Quantitative proteomics identifies redox switches for global translation modulation by mitochondrially produced reactive oxygen species

[1]  C. Joazeiro Ribosomal Stalling During Translation: Providing Substrates for Ribosome-Associated Protein Quality Control. , 2017, Annual review of cell and developmental biology.

[2]  M. Fromont-Racine,et al.  The ribosome-bound quality control complex: from aberrant peptide clearance to proteostasis maintenance , 2017, Current Genetics.

[3]  A. González,et al.  Nutrient sensing and TOR signaling in yeast and mammals , 2017, The EMBO journal.

[4]  B. Kuster,et al.  K+ Efflux-Independent NLRP3 Inflammasome Activation by Small Molecules Targeting Mitochondria. , 2016, Immunity.

[5]  José A. Dianes,et al.  2016 update of the PRIDE database and its related tools , 2016, Nucleic Acids Res..

[6]  Jeremy D O'Connell,et al.  Proteome-wide quantitative multiplexed profiling of protein expression: carbon-source dependency in Saccharomyces cerevisiae , 2015, Molecular biology of the cell.

[7]  Kate S. Carroll,et al.  The Expanding Landscape of the Thiol Redox Proteome* , 2015, Molecular & Cellular Proteomics.

[8]  Maciej Lirski,et al.  Mistargeted mitochondrial proteins activate a proteostatic response in the cytosol , 2015, Nature.

[9]  Colin Echeverría Aitken,et al.  Conformational Differences between Open and Closed States of the Eukaryotic Translation Initiation Complex , 2015, Molecular cell.

[10]  Dean P. Jones,et al.  The cysteine proteome. , 2015, Free radical biology & medicine.

[11]  Xin Jie Chen,et al.  A Cytosolic Network Suppressing Mitochondria-Mediated Proteostatic Stress and Cell Death , 2015, Nature.

[12]  L. Partridge,et al.  Fasting, but Not Aging, Dramatically Alters the Redox Status of Cysteine Residues on Proteins in Drosophila melanogaster , 2015, Cell reports.

[13]  Marcel Deponte,et al.  Enzymatic control of cysteinyl thiol switches in proteins , 2015, Biological chemistry.

[14]  James Vlasblom,et al.  Yeast mitochondrial protein-protein interactions reveal diverse complexes and disease-relevant functional relationships. , 2015, Journal of proteome research.

[15]  Marina V. Rodnina,et al.  Structural basis for the inhibition of the eukaryotic ribosome , 2014, Nature.

[16]  Brendan MacLean,et al.  Panorama: A Targeted Proteomics Knowledge Base , 2014, Journal of proteome research.

[17]  R. Tomar,et al.  Ebselen, a promising antioxidant drug: mechanisms of action and targets of biological pathways , 2014, Molecular Biology Reports.

[18]  Alan Brown,et al.  Structure of the Yeast Mitochondrial Large Ribosomal Subunit , 2014, Science.

[19]  Fernando Antunes,et al.  Hydrogen peroxide sensing, signaling and regulation of transcription factors , 2014, Redox biology.

[20]  A. Aharoni,et al.  Mapping the diatom redox-sensitive proteome provides insight into response to nitrogen stress in the marine environment , 2014, Proceedings of the National Academy of Sciences.

[21]  M. Mann,et al.  Minimal, encapsulated proteomic-sample processing applied to copy-number estimation in eukaryotic cells , 2014, Nature Methods.

[22]  Derek J. Bailey,et al.  The One Hour Yeast Proteome* , 2013, Molecular & Cellular Proteomics.

[23]  U. Jakob,et al.  Oxidant Sensing by Reversible Disulfide Bond Formation* , 2013, The Journal of Biological Chemistry.

[24]  A. Chacińska,et al.  Mitochondrial protein import: Mia40 facilitates Tim22 translocation into the inner membrane of mitochondria , 2013, Molecular biology of the cell.

[25]  D. Ron,et al.  Protein-folding homeostasis in the endoplasmic reticulum and nutritional regulation. , 2012, Cold Spring Harbor perspectives in biology.

[26]  D. Ron,et al.  Uncoupling Proteostasis and Development in Vitro with a Small Molecule Inhibitor of the Pancreatic Endoplasmic Reticulum Kinase, PERK* , 2012, The Journal of Biological Chemistry.

[27]  Jürgen Cox,et al.  1D and 2D annotation enrichment: a statistical method integrating quantitative proteomics with complementary high-throughput data , 2012, BMC Bioinformatics.

[28]  N. Chandel,et al.  Physiological roles of mitochondrial reactive oxygen species. , 2012, Molecular cell.

[29]  U. Jakob,et al.  Quantitative in vivo redox sensors uncover oxidative stress as an early event in life. , 2012, Molecular cell.

[30]  Cole M. Haynes,et al.  Protective Coupling of Mitochondrial Function and Protein Synthesis via the eIF2α Kinase GCN-2 , 2012, PLoS genetics.

[31]  Nicholas T. Ingolia,et al.  The translational landscape of mTOR signalling steers cancer initiation and metastasis , 2012, Nature.

[32]  D. Sabatini,et al.  mTOR Signaling. , 2012, Cold Spring Harbor perspectives in biology.

[33]  P. Walter,et al.  The Unfolded Protein Response: From Stress Pathway to Homeostatic Regulation , 2011, Science.

[34]  D. Higgins,et al.  Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega , 2011, Molecular systems biology.

