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Dimmer KS, Rapaport D. Mitochondrial contact sites as platforms for phospholipid exchange. Biochim Biophys Acta Mol Cell Biol Lipids 2016; 1862:69-80. [PMID: 27477677 DOI: 10.1016/j.bbalip.2016.07.010] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 07/21/2016] [Accepted: 07/22/2016] [Indexed: 12/15/2022]
Abstract
Mitochondria are unique organelles that contain their own - although strongly reduced - genome, and are surrounded by two membranes. While most cellular phospholipid biosynthesis takes place in the ER, mitochondria harbor the whole spectrum of glycerophospholipids common to biological membranes. Mitochondria also contribute to overall phospholipid biosynthesis in cells by producing phosphatidylethanolamine, phosphatidylglycerol, and cardiolipin. Considering these features, it is not surprising that mitochondria maintain highly active exchange of phospholipids with other cellular compartments. In this contribution we describe the transport of phospholipids between mitochondria and other organelles, and discuss recent developments in our understanding of the molecular functions of the protein complexes that mediate these processes. This article is part of a Special Issue entitled: Lipids of Mitochondria edited by Guenther Daum.
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Affiliation(s)
- Kai Stefan Dimmer
- Interfaculty Institute of Biochemistry, University of Tübingen, Hoppe-Seyler-Str. 4, 72076 Tübingen, Germany.
| | - Doron Rapaport
- Interfaculty Institute of Biochemistry, University of Tübingen, Hoppe-Seyler-Str. 4, 72076 Tübingen, Germany
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52
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Abstract
Membrane contact sites between mitochondria and other organelles are important for lipid and ion exchange, membrane dynamics, and signaling. Recent advances are revealing their molecular features and how different types of mitochondria contacts are coordinated with each other for cell function.
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Affiliation(s)
- Andrew Murley
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA 95616, USA
| | - Jodi Nunnari
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA 95616, USA.
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53
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Sinzel M, Tan T, Wendling P, Kalbacher H, Özbalci C, Chelius X, Westermann B, Brügger B, Rapaport D, Dimmer KS. Mcp3 is a novel mitochondrial outer membrane protein that follows a unique IMP-dependent biogenesis pathway. EMBO Rep 2016; 17:965-81. [PMID: 27226123 DOI: 10.15252/embr.201541273] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 04/26/2016] [Indexed: 11/09/2022] Open
Abstract
Mitochondria are separated from the remainder of the eukaryotic cell by the mitochondrial outer membrane (MOM). The MOM plays an important role in different transport processes like lipid trafficking and protein import. In yeast, the ER-mitochondria encounter structure (ERMES) has a central, but poorly defined role in both activities. To understand the functions of the ERMES, we searched for suppressors of the deficiency of one of its components, Mdm10, and identified a novel mitochondrial protein that we named Mdm10 complementing protein 3 (Mcp3). Mcp3 partially rescues a variety of ERMES-related phenotypes. We further demonstrate that Mcp3 is an integral protein of the MOM that follows a unique import pathway. It is recognized initially by the import receptor Tom70 and then crosses the MOM via the translocase of the outer membrane. Mcp3 is next relayed to the TIM23 translocase at the inner membrane, gets processed by the inner membrane peptidase (IMP) and finally integrates into the MOM. Hence, Mcp3 follows a novel biogenesis route where a MOM protein is processed by a peptidase of the inner membrane.
