Uwe Sauer

Summary

Affiliation: Swiss Federal Institute of Technology
Country: Switzerland

Publications

  1. pmc Tradeoff between enzyme and metabolite efficiency maintains metabolic homeostasis upon perturbations in enzyme capacity
    Sarah Maria Fendt
    Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
    Mol Syst Biol 6:356. 2010
  2. ncbi request reprint Genetics. Getting closer to the whole picture
    Uwe Sauer
    Institute of Molecular Systems Biology, ETH Zurich, Switzerland
    Science 316:550-1. 2007
  3. pmc Metabolic networks in motion: 13C-based flux analysis
    Uwe Sauer
    Institute of Molecular Systems Biology, ETH Zurich, Switzerland
    Mol Syst Biol 2:62. 2006
  4. pmc Cyclic AMP-dependent catabolite repression is the dominant control mechanism of metabolic fluxes under glucose limitation in Escherichia coli
    Annik Nanchen
    Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
    J Bacteriol 190:2323-30. 2008
  5. pmc Large-scale 13C-flux analysis reveals distinct transcriptional control of respiratory and fermentative metabolism in Escherichia coli
    Bart R B Haverkorn van Rijsewijk
    Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
    Mol Syst Biol 7:477. 2011
  6. pmc Impact of global transcriptional regulation by ArcA, ArcB, Cra, Crp, Cya, Fnr, and Mlc on glucose catabolism in Escherichia coli
    Annik Perrenoud
    Institute of Biotechnology, ETH Zurich, CH 8093 Zurich, Switzerland
    J Bacteriol 187:3171-9. 2005
  7. ncbi request reprint Differential glucose repression in common yeast strains in response to HXK2 deletion
    Anne Kümmel
    Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
    FEMS Yeast Res 10:322-32. 2010
  8. ncbi request reprint Transient expression and flux changes during a shift from high to low riboflavin production in continuous cultures of Bacillus subtilis
    Nicola Zamboni
    Institute of Biotechnology, ETH Zurich, CH 8093 Zurich, Switzerland
    Biotechnol Bioeng 89:219-32. 2005
  9. pmc Transcriptional regulation is insufficient to explain substrate-induced flux changes in Bacillus subtilis
    Victor Chubukov
    Institute of Molecular System Biology, ETH Zurich, Zurich, Switzerland
    Mol Syst Biol 9:709. 2013
  10. pmc CcpN controls central carbon fluxes in Bacillus subtilis
    Simon Tännler
    Institute of Molecular Systems Biology, ETH Zurich, CH 8093 Zurich, Switzerland
    J Bacteriol 190:6178-87. 2008

Collaborators

Detail Information

Publications89

  1. pmc Tradeoff between enzyme and metabolite efficiency maintains metabolic homeostasis upon perturbations in enzyme capacity
    Sarah Maria Fendt
    Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
    Mol Syst Biol 6:356. 2010
    ..Hence, alteration in one network constituent can be efficiently buffered by converse alterations in the other constituent, implying a passive mechanism to maintain metabolic homeostasis upon perturbations in enzyme capacity...
  2. ncbi request reprint Genetics. Getting closer to the whole picture
    Uwe Sauer
    Institute of Molecular Systems Biology, ETH Zurich, Switzerland
    Science 316:550-1. 2007
  3. pmc Metabolic networks in motion: 13C-based flux analysis
    Uwe Sauer
    Institute of Molecular Systems Biology, ETH Zurich, Switzerland
    Mol Syst Biol 2:62. 2006
    ....
  4. pmc Cyclic AMP-dependent catabolite repression is the dominant control mechanism of metabolic fluxes under glucose limitation in Escherichia coli
    Annik Nanchen
    Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
    J Bacteriol 190:2323-30. 2008
    ....
  5. pmc Large-scale 13C-flux analysis reveals distinct transcriptional control of respiratory and fermentative metabolism in Escherichia coli
    Bart R B Haverkorn van Rijsewijk
    Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
    Mol Syst Biol 7:477. 2011
    ..Thus, E. coli actively limits its galactose catabolism at the expense of otherwise possible faster growth...
  6. pmc Impact of global transcriptional regulation by ArcA, ArcB, Cra, Crp, Cya, Fnr, and Mlc on glucose catabolism in Escherichia coli
    Annik Perrenoud
    Institute of Biotechnology, ETH Zurich, CH 8093 Zurich, Switzerland
    J Bacteriol 187:3171-9. 2005
    ..coli. This control goes well beyond the previously known ArcA-dependent regulation of the TCA cycle during microaerobiosis...
  7. ncbi request reprint Differential glucose repression in common yeast strains in response to HXK2 deletion
    Anne Kümmel
    Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
    FEMS Yeast Res 10:322-32. 2010
    ....
