1
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Sebők-Nagy K, Blastyák A, Juhász G, Páli T. Reversible binding of divalent cations to Ductin protein assemblies-A putative new regulatory mechanism of membrane traffic processes. Front Mol Biosci 2023; 10:1195010. [PMID: 37228584 PMCID: PMC10203432 DOI: 10.3389/fmolb.2023.1195010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 04/24/2023] [Indexed: 05/27/2023] Open
Abstract
Ductins are a family of homologous and structurally similar membrane proteins with 2 or 4 trans-membrane alpha-helices. The active forms of the Ductins are membranous ring- or star-shaped oligomeric assemblies and they provide various pore, channel, gap-junction functions, assist in membrane fusion processes and also serve as the rotor c-ring domain of V-and F-ATPases. All functions of the Ductins have been reported to be sensitive to the presence of certain divalent metal cations (Me2+), most frequently Cu2+ or Ca2+ ions, for most of the better known members of the family, and the mechanism of this effect is not yet known. Given that we have earlier found a prominent Me2+ binding site in a well-characterised Ductin protein, we hypothesise that certain divalent cations can structurally modulate the various functions of Ductin assemblies via affecting their stability by reversible non-covalent binding to them. A fine control of the stability of the assembly ranging from separated monomers through a loosely/weakly to tightly/strongly assembled ring might render precise regulation of Ductin functions possible. The putative role of direct binding of Me2+ to the c-ring subunit of active ATP hydrolase in autophagy and the mechanism of Ca2+-dependent formation of the mitochondrial permeability transition pore are also discussed.
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Affiliation(s)
- Krisztina Sebők-Nagy
- Institute of Biophysics, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary
| | - András Blastyák
- Institute of Genetics, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary
| | - Gábor Juhász
- Institute of Genetics, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary
| | - Tibor Páli
- Institute of Biophysics, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary
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2
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Hassan I, Ebaid H, Alhazza IM, Al-Tamimi J, Rady AM. Disulfiram Enhances the Antineoplastic Activity and Sensitivity of Murine Hepatocellular Carcinoma to 5-FU via Redox Management. Pharmaceuticals (Basel) 2023; 16:169. [PMID: 37259318 PMCID: PMC9967644 DOI: 10.3390/ph16020169] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/05/2023] [Accepted: 01/10/2023] [Indexed: 11/20/2023] Open
Abstract
The efficacy of anticancer drug 5-FU is suppressed due to various factors, including severe side effects and decreased insensitivity during prolonged chemotherapy. Elevated endogenous copper (Cu) levels are one of the prominent hallmark features of cancer cells. In the present investigation, this feature was targeted in diethyl nitrosamine-phenobarbital-induced hepatocellular carcinoma (HCC) in a rat model system by an established anticancer drug, 5-FU, co-administered with copper and its chelating agent, disulfiram. After treatment with the test chemicals in HCC-induced rats, blood and liver samples were subjected to biochemical, molecular, and histopathological analyses. The analysis revealed that reactive oxygen species-mediated oxidative stress is the crucial etiological reason for the pathogenesis of HCC in rats, as evidenced by the significantly compromised activity of major antioxidant enzymes and elevated levels of oxidative damaged products with major histological alterations compared to the control. However, the combination of 5-FU with DSF demonstrated a significant improvement in most of the parameters, followed by 5-FU-Cu in the combination-treated groups. The combination treatment improved the histological details and triggered apoptosis in the cancer cells to a remarkable extent, as the levels of cleaved PARP and caspase-3 were significantly higher than those in the HCC rats treated with the drug alone. The present study envisages that manipulating the Cu-level greatly enhances the antineoplastic activity of 5-FU and sensitizes cancer cells to the increased efficacy of the drug.
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Affiliation(s)
| | | | - Ibrahim M. Alhazza
- Department of Zoology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
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3
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Murray NH, Lewis A, Rincon Pabon JP, Gross ML, Henzler-Wildman K, Pagliarini DJ. 2-Propylphenol Allosterically Modulates COQ8A to Enhance ATPase Activity. ACS Chem Biol 2022; 17:2031-2038. [PMID: 35904798 PMCID: PMC9586199 DOI: 10.1021/acschembio.2c00434] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
COQ8A is an atypical kinase-like protein that aids the biosynthesis of coenzyme Q, an essential cellular cofactor and antioxidant. COQ8A's mode of action remains unclear, in part due to the lack of small molecule tools to probe its function. Here, we blend NMR and hydrogen-deuterium exchange mass spectrometry to help determine how a small CoQ precursor mimetic, 2-propylphenol, modulates COQ8A activity. We identify a likely 2-propylphenol binding site and reveal that this compound modulates a conserved COQ8A domain to increase nucleotide affinity and ATPase activity. Our findings promise to aid further investigations into COQ8A's precise enzymatic function and the design of compounds capable of boosting endogenous CoQ production for therapeutic gain.
