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Goto-Yamada S, Oikawa K, Yamato KT, Kanai M, Hikino K, Nishimura M, Mano S. Image-Based Analysis Revealing the Molecular Mechanism of Peroxisome Dynamics in Plants. Front Cell Dev Biol 2022; 10:883491. [PMID: 35592252 PMCID: PMC9110829 DOI: 10.3389/fcell.2022.883491] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 04/15/2022] [Indexed: 11/13/2022] Open
Abstract
Peroxisomes are present in eukaryotic cells and have essential roles in various biological processes. Plant peroxisomes proliferate by de novo biosynthesis or division of pre-existing peroxisomes, degrade, or replace metabolic enzymes, in response to developmental stages, environmental changes, or external stimuli. Defects of peroxisome functions and biogenesis alter a variety of biological processes and cause aberrant plant growth. Traditionally, peroxisomal function-based screening has been employed to isolate Arabidopsis thaliana mutants that are defective in peroxisomal metabolism, such as lipid degradation and photorespiration. These analyses have revealed that the number, subcellular localization, and activity of peroxisomes are closely related to their efficient function, and the molecular mechanisms underlying peroxisome dynamics including organelle biogenesis, protein transport, and organelle interactions must be understood. Various approaches have been adopted to identify factors involved in peroxisome dynamics. With the development of imaging techniques and fluorescent proteins, peroxisome research has been accelerated. Image-based analyses provide intriguing results concerning the movement, morphology, and number of peroxisomes that were hard to obtain by other approaches. This review addresses image-based analysis of peroxisome dynamics in plants, especially A. thaliana and Marchantia polymorpha.
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Affiliation(s)
- Shino Goto-Yamada
- Małopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Kazusato Oikawa
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Katsuyuki T. Yamato
- Faculty of Biology-Oriented Science and Technology, Kindai University, Wakayama, Japan
| | - Masatake Kanai
- Department of Cell Biology, National Institute for Basic Biology, Okazaki, Japan
| | - Kazumi Hikino
- Department of Cell Biology, National Institute for Basic Biology, Okazaki, Japan
| | - Mikio Nishimura
- Department of Biology, Faculty of Science and Engineering, Konan University, Kobe, Japan
| | - Shoji Mano
- Department of Cell Biology, National Institute for Basic Biology, Okazaki, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Japan
- *Correspondence: Shoji Mano
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2
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TheCellVision.org: A Database for Visualizing and Mining High-Content Cell Imaging Projects. G3-GENES GENOMES GENETICS 2020; 10:3969-3976. [PMID: 32934016 PMCID: PMC7642925 DOI: 10.1534/g3.120.401570] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Advances in genome engineering and high throughput imaging technologies have enabled genome-scale screens of single cells for a variety of phenotypes, including subcellular morphology and protein localization. We constructed TheCellVision.org, a freely available and web-accessible image visualization and data browsing tool that serves as a central repository for fluorescence microscopy images and associated quantitative data produced by high-content screening experiments. Currently, TheCellVision.org hosts ∼575,590 images and associated analysis results from two published high-content screening (HCS) projects focused on the budding yeast Saccharomyces cerevisiae TheCellVision.org allows users to access, visualize and explore fluorescence microscopy images, and to search, compare, and extract data related to subcellular compartment morphology, protein abundance, and localization. Each dataset can be queried independently or as part of a search across multiple datasets using the advanced search option. The website also hosts computational tools associated with the available datasets, which can be applied to other projects and cell systems, a feature we demonstrate using published images of mammalian cells. Providing access to HCS data through websites such as TheCelllVision.org enables new discovery and independent re-analyses of imaging data.
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3
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Alexandrov AI, Dergalev AA. Increasing throughput of manual microscopy of cell suspensions using solid medium pads. MethodsX 2019; 6:329-332. [PMID: 30847282 PMCID: PMC6389654 DOI: 10.1016/j.mex.2019.02.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 02/11/2019] [Indexed: 11/25/2022] Open
Abstract
Microscopy of multiple samples using slides and coverslips is time consuming and good images are sometimes difficult to obtain due to cell movement. Our method involves manual spotting of multiple cell samples onto solid-medium pads, which creates the following benefits: Rapid, high-quality imaging of multiple samples (hundreds per day) by visible and fluorescence microscopy. No need for expensive automated equipment, multi-well plates or large amounts of consumables. Wide range of working cell concentrations.
The method was implemented for S. cerevisiae yeast, however it is likely to be applicable to all types of microorganisms and possibly other microscopic samples such as pollen. The lack of need for automated equipment may also make this method useful for field work.
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Affiliation(s)
- Alexander I Alexandrov
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2 Leninsky Ave., Moscow 119071, Russia.,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Alexander A Dergalev
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2 Leninsky Ave., Moscow 119071, Russia
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4
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Chuartzman SG, Schuldiner M. Database for High Throughput Screening Hits (dHITS): a simple tool to retrieve gene specific phenotypes from systematic screens done in yeast. Yeast 2018; 35:477-483. [PMID: 29574976 PMCID: PMC6055851 DOI: 10.1002/yea.3312] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 03/04/2018] [Accepted: 03/07/2018] [Indexed: 12/21/2022] Open
Abstract
In the last decade several collections of Saccharomyces cerevisiae yeast strains have been created. In these collections every gene is modified in a similar manner such as by a deletion or the addition of a protein tag. Such libraries have enabled a diversity of systematic screens, giving rise to large amounts of information regarding gene functions. However, often papers describing such screens focus on a single gene or a small set of genes and all other loci affecting the phenotype of choice (‘hits’) are only mentioned in tables that are provided as supplementary material and are often hard to retrieve or search. To help unify and make such data accessible, we have created a Database of High Throughput Screening Hits (dHITS). The dHITS database enables information to be obtained about screens in which genes of interest were found as well as the other genes that came up in that screen – all in a readily accessible and downloadable format. The ability to query large lists of genes at the same time provides a platform to easily analyse hits obtained from transcriptional analyses or other screens. We hope that this platform will serve as a tool to facilitate investigation of protein functions to the yeast community.
