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Liu Q, Zhu D, Li N, Chen S, Hu L, Yu J, Xiong Y. Regulation of LRRK2 mRNA stability by ATIC and its substrate AICAR through ARE-mediated mRNA decay in Parkinson's disease. EMBO J 2023; 42:e113410. [PMID: 37366237 PMCID: PMC10390876 DOI: 10.15252/embj.2022113410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 05/08/2023] [Accepted: 05/15/2023] [Indexed: 06/28/2023] Open
Abstract
Mutations in LRRK2 are the most common genetic causes of Parkinson's disease (PD). While the enzymatic activity of LRRK2 has been linked to PD, previous work has also provided support for an important role of elevated LRRK2 protein levels, independent of enzymatic activity, in PD pathogenesis. However, the mechanisms underlying the regulation of LRRK2 protein levels remain unclear. Here, we identify a role for the purine biosynthesis pathway enzyme ATIC in the regulation of LRRK2 levels and toxicity. AICAr, the precursor of ATIC substrate, regulates LRRK2 levels in a cell-type-specific manner in vitro and in mouse tissue. AICAr regulates LRRK2 levels through AUF1-mediated mRNA decay. Upon AICAr treatment, the RNA binding protein AUF1 is recruited to the AU-rich elements (ARE) of LRRK2 mRNA leading to the recruitment of the decapping enzyme complex DCP1/2 and decay of LRRK2 mRNA. AICAr suppresses LRRK2 expression and rescues LRRK2-induced dopaminergic neurodegeneration and neuroinflammation in PD Drosophila and mouse models. Together, this study provides insight into a novel regulatory mechanism of LRRK2 protein levels and function via LRRK2 mRNA decay that is distinct from LRRK2 enzymatic functions.
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Affiliation(s)
- Qinfang Liu
- Department of NeuroscienceUniversity of Connecticut School of MedicineFarmingtonCTUSA
| | - Dong Zhu
- Department of NeuroscienceUniversity of Connecticut School of MedicineFarmingtonCTUSA
| | - Naren Li
- Department of Physiology & NeurobiologyUniversity of ConnecticutStorrsCTUSA
| | - Shifan Chen
- Department of NeuroscienceUniversity of Connecticut School of MedicineFarmingtonCTUSA
| | - Liang Hu
- Department of Physiology & NeurobiologyUniversity of ConnecticutStorrsCTUSA
| | - Jianzhong Yu
- Department of Physiology & NeurobiologyUniversity of ConnecticutStorrsCTUSA
| | - Yulan Xiong
- Department of NeuroscienceUniversity of Connecticut School of MedicineFarmingtonCTUSA
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2
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Li G, Jian T, Liu X, Lv Q, Zhang G, Ling J. Application of Metabolomics in Fungal Research. Molecules 2022; 27:7365. [PMID: 36364192 PMCID: PMC9654507 DOI: 10.3390/molecules27217365] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/23/2022] [Accepted: 10/25/2022] [Indexed: 08/27/2023] Open
Abstract
Metabolomics is an essential method to study the dynamic changes of metabolic networks and products using modern analytical techniques, as well as reveal the life phenomena and their inherent laws. Currently, more and more attention has been paid to the development of metabolic histochemistry in the fungus field. This paper reviews the application of metabolomics in fungal research from five aspects: identification, response to stress, metabolite discovery, metabolism engineering, and fungal interactions with plants.
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Affiliation(s)
- Guangyao Li
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Tongtong Jian
- Hospital of Shandong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Xiaojin Liu
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Qingtao Lv
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Guoying Zhang
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Jianya Ling
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
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3
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An ion-pair free LC-MS/MS method for quantitative metabolite profiling of microbial bioproduction systems. Talanta 2021; 222:121625. [DOI: 10.1016/j.talanta.2020.121625] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 08/31/2020] [Accepted: 09/02/2020] [Indexed: 11/23/2022]
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4
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Sailwal M, Das AJ, Gazara RK, Dasgupta D, Bhaskar T, Hazra S, Ghosh D. Connecting the dots: Advances in modern metabolomics and its application in yeast system. Biotechnol Adv 2020; 44:107616. [DOI: 10.1016/j.biotechadv.2020.107616] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 08/15/2020] [Accepted: 08/17/2020] [Indexed: 12/15/2022]
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5
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Saint-Marc C, Ceschin J, Almyre C, Pinson B, Daignan-Fornier B. Genetic investigation of purine nucleotide imbalance in Saccharomyces cerevisiae. Curr Genet 2020; 66:1163-1177. [PMID: 32780163 DOI: 10.1007/s00294-020-01101-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 07/21/2020] [Accepted: 08/06/2020] [Indexed: 11/28/2022]
Abstract
Because metabolism is a complex balanced process involving multiple enzymes, understanding how organisms compensate for transient or permanent metabolic imbalance is a challenging task that can be more easily achieved in simpler unicellular organisms. The metabolic balance results not only from the combination of individual enzymatic properties, regulation of enzyme abundance, but also from the architecture of the metabolic network offering multiple interconversion alternatives. Although metabolic networks are generally highly resilient to perturbations, metabolic imbalance resulting from enzymatic defect and specific environmental conditions can be designed experimentally and studied. Starting with a double amd1 aah1 mutant that severely and conditionally affects yeast growth, we carefully characterized the metabolic shuffle associated with this defect. We established that the GTP decrease resulting in an adenylic/guanylic nucleotide imbalance was responsible for the growth defect. Identification of several gene dosage suppressors revealed that TAT1, encoding an amino acid transporter, is a robust suppressor of the amd1 aah1 growth defect. We show that TAT1 suppression occurs through replenishment of the GTP pool in a process requiring the histidine biosynthesis pathway. Importantly, we establish that a tat1 mutant exhibits synthetic sickness when combined with an amd1 mutant and that both components of this synthetic phenotype can be suppressed by specific gene dosage suppressors. Together our data point to a strong phenotypic connection between amino acid uptake and GTP synthesis, a connection that could open perspectives for future treatment of related human defects, previously reported as etiologically highly conserved.
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Affiliation(s)
- Christelle Saint-Marc
- IBGC, UMR 5095, Université de Bordeaux, Bordeaux, France.,Centre National de la Recherche Scientifique IBGC, UMR 5095, Bordeaux, France
| | - Johanna Ceschin
- IBGC, UMR 5095, Université de Bordeaux, Bordeaux, France.,Centre National de la Recherche Scientifique IBGC, UMR 5095, Bordeaux, France
| | - Claire Almyre
- IBGC, UMR 5095, Université de Bordeaux, Bordeaux, France.,Centre National de la Recherche Scientifique IBGC, UMR 5095, Bordeaux, France
| | - Benoît Pinson
- IBGC, UMR 5095, Université de Bordeaux, Bordeaux, France.,Centre National de la Recherche Scientifique IBGC, UMR 5095, Bordeaux, France
| | - Bertrand Daignan-Fornier
- IBGC, UMR 5095, Université de Bordeaux, Bordeaux, France. .,Centre National de la Recherche Scientifique IBGC, UMR 5095, Bordeaux, France.
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6
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Minazzato G, Gasparrini M, Amici A, Cianci M, Mazzola F, Orsomando G, Sorci L, Raffaelli N. Functional Characterization of COG1713 (YqeK) as a Novel Diadenosine Tetraphosphate Hydrolase Family. J Bacteriol 2020; 202:e00053-20. [PMID: 32152217 PMCID: PMC7186459 DOI: 10.1128/jb.00053-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 03/03/2020] [Indexed: 12/29/2022] Open
Abstract
Diadenosine tetraphosphate (Ap4A) is a dinucleotide found in both prokaryotes and eukaryotes. In bacteria, its cellular levels increase following exposure to various stress signals and stimuli, and its accumulation is generally correlated with increased sensitivity to a stressor(s), decreased pathogenicity, and enhanced antibiotic susceptibility. Ap4A is produced as a by-product of tRNA aminoacylation, and is cleaved to ADP molecules by hydrolases of the ApaH and Nudix families and/or by specific phosphorylases. Here, considering evidence that the recombinant protein YqeK from Staphylococcus aureus copurified with ADP, and aided by thermal shift and kinetic analyses, we identified the YqeK family of proteins (COG1713) as an unprecedented class of symmetrically cleaving Ap4A hydrolases. We validated the functional assignment by confirming the ability of YqeK to affect in vivo levels of Ap4A in B. subtilis YqeK shows a catalytic efficiency toward Ap4A similar to that of the symmetrically cleaving Ap4A hydrolases of the known ApaH family, although it displays a distinct fold that is typical of proteins of the HD domain superfamily harboring a diiron cluster. Analysis of the available 3D structures of three members of the YqeK family provided hints to the mode of substrate binding. Phylogenetic analysis revealed the occurrence of YqeK proteins in a consistent group of Gram-positive bacteria that lack ApaH enzymes. Comparative genomics highlighted that yqeK and apaH genes share a similar genomic context, where they are frequently found in operons involved in integrated responses to stress signals.IMPORTANCE Elevation of Ap4A level in bacteria is associated with increased sensitivity to heat and oxidative stress, reduced antibiotic tolerance, and decreased pathogenicity. ApaH is the major Ap4A hydrolase in gamma- and betaproteobacteria and has been recently proposed as a novel target to weaken the bacterial resistance to antibiotics. Here, we identified the orphan YqeK protein family (COG1713) as a highly efficient Ap4A hydrolase family, with members distributed in a consistent group of bacterial species that lack the ApaH enzyme. Among them are the pathogens Staphylococcus aureus, Streptococcus pneumoniae, and Mycoplasma pneumoniae By identifying the player contributing to Ap4A homeostasis in these bacteria, we disclose a novel target to develop innovative antibacterial strategies.
