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Jiang PH, Hou CY, Teng SC. An HSP90 cochaperone Ids2 maintains the stability of mitochondrial DNA and ATP synthase. BMC Biol 2021; 19:242. [PMID: 34763695 PMCID: PMC8582188 DOI: 10.1186/s12915-021-01179-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Accepted: 10/28/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Proteostasis unbalance and mitochondrial dysfunction are two hallmarks of aging. While the chaperone folds and activates its clients, it is the cochaperone that determines the specificity of the clients. Ids2 is an HSP90's cochaperone controlling mitochondrial functions, but no in vivo clients of Ids2 have been reported yet. RESULTS We performed a screen of the databases of HSP90 physical interactors, mitochondrial components, and mutants with respiratory defect, and identified Atp3, a subunit of the complex V ATP synthase, as a client of Ids2. Deletion of IDS2 destabilizes Atp3, and an α-helix at the middle region of Ids2 recruits Atp3 to the folding system. Shortage of Ids2 or Atp3 leads to the loss of mitochondrial DNA. The intermembrane space protease Yme1 is critical to maintaining the Atp3 protein level. Moreover, Ids2 is highly induced when cells carry out oxidative respiration. CONCLUSIONS These findings discover a cochaperone essentially for maintaining the stability of mitochondrial DNA and the proteostasis of the electron transport chain-crosstalk between two hallmarks of aging.
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Affiliation(s)
- Pei-Heng Jiang
- Department of Microbiology, College of Medicine, National Taiwan University, No. 1, Sec. 1, Jen-Ai Road, Taipei, 10051, Taiwan
| | - Chen-Yan Hou
- Department of Microbiology, College of Medicine, National Taiwan University, No. 1, Sec. 1, Jen-Ai Road, Taipei, 10051, Taiwan
| | - Shu-Chun Teng
- Department of Microbiology, College of Medicine, National Taiwan University, No. 1, Sec. 1, Jen-Ai Road, Taipei, 10051, Taiwan.
- Center of Precision Medicine, National Taiwan University, Taipei, Taiwan.
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2
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Swamy KBS, Schuyler SC, Leu JY. Protein Complexes Form a Basis for Complex Hybrid Incompatibility. Front Genet 2021; 12:609766. [PMID: 33633780 PMCID: PMC7900514 DOI: 10.3389/fgene.2021.609766] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 01/20/2021] [Indexed: 12/20/2022] Open
Abstract
Proteins are the workhorses of the cell and execute many of their functions by interacting with other proteins forming protein complexes. Multi-protein complexes are an admixture of subunits, change their interaction partners, and modulate their functions and cellular physiology in response to environmental changes. When two species mate, the hybrid offspring are usually inviable or sterile because of large-scale differences in the genetic makeup between the two parents causing incompatible genetic interactions. Such reciprocal-sign epistasis between inter-specific alleles is not limited to incompatible interactions between just one gene pair; and, usually involves multiple genes. Many of these multi-locus incompatibilities show visible defects, only in the presence of all the interactions, making it hard to characterize. Understanding the dynamics of protein-protein interactions (PPIs) leading to multi-protein complexes is better suited to characterize multi-locus incompatibilities, compared to studying them with traditional approaches of genetics and molecular biology. The advances in omics technologies, which includes genomics, transcriptomics, and proteomics can help achieve this end. This is especially relevant when studying non-model organisms. Here, we discuss the recent progress in the understanding of hybrid genetic incompatibility; omics technologies, and how together they have helped in characterizing protein complexes and in turn multi-locus incompatibilities. We also review advances in bioinformatic techniques suitable for this purpose and propose directions for leveraging the knowledge gained from model-organisms to identify genetic incompatibilities in non-model organisms.
