes, 38000 Grenoble, France
| | - Juliette Jouhet
- Laboratoire de Physiologie Cellulaire et Végétale, UMR 5168 CNRS-CEA-INRA-Université Grenoble Alpes, 38000 Grenoble, France.
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Singh M, Metwal M, Kumar VA, Kumar A. Identification and molecular characterization of 48 kDa calcium binding protein as calreticulin from finger millet (Eleusine coracana) using peptide mass fingerprinting and transcript profiling. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2016; 96:672-9. [PMID: 25684084 DOI: 10.1002/jsfa.7139] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Revised: 01/31/2015] [Accepted: 02/12/2015] [Indexed: 05/10/2023]
Abstract
BACKGROUND Attempts were made to identify and characterize the calcium binding proteins (CaBPs) in grain filling stages of finger millet using proteomics, bioinformatics and molecular approaches. RESULTS A distinctly observed blue color band of 48 kDa stained by Stains-all was eluted and analyzed as calreticulin (CRT) using nano liquid chromatography-tandem mass spectrometry (nano LC-MS). Based on the top hits of peptide mass fingerprinting results, conserved primers were designed for isolation of the CRT gene from finger millet using calreticulin sequences of different cereals. The deduced nucleotide sequence analysis of 600 bp amplicon showed up to 91% similarity with CRT gene(s) of rice and other plant species and designated as EcCRT1. Transcript profiling of EcCRT1 showed different levels of relative expression at different stages of developing spikes. The higher expression of EcCRT1 transcripts and protein were observed in later stages of developing spikes which might be due to greater translational synthesis of EcCRT1 protein during seed maturation in finger millet. CONCLUSIONS Preferentially higher synthesis of this CaBP during later stages of grain filling may be responsible for the sequestration of calcium in endoplasmic reticulum of finger millet grains.
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Affiliation(s)
- Manoj Singh
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, GB Pant University of Agriculture and Technology, Pantnagar, 63145, Udham Singh Nagar, India
| | - Mamta Metwal
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, GB Pant University of Agriculture and Technology, Pantnagar, 63145, Udham Singh Nagar, India
| | - Vandana A Kumar
- Department of Biochemistry, College of Basic Sciences and Humanities, GB Pant University of Agriculture and Technology, Pantnagar, 63145, Udham Singh Nagar, India
| | - Anil Kumar
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, GB Pant University of Agriculture and Technology, Pantnagar, 63145, Udham Singh Nagar, India
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35
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Midzak A, Papadopoulos V. Adrenal Mitochondria and Steroidogenesis: From Individual Proteins to Functional Protein Assemblies. Front Endocrinol (Lausanne) 2016; 7:106. [PMID: 27524977 PMCID: PMC4965458 DOI: 10.3389/fendo.2016.00106] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 07/18/2016] [Indexed: 12/13/2022] Open
Abstract
The adrenal cortex is critical for physiological function as the central site of glucocorticoid and mineralocorticoid synthesis. It possesses a great degree of specialized compartmentalization at multiple hierarchical levels, ranging from the tissue down to the molecular levels. In this paper, we discuss this functionalization, beginning with the tissue zonation of the adrenal cortex and how this impacts steroidogenic output. We then discuss the cellular biology of steroidogenesis, placing special emphasis on the mitochondria. Mitochondria are classically known as the "powerhouses of the cell" for their central role in respiratory adenosine triphosphate synthesis, and attention is given to mitochondrial electron transport, in both the context of mitochondrial respiration and mitochondrial steroid metabolism. Building on work demonstrating functional assembly of large protein complexes in respiration, we further review research demonstrating a role for multimeric protein complexes in mitochondrial cholesterol transport, steroidogenesis, and mitochondria-endoplasmic reticulum contact. We aim to highlight with this review the shift in steroidogenic cell biology from a focus on the actions of individual proteins in isolation to the actions of protein assemblies working together to execute cellular functions.