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Affiliation(s)
- Monika Sinzel
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Tao Tan
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Philipp Wendling
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Hubert Kalbacher
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Cagakan Özbalci
- Heidelberg University Biochemistry Center, Heidelberg, Germany
| | - Xenia Chelius
- Cell Biology, University of Bayreuth, Bayreuth, Germany
| | | | - Britta Brügger
- Heidelberg University Biochemistry Center, Heidelberg, Germany
| | - Doron Rapaport
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Kai Stefan Dimmer
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
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54
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Joshi AS, Fei N, Greenberg ML. Get1p and Get2p are required for maintenance of mitochondrial morphology and normal cardiolipin levels. FEMS Yeast Res 2016; 16:fow019. [PMID: 26926495 DOI: 10.1093/femsyr/fow019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/23/2016] [Indexed: 11/13/2022] Open
Abstract
Cardiolipin (CL) is the signature phospholipid of mitochondrial membranes. CL deficiency leads to defects in mitochondrial function. Using a targeted synthetic lethality screen to identify defects that exacerbate CL deficiency, we determined that deletion of mitochondrial morphology genes in cells lacking CL leads to severe growth defects. We show that ER membrane proteins Get1p and Get2p are required for maintaining normal levels of CL. We propose that these proteins regulate the level of CL by maintaining wild type-like tubular mitochondrial morphology. The genetic interactions observed in this study identify novel physiological modifiers that are required for maintenance of CL levels and mitochondrial morphology.
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Affiliation(s)
- Amit S Joshi
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA
| | - Naomi Fei
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA
| | - Miriam L Greenberg
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA
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55
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Wideman JG, Muñoz-Gómez SA. The evolution of ERMIONE in mitochondrial biogenesis and lipid homeostasis: An evolutionary view from comparative cell biology. Biochim Biophys Acta Mol Cell Biol Lipids 2016; 1861:900-912. [PMID: 26825688 DOI: 10.1016/j.bbalip.2016.01.015] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Revised: 01/19/2016] [Accepted: 01/25/2016] [Indexed: 12/17/2022]
Abstract
The ER-mitochondria organizing network (ERMIONE) in Saccharomyces cerevisiae is involved in maintaining mitochondrial morphology and lipid homeostasis. ERMES and MICOS are two scaffolding complexes of ERMIONE that contribute to these processes. ERMES is ancient but has been lost in several lineages including animals, plants, and SAR (stramenopiles, alveolates and rhizaria). On the other hand, MICOS is ancient and has remained present in all organisms bearing mitochondrial cristae. The ERMIONE precursor evolved in the α-proteobacterial ancestor of mitochondria which had the central subunit of MICOS, Mic60. The subsequent evolution of ERMIONE and its interactors in eukaryotes reflects the integrative co-evolution of mitochondria and their hosts and the adaptive paths that some lineages have followed in their specialization to certain environments. By approaching the ERMIONE from a perspective of comparative evolutionary cell biology, we hope to shed light on not only its evolutionary history, but also how ERMIONE components may function in organisms other than S. cerevisiae. This article is part of a Special Issue entitled: The cellular lipid landscape edited by Tim P. Levine and Anant K. Menon.
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Affiliation(s)
| | - Sergio A Muñoz-Gómez
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
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56
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Lang AB, John Peter AT, Walter P, Kornmann B. ER-mitochondrial junctions can be bypassed by dominant mutations in the endosomal protein Vps13. J Cell Biol 2015; 210:883-90. [PMID: 26370498 PMCID: PMC4576869 DOI: 10.1083/jcb.201502105] [Citation(s) in RCA: 177] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Substitutions in Vps13 suppress all measured phenotypic consequences of ERMES deficiency, and Vps13 dynamically localizes to vacuole–mitochondria and to vacuole–nucleus contact sites depending on growth conditions, suggesting that ERMES function can be bypassed by the activity of other contact sites, and that contact sites establish a growth condition–regulated organelle network. The endoplasmic reticulum–mitochondria encounter structure (ERMES) complex tethers the endoplasmic reticulum and the mitochondria. It is thought to facilitate interorganelle lipid exchange and influence mitochondrial dynamics and mitochondrial DNA maintenance. Despite this important role, ERMES is not found in metazoans. Here, we identified single amino acid substitutions in Vps13 (vacuolar protein sorting 13), a large universally conserved eukaryotic protein, which suppress all measured phenotypic consequences of ERMES deficiency. Combined loss of VPS13 and ERMES is lethal, indicating that Vps13 and ERMES function in redundant pathways. Vps13 dynamically localizes to vacuole–mitochondria and to vacuole–nucleus contact sites depending on growth conditions, suggesting that ERMES function can be bypassed by the activity of other contact sites, and that contact sites establish a growth condition–regulated organelle network.