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Affiliation(s)
- Silvia G Chuartzman
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7610001, Israel
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5
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Pesce CG, Zdraljevic S, Peria WJ, Bush A, Repetto MV, Rockwell D, Yu RC, Colman-Lerner A, Brent R. Single-cell profiling screen identifies microtubule-dependent reduction of variability in signaling. Mol Syst Biol 2018; 14:e7390. [PMID: 29618636 PMCID: PMC5884679 DOI: 10.15252/msb.20167390] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Revised: 01/25/2018] [Accepted: 02/06/2018] [Indexed: 01/01/2023] Open
Abstract
Populations of isogenic cells often respond coherently to signals, despite differences in protein abundance and cell state. Previously, we uncovered processes in the Saccharomyces cerevisiae pheromone response system (PRS) that reduced cell-to-cell variability in signal strength and cellular response. Here, we screened 1,141 non-essential genes to identify 50 "variability genes". Most had distinct, separable effects on strength and variability of the PRS, defining these quantities as genetically distinct "axes" of system behavior. Three genes affected cytoplasmic microtubule function: BIM1, GIM2, and GIM4 We used genetic and chemical perturbations to show that, without microtubules, PRS output is reduced but variability is unaffected, while, when microtubules are present but their function is perturbed, output is sometimes lowered, but its variability is always high. The increased variability caused by microtubule perturbations required the PRS MAP kinase Fus3 and a process at or upstream of Ste5, the membrane-localized scaffold to which Fus3 must bind to be activated. Visualization of Ste5 localization dynamics demonstrated that perturbing microtubules destabilized Ste5 at the membrane signaling site. The fact that such microtubule perturbations cause aberrant fate and polarity decisions in mammals suggests that microtubule-dependent signal stabilization might also operate throughout metazoans.
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Affiliation(s)
| | - Stefan Zdraljevic
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | | | - Alan Bush
- IFIBYNE-UBA-CONICET and Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - María Victoria Repetto
- IFIBYNE-UBA-CONICET and Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | | | | | - Alejandro Colman-Lerner
- IFIBYNE-UBA-CONICET and Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Roger Brent
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
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6
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Bersch K, Lobos Matthei I, Thoms S. Multiple Localization by Functional Translational Readthrough. Subcell Biochem 2018; 89:201-219. [PMID: 30378024 DOI: 10.1007/978-981-13-2233-4_8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In a compartmentalized cell, correct protein localization is crucial for function of virtually all cellular processes. From the cytoplasm as a starting point, proteins are imported into organelles by specific targeting signals. Many proteins, however, act in more than one cellular compartment. In this chapter, we discuss mechanisms by which proteins can be targeted to multiple organelles with a focus on a novel gene regulatory mechanism, functional translational readthrough, that permits multiple targeting of proteins to the peroxisome and other organelles. In mammals, lactate and malate dehydrogenase are the best-characterized enzymes whose targeting is controlled by functional translational readthrough.
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Affiliation(s)
- Kristina Bersch
- Department of Child and Adolescent Health, University Medical Center Göttingen, University of Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Germany
| | - Ignacio Lobos Matthei
- Department of Child and Adolescent Health, University Medical Center Göttingen, University of Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Germany
| | - Sven Thoms
- Department of Child and Adolescent Health, University Medical Center Göttingen, University of Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Germany.
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7
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Hofhuis J, Schueren F, Nötzel C, Lingner T, Gärtner J, Jahn O, Thoms S. The functional readthrough extension of malate dehydrogenase reveals a modification of the genetic code. Open Biol 2017; 6:rsob.160246. [PMID: 27881739 PMCID: PMC5133446 DOI: 10.1098/rsob.160246] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 10/21/2016] [Indexed: 01/19/2023] Open
Abstract
Translational readthrough gives rise to C-terminally extended proteins, thereby providing the cell with new protein isoforms. These may have different properties from the parental proteins if the extensions contain functional domains. While for most genes amino acid incorporation at the stop codon is far lower than 0.1%, about 4% of malate dehydrogenase (MDH1) is physiologically extended by translational readthrough and the actual ratio of MDH1x (extended protein) to ‘normal' MDH1 is dependent on the cell type. In human cells, arginine and tryptophan are co-encoded by the MDH1x UGA stop codon. Readthrough is controlled by the 7-nucleotide high-readthrough stop codon context without contribution of the subsequent 50 nucleotides encoding the extension. All vertebrate MDH1x is directed to peroxisomes via a hidden peroxisomal targeting signal (PTS) in the readthrough extension, which is more highly conserved than the extension of lactate dehydrogenase B. The hidden PTS of non-mammalian MDH1x evolved to be more efficient than the PTS of mammalian MDH1x. These results provide insight into the genetic and functional co-evolution of these dually localized dehydrogenases.
