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Marchesan E, Nardin A, Mauri S, Bernardo G, Chander V, Di Paola S, Chinellato M, von Stockum S, Chakraborty J, Herkenne S, Basso V, Schrepfer E, Marin O, Cendron L, Medina DL, Scorrano L, Ziviani E. Activation of Ca 2+ phosphatase Calcineurin regulates Parkin translocation to mitochondria and mitophagy in flies. Cell Death Differ 2024; 31:217-238. [PMID: 38238520 PMCID: PMC10850161 DOI: 10.1038/s41418-023-01251-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 11/23/2023] [Accepted: 12/05/2023] [Indexed: 02/09/2024] Open
Abstract
Selective removal of dysfunctional mitochondria via autophagy is crucial for the maintenance of cellular homeostasis. This event is initiated by the translocation of the E3 ubiquitin ligase Parkin to damaged mitochondria, and it requires the Serine/Threonine-protein kinase PINK1. In a coordinated set of events, PINK1 operates upstream of Parkin in a linear pathway that leads to the phosphorylation of Parkin, Ubiquitin, and Parkin mitochondrial substrates, to promote ubiquitination of outer mitochondrial membrane proteins. Ubiquitin-decorated mitochondria are selectively recruiting autophagy receptors, which are required to terminate the organelle via autophagy. In this work, we show a previously uncharacterized molecular pathway that correlates the activation of the Ca2+-dependent phosphatase Calcineurin to Parkin translocation and Parkin-dependent mitophagy. Calcineurin downregulation or genetic inhibition prevents Parkin translocation to CCCP-treated mitochondria and impairs stress-induced mitophagy, whereas Calcineurin activation promotes Parkin mitochondrial recruitment and basal mitophagy. Calcineurin interacts with Parkin, and promotes Parkin translocation in the absence of PINK1, but requires PINK1 expression to execute mitophagy in MEF cells. Genetic activation of Calcineurin in vivo boosts basal mitophagy in neurons and corrects locomotor dysfunction and mitochondrial respiratory defects of a Drosophila model of impaired mitochondrial functions. Our study identifies Calcineurin as a novel key player in the regulation of Parkin translocation and mitophagy.
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Affiliation(s)
| | - Alice Nardin
- Department of Biology, University of Padova, Padova, Italy
| | - Sofia Mauri
- Department of Biology, University of Padova, Padova, Italy
| | - Greta Bernardo
- Department of Biology, University of Padova, Padova, Italy
| | - Vivek Chander
- Department of Biology, University of Padova, Padova, Italy
| | - Simone Di Paola
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Naples, Italy
- Institute for Experimental Endocrinology and Oncology (IEOS), National Research Council (CNR), Napoli, Italy
| | | | | | | | | | | | - Emilie Schrepfer
- Department of Biology, University of Padova, Padova, Italy
- Dulbecco-Telethon Institute, Venetian Institute of Molecular Medicine (VIMM), Padova, Italy
| | - Oriano Marin
- Department of Biomedical Sciences (DSB), University of Padova, Padova, Italy
| | - Laura Cendron
- Department of Biology, University of Padova, Padova, Italy
| | - Diego L Medina
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Naples, Italy
- Medical Genetics Unit, Department of Medical and Translational Science, Federico II University, Naples, Italy
| | - Luca Scorrano
- Department of Biology, University of Padova, Padova, Italy
- Dulbecco-Telethon Institute, Venetian Institute of Molecular Medicine (VIMM), Padova, Italy
| | - Elena Ziviani
- Department of Biology, University of Padova, Padova, Italy.
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2
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Kushnireva L, Korkotian E, Segal M. Exposure of Cultured Hippocampal Neurons to the Mitochondrial Uncoupler Carbonyl Cyanide Chlorophenylhydrazone Induces a Rapid Growth of Dendritic Processes. Int J Mol Sci 2023; 24:12940. [PMID: 37629119 PMCID: PMC10455170 DOI: 10.3390/ijms241612940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 08/15/2023] [Indexed: 08/27/2023] Open
Abstract
A major route for the influx of calcium ions into neurons uses the STIM-Orai1 voltage-independent channel. Once cytosolic calcium ([Ca2+]i) elevates, it activates mitochondrial and endoplasmic calcium stores to affect downstream molecular pathways. In the present study, we employed a novel drug, carbonyl cyanide chlorophenylhydrazone (CCCP), a mitochondrial uncoupler, to explore the role of mitochondria in cultured neuronal morphology. CCCP caused a sustained elevation of [Ca2+]i and, quite surprisingly, a massive increase in the density of dendritic filopodia and spines in the affected neurons. This morphological change can be prevented in cultures exposed to a calcium-free medium, Orai1 antagonist 2APB, or cells transfected with a mutant Orai1 plasmid. It is suggested that CCCP activates mitochondria through the influx of calcium to cause rapid growth of dendritic processes.
