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Gorospe CM, Carvalho G, Herrera Curbelo A, Marchhart L, Mendes IC, Niedźwiecka K, Wanrooij PH. Mitochondrial membrane potential acts as a retrograde signal to regulate cell cycle progression. Life Sci Alliance 2023; 6:e202302091. [PMID: 37696576 PMCID: PMC10494934 DOI: 10.26508/lsa.202302091] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 08/29/2023] [Accepted: 08/30/2023] [Indexed: 09/13/2023] Open
Abstract
Mitochondria are central to numerous metabolic pathways whereby mitochondrial dysfunction has a profound impact and can manifest in disease. The consequences of mitochondrial dysfunction can be ameliorated by adaptive responses that rely on crosstalk from the mitochondria to the rest of the cell. Such mito-cellular signalling slows cell cycle progression in mitochondrial DNA-deficient (ρ0) Saccharomyces cerevisiae cells, but the initial trigger of the response has not been thoroughly studied. Here, we show that decreased mitochondrial membrane potential (ΔΨm) acts as the initial signal of mitochondrial stress that delays G1-to-S phase transition in both ρ0 and control cells containing mtDNA. Accordingly, experimentally increasing ΔΨm was sufficient to restore timely cell cycle progression in ρ0 cells. In contrast, cellular levels of oxidative stress did not correlate with the G1-to-S delay. Restored G1-to-S transition in ρ0 cells with a recovered ΔΨm is likely attributable to larger cell size, whereas the timing of G1/S transcription remained delayed. The identification of ΔΨm as a regulator of cell cycle progression may have implications for disease states involving mitochondrial dysfunction.
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Affiliation(s)
- Choco Michael Gorospe
- https://ror.org/05kb8h459 Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Gustavo Carvalho
- https://ror.org/05kb8h459 Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Alicia Herrera Curbelo
- https://ror.org/05kb8h459 Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Lisa Marchhart
- https://ror.org/05kb8h459 Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Isabela C Mendes
- https://ror.org/05kb8h459 Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Katarzyna Niedźwiecka
- https://ror.org/05kb8h459 Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Paulina H Wanrooij
- https://ror.org/05kb8h459 Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
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2
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Leite AC, Costa V, Pereira C. Mitochondria and the cell cycle in budding yeast. Int J Biochem Cell Biol 2023; 161:106444. [PMID: 37419443 DOI: 10.1016/j.biocel.2023.106444] [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: 03/10/2023] [Revised: 06/05/2023] [Accepted: 07/03/2023] [Indexed: 07/09/2023]
Abstract
As centers for energy production and essential biosynthetic activities, mitochondria are vital for cell growth and proliferation. Accumulating evidence suggests an integrated regulation of these organelles and the nuclear cell cycle in distinct organisms. In budding yeast, a well-established example of this coregulation is the coordinated movement and positional control of mitochondria during the different phases of the cell cycle. The molecular determinants involved in the inheritance of the fittest mitochondria by the bud also seem to be cell cycle-regulated. In turn, loss of mtDNA or defects in mitochondrial structure or inheritance often lead to a cell cycle delay or arrest, indicating that mitochondrial function can also regulate cell cycle progression, possibly through the activation of cell cycle checkpoints. The up-regulation of mitochondrial respiration at G2/M, presumably to fulfil energetic requirements for progression at this phase, also supports a mitochondria-cell cycle interplay. Cell cycle-linked mitochondrial regulation is accomplished at the transcription level and through post-translational modifications, predominantly protein phosphorylation. Here, we address mitochondria-cell cycle interactions in the yeast Saccharomyces cerevisiae and discuss future challenges in the field.
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Affiliation(s)
- Ana Cláudia Leite
- i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal; IBMC, Instituto de Biologia Celular e Molecular, Universidade do Porto, Portugal; ICBAS, Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Portugal
| | - Vítor Costa
- i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal; IBMC, Instituto de Biologia Celular e Molecular, Universidade do Porto, Portugal; ICBAS, Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Portugal
| | - Clara Pereira
- i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal; IBMC, Instituto de Biologia Celular e Molecular, Universidade do Porto, Portugal.
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3
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Wagner ER, Gasch AP. Advances in S. cerevisiae Engineering for Xylose Fermentation and Biofuel Production: Balancing Growth, Metabolism, and Defense. J Fungi (Basel) 2023; 9:786. [PMID: 37623557 PMCID: PMC10455348 DOI: 10.3390/jof9080786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 07/19/2023] [Accepted: 07/24/2023] [Indexed: 08/26/2023] Open
Abstract
Genetically engineering microorganisms to produce chemicals has changed the industrialized world. The budding yeast Saccharomyces cerevisiae is frequently used in industry due to its genetic tractability and unique metabolic capabilities. S. cerevisiae has been engineered to produce novel compounds from diverse sugars found in lignocellulosic biomass, including pentose sugars, like xylose, not recognized by the organism. Engineering high flux toward novel compounds has proved to be more challenging than anticipated since simply introducing pathway components is often not enough. Several studies show that the rewiring of upstream signaling is required to direct products toward pathways of interest, but doing so can diminish stress tolerance, which is important in industrial conditions. As an example of these challenges, we reviewed S. cerevisiae engineering efforts, enabling anaerobic xylose fermentation as a model system and showcasing the regulatory interplay's controlling growth, metabolism, and stress defense. Enabling xylose fermentation in S. cerevisiae requires the introduction of several key metabolic enzymes but also regulatory rewiring of three signaling pathways at the intersection of the growth and stress defense responses: the RAS/PKA, Snf1, and high osmolarity glycerol (HOG) pathways. The current studies reviewed here suggest the modulation of global signaling pathways should be adopted into biorefinery microbial engineering pipelines to increase efficient product yields.