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Affiliation(s)
- Andrew Midzak
- Research Institute of the McGill University, Montreal, QC, Canada
- *Correspondence: Andrew Midzak, ; Vassilios Papadopoulos,
| | - Vassilios Papadopoulos
- Research Institute of the McGill University, Montreal, QC, Canada
- Department of Biochemistry, McGill University, Montreal, QC, Canada
- Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada
- *Correspondence: Andrew Midzak, ; Vassilios Papadopoulos,
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36
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Bode D, Yu L, Tate P, Pardo M, Choudhary J. Characterization of Two Distinct Nucleosome Remodeling and Deacetylase (NuRD) Complex Assemblies in Embryonic Stem Cells. Mol Cell Proteomics 2015; 15:878-91. [PMID: 26714524 PMCID: PMC4813707 DOI: 10.1074/mcp.m115.053207] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Indexed: 11/26/2022] Open
Abstract
Pluripotency and self-renewal, the defining properties of embryonic stem cells, are brought about by transcriptional programs involving an intricate network of transcription factors and chromatin remodeling complexes. The Nucleosome Remodeling and Deacetylase (NuRD) complex plays a crucial and dynamic role in the regulation of stemness and differentiation. Several NuRD-associated factors have been reported but how they are organized has not been investigated in detail. Here, we have combined affinity purification and blue native polyacrylamide gel electrophoresis followed by protein identification by mass spectrometry and protein correlation profiling to characterize the topology of the NuRD complex. Our data show that in mouse embryonic stem cells the NuRD complex is present as two distinct assemblies of differing topology with different binding partners. Cell cycle regulator Cdk2ap1 and transcription factor Sall4 associate only with the higher mass NuRD assembly. We further establish that only isoform Sall4a, and not Sall4b, associates with NuRD. By contrast, Suz12, a component of the PRC2 Polycomb repressor complex, associates with the lower mass entity. In addition, we identify and validate a novel NuRD-associated protein, Wdr5, a regulatory subunit of the MLL histone methyltransferase complex, which associates with both NuRD entities. Bioinformatic analyses of published target gene sets of these chromatin binding proteins are in agreement with these structural observations. In summary, this study provides an interesting insight into mechanistic aspects of NuRD function in stem cell biology. The relevance of our work has broader implications because of the ubiquitous nature of the NuRD complex. The strategy described here can be more broadly applicable to investigate the topology of the multiple complexes an individual protein can participate in.
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Affiliation(s)
- Daniel Bode
- From the ‡Proteomic Mass Spectrometry, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Lu Yu
- From the ‡Proteomic Mass Spectrometry, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Peri Tate
- §Stem Cell Engineering, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Mercedes Pardo
- From the ‡Proteomic Mass Spectrometry, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK;
| | - Jyoti Choudhary
- From the ‡Proteomic Mass Spectrometry, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
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37
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Schneider J, Mielich-Süss B, Böhme R, Lopez D. In vivo characterization of the scaffold activity of flotillin on the membrane kinase KinC of Bacillus subtilis. MICROBIOLOGY-SGM 2015; 161:1871-1887. [PMID: 26297017 DOI: 10.1099/mic.0.000137] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Scaffold proteins are ubiquitous chaperones that bind to proteins and facilitate the physical interaction of the components of signal transduction pathways or multi-enzymic complexes. In this study, we used a biochemical approach to dissect the molecular mechanism of a membrane-associated scaffold protein, FloT, a flotillin-homologue protein that is localized in functional membrane microdomains of the bacterium Bacillus subtilis. This study provides unambiguous evidence that FloT physically binds to and interacts with the membrane-bound sensor kinase KinC. This sensor kinase activates biofilm formation in B. subtilis in response to the presence of the self-produced signal surfactin. Furthermore, we have characterized the mechanism by which the interaction of FloT with KinC benefits the activity of KinC. Two separate and synergistic effects constitute this mechanism: first, the scaffold activity of FloT promotes more efficient self-interaction of KinC and facilitates dimerization into its active form. Second, the selective binding of FloT to KinC prevents the occurrence of unspecific aggregation between KinC and other proteins that may generate dead-end intermediates that could titrate the activity of KinC. Flotillin proteins appear to play an important role in prokaryotes in promoting effective binding of signalling proteins with their correct protein partners.
