1
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Xian J, Ni L, Liu C, Li J, Cao Y, Qin J, Liu D, Wang X. Genome-Scale Screening of Saccharomyces cerevisiae Deletion Mutants to Gain Molecular Insight into Tolerance to Mercury Ions. J Fungi (Basel) 2024; 10:492. [PMID: 39057376 PMCID: PMC11277898 DOI: 10.3390/jof10070492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 06/19/2024] [Accepted: 06/25/2024] [Indexed: 07/28/2024] Open
Abstract
Mercury (Hg) is a global pollutant and a bioaccumulative toxin that seriously affects the environment. Though increasing information has been obtained on the mechanisms involved in mercury toxicity, there is still a knowledge gap between the adverse effects and action mechanisms, especially at the molecular level. In the current study, we screened a diploid library of Saccharomyces cerevisiae single-gene deletion mutants to identify the nonessential genes associated with increased sensitivity to mercury ions. By genome-scale screening, we identified 64 yeast single-gene deletion mutants. These genes are involved in metabolism, transcription, antioxidant activity, cellular transport, transport facilitation, transport routes, and the cell cycle, as well as in protein synthesis, folding, modification, and protein destination. The concentration of mercury ions was different in the cells of yeast deletion mutants. Moreover, the disruption of antioxidant systems may play a key role in the mercurial toxic effects. The related functions of sensitive genes and signal pathways were further analyzed using bioinformatics-related technologies. Among 64 sensitive genes, 37 genes have human homologous analogs. Our results may provide a meaningful reference for understanding the action mode, cellular detoxification, and molecular regulation mechanisms of mercury toxicity.
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Affiliation(s)
| | | | | | | | | | | | | | - Xue Wang
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo 255049, China; (J.X.); (L.N.); (C.L.); (J.L.); (Y.C.); (J.Q.); (D.L.)
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2
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Hotta N, Kotaka A, Matsumura K, Sasano Y, Hata Y, Harada T, Sugiyama M, Harashima S, Ishida H. Effect of yeast chromosome II aneuploidy on malate production in sake brewing. J Biosci Bioeng 2024; 137:24-30. [PMID: 37989703 DOI: 10.1016/j.jbiosc.2023.10.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 10/08/2023] [Accepted: 10/31/2023] [Indexed: 11/23/2023]
Abstract
Chromosome aneuploidy is a common phenomenon in industrial yeast. Aneuploidy is considered one of the strategies to enhance the industrial properties of Saccharomyces cerevisiae strains. However, the effects of chromosomal aneuploidy on the brewing properties of sake have not been extensively studied. In this study, sake brewing was performed using a series of genome-wide segmental duplicated laboratory S. cerevisiae strains, and the effects of each segmentally duplicated region on sake brewing were investigated. We found that the duplication of specific chromosomal regions affected the production of organic acids and aromatic compounds in sake brewing. As organic acids significantly influence the taste of sake, we focused on the segmental duplication of chromosome II that alters malate levels. Sake yeast Kyokai No. 901 strains with segmental chromosome II duplication were constructed using a polymerase chain reaction-mediated chromosomal duplication method, and sake was brewed using the resultant aneuploid sake yeast strains. The results showed the possibility of developing sake yeast strains exhibiting low malate production without affecting ethanol production capacity. Our study revealed that aneuploidy in yeast alters the brewing properties; in particular, the aneuploidy of chromosome II alters malate production in sake brewing. In conclusion, aneuploidization can be a novel and useful tool to breed sake yeast strains with improved traits, possessing industrial significance.
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Affiliation(s)
- Natsuki Hotta
- Research Institute, Gekkeikan Sake Co., Ltd., 101 Shimotoba-koyanagi-cho, Fushimi-ku, Kyoto 612-8385, Japan.
| | - Atsushi Kotaka
- Research Institute, Gekkeikan Sake Co., Ltd., 101 Shimotoba-koyanagi-cho, Fushimi-ku, Kyoto 612-8385, Japan
| | - Kengo Matsumura
- Research Institute, Gekkeikan Sake Co., Ltd., 101 Shimotoba-koyanagi-cho, Fushimi-ku, Kyoto 612-8385, Japan
| | - Yu Sasano
- Department of Applied Microbial Technology, Faculty of Biotechnology and Life Science, Sojo University, 4-22-1 Ikeda, Nishi-ku, Kumamoto 860-0082, Japan
| | - Yoji Hata
- Research Institute, Gekkeikan Sake Co., Ltd., 101 Shimotoba-koyanagi-cho, Fushimi-ku, Kyoto 612-8385, Japan
| | - Tomoka Harada
- Department of Food Sciences and Biotechnology, Faculty of Life Sciences, Hiroshima Institute of Technology, 2-1-1 Miyake, Saeki-ku, Hiroshima 731-5193, Japan
| | - Minetaka Sugiyama
- Department of Food Sciences and Biotechnology, Faculty of Life Sciences, Hiroshima Institute of Technology, 2-1-1 Miyake, Saeki-ku, Hiroshima 731-5193, Japan
| | - Satoshi Harashima
- Department of Applied Microbial Technology, Faculty of Biotechnology and Life Science, Sojo University, 4-22-1 Ikeda, Nishi-ku, Kumamoto 860-0082, Japan
| | - Hiroki Ishida
- Research Institute, Gekkeikan Sake Co., Ltd., 101 Shimotoba-koyanagi-cho, Fushimi-ku, Kyoto 612-8385, Japan
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3
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Li CY, Jiang HF, Li L, Lai XJ, Liu QR, Yu SB, Yi CL, Chen XQ. Neuroglobin Facilitates Neuronal Oxygenation through Tropic Migration under Hypoxia or Anemia in Rat: How Does the Brain Breathe? Neurosci Bull 2023; 39:1481-1496. [PMID: 36884214 PMCID: PMC10533768 DOI: 10.1007/s12264-023-01040-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 01/03/2023] [Indexed: 03/09/2023] Open
Abstract
The discovery of neuroglobin (Ngb), a brain- or neuron-specific member of the hemoglobin family, has revolutionized our understanding of brain oxygen metabolism. Currently, how Ngb plays such a role remains far from clear. Here, we report a novel mechanism by which Ngb might facilitate neuronal oxygenation upon hypoxia or anemia. We found that Ngb was present in, co-localized to, and co-migrated with mitochondria in the cell body and neurites of neurons. Hypoxia induced a sudden and prominent migration of Ngb towards the cytoplasmic membrane (CM) or cell surface in living neurons, and this was accompanied by the mitochondria. In vivo, hypotonic and anemic hypoxia induced a reversible Ngb migration toward the CM in cerebral cortical neurons in rat brains but did not alter the expression level of Ngb or its cytoplasm/mitochondria ratio. Knock-down of Ngb by RNA interference significantly diminished respiratory succinate dehydrogenase (SDH) and ATPase activity in neuronal N2a cells. Over-expression of Ngb enhanced SDH activity in N2a cells upon hypoxia. Mutation of Ngb at its oxygen-binding site (His64) significantly increased SDH activity and reduced ATPase activity in N2a cells. Taken together, Ngb was physically and functionally linked to mitochondria. In response to an insufficient oxygen supply, Ngb migrated towards the source of oxygen to facilitate neuronal oxygenation. This novel mechanism of neuronal respiration provides new insights into the understanding and treatment of neurological diseases such as stroke and Alzheimer's disease and diseases that cause hypoxia in the brain such as anemia.
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Affiliation(s)
- Chun-Yang Li
- Department of Pathophysiology, Tongji Medical College; Key Laboratory of Neurological Diseases, The Ministry of Education (HUST), Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Hai-Feng Jiang
- Department of Pathophysiology, Tongji Medical College; Key Laboratory of Neurological Diseases, The Ministry of Education (HUST), Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Li Li
- Department of Pathophysiology, Tongji Medical College; Key Laboratory of Neurological Diseases, The Ministry of Education (HUST), Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Xiao-Jing Lai
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, 430023, China
| | - Qian-Rong Liu
- Department of Pathophysiology, Tongji Medical College; Key Laboratory of Neurological Diseases, The Ministry of Education (HUST), Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Shang-Bin Yu
- Department of Pathophysiology, Tongji Medical College; Key Laboratory of Neurological Diseases, The Ministry of Education (HUST), Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Cheng-La Yi
- Department of Traumatic Surgery, Tong-ji Hospital, Tong-ji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
| | - Xiao-Qian Chen
- Department of Pathophysiology, Tongji Medical College; Key Laboratory of Neurological Diseases, The Ministry of Education (HUST), Huazhong University of Science and Technology, Wuhan, 430030, China.
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4
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Seshadri SR, Banarjee C, Barros MH, Fontanesi F. The translational activator Sov1 coordinates mitochondrial gene expression with mitoribosome biogenesis. Nucleic Acids Res 2020; 48:6759-6774. [PMID: 32449921 PMCID: PMC7337963 DOI: 10.1093/nar/gkaa424] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 05/06/2020] [Accepted: 05/07/2020] [Indexed: 02/07/2023] Open
Abstract
Mitoribosome biogenesis is an expensive metabolic process that is essential to maintain cellular respiratory capacity and requires the stoichiometric accumulation of rRNAs and proteins encoded in two distinct genomes. In yeast, the ribosomal protein Var1, alias uS3m, is mitochondrion-encoded. uS3m is a protein universally present in all ribosomes, where it forms part of the small subunit (SSU) mRNA entry channel and plays a pivotal role in ribosome loading onto the mRNA. However, despite its critical functional role, very little is known concerning VAR1 gene expression. Here, we demonstrate that the protein Sov1 is an in bona fide VAR1 mRNA translational activator and additionally interacts with newly synthesized Var1 polypeptide. Moreover, we show that Sov1 assists the late steps of mtSSU biogenesis involving the incorporation of Var1, an event necessary for uS14 and mS46 assembly. Notably, we have uncovered a translational regulatory mechanism by which Sov1 fine-tunes Var1 synthesis with its assembly into the mitoribosome.