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Affiliation(s)
- Krishna B. S. Swamy
- Division of Biological and Life Sciences, School of Arts and Sciences, Ahmedabad University, Ahmedabad, India
| | - Scott C. Schuyler
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Division of Head and Neck Surgery, Department of Otolaryngology, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Jun-Yi Leu
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
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3
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Chen YC, Jiang PH, Chen HM, Chen CH, Wang YT, Chen YJ, Yu CJ, Teng SC. Glucose intake hampers PKA-regulated HSP90 chaperone activity. eLife 2018; 7:39925. [PMID: 30516470 PMCID: PMC6281317 DOI: 10.7554/elife.39925] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 11/22/2018] [Indexed: 12/12/2022] Open
Abstract
Aging is an intricate phenomenon associated with the gradual loss of physiological functions, and both nutrient sensing and proteostasis control lifespan. Although multiple approaches have facilitated the identification of candidate genes that govern longevity, the molecular mechanisms that link aging pathways are still elusive. Here, we conducted a quantitative mass spectrometry screen and identified all phosphorylation/dephosphorylation sites on yeast proteins that significantly responded to calorie restriction, a well-established approach to extend lifespan. Functional screening of 135 potential regulators uncovered that Ids2 is activated by PP2C under CR and inactivated by PKA under glucose intake. ids2Δ or ids2 phosphomimetic cells displayed heat sensitivity and lifespan shortening. Ids2 serves as a co-chaperone to form a complex with Hsc82 or the redundant Hsp82, and phosphorylation impedes its association with chaperone HSP90. Thus, PP2C and PKA may orchestrate glucose sensing and protein folding to enable cells to maintain protein quality for sustained longevity.
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Affiliation(s)
- Yu-Chen Chen
- Department of Microbiology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Pei-Heng Jiang
- Department of Microbiology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Hsuan-Ming Chen
- Department of Microbiology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Chang-Han Chen
- Department of Microbiology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Yi-Ting Wang
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
| | - Yu-Ju Chen
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
| | - Chia-Jung Yu
- Department of Cell and Molecular Biology, College of Medicine, Chang Gung University, Tao-Yuan, Taiwan.,Department of Thoracic Medicine, Chang Gung Memorial Hospital, Tao-Yuan, Taiwan
| | - Shu-Chun Teng
- Department of Microbiology, College of Medicine, National Taiwan University, Taipei, Taiwan.,Center of Precision Medicine, National Taiwan University, Taipei, Taiwan
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4
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Levytskyy RM, Bohovych I, Khalimonchuk O. Metalloproteases of the Inner Mitochondrial Membrane. Biochemistry 2017; 56:4737-4746. [PMID: 28806058 DOI: 10.1021/acs.biochem.7b00663] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The inner mitochondrial membrane (IM) is among the most protein-rich cellular compartments. The metastable IM subproteome where the concentration of proteins is approaching oversaturation creates a challenging protein folding environment with a high probability of protein malfunction or aggregation. Failure to maintain protein homeostasis in such a setting can impair the functional integrity of the mitochondria and drive clinical manifestations. The IM is equipped with a series of highly conserved, proteolytic complexes dedicated to the maintenance of normal protein homeostasis within this mitochondrial subcompartment. Particularly important is a group of membrane-anchored metallopeptidases commonly known as m-AAA and i-AAA proteases, and the ATP-independent Oma1 protease. Herein, we will summarize the current biochemical knowledge of these proteolytic machines and discuss recent advances in our understanding of mechanistic aspects of their functioning.
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Affiliation(s)
- Roman M Levytskyy
- Department of Biochemistry, University of Nebraska-Lincoln , Lincoln, Nebraska 68588-0664, United States
| | - Iryna Bohovych
- Department of Biochemistry, University of Nebraska-Lincoln , Lincoln, Nebraska 68588-0664, United States
| | - Oleh Khalimonchuk
- Department of Biochemistry, University of Nebraska-Lincoln , Lincoln, Nebraska 68588-0664, United States.,Nebraska Redox Biology Center, University of Nebraska-Lincoln , Lincoln, Nebraska 68588-0662, United States.,Fred & Pamela Buffett Cancer Center , Omaha, Nebraska 68106, United States
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5
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Srinivasainagendra V, Sandel MW, Singh B, Sundaresan A, Mooga VP, Bajpai P, Tiwari HK, Singh KK. Migration of mitochondrial DNA in the nuclear genome of colorectal adenocarcinoma. Genome Med 2017; 9:31. [PMID: 28356157 PMCID: PMC5370490 DOI: 10.1186/s13073-017-0420-6] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 03/09/2017] [Indexed: 12/31/2022] Open
Abstract