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Affiliation(s)
- Ellen R. Wagner
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Audrey P. Gasch
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI 53706, USA
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4
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Casamayor A, Ariño J. When Phosphatases Go Mad: The Molecular Basis for Toxicity of Yeast Ppz1. Int J Mol Sci 2022; 23:ijms23084304. [PMID: 35457140 PMCID: PMC9029398 DOI: 10.3390/ijms23084304] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/04/2022] [Accepted: 04/08/2022] [Indexed: 02/04/2023] Open
Abstract
The fact that overexpression of the yeast Ser/Thr protein phosphatase Ppz1 induces a dramatic halt in cell proliferation was known long ago, but only work in the last few years has provided insight into the molecular basis for this toxicity. Overexpression of Ppz1 causes abundant changes in gene expression and modifies the phosphorylation state of more than 150 proteins, including key signaling protein kinases such as Hog1 or Snf1. Diverse cellular processes are altered: halt in translation, failure to properly adapt to low glucose supply, acidification of the cytosol, or depletion of intracellular potassium content are a few examples. Therefore, the toxicity derived from an excess of Ppz1 appears to be multifactorial, the characteristic cell growth blockage thus arising from the combination of various altered processes. Notably, overexpression of the Ppz1 regulatory subunit Hal3 fully counteracts the toxic effects of the phosphatase, and this process involves intracellular relocation of the phosphatase to internal membranes.
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Li L, Wang J, Yang Z, Zhao Y, Jiang H, Jiang L, Hou W, Ye R, He Q, Kupiec M, Luke B, Cao Q, Qi Z, Li Z, Lou H. Metabolic remodeling maintains a reducing environment for rapid activation of the yeast DNA replication checkpoint. EMBO J 2022; 41:e108290. [PMID: 35028974 PMCID: PMC8844976 DOI: 10.15252/embj.2021108290] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 11/04/2021] [Accepted: 12/09/2021] [Indexed: 12/31/2022] Open
Abstract
Nucleotide metabolism fuels normal DNA replication and is also primarily targeted by the DNA replication checkpoint when replication stalls. To reveal a comprehensive interconnection between genome maintenance and metabolism, we analyzed the metabolomic changes upon replication stress in the budding yeast S. cerevisiae. We found that upon treatment of cells with hydroxyurea, glucose is rapidly diverted to the oxidative pentose phosphate pathway (PPP). This effect is mediated by the AMP-dependent kinase, SNF1, which phosphorylates the transcription factor Mig1, thereby relieving repression of the gene encoding the rate-limiting enzyme of the PPP. Surprisingly, NADPH produced by the PPP is required for efficient recruitment of replication protein A (RPA) to single-stranded DNA, providing the signal for the activation of the Mec1/ATR-Rad53/CHK1 checkpoint signaling kinase cascade. Thus, SNF1, best known as a central energy controller, determines a fast mode of replication checkpoint activation through a redox mechanism. These findings establish that SNF1 provides a hub with direct links to cellular metabolism, redox, and surveillance of DNA replication in eukaryotes.
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Affiliation(s)
- Lili Li
- State Key Laboratory of AgrobiotechnologyCollege of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Jie Wang
- State Key Laboratory of Plant Physiology and BiochemistryCollege of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Zijia Yang
- State Key Laboratory of Plant Physiology and BiochemistryCollege of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Yiling Zhao
- Center for Quantitative Biology and Peking‐Tsinghua Center for Life SciencesAcademy for Advanced Interdisciplinary StudiesPeking UniversityBeijingChina
| | - Hui Jiang
- State Key Laboratory of AgrobiotechnologyCollege of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Luguang Jiang
- MOE Key Laboratory of Crop Heterosis and UtilizationNational Maize Improvement Center of ChinaCollege of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Wenya Hou
- Shenzhen University General HospitalGuangdong Key Laboratory for Genome Stability and Disease PreventionShenzhen University School of MedicineShenzhenChina
| | - Risheng Ye
- Department of Medical EducationTexas Tech University Health Sciences Center Paul L. Foster School of MedicineEl PasoTXUSA
| | - Qun He
- State Key Laboratory of AgrobiotechnologyCollege of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Martin Kupiec
- The Shmunis School of Biomedicine and Cancer ResearchTel Aviv UniversityRamat AvivIsrael
| | - Brian Luke
- Institute of Molecular Biology (IMB)MainzGermany,Institute of Developmental Biology and Neurobiology (IDN)Johannes Gutenberg UniversitätMainzGermany
| | - Qinhong Cao
- State Key Laboratory of AgrobiotechnologyCollege of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Zhi Qi
- Center for Quantitative Biology and Peking‐Tsinghua Center for Life SciencesAcademy for Advanced Interdisciplinary StudiesPeking UniversityBeijingChina
| | - Zhen Li
- State Key Laboratory of Plant Physiology and BiochemistryCollege of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Huiqiang Lou