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Affiliation(s)
- Nathan H. Murray
- Department of Biochemistry, University of Wisconsin–Madison, Madison, WI 53706, USA
- Morgridge Institute for Research, Madison, WI 53715, USA
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Adam Lewis
- Department of Biochemistry, University of Wisconsin–Madison, Madison, WI 53706, USA
| | - Juan P. Rincon Pabon
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, USA
| | - Michael L. Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, USA
| | | | - David J. Pagliarini
- Department of Biochemistry, University of Wisconsin–Madison, Madison, WI 53706, USA
- Morgridge Institute for Research, Madison, WI 53715, USA
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Correspondence and requests for materials should be addressed to D.J.P.,
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4
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Kaminska J, Soczewka P, Rzepnikowska W, Zoladek T. Yeast as a Model to Find New Drugs and Drug Targets for VPS13-Dependent Neurodegenerative Diseases. Int J Mol Sci 2022; 23:ijms23095106. [PMID: 35563497 PMCID: PMC9104724 DOI: 10.3390/ijms23095106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/28/2022] [Accepted: 04/30/2022] [Indexed: 12/10/2022] Open
Abstract
Mutations in human VPS13A-D genes result in rare neurological diseases, including chorea-acanthocytosis. The pathogenesis of these diseases is poorly understood, and no effective treatment is available. As VPS13 genes are evolutionarily conserved, the effects of the pathogenic mutations could be studied in model organisms, including yeast, where one VPS13 gene is present. In this review, we summarize advancements obtained using yeast. In recent studies, vps13Δ and vps13-I2749 yeast mutants, which are models of chorea-acanthocytosis, were used to screen for multicopy and chemical suppressors. Two of the suppressors, a fragment of the MYO3 and RCN2 genes, act by downregulating calcineurin activity. In addition, vps13Δ suppression was achieved by using calcineurin inhibitors. The other group of multicopy suppressors were genes: FET4, encoding iron transporter, and CTR1, CTR3 and CCC2, encoding copper transporters. Mechanisms of their suppression rely on causing an increase in the intracellular iron content. Moreover, among the identified chemical suppressors were copper ionophores, which require a functional iron uptake system for activity, and flavonoids, which bind iron. These findings point at areas for further investigation in a higher eukaryotic model of VPS13-related diseases and to new therapeutic targets: calcium signalling and copper and iron homeostasis. Furthermore, the identified drugs are interesting candidates for drug repurposing for these diseases.
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Affiliation(s)
- Joanna Kaminska
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, 02-106 Warsaw, Poland; (J.K.); (P.S.)
| | - Piotr Soczewka
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, 02-106 Warsaw, Poland; (J.K.); (P.S.)
| | - Weronika Rzepnikowska
- Neuromuscular Unit, Mossakowski Medical Research Institute, Polish Academy of Sciences, 02-106 Warsaw, Poland;
| | - Teresa Zoladek
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, 02-106 Warsaw, Poland; (J.K.); (P.S.)
- Correspondence:
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5
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Yamada R, Ando Y, Mitsui R, Mizobata A, Yoshihara S, Tokumoto H, Matsumoto T, Ogino H. Improving carotenoid production in recombinant yeast, Saccharomyces cerevisiae, using ultrasound-irradiated two-phase extractive fermentation. Eng Life Sci 2022; 22:4-12. [PMID: 35024023 PMCID: PMC8727735 DOI: 10.1002/elsc.202100051] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 08/11/2021] [Accepted: 10/10/2021] [Indexed: 12/28/2022] Open
Abstract
Carotenoids are hydrophobic compounds that exhibit excellent bioactivity and can be produced by recombinant S. cerevisiae. Irradiating microorganisms with ultrasonic waves increase the productivity of various useful chemicals. Ultrasonic waves are also used to extract useful chemicals that accumulate in microbial cells. In this study, we aimed to improve the carotenoid production efficiency of a recombinant S. cerevisiae using an ultrasonic-irradiation based two-phase extractive fermentation process. When isopropyl myristate was used as the extraction solvent, a total of 264 mg/L of carotenoid was produced when batches were subjected to ultrasonic-irradiation at 10 W, which was a 1.3-fold increase when compared to the control. Transcriptome analysis suggested that one of the reasons for this improvement was an increase in the number of living cells. In fact, after 96 h of fermentation, the number of living cells increased by 1.4-fold upon irradiation with ultrasonic waves. Consequently, we succeeded in improving the carotenoid production in a recombinant S. cerevisiae strain using a ultrasonic-irradiated two-phase extractive fermentation and isopropyl myristate as the solvent. This fermentation strategy has the potential to be widely applied during the production of hydrophobic chemicals in recombinant yeast, and future research is expected to further develop this process.
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Affiliation(s)
- Ryosuke Yamada
- Department of Chemical EngineeringOsaka Prefecture UniversitySakaiOsakaJapan
| | - Yorichika Ando
- Department of Chemical EngineeringOsaka Prefecture UniversitySakaiOsakaJapan
| | - Ryosuke Mitsui
- Department of Chemical EngineeringOsaka Prefecture UniversitySakaiOsakaJapan
| | - Asuka Mizobata
- Department of Chemical EngineeringOsaka Prefecture UniversitySakaiOsakaJapan
| | - Shizue Yoshihara
- Department of Biological ScienceOsaka Prefecture UniversitySakaiOsakaJapan
| | - Hayato Tokumoto
- Department of Biological ScienceOsaka Prefecture UniversitySakaiOsakaJapan
| | - Takuya Matsumoto
- Department of Chemical EngineeringOsaka Prefecture UniversitySakaiOsakaJapan
| | - Hiroyasu Ogino
- Department of Chemical EngineeringOsaka Prefecture UniversitySakaiOsakaJapan
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6
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Tanaka H, Kreisberg JF, Ideker T. Genetic dissection of complex traits using hierarchical biological knowledge. PLoS Comput Biol 2021; 17:e1009373. [PMID: 34534210 PMCID: PMC8480841 DOI: 10.1371/journal.pcbi.1009373] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 09/29/2021] [Accepted: 08/23/2021] [Indexed: 11/18/2022] Open
Abstract
Despite the growing constellation of genetic loci linked to common traits, these loci have yet to account for most heritable variation, and most act through poorly understood mechanisms. Recent machine learning (ML) systems have used hierarchical biological knowledge to associate genetic mutations with phenotypic outcomes, yielding substantial predictive power and mechanistic insight. Here, we use an ontology-guided ML system to map single nucleotide variants (SNVs) focusing on 6 classic phenotypic traits in natural yeast populations. The 29 identified loci are largely novel and account for ~17% of the phenotypic variance, versus <3% for standard genetic analysis. Representative results show that sensitivity to hydroxyurea is linked to SNVs in two alternative purine biosynthesis pathways, and that sensitivity to copper arises through failure to detoxify reactive oxygen species in fatty acid metabolism. This work demonstrates a knowledge-based approach to amplifying and interpreting signals in population genetic studies. Genome-wide association studies (GWAS) have identified many important loci for common diseases and other traits. However, the loci identified by these studies are almost always many steps away from an understanding of underlying biological mechanisms. Here we develop an approach using hierarchical biological knowledge to identify genes and pathways responsible for phenotypic traits. Variants identified by the new method could explain a substantially greater fraction of heritability than previously reported. Moreover, we identified mechanistic pathways by which each causal variant affects cellular function. For example, we find that sensitivity to hydroxyurea is tied to genetic variants in two alternative purine biosynthesis pathways, and that sensitivity to copper arises through failure to detoxify reactive oxygen species in fatty acid metabolism. The new approach is a potentially transformative concept for understanding the genetic drivers of phenotypic variance, with potential applications in understanding traits in biomedicine and agriculture.