Background Colorectal adenocarcinomas are characterized by abnormal mitochondrial DNA (mtDNA) copy number and genomic instability, but a molecular interaction between mitochondrial and nuclear genome remains unknown. Here we report the discovery of increased copies of nuclear mtDNA (NUMT) in colorectal adenocarcinomas, which supports link between mtDNA and genomic instability in the nucleus. We name this phenomenon of nuclear occurrence of mitochondrial component as numtogenesis. We provide a description of NUMT abundance and distribution in tumor versus matched blood-derived normal genomes. Methods Whole-genome sequence data were obtained for colon adenocarcinoma and rectum adenocarcinoma patients participating in The Cancer Genome Atlas, via the Cancer Genomics Hub, using the GeneTorrent file acquisition tool. Data were analyzed to determine NUMT proportion and distribution on a genome-wide scale. A NUMT suppressor gene was identified by comparing numtogenesis in other organisms. Results Our study reveals that colorectal adenocarcinoma genomes, on average, contains up to 4.2-fold more somatic NUMTs than matched normal genomes. Women colorectal tumors contained more NUMT than men. NUMT abundance in tumor predicted parallel abundance in blood. NUMT abundance positively correlated with GC content and gene density. Increased numtogenesis was observed with higher mortality. We identified YME1L1, a human homolog of yeast YME1 (yeast mitochondrial DNA escape 1) to be frequently mutated in colorectal tumors. YME1L1 was also mutated in tumors derived from other tissues. We show that inactivation of YME1L1 results in increased transfer of mtDNA in the nuclear genome. Conclusions Our study demonstrates increased somatic transfer of mtDNA in colorectal tumors. Our study also reveals sex-based differences in frequency of NUMT occurrence and that NUMT in blood reflects NUMT in tumors, suggesting NUMT may be used as a biomarker for tumorigenesis. We identify YME1L1 as the first NUMT suppressor gene in human and demonstrate that inactivation of YME1L1 induces migration of mtDNA to the nuclear genome. Our study reveals that numtogenesis plays an important role in the development of cancer. Electronic supplementary material The online version of this article (doi:10.1186/s13073-017-0420-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Vinodh Srinivasainagendra
- Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, Alabama, 35294, USA
| | - Michael W Sandel
- Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, Alabama, 35294, USA.,Present address: Department of Biological and Environmental Sciences, School of Natural Sciences and Mathematics, University of West Alabama, Livingston, Alabama, USA
| | - Bhupendra Singh
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, 35294, USA
| | - Aishwarya Sundaresan
- Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, Alabama, 35294, USA
| | - Ved P Mooga
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, 35294, USA
| | - Prachi Bajpai
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, 35294, USA
| | - Hemant K Tiwari
- Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, Alabama, 35294, USA.
| | - Keshav K Singh
- Departments of Genetics, Environmental Health, Center for Free Radical Biology, Center for Aging and UAB Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama, 35294, USA. .,Departments of Pathology, Environmental Health, Center for Free Radical Biology, Center for Aging and UAB Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama, 35294, USA. .,Birmingham Veterans Affairs Medical Center, Birmingham, Alabama, 35294, USA. .,Department of Genetics, School of Medicine, University of Alabama at Birmingham, Kaul Genetics Building, Suite 620, 720 20th St. South, Birmingham, AL, 35294, USA.
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6
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Pasquali F, Agrimonti C, Pagano L, Zappettini A, Villani M, Marmiroli M, White JC, Marmiroli N. Nucleo-mitochondrial interaction of yeast in response to cadmium sulfide quantum dot exposure. JOURNAL OF HAZARDOUS MATERIALS 2017; 324:744-752. [PMID: 27890358 DOI: 10.1016/j.jhazmat.2016.11.053] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 11/16/2016] [Accepted: 11/19/2016] [Indexed: 06/06/2023]
Abstract
Cell sensitivity to quantum dots (QDs) has been attributed to a cascade triggered by oxidative stress leading to apoptosis. The role and function of mitochondria in animal cells are well understood but little information is available on the complex genetic networks that regulate nucleo-mitochondrial interaction. The effect of CdS QD exposure in yeast Saccharomyces cerevisiae was assessed under conditions of limited lethality (<10%), using cell physiological and morphological endpoints. Whole-genomic array analysis and the screening of a deletion mutant library were also carried out. The results showed that QDs: increased the level of reactive oxygen species (ROS) and decreased the level of reduced vs oxidized glutathione (GSH/GSSG); reduced oxygen consumption and the abundance of respiratory cytochromes; disrupted mitochondrial membrane potentials and affected mitochondrial morphology. Exposure affected the capacity of cells to grow on galactose, which requires nucleo-mitochondrial involvement. However, QDs exposure did not materially induce respiratory deficient (RD) mutants but only RD phenocopies. All of these cellular changes were correlated with several key nuclear genes, including TOM5 and FKS1, involved in the maintenance of mitochondrial organization and function. The consequences of these cellular effects are discussed in terms of dysregulation of cell function in response to these "pathological mitochondria".
