1
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Poopanitpan N, Piampratom S, Viriyathanit P, Lertvatasilp T, Horiuchi H, Fukuda R, Kiatwuthinon P. SNF1 plays a crucial role in the utilization of n-alkane and transcriptional regulation of the genes involved in it in the yeast Yarrowia lipolytica. Heliyon 2024; 10:e32886. [PMID: 38975102 PMCID: PMC11226914 DOI: 10.1016/j.heliyon.2024.e32886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 06/10/2024] [Accepted: 06/11/2024] [Indexed: 07/09/2024] Open
Abstract
Yarrowia lipolytica is an ascomycetous yeast that can assimilate hydrophobic carbon sources including oil and n-alkane. The sucrose non-fermenting 1/AMP-activated protein kinase (Snf1/AMPK) complex is involved in the assimilation of non-fermentable carbon sources in various yeasts. However, the role of the Snf1/AMPK complex in n-alkane assimilation in Y. lipolytica has not yet been elucidated. This study aimed to clarify the role of Y. lipolytica SNF1 (YlSNF1) in the utilization of n-alkane. The deletion mutant of YlSNF1 (ΔYlsnf1) exhibited substantial growth defects on n-alkanes of various lengths (C10, C12, C14, and C16), and its growth was restored through the introduction of YlSNF1. Microscopic observations revealed that YlSnf1 tagged with enhanced green fluorescence protein showed dot-like distribution patterns in some cells cultured in the medium containing n-decane, which were not observed in cells cultured in the medium containing glucose or glycerol. The RNA sequencing analysis of ΔYlsnf1 cultured in the medium containing n-decane exhibited 302 downregulated and 131 upregulated genes compared with the wild-type strain cultured in the same medium. Gene ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses suggested that a significant fraction of the downregulated genes functioned in peroxisomes or were involved in the metabolism of n-alkane and fatty acids. Quantitative real-time PCR analysis confirmed the downregulation of 12 genes involved in the metabolism of n-alkane and fatty acid, ALK1-ALK3, ALK5, ADH7, PAT1, POT1, POX2, PEX3, PEX11, YAS1, and HFD3. Furthermore, ΔYlsnf1 exhibited growth defects on the medium containing the metabolites of n-alkane (fatty alcohol and fatty aldehyde). These findings suggest that YlSNF1 plays a crucial role in the utilization of n-alkane in Y. lipolytica. This study provides important insights into the advanced biotechnological applications of this yeast, including the bioconversion of n-alkane to useful chemicals and the bioremediation of petroleum-contaminated environments.
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Affiliation(s)
- Napapol Poopanitpan
- Department of Biochemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
- Interdisciplinary Program in Genetic Engineering, The Graduate School, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
| | - Sorawit Piampratom
- Interdisciplinary Program in Genetic Engineering, The Graduate School, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
| | - Patthanant Viriyathanit
- Department of Biochemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
| | - Threesara Lertvatasilp
- Department of Biochemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
| | - Hiroyuki Horiuchi
- Department of Biotechnology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Ryouichi Fukuda
- Department of Biotechnology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Pichamon Kiatwuthinon
- Department of Biochemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
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2
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Rawat SS, Laxmi A. Sugar signals pedal the cell cycle! FRONTIERS IN PLANT SCIENCE 2024; 15:1354561. [PMID: 38562561 PMCID: PMC10982403 DOI: 10.3389/fpls.2024.1354561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 02/19/2024] [Indexed: 04/04/2024]
Abstract
Cell cycle involves the sequential and reiterative progression of important events leading to cell division. Progression through a specific phase of the cell cycle is under the control of various factors. Since the cell cycle in multicellular eukaryotes responds to multiple extracellular mitogenic cues, its study in higher forms of life becomes all the more important. One such factor regulating cell cycle progression in plants is sugar signalling. Because the growth of organs depends on both cell growth and proliferation, sugars sensing and signalling are key control points linking sugar perception to regulation of downstream factors which facilitate these key developmental transitions. However, the basis of cell cycle control via sugars is intricate and demands exploration. This review deals with the information on sugar and TOR-SnRK1 signalling and how they manoeuvre various events of the cell cycle to ensure proper growth and development.
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Affiliation(s)
| | - Ashverya Laxmi
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
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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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Oz N, Vayndorf EM, Tsuchiya M, McLean S, Turcios-Hernandez L, Pitt JN, Blue BW, Muir M, Kiflezghi MG, Tyshkovskiy A, Mendenhall A, Kaeberlein M, Kaya A. Evidence that conserved essential genes are enriched for pro-longevity factors. GeroScience 2022; 44:1995-2006. [PMID: 35695982 PMCID: PMC9616985 DOI: 10.1007/s11357-022-00604-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 06/03/2022] [Indexed: 02/02/2023] Open
Abstract
At the cellular level, many aspects of aging are conserved across species. This has been demonstrated by numerous studies in simple model organisms like Saccharomyces cerevisiae, Caenorhabdits elegans, and Drosophila melanogaster. Because most genetic screens examine loss of function mutations or decreased expression of genes through reverse genetics, essential genes have often been overlooked as potential modulators of the aging process. By taking the approach of increasing the expression level of a subset of conserved essential genes, we found that 21% of these genes resulted in increased replicative lifespan in S. cerevisiae. This is greater than the ~ 3.5% of genes found to affect lifespan upon deletion, suggesting that activation of essential genes may have a relatively disproportionate effect on increasing lifespan. The results of our experiments demonstrate that essential gene overexpression is a rich, relatively unexplored means of increasing eukaryotic lifespan.
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Affiliation(s)
- Naci Oz
- Department of Biology, Virginia Commonwealth University, Richmond, VA, 23284, USA
| | - Elena M Vayndorf
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Mitsuhiro Tsuchiya
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Samantha McLean
- Department of Biology, Virginia Commonwealth University, Richmond, VA, 23284, USA
| | | | - Jason N Pitt
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Benjamin W Blue
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Michael Muir
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Michael G Kiflezghi
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Alexander Tyshkovskiy
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Alexander Mendenhall
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Matt Kaeberlein
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA.
| | - Alaattin Kaya
- Department of Biology, Virginia Commonwealth University, Richmond, VA, 23284, USA.
- Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, 23298, USA.
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA, 23284, USA.
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5
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Mattam U, Talari NK, Paripati AK, Krishnamoorthy T, Sepuri NBV. Kisspeptin preserves mitochondrial function by inducing mitophagy and autophagy in aging rat brain hippocampus and human neuronal cell line. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1868:118852. [PMID: 32926943 DOI: 10.1016/j.bbamcr.2020.118852] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 09/07/2020] [Accepted: 09/09/2020] [Indexed: 12/20/2022]
Abstract
It has become amply clear that mitochondrial function defined by quality, quantity, dynamics, homeostasis, and regulated by mitophagy and mitochondrial biogenesis is a critical metric of human aging and disease. As a consequence, therapeutic interventions that can improve mitochondrial function can have a profound impact on human health and longevity. Kisspeptins are neuropeptides belonging to the family of metastasis suppressors that are known to regulate functions like fertility, reproduction, and metabolism. Using SKNSH cell line, hippocampus explant cultures and hippocampus of aging Wistar rat models, we show that Kisspeptin-10 (Kp) induces autophagy and mitophagy via calcium, Ca2+/CaM-dependent protein kinase kinase β (CaMKKβ), AMP-activated protein kinase (AMPK), and Unc-51 like autophagy activating kinase (ULK1) signaling pathway that is independent of mammalian target of rapamycin (mTOR). Intriguingly, Kp administration in vivo also results in the enhancement of mitochondrial number, complex I activity, and Adenosine Triphosphate (ATP) levels. This study uncovers potential effects of Kp in protecting mitochondrial health and as a possible therapeutic intervention to hippocampus associated impairments such as memory, cognitive aging, and other diseases linked to mitochondrial dysfunction.
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Affiliation(s)
- Ushodaya Mattam
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad 500046, T.S., India.
| | - Noble Kumar Talari
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad 500046, T.S., India
| | - Arun Kumar Paripati
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad 500046, T.S., India
| | - Thanuja Krishnamoorthy
- Vectrogen Biologicals Pvt Ltd, Hyderabad, BioNEST, School of Life Sciences, University of Hyderabad, Hyderabad 500046, T.S., India
| | - Naresh Babu V Sepuri
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad 500046, T.S., India.
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6
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Evolution of Distinct Responses to Low NAD + Stress by Rewiring the Sir2 Deacetylase Network in Yeasts. Genetics 2020; 214:855-868. [PMID: 32071196 DOI: 10.1534/genetics.120.303087] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 02/12/2020] [Indexed: 01/20/2023] Open
Abstract
Evolutionary adaptation increases the fitness of a species in its environment. It can occur through rewiring of gene regulatory networks, such that an organism responds appropriately to environmental changes. We investigated whether sirtuin deacetylases, which repress transcription and require NAD+ for activity, serve as transcriptional rewiring points that facilitate the evolution of potentially adaptive traits. If so, bringing genes under the control of sirtuins could enable organisms to mount appropriate responses to stresses that decrease NAD+ levels. To explore how the genomic targets of sirtuins shift over evolutionary time, we compared two yeast species, Saccharomyces cerevisiae and Kluyveromyces lactis, that display differences in cellular metabolism and life cycle timing in response to nutrient availability. We identified sirtuin-regulated genes through a combination of chromatin immunoprecipitation and RNA expression. In both species, regulated genes were associated with NAD+ homeostasis, mating, and sporulation, but the specific genes differed. In addition, regulated genes in K. lactis were associated with other processes, including utilization of nonglucose carbon sources, detoxification of arsenic, and production of the siderophore pulcherrimin. Consistent with the species-restricted regulation of these genes, sirtuin deletion affected relevant phenotypes in K. lactis but not S. cerevisiae Finally, sirtuin-regulated gene sets were depleted for broadly conserved genes, consistent with sirtuins regulating processes restricted to a few species. Taken together, these results are consistent with the notion that sirtuins serve as rewiring points that allow species to evolve distinct responses to low NAD+ stress.