  8. ncbi request reprint Transient expression and flux changes during a shift from high to low riboflavin production in continuous cultures of Bacillus subtilis
    Nicola Zamboni
    Institute of Biotechnology, ETH Zurich, CH 8093 Zurich, Switzerland
    Biotechnol Bioeng 89:219-32. 2005
    ..With the possible exception of a slight down-regulation of the purine biosynthesis pathway, genome-wide expression analysis indicated that transcriptional regulation was not responsible for the production decline...
  9. pmc Transcriptional regulation is insufficient to explain substrate-induced flux changes in Bacillus subtilis
    Victor Chubukov
    Institute of Molecular System Biology, ETH Zurich, Zurich, Switzerland
    Mol Syst Biol 9:709. 2013
    ..Surprisingly, substrate changes revealed by metabolomics were also insufficient to explain observed fluxes, leaving a large role for allosteric regulation and enzyme modification in the control of metabolic fluxes...
  10. pmc CcpN controls central carbon fluxes in Bacillus subtilis
    Simon Tännler
    Institute of Molecular Systems Biology, ETH Zurich, CH 8093 Zurich, Switzerland
    J Bacteriol 190:6178-87. 2008
    ..In contrast, derepression of sr1, the third known target of CcpN, plays only a marginal role in ccpN mutant phenotypes...
  11. doi request reprint Multidimensional optimality of microbial metabolism
    Robert Schuetz
    Institute of Molecular Systems Biology, Eidgenossische Technische Hochschule Zurich, Zurich, Switzerland
    Science 336:601-4. 2012
    ..These principles form the forces by which evolution shapes metabolic fluxes in microorganisms' environmental context...
  12. pmc Regulation of yeast central metabolism by enzyme phosphorylation
    Ana Paula Oliveira
    Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
    Mol Syst Biol 8:623. 2012
    ..These results demonstrate the role of phosphorylation in controlling the metabolic flux realised by these three enzymes...
  13. ncbi request reprint TCA cycle activity in Saccharomyces cerevisiae is a function of the environmentally determined specific growth and glucose uptake rates
    Lars M Blank
    Institute of Biotechnology, ETH Zurich, Zurich, Switzerland
    Microbiology 150:1085-93. 2004
    ..While sensing of extracellular glucose concentrations has a general influence on the in vivo TCA cycle activity, the growth-rate-dependent increase in respiratory TCA cycle activity was independent of glucose sensing...
  14. ncbi request reprint The soluble and membrane-bound transhydrogenases UdhA and PntAB have divergent functions in NADPH metabolism of Escherichia coli
    Uwe Sauer
    Institute of Biotechnology, ETH Zurich, CH 8093 Zurich, Switzerland
    J Biol Chem 279:6613-9. 2004
    ..metabolism with an extraordinary flexibility to cope with varying catabolic and anabolic demands, which raises two general questions: why do only a few bacteria contain both isoforms, and how do other organisms manage NADPH metabolism?..
  15. pmc The Bacillus subtilis yqjI gene encodes the NADP+-dependent 6-P-gluconate dehydrogenase in the pentose phosphate pathway
    Nicola Zamboni
    Institute of Biotechnology, ETH Zurich, Zurich, Switzerland
    J Bacteriol 186:4528-34. 2004
    ....
  16. ncbi request reprint Determination of metabolic flux ratios from 13C-experiments and gas chromatography-mass spectrometry data: protocol and principles
    Annik Nanchen
    Institute for Molecular Systems Biology, ETH Zurich, Switzerland
    Methods Mol Biol 358:177-97. 2007
    ..These principles are also implemented in the publicly available software FiatFlux, which directly calculates flux ratios from the mass spectra of amino acids...
  17. pmc Comprehensive quantitative analysis of central carbon and amino-acid metabolism in Saccharomyces cerevisiae under multiple conditions by targeted proteomics
    Roeland Costenoble
    Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
    Mol Syst Biol 7:464. 2011
    ..Interpreted through flux balance modeling, the data indicate that S. cerevisiae retains proteins not necessarily used in a particular environment. Further, the data suggest differential functionality for several metabolic isoenzymes...
  18. doi request reprint Global network reorganization during dynamic adaptations of Bacillus subtilis metabolism
    Joerg Martin Buescher
    Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
    Science 335:1099-103. 2012
    ..Our analysis suggests that global trade-offs and evolutionary constraints provide incentives to favor complex control programs...
  19. doi request reprint Intracellular characterization of aerobic glucose metabolism in seven yeast species by 13C flux analysis and metabolomics
    Stefan Christen
    Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
    FEMS Yeast Res 11:263-72. 2011
    ....
  20. doi request reprint (13)C-based metabolic flux analysis
    Nicola Zamboni
    Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
    Nat Protoc 4:878-92. 2009
    ..The presented protocols take 5-10 d, have been used extensively in the past decade and are exemplified here for the central metabolism of Escherichia coli...
