Untargeted metabolomics unravels functionalities of phosphorylation sites in Saccharomyces cerevisiae

[1]  Horst Wenck,et al.  Acute Activation of Oxidative Pentose Phosphate Pathway as First-Line Response to Oxidative Stress in Human Skin Cells. , 2015, Molecular cell.

[2]  K. Gerdes,et al.  Remarkable Functional Convergence: Alarmone ppGpp Mediates Persistence by Activating Type I and II Toxin-Antitoxins. , 2015, Molecular cell.

[3]  U. Sauer,et al.  Dynamic phosphoproteomics reveals TORC1-dependent regulation of yeast nucleotide and amino acid biosynthesis , 2015, Science Signaling.

[4]  H. Kestler,et al.  Site-specific methylation of Notch1 controls the amplitude and duration of the Notch1 response , 2015, Science Signaling.

[5]  Jack T. Pronk,et al.  CRISPR/Cas9: a molecular Swiss army knife for simultaneous introduction of multiple genetic modifications in Saccharomyces cerevisiae , 2015, FEMS yeast research.

[6]  S. Michnick,et al.  A cell-signaling network temporally resolves specific versus promiscuous phosphorylation. , 2015, Cell reports.

[7]  N. Rowe,et al.  Global diversification of a tropical plant growth form: environmental correlates and historical contingencies in climbing palms , 2015, Front. Genet..

[8]  U. Sauer,et al.  Large-scale functional analysis of the roles of phosphorylation in yeast metabolic pathways , 2014, Science Signaling.

[9]  Alan M. Moses,et al.  Turnover of protein phosphorylation evolving under stabilizing selection , 2014, Front. Genet..

[10]  J. Seebacher,et al.  Memo Is a Copper-Dependent Redox Protein with an Essential Role in Migration and Metastasis , 2014, Science Signaling.

[11]  P. Bork,et al.  Evolution and functional cross‐talk of protein post‐translational modifications , 2013, Molecular systems biology.

[12]  Merja Penttilä,et al.  Yeast oligo-mediated genome engineering (YOGE). , 2013, ACS synthetic biology.

[13]  Susumu Goto,et al.  Data, information, knowledge and principle: back to metabolism in KEGG , 2013, Nucleic Acids Res..

[14]  U. Sauer,et al.  Regulation of yeast central metabolism by enzyme phosphorylation , 2012, Molecular systems biology.

[15]  Francesc Posas,et al.  Response to Hyperosmotic Stress , 2012, Genetics.

[16]  Emmanuel D Levy,et al.  Protein abundance is key to distinguish promiscuous from functional phosphorylation based on evolutionary information , 2012, Philosophical Transactions of the Royal Society B: Biological Sciences.

[17]  Yong Jae Lee,et al.  Reciprocal Phosphorylation of Yeast Glycerol-3-Phosphate Dehydrogenases in Adaptation to Distinct Types of Stress , 2012, Molecular and Cellular Biology.

[18]  W. Lim,et al.  Systematic Functional Prioritization of Protein Posttranslational Modifications , 2012, Cell.

[19]  Peer Bork,et al.  Deciphering a global network of functionally associated post-translational modifications , 2012, Molecular systems biology.

[20]  B. Daignan-Fornier,et al.  Regulation of Amino Acid, Nucleotide, and Phosphate Metabolism in Saccharomyces cerevisiae , 2012, Genetics.

[21]  Uwe Sauer,et al.  The importance of post-translational modifications in regulating Saccharomyces cerevisiae metabolism. , 2012, FEMS yeast research.

[22]  H. Mischak,et al.  Urine Proteome Analysis Reflects Atherosclerotic Disease in an ApoE−/− Mouse Model and Allows the Discovery of New Candidate Biomarkers in Mouse and Human Atherosclerosis* , 2012, Molecular & Cellular Proteomics.

[23]  Andrew J. Oler,et al.  PP4 dephosphorylates Maf1 to couple multiple stress conditions to RNA polymerase III repression , 2012, The EMBO journal.

[24]  Kathryn S. Lilley,et al.  Evaluation and Properties of the Budding Yeast Phosphoproteome , 2012, Molecular & Cellular Proteomics.

[25]  M. Hall,et al.  Target of Rapamycin (TOR) in Nutrient Signaling and Growth Control , 2011, Genetics.

[26]  Edith D. Wong,et al.  Saccharomyces Genome Database: the genomics resource of budding yeast , 2011, Nucleic Acids Res..