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Affiliation(s)
- Gabriele Minazzato
- Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Massimiliano Gasparrini
- Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Adolfo Amici
- Department of Clinical Sciences DISCO, Section of Biochemistry, Polytechnic University of Marche, Ancona, Italy
| | - Michele Cianci
- Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Francesca Mazzola
- Department of Clinical Sciences DISCO, Section of Biochemistry, Polytechnic University of Marche, Ancona, Italy
| | - Giuseppe Orsomando
- Department of Clinical Sciences DISCO, Section of Biochemistry, Polytechnic University of Marche, Ancona, Italy
| | - Leonardo Sorci
- Department of Materials, Environmental Sciences and Urban Planning, Division of Bioinformatics and Biochemistry, Polytechnic University of Marche, Ancona, Italy
| | - Nadia Raffaelli
- Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
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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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Smith ML, Miguez AM, Styczynski MP. Gas Chromatography-Mass Spectrometry Microbial Metabolomics for Applications in Strain Optimization. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2019; 1927:179-189. [PMID: 30788792 DOI: 10.1007/978-1-4939-9142-6_12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Metabolomics is the systems-scale measurement of biochemical intermediates in biological systems; by virtue of its deep and broad study of metabolism, it has great potential for applications in metabolic engineering. While a number of the analytical techniques used widely in metabolomics are familiar to metabolic engineers performing post hoc analyses of product titers, the requirements for accurately capturing metabolism at a systems scale rather than just measuring a single secreted product are much more complicated. Nonetheless, metabolomics (which is still not widely available as an affordable consumer service like many molecular biology services) is within reach of many properly equipped metabolic engineering groups. To this end, we present a detailed metabolomics protocol with application to strain optimization. Specifically, we focus on characterizing metabolism in the yeast Saccharomyces cerevisiae using gas chromatography coupled to mass spectrometry. The measurement of metabolic intermediates that results from such approaches has the potential to enable more informed and rational efforts towards pathway engineering and strain optimization.
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Affiliation(s)
- McKenzie L Smith
- Georgia Tech School of Chemical & Biomolecular Engineering, Atlanta, GA, USA
| | - April M Miguez
- Georgia Tech School of Chemical & Biomolecular Engineering, Atlanta, GA, USA
| | - Mark P Styczynski
- Georgia Tech School of Chemical & Biomolecular Engineering, Atlanta, GA, USA.
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9
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Enhancement of Pyruvate Productivity in Candida glabrata by Deleting the CgADE13 Gene to Improve Acid Tolerance. BIOTECHNOL BIOPROC E 2018. [DOI: 10.1007/s12257-018-0201-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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10
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Rosas Lemus M, Roussarie E, Hammad N, Mougeolle A, Ransac S, Issa R, Mazat JP, Uribe-Carvajal S, Rigoulet M, Devin A. The role of glycolysis-derived hexose phosphates in the induction of the Crabtree effect. J Biol Chem 2018; 293:12843-12854. [PMID: 29907566 DOI: 10.1074/jbc.ra118.003672] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 06/04/2018] [Indexed: 11/06/2022] Open
Abstract
Evidence for the Crabtree effect was first reported by H. Crabtree in 1929 and is defined as the glucose-induced decrease of cellular respiratory flux. This effect was observed in tumor cells and was not detected in most non-tumor cells. A number of hypotheses on the mechanism underlying the Crabtree effect have been formulated. However, to this day, no consensual mechanism for this effect has been described. In a previous study on isolated mitochondria, we have proposed that fructose-1,6-bisphosphate (F1,6bP), which inhibits the respiratory chain, induces the Crabtree effect. Using whole cells from the yeast Saccharomyces cerevisiae as a model, we show here not only that F1,6bP plays a key role in the process but that glucose-6-phosphate (G6P), a hexose that has an effect opposite to that of F1,6bP on the regulation of the respiratory flux, does as well. Thus, these findings reveal that the Crabtree effect strongly depends on the ratio between these two glycolysis-derived hexose phosphates. Last, in silico modeling of the Crabtree effect illustrated the requirement of an inhibition of the respiratory flux by a coordinated variation of glucose-6-phosphate and fructose-1,6-bisphosphate to fit the respiratory rate decrease observed upon glucose addition to cells. In summary, we conclude that two glycolysis-derived hexose phosphates, G6P and F1,6bP, play a key role in the induction of the Crabtree effect.
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Affiliation(s)
- Mónica Rosas Lemus
- Université Bordeaux, IBGC, UMR 5095, 33077 Bordeaux Cedex, France; Institut de Biochimie et Génétique Cellulaires, CNRS UMR 5095, 33077 Bordeaux Cedex, France
| | - Elodie Roussarie
- Université Bordeaux, IBGC, UMR 5095, 33077 Bordeaux Cedex, France; Institut de Biochimie et Génétique Cellulaires, CNRS UMR 5095, 33077 Bordeaux Cedex, France
| | - Noureddine Hammad
- Université Bordeaux, IBGC, UMR 5095, 33077 Bordeaux Cedex, France; Institut de Biochimie et Génétique Cellulaires, CNRS UMR 5095, 33077 Bordeaux Cedex, France
| | - Alexis Mougeolle
- Université Bordeaux, IBGC, UMR 5095, 33077 Bordeaux Cedex, France; Institut de Biochimie et Génétique Cellulaires, CNRS UMR 5095, 33077 Bordeaux Cedex, France
| | - Stéphane Ransac
- Université Bordeaux, IBGC, UMR 5095, 33077 Bordeaux Cedex, France; Institut de Biochimie et Génétique Cellulaires, CNRS UMR 5095, 33077 Bordeaux Cedex, France
| | - Razanne Issa
- Université Bordeaux, IBGC, UMR 5095, 33077 Bordeaux Cedex, France; Institut de Biochimie et Génétique Cellulaires, CNRS UMR 5095, 33077 Bordeaux Cedex, France
| | - Jean-Pierre Mazat
- Université Bordeaux, IBGC, UMR 5095, 33077 Bordeaux Cedex, France; Institut de Biochimie et Génétique Cellulaires, CNRS UMR 5095, 33077 Bordeaux Cedex, France
| | - Salvador Uribe-Carvajal
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, México 04510
| | - Michel Rigoulet
- Université Bordeaux, IBGC, UMR 5095, 33077 Bordeaux Cedex, France; Institut de Biochimie et Génétique Cellulaires, CNRS UMR 5095, 33077 Bordeaux Cedex, France
| | - Anne Devin
- Université Bordeaux, IBGC, UMR 5095, 33077 Bordeaux Cedex, France; Institut de Biochimie et Génétique Cellulaires, CNRS UMR 5095, 33077 Bordeaux Cedex, France.
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11
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Transcriptional Profiling of Saccharomyces cerevisiae Reveals the Impact of Variation of a Single Transcription Factor on Differential Gene Expression in 4NQO, Fermentable, and Nonfermentable Carbon Sources. G3-GENES GENOMES GENETICS 2018; 8:607-619. [PMID: 29208650 PMCID: PMC5919752 DOI: 10.1534/g3.117.300138] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Cellular metabolism can change the potency of a chemical's tumorigenicity. 4-nitroquinoline-1-oxide (4NQO) is a tumorigenic drug widely used on animal models for cancer research. Polymorphisms of the transcription factor Yrr1 confer different levels of resistance to 4NQO in Saccharomyces cerevisiae To study how different Yrr1 alleles regulate gene expression leading to resistance, transcriptomes of three isogenic Scerevisiae strains carrying different Yrr1 alleles were profiled via RNA sequencing (RNA-Seq) and chromatin immunoprecipitation coupled with sequencing (ChIP-Seq) in the presence and absence of 4NQO. In response to 4NQO, all alleles of Yrr1 drove the expression of SNQ2 (a multidrug transporter), which was highest in the presence of 4NQO resistance-conferring alleles, and overexpression of SNQ2 alone was sufficient to overcome 4NQO-sensitive growth. Using shape metrics to refine the ChIP-Seq peaks, Yrr1 strongly associated with three loci including SNQ2 In addition to a known Yrr1 target SNG1, Yrr1 also bound upstream of RPL35B; however, overexpression of these genes did not confer 4NQO resistance. RNA-Seq data also implicated nucleotide synthesis pathways including the de novo purine pathway, and the ribonuclease reductase pathways were downregulated in response to 4NQO. Conversion of a 4NQO-sensitive allele to a 4NQO-resistant allele by a single point mutation mimicked the 4NQO-resistant allele in phenotype, and while the 4NQO resistant allele increased the expression of the ADE genes in the de novo purine biosynthetic pathway, the mutant Yrr1 increased expression of ADE genes even in the absence of 4NQO. These same ADE genes were only increased in the wild-type alleles in the presence of 4NQO, indicating that the point mutation activated Yrr1 to upregulate a pathway normally only activated in response to stress. The various Yrr1 alleles also influenced growth on different carbon sources by altering the function of the mitochondria. Hence, the complement to 4NQO resistance was poor growth on nonfermentable carbon sources, which in turn varied depending on the allele of Yrr1 expressed in the isogenic yeast. The oxidation state of the yeast affected the 4NQO toxicity by altering the reactive oxygen species (ROS) generated by cellular metabolism. The integration of RNA-Seq and ChIP-Seq elucidated how Yrr1 regulates global gene transcription in response to 4NQO and how various Yrr1 alleles confer differential resistance to 4NQO. This study provides guidance for further investigation into how Yrr1 regulates cellular responses to 4NQO, as well as transcriptomic resources for further analysis of transcription factor variation on carbon source utilization.