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Affiliation(s)
- Johannes Schneider
- Research Centre for Infectious Diseases (ZINF), University of Würzburg, Würzburg 97080, Germany
- Institute for Molecular Infection Biology (IMIB), University of Würzburg, Würzburg 97080, Germany
| | - Benjamin Mielich-Süss
- Research Centre for Infectious Diseases (ZINF), University of Würzburg, Würzburg 97080, Germany
- Institute for Molecular Infection Biology (IMIB), University of Würzburg, Würzburg 97080, Germany
| | - Richard Böhme
- Research Centre for Infectious Diseases (ZINF), University of Würzburg, Würzburg 97080, Germany
- Institute for Molecular Infection Biology (IMIB), University of Würzburg, Würzburg 97080, Germany
| | - Daniel Lopez
- Institute for Molecular Infection Biology (IMIB), University of Würzburg, Würzburg 97080, Germany
- National Center for Biotechnology (CNB), Spanish Research Council (CSIC), Madrid 28050, Spain
- Research Centre for Infectious Diseases (ZINF), University of Würzburg, Würzburg 97080, Germany
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38
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D'Haene SE, Sobotka R, Bučinská L, Dekker JP, Komenda J. Interaction of the PsbH subunit with a chlorophyll bound to histidine 114 of CP47 is responsible for the red 77K fluorescence of Photosystem II. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1847:1327-34. [PMID: 26164101 DOI: 10.1016/j.bbabio.2015.07.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 07/03/2015] [Accepted: 07/07/2015] [Indexed: 10/23/2022]
Abstract
A characteristic feature of the active Photosystem II (PSII) complex is a red-shifted low temperature fluorescence emission at about 693nm. The origin of this emission has been attributed to a monomeric 'red' chlorophyll molecule located in the CP47 subunit. However, the identity and function of this chlorophyll remain uncertain. In our previous work, we could not detect the red PSII emission in a mutant of the cyanobacterium Synechocystis sp. PCC 6803 lacking PsbH, a small transmembrane subunit bound to CP47. However, it has not been clear whether the PsbH is structurally essential for the red emission or the observed effect of mutation has been indirectly caused by compromised PSII stability and function. In the present work we performed a detailed spectroscopic characterization of PSII in cells of a mutant lacking PsbH and Photosystem I and we also characterized PSII core complexes isolated from this mutant. In addition, we purified and characterized the CP47 assembly modules containing and lacking PsbH. The results clearly confirm an essential role of PsbH in the origin of the PSII red emission and also demonstrate that PsbH stabilizes the binding of one β-carotene molecule in PSII. Crystal structures of the cyanobacterial PSII show that PsbH directly interacts with a single monomeric chlorophyll ligated by the histidine 114 residue of CP47 and we conclude that this peripheral chlorophyll hydrogen-bonded to PsbH is responsible for the red fluorescence state of CP47. Given the proximity of β-carotene this state could participate in the dissipation of excessive light energy.
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Affiliation(s)
- Sandrine E D'Haene
- Biophysics of Photosynthesis/Physics of Energy, Department of Physics and Astronomy, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1081, Amsterdam 1081 HV, The Netherlands.
| | - Roman Sobotka
- Institute of Microbiology, Laboratory of Photosynthesis, Centre Algatech, Opatovický mlýn, 379 81 Třeboň, Czech Republic; Faculty of Science, University of South Bohemia, Branišovská 31, České Budějovice, Czech Republic
| | - Lenka Bučinská
- Institute of Microbiology, Laboratory of Photosynthesis, Centre Algatech, Opatovický mlýn, 379 81 Třeboň, Czech Republic; Faculty of Science, University of South Bohemia, Branišovská 31, České Budějovice, Czech Republic
| | - Jan P Dekker
- Biophysics of Photosynthesis/Physics of Energy, Department of Physics and Astronomy, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1081, Amsterdam 1081 HV, The Netherlands
| | - Josef Komenda
- Institute of Microbiology, Laboratory of Photosynthesis, Centre Algatech, Opatovický mlýn, 379 81 Třeboň, Czech Republic; Faculty of Science, University of South Bohemia, Branišovská 31, České Budějovice, Czech Republic
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39
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Yang JH, Sarrou I, Martin-Garcia JM, Zhang S, Redding KE, Fromme P. Purification and biochemical characterization of the ATP synthase from Heliobacterium modesticaldum. Protein Expr Purif 2015; 114:1-8. [PMID: 25979464 DOI: 10.1016/j.pep.2015.05.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 04/28/2015] [Accepted: 05/06/2015] [Indexed: 11/26/2022]
Abstract
Heliobacterium modesticaldum is an anaerobic photosynthetic bacterium that grows optimally at pH 6-7 and 52°C and is the only phototrophic member of the Firmicutes phylum family (gram-positive bacteria with low GC content). The ATP synthase of H. modesticaldum was isolated and characterized at the biochemical and biophysical levels. The isolated holoenzyme exhibited the subunit patterns of F-type ATP synthases containing a 5-subunit hydrophilic F1 subcomplex and a 3-subunit hydrophobic F0 subcomplex. ATP hydrolysis by the isolated HF1F0 ATP synthase was successfully detected after pretreatment with different detergents by an in-gel ATPase activity assay, which showed that the highest activity was detected in the presence of mild detergents such as LDAO; moreover, high catalytic activity in the gel was already detected after the initial incubation period of 0.5h. In contrast, HF1F0 showed extremely low ATPase activity in harsher detergents such as TODC. The isolated fully functional enzyme will form the basis for future structural studies.