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Affiliation(s)
| | | | - Luca Pagano
- Department of Life Sciences, University of Parma, Parma, Italy; Stockbridge school of Agriculture, University of Massachusetts, Amherst, MA, USA; The Connecticut Agricultural Experiment Station, New Haven, CT, USA
| | - Andrea Zappettini
- IMEM-CNR - Istituto dei Materiali per l'Elettronica ed il Magnetismo, Parma, Italy
| | - Marco Villani
- IMEM-CNR - Istituto dei Materiali per l'Elettronica ed il Magnetismo, Parma, Italy
| | - Marta Marmiroli
- Department of Life Sciences, University of Parma, Parma, Italy
| | - Jason C White
- The Connecticut Agricultural Experiment Station, New Haven, CT, USA
| | - Nelson Marmiroli
- Department of Life Sciences, University of Parma, Parma, Italy; CINSA - Consorzio Interuniversitario Nazionale per le Scienze Ambientali, University of Parma, Parma, Italy.
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7
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Smakowska E, Skibior-Blaszczyk R, Czarna M, Kolodziejczak M, Kwasniak-Owczarek M, Parys K, Funk C, Janska H. Lack of FTSH4 Protease Affects Protein Carbonylation, Mitochondrial Morphology, and Phospholipid Content in Mitochondria of Arabidopsis: New Insights into a Complex Interplay. PLANT PHYSIOLOGY 2016; 171:2516-35. [PMID: 27297677 PMCID: PMC4972270 DOI: 10.1104/pp.16.00370] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 06/06/2016] [Indexed: 05/04/2023]
Abstract
FTSH4 is one of the inner membrane-embedded ATP-dependent metalloproteases in mitochondria of Arabidopsis (Arabidopsis thaliana). In mutants impaired to express FTSH4, carbonylated proteins accumulated and leaf morphology was altered when grown under a short-day photoperiod, at 22°C, and a long-day photoperiod, at 30°C. To provide better insight into the function of FTSH4, we compared the mitochondrial proteomes and oxyproteomes of two ftsh4 mutants and wild-type plants grown under conditions inducing the phenotypic alterations. Numerous proteins from various submitochondrial compartments were observed to be carbonylated in the ftsh4 mutants, indicating a widespread oxidative stress. One of the reasons for the accumulation of carbonylated proteins in ftsh4 was the limited ATP-dependent proteolytic capacity of ftsh4 mitochondria, arising from insufficient ATP amount, probably as a result of an impaired oxidative phosphorylation (OXPHOS), especially complex V. In ftsh4, we further observed giant, spherical mitochondria coexisting among normal ones. Both effects, the increased number of abnormal mitochondria and the decreased stability/activity of the OXPHOS complexes, were probably caused by the lower amount of the mitochondrial membrane phospholipid cardiolipin. We postulate that the reduced cardiolipin content in ftsh4 mitochondria leads to perturbations within the OXPHOS complexes, generating more reactive oxygen species and less ATP, and to the deregulation of mitochondrial dynamics, causing in consequence the accumulation of oxidative damage.