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Affiliation(s)
- Suhas R Seshadri
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Chitra Banarjee
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Mario H Barros
- Departamento de Microbiologia, Instituto de Ciencias Biomedicas, Universidade de Sao Paulo, Sao Paulo 05508-900, Brazil
| | - Flavia Fontanesi
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
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5
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Moosavi B, Berry EA, Zhu XL, Yang WC, Yang GF. The assembly of succinate dehydrogenase: a key enzyme in bioenergetics. Cell Mol Life Sci 2019; 76:4023-4042. [PMID: 31236625 PMCID: PMC11105593 DOI: 10.1007/s00018-019-03200-7] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 05/30/2019] [Accepted: 06/17/2019] [Indexed: 12/12/2022]
Abstract
Succinate dehydrogenase (SDH) also known as complex II or succinate:quinone oxidoreductase is an enzyme involved in both oxidative phosphorylation and tricarboxylic acid cycle; the processes that generate energy. SDH is a multi-subunit enzyme which requires a series of proteins for its proper assembly at several steps. This enzyme has medical significance as there is a broad range of human diseases from cancers to neurodegeneration related to SDH malfunction. Some of these disorders have recently been linked to defective assembly factors, reinvigorating further research in this area. Apart from that this enzyme has agricultural importance as many fungicides have been/will be designed targeting specifically this enzyme in plant fungal pathogens. In addition, we speculate it might be possible to design novel fungicides specifically targeting fungal assembly factors. Considering the medical and agricultural implications of SDH, the aim of this review is an overview of the SDH assembly factors and critical analysis of controversial issues around them.
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Affiliation(s)
- Behrooz Moosavi
- Key Laboratory of Pesticide and Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, 430079, People's Republic of China
| | - Edward A Berry
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
| | - Xiao-Lei Zhu
- Key Laboratory of Pesticide and Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, 430079, People's Republic of China
| | - Wen-Chao Yang
- Key Laboratory of Pesticide and Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, 430079, People's Republic of China
| | - Guang-Fu Yang
- Key Laboratory of Pesticide and Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, 430079, People's Republic of China.
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6
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Sharma P, Maklashina E, Cecchini G, Iverson TM. Maturation of the respiratory complex II flavoprotein. Curr Opin Struct Biol 2019; 59:38-46. [PMID: 30851631 DOI: 10.1016/j.sbi.2019.01.027] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 01/31/2019] [Indexed: 12/13/2022]
Abstract
Respiratory complexes are complicated multi-subunit cofactor-containing machines that allow cells to harvest energy from the environment. Maturation of these complexes requires protein folding, cofactor insertion, and assembly of multiple subunits into a final, functional complex. Because the intermediate states in complex maturation are transitory, these processes are poorly understood. This review gives an overview of the process of maturation in respiratory complex II with a focus on recent structural studies on intermediates formed during covalent flavinylation of the catalytic subunit, SDHA. Covalent flavinylation has an evolutionary significance because variants of complex II enzymes with the covalent ligand removed by mutagenesis cannot oxidize succinate, but can still perform the reverse reaction and reduce fumarate. Since succinate oxidation is a key step of aerobic respiration, the covalent bond of complex II appears to be important for aerobic life.
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Affiliation(s)
- Pankaj Sharma
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, United States
| | - Elena Maklashina
- Molecular Biology Division, San Francisco VA Health Care System, San Francisco, CA 94121, United States; Department of Biochemistry & Biophysics, University of California, San Francisco, CA 94158, United States
| | - Gary Cecchini
- Molecular Biology Division, San Francisco VA Health Care System, San Francisco, CA 94121, United States; Department of Biochemistry & Biophysics, University of California, San Francisco, CA 94158, United States.
| | - T M Iverson
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, United States; Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, United States; Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, United States; Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN 37232, United States.
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7
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Liu W, Luo Z, Wang Y, Pham NT, Tuck L, Pérez-Pi I, Liu L, Shen Y, French C, Auer M, Marles-Wright J, Dai J, Cai Y. Rapid pathway prototyping and engineering using in vitro and in vivo synthetic genome SCRaMbLE-in methods. Nat Commun 2018; 9:1936. [PMID: 29789543 PMCID: PMC5964202 DOI: 10.1038/s41467-018-04254-0] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 04/11/2018] [Indexed: 12/11/2022] Open
Abstract
Exogenous pathway optimization and chassis engineering are two crucial methods for heterologous pathway expression. The two methods are normally carried out step-wise and in a trial-and-error manner. Here we report a recombinase-based combinatorial method (termed "SCRaMbLE-in") to tackle both challenges simultaneously. SCRaMbLE-in includes an in vitro recombinase toolkit to rapidly prototype and diversify gene expression at the pathway level and an in vivo genome reshuffling system to integrate assembled pathways into the synthetic yeast genome while combinatorially causing massive genome rearrangements in the host chassis. A set of loxP mutant pairs was identified to maximize the efficiency of the in vitro diversification. Exemplar pathways of β-carotene and violacein were successfully assembled, diversified, and integrated using this SCRaMbLE-in method. High-throughput sequencing was performed on selected engineered strains to reveal the resulting genotype-to-phenotype relationships. The SCRaMbLE-in method proves to be a rapid, efficient, and universal method to fast track the cycle of engineering biology.
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Affiliation(s)
- Wei Liu
- School of Biological Sciences, The King's Buildings, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Zhouqing Luo
- Center for Synthetic Genomics, Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, China
| | - Yun Wang
- BGI-Shenzhen, Beishan Industrial Zone, 518083, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Jinsha Road, 518120, Shenzhen, China.,Guangdong Provincial Key Laboratory of Genome Read and Write, Jinsha Road, 518120, Shenzhen, China
| | - Nhan T Pham
- School of Biological Sciences, The King's Buildings, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Laura Tuck
- School of Biological Sciences, The King's Buildings, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Irene Pérez-Pi
- School of Biological Sciences, The King's Buildings, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Longying Liu
- BGI-Shenzhen, Beishan Industrial Zone, 518083, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Jinsha Road, 518120, Shenzhen, China.,Guangdong Provincial Key Laboratory of Genome Read and Write, Jinsha Road, 518120, Shenzhen, China
| | - Yue Shen
- School of Biological Sciences, The King's Buildings, University of Edinburgh, Edinburgh, EH9 3BF, UK.,BGI-Shenzhen, Beishan Industrial Zone, 518083, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Jinsha Road, 518120, Shenzhen, China.,Guangdong Provincial Key Laboratory of Genome Read and Write, Jinsha Road, 518120, Shenzhen, China.,Manchester Institute of Biotechnology, University of Manchester, Manchester, M1 7DN, UK
| | - Chris French
- School of Biological Sciences, The King's Buildings, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Manfred Auer
- School of Biological Sciences, The King's Buildings, University of Edinburgh, Edinburgh, EH9 3BF, UK.,Edinburgh Medical School, Biomedical Sciences, The King's Buildings, Edinburgh, EH9 3BF, UK
| | - Jon Marles-Wright
- School of Natural and Environmental Sciences, Devonshire Building, Newcastle University, Newcastle upon, Tyne, NE1 7RX, UK
| | - Junbiao Dai
- Center for Synthetic Genomics, Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, China.
| | - Yizhi Cai
- Center for Synthetic Genomics, Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, China. .,Manchester Institute of Biotechnology, University of Manchester, Manchester, M1 7DN, UK.
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8
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Deniset JF, Hedley TE, Hlaváčková M, Chahine MN, Dibrov E, O'Hara K, Maddaford GG, Nelson D, Maddaford TG, Fandrich R, Kardami E, Pierce GN. Heat shock protein 60 involvement in vascular smooth muscle cell proliferation. Cell Signal 2018; 47:44-51. [PMID: 29596871 DOI: 10.1016/j.cellsig.2018.03.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 03/23/2018] [Accepted: 03/23/2018] [Indexed: 10/17/2022]
Abstract
AIM Heat shock protein 60 (Hsp60) is a mediator of stress-induced vascular smooth muscle cell (VSMC) proliferation. This study will determine, first, if the mitochondrial or cytoplasmic localization of Hsp60 is critical to VSMC proliferation and, second, the mechanism of Hsp60 induction of VSMC proliferation with a focus on modification of nucleocytoplasmic trafficking. METHODS AND RESULTS Hsp60 was overexpressed in primary rabbit VSMCs with or without a mitochondrial targeting sequence (AdHsp60mito-). Both interventions induced an increase in VSMC PCNA expression and proliferation. The increase in VSMC PCNA expression and growth was not observed after siRNA-mediated knockdown of Hsp60 expression. Nuclear protein import in VSMC was measured by fluorescent microscopy using a microinjected fluorescent import substrate. Nuclear protein import was stimulated by both AdHsp60 and AdHsp60mito- treatments. AdHsp60 treatment also induced increases in nucleoporin (Nup) 62, Nup153, importin-α, importin-β and Ran expression as well as cellular ATP levels compared to control. AdHsp60mito- treatment induced an up-regulation in importin-α, importin-β and Ran expression compared to control. Hsp60 knockdown did not change nuclear protein import nor the expression of any nuclear transport receptors or nucleoporins. Both heat shock treatment and Hsp60 overexpression promoted the interaction of Ran with Hsp60. CONCLUSIONS VSMC proliferation can be modulated via an Hsp60 dependent, cytosol localized mechanism that in part involves a stimulation of nuclear protein import through an interaction with Ran. This novel cellular signaling role for Hsp60 may be important in growth-based vascular pathologies like atherosclerosis and hypertension.