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Affiliation(s)
- Jay-How Yang
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287-1604, USA; Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Iosifina Sarrou
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287-1604, USA; Institute of Molecular Biology & Biotechnology, Foundation for Research & Technology-Hellas, Nikolaou Plastira 100, GR-70013 Heraklion, Crete, Greece
| | - Jose M Martin-Garcia
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287-1604, USA; Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Shangji Zhang
- School of Life Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Kevin E Redding
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Petra Fromme
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287-1604, USA; Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ 85287-1604, USA.
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40
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Boelt SG, Houen G, Højrup P. Agarose gel shift assay reveals that calreticulin favors substrates with a quaternary structure in solution. Anal Biochem 2015; 481:33-42. [PMID: 25908558 DOI: 10.1016/j.ab.2015.04.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Revised: 04/13/2015] [Accepted: 04/13/2015] [Indexed: 10/23/2022]
Abstract
Here we present an agarose gel shift assay that, in contrast to other electrophoresis approaches, is loaded in the center of the gel. This allows proteins to migrate in either direction according to their isoelectric points. Therefore, the presented assay enables a direct visualization, separation, and prefractionation of protein interactions in solution independent of isoelectric point. We demonstrate that this assay is compatible with immunochemical methods and mass spectrometry. The assay was used to investigate interactions with several potential substrates for calreticulin, a chaperone that is involved in different biological aspects through interaction with other proteins. The current analytical assays used to investigate these interactions are mainly spectroscopic aggregation assays or solid phase assays that do not provide a direct visualization of the stable protein complex but rather provide an indirect measure of interactions. Therefore, no interaction studies between calreticulin and substrates in solution have been investigated previously. The results presented here indicate that calreticulin has a preference for substrates with a quaternary structure and primarily β-sheets in their secondary structure. It is also demonstrated that the agarose gel shift assay is useful in the study of other protein interactions and can be used as an alternative method to native polyacrylamide gel electrophoresis.
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Affiliation(s)
- Sanne Grundvad Boelt
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense, Denmark; Department of Autoimmunology and Biomarkers, Statens Serum Institut, DK-2300 Copenhagen, Denmark
| | - Gunnar Houen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense, Denmark; Department of Autoimmunology and Biomarkers, Statens Serum Institut, DK-2300 Copenhagen, Denmark
| | - Peter Højrup
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense, Denmark.
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41
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Meisrimler CN, Schwendke A, Lüthje S. Two-dimensional phos-tag zymograms for tracing phosphoproteins by activity in-gel staining. FRONTIERS IN PLANT SCIENCE 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] [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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Almeida AM, Bassols A, Bendixen E, Bhide M, Ceciliani F, Cristobal S, Eckersall PD, Hollung K, Lisacek F, Mazzucchelli G, McLaughlin M, Miller I, Nally JE, Plowman J, Renaut J, Rodrigues P, Roncada P, Staric J, Turk R. Animal board invited review: advances in proteomics for animal and food sciences. Animal 2015; 9:1-17. [PMID: 25359324 PMCID: PMC4301196 DOI: 10.1017/s1751731114002602] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 09/27/2014] [Indexed: 01/15/2023] Open
Abstract
Animal production and health (APH) is an important sector in the world economy, representing a large proportion of the budget of all member states in the European Union and in other continents. APH is a highly competitive sector with a strong emphasis on innovation and, albeit with country to country variations, on scientific research. Proteomics (the study of all proteins present in a given tissue or fluid - i.e. the proteome) has an enormous potential when applied to APH. Nevertheless, for a variety of reasons and in contrast to disciplines such as plant sciences or human biomedicine, such potential is only now being tapped. To counter such limited usage, 6 years ago we created a consortium dedicated to the applications of Proteomics to APH, specifically in the form of a Cooperation in Science and Technology (COST) Action, termed FA1002--Proteomics in Farm Animals: www.cost-faproteomics.org. In 4 years, the consortium quickly enlarged to a total of 31 countries in Europe, as well as Israel, Argentina, Australia and New Zealand. This article has a triple purpose. First, we aim to provide clear examples on the applications and benefits of the use of proteomics in all aspects related to APH. Second, we provide insights and possibilities on the new trends and objectives for APH proteomics applications and technologies for the years to come. Finally, we provide an overview and balance of the major activities and accomplishments of the COST Action on Farm Animal Proteomics. These include activities such as the organization of seminars, workshops and major scientific conferences, organization of summer schools, financing Short-Term Scientific Missions (STSMs) and the generation of scientific literature. Overall, the Action has attained all of the proposed objectives and has made considerable difference by putting proteomics on the global map for animal and veterinary researchers in general and by contributing significantly to reduce the East-West and North-South gaps existing in the European farm animal research. Future activities of significance in the field of scientific research, involving members of the action, as well as others, will likely be established in the future.