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Affiliation(s)
- Elwira Smakowska
- Faculty of Biotechnology, University of Wroclaw, 50-383 Wroclaw, Poland (E.S., R.S.-B, M.C., M.K., M.K.-O., K.P., H.J.); andDepartment of Chemistry, Umeå University, 901 87 Umea, Sweden (C.F.)
| | - Renata Skibior-Blaszczyk
- Faculty of Biotechnology, University of Wroclaw, 50-383 Wroclaw, Poland (E.S., R.S.-B, M.C., M.K., M.K.-O., K.P., H.J.); andDepartment of Chemistry, Umeå University, 901 87 Umea, Sweden (C.F.)
| | - Malgorzata Czarna
- Faculty of Biotechnology, University of Wroclaw, 50-383 Wroclaw, Poland (E.S., R.S.-B, M.C., M.K., M.K.-O., K.P., H.J.); andDepartment of Chemistry, Umeå University, 901 87 Umea, Sweden (C.F.)
| | - Marta Kolodziejczak
- Faculty of Biotechnology, University of Wroclaw, 50-383 Wroclaw, Poland (E.S., R.S.-B, M.C., M.K., M.K.-O., K.P., H.J.); andDepartment of Chemistry, Umeå University, 901 87 Umea, Sweden (C.F.)
| | - Malgorzata Kwasniak-Owczarek
- Faculty of Biotechnology, University of Wroclaw, 50-383 Wroclaw, Poland (E.S., R.S.-B, M.C., M.K., M.K.-O., K.P., H.J.); andDepartment of Chemistry, Umeå University, 901 87 Umea, Sweden (C.F.)
| | - Katarzyna Parys
- Faculty of Biotechnology, University of Wroclaw, 50-383 Wroclaw, Poland (E.S., R.S.-B, M.C., M.K., M.K.-O., K.P., H.J.); andDepartment of Chemistry, Umeå University, 901 87 Umea, Sweden (C.F.)
| | - Christiane Funk
- Faculty of Biotechnology, University of Wroclaw, 50-383 Wroclaw, Poland (E.S., R.S.-B, M.C., M.K., M.K.-O., K.P., H.J.); andDepartment of Chemistry, Umeå University, 901 87 Umea, Sweden (C.F.)
| | - Hanna Janska
- Faculty of Biotechnology, University of Wroclaw, 50-383 Wroclaw, Poland (E.S., R.S.-B, M.C., M.K., M.K.-O., K.P., H.J.); andDepartment of Chemistry, Umeå University, 901 87 Umea, Sweden (C.F.)
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8
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Lindahl PA, Moore MJ. Labile Low-Molecular-Mass Metal Complexes in Mitochondria: Trials and Tribulations of a Burgeoning Field. Biochemistry 2016; 55:4140-53. [PMID: 27433847 DOI: 10.1021/acs.biochem.6b00216] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Iron, copper, zinc, manganese, cobalt, and molybdenum play important roles in mitochondrial biochemistry, serving to help catalyze reactions in numerous metalloenzymes. These metals are also found in labile "pools" within mitochondria. Although the composition and cellular function of these pools are largely unknown, they are thought to be comprised of nonproteinaceous low-molecular-mass (LMM) metal complexes. Many problems must be solved before these pools can be fully defined, especially problems stemming from the lability of such complexes. This lability arises from inherently weak coordinate bonds between ligands and metals. This is an advantage for catalysis and trafficking, but it makes characterization difficult. The most popular strategy for investigating such pools is to detect them using chelator probes with fluorescent properties that change upon metal coordination. Characterization is limited because of the inevitable destruction of the complexes during their detection. Moreover, probes likely react with more than one type of metal complex, confusing analyses. An alternative approach is to use liquid chromatography (LC) coupled with inductively coupled plasma mass spectrometry (ICP-MS). With help from a previous lab member, the authors recently developed an LC-ICP-MS approach to analyze LMM extracts from yeast and mammalian mitochondria. They detected several metal complexes, including Fe580, Fe1100, Fe1500, Cu5000, Zn1200, Zn1500, Mn1100, Mn2000, Co1200, Co1500, and Mo780 (numbers refer to approximate masses in daltons). Many of these may be used to metalate apo-metalloproteins as they fold inside the organelle. The LC-based approach also has challenges, e.g., in distinguishing artifactual metal complexes from endogenous ones, due to the fact that cells must be disrupted to form extracts before they are passed through chromatography columns prior to analysis. Ultimately, both approaches will be needed to characterize these intriguing complexes and to elucidate their roles in mitochondrial biochemistry.
