System-Level Insights into Yeast Metabolism by Thermodynamic Analysis of Elementary Flux Modes

U Sauer, 2006, Metabolic networks in motion: 13C-based ux analysis., Mol Syst Biol, 2, 62, 10.1038/msb4100109

N Zamboni, 2009, Novel biological insights through metabolomics and 13C-ux analysis., Curr Opin Microbiol, 12, 553, 10.1016/j.mib.2009.08.003

T Fuhrer, 2009, Different biochemical mechanisms ensure network-wide balancing of reducing equivalents in microbial metabolism., J Bacteriol, 191, 2112, 10.1128/JB.01523-08

SM Fendt, 2010, Transcriptional regulation of respiration in yeast metabolizing differently repressive carbon substrates., BMC Syst Biol, 4, 12, 10.1186/1752-0509-4-12

RJ Kleijn, 2007, Metabolic flux analysis of a glycerol-overproducing Saccharomyces cerevisiae strain based on GC-MS, LC-MS and NMRderived C-labelling data., FEMS Yeast Res, 7, 216, 10.1111/j.1567-1364.2006.00180.x

N Zamboni, 2009, (13)C-based metabolic flux analysis., Nat Protoc, 4, 878, 10.1038/nprot.2009.58

N Zamboni, 2010, (13)C metabolic flux analysis in complex systems., Curr Opin Biotechnol, 22, 103, 10.1016/j.copbio.2010.08.009

U Sonnewald, 2004, Intracellular metabolic compartmentation assessed by 13C magnetic resonance spectroscopy., Neurochem Int, 45, 305, 10.1016/j.neuint.2003.10.010

J Niklas, 2010, Metabolic ux analysis in eukaryotes., Curr Opin Biotechnol, 21, 63, 10.1016/j.copbio.2010.01.011

KJ Kauffman, 2003, Advances in flux balance analysis., Curr Opin Biotechnol, 14, 491, 10.1016/j.copbio.2003.08.001

PDN Pissarra, 1997, Thermodynamics of Metabolic Pathways for Penicillin Production: Analysis of Thermodynamic Feasibility and Free Energy Changes During Fed-Batch Cultivation., Biotechnol Prog, 13, 156, 10.1021/bp970010c

A Kümmel, 2006, Putative regulatory sites unraveled by networkembedded thermodynamic analysis of metabolome data., Mol Syst Biol, 2, 2006.0034, 10.1038/msb4100074

AM Feist, 2007, A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information., Mol Syst Biol, 3, 121, 10.1038/msb4100155

A Hoppe, 2007, Including metabolite concentrations into flux balance analysis: Thermodynamic realizability as a constraint on flux distributions in metabolic networks., BMC Syst Biol, 1, 23, 10.1186/1752-0509-1-23

CS Henry, 2007, Thermodynamics-Based Metabolic Flux Analysis., Biophys J, 92, 1792, 10.1529/biophysj.106.093138

Ma Orman, 2012, Metabolic network analysis of perfused livers under fed and fasted states: Incorporating thermodynamic and futile-cycleassociated regulatory constraints., J Theor Biol, 293, 101, 10.1016/j.jtbi.2011.10.019

S Schuster, 1994, On elementary ux modes in biochemical reaction systems at steady state., J Biol Syst, 2, 165, 10.1142/S0218339094000131

S Klamt, 2005, Algorithmic approaches for computing elementary modes in large biochemical reaction networks., Syst Biol (Stevenage), 152, 249, 10.1049/ip-syb:20050035

M Terzer, 2008, Large-scale computation of elementary flux modes with bit pattern trees., Bioinformatics, 24, 2229, 10.1093/bioinformatics/btn401

S Schuster, 1999, Detection of elementary flux modes in biochemical networks: a promising tool for pathway analysis and metabolic engineering., Trends Biotechnol, 17, 53, 10.1016/S0167-7799(98)01290-6

NC Duarte, 2004, Reconstruction and Validation of Saccharomyces cerevisiae iND750, a Fully Compartmentalized Genome-Scale Metabolic Model., Genome Res, 14, 1298, 10.1101/gr.2250904

R Mahadevan, 2003, The effects of alternate optimal solutions in constraint-based genome-scale metabolic models., Metab Eng, 5, 264, 10.1016/j.ymben.2003.09.002

N Zamboni, 2008, anNET: a tool for network-embedded thermodynamic analysis of quantitative metabolome data., BMC bioinformatics, 9, 199, 10.1186/1471-2105-9-199

L Palmieri, 1999, Identification of the Yeast Mitochondrial Transporter for Oxaloacetate and Sulfate., J Biol Chem, 274, 22184, 10.1074/jbc.274.32.22184

DK Breslow, 2008, A comprehensive strategy enabling high-resolution functional analysis of the yeast genome., Nat Methods, 5, 711, 10.1038/nmeth.1234

ND Price, 2002, Extreme Pathways and Kirchhoff's Second Law., Biophys J, 83, 2879, 10.1016/S0006-3495(02)75297-1

BM Bakker, 2001, Stoichiometry and compartmentation of NADH metabolism in Saccharomyces cerevisiae., FEMS Microbiol Rev, 25, 15, 10.1111/j.1574-6976.2001.tb00570.x

R Schütz, 2007, Systematic evaluation of objective functions for predicting intracellular uxes in Escherichia coli., Mol Syst Biol, 3, 119, 10.1038/msb4100162

R Schütz, 2009, Model-driven identification of operating principles in metabolic networks [Ph.D. thesis]