[35]  D. Reichmann,et al.  Using Quantitative Redox Proteomics to Dissect the Yeast Redoxome* , 2011, The Journal of Biological Chemistry.

[36]  T. Finkel Signal Transduction by Mitochondrial Oxidants* , 2011, The Journal of Biological Chemistry.

[37]  T. Langer,et al.  Presequence‐dependent folding ensures MrpL32 processing by the m‐AAA protease in mitochondria , 2011, The EMBO journal.

[38]  C. Grant Regulation of translation by hydrogen peroxide. , 2011, Antioxidants & redox signaling.

[39]  M. Mann,et al.  Andromeda: a peptide search engine integrated into the MaxQuant environment. , 2011, Journal of proteome research.

[40]  Dean P. Jones,et al.  Protein Cysteines Map to Functional Networks According to Steady-state Level of Oxidation. , 2011, Journal of proteomics & bioinformatics.

[41]  D. Jones,et al.  Redox sensing: orthogonal control in cell cycle and apoptosis signalling , 2010, Journal of internal medicine.

[42]  Brendan MacLean,et al.  Bioinformatics Applications Note Gene Expression Skyline: an Open Source Document Editor for Creating and Analyzing Targeted Proteomics Experiments , 2022 .

[43]  Karl Bihlmaier,et al.  Systematic analysis of the twin cx(9)c protein family. , 2009, Journal of molecular biology.

[44]  A. Hinnebusch,et al.  Regulation of Translation Initiation in Eukaryotes: Mechanisms and Biological Targets , 2009, Cell.

[45]  Reinout Raijmakers,et al.  Multiplex peptide stable isotope dimethyl labeling for quantitative proteomics , 2009, Nature Protocols.

[46]  M. Mann,et al.  MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification , 2008, Nature Biotechnology.

[47]  N. Pfanner,et al.  Mitochondrial protein import: precursor oxidation in a ternary complex with disulfide carrier and sulfhydryl oxidase , 2008, The Journal of cell biology.

[48]  Martin Vingron,et al.  Ontologizer 2.0 - a multifunctional tool for GO term enrichment analysis and data exploration , 2008, Bioinform..

[49]  J. Strahler,et al.  Quantifying changes in the thiol redox proteome upon oxidative stress in vivo , 2008, Proceedings of the National Academy of Sciences.

[50]  J. Momand,et al.  Prediction of reversibly oxidized protein cysteine thiols using protein structure properties , 2008, Protein science : a publication of the Protein Society.

[51]  M. Toledano,et al.  ROS as signalling molecules: mechanisms that generate specificity in ROS homeostasis , 2007, Nature Reviews Molecular Cell Biology.

[52]  N. Pfanner,et al.  Novel mitochondrial intermembrane space proteins as substrates of the MIA import pathway. , 2007, Journal of molecular biology.

[53]  S. Marklund,et al.  The coupling between disulphide status, metallation and dimer interface strength in Cu/Zn superoxide dismutase. , 2007, Journal of molecular biology.

[54]  P. Walter,et al.  Intracellular signaling by the unfolded protein response. , 2006, Annual review of cell and developmental biology.

[55]  Julian N. Selley,et al.  Global Translational Responses to Oxidative Stress Impact upon Multiple Levels of Protein Synthesis* , 2006, Journal of Biological Chemistry.

[56]  U. Jakob,et al.  Zinc center as redox switch--new function for an old motif. , 2006, Antioxidants & redox signaling.

[57]  N. Pfanner,et al.  Isolation of yeast mitochondria. , 2006, Methods in molecular biology.

[58]  C. Proud eIF2 and the control of cell physiology. , 2005, Seminars in cell & developmental biology.

[59]  N. Pfanner,et al.  Essential role of Mia40 in import and assembly of mitochondrial intermembrane space proteins , 2004, The EMBO journal.

[60]  M. Simon,et al.  Regulation of Transcription and Translation by Hypoxia , 2004, Cancer biology & therapy.

[61]  G. Crooks,et al.  WebLogo: a sequence logo generator. , 2004, Genome research.

[62]  C. Grant,et al.  Protein S-thiolation targets glycolysis and protein synthesis in response to oxidative stress in the yeast Saccharomyces cerevisiae. , 2003, The Biochemical journal.

[63]  M. Ahmad,et al.  Molecular mechanisms of N-acetylcysteine actions , 2003, Cellular and Molecular Life Sciences CMLS.

[64]  N. Grishin Treble clef finger--a functionally diverse zinc-binding structural motif. , 2001, Nucleic acids research.

[65]  M. Clemens Initiation Factor eIF2α Phosphorylation in Stress Responses and Apoptosis , 2001 .

[66]  M. Clemens Initiation factor eIF2 alpha phosphorylation in stress responses and apoptosis. , 2001, Progress in molecular and subcellular biology.

[67]  U. Jakob,et al.  Redox Switch of Hsp33 Has a Novel Zinc-binding Motif* , 2000, The Journal of Biological Chemistry.

[68]  B. Snel,et al.  STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene. , 2000, Nucleic acids research.

[69]  P. Csutora,et al.  Relationship between the occurrence of cysteine in proteins and the complexity of organisms. , 2000, Molecular biology and evolution.

[70]  V. Kushnirov Rapid and reliable protein extraction from yeast , 2000, Yeast.

[71]  E. Stadtman,et al.  Carbonyl assays for determination of oxidatively modified proteins. , 1994, Methods in enzymology.