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7
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Pinson B, Ceschin J, Saint-Marc C, Daignan-Fornier B. Dual control of NAD + synthesis by purine metabolites in yeast. eLife 2019; 8:43808. [PMID: 30860478 PMCID: PMC6430606 DOI: 10.7554/elife.43808] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 03/11/2019] [Indexed: 12/13/2022] Open
Abstract
Metabolism is a highly integrated process resulting in energy and biomass production. While individual metabolic routes are well characterized, the mechanisms ensuring crosstalk between pathways are poorly described, although they are crucial for homeostasis. Here, we establish a co-regulation of purine and pyridine metabolism in response to external adenine through two separable mechanisms. First, adenine depletion promotes transcriptional upregulation of the de novo NAD+ biosynthesis genes by a mechanism requiring the key-purine intermediates ZMP/SZMP and the Bas1/Pho2 transcription factors. Second, adenine supplementation favors the pyridine salvage route resulting in an ATP-dependent increase of intracellular NAD+. This control operates at the level of the nicotinic acid mononucleotide adenylyl-transferase Nma1 and can be bypassed by overexpressing this enzyme. Therefore, in yeast, pyridine metabolism is under the dual control of ZMP/SZMP and ATP, revealing a much wider regulatory role for these intermediate metabolites in an integrated biosynthesis network.
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Affiliation(s)
- Benoît Pinson
- IBGCUniversité de Bordeaux UMR 5095BordeauxFrance
- Centre National de la Recherche Scientifique IBGC UMR 5095BordeauxFrance
| | - Johanna Ceschin
- IBGCUniversité de Bordeaux UMR 5095BordeauxFrance
- Centre National de la Recherche Scientifique IBGC UMR 5095BordeauxFrance
| | - Christelle Saint-Marc
- IBGCUniversité de Bordeaux UMR 5095BordeauxFrance
- Centre National de la Recherche Scientifique IBGC UMR 5095BordeauxFrance
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8
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Modulatory Effects of Dietary Amino Acids on Neurodegenerative Diseases. ADVANCES IN NEUROBIOLOGY 2018; 12:401-14. [PMID: 27651266 DOI: 10.1007/978-3-319-28383-8_22] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
Proteins are playing a vital role in maintaining the cellular integrity and function, as well as for brain cells. Protein intake and supplementation of individual amino acids can affect the brain functioning and mental health, and many of the neurotransmitters in the brain are made from amino acids. The amino acid supplementation has been found to reduce symptoms, as they are converted into neurotransmitters which in turn extenuate the mental disorders. The biosynthesis of amino acids in the brain is regulated by the concentration of amino acids in plasma. The brain diseases such as depression, bipolar disorder, schizophrenia, obsessive-compulsive disorder (OCD), and Alzheimer's (AD), Parkinson's (PD), and Huntington's diseases (HD) are the most common mental disorders that are currently widespread in numerous countries. The intricate biochemical and molecular machinery contributing to the neurological disorders is still unknown, and in this chapter, we revealed the involvement of dietary amino acids on neurological diseases.
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9
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Mojardín L, Vega M, Moreno F, Schmitz HP, Heinisch JJ, Rodicio R. Lack of the NAD+-dependent glycerol 3-phosphate dehydrogenase impairs the function of transcription factors Sip4 and Cat8 required for ethanol utilization in Kluyveromyces lactis. Fungal Genet Biol 2018; 111:16-29. [DOI: 10.1016/j.fgb.2017.11.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Revised: 11/19/2017] [Accepted: 11/21/2017] [Indexed: 11/25/2022]
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10
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Lutchman V, Dakik P, McAuley M, Cortes B, Ferraye G, Gontmacher L, Graziano D, Moukhariq FZ, Simard É, Titorenko VI. Six plant extracts delay yeast chronological aging through different signaling pathways. Oncotarget 2018; 7:50845-50863. [PMID: 27447556 PMCID: PMC5239441 DOI: 10.18632/oncotarget.10689] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 07/07/2016] [Indexed: 01/19/2023] Open
Abstract
Our recent study has revealed six plant extracts that slow yeast chronological aging more efficiently than any chemical compound yet described. The rate of aging in yeast is controlled by an evolutionarily conserved network of integrated signaling pathways and protein kinases. Here, we assessed how single-gene-deletion mutations eliminating each of these pathways and kinases affect the aging-delaying efficiencies of the six plant extracts. Our findings imply that these extracts slow aging in the following ways: 1) plant extract 4 decreases the efficiency with which the pro-aging TORC1 pathway inhibits the anti-aging SNF1 pathway; 2) plant extract 5 mitigates two different branches of the pro-aging PKA pathway; 3) plant extract 6 coordinates processes that are not assimilated into the network of presently known signaling pathways/protein kinases; 4) plant extract 8 diminishes the inhibitory action of PKA on SNF1; 5) plant extract 12 intensifies the anti-aging protein kinase Rim15; and 6) plant extract 21 inhibits a form of the pro-aging protein kinase Sch9 that is activated by the pro-aging PKH1/2 pathway.
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Affiliation(s)
- Vicky Lutchman
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | - Pamela Dakik
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | - Mélissa McAuley
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | - Berly Cortes
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | - George Ferraye
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | - Leonid Gontmacher
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | - David Graziano
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | | | - Éric Simard
- Idunn Technologies Inc., Rosemere, Quebec, Canada
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11
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Kanamori KS, de Oliveira GC, Auxiliadora-Martins M, Schoon RA, Reid JM, Chini EN. Two Different Methods of Quantification of Oxidized Nicotinamide Adenine Dinucleotide (NAD +) and Reduced Nicotinamide Adenine Dinucleotide (NADH) Intracellular Levels: Enzymatic Coupled Cycling Assay and Ultra-performance Liquid Chromatography (UPLC)-Mass Spectrometry. Bio Protoc 2018; 8:e2937. [PMID: 30101155 DOI: 10.21769/bioprotoc.2937] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Current studies on the age-related development of metabolic dysfunction and frailty are each day in more evidence. It is known, as aging progresses, nicotinamide adenine dinucleotide (NAD+) levels decrease in an expected physiological process. Recent studies have shown that a reduction in NAD+ is a key factor for the development of age-associated metabolic decline. Increased NAD+ levels in vivo results in activation of pro-longevity and health span-related factors. Also, it improves several physiological and metabolic parameters of aging, including muscle function, exercise capacity, glucose tolerance, and cardiac function in mouse models of natural and accelerated aging. Given the importance of monitoring cellular NAD+ and NADH levels, it is crucial to have a trustful method to do so. This protocol has the purpose of describing the NAD+ and NADH extraction from tissues and cells in an efficient and widely applicable assay as well as its graphic and quantitative analysis.
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Affiliation(s)
- Karina S Kanamori
- Signal Transduction and Molecular Nutrition Laboratory, Kogod Aging Center, Department of Anesthesiology and Perioperative Medicine, Mayo Clinic College of Medicine, Rochester, USA
| | - Guilherme C de Oliveira
- Signal Transduction and Molecular Nutrition Laboratory, Kogod Aging Center, Department of Anesthesiology and Perioperative Medicine, Mayo Clinic College of Medicine, Rochester, USA
| | - Maria Auxiliadora-Martins
- Fundação de Apoio ao Ensino, Pesquisa e Assistência do Hospital das Clínicas da Faculdade de Medicina de Ribeirão Preto da Universidade de São Paulo (FAEPA), São Paulo, Brazil
| | - Renee A Schoon
- Oncology Research, Mayo Clinic College of Medicine, Rochester, USA
| | - Joel M Reid
- Oncology Research, Mayo Clinic College of Medicine, Rochester, USA
| | - Eduardo N Chini
- Signal Transduction and Molecular Nutrition Laboratory, Kogod Aging Center, Department of Anesthesiology and Perioperative Medicine, Mayo Clinic College of Medicine, Rochester, USA
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12
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Perić M, Lovrić A, Šarić A, Musa M, Bou Dib P, Rudan M, Nikolić A, Sobočanec S, Mikecin AM, Dennerlein S, Milošević I, Vlahoviček K, Raimundo N, Kriško A. TORC1-mediated sensing of chaperone activity alters glucose metabolism and extends lifespan. Aging Cell 2017; 16:994-1005. [PMID: 28613034 PMCID: PMC5595670 DOI: 10.1111/acel.12623] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/27/2017] [Indexed: 11/28/2022] Open
Abstract
Protein quality control mechanisms, required for normal cellular functioning, encompass multiple functions related to protein production and maintenance. However, the existence of communication between proteostasis and metabolic networks and its underlying mechanisms remain elusive. Here, we report that enhanced chaperone activity and consequent improved proteostasis are sensed by TORC1 via the activity of Hsp82. Chaperone enrichment decreases the level of Hsp82, which deactivates TORC1 and leads to activation of Snf1/AMPK, regardless of glucose availability. This mechanism culminates in the extension of yeast replicative lifespan (RLS) that is fully reliant on both TORC1 deactivation and Snf1/AMPK activation. Specifically, we identify oxygen consumption increase as the downstream effect of Snf1 activation responsible for the entire RLS extension. Our results set a novel paradigm for the role of proteostasis in aging: modulation of the misfolded protein level can affect cellular metabolic features as well as mitochondrial activity and consequently modify lifespan. The described mechanism is expected to open new avenues for research of aging and age‐related diseases.