- South China HospitalHealth Science CenterGuangdong Key Laboratory of Genome Instability and Disease PreventionShenzhen University School of MedicineShenzhenChina
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Chen X, Lu Z, Chen Y, Wu R, Luo Z, Lu Q, Guan N, Chen D. Deletion of the MBP1 Gene, Involved in the Cell Cycle, Affects Respiration and Pseudohyphal Differentiation in Saccharomyces cerevisiae. Microbiol Spectr 2021; 9:e0008821. [PMID: 34346754 PMCID: PMC8552743 DOI: 10.1128/spectrum.00088-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 05/03/2021] [Indexed: 11/20/2022] Open
Abstract
Mbp1p is a component of MBF (MluI cell cycle box binding factor, Mbp1p-Swi6p) and is well known to regulate the G1-S transition of the cell cycle. However, few studies have provided clues regarding its role in fermentation. This work aimed to recognize the function of the MBP1 gene in ethanol fermentation in a wild-type industrial Saccharomyces cerevisiae strain. MBP1 deletion caused an obvious decrease in the final ethanol concentration under oxygen-limited (without agitation), but not under aerobic, conditions (130 rpm). Furthermore, the mbp1Δ strain showed 84% and 35% decreases in respiration intensity under aerobic and oxygen-limited conditions, respectively. These findings indicate that MBP1 plays an important role in responding to variations in oxygen content and is involved in the regulation of respiration and fermentation. Unexpectedly, mbp1Δ also showed pseudohyphal growth, in which cells elongated and remained connected in a multicellular arrangement on yeast extract-peptone-dextrose (YPD) plates. In addition, mbp1Δ showed an increase in cell volume, associated with a decrease in the fraction of budded cells. These results provide more detailed information about the function of MBP1 and suggest some clues to efficiently improve ethanol production by industrially engineered yeast strains. IMPORTANCE Saccharomyces cerevisiae is an especially favorable organism used for ethanol production. However, inhibitors and high osmolarity conferred by fermentation broth, and high concentrations of ethanol as fermentation runs to completion, affect cell growth and ethanol production. Therefore, yeast strains with high performance, such as rapid growth, high tolerance, and high ethanol productivity, are highly desirable. Great efforts have been made to improve their performance by evolutionary engineering, and industrial strains may be a better start than laboratory ones for industrial-scale ethanol production. The significance of our research is uncovering the function of MBP1 in ethanol fermentation in a wild-type industrial S. cerevisiae strain, which may provide clues to engineer better-performance yeast in producing ethanol. Furthermore, the results that lacking MBP1 caused pseudohyphal growth on YPD plates could shed light on the development of xylose-fermenting S. cerevisiae, as using xylose as the sole carbon source also caused pseudohyphal growth.
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Affiliation(s)
- Xiaoling Chen
- National Engineering Research Center for Non-Food Biorefinery, Guangxi Academy of Sciences, Nanning, Guangxi, People’s Republic of China
| | - Zhilong Lu
- National Engineering Research Center for Non-Food Biorefinery, Guangxi Academy of Sciences, Nanning, Guangxi, People’s Republic of China
| | - Ying Chen
- National Engineering Research Center for Non-Food Biorefinery, Guangxi Academy of Sciences, Nanning, Guangxi, People’s Republic of China
| | - Renzhi Wu
- National Engineering Research Center for Non-Food Biorefinery, Guangxi Academy of Sciences, Nanning, Guangxi, People’s Republic of China
| | - Zhenzhen Luo
- National Engineering Research Center for Non-Food Biorefinery, Guangxi Academy of Sciences, Nanning, Guangxi, People’s Republic of China
| | - Qi Lu
- National Engineering Research Center for Non-Food Biorefinery, Guangxi Academy of Sciences, Nanning, Guangxi, People’s Republic of China
| | - Ni Guan
- National Engineering Research Center for Non-Food Biorefinery, Guangxi Academy of Sciences, Nanning, Guangxi, People’s Republic of China
| | - Dong Chen
- National Engineering Research Center for Non-Food Biorefinery, Guangxi Academy of Sciences, Nanning, Guangxi, People’s Republic of China
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7
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Simpson-Lavy K, Kupiec M. Noise buffering by biomolecular condensates in glucose sensing. Curr Opin Cell Biol 2020; 69:1-6. [PMID: 33388622 DOI: 10.1016/j.ceb.2020.12.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 11/26/2020] [Accepted: 12/01/2020] [Indexed: 02/05/2023]
Abstract
Many cellular processes involve buffering mechanisms against noise to enhance state stability. Such processes include the cell cycle and the switch between respiration and fermentation. In recent years, protein aggregation/condensation has emerged as an important regulatory mechanism. In this article, we examine the regulation of Std1, an activator of the Snf1/AMPK kinase, by sequestration into foci of liquid drops, and how foci of metabolic signaling and enzymatic proteins are regulated by chaperones, anti-aggregases and by phosphorylation.
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Affiliation(s)
- Kobi Simpson-Lavy
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Ramat Aviv, 69978, Israel
| | - Martin Kupiec
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Ramat Aviv, 69978, Israel.
