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Quirós PM, Mottis A, Auwerx J. Mitonuclear communication in homeostasis and stress. Nat Rev Mol Cell Biol 2016; 17:213-26. [PMID: 26956194 DOI: 10.1038/nrm.2016.23] [Citation(s) in RCA: 479] [Impact Index Per Article: 59.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Mitochondria participate in crucial cellular processes such as energy harvesting and intermediate metabolism. Although mitochondria possess their own genome--a vestige of their bacterial origins and endosymbiotic evolution--most mitochondrial proteins are encoded in the nucleus. The expression of the mitochondrial proteome hence requires tight coordination between the two genomes to adapt mitochondrial function to the ever-changing cellular milieu. In this Review, we focus on the pathways that coordinate the communication between mitochondria and the nucleus during homeostasis and mitochondrial stress. These pathways include nucleus-to-mitochondria (anterograde) and mitochondria-to-nucleus (retrograde) communication, mitonuclear feedback signalling and proteostasis regulation, the integrated stress response and non-cell-autonomous communication. We discuss how mitonuclear communication safeguards cellular and organismal fitness and regulates lifespan.
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Affiliation(s)
- Pedro M Quirós
- Laboratory for Integrative and Systems Physiology, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Adrienne Mottis
- Laboratory for Integrative and Systems Physiology, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Johan Auwerx
- Laboratory for Integrative and Systems Physiology, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
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52
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Mitochondrial emitted electromagnetic signals mediate retrograde signaling. Med Hypotheses 2015; 85:810-8. [DOI: 10.1016/j.mehy.2015.10.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2015] [Revised: 09/25/2015] [Accepted: 10/09/2015] [Indexed: 12/19/2022]
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53
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Mitochondrial Retrograde Signaling: Triggers, Pathways, and Outcomes. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2015; 2015:482582. [PMID: 26583058 PMCID: PMC4637108 DOI: 10.1155/2015/482582] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 05/08/2015] [Accepted: 05/13/2015] [Indexed: 12/22/2022]
Abstract
Mitochondria are essential organelles for eukaryotic homeostasis. Although these organelles possess their own DNA, the vast majority (>99%) of mitochondrial proteins are encoded in the nucleus. This situation makes systems that allow the communication between mitochondria and the nucleus a requirement not only to coordinate mitochondrial protein synthesis during biogenesis but also to communicate eventual mitochondrial malfunctions, triggering compensatory responses in the nucleus. Mitochondria-to-nucleus retrograde signaling has been described in various organisms, albeit with differences in effector pathways, molecules, and outcomes, as discussed in this review.
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54
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A respiratory chain controlled signal transduction cascade in the mitochondrial intermembrane space mediates hydrogen peroxide signaling. Proc Natl Acad Sci U S A 2015; 112:E5679-88. [PMID: 26438848 DOI: 10.1073/pnas.1517932112] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Reactive oxygen species (ROS) such as hydrogen peroxide (H2O2) govern cellular homeostasis by inducing signaling. H2O2 modulates the activity of phosphatases and many other signaling molecules through oxidation of critical cysteine residues, which led to the notion that initiation of ROS signaling is broad and nonspecific, and thus fundamentally distinct from other signaling pathways. Here, we report that H2O2 signaling bears hallmarks of a regular signal transduction cascade. It is controlled by hierarchical signaling events resulting in a focused response as the results place the mitochondrial respiratory chain upstream of tyrosine-protein kinase Lyn, Lyn upstream of tyrosine-protein kinase SYK (Syk), and Syk upstream of numerous targets involved in signaling, transcription, translation, metabolism, and cell cycle regulation. The active mediators of H2O2 signaling colocalize as H2O2 induces mitochondria-associated Lyn and Syk phosphorylation, and a pool of Lyn and Syk reside in the mitochondrial intermembrane space. Finally, the same intermediaries control the signaling response in tissues and species responsive to H2O2 as the respiratory chain, Lyn, and Syk were similarly required for H2O2 signaling in mouse B cells, fibroblasts, and chicken DT40 B cells. Consistent with a broad role, the Syk pathway is coexpressed across tissues, is of early metazoan origin, and displays evidence of evolutionary constraint in the human. These results suggest that H2O2 signaling is under control of a signal transduction pathway that links the respiratory chain to the mitochondrial intermembrane space-localized, ubiquitous, and ancient Syk pathway in hematopoietic and nonhematopoietic cells.
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Lee YK, Jee BA, Kwon SM, Yoon YS, Xu WG, Wang HJ, Wang XW, Thorgeirsson SS, Lee JS, Woo HG, Yoon G. Identification of a mitochondrial defect gene signature reveals NUPR1 as a key regulator of liver cancer progression. Hepatology 2015; 62:1174-89. [PMID: 26173068 PMCID: PMC6312643 DOI: 10.1002/hep.27976] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 06/11/2015] [Accepted: 07/06/2015] [Indexed: 02/01/2023]
Abstract
UNLABELLED Many cancer cells require more glycolytic adenosine triphosphate production due to a mitochondrial respiratory defect. However, the roles of mitochondrial defects in cancer development and progression remain unclear. To address the role of transcriptomic regulation by mitochondrial defects in liver cancer cells, we performed gene expression profiling for three different cell models of mitochondrial defects: cells with chemical respiratory inhibition (rotenone, thenoyltrifluoroacetone, antimycin A, and oligomycin), cells with mitochondrial DNA depletion (Rho0), and liver cancer cells harboring mitochondrial defects (SNU354 and SNU423). By comparing gene expression in the three models, we identified 10 common mitochondrial defect-related genes that may be responsible for retrograde signaling from cancer cell mitochondria to the intracellular transcriptome. The concomitant expression of the 10 common mitochondrial defect genes is significantly associated with poor prognostic outcomes in liver cancers, suggesting their functional and clinical relevance. Among the common mitochondrial defect genes, we found that nuclear protein 1 (NUPR1) is one of the key transcription regulators. Knockdown of NUPR1 suppressed liver cancer cell invasion, which was mediated in a Ca(2+) signaling-dependent manner. In addition, by performing an NUPR1-centric network analysis and promoter binding assay, granulin was identified as a key downstream effector of NUPR1. We also report association of the NUPR1-granulin pathway with mitochondrial defect-derived glycolytic activation in human liver cancer. CONCLUSION Mitochondrial respiratory defects and subsequent retrograde signaling, particularly the NUPR1-granulin pathway, play pivotal roles in liver cancer progression.
