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Leiro M, Ventura R, Rojo-Querol N, Hernández-Alvarez MI. Endoplasmic Reticulum Isolation: An Optimized Approach into Cells and Mouse Liver Fractionation. Bio Protoc 2023; 13:e4803. [PMID: 37719073 PMCID: PMC10501922 DOI: 10.21769/bioprotoc.4803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 06/08/2023] [Accepted: 06/13/2023] [Indexed: 09/19/2023] Open
Abstract
The subfractionation of the endoplasmic reticulum (ER) is a widely used technique in cell biology. However, current protocols present limitations such as low yield, the use of large number of dishes, and contamination with other organelles. Here, we describe an improved method for ER subfractionation that solves other reported methods' main limitations of being time consuming and requiring less starting material. Our protocol involves a combination of different centrifugations and special buffer incubations as well as a fine-tuned method for homogenization followed by western blotting to confirm the purity of the fractions. This protocol contains a method to extract clean ER samples from cells using only five (150 mm) dishes instead of over 50 plates needed in other protocols. In addition, in this article we not only propose a new cell fractionation approach but also an optimized method to isolate pure ER fractions from one mouse liver instead of three, which are commonly used in other protocols. The protocols described here are optimized for time efficiency and designed for seamless execution in any laboratory, eliminating the need for special/patented reagents. Key features • Subcellular fractionation from cells and mouse liver. • Uses only five dishes (150 mm) or one mouse liver to extract highly enriched endoplasmic reticulum without mitochondrial-associated membrane contamination. • These protocols require the use of ultracentrifuges, dounce homogenizers, and/or Teflon Potter Elvehjem. As a result, highly enriched/clean samples are obtained. Graphical overview.
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Affiliation(s)
- Marc Leiro
- Departament de Bioquímica i Biomedicina Molecular, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
| | - Raúl Ventura
- Departament de Bioquímica i Biomedicina Molecular, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Spain
| | - Nil Rojo-Querol
- Departament de Bioquímica i Biomedicina Molecular, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
| | - María Isabel Hernández-Alvarez
- Departament de Bioquímica i Biomedicina Molecular, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, Madrid, Spain
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Rozsivalova DH, Popovic M, Kaul H, Trifunovic A. Isolation of Functional Mitochondria and Pure mtDNA from Murine Tissues. Methods Mol Biol 2023; 2615:3-16. [PMID: 36807780 DOI: 10.1007/978-1-0716-2922-2_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
Detailed analysis of mitochondrial function cannot be achieved without good quality preparations of isolated mitochondria. Ideally, the isolation protocol should be quick, while producing a reasonably pure pool of mitochondria that are still intact and coupled. Here, we describe a fast and simple method for the purification of mammalian mitochondria relying on isopycnic density gradient centrifugation. We describe specific steps that should be taken into consideration when functional mitochondria from different tissues should be isolated. This protocol is suitable for the analysis of many aspects of the organelle's structure and function.
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Affiliation(s)
- Dieu Hien Rozsivalova
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD) and Institute for Mitochondrial Diseases and Aging, Medical Faculty, University of Cologne, Cologne, Germany
| | - Milica Popovic
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD) and Institute for Mitochondrial Diseases and Aging, Medical Faculty, University of Cologne, Cologne, Germany
| | - Harshita Kaul
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD) and Institute for Mitochondrial Diseases and Aging, Medical Faculty, University of Cologne, Cologne, Germany
| | - Aleksandra Trifunovic
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD) and Institute for Mitochondrial Diseases and Aging, Medical Faculty, University of Cologne, Cologne, Germany.
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Li H. Rapid Isolation of Functional Synaptic Vesicles from Tissues Through Cryogrinding, Ultracentrifugation, and Size Exclusion Chromatography. Methods Mol Biol 2022; 2417:121-130. [PMID: 35099796 DOI: 10.1007/978-1-0716-1916-2_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Many biochemical and biophysical related questions require the isolation of functional synaptic vesicles. Isolated synaptic vesicles can be used for transporter kinetics studies, synaptic vesicle content analysis and immuno-labeling of specific synaptic vesicle proteins, etc. Here I describe a fast and reliable isolation procedure to allow researchers to isolate a large amount, as well as physiologically functional synaptic vesicles, by following the subsequent order of cryogrinding, gradient ultracentrifugation, and size exclusion liquid chromatography. This process enriches over 90% of the synaptic vesicle population, with low contamination of Golgi or endoplasmic reticulum vesicles.
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Affiliation(s)
- Huinan Li
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA.
- Laboratory for Genomics Research, University of California San Francisco, San Francisco, CA, USA.