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Affiliation(s)
- Justin F Deniset
- Institute of Cardiovascular Sciences, Albrechtsen Research Centre, St Boniface Hospital, Canada; Departments of Physiology and Pathophysiology, Canada
| | - Thomas E Hedley
- Institute of Cardiovascular Sciences, Albrechtsen Research Centre, St Boniface Hospital, Canada; Departments of Physiology and Pathophysiology, Canada
| | - Markéta Hlaváčková
- Institute of Physiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Mirna N Chahine
- Institute of Cardiovascular Sciences, Albrechtsen Research Centre, St Boniface Hospital, Canada; Departments of Physiology and Pathophysiology, Canada
| | - Elena Dibrov
- Institute of Cardiovascular Sciences, Albrechtsen Research Centre, St Boniface Hospital, Canada; Departments of Physiology and Pathophysiology, Canada
| | - Kim O'Hara
- Institute of Cardiovascular Sciences, Albrechtsen Research Centre, St Boniface Hospital, Canada; Departments of Physiology and Pathophysiology, Canada
| | - Graham G Maddaford
- Institute of Cardiovascular Sciences, Albrechtsen Research Centre, St Boniface Hospital, Canada; Departments of Physiology and Pathophysiology, Canada
| | - David Nelson
- Institute of Cardiovascular Sciences, Albrechtsen Research Centre, St Boniface Hospital, Canada; Departments of Physiology and Pathophysiology, Canada
| | - Thane G Maddaford
- Institute of Cardiovascular Sciences, Albrechtsen Research Centre, St Boniface Hospital, Canada; Departments of Physiology and Pathophysiology, Canada
| | - Robert Fandrich
- Institute of Cardiovascular Sciences, Albrechtsen Research Centre, St Boniface Hospital, Canada; Anatomy and Cell Biology, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Elissavet Kardami
- Institute of Cardiovascular Sciences, Albrechtsen Research Centre, St Boniface Hospital, Canada; Anatomy and Cell Biology, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Grant N Pierce
- Institute of Cardiovascular Sciences, Albrechtsen Research Centre, St Boniface Hospital, Canada; Departments of Physiology and Pathophysiology, Canada.
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9
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Dubinski AF, Camasta R, Soule TGB, Reed BH, Glerum DM. Consequences of cytochrome c oxidase assembly defects for the yeast stationary phase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1859:445-458. [PMID: 29567354 DOI: 10.1016/j.bbabio.2018.03.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 03/13/2018] [Accepted: 03/19/2018] [Indexed: 12/24/2022]
Abstract
The assembly of cytochrome c oxidase (COX) is essential for a functional mitochondrial respiratory chain, although the consequences of a loss of assembled COX at yeast stationary phase, an excellent model for terminally differentiated cells in humans, remain largely unexamined. In this study, we show that a wild-type respiratory competent yeast strain at stationary phase is characterized by a decreased oxidative capacity, as seen by a reduction in the amount of assembled COX and by a decrease in protein levels of several COX assembly factors. In contrast, loss of assembled COX results in the decreased abundance of many mitochondrial proteins at stationary phase, which is likely due to decreased membrane potential and changes in mitophagy. In addition to an altered mitochondrial proteome, COX assembly mutants display unexpected changes in markers of cellular oxidative stress at stationary phase. Our results suggest that mitochondria may not be a major source of reactive oxygen species at stationary phase in cells lacking an intact respiratory chain.
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Affiliation(s)
- Alicia F Dubinski
- Department of Biology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Raffaele Camasta
- Department of Biology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Tyler G B Soule
- Department of Biology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Bruce H Reed
- Department of Biology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - D Moira Glerum
- Department of Biology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada; Waterloo Institute of Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada.
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10
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Sharma P, Maklashina E, Cecchini G, Iverson TM. Crystal structure of an assembly intermediate of respiratory Complex II. Nat Commun 2018; 9:274. [PMID: 29348404 PMCID: PMC5773532 DOI: 10.1038/s41467-017-02713-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 12/20/2017] [Indexed: 02/06/2023] Open
Abstract
Flavin is covalently attached to the protein scaffold in ~10% of flavoenzymes. However, the mechanism of covalent modification is unclear, due in part to challenges in stabilizing assembly intermediates. Here, we capture the structure of an assembly intermediate of the Escherichiacoli Complex II (quinol:fumarate reductase (FrdABCD)). The structure contains the E. coli FrdA subunit bound to covalent FAD and crosslinked with its assembly factor, SdhE. The structure contains two global conformational changes as compared to prior structures of the mature protein: the rotation of a domain within the FrdA subunit, and the destabilization of two large loops of the FrdA subunit, which may create a tunnel to the active site. We infer a mechanism for covalent flavinylation. As supported by spectroscopic and kinetic analyses, we suggest that SdhE shifts the conformational equilibrium of the FrdA active site to disfavor succinate/fumarate interconversion and enhance covalent flavinylation. The mechanism for covalent flavinylation of flavoenzymes is still unclear. Here, the authors propose a mechanism based on the crystal structure of a flavinylation assembly intermediate of the E. coli respiratory Complex II comprising the E. coli FrdA subunit bound to covalent FAD and crosslinked with its assembly factor SdhE.
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Affiliation(s)
- Pankaj Sharma
- Department of Pharmacology, Vanderbilt University, Nashville, TN, 37232, USA
| | - Elena Maklashina
- Molecular Biology Division, San Francisco VA Health Care System, San Francisco, CA, 94121, USA.,Department of Biochemistry & Biophysics, University of California, San Francisco, CA, 94158, USA
| | - Gary Cecchini
- Molecular Biology Division, San Francisco VA Health Care System, San Francisco, CA, 94121, USA. .,Department of Biochemistry & Biophysics, University of California, San Francisco, CA, 94158, USA.
| | - T M Iverson
- Department of Pharmacology, Vanderbilt University, Nashville, TN, 37232, USA. .,Department of Biochemistry, Vanderbilt University, Nashville, TN, 37232, USA. .,Center for Structural Biology, Vanderbilt University, Nashville, TN, 37232, USA. .,Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN, 37232, USA.
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11
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Zafreen L, Walker-Kopp N, Huang LS, Berry E. In-vitro, SDH5-dependent flavinylation of immobilized human respiratory complex II flavoprotein. Arch Biochem Biophys 2016; 604:47-56. [PMID: 27296776 DOI: 10.1016/j.abb.2016.06.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 06/03/2016] [Accepted: 06/09/2016] [Indexed: 10/21/2022]
Abstract
Mitochondrial Complex II (Succinate: ubiquinone oxidoreductase) has a covalently bound FAD cofactor in its largest subunit (SDHA), which accepts electrons from oxidation of succinate during catalysis. The mechanism of flavin attachment, and factors involved, have not been fully elucidated. The recent report of an assembly factor SDH5 (SDHAF2, SDHE) required for flavinylation (Hao et al., 2009 Science 325, 1139-1142) raises the prospect of achieving flavinylation in a completely defined system, which would facilitate elucidation of the precise role played by SDH5 and other factors. At this time that goal has not been achieved, and the actual function of SDH5 is still unknown. We have developed a procedure for in-vitro flavinylation of recombinant human apo-SDHA, immobilized on Ni-IMAC resin by a His tag, in a chemically defined medium. In this system flavinylation has a pH optimum of 6.5 and is completely dependent on added SDH5. The results suggest that FAD interacts noncovalently with SDHA in the absence of SDH5. This system will be useful in understanding the process of flavinylation of SDHA and the role of SDH5 in this process.
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Affiliation(s)
- Lala Zafreen
- Dept. of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Nancy Walker-Kopp
- Dept. of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Li-Shar Huang
- Dept. of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Edward Berry
- Dept. of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA.
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12
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Niedzwiecka K, Kabala AM, Lasserre JP, Tribouillard-Tanvier D, Golik P, Dautant A, di Rago JP, Kucharczyk R. Yeast models of mutations in the mitochondrial ATP6 gene found in human cancer cells. Mitochondrion 2016; 29:7-17. [PMID: 27083309 DOI: 10.1016/j.mito.2016.04.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 04/08/2016] [Accepted: 04/08/2016] [Indexed: 01/09/2023]
Abstract
Since the discovery of somatic mtDNA mutations in tumor cells, multiple studies have focused on establishing a causal relationship between those changes and alterations in energy metabolism, a hallmark of cancer cells. Yet the consequences of these mutations on mitochondrial function remain largely unknown. In this study, Saccharomyces cerevisiae has been used as a model to investigate the functional consequences of four cancer-associated missense mutations (8914C>A, 8932C>T, 8953A>G, 9131T>C) found in the mitochondrial MT-ATP6 gene. This gene encodes the a-subunit of F1FO-ATP synthase, which catalyzes the last steps of ATP production in mitochondria. Although the four studied mutations affected well-conserved residues of the a-subunit, only one of them (8932C>T) had a significant impact on mitochondrial function, due to a less efficient incorporation of the a-subunit into ATP synthase. Our findings indicate that these ATP6 genetic variants found in human tumors are neutral mitochondrial genome substitutions with a limited, if any, impact on the energetic function of mitochondria.
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Affiliation(s)
- Katarzyna Niedzwiecka
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Anna Magdalena Kabala
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland; Institut de Biochimie et Génétique Cellulaires, CNRS UMR5095, Université de Bordeaux, 1 rue Camille Saint-Saëns, 33077 Bordeaux Cedex, France
| | - Jean-Paul Lasserre
- Institut de Biochimie et Génétique Cellulaires, CNRS UMR5095, Université de Bordeaux, 1 rue Camille Saint-Saëns, 33077 Bordeaux Cedex, France
| | - Déborah Tribouillard-Tanvier
- Institut de Biochimie et Génétique Cellulaires, CNRS UMR5095, Université de Bordeaux, 1 rue Camille Saint-Saëns, 33077 Bordeaux Cedex, France
| | - Pawel Golik
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland; Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Poland
| | - Alain Dautant
- Institut de Biochimie et Génétique Cellulaires, CNRS UMR5095, Université de Bordeaux, 1 rue Camille Saint-Saëns, 33077 Bordeaux Cedex, France
| | - Jean-Paul di Rago
- Institut de Biochimie et Génétique Cellulaires, CNRS UMR5095, Université de Bordeaux, 1 rue Camille Saint-Saëns, 33077 Bordeaux Cedex, France
| | - Roza Kucharczyk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland.