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Affiliation(s)
- Young-Kyoung Lee
- Department of Biochemistry, Ajou University School of Medicine, Suwon, Korea,Department of Biomedical Science, Graduate School, Ajou University, Suwon, Korea
| | - Byul A. Jee
- Department of Physiology, Ajou University School of Medicine, Suwon, Korea,Department of Biomedical Science, Graduate School, Ajou University, Suwon, Korea
| | - So Mee Kwon
- Department of Physiology, Ajou University School of Medicine, Suwon, Korea,Department of Biomedical Science, Graduate School, Ajou University, Suwon, Korea
| | - Young-Sil Yoon
- Department of Biochemistry, Ajou University School of Medicine, Suwon, Korea
| | - Wei Guang Xu
- Department of Surgery, Ajou University School of Medicine, Suwon, Korea
| | - Hee-Jung Wang
- Department of Surgery, Ajou University School of Medicine, Suwon, Korea
| | - Xin Wei Wang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Snorri S. Thorgeirsson
- Laboratory of Experimental Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Jae-Seon Lee
- Department of Biomedical Sciences and Hypoxia-Related Disease Research Center, Inha University College of Medicine, Incheon, Korea
| | - Hyun Goo Woo
- Department of Physiology, Ajou University School of Medicine, Suwon, Korea,Department of Biomedical Science, Graduate School, Ajou University, Suwon, Korea
| | - Gyesoon Yoon
- Department of Biochemistry, Ajou University School of Medicine, Suwon, Korea,Department of Biomedical Science, Graduate School, Ajou University, Suwon, Korea
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56
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Jazwinski S. Mitochondria to nucleus signaling and the role of ceramide in its integration into the suite of cell quality control processes during aging. Ageing Res Rev 2015; 23:67-74. [PMID: 25555678 DOI: 10.1016/j.arr.2014.12.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 12/15/2014] [Accepted: 12/22/2014] [Indexed: 12/26/2022]
Abstract
Mitochondria to nucleus signaling has been the most extensively studied mode of inter-organelle communication. The first signaling pathway in this category of information transfer to be discovered was the retrograde response, with its own set of signal transduction proteins. The finding that this pathway compensates for mitochondrial dysfunction to extend the replicative lifespan of yeast cells has generated additional impetus for its study. This research has demonstrated crosstalk between the retrograde response and the target of rapamycin (TOR), small GTPase RAS, and high-osmolarity glycerol (HOG) pathways in yeast, all of which are key players in replicative lifespan. More recently, the retrograde response has been implicated in the diauxic shift and survival in stationary phase, extending its operation to the yeast chronological lifespan as well. In this capacity, the retrograde response may cooperate with other, related mitochondria to nucleus signaling pathways. Counterparts of the retrograde response are found in the roundworm, the fruit fly, the mouse, and even in human cells in tissue culture. The exciting realization that the retrograde response is embedded in the network of cellular quality control processes has emerged over the past few years. Most strikingly, it is closely integrated with autophagy and the selective brand of this quality control process, mitophagy. This coordination depends on TOR, and it engages ceramide/sphingolipid signaling. The yeast LAG1 ceramide synthase gene was the first longevity gene cloned as such, and its orthologs hyl-1 and hyl-2 determine worm lifespan. Thus, the involvement of ceramide signaling in quality control gives these findings cellular context. The retrograde response and ceramide are essential components of a lifespan maintenance process that likely evolved as a cytoprotective mechanism to defend the organism from diverse stressors.
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Dokudovskaya S, Rout MP. SEA you later alli-GATOR--a dynamic regulator of the TORC1 stress response pathway. J Cell Sci 2015; 128:2219-28. [PMID: 25934700 DOI: 10.1242/jcs.168922] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Cells constantly adapt to various environmental changes and stresses. The way in which nutrient and stress levels in a cell feed back to control metabolism and growth are, unsurprisingly, extremely complex, as responding with great sensitivity and speed to the 'feast or famine, slack or stress' status of its environment is a central goal for any organism. The highly conserved target of rapamycin complex 1 (TORC1) controls eukaryotic cell growth and response to a variety of signals, including nutrients, hormones and stresses, and plays the key role in the regulation of autophagy. A lot of attention has been paid recently to the factors in this pathway functioning upstream of TORC1. In this Commentary, we focus on a major, newly discovered upstream regulator of TORC1--the multiprotein SEA complex, also known as GATOR. We describe the structural and functional features of the yeast complex and its mammalian homolog, and their involvement in the regulation of the TORC1 pathway and TORC1-independent processes. We will also provide an overview of the consequences of GATOR deregulation in cancer and other diseases.
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Affiliation(s)
- Svetlana Dokudovskaya
- CNRS UMR 8126, Université Paris-Sud 11, Institut Gustave Roussy, 114, rue Edouard Vaillant, 94805, Villejuif, France
| | - Michael P Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
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58
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Mechanisms by which different functional states of mitochondria define yeast longevity. Int J Mol Sci 2015; 16:5528-54. [PMID: 25768339 PMCID: PMC4394491 DOI: 10.3390/ijms16035528] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 03/05/2015] [Accepted: 03/05/2015] [Indexed: 12/17/2022] Open
Abstract
Mitochondrial functionality is vital to organismal physiology. A body of evidence supports the notion that an age-related progressive decline in mitochondrial function is a hallmark of cellular and organismal aging in evolutionarily distant eukaryotes. Studies of the baker’s yeast Saccharomyces cerevisiae, a unicellular eukaryote, have led to discoveries of genes, signaling pathways and chemical compounds that modulate longevity-defining cellular processes in eukaryotic organisms across phyla. These studies have provided deep insights into mechanistic links that exist between different traits of mitochondrial functionality and cellular aging. The molecular mechanisms underlying the essential role of mitochondria as signaling organelles in yeast aging have begun to emerge. In this review, we discuss recent progress in understanding mechanisms by which different functional states of mitochondria define yeast longevity, outline the most important unanswered questions and suggest directions for future research.
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59
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Yeast as a tool to study mitochondrial retrograde pathway en route to cell stress response. Methods Mol Biol 2015; 1265:321-31. [PMID: 25634284 DOI: 10.1007/978-1-4939-2288-8_22] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Mitochondrial retrograde signaling is a mitochondria-to-nucleus communication pathway, conserved from yeast to humans, by which dysfunctional mitochondria relay signals that lead to cell stress adaptation in physiopathological conditions by changes in nuclear gene expression. The best comprehension of components and regulation of retrograde signaling have been obtained in Saccharomyces cerevisiae, where retrograde target gene expression is regulated by RTG genes. In this chapter, we describe the methods to measure mitochondrial retrograde pathway activation in yeast cells by monitoring the mRNA levels of RTG target genes, such as those encoding for peroxisomal citrate synthase, aconitase, and NAD(+)-specific isocitrate dehydrogenase subunit 1, as well as the phosphorylation status of Rtg1/3p transcriptional factor which controls RTG target gene transcription.
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60
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Chang HW, Shtessel L, Lee SS. Collaboration between mitochondria and the nucleus is key to long life in Caenorhabditis elegans. Free Radic Biol Med 2015; 78:168-78. [PMID: 25450327 PMCID: PMC4280335 DOI: 10.1016/j.freeradbiomed.2014.10.576] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 10/22/2014] [Accepted: 10/23/2014] [Indexed: 02/07/2023]
Abstract
Recent findings in diverse organisms strongly support a conserved role for mitochondrial electron transport chain dysfunction in longevity modulation, but the underlying mechanisms are not well understood. One way cells cope with mitochondrial dysfunction is through a retrograde transcriptional reprogramming response. In this review, we primarily focus on the work that has been performed in Caenorhabditis elegans to elucidate these mechanisms. We describe several transcription factors that participate in mitochondria-to-nucleus signaling and discuss how they mediate the relationship between mitochondrial dysfunction and life span.
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Affiliation(s)
- Hsin-Wen Chang
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14850, USA
| | - Ludmila Shtessel
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14850, USA
| | - Siu Sylvia Lee
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14850, USA.