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8
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Velázquez D, Albacar M, Zhang C, Calafí C, López-Malo M, Torres-Torronteras J, Martí R, Kovalchuk SI, Pinson B, Jensen ON, Daignan-Fornier B, Casamayor A, Ariño J. Yeast Ppz1 protein phosphatase toxicity involves the alteration of multiple cellular targets. Sci Rep 2020; 10:15613. [PMID: 32973189 PMCID: PMC7519054 DOI: 10.1038/s41598-020-72391-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Accepted: 08/31/2020] [Indexed: 12/13/2022] Open
Abstract
Control of the protein phosphorylation status is a major mechanism for regulation of cellular processes, and its alteration often lead to functional disorders. Ppz1, a protein phosphatase only found in fungi, is the most toxic protein when overexpressed in Saccharomyces cerevisiae. To investigate the molecular basis of this phenomenon, we carried out combined genome-wide transcriptomic and phosphoproteomic analyses. We have found that Ppz1 overexpression causes major changes in gene expression, affecting ~ 20% of the genome, together with oxidative stress and increase in total adenylate pools. Concurrently, we observe changes in the phosphorylation pattern of near 400 proteins (mainly dephosphorylated), including many proteins involved in mitotic cell cycle and bud emergence, rapid dephosphorylation of Snf1 and its downstream transcription factor Mig1, and phosphorylation of Hog1 and its downstream transcription factor Sko1. Deletion of HOG1 attenuates the growth defect of Ppz1-overexpressing cells, while that of SKO1 aggravates it. Our results demonstrate that Ppz1 overexpression has a widespread impact in the yeast cells and reveals new aspects of the regulation of the cell cycle.
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Affiliation(s)
- Diego Velázquez
- Institut de Biotecnologia i Biomedicina & Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Marcel Albacar
- Institut de Biotecnologia i Biomedicina & Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Chunyi Zhang
- Institut de Biotecnologia i Biomedicina & Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Carlos Calafí
- Institut de Biotecnologia i Biomedicina & Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - María López-Malo
- Institut de Biotecnologia i Biomedicina & Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
- Institute of Bioengineering, School of Engineering, Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland
| | - Javier Torres-Torronteras
- Research Group on Neuromuscular and Mitochondrial Diseases, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, and Biomedical Network Research Centre on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Barcelona, Spain
| | - Ramón Martí
- Research Group on Neuromuscular and Mitochondrial Diseases, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, and Biomedical Network Research Centre on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Barcelona, Spain
| | - Sergey I Kovalchuk
- Department of Biochemistry & Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
- Laboratory of Bioinformatic Approaches in Combinatorial Chemistry and Biology, Department of Functioning of Living Systems, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Benoit Pinson
- Bordeaux University, IBGC CNRS UMR 5095, Bordeaux, France
- Service Analyses Metaboliques TBMcore CNRS UMS3427/INSERM US05, Université de Bordeaux, Bordeaux, France
| | - Ole N Jensen
- Department of Biochemistry & Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
| | | | - Antonio Casamayor
- Institut de Biotecnologia i Biomedicina & Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Joaquín Ariño
- Institut de Biotecnologia i Biomedicina & Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain.
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9
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Bonomelli B, Martegani E, Colombo S. Lack of SNF1 induces localization of active Ras in mitochondria and triggers apoptosis in the yeast Saccharomyces cerevisiae. Biochem Biophys Res Commun 2019; 523:130-134. [PMID: 31837801 DOI: 10.1016/j.bbrc.2019.12.023] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 12/05/2019] [Indexed: 11/26/2022]
Abstract
In previous papers we showed that activated Ras proteins are localized to the plasma membrane and in the nucleus in wild-type yeast cells growing exponentially on glucose, while an aberrant accumulation of activated Ras in mitochondria correlated to mitochondrial dysfunction, accumulation of ROS and regulated cell death. Here we show that also in a strain lacking Snf1, the homolog of the AMP-activated protein kinase (AMPK) in Saccharomyces cerevisiae, activated Ras proteins accumulate mainly in these organelles, suggesting an antiapoptotic role for this protein, beside its well-known function in glucose repression. Indeed, in this paper we show that Snf1 protects against apoptosis in Saccharomyces cerevisiae. In particular, following treatment with acetic acid, a well-known inducer of apoptosis in this microorganism, snf1Δ cells show a significant reduction in cell survival and a higher level of ROS when compared with wild-type cells. More importantly, untreated snf1Δ cells show a higher percentage of apoptotic cells compared with wild-type cells, which further increases upon treatment with acetic acid. In order to determine whether the role of Snf1 in regulated cell death is dependent on its catalytic activity, we characterized the Snf1-S214E strain, expressing a catalytically inactive form of Snf1. Data on active Ras proteins localization, cell survival, level of ROS and percentage of apoptotic cells are congruent and suggest that the antiapoptotic role of Snf1 is independent on its kinase activity.
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Affiliation(s)
- Barbara Bonomelli
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza Della Scienza 2, 20126, Milan, Italy
| | - Enzo Martegani
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza Della Scienza 2, 20126, Milan, Italy; SysBio Centre of Systems Biology, Piazza Della Scienza 2, 20126, Milan, Italy
| | - Sonia Colombo
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza Della Scienza 2, 20126, Milan, Italy; SysBio Centre of Systems Biology, Piazza Della Scienza 2, 20126, Milan, Italy.