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Affiliation(s)
- Julia Hofhuis
- Department of Pediatrics and Adolescent Medicine, University Medical Center Göttingen, University of Göttingen, 37075 Göttingen, Germany
| | - Fabian Schueren
- Department of Pediatrics and Adolescent Medicine, University Medical Center Göttingen, University of Göttingen, 37075 Göttingen, Germany
| | - Christopher Nötzel
- Department of Pediatrics and Adolescent Medicine, University Medical Center Göttingen, University of Göttingen, 37075 Göttingen, Germany
| | - Thomas Lingner
- Microarray and Deep Sequencing Core Facility, University Medical Center Göttingen, University of Göttingen, 37077 Göttingen, Germany
| | - Jutta Gärtner
- Department of Pediatrics and Adolescent Medicine, University Medical Center Göttingen, University of Göttingen, 37075 Göttingen, Germany
| | - Olaf Jahn
- Proteomics Group, Max Planck Institute of Experimental Medicine, 37075 Göttingen, Germany
| | - Sven Thoms
- Department of Pediatrics and Adolescent Medicine, University Medical Center Göttingen, University of Göttingen, 37075 Göttingen, Germany
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8
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Yofe I, Soliman K, Chuartzman SG, Morgan B, Weill U, Yifrach E, Dick TP, Cooper SJ, Ejsing CS, Schuldiner M, Zalckvar E, Thoms S. Pex35 is a regulator of peroxisome abundance. J Cell Sci 2017; 130:791-804. [PMID: 28049721 DOI: 10.1242/jcs.187914] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 11/24/2016] [Indexed: 12/12/2022] Open
Abstract
Peroxisomes are cellular organelles with vital functions in lipid, amino acid and redox metabolism. The cellular formation and dynamics of peroxisomes are governed by PEX genes; however, the regulation of peroxisome abundance is still poorly understood. Here, we use a high-content microscopy screen in Saccharomyces cerevisiae to identify new regulators of peroxisome size and abundance. Our screen led to the identification of a previously uncharacterized gene, which we term PEX35, which affects peroxisome abundance. PEX35 encodes a peroxisomal membrane protein, a remote homolog to several curvature-generating human proteins. We systematically characterized the genetic and physical interactome as well as the metabolome of mutants in PEX35, and we found that Pex35 functionally interacts with the vesicle-budding-inducer Arf1. Our results highlight the functional interaction between peroxisomes and the secretory pathway.
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Affiliation(s)
- Ido Yofe
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Kareem Soliman
- Department of Child and Adolescent Health, University Medical Center, Göttingen 37075, Germany
| | - Silvia G Chuartzman
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Bruce Morgan
- Department of Cellular Biochemistry, University of Kaiserslautern, Kaiserslautern 67653, Germany.,Division of Redox Regulation, ZMBH-DKFZ Alliance, German Cancer Research Center (DKFZ), Heidelberg 69121, Germany
| | - Uri Weill
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Eden Yifrach
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Tobias P Dick
- Division of Redox Regulation, ZMBH-DKFZ Alliance, German Cancer Research Center (DKFZ), Heidelberg 69121, Germany
| | - Sara J Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Christer S Ejsing
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense 5230, Denmark
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Einat Zalckvar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Sven Thoms
- Department of Child and Adolescent Health, University Medical Center, Göttingen 37075, Germany
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9
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Styles EB, Friesen H, Boone C, Andrews BJ. High-Throughput Microscopy-Based Screening in Saccharomyces cerevisiae. Cold Spring Harb Protoc 2016; 2016:pdb.top087593. [PMID: 27037080 DOI: 10.1101/pdb.top087593] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The budding yeastSaccharomyces cerevisiaehas served as the pioneer model organism for virtually all genome-scale methods, including genome sequencing, DNA microarrays, gene deletion collections, and a variety of proteomic platforms. Yeast has also provided a test-bed for the development of systematic fluorescence-based imaging screens to enable the analysis of protein localization and abundance in vivo. Especially important has been the integration of high-throughput microscopy with automated image-processing methods, which has allowed researchers to overcome issues associated with manual image analysis and acquire unbiased, quantitative data. Here we provide an introduction to automated imaging in budding yeast.
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Affiliation(s)
- Erin B Styles
- The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Helena Friesen
- The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Charles Boone
- The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Brenda J Andrews
- The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
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10
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Wolinski H, Kohlwein SD. Microscopic and spectroscopic techniques to investigate lipid droplet formation and turnover in yeast. Methods Mol Biol 2015; 1270:289-305. [PMID: 25702125 DOI: 10.1007/978-1-4939-2309-0_21] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
In spite of some progress in understanding the molecular basis of lipid-associated disorders, major questions about the regulation of synthesis and degradation of lipids and the interaction of these processes with other aspects of cellular physiology are still unresolved. Studies in reference organisms such as various yeast species, the fruit fly Drosophila melanogaster, or the nematode Caenorhabditis elegans complement efforts in mouse models as well as clinical studies in humans to address these questions. Imaging techniques play a pivotal role in understanding lipid droplet biology, and the implementation of imaging-based high-content screens of mutant collections has led to the identification of novel molecular players. This study focuses on novel fluorescent probes as well as spectroscopic imaging techniques to investigate lipid droplet formation and turnover in yeast. The application and limitations of such techniques in understanding lipid storage and turnover are discussed.