  21. doi request reprint Screening of Bacillus subtilis transposon mutants with altered riboflavin production
    Simon Tännler
    Institute of Molecular Systems Biology, ETH Zurich, CH 8093 Zurich, Switzerland
    Metab Eng 10:216-26. 2008
    ..This improvement was also verified under the more process-relevant conditions of a glucose-limited fed-batch culture...
  22. pmc Nonlinear dependency of intracellular fluxes on growth rate in miniaturized continuous cultures of Escherichia coli
    Annik Nanchen
    Institute of Molecular Systems Biology, ETH Zurich, CH 8093 Zurich, Switzerland
    Appl Environ Microbiol 72:1164-72. 2006
    ....
  23. pmc Unraveling condition-dependent networks of transcription factors that control metabolic pathway activity in yeast
    Sarah Maria Fendt
    Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
    Mol Syst Biol 6:432. 2010
    ....
  24. pmc Metabolic fluxes during strong carbon catabolite repression by malate in Bacillus subtilis
    Roelco J Kleijn
    Institute of Molecular System Biology, ETH Zurich, CH 8093 Zurich, Switzerland
    J Biol Chem 285:1587-96. 2010
    ..Co-utilization of glucose and malate resulted in a synergistic decrease of the respiratory tricarboxylic acid cycle flux...
  25. ncbi request reprint Knockout of the high-coupling cytochrome aa3 oxidase reduces TCA cycle fluxes in Bacillus subtilis
    Nicola Zamboni
    Institute of Biotechnology, ETH Zurich, CH 8093, Zurich, Switzerland
    FEMS Microbiol Lett 226:121-6. 2003
    ..Since the product-corrected biomass yields were identical in mutants and parent, the results show that efficient ATP generation is not overly important for exponential growth of B. subtilis in batch culture...
  26. pmc Transcriptional regulation of respiration in yeast metabolizing differently repressive carbon substrates
    Sarah Maria Fendt
    Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
    BMC Syst Biol 4:12. 2010
    ..While many key regulators are known for these extreme cases, we focus here on regulators that are relevant at intermediate levels of respiration...
  27. ncbi request reprint Fermentation performance of engineered and evolved xylose-fermenting Saccharomyces cerevisiae strains
    Marco Sonderegger
    Institute of Biotechnology, ETH Zurich, CH 8093 Zurich, Switzerland
    Biotechnol Bioeng 87:90-8. 2004
    ....
  28. pmc Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli
    Robert Schuetz
    Institute of Molecular Systems Biology, ETH Zurich, Switzerland
    Mol Syst Biol 3:119. 2007
    ....
  29. pmc Identification of furfural as a key toxin in lignocellulosic hydrolysates and evolution of a tolerant yeast strain
    Dominik Heer
    ETH Zurich, Institute of Molecular Systems Biology, Zurich, Switzerland
    Microb Biotechnol 1:497-506. 2008
    ..The improved resistance of our evolved strains was based on their capacity to remain viable in a toxic environment during the prolonged, furfural induced lag phase...
  30. pmc 13C-flux analysis reveals NADPH-balancing transhydrogenation cycles in stationary phase of nitrogen-starving Bacillus subtilis
    Martin Rühl
    Institute of Molecular Systems Biology, ETH Zurich, CH 8093 Zurich, Switzerland
    J Biol Chem 287:27959-70. 2012
    ..Overall, we demonstrate the interplay between several metabolic mechanisms that concertedly enable network-wide NADPH homeostasis under conditions of high catabolic NADPH production in the absence of cell growth in B. subtilis...
  31. doi request reprint Collisional fragmentation of central carbon metabolites in LC-MS/MS increases precision of ¹³C metabolic flux analysis
    Martin Rühl
    Institute of Molecular Systems Biology, ETH Zurich, Dr Nicola Zamboni, Wolfgang Pauli Str 16, CH 8093 Zurich, Switzerland
    Biotechnol Bioeng 109:763-71. 2012
    ..In the future, this catalogue will enable comprehensive in silico calculability analyses to identify the most sensitive measurements and direct experimental design...
  32. ncbi request reprint Metabolic-flux and network analysis in fourteen hemiascomycetous yeasts
    Lars M Blank
    Institute of Biotechnology, Building HPT E58, ETH Zurich, 8093 Zurich, Switzerland
    FEMS Yeast Res 5:545-58. 2005
    ..In most yeasts, the PP pathway activity appears to be driven exclusively by the demand for NADPH...
  33. pmc Resistance of Saccharomyces cerevisiae to high concentrations of furfural is based on NADPH-dependent reduction by at least two oxireductases
    Dominik Heer
    Institute of Molecular Systems Biology, HPT E77, Wolfgang Pauli Str 16, 8093 Zurich, Switzerland
    Appl Environ Microbiol 75:7631-8. 2009
    ..By overexpressing the ADH7 gene and the ORF YKL071W, we inversely engineered significantly increased furfural resistance in the parent strain, thereby demonstrating that these two enzymes are key elements of the resistance phenotype...