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Affiliation(s)
| | | | - Peter Walter
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158 Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158
| | - Benoît Kornmann
- ETH Zürich, Institute of Biochemistry, 8093 Zürich, Switzerland
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57
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Phillips MJ, Voeltz GK. Structure and function of ER membrane contact sites with other organelles. Nat Rev Mol Cell Biol 2015; 17:69-82. [PMID: 26627931 DOI: 10.1038/nrm.2015.8] [Citation(s) in RCA: 638] [Impact Index Per Article: 70.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The endoplasmic reticulum (ER) is the largest organelle in the cell, and its functions have been studied for decades. The past several years have provided novel insights into the existence of distinct domains between the ER and other organelles, known as membrane contact sites (MCSs). At these contact sites, organelle membranes are closely apposed and tethered, but do not fuse. Here, various protein complexes can work in concert to perform specialized functions such as binding, sensing and transferring molecules, as well as engaging in organelle biogenesis and dynamics. This Review describes the structure and functions of MCSs, primarily focusing on contacts of the ER with mitochondria and endosomes.
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Affiliation(s)
- Melissa J Phillips
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado 80309, USA
| | - Gia K Voeltz
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado 80309, USA
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58
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Human Mitochondrial DNA-Protein Complexes Attach to a Cholesterol-Rich Membrane Structure. Sci Rep 2015; 5:15292. [PMID: 26478270 PMCID: PMC4609938 DOI: 10.1038/srep15292] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 09/22/2015] [Indexed: 01/05/2023] Open
Abstract
The helicase Twinkle is indispensable for mtDNA replication in nucleoids. Previously, we showed that Twinkle is tightly membrane-associated even in the absence of mtDNA, which suggests that Twinkle is part of a membrane-attached replication platform. Here we show that this platform is a cholesterol-rich membrane structure. We fractionated mitochondrial membrane preparations on flotation gradients and show that membrane-associated nucleoids accumulate at the top of the gradient. This fraction was shown to be highly enriched in cholesterol, a lipid that is otherwise low abundant in mitochondria. In contrast, more common mitochondrial lipids, and abundant inner-membrane associated proteins concentrated in the bottom-half of these gradients. Gene silencing of ATAD3, a protein with proposed functions related to nucleoid and mitochondrial cholesterol homeostasis, modified the distribution of cholesterol and nucleoids in the gradient in an identical fashion. Both cholesterol and ATAD3 were previously shown to be enriched in ER-mitochondrial junctions, and we detect nucleoid components in biochemical isolates of these structures. Our data suggest an uncommon membrane composition that accommodates platforms for replicating mtDNA, and reconcile apparently disparate functions of ATAD3. We suggest that mtDNA replication platforms are organized in connection with ER-mitochondrial junctions, facilitated by a specialized membrane architecture involving mitochondrial cholesterol.
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59
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Murley A, Sarsam RD, Toulmay A, Yamada J, Prinz WA, Nunnari J. Ltc1 is an ER-localized sterol transporter and a component of ER-mitochondria and ER-vacuole contacts. ACTA ACUST UNITED AC 2015; 209:539-48. [PMID: 25987606 PMCID: PMC4442815 DOI: 10.1083/jcb.201502033] [Citation(s) in RCA: 204] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 04/21/2015] [Indexed: 11/22/2022]
Abstract
Organelle contact sites perform fundamental functions in cells, including lipid and ion homeostasis, membrane dynamics, and signaling. Using a forward proteomics approach in yeast, we identified new ER-mitochondria and ER-vacuole contacts specified by an uncharacterized protein, Ylr072w. Ylr072w is a conserved protein with GRAM and VASt domains that selectively transports sterols and is thus termed Ltc1, for Lipid transfer at contact site 1. Ltc1 localized to ER-mitochondria and ER-vacuole contacts via the mitochondrial import receptors Tom70/71 and the vacuolar protein Vac8, respectively. At mitochondria, Ltc1 was required for cell viability in the absence of Mdm34, a subunit of the ER-mitochondria encounter structure. At vacuoles, Ltc1 was required for sterol-enriched membrane domain formation in response to stress. Increasing the proportion of Ltc1 at vacuoles was sufficient to induce sterol-enriched vacuolar domains without stress. Thus, our data support a model in which Ltc1 is a sterol-dependent regulator of organelle and cellular homeostasis via its dual localization to ER-mitochondria and ER-vacuole contact sites.