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Affiliation(s)
- A. M. Almeida
- Instituto de Investigação Científica Tropical, CVZ – Centro de Veterinária e Zootecnia, Av. Univ. Técnica, 1300-477 Lisboa, Portugal
- CIISA – Centro Interdisciplinar de Investigação em Sanidade Animal, 1300-477 Lisboa, Portugal
- ITQB – Instituto de Tecnologia Química e Biológica da UNL, 2780-157 Oeiras, Portugal
- IBET – Instituto de Biologia Experimental e Tecnológica, 2780-157 Oeiras, Portugal
| | - A. Bassols
- Departament de Bioquímica i Biologia Molecular, Facultat de Veterinària, Universitat Autònoma de Barcelona,08193 Cerdanyola del Vallès, Spain
| | - E. Bendixen
- Institute of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - M. Bhide
- Laboratory of Biomedical Microbiology and Immunology, University of Veterinary Medicine and Pharmacy, Komenskeho-73 Kosice, Slovakia
| | - F. Ceciliani
- Department of Veterinary Science and Public Health, Università di Milano, Via Celoria 10, 20133 Milano, Italy
| | - S. Cristobal
- Department of Clinical and Experimental Medicine, Division of Cell Biology, Faculty of Health Science, Linköping University, SE-581 85 Linköping, Sweden
- IKERBASQUE, Basque Foundation for Science, Department of Physiology, Faculty of Medicine and Dentistry, University of Basque Country,48940 Leioa, Bizkaia, Spain
| | - P. D. Eckersall
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Garscube Estate, Glasgow G61 1QH, UK
| | - K. Hollung
- Nofima AS, PO Box 210, NO-1431 Aas, Norway
| | - F. Lisacek
- Swiss Institute of Bioinformatics, CMU – Rue Michel-Servet 1, 1211 Geneva 4, Switzerland
| | - G. Mazzucchelli
- Mass Spectrometry Laboratory, GIGA-Research, Department of Chemistry, University of Liège, 4000 Liège, Belgium
| | - M. McLaughlin
- Division of Veterinary Bioscience, School of Veterinary Medicine, University of Glasgow, Garscube Estate, Glasgow G61 1QH, UK
| | - I. Miller
- Institute of Medical Biochemistry, University of Veterinary Medicine, Veterinaerplatz 1, A-1210 Vienna, Austria
| | - J. E. Nally
- National Animal Disease Center, Bacterial Diseases of Livestock Research Unit, Agricultural Research Service, United States Department of Agriculture, Ames, IA 50010, USA
| | - J. Plowman
- Food & Bio-Based Products, AgResearch, Lincoln Research Centre, Christchurch 8140, New Zealand
| | - J. Renaut
- Department of Environment and Agrobiotechnologies, Centre de Recherche Public – Gabriel Lippmann, 41 rue du Brill, L-4422 Belvaux, Luxembourg
| | - P. Rodrigues
- CCMAR – Centre of Marine Sciences of Algarve, University of Algarve, Campus de Gambelas, 8005-139 Faro, Portugal
| | - P. Roncada
- Department of Veterinary Science and Public Health, Istituto Sperimentale Italiano L. Spallanzani Milano, University of Milano, 20133 Milano, Italy
| | - J. Staric
- Clinic for Ruminants with Ambulatory Clinic, Veterinary Faculty, University of Ljubljana, Gerbičeva 60, 1000 Ljubljana, Slovenia
| | - R. Turk
- Department of Pathophysiology, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, 10000 Zagreb, Croatia
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Abstract
In recent years, a number of advancements have been made in the study of entire mitochondrial proteomes in both physiological and pathological conditions. Naturally occurring iodothyronines (i.e., T3 and T2) greatly influence mitochondrial oxidative capacity, directly or indirectly affecting the structure and function of the respiratory chain components. Blue native PAGE (BN-PAGE) can be used to isolate enzymatically active oxidative phosphorylation (OXPHOS) complexes in one step, allowing the clinical diagnosis of mitochondrial metabolism by monitoring OXPHOS catalytic and/or structural features. Protocols for isolating mammalian liver mitochondria and subsequent one-dimensional (1D) BN-PAGE will be described in relation to the impact of thyroid hormones on mitochondrial bioenergetics.