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Affiliation(s)
- Heimo Wolinski
- Institute of Molecular Biosciences, BioTechMed-Graz, University of Graz, Humboldtstrasse 50/II, 8010, Graz, Austria
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11
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Mattiazzi Ušaj M, Brložnik M, Kaferle P, Žitnik M, Wolinski H, Leitner F, Kohlwein SD, Zupan B, Petrovič U. Genome-Wide Localization Study of Yeast Pex11 Identifies Peroxisome-Mitochondria Interactions through the ERMES Complex. J Mol Biol 2015; 427:2072-87. [PMID: 25769804 PMCID: PMC4429955 DOI: 10.1016/j.jmb.2015.03.004] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 03/01/2015] [Accepted: 03/04/2015] [Indexed: 11/29/2022]
Abstract
Pex11 is a peroxin that regulates the number of peroxisomes in eukaryotic cells. Recently, it was found that a mutation in one of the three mammalian paralogs, PEX11β, results in a neurological disorder. The molecular function of Pex11, however, is not known. Saccharomyces cerevisiae Pex11 has been shown to recruit to peroxisomes the mitochondrial fission machinery, thus enabling proliferation of peroxisomes. This process is essential for efficient fatty acid β-oxidation. In this study, we used high-content microscopy on a genome-wide scale to determine the subcellular localization pattern of yeast Pex11 in all non-essential gene deletion mutants, as well as in temperature-sensitive essential gene mutants. Pex11 localization and morphology of peroxisomes was profoundly affected by mutations in 104 different genes that were functionally classified. A group of genes encompassing MDM10, MDM12 and MDM34 that encode the mitochondrial and cytosolic components of the ERMES complex was analyzed in greater detail. Deletion of these genes caused a specifically altered Pex11 localization pattern, whereas deletion of MMM1, the gene encoding the fourth, endoplasmic-reticulum-associated component of the complex, did not result in an altered Pex11 localization or peroxisome morphology phenotype. Moreover, we found that Pex11 and Mdm34 physically interact and that Pex11 plays a role in establishing the contact sites between peroxisomes and mitochondria through the ERMES complex. Based on these results, we propose that the mitochondrial/cytosolic components of the ERMES complex establish a direct interaction between mitochondria and peroxisomes through Pex11. Molecular function of Pex11, a protein with roles in metabolism and disease, is unknown. Genome-wide screening determined subcellular localization of Pex11-GFP in yeast. Mutants defective in components of the ERMES complex show altered Pex11 localization. Pex11 physically interacts with the ERMES complex component Mdm34. ERMES complex and Pex11 mediate interaction between mitochondria and peroxisomes.
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Affiliation(s)
- M Mattiazzi Ušaj
- Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia
| | - M Brložnik
- Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia
| | - P Kaferle
- Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia
| | - M Žitnik
- Faculty of Computer and Information Science, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia
| | - H Wolinski
- Institute of Molecular Biosciences, University of Graz, BioTechMed Graz, Humboldtstrasse 50, A-8010 Graz, Austria
| | - F Leitner
- Institute of Molecular Biosciences, University of Graz, BioTechMed Graz, Humboldtstrasse 50, A-8010 Graz, Austria
| | - S D Kohlwein
- Institute of Molecular Biosciences, University of Graz, BioTechMed Graz, Humboldtstrasse 50, A-8010 Graz, Austria
| | - B Zupan
- Faculty of Computer and Information Science, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia; Department of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - U Petrovič
- Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia.
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12
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Schuldiner M, Zalckvar E. Peroxisystem: Harnessing systems cell biology to study peroxisomes. Biol Cell 2015; 107:89-97. [DOI: 10.1111/boc.201400091] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 01/05/2015] [Indexed: 12/14/2022]
Affiliation(s)
- Maya Schuldiner
- Department of Molecular Genetics; Weizmann Institute of Science; Rehovot 7610001 Israel
| | - Einat Zalckvar
- Department of Molecular Genetics; Weizmann Institute of Science; Rehovot 7610001 Israel
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13
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Cohen Y, Klug YA, Dimitrov L, Erez Z, Chuartzman SG, Elinger D, Yofe I, Soliman K, Gärtner J, Thoms S, Schekman R, Elbaz-Alon Y, Zalckvar E, Schuldiner M. Peroxisomes are juxtaposed to strategic sites on mitochondria. MOLECULAR BIOSYSTEMS 2014; 10:1742-8. [PMID: 24722918 DOI: 10.1039/c4mb00001c] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Peroxisomes are ubiquitous and dynamic organelles that house many important pathways of cellular metabolism. In recent years it has been demonstrated that mitochondria are tightly connected with peroxisomes and are defective in several peroxisomal diseases. Indeed, these two organelles share metabolic routes as well as resident proteins and, at least in mammals, are connected via a vesicular transport pathway. However the exact extent of cross-talk between peroxisomes and mitochondria remains unclear. Here we used a combination of high throughput genetic manipulations of yeast libraries alongside high content screens to systematically unravel proteins that affect the transport of peroxisomal proteins and peroxisome biogenesis. Follow up work on the effector proteins that were identified revealed that peroxisomes are not randomly distributed in cells but are rather localized to specific mitochondrial subdomains such as mitochondria-ER junctions and sites of acetyl-CoA synthesis. Our approach highlights the intricate geography of the cell and suggests an additional layer of organization as a possible way to enable efficient metabolism. Our findings pave the way for further studying the machinery aligning mitochondria and peroxisomes, the role of the juxtaposition, as well as its regulation during various metabolic conditions. More broadly, the approaches used here can be easily applied to study any organelle of choice, facilitating the discovery of new aspects in cell biology.
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Affiliation(s)
- Yifat Cohen
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel.