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13
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Maklashina E, Rajagukguk S, Starbird CA, McDonald WH, Koganitsky A, Eisenbach M, Iverson TM, Cecchini G. Binding of the Covalent Flavin Assembly Factor to the Flavoprotein Subunit of Complex II. J Biol Chem 2015; 291:2904-16. [PMID: 26644464 DOI: 10.1074/jbc.m115.690396] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Indexed: 01/23/2023] Open
Abstract
Escherichia coli harbors two highly conserved homologs of the essential mitochondrial respiratory complex II (succinate:ubiquinone oxidoreductase). Aerobically the bacterium synthesizes succinate:quinone reductase as part of its respiratory chain, whereas under microaerophilic conditions, the quinol:fumarate reductase can be utilized. All complex II enzymes harbor a covalently bound FAD co-factor that is essential for their ability to oxidize succinate. In eukaryotes and many bacteria, assembly of the covalent flavin linkage is facilitated by a small protein assembly factor, termed SdhE in E. coli. How SdhE assists with formation of the covalent flavin bond and how it binds the flavoprotein subunit of complex II remain unknown. Using photo-cross-linking, we report the interaction site between the flavoprotein of complex II and the SdhE assembly factor. These data indicate that SdhE binds to the flavoprotein between two independently folded domains and that this binding mode likely influences the interdomain orientation. In so doing, SdhE likely orients amino acid residues near the dicarboxylate and FAD binding site, which facilitates formation of the covalent flavin linkage. These studies identify how the conserved SdhE assembly factor and its homologs participate in complex II maturation.
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Affiliation(s)
- Elena Maklashina
- From the Molecular Biology Division, Veterans Affairs Medical Center, San Francisco, California 94121, the Department of Biochemistry & Biophysics, University of California, San Francisco, California 94158
| | - Sany Rajagukguk
- From the Molecular Biology Division, Veterans Affairs Medical Center, San Francisco, California 94121
| | | | - W Hayes McDonald
- the Department of Biochemistry and Mass Spectrometry Research Center
| | - Anna Koganitsky
- the Department of Biological Chemistry, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Michael Eisenbach
- the Department of Biological Chemistry, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Tina M Iverson
- the Department of Biochemistry and Mass Spectrometry Research Center, the Department of Pharmacology, the Center for Structural Biology, and the Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37232, and
| | - Gary Cecchini
- From the Molecular Biology Division, Veterans Affairs Medical Center, San Francisco, California 94121, the Department of Biochemistry & Biophysics, University of California, San Francisco, California 94158,
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14
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Kito K, Ito H, Nohara T, Ohnishi M, Ishibashi Y, Takeda D. Yeast Interspecies Comparative Proteomics Reveals Divergence in Expression Profiles and Provides Insights into Proteome Resource Allocation and Evolutionary Roles of Gene Duplication. Mol Cell Proteomics 2015; 15:218-35. [PMID: 26560065 DOI: 10.1074/mcp.m115.051854] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Indexed: 11/06/2022] Open
Abstract
Omics analysis is a versatile approach for understanding the conservation and diversity of molecular systems across multiple taxa. In this study, we compared the proteome expression profiles of four yeast species (Saccharomyces cerevisiae, Saccharomyces mikatae, Kluyveromyces waltii, and Kluyveromyces lactis) grown on glucose- or glycerol-containing media. Conserved expression changes across all species were observed only for a small proportion of all proteins differentially expressed between the two growth conditions. Two Kluyveromyces species, both of which exhibited a high growth rate on glycerol, a nonfermentative carbon source, showed distinct species-specific expression profiles. In K. waltii grown on glycerol, proteins involved in the glyoxylate cycle and gluconeogenesis were expressed in high abundance. In K. lactis grown on glycerol, the expression of glycolytic and ethanol metabolic enzymes was unexpectedly low, whereas proteins involved in cytoplasmic translation, including ribosomal proteins and elongation factors, were highly expressed. These marked differences in the types of predominantly expressed proteins suggest that K. lactis optimizes the balance of proteome resource allocation between metabolism and protein synthesis giving priority to cellular growth. In S. cerevisiae, about 450 duplicate gene pairs were retained after whole-genome duplication. Intriguingly, we found that in the case of duplicates with conserved sequences, the total abundance of proteins encoded by a duplicate pair in S. cerevisiae was similar to that of protein encoded by nonduplicated ortholog in Kluyveromyces yeast. Given the frequency of haploinsufficiency, this observation suggests that conserved duplicate genes, even though minor cases of retained duplicates, do not exhibit a dosage effect in yeast, except for ribosomal proteins. Thus, comparative proteomic analyses across multiple species may reveal not only species-specific characteristics of metabolic processes under nonoptimal culture conditions but also provide valuable insights into intriguing biological principles, including the balance of proteome resource allocation and the role of gene duplication in evolutionary history.
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Affiliation(s)
- Keiji Kito
- From the ‡Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, 214-8571, Japan
| | - Haruka Ito
- From the ‡Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, 214-8571, Japan
| | - Takehiro Nohara
- From the ‡Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, 214-8571, Japan
| | - Mihoko Ohnishi
- From the ‡Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, 214-8571, Japan
| | - Yuko Ishibashi
- From the ‡Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, 214-8571, Japan
| | - Daisuke Takeda
- From the ‡Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, 214-8571, Japan
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15
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Abstract
Permeabilization of the outer mitochondrial membrane that leads to the release of cytochrome c and several other apoptogenic proteins from mitochondria into cytosol represents a commitment point of apoptotic pathway in mammalian cells. This crucial event is governed by proteins of the Bcl-2 family. Molecular mechanisms, by which Bcl-2 family proteins permeabilize mitochondrial membrane, remain under dispute. Although yeast does not have apparent homologues of these proteins, when mammalian members of Bcl-2 family are expressed in yeast, they retain their activity, making yeast an attractive model system, in which to study their action. This review focuses on using yeast expressing mammalian proteins of the Bcl-2 family as a tool to investigate mechanisms, by which these proteins permeabilize mitochondrial membranes, mechanisms, by which pro- and antiapoptotic members of this family interact, and involvement of other cellular components in the regulation of programmed cell death by Bcl-2 family proteins.
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Affiliation(s)
- Peter Polčic
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University, Bratislava, Slovak Republic
| | - Petra Jaká
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University, Bratislava, Slovak Republic
| | - Marek Mentel
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University, Bratislava, Slovak Republic
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16
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Her YF, Maher LJ. Succinate Dehydrogenase Loss in Familial Paraganglioma: Biochemistry, Genetics, and Epigenetics. Int J Endocrinol 2015; 2015:296167. [PMID: 26294907 PMCID: PMC4532907 DOI: 10.1155/2015/296167] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 07/05/2015] [Indexed: 01/14/2023] Open
Abstract
It is counterintuitive that metabolic defects reducing ATP production can cause, rather than protect from, cancer. Yet this is precisely the case for familial paraganglioma, a form of neuroendocrine malignancy caused by loss of succinate dehydrogenase in the tricarboxylic acid cycle. Here we review biochemical, genetic, and epigenetic considerations in succinate dehydrogenase loss and present leading models and mysteries associated with this fascinating and important tumor.
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Affiliation(s)
- Yeng F. Her
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN 55905, USA
- Mayo Clinic Medical Scientist Training Program, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN 55905, USA
| | - L. James Maher
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN 55905, USA
- *L. James Maher III:
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17
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Mitochondrial Ca(2+) influx targets cardiolipin to disintegrate respiratory chain complex II for cell death induction. Cell Death Differ 2014; 21:1733-45. [PMID: 24948011 DOI: 10.1038/cdd.2014.84] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Revised: 04/23/2014] [Accepted: 05/15/2014] [Indexed: 12/22/2022] Open
Abstract
Massive Ca(2+) influx into mitochondria is critically involved in cell death induction but it is unknown how this activates the organelle for cell destruction. Using multiple approaches including subcellular fractionation, FRET in intact cells, and in vitro reconstitutions, we show that mitochondrial Ca(2+) influx prompts complex II of the respiratory chain to disintegrate, thereby releasing an enzymatically competent sub-complex that generates excessive reactive oxygen species (ROS) for cell death induction. This Ca(2+)-dependent dissociation of complex II is also observed in model membrane systems, but not when cardiolipin is replaced with a lipid devoid of Ca(2+) binding. Cardiolipin is known to associate with complex II and upon Ca(2+) binding coalesces into separate homotypic clusters. When complex II is deprived of this lipid, it disintegrates for ROS formation and cell death. Our results reveal Ca(2+) binding to cardiolipin for complex II disintegration as a pivotal step for oxidative stress and cell death induction.
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18
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Hwang MS, Rohlena J, Dong LF, Neuzil J, Grimm S. Powerhouse down: Complex II dissociation in the respiratory chain. Mitochondrion 2014; 19 Pt A:20-8. [PMID: 24933571 DOI: 10.1016/j.mito.2014.06.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Revised: 05/28/2014] [Accepted: 06/04/2014] [Indexed: 12/12/2022]
Abstract
Complex II of the respiratory chain (RC) recently emerged as a prominent regulator of cell death. In both cancer cells as well as neurodegenerative diseases, mutations in subunits have been found along with other genetic alterations indirectly affecting this complex. Anticancer compounds were developed that target complex II and cause cell death in a tumor-specific way. Our mechanistic understanding of how complex II is activated for cell death induction has recently been made clearer in recent studies, the results of which are covered in this review. This protein assembly is specifically activated for cell death via the dissociation of its SDHA and SDHB subunits from the membrane-anchoring proteins through pH change or mitochondrial Ca(2+) influx. The SDH activity contained in the SDHA/SDHB subcomplex remains intact and then generates, in an uncontrolled fashion, excessive amounts of reactive oxygen species (ROS) for cell death. Future studies on this mitochondrial complex will further elucidate it as a target for cancer treatments and reveal its role as a nexus for many diverse stimuli in cell death signaling.
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Affiliation(s)
- Ming-Shih Hwang
- Division of Experimental Medicine, Imperial College London, Hammersmith Campus, Du Cane Road, London W12 0NN, UK
| | - Jakub Rohlena
- Institute of Biotechnology, Academy of Sciences of the Czech Republic, Prague 142 20, Czech Republic
| | - Lan-Feng Dong
- School of Medical Science, Griffith Health Institute, Griffith University, Southport Qld 4222, Australia
| | - Jiri Neuzil
- Institute of Biotechnology, Academy of Sciences of the Czech Republic, Prague 142 20, Czech Republic; School of Medical Science, Griffith Health Institute, Griffith University, Southport Qld 4222, Australia
| | - Stefan Grimm
- Division of Experimental Medicine, Imperial College London, Hammersmith Campus, Du Cane Road, London W12 0NN, UK.