[27]  Nicola Zamboni,et al.  High-throughput, accurate mass metabolome profiling of cellular extracts by flow injection-time-of-flight mass spectrometry. , 2011, Analytical chemistry.

[28]  Jonathan J. Ellis,et al.  Predicting Protein Kinase Specificity: Predikin Update and Performance in the DREAM4 Challenge , 2011, PloS one.

[29]  Jean-François Dartigues,et al.  Association of Plasma Aß Peptides with Blood Pressure in the Elderly , 2011, PloS one.

[30]  Patrick G. A. Pedrioli,et al.  Phosphoproteomic Analysis Reveals Interconnected System-Wide Responses to Perturbations of Kinases and Phosphatases in Yeast , 2010, Science Signaling.

[31]  P. Kemmeren,et al.  Functional Overlap and Regulatory Links Shape Genetic Interactions between Signaling Pathways , 2010, Cell.

[32]  Neil Swainston,et al.  Further developments towards a genome-scale metabolic model of yeast , 2010, BMC Systems Biology.

[33]  C. Nombela,et al.  The high‐osmolarity glycerol (HOG) and cell wall integrity (CWI) signalling pathways interplay: a yeast dialogue between MAPK routes , 2010, Yeast.

[34]  M. Mann,et al.  Decoding signalling networks by mass spectrometry-based proteomics , 2010, Nature Reviews Molecular Cell Biology.

[35]  Limsoon Wong,et al.  Genome-wide analysis of regions similar to promoters of histone genes , 2010, BMC Systems Biology.

[36]  B. Zhao,et al.  Loops Govern SH2 Domain Specificity by Controlling Access to Binding Pockets , 2010, Science Signaling.

[37]  Joerg M. Buescher,et al.  Ultrahigh performance liquid chromatography-tandem mass spectrometry method for fast and robust quantification of anionic and aromatic metabolites. , 2010, Analytical chemistry.

[38]  Bruce Stillman,et al.  Deciphering Protein Kinase Specificity through Large-scale Analysis of Materials Supplemental Deciphering Protein Kinase Specificity through Large-scale Analysis of Yeast Phosphorylation Site Motifs , 2010 .

[39]  C. Rodrigues-Pousada,et al.  Yap4 PKA‐ and GSK3‐dependent phosphorylation affects its stability but not its nuclear localization , 2009, Yeast.

[40]  Farren J. Isaacs,et al.  Programming cells by multiplex genome engineering and accelerated evolution , 2009, Nature.

[41]  A. Whetton,et al.  Mutation of a Phosphorylatable Residue in Put3p Affects the Magnitude of Rapamycin-induced PUT1 Activation in a Gat1p-dependent Manner* , 2009, The Journal of Biological Chemistry.

[42]  T. Höfer,et al.  Multisite protein phosphorylation – from molecular mechanisms to kinetic models , 2009, The FEBS journal.

[43]  C. Landry,et al.  Weak functional constraints on phosphoproteomes. , 2009, Trends in genetics : TIG.

[44]  Ricard Solé,et al.  Dynamic Signaling in the Hog1 MAPK Pathway Relies on High Basal Signal Transduction , 2009, Science Signaling.

[45]  A. Casamayor,et al.  Normal Function of the Yeast TOR Pathway Requires the Type 2C Protein Phosphatase Ptc1 , 2009, Molecular and Cellular Biology.

[46]  Timothy C Elston,et al.  Control of MAPK Specificity by Feedback Phosphorylation of Shared Adaptor Protein Ste50* , 2008, Journal of Biological Chemistry.

[47]  Ruedi Aebersold,et al.  PhosphoPep—a database of protein phosphorylation sites in model organisms , 2008, Nature Biotechnology.

[48]  Yoav Arava,et al.  Yeast translational response to high salinity: global analysis reveals regulation at multiple levels. , 2008, RNA.

[49]  Robbie Loewith,et al.  Caffeine extends yeast lifespan by targeting TORC1 , 2008, Molecular microbiology.

[50]  C. Nombela,et al.  The sequential activation of the yeast HOG and SLT2 pathways is required for cell survival to cell wall stress. , 2007, Molecular biology of the cell.

[51]  Mehdi Mollapour,et al.  Hog1 Mitogen-Activated Protein Kinase Phosphorylation Targets the Yeast Fps1 Aquaglyceroporin for Endocytosis, Thereby Rendering Cells Resistant to Acetic Acid , 2007, Molecular and Cellular Biology.