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14
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Abstract
Peroxisomes carry out various oxidative reactions that are tightly regulated to adapt to the changing needs of the cell and varying external environments. Accordingly, they are remarkably fluid and can change dramatically in abundance, size, shape and content in response to numerous cues. These dynamics are controlled by multiple aspects of peroxisome biogenesis that are coordinately regulated with each other and with other cellular processes. Ongoing studies are deciphering the diverse molecular mechanisms that underlie biogenesis and how they cooperate to dynamically control peroxisome utility. These important challenges should lead to an understanding of peroxisome dynamics that can be capitalized upon for bioengineering and the development of therapies to improve human health.
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Affiliation(s)
- Jennifer J Smith
- 1] Seattle Biomedical Research Institute, 307 Westlake Avenue North, 98109-5240, USA. [2] Institute for Systems Biology, 401 Terry Avenue North, Seattle, Washington 98109-5219, USA
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15
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Abstract
Microscopic imaging techniques play a pivotal role in the life sciences. Here we describe labeling and imaging methods for live yeast cell imaging. Yeast is an excellent reference organism for biomedical research to investigate fundamental cellular processes, and has gained great popularity also for large-scale imaging-based screens. Methods are described to label live yeast cells with organelle-specific fluorescent dyes or GFP-tagged proteins, and how cells are maintained viable over extended periods of time during microscopy. We point out common pitfalls and potential microscopy artifacts arising from inhomogeneous labeling and depending on cellular physiology. Application and limitation of bleaching techniques to address dynamic processes in the yeast cell are described.
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Affiliation(s)
- Heimo Wolinski
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
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16
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Radulovic M, Knittelfelder O, Cristobal-Sarramian A, Kolb D, Wolinski H, Kohlwein SD. The emergence of lipid droplets in yeast: current status and experimental approaches. Curr Genet 2013; 59:231-42. [PMID: 24057105 PMCID: PMC3824194 DOI: 10.1007/s00294-013-0407-9] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Revised: 09/11/2013] [Accepted: 09/11/2013] [Indexed: 11/28/2022]
Abstract
The ‘discovery’ of lipid droplets as a metabolically highly active subcellular organelle has sparked great scientific interest in its research in recent years. The previous view of a rather inert storage pool of neutral lipids—triacylglycerol and sterols or steryl esters—has markedly changed. Driven by the endemic dimensions of lipid-associated disorders on the one hand, and the promising biotechnological application to generate oils (‘biodiesel’) from single-celled organisms on the other, multiple model organisms are exploited in basic and applied research to develop a better understanding of biogenesis and metabolism of this organelle. This article summarizes the current status of LD research in yeast and experimental approaches to obtain insight into the regulatory and structural components driving lipid droplet formation and their physiological and pathophysiological roles in lipid homeostasis.
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Affiliation(s)
- Maja Radulovic
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50/II, 8010, Graz, Austria
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17
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Lipid droplets and peroxisomes: key players in cellular lipid homeostasis or a matter of fat--store 'em up or burn 'em down. Genetics 2013; 193:1-50. [PMID: 23275493 PMCID: PMC3527239 DOI: 10.1534/genetics.112.143362] [Citation(s) in RCA: 166] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Lipid droplets (LDs) and peroxisomes are central players in cellular lipid homeostasis: some of their main functions are to control the metabolic flux and availability of fatty acids (LDs and peroxisomes) as well as of sterols (LDs). Both fatty acids and sterols serve multiple functions in the cell—as membrane stabilizers affecting membrane fluidity, as crucial structural elements of membrane-forming phospholipids and sphingolipids, as protein modifiers and signaling molecules, and last but not least, as a rich carbon and energy source. In addition, peroxisomes harbor enzymes of the malic acid shunt, which is indispensable to regenerate oxaloacetate for gluconeogenesis, thus allowing yeast cells to generate sugars from fatty acids or nonfermentable carbon sources. Therefore, failure of LD and peroxisome biogenesis and function are likely to lead to deregulated lipid fluxes and disrupted energy homeostasis with detrimental consequences for the cell. These pathological consequences of LD and peroxisome failure have indeed sparked great biomedical interest in understanding the biogenesis of these organelles, their functional roles in lipid homeostasis, interaction with cellular metabolism and other organelles, as well as their regulation, turnover, and inheritance. These questions are particularly burning in view of the pandemic development of lipid-associated disorders worldwide.
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18
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An active-contour based algorithm for the automated segmentation of dense yeast populations on transmission microscopy images. ACTA ACUST UNITED AC 2012. [DOI: 10.1007/s00791-012-0178-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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19
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Mattiazzi M, Petrovič U, Križaj I. Yeast as a model eukaryote in toxinology: a functional genomics approach to studying the molecular basis of action of pharmacologically active molecules. Toxicon 2012; 60:558-71. [PMID: 22465496 DOI: 10.1016/j.toxicon.2012.03.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Accepted: 03/13/2012] [Indexed: 10/28/2022]
Abstract
Yeast Saccharomyces cerevisiae has proven to be a relevant and convenient model organism for the study of diverse biological phenomena, due to its straightforward genetics, cost-effectiveness and rapid growth, combined with the typical characteristics of a eukaryotic cell. More than 40% of yeast proteins share at least part of their primary amino acid sequence with the corresponding human protein, making yeast a valuable model in biomedical research. In the last decade, high-throughput and genome-wide experimental approaches developed in yeast have paved the way to functional genomics that aims at a global understanding of the relationship between genotype and phenotype. In this review we first present the yeast strain and plasmid collections for genome-wide experimental approaches to study complex interactions between genes, proteins and endo- or exogenous small molecules. We describe methods for protein-protein, protein-DNA, genetic and chemo-genetic interactions, as well as localization studies, focussing on their application in research on small pharmacologically active molecules. Next we review the use of yeast as a model organism in neurobiology, emphasizing work done towards elucidating the pathogenesis of neurodegenerative diseases and the mechanism of action of neurotoxic phospholipases A(2).