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61
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Nishida-Aoki N, Mori H, Kuroda K, Ueda M. Activation of the mitochondrial signaling pathway in response to organic solvent stress in yeast. Curr Genet 2014; 61:153-64. [DOI: 10.1007/s00294-014-0463-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Revised: 11/18/2014] [Accepted: 11/19/2014] [Indexed: 10/24/2022]
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62
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Mitochondrial dysfunction in cancer chemoresistance. Biochem Pharmacol 2014; 92:62-72. [DOI: 10.1016/j.bcp.2014.07.027] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Revised: 07/25/2014] [Accepted: 07/28/2014] [Indexed: 12/19/2022]
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63
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Padman BS, Bach M, Lucarelli G, Prescott M, Ramm G. The protonophore CCCP interferes with lysosomal degradation of autophagic cargo in yeast and mammalian cells. Autophagy 2014; 9:1862-75. [DOI: 10.4161/auto.26557] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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64
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Rodríguez-Lombardero S, Rodríguez-Belmonte ME, González-Siso MI, Vizoso-Vázquez Á, Valdiglesias V, Laffón B, Cerdán ME. Proteomic analyses reveal that Sky1 modulates apoptosis and mitophagy in Saccharomyces cerevisiae cells exposed to cisplatin. Int J Mol Sci 2014; 15:12573-90. [PMID: 25029545 PMCID: PMC4139861 DOI: 10.3390/ijms150712573] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Revised: 07/02/2014] [Accepted: 07/02/2014] [Indexed: 12/11/2022] Open
Abstract
Sky1 is the only member of the SR (Serine–Arginine) protein kinase family in Saccharomyces cerevisiae. When yeast cells are treated with the anti-cancer drug cisplatin, Sky1 kinase activity is necessary to produce the cytotoxic effect. In this study, proteome changes in response to this drug and/or SKY1 deletion have been evaluated in order to understand the role of Sky1 in the response of yeast cells to cisplatin. Results reveal differential expression of proteins previously related to the oxidative stress response, DNA damage, apoptosis and mitophagy. With these precedents, the role of Sky1 in apoptosis, necrosis and mitophagy has been evaluated by flow-cytometry, fluorescence microscopy, biosensors and fluorescence techniques. After cisplatin treatment, an apoptotic-like process diminishes in the ∆sky1 strain in comparison to the wild-type. The treatment does not affect mitophagy in the wild-type strain, while an increase is observed in the ∆sky1 strain. The increased resistance to cisplatin observed in the ∆sky1 strain may be attributable to a decrease of apoptosis and an increase of mitophagy.
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Affiliation(s)
- Silvia Rodríguez-Lombardero
- EXPRELA Group, Department of Cellular and Molecular Biology, University of A Coruña, Campus A Coruña, A Coruña E15071, Spain.
| | - M Esther Rodríguez-Belmonte
- EXPRELA Group, Department of Cellular and Molecular Biology, University of A Coruña, Campus A Coruña, A Coruña E15071, Spain.
| | - M Isabel González-Siso
- EXPRELA Group, Department of Cellular and Molecular Biology, University of A Coruña, Campus A Coruña, A Coruña E15071, Spain.
| | - Ángel Vizoso-Vázquez
- EXPRELA Group, Department of Cellular and Molecular Biology, University of A Coruña, Campus A Coruña, A Coruña E15071, Spain.
| | - Vanessa Valdiglesias
- DICOMOSA Group, Department of Psychology, Area of Psychobiology, University of A Coruña, Campus A Coruña, A Coruña E15071, Spain.
| | - Blanca Laffón
- DICOMOSA Group, Department of Psychology, Area of Psychobiology, University of A Coruña, Campus A Coruña, A Coruña E15071, Spain.
| | - M Esperanza Cerdán
- EXPRELA Group, Department of Cellular and Molecular Biology, University of A Coruña, Campus A Coruña, A Coruña E15071, Spain.
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65
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Kenney MC, Chwa M, Atilano SR, Falatoonzadeh P, Ramirez C, Malik D, Tarek M, Cáceres-del-Carpio J, Nesburn AB, Boyer DS, Kuppermann BD, Vawter M, Jazwinski SM, Miceli M, Wallace DC, Udar N. Inherited mitochondrial DNA variants can affect complement, inflammation and apoptosis pathways: insights into mitochondrial-nuclear interactions. Hum Mol Genet 2014; 23:3537-51. [PMID: 24584571 PMCID: PMC4049308 DOI: 10.1093/hmg/ddu065] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 02/03/2014] [Accepted: 02/10/2014] [Indexed: 12/21/2022] Open
Abstract
Age-related macular degeneration (AMD) is the leading cause of vision loss in developed countries. While linked to genetic polymorphisms in the complement pathway, there are many individuals with high risk alleles that do not develop AMD, suggesting that other 'modifiers' may be involved. Mitochondrial (mt) haplogroups, defined by accumulations of specific mtDNA single nucleotide polymorphisms (SNPs) which represent population origins, may be one such modifier. J haplogroup has been associated with high risk for AMD while the H haplogroup is protective. It has been difficult to assign biological consequences for haplogroups so we created human ARPE-19 cybrids (cytoplasmic hybrids), which have identical nuclei but mitochondria of either J or H haplogroups, to investigate their effects upon bioenergetics and molecular pathways. J cybrids have altered bioenergetic profiles compared with H cybrids. Q-PCR analyses show significantly lower expression levels for seven respiratory complex genes encoded by mtDNA. J and H cybrids have significantly altered expression of eight nuclear genes of the alternative complement, inflammation and apoptosis pathways. Sequencing of the entire mtDNA was carried out for all the cybrids to identify haplogroup and non-haplogroup defining SNPs. mtDNA can mediate cellular bioenergetics and expression levels of nuclear genes related to complement, inflammation and apoptosis. Sequencing data suggest that observed effects are not due to rare mtDNA variants but rather the combination of SNPs representing the J versus H haplogroups. These findings represent a paradigm shift in our concepts of mt-nuclear interactions.
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Affiliation(s)
- M Cristina Kenney
- Gavin Herbert Eye Institute, Department of Pathology and Laboratory Medicine,
| | | | | | | | | | | | | | | | - Anthony B Nesburn
- Gavin Herbert Eye Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - David S Boyer
- Retina-Vitreous Associates Medical Group, Beverly Hills, CA, USA
| | | | - Marquis Vawter
- Functional Genomics Laboratory, Department of Psychiatry and Human Behavior, University of California Irvine, Irvine, CA, USA
| | | | - Michael Miceli
- Tulane Center for Aging, Tulane University, New Orleans, LA, USA
| | - Douglas C Wallace
- Children's Hospital of Philadelphia, Center for Mitochondrial and Epigenomic Medicine, Philadelphia, PA, USA
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66
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Kerchev PI, De Clercq I, Denecker J, Mühlenbock P, Kumpf R, Nguyen L, Audenaert D, Dejonghe W, Van Breusegem F. Mitochondrial perturbation negatively affects auxin signaling. MOLECULAR PLANT 2014; 7:1138-50. [PMID: 24903751 DOI: 10.1093/mp/ssu071] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Mitochondria are crucial players in the signaling and metabolic homeostasis of the plant cell. The molecular components that orchestrate the underlying processes, however, are largely unknown. Using a chemical biology approach, we exploited the responsiveness of Arabidopsis UDP-glucosyltransferase-encoding UGT74E2 towards mitochondrial perturbation in order to look for novel mechanisms regulating mitochondria-to-nucleus communication. The most potent inducers of UGT74E2 shared a (2-furyl)acrylate (FAA) substructure that negatively affected mitochondrial function and was identified before as an auxin transcriptional inhibitor. Based on these premises, we demonstrated that perturbed mitochondria negatively affect the auxin signaling machinery. Moreover, chemical perturbation of polar auxin transport and auxin biosynthesis was sufficient to induce mitochondrial retrograde markers and their transcript abundance was constitutively elevated in the absence of the auxin transcriptional activators ARF7 and ARF19.