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19
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Damiano M, Diguet E, Malgorn C, D'Aurelio M, Galvan L, Petit F, Benhaim L, Guillermier M, Houitte D, Dufour N, Hantraye P, Canals JM, Alberch J, Delzescaux T, Déglon N, Beal MF, Brouillet E. A role of mitochondrial complex II defects in genetic models of Huntington's disease expressing N-terminal fragments of mutant huntingtin. Hum Mol Genet 2013; 22:3869-82. [PMID: 23720495 PMCID: PMC3766181 DOI: 10.1093/hmg/ddt242] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Huntington's disease (HD) is a neurodegenerative disorder caused by an abnormal expansion of a CAG repeat encoding a polyglutamine tract in the huntingtin (Htt) protein. The mutation leads to neuronal death through mechanisms which are still unknown. One hypothesis is that mitochondrial defects may play a key role. In support of this, the activity of mitochondrial complex II (C-II) is preferentially reduced in the striatum of HD patients. Here, we studied C-II expression in different genetic models of HD expressing N-terminal fragments of mutant Htt (mHtt). Western blot analysis showed that the expression of the 30 kDa Iron–Sulfur (Ip) subunit of C-II was significantly reduced in the striatum of the R6/1 transgenic mice, while the levels of the FAD containing catalytic 70 kDa subunit (Fp) were not significantly changed. Blue native gel analysis showed that the assembly of C-II in mitochondria was altered early in N171-82Q transgenic mice. Early loco-regional reduction in C-II activity and Ip protein expression was also demonstrated in a rat model of HD using intrastriatal injection of lentiviral vectors encoding mHtt. Infection of the rat striatum with a lentiviral vector coding the C-II Ip or Fp subunits induced a significant overexpression of these proteins that led to significant neuroprotection of striatal neurons against mHtt neurotoxicity. These results obtained in vivo support the hypothesis that structural and functional alterations of C-II induced by mHtt may play a critical role in the degeneration of striatal neurons in HD and that mitochondrial-targeted therapies may be useful in its treatment.
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Affiliation(s)
- Maria Damiano
- The first two authors contributed equally to the present study
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20
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Grimm S. Respiratory chain complex II as general sensor for apoptosis. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1827:565-72. [DOI: 10.1016/j.bbabio.2012.09.009] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Revised: 09/09/2012] [Accepted: 09/10/2012] [Indexed: 01/05/2023]
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21
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Kim HJ, Winge DR. Emerging concepts in the flavinylation of succinate dehydrogenase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1827:627-36. [PMID: 23380393 DOI: 10.1016/j.bbabio.2013.01.012] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Revised: 01/14/2013] [Accepted: 01/18/2013] [Indexed: 12/28/2022]
Abstract
The Succinate Dehydrogenase (SDH) heterotetrameric complex catalyzes the oxidation of succinate to fumarate in the tricarboxylic acid (TCA) cycle and in the aerobic respiratory chains of eukaryotes and bacteria. Essential in this catalysis is the covalently-linked cofactor flavin adenine dinucleotide (FAD) in subunit1 (Sdh1) of the SDH enzyme complex. The mechanism of FAD insertion and covalent attachment to Sdh1 is unknown. Our working concept of this flavinylation process has relied mostly on foundational works from the 1990s and by applying the principles learned from other enzymes containing a similarly linked FAD. The discovery of the flavinylation factor Sdh5, however, has provided new insight into the possible mechanism associated with Sdh1 flavinylation. This review focuses on encapsulating prior and recent advances towards understanding the mechanism associated with flavinylation of Sdh1 and how this flavinylation process affects the overall assembly of SDH. This article is part of a Special Issue entitled: Respiratory complex II: Role in cellular physiology and disease.
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Affiliation(s)
- Hyung J Kim
- Department of Medicine and Biochemistry, University of Utah Health Sciences Center, Salt Lake City, UT 84132, USA
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22
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Jain-Ghai S, Cameron JM, Al Maawali A, Blaser S, MacKay N, Robinson B, Raiman J. Complex II deficiency--a case report and review of the literature. Am J Med Genet A 2013; 161A:285-94. [PMID: 23322652 DOI: 10.1002/ajmg.a.35714] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2011] [Accepted: 09/15/2012] [Indexed: 11/07/2022]
Abstract
Complex II deficiency is a rare cause of mitochondrial respiratory chain defects with a prevalence of 2-23%. It is exclusively nuclear encoded and functions in the citric acid cycle by oxidizing succinate to fumarate and in the mitochondrial electron transport chain (ETC) by transferring electrons to ubiquinone. Of the four subunits, SDHA and SDHB are catalytic and SDHC and SDHD are anchoring. Mutations in SDHA and SDHAF1 (assembly factor) have been found in patients with CII deficiency and a mitochondrial phenotype. We present a patient with CII deficiency with a previously undescribed phenotype of dilated cardiomyopathy, left ventricular noncompaction, failure to thrive, hypotonia, and developmental delay. Also, a comprehensive review of 36 cases published in the literature was undertaken. The results show that CII deficiency has a variable phenotype with no correlation with residual complex activity in muscle although the phenotype and enzyme activities are comparable within a family. For some, the condition was fatal in infancy, others had multisystem involvement and some had onset in adulthood with mild symptoms and normal cognition. Neurological involvement is most commonly observed and brain imaging commonly shows leukoencephalopathy, Leigh syndrome, or cerebellar atrophy. Mutations in SDHAF1 are associated with leukoencephalopathy. Other organ systems like heart, muscle, and eyes are only involved in about 50% of the cases but cardiomyopathy is associated with high mortality and morbidity. In some patients, riboflavin has provided clinical improvement.
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Affiliation(s)
- Shailly Jain-Ghai
- The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada.
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23
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Park K, Botelho SC, Hong J, Österberg M, Kim H. Dissecting stop transfer versus conservative sorting pathways for mitochondrial inner membrane proteins in vivo. J Biol Chem 2012. [PMID: 23184936 DOI: 10.1074/jbc.m112.409748] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Mitochondrial inner membrane proteins that carry an N-terminal presequence are sorted by one of two pathways: stop transfer or conservative sorting. However, the sorting pathway is known for only a small number of proteins, in part due to the lack of robust experimental tools with which to study. Here we present an approach that facilitates determination of inner membrane protein sorting pathways in vivo by fusing a mitochondrial inner membrane protein to the C-terminal part of Mgm1p containing the rhomboid cleavage region. We validated the Mgm1 fusion approach using a set of proteins for which the sorting pathway is known, and determined sorting pathways of inner membrane proteins for which the sorting mode was previously uncharacterized. For Sdh4p, a multispanning membrane protein, our results suggest that both conservative sorting and stop transfer mechanisms are required for insertion. Furthermore, the sorting process of Mgm1 fusion proteins was analyzed under different growth conditions and yeast mutant strains that were defective in the import motor or the m-AAA protease function. Our results show that the sorting of mitochondrial proteins carrying moderately hydrophobic transmembrane segments is sensitive to cellular conditions, implying that mitochondrial import and membrane sorting in the physiological environment may be dynamically tuned.
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Affiliation(s)
- Kwangjin Park
- School of Biological Sciences, Seoul National University, Building 504-421, Seoul 151-747, South Korea
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24
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Kluckova K, Bezawork-Geleta A, Rohlena J, Dong L, Neuzil J. Mitochondrial complex II, a novel target for anti-cancer agents. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1827:552-64. [PMID: 23142170 DOI: 10.1016/j.bbabio.2012.10.015] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Revised: 10/28/2012] [Accepted: 10/29/2012] [Indexed: 12/22/2022]
Abstract
With the arrival of the third millennium, in spite of unprecedented progress in molecular medicine, cancer remains as untamed as ever. The complexity of tumours, dictating the potential response of cancer cells to anti-cancer agents, has been recently highlighted in a landmark paper by Weinberg and Hanahan on hallmarks of cancer [1]. Together with the recently published papers on the complexity of tumours in patients and even within the same tumour (see below), the cure for this pathology seems to be an elusive goal. Indisputably, the strategy ought to be changed, searching for targets that are generally invariant across the landscape of neoplastic diseases. One such target appears to be the mitochondrial complex II (CII) of the electron transfer chain, a recent focus of research. We document and highlight this particularly intriguing target in this review paper and give examples of drugs that use CII as their molecular target. This article is part of a Special Issue entitled: Respiratory complex II: Role in cellular physiology and disease.
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Affiliation(s)
- Katarina Kluckova
- Institute of Biotechnology, Czech Academy of Sciences, Prague, Czech Republic
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25
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Iverson TM, Maklashina E, Cecchini G. Structural basis for malfunction in complex II. J Biol Chem 2012; 287:35430-35438. [PMID: 22904323 DOI: 10.1074/jbc.r112.408419] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Complex II couples oxidoreduction of succinate and fumarate at one active site with that of quinol/quinone at a second distinct active site over 40 Å away. This process links the Krebs cycle to oxidative phosphorylation and ATP synthesis. The pathogenic mutation or inhibition of human complex II or its assembly factors is often associated with neurodegeneration or tumor formation in tissues derived from the neural crest. This brief overview of complex II correlates the clinical presentations of a large number of symptom-associated alterations in human complex II activity and assembly with the biochemical manifestations of similar alterations in the complex II homologs from Escherichia coli. These analyses provide clues to the molecular basis for diseases associated with aberrant complex II function.
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Affiliation(s)
- Tina M Iverson
- Department of Pharmacology and Biochemistry, Vanderbilt University Medical Center, Nashville, Tennessee 37232.
| | - Elena Maklashina
- Molecular Biology Division, Veterans Affairs Medical Center, San Francisco, California 94121; Department of Biochemistry and Biophysics, University of California, San Francisco, California 94158
| | - Gary Cecchini
- Molecular Biology Division, Veterans Affairs Medical Center, San Francisco, California 94121; Department of Biochemistry and Biophysics, University of California, San Francisco, California 94158.