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Affiliation(s)
- Mojca Mattiazzi
- Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Ljubljana, Slovenia
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20
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Kabran P, Rossignol T, Gaillardin C, Nicaud JM, Neuvéglise C. Alternative splicing regulates targeting of malate dehydrogenase in Yarrowia lipolytica. DNA Res 2012; 19:231-44. [PMID: 22368181 PMCID: PMC3372373 DOI: 10.1093/dnares/dss007] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Alternative pre-mRNA splicing is a major mechanism contributing to the proteome complexity of most eukaryotes, especially mammals. In less complex organisms, such as yeasts, the numbers of genes that contain introns are low and cases of alternative splicing (AS) with functional implications are rare. We report the first case of AS with functional consequences in the yeast Yarrowia lipolytica. The splicing pattern was found to govern the cellular localization of malate dehydrogenase, an enzyme of the central carbon metabolism. This ubiquitous enzyme is involved in the tricarboxylic acid cycle in mitochondria and in the glyoxylate cycle, which takes place in peroxisomes and the cytosol. In Saccharomyces cerevisiae, three genes encode three compartment-specific enzymes. In contrast, only two genes exist in Y. lipolytica. One gene (YlMDH1, YALI0D16753g) encodes a predicted mitochondrial protein, whereas the second gene (YlMDH2, YALI0E14190g) generates the cytosolic and peroxisomal forms through the alternative use of two 3'-splice sites in the second intron. Both splicing variants were detected in cDNA libraries obtained from cells grown under different conditions. Mutants expressing the individual YlMdh2p isoforms tagged with fluorescent proteins confirmed that they localized to either the cytosolic or the peroxisomal compartment.
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21
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Wolinski H, Bredies K, Kohlwein SD. Quantitative imaging of lipid metabolism in yeast: from 4D analysis to high content screens of mutant libraries. Methods Cell Biol 2012; 108:345-65. [PMID: 22325610 DOI: 10.1016/b978-0-12-386487-1.00016-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Due to their central role in cellular fat storage and lipid homeostasis, lipid droplets (LD) have attracted great interest in biomedical research. The integration of both biochemical and genetic tools and the use of model organisms have greatly contributed to the understanding of LD metabolism and its regulation. However, many important aspects such as LD biogenesis, intracellular dynamics, or their potential degradation by autophagy are still poorly understood. Microscopic techniques, in particular fluorescence microscopy using LD specific dyes or fluorescent protein tagging, represent excellent experimental tools to study the dynamic nature of both the protein and lipid content of LD. Single cell systems in culture are particularly suited to identify and characterize proteins required for LD formation and turnover, using genetic knock-down or gene deletion strategies. Here we describe experimental setups to investigate LD dynamics and turnover in yeast, using various labeling techniques suitable for three-dimensional imaging over time (4D imaging), quantitative microscopy and imaging-based screens of mutant libraries. Also, implementation of coherent anti-Stokes Raman scattering (CARS) microscopy as an emerging tool for label-free lipid imaging in living cells will be discussed.
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Affiliation(s)
- Heimo Wolinski
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
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22
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Oheim M. Advances and challenges in high-throughput microscopy for live-cell subcellular imaging. Expert Opin Drug Discov 2011; 6:1299-315. [DOI: 10.1517/17460441.2011.637105] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Martin Oheim
- INSERM U603, CNRS UMR 8154, Université Paris Descartes, PRES Sorbonne Paris Cité, Laboratory of Neurophysiology and New Microscopies, F-75006 Paris, France ;
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23
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Tower RJ, Fagarasanu A, Aitchison JD, Rachubinski RA. The peroxin Pex34p functions with the Pex11 family of peroxisomal divisional proteins to regulate the peroxisome population in yeast. Mol Biol Cell 2011; 22:1727-38. [PMID: 21441307 PMCID: PMC3093324 DOI: 10.1091/mbc.e11-01-0084] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Peroxisomes are ubiquitous organelles involved in diverse metabolic processes, most notably the metabolism of lipids and the detoxification of reactive oxygen species. Peroxisomes are highly dynamic and change in size and number in response to both intra- and extracellular cues. In the yeast Saccharomyces cerevisiae, peroxisome growth and division are controlled by both the differential import of soluble matrix proteins and a specialized divisional machinery that includes peroxisome-specific factors, such as members of the Pex11 protein family, and general organelle divisional factors, such as the dynamin-related protein Vps1p. Global yeast two-hybrid analyses have demonstrated interactions between the product of the S. cerevisiae gene of unknown function, YCL056c, and Pex proteins involved in peroxisome biogenesis. Here we show that the protein encoded by YCL056c, renamed Pex34p, is a peroxisomal integral membrane protein that acts independently and also in concert with the Pex11 protein family members Pex11p, Pex25p, and Pex27p to control the peroxisome populations of cells under conditions of both peroxisome proliferation and constitutive peroxisome division. Yeast two-hybrid analysis showed that Pex34p interacts physically with itself and with Pex11p, Pex25p, and Pex27p but not with Vps1p. Pex34p can act as a positive effector of peroxisome division as its overexpression leads to increased numbers of peroxisomes in wild type and pex34Δ cells. Pex34p requires the Pex11 family proteins to promote peroxisome division. Our discovery of Pex34p as a protein involved in the already complex control of peroxisome populations emphasizes the necessity of cells to strictly regulate their peroxisome populations to be able to respond appropriately to changing environmental conditions.
