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Sankaranarayanan S, Haag C, Petzsch P, Köhrer K, Matuszyńska A, Zarnack K, Feldbrügge M. The mRNA stability factor Khd4 defines a specific mRNA regulon for membrane trafficking in the pathogen Ustilago maydis. Proc Natl Acad Sci U S A 2023; 120:e2301731120. [PMID: 37590419 PMCID: PMC10450656 DOI: 10.1073/pnas.2301731120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 07/10/2023] [Indexed: 08/19/2023] Open
Abstract
Fungal pathogens depend on sophisticated gene expression programs for successful infection. A crucial component is RNA regulation mediated by RNA-binding proteins (RBPs). However, little is known about the spatiotemporal RNA control mechanisms during fungal pathogenicity. Here, we discover that the RBP Khd4 defines a distinct mRNA regulon to orchestrate membrane trafficking during pathogenic development of Ustilago maydis. By establishing hyperTRIBE for fungal RBPs, we generated a comprehensive transcriptome-wide map of Khd4 interactions in vivo. We identify a defined set of target mRNAs enriched for regulatory proteins involved, e.g., in GTPase signaling. Khd4 controls the stability of target mRNAs via its cognate regulatory element AUACCC present in their 3' untranslated regions. Studying individual examples reveals a unique link between Khd4 and vacuole maturation. Thus, we uncover a distinct role for an RNA stability factor defining a specific mRNA regulon for membrane trafficking during pathogenicity.
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Affiliation(s)
- Srimeenakshi Sankaranarayanan
- Institute of Microbiology, Cluster of Excellence on Plant Sciences, Heinrich Heine University Düsseldorf, Düsseldorf40204, Germany
| | - Carl Haag
- Institute of Microbiology, Cluster of Excellence on Plant Sciences, Heinrich Heine University Düsseldorf, Düsseldorf40204, Germany
| | - Patrick Petzsch
- Biologisch-Medizinisches Forschungszentrum, Heinrich Heine University Düsseldorf, Düsseldorf40204, Germany
| | - Karl Köhrer
- Biologisch-Medizinisches Forschungszentrum, Heinrich Heine University Düsseldorf, Düsseldorf40204, Germany
| | - Anna Matuszyńska
- Department of Biology, Computational Life Science, Rheinisch-Westfälische Technische Hochschule Aachen University, Aachen52074, Germany
| | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt a.M.60438, Germany
- Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt a.M.60438, Germany
| | - Michael Feldbrügge
- Institute of Microbiology, Cluster of Excellence on Plant Sciences, Heinrich Heine University Düsseldorf, Düsseldorf40204, Germany
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2
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Tang H, Huang X, Pang S. Regulation of the lysosome by sphingolipids: potential role in aging. J Biol Chem 2022; 298:102118. [PMID: 35691340 PMCID: PMC9257404 DOI: 10.1016/j.jbc.2022.102118] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 06/01/2022] [Accepted: 06/04/2022] [Indexed: 02/04/2023] Open
Abstract
Sphingolipids are a class of bioactive complex lipids that have been closely associated with aging and aging-related diseases. However, the mechanism through which sphingolipids control aging has long been a mystery. Emerging studies reveal that sphingolipids exert tight control over lysosomal homeostasis and function, as evidenced by sphingolipid-related diseases, including but not limited to lysosomal storage disorders. These diseases are defined by primary lysosomal defects and a few secondary defects such as mitochondrial dysfunction. Intriguingly, recent research indicates that the majority of these defects are also associated with aging, implying that sphingolipid-related diseases and aging may share common mechanisms. We propose that the lysosome is a pivotal hub for sphingolipid-mediated aging regulation. This review discusses the critical roles of sphingolipid metabolism in regulating various lysosomal functions, with an emphasis on how such regulation may contribute to aging and aging-related diseases.
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Affiliation(s)
- Haiqing Tang
- School of Life Sciences, Chongqing University, Chongqing, 401331, China
| | - Xiaokun Huang
- School of Life Sciences, Chongqing University, Chongqing, 401331, China
| | - Shanshan Pang
- School of Life Sciences, Chongqing University, Chongqing, 401331, China.
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3
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The Role of Sch9 and the V-ATPase in the Adaptation Response to Acetic Acid and the Consequences for Growth and Chronological Lifespan. Microorganisms 2021; 9:microorganisms9091871. [PMID: 34576766 PMCID: PMC8472237 DOI: 10.3390/microorganisms9091871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 08/20/2021] [Accepted: 08/30/2021] [Indexed: 11/17/2022] Open
Abstract
Studies with Saccharomyces cerevisiae indicated that non-physiologically high levels of acetic acid promote cellular acidification, chronological aging, and programmed cell death. In the current study, we compared the cellular lipid composition, acetic acid uptake, intracellular pH, growth, and chronological lifespan of wild-type cells and mutants lacking the protein kinase Sch9 and/or a functional V-ATPase when grown in medium supplemented with different acetic acid concentrations. Our data show that strains lacking the V-ATPase are especially more susceptible to growth arrest in the presence of high acetic acid concentrations, which is due to a slower adaptation to the acid stress. These V-ATPase mutants also displayed changes in lipid homeostasis, including alterations in their membrane lipid composition that influences the acetic acid diffusion rate and changes in sphingolipid metabolism and the sphingolipid rheostat, which is known to regulate stress tolerance and longevity of yeast cells. However, we provide evidence that the supplementation of 20 mM acetic acid has a cytoprotective and presumable hormesis effect that extends the longevity of all strains tested, including the V-ATPase compromised mutants. We also demonstrate that the long-lived sch9Δ strain itself secretes significant amounts of acetic acid during stationary phase, which in addition to its enhanced accumulation of storage lipids may underlie its increased lifespan.