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Affiliation(s)
- Matea Perić
- Mediterranean Institute for Life Sciences; Mestrovicevo setaliste 45 21000 Split Croatia
| | - Anita Lovrić
- Mediterranean Institute for Life Sciences; Mestrovicevo setaliste 45 21000 Split Croatia
| | - Ana Šarić
- Division of Molecular Medicine; Rudjer Boskovic Institute; Bijenicka 54 10000 Zagreb Croatia
| | - Marina Musa
- Mediterranean Institute for Life Sciences; Mestrovicevo setaliste 45 21000 Split Croatia
| | - Peter Bou Dib
- Institut für Zellbiochemie; Universitätsmedizin Göttingen; Humboldtallee 23 D-37073 Göttingen Germany
| | - Marina Rudan
- Mediterranean Institute for Life Sciences; Mestrovicevo setaliste 45 21000 Split Croatia
| | - Andrea Nikolić
- Mediterranean Institute for Life Sciences; Mestrovicevo setaliste 45 21000 Split Croatia
| | - Sandra Sobočanec
- Division of Molecular Medicine; Rudjer Boskovic Institute; Bijenicka 54 10000 Zagreb Croatia
| | - Ana-Matea Mikecin
- Division of Molecular Medicine; Rudjer Boskovic Institute; Bijenicka 54 10000 Zagreb Croatia
| | - Sven Dennerlein
- Institut für Zellbiochemie; Universitätsmedizin Göttingen; Humboldtallee 23 D-37073 Göttingen Germany
| | - Ira Milošević
- European Neuroscience Institute; Grisebachstraße 5 37077 Göttingen Germany
| | - Kristian Vlahoviček
- Bioinformatics Group; Division of Biology; Department of Molecular Biology; Faculty of Science; University of Zagreb; Zagreb Croatia
| | - Nuno Raimundo
- Institut für Zellbiochemie; Universitätsmedizin Göttingen; Humboldtallee 23 D-37073 Göttingen Germany
| | - Anita Kriško
- Mediterranean Institute for Life Sciences; Mestrovicevo setaliste 45 21000 Split Croatia
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13
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Kimura Y, Irie K, Mizuno T. Expression control of the AMPK regulatory subunit and its functional significance in yeast ER stress response. Sci Rep 2017; 7:46713. [PMID: 28429799 PMCID: PMC5399461 DOI: 10.1038/srep46713] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 03/24/2017] [Indexed: 12/30/2022] Open
Abstract
AMP-activated protein kinase (AMPK) is an evolutionarily conserved heterotrimeric kinase complex consisting of a catalytic subunit, α, and two regulatory subunits, β and γ. Previously, we demonstrated that Snf1, the Saccharomyces cerevisiae ortholog of AMPK, negatively regulates the unfolded protein response (UPR) pathway and the Hog1 MAP kinase pathway in ER stress response. However, it remains unclear how the alternate three β subunits, Sip1, Sip2, and Gal83, of the Snf1 complex participate in ER stress response. Here, we show that Gal83 plays a major role in Snf1-mediated downregulation of the UPR and Hog1 pathways. Gal83 is the most abundant β subunit in the normal state and further induced by ER stress. This induction is mediated via activation of the GAL83 promoter by the UPR. When expressed under the control of the GAL83 promoter, Sip2 exhibits potent functional activity equivalent to Gal83. Our results suggest that the functional significance of the β subunit of Snf1 AMPK in ER stress response is defined by modulation of the expression level through regulation of the promoter activity.
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Affiliation(s)
- Yuichi Kimura
- Department of Molecular Cell Biology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Kenji Irie
- Department of Molecular Cell Biology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Tomoaki Mizuno
- Department of Molecular Cell Biology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
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14
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He X, Li C, Ke R, Luo L, Huang D. Down-regulation of adenosine monophosphate–activated protein kinase activity: A driver of cancer. Tumour Biol 2017; 39:1010428317697576. [PMID: 28381161 DOI: 10.1177/1010428317697576] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Adenosine monophosphate–activated protein kinase (AMPK), a serine/threonine protein kinase, is known as “intracellular energy sensor and regulator.” AMPK regulates multiple cellular processes including protein and lipid synthesis, cell proliferation, invasion, migration, and apoptosis. Moreover, AMPK plays a key role in the regulation of “Warburg effect” in cancer cells. AMPK activity is down-regulated in most tumor tissues compared with the corresponding adjacent paracancerous or normal tissues, indicating that the decline in AMPK activity is closely associated with the development and progression of cancer. Therefore, understanding the mechanism of AMPK deactivation during cancer progression is of pivotal importance as it may identify AMPK as a valid therapeutic target for cancer treatment. Here, we review the mechanisms by which AMPK is down-regulated in cancer.
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Affiliation(s)
- Xiaoling He
- Department of Gastroenterology and Research Institute of Digestive Diseases, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Cong Li
- Department of Gastroenterology and Research Institute of Digestive Diseases, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Rong Ke
- Department of Gastroenterology and Research Institute of Digestive Diseases, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Lingyu Luo
- Department of Gastroenterology and Research Institute of Digestive Diseases, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Deqiang Huang
- Department of Gastroenterology and Research Institute of Digestive Diseases, The First Affiliated Hospital of Nanchang University, Nanchang, China
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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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Rippert D, Backhaus K, Rodicio R, Heinisch JJ. Cell wall synthesis and central carbohydrate metabolism are interconnected by the SNF1/Mig1 pathway in Kluyveromyces lactis. Eur J Cell Biol 2017; 96:70-81. [DOI: 10.1016/j.ejcb.2016.12.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 12/21/2016] [Accepted: 12/22/2016] [Indexed: 11/12/2022] Open
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17
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Salminen A, Kauppinen A, Kaarniranta K. AMPK/Snf1 signaling regulates histone acetylation: Impact on gene expression and epigenetic functions. Cell Signal 2016; 28:887-95. [PMID: 27010499 DOI: 10.1016/j.cellsig.2016.03.009] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 03/18/2016] [Indexed: 01/22/2023]
Abstract
AMP-activated protein kinase (AMPK) and its yeast homolog, Snf1, are critical regulators in the maintenance of energy metabolic balance not only stimulating energy production but also inhibiting energy-consuming processes. The AMPK/Snf1 signaling controls energy metabolism by specific phosphorylation of many metabolic enzymes and transcription factors, enhancing or suppressing their functions. The AMPK/Snf1 complexes can be translocated from cytoplasm into nuclei where they are involved in the regulation of transcription. Recent studies have indicated that AMPK/Snf1 activation can control histone acetylation through different mechanisms affecting not only gene transcription but also many other epigenetic functions. For instance, AMPK/Snf1 enzymes can phosphorylate the histone H3S10 (yeast) and H2BS36 (mammalian) sites which activate specific histone acetyltransferases (HAT), consequently enhancing histone acetylation. Moreover, nuclear AMPK can phosphorylate type 2A histone deacetylases (HDAC), e.g. HDAC4 and HDAC5, triggering their export from nuclei thus promoting histone acetylation reactions. AMPK activation can also increase the level of acetyl CoA, e.g. by inhibiting fatty acid and cholesterol syntheses. Acetyl CoA is a substrate for HATs, thus increasing their capacity for histone acetylation. On the other hand, AMPK can stimulate the activity of nicotinamide phosphoribosyltransferase (NAMPT) which increases the level of NAD(+). NAD(+) is a substrate for nuclear sirtuins, especially for SIRT1 and SIRT6, which deacetylate histones and transcription factors, e.g. those regulating ribosome synthesis and circadian clocks. Histone acetylation is an important epigenetic modification which subsequently can affect chromatin remodeling, e.g. via bromodomain proteins. We will review the signaling mechanisms of AMPK/Snf1 in the control of histone acetylation and subsequently clarify their role in the epigenetic regulation of ribosome synthesis and circadian clocks.
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Affiliation(s)
- Antero Salminen
- Department of Neurology, Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland.
| | - Anu Kauppinen
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland
| | - Kai Kaarniranta
- Department of Ophthalmology, Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland; Department of Ophthalmology, Kuopio University Hospital, Kuopio, Finland
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18
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Molon M, Szajwaj M, Tchorzewski M, Skoczowski A, Niewiadomska E, Zadrag-Tecza R. The rate of metabolism as a factor determining longevity of the Saccharomyces cerevisiae yeast. AGE (DORDRECHT, NETHERLANDS) 2016; 38:11. [PMID: 26783001 PMCID: PMC5005888 DOI: 10.1007/s11357-015-9868-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 12/22/2015] [Indexed: 05/13/2023]
Abstract
Despite many controversies, the yeast Saccharomyces cerevisiae continues to be used as a model organism for the study of aging. Numerous theories and hypotheses have been created for several decades, yet basic mechanisms of aging have remained unclear. Therefore, the principal aim of this work is to propose a possible mechanism leading to increased longevity in yeast. In this paper, we suggest for the first time that there is a link between decreased metabolic activity, fertility and longevity expressed as time of life in yeast. Determination of reproductive potential and total lifespan with the use of fob1Δ and sfp1Δ mutants allows us to compare the "longevity" presented as the number of produced daughters with the longevity expressed as the time of life. The results of analyses presented in this paper suggest the need for a change in the definition of longevity of yeast by taking into consideration the time parameter. The mutants that have been described as "long-lived" in the literature, such as the fob1Δ mutant, have an increased reproductive potential but live no longer than their standard counterparts. On the other hand, the sfp1Δ mutant and the wild-type strain produce a similar number of daughter cells, but the former lives much longer. Our results demonstrate a correlation between the decreased efficiency of the translational apparatus and the longevity of the sfp1Δ mutant. We suggest that a possible factor regulating the lifespan is the rate of cell metabolism. To measure the basic metabolism of the yeast cells, we used the isothermal microcalorimetry method. In the case of sfp1Δ, the flow of energy, ATP concentration, polysome profile and translational fitness are significantly lower in comparison with the wild-type strain and the fob1Δ mutant.