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Affiliation(s)
- Hidenori Tanaka
- Department of Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Jason F. Kreisberg
- Department of Medicine, University of California San Diego, La Jolla, California, United States of America
- * E-mail: (JFK); (TI)
| | - Trey Ideker
- Department of Medicine, University of California San Diego, La Jolla, California, United States of America
- * E-mail: (JFK); (TI)
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7
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A CRISPR Interference Screen of Essential Genes Reveals that Proteasome Regulation Dictates Acetic Acid Tolerance in Saccharomyces cerevisiae. mSystems 2021; 6:e0041821. [PMID: 34313457 PMCID: PMC8407339 DOI: 10.1128/msystems.00418-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
CRISPR interference (CRISPRi) is a powerful tool to study cellular physiology under different growth conditions, and this technology provides a means for screening changed expression of essential genes. In this study, a Saccharomyces cerevisiae CRISPRi library was screened for growth in medium supplemented with acetic acid. Acetic acid is a growth inhibitor challenging the use of yeast for the industrial conversion of lignocellulosic biomasses. Tolerance to acetic acid that is released during biomass hydrolysis is crucial for cell factories to be used in biorefineries. The CRISPRi library screened consists of >9,000 strains, where >98% of all essential and respiratory growth-essential genes were targeted with multiple guide RNAs (gRNAs). The screen was performed using the high-throughput, high-resolution Scan-o-matic platform, where each strain is analyzed separately. Our study identified that CRISPRi targeting of genes involved in vesicle formation or organelle transport processes led to severe growth inhibition during acetic acid stress, emphasizing the importance of these intracellular membrane structures in maintaining cell vitality. In contrast, strains in which genes encoding subunits of the 19S regulatory particle of the 26S proteasome were downregulated had increased tolerance to acetic acid, which we hypothesize is due to ATP salvage through an increased abundance of the 20S core particle that performs ATP-independent protein degradation. This is the first study where high-resolution CRISPRi library screening paves the way to understanding and bioengineering the robustness of yeast against acetic acid stress. IMPORTANCE Acetic acid is inhibitory to the growth of the yeast Saccharomyces cerevisiae, causing ATP starvation and oxidative stress, which leads to the suboptimal production of fuels and chemicals from lignocellulosic biomass. In this study, where each strain of a CRISPRi library was characterized individually, many essential and respiratory growth-essential genes that regulate tolerance to acetic acid were identified, providing a new understanding of the stress response of yeast and new targets for the bioengineering of industrial yeast. Our findings on the fine-tuning of the expression of proteasomal genes leading to increased tolerance to acetic acid suggest that this could be a novel strategy for increasing stress tolerance, leading to improved strains for the production of biobased chemicals.
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8
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Helsen J, Voordeckers K, Vanderwaeren L, Santermans T, Tsontaki M, Verstrepen KJ, Jelier R. Gene Loss Predictably Drives Evolutionary Adaptation. Mol Biol Evol 2021; 37:2989-3002. [PMID: 32658971 PMCID: PMC7530610 DOI: 10.1093/molbev/msaa172] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Loss of gene function is common throughout evolution, even though it often leads to reduced fitness. In this study, we systematically evaluated how an organism adapts after deleting genes that are important for growth under oxidative stress. By evolving, sequencing, and phenotyping over 200 yeast lineages, we found that gene loss can enhance an organism’s capacity to evolve and adapt. Although gene loss often led to an immediate decrease in fitness, many mutants rapidly acquired suppressor mutations that restored fitness. Depending on the strain’s genotype, some ultimately even attained higher fitness levels than similarly adapted wild-type cells. Further, cells with deletions in different modules of the genetic network followed distinct and predictable mutational trajectories. Finally, losing highly connected genes increased evolvability by facilitating the emergence of a more diverse array of phenotypes after adaptation. Together, our findings show that loss of specific parts of a genetic network can facilitate adaptation by opening alternative evolutionary paths.