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Affiliation(s)
- Pavel Ivanov Kerchev
- a Department of Plant Systems Biology, VIB, Ghent University, B-9052 Gent, Belgium b Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Inge De Clercq
- a Department of Plant Systems Biology, VIB, Ghent University, B-9052 Gent, Belgium b Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Jordi Denecker
- a Department of Plant Systems Biology, VIB, Ghent University, B-9052 Gent, Belgium b Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | | | - Robert Kumpf
- a Department of Plant Systems Biology, VIB, Ghent University, B-9052 Gent, Belgium b Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Long Nguyen
- d VIB Compound Screening Facility, B-9052 Gent, Belgium
| | - Dominique Audenaert
- a Department of Plant Systems Biology, VIB, Ghent University, B-9052 Gent, Belgium b Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium d VIB Compound Screening Facility, B-9052 Gent, Belgium
| | - Wim Dejonghe
- a Department of Plant Systems Biology, VIB, Ghent University, B-9052 Gent, Belgium b Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Frank Van Breusegem
- a Department of Plant Systems Biology, VIB, Ghent University, B-9052 Gent, Belgium b Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
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67
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Carmona-Gutierrez D, Büttner S. The many ways to age for a single yeast cell. Yeast 2014; 31:289-98. [PMID: 24842537 PMCID: PMC4140606 DOI: 10.1002/yea.3020] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Revised: 05/07/2014] [Accepted: 05/09/2014] [Indexed: 12/17/2022] Open
Abstract
The identification and characterization of the molecular determinants governing ageing represents the key to counteracting age-related diseases and eventually prolonging our health span. A large number of fundamental insights into the ageing process have been provided by research into the budding yeast Saccharomyces cerevisiae, which couples a wide array of technical advantages with a high degree of genetic, proteomic and mechanistic conservation. Indeed, this unicellular organism harbours regulatory pathways, such as those related to programmed cell death or nutrient signalling, that are crucial for ageing control and are reminiscent of other eukaryotes, including mammals. Here, we summarize and discuss three different paradigms of yeast ageing: replicative, chronological and colony ageing. We address their physiological relevance as well as the specific and common characteristics and regulators involved, providing an overview of the network underlying ageing in one of the most important eukaryotic model organisms.
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Abstract
For many years, mitochondria were viewed as semiautonomous organelles, required only for cellular energetics. This view has been largely supplanted by the concept that mitochondria are fully integrated into the cell and that mitochondrial stresses rapidly activate cytosolic signaling pathways that ultimately alter nuclear gene expression. Remarkably, this coordinated response to mild mitochondrial stress appears to leave the cell less susceptible to subsequent perturbations. This response, termed mitohormesis, is being rapidly dissected in many model organisms. A fuller understanding of mitohormesis promises to provide insight into our susceptibility for disease and potentially provide a unifying hypothesis for why we age.
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Affiliation(s)
- Jeanho Yun
- Center for Molecular Medicine, National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892, USA; Department of Biochemistry and Mitochondria Hub Regulation Center, College of Medicine, Dong-A University, Busan 602-714, South Korea
| | - Toren Finkel
- Center for Molecular Medicine, National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892, USA.
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69
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Yan H, Zhao Y, Jiang L. The putative transcription factor CaRtg3 is involved in tolerance to cations and antifungal drugs as well as serum-induced filamentation in Candida albicans. FEMS Yeast Res 2014; 14:614-23. [PMID: 24606409 DOI: 10.1111/1567-1364.12148] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Revised: 02/07/2014] [Accepted: 02/23/2014] [Indexed: 11/28/2022] Open
Abstract
The activated retrograde (RTG) pathway controls transcription of target genes through a heterodimer of transcription factors, Rtg1 and Rtg3, in Saccharomyces cerevisiae. Here, we have identified the sole homologous gene CaRTG3 that encodes a protein of 520 amino acids with characteristics of the basic helix-loop-helix/leucine zipper (bHLH/Zip) family in Candida albicans. Deletion of CaRTG3 results in C. albicans cells being sensitive to high concentrations of calcium and lithium cations as well as sodium dodecyl sulfate and activates the calcium/calcineurin signaling pathway in C. albicans cells. CaRTG3 is also involved in the tolerance of C. albicans cells to the antifungal drugs azoles and terbinafine, but not to the antifungal drugs casponfungin and amphotericin B as well as the cell-wall-damaging reagents Calcoflour White and Congo red. In contrast to ScRtg3, CaRtg3 is not involved in the osmolar response and is constitutively localized in the nucleus. However, deletion of CaRTG3 results in a delay in serum-induced filamentation of C. albicans cells. Therefore, CaRtg3 plays a role in tolerance to cations and antifungal drugs as well as serum-induced filamentation in C. albicans.
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Affiliation(s)
- Hongbo Yan
- The National Engineering Laboratory for Cereal Fermentation Technology, School of Biotechnology, Jiangnan University, Wuxi, China
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70
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Long YC, Tan TMC, Takao I, Tang BL. The biochemistry and cell biology of aging: metabolic regulation through mitochondrial signaling. Am J Physiol Endocrinol Metab 2014; 306:E581-91. [PMID: 24452454 DOI: 10.1152/ajpendo.00665.2013] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Cellular and organ metabolism affects organismal lifespan. Aging is characterized by increased risks for metabolic disorders, with age-associated degenerative diseases exhibiting varying degrees of mitochondrial dysfunction. The traditional view of the role of mitochondria generated reactive oxygen species (ROS) in cellular aging, assumed to be causative and simply detrimental for a long time now, is in need of reassessment. While there is little doubt that high levels of ROS are detrimental, mounting evidence points toward a lifespan extension effect exerted by mild to moderate ROS elevation. Dietary caloric restriction, inhibition of insulin-like growth factor-I signaling, and inhibition of the nutrient-sensing mechanistic target of rapamycin are robust longevity-promoting interventions. All of these appear to elicit mitochondrial retrograde signaling processes (defined as signaling from the mitochondria to the rest of the cell, for example, the mitochondrial unfolded protein response, or UPR(mt)). The effects of mitochondrial retrograde signaling may even spread to other cells/tissues in a noncell autonomous manner by yet unidentified signaling mediators. Multiple recent publications support the notion that an evolutionarily conserved, mitochondria-initiated signaling is central to the genetic and epigenetic regulation of cellular aging and organismal lifespan.
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Affiliation(s)
- Yun Chau Long
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University Health System, Singapore; and
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71
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Jazwinski SM. The retrograde response: a conserved compensatory reaction to damage from within and from without. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2014; 127:133-54. [PMID: 25149216 DOI: 10.1016/b978-0-12-394625-6.00005-2] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The retrograde response was discovered in Saccharomyces cerevisiae as a signaling pathway from the mitochondrion to the nucleus that triggers an array of gene regulatory changes in the latter. The activation of the retrograde response compensates for the deficits associated with aging, and thus it extends yeast replicative life span. The retrograde response is activated by the progressive decline in mitochondrial membrane potential during aging that is the result of increasing mitochondrial dysfunction. The ensuing metabolic adaptations and stress resistance can only delay the inevitable demise of the yeast cell. The retrograde response is embedded in a network of signal transduction pathways that impinge upon virtually every aspect of cell physiology. Thus, its manifestations are complicated. Many of these pathways have been implicated in life span regulation quite independently of the retrograde response. Together, they operate in a delicate balance in promoting longevity. The retrograde response is closely aligned with cell quality control, often performing when quality control is not sufficient to assure longevity. Among the key pathways related to this aspect of retrograde signaling are target of rapamycin and ceramide signaling. The retrograde response can also be found in other organisms, including Caenorhabditis elegans, Drosophila melanogaster, mouse, and human, where it exhibits an ever-increasing complexity that may be corralled by the transcription factor NFκB. The retrograde response may have evolved as a cytoprotective mechanism that senses and defends the organism from pathogens and environmental toxins.
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Affiliation(s)
- S Michal Jazwinski
- Tulane Center for Aging and Department of Medicine, Tulane University Health Sciences Center, New Orleans, Louisiana, USA
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72
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Abstract
SIGNIFICANCE The mitochondrial genetic system is responsible for the production of a few core-subunits of the respiratory chain and ATP synthase, the membrane protein complexes driving oxidative phosphorylation (OXPHOS). Efficiency and accuracy of mitochondrial protein synthesis determines how efficiently new OXPHOS complexes can be made. RECENT ADVANCES The system responsible for expression of the mitochondrial-encoded subunits developed from that of the bacterial ancestor of mitochondria. Importantly, many aspects of genome organization, transcription, and translation have diverged during evolution. Recent research has provided new insights into the architecture, regulation, and organelle-specific features of mitochondrial translation. Mitochondrial ribosomes contain a number of proteins absent from prokaryotic ribosomes, implying that in mitochondria, ribosomes were tailored to fit the requirements of the organelle. In addition, mitochondrial gene expression is regulated post-transcriptionally by a number of mRNA-specific translational activators. At least in yeast, these factors can regulate translation in respect to OXPHOS complex assembly to adjust the level of newly synthesized proteins to amounts that can be successfully assembled into respiratory chain complexes. CRITICAL ISSUES Mitochondrial gene expression is determining aging in eukaryotes, and a number of recent reports indicate that efficiency of translation directly influences this process. FUTURE DIRECTIONS Here we will summarize recent advances in our understanding of mitochondrial protein synthesis by comparing the knowledge acquired in the systems most commonly used to study mitochondrial biogenesis. However, many steps have not been understood mechanistically. Innovative biochemical and genetic approaches have to be elaborated to shed light on these important processes.