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10
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Baro B, Játiva S, Calabria I, Vinaixa J, Bech-Serra JJ, de LaTorre C, Rodrigues J, Hernáez ML, Gil C, Barceló-Batllori S, Larsen MR, Queralt E. SILAC-based phosphoproteomics reveals new PP2A-Cdc55-regulated processes in budding yeast. Gigascience 2018; 7:4982941. [PMID: 29688323 PMCID: PMC5967524 DOI: 10.1093/gigascience/giy047] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 04/18/2018] [Indexed: 01/12/2023] Open
Abstract
Background Protein phosphatase 2A (PP2A) is a family of conserved serine/threonine phosphatases involved in several essential aspects of cell growth and proliferation. PP2ACdc55 phosphatase has been extensively related to cell cycle events in budding yeast; however, few PP2ACdc55 substrates have been identified. Here, we performed a quantitative mass spectrometry approach to reveal new substrates of PP2ACdc55 phosphatase and new PP2A-related processes in mitotic arrested cells. Results We identified 62 statistically significant PP2ACdc55 substrates involved mainly in actin-cytoskeleton organization. In addition, we validated new PP2ACdc55 substrates such as Slk19 and Lte1, involved in early and late anaphase pathways, and Zeo1, a component of the cell wall integrity pathway. Finally, we constructed docking models of Cdc55 and its substrate Mob1. We found that the predominant interface on Cdc55 is mediated by a protruding loop consisting of residues 84–90, thus highlighting the relevance of these aminoacids for substrate interaction. Conclusions We used phosphoproteomics of Cdc55-deficient cells to uncover new PP2ACdc55 substrates and functions in mitosis. As expected, several hyperphosphorylated proteins corresponded to Cdk1-dependent substrates, although other kinases’ consensus motifs were also enriched in our dataset, suggesting that PP2ACdc55 counteracts and regulates other kinases distinct from Cdk1. Indeed, Pkc1 emerged as a novel node of PP2ACdc55 regulation, highlighting a major role of PP2ACdc55 in actin cytoskeleton and cytokinesis, gene ontology terms significantly enriched in the PP2ACdc55-dependent phosphoproteome.
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Affiliation(s)
- Barbara Baro
- Cell Cycle Group, Cancer Epigenetics and Biology Program, Institut d'Investigacions Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Soraya Játiva
- Cell Cycle Group, Cancer Epigenetics and Biology Program, Institut d'Investigacions Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Inés Calabria
- Cell Cycle Group, Cancer Epigenetics and Biology Program, Institut d'Investigacions Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Judith Vinaixa
- Cell Cycle Group, Cancer Epigenetics and Biology Program, Institut d'Investigacions Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Joan-Josep Bech-Serra
- IDIBELL Proteomics Unit, Institut d'Investigacions Biomèdica de Bellvitge, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Carolina de LaTorre
- IDIBELL Proteomics Unit, Institut d'Investigacions Biomèdica de Bellvitge, L'Hospitalet de Llobregat, Barcelona, Spain
| | - João Rodrigues
- Structural Biology Department, School of Medicine, Stanford, California, USA
| | - María Luisa Hernáez
- Proteomics Unit, Parque Científico de Madrid, Facultad de Farmacia, Universidad Complutense de Madrid, Madrid, Spain
| | - Concha Gil
- Proteomics Unit, Parque Científico de Madrid, Facultad de Farmacia, Universidad Complutense de Madrid, Madrid, Spain
| | - Silvia Barceló-Batllori
- IDIBELL Proteomics Unit, Institut d'Investigacions Biomèdica de Bellvitge, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Martin R Larsen
- Department of Biochemistry and Molecular Biology, Odense M, Denmark
| | - Ethel Queralt
- Cell Cycle Group, Cancer Epigenetics and Biology Program, Institut d'Investigacions Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
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11
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Tripodi F, Castoldi A, Nicastro R, Reghellin V, Lombardi L, Airoldi C, Falletta E, Maffioli E, Scarcia P, Palmieri L, Alberghina L, Agrimi G, Tedeschi G, Coccetti P. Methionine supplementation stimulates mitochondrial respiration. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2018; 1865:1901-1913. [PMID: 30290237 DOI: 10.1016/j.bbamcr.2018.09.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 08/28/2018] [Accepted: 09/23/2018] [Indexed: 10/28/2022]
Abstract
Mitochondria play essential metabolic functions in eukaryotes. Although their major role is the generation of energy in the form of ATP, they are also involved in maintenance of cellular redox state, conversion and biosynthesis of metabolites and signal transduction. Most mitochondrial functions are conserved in eukaryotic systems and mitochondrial dysfunctions trigger several human diseases. By using multi-omics approach, we investigate the effect of methionine supplementation on yeast cellular metabolism, considering its role in the regulation of key cellular processes. Methionine supplementation induces an up-regulation of proteins related to mitochondrial functions such as TCA cycle, electron transport chain and respiration, combined with an enhancement of mitochondrial pyruvate uptake and TCA cycle activity. This metabolic signature is more noticeable in cells lacking Snf1/AMPK, the conserved signalling regulator of energy homeostasis. Remarkably, snf1Δ cells strongly depend on mitochondrial respiration and suppression of pyruvate transport is detrimental for this mutant in methionine condition, indicating that respiration mostly relies on pyruvate flux into mitochondrial pathways. These data provide new insights into the regulation of mitochondrial metabolism and extends our understanding on the role of methionine in regulating energy signalling pathways.
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Affiliation(s)
- Farida Tripodi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy; SYSBIO, Centre of Systems Biology, Milan, Italy
| | - Andrea Castoldi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Raffaele Nicastro
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Veronica Reghellin
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Linda Lombardi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Cristina Airoldi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy; SYSBIO, Centre of Systems Biology, Milan, Italy
| | | | - Elisa Maffioli
- DIMEVET - Department of Veterinary Medicine, University of Milano, Milan, Italy
| | - Pasquale Scarcia
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, Italy
| | - Luigi Palmieri
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, Italy
| | - Lilia Alberghina
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy; SYSBIO, Centre of Systems Biology, Milan, Italy
| | - Gennaro Agrimi
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, Italy.
| | - Gabriella Tedeschi
- DIMEVET - Department of Veterinary Medicine, University of Milano, Milan, Italy.
| | - Paola Coccetti
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy; SYSBIO, Centre of Systems Biology, Milan, Italy.