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Affiliation(s)
- Mateusz Molon
- Department of Biochemistry and Cell Biology, University of Rzeszow, Zelwerowicza 4, Rzeszow, 35-601, Poland.
| | - Monika Szajwaj
- Department of Molecular Biology, Maria Curie-Sklodowska University, Lublin, Poland
| | - Marek Tchorzewski
- Department of Molecular Biology, Maria Curie-Sklodowska University, Lublin, Poland
| | | | - Ewa Niewiadomska
- The Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, Krakow, Poland
| | - Renata Zadrag-Tecza
- Department of Biochemistry and Cell Biology, University of Rzeszow, Zelwerowicza 4, Rzeszow, 35-601, Poland
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19
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Sugar and Glycerol Transport in Saccharomyces cerevisiae. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 892:125-168. [PMID: 26721273 DOI: 10.1007/978-3-319-25304-6_6] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
In Saccharomyces cerevisiae the process of transport of sugar substrates into the cell comprises a complex network of transporters and interacting regulatory mechanisms. Members of the large family of hexose (HXT) transporters display uptake efficiencies consistent with their environmental expression and play physiological roles in addition to feeding the glycolytic pathway. Multiple glucose-inducing and glucose-independent mechanisms serve to regulate expression of the sugar transporters in yeast assuring that expression levels and transporter activity are coordinated with cellular metabolism and energy needs. The expression of sugar transport activity is modulated by other nutritional and environmental factors that may override glucose-generated signals. Transporter expression and activity is regulated transcriptionally, post-transcriptionally and post-translationally. Recent studies have expanded upon this suite of regulatory mechanisms to include transcriptional expression fine tuning mediated by antisense RNA and prion-based regulation of transcription. Much remains to be learned about cell biology from the continued analysis of this dynamic process of substrate acquisition.
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20
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Mesquita I, Moreira D, Sampaio-Marques B, Laforge M, Cordeiro-da-Silva A, Ludovico P, Estaquier J, Silvestre R. AMPK in Pathogens. EXPERIENTIA SUPPLEMENTUM (2012) 2016; 107:287-323. [PMID: 27812985 DOI: 10.1007/978-3-319-43589-3_12] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
During host-pathogen interactions, a complex web of events is crucial for the outcome of infection. Pathogen recognition triggers powerful cellular signaling events that is translated into the induction and maintenance of innate and adaptive host immunity against infection. In opposition, pathogens employ active mechanisms to manipulate host cell regulatory pathways toward their proliferation and survival. Among these, subversion of host cell energy metabolism by pathogens is currently recognized to play an important role in microbial growth and persistence. Extensive studies have documented the role of AMP-activated protein kinase (AMPK) signaling, a central cellular hub involved in the regulation of energy homeostasis, in host-pathogen interactions. Here, we highlight the most recent advances detailing how pathogens hijack cellular metabolism by suppressing or increasing the activity of the host energy sensor AMPK. We also address the role of lower eukaryote AMPK orthologues in the adaptive process to the host microenvironment and their contribution for pathogen survival, differentiation, and growth. Finally, we review the effects of pharmacological or genetic AMPK modulation on pathogen growth and persistence.
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Affiliation(s)
- Inês Mesquita
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal.,ICVS/3Bs-PT Government Associate Laboratory, Guimarães, Braga, Portugal
| | - Diana Moreira
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal.,Departamento de Ciências Biológicas, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Belém Sampaio-Marques
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal.,ICVS/3Bs-PT Government Associate Laboratory, Guimarães, Braga, Portugal
| | | | - Anabela Cordeiro-da-Silva
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal.,Departamento de Ciências Biológicas, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Paula Ludovico
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal.,ICVS/3Bs-PT Government Associate Laboratory, Guimarães, Braga, Portugal
| | - Jérôme Estaquier
- CNRS FR 3636, Université Paris Descartes, Paris, France.,Centre de Recherche du CHU de Québec, Université Laval, Québec, QC, Canada
| | - Ricardo Silvestre
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal. .,ICVS/3Bs-PT Government Associate Laboratory, Guimarães, Braga, Portugal.
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21
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Sanz P, Viana R, Garcia-Gimeno MA. AMPK in Yeast: The SNF1 (Sucrose Non-fermenting 1) Protein Kinase Complex. EXPERIENTIA SUPPLEMENTUM (2012) 2016; 107:353-374. [PMID: 27812987 DOI: 10.1007/978-3-319-43589-3_14] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
In yeast, SNF1 protein kinase is the orthologue of mammalian AMPK complex. It is a trimeric complex composed of Snf1 protein kinase (orthologue of AMPKα catalytic subunit), Snf4 (orthologue of AMPKγ regulatory subunit), and a member of the Gal83/Sip1/Sip2 family of proteins (orthologues of AMPKβ subunit) that act as scaffolds and also regulate the subcellular localization of the complex. In this chapter, we review the recent literature on the characteristics of SNF1 complex subunits, the structure and regulation of the activity of the SNF1 complex, its role at the level of transcriptional regulation of relevant target genes and also at the level of posttranslational modification of targeted substrates. We also review the crosstalk of SNF1 complex activity with other key protein kinase pathways such as cAMP-PKA, TORC1, and PAS kinase.
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Affiliation(s)
- Pascual Sanz
- Instituto de Biomedicina de Valencia, CSIC and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER-ISCiii), Jaime Roig 11, 46010, Valencia, Spain.
| | - Rosa Viana
- Instituto de Biomedicina de Valencia, CSIC and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER-ISCiii), Jaime Roig 11, 46010, Valencia, Spain
| | - Maria Adelaida Garcia-Gimeno
- Department of Biotecnología, Escuela Técnica Superior de Ingeniería Agronómica y del Medio Natural (ETSIAMN), Universitat Politécnica de Valencia, Valencia, Spain
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22
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Tsang F, Lin SJ. Less is more: Nutrient limitation induces cross-talk of nutrient sensing pathways with NAD + homeostasis and contributes to longevity. ACTA ACUST UNITED AC 2015; 10:333-357. [PMID: 27683589 DOI: 10.1007/s11515-015-1367-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Nutrient sensing pathways and their regulation grant cells control over their metabolism and growth in response to changing nutrients. Factors that regulate nutrient sensing can also modulate longevity. Reduced activity of nutrient sensing pathways such as glucose-sensing PKA, nitrogen-sensing TOR and S6 kinase homolog Sch9 have been linked to increased life span in the yeast, Saccharomyces cerevisiae, and higher eukaryotes. Recently, reduced activity of amino acid sensing SPS pathway was also shown to increase yeast life span. Life span extension by reduced SPS activity requires enhanced NAD+ (nicotinamide adenine dinucleotide, oxidized form) and nicotinamide riboside (NR, a NAD+ precursor) homeostasis. Maintaining adequate NAD+ pools has been shown to play key roles in life span extension, but factors regulating NAD+ metabolism and homeostasis are not completely understood. Recently, NAD+ metabolism was also linked to the phosphate (Pi)-sensing PHO pathway in yeast. Canonical PHO activation requires Pi-starvation. Interestingly, NAD+ depletion without Pi-starvation was sufficient to induce PHO activation, increasing NR production and mobilization. Moreover, SPS signaling appears to function in parallel with PHO signaling components to regulate NR/NAD+ homeostasis. These studies suggest that NAD+ metabolism is likely controlled by and/or coordinated with multiple nutrient sensing pathways. Indeed, cross-regulation of PHO, PKA, TOR and Sch9 pathways was reported to potentially affect NAD+ metabolism; though detailed mechanisms remain unclear. This review discusses yeast longevity-related nutrient sensing pathways and possible mechanisms of life span extension, regulation of NAD+ homeostasis, and cross-talk among nutrient sensing pathways and NAD+ homeostasis.
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Affiliation(s)
- Felicia Tsang
- Department of Microbiology and Molecular Genetics, College of Biological Sciences, University of California, Davis, CA 95616, USA
| | - Su-Ju Lin
- Department of Microbiology and Molecular Genetics, College of Biological Sciences, University of California, Davis, CA 95616, USA
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23
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Quantifying intracellular metabolites in yeast using a matrix with minimal interference from naturally occurring analytes. Anal Biochem 2015; 487:17-26. [PMID: 26142219 DOI: 10.1016/j.ab.2015.06.033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Revised: 06/25/2015] [Accepted: 06/26/2015] [Indexed: 12/13/2022]
Abstract
For quantification of intracellular metabolites, mass spectrometry combined with liquid chromatography, capillary electrophoresis, or gas chromatography is currently the method of choice, especially when combined with stable isotope-labeled internal standards (SIL-ISs). Due to the difficulties in finding a biological matrix free of intracellular metabolites, a standard addition based validation is needed. Here, we present an alternative by producing a matrix with minimal signal interferences on both the analytes and their SIL-ISs. The matrix was obtained by cultivating Saccharomyces cerevisiae in [(13)C6]glucose/nonlabeled glucose (50:50, w/w) growth medium. The areas of both (12)C6 and (13)C6 fractions of ATP in the matrix were measured to be 2% of the sum of the areas of all ATP isotopes detected. The matrix allowed for spiking of both the nonlabeled and SIL-ISs and more straightforward validation. The intra- and inter-day accuracy and precision were ⩾80% and ⩽20%, respectively. The methodology was used for quantification of nucleotides, coenzymes, and redox compounds from Saccharomyces cerevisiae. The determined energy charge ratio was 0.9, whereas the Mal-CoA/Ac-CoA ratio was 0.04. The analysis of the redox compounds was challenging due to the oxidation of NADH and NADPH, when dissolved in water or tributylamine. The oxidation was reduced by dissolving them in ammonium acetate solution (pH 8.0).
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24
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Chen CNJ, Lin SY, Liao YH, Li ZJ, Wong AMK. Late-onset caloric restriction alters skeletal muscle metabolism by modulating pyruvate metabolism. Am J Physiol Endocrinol Metab 2015; 308:E942-9. [PMID: 26032513 DOI: 10.1152/ajpendo.00508.2014] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 04/07/2015] [Indexed: 12/20/2022]
Abstract
Caloric restriction (CR) attenuates age-related muscle loss. However, the underlying mechanism responsible for this attenuation is not fully understood. This study evaluated the role of energy metabolism in the CR-induced attenuation of muscle loss. The aims of this study were twofold: 1) to evaluate the effect of CR on energy metabolism and determine its relationship with muscle mass, and 2) to determine whether the effects of CR are age dependent. Young and middle-aged rats were randomized into either 40% CR or ad libitum (AL) diet groups for 14 wk. Major energy-producing pathways in muscles, i.e., glycolysis and mitochondrial oxidative phosphorylation (OXPHOS), were examined. We found that the effects of CR were age dependent. CR improved muscle metabolism and normalized muscle mass in middle-aged animals but not young animals. CR decreased glycolysis and increased the cellular dependency for OXPHOS vs. glycolysis in muscles of middle-aged rats, which was associated with the improvement of normalized muscle mass. The metabolic reprogramming induced by CR was related to modulation of pyruvate metabolism and increased mitochondrial biogenesis. Compared with animals fed AL, middle-aged animals with CR had lower lactate dehydrogenase A content and greater mitochondrial pyruvate carrier content. Markers of mitochondrial biogenesis, including AMPK activation levels and SIRT1 and COX-IV content, also showed increased levels. In conclusion, 14 wk of CR improved muscle metabolism and preserved muscle mass in middle-aged animals but not in young developing animals. CR-attenuated age-related muscle loss is associated with reprogramming of the metabolic pathway from glycolysis to OXPHOS.