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Kim JY, Kwak PB, Gebert M, Duong HA, Weitz CJ. Purification and Analysis of PERIOD Protein Complexes of the Mammalian Circadian Clock. Methods Enzymol 2015; 551:197-210. [DOI: 10.1016/bs.mie.2014.10.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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45
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Chen JJ, Genereux JC, Qu S, Hulleman JD, Shoulders MD, Wiseman RL. ATF6 activation reduces the secretion and extracellular aggregation of destabilized variants of an amyloidogenic protein. CHEMISTRY & BIOLOGY 2014; 21:1564-74. [PMID: 25444553 PMCID: PMC4254654 DOI: 10.1016/j.chembiol.2014.09.009] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Revised: 08/30/2014] [Accepted: 09/08/2014] [Indexed: 12/19/2022]
Abstract
Systemic amyloidoses result from the aberrant secretion of destabilized, amyloidogenic proteins to the serum where they aggregate into proteotoxic soluble aggregates and amyloid fibrils. Few therapeutic approaches exist to attenuate extracellular pathologic aggregation of amyloidogenic proteins, necessitating the development of new strategies to intervene in these devastating disorders. We show that stress-independent activation of the Unfolded Protein Response-associated transcription factor ATF6 increases ER quality control stringency for the amyloidogenic protein transthyretin (TTR), preferentially reducing secretion of disease-associated TTR variants to an extent corresponding to the variants' destabilization of the TTR tetramer. This decrease in destabilized TTR variant secretion attenuates extracellular, concentration-dependent aggregation of amyloidogenic TTRs into soluble aggregates commonly associated with proteotoxicity in disease. Collectively, our results indicate that increasing ER quality control stringency through ATF6 activation is a strategy to attenuate pathologic aggregation of a destabilized, amyloidogenic protein, revealing a potential approach to intervene in systemic amyloid disease pathology.
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Affiliation(s)
- John J Chen
- Department of Molecular and Experimental Medicine and Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Joseph C Genereux
- Department of Molecular and Experimental Medicine and Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Song Qu
- Department of Molecular and Experimental Medicine and Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - John D Hulleman
- Department of Molecular and Experimental Medicine and Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Matthew D Shoulders
- Department of Molecular and Experimental Medicine and Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - R Luke Wiseman
- Department of Molecular and Experimental Medicine and Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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Verma N, Pink M, Petrat F, Rettenmeier AW, Schmitz-Spanke S. Proteomic Analysis of Human Bladder Epithelial Cells by 2D Blue Native SDS-PAGE Reveals TCDD-Induced Alterations of Calcium and Iron Homeostasis Possibly Mediated by Nitric Oxide. J Proteome Res 2014; 14:202-13. [DOI: 10.1021/pr501051f] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Nisha Verma
- Gene
Center, Ludwig-Maximilians-University, Feodor-Lynen-Str. 25, 81377 Munich, Germany
| | - Mario Pink
- Institute
and Outpatient Clinic of Occupational, Social and Environmental Medicine, University of Erlangen-Nuremberg, Schillerstr. 25/29, 91054 Erlangen, Germany
| | | | | | - Simone Schmitz-Spanke
- Institute
and Outpatient Clinic of Occupational, Social and Environmental Medicine, University of Erlangen-Nuremberg, Schillerstr. 25/29, 91054 Erlangen, Germany
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47
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Todd K, Fossati S, Ghiso J, Rostagno A. Mitochondrial dysfunction induced by a post-translationally modified amyloid linked to a familial mutation in an alternative model of neurodegeneration. Biochim Biophys Acta Mol Basis Dis 2014; 1842:2457-67. [PMID: 25261792 DOI: 10.1016/j.bbadis.2014.09.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 09/18/2014] [Accepted: 09/19/2014] [Indexed: 01/25/2023]
Abstract