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12
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Coccetti P, Nicastro R, Tripodi F. Conventional and emerging roles of the energy sensor Snf1/AMPK in Saccharomyces cerevisiae. MICROBIAL CELL 2018; 5:482-494. [PMID: 30483520 PMCID: PMC6244292 DOI: 10.15698/mic2018.11.655] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
All proliferating cells need to match metabolism, growth and cell cycle progression with nutrient availability to guarantee cell viability in spite of a changing environment. In yeast, a signaling pathway centered on the effector kinase Snf1 is required to adapt to nutrient limitation and to utilize alternative carbon sources, such as sucrose and ethanol. Snf1 shares evolutionary conserved functions with the AMP-activated Kinase (AMPK) in higher eukaryotes which, activated by energy depletion, stimulates catabolic processes and, at the same time, inhibits anabolism. Although the yeast Snf1 is best known for its role in responding to a number of stress factors, in addition to glucose limitation, new unconventional roles of Snf1 have recently emerged, even in glucose repressing and unstressed conditions. Here, we review and integrate available data on conventional and non-conventional functions of Snf1 to better understand the complexity of cellular physiology which controls energy homeostasis.
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Affiliation(s)
- Paola Coccetti
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy.,SYSBIO, Centre of Systems Biology, Milan, Italy
| | - Raffaele Nicastro
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy.,Present address: Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Farida Tripodi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy.,SYSBIO, Centre of Systems Biology, Milan, Italy
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13
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Tripodi F, Fraschini R, Zocchi M, Reghellin V, Coccetti P. Snf1/AMPK is involved in the mitotic spindle alignment in Saccharomyces cerevisiae. Sci Rep 2018; 8:5853. [PMID: 29643469 PMCID: PMC5895576 DOI: 10.1038/s41598-018-24252-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 03/01/2018] [Indexed: 12/17/2022] Open
Abstract
Before anaphase onset, budding yeast cells must align the mitotic spindle parallel to the mother-bud axis to ensure proper chromosome segregation. The protein kinase Snf1/AMPK is a highly conserved energy sensor, essential for adaptation to glucose limitation and in response to cellular stresses. However, recent findings indicate that it plays important functions also in non-limiting glucose conditions. Here we report a novel role of Snf1/AMPK in the progression through mitosis in glucose-repressing condition. We show that active Snf1 is localized to the bud neck from bud emergence to cytokinesis in a septin-dependent manner. In addition, loss of Snf1 induces a delay of the metaphase to anaphase transition that is due to a defect in the correct alignment of the mitotic spindle. In particular, genetic data indicate that Snf1 promotes spindle orientation acting in parallel with Dyn1 and in concert with Kar9. Altogether this study describes a new role for Snf1 in mitosis and connects cellular metabolism to mitosis progression.
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Affiliation(s)
- Farida Tripodi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milano, Italy. .,SYSBIO, Centre of Systems Biology, Milan, Italy.
| | - Roberta Fraschini
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milano, Italy
| | - Monica Zocchi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milano, Italy.,Museo della Scienza e della Tecnologia Leonardo da Vinci, Milano, Italy
| | - Veronica Reghellin
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milano, Italy.,Eurofins BioPharma, Vimodrone, Italy
| | - Paola Coccetti
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milano, Italy. .,SYSBIO, Centre of Systems Biology, Milan, Italy.
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14
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Galello F, Pautasso C, Reca S, Cañonero L, Portela P, Moreno S, Rossi S. Transcriptional regulation of the protein kinase a subunits inSaccharomyces cerevisiaeduring fermentative growth. Yeast 2017; 34:495-508. [DOI: 10.1002/yea.3252] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 07/26/2017] [Accepted: 08/09/2017] [Indexed: 11/08/2022] Open
Affiliation(s)
- Fiorella Galello
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento Química Biológica and CONICET - Universidad de Buenos Aires; Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; Buenos Aires Argentina
| | - Constanza Pautasso
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento Química Biológica and CONICET - Universidad de Buenos Aires; Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; Buenos Aires Argentina
| | - Sol Reca
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento Química Biológica and CONICET - Universidad de Buenos Aires; Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; Buenos Aires Argentina
| | - Luciana Cañonero
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento Química Biológica and CONICET - Universidad de Buenos Aires; Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; Buenos Aires Argentina
| | - Paula Portela
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento Química Biológica and CONICET - Universidad de Buenos Aires; Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; Buenos Aires Argentina
| | - Silvia Moreno
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento Química Biológica and CONICET - Universidad de Buenos Aires; Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; Buenos Aires Argentina
| | - Silvia Rossi
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento Química Biológica and CONICET - Universidad de Buenos Aires; Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; Buenos Aires Argentina
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15
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Kanshin E, Giguère S, Jing C, Tyers M, Thibault P. Machine Learning of Global Phosphoproteomic Profiles Enables Discrimination of Direct versus Indirect Kinase Substrates. Mol Cell Proteomics 2017; 16:786-798. [PMID: 28265048 DOI: 10.1074/mcp.m116.066233] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 02/13/2017] [Indexed: 12/12/2022] Open
Abstract
Mass spectrometry allows quantification of tens of thousands of phosphorylation sites from minute amounts of cellular material. Despite this wealth of information, our understanding of phosphorylation-based signaling is limited, in part because it is not possible to deconvolute substrate phosphorylation that is directly mediated by a particular kinase versus phosphorylation that is mediated by downstream kinases. Here, we describe a framework for assignment of direct in vivo kinase substrates using a combination of selective chemical inhibition, quantitative phosphoproteomics, and machine learning techniques. Our workflow allows classification of phosphorylation events following inhibition of an analog-sensitive kinase into kinase-independent effects of the inhibitor, direct effects on cognate substrates, and indirect effects mediated by downstream kinases or phosphatases. We applied this method to identify many direct targets of Cdc28 and Snf1 kinases in the budding yeast Saccharomyces cerevisiae Global phosphoproteome analysis of acute time-series demonstrated that dephosphorylation of direct kinase substrates occurs more rapidly compared with indirect substrates, both after inhibitor treatment and under a physiological nutrient shift in wt cells. Mutagenesis experiments revealed a high proportion of functionally relevant phosphorylation sites on Snf1 targets. For example, Snf1 itself was inhibited through autophosphorylation on Ser391 and new phosphosites were discovered that modulate the activity of the Reg1 regulatory subunit of the Glc7 phosphatase and the Gal83 β-subunit of SNF1 complex. This methodology applies to any kinase for which a functional analog sensitive version can be constructed to facilitate the dissection of the global phosphorylation network.