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4
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Flotillin-Dependent Membrane Microdomains Are Required for Functional Phagolysosomes against Fungal Infections. Cell Rep 2021; 32:108017. [PMID: 32814035 PMCID: PMC10054021 DOI: 10.1016/j.celrep.2020.108017] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 04/03/2020] [Accepted: 07/17/2020] [Indexed: 11/23/2022] Open
Abstract
Lipid rafts form signaling platforms on biological membranes with incompletely characterized role in immune response to infection. Here we report that lipid-raft microdomains are essential components of phagolysosomal membranes of macrophages and depend on flotillins. Genetic deletion of flotillins demonstrates that the assembly of both major defense complexes vATPase and NADPH oxidase requires membrane microdomains. Furthermore, we describe a virulence mechanism leading to dysregulation of membrane microdomains by melanized wild-type conidia of the important human-pathogenic fungus Aspergillus fumigatus resulting in reduced phagolysosomal acidification. We show that phagolysosomes with ingested melanized conidia contain a reduced amount of free Ca2+ ions and that inhibition of Ca2+-dependent calmodulin activity led to reduced lipid-raft formation. We identify a single-nucleotide polymorphism in the human FLOT1 gene resulting in heightened susceptibility for invasive aspergillosis in hematopoietic stem cell transplant recipients. Collectively, flotillin-dependent microdomains on the phagolysosomal membrane play an essential role in protective antifungal immunity.
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5
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Zhang LB, Qiu TT, Guan Y, Huang ZH, Ye XY. Analyses of transcriptomics and metabolomics reveal pathway of vacuolar Sur7 contributed to biocontrol potential of entomopathogenic Beauveria bassiana. J Invertebr Pathol 2021; 181:107564. [PMID: 33689762 DOI: 10.1016/j.jip.2021.107564] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 02/23/2021] [Accepted: 02/26/2021] [Indexed: 01/21/2023]
Abstract
Beauveria bassiana is a critical entomopathogenic fungus for pest biocontrol, whose efficiency depends on fungal development and stress resistance. Unlike its revealed location in plasma membrane patches in other organisms, B. bassiana Sur7 specifically localized in vacuoles. This vacuolar Sur7 was previously demonstrated to affect stress tolerance, hyphal development and virulence. There, however, remain more mechanistic details to be explored. In this study, transcriptomics and metabolomics were applied to investigate the mechanism of vacuolar Sur7. Analyses of transcriptomics and metabolomics displayed many differentially expressed genes and abundant metabolites in response to Sur7 loss, respectively. Together with genes associated with vacuolar biofunction (including transportation and hydrolysis), the altered metabolites contributed to cell wall construction and stress resistance. Particularly, an N-acetylglucosamine-associated Brg1/Nrg1 pathway was enriched and partially affected by Sur7. Absence of Sur7 changed the expression level of Brg1/Nrg1 pathway-related transcript factors, which interfered with downstream phenotype of sporulation. In addition, Sur7 was involved in the accumulation of sphingoid bases, which may affect sphingolipid-related signaling pathway. Although experimental evidence is further required, our studies provide a preliminary framework for future exploring the regulatory mechanism of Sur7, and give a new version of metabolic agency connecting Sur7 and downstream signaling pathway.
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Affiliation(s)
- Long-Bin Zhang
- Fujian Key Laboratory of Marine Enzyme Engineering, College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian 350116, China.
| | - Ting-Ting Qiu
- Fujian Key Laboratory of Marine Enzyme Engineering, College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian 350116, China
| | - Yi Guan
- Fujian Key Laboratory of Marine Enzyme Engineering, College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian 350116, China
| | - Zhi-Hong Huang
- Chemical Engineering Institution, Huaqiao University, Xiamen, Fujian 361021, China
| | - Xiu-Yun Ye
- Fujian Key Laboratory of Marine Enzyme Engineering, College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian 350116, China
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6
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Sun L, Liao K. The Effect of Honokiol on Ergosterol Biosynthesis and Vacuole Function in Candida albicans. J Microbiol Biotechnol 2020; 30:1835-1842. [PMID: 33263334 PMCID: PMC9728367 DOI: 10.4014/jmb.2008.08019] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 10/16/2020] [Accepted: 11/24/2020] [Indexed: 12/15/2022]
Abstract
Ergosterol, an essential constituent of membrane lipids of yeast, is distributed in both the cell membrane and intracellular endomembrane components such as vacuoles. Honokiol, a major polyphenol isolated from Magnolia officinalis, has been shown to inhibit the growth of Candida albicans. Here, we assessed the effect of honokiol on ergosterol biosynthesis and vacuole function in C. albicans. Honokiol could decrease the ergosterol content and upregulate the expression of genes related with the ergosterol biosynthesis pathway. The exogenous supply of ergosterol attenuated the toxicity of honokiol against C. albicans. Honokiol treatment could induce cytosolic acidification by blocking the activity of the plasma membrane Pma1p H+-ATPase. Furthermore, honokiol caused abnormalities in vacuole morphology and function. Concomitant ergosterol feeding to some extent restored the vacuolar morphology and the function of acidification in cells treated by honokiol. Honokiol also disrupted the intracellular calcium homeostasis. Amiodarone attenuated the antifungal effects of honokiol against C. albicans, probably due to the activation of the calcineurin signaling pathway which is involved in honokiol tolerance. In conclusion, this study demonstrated that honokiol could inhibit ergosterol biosynthesis and decrease Pma 1p H+-ATPase activity, which resulted in the abnormal pH in vacuole and cytosol.