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12
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Wu J, Luo Q, Liu J, Chen X, Liu L. Enhanced pyruvate production in Candida glabrata by overexpressing the CgAMD1 gene to improve acid tolerance. Biotechnol Lett 2017; 40:143-149. [PMID: 28983762 DOI: 10.1007/s10529-017-2452-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 09/27/2017] [Indexed: 10/18/2022]
Abstract
OBJECTIVES To enhance acid tolerance of Candida glabrata for pyruvate production by engineering AMP metabolism. RESULTS The physiological function of AMP deaminase in AMP metabolism from C. glabrata was investigated by deleting or overexpresseing the corresponding gene, CgAMD1. At pH 4, CgAMD1 overexpression resulted in 59 and 51% increases in biomass and cell viability compared to those of wild type strain, respectively. In addition, the intracellular ATP level of strain Cgamd1Δ/CgAMD1 was down-regulated by 22%, which led to a 94% increase in pyruvate production. Further, various strengths of CgAMD1 expression cassettes were designed, thus resulting in a 59% increase in pyruvate production at pH 4. Strain Cgamd1Δ/CgAMD1 (H) was grown in a 30 l batch bioreactor at pH 4, and pyruvate reached 46.1 g/l. CONCLUSION CgAMD1 overexpression plays an active role in improving acid tolerance and pyruvate fermentation performance of C. glabrata at pH 4.
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Affiliation(s)
- Jing Wu
- School of Pharmaceutical Science, Jiangnan University, Wuxi, 214122, China
| | - Qiuling Luo
- School of Pharmaceutical Science, Jiangnan University, Wuxi, 214122, China.,State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China
| | - Jia Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China. .,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China.
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
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13
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Ewald J, Bartl M, Dandekar T, Kaleta C. Optimality principles reveal a complex interplay of intermediate toxicity and kinetic efficiency in the regulation of prokaryotic metabolism. PLoS Comput Biol 2017; 13:e1005371. [PMID: 28212377 PMCID: PMC5315294 DOI: 10.1371/journal.pcbi.1005371] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 01/19/2017] [Indexed: 11/18/2022] Open
Abstract
A precise and rapid adjustment of fluxes through metabolic pathways is crucial for organisms to prevail in changing environmental conditions. Based on this reasoning, many guiding principles that govern the evolution of metabolic networks and their regulation have been uncovered. To this end, methods from dynamic optimization are ideally suited since they allow to uncover optimality principles behind the regulation of metabolic networks. We used dynamic optimization to investigate the influence of toxic intermediates in connection with the efficiency of enzymes on the regulation of a linear metabolic pathway. Our results predict that transcriptional regulation favors the control of highly efficient enzymes with less toxic upstream intermediates to reduce accumulation of toxic downstream intermediates. We show that the derived optimality principles hold by the analysis of the interplay between intermediate toxicity and pathway regulation in the metabolic pathways of over 5000 sequenced prokaryotes. Moreover, using the lipopolysaccharide biosynthesis in Escherichia coli as an example, we show how knowledge about the relation of regulation, kinetic efficiency and intermediate toxicity can be used to identify drug targets, which control endogenous toxic metabolites and prevent microbial growth. Beyond prokaryotes, we discuss the potential of our findings for the development of antifungal drugs.
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Affiliation(s)
- Jan Ewald
- Research Group Theoretical Systems Biology, Department of Bioinformatics, Friedrich-Schiller-Universität Jena, Jena, Germany
| | - Martin Bartl
- Research Group Theoretical Systems Biology, Department of Bioinformatics, Friedrich-Schiller-Universität Jena, Jena, Germany
| | - Thomas Dandekar
- Department of Bioinformatics, Biocenter, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Christoph Kaleta
- Research Group Medical Systems Biology, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
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14
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Gil A, Siegel D, Bonsing-Vedelaar S, Permentier H, Reijngoud DJ, Dekker F, Bischoff R. The degradation of nucleotide triphosphates extracted under boiling ethanol conditions is prevented by the yeast cellular matrix. Metabolomics 2017; 13:1. [PMID: 27980501 PMCID: PMC5126204 DOI: 10.1007/s11306-016-1140-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 11/11/2016] [Indexed: 11/03/2022]
Abstract
INTRODUCTION Boiling ethanol extraction is a frequently used method for metabolomics studies of biological samples. However, the stability of several central carbon metabolites, including nucleotide triphosphates, and the influence of the cellular matrix on their degradation have not been addressed. OBJECTIVES To study how a complex cellular matrix extracted from yeast (Saccharomyces cerevisiae) may affect the degradation profiles of nucleotide triphosphates extracted under boiling ethanol conditions. METHODS We present a double-labelling LC-MS approach with a 13C-labeled yeast cellular extract as complex surrogate matrix, and 13C15N-labeled nucleotides as internal standards, to study the effect of the yeast matrix on the degradation of nucleotide triphosphates. RESULTS While nucleotide triphosphates were degraded to the corresponding diphosphates in pure solutions, degradation was prevented in the presence of the yeast matrix under typical boiling ethanol extraction conditions. CONCLUSIONS Extraction of biological samples under boiling ethanol extraction conditions that rapidly inactivate enzyme activity are suitable for labile central energy metabolites such as nucleotide triphosphates due to the stabilizing effect of the yeast matrix. The basis of this phenomenon requires further study.
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Affiliation(s)
- Andres Gil
- 0000 0004 0407 1981grid.4830.fDepartment of Pharmacy, Analytical Biochemistry, University of Groningen, Antonius Deusinglaan 1, Building 3226, Room 601, 9713 AV Groningen, The Netherlands
| | - David Siegel
- 0000 0004 0407 1981grid.4830.fDepartment of Pharmacy, Analytical Biochemistry, University of Groningen, Antonius Deusinglaan 1, Building 3226, Room 601, 9713 AV Groningen, The Netherlands
| | - Silke Bonsing-Vedelaar
- 0000 0004 0407 1981grid.4830.fBiomolecular Sciences and Biotechnology Institute, Molecular Systems Biology, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Hjalmar Permentier
- 0000 0004 0407 1981grid.4830.fDepartment of Pharmacy, Interfaculty Mass Spectrometry Center, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Dirk-Jan Reijngoud
- 0000 0004 0407 1981grid.4830.fUniversity Medical Center Groningen, Department of Pediatrics, Center for Liver, Digestive and Metabolic Diseases, University of Groningen, PO Box 30.001, 9700 RB Groningen, The Netherlands
| | - Frank Dekker
- 0000 0004 0407 1981grid.4830.fDepartment of Pharmacy, Pharmaceutical Gene Modulation, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Rainer Bischoff
- 0000 0004 0407 1981grid.4830.fDepartment of Pharmacy, Analytical Biochemistry, University of Groningen, Antonius Deusinglaan 1, Building 3226, Room 601, 9713 AV Groningen, The Netherlands
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15
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A capillary zone electrophoresis method for adenine nucleotides analysis in Saccharomyces cerevisiae. J Chromatogr B Analyt Technol Biomed Life Sci 2015; 1008:156-163. [PMID: 26655107 DOI: 10.1016/j.jchromb.2015.11.040] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 11/19/2015] [Accepted: 11/21/2015] [Indexed: 02/04/2023]
Abstract
Adenosine triphosphate and its metabolites are involved in the cellular metabolism process in Saccharomyces cerevisiae. It is very important to simultaneously determine the relative contents of ATP and its metabolites in yeast. In this study, an effective capillary zone electrophoresis method with high selectivity was established. The calibration curves were linear in the concentration range from 1 to 20mg/L (ATP and cAMP) and 2 to 40mg/L (ADP and AMP) with excellent correlation coefficients (r(2))>0.999. The recovery of ATP, ADP, AMP, and cAMP were 99.4%, 94.7%, 100.3% and 99.6%, respectively. Simple sample preparation and easy detection of ATP and its metabolites make this method suitable for the study of changes in the four adenine nucleotides levels caused by caloric restriction in yeast. It is expected that the current method may contribute to further energy metabolism and related investigations of yeast.
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16
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Volkov V. Quantitative description of ion transport via plasma membrane of yeast and small cells. FRONTIERS IN PLANT SCIENCE 2015; 6:425. [PMID: 26113853 PMCID: PMC4462678 DOI: 10.3389/fpls.2015.00425] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 05/26/2015] [Indexed: 05/21/2023]
Abstract
Modeling of ion transport via plasma membrane needs identification and quantitative understanding of the involved processes. Brief characterization of main ion transport systems of a yeast cell (Pma1, Ena1, TOK1, Nha1, Trk1, Trk2, non-selective cation conductance) and determining the exact number of molecules of each transporter per a typical cell allow us to predict the corresponding ion flows. In this review a comparison of ion transport in small yeast cell and several animal cell types is provided. The importance of cell volume to surface ratio is emphasized. The role of cell wall and lipid rafts is discussed in respect to required increase in spatial and temporary resolution of measurements. Conclusions are formulated to describe specific features of ion transport in a yeast cell. Potential directions of future research are outlined based on the assumptions.