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Affiliation(s)
- Chiao-Nan Joyce Chen
- Department of Physical Therapy, Medical School, Chang Gung University, Tao-Yuan, Taiwan; Healthy Aging Research Center, Chang Gung University, Tao-Yuan, Taiwan;
| | - Shang-Ying Lin
- Department of Physical Therapy, Medical School, Chang Gung University, Tao-Yuan, Taiwan
| | - Yi-Hung Liao
- Department of Exercise and Health Science, College of Human Development and Health, National Taipei University of Nursing and Health Sciences, Taipei, Taiwan; and
| | - Zhen-Jie Li
- Department of Physical Therapy, Medical School, Chang Gung University, Tao-Yuan, Taiwan
| | - Alice May-Kuen Wong
- Department of Physical Medicine and Rehabilitation, Chang Gung Memorial Hospital, Taipei, Taiwan
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25
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Shashkova S, Welkenhuysen N, Hohmann S. Molecular communication: crosstalk between the Snf1 and other signaling pathways. FEMS Yeast Res 2015; 15:fov026. [DOI: 10.1093/femsyr/fov026] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/15/2015] [Indexed: 02/02/2023] Open
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26
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Ruetenik A, Barrientos A. Dietary restriction, mitochondrial function and aging: from yeast to humans. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1847:1434-47. [PMID: 25979234 DOI: 10.1016/j.bbabio.2015.05.005] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 04/30/2015] [Accepted: 05/05/2015] [Indexed: 12/20/2022]
Abstract
Dietary restriction (DR) attenuates many detrimental effects of aging and consequently promotes health and increases longevity across organisms. While over the last 15 years extensive research has been devoted towards understanding the biology of aging, the precise mechanistic aspects of DR are yet to be settled. Abundant experimental evidence indicates that the DR effect on stimulating health impinges several metabolic and stress-resistance pathways. Downstream effects of these pathways include a reduction in cellular damage induced by oxidative stress, enhanced efficiency of mitochondrial functions and maintenance of mitochondrial dynamics and quality control, thereby attenuating age-related declines in mitochondrial function. However, the literature also accumulates conflicting evidence regarding how DR ameliorates mitochondrial performance and whether that is enough to slow age-dependent cellular and organismal deterioration. Here, we will summarize the current knowledge about how and to which extent the influence of different DR regimes on mitochondrial biogenesis and function contribute to postpone the detrimental effects of aging on health-span and lifespan. This article is part of a Special Issue entitled: Mitochondrial Dysfunction in Aging.
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Affiliation(s)
| | - Antoni Barrientos
- Neuroscience Graduate Program; Department of Neurology, University of Miami Miller School of Medicine, Miami, FL 33136, USA.
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27
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Hsu HE, Liu TN, Yeh CS, Chang TH, Lo YC, Kao CF. Feedback Control of Snf1 Protein and Its Phosphorylation Is Necessary for Adaptation to Environmental Stress. J Biol Chem 2015; 290:16786-96. [PMID: 25947383 DOI: 10.1074/jbc.m115.639443] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Indexed: 12/26/2022] Open
Abstract
Snf1, a member of the AMP-activated protein kinase family, plays a critical role in metabolic energy control in yeast cells. Snf1 activity is activated by phosphorylation of Thr-210 on the activation loop of its catalytic subunit; following activation, Snf1 regulates stress-responsive transcription factors. Here, we report that the level of Snf1 protein is dramatically decreased in a UBP8- and UBP10-deleted yeast mutant (ubp8Δ ubp10Δ), and this is independent of transcriptional regulation and proteasome-mediated degradation. Surprisingly, most Snf1-mediated functions, including glucose limitation regulation, utilization of alternative carbon sources, stress responses, and aging, are unaffected in this strain. Snf1 phosphorylation in ubp8Δ ubp10Δ cells is hyperactivated upon stress, which may compensate for the loss of the Snf1 protein and protect cells against stress and aging. Furthermore, artificial elevation of Snf1 phosphorylation (accomplished through deletion of REG1, which encodes a protein that regulates Snf1 dephosphorylation) restored Snf1 protein levels and the regulation of Snf1 activity in ubp8Δ ubp10Δ cells. Our results reveal the existence of a feedback loop that controls Snf1 protein level and its phosphorylation, which is masked by Ubp8 and Ubp10 through an unknown mechanism. We propose that this dynamic modulation of Snf1 phosphorylation and its protein level may be important for adaptation to environmental stress.
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Affiliation(s)
- Hsiang-En Hsu
- From the Graduate Institute of Life Sciences, National Defense Medical Center, Taipei 11490, Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taipei, Taiwan
| | - Tzu-Ning Liu
- the Institute of Food Science and Technology, College of Bio-Resources and Agriculture, National Taiwan University, Taipei 10617
| | - Chung-Shu Yeh
- the Institute of Biochemistry and Molecular Biology, National Yang Ming University, Taipei 11221, and the Genomics Research Center and
| | - Tien-Hsien Chang
- the Institute of Biochemistry and Molecular Biology, National Yang Ming University, Taipei 11221, and the Genomics Research Center and
| | - Yi-Chen Lo
- the Institute of Food Science and Technology, College of Bio-Resources and Agriculture, National Taiwan University, Taipei 10617,
| | - Cheng-Fu Kao
- From the Graduate Institute of Life Sciences, National Defense Medical Center, Taipei 11490, Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taipei, Taiwan
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28
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Jiao R, Postnikoff S, Harkness TA, Arnason TG. The SNF1 Kinase Ubiquitin-associated Domain Restrains Its Activation, Activity, and the Yeast Life Span. J Biol Chem 2015; 290:15393-15404. [PMID: 25869125 DOI: 10.1074/jbc.m115.647032] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Indexed: 02/04/2023] Open
Abstract
The enzyme family of heterotrimeric AMP-dependent protein kinases is activated upon low energy states, conferring a switch toward energy-conserving metabolic pathways through immediate kinase actions on enzyme targets and delayed alterations in gene expression through its nuclear relocalization. This family is evolutionarily conserved, including the presence of a ubiquitin-associated (UBA) motif in most catalytic subunits. The potential for the UBA domain to promote protein associations or direct subcellular location, as seen in other UBA-containing proteins, led us to query whether the UBA domain within the yeast AMP-dependent protein kinase ortholog, SNF1 kinase, was important in these aspects of its regulation. Here, we demonstrate that conserved UBA motif mutations significantly alter SNF1 kinase activation and biological activity, including enhanced allosteric subunit associations and increased oxidative stress resistance and life span. Significantly, the enhanced UBA-dependent longevity and oxidative stress response are at least partially dependent on the Fkh1 and Fkh2 stress response transcription factors, which in turn are shown to influence Snf1 gene expression.
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Affiliation(s)
- Rubin Jiao
- Departments of Anatomy and Cell Biology and University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada
| | - Spike Postnikoff
- Departments of Anatomy and Cell Biology and University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada
| | - Troy A Harkness
- Departments of Anatomy and Cell Biology and University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada
| | - Terra G Arnason
- Departments of Anatomy and Cell Biology and University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada; Medicine, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada.
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29
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Yao Y, Tsuchiyama S, Yang C, Bulteau AL, He C, Robison B, Tsuchiya M, Miller D, Briones V, Tar K, Potrero A, Friguet B, Kennedy BK, Schmidt M. Proteasomes, Sir2, and Hxk2 form an interconnected aging network that impinges on the AMPK/Snf1-regulated transcriptional repressor Mig1. PLoS Genet 2015; 11:e1004968. [PMID: 25629410 PMCID: PMC4309596 DOI: 10.1371/journal.pgen.1004968] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 12/19/2014] [Indexed: 01/20/2023] Open
Abstract
Elevated proteasome activity extends lifespan in model organisms such as yeast, worms and flies. This pro-longevity effect might be mediated by improved protein homeostasis, as this protease is an integral module of the protein homeostasis network. Proteasomes also regulate cellular processes through temporal and spatial degradation of signaling pathway components. Here we demonstrate that the regulatory function of the proteasome plays an essential role in aging cells and that the beneficial impact of elevated proteasome capacity on lifespan partially originates from deregulation of the AMPK signaling pathway. Proteasome-mediated lifespan extension activity was carbon-source dependent and cells with enhancement proteasome function exhibited increased respiratory activity and oxidative stress response. These findings suggested that the pro-aging impact of proteasome upregulation might be related to changes in the metabolic state through a premature induction of respiration. Deletion of yeast AMPK, SNF1, or its activator SNF4 abrogated proteasome-mediated lifespan extension, supporting this hypothesis as the AMPK pathway regulates metabolism. We found that the premature induction of respiration in cells with increased proteasome activity originates from enhanced turnover of Mig1, an AMPK/Snf1 regulated transcriptional repressor that prevents the induction of genes required for respiration. Increasing proteasome activity also resulted in partial relocation of Mig1 from the nucleus to the mitochondria. Collectively, the results argue for a model in which elevated proteasome activity leads to the uncoupling of Snf1-mediated Mig1 regulation, resulting in a premature activation of respiration and thus the induction of a mitohormetic response, beneficial to lifespan. In addition, we observed incorrect Mig1 localization in two other long-lived yeast aging models: cells that overexpress SIR2 or deleted for the Mig1-regulator HXK2. Finally, compromised proteasome function blocks lifespan extension in both strains. Thus, our findings suggest that proteasomes, Sir2, Snf1 and Hxk2 form an interconnected aging network that controls metabolism through coordinated regulation of Mig1. Advanced cellular age is associated with decreased efficiency of the proteostasis network. The proteasome, a protease in the cytoplasm and nuclei of eukaryotic cells, is an important component of this network. Recent studies demonstrate that increased proteasome capacity has a positive impact on longevity. The underlying mechanisms, however, have not been fully identified. Here we report that proteasomes are involved in regulating the AMP-activated kinase (AMPK) pathway and thus participate in correct metabolic adaptation. We find that Mig1, a transcriptional repressor downstream of yeast AMPK, Snf1, is a proteasome target and a negative regulator of lifespan. Increased proteasome activity results in enhanced turnover and incorrect localization of Mig1. The reduced Mig1 levels result in the induction of respiration and upregulation of the oxidative stress response. Premature Mig1 inactivation is also observed in two additional long-lived strains that overexpress SIR2 or are deleted for HXK2 and lifespan extension in both strains requires correct proteasome function. Our results uncover an interconnected network comprised of the proteasome, Sir2 and AMPK/Hxk2 signaling that impacts longevity through regulation of Mig1 and modulates respiratory metabolism. Mechanistic information on the cross-communication between these pathways is expected to facilitate the identification of novel pro-aging interventions.