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Affiliation(s)
- Andrew Murley
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA 95616
| | - Reta D Sarsam
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA 95616
| | - Alexandre Toulmay
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Justin Yamada
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA 95616
| | - William A Prinz
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Jodi Nunnari
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA 95616
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60
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Lang A, John Peter AT, Kornmann B. ER-mitochondria contact sites in yeast: beyond the myths of ERMES. Curr Opin Cell Biol 2015; 35:7-12. [PMID: 25836730 DOI: 10.1016/j.ceb.2015.03.002] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 03/10/2015] [Accepted: 03/10/2015] [Indexed: 10/23/2022]
Abstract
A standout feature of eukaryotic cells is the presence of organelles with distinct chemical compositions and physical properties, which aid in the accomplishment of specialized metabolic tasks. This complex topology, however, makes a permanent crosstalk between the organelles a necessity for the coordination of cellular function. While molecule exchange between organelles via the vesicular transport system has been extensively studied, communication via direct connections has only recently become a new matter of interest. These direct connections termed membrane contact sites (MCSs) represent zones of close proximity (10-30nm) between two organelles. Research in the past years has revealed a number of MCSs especially between the ER and almost every other organelle [1(•)]. In particular, the MCSs between the ER and the mitochondria have undergone intense investigation. While the quest for ER-mitochondria MCS components in human cells has led to the revelation of an ever growing number of potential factors, studies in the simpler eukaryote Saccharomyces cerevisiae revealed the actual existence of a molecular tether between the two organelles [2(••)].
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Affiliation(s)
- Alexander Lang
- Institute of Biochemistry, ETH Zurich, 8093 Zürich, Switzerland
| | | | - Benoît Kornmann
- Institute of Biochemistry, ETH Zurich, 8093 Zürich, Switzerland.
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61
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Membrane contact sites, gateways for lipid homeostasis. Curr Opin Cell Biol 2015; 33:82-87. [PMID: 25569848 DOI: 10.1016/j.ceb.2014.12.004] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 12/08/2014] [Accepted: 12/15/2014] [Indexed: 12/21/2022]
Abstract
Maintaining the proper lipid composition of cellular membranes is critical for numerous cellular processes but mechanisms of membrane lipid homeostasis are not well understood. There is growing evidence that membrane contact sites (MCSs), regions where two organelles come in close proximity to one another, play major roles in the regulation of intracellular lipid composition and distribution. MCSs are thought to mediate the exchange of lipids and signals between organelles. In this review, we discuss how lipid exchange occurs at MCSs and evidence for roles of MCSs in regulating lipid synthesis and degradation. We also discuss how networks of organelles connected by MCSs may modulate cellular lipid homeostasis and help determine organelle lipid composition.
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62
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Stefely JA, Reidenbach AG, Ulbrich A, Oruganty K, Floyd BJ, Jochem A, Saunders JM, Johnson IE, Minogue CE, Wrobel RL, Barber GE, Lee D, Li S, Kannan N, Coon JJ, Bingman CA, Pagliarini DJ. Mitochondrial ADCK3 employs an atypical protein kinase-like fold to enable coenzyme Q biosynthesis. Mol Cell 2014; 57:83-94. [PMID: 25498144 DOI: 10.1016/j.molcel.2014.11.002] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 10/13/2014] [Accepted: 11/04/2014] [Indexed: 10/24/2022]
Abstract
The ancient UbiB protein kinase-like family is involved in isoprenoid lipid biosynthesis and is implicated in human diseases, but demonstration of UbiB kinase activity has remained elusive for unknown reasons. Here, we quantitatively define UbiB-specific sequence motifs and reveal their positions within the crystal structure of a UbiB protein, ADCK3. We find that multiple UbiB-specific features are poised to inhibit protein kinase activity, including an N-terminal domain that occupies the typical substrate binding pocket and a unique A-rich loop that limits ATP binding by establishing an unusual selectivity for ADP. A single alanine-to-glycine mutation of this loop flips this coenzyme selectivity and enables autophosphorylation but inhibits coenzyme Q biosynthesis in vivo, demonstrating functional relevance for this unique feature. Our work provides mechanistic insight into UbiB enzyme activity and establishes a molecular foundation for further investigation of how UbiB family proteins affect diseases and diverse biological pathways.