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Affiliation(s)
- Jana Helsen
- Laboratory of Predictive Genetics and Multicellular Systems, CMPG, KU Leuven, Leuven, Belgium.,Laboratory of Genetics and Genomics, CMPG, KU Leuven, Leuven, Belgium.,Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, Belgium
| | - Karin Voordeckers
- Laboratory of Genetics and Genomics, CMPG, KU Leuven, Leuven, Belgium.,Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, Belgium
| | - Laura Vanderwaeren
- Laboratory of Predictive Genetics and Multicellular Systems, CMPG, KU Leuven, Leuven, Belgium.,Laboratory of Genetics and Genomics, CMPG, KU Leuven, Leuven, Belgium.,Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, Belgium
| | - Toon Santermans
- Laboratory of Predictive Genetics and Multicellular Systems, CMPG, KU Leuven, Leuven, Belgium
| | - Maria Tsontaki
- Laboratory of Genetics and Genomics, CMPG, KU Leuven, Leuven, Belgium.,Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, Belgium
| | - Kevin J Verstrepen
- Laboratory of Genetics and Genomics, CMPG, KU Leuven, Leuven, Belgium.,Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, Belgium
| | - Rob Jelier
- Laboratory of Predictive Genetics and Multicellular Systems, CMPG, KU Leuven, Leuven, Belgium
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9
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Garza NM, Griffin AT, Zulkifli M, Qiu C, Kaplan CD, Gohil VM. A genome-wide copper-sensitized screen identifies novel regulators of mitochondrial cytochrome c oxidase activity. J Biol Chem 2021; 296:100485. [PMID: 33662401 PMCID: PMC8027276 DOI: 10.1016/j.jbc.2021.100485] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/22/2021] [Accepted: 02/25/2021] [Indexed: 11/30/2022] Open
Abstract
Copper is essential for the activity and stability of cytochrome c oxidase (CcO), the terminal enzyme of the mitochondrial respiratory chain. Loss-of-function mutations in genes required for copper transport to CcO result in fatal human disorders. Despite the fundamental importance of copper in mitochondrial and organismal physiology, systematic identification of genes that regulate mitochondrial copper homeostasis is lacking. To discover these genes, we performed a genome-wide screen using a library of DNA-barcoded yeast deletion mutants grown in copper-supplemented media. Our screen recovered a number of genes known to be involved in cellular copper homeostasis as well as genes previously not linked to mitochondrial copper biology. These newly identified genes include the subunits of the adaptor protein 3 complex (AP-3) and components of the cellular pH-sensing pathway Rim20 and Rim21, both of which are known to affect vacuolar function. We find that AP-3 and Rim mutants exhibit decreased vacuolar acidity, which in turn perturbs mitochondrial copper homeostasis and CcO function. CcO activity of these mutants could be rescued by either restoring vacuolar pH or supplementing growth media with additional copper. Consistent with these genetic data, pharmacological inhibition of the vacuolar proton pump leads to decreased mitochondrial copper content and a concomitant decrease in CcO abundance and activity. Taken together, our study uncovered novel genetic regulators of mitochondrial copper homeostasis and provided a mechanism by which vacuolar pH impacts mitochondrial respiration through copper homeostasis.
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Affiliation(s)
- Natalie M Garza
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
| | - Aaron T Griffin
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
| | - Mohammad Zulkifli
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
| | - Chenxi Qiu
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
| | - Craig D Kaplan
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
| | - Vishal M Gohil
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA.
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10
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Soczewka P, Tribouillard-Tanvier D, di Rago JP, Zoladek T, Kaminska J. Targeting Copper Homeostasis Improves Functioning of vps13Δ Yeast Mutant Cells, a Model of VPS13-Related Diseases. Int J Mol Sci 2021; 22:2248. [PMID: 33668157 PMCID: PMC7956333 DOI: 10.3390/ijms22052248] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 02/12/2021] [Accepted: 02/19/2021] [Indexed: 01/01/2023] Open
Abstract
Ion homeostasis is crucial for organism functioning, and its alterations may cause diseases. For example, copper insufficiency and overload are associated with Menkes and Wilson's diseases, respectively, and iron imbalance is observed in Parkinson's and Alzheimer's diseases. To better understand human diseases, Saccharomyces cerevisiae yeast are used as a model organism. In our studies, we used the vps13Δ yeast strain as a model of rare neurological diseases caused by mutations in VPS13A-D genes. In this work, we show that overexpression of genes encoding copper transporters, CTR1, CTR3, and CCC2, or the addition of copper salt to the medium, improved functioning of the vps13Δ mutant. We show that their mechanism of action, at least partially, depends on increasing iron content in the cells by the copper-dependent iron uptake system. Finally, we present that treatment with copper ionophores, disulfiram, elesclomol, and sodium pyrithione, also resulted in alleviation of the defects observed in vps13Δ cells. Our study points at copper and iron homeostasis as a potential therapeutic target for further investigation in higher eukaryotic models of VPS13-related diseases.
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Affiliation(s)
- Piotr Soczewka
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland;
| | - Déborah Tribouillard-Tanvier
- IBGC, UMR 5095, CNRS, Université de Bordeaux, F-33000 Bordeaux, France; (D.T.-T.); (J.-P.d.R.)
- Institut National de la Santé et de la Recherche Médicale (INSERM), F-33077 Bordeaux, France
| | - Jean-Paul di Rago
- IBGC, UMR 5095, CNRS, Université de Bordeaux, F-33000 Bordeaux, France; (D.T.-T.); (J.-P.d.R.)
| | - Teresa Zoladek
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland;
| | - Joanna Kaminska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland;
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11
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Stenger M, Le DT, Klecker T, Westermann B. Systematic analysis of nuclear gene function in respiratory growth and expression of the mitochondrial genome in S. cerevisiae. MICROBIAL CELL 2020; 7:234-249. [PMID: 32904421 PMCID: PMC7453639 DOI: 10.15698/mic2020.09.729] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The production of metabolic energy in form of ATP by oxidative phosphorylation depends on the coordinated action of hundreds of nuclear-encoded mitochondrial proteins and a handful of proteins encoded by the mitochondrial genome (mtDNA). We used the yeast Saccharomyces cerevisiae as a model system to systematically identify the genes contributing to this process. Integration of genome-wide high-throughput growth assays with previously published large data sets allowed us to define with high confidence a set of 254 nuclear genes that are indispensable for respiratory growth. Next, we induced loss of mtDNA in the yeast deletion collection by growth on ethidium bromide-containing medium and identified twelve genes that are essential for viability in the absence of mtDNA (i.e. petite-negative). Replenishment of mtDNA by cytoduction showed that respiratory-deficient phenotypes are highly variable in many yeast mutants. Using a mitochondrial genome carrying a selectable marker, ARG8m, we screened for mutants that are specifically defective in maintenance of mtDNA and mitochondrial protein synthesis. We found that up to 176 nuclear genes are required for expression of mitochondria-encoded proteins during fermentative growth. Taken together, our data provide a comprehensive picture of the molecular processes that are required for respiratory metabolism in a simple eukaryotic cell.