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Affiliation(s)
- Vadim Volkov
- *Correspondence: Vadim Volkov, Faculty of Life Sciences, School of Human Sciences, London Metropolitan University, 166-220 Holloway Road, London N7 8DB, UK
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17
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A Ralstonia solanacearum type III effector directs the production of the plant signal metabolite trehalose-6-phosphate. mBio 2014; 5:mBio.02065-14. [PMID: 25538193 PMCID: PMC4278537 DOI: 10.1128/mbio.02065-14] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The plant pathogen Ralstonia solanacearum possesses two genes encoding a trehalose-6-phosphate synthase (TPS), an enzyme of the trehalose biosynthetic pathway. One of these genes, named ripTPS, was found to encode a protein with an additional N-terminal domain which directs its translocation into host plant cells through the type 3 secretion system. RipTPS is a conserved effector in the R. solanacearum species complex, and homologues were also detected in other bacterial plant pathogens. Functional analysis of RipTPS demonstrated that this type 3 effector synthesizes trehalose-6-phosphate and identified residues essential for this enzymatic activity. Although trehalose-6-phosphate is a key signal molecule in plants that regulates sugar status and carbon assimilation, the disruption of ripTPS did not alter the virulence of R. solanacearum on plants. However, heterologous expression assays showed that this effector specifically elicits a hypersensitive-like response on tobacco that is independent of its enzymatic activity and is triggered by the C-terminal half of the protein. Recognition of this effector by the plant immune system is suggestive of a role during the infectious process. Ralstonia solanacearum, the causal agent of bacterial wilt disease, infects more than two hundred plant species, including economically important crops. The type III secretion system plays a major role in the pathogenicity of this bacterium, and approximately 70 effector proteins have been shown to be translocated into host plant cells. This study provides the first description of a type III effector endowed with a trehalose-6-phosphate synthase enzymatic activity and illustrates a new mechanism by which the bacteria may manipulate the plant metabolism upon infection. In recent years, trehalose-6-phosphate has emerged as an essential signal molecule in plants, connecting plant metabolism and development. The finding that a bacterial pathogen could induce the production of trehalose-6-phosphate in plant cells further highlights the importance of this metabolite in multiple aspects of the molecular physiology of plants.
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18
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Tocco A, Pinson B, Thiébaud P, Thézé N, Massé K. Comparative genomic and expression analysis of the adenosine signaling pathway members in Xenopus. Purinergic Signal 2014; 11:59-77. [PMID: 25319637 DOI: 10.1007/s11302-014-9431-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 09/30/2014] [Indexed: 12/13/2022] Open
Abstract
Adenosine is an endogenous molecule that regulates many physiological processes via the activation of four specific G-protein-coupled ADORA receptors. Extracellular adenosine may originate either from the hydrolysis of released ATP by the ectonucleotidases or from cellular exit via the equilibrative nucleoside transporters (SLC29A). Adenosine extracellular concentration is also regulated by its successive hydrolysis into uric acid by membrane-bound enzymes or by cell influx via the concentrative nucleoside transporters (SLC28A). All of these members constitute the adenosine signaling pathway and regulate adenosine functions. Although the roles of this pathway are quite well understood in adults, little is known regarding its functions during vertebrate embryogenesis. We have used Xenopus laevis as a model system to provide a comparative expression map of the different members of this pathway during vertebrate development. We report the characterization of the different enzymes, receptors, and nucleoside transporters in both X. laevis and X. tropicalis, and we demonstrate by phylogenetic analyses the high level of conservation of these members between amphibians and mammals. A thorough expression analysis of these members during development and in the adult frog reveals that each member displays distinct specific expression patterns. These data suggest potentially different developmental roles for these proteins and therefore for extracellular adenosine. In addition, we show that adenosine levels during amphibian embryogenesis are very low, confirming that they must be tightly controlled for normal development.
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Affiliation(s)
- Alice Tocco
- Université de Bordeaux, CIRID UMR 5164, F-33000, Bordeaux, France
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19
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Walther T, Létisse F, Peyriga L, Alkim C, Liu Y, Lardenois A, Martin-Yken H, Portais JC, Primig M, François J. Developmental stage dependent metabolic regulation during meiotic differentiation in budding yeast. BMC Biol 2014; 12:60. [PMID: 25178389 PMCID: PMC4176597 DOI: 10.1186/s12915-014-0060-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Indexed: 12/12/2022] Open
Abstract
Background The meiotic developmental pathway in yeast enables both differentiation of vegetative cells into haploid spores that ensure long-term survival, and recombination of the parental DNA to create genetic diversity. Despite the importance of proper metabolic regulation for the supply of building blocks and energy, little is known about the reprogramming of central metabolic pathways in meiotically differentiating cells during passage through successive developmental stages. Results Metabolic regulation during meiotic differentiation in budding yeast was analyzed by integrating information on genome-wide transcriptional activity, 26 enzymatic activities in the central metabolism, the dynamics of 67 metabolites, and a metabolic flux analysis at mid-stage meiosis. Analyses of mutants arresting sporulation at defined stages demonstrated that metabolic reprogramming is tightly controlled by the progression through the developmental pathway. The correlation between transcript levels and enzymatic activities in the central metabolism varies significantly in a developmental stage-dependent manner. The complete loss of phosphofructokinase activity at mid-stage meiosis enables a unique setup of the glycolytic pathway which facilitates carbon flux repartitioning into synthesis of spore wall precursors during the co-assimilation of glycogen and acetate. The need for correct homeostasis of purine nucleotides during the meiotic differentiation was demonstrated by the sporulation defect of the AMP deaminase mutant amd1, which exhibited hyper-accumulation of ATP accompanied by depletion of guanosine nucleotides. Conclusions Our systems-level analysis shows that reprogramming of the central metabolism during the meiotic differentiation is controlled at different hierarchical levels to meet the metabolic and energetic needs at successive developmental stages. Electronic supplementary material The online version of this article (doi:10.1186/s12915-014-0060-x) contains supplementary material, which is available to authorized users.
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20
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Global LC/MS Metabolomics Profiling of Calcium Stressed and Immunosuppressant Drug Treated Saccharomyces cerevisiae. Metabolites 2013; 3:1102-17. [PMID: 24958268 PMCID: PMC3937837 DOI: 10.3390/metabo3041102] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 11/20/2013] [Accepted: 11/25/2013] [Indexed: 11/17/2022] Open
Abstract
Previous studies have shown that calcium stressed Saccharomyces cerevisiae, challenged with immunosuppressant drugs FK506 and Cyclosporin A, responds with comprehensive gene expression changes and attenuation of the generalized calcium stress response. Here, we describe a global metabolomics workflow for investigating the utility of tracking corresponding phenotypic changes. This was achieved by efficiently analyzing relative abundance differences between intracellular metabolite pools from wild-type and calcium stressed cultures, with and without prior immunosuppressant drugs exposure. We used pathway database content from WikiPathways and YeastCyc to facilitate the projection of our metabolomics profiling results onto biological pathways. A key challenge was to increase the coverage of the detected metabolites. This was achieved by applying both reverse phase (RP) and aqueous normal phase (ANP) chromatographic separations, as well as electrospray ionization (ESI) and atmospheric pressure chemical ionization (APCI) sources for detection in both ion polarities. Unsupervised principle component analysis (PCA) and ANOVA results revealed differentiation between wild-type controls, calcium stressed and immunosuppressant/calcium challenged cells. Untargeted data mining resulted in 247 differentially expressed, annotated metabolites, across at least one pair of conditions. A separate, targeted data mining strategy identified 187 differential, annotated metabolites. All annotated metabolites were subsequently mapped onto curated pathways from YeastCyc and WikiPathways for interactive pathway analysis and visualization. Dozens of pathways showed differential responses to stress conditions based on one or more matches to the list of annotated metabolites or to metabolites that had been identified further by MS/MS. The purine salvage, pantothenate and sulfur amino acid pathways were flagged as being enriched, which is consistent with previously published literature for transcriptomics analysis. Thus, broad discovery-based data mining combined with targeted pathway projections can be an important asset for rapidly distilling, testing and evaluating a large amount of information for further investigation.
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21
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Metabolic phenotypes of Saccharomyces cerevisiae mutants with altered trehalose 6-phosphate dynamics. Biochem J 2013; 454:227-37. [PMID: 23763276 DOI: 10.1042/bj20130587] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
In Saccharomyces cerevisiae, synthesis of T6P (trehalose 6-phosphate) is essential for growth on most fermentable carbon sources. In the present study, the metabolic response to glucose was analysed in mutants with different capacities to accumulate T6P. A mutant carrying a deletion in the T6P synthase encoding gene, TPS1, which had no measurable T6P, exhibited impaired ethanol production, showed diminished plasma membrane H⁺-ATPase activation, and became rapidly depleted of nearly all adenine nucleotides which were irreversibly converted into inosine. Deletion of the AMP deaminase encoding gene, AMD1, in the tps1 strain prevented inosine formation, but did not rescue energy balance or growth on glucose. Neither the 90%-reduced T6P content observed in a tps1 mutant expressing the Tps1 protein from Yarrowia lipolytica, nor the hyperaccumulation of T6P in the tps2 mutant had significant effects on fermentation rates, growth on fermentable carbon sources or plasma membrane H⁺-ATPase activation. However, intracellular metabolite dynamics and pH homoeostasis were strongly affected by changes in T6P concentrations. Hyperaccumulation of T6P in the tps2 mutant caused an increase in cytosolic pH and strongly reduced growth rates on non-fermentable carbon sources, emphasizing the crucial role of the trehalose pathway in the regulation of respiratory and fermentative metabolism.
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22
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Changes in intracellular metabolite pools during growth of adherent MDCK cells in two different media. Appl Microbiol Biotechnol 2013; 98:385-97. [PMID: 24169951 DOI: 10.1007/s00253-013-5329-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Revised: 09/27/2013] [Accepted: 10/10/2013] [Indexed: 10/26/2022]
Abstract
In bioprocess engineering, the growth of continuous cell lines is mainly studied with respect to the changes in cell concentration, the resulting demand for substrates, and the accumulation of extracellular metabolites. The underlying metabolic process rests upon intracellular metabolite pools and their interaction with enzymes in the form of substrates, products, or allosteric effectors. Here, we quantitatively analyze time courses of 29 intracellular metabolites of adherent Madin-Darby canine kidney cells during cultivation in a serum-containing medium and a serum-free medium. The cells, which originated from the same pre-culture, showed similar overall growth behavior and only slight differences in their demand for the substrates glucose (GLC), glutamine (GLN), and glutamate (GLU). Analysis of intracellular metabolites, which mainly cover the glycolytic pathway, the citric acid cycle, and the nucleotide pools, revealed surprisingly similar dynamics for both cultivation conditions. Instead of a strong influence of the medium, we rather observed a growth phase-specific behavior in glycolysis and in the lower citric acid cycle. Furthermore, analysis of the lower part of glycolysis suggests the well-known regulation of pyruvate kinase by fructose 1,6-bisphosphate. The upper citric acid cycle (citrate, cis-aconitate, and isocitrate) is apparently uncoupled from the lower part (α-ketoglutarate, succinate, fumarate, and malate), which is in line with the characteristics of a truncated cycle. Decreased adenosine triphosphate and guanosine triphosphate pools, as well as a relatively low energy charge soon after inoculation of cells, indicate a high demand for cellular energy and the consumption of nucleotides for biosynthesis. We finally conclude that, with sufficient availability of substrates, the dynamics of GLC and GLN/GLU metabolism is influenced mainly by the cellular growth regime and regulatory function of key enzymes.