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26
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Assembly Factors of Human Mitochondrial Respiratory Chain Complexes: Physiology and Pathophysiology. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 748:65-106. [DOI: 10.1007/978-1-4614-3573-0_4] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Hacioglu E, Demir AB, Koc A. Identification of respiratory chain gene mutations that shorten replicative life span in yeast. Exp Gerontol 2011; 47:149-53. [PMID: 22137892 DOI: 10.1016/j.exger.2011.11.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2011] [Revised: 11/14/2011] [Accepted: 11/15/2011] [Indexed: 11/19/2022]
Abstract
Aging is the progressive accumulation of alterations in cells that elevates the risk of death. The mitochondrial theory of aging postulates that free radicals produced by the mitochondrial respiratory system contribute to the aging process. However, the roles of individual electron transfer chain (ETC) components in cellular aging have not been elucidated. In this study, we analyzed the replicative life span of 73 yeast deletion mutants lacking the genes of the mitochondrial electron transfer chain system, and found that nine of these mutants (Δnde1, Δtcm62, Δrip1, Δcyt1, Δqrc8, Δpet117, Δcox11, Δatp11, Δfmc1) had significantly shorter life spans. These mutants had lower rates of respiration and were slightly sensitive to exogenous administration of hydrogen peroxide. However, only two of them, Δnde1 and Δfmc1, produced higher amounts of intrinsic superoxide radicals in the presence of glucose compared to that of wild type cells. Interestingly, there were no significant alterations in the mitochondrial membrane potentials of these mutants. We speculate that the shorter life spans of ETC mutants result from multiple mechanisms including the low respiration rate and low energy production rather than just a ROS-dependent path.
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Affiliation(s)
- Elise Hacioglu
- Izmir Institute of Technology, Department of Molecular Biology and Genetics, 35430 Urla, Izmir, Turkey
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Diaz F, Kotarsky H, Fellman V, Moraes CT. Mitochondrial disorders caused by mutations in respiratory chain assembly factors. Semin Fetal Neonatal Med 2011; 16:197-204. [PMID: 21680271 PMCID: PMC3152982 DOI: 10.1016/j.siny.2011.05.004] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Mitochondrial diseases involve the dysfunction of the oxidative phosphorylation (OXPHOS) system. This group of diseases presents with heterogeneous clinical symptoms affecting mainly organs with high energy demands. Defects in the multimeric complexes comprising the OXPHOS system have a dual genetic origin, mitochondrial or nuclear DNA. Although many nuclear DNA mutations involve genes coding for subunits of the respiratory complexes, the majority of mutations found to date affect factors that do not form part of the final complexes. These assembly factors or chaperones have multiple functions ranging from cofactor insertion to proper assembly/stability of the complexes. Although significant progress has been made in the last few years in the discovery of new assembly factors, the function of many remains elusive. Here, we describe assembly factors or chaperones that are required for respiratory chain complex assembly and their clinical relevance.
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Affiliation(s)
- Francisca Diaz
- Department of Neurology, University of Miami Miller School of Medicine, Miami, Florida, USA.
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29
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Abstract
Mutations in cancer cells affecting subunits of the respiratory chain (RC) indicate a central role of oxidative phosphorylation for tumourigenesis. Recent studies have suggested that such mutations of RC complexes impact apoptosis induction. We review here the evidence for this hypothesis, which in particular emerged from work on how complex I and II mediate signals for apoptosis. Both protein aggregates are specifically inhibited for apoptosis induction through different means by exploiting with protease activation and pH change, two widespread but independent features of dying cells. Nevertheless, both converge on forming reactive oxygen species for the demise of the cell. Investigations into these mitochondrial processes will remain a rewarding area for unravelling the causes of tumourigenesis and for discovering interference options.
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Tower RJ, Fagarasanu A, Aitchison JD, Rachubinski RA. The peroxin Pex34p functions with the Pex11 family of peroxisomal divisional proteins to regulate the peroxisome population in yeast. Mol Biol Cell 2011; 22:1727-38. [PMID: 21441307 PMCID: PMC3093324 DOI: 10.1091/mbc.e11-01-0084] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Peroxisomes are ubiquitous organelles involved in diverse metabolic processes, most notably the metabolism of lipids and the detoxification of reactive oxygen species. Peroxisomes are highly dynamic and change in size and number in response to both intra- and extracellular cues. In the yeast Saccharomyces cerevisiae, peroxisome growth and division are controlled by both the differential import of soluble matrix proteins and a specialized divisional machinery that includes peroxisome-specific factors, such as members of the Pex11 protein family, and general organelle divisional factors, such as the dynamin-related protein Vps1p. Global yeast two-hybrid analyses have demonstrated interactions between the product of the S. cerevisiae gene of unknown function, YCL056c, and Pex proteins involved in peroxisome biogenesis. Here we show that the protein encoded by YCL056c, renamed Pex34p, is a peroxisomal integral membrane protein that acts independently and also in concert with the Pex11 protein family members Pex11p, Pex25p, and Pex27p to control the peroxisome populations of cells under conditions of both peroxisome proliferation and constitutive peroxisome division. Yeast two-hybrid analysis showed that Pex34p interacts physically with itself and with Pex11p, Pex25p, and Pex27p but not with Vps1p. Pex34p can act as a positive effector of peroxisome division as its overexpression leads to increased numbers of peroxisomes in wild type and pex34Δ cells. Pex34p requires the Pex11 family proteins to promote peroxisome division. Our discovery of Pex34p as a protein involved in the already complex control of peroxisome populations emphasizes the necessity of cells to strictly regulate their peroxisome populations to be able to respond appropriately to changing environmental conditions.
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Affiliation(s)
- Robert J Tower
- Department of Cell Biology, University of Alberta, Edmonton, Alberta, Canada Institute for Systems Biology, Seattle, WA 98103, USA
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31
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Rutter J, Winge DR, Schiffman JD. Succinate dehydrogenase - Assembly, regulation and role in human disease. Mitochondrion 2010; 10:393-401. [PMID: 20226277 PMCID: PMC2874626 DOI: 10.1016/j.mito.2010.03.001] [Citation(s) in RCA: 291] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/05/2010] [Indexed: 12/18/2022]
Abstract
Succinate dehydrogenase (or Electron Transport Chain Complex II) has been the subject of a focused but significant renaissance. This complex, which has been the least studied of the mitochondrial respiratory complexes has seen renewed interest due to the discovery of its role in human disease. Under this heightened scrutiny, the succinate dehydrogenase complex has proven to be a fascinating machine, whose regulation and assembly requires additional factors that are beginning to be discovered. Mutations in these factors and in the structural subunits of the complex itself cause a variety of human diseases. The mechanisms underlying the pathogenesis of SDH mutations is beginning to be understood.
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Affiliation(s)
- Jared Rutter
- Departments of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, United States.
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32
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Lenaz G, Genova ML. Structure and organization of mitochondrial respiratory complexes: a new understanding of an old subject. Antioxid Redox Signal 2010; 12:961-1008. [PMID: 19739941 DOI: 10.1089/ars.2009.2704] [Citation(s) in RCA: 193] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The enzymatic complexes of the mitochondrial respiratory chain have been extensively investigated in their structural and functional properties. A clear distinction is possible today between three complexes in which the difference in redox potential allows proton translocation (complexes I, III, and IV) and those having the mere function to convey electrons to the respiratory chain. We also have a clearer understanding of the structure and function of most respiratory complexes, of their biogenesis and regulation, and of their capacity to generate reactive oxygen species. Past investigations led to the conclusion that the complexes are randomly dispersed and functionally connected by diffusion of smaller redox components, coenzyme Q and cytochrome c. More-recent investigations by native gel electrophoresis and single-particle image processing showed the existence of supramolecular associations. Flux-control analysis demonstrated that complexes I and III in mammals and I, III, and IV in plants kinetically behave as single units, suggesting the existence of substrate channeling. This review discusses conditions affecting the formation of supercomplexes that, besides kinetic advantage, have a role in the stability and assembly of the individual complexes and in preventing excess oxygen radical formation. Disruption of supercomplex organization may lead to functional derangements responsible for pathologic changes.
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Affiliation(s)
- Giorgio Lenaz
- Dipartimento di Biochimica "G. Moruzzi," Alma Mater Studiorum, Università di Bologna, Bologna, Italy.
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33
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Hao HX, Khalimonchuk O, Schraders M, Dephoure N, Bayley JP, Kunst H, Devilee P, Cremers CWRJ, Schiffman JD, Bentz BG, Gygi SP, Winge DR, Kremer H, Rutter J. SDH5, a gene required for flavination of succinate dehydrogenase, is mutated in paraganglioma. Science 2009; 325:1139-42. [PMID: 19628817 DOI: 10.1126/science.1175689] [Citation(s) in RCA: 539] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Mammalian mitochondria contain about 1100 proteins, nearly 300 of which are uncharacterized. Given the well-established role of mitochondrial defects in human disease, functional characterization of these proteins may shed new light on disease mechanisms. Starting with yeast as a model system, we investigated an uncharacterized but highly conserved mitochondrial protein (named here Sdh5). Both yeast and human Sdh5 interact with the catalytic subunit of the succinate dehydrogenase (SDH) complex, a component of both the electron transport chain and the tricarboxylic acid cycle. Sdh5 is required for SDH-dependent respiration and for Sdh1 flavination (incorporation of the flavin adenine dinucleotide cofactor). Germline loss-of-function mutations in the human SDH5 gene, located on chromosome 11q13.1, segregate with disease in a family with hereditary paraganglioma, a neuroendocrine tumor previously linked to mutations in genes encoding SDH subunits. Thus, a mitochondrial proteomics analysis in yeast has led to the discovery of a human tumor susceptibility gene.
