Systematic analysis of Ca2+ homeostasis in Saccharomyces cerevisiae based on chemical-genetic interaction profiles

The global landscape of Ca2+ homeostasis in budding yeast is deciphered. Quantified morphological responses under high concentration of Ca2+ and obtained high-dimensional Ca2+-genetic interaction profiles show functional gene clusters, which are used to build a global network among the Ca2+ homeostasis units acting in various cellular compartments.

[1]  O. Oltmanns,et al.  Biosynthesis of Riboflavine in Saccharomyces cerevisiae: the Role of Genes rib1 and rib7 , 1972, Journal of bacteriology.

[2]  H. Akaike,et al.  Information Theory and an Extension of the Maximum Likelihood Principle , 1973 .

[3]  Y. Eilam.  Studies on calcium efflux in the yeast Saccharomyces cerevisiae. , 1982, Microbios.

[4]  P. McCullagh,et al.  Generalized Linear Models , 1984 .

[5]  Y. Eilam,et al.  Cytoplasmic Ca2+Homeostasis Maintained by a Vacuolar Ca2+Transport System in the Yeast Saccharomyces cerevisiae , 1985 .

[6]  Y. Anraku,et al.  Isolation and characterization of Ca2+-sensitive mutants of Saccharomyces cerevisiae. , 1986, Journal of general microbiology.

[7]  Y. Anraku,et al.  Calcium-sensitive cls4 mutant of Saccharomyces cerevisiae with a defect in bud formation , 1986, Journal of bacteriology.

[8]  J. Heitman,et al.  FK 506-binding protein proline rotamase is a target for the immunosuppressive agent FK 506 in Saccharomyces cerevisiae. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[9]  Y. Anraku,et al.  VMA11, a novel gene that encodes a putative proteolipid, is indispensable for expression of yeast vacuolar membrane H(+)-ATPase activity. , 1991, The Journal of biological chemistry.

[10]  Y. Anraku,et al.  Calcium-sensitive cls mutants of Saccharomyces cerevisiae showing a Pet- phenotype are ascribable to defects of vacuolar membrane H(+)-ATPase activity. , 1991, The Journal of biological chemistry.

[11]  Y. Anraku,et al.  Genes for directing vacuolar morphogenesis in Saccharomyces cerevisiae. I. Isolation and characterization of two classes of vam mutants. , 1992, The Journal of biological chemistry.

[12]  T. Stevens,et al.  VMA12 is essential for assembly of the vacuolar H(+)-ATPase subunits onto the vacuolar membrane in Saccharomyces cerevisiae. , 1993, The Journal of biological chemistry.

[13]  Y. Eilam,et al.  Calcium homeostasis in yeast cells exposed to high concentrations of calcium Roles of vacuolar H+‐ATPase and cellular ATP , 1993, FEBS Letters.

[14]  T. Stevens,et al.  VMA13 encodes a 54-kDa vacuolar H(+)-ATPase subunit required for activity but not assembly of the enzyme complex in Saccharomyces cerevisiae. , 1993, The Journal of biological chemistry.

[15]  M. Manolson,et al.  The VPH2 gene encodes a 25 kDa protein required for activity of the yeast vacuolar H+‐ATPase , 1993, Yeast.

[16]  K. Gable,et al.  Regulation of cellular Ca2+ by yeast vacuoles. , 1994, The Journal of biological chemistry.

[17]  Y. Anraku,et al.  MID1, a novel Saccharomyces cerevisiae gene encoding a plasma membrane protein, is required for Ca2+ influx and mating , 1994, Molecular and cellular biology.

[18]  G. Fink,et al.  Calcineurin-dependent growth control in Saccharomyces cerevisiae mutants lacking PMC1, a homolog of plasma membrane Ca2+ ATPases , 1994, The Journal of cell biology.

[19]  A. Bognar,et al.  Cloning and molecular characterization of three genes, including two genes encoding serine hydroxymethyltransferases, whose inactivation is required to render yeast auxotrophic for glycine. , 1994, The Journal of biological chemistry.

[20]  K. Gable,et al.  A novel protein, CSG2p, is required for Ca2+ regulation in Saccharomyces cerevisiae. , 1994, The Journal of biological chemistry.

[21]  J. Revuelta,et al.  The Saccharomyces cerevisiae RIB4 Gene Codes for 6,7-Dimethyl- 8-ribityllumazine Synthase Involved in Riboflavin Biosynthesis , 1995, The Journal of Biological Chemistry.

[22]  Y. Anraku,et al.  Cooperation of Calcineurin and Vacuolar H+-ATPase in Intracellular Ca2+Homeostasis of Yeast Cells * , 1995, The Journal of Biological Chemistry.

