Experts and Doctors on saccharomyces cerevisiae in Berkeley, California, United States

Summary

Locale: Berkeley, California, United States
Topic: saccharomyces cerevisiae

Top Publications

  1. Cyert M, Kunisawa R, Kaim D, Thorner J. Yeast has homologs (CNA1 and CNA2 gene products) of mammalian calcineurin, a calmodulin-regulated phosphoprotein phosphatase. Proc Natl Acad Sci U S A. 1991;88:7376-80 pubmed
    ..Thus, calcineurin action antagonizes the mating-pheromone response pathway. ..
  2. d Enfert C, Barlowe C, Nishikawa S, Nakano A, Schekman R. Structural and functional dissection of a membrane glycoprotein required for vesicle budding from the endoplasmic reticulum. Mol Cell Biol. 1991;11:5727-34 pubmed
    ..Sar1p membrane association was enhanced by elevated levels of Sec12p. These results suggest that the cytoplasmic domain of Sec12p interacts with Sar1p and that the complex may function to promote vesicle formation. ..
  3. Basson M, Thorsness M, Finer Moore J, Stroud R, Rine J. Structural and functional conservation between yeast and human 3-hydroxy-3-methylglutaryl coenzyme A reductases, the rate-limiting enzyme of sterol biosynthesis. Mol Cell Biol. 1988;8:3797-808 pubmed
    ..The availability of yeast cells whose growth depends on human HMG-CoA reductase may provide a microbial screen to identify new drugs that can modulate cholesterol biosynthesis. ..
  4. Corsi A, Schekman R. Mechanism of polypeptide translocation into the endoplasmic reticulum. J Biol Chem. 1996;271:30299-302 pubmed
  5. Goode B, Drubin D, Lappalainen P. Regulation of the cortical actin cytoskeleton in budding yeast by twinfilin, a ubiquitous actin monomer-sequestering protein. J Cell Biol. 1998;142:723-33 pubmed
    ..Taken together, these results demonstrate that twinfilin is a novel, highly conserved actin monomer-sequestering protein involved in regulation of the cortical actin cytoskeleton. ..
  6. Belmont L, Drubin D. The yeast V159N actin mutant reveals roles for actin dynamics in vivo. J Cell Biol. 1998;142:1289-99 pubmed
    ..Analysis of the cables in these double-mutant cells supports a role for fimbrin in organizing cytoplasmic cables and for Mdm20p and tropomyosin in excluding cofilin from the cables. ..
  7. Kurihara T, Hamamoto S, Gimeno R, Kaiser C, Schekman R, Yoshihisa T. Sec24p and Iss1p function interchangeably in transport vesicle formation from the endoplasmic reticulum in Saccharomyces cerevisiae. Mol Biol Cell. 2000;11:983-98 pubmed
    ..Abundant proteins in the purified vesicles produced with Sec23p/Iss1p were indistinguishable from those in the regular COPII vesicles produced with Sec23p/Sec24p. ..
  8. Schild D, Lio Y, Collins D, Tsomondo T, Chen D. Evidence for simultaneous protein interactions between human Rad51 paralogs. J Biol Chem. 2000;275:16443-9 pubmed
    ..These results suggest that these proteins may participate in one complex or multiple smaller ones. ..
  9. Hagstrom K, Holmes V, Cozzarelli N, Meyer B. C. elegans condensin promotes mitotic chromosome architecture, centromere organization, and sister chromatid segregation during mitosis and meiosis. Genes Dev. 2002;16:729-42 pubmed
    ..These results imply that condensin is not simply required for compaction, but plays a more complex role in chromosome architecture that is essential for mitotic and meiotic sister chromatid segregation. ..

More Information

Publications232 found, 100 shown here

  1. Weilbaecher R, Awrey D, Edwards A, Kane C. Intrinsic transcript cleavage in yeast RNA polymerase II elongation complexes. J Biol Chem. 2003;278:24189-99 pubmed
    ..A mutant RNA polymerase previously shown to be refractory to TFIIS-induced transcript cleavage is essentially identical to the wild type polymerase in all tested aspects of intrinsic cleavage. ..
  2. Versele M, Gullbrand B, Shulewitz M, Cid V, Bahmanyar S, Chen R, et al. Protein-protein interactions governing septin heteropentamer assembly and septin filament organization in Saccharomyces cerevisiae. Mol Biol Cell. 2004;15:4568-83 pubmed
    ..These data provide novel insights about the connectivity among the five individual septins in functional septin heteropentamers and the organization of septin filaments. ..