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Kuhnert F, Weber APM. In Vivo Epitope Tagging of Plant Mitochondria. Methods Mol Biol 2022; 2379:253-264. [PMID: 35188666 DOI: 10.1007/978-1-0716-1791-5_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Mitochondria play a key role in cellular metabolism. Analyses of the genome, the proteome, metabolic, physiological, and biochemical functions of mitochondria frequently require the isolation of intact and functional mitochondria from various plant tissues with sufficient yield. For this purpose, we generated a transgenic Arabidopsis thaliana (Arabidopsis) line which presents a triple hemagglutinin tag on the surface of the outer mitochondrial membrane. The affinity tag enables immunocapture of the organelles in a single step. This chapter gives detailed instructions on how to generate transgenic Arabidopsis lines harboring a ubiquitously expressed 3xHA-sGFP-TOM5 mitochondrial fusion protein that is targeted to the outer mitochondrial membrane and enables purification of the organelles in a single step.
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Affiliation(s)
- Franziska Kuhnert
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Science (CEPLAS), Heinrich Heine University, Universitätsstrasse 1, Düsseldorf, Germany
| | - Andreas P M Weber
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Science (CEPLAS), Heinrich Heine University, Universitätsstrasse 1, Düsseldorf, Germany.
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Ishii M, Beeson G, Beeson C, Rohrer B. Isolation of Mitochondria from Retinal Pigment Epithelial Cell Cultures and an Application of High-Resolution Respirometric Assay (XF e96 Seahorse Assay). Methods Mol Biol 2021; 2277:423-431. [PMID: 34080166 DOI: 10.1007/978-1-0716-1270-5_26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Intracellular Ca2+ is strictly regulated to maintain optimal levels for function of cellular organelles as well as mitochondrial respiratory signaling at the tricarboxylic acid cycle and electron transport chain level. Optimal Ca2+ concentration for these processes vary between cell types. Furthermore, exposure of mitochondria to sustained, elevated levels of Ca2+ induces mitochondrial Ca2+ overload and damage to mitochondrial oxidative phosphorylation and ATP production. Isolated mitochondria are widely used to study mitochondrial physiology and drug effects on mitochondrial metabolism and respiratory function. However, isolated mitochondria are easily damaged during the mitochondrial isolation process. The present article describes a mitochondrial isolation method using Ca2+-chelation to minimize mitochondrial damage. We follow up the isolation process with an application that requires an optimized buffer Ca2+ concentration: the characterization of their respiratory function using a high-resolution respirometric assay.
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Affiliation(s)
- Masaaki Ishii
- Department of Ophthalmology, Medical University of South Carolina, Charleston, SC, USA.
| | - Gyda Beeson
- Department of Drug Discovery and Biomedical Sciences, Medical University of South Carolina, Charleston, SC, USA
| | - Craig Beeson
- Department of Drug Discovery and Biomedical Sciences, Medical University of South Carolina, Charleston, SC, USA
| | - Bärbel Rohrer
- Department of Ophthalmology, Medical University of South Carolina, Charleston, SC, USA.
- Ralph H. Johnson VA Medical Center, Charleston, SC, USA.
- Department of Neurosciences, Medical University of South Carolina, Charleston, SC, USA.
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Abstract
Endosomal microautophagy (eMI) is a type of autophagy that allows for the selective uptake and degradation of cytosolic proteins in late endosome/multi-vesicular bodies (LE/MVB). This process starts with the recognition of a pentapeptide amino acid KFERQ-like targeting motif in the substrate protein by the hsc70 chaperone, which then enables binding and subsequent uptake of the protein into the LE/MVB compartment. The recognition of a KFERQ-like motif by hsc70 is the same initial step in chaperone-mediated autophagy (CMA), a form of selective autophagy that degrades the hsc70-targeted proteins in lysosomes in a LAMP-2A dependent manner. The shared step of substrate recognition by hsc70, originally identified for CMA, makes it now necessary to differentiate between the two pathways. Here, we detail biochemical and imaging-based methods to track eMI activity in vitro with isolated LE/MVBs and in cells in culture using fluorescent reporters and highlight approaches to distinguish whether a protein is a substrate of eMI or CMA.
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Affiliation(s)
- Gregory J Krause
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, New York, NY, United States; Institute for Aging Studies, Albert Einstein College of Medicine, New York, NY, United States
| | - Ana Maria Cuervo
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, New York, NY, United States; Institute for Aging Studies, Albert Einstein College of Medicine, New York, NY, United States.