[52]  T. Cooper,et al.  Differing responses of Gat1 and Gln3 phosphorylation and localization to rapamycin and methionine sulfoximine treatment in Saccharomyces cerevisiae. , 2006, FEMS yeast research.

[53]  Martha S. Cyert,et al.  Integration of Stress Responses: Modulation of Calcineurin Signaling in Saccharomyces cerevisiae by Protein Kinase A , 2004, Eukaryotic Cell.

[54]  David Y. Thomas,et al.  Phosphorylation of the MAPKKK Regulator Ste50p in Saccharomyces cerevisiae: a Casein Kinase I Phosphorylation Site Is Required for Proper Mating Function , 2003, Eukaryotic Cell.

[55]  G. Carman,et al.  Phosphorylation of CTP Synthetase on Ser36, Ser330, Ser354, and Ser454 Regulates the Levels of CTP and Phosphatidylcholine Synthesis in Saccharomyces cerevisiae* , 2003, Journal of Biological Chemistry.

[56]  M. Whiteway,et al.  Negative Regulation of MAPKK by Phosphorylation of a Conserved Serine Residue Equivalent to Ser212 of MEK1* , 2003, The Journal of Biological Chemistry.

[57]  F. Posas,et al.  Targeting the MEF2-Like Transcription Factor Smp1 by the Stress-Activated Hog1 Mitogen-Activated Protein Kinase , 2003, Molecular and Cellular Biology.

[58]  John D. Storey A direct approach to false discovery rates , 2002 .

[59]  K. Arndt,et al.  TIP41 interacts with TAP42 and negatively regulates the TOR signaling pathway. , 2001, Molecular cell.

[60]  E. de Nadal,et al.  Regulation of the Sko1 transcriptional repressor by the Hog1 MAP kinase in response to osmotic stress , 2001, The EMBO journal.

[61]  I. Sadowski,et al.  Multiple Signals Regulate GALTranscription in Yeast , 2000, Molecular and Cellular Biology.

[62]  J. Nielsen,et al.  Anaerobic and aerobic batch cultivations of Saccharomyces cerevisiae mutants impaired in glycerol synthesis , 2000, Yeast.

[63]  M. Cyert,et al.  Yeast calcineurin regulates nuclear localization of the Crz1p transcription factor through dephosphorylation. , 1999, Genes & development.

[64]  Pamela A. Silver,et al.  Regulated nucleo/cytoplasmic exchange of HOG1 MAPK requires the importin β homologs NMD5 and XPO1 , 1998, The EMBO journal.

[65]  J M Thevelein,et al.  The two isoenzymes for yeast NAD+‐dependent glycerol 3‐phosphate dehydrogenase encoded by GPD1 and GPD2 have distinct roles in osmoadaptation and redox regulation , 1997, The EMBO journal.

[66]  T. Maeda,et al.  Activation of yeast PBS2 MAPKK by MAPKKKs or by binding of an SH3-containing osmosensor. , 1995, Science.

[67]  H. Ruis,et al.  The HOG pathway controls osmotic regulation of transcription via the stress response element (STRE) of the Saccharomyces cerevisiae CTT1 gene. , 1994, The EMBO journal.

[68]  Tatsuya Maeda,et al.  A two-component system that regulates an osmosensing MAP kinase cascade in yeast , 1994, Nature.

[69]  W. A. Scheffers,et al.  Effect of benzoic acid on metabolic fluxes in yeasts: A continuous‐culture study on the regulation of respiration and alcoholic fermentation , 1992, Yeast.

[70]  L. Reed,et al.  Phosphorylation-dephosphorylation of pyruvate dehydrogenase from bakers' yeast. , 1986, Biochemistry.

[71]  Ruedi Aebersold,et al.  Mass spectrometry‐driven phosphoproteomics: patterning the systems biology mosaic , 2014, Wiley interdisciplinary reviews. Developmental biology.

[72]  Advin K. Mathew METABOLOMICS: THE APOGEE OF THE OMICS TRILOGY , 2013 .

[73]  R. Aebersold,et al.  Quantitative analysis of protein phosphorylation on a system-wide scale by mass spectrometry-based proteomics. , 2010, Methods in enzymology.

[74]  Francesca Storici,et al.  The delitto perfetto approach to in vivo site-directed mutagenesis and chromosome rearrangements with synthetic oligonucleotides in yeast. , 2006, Methods in enzymology.