  3. Ballon D, Flanary P, Gladue D, Konopka J, Dohlman H, Thorner J. DEP-domain-mediated regulation of GPCR signaling responses. Cell. 2006;126:1079-93 pubmed
    ..DEP-domain-mediated targeting of effectors and regulators to specific GPCRs provides a means to dictate the nature, duration, and specificity of the response. ..
  4. Gilbert W, Zhou K, Butler T, Doudna J. Cap-independent translation is required for starvation-induced differentiation in yeast. Science. 2007;317:1224-7 pubmed
    ..A 5'UTR mutation that impairs IRES activity compromises invasive growth, which indicates that cap-independent translation is required for physiological adaptation to stress. ..
  5. Schulze J, Kane C, Ruiz Manzano A. The YEATS domain of Taf14 in Saccharomyces cerevisiae has a negative impact on cell growth. Mol Genet Genomics. 2010;283:365-80 pubmed publisher
    ..Thus, this highly conserved domain should be considered part of a negative regulatory loop in cell growth. ..
  6. Okreglak V, Drubin D. Loss of Aip1 reveals a role in maintaining the actin monomer pool and an in vivo oligomer assembly pathway. J Cell Biol. 2010;188:769-77 pubmed publisher
  7. Weinberg J, Drubin D. Clathrin-mediated endocytosis in budding yeast. Trends Cell Biol. 2012;22:1-13 pubmed publisher
  8. Parsons H, Christiansen K, Knierim B, Carroll A, Ito J, Batth T, et al. Isolation and proteomic characterization of the Arabidopsis Golgi defines functional and novel components involved in plant cell wall biosynthesis. Plant Physiol. 2012;159:12-26 pubmed publisher
    ..Overall, these data show key proteins involved in primary cell wall synthesis and include a mixture of well-characterized and unknown proteins whose biological roles and importance as targets for future research can now be realized...
  9. Peters T, Miller A, Tourette C, Agren H, Hubbard A, Hughes R. Genomic Analysis of ATP Efflux in Saccharomyces cerevisiae. G3 (Bethesda). 2015;6:161-70 pubmed publisher
    ..These results will facilitate analysis of ATP efflux mechanisms in higher eukaryotes. ..
  10. Pugh B, Tjian R. Mechanism of transcriptional activation by Sp1: evidence for coactivators. Cell. 1990;61:1187-97 pubmed
    ..At promoters lacking a TATA box, an additional activity distinct from coactivators is required for Sp1 activation of transcription. ..
  11. Ehrenhofer Murray A, Rivier D, Rine J. The role of Sas2, an acetyltransferase homologue of Saccharomyces cerevisiae, in silencing and ORC function. Genetics. 1997;145:923-34 pubmed
    ..Moreover, sas2 delta had opposing effects on silencing of HML and HMR. The putative Sas2 protein bears similarities to known protein acetyltransferases. Several models for the role of Sas2 in silencing are discussed. ..
  12. Inouye C, Dhillon N, Durfee T, Zambryski P, Thorner J. Mutational analysis of STE5 in the yeast Saccharomyces cerevisiae: application of a differential interaction trap assay for examining protein-protein interactions. Genetics. 1997;147:479-92 pubmed
    ..Ste5 mutants defective in association with Ste11 or Ste7 showed strong interallelic complementation when co-expressed, suggesting that the functional form of Ste5 in vivo is an oligomer. ..
  13. Drees B, Sundin B, Brazeau E, Caviston J, Chen G, Guo W, et al. A protein interaction map for cell polarity development. J Cell Biol. 2001;154:549-71 pubmed
    ..In total, a network of interactions that provide an integrated response of signaling proteins, the cytoskeleton, and organelles to the spatial cues that direct polarity development was revealed. ..
  14. Fischer N, Weis K. The DEAD box protein Dhh1 stimulates the decapping enzyme Dcp1. EMBO J. 2002;21:2788-97 pubmed
    ..We propose that the DEAD box protein Dhh1 regulates the access of the decapping enzyme to the m(7)G cap by modulating the structure at the 5' end of mRNAs. ..
  15. Miller E, Antonny B, Hamamoto S, Schekman R. Cargo selection into COPII vesicles is driven by the Sec24p subunit. EMBO J. 2002;21:6105-13 pubmed
    ..Our data suggest that the principle role of Sec24p is to discriminate cargo molecules for incorporation into COPII vesicles...
  16. Okreglak V, Drubin D. Cofilin recruitment and function during actin-mediated endocytosis dictated by actin nucleotide state. J Cell Biol. 2007;178:1251-64 pubmed
    ..These results suggest that cofilin-mediated actin filament flux is required for the multiple steps of endocytic trafficking. ..