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Affiliation(s)
- Lingmei Sun
- Department of Pharmacology, Medical School of Southeast University, Nanjing 20009, P.R. China,Corresponding authors L.Sun Phone: +86-25-83272525 E-mail:
| | - Kai Liao
- Department of Pathology and Pathophysiology, Medical School of Southeast University, Nanjing 10009, P.R. China,K.Liao E-mail:
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7
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Hurst LR, Fratti RA. Lipid Rafts, Sphingolipids, and Ergosterol in Yeast Vacuole Fusion and Maturation. Front Cell Dev Biol 2020; 8:539. [PMID: 32719794 PMCID: PMC7349313 DOI: 10.3389/fcell.2020.00539] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 06/09/2020] [Indexed: 01/15/2023] Open
Abstract
The Saccharomyces cerevisiae lysosome-like vacuole is a useful model for studying membrane fusion events and organelle maturation processes utilized by all eukaryotes. The vacuolar membrane is capable of forming micrometer and nanometer scale domains that can be visualized using microscopic techniques and segregate into regions with surprisingly distinct lipid and protein compositions. These lipid raft domains are liquid-ordered (L o ) like regions that are rich in sphingolipids, phospholipids with saturated acyl chains, and ergosterol. Recent studies have shown that these lipid rafts contain an enrichment of many different proteins that function in essential activities such as nutrient transport, organelle contact, membrane trafficking, and homotypic fusion, suggesting that they are biologically relevant regions within the vacuole membrane. Here, we discuss recent developments and the current understanding of sphingolipid and ergosterol function at the vacuole, the composition and function of lipid rafts at this organelle and how the distinct lipid and protein composition of these regions facilitates the biological processes outlined above.
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Affiliation(s)
- Logan R Hurst
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Rutilio A Fratti
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, United States.,Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
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8
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Hui L, Soliman ML, Geiger NH, Miller NM, Afghah Z, Lakpa KL, Chen X, Geiger JD. Acidifying Endolysosomes Prevented Low-Density Lipoprotein-Induced Amyloidogenesis. J Alzheimers Dis 2020; 67:393-410. [PMID: 30594929 DOI: 10.3233/jad-180941] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Cholesterol dyshomeostasis has been linked to the pathogenesis of sporadic Alzheimer's disease (AD). In furthering the understanding of mechanisms by which increased levels of circulating cholesterol augments the risk of developing sporadic AD, others and we have reported that low-density lipoprotein (LDL) enters brain parenchyma by disrupting the blood-brain barrier and that endolysosome de-acidification plays a role in LDL-induced amyloidogenesis in neurons. Here, we tested the hypothesis that endolysosome de-acidification was central to amyloid-β (Aβ) generation and that acidifying endolysosomes protects against LDL-induced increases in Aβ levels in neurons. We demonstrated that LDL, but not HDL, de-acidified endolysosomes and increased intraneuronal and secreted levels of Aβ. ML-SA1, an agonist of endolysosome-resident TRPML1 channels, acidified endolysosomes, and TRPML1 knockdown attenuated ML-SA1-induced endolysosome acidification. ML-SA1 blocked LDL-induced increases in intraneuronal and secreted levels of Aβ as well as Aβ accumulation in endolysosomes, prevented BACE1 accumulation in endolysosomes, and decreased BACE1 activity levels. LDL downregulated TRPML1 protein levels, and TRPML1 knockdown worsens LDL-induced increases in Aβ. Our findings suggest that endolysosome acidification by activating TRPML1 may represent a protective strategy against sporadic AD.
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Affiliation(s)
- Liang Hui
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND, USA
| | - Mahmoud L Soliman
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND, USA
| | - Nicholas H Geiger
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND, USA
| | - Nicole M Miller
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND, USA
| | - Zahra Afghah
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND, USA
| | - Koffi L Lakpa
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND, USA
| | - Xuesong Chen
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND, USA
| | - Jonathan D Geiger
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND, USA
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9
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Aufschnaiter A, Büttner S. The vacuolar shapes of ageing: From function to morphology. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2019; 1866:957-970. [PMID: 30796938 DOI: 10.1016/j.bbamcr.2019.02.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 02/13/2019] [Accepted: 02/15/2019] [Indexed: 12/21/2022]
Abstract
Cellular ageing results in accumulating damage to various macromolecules and the progressive decline of organelle function. Yeast vacuoles as well as their counterpart in higher eukaryotes, the lysosomes, emerge as central organelles in lifespan determination. These acidic organelles integrate enzymatic breakdown and recycling of cellular waste with nutrient sensing, storage, signalling and mobilization. Establishing physical contact with virtually all other organelles, vacuoles serve as hubs of cellular homeostasis. Studies in Saccharomyces cerevisiae contributed substantially to our understanding of the ageing process per se and the multifaceted roles of vacuoles/lysosomes in the maintenance of cellular fitness with progressing age. Here, we discuss the multiple roles of the vacuole during ageing, ranging from vacuolar dynamics and acidification as determinants of lifespan to the function of this organelle as waste bin, recycling facility, nutrient reservoir and integrator of nutrient signalling.
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Affiliation(s)
- Andreas Aufschnaiter
- Institute of Molecular Biosciences, University of Graz, Humboldtstraße 50, 8010 Graz, Austria
| | - Sabrina Büttner
- Institute of Molecular Biosciences, University of Graz, Humboldtstraße 50, 8010 Graz, Austria; Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrhenius väg 20C, 106 91 Stockholm, Sweden.