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Affiliation(s)
- Yanhua Yao
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, New York, United States of America
| | | | - Ciyu Yang
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, New York, United States of America
| | | | - Chong He
- Buck Institute, Novato, California, United States of America
| | - Brett Robison
- Buck Institute, Novato, California, United States of America
| | | | - Delana Miller
- Buck Institute, Novato, California, United States of America
| | - Valeria Briones
- Buck Institute, Novato, California, United States of America
| | - Krisztina Tar
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, New York, United States of America
| | - Anahi Potrero
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, New York, United States of America
| | - Bertrand Friguet
- Laboratoire de Biologie Cellulaire du Vieillissement, UR4-IFR83, Université Pierre et Marie Curie-Paris 6, Paris, France
| | - Brian K. Kennedy
- Buck Institute, Novato, California, United States of America
- * E-mail: (MS); (BKK)
| | - Marion Schmidt
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, New York, United States of America
- * E-mail: (MS); (BKK)
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30
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Conrad M, Schothorst J, Kankipati HN, Van Zeebroeck G, Rubio-Texeira M, Thevelein JM. Nutrient sensing and signaling in the yeast Saccharomyces cerevisiae. FEMS Microbiol Rev 2014; 38:254-99. [PMID: 24483210 PMCID: PMC4238866 DOI: 10.1111/1574-6976.12065] [Citation(s) in RCA: 419] [Impact Index Per Article: 41.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Revised: 12/23/2013] [Accepted: 01/22/2014] [Indexed: 02/04/2023] Open
Abstract
The yeast Saccharomyces cerevisiae has been a favorite organism for pioneering studies on nutrient-sensing and signaling mechanisms. Many specific nutrient responses have been elucidated in great detail. This has led to important new concepts and insight into nutrient-controlled cellular regulation. Major highlights include the central role of the Snf1 protein kinase in the glucose repression pathway, galactose induction, the discovery of a G-protein-coupled receptor system, and role of Ras in glucose-induced cAMP signaling, the role of the protein synthesis initiation machinery in general control of nitrogen metabolism, the cyclin-controlled protein kinase Pho85 in phosphate regulation, nitrogen catabolite repression and the nitrogen-sensing target of rapamycin pathway, and the discovery of transporter-like proteins acting as nutrient sensors. In addition, a number of cellular targets, like carbohydrate stores, stress tolerance, and ribosomal gene expression, are controlled by the presence of multiple nutrients. The protein kinase A signaling pathway plays a major role in this general nutrient response. It has led to the discovery of nutrient transceptors (transporter receptors) as nutrient sensors. Major shortcomings in our knowledge are the relationship between rapid and steady-state nutrient signaling, the role of metabolic intermediates in intracellular nutrient sensing, and the identity of the nutrient sensors controlling cellular growth.
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Affiliation(s)
- Michaela Conrad
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU LeuvenLeuven-Heverlee, Flanders, Belgium
- Department of Molecular Microbiology, VIBLeuven-Heverlee, Flanders, Belgium
| | - Joep Schothorst
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU LeuvenLeuven-Heverlee, Flanders, Belgium
- Department of Molecular Microbiology, VIBLeuven-Heverlee, Flanders, Belgium
| | - Harish Nag Kankipati
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU LeuvenLeuven-Heverlee, Flanders, Belgium
- Department of Molecular Microbiology, VIBLeuven-Heverlee, Flanders, Belgium
| | - Griet Van Zeebroeck
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU LeuvenLeuven-Heverlee, Flanders, Belgium
- Department of Molecular Microbiology, VIBLeuven-Heverlee, Flanders, Belgium
| | - Marta Rubio-Texeira
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU LeuvenLeuven-Heverlee, Flanders, Belgium
- Department of Molecular Microbiology, VIBLeuven-Heverlee, Flanders, Belgium
| | - Johan M Thevelein
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU LeuvenLeuven-Heverlee, Flanders, Belgium
- Department of Molecular Microbiology, VIBLeuven-Heverlee, Flanders, Belgium
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31
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Mutations in SNF1 complex genes affect yeast cell wall strength. Eur J Cell Biol 2013; 92:383-95. [DOI: 10.1016/j.ejcb.2014.01.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Revised: 12/19/2013] [Accepted: 01/02/2014] [Indexed: 01/01/2023] Open
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32
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Siegel D, Permentier H, Reijngoud DJ, Bischoff R. Chemical and technical challenges in the analysis of central carbon metabolites by liquid-chromatography mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 2013; 966:21-33. [PMID: 24326023 DOI: 10.1016/j.jchromb.2013.11.022] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Revised: 11/10/2013] [Accepted: 11/12/2013] [Indexed: 11/18/2022]
Abstract
This review deals with chemical and technical challenges in the analysis of small-molecule metabolites involved in central carbon and energy metabolism via liquid-chromatography mass-spectrometry (LC-MS). The covered analytes belong to the prominent pathways in biochemical carbon oxidation such as glycolysis or the tricarboxylic acid cycle and, for the most part, share unfavorable properties such as a high polarity, chemical instability or metal-affinity. The topic is introduced by selected examples on successful applications of metabolomics in the clinic. In the core part of the paper, the structural features of important analyte classes such as nucleotides, coenzyme A thioesters or carboxylic acids are linked to "problematic hotspots" along the analytical chain (sample preparation and-storage, separation and detection). We discuss these hotspots from a chemical point of view, covering issues such as analyte degradation or interactions with metals and other matrix components. Based on this understanding we propose solutions wherever available. A major notion derived from these considerations is that comprehensive carbon metabolomics inevitably requires multiple, complementary analytical approaches covering different chemical classes of metabolites.
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Affiliation(s)
- David Siegel
- University of Groningen, Department of Pharmacy, Analytical Biochemistry, Antonius-Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Hjalmar Permentier
- University of Groningen, Department of Pharmacy, Mass Spectrometry Core Facility, Antonius-Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Dirk-Jan Reijngoud
- University Medical Center Groningen, Department of Pediatrics, Center for Liver, Digestive and Metabolic Diseases, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Rainer Bischoff
- University of Groningen, Department of Pharmacy, Analytical Biochemistry, Antonius-Deusinglaan 1, 9713 AV Groningen, The Netherlands.
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33
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Wasko BM, Kaeberlein M. Yeast replicative aging: a paradigm for defining conserved longevity interventions. FEMS Yeast Res 2013; 14:148-59. [PMID: 24119093 DOI: 10.1111/1567-1364.12104] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Revised: 08/22/2013] [Accepted: 09/26/2013] [Indexed: 12/15/2022] Open
Abstract
The finite replicative life span of budding yeast mother cells was demonstrated as early as 1959, but the idea that budding yeast could be used to model aging of multicellular eukaryotes did not enter the scientific mainstream until relatively recently. Despite continued skepticism by some, there are now abundant data that several interventions capable of extending yeast replicative life span have a similar effect in multicellular eukaryotes including nematode worms, fruit flies, and rodents. In particular, dietary restriction, mTOR signaling, and sirtuins are among the most studied longevity interventions in the field. Here, we describe key conserved longevity pathways in yeast and discuss relationships that may help explain how such broad conservation of aging processes could have evolved.
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Affiliation(s)
- Brian M Wasko
- Department of Pathology, University of Washington, Seattle, WA, USA
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34
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Seifar RM, Ras C, Deshmukh AT, Bekers KM, Suarez-Mendez CA, da Cruz AL, van Gulik WM, Heijnen JJ. Quantitative analysis of intracellular coenzymes in Saccharomyces cerevisiae using ion pair reversed phase ultra high performance liquid chromatography tandem mass spectrometry. J Chromatogr A 2013; 1311:115-20. [DOI: 10.1016/j.chroma.2013.08.076] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Revised: 08/20/2013] [Accepted: 08/21/2013] [Indexed: 11/17/2022]
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35
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Lee S, Gaspar ML, Aregullin MA, Jesch SA, Henry SA. Activation of protein kinase C-mitogen-activated protein kinase signaling in response to inositol starvation triggers Sir2p-dependent telomeric silencing in yeast. J Biol Chem 2013; 288:27861-71. [PMID: 23943620 DOI: 10.1074/jbc.m113.493072] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Depriving wild type yeast of inositol, a soluble precursor for phospholipid, phosphoinositide, and complex sphingolipid synthesis, activates the protein kinase C (PKC)-MAPK signaling pathway, which plays a key role in the activation of NAD(+)-dependent telomeric silencing. We now report that triggering PKC-MAPK signaling by inositol deprivation or by blocking inositol-containing sphingolipid synthesis with aureobasidin A results in increased telomeric silencing regulated by the MAPK, Slt2p, and the NAD(+)-dependent deacetylase, Sir2p. Consistent with the dependence on NAD(+) in Sir2p-regulated silencing, we found that inositol depletion induces the expression of BNA2, which is required for the de novo synthesis of NAD(+). Moreover, telomeric silencing is greatly reduced in bna2Δ and npt1Δ mutants, which are defective in de novo and salvage pathways for NAD(+) synthesis, respectively. Surprisingly, however, omitting nicotinic acid from the growth medium, which reduces cellular NAD(+) levels, leads to increased telomeric silencing in the absence of inositol and/or at high temperature. This increase in telomeric silencing in response to inositol starvation is correlated to chronological life span extension but is Sir2p-independent. We conclude that activation of the PKC-MAPK signaling by interruption of inositol sphingolipid synthesis leads to increased Sir2p-dependent silencing and is dependent upon the de novo and salvage pathways for NAD(+) synthesis but is not correlated with cellular NAD(+) levels.