  17. Halley J, Kaplan T, Wang A, Kobor M, Rine J. Roles for H2A.Z and its acetylation in GAL1 transcription and gene induction, but not GAL1-transcriptional memory. PLoS Biol. 2010;8:e1000401 pubmed publisher
    ..Z were due to the SWR1 complex's activity rather than to the absence of H2A.Z per se. These results highlight the need to reevaluate all studies on the phenotypes of cells lacking H2A.Z. ..
  18. Galazka J, Tian C, Beeson W, Martinez B, Glass N, Cate J. Cellodextrin transport in yeast for improved biofuel production. Science. 2010;330:84-6 pubmed publisher
    ..In simultaneous saccharification and fermentation experiments, the engineered yeast strains more rapidly convert cellulose to ethanol when compared with yeast lacking this system. ..
  19. Gaytán B, Loguinov A, Lantz S, Lerot J, Denslow N, Vulpe C. Functional profiling discovers the dieldrin organochlorinated pesticide affects leucine availability in yeast. Toxicol Sci. 2013;132:347-58 pubmed publisher
    ..Many yeast genes described in this study have human orthologs that may modulate dieldrin toxicity in humans. ..
  20. Matyskiela M, Lander G, Martin A. Conformational switching of the 26S proteasome enables substrate degradation. Nat Struct Mol Biol. 2013;20:781-8 pubmed publisher
    ..Notably, Rpn11 moves from an occluded position to directly above the central pore, thus facilitating substrate deubiquitination concomitant with translocation. ..
  21. Gossen M, Pak D, Hansen S, Acharya J, Botchan M. A Drosophila homolog of the yeast origin recognition complex. Science. 1995;270:1674-7 pubmed
    ..These studies will enable direct testing of the initiator-based model of replication in a metazoan. ..
  22. Ma D, Cook J, Thorner J. Phosphorylation and localization of Kss1, a MAP kinase of the Saccharomyces cerevisiae pheromone response pathway. Mol Biol Cell. 1995;6:889-909 pubmed
    ..Indirect immunofluorescence demonstrated that Kss1 is concentrated in the nucleus and that its distribution is not altered detectably during signaling. ..
  23. Duden R, Hosobuchi M, Hamamoto S, Winey M, Byers B, Schekman R. Yeast beta- and beta'-coat proteins (COP). Two coatomer subunits essential for endoplasmic reticulum-to-Golgi protein traffic. J Biol Chem. 1994;269:24486-95 pubmed
    ..Genetic interactions connect sec27-1 and sec21-1 (coatomer gamma subunit) with the ARF1 and ARF2 genes and with the SEC22, BET1, and BOS1 genes, which encode membrane proteins involved in ER-to-Golgi transport. ..
  24. Machin N, Lee J, Barnes G. Microtubule stability in budding yeast: characterization and dosage suppression of a benomyl-dependent tubulin mutant. Mol Biol Cell. 1995;6:1241-59 pubmed
    ..As tub2-404 mutants are also defective for spindle elongation, this provides additional support for a role for JSN1 during anaphase...
  25. Springer S, Schekman R. Nucleation of COPII vesicular coat complex by endoplasmic reticulum to Golgi vesicle SNAREs. Science. 1998;281:698-700 pubmed
    ..The data suggest that transmembrane proteins can be taken up into COPII vesicles by direct interactions with the coat proteins and may play a structural role in the assembly of the COPII coat complex...
  26. Adamkewicz J, Mueller C, Hansen K, Prud homme W, Thorner J. Purification and enzymic properties of Mot1 ATPase, a regulator of basal transcription in the yeast Saccharomyces cerevisiae. J Biol Chem. 2000;275:21158-68 pubmed
    ..Thus, Mot1 most likely promotes release of TBP from TATA-containing DNA by causing a structural change in TBP itself, rather than by strand unwinding. ..
  27. Ladurner A, Inouye C, Jain R, Tjian R. Bromodomains mediate an acetyl-histone encoded antisilencing function at heterochromatin boundaries. Mol Cell. 2003;11:365-76 pubmed
    ..These data suggest an active role for Bdf1 in euchromatin maintenance and antisilencing through a histone tail-encoded boundary function. ..
  28. Versele M, Thorner J. Septin collar formation in budding yeast requires GTP binding and direct phosphorylation by the PAK, Cla4. J Cell Biol. 2004;164:701-15 pubmed
    ..Cla4 interacts directly with and phosphorylates certain septins in vitro and in vivo. Thus, septin collar formation may correspond to septin filament assembly, and requires both GTP binding and Cla4-mediated phosphorylation of septins. ..