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10
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McCarthy JK, Smith SR, McCrow JP, Tan M, Zheng H, Beeri K, Roth R, Lichtle C, Goodenough U, Bowler CP, Dupont CL, Allen AE. Nitrate Reductase Knockout Uncouples Nitrate Transport from Nitrate Assimilation and Drives Repartitioning of Carbon Flux in a Model Pennate Diatom. THE PLANT CELL 2017; 29:2047-2070. [PMID: 28765511 PMCID: PMC5590495 DOI: 10.1105/tpc.16.00910] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 06/06/2017] [Accepted: 07/29/2017] [Indexed: 05/03/2023]
Abstract
The ecological prominence of diatoms in the ocean environment largely results from their superior competitive ability for dissolved nitrate (NO3-). To investigate the cellular and genetic basis of diatom NO3- assimilation, we generated a knockout in the nitrate reductase gene (NR-KO) of the model pennate diatom Phaeodactylum tricornutum In NR-KO cells, N-assimilation was abolished although NO3- transport remained intact. Unassimilated NO3- accumulated in NR-KO cells, resulting in swelling and associated changes in biochemical composition and physiology. Elevated expression of genes encoding putative vacuolar NO3- chloride channel transporters plus electron micrographs indicating enlarged vacuoles suggested vacuolar storage of NO3- Triacylglycerol concentrations in the NR-KO cells increased immediately following the addition of NO3-, and these increases coincided with elevated gene expression of key triacylglycerol biosynthesis components. Simultaneously, induction of transcripts encoding proteins involved in thylakoid membrane lipid recycling suggested more abrupt repartitioning of carbon resources in NR-KO cells compared with the wild type. Conversely, ribosomal structure and photosystem genes were immediately deactivated in NR-KO cells following NO3- addition, followed within hours by deactivation of genes encoding enzymes for chlorophyll biosynthesis and carbon fixation and metabolism. N-assimilation pathway genes respond uniquely, apparently induced simultaneously by both NO3- replete and deplete conditions.
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Affiliation(s)
- James K McCarthy
- Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, California 92037
| | - Sarah R Smith
- Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, California 92037
- Integrative Oceanography Division, Scripps Institution of Oceanography, UC San Diego, La Jolla, California 92037
| | - John P McCrow
- Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, California 92037
| | - Maxine Tan
- Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, California 92037
| | - Hong Zheng
- Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, California 92037
| | - Karen Beeri
- Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, California 92037
| | - Robyn Roth
- Department of Biology, Washington University, St. Louis, Missouri 63130
| | - Christian Lichtle
- Institut de Biologie de l'École Normale Supérieure, École Normale Supérieure, Paris Sciences et Lettres Research University, CNRS UMR8197 INSERM U1024, 75005 Paris, France
| | - Ursula Goodenough
- Department of Biology, Washington University, St. Louis, Missouri 63130
| | - Chris P Bowler
- Institut de Biologie de l'École Normale Supérieure, École Normale Supérieure, Paris Sciences et Lettres Research University, CNRS UMR8197 INSERM U1024, 75005 Paris, France
| | - Christopher L Dupont
- Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, California 92037
| | - Andrew E Allen
- Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, California 92037
- Integrative Oceanography Division, Scripps Institution of Oceanography, UC San Diego, La Jolla, California 92037
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11
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Sharma S, Wilkens S. Biolayer interferometry of lipid nanodisc-reconstituted yeast vacuolar H + -ATPase. Protein Sci 2017; 26:1070-1079. [PMID: 28241399 DOI: 10.1002/pro.3143] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 02/15/2017] [Accepted: 02/17/2017] [Indexed: 01/24/2023]
Abstract
Vacuolar H+ -ATPase (V-ATPase) is a large, multisubunit membrane protein complex responsible for the acidification of subcellular compartments and the extracellular space. V-ATPase activity is regulated by reversible disassembly, resulting in cytosolic V1 -ATPase and membrane-integral V0 proton channel sectors. Reversible disassembly is accompanied by transient interaction with cellular factors and assembly chaperones. Quantifying protein-protein interactions involving membrane proteins, however, is challenging. Here we present a novel method to determine kinetic constants of membrane protein-protein interactions using biolayer interferometry (BLI). Yeast vacuoles are solubilized, vacuolar proteins are reconstituted into lipid nanodiscs with native vacuolar lipids and biotinylated membrane scaffold protein (MSP) followed by affinity purification of nanodisc-reconstituted V-ATPase (V1 V0 ND). We show that V1 V0 ND can be immobilized on streptavidin-coated BLI sensors to quantitate binding of a pathogen derived inhibitor and to measure the kinetics of nucleotide dependent enzyme dissociation.