  34. doi request reprint Dynamic flux responses in riboflavin overproducing Bacillus subtilis to increasing glucose limitation in fed-batch culture
    Martin Rühl
    Institute of Molecular Systems Biology, ETH Zurich, Wolfgang Pauli Str 16, CH 8093 Zurich, Switzerland
    Biotechnol Bioeng 105:795-804. 2010
    ..As a consequence, higher catabolic NADPH formation occurred than was necessary to satisfy the anabolic demands, suggesting a transhydrogenase-like mechanism to close the balance of reducing equivalents...
  35. ncbi request reprint Non-stationary (13)C-metabolic flux ratio analysis
    Manuel Hörl
    Institute of Molecular Systems Biology, ETH Zurich, Wolfgang Pauli Str 16, 8093, Zurich, Switzerland PhD Program Systems Biology, Life Science Zurich Graduate School, Zurich, Switzerland
    Biotechnol Bioeng 110:3164-76. 2013
    ..Hence this approach paves the road to targeted (13)C-MFA in dynamic systems with multiple carbon sources and towards rich media...
  36. pmc Molecular basis for anaerobic growth of Saccharomyces cerevisiae on xylose, investigated by global gene expression and metabolic flux analysis
    Marco Sonderegger
    Institute of Biotechnology, ETH Zurich, CH 8093 Zurich, Switzerland
    Appl Environ Microbiol 70:2307-17. 2004
    ..We concluded that anaerobic growth of the yeast on xylose is ultimately limited by the rate of ATP production and not by the redox balance per se, although the redox imbalance, in turn, limits ATP production...
  37. doi request reprint Systematic identification of allosteric protein-metabolite interactions that control enzyme activity in vivo
    Hannes Link
    Institute of Molecular System Biology, ETH Zurich, Zurich, Switzerland
    Nat Biotechnol 31:357-61. 2013
    ..Thus, from large sets of putative allosteric interactions, our approach can identify the most likely ones and provide hypotheses about their function...
  38. pmc Dissecting specific and global transcriptional regulation of bacterial gene expression
    Luca Gerosa
    Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
    Mol Syst Biol 9:658. 2013
    ....
  39. doi request reprint Cross-platform comparison of methods for quantitative metabolomics of primary metabolism
    Jörg Martin Büscher
    Institute of Molecular Systems Biology, ETH Zurich, Wolfgang Pauli Strasse 16, 8093 Zurich, Switzerland
    Anal Chem 81:2135-43. 2009
    ..Therefore, suitable internal standards, such as (13)C-labeled biomass extracts, are mandatory for quantitative metabolomics with any methods...
  40. pmc Large-scale 13C-flux analysis reveals mechanistic principles of metabolic network robustness to null mutations in yeast
    Lars M Blank
    Institute of Biotechnology, ETH Zurich, 8093 Zurich, Switzerland
    Genome Biol 6:R49. 2005
    ..Here we identify key experiments in a systems biology approach with a genome-scale model of Saccharomyces cerevisiae metabolism, thereby reducing the workload for experimental network analyses and functional genomics...
  41. pmc Different biochemical mechanisms ensure network-wide balancing of reducing equivalents in microbial metabolism
    Tobias Fuhrer
    Institute of Molecular Systems Biology, ETH Zurich, Switzerland
    J Bacteriol 191:2112-21. 2009
    ..coli and B. subtilis, was the lack of cofactor specificity in the oxidative pentose phosphate pathway, which contrasts with the textbook view of the pentose phosphate pathway dehydrogenases as being NADP+ dependent...
  42. pmc Computational prediction and experimental verification of the gene encoding the NAD+/NADP+-dependent succinate semialdehyde dehydrogenase in Escherichia coli
    Tobias Fuhrer
    Institute of Molecular Systems Biology, ETH Zurich, CH 8093 Zurich, Switzerland
    J Bacteriol 189:8073-8. 2007
    ..Analysis of available genome sequences demonstrated that orthologs of both yneI and gabD are broadly distributed across phylogenetic space...
  43. ncbi request reprint Systems biology of microbial metabolism
    Matthias Heinemann
    ETH Zurich, Institute of Molecular Systems Biology, Wolfgang Pauli Str 16, 8093 Zurich, Switzerland
    Curr Opin Microbiol 13:337-43. 2010
    ....
  44. pmc FiatFlux--a software for metabolic flux analysis from 13C-glucose experiments
    Nicola Zamboni
    Institute of Biotechnology, ETH Zurich, 8093 Zurich, Switzerland
    BMC Bioinformatics 6:209. 2005
    ..A conceptual simplification of flux analysis is the analytical determination of metabolic flux ratios exclusively from MS data, which can then be used in a second step to estimate absolute in vivo fluxes...
  45. ncbi request reprint The importance of post-translational modifications in regulating Saccharomyces cerevisiae metabolism
    Ana Paula Oliveira
    Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
    FEMS Yeast Res 12:104-17. 2012
    ..cerevisiae and reviews their underlying mechanistic principles - both at the individual enzyme level and in the context of the entire metabolic network operation...