  29. Kobor M, Venkatasubrahmanyam S, Meneghini M, Gin J, Jennings J, Link A, et al. A protein complex containing the conserved Swi2/Snf2-related ATPase Swr1p deposits histone variant H2A.Z into euchromatin. PLoS Biol. 2004;2:E131 pubmed
    ..Metazoan orthologs of Swr1p (Drosophila Domino; human SRCAP and p400) may have analogous functions...
  30. Babiarz J, Halley J, Rine J. Telomeric heterochromatin boundaries require NuA4-dependent acetylation of histone variant H2A.Z in Saccharomyces cerevisiae. Genes Dev. 2006;20:700-10 pubmed
    ..Taken together, these results show a role for H2A.Z acetylation in restricting silent chromatin, and reveal that acetylation of H2A.Z and H4 can contribute to a common function essential to life. ..
  31. Kustu S, Inwood W. Biological gas channels for NH3 and CO2: evidence that Rh (Rhesus) proteins are CO2 channels. Transfus Clin Biol. 2006;13:103-10 pubmed
  32. Toret C, Lee L, Sekiya Kawasaki M, Drubin D. Multiple pathways regulate endocytic coat disassembly in Saccharomyces cerevisiae for optimal downstream trafficking. Traffic. 2008;9:848-59 pubmed publisher
    ..In total, at least four separate processes are important for disassembly of endocytic complexes and efficient downstream trafficking of endocytic cargo. ..
  33. Fox J, Levine S, Blanch H, Clark D. An evaluation of cellulose saccharification and fermentation with an engineered Saccharomyces cerevisiae capable of cellobiose and xylose utilization. Biotechnol J. 2012;7:361-73 pubmed publisher
    ..Strains with improved cellobiose utilization are therefore unlikely to allow higher titers to be reached more quickly in SSF than in SHF. ..
  34. Ziman M, Chuang J, Tsung M, Hamamoto S, Schekman R. Chs6p-dependent anterograde transport of Chs3p from the chitosome to the plasma membrane in Saccharomyces cerevisiae. Mol Biol Cell. 1998;9:1565-76 pubmed
  35. Chen Y, Holcomb C, Moore H. Expression and localization of two low molecular weight GTP-binding proteins, Rab8 and Rab10, by epitope tag. Proc Natl Acad Sci U S A. 1993;90:6508-12 pubmed
    ..This approach should provide a general tool for the analyses of other members of the YPT/SEC4/rab gene family. ..
  36. Fraser H, Hirsh A, Giaever G, Kumm J, Eisen M. Noise minimization in eukaryotic gene expression. PLoS Biol. 2004;2:e137 pubmed
    ..Our results support the hypothesis that noise in gene expression is a biologically important variable, is generally detrimental to organismal fitness, and is subject to natural selection. ..
  37. Howes S, Geyer E, LaFrance B, Zhang R, Kellogg E, Westermann S, et al. Structural differences between yeast and mammalian microtubules revealed by cryo-EM. J Cell Biol. 2017;216:2669-2677 pubmed publisher
    ..These differences may reflect adaptations to the demands of different cell size or range of physiological growth temperatures. ..
  38. Huttner I, Strahl T, Osawa M, King D, Ames J, Thorner J. Molecular interactions of yeast frequenin (Frq1) with the phosphatidylinositol 4-kinase isoform, Pik1. J Biol Chem. 2003;278:4862-74 pubmed
    ..This study defines the segment of Pik1 required for high affinity binding of Frq1. ..
  39. North M, Steffen J, Loguinov A, Zimmerman G, Vulpe C, Eide D. Genome-wide functional profiling identifies genes and processes important for zinc-limited growth of Saccharomyces cerevisiae. PLoS Genet. 2012;8:e1002699 pubmed publisher
    ..Thus, functional profiling has provided many new insights into genes and processes that are needed for cells to thrive under the stress of zinc deficiency. ..
  40. Eby J, Holly S, van Drogen F, Grishin A, Peter M, Drubin D, et al. Actin cytoskeleton organization regulated by the PAK family of protein kinases. Curr Biol. 1998;8:967-70 pubmed
    ..Thus, PAKs are effectors of Cdc42 in pathways that regulate the organization of the cortical actin cytoskeleton. ..
  41. Osborne E, Dudoit S, Rine J. The establishment of gene silencing at single-cell resolution. Nat Genet. 2009;41:800-6 pubmed publisher
    ..Our findings showed that removal of methyl modifications at H3K4 and H3K79 were important steps in silent chromatin formation and that Jhd2 and Set1 had competing roles in the process. ..
