The cytoplasmic synthesis and coupled membrane translocation of eukaryotic polyphosphate by signal-activated VTC complex

[1]  Tingting Zou,et al.  Mechanistic insights into the regulation of plant phosphate homeostasis by the rice SPX2 – PHR2 complex , 2021, Nature communications.

[2]  Weiman Xing,et al.  Mechanism of phosphate sensing and signaling revealed by rice SPX1-PHR2 complex structure , 2021, Nature Communications.

[3]  S. Keeney,et al.  Computed structures of core eukaryotic protein complexes , 2021, Science.

[4]  Boyu Zhao,et al.  A phosphate starvation response-centered network regulates mycorrhizal symbiosis , 2021, Cell.

[5]  Tingting Zou,et al.  AimR Adopts Preexisting Dimer Conformations for Specific Target Recognition in Lysis-Lysogeny Decisions of Bacillus Phage phi3T , 2021, Biomolecules.

[6]  Ryokichi Koyama,et al.  The enzymatic activity of inositol hexakisphosphate kinase controls circulating phosphate in mammals , 2021, Nature Communications.

[7]  Oriol Vinyals,et al.  Highly accurate protein structure prediction with AlphaFold , 2021, Nature.

[8]  Nam Ki Lee,et al.  FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices , 2021, eLife.

[9]  Dong Si,et al.  DeepTracer for fast de novo cryo-EM protein structure modeling and special studies on CoV-related complexes , 2020, Proceedings of the National Academy of Sciences.

[10]  A. Grossman,et al.  Metabolic control of acclimation to nutrient deprivation dependent on polyphosphate synthesis , 2020, Science Advances.

[11]  A. Saiardi,et al.  Inorganic polyphosphate in mammals: where's Wally? , 2020, Biochemical Society transactions.

[12]  Huanchen Wang,et al.  Control of XPR1-dependent cellular phosphate efflux by InsP8 is an exemplar for functionally-exclusive inositol pyrophosphate signaling , 2020, Proceedings of the National Academy of Sciences.

[13]  A. Fernie,et al.  A genetically validated approach to detect inorganic polyphosphates in plants. , 2019, The Plant journal : for cell and molecular biology.

[14]  W. Müller,et al.  Inorganic Polyphosphates As Storage for and Generator of Metabolic Energy in the Extracellular Matrix , 2019, Chemical reviews.

[15]  M. Hothorn,et al.  Identity and functions of inorganic and inositol polyphosphates in plants , 2019, The New phytologist.

[16]  Zhu Liu,et al.  Structural basis for the recognition of K48-linked Ub chain by proteasomal receptor Rpn13 , 2019, bioRxiv.

[17]  Bonnie Berger,et al.  Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs , 2018, Nature Methods.

[18]  U. Jakob,et al.  Inorganic polyphosphate, a multifunctional polyanionic protein scaffold , 2018, The Journal of Biological Chemistry.

[19]  Nam Ki Lee,et al.  Publisher Correction: Precision and accuracy of single-molecule FRET measurements—a multi-laboratory benchmark study , 2018, Nature Methods.

[20]  Antonino Ingargiola,et al.  Toward dynamic structural biology: Two decades of single-molecule Förster resonance energy transfer , 2018, Science.

[21]  Randy J Read,et al.  Real-space refinement in PHENIX for cryo-EM and crystallography , 2018, bioRxiv.

[22]  Christopher J. Williams,et al.  MolProbity: More and better reference data for improved all‐atom structure validation , 2018, Protein science : a publication of the Protein Society.

[23]  G. Clore,et al.  Xplor‐NIH for molecular structure determination from NMR and other data sources , 2018, Protein science : a publication of the Protein Society.

[24]  Nam Ki Lee,et al.  Precision and accuracy of single-molecule FRET measurements—a multi-laboratory benchmark study , 2017, Nature Methods.

[25]  Zhu Liu,et al.  Ubiquitin S65 phosphorylation engenders a pH-sensitive conformational switch , 2017, Proceedings of the National Academy of Sciences.