  46. pmc Metabolic engineering of a phosphoketolase pathway for pentose catabolism in Saccharomyces cerevisiae
    Marco Sonderegger
    Institute of Biotechnology, ETH Zurich, CH 8093 Zurich, Switzerland
    Appl Environ Microbiol 70:2892-7. 2004
    ..By combining the phosphoketolase pathway with the ald6 mutation, which reduced acetate formation, a strain with an ethanol yield 20% higher and a xylose fermentation rate 40% higher than those of its parent was engineered...
  47. pmc Experimental identification and quantification of glucose metabolism in seven bacterial species
    Tobias Fuhrer
    Institute of Biotechnology, ETH Zurich, CH 8093 Zurich, Switzerland
    J Bacteriol 187:1581-90. 2005
    ..Overall, the results suggest that metabolic data from model species with extensive industrial and laboratory history are not representative of microbial metabolism, at least not quantitatively...
  48. pmc Model-independent fluxome profiling from 2H and 13C experiments for metabolic variant discrimination
    Nicola Zamboni
    Institute of Biotechnology, ETH Zurich, CH 8093 Zurich, Switzerland
    Genome Biol 5:R99. 2004
    ..The approach is flexible and paves the way to large-scale fluxome profiling of any biological system and condition...
  49. ncbi request reprint Large-scale in vivo flux analysis shows rigidity and suboptimal performance of Bacillus subtilis metabolism
    Eliane Fischer
    Institute of Biotechnology, ETH Zurich, CH 8093 Zurich, Switzerland
    Nat Genet 37:636-40. 2005
    ..Network rigidity and robustness are probably universal functional design principles, whereas the standby mode may be more specific...
  50. doi request reprint Local requirement of the Drosophila insulin binding protein imp-L2 in coordinating developmental progression with nutritional conditions
    Ladan Sarraf-Zadeh
    Institute for Molecular Systems Biology IMSB, ETH Zurich, Zurich 8093, Switzerland
    Dev Biol 381:97-106. 2013
    ..Taken together our results suggest that Imp-L2-expressing neurons sense the nutritional state of Drosophila larvae and coordinate dietary information and ecdysone production to adjust developmental timing under starvation conditions...
  51. ncbi request reprint The PEP-pyruvate-oxaloacetate node as the switch point for carbon flux distribution in bacteria
    Uwe Sauer
    Institute of Biotechnology, ETH Zurich, Switzerland
    FEMS Microbiol Rev 29:765-94. 2005
    ..The present knowledge unequivocally reveals the PEP-pyruvate-oxaloacetate nodes of bacteria to be a fascinating target of metabolic engineering in order to achieve optimized metabolite production...
  52. pmc Metabolic functions of duplicate genes in Saccharomyces cerevisiae
    Lars Kuepfer
    Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
    Genome Res 15:1421-30. 2005
    ..Thus, at least for metabolism, persistence of the paralog fraction in the genome can be better explained with an array of different, often overlapping functional roles...
  53. pmc Efficient classification of complete parameter regions based on semidefinite programming
    Lars Kuepfer
    Institute of Molecular Systems Biology, ETH Zurich, CH 8093 Zurich, Switzerland
    BMC Bioinformatics 8:12. 2007
    ..Consequently, it is impossible to conclude that the "best" solution was identified or that no good solution exists, because parameter spaces typically cannot be explored in a reasonable amount of time...
  54. pmc Topological augmentation to infer hidden processes in biological systems
    Mikael Sunnåker
    Department of Biosystems Science and Engineering Swiss Institute of Bioinformatics, ETH Zurich, 4058 Basel, Switzerland, Competence Center for Systems Physiology and Metabolic Diseases, ETH Zurich, 8093 Zurich, Switzerland, Institute of Evolutionary Biology and Environmental Studies Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland, Institute for Molecular Systems Biology, 8093 Zurich, Switzerland and The Santa Fe Institute, Santa Fe, 87501 New Mexico, USA
    Bioinformatics 30:221-7. 2014
    ..Here we present a method called topological augmentation to infer this structure in a statistically rigorous and systematic way from prior knowledge and experimental data...
  55. pmc Subpopulation-specific metabolic pathway usage in mixed cultures as revealed by reporter protein-based 13C analysis
    Martin Rühl
    Institute of Molecular Systems Biology, ETH Zurich, Wolfgang Pauli Str 16, 8093 Zurich, Switzerland
    Appl Environ Microbiol 77:1816-21. 2011
    ..The reporter method quantitatively resolved the expected mutant-specific metabolic phenotypes down to subpopulation fractions of about 1%...
  56. ncbi request reprint Experimental tests for an evolutionary trade-off between growth rate and yield in E. coli
    Maja Novak
    Institute of Integrative Biology, Eldgenossische Technische Hochschule Zurich, 8092 Zurich, Switzerland
    Am Nat 168:242-51. 2006
    ..The observation of a trade-off within, but not between, populations suggests that the populations evolved different genetic solutions for growth in the selective environment, which in turn led to different physiological constraints...