Familial British dementia (FBD) is an early-onset non-amyloid-β (Aβ) cerebral amyloidosis that presents with severe cognitive decline and strikingly similar neuropathological features to those present in Alzheimer's disease (AD). FBD is associated with a T to A single nucleotide transition in the stop codon of a gene encoding BRI2, leading to the production of an elongated precursor protein. Furin-like proteolytic processing at its C-terminus releases a longer-than-normal 34 amino acid peptide, ABri, exhibiting amyloidogenic properties not seen in its 23 amino acid physiologic counterpart Bri1-23. Deposited ABri exhibits abundant post-translational pyroglutamate (pE) formation at the N-terminus, a feature seen in truncated forms of Aβ found in AD deposits, and co-exists with neurofibrillary tangles almost identical to those found in AD. We tested the impact of the FBD mutation alone and in conjunction with the pE post-translational modification on the structural properties and associated neurotoxicity of the ABri peptide. The presence of pE conferred to the ABri molecule enhanced hydrophobicity and accelerated aggregation/fibrillization properties. ABri pE was capable of triggering oxidative stress, loss of mitochondrial membrane potential and activation of caspase-mediated apoptotic mechanisms in neuronal cells, whereas homologous peptides lacking the elongated C-terminus and/or the N-terminal pE were unable to induce similar detrimental cellular pathways. The data indicate that the presence of N-terminal pE is not in itself sufficient to induce pathogenic changes in the physiologic Bri1-23 peptides but that its combination with the ABri mutation is critical for the molecular pathogenesis of FBD.
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Affiliation(s)
- Krysti Todd
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
| | - Silvia Fossati
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
| | - Jorge Ghiso
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA; Department of Psychiatry, New York University School of Medicine, New York, NY 10016, USA.
| | - Agueda Rostagno
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA.
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48
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Enriquez JA, Lenaz G. Coenzyme q and the respiratory chain: coenzyme q pool and mitochondrial supercomplexes. Mol Syndromol 2014; 5:119-40. [PMID: 25126045 DOI: 10.1159/000363364] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Two alternative models of organization of the mitochondrial electron transport chain (mETC) have been alternatively favored or questioned by the accumulation evidences of different sources, the solid model or the random collision model. Both agree in the number of respiratory complexes (I-IV) that participate in the mETC, but while the random collision model proposes that Complexes I-IV do not interact physically and that electrons are transferred between them by coenzyme Q and cytochrome c, the solid model proposes that all complexes super-assemble in the so-called respirasome. Recently, the plasticity model has been developed to incorporate the solid and the random collision model as extreme situations of a dynamic organization, allowing super-assembly free movement of the respiratory complexes. In this review, we evaluate the supporting evidences of each model and the implications of the super-assembly in the physiological role of coenzyme Q.
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Affiliation(s)
| | - Giorgio Lenaz
- Dipartimento di Scienze Biomediche e Neuromotorie, Università di Bologna, Bologna, Italy
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49
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Weiland F, Zammit CM, Reith F, Hoffmann P. High resolution two-dimensional electrophoresis of native proteins. Electrophoresis 2014; 35:1893-902. [DOI: 10.1002/elps.201400060] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 02/27/2014] [Accepted: 03/07/2014] [Indexed: 11/07/2022]
Affiliation(s)
- Florian Weiland
- Adelaide Proteomics Centre; University of Adelaide; Adelaide Australia
| | - Carla M. Zammit
- Earth Sciences; University of Queensland; Brisbane Australia
| | - Frank Reith
- School of Earth and Environmental Sciences; University of Adelaide; Adelaide Australia
| | - Peter Hoffmann
- Adelaide Proteomics Centre; University of Adelaide; Adelaide Australia
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50
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Functional role of mitochondrial respiratory supercomplexes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1837:427-43. [DOI: 10.1016/j.bbabio.2013.11.002] [Citation(s) in RCA: 224] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Revised: 10/30/2013] [Accepted: 11/02/2013] [Indexed: 12/30/2022]
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