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Affiliation(s)
- Liliia Kushnireva
- Faculty of Biology, Perm State University, 614068 Perm, Russia;
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel;
| | - Eduard Korkotian
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel;
| | - Menahem Segal
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel;
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Coleman CE, Landin C, Neuer A, Sayegh FM, Marshall PA. Calmodulin kinase 2 genetically interacts with Rch1p to negatively regulate calcium import into Saccharomyces cerevisiae after extracellular calcium pulse. Arch Microbiol 2022; 204:519. [DOI: 10.1007/s00203-022-03095-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 06/20/2022] [Accepted: 06/21/2022] [Indexed: 01/18/2023]
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Padilla-Garfias F, Ríos-Cifuentes L, Sánchez NS, Calahorra M, Peña A. Study of the mechanism of ε-poly-l-lysine as an antifungal on Candida albicans and Saccharomyces cerevisiae. Biochim Biophys Acta Gen Subj 2022; 1866:130197. [PMID: 35732210 DOI: 10.1016/j.bbagen.2022.130197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 06/14/2022] [Accepted: 06/14/2022] [Indexed: 10/17/2022]
Abstract
The antimicrobial activity of ε-poly-l-lysine (EPL) has been documented, but its antifungal activity on yeast is not well defined and its mechanism of action has been vaguely explained. Our studies revealed that on both, Candida albicans and Saccharomyces cerevisiae, the minimum inhibitory concentration (MIC) and the minimum fungicidal concentration (MFC) were 250 μg·mL-1; EPL produced a K+ and Ca2+ efflux, and at higher concentrations also an efflux of material absorbing at 260 nm, small peptides, and phosphate is produced, along with the inhibition of fermentation and extracellular acidification and respiration. Moreover, growth was inhibited, reactive oxygen species (ROS) production increased, and cell viability decreased. The polycation also produced plasma membrane potential hyperpolarization. The effects were dependent both on the cell quantity and polycation concentration, as well as the media used. The plasma membrane disruption was confirmed by TEM and PI staining.
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Affiliation(s)
- Francisco Padilla-Garfias
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, CDMX, 04510, México, CDMX, Mexico
| | - Laura Ríos-Cifuentes
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, CDMX, 04510, México, CDMX, Mexico
| | - Norma Silvia Sánchez
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, CDMX, 04510, México, CDMX, Mexico
| | - Martha Calahorra
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, CDMX, 04510, México, CDMX, Mexico
| | - Antonio Peña
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, CDMX, 04510, México, CDMX, Mexico.
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5
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Coordinated glucose-induced Ca 2+ and pH responses in yeast Saccharomyces cerevisiae. Cell Calcium 2021; 100:102479. [PMID: 34610487 DOI: 10.1016/j.ceca.2021.102479] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 09/23/2021] [Accepted: 09/24/2021] [Indexed: 12/13/2022]
Abstract
Ca2+ and pH homeostasis are closely intertwined and this interrelationship is crucial in the cells' ability to adapt to varying environmental conditions. To further understand this Ca2+-pH link, cytosolic Ca2+ was monitored using the aequorin-based bioluminescent assay in parallel with fluorescence reporter-based assays to monitor plasma membrane potentials and intracellular (cytosolic and vacuolar) pH in yeast Saccharomyces cerevisiae. At external pH 5, starved yeast cells displayed depolarized membrane potentials and responded to glucose re-addition with small Ca2+ transients accompanied by cytosolic alkalinization and profound vacuolar acidification. In contrast, starved cells at external pH 7 were hyperpolarized and glucose re-addition induced large Ca2+ transients and vacuolar alkalinization. In external Ca2+-free medium, glucose-induced pH responses were not affected but Ca2+ transients were abolished, indicating that the intracellular [Ca2+] increase was not prerequisite for activation of the two primary proton pumps, being Pma1 at the plasma membrane and the vacuolar and Golgi localized V-ATPases. A reduction in Pma1 expression resulted in membrane depolarization and reduced Ca2+ transients, indicating that the membrane hyperpolarization generated by Pma1 activation governed the Ca2+ influx that is associated with glucose-induced Ca2+ transients. Loss of V-ATPase activity through concanamycin A inhibition did not alter glucose-induced cytosolic pH responses but affected vacuolar pH changes and Ca2+ transients, indicating that the V-ATPase established vacuolar proton gradient is substantial for organelle H+/Ca2+ exchange. Finally, a systematic analysis of yeast deletion strains allowed us to reveal an essential role for both the vacuolar H+/Ca2+ exchanger Vcx1 and the Golgi exchanger Gdt1 in the dissipation of intracellular Ca2+.