  57. ncbi request reprint Single-gene knockout of a novel regulatory element confers ethionine resistance and elevates methionine production in Corynebacterium glutamicum
    Jörg Mampel
    Institute of Biotechnology, Swiss Federal Institute of Technology ETH, Zurich 8093, Switzerland
    Appl Microbiol Biotechnol 68:228-36. 2005
    ..Complementation of the mutant strain with plasmid-borne NCgl2640 restored the wild-type phenotype for metY and sulfite reductase...
  58. ncbi request reprint Inverse metabolic engineering with phosphagen kinase systems improves the cellular energy state
    Uwe Sauer
    Institute of Biotechnology, Swiss Federal Institute of Technology ETH Zurich, CH 8093
    Metab Eng 6:220-8. 2004
    ..Examples are discussed that illustrate how microbial metabolism can be tailored for large-scale industrial processes with imperfect mixing and how the liver can be protected from metabolic insults or stimulated for better regeneration...
  59. pmc Metabolic flux responses to pyruvate kinase knockout in Escherichia coli
    Marcel Emmerling
    Institute of Biotechnology, ETH Zurich, CH 8093 Zurich, Switzerland
    J Bacteriol 184:152-64. 2002
    ..Reliability of the flux estimates thus obtained was verified by statistical error analysis and by comparison to intracellular carbon flux ratios that were independently calculated from the same NMR data by metabolic flux ratio analysis...
  60. ncbi request reprint High-throughput metabolic flux analysis based on gas chromatography-mass spectrometry derived 13C constraints
    Eliane Fischer
    Institute of Biotechnology, ETH Zürich CH 8093, Zurich, Switzerland
    Anal Biochem 325:308-16. 2004
    ..coli shake flasks and 1-ml deep-well microtiter plates. Due to its simplicity, speed, and robustness, 13C-constrained metabolic flux balancing is promising for routine and high-throughput analysis on a miniaturized scale...
  61. ncbi request reprint High-throughput phenomics: experimental methods for mapping fluxomes
    Uwe Sauer
    Institute of Biotechnology, ETH Zurich, CH 8093 Zurich, Switzerland
    Curr Opin Biotechnol 15:58-63. 2004
    ..This review highlights recent developments towards high-throughput flux analysis...
  62. ncbi request reprint Functional expression of arginine kinase improves recovery from pH stress of Escherichia coli
    Fabrizio Canonaco
    Institute of Biotechnology, ETH Zurich, CH 8093 Zurich, Switzerland
    Biotechnol Lett 25:1013-7. 2003
    ..This effect is presumably caused by the physiological function of arginine kinase as a short term energy buffer in the form of phosphoarginine, but a pH-buffering effect cannot be excluded...
  63. doi request reprint Cra regulates the cross-talk between the two branches of the phosphoenolpyruvate : phosphotransferase system of Pseudomonas putida
    Max Chavarría
    Systems Biology Program, Centro Nacional de Biotecnologia, 28049 Cantoblanco Madrid, Spain
    Environ Microbiol 15:121-32. 2013
    ..The Cra/F1P duo seems to not only control the expression of the PTS(Fru) but also checks the activity of the PTS(Ntr) in vivo...
  64. ncbi request reprint Ensemble modeling for analysis of cell signaling dynamics
    Lars Kuepfer
    Institute of Molecular Systems Biology, ETH Zurich, 8092 Zurich, Switzerland
    Nat Biotechnol 25:1001-6. 2007
    ..Beyond revising our picture of TOR signaling, we expect ensemble modeling to help elucidate other insufficiently characterized cellular circuits...
  65. ncbi request reprint Long-term continuous evolution of acetate resistant Acetobacter aceti
    Peter Steiner
    Institute of Biotechnology, ETH Zurich, CH 8093 Zurich, Switzerland
    Biotechnol Bioeng 84:40-4. 2003
    ..Intracellular acetate concentrations were significantly lower in evolved A. aceti, when compared to wild-type A. aceti and E. coli, indicating that cytoplasmatic anion accumulation is an important component of acetate toxicity...
  66. ncbi request reprint Ultrahigh performance liquid chromatography-tandem mass spectrometry method for fast and robust quantification of anionic and aromatic metabolites
    Joerg Martin Buescher
    Institute of Molecular Systems Biology, ETH Zurich, Switzerland
    Anal Chem 82:4403-12. 2010
    ..5-50 mg dry cell weight. We recommend this method for routine and yet comprehensive quantification of primary metabolites in a wide variety of biological matrices...