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Affiliation(s)
- Stuti Sharma
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University 750 East Adams Street, Syracuse, New York, 13210
| | - Stephan Wilkens
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University 750 East Adams Street, Syracuse, New York, 13210
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12
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Colacurcio DJ, Nixon RA. Disorders of lysosomal acidification-The emerging role of v-ATPase in aging and neurodegenerative disease. Ageing Res Rev 2016; 32:75-88. [PMID: 27197071 DOI: 10.1016/j.arr.2016.05.004] [Citation(s) in RCA: 299] [Impact Index Per Article: 37.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 05/02/2016] [Accepted: 05/13/2016] [Indexed: 12/21/2022]
Abstract
Autophagy and endocytosis deliver unneeded cellular materials to lysosomes for degradation. Beyond processing cellular waste, lysosomes release metabolites and ions that serve signaling and nutrient sensing roles, linking the functions of the lysosome to various pathways for intracellular metabolism and nutrient homeostasis. Each of these lysosomal behaviors is influenced by the intraluminal pH of the lysosome, which is maintained in the low acidic range by a proton pump, the vacuolar ATPase (v-ATPase). New reports implicate altered v-ATPase activity and lysosomal pH dysregulation in cellular aging, longevity, and adult-onset neurodegenerative diseases, including forms of Parkinson disease and Alzheimer disease. Genetic defects of subunits composing the v-ATPase or v-ATPase-related proteins occur in an increasingly recognized group of familial neurodegenerative diseases. Here, we review the expanding roles of the v-ATPase complex as a platform regulating lysosomal hydrolysis and cellular homeostasis. We discuss the unique vulnerability of neurons to persistent low level lysosomal dysfunction and review recent clinical and experimental studies that link dysfunction of the v-ATPase complex to neurodegenerative diseases across the age spectrum.
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13
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Jansen EJR, Timal S, Ryan M, Ashikov A, van Scherpenzeel M, Graham LA, Mandel H, Hoischen A, Iancu TC, Raymond K, Steenbergen G, Gilissen C, Huijben K, van Bakel NHM, Maeda Y, Rodenburg RJ, Adamowicz M, Crushell E, Koenen H, Adams D, Vodopiutz J, Greber-Platzer S, Müller T, Dueckers G, Morava E, Sykut-Cegielska J, Martens GJM, Wevers RA, Niehues T, Huynen MA, Veltman JA, Stevens TH, Lefeber DJ. ATP6AP1 deficiency causes an immunodeficiency with hepatopathy, cognitive impairment and abnormal protein glycosylation. Nat Commun 2016; 7:11600. [PMID: 27231034 PMCID: PMC4894975 DOI: 10.1038/ncomms11600] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 04/12/2016] [Indexed: 02/07/2023] Open
Abstract
The V-ATPase is the main regulator of intra-organellar acidification. Assembly of this complex has extensively been studied in yeast, while limited knowledge exists for man. We identified 11 male patients with hemizygous missense mutations in ATP6AP1, encoding accessory protein Ac45 of the V-ATPase. Homology detection at the level of sequence profiles indicated Ac45 as the long-sought human homologue of yeast V-ATPase assembly factor Voa1. Processed wild-type Ac45, but not its disease mutants, restored V-ATPase-dependent growth in Voa1 mutant yeast. Patients display an immunodeficiency phenotype associated with hypogammaglobulinemia, hepatopathy and a spectrum of neurocognitive abnormalities. Ac45 in human brain is present as the common, processed ∼40-kDa form, while liver shows a 62-kDa intact protein, and B-cells a 50-kDa isoform. Our work unmasks Ac45 as the functional ortholog of yeast V-ATPase assembly factor Voa1 and reveals a novel link of tissue-specific V-ATPase assembly with immunoglobulin production and cognitive function.
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Affiliation(s)
- Eric J. R. Jansen
- Department of Molecular Animal Physiology, Donders Institute for Brain, Cognition and Behaviour, Centre for Neuroscience and Radboud Institute for Molecular Life Sciences, Faculty of Science, Radboud University, 6525 GA Nijmegen, The Netherlands
| | - Sharita Timal
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Margret Ryan
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, USA
| | - Angel Ashikov
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Monique van Scherpenzeel
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Laurie A. Graham
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, USA
| | - Hanna Mandel
- Metabolic Unit, Rambam Health Care Center, Rappaport School of Medicine, Technion, 3109601 Haifa, Israel
| | - Alexander Hoischen
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences and Donders Centre for Neuroscience, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Theodore C. Iancu
- The Milman-David Biomedical Research Unit, 24 Hazevi Avenue, 34355 Haifa, Israel
| | - Kimiyo Raymond
- Department of Laboratory Medicine and Pathology, Mayo College of Medicine, Rochester, Minnesota 55905, USA
| | - Gerry Steenbergen
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences and Donders Centre for Neuroscience, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Karin Huijben
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Nick H. M. van Bakel
- Department of Molecular Animal Physiology, Donders Institute for Brain, Cognition and Behaviour, Centre for Neuroscience and Radboud Institute for Molecular Life Sciences, Faculty of Science, Radboud University, 6525 GA Nijmegen, The Netherlands
| | - Yusuke Maeda
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Richard J. Rodenburg
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Department of Pediatrics, Nijmegen Centre for Mitochondrial Disorders (NCMD), Radboud university medical center, 6525 GA Nijmegen, The Netherlands
| | - Maciej Adamowicz
- Protein Laboratory, Children's Memorial Health Institute, 04730 Warsaw, Poland
| | - Ellen Crushell