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Schober AF, R�o B�rtulos C, Bischoff A, Lepetit B, Gruber A, Kroth PG. Organelle Studies and Proteome Analyses of Mitochondria and Plastids Fractions from the Diatom Thalassiosira pseudonana. Plant Cell Physiol 2019; 60:1811-1828. [PMID: 31179502 PMCID: PMC6683858 DOI: 10.1093/pcp/pcz097] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 05/14/2019] [Indexed: 05/19/2023]
Abstract
Diatoms are unicellular algae and evolved by secondary endosymbiosis, a process in which a red alga-like eukaryote was engulfed by a heterotrophic eukaryotic cell. This gave rise to plastids of remarkable complex architecture and ultrastructure that require elaborate protein importing, trafficking, signaling and intracellular cross-talk pathways. Studying both plastids and mitochondria and their distinctive physiological pathways in organello may greatly contribute to our understanding of photosynthesis, mitochondrial respiration and diatom evolution. The isolation of such complex organelles, however, is still demanding, and existing protocols are either limited to a few species (for plastids) or have not been reported for diatoms so far (for mitochondria). In this work, we present the first isolation protocol for mitochondria from the model diatom Thalassiosira pseudonana. Apart from that, we extended the protocol so that it is also applicable for the purification of a high-quality plastids fraction, and provide detailed structural and physiological characterizations of the resulting organelles. Isolated mitochondria were structurally intact, showed clear evidence of mitochondrial respiration, but the fractions still contained residual cell fragments. In contrast, plastid isolates were virtually free of cellular contaminants, featured structurally preserved thylakoids performing electron transport, but lost most of their stromal components as concluded from Western blots and mass spectrometry. Liquid chromatography electrospray-ionization mass spectrometry studies on mitochondria and thylakoids, moreover, allowed detailed proteome analyses which resulted in extensive proteome maps for both plastids and mitochondria thus helping us to broaden our understanding of organelle metabolism and functionality in diatoms.
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Affiliation(s)
- Alexander F Schober
- Plant Ecophysiology, Department of Biology, University of Konstanz, Konstanz, Germany
- Corresponding author: E-mail, ; Fax, +49(0)7531-88-4047
| | - Carolina R�o B�rtulos
- Plant Ecophysiology, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Annsophie Bischoff
- Plant Ecophysiology, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Bernard Lepetit
- Plant Ecophysiology, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Ansgar Gruber
- Plant Ecophysiology, Department of Biology, University of Konstanz, Konstanz, Germany
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branišovsk� 1160/31, Česk� Budějovice, Czech Republic
| | - Peter G Kroth
- Plant Ecophysiology, Department of Biology, University of Konstanz, Konstanz, Germany
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Abstract
Mitochondria serve as the center stage for a number of cellular processes, including energy production, apoptosis, ion homeostasis, iron and copper processing, steroid metabolism, de novo pyrimidine, and heme biosynthesis. The study of mitochondrial function often requires the purification of intact and respiratory-competent organelles. Here, we provide detailed protocols to isolate functional mitochondria from various types of mammalian cells and mouse tissues, in both crude and pure forms. We introduce the use of nitrogen cavitation for the disruption of plasma membrane and the reproducible isolation of mitochondria-enriched fractions of high yield. Mitochondria that are isolated by these procedures are intact and coupled and can directly be used for several downstream analyses, such as measurements of oxygen consumption and calcium buffering capacity.
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Affiliation(s)
- Jennifer Wettmarshausen
- Genzentrum, Department of Biochemistry, Ludwig-Maximilians University, Feodor-Lynen Strasse 25, 81377, Munich, Germany
- Institute for Diabetes and Obesity, Helmholtz Zentrum München, 85764, Neuherberg, Germany
| | - Fabiana Perocchi
- Gene Center, LMU Munich and Institute for Diabetes and Obesity, Helmholtz Zentrum München, Munich, Germany.
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Abstract
Isolation of various subcellular compartments followed by a high-coverage proteomic analysis provides an unparalleled foundation for the functional analyses of proteins. Analyses of tonoplast preparations free of major contaminants provide insights into vesicular fusion machinery, solute transport, and the vacuole association with the cytoskeleton, whereas analyses of the vacuolar lumen have yielded numerous soluble glycosidases, proteases, and proteins involved in stress responses. In addition, vacuolar lumen preparations have also allowed characterization of a luminal solute content in response to various abiotic stresses. Here, I revisit and update one of the most successful methodologies for vacuole and tonoplast isolation.
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Affiliation(s)
- Jan Zouhar
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, I.N.I.A. Parque Científico y Tecnológico, Campus de Montegancedo, 28223, Pozuelo de Alarcón, Spain.
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Abstract
Chaperone-mediated autophagy (CMA) is a multistep process that involves selective degradation and digestion of a pool of soluble cytosolic proteins in lysosomes. Cytosolic substrates are selectively identified and targeted by chaperones to lysosomes where they are subsequently translocated into the organelle lumen through a dedicated CMA-associated lysosomal membrane receptor/translocation complex. CMA contributes to maintaining a functional proteome, through elimination of altered proteins, and participates in the cellular energetic balance through amino acid recycling. Defective or dysfunctional CMA has been associated with human pathologies such as neurodegeneration, cancer, immunodeficiency or diabetes, increasing the overall interest in methods to monitor this selective autophagic pathway. Here, we describe approaches used to study CMA in different experimental models.
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Affiliation(s)
- Bindi Patel
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Institute for Aging Studies, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Ana Maria Cuervo
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Institute for Aging Studies, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
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