GN Vemuri, 2007, Increasing NADH oxidation reduces overow metabolism in Saccharomyces cerevisiae., Proc Natl Acad Sci U S A, 104, 2402, 10.1073/pnas.0607469104

M Rigoulet, 2004, Organization and regulation of the cytosolic NADH metabolism in the yeast Saccharomyces cerevisiae., Mol Cell Biochem, 256–257, 73, 10.1023/B:MCBI.0000009888.79484.fd

CAM Marres, 1991, Isolation and inactivation of the nuclear gene encoding the rotenone-insensitive internal NADH: ubiquinone oxidoreductase of mitochondria from Saccharomyces cerevisiae., Eur J Biochem, 195, 857, 10.1111/j.1432-1033.1991.tb15775.x

S Todisco, 2006, Identification of the Mitochondrial NAD+ Transporter in Saccharomyces cerevisiae., J Biol Chem, 281, 1524, 10.1074/jbc.M510425200

G von Jagow, 1970, Pathways of hydrogen in mitochondria of Saccharomyces carlsbergensis., Eur J Biochem, 12, 583, 10.1111/j.1432-1033.1970.tb00890.x

MD Jankowski, 2008, Group Contribution Method for Thermodynamic Analysis of Complex Metabolic Networks., Biophys J, 95, 1487, 10.1529/biophysj.107.124784

X Li, 2010, A Database of Thermodynamic Quantities for the Reactions of Glycolysis and the Tricarboxylic Acid Cycle., J Phys Chem B, 114, 16068, 10.1021/jp911381p

JM Buescher, 2010, Ultrahigh performance liquid chromatographytandem mass spectrometry method for fast and robust quantification of anionic and aromatic metabolites., Anal Chem, 82, 4403, 10.1021/ac100101d

M Terzer, 2009, Large scale methods to enumerate extreme rays and elementary modes [Ph.D. thesis]

C Kaleta, 2009, Can the whole be less than the sum of its parts? Pathway analysis in genome-scale metabolic networks using elementary flux patterns., Genome Res, 19, 1872, 10.1101/gr.090639.108

A Kümmel, 2008, Integrating Thermodynamics-based Modeling and Quantitative Experimental Data for Studying Microbial Metabolism [Ph.D. thesis]

SM Fendt, 2010, Tradeoff between enzyme and metabolite efficiency maintains metabolic homeostasis upon perturbations in enzyme capacity., Mol Syst Biol, 6, 356, 10.1038/msb.2010.11

JC Ewald, 2010, Unraveling Yeast's Response to its Environment by Novel Metabolomics Approaches [Ph.D. thesis]

M Kunze, 2002, Targeting of malate synthase 1 to the peroxisomes of Saccharomyces cerevisiae cells depends on growth on oleic acid medium., Eur J Biochem, 269, 915, 10.1046/j.0014-2956.2001.02727.x

WK Huh, 2003, Global analysis of protein localization in budding yeast., Nature, 425, 686, 10.1038/nature02026

LM Blank, 2005, Metabolic-flux and network analysis in fourteen hemiascomycetous yeasts., FEMS Yeast Res, 5, 545, 10.1016/j.femsyr.2004.09.008

H Maaheimo, 2001, Central carbon metabolism of Saccharomyces cerevisiae explored by biosynthetic fractional 13C labeling of common amino acids., Eur J Biochem, 268, 2464, 10.1046/j.1432-1327.2001.02126.x

L Valenzuela, 1998, Regulation of expression of GLT1, the gene encoding glutamate synthase in Saccharomyces cerevisiae., J Bacteriol, 180, 3533, 10.1128/JB.180.14.3533-3540.1998

T Schlösser, 2004, Alanine : glyoxylate aminotransferase of Saccharomyces cerevisiae-encoding gene AGX1 and metabolic significance., Yeast, 21, 63, 10.1002/yea.1058

EK Kastanos, 1997, Role of mitochondrial and cytoplasmic serine hydroxymethyltransferase isozymes in de novo purine synthesis in Saccharomyces cerevisiae., Biochemistry, 36, 14956, 10.1021/bi971610n

N Monschau, 2006, Identification of Saccharomyces cerevisiae GLY1 as a threonine aldolase: a key enzyme in glycine biosynthesis., FEMS Microbiol Lett, 150, 55, 10.1111/j.1574-6968.1997.tb10349.x

DA Beard, 2005, Thermodynamic-Based Computational Profiling of Cellular Regulatory Control in Hepatocyte Metabolism., Am J Physiol Endocrinol Metab, 288, 633, 10.1152/ajpendo.00239.2004

C Auesukaree, 2004, Intracellular Phosphate Serves as a Signal for the Regulation of the PHO Pathway in Saccharomyces cerevisiae., J Biol Chem, 279, 17289, 10.1074/jbc.M312202200

Y Takehara, 1995, Oxygen-Dependent Regulation of Mitochondrial Energy Metabolism by Nitric Oxide., Arch Biochem Biophys, 323, 27, 10.1006/abbi.1995.0005

MTAP Kresnowati, 2007, Measurement of fast dynamic intracellular pH in Saccharomyces cerevisiae using benzoic acid pulse., Biotechnol Bioeng, 97, 86, 10.1002/bit.21179

R Orij, 2009, In vivo measurement of cytosolic and mitochondrial pH using a pH-sensitive GFP derivative in Saccharomyces cerevisiae reveals a relation between intracellular pH and growth., Microbiology, 155, 268, 10.1099/mic.0.022038-0

SJ Jol, 2010, Thermodynamic Calculations for Biochemical Transport and Reaction Processes in Metabolic Networks., Biophys J, 99, 3139, 10.1016/j.bpj.2010.09.043