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Protonophore FCCP provides fitness advantage to PDR-deficient yeast cells. J Bioenerg Biomembr 2020; 52:383-395. [DOI: 10.1007/s10863-020-09849-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 08/06/2020] [Indexed: 01/02/2023]
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7
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Chakraborty J, Caicci F, Roy M, Ziviani E. Investigating mitochondrial autophagy by routine transmission electron microscopy: Seeing is believing? Pharmacol Res 2020; 160:105097. [PMID: 32739423 DOI: 10.1016/j.phrs.2020.105097] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 07/15/2020] [Accepted: 07/22/2020] [Indexed: 01/13/2023]
Abstract
Mitochondrial autophagy is affected in many diseases. In the past few years, the multiple-steps process of selective degradation of mitochondria has been dissected in details by combining outcomes from different approaches. Perhaps one of the most rigorous methods to clearly visualise mitochondria undergoing autophagic engulfment and degradation, is transmission electron microscopy (TEM). In this opinion paper, we want to give a brief summary of the mitophagic process, and by which means mitophagy can be addressed, including TEM analysis. We will report examples of autophagy and mitophagy-related TEM images, and discuss how to decipher the different steps of the mitophagic process by routine TEM. In our opinion, this technique can be used as a powerful confirmatory approach for mitochondrial autophagy and can provide details of the organelle fate throughout the course of mitophagy with no substantial sample manipulation.
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Affiliation(s)
- Joy Chakraborty
- Department of Cell Biology and Physiology, CSIR-Indian Institute of Chemical Biology-TRUE Campus, Sector V, Salt Lake, Kolkata, India
| | | | - Moumita Roy
- Department of Cell Biology and Physiology, CSIR-Indian Institute of Chemical Biology-TRUE Campus, Sector V, Salt Lake, Kolkata, India
| | - Elena Ziviani
- Department of Biology, University of Padova, Padova, Italy.
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Castanheira DD, Santana EP, Godoy-Santos F, Diniz RHS, Faria-Oliveira F, Pereira RR, Trópia MJM, Castro IM, Brandão RL. Lpx1p links glucose-induced calcium signaling and plasma membrane H+-ATPase activation in Saccharomyces cerevisiae cells. FEMS Yeast Res 2018; 18:4643176. [PMID: 29177424 DOI: 10.1093/femsyr/fox088] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 11/17/2017] [Indexed: 11/12/2022] Open
Abstract
In yeast, as in other eukaryotes, calcium plays an essential role in signaling transduction to regulate different processes. Many pieces of evidence suggest that glucose-induced activation of plasma membrane H+-ATPase, essential for yeast physiology, is related to calcium signaling. Until now, no protein that could be regulated by calcium in this context has been identified. Lpx1p, a serine-protease that is also involved in the glucose-induced activation of the plasma membrane H+-ATPase, could be a candidate to respond to intracellular calcium signaling involved in this process. In this work, by using different approaches, we obtained many pieces of evidence suggesting that the requirement of calcium signaling for activation of the plasma membrane H+-ATPase is due to its requirement for activation of Lpx1p. According to the current model, activation of Lpx1p would cause hydrolysis of an acetylated tubulin that maintains the plasma membrane H+-ATPase in an inactive state. Therefore, after its activation, Lpx1p would hydrolyze the acetylated tubulin making the plasma membrane H+-ATPase accessible for phosphorylation by at least one protein kinase.
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Affiliation(s)
- Diogo Dias Castanheira
- Laboratório de Biologia Celular e Molecular, Núcleo de Pesquisas em Ciências Biológicas, Escola de Farmácia, Universidade Federal de Ouro Preto, Campus do Morro do Cruzeiro, Ouro Preto, MG 35.400-000, Brazil
| | - Eduardo Perovano Santana
- Laboratório de Biologia Celular e Molecular, Núcleo de Pesquisas em Ciências Biológicas, Escola de Farmácia, Universidade Federal de Ouro Preto, Campus do Morro do Cruzeiro, Ouro Preto, MG 35.400-000, Brazil
| | - Fernanda Godoy-Santos
- Laboratório de Biologia Celular e Molecular, Núcleo de Pesquisas em Ciências Biológicas, Escola de Farmácia, Universidade Federal de Ouro Preto, Campus do Morro do Cruzeiro, Ouro Preto, MG 35.400-000, Brazil
| | - Raphael Hermano Santos Diniz
- Laboratório de Biologia Celular e Molecular, Núcleo de Pesquisas em Ciências Biológicas, Escola de Farmácia, Universidade Federal de Ouro Preto, Campus do Morro do Cruzeiro, Ouro Preto, MG 35.400-000, Brazil
| | - Fábio Faria-Oliveira
- Laboratório de Biologia Celular e Molecular, Núcleo de Pesquisas em Ciências Biológicas, Escola de Farmácia, Universidade Federal de Ouro Preto, Campus do Morro do Cruzeiro, Ouro Preto, MG 35.400-000, Brazil
| | - Renata Rebeca Pereira
- Laboratório de Biologia Celular e Molecular, Núcleo de Pesquisas em Ciências Biológicas, Escola de Farmácia, Universidade Federal de Ouro Preto, Campus do Morro do Cruzeiro, Ouro Preto, MG 35.400-000, Brazil