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Affiliation(s)
- Jonathan A Stefely
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Andrew G Reidenbach
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Arne Ulbrich
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | | | - Brendan J Floyd
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Adam Jochem
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jaclyn M Saunders
- Mitochondrial Protein Partnership, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Isabel E Johnson
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Catherine E Minogue
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Russell L Wrobel
- Mitochondrial Protein Partnership, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Grant E Barber
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - David Lee
- Department of Medicine and UCSD DXMS Proteomics Resource, University of California, San Diego, La Jolla, CA 92023, USA
| | - Sheng Li
- Department of Medicine and UCSD DXMS Proteomics Resource, University of California, San Diego, La Jolla, CA 92023, USA
| | - Natarajan Kannan
- Department of Biochemistry, University of Georgia, Athens, GA 30602, USA
| | - Joshua J Coon
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Craig A Bingman
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Mitochondrial Protein Partnership, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - David J Pagliarini
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Mitochondrial Protein Partnership, University of Wisconsin-Madison, Madison, WI 53706, USA.
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63
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Association between paraoxonases gene expression and oxidative stress in hepatotoxicity induced by CCl4. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2014; 2014:893212. [PMID: 25478064 PMCID: PMC4248367 DOI: 10.1155/2014/893212] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Revised: 08/22/2014] [Accepted: 08/22/2014] [Indexed: 12/29/2022]
Abstract
Objectives. The purpose of the study is to evaluate the hepatoprotective effect of rutin in carbon tetrachloride- (CCl4-) induced liver injuries in rat model. Methods. Forty male Wistar albino rats were divided into four groups. Group I was the control group and received dimethyl sulphoxide (DMSO) and olive oil. Group II received rutin. Groups III was treated with CCl4. Group IV was administered rutin after 48 h of CCl4 treatment. Liver enzymes level, lipid profile, lipid peroxidation, and hydrogen peroxide were measured. The genes expression levels were monitored by real time RT-PCR and western blot techniques. Results. CCl4 group showed significant increase in alanine aminotransferase (ALT), aspartate aminotransferase (AST), thiobarbituric acid reactive substances (TBAR), hydrogen peroxide (H2O2), and lipid profile and a significant decrease in glutathione peroxidase (GPx), glutathione S transferase (GST), catalase (CAT), paraoxonase-1 (PON-1), paraoxonase-3 (PON-3), peroxisome proliferator activated receptor delta (PPAR-δ), and ATP-binding cassette transporter 1 (ABAC1) genes expression levels. Interestingly, rutin supplementation completely reversed the biochemical and gene expression levels induced by CCl4 to control values. Conclusion. CCl4 administration causes aberration of genes expression levels in oxidative stress pathway resulting in DNA damage and hepatotoxicity. Rutin causes hepatoprotective effect through enhancing the antioxidant genes.