  67. doi request reprint Somewhat in control--the role of transcription in regulating microbial metabolic fluxes
    Karl Kochanowski
    Institute of Molecular Systems Biology, ETH Zurich, Wolfgang Pauli Str 16, CH 8093 Zurich, Switzerland Life Science Zurich PhD Program on Systems Biology, Zurich, Switzerland
    Curr Opin Biotechnol 24:987-93. 2013
    ..Several studies have found examples of demonstrably suboptimal regulation of gene expression, and improvements to the regulatory network have been investigated in laboratory evolution experiments. ..
  68. ncbi request reprint Reducing maintenance metabolism by metabolic engineering of respiration improves riboflavin production by Bacillus subtilis
    Nicola Zamboni
    Institute of Biotechnology, Swiss Federal Institute of Technology Zurich, ETH Zurich, Honggerberg, CH 8093, Zurich, Switzerland
    Metab Eng 5:49-55. 2003
    ..The reduction of maintenance metabolism, in turn, significantly improved the yield of recombinant riboflavin and B. subtilis biomass in fed-batch cultures...
  69. ncbi request reprint Novel biological insights through metabolomics and 13C-flux analysis
    Nicola Zamboni
    Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
    Curr Opin Microbiol 12:553-8. 2009
    ..Integration of metabolomics, (13)C-flux analysis and other data enable the condition-dependent characterization of regulatory circuits that ultimately govern the metabolic phenotype...
  70. ncbi request reprint Regulation and control of metabolic fluxes in microbes
    Luca Gerosa
    Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
    Curr Opin Biotechnol 22:566-75. 2011
    ....
  71. doi request reprint Nontargeted profiling of coenzyme A thioesters in biological samples by tandem mass spectrometry
    Michael Zimmermann
    Institute of Molecular Systems Biology, ETH Zurich, Wolfgang Pauli Strasse 16, 8093 Zurich, Switzerland
    Anal Chem 85:8284-90. 2013
    ..This demonstrates the power of our method for untargeted profiling of CoA-thioesters and adds a missing link in mycobacterial cholesterol catabolism. ..
  72. doi request reprint The IHF regulon of exponentially growing Pseudomonas putida cells
    Rafael Silva-Rocha
    Systems Biology Program, Centro Nacional de Biotecnologia, 28049 Cantoblanco Madrid, Spain
    Environ Microbiol 15:49-63. 2013
    ..Taken together, the data suggest that IHF plays a role in the physiological shift that sets P. putida for entering stationary phase...
  73. ncbi request reprint A novel metabolic cycle catalyzes glucose oxidation and anaplerosis in hungry Escherichia coli
    Eliane Fischer
    Institute of Biotechnology, ETH Zurich, CH 8093 Zurich, Switzerland
    J Biol Chem 278:46446-51. 2003
    ....
  74. pmc Maintenance metabolism and carbon fluxes in Bacillus species
    Simon Tännler
    Institute of Molecular Systems Biology, ETH Zurich, CH 8093 Zurich, Switzerland
    Microb Cell Fact 7:19. 2008
    ..abstract:..
  75. ncbi request reprint Genome engineering reveals large dispensable regions in Bacillus subtilis
    Helga Westers
    Department of Pharmaceutical Biology, University of Groningen, Groningen, The Netherlands
    Mol Biol Evol 20:2076-90. 2003
    ..We show that genome engineering is a feasible strategy for functional analysis of large gene clusters, and that removal of dispensable genomic regions may pave the way toward an optimized Bacillus cell factory...
  76. pmc Intracellular carbon fluxes in riboflavin-producing Bacillus subtilis during growth on two-carbon substrate mixtures
    Michael Dauner
    Institute of Biotechnology, ETH Zurich, CH 8093 Zurich, Switzerland
    Appl Environ Microbiol 68:1760-71. 2002
    ..The in vivo activity of the gluconeogenic phosphoenolpyruvate carboxykinase was found to be relatively high in all experiments, with the sole exception of the gluconate-cofed culture...
  77. ncbi request reprint Functional expression of phosphagen kinase systems confers resistance to transient stresses in Saccharomyces cerevisiae by buffering the ATP pool
    Fabrizio Canonaco
    Institute of Biotechnology, Eidgenössiche Technische Hochschule Zurich, CH 8093 Zurich, Switzerland
    J Biol Chem 277:31303-9. 2002
    ..Thus, our results demonstrate that temporal energy buffering is an intrinsic property of phosphagen kinases that can be transferred to phylogenetically very distant organisms...
  78. pmc YtsJ has the major physiological role of the four paralogous malic enzyme isoforms in Bacillus subtilis
    Guillaume Lerondel
    Microbiologie et Genetique Moleculaire, INRA UMR1238 CNRS UMR2585 and INAP G, F 78850 Thiverval Grignon, France
    J Bacteriol 188:4727-36. 2006
    ..coli partially suppressed it. These results suggest an additional physiological role of YtsJ beyond that of malate-to-pyruvate conversion...