| | - Maria José Magalhães Trópia
- Laboratório de Biologia Celular e Molecular, Núcleo de Pesquisas em Ciências Biológicas, Escola de Farmácia, Universidade Federal de Ouro Preto, Campus do Morro do Cruzeiro, Ouro Preto, MG 35.400-000, Brazil
| | - Ieso Miranda Castro
- Laboratório de Biologia Celular e Molecular, Núcleo de Pesquisas em Ciências Biológicas, Escola de Farmácia, Universidade Federal de Ouro Preto, Campus do Morro do Cruzeiro, Ouro Preto, MG 35.400-000, Brazil
| | - Rogelio Lopes Brandão
- Laboratório de Biologia Celular e Molecular, Núcleo de Pesquisas em Ciências Biológicas, Escola de Farmácia, Universidade Federal de Ouro Preto, Campus do Morro do Cruzeiro, Ouro Preto, MG 35.400-000, Brazil
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Zahumenský J, Jančíková I, Drietomská A, Švenkrtová A, Hlaváček O, Hendrych T, Plášek J, Sigler K, Gášková D. Yeast Tok1p channel is a major contributor to membrane potential maintenance under chemical stress. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:1974-1985. [PMID: 28669766 DOI: 10.1016/j.bbamem.2017.06.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 06/02/2017] [Accepted: 06/27/2017] [Indexed: 11/17/2022]
Abstract
Tok1p is a highly specific yeast plasma membrane potassium channel with strong outward directionality. Its opening is induced by membrane depolarization. Although the biophysical properties of Tok1p are well-described, its potentially important physiological role is currently largely unexplored. To address this issue, we examined the Tok1p activity following chemically-induced depolarization by measuring changes of plasma membrane potential (ΔΨ) using the diS-C3(3) fluorescence assay in a Tok1p-expressing and a Tok1p-deficient strain. We report that Tok1p channel activity in response to chemical stress does not depend solely on the extent of depolarization, as might have been expected, but may also be negatively influenced by accompanying effects of the used compound. The stressors may interact with the plasma membrane or the channel itself, or cause cytosolic acidification. All of these effects may negatively influence the Tok1p channel opening. While ODDC-induced depolarization exhibits the cleanest Tok1p activation, restoring an astonishing 75% of lost ΔΨ, higher BAC concentrations reduce Tok1p activity, probably because of direct interactions with the channel and/or its lipid microenvironment. This is not only the first study of the physiological role of Tok1p in ΔΨ maintenance under chemical stress, but also the first estimate of the extent of depolarization the channel is able to counterbalance.
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Affiliation(s)
- Jakub Zahumenský
- Charles University, Faculty of Mathematics and Physics, Institute of Physics, Prague 121 16, Czech Republic
| | - Iva Jančíková
- Charles University, Faculty of Mathematics and Physics, Institute of Physics, Prague 121 16, Czech Republic
| | - Andrea Drietomská
- Charles University, Faculty of Mathematics and Physics, Institute of Physics, Prague 121 16, Czech Republic
| | - Andrea Švenkrtová
- Institute of Microbiology, CR Academy of Sciences, Prague 142 20, Czech Republic; Institute of Chemical Technology, Faculty of Food and Biochemical Technology, Prague 166 28, Czech Republic
| | - Otakar Hlaváček
- Institute of Microbiology, CR Academy of Sciences, Prague 142 20, Czech Republic
| | - Tomáš Hendrych
- Department of Genetics and Microbiology, Faculty of Science, Charles University, Prague 128 44, Czech Republic
| | - Jaromír Plášek
- Charles University, Faculty of Mathematics and Physics, Institute of Physics, Prague 121 16, Czech Republic
| | - Karel Sigler
- Institute of Microbiology, CR Academy of Sciences, Prague 142 20, Czech Republic
| | - Dana Gášková
- Charles University, Faculty of Mathematics and Physics, Institute of Physics, Prague 121 16, Czech Republic.
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Yenush L. Potassium and Sodium Transport in Yeast. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 892:187-228. [DOI: 10.1007/978-3-319-25304-6_8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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11
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Mazón MJ, Eraso P, Portillo F. Specific phosphoantibodies reveal two phosphorylation sites in yeast Pma1 in response to glucose. FEMS Yeast Res 2015; 15:fov030. [PMID: 26019146 DOI: 10.1093/femsyr/fov030] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/21/2015] [Indexed: 11/14/2022] Open
Abstract
Glucose triggers post-translational modifications of the Saccharomyces cerevisiae plasma membrane H(+)-ATPase (Pma1) that lead to an increase in enzyme activity. The activation results from changes in two kinetic parameters: an increase in the affinity of the enzyme for ATP, depending on Ser899, and an increase in the Vmax involving Ser911/Thr912. Using phosphospecific antibodies, we show that Ser899 and Ser911/Thr912 are phosphorylated in vivo during glucose activation and that protein phosphatase Glc7 is involved in the dephosphorylation of Ser899 upon glucose starvation.