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64
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Affiliation(s)
- Katherine Labbé
- Department of Molecular and Cellular Biology, University of California, Davis, California 95616; , ,
| | - Andrew Murley
- Department of Molecular and Cellular Biology, University of California, Davis, California 95616; , ,
| | - Jodi Nunnari
- Department of Molecular and Cellular Biology, University of California, Davis, California 95616; , ,
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65
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Khadria AS, Mueller BK, Stefely JA, Tan CH, Pagliarini DJ, Senes A. A Gly-zipper motif mediates homodimerization of the transmembrane domain of the mitochondrial kinase ADCK3. J Am Chem Soc 2014; 136:14068-77. [PMID: 25216398 PMCID: PMC4195374 DOI: 10.1021/ja505017f] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Interactions between α-helices within the hydrophobic environment of lipid bilayers are integral to the folding and function of transmembrane proteins; however, the major forces that mediate these interactions remain debated, and our ability to predict these interactions is still largely untested. We recently demonstrated that the frequent transmembrane association motif GASright, the GxxxG-containing fold of the glycophorin A dimer, is optimal for the formation of extended networks of Cα-H hydrogen bonds, supporting the hypothesis that these bonds are major contributors to association. We also found that optimization of Cα-H hydrogen bonding and interhelical packing is sufficient to computationally predict the structure of known GASright dimers at near atomic level. Here, we demonstrate that this computational method can be used to characterize the structure of a protein not previously known to dimerize, by predicting and validating the transmembrane dimer of ADCK3, a mitochondrial kinase. ADCK3 is involved in the biosynthesis of the redox active lipid, ubiquinone, and human ADCK3 mutations cause a cerebellar ataxia associated with ubiquinone deficiency, but the biochemical functions of ADCK3 remain largely undefined. Our experimental analyses show that the transmembrane helix of ADCK3 oligomerizes, with an interface based on an extended Gly-zipper motif, as predicted by our models. The data provide strong evidence for the hypothesis that optimization of Cα-H hydrogen bonding is an important factor in the association of transmembrane helices. This work also provides a structural foundation for investigating the role of transmembrane association in regulating the biological activity of ADCK3.
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Affiliation(s)
- Ambalika S Khadria
- Department of Biochemistry, University of Wisconsin-Madison , 433 Babcock Drive, Madison, Wisconsin 53706, United States
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66
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Abstract
In this issue of Developmental Cell, Elbaz-Alon et al. (2014) and Hönscher et al. (2014) describe a contact site between mitochondria and the lysosome-like yeast vacuole named vCLAMP (vacuole and mitochondria patch). They show that vCLAMP plays a role in lipid exchange, thereby linking mitochondria to the endomembrane system.
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Affiliation(s)
- Till Klecker
- Institut für Zellbiologie, Universität Bayreuth, 95440 Bayreuth, Germany
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67
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Prinz WA. Bridging the gap: membrane contact sites in signaling, metabolism, and organelle dynamics. ACTA ACUST UNITED AC 2014; 205:759-69. [PMID: 24958771 PMCID: PMC4068136 DOI: 10.1083/jcb.201401126] [Citation(s) in RCA: 296] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Regions of close apposition between two organelles, often referred to as membrane contact sites (MCSs), mostly form between the endoplasmic reticulum and a second organelle, although contacts between mitochondria and other organelles have also begun to be characterized. Although these contact sites have been noted since cells first began to be visualized with electron microscopy, the functions of most of these domains long remained unclear. The last few years have witnessed a dramatic increase in our understanding of MCSs, revealing the critical roles they play in intracellular signaling, metabolism, the trafficking of metabolites, and organelle inheritance, division, and transport.
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Affiliation(s)
- William A Prinz
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892
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68
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Tamura Y, Sesaki H, Endo T. Phospholipid transport via mitochondria. Traffic 2014; 15:933-45. [PMID: 24954234 DOI: 10.1111/tra.12188] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Revised: 06/16/2014] [Accepted: 06/16/2014] [Indexed: 12/27/2022]
Abstract
In eukaryotic cells, complex membrane structures called organelles are highly developed to exert specialized functions. Mitochondria are one of such organelles consisting of the outer and inner membranes (OM and IM) with characteristic protein and phospholipid compositions. Maintaining proper phospholipid compositions of the membranes is crucial for mitochondrial integrity, thereby contributing to normal cell activities. As cellular locations for phospholipid synthesis are restricted to specific compartments such as the endoplasmic reticulum (ER) membrane and the mitochondrial inner membrane, newly synthesized phospholipids have to be transported and distributed properly from the ER or mitochondria to other cellular membranes. Although understanding of molecular mechanisms of phospholipid transport are much behind those of protein transport, recent studies using yeast as a model system began to provide intriguing insights into phospholipid exchange between the ER and mitochondria as well as between the mitochondrial OM and IM. In this review, we summarize the latest findings of phospholipid transport via mitochondria and discuss the implicated molecular mechanisms.