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Affiliation(s)
- Kirsten Kehrein
- 1 Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University , Stockholm, Sweden
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73
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Sousa M, Duarte AM, Fernandes TR, Chaves SR, Pacheco A, Leão C, Côrte-Real M, Sousa MJ. Genome-wide identification of genes involved in the positive and negative regulation of acetic acid-induced programmed cell death in Saccharomyces cerevisiae. BMC Genomics 2013; 14:838. [PMID: 24286259 PMCID: PMC4046756 DOI: 10.1186/1471-2164-14-838] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Accepted: 11/14/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Acetic acid is mostly known as a toxic by-product of alcoholic fermentation carried out by Saccharomyces cerevisiae, which it frequently impairs. The more recent finding that acetic acid triggers apoptotic programmed cell death (PCD) in yeast sparked an interest to develop strategies to modulate this process, to improve several biotechnological applications, but also for biomedical research. Indeed, acetate can trigger apoptosis in cancer cells, suggesting its exploitation as an anticancer compound. Therefore, we aimed to identify genes involved in the positive and negative regulation of acetic acid-induced PCD by optimizing a functional analysis of a yeast Euroscarf knock-out mutant collection. RESULTS The screen consisted of exposing the mutant strains to acetic acid in YPD medium, pH 3.0, in 96-well plates, and subsequently evaluating the presence of culturable cells at different time points. Several functional categories emerged as greatly relevant for modulation of acetic acid-induced PCD (e.g.: mitochondrial function, transcription of glucose-repressed genes, protein synthesis and modifications, and vesicular traffic for protection, or amino acid transport and biosynthesis, oxidative stress response, cell growth and differentiation, protein phosphorylation and histone deacetylation for its execution). Known pro-apoptotic and anti-apoptotic genes were found, validating the approach developed. Metabolism stood out as a main regulator of this process, since impairment of major carbohydrate metabolic pathways conferred resistance to acetic acid-induced PCD. Among these, lipid catabolism arose as one of the most significant new functions identified. The results also showed that many of the cellular and metabolic features that constitute hallmarks of tumour cells (such as higher glycolytic energetic dependence, lower mitochondrial functionality, increased cell division and metabolite synthesis) confer sensitivity to acetic acid-induced PCD, potentially explaining why tumour cells are more susceptible to acetate than untransformed cells and reinforcing the interest in exploiting this acid in cancer therapy. Furthermore, our results clearly establish a connection between cell proliferation and cell death regulation, evidencing a conserved developmental role of programmed cell death in unicellular eukaryotes. CONCLUSIONS This work advanced the characterization of acetic acid-induced PCD, providing a wealth of new information on putative molecular targets for its control with impact both in biotechnology and biomedicine.
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Affiliation(s)
- Marlene Sousa
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, Universidade do Minho, Campus de Gualtar, 4710-057 Braga, Portugal.
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Guaragnella N, Palermo V, Galli A, Moro L, Mazzoni C, Giannattasio S. The expanding role of yeast in cancer research and diagnosis: insights into the function of the oncosuppressors p53 and BRCA1/2. FEMS Yeast Res 2013; 14:2-16. [PMID: 24103154 DOI: 10.1111/1567-1364.12094] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Revised: 07/26/2013] [Accepted: 09/12/2013] [Indexed: 12/16/2022] Open
Abstract
When the glucose supply is high, despite the presence of oxygen, Saccharomyces cerevisiae uses fermentation as its main metabolic pathway and switches to oxidative metabolism only when this carbon source is limited. There are similarities between glucose-induced repression of oxidative metabolism of yeast and metabolic reprogramming of tumor cells. The glucose-induced repression of oxidative metabolism is regulated by oncogene homologues in yeast, such as RAS and Sch9p, the yeast homologue of Akt. Yeast also undergoes an apoptosis-like programmed cell death process sharing several features with mammalian apoptosis, including oxidative stress and a major role played by mitochondria. Evasion of apoptosis and sustained proliferative signaling are hallmarks of cancer. This, together with the possibility of heterologous expression of human genes in yeast, has allowed new insights to be obtained into the function of mammalian oncogenes/oncosuppressors. Here, we elaborate on the similarities between tumor and yeast cells underpinning the use of this model organism in cancer research. We also review the achievements obtained through heterologous expression in yeast of p53, BRCA1, and BRCA2, which are among the best-known cancer-susceptibility genes, with the aim of understanding their role in tumorigenesis. Yeast-cell-based functional assays for cancer genetic testing will also be dealt with.
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75
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Hofmann NR. Endoplasmic reticulum-localized transcription factors and mitochondrial retrograde regulation. THE PLANT CELL 2013; 25:3151. [PMID: 24045018 PMCID: PMC3809523 DOI: 10.1105/tpc.113.250912] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
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76
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Guha M, Avadhani NG. Mitochondrial retrograde signaling at the crossroads of tumor bioenergetics, genetics and epigenetics. Mitochondrion 2013; 13:577-91. [PMID: 24004957 DOI: 10.1016/j.mito.2013.08.007] [Citation(s) in RCA: 146] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Revised: 08/20/2013] [Accepted: 08/27/2013] [Indexed: 12/25/2022]
Abstract
Mitochondria play a central role not only in energy production but also in the integration of metabolic pathways as well as signals for apoptosis and autophagy. It is becoming increasingly apparent that mitochondria in mammalian cells play critical roles in the initiation and propagation of various signaling cascades. In particular, mitochondrial metabolic and respiratory states and status on mitochondrial genetic instability are communicated to the nucleus as an adaptive response through retrograde signaling. Each mammalian cell contains multiple copies of the mitochondrial genome (mtDNA). A reduction in mtDNA copy number has been reported in various human pathological conditions such as diabetes, obesity, neurodegenerative disorders, aging and cancer. Reduction in mtDNA copy number disrupts mitochondrial membrane potential (Δψm) resulting in dysfunctional mitochondria. Dysfunctional mitochondria trigger retrograde signaling and communicate their changing metabolic and functional state to the nucleus as an adaptive response resulting in an altered nuclear gene expression profile and altered cell physiology and morphology. In this review, we provide an overview of the various modes of mitochondrial retrograde signaling focusing particularly on the Ca(2+)/Calcineurin mediated retrograde signaling. We discuss the contribution of the key factors of the pathway such as Calcineurin, IGF1 receptor, Akt kinase and HnRNPA2 in the propagation of signaling and their role in modulating genetic and epigenetic changes favoring cellular reprogramming towards tumorigenesis.
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Affiliation(s)
- Manti Guha
- Department of Animal Biology and the Mari Lowe Center for Comparative Oncology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States.