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Affiliation(s)
- Maria Stenger
- Zellbiologie, Universität Bayreuth, 95440 Bayreuth, Germany
| | - Duc Tung Le
- Zellbiologie, Universität Bayreuth, 95440 Bayreuth, Germany
| | - Till Klecker
- Zellbiologie, Universität Bayreuth, 95440 Bayreuth, Germany
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12
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Sobh A, Loguinov A, Stornetta A, Balbo S, Tagmount A, Zhang L, Vulpe CD. Genome-Wide CRISPR Screening Identifies the Tumor Suppressor Candidate OVCA2 As a Determinant of Tolerance to Acetaldehyde. Toxicol Sci 2020; 169:235-245. [PMID: 31059574 DOI: 10.1093/toxsci/kfz037] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Acetaldehyde, a metabolite of ethanol, is a cellular toxicant and a human carcinogen. A genome-wide CRISPR-based loss-of-function screen in erythroleukemic K562 cells revealed candidate genetic contributors affecting acetaldehyde cytotoxicity. Secondary screening exposing cells to a lower acetaldehyde dose simultaneously validated multiple candidate genes whose loss results in increased sensitivity to acetaldehyde. Disruption of genes encoding components of various DNA repair pathways increased cellular sensitivity to acetaldehyde. Unexpectedly, the tumor suppressor gene OVCA2, whose function is unknown, was identified in our screen as a determinant of acetaldehyde tolerance. Disruption of the OVCA2 gene resulted in increased acetaldehyde sensitivity and higher accumulation of the acetaldehyde-derived DNA adduct N2-ethylidene-dG. Together these results are consistent with a role for OVCA2 in adduct removal and/or DNA repair.
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Affiliation(s)
- Amin Sobh
- Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, Florida.,Department of Nutritional Sciences & Toxicology, Comparative Biochemistry Program, University of California, Berkeley, California
| | - Alex Loguinov
- Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, Florida
| | - Alessia Stornetta
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
| | - Silvia Balbo
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota.,Division of Environmental Health Sciences, University of Minnesota, Minneapolis, Minnesota
| | - Abderrahmane Tagmount
- Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, Florida
| | - Luoping Zhang
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, California
| | - Chris D Vulpe
- Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, Florida
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13
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Afonso J, Coutinho LL, Tizioto PC, da Silva Diniz WJ, de Lima AO, Rocha MIP, Buss CE, Andrade BGN, Piaya O, da Silva JV, Lins LA, Gromboni CF, Nogueira ARA, Fortes MRS, Mourao GB, de Almeida Regitano LC. Muscle transcriptome analysis reveals genes and metabolic pathways related to mineral concentration in Bos indicus. Sci Rep 2019; 9:12715. [PMID: 31481722 PMCID: PMC6722098 DOI: 10.1038/s41598-019-49089-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 08/02/2019] [Indexed: 01/18/2023] Open
Abstract
Mineral content affects the biological processes underlying beef quality. Muscle mineral concentration depends not only on intake-outtake balance and muscle type, but also on age, environment, breed, and genetic factors. To unveil the genetic factors involved in muscle mineral concentration, we applied a pairwise differential gene expression analysis in groups of Nelore steers genetically divergent for nine different mineral concentrations. Here, based on significant expression differences between contrasting groups, we presented candidate genes for the genetic regulation of mineral concentration in muscle. Functional enrichment and protein-protein interaction network analyses were carried out to search for gene regulatory processes concerning each mineral. The core genetic regulation for all minerals studied, except Zn, seems to rest on interactions between components of the extracellular matrix. Regulation of adipogenesis-related pathways was also significant in our results. Antagonistic patterns of gene expression for fatty acid metabolism-related genes may explain the Cu and Zn antagonistic effect on fatty acid accumulation. Our results shed light on the role of these minerals on cell function.
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Affiliation(s)
- Juliana Afonso
- Department of Evolutionary Genetics and Molecular Biology, Federal University of São Carlos, São Carlos, Brazil
| | | | | | | | - Andressa Oliveira de Lima
- Department of Evolutionary Genetics and Molecular Biology, Federal University of São Carlos, São Carlos, Brazil
| | - Marina Ibelli Pereira Rocha
- Department of Evolutionary Genetics and Molecular Biology, Federal University of São Carlos, São Carlos, Brazil
| | - Carlos Eduardo Buss
- Department of Evolutionary Genetics and Molecular Biology, Federal University of São Carlos, São Carlos, Brazil
| | | | - Otávio Piaya
- Department of Evolutionary Genetics and Molecular Biology, Federal University of São Carlos, São Carlos, Brazil
| | | | - Laura Albuquerque Lins
- Animal Science department, Laboratory of Molecular Genetics. São Paulo State University, Jaboticabal, Brazil
| | | | | | - Marina Rufino Salinas Fortes
- School of Chemistry and Molecular Biosciences, Faculty of Sciences, The University of Queensland, Brisbane, Australia
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14
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McColl AI, Bleackley MR, Anderson MA, Lowe RGT. Resistance to the Plant Defensin NaD1 Features Modifications to the Cell Wall and Osmo-Regulation Pathways of Yeast. Front Microbiol 2018; 9:1648. [PMID: 30087664 PMCID: PMC6066574 DOI: 10.3389/fmicb.2018.01648] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 07/02/2018] [Indexed: 11/24/2022] Open
Abstract
Over the last few decades, the emergence of resistance to commonly used antifungal molecules has become a major barrier to effective treatment of recurrent life-threatening fungal diseases. Resistance combined with the increased incidence of fungal diseases has created the need for new antifungals, such as the plant defensin NaD1, with different mechanisms of action to broaden treatment options. Antimicrobial peptides produced in plants and animals are promising new molecules in the arsenal of antifungal agents because they have different mechanisms of action to current antifungals and are often targeted specifically to fungal pathogens (van der Weerden et al., 2013). A key step in the development of novel antifungals is an understanding of the potential for the fungus to develop resistance. Here, we have used the prototypic plant defensin NaD1 in serial passages with the model fungus Saccharomyces cerevisiae to examine the evolution of resistance to plant antifungal peptides. The yeast strains did develop tolerance to NaD1, but it occurred more slowly than to the clinically used antifungal caspofungin. Sequencing the genomes of the strains with increased tolerance failed to identify any ‘hotspot’ mutations associated with increased tolerance to NaD1 and led to the identification of 12 genes that are involved in resistance. Characterization of the strains with increased tolerance to NaD1 also revealed changes in tolerance to abiotic stressors. Resistance developed slowly via an accumulation of single nucleotide mutations and had a fitness penalty associated with it. One of the genes identified FPS1, revealed that there is a common mechanism of resistance to NaD1 that involves the osmotic stress response pathway. These data indicate that it is more difficult to generate resistance to antimicrobial peptides such as NaD1 compared to small molecule antifungals.