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Affiliation(s)
- Robert J Tower
- Department of Cell Biology, University of Alberta, Edmonton, Alberta, Canada Institute for Systems Biology, Seattle, WA 98103, USA
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24
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van Zutphen T, van der Klei IJ. Quantitative analysis of organelle abundance, morphology and dynamics. Curr Opin Biotechnol 2011; 22:127-32. [DOI: 10.1016/j.copbio.2010.10.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2010] [Revised: 10/27/2010] [Accepted: 10/27/2010] [Indexed: 10/18/2022]
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25
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Salomon S, Grunewald D, Stüber K, Schaaf S, MacLean D, Schulze-Lefert P, Robatzek S. High-throughput confocal imaging of intact live tissue enables quantification of membrane trafficking in Arabidopsis. PLANT PHYSIOLOGY 2010; 154:1096-104. [PMID: 20841454 PMCID: PMC2971591 DOI: 10.1104/pp.110.160325] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2010] [Accepted: 09/13/2010] [Indexed: 05/19/2023]
Abstract
Membrane compartmentalization and trafficking within and between cells is considered an essential cellular property of higher eukaryotes. We established a high-throughput imaging method suitable for the quantitative detection of membrane compartments at subcellular resolution in intact epidermal tissue. Whole Arabidopsis (Arabidopsis thaliana) cotyledon leaves were subjected to quantitative confocal laser microscopy using automated image acquisition, computational pattern recognition, and quantification of membrane compartments. This revealed that our method is sensitive and reliable to detect distinct endomembrane compartments. We applied quantitative confocal laser microscopy to a transgenic line expressing GFP-2xFYVE as a marker for endosomal compartments during biotic or abiotic stresses, and detected markedly quantitative adaptations in response to changing environments. Using a transgenic line expressing the plasma membrane-resident syntaxin GFP-PEN1, we quantified the pathogen-inducible extracellular accumulation of this fusion protein at fungal entry sites. Our protocol provides a platform to study the quantitative and dynamic changes of endomembrane trafficking, and potential adaptations of this machinery to physiological stress.
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26
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Mirzaei M, Pla-Roca M, Safavieh R, Nazarova E, Safavieh M, Li H, Vogel J, Juncker D. Microfluidic perfusion system for culturing and imaging yeast cell microarrays and rapidly exchanging media. LAB ON A CHIP 2010; 10:2449-2457. [PMID: 20714499 DOI: 10.1039/c004857g] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
High resolution live cell microscopy is increasingly used to detect cellular dynamics in response to drugs and chemicals, but it depends on complex and expensive liquid handling devices that have limited its wider adoption. Here, we present a microfluidic perfusion system that is built without using specialized microfabrication infrastructure, simple to use because only a pipette is needed for liquid handling, and yet allows for rapid media exchange and simultaneous fluorescence microscopy imaging. Yeast cells may be introduced from a culture, or spotted as arrays on a coverslip, and are sandwiched with a 20 mum thick track-etched membrane. A second coverslip and a mesh with 120 mum porosity are placed on top, forming a microfluidic conduit for lateral flow of solutions by capillary effects. Solutions introduced through the inlet flow through the mesh and chemicals diffuse vertically across the membrane to the cells trapped below. Solutions are exchanged by adding a new sample to the inlet. Using this system, we studied the dynamic response of F-actin in living yeast expressing Sac6-EGFP-a protein associated with discrete F-actin structures called "patches"-to the drug latrunculin A, a well known inhibitor of actin polymerization. We observed that the patches disappeared in 85% of the cells within 5 min, and re-assembled in 45 min following exchange of the drug with media. The perfusion system presented here is a simple, inexpensive device suited for analysis of drug dose-response and regeneration of single cells and arrays of cells.
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Affiliation(s)
- Maryam Mirzaei
- Biomedical Engineering Department, McGill University, Montréal, QC, Canada
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27
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Walling MA, Wang S, Shi H, Shepard JRE. Quantum dots for positional registration in live cell-based arrays. Anal Bioanal Chem 2010; 398:1263-71. [DOI: 10.1007/s00216-010-4053-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2010] [Revised: 07/14/2010] [Accepted: 07/20/2010] [Indexed: 11/29/2022]
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28
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Saleem RA, Long-O'Donnell R, Dilworth DJ, Armstrong AM, Jamakhandi AP, Wan Y, Knijnenburg TA, Niemistö A, Boyle J, Rachubinski RA, Shmulevich I, Aitchison JD. Genome-wide analysis of effectors of peroxisome biogenesis. PLoS One 2010; 5:e11953. [PMID: 20694151 PMCID: PMC2915925 DOI: 10.1371/journal.pone.0011953] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2010] [Accepted: 07/12/2010] [Indexed: 11/19/2022] Open
Abstract
Peroxisomes are intracellular organelles that house a number of diverse metabolic processes, notably those required for beta-oxidation of fatty acids. Peroxisomes biogenesis can be induced by the presence of peroxisome proliferators, including fatty acids, which activate complex cellular programs that underlie the induction process. Here, we used multi-parameter quantitative phenotype analyses of an arrayed mutant collection of yeast cells induced to proliferate peroxisomes, to establish a comprehensive inventory of genes required for peroxisome induction and function. The assays employed include growth in the presence of fatty acids, and confocal imaging and flow cytometry through the induction process. In addition to the classical phenotypes associated with loss of peroxisomal functions, these studies identified 169 genes required for robust signaling, transcription, normal peroxisomal development and morphologies, and transmission of peroxisomes to daughter cells. These gene products are localized throughout the cell, and many have indirect connections to peroxisome function. By integration with extant data sets, we present a total of 211 genes linked to peroxisome biogenesis and highlight the complex networks through which information flows during peroxisome biogenesis and function.