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De Clercq I, Vermeirssen V, Van Aken O, Vandepoele K, Murcha MW, Law SR, Inzé A, Ng S, Ivanova A, Rombaut D, van de Cotte B, Jaspers P, Van de Peer Y, Kangasjärvi J, Whelan J, Van Breusegem F. The membrane-bound NAC transcription factor ANAC013 functions in mitochondrial retrograde regulation of the oxidative stress response in Arabidopsis. THE PLANT CELL 2013; 25:3472-90. [PMID: 24045019 PMCID: PMC3809544 DOI: 10.1105/tpc.113.117168] [Citation(s) in RCA: 250] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Revised: 08/06/2013] [Accepted: 08/26/2013] [Indexed: 05/18/2023]
Abstract
Upon disturbance of their function by stress, mitochondria can signal to the nucleus to steer the expression of responsive genes. This mitochondria-to-nucleus communication is often referred to as mitochondrial retrograde regulation (MRR). Although reactive oxygen species and calcium are likely candidate signaling molecules for MRR, the protein signaling components in plants remain largely unknown. Through meta-analysis of transcriptome data, we detected a set of genes that are common and robust targets of MRR and used them as a bait to identify its transcriptional regulators. In the upstream regions of these mitochondrial dysfunction stimulon (MDS) genes, we found a cis-regulatory element, the mitochondrial dysfunction motif (MDM), which is necessary and sufficient for gene expression under various mitochondrial perturbation conditions. Yeast one-hybrid analysis and electrophoretic mobility shift assays revealed that the transmembrane domain-containing no apical meristem/Arabidopsis transcription activation factor/cup-shaped cotyledon transcription factors (ANAC013, ANAC016, ANAC017, ANAC053, and ANAC078) bound to the MDM cis-regulatory element. We demonstrate that ANAC013 mediates MRR-induced expression of the MDS genes by direct interaction with the MDM cis-regulatory element and triggers increased oxidative stress tolerance. In conclusion, we characterized ANAC013 as a regulator of MRR upon stress in Arabidopsis thaliana.
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Affiliation(s)
- Inge De Clercq
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Vanessa Vermeirssen
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Olivier Van Aken
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley 6009, Western Australia, Australia
| | - Klaas Vandepoele
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Monika W. Murcha
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley 6009, Western Australia, Australia
| | - Simon R. Law
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley 6009, Western Australia, Australia
| | - Annelies Inzé
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Sophia Ng
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley 6009, Western Australia, Australia
| | - Aneta Ivanova
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley 6009, Western Australia, Australia
| | - Debbie Rombaut
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Brigitte van de Cotte
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Pinja Jaspers
- Plant Biology, Department of Biological and Environmental Sciences, University of Helsinki, FI-00014 Helsinki, Finland
| | - Yves Van de Peer
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Jaakko Kangasjärvi
- Plant Biology, Department of Biological and Environmental Sciences, University of Helsinki, FI-00014 Helsinki, Finland
| | - James Whelan
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley 6009, Western Australia, Australia
- Department of Botany, School of Life Science, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Frank Van Breusegem
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
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Guaragnella N, Ždralević M, Lattanzio P, Marzulli D, Pracheil T, Liu Z, Passarella S, Marra E, Giannattasio S. Yeast growth in raffinose results in resistance to acetic-acid induced programmed cell death mostly due to the activation of the mitochondrial retrograde pathway. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2013; 1833:2765-2774. [PMID: 23906793 DOI: 10.1016/j.bbamcr.2013.07.017] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Revised: 06/27/2013] [Accepted: 07/19/2013] [Indexed: 12/22/2022]
Abstract
In order to investigate whether and how a modification of mitochondrial metabolism can affect yeast sensitivity to programmed cell death (PCD) induced by acetic acid (AA-PCD), yeast cells were grown on raffinose, as a sole carbon source, which, differently from glucose, favours mitochondrial respiration. We found that, differently from glucose-grown cells, raffinose-grown cells were mostly resistant to AA-PCD and that this was due to the activation of mitochondrial retrograde (RTG) response, which increased with time, as revealed by the up-regulation of the peroxisomal isoform of citrate synthase and isocitrate dehydrogenase isoform 1, RTG pathway target genes. Accordingly, the deletion of RTG2 and RTG3, a positive regulator and a transcription factor of the RTG pathway, resulted in AA-PCD, as shown by TUNEL assay. Neither deletion in raffinose-grown cells of HAP4, encoding the positive regulatory subunit of the Hap2,3,4,5 complex nor constitutive activation of the RTG pathway in glucose-grown cells due to deletion of MKS1, a negative regulator of RTG pathway, had effect on yeast AA-PCD. The RTG pathway was found to be activated in yeast cells containing mitochondria, in which membrane potential was measured, capable to consume oxygen in a manner stimulated by the uncoupler CCCP and inhibited by the respiratory chain inhibitor antimycin A. AA-PCD resistance in raffinose-grown cells occurs with a decrease in both ROS production and cytochrome c release as compared to glucose-grown cells en route to AA-PCD.
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Affiliation(s)
| | - Maša Ždralević
- CNR, Istituto di Biomembrane e Bioenergetica, Via Amendola 165/a, 70126 Bari, Italy
| | - Paolo Lattanzio
- CNR, Istituto di Biomembrane e Bioenergetica, Via Amendola 165/a, 70126 Bari, Italy
| | - Domenico Marzulli
- CNR, Istituto di Biomembrane e Bioenergetica, Via Amendola 165/a, 70126 Bari, Italy
| | - Tammy Pracheil
- Department of Biological Sciences, University of New Orleans, 2000 Lakeshore Drive, New Orleans, LA 70148, USA
| | - Zhengchang Liu
- Department of Biological Sciences, University of New Orleans, 2000 Lakeshore Drive, New Orleans, LA 70148, USA
| | - Salvatore Passarella
- Dipartimento di Medicina e Scienze per la Salute, Università del Molise, Via de Sanctis, 86100 Campobasso, Italy
| | - Ersilia Marra
- CNR, Istituto di Biomembrane e Bioenergetica, Via Amendola 165/a, 70126 Bari, Italy
| | - Sergio Giannattasio
- CNR, Istituto di Biomembrane e Bioenergetica, Via Amendola 165/a, 70126 Bari, Italy.
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79
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Leonov A, Titorenko VI. A network of interorganellar communications underlies cellular aging. IUBMB Life 2013; 65:665-74. [PMID: 23818261 DOI: 10.1002/iub.1183] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2013] [Accepted: 04/19/2013] [Indexed: 01/07/2023]
Abstract
Organelles within a eukaryotic cell respond to age-related intracellular stresses and environmental factors by altering their functional states to generate, direct and process the flow of interorganellar information that is essential for establishing a pro- or antiaging cellular pattern. The scope of this review is to critically analyze recent progress in understanding how various intercompartmental (i.e., organelle-organelle and organelle-cytosol) communications regulate cellular aging in evolutionarily distant eukaryotes. Our analysis suggests a model for an intricate network of intercompartmental communications that underly cellular aging in eukaryotic organisms across phyla. This proposed model posits that the numerous directed, coordinated and regulated organelle-organelle and organelle-cytosol communications integrated into this network define the long-term viability of a eukaryotic cell and, thus, are critical for regulating cellular aging.