  42. Barlowe C, Schekman R. SEC12 encodes a guanine-nucleotide-exchange factor essential for transport vesicle budding from the ER. Nature. 1993;365:347-9 pubmed
    ..8). We propose that Sec12 catalyses Sar1 guanine-nucleotide exchange in a process that recruits Sar1 to a vesicle formation site on the ER membrane. ..
  43. Karbstein K, Jonas S, Doudna J. An essential GTPase promotes assembly of preribosomal RNA processing complexes. Mol Cell. 2005;20:633-43 pubmed
    ..Together, these data suggest that Bms1 functions as a GTP-regulated switch to deliver Rcl1 to preribosomes, providing molecular insight into preribosome assembly. ..
  44. Sadhu M, Guan Q, Li F, Sales Lee J, Iavarone A, Hammond M, et al. Nutritional control of epigenetic processes in yeast and human cells. Genetics. 2013;195:831-44 pubmed publisher
    ..Histone methylation was also found to respond to nutritional deficiency in the fission yeast Schizosaccharomyces pombe and in human cells in culture. ..
  45. Hoey T, Dynlacht B, Peterson M, Pugh B, Tjian R. Isolation and characterization of the Drosophila gene encoding the TATA box binding protein, TFIID. Cell. 1990;61:1179-86 pubmed
  46. Salama N, Chuang J, Schekman R. Sec31 encodes an essential component of the COPII coat required for transport vesicle budding from the endoplasmic reticulum. Mol Biol Cell. 1997;8:205-17 pubmed
    ..Sec31p is a phosphoprotein and treatment of the Sec31p-containing fraction with alkaline phosphatase results in a 50-75% inhibition of transport vesicle formation activity in an ER membrane budding assay. ..
  47. Matsuoka K, Orci L, Amherdt M, Bednarek S, Hamamoto S, Schekman R, et al. COPII-coated vesicle formation reconstituted with purified coat proteins and chemically defined liposomes. Cell. 1998;93:263-75 pubmed
    ..These observations suggest that the assembly of the COPII coat on the ER occurs by a sequential binding of coat proteins to specific lipids and that this assembly promotes the budding of COPII-coated vesicles...
  48. Courchesne W, Kunisawa R, Thorner J. A putative protein kinase overcomes pheromone-induced arrest of cell cycling in S. cerevisiae. Cell. 1989;58:1107-19 pubmed
    ..pombe) gene products. The recovery-promoting activity of the KSS1 gene requires a functional WHI1 gene, which encodes a yeast homolog to animal cyclins, suggesting that the KSS1 and WHI1 proteins act in the same growth control pathway. ..
  49. Lim M, Dailey D, Martin G, Thorner J. Yeast MCK1 protein kinase autophosphorylates at tyrosine and serine but phosphorylates exogenous substrates at serine and threonine. J Biol Chem. 1993;268:21155-64 pubmed
    ..These findings demonstrate that Mck1 is a member of a novel class of protein kinases that displays the ability to phosphorylate all three hydroxyamino acids in proteins. ..
  50. Zdraljevic S, Wagner D, Cheng K, Ruohonen L, Jantti J, Penttila M, et al. Single-cell measurements of enzyme levels as a predictive tool for cellular fates during organic acid production. Appl Environ Microbiol. 2013;79:7569-82 pubmed publisher
    ..Our results demonstrate a generalizable approach that takes advantage of the cell-to-cell variation of a clonal population to uncover causal relationships in the toxicity of engineered pathways. ..
  51. Fujita K, Kubo I. Antifungal activity of octyl gallate. Int J Food Microbiol. 2002;79:193-201 pubmed
  52. Neufeld T, Rubin G. The Drosophila peanut gene is required for cytokinesis and encodes a protein similar to yeast putative bud neck filament proteins. Cell. 1994;77:371-9 pubmed
    ..Our results suggest that this class of proteins is involved in aspects of cytokinesis that have been conserved between flies and yeast. ..
  53. Ayscough K, Stryker J, Pokala N, Sanders M, Crews P, Drubin D. High rates of actin filament turnover in budding yeast and roles for actin in establishment and maintenance of cell polarity revealed using the actin inhibitor latrunculin-A. J Cell Biol. 1997;137:399-416 pubmed
    ..Finally, transient actin depolymerization caused many cells to abandon one bud site or mating projection and to initiate growth at a second site. Thus, actin filaments are also required for maintenance of an axis of cell polarity. ..