[23]  D. Stillman,et al.  Mutations in the homologous ZDS1 and ZDS2 genes affect cell cycle progression , 1996, Molecular and Cellular Biology.

[24]  M. Cyert,et al.  The product of HUM1, a novel yeast gene, is required for vacuolar Ca2+/H+ exchange and is related to mammalian Na+/Ca2+ exchangers , 1996, Molecular and cellular biology.

[25]  G. Fink,et al.  Calcineurin inhibits VCX1-dependent H+/Ca2+ exchange and induces Ca2+ ATPases in Saccharomyces cerevisiae , 1996, Molecular and cellular biology.

[26]  Y. Anraku,et al.  Yeast Cls2p/Csg2p localized on the endoplasmic reticulum membrane regulates a non‐exchangeable intracellular Ca2+ pool cooperatively with calcineurin , 1996, FEBS letters.

[27]  M. Cyert,et al.  Calcineurin acts through the CRZ1/TCN1-encoded transcription factor to regulate gene expression in yeast. , 1997, Genes & development.

[28]  D. Sanders,et al.  The Saccharomyces cerevisiae CCH1 gene is involved in calcium influx and mating , 1997, FEBS letters.

[29]  P. Philippsen,et al.  Additional modules for versatile and economical PCR‐based gene deletion and modification in Saccharomyces cerevisiae , 1998, Yeast.

[30]  H. Sahm,et al.  Threonine Aldolase Overexpression plus Threonine Supplementation Enhanced Riboflavin Production inAshbya gossypii , 1998, Applied and Environmental Microbiology.

[31]  Ronald W. Davis,et al.  Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. , 1999, Science.

[32]  P. Kane,et al.  Cytosolic Ca2+ Homeostasis Is a Constitutive Function of the V-ATPase in Saccharomyces cerevisiae * , 2000, The Journal of Biological Chemistry.

[33]  W. Robberecht,et al.  Abnormal intracellular ca(2+)homeostasis and disease. , 2000, Cell calcium.

[34]  Yoh WadaSB,et al.  Genes for Directing Vacuolar Morphogenesis in Saccharomyces cerevisiae 11 , 2001 .

[35]  Hidetoshi Shimodaira.  An approximately unbiased test of phylogenetic tree selection. , 2002, Systematic biology.

[36]  D. Botstein,et al.  Genome-wide Analysis of Gene Expression Regulated by the Calcineurin/Crz1p Signaling Pathway in Saccharomyces cerevisiae * , 2002, The Journal of Biological Chemistry.

[37]  M. Cyert,et al.  Internal Ca2+ release in yeast is triggered by hypertonic shock and mediated by a TRP channel homologue , 2002, The Journal of cell biology.

[38]  A. Kihara,et al.  Csg1p and Newly Identified Csh1p Function in Mannosylinositol Phosphorylceramide Synthesis by Interacting with Csg2p* , 2003, Journal of Biological Chemistry.

[39]  M. Cyert.  Calcineurin signaling in Saccharomyces cerevisiae: how yeast go crazy in response to stress. , 2003, Biochemical and biophysical research communications.

[40]  N. Demaurex,et al.  Measurements of the free luminal ER Ca(2+) concentration with targeted "cameleon" fluorescent proteins. , 2003, Cell calcium.

[41]  Shinichi Morishita,et al.  Development of Image Processing Program for Yeast Cell Morphology , 2004, J. Bioinform. Comput. Biol..

[42]  Gary D Bader,et al.  Global Mapping of the Yeast Genetic Interaction Network , 2004, Science.

[43]  Michael D. Abràmoff,et al.  Image processing with ImageJ , 2004 .

[44]  Y. Anraku,et al.  The CLS2 gene encodes a protein with multiple membrane-spanning domains that is important Ca2+ tolerance in yeast , 1995, Molecular and General Genetics MGG.

[45]  K. Hirschi,et al.  Functional dependence on calcineurin by variants of the Saccharomyces cerevisiae vacuolar Ca2+/H+ exchanger Vcx1p , 2004, Molecular microbiology.

[46]  T. Hughes,et al.  Exploration of Essential Gene Functions via Titratable Promoter Alleles , 2004, Cell.

[47]  Taro L. Saito,et al.  High-dimensional and large-scale phenotyping of yeast mutants. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[48]  P. Kane,et al.  A Genomic Screen for Yeast Vacuolar Membrane ATPase Mutants , 2005, Genetics.

[49]  Sean R. Collins,et al.  Exploration of the Function and Organization of the Yeast Early Secretory Pathway through an Epistatic Miniarray Profile , 2005, Cell.