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Affiliation(s)
- Anna Leonov
- Department of Biology, Concordia University, Montreal, QC, Canada
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80
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Beach A, Richard VR, Leonov A, Burstein MT, Bourque SD, Koupaki O, Juneau M, Feldman R, Iouk T, Titorenko VI. Mitochondrial membrane lipidome defines yeast longevity. Aging (Albany NY) 2013; 5:551-74. [PMID: 23924582 PMCID: PMC3765583 DOI: 10.18632/aging.100578] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2013] [Accepted: 07/16/2013] [Indexed: 12/22/2022]
Abstract
Our studies revealed that lithocholic acid (LCA), a bile acid, is a potent anti-aging natural compound that in yeast cultured under longevity-extending caloric restriction (CR) conditions acts in synergy with CR to enable a significant further increase in chronological lifespan. Here, we investigate a mechanism underlying this robust longevity-extending effect of LCA under CR. We found that exogenously added LCA enters yeast cells, is sorted to mitochondria, resides mainly in the inner mitochondrial membrane, and also associates with the outer mitochondrial membrane. LCA elicits an age-related remodeling of glycerophospholipid synthesis and movement within both mitochondrial membranes, thereby causing substantial changes in mitochondrial membrane lipidome and triggering major changes in mitochondrial size, number and morphology. In synergy, these changes in the membrane lipidome and morphology of mitochondria alter the age-related chronology of mitochondrial respiration, membrane potential, ATP synthesis and reactive oxygen species homeostasis. The LCA-driven alterations in the age-related dynamics of these vital mitochondrial processes extend yeast longevity. In sum, our findings suggest a mechanism underlying the ability of LCA to delay chronological aging in yeast by accumulating in both mitochondrial membranes and altering their glycerophospholipid compositions. We concluded that mitochondrial membrane lipidome plays an essential role in defining yeast longevity.
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Affiliation(s)
- Adam Beach
- Department of Biology, Concordia University, Montreal, Quebec H4B 1R6, Canada
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81
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Giannattasio S, Guaragnella N, Arbini AA, Moro L. Stress-related mitochondrial components and mitochondrial genome as targets of anticancer therapy. Chem Biol Drug Des 2013; 81:102-12. [PMID: 23253132 DOI: 10.1111/cbdd.12057] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In addition to their role as cell powerhouse mitochondria are key organelles in the processes deciding about cell life or death that are crucial for tumor cell growth and survival, as well as for tumor cell ability to metastasize. Alterations in mitochondrial structure and functions have long been observed in cancer cells, thus targeting mitochondria as an anticancer therapeutic strategy has gained momentum recently. We will review the achievements and perspectives in the elucidation of the molecular basis for developing mitochondrial-targeted compounds as potential anticancer agents with special attention to mitochondrial DNA mutations and mitochondrial dysfunction. Molecules/agents candidate to affect mitochondrial metabolism in cancer cells will be dealt with, with a particular focus on approaches targeting defects in the mitochondrial genome.
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Affiliation(s)
- Sergio Giannattasio
- Institute of Biomembranes and Bioenergetics, National Research Council, Via Amendola 165/a, 70126 Bari, Italy.
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82
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Zhang F, Pracheil T, Thornton J, Liu Z. Adenosine Triphosphate (ATP) Is a Candidate Signaling Molecule in the Mitochondria-to-Nucleus Retrograde Response Pathway. Genes (Basel) 2013; 4:86-100. [PMID: 24605246 PMCID: PMC3899953 DOI: 10.3390/genes4010086] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Revised: 03/09/2013] [Accepted: 03/15/2013] [Indexed: 01/08/2023] Open
Abstract
Intracellular communication from the mitochondria to the nucleus is achieved via the retrograde response. In budding yeast, the retrograde response, also known as the RTG pathway, is regulated positively by Rtg1, Rtg2, Rtg3 and Grr1 and negatively by Mks1, Lst8 and two 14-3-3 proteins, Bmh1/2. Activation of retrograde signaling leads to activation of Rtg1/3, two basic helix-loop-helix leucine zipper transcription factors. Rtg1/3 activation requires Rtg2, a cytoplasmic protein with an N-terminal adenosine triphosphate (ATP) binding domain belonging to the actin/Hsp70/sugar kinase superfamily. The critical regulatory step of the retrograde response is the interaction between Rtg2 and Mks1. Rtg2 binds to and inactivates Mks1, allowing for activation of Rtg1/3 and the RTG pathway. When the pathway is inactive, Mks1 has dissociated from Rtg2 and bound to Bmh1/2, preventing activation of Rtg1/3. What signals association or disassociation of Mks1 and Rtg2 is unknown. Here, we show that ATP at physiological concentrations dissociates Mks1 from Rtg2 in a highly cooperative fashion. We report that ATP-mediated dissociation of Mks1 from Rtg2 is conserved in two other fungal species, K. lactis and K. waltii. Activation of Rtg1/3 upregulates expression of genes encoding enzymes catalyzing the first three reactions of the Krebs cycle, which is coupled to ATP synthesis through oxidative phosphorylation. Therefore, we propose that the retrograde response is an ATP homeostasis pathway coupling ATP production with ATP-mediated repression of the retrograde response by releasing Mks1 from Rtg2.
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Affiliation(s)
- Feng Zhang
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA; E-Mails: (F.Z.); (J.T.)
| | - Tammy Pracheil
- Department of Biological Sciences, University of New Orleans, 2000 Lakeshore Drive, New Orleans, LA 70148, USA; E-Mail:
| | - Janet Thornton
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA; E-Mails: (F.Z.); (J.T.)
| | - Zhengchang Liu
- Department of Biological Sciences, University of New Orleans, 2000 Lakeshore Drive, New Orleans, LA 70148, USA; E-Mail:
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +1-504-280-6314; Fax: +1-504-280-6121
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Giannattasio S, Guaragnella N, Zdralević M, Marra E. Molecular mechanisms of Saccharomyces cerevisiae stress adaptation and programmed cell death in response to acetic acid. Front Microbiol 2013; 4:33. [PMID: 23430312 PMCID: PMC3576806 DOI: 10.3389/fmicb.2013.00033] [Citation(s) in RCA: 103] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Accepted: 02/05/2013] [Indexed: 01/07/2023] Open
Abstract
Beyond its classical biotechnological applications such as food and beverage production or as a cell factory, the yeast Saccharomyces cerevisiae is a valuable model organism to study fundamental mechanisms of cell response to stressful environmental changes. Acetic acid is a physiological product of yeast fermentation and it is a well-known food preservative due to its antimicrobial action. Acetic acid has recently been shown to cause yeast cell death and aging. Here we shall focus on the molecular mechanisms of S. cerevisiae stress adaptation and programmed cell death in response to acetic acid. We shall elaborate on the intracellular signaling pathways involved in the cross-talk of pro-survival and pro-death pathways underlying the importance of understanding fundamental aspects of yeast cell homeostasis to improve the performance of a given yeast strain in biotechnological applications.
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Affiliation(s)
- Sergio Giannattasio
- Istituto di Biomembrane e Bioenergetica, Consiglio Nazionale delle Ricerche Bari, Italy
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84
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Kenney MC, Chwa M, Atilano SR, Pavlis JM, Falatoonzadeh P, Ramirez C, Malik D, Hsu T, Woo G, Soe K, Nesburn AB, Boyer DS, Kuppermann BD, Jazwinski SM, Miceli MV, Wallace DC, Udar N. Mitochondrial DNA variants mediate energy production and expression levels for CFH, C3 and EFEMP1 genes: implications for age-related macular degeneration. PLoS One 2013; 8:e54339. [PMID: 23365660 PMCID: PMC3554762 DOI: 10.1371/journal.pone.0054339] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Accepted: 12/10/2012] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Mitochondrial dysfunction is associated with the development and progression of age-related macular degeneration (AMD). Recent studies using populations from the United States and Australia have demonstrated that AMD is associated with mitochondrial (mt) DNA haplogroups (as defined by combinations of mtDNA polymorphisms) that represent Northern European Caucasians. The aim of this study was to use the cytoplasmic hybrid (cybrid) model to investigate the molecular and biological functional consequences that occur when comparing the mtDNA H haplogroup (protective for AMD) versus J haplogroup (high risk for AMD). METHODOLOGY/PRINCIPAL FINDINGS Cybrids were created by introducing mitochondria from individuals with either H or J haplogroups into a human retinal epithelial cell line (ARPE-19) that was devoid of mitochondrial DNA (Rho0). In cybrid lines, all of the cells carry the same nuclear genes but vary in mtDNA content. The J cybrids had significantly lower levels of ATP and reactive oxygen/nitrogen species production, but increased lactate levels and rates of growth. Q-PCR analyses showed J cybrids had decreased expressions for CFH, C3, and EFEMP1 genes, high risk genes for AMD, and higher expression for MYO7A, a gene associated with retinal degeneration in Usher type IB syndrome. The H and J cybrids also have comparatively altered expression of nuclear genes involved in pathways for cell signaling, inflammation, and metabolism. CONCLUSION/SIGNIFICANCE Our findings demonstrate that mtDNA haplogroup variants mediate not only energy production and cell growth, but also cell signaling for major molecular pathways. These data support the hypothesis that mtDNA variants play important roles in numerous cellular functions and disease processes, including AMD.