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Affiliation(s)
- Amanda I McColl
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - Mark R Bleackley
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - Marilyn A Anderson
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - Rohan G T Lowe
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
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15
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Comstra HS, McArthy J, Rudin-Rush S, Hartwig C, Gokhale A, Zlatic SA, Blackburn JB, Werner E, Petris M, D'Souza P, Panuwet P, Barr DB, Lupashin V, Vrailas-Mortimer A, Faundez V. The interactome of the copper transporter ATP7A belongs to a network of neurodevelopmental and neurodegeneration factors. eLife 2017; 6. [PMID: 28355134 PMCID: PMC5400511 DOI: 10.7554/elife.24722] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 03/28/2017] [Indexed: 02/04/2023] Open
Abstract
Genetic and environmental factors, such as metals, interact to determine neurological traits. We reasoned that interactomes of molecules handling metals in neurons should include novel metal homeostasis pathways. We focused on copper and its transporter ATP7A because ATP7A null mutations cause neurodegeneration. We performed ATP7A immunoaffinity chromatography and identified 541 proteins co-isolating with ATP7A. The ATP7A interactome concentrated gene products implicated in neurodegeneration and neurodevelopmental disorders, including subunits of the Golgi-localized conserved oligomeric Golgi (COG) complex. COG null cells possess altered content and subcellular localization of ATP7A and CTR1 (SLC31A1), the transporter required for copper uptake, as well as decreased total cellular copper, and impaired copper-dependent metabolic responses. Changes in the expression of ATP7A and COG subunits in Drosophila neurons altered synapse development in larvae and copper-induced mortality of adult flies. We conclude that the ATP7A interactome encompasses a novel COG-dependent mechanism to specify neuronal development and survival.
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Affiliation(s)
- Heather S Comstra
- Departments of Cell Biology, Emory University, Atlanta, United States
| | - Jacob McArthy
- School of Biological Sciences, Illinois State University, Normal, United States
| | | | - Cortnie Hartwig
- Department of Chemistry, Agnes Scott College, Decatur, Georgia
| | - Avanti Gokhale
- Departments of Cell Biology, Emory University, Atlanta, United States
| | | | - Jessica B Blackburn
- Department of Physiology and Biophysics, University of Arkansas for Medical Sciences, Little Rock, United States
| | - Erica Werner
- Department of Biochemistry, Emory University, Atlanta, United States
| | - Michael Petris
- Department of Biochemistry, University of Missouri, Columbia, United States
| | - Priya D'Souza
- Rollins School of Public Health, Emory University, Atlanta, United States
| | - Parinya Panuwet
- Rollins School of Public Health, Emory University, Atlanta, United States
| | - Dana Boyd Barr
- Rollins School of Public Health, Emory University, Atlanta, United States
| | - Vladimir Lupashin
- Department of Physiology and Biophysics, University of Arkansas for Medical Sciences, Little Rock, United States
| | | | - Victor Faundez
- Departments of Cell Biology, Emory University, Atlanta, United States
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16
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Smith JD, Schlecht U, Xu W, Suresh S, Horecka J, Proctor MJ, Aiyar RS, Bennett RAO, Chu A, Li YF, Roy K, Davis RW, Steinmetz LM, Hyman RW, Levy SF, St Onge RP. A method for high-throughput production of sequence-verified DNA libraries and strain collections. Mol Syst Biol 2017; 13:913. [PMID: 28193641 PMCID: PMC5327727 DOI: 10.15252/msb.20167233] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The low costs of array‐synthesized oligonucleotide libraries are empowering rapid advances in quantitative and synthetic biology. However, high synthesis error rates, uneven representation, and lack of access to individual oligonucleotides limit the true potential of these libraries. We have developed a cost‐effective method called Recombinase Directed Indexing (REDI), which involves integration of a complex library into yeast, site‐specific recombination to index library DNA, and next‐generation sequencing to identify desired clones. We used REDI to generate a library of ~3,300 DNA probes that exhibited > 96% purity and remarkable uniformity (> 95% of probes within twofold of the median abundance). Additionally, we created a collection of ~9,000 individually accessible CRISPR interference yeast strains for > 99% of genes required for either fermentative or respiratory growth, demonstrating the utility of REDI for rapid and cost‐effective creation of strain collections from oligonucleotide pools. Our approach is adaptable to any complex DNA library, and fundamentally changes how these libraries can be parsed, maintained, propagated, and characterized.