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Affiliation(s)
- María J Mazón
- Departamento de Bioquímica and Instituto de Investigaciones Biomédicas 'Alberto Sols', Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, Arturo Duperier, 4, 28029 Madrid, Spain
| | - Pilar Eraso
- Departamento de Bioquímica and Instituto de Investigaciones Biomédicas 'Alberto Sols', Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, Arturo Duperier, 4, 28029 Madrid, Spain
| | - Francisco Portillo
- Departamento de Bioquímica and Instituto de Investigaciones Biomédicas 'Alberto Sols', Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, Arturo Duperier, 4, 28029 Madrid, Spain
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Pereira RR, Castanheira D, Teixeira JA, Bouillet LEM, Ribeiro EMC, Trópia MMJ, Alvarez F, Correa LFM, Mota BEF, Conceição LEFR, Castro IM, Brandão RL. Detailed search for protein kinase(s) involved in plasma membrane H+−ATPase activity regulation of yeast cells. FEMS Yeast Res 2015; 15:fov003. [DOI: 10.1093/femsyr/fov003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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13
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Walker ME, Nguyen TD, Liccioli T, Schmid F, Kalatzis N, Sundstrom JF, Gardner JM, Jiranek V. Genome-wide identification of the Fermentome; genes required for successful and timely completion of wine-like fermentation by Saccharomyces cerevisiae. BMC Genomics 2014. [DOI: 10.1186/1471-2164-15-552 and 1880=1880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023] Open
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14
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Walker ME, Nguyen TD, Liccioli T, Schmid F, Kalatzis N, Sundstrom JF, Gardner JM, Jiranek V. Genome-wide identification of the Fermentome; genes required for successful and timely completion of wine-like fermentation by Saccharomyces cerevisiae. BMC Genomics 2014. [DOI: 10.1186/1471-2164-15-552 order by 1-- -] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023] Open
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15
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Walker ME, Nguyen TD, Liccioli T, Schmid F, Kalatzis N, Sundstrom JF, Gardner JM, Jiranek V. Genome-wide identification of the Fermentome; genes required for successful and timely completion of wine-like fermentation by Saccharomyces cerevisiae. BMC Genomics 2014. [DOI: 10.1186/1471-2164-15-552 order by 8029-- -] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023] Open
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16
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Walker ME, Nguyen TD, Liccioli T, Schmid F, Kalatzis N, Sundstrom JF, Gardner JM, Jiranek V. Genome-wide identification of the Fermentome; genes required for successful and timely completion of wine-like fermentation by Saccharomyces cerevisiae. BMC Genomics 2014. [DOI: 10.1186/1471-2164-15-552 order by 8029-- #] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023] Open
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17
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Walker ME, Nguyen TD, Liccioli T, Schmid F, Kalatzis N, Sundstrom JF, Gardner JM, Jiranek V. Genome-wide identification of the Fermentome; genes required for successful and timely completion of wine-like fermentation by Saccharomyces cerevisiae. BMC Genomics 2014. [DOI: 10.1186/1471-2164-15-552 order by 1-- gadu] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023] Open
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18
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Walker ME, Nguyen TD, Liccioli T, Schmid F, Kalatzis N, Sundstrom JF, Gardner JM, Jiranek V. Genome-wide identification of the Fermentome; genes required for successful and timely completion of wine-like fermentation by Saccharomyces cerevisiae. BMC Genomics 2014. [DOI: 10.1186/1471-2164-15-552 order by 1-- #] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023] Open
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19
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Walker ME, Nguyen TD, Liccioli T, Schmid F, Kalatzis N, Sundstrom JF, Gardner JM, Jiranek V. Genome-wide identification of the Fermentome; genes required for successful and timely completion of wine-like fermentation by Saccharomyces cerevisiae. BMC Genomics 2014. [DOI: 10.1186/1471-2164-15-552 order by 8029-- awyx] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023] Open
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20
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Walker ME, Nguyen TD, Liccioli T, Schmid F, Kalatzis N, Sundstrom JF, Gardner JM, Jiranek V. Genome-wide identification of the Fermentome; genes required for successful and timely completion of wine-like fermentation by Saccharomyces cerevisiae. BMC Genomics 2014; 15:552. [PMID: 24993029 PMCID: PMC4099481 DOI: 10.1186/1471-2164-15-552] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Accepted: 06/27/2014] [Indexed: 12/21/2022] Open
Abstract