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Affiliation(s)
- M Cristina Kenney
- Gavin Herbert Eye Institute, University of California Irvine, Irvine, California, United States of America.
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85
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Essential roles of peroxisomally produced and metabolized biomolecules in regulating yeast longevity. Subcell Biochem 2013; 69:153-67. [PMID: 23821148 DOI: 10.1007/978-94-007-6889-5_9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The essential role of the peroxisome in oxidizing fatty acids, maintaining reactive oxygen species homeostasis and replenishing tricarboxylic acid cycle intermediates is well known. Recent findings have broadened a spectrum of biomolecules that are synthesized and metabolized in peroxisomes. Emergent evidence supports the view that, by releasing various biomolecules known to modulate essential cellular processes, the peroxisome not only operates as an organizing platform for several developmental and differentiation programs but is also actively involved in defining the replicative and chronological age of a eukaryotic cell. The scope of this chapter is to summarize the evidence that the peroxisome defines yeast longevity by operating as a system controller that: (1) modulates levels of non-esterified fatty acids and diacylglycerol; (2) replenishes tricarboxylic acid cycle intermediates destined for mitochondria; and (3) contributes to the synthesis of polyamines. We critically evaluate molecular mechanisms underlying the essential role of peroxisomally produced and metabolized biomolecules in governing cellular aging in yeast.
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86
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Ng S, Giraud E, Duncan O, Law SR, Wang Y, Xu L, Narsai R, Carrie C, Walker H, Day DA, Blanco NE, Strand Å, Whelan J, Ivanova A. Cyclin-dependent kinase E1 (CDKE1) provides a cellular switch in plants between growth and stress responses. J Biol Chem 2012; 288:3449-59. [PMID: 23229550 DOI: 10.1074/jbc.m112.416727] [Citation(s) in RCA: 100] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Plants must deal effectively with unfavorable growth conditions that necessitate a coordinated response to integrate cellular signals with mitochondrial retrograde signals. A genetic screen was carried out to identify regulators of alternative oxidase (rao mutants), using AOX1a expression as a model system to study retrograde signaling in plants. Two independent rao1 mutant alleles identified CDKE1 as a central nuclear component integrating mitochondrial retrograde signals with energy signals under stress. CDKE1 is also necessary for responses to general cellular stresses, such as H(2)O(2) and cold that act, at least in part, via anterograde pathways, and integrates signals from central energy/stress sensing kinase signal transduction pathways within the nucleus. Together, these results place CDKE1 as a central kinase integrating diverse cellular signals and shed light on a mechanism by which plants can effectively switch between growth and stress responses.
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Affiliation(s)
- Sophia Ng
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, 35 Stirling Highway, Crawley, Western Australia 6009, Australia
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87
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Nargang FE, Adames K, Rüb C, Cheung S, Easton N, Nargang CE, Chae MS. Identification of genes required for alternative oxidase production in the Neurospora crassa gene knockout library. G3 (BETHESDA, MD.) 2012; 2:1345-56. [PMID: 23173086 PMCID: PMC3484665 DOI: 10.1534/g3.112.004218] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2012] [Accepted: 09/04/2012] [Indexed: 01/22/2023]
Abstract
The alternative oxidase (AOX) of Neurospora crassa transfers electrons from ubiquinol to oxygen. The enzyme is not expressed under normal conditions. However, when the function of the standard electron transport chain is compromised, AOX is induced, providing cells with a means to continue respiration and growth. Induction of the enzyme represents a form of retrograde regulation because AOX is encoded by a nuclear gene that responds to signals produced from inefficiently functioning mitochondria. To identify genes required for AOX expression, we have screened the N. crassa gene knockout library for strains that are unable to grow in the presence of antimycin A, an inhibitor of complex III of the standard electron transport chain. From the 7800 strains containing knockouts of different genes, we identified 62 strains that have reduced levels of AOX when grown under conditions known to induce the enzyme. Some strains have virtually no AOX, whereas others have only a slight reduction of the protein. A broad range of seemingly unrelated functions are represented in the knockouts. For example, we identified transcription factors, kinases, the mitochondrial import receptor Tom70, three subunits of the COP9 signalosome, a monothiol glutaredoxin, and several hypothetical proteins as being required for wild-type levels of AOX production. Our results suggest that defects in many signaling or metabolic pathways have a negative effect on AOX expression and imply that complex systems control production of the enzyme.
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Affiliation(s)
- Frank E Nargang
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada.
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88
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Titorenko VI, Harkness TAA. The spatiotemporal dynamics of longevity-defining cellular processes and its modulation by genetic, dietary, and pharmacological anti-aging interventions. Front Physiol 2012; 3:419. [PMID: 23118730 PMCID: PMC3484328 DOI: 10.3389/fphys.2012.00419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2012] [Accepted: 10/16/2012] [Indexed: 11/13/2022] Open
Affiliation(s)
| | - Troy A. A. Harkness
- Department of Anatomy and Cell Biology, University of SaskatchewanSaskatoon, SK, Canada,*Correspondence: ;
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89
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Jia D, Park JH, Jung KH, Levine H, Kaipparettu BA. [Experience in the management of children with diabetes mellitus]. Cells 1966. [PMID: 29534029 PMCID: PMC5870353 DOI: 10.3390/cells7030021] [Citation(s) in RCA: 153] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Aerobic glycolysis, also referred to as the Warburg effect, has been regarded as the dominant metabolic phenotype in cancer cells for a long time. More recently, it has been shown that mitochondria in most tumors are not defective in their ability to carry out oxidative phosphorylation (OXPHOS). Instead, in highly aggressive cancer cells, mitochondrial energy pathways are reprogrammed to meet the challenges of high energy demand, better utilization of available fuels and macromolecular synthesis for rapid cell division and migration. Mitochondrial energy reprogramming is also involved in the regulation of oncogenic pathways via mitochondria-to-nucleus retrograde signaling and post-translational modification of oncoproteins. In addition, neoplastic mitochondria can engage in crosstalk with the tumor microenvironment. For example, signals from cancer-associated fibroblasts can drive tumor mitochondria to utilize OXPHOS, a process known as the reverse Warburg effect. Emerging evidence shows that cancer cells can acquire a hybrid glycolysis/OXPHOS phenotype in which both glycolysis and OXPHOS can be utilized for energy production and biomass synthesis. The hybrid glycolysis/OXPHOS phenotype facilitates metabolic plasticity of cancer cells and may be specifically associated with metastasis and therapy-resistance. Moreover, cancer cells can switch their metabolism phenotypes in response to external stimuli for better survival. Taking into account the metabolic heterogeneity and plasticity of cancer cells, therapies targeting cancer metabolic dependency in principle can be made more effective.
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Affiliation(s)
- Dongya Jia
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA.
- Systems, Synthetic and Physical Biology Program, Rice University, Houston, TX 77005, USA.
| | - Jun Hyoung Park
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Kwang Hwa Jung
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Herbert Levine
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA.
- Department of Bioengineering, Rice University, Houston, TX 77005, USA.
- Department of Biosciences, Rice University, Houston, TX 77005, USA.
- Physics and Astronomy, Rice University, Houston, TX 77005, USA.
| | - Benny Abraham Kaipparettu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA.
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