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Affiliation(s)
- Paul A Lindahl
- Department of Chemistry, Texas A&M University , College Station, Texas 77843-3255, United States.,Department of Biochemistry and Biophysics, Texas A&M University , College Station, Texas 77843-2128, United States
| | - Michael J Moore
- Department of Chemistry, Texas A&M University , College Station, Texas 77843-3255, United States
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9
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Rühle T, Leister D. Assembly of F1F0-ATP synthases. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1847:849-60. [PMID: 25667968 DOI: 10.1016/j.bbabio.2015.02.005] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Revised: 01/28/2015] [Accepted: 02/02/2015] [Indexed: 12/31/2022]
Abstract
F1F0-ATP synthases are multimeric protein complexes and common prerequisites for their correct assembly are (i) provision of subunits in appropriate relative amounts, (ii) coordination of membrane insertion and (iii) avoidance of assembly intermediates that uncouple the proton gradient or wastefully hydrolyse ATP. Accessory factors facilitate these goals and assembly occurs in a modular fashion. Subcomplexes common to bacteria and mitochondria, but in part still elusive in chloroplasts, include a soluble F1 intermediate, a membrane-intrinsic, oligomeric c-ring, and a membrane-embedded subcomplex composed of stator subunits and subunit a. The final assembly step is thought to involve association of the preformed F1-c10-14 with the ab2 module (or the ab8-stator module in mitochondria)--mediated by binding of subunit δ in bacteria or OSCP in mitochondria, respectively. Despite the common evolutionary origin of F1F0-ATP synthases, the set of auxiliary factors required for their assembly in bacteria, mitochondria and chloroplasts shows clear signs of evolutionary divergence. This article is part of a Special Issue entitled: Chloroplast Biogenesis.
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Affiliation(s)
- Thilo Rühle
- Plant Molecular Biology (Botany), Department Biology I, Ludwig-Maximilians-Universität München (LMU), Großhaderner Straße 2, 82152 Planegg-Martinsried, Germany.
| | - Dario Leister
- Plant Molecular Biology (Botany), Department Biology I, Ludwig-Maximilians-Universität München (LMU), Großhaderner Straße 2, 82152 Planegg-Martinsried, Germany.
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10
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Abstract
The mitochondrion is arguably the most complex organelle in the budding yeast cell cytoplasm. It is essential for viability as well as respiratory growth. Its innermost aqueous compartment, the matrix, is bounded by the highly structured inner membrane, which in turn is bounded by the intermembrane space and the outer membrane. Approximately 1000 proteins are present in these organelles, of which eight major constituents are coded and synthesized in the matrix. The import of mitochondrial proteins synthesized in the cytoplasm, and their direction to the correct soluble compartments, correct membranes, and correct membrane surfaces/topologies, involves multiple pathways and macromolecular machines. The targeting of some, but not all, cytoplasmically synthesized mitochondrial proteins begins with translation of messenger RNAs localized to the organelle. Most proteins then pass through the translocase of the outer membrane to the intermembrane space, where divergent pathways sort them to the outer membrane, inner membrane, and matrix or trap them in the intermembrane space. Roughly 25% of mitochondrial proteins participate in maintenance or expression of the organellar genome at the inner surface of the inner membrane, providing 7 membrane proteins whose synthesis nucleates the assembly of three respiratory complexes.
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11
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Lionaki E, Tavernarakis N. Oxidative stress and mitochondrial protein quality control in aging. J Proteomics 2013; 92:181-94. [PMID: 23563202 DOI: 10.1016/j.jprot.2013.03.022] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Revised: 02/22/2013] [Accepted: 03/25/2013] [Indexed: 12/17/2022]
Abstract
Mitochondrial protein quality control incorporates an elaborate network of chaperones and proteases that survey the organelle for misfolded or unfolded proteins and toxic aggregates. Repair of misfolded or aggregated protein and proteolytic removal of irreversibly damaged proteins are carried out by the mitochondrial protein quality control system. Initial maturation and folding of the nuclear or mitochondrial-encoded mitochondrial proteins are mediated by processing peptidases and chaperones that interact with the protein translocation machinery. Mitochondrial proteins are subjected to cumulative oxidative damage. Thus, impairment of quality control processes may cause mitochondrial dysfunction. Aging has been associated with a marked decline in the effectiveness of mitochondrial protein quality control. Here, we present an overview of the chaperones and proteases involved in the initial folding and maturation of new, incoming precursor molecules, and the subsequent repair and removal of oxidized aggregated proteins. In addition, we highlight the link between mitochondrial protein quality control mechanisms and the aging process. This article is part of a Special Issue entitled: Posttranslational Protein modifications in biology and Medicine.