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23
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Trammell SA, Brenner C. Targeted, LCMS-based Metabolomics for Quantitative Measurement of NAD(+) Metabolites. Comput Struct Biotechnol J 2013; 4:e201301012. [PMID: 24688693 PMCID: PMC3962138 DOI: 10.5936/csbj.201301012] [Citation(s) in RCA: 140] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Revised: 05/09/2013] [Accepted: 05/09/2013] [Indexed: 01/07/2023] Open
Abstract
Nicotinamide adenine dinucleotide (NAD+) is a coenzyme for hydride transfer reactions and a substrate for sirtuins and other NAD+-consuming enzymes. The abundance of NAD +, NAD+ biosynthetic intermediates, and related nucleotides reflects the metabolic state of cells and tissues. High performance liquid chromatography (HPLC) followed by ultraviolet-visible (UV-Vis) spectroscopic analysis of NAD+ metabolites does not offer the specificity and sensitivity necessary for robust quantification of complex samples. Thus, we developed a targeted, quantitative assay of the NAD+ metabolome with the use of HPLC coupled to mass spectrometry. Here we discuss NAD+ metabolism as well as the technical challenges required for reliable quantification of the NAD+ metabolites. The new method incorporates new separations and improves upon a previously published method that suffered from the problem of ionization suppression for particular compounds.
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Affiliation(s)
- Samuel Aj Trammell
- Department of Biochemistry ; Interdisciplinary Graduate Program in Genetics Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Charles Brenner
- Department of Biochemistry ; Interdisciplinary Graduate Program in Genetics Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
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24
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The PGM3 gene encodes the major phosphoribomutase in the yeast Saccharomyces cerevisiae. FEBS Lett 2012; 586:4114-8. [PMID: 23103740 DOI: 10.1016/j.febslet.2012.09.042] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Revised: 09/21/2012] [Accepted: 09/27/2012] [Indexed: 11/20/2022]
Abstract
The phosphoglucomutases (PGM) Pgm1, Pgm2, and Pgm3 of the yeast Saccharomyces cerevisiae were tested for their ability to interconvert ribose-1-phosphate and ribose-5-phosphate. The purified proteins were studied in vitro with regard to their kinetic properties on glucose-1-phosphate and ribose-1-phosphate. All tested enzymes were active on both substrates with Pgm1 exhibiting only residual activity on ribose-1-phosphate. The Pgm2 and Pgm3 proteins had almost equal kinetic properties on ribose-1-phosphate, but Pgm2 had a 2000 times higher preference for glucose-1-phosphate when compared to Pgm3. The in vivo function of the PGMs was characterized by monitoring ribose-1-phosphate kinetics following a perturbation of the purine nucleotide balance. Only mutants with a deletion of PGM3 hyper-accumulated ribose-1-phosphate. We conclude that Pgm3 functions as the major phosphoribomutase in vivo.
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25
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Verma M, Zakhartsev M, Reuss M, Westerhoff HV. 'Domino' systems biology and the 'A' of ATP. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1827:19-29. [PMID: 23031542 DOI: 10.1016/j.bbabio.2012.09.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Revised: 09/17/2012] [Accepted: 09/23/2012] [Indexed: 11/30/2022]
Abstract
We develop a strategic 'domino' approach that starts with one key feature of cell function and the main process providing for it, and then adds additional processes and components only as necessary to explain provoked experimental observations. The approach is here applied to the energy metabolism of yeast in a glucose limited chemostat, subjected to a sudden increase in glucose. The puzzles addressed include (i) the lack of increase in adenosine triphosphate (ATP) upon glucose addition, (ii) the lack of increase in adenosine diphosphate (ADP) when ATP is hydrolyzed, and (iii) the rapid disappearance of the 'A' (adenine) moiety of ATP. Neither the incorporation of nucleotides into new biomass, nor steady de novo synthesis of adenosine monophosphate (AMP) explains. Cycling of the 'A' moiety accelerates when the cell's energy state is endangered, another essential domino among the seven required for understanding of the experimental observations. This new domino analysis shows how strategic experimental design and observations in tandem with theory and modeling may identify and resolve important paradoxes. It also highlights the hitherto unexpected role of the 'A' component of ATP.
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Affiliation(s)
- Malkhey Verma
- Manchester Centre for Integrative Systems Biology, Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK
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27
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Schlecht U, St Onge RP, Walther T, François JM, Davis RW. Cationic amphiphilic drugs are potent inhibitors of yeast sporulation. PLoS One 2012; 7:e42853. [PMID: 22905177 PMCID: PMC3414501 DOI: 10.1371/journal.pone.0042853] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2012] [Accepted: 07/12/2012] [Indexed: 11/18/2022] Open
Abstract
Meiosis is a highly regulated developmental process that occurs in all eukaryotes that engage in sexual reproduction. Previous epidemiological work shows that male and female infertility is rising and environmental factors, including pollutants such as organic solvents, are thought to play a role in this phenomenon. To better understand how organic compounds interfere with meiotic development, the model organism Saccharomyces cerevisiae was exposed to 446 bioactive molecules while undergoing meiotic development, and sporulation efficiency was quantified employing two different high-throughput assays. 12 chemicals were identified that strongly inhibited spore formation but did not interfere with vegetative growth. Many of these chemicals are known to bind to monoamine-receptors in higher eukaryotes and are cationic amphiphilic drugs. A detailed analysis of one of these drugs, tripelennamine, revealed that it induces sporulation-specific cytotoxicity and a strong inhibition of meiotic M phase. The drug, however, only mildly interfered with pre-meiotic DNA synthesis and the early meiotic transcriptional program. Chemical-genomic screening identified genes involved in autophagy as hypersensitive to tripelennamine. In addition, we found that growing and sporulating yeast cells heterozygous for the aminophospholipid translocase, NEO1, are haploinsufficient in the presence of the drug.
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Affiliation(s)
- Ulrich Schlecht
- Stanford Genome Technology Center, Stanford University, Palo Alto, California, United States of America.
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28
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Yoboue ED, Augier E, Galinier A, Blancard C, Pinson B, Casteilla L, Rigoulet M, Devin A. cAMP-induced mitochondrial compartment biogenesis: role of glutathione redox state. J Biol Chem 2012; 287:14569-78. [PMID: 22396541 DOI: 10.1074/jbc.m111.302786] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Cell fate and proliferation are tightly linked to the regulation of the mitochondrial energy metabolism. Hence, mitochondrial biogenesis regulation, a complex process that requires a tight coordination in the expression of the nuclear and mitochondrial genomes, has a major impact on cell fate and is of high importance. Here, we studied the molecular mechanisms involved in the regulation of mitochondrial biogenesis through a nutrient-sensing pathway, the Ras-cAMP pathway. Activation of this pathway induces a decrease in the cellular phosphate potential that alleviates the redox pressure on the mitochondrial respiratory chain. One of the cellular consequences of this modulation of cellular phosphate potential is an increase in the cellular glutathione redox state. The redox state of the glutathione disulfide-glutathione couple is a well known important indicator of the cellular redox environment, which is itself tightly linked to mitochondrial activity, mitochondria being the main cellular producer of reactive oxygen species. The master regulator of mitochondrial biogenesis in yeast (i.e. the transcriptional co-activator Hap4p) is positively regulated by the cellular glutathione redox state. Using a strain that is unable to modulate its glutathione redox state (Δglr1), we pinpoint a positive feedback loop between this redox state and the control of mitochondrial biogenesis. This is the first time that control of mitochondrial biogenesis through glutathione redox state has been shown.
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Affiliation(s)
- Edgar D Yoboue
- CNRS, Institut de Biochimie et Génétique Cellulaires, UMR 5095, F-33000 Bordeaux, France
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29
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Servant G, Pinson B, Tchalikian-Cosson A, Coulpier F, Lemoine S, Pennetier C, Bridier-Nahmias A, Todeschini AL, Fayol H, Daignan-Fornier B, Lesage P. Tye7 regulates yeast Ty1 retrotransposon sense and antisense transcription in response to adenylic nucleotides stress. Nucleic Acids Res 2012; 40:5271-82. [PMID: 22379133 PMCID: PMC3384299 DOI: 10.1093/nar/gks166] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Transposable elements play a fundamental role in genome evolution. It is proposed that their mobility, activated under stress, induces mutations that could confer advantages to the host organism. Transcription of the Ty1 LTR-retrotransposon of Saccharomyces cerevisiae is activated in response to a severe deficiency in adenylic nucleotides. Here, we show that Ty2 and Ty3 are also stimulated under these stress conditions, revealing the simultaneous activation of three active Ty retrotransposon families. We demonstrate that Ty1 activation in response to adenylic nucleotide depletion requires the DNA-binding transcription factor Tye7. Ty1 is transcribed in both sense and antisense directions. We identify three Tye7 potential binding sites in the region of Ty1 DNA sequence where antisense transcription starts. We show that Tye7 binds to Ty1 DNA and regulates Ty1 antisense transcription. Altogether, our data suggest that, in response to adenylic nucleotide reduction, TYE7 is induced and activates Ty1 mRNA transcription, possibly by controlling Ty1 antisense transcription. We also provide the first evidence that Ty1 antisense transcription can be regulated by environmental stress conditions, pointing to a new level of control of Ty1 activity by stress, as Ty1 antisense RNAs play an important role in regulating Ty1 mobility at both the transcriptional and post-transcriptional stages.