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Affiliation(s)
- Yasushi Tamura
- Research Center for Materials Science, Nagoya University, Nagoya, 464-8602, Japan
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Klecker T, Böckler S, Westermann B. Making connections: interorganelle contacts orchestrate mitochondrial behavior. Trends Cell Biol 2014; 24:537-45. [PMID: 24786308 DOI: 10.1016/j.tcb.2014.04.004] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 04/01/2014] [Accepted: 04/02/2014] [Indexed: 01/07/2023]
Abstract
Mitochondria are highly dynamic organelles. During their life cycle they frequently fuse and divide, and damaged mitochondria are removed by autophagic degradation. These processes serve to maintain mitochondrial function and ensure optimal energy supply for the cell. It has recently become clear that this complex mitochondrial behavior is governed to a large extent by interactions with other organelles. In this review, we describe mitochondrial contacts with the endoplasmic reticulum (ER), plasma membrane, and peroxisomes. In particular, we highlight how mitochondrial fission, distribution, inheritance, and turnover are orchestrated by interorganellar contacts in yeast and metazoa. These interactions are pivotal for the integration of the dynamic mitochondrial network into the architecture of eukaryotic cells.
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Affiliation(s)
- Till Klecker
- Institut für Zellbiologie, Universität Bayreuth, 95440 Bayreuth, Germany
| | - Stefan Böckler
- Institut für Zellbiologie, Universität Bayreuth, 95440 Bayreuth, Germany
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70
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Böckler S, Westermann B. Mitochondrial ER contacts are crucial for mitophagy in yeast. Dev Cell 2014; 28:450-8. [PMID: 24530295 DOI: 10.1016/j.devcel.2014.01.012] [Citation(s) in RCA: 164] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Revised: 12/20/2013] [Accepted: 01/13/2014] [Indexed: 10/25/2022]
Abstract
Damaged and superfluous mitochondria are removed from the cell by selective autophagy, a process termed mitophagy. This serves to maintain the proper quantity and quality of the organelle. Mitophagy is executed by an evolutionarily conserved pathway, many components of which were first discovered and characterized in yeast. In a systematic screen of a yeast deletion collection, we identified ERMES, a complex connecting mitochondria and the endoplasmic reticulum (ER), as an important factor contributing to the selective degradation of mitochondria. We show that efficient mitophagy depends on mitochondrial ER tethering. ERMES colocalizes with sites of mitophagosome biogenesis and affects the formation of the isolation membrane that engulfs the organelles destined for degradation. These results provide insights into the cellular mechanisms that govern organelle homeostasis.
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Affiliation(s)
- Stefan Böckler
- Institut für Zellbiologie, Universität Bayreuth, 95440 Bayreuth, Germany
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71
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Formation and regulation of mitochondrial membranes. Int J Cell Biol 2014; 2014:709828. [PMID: 24578708 PMCID: PMC3918842 DOI: 10.1155/2014/709828] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Revised: 11/04/2013] [Accepted: 11/05/2013] [Indexed: 01/09/2023] Open
Abstract
Mitochondrial membrane phospholipids are essential for the mitochondrial architecture, the activity of respiratory proteins, and the transport of proteins into the mitochondria. The accumulation of phospholipids within mitochondria depends on a coordinate synthesis, degradation, and trafficking of phospholipids between the endoplasmic reticulum (ER) and mitochondria as well as intramitochondrial lipid trafficking. Several studies highlight the contribution of dietary fatty acids to the remodeling of phospholipids and mitochondrial membrane homeostasis. Understanding the role of phospholipids in the mitochondrial membrane and their metabolism will shed light on the molecular mechanisms involved in the regulation of mitochondrial function and in the mitochondrial-related diseases.