  54. Valdivia R, Baggott D, Chuang J, Schekman R. The yeast clathrin adaptor protein complex 1 is required for the efficient retention of a subset of late Golgi membrane proteins. Dev Cell. 2002;2:283-94 pubmed
    ..Similarly, in AP-1 deficient cells, the resident TGN/early endosome syntaxin, Tlg1p, is missorted. We propose that clathrin and AP-1 act to recycle Chs3p and Tlg1p from the early endosome to the TGN. ..
  55. Truckses D, Bloomekatz J, Thorner J. The RA domain of Ste50 adaptor protein is required for delivery of Ste11 to the plasma membrane in the filamentous growth signaling pathway of the yeast Saccharomyces cerevisiae. Mol Cell Biol. 2006;26:912-28 pubmed
    ..Thus, Ste50 serves as an adaptor to tether Ste11 to the plasma membrane and can do so via association with Cdc42, thereby permitting the encounter of Ste11 with activated Ste20. ..
  56. Nakajima Y, Tyers R, Wong C, Yates J, Drubin D, Barnes G. Nbl1p: a Borealin/Dasra/CSC-1-like protein essential for Aurora/Ipl1 complex function and integrity in Saccharomyces cerevisiae. Mol Biol Cell. 2009;20:1772-84 pubmed publisher
    ..Our biological and computational analyses therefore establish that the fundamental design of the CPC is conserved from Fungi to Animalia. ..
  57. Achstetter T, Franzusoff A, Field C, Schekman R. SEC7 encodes an unusual, high molecular weight protein required for membrane traffic from the yeast Golgi apparatus. J Biol Chem. 1988;263:11711-7 pubmed
    ..This domain in Sec7p may serve a structural role to interact with lipids or proteins on the cytoplasmic surface of the Golgi apparatus. ..
  58. Whistler J, Rine J. Ras2 and Ras1 protein phosphorylation in Saccharomyces cerevisiae. J Biol Chem. 1997;272:18790-800 pubmed
    ..This site, when mutated to alanine, led to promiscuous phosphorylation of Ras2 protein on nearby serine residues. A decrease in phosphorylation may lead to a decrease in signaling through the Ras-cAMP pathway. ..
  59. Bardwell L, Cook J, Voora D, Baggott D, Martinez A, Thorner J. Repression of yeast Ste12 transcription factor by direct binding of unphosphorylated Kss1 MAPK and its regulation by the Ste7 MEK. Genes Dev. 1998;12:2887-98 pubmed
  60. Strahl T, Hama H, DeWald D, Thorner J. Yeast phosphatidylinositol 4-kinase, Pik1, has essential roles at the Golgi and in the nucleus. J Cell Biol. 2005;171:967-79 pubmed
    ..Catalytically inactive derivatives of these compartment-restricted Pik1 constructs indicated that PtdIns4P must be generated both in the nucleus and at the Golgi for normal cell function. ..
  61. Zill O, Rine J. Interspecies variation reveals a conserved repressor of alpha-specific genes in Saccharomyces yeasts. Genes Dev. 2008;22:1704-16 pubmed publisher
    ..cerevisiae. We suggest that a comprehensive understanding of some genetic pathways may be best attained through the expanded phenotypic space provided by study of those pathways in multiple related organisms. ..
  62. Gill G, Tjian R. A highly conserved domain of TFIID displays species specificity in vivo. Cell. 1991;65:333-40 pubmed
    ..Thus, the C-terminal conserved domain of TFIID, as well as the N-terminal divergent domain, appears to be involved in species-specific interactions. ..
  63. Strahl T, Huttner I, Lusin J, Osawa M, King D, Thorner J, et al. Structural insights into activation of phosphatidylinositol 4-kinase (Pik1) by yeast frequenin (Frq1). J Biol Chem. 2007;282:30949-59 pubmed
    ..Frq1 may activate Pik1 by facilitating membrane targeting via the exposed N-myristoyl group and by imposing a structural transition that promotes association of the lipid kinase unique motif with the kinase domain. ..
  64. Garrenton L, Stefan C, McMurray M, Emr S, Thorner J. Pheromone-induced anisotropy in yeast plasma membrane phosphatidylinositol-4,5-bisphosphate distribution is required for MAPK signaling. Proc Natl Acad Sci U S A. 2010;107:11805-10 pubmed publisher
  65. Kirby J, Nishimoto M, Park J, Withers S, Nowroozi F, Behrendt D, et al. Cloning of casbene and neocembrene synthases from Euphorbiaceae plants and expression in Saccharomyces cerevisiae. Phytochemistry. 2010;71:1466-73 pubmed publisher
    ..Casbene production levels of 31 mg/L were achieved in S. cerevisiae and we discuss strategies to further increase production by maximizing flux through the mevalonate pathway...