Background Wine fermentation is a harsh ecological niche to which wine yeast are well adapted. The initial high osmotic pressure and acidity of grape juice is followed by nutrient depletion and increasing concentrations of ethanol as the fermentation progresses. Yeast’s adaptation to these and many other environmental stresses, enables successful completion of high-sugar fermentations. Earlier transcriptomic and growth studies have tentatively identified genes important for high-sugar fermentation. Whilst useful, such studies did not consider extended growth (>5 days) in a temporally dynamic multi-stressor environment such as that found in many industrial fermentation processes. Here, we identify genes whose deletion has minimal or no effect on growth, but results in failure to achieve timely completion of the fermentation of a chemically defined grape juice with 200 g L−1 total sugar. Results Micro- and laboratory-scale experimental fermentations were conducted to identify 72 clones from ~5,100 homozygous diploid single-gene yeast deletants, which exhibited protracted fermentation in a high-sugar medium. Another 21 clones (related by gene function, but initially eliminated from the screen because of possible growth defects) were also included. Clustering and numerical enrichment of genes annotated to specific Gene Ontology (GO) terms highlighted the vacuole’s role in ion homeostasis and pH regulation, through vacuole acidification. Conclusion We have identified 93 genes whose deletion resulted in the duration of fermentation being at least 20% longer than the wild type. An extreme phenotype, ‘stuck’ fermentation, was also observed when DOA4, NPT1, PLC1, PTK2, SIN3, SSQ1, TPS1, TPS2 or ZAP1 were deleted. These 93 Fermentation Essential Genes (FEG) are required to complete an extended high-sugar (wine-like) fermentation. Their importance is highlighted in our Fermentation Relevant Yeast Genes (FRYG) database, generated from literature and the fermentation-relevant phenotypic characteristics of null mutants described in the Saccharomyces Genome Database. The 93-gene set is collectively referred to as the ‘Fermentome’. The fact that 10 genes highlighted in this study have not previously been linked to fermentation-related stresses, supports our experimental rationale. These findings, together with investigations of the genetic diversity of industrial strains, are crucial for understanding the mechanisms behind yeast’s response and adaptation to stresses imposed during high-sugar fermentations. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-552) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | - Vladimir Jiranek
- School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, SA 5064, Australia.
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Gómez-Sánchez R, Gegg ME, Bravo-San Pedro JM, Niso-Santano M, Alvarez-Erviti L, Pizarro-Estrella E, Gutiérrez-Martín Y, Alvarez-Barrientos A, Fuentes JM, González-Polo RA, Schapira AHV. Mitochondrial impairment increases FL-PINK1 levels by calcium-dependent gene expression. Neurobiol Dis 2013; 62:426-40. [PMID: 24184327 PMCID: PMC3898697 DOI: 10.1016/j.nbd.2013.10.021] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Revised: 10/06/2013] [Accepted: 10/22/2013] [Indexed: 01/02/2023] Open
Abstract
Mutations of the PTEN-induced kinase 1 (PINK1) gene are a cause of autosomal recessive Parkinson's disease (PD). This gene encodes a mitochondrial serine/threonine kinase, which is partly localized to mitochondria, and has been shown to play a role in protecting neuronal cells from oxidative stress and cell death, perhaps related to its role in mitochondrial dynamics and mitophagy. In this study, we report that increased mitochondrial PINK1 levels observed in human neuroblastoma SH-SY5Y cells after carbonyl cyanide m-chlorophelyhydrazone (CCCP) treatment were due to de novo protein synthesis, and not just increased stabilization of full length PINK1 (FL-PINK1). PINK1 mRNA levels were significantly increased by 4-fold after 24h. FL-PINK1 protein levels at this time point were significantly higher than vehicle-treated, or cells treated with CCCP for 3h, despite mitochondrial content being decreased by 29%. We have also shown that CCCP dissipated the mitochondrial membrane potential (Δψm) and induced entry of extracellular calcium through L/N-type calcium channels. The calcium chelating agent BAPTA-AM impaired the CCCP-induced PINK1 mRNA and protein expression. Furthermore, CCCP treatment activated the transcription factor c-Fos in a calcium-dependent manner. These data indicate that PINK1 expression is significantly increased upon CCCP-induced mitophagy in a calcium-dependent manner. This increase in expression continues after peak Parkin mitochondrial translocation, suggesting a role for PINK1 in mitophagy that is downstream of ubiquitination of mitochondrial substrates. This sensitivity to intracellular calcium levels supports the hypothesis that PINK1 may also play a role in cellular calcium homeostasis and neuroprotection.