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Affiliation(s)
- Sojin Lee
- From the Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853
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36
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Wei Y, Zhang YJ, Cai Y. Growth or longevity: the TOR’s decision on lifespan regulation. Biogerontology 2013; 14:353-63. [DOI: 10.1007/s10522-013-9435-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Accepted: 05/21/2013] [Indexed: 11/28/2022]
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37
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Rodríguez-Colman MJ, Sorolla MA, Vall-Llaura N, Tamarit J, Ros J, Cabiscol E. The FOX transcription factor Hcm1 regulates oxidative metabolism in response to early nutrient limitation in yeast. Role of Snf1 and Tor1/Sch9 kinases. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2013; 1833:2004-15. [PMID: 23481038 DOI: 10.1016/j.bbamcr.2013.02.015] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2012] [Revised: 02/13/2013] [Accepted: 02/15/2013] [Indexed: 02/07/2023]
Abstract
Within Saccharomyces cerevisiae, Hcm1is a member of the forkhead transcription factor family with a role in chromosome organization. Our group recently described its involvement in mitochondrial biogenesis and stress resistance, and reports here that Hcm1 played a role in adaptation to respiratory metabolism when glucose or nitrogen was decreased. Regulation of Hcm1 activity occurs in at least three ways: i) protein quantity, ii) subcellular localization, and iii) transcriptional activity. Transcriptional activity was measured using a reporter gene fused to a promoter that contains a binding site for Hcm1. We also analyzed the levels of several genes whose expression is known to be regulated by Hcm1 levels and the role of the main kinases known to respond to nutrients. Lack of sucrose-nonfermenting (Snf1) kinase increases cytoplasmic localization of Hcm1, whereas Δtor1 cells showed a mild increase in nuclear Hcm1. In vitro experiments showed that Snf1 clearly phosphorylates Hcm1 while Sch9 exerts a milder phosphorylation. Although in vitroTor1 does not directly phosphorylate Hcm1, in vivo rapamycin treatment increases nuclear Hcm1. We conclude that Hcm1 participates in the adaptation of cells from fermentation to respiratory metabolism during nutrient scarcity. According to our hypothesis, when nutrient levels decrease, Snf1 phosphorylates Hcm1. This results in a shift from the cytoplasm to the nucleus and increased transcriptional activity of genes involved in respiration, use of alternative energy sources, NAD synthesis and oxidative stress resistance.
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38
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PdSNF1, a sucrose non-fermenting protein kinase gene, is required for Penicillium digitatum conidiation and virulence. Appl Microbiol Biotechnol 2013; 97:5433-45. [DOI: 10.1007/s00253-012-4593-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Revised: 11/11/2012] [Accepted: 11/13/2012] [Indexed: 10/27/2022]
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39
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Abstract
Availability of key nutrients, such as sugars, amino acids, and nitrogen compounds, dictates the developmental programs and the growth rates of yeast cells. A number of overlapping signaling networks--those centered on Ras/protein kinase A, AMP-activated kinase, and target of rapamycin complex I, for instance--inform cells on nutrient availability and influence the cells' transcriptional, translational, posttranslational, and metabolic profiles as well as their developmental decisions. Here I review our current understanding of the structures of the networks responsible for assessing the quantity and quality of carbon and nitrogen sources. I review how these signaling pathways impinge on transcriptional, metabolic, and developmental programs to optimize survival of cells under different environmental conditions. I highlight the profound knowledge we have gained on the structure of these signaling networks but also emphasize the limits of our current understanding of the dynamics of these signaling networks. Moreover, the conservation of these pathways has allowed us to extrapolate our finding with yeast to address issues of lifespan, cancer metabolism, and growth control in more complex organisms.
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Affiliation(s)
- James R Broach
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA.
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40
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Abstract
For unicellular organisms, the decision to enter the cell cycle can be viewed most fundamentally as a metabolic problem. A cell must assess its nutritional and metabolic status to ensure it can synthesize sufficient biomass to produce a new daughter cell. The cell must then direct the appropriate metabolic outputs to ensure completion of the division process. Herein, we discuss the changes in metabolism that accompany entry to, and exit from, the cell cycle for the unicellular eukaryote Saccharomyces cerevisiae. Studies of budding yeast under continuous, slow-growth conditions have provided insights into the essence of these metabolic changes at unprecedented temporal resolution. Some of these mechanisms by which cell growth and proliferation are coordinated with metabolism are likely to be conserved in multicellular organisms. An improved understanding of the metabolic basis of cell cycle control promises to reveal fundamental principles governing tumorigenesis, metazoan development, niche expansion, and many additional aspects of cell and organismal growth control.
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Affiliation(s)
- Ling Cai
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9038, USA.
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41
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Abstract
AMPK (AMP-activated protein kinase) is one of the key players in maintaining intracellular homoeostasis. AMPK is well known as an energy sensor and can be activated by increased intracellular AMP levels. Generally, the activation of AMPK turns on catabolic pathways that generate ATP, while inhibiting cell proliferation and biosynthetic processes that consume ATP. In recent years, intensive investigations on the regulation and the function of AMPK indicates that AMPK not only functions as an intracellular energy sensor and regulator, but is also a general stress sensor that is important in maintaining intracellular homoeostasis during many kinds of stress challenges. In the present paper, we will review recent literature showing that AMPK functions far beyond its proposed energy sensor and regulator function. AMPK regulates ROS (reactive oxygen species)/redox balance, autophagy, cell proliferation, cell apoptosis, cellular polarity, mitochondrial function and genotoxic response, either directly or indirectly via numerous downstream pathways under physiological and pathological conditions.
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42
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Cantó C, Auwerx J. Calorie restriction: is AMPK a key sensor and effector? Physiology (Bethesda) 2012; 26:214-24. [PMID: 21841070 DOI: 10.1152/physiol.00010.2011] [Citation(s) in RCA: 173] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Dietary restriction can extend life span in most organisms tested to date, suggesting that mechanisms sensing nutrient and energy availability might regulate longevity. The AMP-activated protein kinase (AMPK) has emerged as a key energy sensor with the ability to transcriptionally reprogram the cell and metabolically adapt to external cues. In this review, we will discuss the possible role of AMPK in the beneficial effects of calorie restriction on health and life span.
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Affiliation(s)
- Carles Cantó
- Laboratory of Integrative and Systems Physiology and Nestle Chair in Energy Metabolism, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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Mair W, Steffen KK, Dillin A. SIP-ing the elixir of youth. Cell 2011; 146:859-60. [PMID: 21925309 DOI: 10.1016/j.cell.2011.08.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AMP-activated protein kinase (AMPK) is a conserved cellular fuel gauge previously implicated in aging. In this issue, Lu et al. (2011) describe how age-related deacetylation of Sip2, a subunit of the AMPK homolog in yeast, acts as a life span clock that can be wound backward or forward to modulate longevity.
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Affiliation(s)
- William Mair
- The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
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44
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Ghillebert R, Swinnen E, Wen J, Vandesteene L, Ramon M, Norga K, Rolland F, Winderickx J. The AMPK/SNF1/SnRK1 fuel gauge and energy regulator: structure, function and regulation. FEBS J 2011; 278:3978-90. [PMID: 21883929 DOI: 10.1111/j.1742-4658.2011.08315.x] [Citation(s) in RCA: 152] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
All life forms on earth require a continuous input and monitoring of carbon and energy supplies. The AMP-activated kinase (AMPK)/sucrose non-fermenting1 (SNF1)/Snf1-related kinase1 (SnRK1) protein kinases are evolutionarily conserved metabolic sensors found in all eukaryotic organisms from simple unicellular fungi (yeast SNF1) to animals (AMPK) and plants (SnRK1). Activated by starvation and energy-depleting stress conditions, they enable energy homeostasis and survival by up-regulating energy-conserving and energy-producing catabolic processes, and by limiting energy-consuming anabolic metabolism. In addition, they control normal growth and development as well as metabolic homeostasis at the organismal level. As such, the AMPK/SNF1/SnRK1 kinases act in concert with other central signaling components to control carbohydrate uptake and metabolism, fatty acid and lipid biosynthesis and the storage of carbon energy reserves. Moreover, they have a tremendous impact on developmental processes that are triggered by environmental changes such as nutrient depletion or stress. Although intensive research by many groups has partly unveiled the factors that regulate AMPK/SNF1/SnRK1 kinase activity as well as the pathways and substrates they control, several fundamental issues still await to be clarified. In this review, we will highlight these issues and focus on the structure, function and regulation of the AMPK/SNF1/SnRK1 kinases.
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Affiliation(s)
- Ruben Ghillebert
- Department of Biology, Laboratory for Functional Biology, Katholieke Universiteit Leuven, Heverlee, Belgium
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45
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Acetylation of yeast AMPK controls intrinsic aging independently of caloric restriction. Cell 2011; 146:969-79. [PMID: 21906795 DOI: 10.1016/j.cell.2011.07.044] [Citation(s) in RCA: 114] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2011] [Revised: 05/02/2011] [Accepted: 07/29/2011] [Indexed: 12/15/2022]
Abstract
Acetylation of histone and nonhistone proteins is an important posttranslational modification affecting many cellular processes. Here, we report that NuA4 acetylation of Sip2, a regulatory β subunit of the Snf1 complex (yeast AMP-activated protein kinase), decreases as cells age. Sip2 acetylation, controlled by antagonizing NuA4 acetyltransferase and Rpd3 deacetylase, enhances interaction with Snf1, the catalytic subunit of Snf1 complex. Sip2-Snf1 interaction inhibits Snf1 activity, thus decreasing phosphorylation of a downstream target, Sch9 (homolog of Akt/S6K), and ultimately leading to slower growth but extended replicative life span. Sip2 acetylation mimetics are more resistant to oxidative stress. We further demonstrate that the anti-aging effect of Sip2 acetylation is independent of extrinsic nutrient availability and TORC1 activity. We propose a protein acetylation-phosphorylation cascade that regulates Sch9 activity, controls intrinsic aging, and extends replicative life span in yeast.