- Temple Street Children's University Hospital, Temple Street, Dublin 1, DC01 YC67, Ireland
| | - Hans Koenen
- Department of Laboratory Medicine, Medical Immunology, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Darius Adams
- Personalized Genomic Medicine Pediatric Genetics and Metabolism Goryeb Children's Hospital, Morristown, New Jersey 07960, USA
| | - Julia Vodopiutz
- Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, 1090 Vienna, Austria
| | - Susanne Greber-Platzer
- Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, 1090 Vienna, Austria
| | - Thomas Müller
- Department of Pediatrics I, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Gregor Dueckers
- HELIOS Kliniken Krefeld, Children's Hospital, Lutherplatz 40, 47805 Krefeld, Germany
| | - Eva Morava
- Department of Pediatrics, Tulane University Medical School, New Orleans, Los Angeles 70112, USA
- Department of Pediatrics, University Medical School of Leuven, 3000 Leuven, Belgium
- Department of Pediatrics, Radboudumc, 6525GA, Nijmegen, The Netherlands
| | | | - Gerard J. M. Martens
- Department of Molecular Animal Physiology, Donders Institute for Brain, Cognition and Behaviour, Centre for Neuroscience and Radboud Institute for Molecular Life Sciences, Faculty of Science, Radboud University, 6525 GA Nijmegen, The Netherlands
| | - Ron A. Wevers
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Tim Niehues
- HELIOS Kliniken Krefeld, Children's Hospital, Lutherplatz 40, 47805 Krefeld, Germany
| | - Martijn A. Huynen
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525GA Nijmegen, The Netherlands
| | - Joris A. Veltman
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences and Donders Centre for Neuroscience, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Department of Clinical Genetics, Maastricht University Medical Centre, 6229HX Maastricht, The Netherlands
| | - Tom H. Stevens
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, USA
| | - Dirk J. Lefeber
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
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14
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Mallela SK, Almeida R, Ejsing CS, Conzelmann A. Functions of Ceramide Synthase Paralogs YPR114w and YJR116w of Saccharomyces cerevisiae. PLoS One 2016; 11:e0145831. [PMID: 26752183 PMCID: PMC4713442 DOI: 10.1371/journal.pone.0145831] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 11/04/2015] [Indexed: 12/22/2022] Open
Abstract
Ceramide is synthesized in yeast by two redundant acyl-CoA dependent synthases, Lag1 and Lac1. In lag1∆ lac1∆ cells, free fatty acids and sphingoid bases are elevated, and ceramides are produced through the redundant alkaline ceramidases Ypc1 and Ydc1, working backwards. Even with all four of these genes deleted, cells are surviving and continue to contain small amounts of complex sphingolipids. Here we show that these residual sphingolipids are not synthesized by YPR114w or YJR116w, proteins of unknown function showing a high degree of homology to Lag1 and Lac1. Indeed, the hextuple lag1∆ lac1∆ ypc1∆ ydc1∆ ypr114w∆ yjr116w∆ mutant still contains ceramides and complex sphingolipids. Yjr116w∆ exhibit an oxygen-dependent hypersensitivity to Cu2+ due to an increased mitochondrial production of reactive oxygen species (ROS) and a mitochondrially orchestrated programmed cell death in presence of copper, but also a general copper hypersensitivity that cannot be counteracted by the antioxidant N-acetyl-cysteine (NAC). Myriocin efficiently represses the synthesis of sphingoid bases of ypr114w∆, but not its growth. Both yjr116w∆ and ypr114w∆ have fragmented vacuoles and produce less ROS than wild type, before and after diauxic shift. Ypr114w∆/ypr114w∆ have an increased chronological life span. Thus, Yjr116w and Ypr114w are related, but not functionally redundant.
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Affiliation(s)
- Shamroop K. Mallela
- Division of Biochemistry, Department of Biology, University of Fribourg, Chemin du Musée 10, Fribourg, CH-1700, Switzerland
| | - Reinaldo Almeida
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230, Odense M, Denmark
| | - Christer S. Ejsing
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230, Odense M, Denmark
| | - Andreas Conzelmann
- Division of Biochemistry, Department of Biology, University of Fribourg, Chemin du Musée 10, Fribourg, CH-1700, Switzerland
- * E-mail:
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15
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Tani M. Structure–Function Relationship of Complex Sphingolipids in Yeast. TRENDS GLYCOSCI GLYC 2016. [DOI: 10.4052/tigg.1509.1j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Motohiro Tani
- Department of Chemistry, Faculty of Sciences, Kyushu University
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16
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Affiliation(s)
- Motohiro Tani
- Department of Chemistry, Faculty of Sciences, Kyushu University
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17
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Abstract
Maintenance of cellular homeostasis requires tight and coordinated control of numerous metabolic pathways, which are governed by interconnected networks of signaling pathways and energy-sensing regulators. Autophagy, a lysosomal degradation pathway by which the cell self-digests its own components, has over the past decade been recognized as an essential part of metabolism. Autophagy not only rids the cell of excessive or damaged organelles, misfolded proteins, and invading microorganisms, it also provides nutrients to maintain crucial cellular functions. Besides serving as essential structural moieties of biomembranes, lipids including sphingolipids are increasingly being recognized as central regulators of a number of important cellular processes, including autophagy. In the present review we describe how sphingolipids, with special emphasis on ceramides and sphingosine-1-phosphate, can act as physiological regulators of autophagy in relation to cellular and organismal growth, survival, and aging.