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Affiliation(s)
- Evgeny Kanshin
- From the ‡Institute for Research in Immunology and Cancer
| | | | - Cheng Jing
- From the ‡Institute for Research in Immunology and Cancer
| | - Mike Tyers
- From the ‡Institute for Research in Immunology and Cancer, .,§Department of Medicine
| | - Pierre Thibault
- From the ‡Institute for Research in Immunology and Cancer, .,¶Department of Chemistry, Université de Montréal, C.P. 6128, Succursale centre-ville, Montréal, Québec, H3C 3J7, Canada
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16
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Nicastro R, Tripodi F, Gaggini M, Castoldi A, Reghellin V, Nonnis S, Tedeschi G, Coccetti P. Snf1 Phosphorylates Adenylate Cyclase and Negatively Regulates Protein Kinase A-dependent Transcription in Saccharomyces cerevisiae. J Biol Chem 2015; 290:24715-26. [PMID: 26309257 DOI: 10.1074/jbc.m115.658005] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Indexed: 11/06/2022] Open
Abstract
In eukaryotes, nutrient availability and metabolism are coordinated by sensing mechanisms and signaling pathways, which influence a broad set of cellular functions such as transcription and metabolic pathways to match environmental conditions. In yeast, PKA is activated in the presence of high glucose concentrations, favoring fast nutrient utilization, shutting down stress responses, and boosting growth. On the contrary, Snf1/AMPK is activated in the presence of low glucose or alternative carbon sources, thus promoting an energy saving program through transcriptional activation and phosphorylation of metabolic enzymes. The PKA and Snf1/AMPK pathways share common downstream targets. Moreover, PKA has been reported to negatively influence the activation of Snf1/AMPK. We report a new cross-talk mechanism with a Snf1-dependent regulation of the PKA pathway. We show that Snf1 and adenylate cyclase (Cyr1) interact in a nutrient-independent manner. Moreover, we identify Cyr1 as a Snf1 substrate and show that Snf1 activation state influences Cyr1 phosphorylation pattern, cAMP intracellular levels, and PKA-dependent transcription.
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Affiliation(s)
- Raffaele Nicastro
- From the Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milan, Italy, SYSBIO, Centre of Systems Biology, 20126 Milan, Italy
| | - Farida Tripodi
- From the Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milan, Italy, SYSBIO, Centre of Systems Biology, 20126 Milan, Italy
| | - Marco Gaggini
- From the Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milan, Italy, SYSBIO, Centre of Systems Biology, 20126 Milan, Italy
| | - Andrea Castoldi
- From the Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milan, Italy, SYSBIO, Centre of Systems Biology, 20126 Milan, Italy
| | - Veronica Reghellin
- From the Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milan, Italy, SYSBIO, Centre of Systems Biology, 20126 Milan, Italy
| | - Simona Nonnis
- Dipartimento di Patologia Animale, Igiene e Sanità Pubblica Veterinaria-Biochemistry, University of Milano, 20133 Milan, Italy, and the Filarete Foundation, 20139 Milan, Italy
| | - Gabriella Tedeschi
- Dipartimento di Patologia Animale, Igiene e Sanità Pubblica Veterinaria-Biochemistry, University of Milano, 20133 Milan, Italy, and the Filarete Foundation, 20139 Milan, Italy
| | - Paola Coccetti
- From the Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milan, Italy, SYSBIO, Centre of Systems Biology, 20126 Milan, Italy,
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17
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Protein kinase Snf1 is involved in the proper regulation of the unfolded protein response in Saccharomyces cerevisiae. Biochem J 2015; 468:33-47. [PMID: 25730376 DOI: 10.1042/bj20140734] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Glc7 is the only catalytic subunit of the protein phosphatase type 1 in the yeast S. cerevisiae and, together with its regulatory subunits, is involved in many essential processes. Analysis of the non-essential mutants in the regulatory subunits of Glc7 revealed that the lack of Reg1, and no other subunit, causes hypersensitivity to unfolded protein response (UPR)-inducers, which was concomitant with an augmented UPR element-dependent transcriptional response. The Glc7-Reg1 complex takes part in the regulation of the yeast AMP-activated serine/threonine protein kinase Snf1 in response to glucose. We demonstrate in the present study that the observed phenotypes of reg1 mutant cells are attributable to the inappropriate activation of Snf1. Indeed, growth in the presence of limited concentrations of glucose, where Snf1 is active, or expression of active forms of Snf1 in a wild-type strain increased the sensitivity to the UPR-inducer tunicamycin. Furthermore, reg1 mutant cells showed a sustained HAC1 mRNA splicing and KAR2 mRNA levels during the recovery phase of the UPR, and dysregulation of the Ire1-oligomeric equilibrium. Finally, overexpression of protein phosphatases Ptc2 and Ptc3 alleviated the growth defect of reg1 cells under endoplasmic reticulum (ER) stress conditions. Altogether, our results reveal that Snf1 plays an important role in the attenuation of the UPR, as well as identifying the protein kinase and its effectors as possible pharmacological targets for human diseases that are associated with insufficient UPR activation.