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Affiliation(s)
- Rubén Gómez-Sánchez
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Departamento de Bioquímica y Biología Molecular y Genética, Universidad de Extremadura, F. Enfermería y Terapia Ocupacional, 10003 Cáceres, Spain
| | - Matthew E Gegg
- Department of Clinical Neurosciences, Institute of Neurology, University College London, London NW3 2PF, UK
| | - José M Bravo-San Pedro
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Departamento de Bioquímica y Biología Molecular y Genética, Universidad de Extremadura, F. Enfermería y Terapia Ocupacional, 10003 Cáceres, Spain; INSERM, U848, Institut Gustave Roussy, Université Paris Sud, Paris 11, F-94805 Villejuif, France
| | - Mireia Niso-Santano
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Departamento de Bioquímica y Biología Molecular y Genética, Universidad de Extremadura, F. Enfermería y Terapia Ocupacional, 10003 Cáceres, Spain; INSERM, U848, Institut Gustave Roussy, Université Paris Sud, Paris 11, F-94805 Villejuif, France
| | - Lydia Alvarez-Erviti
- Department of Clinical Neurosciences, Institute of Neurology, University College London, London NW3 2PF, UK
| | - Elisa Pizarro-Estrella
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Departamento de Bioquímica y Biología Molecular y Genética, Universidad de Extremadura, F. Enfermería y Terapia Ocupacional, 10003 Cáceres, Spain
| | - Yolanda Gutiérrez-Martín
- Servicio de Técnicas Aplicadas a las Biociencias, Universidad de Extremadura, 06071 Badajoz, Spain
| | | | - José M Fuentes
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Departamento de Bioquímica y Biología Molecular y Genética, Universidad de Extremadura, F. Enfermería y Terapia Ocupacional, 10003 Cáceres, Spain.
| | - Rosa Ana González-Polo
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Departamento de Bioquímica y Biología Molecular y Genética, Universidad de Extremadura, F. Enfermería y Terapia Ocupacional, 10003 Cáceres, Spain.
| | - Anthony H V Schapira
- Department of Clinical Neurosciences, Institute of Neurology, University College London, London NW3 2PF, UK
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Campetelli AN, Monesterolo NE, Previtali G, Santander VS, Amaiden MR, Arce CA, Valdez-Taubas J, Casale CH. Activation of H+-ATPase by glucose in Saccharomyces cerevisiae involves a membrane serine protease. Biochim Biophys Acta Gen Subj 2013; 1830:3593-603. [DOI: 10.1016/j.bbagen.2013.03.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Revised: 02/05/2013] [Accepted: 03/07/2013] [Indexed: 12/26/2022]
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Monitoring of real changes of plasma membrane potential by diS-C3(3) fluorescence in yeast cell suspensions. J Bioenerg Biomembr 2012; 44:559-69. [DOI: 10.1007/s10863-012-9458-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2012] [Accepted: 06/21/2012] [Indexed: 11/27/2022]
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Bouillet L, Cardoso A, Perovano E, Pereira R, Ribeiro E, Trópia M, Fietto L, Tisi R, Martegani E, Castro I, Brandão R. The involvement of calcium carriers and of the vacuole in the glucose-induced calcium signaling and activation of the plasma membrane H+-ATPase in Saccharomyces cerevisiae cells. Cell Calcium 2012; 51:72-81. [DOI: 10.1016/j.ceca.2011.10.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2011] [Accepted: 10/31/2011] [Indexed: 11/30/2022]
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Martins A, Machado L, Costa S, Cerca P, Spengler G, Viveiros M, Amaral L. Role of calcium in the efflux system of Escherichia coli. Int J Antimicrob Agents 2011; 37:410-4. [PMID: 21419607 DOI: 10.1016/j.ijantimicag.2011.01.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2010] [Revised: 01/11/2011] [Accepted: 01/13/2011] [Indexed: 10/18/2022]
Abstract
Efflux of antibiotics by Escherichia coli AG100 is performed by a variety of efflux pumps, ensuring survival of the bacterium in widely diverse media. At pH 5, efflux is independent of metabolic energy during the period of time the assay is conducted; at pH 8 it is totally dependent upon metabolic energy. Because calcium ions (Ca(2+)) are important for membrane transport channels and the activity of ATPases that provide energy functions, the role of Ca(2+) in the extrusion of an efflux pump substrate under conditions that challenge the bacterium was investigated. Real-time accumulation and efflux of ethidium bromide (EtBr) by E. coli K-12 AG100 strain [argE3 thi-1 rpsL xyl mtl Δ(gal-uvrB) supE44] was determined by a semi-automated fluorometric method in the presence and absence of Ca(2+) and agents that are known to inhibit access of calcium to enzymes that provide energy. Chlorpromazine (CPZ), an inhibitor of calcium binding to proteins (calcium-dependent enzymes), and ethylene diamine tetra-acetic acid (EDTA), a chelator of Ca(2+), increased accumulation and efflux of EtBr at pH 8 but not at pH 5. Ca(2+) reverses these effects when the assay is conducted at pH 8. In conclusion, the activity of the efflux pump system of E. coli is dependent upon metabolic energy at pH 8. Because at pH 8 hydrolysis of ATP is favoured and contributes protons for activation of the AcrAB-TolC efflux pump, CPZ is suspected of having its effects on accumulation/efflux of EtBr by indirectly affecting ATPase activity that is dependent upon Ca(2+).