  79. pmc Metabolic-flux profiling of the yeasts Saccharomyces cerevisiae and Pichia stipitis
    Jocelyne Fiaux
    Institute of Molecular Biology and Biophysics, ETH Zurich, CH 8093 Zurich, Switzerland
    Eukaryot Cell 2:170-80. 2003
    ..cerevisiae has a generally high catabolic capacity by overexpressing the Escherichia coli transhydrogenase UdhA in phosphoglucose isomerase-deficient S. cerevisiae...
  80. ncbi request reprint Metabolic flux profiling of Escherichia coli mutants in central carbon metabolism using GC-MS
    Eliane Fischer
    Institute of Biotechnology, ETH Zurich, CH 8093 Zurich, Switzerland
    Eur J Biochem 270:880-91. 2003
    ..Overall, our results provide quantitative insight into flux changes that bring about the resilience of metabolic networks to disruption...
  81. pmc Evolutionary engineering of Saccharomyces cerevisiae for anaerobic growth on xylose
    Marco Sonderegger
    Institute of Biotechnology, ETH Zurich, Switzerland
    Appl Environ Microbiol 69:1990-8. 2003
    ..However, as a consequence of their improved xylose catabolism, these clones produced up to 19% more ethanol than the parental TMB3001 strain produced under process-like conditions from a mixture of glucose and xylose...
  82. pmc Oxygen- and glucose-dependent regulation of central carbon metabolism in Pichia anomala
    Elisabeth Fredlund
    Department of Microbiology, Swedish University of Agricultural Sciences, P O Box 7025, SE 750 07 Uppsala, Sweden
    Appl Environ Microbiol 70:5905-11. 2004
    ..Overall, our results demonstrate that P. anomala exhibits a Pasteur effect and not a Crabtree effect, i.e., oxygen availability, but not glucose concentration, is the main stimulus for the regulation of the central carbon metabolism...
  83. pmc Multiple and interconnected pathways for L-lysine catabolism in Pseudomonas putida KT2440
    Olga Revelles
    Estacion Experimental del Zaidin, Consejo Superior de Investigaciones Cientificas, C Prof Albareda 1, 18008 Granada, Spain
    J Bacteriol 187:7500-10. 2005
    ..This study establishes an unequivocal relationship between gene and pathway enzymes in the metabolism of L-lysine, which is of crucial importance for the successful colonization of the rhizosphere of plants by this microorganism...
  84. ncbi request reprint Latent pathway activation and increased pathway capacity enable Escherichia coli adaptation to loss of key metabolic enzymes
    Stephen S Fong
    Department of Chemical and Life Science Engineering, Virginia Commonwealth University, Richmond 28284 3028, USA
    J Biol Chem 281:8024-33. 2006
    ..coli to compensate for genetic perturbations and the utility of combining multiple high throughput data sets to differentiate between causal and noncausal mechanistic changes...
  85. ncbi request reprint Selection of quiescent Escherichia coli with high metabolic activity
    Marco Sonderegger
    Metab Eng 7:4-9. 2005
    ..The metabolically most active clones were identified by screening for high specific glucose uptake rates during ammonium starvation-induced stationary phase in deep-well microtiter plates...
  86. pmc Convergent peripheral pathways catalyze initial glucose catabolism in Pseudomonas putida: genomic and flux analysis
    Teresa del Castillo
    Department of Environmental Protection, Estacion Experimental del Zaidin, Consejo Superior de Investigaciones Cientificas, C Prof Albareda, 1, E 18008 Granada, Spain
    J Bacteriol 189:5142-52. 2007
    ..It can therefore be concluded that the glucokinase pathway is a sine qua non condition for P. putida to grow with glucose...
  87. ncbi request reprint The phosphoenolpyruvate carboxykinase also catalyzes C3 carboxylation at the interface of glycolysis and the TCA cycle of Bacillus subtilis
    Nicola Zamboni
    Institute of Biotechnology, Swiss Federal Institute of Technology Zurich ETH ETH Zürich, Zurich 8093, Switzerland
    Metab Eng 6:277-84. 2004
    ..Presumably as a consequence of the unfavorable kinetics of an ATP-synthesizing anaplerotic PEP carboxykinase reaction, such pyruvate carboxylase mutants grow slowly or, as in the case of wild-type 168, not at all...
  88. ncbi request reprint Evolutionary engineering of multiple-stress resistant Saccharomyces cerevisiae
    Z Petek Cakar
    Department of Molecular Biology and Genetics, Faculty of Science and Letters, Istanbul Technical University, Maslak, TR 34469 Istanbul, Turkey
    FEMS Yeast Res 5:569-78. 2005
    ..General selection guidelines for improving multiple-stress resistance in S. cerevisiae are presented and discussed...
  89. ncbi request reprint Robustness of cellular functions
    Jörg Stelling
    Max Planck Institute for Dynamics of Complex Technical Systems, D 39106 Magdeburg, Germany
    Cell 118:675-85. 2004
    ..Robustness may be a key to understanding cellular complexity, elucidating design principles, and fostering closer interactions between experimentation and theory...