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Affiliation(s)
- Justin D Smith
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Ulrich Schlecht
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA.,Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Weihong Xu
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA.,Department of Surgery, Harvard Medical School and Massachusetts General Hospital, Boston, MA, USA
| | - Sundari Suresh
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA.,Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Joe Horecka
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA.,Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Michael J Proctor
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA.,Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Raeka S Aiyar
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA.,Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Richard A O Bennett
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA.,Department of Biochemistry and Cellular Biology, Stony Brook University, Stony Brook, NY, USA
| | - Angela Chu
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA.,Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Yong Fuga Li
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA
| | - Kevin Roy
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Ronald W Davis
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.,Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Lars M Steinmetz
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.,European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Richard W Hyman
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA.,Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Sasha F Levy
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA.,Department of Biochemistry and Cellular Biology, Stony Brook University, Stony Brook, NY, USA
| | - Robert P St Onge
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA .,Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
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17
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Tfp1 is required for ion homeostasis, fluconazole resistance and N-Acetylglucosamine utilization in Candida albicans. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1853:2731-44. [PMID: 26255859 DOI: 10.1016/j.bbamcr.2015.08.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Revised: 07/31/2015] [Accepted: 08/05/2015] [Indexed: 11/23/2022]
Abstract
The vacuolar-type H+-ATPase (V-ATPase) is crucial for the maintenance of ion homeostasis. Dysregulation of ion homeostasis affects various aspects of cellular processes. However, the importance of V-ATPase in Candida albicans is not totally clear. In this study, we demonstrated the essential roles of V-ATPase through Tfp1, a putative V-ATPase subunit. Deletion of TFP1 led to generation of an iron starvation signal and reduced total iron content, which was associated with mislocalization of Fet34p that was finally due to disorders in copper homeostasis. Furthermore, the tfp1∆/∆ mutant exhibited weaker growth and lower aconitase activity on nonfermentable carbon sources, and iron or copper addition partially rescued the growth defect. In addition, the tfp1∆/∆ mutant also showed elevated cytosolic calcium levels in normal or low calcium medium that were relevant to calcium release from vacuole. Kinetics of cytosolic calcium response to an alkaline pulse and VCX1 (VCX1 encodes a putative vacuolar Ca2+/H+ exchanger) overexpression assays indicated that the cytosolic calcium status was in relation to Vcx1 activity. Spot assay and concentration-kill curve demonstrated that the tfp1∆/∆ mutant was hypersensitive to fluconazole, which was attributed to reduced ergosterol biosynthesis and CDR1 efflux pump activity, and iron/calcium dysregulation. Interestingly, carbon source utilization tests found the tfp1∆/∆ mutant was defective for growth on N-Acetylglucosamine (GlcNAc) plate, which was associated with ATP depletion due to the decreased ability to catabolize GlcNAc. Taken together, our study gives new insights into functions of Tfp1, and provides the potential to better exploit V-ATPase as an antifungal target.
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18
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Alesso CA, Discola KF, Monteiro G. The gene ICS3 from the yeast Saccharomyces cerevisiae is involved in copper homeostasis dependent on extracellular pH. Fungal Genet Biol 2015; 82:43-50. [PMID: 26127016 DOI: 10.1016/j.fgb.2015.06.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 06/08/2015] [Accepted: 06/10/2015] [Indexed: 11/18/2022]
Abstract
In the yeast Saccharomyces cerevisiae, many genes are involved in the uptake, transport, storage and detoxification of copper. Large scale studies have noted that deletion of the gene ICS3 increases sensitivity to copper, Sortin 2 and acid exposure. Here, we report a study on the Δics3 strain, in which ICS3 is related to copper homeostasis, affecting the intracellular accumulation of this metal. This strain is sensitive to hydrogen peroxide and copper exposure, but not to other tested transition metals. At pH 6.0, the Δics3 strain accumulates a larger amount of intracellular copper than the wild-type strain, explaining the sensitivity to oxidants in this condition. Unexpectedly, sensitivity to copper exposure only occurs in acidic conditions. This can be explained by the fact that the exposure of Δics3 cells to high copper concentrations at pH 4.0 results in over-accumulation of copper and iron. Moreover, the expression of ICS3 increases in acidic pH, and this is correlated with CCC2 gene expression, since both genes are regulated by Rim101 from the pH regulon. CCC2 is also upregulated in Δics3 in acidic pH. Together, these data indicate that ICS3 is involved in copper homeostasis and is dependent on extracellular pH.
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Affiliation(s)
- C A Alesso
- Departamento de Tecnologia Bioquímico-Farmacêutica, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, Brazil
| | - K F Discola
- Departamento de Tecnologia Bioquímico-Farmacêutica, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, Brazil
| | - G Monteiro
- Departamento de Tecnologia Bioquímico-Farmacêutica, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, Brazil.
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19
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Aiyar RS, Bohnert M, Duvezin-Caubet S, Voisset C, Gagneur J, Fritsch ES, Couplan E, von der Malsburg K, Funaya C, Soubigou F, Courtin F, Suresh S, Kucharczyk R, Evrard J, Antony C, St Onge RP, Blondel M, di Rago JP, van der Laan M, Steinmetz LM. Mitochondrial protein sorting as a therapeutic target for ATP synthase disorders. Nat Commun 2014; 5:5585. [PMID: 25519239 PMCID: PMC4284804 DOI: 10.1038/ncomms6585] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Accepted: 10/16/2014] [Indexed: 11/09/2022] Open
Abstract
Mitochondrial diseases are systemic, prevalent and often fatal; yet treatments remain scarce. Identifying molecular intervention points that can be therapeutically targeted remains a major challenge, which we confronted via a screening assay we developed. Using yeast models of mitochondrial ATP synthase disorders, we screened a drug repurposing library, and applied genomic and biochemical techniques to identify pathways of interest. Here we demonstrate that modulating the sorting of nuclear-encoded proteins into mitochondria, mediated by the TIM23 complex, proves therapeutic in both yeast and patient-derived cells exhibiting ATP synthase deficiency. Targeting TIM23-dependent protein sorting improves an array of phenotypes associated with ATP synthase disorders, including biogenesis and activity of the oxidative phosphorylation machinery. Our study establishes mitochondrial protein sorting as an intervention point for ATP synthase disorders, and because of the central role of this pathway in mitochondrial biogenesis, it holds broad value for the treatment of mitochondrial diseases.