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Affiliation(s)
- Eirini Lionaki
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion 71110, Crete, Greece
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12
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Abstract
This review focuses on organellar AAA/FtsH proteases, whose proteolytic and chaperone-like activity is a crucial component of the protein quality control systems of mitochondrial and chloroplast membranes. We compare the AAA/FtsH proteases from yeast, mammals and plants. The nature of the complexes formed by AAA/FtsH proteases and the current view on their involvement in degradation of non-native organellar proteins or assembly of membrane complexes are discussed. Additional functions of AAA proteases not directly connected with protein quality control found in yeast and mammals but not yet in plants are also described shortly. Following an overview of the molecular functions of the AAA/FtsH proteases we discuss physiological consequences of their inactivation in yeast, mammals and plants. The molecular basis of phenotypes associated with inactivation of the AAA/FtsH proteases is not fully understood yet, with the notable exception of those observed in m-AAA protease-deficient yeast cells, which are caused by impaired maturation of mitochondrial ribosomal protein. Finally, examples of cytosolic events affecting protein quality control in mitochondria and chloroplasts are given. This article is part of a Special Issue entitled: Protein Import and Quality Control in Mitochondria and Plastids.
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Affiliation(s)
- Hanna Janska
- Department of Biotechnology, University of Wroclaw, Przybyszewskiego 63/77, 51-148 Wroclaw, Poland.
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13
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Delaney JR, Ahmed U, Chou A, Sim S, Carr D, Murakami CJ, Schleit J, Sutphin GL, An EH, Castanza A, Fletcher M, Higgins S, Jelic M, Klum S, Muller B, Peng ZJ, Rai D, Ros V, Singh M, Wende HV, Kennedy BK, Kaeberlein M. Stress profiling of longevity mutants identifies Afg3 as a mitochondrial determinant of cytoplasmic mRNA translation and aging. Aging Cell 2013; 12:156-66. [PMID: 23167605 DOI: 10.1111/acel.12032] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/06/2012] [Indexed: 01/05/2023] Open
Abstract
Although environmental stress likely plays a significant role in promoting aging, the relationship remains poorly understood. To characterize this interaction in a more comprehensive manner, we examined the stress response profiles for 46 long-lived yeast mutant strains across four different stress conditions (oxidative, ER, DNA damage, and thermal), grouping genes based on their associated stress response profiles. Unexpectedly, cells lacking the mitochondrial AAA protease gene AFG3 clustered strongly with long-lived strains lacking cytosolic ribosomal proteins of the large subunit. Similar to these ribosomal protein mutants, afg3Δ cells show reduced cytoplasmic mRNA translation, enhanced resistance to tunicamycin that is independent of the ER unfolded protein response, and Sir2-independent but Gcn4-dependent lifespan extension. These data demonstrate an unexpected link between a mitochondrial protease, cytoplasmic mRNA translation, and aging.
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Affiliation(s)
| | - Umema Ahmed
- Department of Pathology; University of Washington; Seattle; WA; USA
| | - Annie Chou
- Department of Pathology; University of Washington; Seattle; WA; USA
| | - Sylvia Sim
- Department of Pathology; University of Washington; Seattle; WA; USA
| | - Daniel Carr
- Department of Pathology; University of Washington; Seattle; WA; USA
| | | | - Jennifer Schleit
- Department of Pathology; University of Washington; Seattle; WA; USA
| | | | - Elroy H. An
- Department of Pathology; University of Washington; Seattle; WA; USA
| | - Anthony Castanza
- Department of Pathology; University of Washington; Seattle; WA; USA
| | - Marissa Fletcher
- Department of Pathology; University of Washington; Seattle; WA; USA
| | - Sean Higgins
- Department of Pathology; University of Washington; Seattle; WA; USA
| | - Monika Jelic
- Department of Pathology; University of Washington; Seattle; WA; USA
| | - Shannon Klum
- Department of Pathology; University of Washington; Seattle; WA; USA
| | - Brian Muller
- Department of Pathology; University of Washington; Seattle; WA; USA
| | - Zhao J. Peng
- Department of Pathology; University of Washington; Seattle; WA; USA
| | - Dilreet Rai
- Department of Pathology; University of Washington; Seattle; WA; USA
| | - Vanessa Ros
- Department of Pathology; University of Washington; Seattle; WA; USA
| | - Minnie Singh
- Department of Pathology; University of Washington; Seattle; WA; USA
| | - Helen V. Wende
- Department of Pathology; University of Washington; Seattle; WA; USA
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14
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Abstract
Cruentaren A, an antifungal benzolactone produced by the myxobacterium Byssovorax cruenta, is highly cytotoxic against various human cancer cell lines and a highly selective inhibitor of mitochondrial F-ATPase. A convergent and efficient synthesis of cruentaren A is reported, based upon a diastereoselective alkylation, a series of stereoselective aldol reactions utilizing Myers' pseudoephedrine propionamide, an acyl bromide mediated esterification, and a ring-closing metathesis (RCM) as the key steps. The RCM reaction was applied for the first time toward the total synthesis of cruentaren A, which led to a convergent and efficient synthesis of the natural product.