[50]  D. Kosman,et al.  Evidence for iron channeling in the Fet3p-Ftr1p high-affinity iron uptake complex in the yeast plasma membrane. , 2006, Biochemistry.

[51]  Hidetoshi Shimodaira,et al.  Pvclust: an R package for assessing the uncertainty in hierarchical clustering , 2006, Bioinform..

[52]  W. Wickner,et al.  Bem1p Is a Positive Regulator of the Homotypic Fusion of Yeast Vacuoles* , 2006, Journal of Biological Chemistry.

[53]  J. Kaandorp,et al.  Mathematical modeling of calcium homeostasis in yeast cells. , 2006, Cell calcium.

[54]  P. Kane.  The Where, When, and How of Organelle Acidification by the Yeast Vacuolar H+-ATPase , 2006, Microbiology and Molecular Biology Reviews.

[55]  Y. Ohya,et al.  Diversity of Ca2+-Induced Morphology Revealed by Morphological Phenotyping of Ca2+-Sensitive Mutants of Saccharomyces cerevisiae , 2007, Eukaryotic Cell.

[56]  Robert P. St.Onge,et al.  Defining genetic interaction , 2008, Proceedings of the National Academy of Sciences.

[57]  Sasha F. Levy,et al.  Network Hubs Buffer Environmental Variation in Saccharomyces cerevisiae , 2008, PLoS biology.

[58]  Kathryn A. O’Donnell,et al.  Toward a comprehensive temperature-sensitive mutant repository of the essential genes of Saccharomyces cerevisiae. , 2008, Molecular cell.

[59]  B. Andrews,et al.  Systematic mapping of genetic interaction networks. , 2009, Annual review of genetics.

[60]  J. Kaandorp,et al.  Simulating calcium influx and free calcium concentrations in yeast. , 2009, Cell calcium.

[61]  S. Collins,et al.  Comprehensive Characterization of Genes Required for Protein Folding in the Endoplasmic Reticulum , 2009, Science.

[62]  A. Beck,et al.  Properties of the intracellular transient receptor potential (TRP) channel in yeast, Yvc1 , 2010, FEBS letters.

[63]  Gary D Bader,et al.  The Genetic Landscape of a Cell , 2010, Science.

[64]  D. Naiman,et al.  New Regulators of a High Affinity Ca2+ Influx System Revealed through a Genome-wide Screen in Yeast* , 2011, The Journal of Biological Chemistry.

[65]  Frederick S. Vizeacoumar,et al.  Systematic exploration of essential yeast gene function with temperature-sensitive mutants , 2011, Nature Biotechnology.

[66]  K. Cunningham.  Acidic calcium stores of Saccharomyces cerevisiae. , 2011, Cell calcium.

[67]  I. Kozone,et al.  Analysis of the biological activity of a novel 24-membered macrolide JBIR-19 in Saccharomyces cerevisiae by the morphological imaging program CalMorph. , 2012, FEMS yeast research.

[68]  Zhaolei Zhang,et al.  PhenoM: a database of morphological phenotypes caused by mutation of essential genes in Saccharomyces cerevisiae , 2011, Nucleic Acids Res..

[69]  Shinsuke Ohnuki,et al.  Single-cell phenomics reveals intra-species variation of phenotypic noise in yeast , 2013, BMC Systems Biology.

[70]  C. Myers,et al.  Genetic interaction networks: toward an understanding of heritability. , 2013, Annual review of genomics and human genetics.

[71]  Y. Ohya,et al.  Profilin is required for Ca2+ homeostasis and Ca2+-modulated bud formation in yeast , 2013, Molecular Genetics and Genomics.

[72]  Linghuo Jiang,et al.  Activation of calcineurin is mainly responsible for the calcium sensitivity of gene deletion mutations in the genome of budding yeast. , 2013, Genomics.

[73]  J. Bader,et al.  A DNA Integrity Network in the Yeast Saccharomyces cerevisiae , 2013, Cell.

[74]  M. Cyert,et al.  Regulation of Cation Balance in Saccharomyces cerevisiae , 2013, Genetics.

[75]  H. Balderhaar,et al.  CORVET and HOPS tethering complexes – coordinators of endosome and lysosome fusion , 2013, Journal of Cell Science.

[76]  Y. Ohya,et al.  Unveiling nonessential gene deletions that confer significant morphological phenotypes beyond natural yeast strains , 2014, BMC Genomics.

[77]  Adam P. Rosebrock,et al.  A global genetic interaction network maps a wiring diagram of cellular function , 2016, Science.