[26]  A. Mayer,et al.  Inositol Pyrophosphate Specificity of the SPX-Dependent Polyphosphate Polymerase VTC. , 2017, ACS chemical biology.

[27]  David J. Fleet,et al.  cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination , 2017, Nature Methods.

[28]  A. Mayer,et al.  Vtc5, a Novel Subunit of the Vacuolar Transporter Chaperone Complex, Regulates Polyphosphate Synthesis and Phosphate Homeostasis in Yeast* , 2016, The Journal of Biological Chemistry.

[29]  M. Chapman,et al.  Polyphosphate: A Conserved Modifier of Amyloidogenic Processes. , 2016, Molecular cell.

[30]  A. Saiardi,et al.  Control of eukaryotic phosphate homeostasis by inositol polyphosphate sensor domains , 2016, Science.

[31]  D. Geschwind,et al.  Mutations in XPR1 cause primary familial brain calcification associated with altered phosphate export , 2015, Nature Genetics.

[32]  A. Saiardi,et al.  Protein polyphosphorylation of lysine residues by inorganic polyphosphate. , 2015, Molecular cell.

[33]  Nathaniel Echols,et al.  EMRinger: Side-chain-directed model and map validation for 3D Electron Cryomicroscopy , 2015, Nature Methods.

[34]  Alan Brown,et al.  Tools for macromolecular model building and refinement into electron cryo-microscopy reconstructions , 2015, Acta crystallographica. Section D, Biological crystallography.

[35]  S. Shears Inositol pyrophosphates: why so many phosphates? , 2015, Advances in biological regulation.

[36]  A. Mayer,et al.  Coupled synthesis and translocation restrains polyphosphate to acidocalcisome-like vacuoles and prevents its toxicity , 2014, Journal of Cell Science.

[37]  Yanyu Zhao,et al.  Three-dimensional structure of human γ-secretase , 2014, Nature.

[38]  R. Bender,et al.  Polyphosphate is a primordial chaperone. , 2014, Molecular cell.

[39]  Hemant D. Tagare,et al.  The Local Resolution of Cryo-EM Density Maps , 2013, Nature Methods.

[40]  R. Henderson,et al.  High-resolution noise substitution to measure overfitting and validate resolution in 3D structure determination by single particle electron cryomicroscopy☆ , 2013, Ultramicroscopy.

[41]  R. Docampo,et al.  Polyphosphate and Its Diverse Functions in Host Cells and Pathogens , 2013, PLoS pathogens.

[42]  A. Gourine,et al.  Signalling properties of inorganic polyphosphate in the mammalian brain , 2013, Nature Communications.

[43]  Claus A M Seidel,et al.  A toolkit and benchmark study for FRET-restrained high-precision structural modeling , 2012, Nature Methods.

[44]  A. Saiardi,et al.  Influence of Inositol Pyrophosphates on Cellular Energy Dynamics , 2011, Science.

[45]  A. Saiardi,et al.  Identification of an Evolutionarily Conserved Family of Inorganic Polyphosphate Endopolyphosphatases* , 2011, The Journal of Biological Chemistry.

[46]  M. Gómez-García,et al.  Inorganic Polyphosphate and Energy Metabolism in Mammalian Cells* , 2010, The Journal of Biological Chemistry.

[47]  T. Renné,et al.  Platelet Polyphosphates Are Proinflammatory and Procoagulant Mediators In Vivo , 2009, Cell.

[48]  Arthur Kornberg,et al.  Inorganic polyphosphate: essential for growth and survival. , 2009, Annual review of biochemistry.

[49]  V. Rybin,et al.  Catalytic Core of a Membrane-Associated Eukaryotic Polyphosphate Polymerase , 2009, Science.

[50]  M. Grynpas,et al.  Relationships between polyphosphate chemistry, biochemistry and apatite biomineralization. , 2008, Chemical reviews.

[51]  Martin Parniske,et al.  Arbuscular mycorrhiza: the mother of plant root endosymbioses , 2008, Nature Reviews Microbiology.