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Affiliation(s)
- Raeka S Aiyar
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany
| | - Maria Bohnert
- Institut für Biochemie und Molekularbiologie, ZBMZ, Universität Freiburg, 79104 Freiburg, Germany
| | - Stéphane Duvezin-Caubet
- 1] Université Bordeaux, IBGC, UMR 5095, F-33000 Bordeaux, France [2] CNRS, IBGC, UMR 5095, F-33000 Bordeaux, France
| | - Cécile Voisset
- Institut National de la Santé et de la Recherche Médicale UMR1078; Université de Bretagne Occidentale, Faculté de Médecine et des Sciences de la Santé; Etablissement Français du Sang (EFS) Bretagne; CHRU Brest, Hôpital Morvan, Laboratoire de Génétique Moléculaire, Brest F-29200, France
| | - Julien Gagneur
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany
| | - Emilie S Fritsch
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany
| | - Elodie Couplan
- Institut National de la Santé et de la Recherche Médicale UMR1078; Université de Bretagne Occidentale, Faculté de Médecine et des Sciences de la Santé; Etablissement Français du Sang (EFS) Bretagne; CHRU Brest, Hôpital Morvan, Laboratoire de Génétique Moléculaire, Brest F-29200, France
| | - Karina von der Malsburg
- 1] Institut für Biochemie und Molekularbiologie, ZBMZ, Universität Freiburg, 79104 Freiburg, Germany [2] BIOSS Centre for Biological Signalling Studies, Universität Freiburg, 79104 Freiburg, Germany
| | - Charlotta Funaya
- European Molecular Biology Laboratory (EMBL), Electron Microscopy Core Facility, 69117 Heidelberg, Germany
| | - Flavie Soubigou
- Institut National de la Santé et de la Recherche Médicale UMR1078; Université de Bretagne Occidentale, Faculté de Médecine et des Sciences de la Santé; Etablissement Français du Sang (EFS) Bretagne; CHRU Brest, Hôpital Morvan, Laboratoire de Génétique Moléculaire, Brest F-29200, France
| | - Florence Courtin
- 1] Université Bordeaux, IBGC, UMR 5095, F-33000 Bordeaux, France [2] CNRS, IBGC, UMR 5095, F-33000 Bordeaux, France
| | - Sundari Suresh
- Stanford Genome Technology Center, Stanford University, Palo Alto, California 94304, USA
| | - Roza Kucharczyk
- Department of Genetics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Justine Evrard
- Institut National de la Santé et de la Recherche Médicale UMR1078; Université de Bretagne Occidentale, Faculté de Médecine et des Sciences de la Santé; Etablissement Français du Sang (EFS) Bretagne; CHRU Brest, Hôpital Morvan, Laboratoire de Génétique Moléculaire, Brest F-29200, France
| | - Claude Antony
- European Molecular Biology Laboratory (EMBL), Electron Microscopy Core Facility, 69117 Heidelberg, Germany
| | - Robert P St Onge
- Stanford Genome Technology Center, Stanford University, Palo Alto, California 94304, USA
| | - Marc Blondel
- Institut National de la Santé et de la Recherche Médicale UMR1078; Université de Bretagne Occidentale, Faculté de Médecine et des Sciences de la Santé; Etablissement Français du Sang (EFS) Bretagne; CHRU Brest, Hôpital Morvan, Laboratoire de Génétique Moléculaire, Brest F-29200, France
| | - Jean-Paul di Rago
- 1] Université Bordeaux, IBGC, UMR 5095, F-33000 Bordeaux, France [2] CNRS, IBGC, UMR 5095, F-33000 Bordeaux, France
| | - Martin van der Laan
- 1] Institut für Biochemie und Molekularbiologie, ZBMZ, Universität Freiburg, 79104 Freiburg, Germany [2] BIOSS Centre for Biological Signalling Studies, Universität Freiburg, 79104 Freiburg, Germany
| | - Lars M Steinmetz
- 1] European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany [2] Stanford Genome Technology Center, Stanford University, Palo Alto, California 94304, USA [3] Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
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20
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Stefely JA, Reidenbach AG, Ulbrich A, Oruganty K, Floyd BJ, Jochem A, Saunders JM, Johnson IE, Minogue CE, Wrobel RL, Barber GE, Lee D, Li S, Kannan N, Coon JJ, Bingman CA, Pagliarini DJ. Mitochondrial ADCK3 employs an atypical protein kinase-like fold to enable coenzyme Q biosynthesis. Mol Cell 2014; 57:83-94. [PMID: 25498144 DOI: 10.1016/j.molcel.2014.11.002] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 10/13/2014] [Accepted: 11/04/2014] [Indexed: 10/24/2022]
Abstract
The ancient UbiB protein kinase-like family is involved in isoprenoid lipid biosynthesis and is implicated in human diseases, but demonstration of UbiB kinase activity has remained elusive for unknown reasons. Here, we quantitatively define UbiB-specific sequence motifs and reveal their positions within the crystal structure of a UbiB protein, ADCK3. We find that multiple UbiB-specific features are poised to inhibit protein kinase activity, including an N-terminal domain that occupies the typical substrate binding pocket and a unique A-rich loop that limits ATP binding by establishing an unusual selectivity for ADP. A single alanine-to-glycine mutation of this loop flips this coenzyme selectivity and enables autophosphorylation but inhibits coenzyme Q biosynthesis in vivo, demonstrating functional relevance for this unique feature. Our work provides mechanistic insight into UbiB enzyme activity and establishes a molecular foundation for further investigation of how UbiB family proteins affect diseases and diverse biological pathways.
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Affiliation(s)
- Jonathan A Stefely
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Andrew G Reidenbach
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Arne Ulbrich
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | | | - Brendan J Floyd
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Adam Jochem
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jaclyn M Saunders
- Mitochondrial Protein Partnership, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Isabel E Johnson
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Catherine E Minogue
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Russell L Wrobel
- Mitochondrial Protein Partnership, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Grant E Barber
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - David Lee
- Department of Medicine and UCSD DXMS Proteomics Resource, University of California, San Diego, La Jolla, CA 92023, USA
| | - Sheng Li
- Department of Medicine and UCSD DXMS Proteomics Resource, University of California, San Diego, La Jolla, CA 92023, USA
| | - Natarajan Kannan
- Department of Biochemistry, University of Georgia, Athens, GA 30602, USA
| | - Joshua J Coon
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Craig A Bingman
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Mitochondrial Protein Partnership, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - David J Pagliarini
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Mitochondrial Protein Partnership, University of Wisconsin-Madison, Madison, WI 53706, USA.
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