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72
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Flinner N, Ellenrieder L, Stiller SB, Becker T, Schleiff E, Mirus O. Mdm10 is an ancient eukaryotic porin co-occurring with the ERMES complex. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2013; 1833:3314-3325. [PMID: 24135058 DOI: 10.1016/j.bbamcr.2013.10.006] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Revised: 09/20/2013] [Accepted: 10/07/2013] [Indexed: 12/17/2022]
Abstract
Mitochondrial β-barrel proteins fulfill central functions in the outer membrane like metabolite exchange catalyzed by the voltage-dependent anion channel (VDAC) and protein biogenesis by the central components of the preprotein translocase of the outer membrane (Tom40) or of the sorting and assembly machinery (Sam50). The mitochondrial division and morphology protein Mdm10 is another essential outer membrane protein with proposed β-barrel fold, which has so far only been found in Fungi. Mdm10 is part of the endoplasmic reticulum mitochondria encounter structure (ERMES), which tethers the ER to mitochondria and associates with the SAM complex. In here, we provide evidence that Mdm10 phylogenetically belongs to the VDAC/Tom40 superfamily. Contrary to Tom40 and VDAC, Mdm10 exposes long loops towards both sides of the membrane. Analyses of single loop deletion mutants of Mdm10 in the yeast Saccharomyces cerevisiae reveal that the loops are dispensable for Mdm10 function. Sequences similar to fungal Mdm10 can be found in species from Excavates to Fungi, but neither in Metazoa nor in plants. Strikingly, the presence of Mdm10 coincides with the appearance of the other ERMES components. Mdm10's presence in both unikonts and bikonts indicates an introduction at an early time point in eukaryotic evolution.
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Affiliation(s)
- Nadine Flinner
- JWGU Frankfurt am Main, Cluster of Excellence Macromolecular Complexes, Centre of Membrane Proteomics, Department of Biosciences, Max-von-Laue Str. 9, 60438 Frankfurt, Germany
| | - Lars Ellenrieder
- Institut für Biochemie und Molekularbiologie, Universität Freiburg, D-79104 Freiburg, Germany; Fakultät für Biologie, Universität Freiburg, D-79104 Freiburg, Germany
| | - Sebastian B Stiller
- Institut für Biochemie und Molekularbiologie, Universität Freiburg, D-79104 Freiburg, Germany; Fakultät für Biologie, Universität Freiburg, D-79104 Freiburg, Germany
| | - Thomas Becker
- Institut für Biochemie und Molekularbiologie, Universität Freiburg, D-79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, Universität Freiburg, D-79104 Freiburg, Germany
| | - Enrico Schleiff
- JWGU Frankfurt am Main, Cluster of Excellence Macromolecular Complexes, Centre of Membrane Proteomics, Department of Biosciences, Max-von-Laue Str. 9, 60438 Frankfurt, Germany.
| | - Oliver Mirus
- JWGU Frankfurt am Main, Cluster of Excellence Macromolecular Complexes, Centre of Membrane Proteomics, Department of Biosciences, Max-von-Laue Str. 9, 60438 Frankfurt, Germany
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73
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Scharwey M, Tatsuta T, Langer T. Mitochondrial lipid transport at a glance. J Cell Sci 2013; 126:5317-23. [DOI: 10.1242/jcs.134130] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Lipids are the building blocks of cellular membranes and are synthesized at distinct parts of the cell. A precise control of lipid synthesis and distribution is crucial for cell function and survival. The endoplasmic reticulum (ER) is the major lipid-synthesizing organelle. However, a subset of lipids is synthesized within mitochondria, and this aspect has become a focus of recent lipid research. Mitochondria form a dynamic membrane network that is reshaped by fusion and fission events. Their functionality therefore depends on a continuous lipid supply from the ER and the distribution of lipids between both mitochondrial membranes. The mechanisms of mitochondrial lipid trafficking are only now emerging and appear to involve membrane contact sites and lipid transfer proteins. In this Cell Science at a Glance article, we will discuss recent discoveries in the field of mitochondrial lipid trafficking that build on long-standing observations and shed new light on the shuttling of membrane lipids between mitochondria and other organelles.
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