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Affiliation(s)
- Huai-Xiang Hao
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
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34
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Mutations in the heme b-binding residue of SDHC inhibit assembly of respiratory chain complex II in mammalian cells. Mitochondrion 2009; 9:254-60. [DOI: 10.1016/j.mito.2009.03.004] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2009] [Revised: 03/05/2009] [Accepted: 03/10/2009] [Indexed: 11/22/2022]
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35
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Endoplasmic reticulum-associated secretory proteins Sec20p, Sec39p, and Dsl1p are involved in peroxisome biogenesis. EUKARYOTIC CELL 2009; 8:830-43. [PMID: 19346454 DOI: 10.1128/ec.00024-09] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Two pathways have been identified for peroxisome formation: (i) growth and division and (ii) de novo synthesis. Recent experiments determined that peroxisomes originate at the endoplasmic reticulum (ER). Although many proteins have been implicated in the peroxisome biogenic program, no proteins in the eukaryotic secretory pathway have been identified as having roles in peroxisome formation. Using the yeast Saccharomyces cerevisiae regulatable Tet promoter Hughes clone collection, we found that repression of the ER-associated secretory proteins Sec20p and Sec39p resulted in mislocalization of the peroxisomal matrix protein chimera Pot1p-green fluorescent protein (GFP) to the cytosol. Likewise, the peroxisomal membrane protein chimera Pex3p-GFP localized to tubular-vesicular structures in cells suppressed for Sec20p, Sec39p, and Dsl1p, which form a complex at the ER. Loss of Sec39p attenuated formation of Pex3p-derived peroxisomal structures following galactose induction of Pex3p-GFP expression from the GAL1 promoter. Expression of Sec20p, Sec39p, and Dsl1p was moderately increased in yeast grown under conditions that proliferate peroxisomes, and Sec20p, Sec39p, and Dsl1p were found to cofractionate with peroxisomes and colocalize with Pex3p-monomeric red fluorescent protein under these conditions. Our results show that SEC20, SEC39, and DSL1 are essential secretory genes involved in the early stages of peroxisome assembly, and this work is the first to identify and characterize an ER-associated secretory machinery involved in peroxisome biogenesis.
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36
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Abstract
Understanding the effect of genetic sequence variation on phenotype is a major challenge that lies at the heart of genetics. We developed GOLPH (GenOmic Linkage to PHenotype), a statistical method to identify genetic interactions, and used it to characterize the landscape of genetic interactions between gene expression quantitative trait loci. Our results reveal that allele-specific interactions, in which a gene only exerts an influence on the phenotype in the presence of a particular allele at the primary locus, are widespread and that genetic interactions are predominantly nonadditive. The data portray a complex picture in which interacting loci influence the expression of modules of coexpressed genes involved in coherent biological processes and pathways. We show that genetic variation at a single gene can have a major impact on the global transcriptional response, altering interactions between genes through shutdown or activation of pathways. Thus, different cellular states occur not only in response to the external environment but also result from intrinsic genetic variation.
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37
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Shlomi T. Metabolic Network-Based Interpretation of Gene Expression Data Elucidates Human Cellular Metabolism. Biotechnol Genet Eng Rev 2009; 26:281-96. [DOI: 10.5661/bger-26-281] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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38
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Sun W, Yuan S, Li KC. Trait-trait dynamic interaction: 2D-trait eQTL mapping for genetic variation study. BMC Genomics 2008; 9:242. [PMID: 18498664 PMCID: PMC2432080 DOI: 10.1186/1471-2164-9-242] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2007] [Accepted: 05/23/2008] [Indexed: 11/11/2022] Open
Abstract
Background Many studies have shown that the abundance level of gene expression is heritable. Analogous to the traditional genetic study, most researchers treat the expression of one gene as a quantitative trait and map it to expression quantitative trait loci (eQTL). This is 1D-trait mapping. 1D-trait mapping ignores the trait-trait interaction completely, which is a major shortcoming. Results To overcome this limitation, we study the expression of a pair of genes and treat the variation in their co-expression pattern as a two dimensional quantitative trait. We develop a method to find gene pairs, whose co-expression patterns, including both signs and strengths, are mediated by genetic variations and map these 2D-traits to the corresponding genetic loci. We report several applications by combining 1D-trait mapping with 2D-trait mapping, including the contribution of genetic variations to the perturbations in the regulatory mechanisms of yeast metabolic pathways. Conclusion Our approach of 2D-trait mapping provides a novel and effective way to connect the genetic variation with higher order biological modules via gene expression profiles.
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Affiliation(s)
- Wei Sun
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, 27599, USA.
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39
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Giancaspero TA, Wait R, Boles E, Barile M. Succinate dehydrogenase flavoprotein subunit expression in Saccharomyces cerevisiae--involvement of the mitochondrial FAD transporter, Flx1p. FEBS J 2008; 275:1103-17. [PMID: 18279395 DOI: 10.1111/j.1742-4658.2008.06270.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The mitochondrial FAD transporter, Flx1p, is a member of the mitochondrial carrier family responsible for FAD transport in Saccharomyces cerevisiae. It has also been suggested that it has a role in maintaining the normal activity of mitochondrial FAD-binding enzymes, including lipoamide dehydrogenase and succinate dehydrogenase flavoprotein subunit Sdh1p. A decrease in the amount of Sdh1p in the flx1Delta mutant strain has been determined here to be due to a post-transcriptional control that involves regulatory sequences located upstream of the SDH1 coding sequence. The SDH1 coding sequence and the regulatory sequences located downstream of the SDH1 coding region, as well as protein import and cofactor attachment, seem to be not involved in the decrease in the amount of protein.
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Affiliation(s)
- Teresa A Giancaspero
- Dipartimento di Biochimica e Biologia Molecolare E. Quagliariello, Università degli Studi di Bari, Via Orabona 4, Bari, Italy
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40
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Szeto SSW, Reinke SN, Sykes BD, Lemire BD. Ubiquinone-binding Site Mutations in the Saccharomyces cerevisiae Succinate Dehydrogenase Generate Superoxide and Lead to the Accumulation of Succinate. J Biol Chem 2007; 282:27518-27526. [PMID: 17636259 DOI: 10.1074/jbc.m700601200] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The mitochondrial succinate dehydrogenase (SDH) is an essential component of the electron transport chain and of the tricarboxylic acid cycle. Also known as complex II, this tetrameric enzyme catalyzes the oxidation of succinate to fumarate and reduces ubiquinone. Mutations in the human SDHB, SDHC, and SDHD genes are tumorigenic, leading to the development of several types of tumors, including paraganglioma and pheochromocytoma. The mechanisms linking SDH mutations to oncogenesis are still unclear. In this work, we used the yeast SDH to investigate the molecular and catalytic effects of tumorigenic or related mutations. We mutated Arg(47) of the Sdh3p subunit to Cys, Glu, and Lys and Asp(88) of the Sdh4p subunit to Asn, Glu, and Lys. Both Arg(47) and Asp(88) are conserved residues, and Arg(47) is a known site of cancer causing mutations in humans. All of the mutants examined have reduced ubiquinone reductase activities. The SDH3 R47K, SDH4 D88E, and SDH4 D88N mutants are sensitive to hyperoxia and paraquat and have elevated rates of superoxide production in vitro and in vivo. We also observed the accumulation and secretion of succinate. Succinate can inhibit prolyl hydroxylase enzymes, which initiate a proliferative response through the activation of hypoxia-inducible factor 1alpha. We suggest that SDH mutations can promote tumor formation by contributing to both reactive oxygen species production and to a proliferative response normally induced by hypoxia via the accumulation of succinate.
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Affiliation(s)
- Samuel S W Szeto
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Stacey N Reinke
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Brian D Sykes
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Bernard D Lemire
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada.
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41
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Silkin Y, Oyedotun KS, Lemire BD. The role of Sdh4p Tyr-89 in ubiquinone reduction by the Saccharomyces cerevisiae succinate dehydrogenase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2006; 1767:143-50. [PMID: 17208193 DOI: 10.1016/j.bbabio.2006.11.017] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2006] [Revised: 11/02/2006] [Accepted: 11/09/2006] [Indexed: 01/10/2023]
Abstract
Succinate dehydrogenase (complex II or succinate:ubiquinone oxidoreductase) is a tetrameric, membrane-bound enzyme that catalyzes the oxidation of succinate and the reduction of ubiquinone in the mitochondrial respiratory chain. Two electrons from succinate are transferred one at a time through a flavin cofactor and a chain of iron-sulfur clusters to reduce ubiquinone to an ubisemiquinone intermediate and to ubiquinol. Residues that form the proximal quinone-binding site (Q(P)) must recognize ubiquinone, stabilize the ubisemiquinone intermediate, and protonate the ubiquinone to ubiquinol, while minimizing the production of reactive oxygen species. We have investigated the role of the yeast Sdh4p Tyr-89, which forms a hydrogen bond with ubiquinone in the Q(P) site. This tyrosine residue is conserved in all succinate:ubiquinone oxidoreductases studied to date. In the human SDH, mutation of this tyrosine to cysteine results in paraganglioma, tumors of the parasympathetic ganglia in the head and neck. We demonstrate that Tyr-89 is essential for ubiquinone reductase activity and that mutation of Tyr-89 to other residues does not increase the production of reactive oxygen species. Our results support a role for Tyr-89 in the protonation of ubiquinone and argue that the generation of reactive oxygen species is not causative of tumor formation.