  66. Enquist Newman M, Faust A, Bravo D, Santos C, Raisner R, Hanel A, et al. Efficient ethanol production from brown macroalgae sugars by a synthetic yeast platform. Nature. 2014;505:239-43 pubmed publisher
    ..These results show that all major sugars in brown macroalgae can be used as feedstocks for biofuels and value-added renewable chemicals in a manner that is comparable to traditional arable-land-based feedstocks. ..
  67. Soupene E, He L, Yan D, Kustu S. Ammonia acquisition in enteric bacteria: physiological role of the ammonium/methylammonium transport B (AmtB) protein. Proc Natl Acad Sci U S A. 1998;95:7030-4 pubmed
  68. Roelants F, Torrance P, Bezman N, Thorner J. Pkh1 and Pkh2 differentially phosphorylate and activate Ypk1 and Ykr2 and define protein kinase modules required for maintenance of cell wall integrity. Mol Biol Cell. 2002;13:3005-28 pubmed
    ..Thus, Pkh1-Ypk1 and Pkh2-Ykr2 function in a novel pathway for cell wall integrity that acts in parallel with the Pkc1-dependent pathway. ..
  69. Zeitler B, Weis K. The FG-repeat asymmetry of the nuclear pore complex is dispensable for bulk nucleocytoplasmic transport in vivo. J Cell Biol. 2004;167:583-90 pubmed
    ..These findings suggest that the biased distribution of FG repeats is not required for major nucleocytoplasmic trafficking events across the NPC. ..
  70. Shiba Y, Paradise E, Kirby J, Ro D, Keasling J. Engineering of the pyruvate dehydrogenase bypass in Saccharomyces cerevisiae for high-level production of isoprenoids. Metab Eng. 2007;9:160-8 pubmed
    ..This work will be generally applicable to the production of a broad range of isoprenoids in yeast. ..
  71. Fox C, Ehrenhofer Murray A, Loo S, Rine J. The origin recognition complex, SIR1, and the S phase requirement for silencing. Science. 1997;276:1547-51 pubmed
    ..Thus, the role of ORC in silencing was separable from its role in initiation, and the role of S phase in silencing was independent of replication initiation at the silencers. ..
  72. Zill O, Scannell D, Teytelman L, Rine J. Co-evolution of transcriptional silencing proteins and the DNA elements specifying their assembly. PLoS Biol. 2010;8:e1000550 pubmed publisher
    ..The results presented here, and in particular the high resolution ChIP-Seq localization of the Sir4 protein, provided unanticipated insights into the mechanism of silent chromatin assembly in yeast...
  73. Denby C, Im J, Yu R, Pesce C, Brem R. Negative feedback confers mutational robustness in yeast transcription factor regulation. Proc Natl Acad Sci U S A. 2012;109:3874-8 pubmed publisher
    ..We suggest that regulatory feedback may be an important element of the network architectures that confer mutational robustness across biology. ..
  74. Ishibashi T, Dangkulwanich M, Coello Y, Lionberger T, Lubkowska L, Ponticelli A, et al. Transcription factors IIS and IIF enhance transcription efficiency by differentially modifying RNA polymerase pausing dynamics. Proc Natl Acad Sci U S A. 2014;111:3419-24 pubmed publisher
    ..Our findings help elucidate the molecular mechanisms by which transcription factors modulate gene expression...
  75. Worden E, Dong K, Martin A. An AAA Motor-Driven Mechanical Switch in Rpn11 Controls Deubiquitination at the 26S Proteasome. Mol Cell. 2017;67:799-811.e8 pubmed publisher
    ..The AAA+ motor-driven acceleration of Rpn11 is therefore important to ensure that poly-ubiquitin chains are removed only from committed substrates and fast enough to prevent their co-degradation. ..
  76. Fish R, Ammerman M, Davie J, Lu B, Pham C, Howe L, et al. Genetic interactions between TFIIF and TFIIS. Genetics. 2006;173:1871-84 pubmed
    ..Together, these results suggest a physiologically relevant functional connection between TFIIS and TFIIF. ..
  77. Westfall P, Thorner J. Analysis of mitogen-activated protein kinase signaling specificity in response to hyperosmotic stress: use of an analog-sensitive HOG1 allele. Eukaryot Cell. 2006;5:1215-28 pubmed
    ..Finally, our results demonstrate a role for active Hog1 in maintaining signaling specificity under conditions of persistently high external osmolarity. ..