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Affiliation(s)
- Eva Bang Harvald
- Villum Center for Bioanalytical Sciences, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
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18
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Tani M, Toume M. Alteration of complex sphingolipid composition and its physiological significance in yeast Saccharomyces cerevisiae lacking vacuolar ATPase. Microbiology (Reading) 2015; 161:2369-83. [DOI: 10.1099/mic.0.000187] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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19
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Teixeira V, Medeiros TC, Vilaça R, Ferreira J, Moradas-Ferreira P, Costa V. Ceramide signaling targets the PP2A-like protein phosphatase Sit4p to impair vacuolar function, vesicular trafficking and autophagy in Isc1p deficient cells. Biochim Biophys Acta Mol Cell Biol Lipids 2015; 1861:21-33. [PMID: 26477382 DOI: 10.1016/j.bbalip.2015.10.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 09/09/2015] [Accepted: 10/14/2015] [Indexed: 02/02/2023]
Abstract
The vacuoles play important roles in cellular homeostasis and their functions include the digestion of cytoplasmic material and organelles derived from autophagy. Conserved nutrient signaling pathways regulate vacuolar function and autophagy, ensuring normal cell and organismal development and aging. Recent evidence implicates sphingolipids in the modulation of these processes, but the impact of ceramide signaling on vacuolar dynamics and autophagy remains largely unknown. Here, we show that yeast cells lacking Isc1p, an orthologue of mammalian neutral sphingomyelinase type 2, exhibit vacuolar fragmentation and dysfunctions, namely decreased Pep4p-mediated proteolysis and V-ATPase activity, which impairs vacuolar acidification. Moreover, these phenotypes are suppressed by downregulation of the ceramide-activated protein phosphatase Sit4p. The isc1Δ cells also exhibit defective Cvt and vesicular trafficking in a Sit4p-dependent manner, ultimately contributing to a reduced autophagic flux. Importantly, these phenotypes are also suppressed by downregulation of the nutrient signaling kinase TORC1, which is known to inhibit Sit4p and autophagy, or Sch9p. These results support a model in which Sit4p functions downstream of Isc1p in a TORC1-independent, ceramide-dependent signaling branch that impairs vacuolar function and vesicular trafficking, leading to autophagic defects in yeast.
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Affiliation(s)
- Vitor Teixeira
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen s/n, 4200-135 Porto, Portugal; IBMC, Instituto de Biologia Molecular e Celular, Rua do Campo Alegre, 823, 4150-180 Porto, Portugal; ICBAS, Instituto de Ciências Biomédicas Abel Salazar, Departamento de Biologia Molecular, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
| | - Tânia C Medeiros
- IBMC, Instituto de Biologia Molecular e Celular, Rua do Campo Alegre, 823, 4150-180 Porto, Portugal
| | - Rita Vilaça
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen s/n, 4200-135 Porto, Portugal; IBMC, Instituto de Biologia Molecular e Celular, Rua do Campo Alegre, 823, 4150-180 Porto, Portugal
| | - João Ferreira
- IBMC, Instituto de Biologia Molecular e Celular, Rua do Campo Alegre, 823, 4150-180 Porto, Portugal
| | - Pedro Moradas-Ferreira
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen s/n, 4200-135 Porto, Portugal; IBMC, Instituto de Biologia Molecular e Celular, Rua do Campo Alegre, 823, 4150-180 Porto, Portugal; ICBAS, Instituto de Ciências Biomédicas Abel Salazar, Departamento de Biologia Molecular, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
| | - Vítor Costa
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen s/n, 4200-135 Porto, Portugal; IBMC, Instituto de Biologia Molecular e Celular, Rua do Campo Alegre, 823, 4150-180 Porto, Portugal; ICBAS, Instituto de Ciências Biomédicas Abel Salazar, Departamento de Biologia Molecular, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal.
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20
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Zhang C, Hicks GR, Raikhel NV. Molecular Composition of Plant Vacuoles: Important but Less Understood Regulations and Roles of Tonoplast Lipids. PLANTS 2015; 4:320-33. [PMID: 27135331 PMCID: PMC4844321 DOI: 10.3390/plants4020320] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 05/21/2015] [Accepted: 06/03/2015] [Indexed: 11/16/2022]
Abstract
The vacuole is an essential organelle for plant growth and development. It is the location for the storage of nutrients; such as sugars and proteins; and other metabolic products. Understanding the mechanisms of vacuolar trafficking and molecule transport across the vacuolar membrane is of great importance in understanding basic plant development and cell biology and for crop quality improvement. Proteins play important roles in vacuolar trafficking; such proteins include Rab GTPase signaling proteins; cargo recognition receptors; and SNAREs (Soluble NSF Attachment Protein Receptors) that are involved in membrane fusion. Some vacuole membrane proteins also serve as the transporters or channels for transport across the tonoplast. Less understood but critical are the roles of lipids in vacuolar trafficking. In this review, we will first summarize molecular composition of plant vacuoles and we will then discuss our latest understanding on the role of lipids in plant vacuolar trafficking and a surprising connection to ribosome function through the study of ribosomal mutants.
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Affiliation(s)
- Chunhua Zhang
- Center for Plant Cell Biology & Department of Botany and Plant Sciences, University of California, 900 University Ave., Riverside, CA 92521, USA.
| | - Glenn R Hicks
- Center for Plant Cell Biology & Department of Botany and Plant Sciences, University of California, 900 University Ave., Riverside, CA 92521, USA.
| | - Natasha V Raikhel
- Center for Plant Cell Biology & Department of Botany and Plant Sciences, University of California, 900 University Ave., Riverside, CA 92521, USA.