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Affiliation(s)
- Ana Martins
- Unit of Mycobacteriology, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Rua da Junqueira 96, 1349-008 Lisbon, Portugal
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Cunningham KW. Acidic calcium stores of Saccharomyces cerevisiae. Cell Calcium 2011; 50:129-38. [PMID: 21377728 DOI: 10.1016/j.ceca.2011.01.010] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2010] [Revised: 01/25/2011] [Accepted: 01/31/2011] [Indexed: 02/06/2023]
Abstract
Fungi and animals constitute sister kingdoms in the eukaryotic domain of life. The major classes of transporters, channels, sensors, and effectors that move and respond to calcium ions were already highly networked in the common ancestor of fungi and animals. Since that time, some key components of the network have been moved, altered, relocalized, lost, or duplicated in the fungal and animal lineages and at the same time some of the regulatory circuitry has been dramatically rewired. Today the calcium transport and signaling networks in fungi provide a fresh perspective on the scene that has emerged from studies of the network in animal cells. This review provides an overview of calcium signaling networks in fungi, particularly the model yeast Saccharomyces cerevisiae, with special attention to the dominant roles of acidic calcium stores in fungal cell physiology.
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Affiliation(s)
- Kyle W Cunningham
- Department of Biology, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA.
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Zhou J, Liu L, Chen J. Improved ATP supply enhances acid tolerance of Candida glabrata during pyruvic acid production. J Appl Microbiol 2010; 110:44-53. [PMID: 20880146 DOI: 10.1111/j.1365-2672.2010.04865.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
AIMS A major problem in industrial fermentation of organic acids with micro-organisms is to ensure a suitable pH in the culture broth. To circumvent this problem, we investigated the effect of citrate, which is a widely used auxiliary energy co-substrate, on cell growth, organic acid production and pH homeostasis among extracellular environment, cytoplasm and vacuole, in the pyruvic acid production by Candida glabrata CCTCC M202019 under different pH conditions. METHODS AND RESULTS Analysis of intracellular ATP regeneration, cytoplasmic and vacuolar pH values under different culture conditions points towards a relief of stress when C. glabrata is exposed to lower pH, if citrate is added. When 50 mmol l(-1) citrate was added to the culture medium, the intracellular ATP concentrations increased by 20·5% (pH 5·5), 20·4% (pH 5·0) and 39·3% (pH 4·5), and higher pH gradients among the culture broth, cell cytoplasm and vacuoles resulted. As a consequence, the cell growth and pyruvic acid production of C. glabrata CCTCC M202019 were significantly improved under pH 5·0 and 4·5. CONCLUSIONS The acid tolerance of yeast can be improved by enhancing the ATP supply, which helps to maintain higher pH gradients in the system. SIGNIFICANCE AND IMPACT OF THE STUDY The results presented here expand our understanding of the physiological characteristics in eukaryotic micro-organisms under low pH conditions and provide a potential route for the further improvement of organic acids production process by process optimization or metabolic engineering.
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Affiliation(s)
- J Zhou
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
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Abstract
The maintenance of appropriate intracellular concentrations of alkali metal cations, principally K(+) and Na(+), is of utmost importance for living cells, since they determine cell volume, intracellular pH, and potential across the plasma membrane, among other important cellular parameters. Yeasts have developed a number of strategies to adapt to large variations in the concentrations of these cations in the environment, basically by controlling transport processes. Plasma membrane high-affinity K(+) transporters allow intracellular accumulation of this cation even when it is scarce in the environment. Exposure to high concentrations of Na(+) can be tolerated due to the existence of an Na(+), K(+)-ATPase and an Na(+), K(+)/H(+)-antiporter, which contribute to the potassium balance as well. Cations can also be sequestered through various antiporters into intracellular organelles, such as the vacuole. Although some uncertainties still persist, the nature of the major structural components responsible for alkali metal cation fluxes across yeast membranes has been defined within the last 20 years. In contrast, the regulatory components and their interactions are, in many cases, still unclear. Conserved signaling pathways (e.g., calcineurin and HOG) are known to participate in the regulation of influx and efflux processes at the plasma membrane level, even though the molecular details are obscure. Similarly, very little is known about the regulation of organellar transport and homeostasis of alkali metal cations. The aim of this review is to provide a comprehensive and up-to-date vision of the mechanisms responsible for alkali metal cation transport and their regulation in the model yeast Saccharomyces cerevisiae and to establish, when possible, comparisons with other yeasts and higher plants.
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Current awareness on yeast. Yeast 2008. [DOI: 10.1002/yea.1558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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