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Affiliation(s)
- Géraldine Servant
- CNRS UPR9073, associated with Univ Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-chimique, F-75005 Paris, France
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Development of quenching and washing protocols for quantitative intracellular metabolite analysis of uninfected and baculovirus-infected insect cells. Methods 2011; 56:396-407. [PMID: 22166686 DOI: 10.1016/j.ymeth.2011.11.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Revised: 11/25/2011] [Accepted: 11/28/2011] [Indexed: 11/21/2022] Open
Abstract
Metabolomics refer to the global analysis of small molecule metabolites in a biological system, and can be a powerful tool to elucidate and optimize cellular processes, particularly when integrated into a systems biology framework. Determining the endometabolome in cultured animal cells is especially challenging, due to the conflicting demands for rapid quenching of metabolism and retention of membrane integrity, while cells are separated from the complex medium. The challenge is magnified in virus infected cells due to increased membrane fragility. This paper describes an effective methodology for quantitative intracellular metabolite analysis of the baculovirus-insect cell expression system, an important platform for the production of heterologous proteins and baculovirus-based biopesticides. These two applications were represented by Spodoptera frugiperda (Sf9) and Helicoverpa zea (HzAM1) cells infected with recombinant Autographa californica and wild-type Helicoverpa armigera nucleopolyhedroviruses (AcMNPV and HaSNPV), respectively. Specifically, an ice-cold quenching solution comprising 1.1% w/v NaCl and 0.2% w/v Pluronic® F-68 (NaCl+P) was found to be efficacious in preserving cell viability and minimizing cell leakage during quenching and centrifugation-based washing procedures (prior to extraction using cold 50% v/v acetonitrile). Good recoveries of intracellular adenosine triphosphate, total adenosine phosphates and amino acids were obtained after just one wash step, for both uninfected and infected insect cells. The ability to implement wash steps is critical, as insect cell media are metabolites-rich, while infected insect cells are much more fragile than their uninfected counterparts. Hence, a promising methodology has been developed to facilitate endometabolomic analysis of insect cell-baculovirus systems for bioprocess optimization.
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Vielhauer O, Zakhartsev M, Horn T, Takors R, Reuss M. Simplified absolute metabolite quantification by gas chromatography–isotope dilution mass spectrometry on the basis of commercially available source material. J Chromatogr B Analyt Technol Biomed Life Sci 2011; 879:3859-70. [DOI: 10.1016/j.jchromb.2011.10.036] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2011] [Revised: 10/21/2011] [Accepted: 10/25/2011] [Indexed: 02/08/2023]
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Laporte D, Lebaudy A, Sahin A, Pinson B, Ceschin J, Daignan-Fornier B, Sagot I. Metabolic status rather than cell cycle signals control quiescence entry and exit. ACTA ACUST UNITED AC 2011; 192:949-57. [PMID: 21402786 PMCID: PMC3063145 DOI: 10.1083/jcb.201009028] [Citation(s) in RCA: 96] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Quiescence is defined as a temporary arrest of proliferation, yet it likely encompasses various cellular situations. Our knowledge about this widespread cellular state remains limited. In particular, little is known about the molecular determinants that orchestrate quiescence establishment and exit. Here we show that upon carbon source exhaustion, budding yeast can enter quiescence from all cell cycle phases. Moreover, using cellular structures that are candidate markers for quiescence, we found that the first steps of quiescence exit can be triggered independently of cell growth and proliferation by the sole addition of glucose in both Saccharomyces cerevisiae and Schizosaccharomyces pombe. Importantly, glucose needs to be internalized and catabolized all the way down to glycolysis to mobilize quiescent cell specific structures, but, strikingly, ATP replenishment is apparently not the key signal. Altogether, these findings strongly suggest that quiescence entry and exit primarily rely on cellular metabolic status and can be uncoupled from the cell cycle.
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Affiliation(s)
- Damien Laporte
- Université de Bordeaux, Institut de Biochimie et Génétique Cellulaires, UMR 5095, F-33000 Bordeaux, France
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Karhumaa K, Wu B, Kielland-Brandt MC. Conditions with high intracellular glucose inhibit sensing through glucose sensor Snf3 in Saccharomyces cerevisiae. J Cell Biochem 2010; 110:920-5. [PMID: 20564191 DOI: 10.1002/jcb.22605] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Gene expression in micro-organisms is regulated according to extracellular conditions and nutrient concentrations. In Saccharomyces cerevisiae, non-transporting sensors with high sequence similarity to transporters, that is, transporter-like sensors, have been identified for sugars as well as for amino acids. An alternating-access model of the function of transporter-like sensors has been previously suggested based on amino acid sensing, where intracellular ligand inhibits binding of extracellular ligand. Here we studied the effect of intracellular glucose on sensing of extracellular glucose through the transporter-like sensor Snf3 in yeast. Sensing through Snf3 was determined by measuring degradation of Mth1 protein. High intracellular glucose concentrations were achieved by using yeast strains lacking monohexose transporters which were grown on maltose. The apparent affinity of extracellular glucose to Snf3 was measured for cells grown in non-fermentative medium or on maltose. The apparent affinity for glucose was lowest when the intracellular glucose concentration was high. The results conform to an alternating-access model for transporter-like sensors.
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Ahmed AESI, Wardell JN, Thumser AE, Avignone-Rossa CA, Cavalli G, Hay JN, Bushell ME. Metabolomic profiling can differentiate between bactericidal effects of free and polymer bound halogen. J Appl Polym Sci 2010. [DOI: 10.1002/app.32731] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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35
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Meyer H, Liebeke M, Lalk M. A protocol for the investigation of the intracellular Staphylococcus aureus metabolome. Anal Biochem 2010; 401:250-9. [PMID: 20211591 DOI: 10.1016/j.ab.2010.03.003] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2009] [Revised: 02/10/2010] [Accepted: 03/02/2010] [Indexed: 12/01/2022]
Abstract
Systems biology studies assume the acquisition of reliable and reproducible data sets. Metabolomics, in particular, requires comprehensive evaluated workflows to enable the analysis of hundreds of different compounds. Therefore, a protocol to elucidate the metabolome of the gram-positive pathogen, Staphylococcus aureus COL strain, grown in a chemically defined medium is introduced here. Different standard operating procedures in the field of metabolome experiments were tested for common pitfalls. These included suitable and fast sampling processes, efficient metabolite extraction, quenching effectiveness (energy charge), and estimation of leakage and recovery of metabolites. Moreover, a cell disruption protocol for S. aureus was developed and optimized for metabolome analyses, for the express purpose of obtaining reproducible data. We used complementary methods (e.g., gas chromatography and/or liquid chromatography coupled with mass spectrometry) to detect the highly chemically diverse groups of metabolites for a global insight into the intracellular metabolism of S. aureus.
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Affiliation(s)
- Hanna Meyer
- Department of Pharmaceutical Biology, Friedrich-Ludwig Jahn Street 15, 17489 Greifswald, Ernst-Moritz-Arndt University of Greifswald, Germany
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Crutchfield CA, Lu W, Melamud E, Rabinowitz JD. Mass spectrometry-based metabolomics of yeast. Methods Enzymol 2010; 470:393-426. [PMID: 20946819 DOI: 10.1016/s0076-6879(10)70016-1] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Driven by the advent of metabolomics, recent years have seen renewed interest in the investigation of yeast metabolism. Here we provide a practical guide to metabolomic analysis of yeast using liquid chromatography-mass spectrometry (LC-MS). We begin with background on LC-MS and its utility in studying yeast metabolism. We then describe key issues involved at each step of a typical yeast metabolomics experiment: in experimental design, cell culture, metabolite extraction, LC-MS, and data processing and analysis. Throughout, we highlight interdependencies between the steps that are relevant to developing an integrated workflow which effectively leverages LC-MS to reveal yeast biology.
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Affiliation(s)
- Christopher A Crutchfield
- Lewis-Sigler Institute for Integrative Genomics, Department of Chemistry, Princeton University, Princeton, New Jersey, USA
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Evans C, Bogan KL, Song P, Burant CF, Kennedy RT, Brenner C. NAD+ metabolite levels as a function of vitamins and calorie restriction: evidence for different mechanisms of longevity. BMC CHEMICAL BIOLOGY 2010; 10:2. [PMID: 20175898 PMCID: PMC2834649 DOI: 10.1186/1472-6769-10-2] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2009] [Accepted: 02/22/2010] [Indexed: 12/01/2022]
Abstract
BACKGROUND NAD+ is a coenzyme for hydride transfer enzymes and a substrate for sirtuins and other NAD+-dependent ADPribose transfer enzymes. In wild-type Saccharomyces cerevisiae, calorie restriction accomplished by glucose limitation extends replicative lifespan in a manner that depends on Sir2 and the NAD+ salvage enzymes, nicotinic acid phosphoribosyl transferase and nicotinamidase. Though alterations in the NAD+ to nicotinamide ratio and the NAD+ to NADH ratio are anticipated by models to account for the effects of calorie restriction, the nature of a putative change in NAD+ metabolism requires analytical definition and quantification of the key metabolites. RESULTS Hydrophilic interaction chromatography followed by tandem electrospray mass spectrometry were used to identify the 12 compounds that constitute the core NAD+ metabolome and 6 related nucleosides and nucleotides. Whereas yeast extract and nicotinic acid increase net NAD+ synthesis in a manner that can account for extended lifespan, glucose restriction does not alter NAD+ or nicotinamide levels in ways that would increase Sir2 activity. CONCLUSIONS The results constrain the possible mechanisms by which calorie restriction may regulate Sir2 and suggest that provision of vitamins and calorie restriction extend lifespan by different mechanisms.