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21
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Yucel EB, Eraslan S, Ulgen KO. The impact of medium acidity on the chronological life span ofSaccharomyces cerevisiae - lipids, signaling cascades, mitochondrial and vacuolar functions. FEBS J 2014; 281:1281-303. [DOI: 10.1111/febs.12705] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2013] [Revised: 12/20/2013] [Accepted: 12/23/2013] [Indexed: 12/18/2022]
Affiliation(s)
- Esra B. Yucel
- Department of Chemical Engineering; Boğaziçi University; Istanbul Turkey
| | - Serpil Eraslan
- Department of Chemical Engineering; Boğaziçi University; Istanbul Turkey
| | - Kutlu O. Ulgen
- Department of Chemical Engineering; Boğaziçi University; Istanbul Turkey
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22
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Abstract
Continuous synthesis of all cellular components requires their constant turnover in order for a cell to achieve homeostasis. To this end, eukaryotic cells are endowed with two degradation pathways - the ubiquitin-proteasome system and the lysosomal pathway. The latter pathway is partly fed by autophagy, which targets intracellular material in distinct vesicles, termed autophagosomes, to the lysosome. Central to this pathway is a set of key autophagy proteins, including the ubiquitin-like modifier Atg8, that orchestrate autophagosome initiation and biogenesis. In higher eukaryotes, the Atg8 family comprises six members known as the light chain 3 (LC3) or γ-aminobutyric acid (GABA)-receptor-associated protein (GABARAP) proteins. Considerable effort during the last 15 years to decipher the molecular mechanisms that govern autophagy has significantly advanced our understanding of the functioning of this protein family. In this Cell Science at a Glance article and the accompanying poster, we present the current LC3 protein interaction network, which has been and continues to be vital for gaining insight into the regulation of autophagy.
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Affiliation(s)
- Philipp Wild
- Institute of Biochemistry II, Goethe University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
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23
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Lee YJ, Huang X, Kropat J, Henras A, Merchant SS, Dickson RC, Chanfreau GF. Sphingolipid signaling mediates iron toxicity. Cell Metab 2012; 16:90-6. [PMID: 22768841 PMCID: PMC3653578 DOI: 10.1016/j.cmet.2012.06.004] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Revised: 03/04/2012] [Accepted: 06/14/2012] [Indexed: 01/24/2023]
Abstract
Iron constitutes a major source of toxicity due to its ability to generate reactive oxygen species that can damage cellular macromolecules. However, the precise mechanism by which exposure to high iron concentrations results in cellular toxicity remains unknown. Here we identify sphingolipid synthesis and signaling as a major mediator of iron toxicity in S. cerevisiae. Inhibition of sphingolipid synthesis by myriocin treatment or after overexpression of the negative regulator Orm2p confers resistance to high iron. High iron conditions upregulate sphingolipid synthesis, and increasing sphingolipid levels by inactivating Orm2p exacerbates sensitivity to iron. Toxicity is mediated by sphingolipid signaling, as inactivation of the sphingolipid-activated protein kinases Pkh1p and Ypk1p and of the transcription factor Smp1p also enhances resistance to high iron conditions. These results demonstrate an unexpected connection between sphingolipid flux and iron toxicity and show that activation of a signal transduction cascade contributes to iron-mediated cellular toxicity.
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Affiliation(s)
- Yueh-Jung Lee
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095-1569, USA
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24
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Aguileta G, Lengelle J, Chiapello H, Giraud T, Viaud M, Fournier E, Rodolphe F, Marthey S, Ducasse A, Gendrault A, Poulain J, Wincker P, Gout L. Genes under positive selection in a model plant pathogenic fungus, Botrytis. INFECTION GENETICS AND EVOLUTION 2012; 12:987-96. [PMID: 22406010 DOI: 10.1016/j.meegid.2012.02.012] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2011] [Revised: 02/15/2012] [Accepted: 02/23/2012] [Indexed: 11/29/2022]
Abstract
The rapid evolution of particular genes is essential for the adaptation of pathogens to new hosts and new environments. Powerful methods have been developed for detecting targets of selection in the genome. Here we used divergence data to compare genes among four closely related fungal pathogens adapted to different hosts to elucidate the functions putatively involved in adaptive processes. For this goal, ESTs were sequenced in the specialist fungal pathogens Botrytis tulipae and Botrytis ficariarum, and compared with genome sequences of Botrytis cinerea and Sclerotinia sclerotiorum, responsible for diseases on over 200 plant species. A maximum likelihood-based analysis of 642 predicted orthologs detected 21 genes showing footprints of positive selection. These results were validated by resequencing nine of these genes in additional Botrytis species, showing they have also been rapidly evolving in other related species. Twenty of the 21 genes had not previously been identified as pathogenicity factors in B. cinerea, but some had functions related to plant-fungus interactions. The putative functions were involved in respiratory and energy metabolism, protein and RNA metabolism, signal transduction or virulence, similarly to what was detected in previous studies using the same approach in other pathogens. Mutants of B. cinerea were generated for four of these genes as a first attempt to elucidate their functions.
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Affiliation(s)
- Gabriela Aguileta
- Ecologie, Systématique et Evolution, Université Paris-Sud UMR8079, F-91405 Orsay Cedex, France
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25
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Su X, Chen W, Lee W, Jiang H, Zhang S, Lin H. YBR246W is required for the third step of diphthamide biosynthesis. J Am Chem Soc 2011; 134:773-6. [PMID: 22188241 DOI: 10.1021/ja208870a] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Diphthamide, the target of diphtheria toxin, is a post-translationally modified histidine residue that is found in archaeal and eukaryotic translation elongation factor 2. The biosynthesis and function of this modification has attracted the interest of many biochemists for decades. The biosynthesis has been known to proceed in three steps. Proteins required for the first and second steps have been identified, but the protein(s) required for the last step have remained elusive. Here we demonstrate that the YBR246W gene in yeast is required for the last step of diphthamide biosynthesis, as the deletion of YBR246W leads to the accumulation of diphthine, which is the enzymatic product of the second step of the biosynthesis. This discovery will provide important information leading to the complete elucidation of the full biosynthesis pathway of diphthamide.
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Affiliation(s)
- Xiaoyang Su
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
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