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Affiliation(s)
| | | | - Brian S. J. Blagg
- Department of Medicinal Chemistry, The University of Kansas, 1251 Wescoe Hall Dr, Malott 4070, Lawrence, Kansas 66045-7562
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15
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Protein quality control in organelles - AAA/FtsH story. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2012; 1833:381-7. [PMID: 22498346 DOI: 10.1016/j.bbamcr.2012.03.016] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2012] [Revised: 03/26/2012] [Accepted: 03/27/2012] [Indexed: 11/23/2022]
Abstract
This review focuses on organellar AAA/FtsH proteases, whose proteolytic and chaperone-like activity is a crucial component of the protein quality control systems of mitochondrial and chloroplast membranes. We compare the AAA/FtsH proteases from yeast, mammals and plants. The nature of the complexes formed by AAA/FtsH proteases and the current view on their involvement in degradation of non-native organellar proteins or assembly of membrane complexes are discussed. Additional functions of AAA proteases not directly connected with protein quality control found in yeast and mammals but not yet in plants are also described shortly. Following an overview of the molecular functions of the AAA/FtsH proteases we discuss physiological consequences of their inactivation in yeast, mammals and plants. The molecular basis of phenotypes associated with inactivation of the AAA/FtsH proteases is not fully understood yet, with the notable exception of those observed in m-AAA protease-deficient yeast cells, which are caused by impaired maturation of mitochondrial ribosomal protein. Finally, examples of cytosolic events affecting protein quality control in mitochondria and chloroplasts are given. This article is part of a Special Issue entitled: Protein Import and Quality Control in Mitochondria and Plastids.
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16
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da Silva VCH, Ramos CHI. The network interaction of the human cytosolic 90 kDa heat shock protein Hsp90: A target for cancer therapeutics. J Proteomics 2012; 75:2790-802. [PMID: 22236519 DOI: 10.1016/j.jprot.2011.12.028] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2011] [Revised: 12/18/2011] [Accepted: 12/19/2011] [Indexed: 10/14/2022]
Abstract
In the cell, proteins interact within a network in which a small number of proteins are highly connected nodes or hubs. A disturbance in the hub proteins usually has a higher impact on the cell physiology than a disturbance in poorly connected nodes. In eukaryotes, the cytosolic Hsp90 is considered to be a hub protein as it interacts with molecular chaperones and co-chaperones, and has key regulatory proteins as clients, such as transcriptional factors, protein kinases and hormone receptors. The large number of Hsp90 partners suggests that Hsp90 is involved in very important functions, such as signaling, proteostasis and epigenetics. Some of these functions are dysregulated in cancer, making Hsp90 a potential target for therapeutics. The number of Hsp90 interactors appears to be so large that a precise answer to the question of how many proteins interact with this chaperone has no definitive answer yet, not even if the question refers to specific Hsp90s as one of the human cytosolic forms. Here we review the major chaperones and co-chaperones that interact with cytosolic Hsp90s, highlighting the latest findings regarding client proteins and the role that posttranslational modifications have on the function and interactions of these molecular chaperones. This article is part of a Special Issue entitled: Proteomics: The clinical link.
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Affiliation(s)
- Viviane C H da Silva
- Institute of Chemistry, University of Campinas-UNICAMP. P.O. Box 6154, 13083-970, Campinas, SP, Brazil
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