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Affiliation(s)
- Charles Evans
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
- Michigan Metabolomics and Obesity Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Katrina L Bogan
- Biochemistry Graduate Program, Dartmouth Medical School, Lebanon, NH 03756, USA
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Peng Song
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Charles F Burant
- Michigan Metabolomics and Obesity Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Robert T Kennedy
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Chemistry, University of Michigan, 930 N University Ave, Ann Arbor, MI 48109, USA
| | - Charles Brenner
- Biochemistry Graduate Program, Dartmouth Medical School, Lebanon, NH 03756, USA
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
- Department of Biochemistry, Carver College of Medicine, University of Iowa, 51 Newton Rd, 4-403 BSB, Iowa City, IA 52242, USA
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Álvarez-Sánchez B, Priego-Capote F, Castro MLD. Metabolomics analysis II. Preparation of biological samples prior to detection. Trends Analyt Chem 2010. [DOI: 10.1016/j.trac.2009.12.004] [Citation(s) in RCA: 123] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Walther T, Novo M, Rössger K, Létisse F, Loret MO, Portais JC, François JM. Control of ATP homeostasis during the respiro-fermentative transition in yeast. Mol Syst Biol 2010; 6:344. [PMID: 20087341 PMCID: PMC2824524 DOI: 10.1038/msb.2009.100] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2009] [Accepted: 11/07/2009] [Indexed: 11/09/2022] Open
Abstract
Respiring Saccharomyces cerevisiae cells respond to a sudden increase in glucose concentration by a pronounced drop of their adenine nucleotide content ([ATP]+[ADP]+[AMP]=[AXP]). The unknown fate of 'lost' AXP nucleotides represented a long-standing problem for the understanding of the yeast's physiological response to changing growth conditions. Transient accumulation of the purine salvage pathway intermediate, inosine, accounted for the apparent loss of adenine nucleotides. Conversion of AXPs into inosine was facilitated by AMP deaminase, Amd1, and IMP-specific 5'-nucleotidase, Isn1. Inosine recycling into the AXP pool was facilitated by purine nucleoside phosphorylase, Pnp1, and joint action of the phosphoribosyltransferases, Hpt1 and Xpt1. Analysis of changes in 24 intracellular metabolite pools during the respiro-fermentative growth transition in wild-type, amd1, isn1, and pnp1 strains revealed that only the amd1 mutant exhibited significant deviations from the wild-type behavior. Moreover, mutants that were blocked in inosine production exhibited delayed growth acceleration after glucose addition. It is proposed that interconversion of adenine nucleotides and inosine facilitates rapid and energy-cost efficient adaptation of the AXP pool size to changing environmental conditions.
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Affiliation(s)
- Thomas Walther
- Université de Toulouse, INSA, UPS, INP, Toulouse, France.
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40
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Canelas AB, ten Pierick A, Ras C, Seifar RM, van Dam JC, van Gulik WM, Heijnen JJ. Quantitative evaluation of intracellular metabolite extraction techniques for yeast metabolomics. Anal Chem 2009; 81:7379-89. [PMID: 19653633 DOI: 10.1021/ac900999t] [Citation(s) in RCA: 256] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Accurate determination of intracellular metabolite levels requires well-validated procedures for sampling and sample treatment. Several methods exist for metabolite extraction, but the literature is contradictory regarding the adequacy and performance of each technique. Using a strictly quantitative approach, we have re-evaluated five methods (hot water, HW; boiling ethanol, BE; chloroform-methanol, CM; freezing-thawing in methanol, FTM; acidic acetonitrile-methanol, AANM) for the extraction of 44 intracellular metabolites (phosphorylated intermediates, amino acids, organic acids, nucleotides) from S. cerevisiae cells. Two culture modes were investigated (batch and chemostat) to check for growth condition dependency, and three targeted platforms were employed (two LC-MS and one GC/MS) to exclude analytical bias. Additionally, for the determination of metabolite recoveries, we applied a novel approach based on addition of (13)C-labeled internal standards at different stages of sample processing. We found that the choice of extraction method can drastically affect measured metabolite levels, to an extent that for some metabolites even the direction of changes between growth conditions can be inverted. The best performances, in terms of efficacy and metabolite recoveries, were achieved with BE and CM, which yielded nearly identical levels for the metabolites analyzed. According to our results, AANM performs poorly in yeast and FTM cannot be considered adequate as an extraction method, as it does not ensure inactivation of enzymatic activity.
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Affiliation(s)
- André B Canelas
- Department of Biotechnology, Kluyver Centre for Genomics of Industrial Fermentation, Delft University of Technology, Julianalaan 67, 2628 BC, The Netherlands.
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41
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Spura J, Christian Reimer L, Wieloch P, Schreiber K, Buchinger S, Schomburg D. A method for enzyme quenching in microbial metabolome analysis successfully applied to gram-positive and gram-negative bacteria and yeast. Anal Biochem 2009; 394:192-201. [DOI: 10.1016/j.ab.2009.07.016] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2009] [Revised: 07/10/2009] [Accepted: 06/14/2009] [Indexed: 10/20/2022]
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42
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Bogan KL, Evans C, Belenky P, Song P, Burant CF, Kennedy R, Brenner C. Identification of Isn1 and Sdt1 as glucose- and vitamin-regulated nicotinamide mononucleotide and nicotinic acid mononucleotide [corrected] 5'-nucleotidases responsible for production of nicotinamide riboside and nicotinic acid riboside. J Biol Chem 2009; 284:34861-9. [PMID: 19846558 DOI: 10.1074/jbc.m109.056689] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Recently, we discovered that nicotinamide riboside and nicotinic acid riboside are biosynthetic precursors of NAD(+), which are utilized through two pathways consisting of distinct enzymes. In addition, we have shown that exogenously supplied nicotinamide riboside is imported into yeast cells by a dedicated transporter, and it extends replicative lifespan on high glucose medium. Here, we show that nicotinamide riboside and nicotinic acid riboside are authentic intracellular metabolites in yeast. Secreted nicotinamide riboside was detected with a biological assay, and intracellular levels of nicotinamide riboside, nicotinic acid riboside, and other NAD(+) metabolites were determined by a liquid chromatography-mass spectrometry method. A biochemical genomic screen indicated that three yeast enzymes possess nicotinamide mononucleotide 5'-nucleotidase activity in vitro. Metabolic profiling of knock-out mutants established that Isn1 and Sdt1 are responsible for production of nicotinamide riboside and nicotinic acid riboside in cells. Isn1, initially classified as an IMP-specific 5'-nucleotidase, and Sdt1, initially classified as a pyrimidine 5'-nucleotidase, are additionally responsible for dephosphorylation of pyridine mononucleotides. Sdt1 overexpression is growth-inhibitory to cells in a manner that depends on its active site and correlates with reduced cellular NAD(+). Expression of Isn1 protein is positively regulated by the availability of nicotinic acid and glucose. These results reveal unanticipated and highly regulated steps in NAD(+) metabolism.
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Affiliation(s)
- Katrina L Bogan
- Biochemistry Graduate Program, Dartmouth Medical School, Lebanon, New Hampshire 03756, USA
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43
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Vrabl P, Mutschlechner W, Burgstaller W. Dynamics of energy charge and adenine nucleotides during uncoupling of catabolism and anabolism in Penicillium ochrochloron. ACTA ACUST UNITED AC 2009; 113:1422-32. [PMID: 19818403 DOI: 10.1016/j.mycres.2009.09.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2009] [Revised: 09/28/2009] [Accepted: 09/29/2009] [Indexed: 10/20/2022]
Abstract
Filamentous fungi are able to spill energy when exposed to energy excess by uncoupling catabolism from anabolism, e.g. via overflow metabolism. In current study we tested the hypothesis that overflow metabolism is regulated via the energetic status of the hyphae (i.e. energy charge, ATP concentration). This hypothesis was studied in Penicillium ochrochloron during the steady state of glucose- or ammonium-limited chemostat cultures as well as during three transient states ((i) glucose pulse to a glucose-limited chemostat, (ii) shift from glucose-limited to ammonium-limited conditions in a chemostat, and (iii) ammonium exhaustion in batch culture). Organic acids were excreted under all conditions, even during exponential growth in batch culture as well as under glucose-limited conditions in a chemostat. Partial uncoupling of catabolism and anabolism via overflow metabolism was thus constitutively present. Under all tested conditions, overflow metabolism was independent of the energy charge or the ATP concentration of the hyphae. There was a reciprocal correlation between glucose uptake rate and intracellular adenine nucleotide content. During all transients states a rapid decrease in energy charge and the concentrations of nucleotides was observed shortly after a change in glycolytic flux ("ATP paradoxon"). A possible connection between the change in adenine nucleotide concentrations and the purine salvage pathway is discussed.
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Affiliation(s)
- Pamela Vrabl
- University of Innsbruck, Institute of Microbiology, Technikerstrasse 25, 6020 Innsbruck, Austria.