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Affiliation(s)
- Ramsey A. Saleem
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Rose Long-O'Donnell
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - David J. Dilworth
- Institute for Systems Biology, Seattle, Washington, United States of America
| | | | | | - Yakun Wan
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Theo A. Knijnenburg
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Antti Niemistö
- Institute for Systems Biology, Seattle, Washington, United States of America
- Department of Signal Processing, Tampere University of Technology, Tampere, Finland
| | - John Boyle
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Richard A. Rachubinski
- Department of Cell Biology, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Ilya Shmulevich
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - John D. Aitchison
- Institute for Systems Biology, Seattle, Washington, United States of America
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29
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Obese and anorexic yeasts: Experimental models to understand the metabolic syndrome and lipotoxicity. Biochim Biophys Acta Mol Cell Biol Lipids 2010; 1801:222-9. [DOI: 10.1016/j.bbalip.2009.12.016] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2009] [Revised: 12/23/2009] [Accepted: 12/24/2009] [Indexed: 12/23/2022]
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30
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Huh S, Lee D, Murphy RF. Efficient framework for automated classification of subcellular patterns in budding yeast. Cytometry A 2010; 75:934-40. [PMID: 19753630 DOI: 10.1002/cyto.a.20793] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Fluorescent-tagging and digital imaging are widely used to determine the subcellular location of proteins. An extensive publicly available collection of images for most proteins expressed in the yeast S. cerevisae has provided both an important source of information on protein location but also a testbed for methods designed to automate the assignment of locations to unknown proteins. The first system for automated classification of subcellular patterns in these yeast images utilized a computationally expensive method for segmentation of images into individual cells and achieved an overall accuracy of 81%. The goal of the present study was to improve on both the computational efficiency and accuracy of this task. Numerical features derived from applying Gabor filters to small image patches were implemented so that patterns could be classified without segmentation into single cells. When tested on 20 classes of images visually classified as showing a single subcellular pattern, an overall accuracy of 87.8% was achieved, with 2330 images out of 2655 images in the UCSF dataset being correctly classified. On the 4 largest classes of these images, 95.3% accuracy was achieved. The improvement over the previous approach is not only in classification accuracy but also in computational efficiency, with the new approach taking about 1 h on a desktop computer to complete all steps required to perform a 6-fold cross validation on all images.
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Affiliation(s)
- Seungil Huh
- Robotics Institute, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
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31
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Petschnigg J, Wolinski H, Kolb D, Zellnig G, Kurat CF, Natter K, Kohlwein SD. Good fat, essential cellular requirements for triacylglycerol synthesis to maintain membrane homeostasis in yeast. J Biol Chem 2009; 284:30981-93. [PMID: 19608739 PMCID: PMC2781499 DOI: 10.1074/jbc.m109.024752] [Citation(s) in RCA: 165] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2009] [Revised: 07/16/2009] [Indexed: 12/29/2022] Open
Abstract
Storage triacylglycerols (TAG) and membrane phospholipids share common precursors, i.e. phosphatidic acid and diacylglycerol, in the endoplasmic reticulum. In addition to providing a biophysically rather inert storage pool for fatty acids, TAG synthesis plays an important role to buffer excess fatty acids (FA). The inability to incorporate exogenous oleic acid into TAG in a yeast mutant lacking the acyltransferases Lro1p, Dga1p, Are1p, and Are2p contributing to TAG synthesis results in dysregulation of lipid synthesis, massive proliferation of intracellular membranes, and ultimately cell death. Carboxypeptidase Y trafficking from the endoplasmic reticulum to the vacuole is severely impaired, but the unfolded protein response is only moderately up-regulated, and dispensable for membrane proliferation, upon exposure to oleic acid. FA-induced toxicity is specific to oleic acid and much less pronounced with palmitoleic acid and is not detectable with the saturated fatty acids, palmitic and stearic acid. Palmitic acid supplementation partially suppresses oleic acid-induced lipotoxicity and restores carboxypeptidase Y trafficking to the vacuole. These data show the following: (i) FA uptake is not regulated by the cellular lipid requirements; (ii) TAG synthesis functions as a crucial intracellular buffer for detoxifying excess unsaturated fatty acids; (iii) membrane lipid synthesis and proliferation are responsive to and controlled by a balanced fatty acid composition.
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Affiliation(s)
- Julia Petschnigg
- From the Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50/II, A8010 Graz and
| | - Heimo Wolinski
- From the Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50/II, A8010 Graz and
| | - Dagmar Kolb
- From the Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50/II, A8010 Graz and
| | - Günther Zellnig
- Institute of Plant Sciences, University of Graz, A8010 Graz, Austria
| | - Christoph F. Kurat
- From the Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50/II, A8010 Graz and
| | - Klaus Natter
- From the Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50/II, A8010 Graz and
| | - Sepp D. Kohlwein
- From the Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50/II, A8010 Graz and
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32
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Current awareness on yeast. Yeast 2009. [DOI: 10.1002/yea.1622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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