[52]  Mike Heilemann,et al.  A reducing and oxidizing system minimizes photobleaching and blinking of fluorescent dyes. , 2008, Angewandte Chemie.

[53]  R. French,et al.  High Sensitivity, Quantitative Measurements of Polyphosphate Using a New DAPI-Based Approach , 2008, Journal of Fluorescence.

[54]  M. Duchen,et al.  Targeted polyphosphatase expression alters mitochondrial metabolism and inhibits calcium-dependent cell death , 2007, Proceedings of the National Academy of Sciences.

[55]  N. Amrhein,et al.  Systematic screening of polyphosphate (poly P) levels in yeast mutant cells reveals strong interdependence with primary metabolism , 2006, Genome Biology.

[56]  F. Ruiz,et al.  Inorganic polyphosphate and specific induction of apoptosis in human plasma cells. , 2006, Haematologica.

[57]  Christoph Bräuchle,et al.  Pulsed interleaved excitation. , 2005, Biophysical journal.

[58]  E. O’Shea,et al.  An intracellular phosphate buffer filters transient fluctuations in extracellular phosphate levels. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[59]  Nam Ki Lee,et al.  Accurate FRET measurements within single diffusing biomolecules using alternating-laser excitation. , 2005, Biophysical journal.

[60]  Peter Rohloff,et al.  Acidocalcisomes ? conserved from bacteria to man , 2005, Nature Reviews Microbiology.

[61]  Arthur Kornberg,et al.  Inorganic polyphosphate in the origin and survival of species. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[62]  Michael Knop,et al.  A versatile toolbox for PCR‐based tagging of yeast genes: new fluorescent proteins, more markers and promoter substitution cassettes , 2004, Yeast.

[63]  A. Kornberg,et al.  Inorganic polyphosphate stimulates mammalian TOR, a kinase involved in the proliferation of mammary cancer cells , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[64]  A. Mayer,et al.  Role of the Vtc proteins in V-ATPase stability and membrane trafficking , 2003, Journal of Cell Science.

[65]  M. Mann,et al.  The Vtc proteins in vacuole fusion: coupling NSF activity to V0 trans‐complex formation , 2002, The EMBO journal.

[66]  A Kornberg,et al.  Role of Inorganic Polyphosphate in Promoting Ribosomal Protein Degradation by the Lon Protease in E. coli , 2001, Science.

[67]  P. Brown,et al.  New components of a system for phosphate accumulation and polyphosphate metabolism in Saccharomyces cerevisiae revealed by genomic expression analysis. , 2000, Molecular biology of the cell.

[68]  A. Kornberg,et al.  Polyphosphate kinase is essential for biofilm development, quorum sensing, and virulence of Pseudomonas aeruginosa. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[69]  A. Kornberg Inorganic polyphosphate: a molecule of many functions. , 2003, Annual review of biochemistry.

[70]  Stewart Shuman,et al.  Structure and Mechanism of Yeast RNA Triphosphatase An Essential Component of the mRNA Capping Apparatus , 1999, Cell.

[71]  Adiel Cohen,et al.  A Novel Family of Yeast Chaperons Involved in the Distribution of V-ATPase and Other Membrane Proteins* , 1999, The Journal of Biological Chemistry.

[72]  B. Wallace,et al.  HOLE: a program for the analysis of the pore dimensions of ion channel structural models. , 1996, Journal of molecular graphics.

[73]  S. Kohlwein,et al.  Phospholipid synthesis and lipid composition of subcellular membranes in the unicellular eukaryote Saccharomyces cerevisiae , 1991, Journal of bacteriology.

[74]  N. Greenfield,et al.  Effects of growth state and amines on cytoplasmic and vacuolar pH, phosphate and polyphosphate levels in Saccharomyces cerevisiae: a 31P-nuclear magnetic resonance study. , 1987, Biochimica et biophysica acta.

[75]  Y. Anraku,et al.  Properties of H+-translocating adenosine triphosphatase in vacuolar membranes of SAccharomyces cerevisiae. , 1981, The Journal of biological chemistry.