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18
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Nicastro R, Tripodi F, Guzzi C, Reghellin V, Khoomrung S, Capusoni C, Compagno C, Airoldi C, Nielsen J, Alberghina L, Coccetti P. Enhanced amino acid utilization sustains growth of cells lacking Snf1/AMPK. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1853:1615-25. [PMID: 25841981 DOI: 10.1016/j.bbamcr.2015.03.014] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/03/2015] [Revised: 03/16/2015] [Accepted: 03/25/2015] [Indexed: 01/02/2023]
Abstract
The metabolism of proliferating cells shows common features even in evolutionary distant organisms such as mammals and yeasts, for example the requirement for anabolic processes under tight control of signaling pathways. Analysis of the rewiring of metabolism, which occurs following the dysregulation of signaling pathways, provides new knowledge about the mechanisms underlying cell proliferation. The key energy regulator in yeast Snf1 and its mammalian ortholog AMPK have earlier been shown to have similar functions at glucose limited conditions and here we show that they also have analogies when grown with glucose excess. We show that loss of Snf1 in cells growing in 2% glucose induces an extensive transcriptional reprogramming, enhances glycolytic activity, fatty acid accumulation and reliance on amino acid utilization for growth. Strikingly, we demonstrate that Snf1/AMPK-deficient cells remodel their metabolism fueling mitochondria and show glucose and amino acids addiction, a typical hallmark of cancer cells.
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Affiliation(s)
- Raffaele Nicastro
- SYSBIO, Centre of Systems Biology, Milan, Italy; Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Farida Tripodi
- SYSBIO, Centre of Systems Biology, Milan, Italy; Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Cinzia Guzzi
- SYSBIO, Centre of Systems Biology, Milan, Italy; Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Veronica Reghellin
- SYSBIO, Centre of Systems Biology, Milan, Italy; Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Sakda Khoomrung
- Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Claudia Capusoni
- Department of Food, Environmental and Nutritional Sciences, University of Milan, Milan, Italy
| | - Concetta Compagno
- Department of Food, Environmental and Nutritional Sciences, University of Milan, Milan, Italy
| | - Cristina Airoldi
- SYSBIO, Centre of Systems Biology, Milan, Italy; Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Jens Nielsen
- Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
| | - Lilia Alberghina
- SYSBIO, Centre of Systems Biology, Milan, Italy; Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Paola Coccetti
- SYSBIO, Centre of Systems Biology, Milan, Italy; Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy.
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19
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Tripodi F, Nicastro R, Reghellin V, Coccetti P. Post-translational modifications on yeast carbon metabolism: Regulatory mechanisms beyond transcriptional control. Biochim Biophys Acta Gen Subj 2015; 1850:620-7. [DOI: 10.1016/j.bbagen.2014.12.010] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Revised: 12/05/2014] [Accepted: 12/08/2014] [Indexed: 12/19/2022]
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20
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Chasman D, Ho YH, Berry DB, Nemec CM, MacGilvray ME, Hose J, Merrill AE, Lee MV, Will JL, Coon JJ, Ansari AZ, Craven M, Gasch AP. Pathway connectivity and signaling coordination in the yeast stress-activated signaling network. Mol Syst Biol 2014; 10:759. [PMID: 25411400 PMCID: PMC4299600 DOI: 10.15252/msb.20145120] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Stressed cells coordinate a multi-faceted response spanning many levels of physiology. Yet
knowledge of the complete stress-activated regulatory network as well as design principles for
signal integration remains incomplete. We developed an experimental and computational approach to
integrate available protein interaction data with gene fitness contributions, mutant transcriptome
profiles, and phospho-proteome changes in cells responding to salt stress, to infer the
salt-responsive signaling network in yeast. The inferred subnetwork presented many novel predictions
by implicating new regulators, uncovering unrecognized crosstalk between known pathways, and
pointing to previously unknown ‘hubs’ of signal integration. We exploited these
predictions to show that Cdc14 phosphatase is a central hub in the network and that modification of
RNA polymerase II coordinates induction of stress-defense genes with reduction of growth-related
transcripts. We find that the orthologous human network is enriched for cancer-causing genes,
underscoring the importance of the subnetwork's predictions in understanding stress
biology.
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Affiliation(s)
- Deborah Chasman
- Department of Computer Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Yi-Hsuan Ho
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, USA
| | - David B Berry
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, USA
| | - Corey M Nemec
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | | | - James Hose
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, USA
| | - Anna E Merrill
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - M Violet Lee
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Jessica L Will
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, USA
| | - Joshua J Coon
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA Department of Biological Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Aseem Z Ansari
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA
| | - Mark Craven
- Department of Computer Sciences, University of Wisconsin-Madison, Madison, WI, USA Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, USA
| | - Audrey P Gasch
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, USA Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA
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