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44
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Phenotypic consequences of purine nucleotide imbalance in Saccharomyces cerevisiae. Genetics 2009; 183:529-38, 1SI-7SI. [PMID: 19635936 DOI: 10.1534/genetics.109.105858] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Coordinating homeostasis of multiple metabolites is a major task for living organisms, and complex interconversion pathways contribute to achieving the proper balance of metabolites. AMP deaminase (AMPD) is such an interconversion enzyme that allows IMP synthesis from AMP. In this article, we show that, under specific conditions, lack of AMPD activity impairs growth. Under these conditions, we found that the intracellular guanylic nucleotide pool was severely affected. In vivo studies of two AMPD homologs, Yjl070p and Ybr284p, indicate that these proteins have no detectable AMP, adenosine, or adenine deaminase activity; we show that overexpression of YJL070c instead mimics a loss of AMPD function. Expression of the yeast transcriptome was monitored in a AMPD-deficient mutant in a strain overexpressing YJL070c and in cells treated with the immunosuppressive drug mycophenolic acid, three conditions that lead to severe depletion of the guanylic nucleotide pool. These three conditions resulted in the up- or downregulation of multiple transcripts, 244 of which are common to at least two conditions and 71 to all three conditions. These transcriptome results, combined with specific mutant analysis, point to threonine metabolism as exquisitely sensitive to the purine nucleotide balance.
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45
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Kitanovic A, Walther T, Loret MO, Holzwarth J, Kitanovic I, Bonowski F, Van Bui N, Francois JM, Wölfl S. Metabolic response to MMS-mediated DNA damage in Saccharomyces cerevisiae is dependent on the glucose concentration in the medium. FEMS Yeast Res 2009; 9:535-51. [PMID: 19341380 DOI: 10.1111/j.1567-1364.2009.00505.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Maintenance and adaptation of energy metabolism could play an important role in the cellular ability to respond to DNA damage. A large number of studies suggest that the sensitivity of cells to oxidants and oxidative stress depends on the activity of cellular metabolism and is dependent on the glucose concentration. In fact, yeast cells that utilize fermentative carbon sources and hence rely mainly on glycolysis for energy appear to be more sensitive to oxidative stress. Here we show that treatment of the yeast Saccharomyces cerevisiae growing on a glucose-rich medium with the DNA alkylating agent methyl methanesulphonate (MMS) triggers a rapid inhibition of respiration and enhances reactive oxygen species (ROS) production, which is accompanied by a strong suppression of glycolysis. Further, diminished activity of pyruvate kinase and glyceraldehyde-3-phosphate dehydrogenase upon MMS treatment leads to a diversion of glucose carbon to glycerol, trehalose and glycogen accumulation and an increased flux through the pentose-phosphate pathway. Such conditions finally result in a significant decline in the ATP level and energy charge. These effects are dependent on the glucose concentration in the medium. Our results clearly demonstrate that calorie restriction reduces MMS toxicity through increased respiration and reduced ROS accumulation, enhancing the survival and recovery of cells.
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Affiliation(s)
- Ana Kitanovic
- Institute for Pharmacy and Molecular Biotechnology, Ruperto-Carola University of Heidelberg, Heidelberg, Germany
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46
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Díaz-Ruiz R, Avéret N, Araiza D, Pinson B, Uribe-Carvajal S, Devin A, Rigoulet M. Mitochondrial oxidative phosphorylation is regulated by fructose 1,6-bisphosphate. A possible role in Crabtree effect induction? J Biol Chem 2008; 283:26948-55. [PMID: 18682403 DOI: 10.1074/jbc.m800408200] [Citation(s) in RCA: 113] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In numerous cell types, tumoral cells, proliferating cells, bacteria, and yeast, respiration is inhibited when high concentrations of glucose are added to the culture medium. This phenomenon has been named the "Crabtree effect." We used yeast to investigate (i) the short term event(s) associated with the Crabtree effect and (ii) a putative role of hexose phosphates in the inhibition of respiration. Indeed, yeast divide into "Crabtree-positive," where the Crabtree effect occurs, and "Crabtree-negative," where it does not. In mitochondria isolated from these two categories of yeast, we found that low, physiological concentrations of glucose 6-phosphate and fructose 6-phosphate slightly (20%) stimulated the respiratory flux and that this effect was strongly antagonized by fructose 1,6-bisphosphate (F16bP). On the other hand, F16bP by itself was able to inhibit mitochondrial respiration only in mitochondria isolated from a Crabtree-positive strain. Using permeabilized spheroplasts from Crabtree-positive yeast, we have shown that the sole effect observed at physiological concentrations of hexose phosphates is an inhibition of oxidative phosphorylation by F16bP. This F16bP-mediated inhibition was also observed in isolated rat liver mitochondria, extending this process to mammalian cells. From these results and taking into account that F16bP is able to accumulate in the cell cytoplasm, we propose that F16bP regulates oxidative phosphorylation and thus participates in the establishment of the Crabtree effect.
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Affiliation(s)
- Rodrigo Díaz-Ruiz
- Université Victor Segalen Bordeaux 2, 1 Rue Camille Saint-Saëns, 33077 Bordeaux cedex, France
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47
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Bolten CJ, Wittmann C. Appropriate sampling for intracellular amino acid analysis in five phylogenetically different yeasts. Biotechnol Lett 2008; 30:1993-2000. [PMID: 18604477 DOI: 10.1007/s10529-008-9789-z] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2008] [Revised: 06/09/2008] [Accepted: 06/12/2008] [Indexed: 11/26/2022]
Abstract
Methanol quenching and fast filtration, the two most common sampling protocols in microbial metabolome analysis, were validated for intracellular amino acid analysis in phylogenetically different yeast strains comprising Saccharomyces cerevisiae, Kluyveromyces marxianus, Pichia pastoris, Schizosaccharomyces pombe and Zygosaccharomyces bailii. With only few exceptions for selected amino acids, all yeasts exhibited negligible metabolite leakage during quenching with 60% cold buffered methanol. Slightly higher leakage was observed with increasing methanol content in the quenching solution. Fast filtration resulted in identical levels for intracellular amino acids in all strains tested. The results clearly demonstrate the validity of both approaches for leakage-free sampling of amino acids in yeast.
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Affiliation(s)
- Christoph J Bolten
- Biotechnology Department, Biochemistry Institute, Westfalian Wilhelms-University, Munster, Germany
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48
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Geng X, Zhang S, Wang Q, Zhao Z(K. Determination of organic acids in the presence of inorganic anions by ion chromatography with suppressed conductivity detection. J Chromatogr A 2008; 1192:187-90. [DOI: 10.1016/j.chroma.2008.03.073] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2007] [Revised: 03/24/2008] [Accepted: 03/27/2008] [Indexed: 10/22/2022]
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49
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Gauthier S, Coulpier F, Jourdren L, Merle M, Beck S, Konrad M, Daignan-Fornier B, Pinson B. Co-regulation of yeast purine and phosphate pathways in response to adenylic nucleotide variations. Mol Microbiol 2008; 68:1583-94. [PMID: 18433446 DOI: 10.1111/j.1365-2958.2008.06261.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Adenylate kinase (Adk1p) is a pivotal enzyme in both energetic and adenylic nucleotide metabolisms. In this paper, using a transcriptomic analysis, we show that the lack of Adk1p strongly induced expression of the PHO and ADE genes involved in phosphate utilization and AMP de novo biosynthesis respectively. Isolation and characterization of adk1 point mutants affecting PHO5 expression revealed that all these mutations also severely affected Adk1p catalytic activity, as well as PHO84 and ADE1 transcription. Furthermore, overexpression of distantly related enzymes such as human adenylate kinase or yeast UMP kinase was sufficient to restore regulation. These results demonstrate that adenylate kinase catalytic activity is critical for proper regulation of the PHO and ADE pathways. We also establish that adk1 deletion and purine limitation have similar effects on both adenylic nucleotide pool and PHO84 or ADE17 expression. Finally, we show that, in the adk1 mutant, upregulation of ADE1 depends on synthesis of the previously described effector(s) (S)AICAR ((N-succinyl)-5-aminoimidazol-4-carboxamide ribotide), while upregulation of PHO84 necessitates the Spl2p positive regulator. This work reveals that adenylic nucleotide availability is a key signal used by yeast to co-ordinate phosphate utilization and purine synthesis.
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Affiliation(s)
- Sébastien Gauthier
- Université Victor Segalen/Bordeaux 2, Institut de Biochimie et Génétique Cellulaires, Bordeaux, France
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Winder CL, Dunn WB, Schuler S, Broadhurst D, Jarvis R, Stephens GM, Goodacre R. Global Metabolic Profiling of Escherichia coli Cultures: an Evaluation of Methods for Quenching and Extraction of Intracellular Metabolites. Anal Chem 2008; 80:2939-48. [DOI: 10.1021/ac7023409] [Citation(s) in RCA: 246] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Catherine L. Winder
- School of Chemistry, The Manchester Centre for Integrative Systems Biology, and School of Chemical Engineering and Analytical Sciences, and The Manchester Interdisciplinary Biocentre, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Warwick B. Dunn
- School of Chemistry, The Manchester Centre for Integrative Systems Biology, and School of Chemical Engineering and Analytical Sciences, and The Manchester Interdisciplinary Biocentre, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Stephanie Schuler
- School of Chemistry, The Manchester Centre for Integrative Systems Biology, and School of Chemical Engineering and Analytical Sciences, and The Manchester Interdisciplinary Biocentre, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - David Broadhurst
- School of Chemistry, The Manchester Centre for Integrative Systems Biology, and School of Chemical Engineering and Analytical Sciences, and The Manchester Interdisciplinary Biocentre, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Roger Jarvis
- School of Chemistry, The Manchester Centre for Integrative Systems Biology, and School of Chemical Engineering and Analytical Sciences, and The Manchester Interdisciplinary Biocentre, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Gillian M. Stephens
- School of Chemistry, The Manchester Centre for Integrative Systems Biology, and School of Chemical Engineering and Analytical Sciences, and The Manchester Interdisciplinary Biocentre, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Royston Goodacre
- School of Chemistry, The Manchester Centre for Integrative Systems Biology, and School of Chemical Engineering and Analytical Sciences, and The Manchester Interdisciplinary Biocentre, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
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