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Affiliation(s)
- Yuri Silkin
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2H7
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42
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Grad LI, Lemire BD. Riboflavin enhances the assembly of mitochondrial cytochrome c oxidase in C. elegans NADH-ubiquinone oxidoreductase mutants. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2006; 1757:115-22. [PMID: 16443191 DOI: 10.1016/j.bbabio.2005.11.009] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2005] [Revised: 10/21/2005] [Accepted: 11/28/2005] [Indexed: 12/12/2022]
Abstract
Mitochondrial respiratory chain dysfunction is responsible for a large variety of early and late-onset diseases. NADH-ubiquinone oxidoreductase (complex I) defects constitute the most commonly observed mitochondrial disorders. We have generated Caenorhabditis elegans strains with mutations in the 51 kDa active site subunit of complex I. These strains exhibit decreased NADH-dependent respiration and lactic acidosis, hallmark features of complex I deficiency. Surprisingly, the mutants display a significant decrease in the amount and activity of cytochrome c oxidase (complex IV). The metabolic and reproductive fitness of the mutants is markedly improved by riboflavin. In this study, we have examined how the assembly and activity of complexes I and IV are affected by riboflavin. Our results reveal that the mutations result in variable steady-state levels of different complex I subunits and in a significant reduction in the amount of COXI subunit. Using native gel electrophoresis, we detected assembly intermediates for both complexes I and IV. Riboflavin promotes the assembly of both complexes, resulting in increased catalytic activities. We propose that one primary pathogenic mechanism of some complex I mutations is to destabilize complex IV. Enhancing complex I assembly with riboflavin results in the added benefit of partially reversing the complex IV deficit.
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Affiliation(s)
- Leslie I Grad
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2H7
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43
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Grad LI, Sayles LC, Lemire BD. Introduction of an additional pathway for lactate oxidation in the treatment of lactic acidosis and mitochondrial dysfunction in Caenorhabditis elegans. Proc Natl Acad Sci U S A 2005; 102:18367-72. [PMID: 16344465 PMCID: PMC1311736 DOI: 10.1073/pnas.0506939102] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Mitochondrial dysfunction, with an estimated incidence of 1 in 5,000 births, is associated with a wide variety of multisystem degenerative diseases. Among the most prevalent forms of dysfunction are defects in the NADH:ubiquinone oxidoreductase (complex I). Caenorhabditis elegans strains with complex I mutations exhibit characteristic features of human mitochondrial disease including decreased rates of respiration and lactic acidosis. We hypothesized that introducing an additional pathway for the direct oxidation of lactate would be beneficial for energy metabolism. The yeast CYB2 gene encodes an L-lactate:cytochrome c oxidoreductase that oxidizes lactate, donates electrons directly into the mitochondrial respiratory chain, and supports lactate-dependent respiration. Cyb2p expression markedly increases lifespan, fertility, respiration rates, and ATP content in complex I-deficient animals. Our results indicate that metabolic imbalance leading to lactic acidosis and energy depletion are central mechanisms of pathogenesis in mitochondrial dysfunction and that introduction of an additional pathway for lactate oxidation should be considered as a treatment.
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Affiliation(s)
- Leslie I Grad
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada T6G 2H7
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44
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Romano JD, Kolter R. Pseudomonas-Saccharomyces interactions: influence of fungal metabolism on bacterial physiology and survival. J Bacteriol 2005; 187:940-8. [PMID: 15659672 PMCID: PMC545695 DOI: 10.1128/jb.187.3.940-948.2005] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Fungal-bacterial interactions are ubiquitous, yet their molecular basis is only poorly understood. In this study, a novel beneficial interaction between a strain of Pseudomonas putida and the fungus Saccharomyces cerevisiae was identified. When the bacteria were incubated alone in grape juice or in synthetic medium containing various concentrations of glucose, they lost viability rapidly during stationary phase. However, when the bacteria were incubated in these media in the presence of the fungus, their stationary phase survival improved dramatically. On agar plates containing glucose, the beneficial effects of the fungus were manifested in robust bacterial growth and exopolysaccharide production that led to visible mucoidy. In contrast, bacteria grew poorly and were nonmucoid in such media in the absence of the fungus. By using the available S. cerevisiae deletion library, yeast mutants that were unable to mediate this beneficial interaction were identified. These mutants revealed that the beneficial effect on bacterial physiology and survival was mediated by the ability of the fungus to metabolize the available glucose and consequent effects on the medium's pH. In natural environments where the concentration of glucose is high, it is likely that the presence of fungi has had profound beneficial effects on the physiology and survival of certain P. putida strains throughout their natural history.
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Affiliation(s)
- Julia D Romano
- Department of Microbiology and Molecular Genetics, Harvard Medical School, 200 Longwood Ave., Boston, MA 02115, USA
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45
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Cardol P, González-Halphen D, Reyes-Prieto A, Baurain D, Matagne RF, Remacle C. The mitochondrial oxidative phosphorylation proteome of Chlamydomonas reinhardtii deduced from the Genome Sequencing Project. PLANT PHYSIOLOGY 2005; 137:447-59. [PMID: 15710684 PMCID: PMC1065347 DOI: 10.1104/pp.104.054148] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2004] [Revised: 11/25/2004] [Accepted: 11/25/2004] [Indexed: 05/20/2023]
Affiliation(s)
- Pierre Cardol
- Genetics of Microorganisms , Institute of Plant Biology B22, University of Liege, B-4000 Liege, Belgium
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46
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Akesson M, Förster J, Nielsen J. Integration of gene expression data into genome-scale metabolic models. Metab Eng 2004; 6:285-93. [PMID: 15491858 DOI: 10.1016/j.ymben.2003.12.002] [Citation(s) in RCA: 144] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2003] [Accepted: 12/10/2003] [Indexed: 10/26/2022]
Abstract
A framework for integration of transcriptome data into stoichiometric metabolic models to obtain improved flux predictions is presented. The key idea is to exploit the regulatory information in the expression data to give additional constraints on the metabolic fluxes in the model. Measurements of gene expression from chemostat and batch cultures of Saccharomyces cerevisiae were combined with a recently developed genome-scale model, and the computed metabolic flux distributions were compared to experimental values from carbon labeling experiments and metabolic network analysis. The integration of expression data resulted in improved predictions of metabolic behavior in batch cultures, enabling quantitative predictions of exchange fluxes as well as qualitative estimations of changes in intracellular fluxes. A critical discussion of correlation between gene expression and metabolic fluxes is given.
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Affiliation(s)
- Mats Akesson
- Center for Microbial Biotechnology, BioCentrum-DTU, Technical University of Denmark, Building 223, DK-2800 Kgs. Lyngby, Denmark.
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47
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Nijtmans LG, Ugalde C, van den Heuvel LP, Smeitink JA. Function and dysfunction of the oxidative phosphorylation system. MITOCHONDRIAL FUNCTION AND BIOGENESIS 2004. [DOI: 10.1007/b95715] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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48
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Abstract
Complex II is the only membrane-bound component of the Krebs cycle and in addition functions as a member of the electron transport chain in mitochondria and in many bacteria. A recent X-ray structural solution of members of the complex II family of proteins has provided important insights into their function. One feature of the complex II structures is a linear electron transport chain that extends from the flavin and iron-sulfur redox cofactors in the membrane extrinsic domain to the quinone and b heme cofactors in the membrane domain. Exciting recent developments in relation to disease in humans and the formation of reactive oxygen species by complex II point to its overall importance in cellular physiology.
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Affiliation(s)
- Gary Cecchini
- Molecular Biology Division, Veterans Administration Medical Center, San Francisco, California 94121, USA.
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49
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Hirono S, Dibrov E, Hurtado C, Kostenuk A, Ducas R, Pierce GN. Chlamydia pneumoniae stimulates proliferation of vascular smooth muscle cells through induction of endogenous heat shock protein 60. Circ Res 2003; 93:710-6. [PMID: 14500333 DOI: 10.1161/01.res.0000095720.46043.f2] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Chlamydia pneumoniae infection has been linked with atherosclerosis. However, the mechanism responsible for the atherogenic effects of C pneumoniae remains unclear. Heat shock proteins (HSPs) have been found in atherosclerotic lesions. HSPs of HSP70 and HSP90 families are involved in the regulation of cell cycle progression and cell proliferation. We assessed the hypothesis that HSP60 is induced in vascular cells infected with C pneumoniae and stimulates cell proliferation. Rabbit vascular smooth muscle cells (VSMCs) and human umbilical vein endothelial cells (HUVECs) were infected with C pneumoniae. Western blot analysis demonstrated the induction of endogenous HSP60 expression in C pneumoniae-infected VSMCs. C pneumoniae infection significantly increased the number of VSMCs, and the mitogenic effect correlated with the expression level of endogenous HSP60. In contrast to VSMCs, C pneumoniae infection had no effect on the expression level of HSP60 and did not stimulate cell proliferation in HUVECs. Exogenous addition of recombinant chlamydial HSP60 had no mitogenic effect on VSMCs and HUVECs. However, overexpression of HSP60 within VSMCs by infection with adenovirus encoding human HSP60 resulted in a significant increase in cell numbers compared with uninfected VSMCs. These results suggest that overexpression of endogenous HSP60 may be a central intracellular event responsible for the mitogenic effects induced by C pneumoniae infection. In addition to C pneumoniae, other infectious agents and atherogenic risk factors may also stimulate VSMC proliferation and contribute to the lesion formation through the induction of HSP60.
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Affiliation(s)
- Satoru Hirono
- Division of Stroke and Vascular Disease, St Boniface General Hospital Research Centre, and the Department of Physiology, Faculty of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
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50
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Butcher RA, Schreiber SL. A small molecule suppressor of FK506 that targets the mitochondria and modulates ionic balance in Saccharomyces cerevisiae. CHEMISTRY & BIOLOGY 2003; 10:521-31. [PMID: 12837385 DOI: 10.1016/s1074-5521(03)00108-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
FK506 inhibits the evolutionarily conserved, Ca(2+)-dependent phosphatase calcineurin, which in yeast is essential for growth during sodium stress. We undertook a chemical genetic modifier screen to identify small molecules that suppress the ability of FK506 to inhibit yeast growth in high NaCl. One of these small molecule suppressors, SFK1 (suppressor of FK506 1), causes a mitochondrially induced death in low salt, concomitant with the release of reactive oxygen species. Biochemically, SFK1 interacts with Por1p, a channel protein in the outer mitochondrial membrane, suggesting that SFK1 interacts with the mitochondria directly. A genome-wide screen of yeast deletion strains for hypersensitivity to SFK1 yielded several strains with impaired mitochondrial function, as well as several with reduced sodium tolerance. Our data link ionic balance to mitochondrial function and suggest a role for calcineurin in mediating this signaling network.
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Affiliation(s)
- Rebecca A Butcher
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
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