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Abstract
In this study, a reverse-engineering strategy was used to infer and analyze the structure and function of an aging and glucose repressed gene regulatory network in the budding yeast Saccharomyces cerevisiae. The method uses transcriptional perturbations to model the functional interactions between genes as a system of first-order ordinary differential equations. The resulting network model correctly identified the known interactions of key regulators in a 10-gene network from the Snf1 signaling pathway, which is required for expression of glucose-repressed genes upon calorie restriction. The majority of interactions predicted by the network model were confirmed using promoter-reporter gene fusions in gene-deletion mutants and chromatin immunoprecipitation experiments, revealing a more complex network architecture than previously appreciated. The reverse-engineered network model also predicted an unexpected role for transcriptional regulation of the SNF1 gene by hexose kinase enzyme/transcriptional repressor Hxk2, Mediator subunit Med8, and transcriptional repressor Mig1. These interactions were validated experimentally and used to design new experiments demonstrating Snf1 and its transcriptional regulators Hxk2 and Mig1 as modulators of chronological lifespan. This work demonstrates the value of using network inference methods to identify and characterize the regulators of complex phenotypes, such as aging.
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47
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Van de Velde S, Thevelein JM. Cyclic AMP-Protein Kinase A and Snf1 Signaling Mechanisms Underlie the Superior Potency of Sucrose for Induction of Filamentation in
Saccharomyces cerevisiae. EUKARYOTIC CELL 2008; 7:286-93. [PMID: 17890371 PMCID: PMC2238163 DOI: 10.1128/ec.00276-07] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
ABSTRACT
Under specific environmental conditions, the yeast
Saccharomyces cerevisiae
can undergo a morphological switch to a pseudohyphal growth pattern. Pseudohyphal differentiation is generally studied upon induction by nitrogen limitation in the presence of glucose. It is known to be controlled by several signaling pathways, including mitogen-activated protein kinase, cyclic AMP-protein kinase A (cAMP-PKA), and Snf1 kinase pathways. We show that the alpha-glucoside sugars maltose and maltotriose, and especially sucrose, are more potent inducers of filamentation than glucose. Sucrose even induces filamentation in nitrogen-rich media and in the
mep2
Δ
/mep2
Δ ammonium permease mutant on ammonium-limiting medium. We demonstrate that glucose also inhibits filamentation by means of a pathway parallel to the cAMP-PKA pathway. Deletion of
HXK2
shifted the pseudohyphal growth pattern on glucose to that of sucrose, while deletion of
SNF4
abrogated filamentation on both sugars, indicating a negative role of glucose repression and a positive role for Snf1 activity in the control of filamentation. In all strains and in all media, sucrose induction of filamentation is greatly diminished by deletion of the sucrose/glucose-sensing G-protein-coupled receptor Gpr1, whereas it has no effect on induction by maltose and maltotriose. The competence of alpha-glucoside sugars to induce filamentation is reflected in the increased expression of the cell surface flocculin gene
FLO11
. In addition, sucrose is the only alpha-glucoside sugar capable of rapidly inducing
FLO11
expression in a Gpr1-dependent manner, reflecting the sensitivity of Gpr1 for this sugar and its involvement in rapid sucrose signaling. Our study identifies sucrose as the most potent nutrient inducer of pseudohyphal growth and shows that glucose inactivation of Snf1 kinase signaling is responsible for the lower potency of glucose.
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Affiliation(s)
- Sam Van de Velde
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, Katholieke Universiteit Leuven, and Department ofMolecular Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
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48
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Pierre M, Traverso JA, Boisson B, Domenichini S, Bouchez D, Giglione C, Meinnel T. N-myristoylation regulates the SnRK1 pathway in Arabidopsis. THE PLANT CELL 2007; 19:2804-21. [PMID: 17827350 PMCID: PMC2048702 DOI: 10.1105/tpc.107.051870] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Cotranslational and posttranslational modifications are increasingly recognized as important in the regulation of numerous essential cellular functions. N-myristoylation is a lipid modification ensuring the proper function and intracellular trafficking of proteins involved in many signaling pathways. Arabidopsis thaliana, like human, has two tightly regulated N-myristoyltransferase (NMT) genes, NMT1 and NMT2. Characterization of knockout mutants showed that NMT1 was strictly required for plant viability, whereas NMT2 accelerated flowering. NMT1 impairment induced extremely severe defects in the shoot apical meristem during embryonic development, causing growth arrest after germination. A transgenic plant line with an inducible NMT1 gene demonstrated that NMT1 expression had further effects at later stages. NMT2 did not compensate for NMT1 in the nmt1-1 mutant, but NMT2 overexpression resulted in shoot and root meristem abnormalities. Various data from complementation experiments in the nmt1-1 background, using either yeast or human NMTs, demonstrated a functional link between the developmental arrest of nmt1-1 mutants and the myristoylation state of an extremely small set of protein targets. We show here that protein N-myristoylation is systematically associated with shoot meristem development and that SnRK1 (for SNF1-related kinase) is one of its essential primary targets.
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Affiliation(s)
- Michèle Pierre
- Protein Maturation and Cell Fate, Institut des Sciences du Végétal, Unité Propre de Recherche 2355, Centre National de la Recherche Scientifique, F-91198, Gif-sur-Yvette Cedex, France
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49
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Rosnoblet C, Aubry C, Leprince O, Vu BL, Rogniaux H, Buitink J. The regulatory gamma subunit SNF4b of the sucrose non-fermenting-related kinase complex is involved in longevity and stachyose accumulation during maturation of Medicago truncatula seeds. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2007; 51:47-59. [PMID: 17488238 DOI: 10.1111/j.1365-313x.2007.03116.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
The sucrose non-fermenting-related kinase complex (SnRK1) is a heterotrimeric complex that plays a central role in metabolic adaptation to nutritional or environmental stresses. Here we investigate the role of a regulatory gamma-subunit of the complex, MtSNF4b, in Medicago truncatula seeds. Western blot indicated that MtSNF4b accumulated during seed filling, whereas it disappeared during imbibition of mature seeds. Gel filtration chromatography suggested that MtSNF4b assembled into a complex (450-600 kDa) at the onset of maturation drying, and dissociated during subsequent imbibition. Drying of desiccation-tolerant radicles led to a reassembly of the complex, in contrast to sensitive tissues. Silencing of MtSNF4b using a RNA interference (RNAi) approach resulted in a phenotype with reduced seed longevity, evident from the reduction in both germination percentage and seedling vigour in aged RNAi MtSNF4b seeds compared with the wild-type seeds. In parallel to the assembly of the complex, seeds of the RNAi MtSNF4b lines showed impaired accumulation of raffinose family oligosaccharides compared with control seeds. In mature seeds, the amount of stachyose was reduced by 50-80%, whereas the sucrose content was 60% higher. During imbibition, the differences in non-reducing sugar compared with the control disappeared in parallel to the disassembly of the complex. No difference was observed in dry weight or reserve accumulation such as proteins, lipids and starch. These data suggest that the regulatory gamma-subunit MtSNF4b confers a specific and temporal function to SnRK1 complexes in seeds, improving seed longevity and affecting the non-reducing sugar content at later stages of seed maturation.
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Affiliation(s)
- Claire Rosnoblet
- Unité Mixte de Recherche 1191 Physiologie Moléculaire des Semences (Université d'Angers, Institut National d'Horticulture, Institut National de la Recherche Agronomique), 16 boulevard Lavoisier, 49045 Angers, France
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50
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Alkhalfioui F, Renard M, Vensel WH, Wong J, Tanaka CK, Hurkman WJ, Buchanan BB, Montrichard F. Thioredoxin-linked proteins are reduced during germination of Medicago truncatula seeds. PLANT PHYSIOLOGY 2007; 144:1559-79. [PMID: 17513483 PMCID: PMC1914137 DOI: 10.1104/pp.107.098103] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Germination of cereals is accompanied by extensive change in the redox state of seed proteins. Proteins present in oxidized form in dry seeds are converted to the reduced state following imbibition. Thioredoxin (Trx) appears to play a role in this transition in cereals. It is not known, however, whether Trx-linked redox changes are restricted to cereals or whether they take place more broadly in germinating seeds. To gain information on this point, we have investigated a model legume, Medicago truncatula. Two complementary gel-based proteomic approaches were followed to identify Trx targets in seeds: Proteins were (1) labeled with a thiol-specific probe, monobromobimane (mBBr), following in vitro reduction by an NADP/Trx system, or (2) isolated on a mutant Trx affinity column. Altogether, 111 Trx-linked proteins were identified with few differences between axes and cotyledons. Fifty nine were new, 34 found previously in cereal or peanut seeds, and 18 in other plants or photosynthetic organisms. In parallel, the redox state of proteins assessed in germinating seeds using mBBr revealed that a substantial number of proteins that are oxidized or partly reduced in dry seeds became more reduced upon germination. The patterns were similar for proteins reduced in vivo during germination or in vitro by Trx. In contrast, glutathione and glutaredoxin were less effective as reductants in vitro. Overall, more than half of the potential targets identified with the mBBr labeling procedure were reduced during germination. The results provide evidence that Trx functions in the germination of seeds of dicotyledons as well as monocotyledons.
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Affiliation(s)
- Fatima Alkhalfioui
- Physiologie Moléculaire des Semences, Unité Mixte de Recherche 1191, Université d'Angers, Institut National d'Horticulture, Institut National de la Recherche Agronomique, Anjou Recherche Semences, Angers Cedex 01, France
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