  78. Nakajima Y, Cormier A, Tyers R, Pigula A, Peng Y, Drubin D, et al. Ipl1/Aurora-dependent phosphorylation of Sli15/INCENP regulates CPC-spindle interaction to ensure proper microtubule dynamics. J Cell Biol. 2011;194:137-53 pubmed publisher
  79. Vinh D, Drubin D. A yeast TCP-1-like protein is required for actin function in vivo. Proc Natl Acad Sci U S A. 1994;91:9116-20 pubmed
    ..Taken together, these findings demonstrate that TCP-1-like proteins are required for actin and tubulin function in vivo. ..
  80. Spang A, Schekman R. Reconstitution of retrograde transport from the Golgi to the ER in vitro. J Cell Biol. 1998;143:589-99 pubmed
    ..Putative retrograde carriers (COPI vesicles) generated from Golgi-enriched membranes contain v-SNAREs as well as Emp47p as cargo...
  81. Teytelman L, Ozaydin B, Zill O, Lefrançois P, Snyder M, Rine J, et al. Impact of chromatin structures on DNA processing for genomic analyses. PLoS ONE. 2009;4:e6700 pubmed publisher
    ..These results established the pervasiveness of this bias genome-wide, and suggested that this bias can be used to detect differences in chromatin structures across the genome. ..
  82. Green E, Jiang Y, Joyner R, Weis K. A negative feedback loop at the nuclear periphery regulates GAL gene expression. Mol Biol Cell. 2012;23:1367-75 pubmed publisher
  83. Geyer C, Colman Lerner A, Brent R. "Mutagenesis" by peptide aptamers identifies genetic network members and pathway connections. Proc Natl Acad Sci U S A. 1999;96:8567-72 pubmed
    ..Forward genetic analysis with peptide aptamer "mutagens" should be particularly useful in elucidating genetic networks in organisms and processes for which classical genetics is not feasible. ..
  84. Garrenton L, Braunwarth A, Irniger S, Hurt E, Kunzler M, Thorner J. Nucleus-specific and cell cycle-regulated degradation of mitogen-activated protein kinase scaffold protein Ste5 contributes to the control of signaling competence. Mol Cell Biol. 2009;29:582-601 pubmed publisher
  85. Rockwell N, Wolfger H, Kuchler K, Thorner J. ABC transporter Pdr10 regulates the membrane microenvironment of Pdr12 in Saccharomyces cerevisiae. J Membr Biol. 2009;229:27-52 pubmed publisher
    ..Pdr10 therefore acts as a negative regulator for incorporation of Pdr12 into detergent-resistant membranes, a novel role for members of the ABC transporter superfamily...
  86. Otero L, Ashe M, Sachs A. The yeast poly(A)-binding protein Pab1p stimulates in vitro poly(A)-dependent and cap-dependent translation by distinct mechanisms. EMBO J. 1999;18:3153-63 pubmed
    ..These data show that Pab1p has at least two biochemically distinct activities in translation extracts. ..
  87. Rubin G, Yandell M, Wortman J, Gabor Miklos G, Nelson C, Hariharan I, et al. Comparative genomics of the eukaryotes. Science. 2000;287:2204-15 pubmed
    ..The fly has orthologs to 177 of the 289 human disease genes examined and provides the foundation for rapid analysis of some of the basic processes involved in human disease. ..
  88. Pierstorff E, Kane C. Genetic interactions between an RNA polymerase II phosphatase and centromeric elements in Saccharomyces cerevisiae. Mol Genet Genomics. 2004;271:603-15 pubmed
    ..The mechanism of suppression and regulation of Fcp1-2 protein activity by centromeric DNA is discussed. ..
  89. Roelants F, Torrance P, Thorner J. Differential roles of PDK1- and PDK2-phosphorylation sites in the yeast AGC kinases Ypk1, Pkc1 and Sch9. Microbiology. 2004;150:3289-304 pubmed
  90. Beh C, Cool L, Phillips J, Rine J. Overlapping functions of the yeast oxysterol-binding protein homologues. Genetics. 2001;157:1117-40 pubmed
    ..Our findings indicated that OSH genes performed a multitude of nonessential roles defined by specific subsets of the genes and that most shared at least one essential role potentially linked to changes in sterol lipid levels. ..
  91. Wang H, Wang J, Ding F, Callahan K, Bratkowski M, Butler J, et al. Architecture of the yeast Rrp44 exosome complex suggests routes of RNA recruitment for 3' end processing. Proc Natl Acad Sci U S A. 2007;104:16844-9 pubmed
    ..The Rrp44-exosome (RE) architecture suggests an active site sequestration mechanism for strict control of 3' exoribonuclease activity in the RE complex. ..
  92. Goltsev Y, Papatsenko D. Time warping of evolutionary distant temporal gene expression data based on noise suppression. BMC Bioinformatics. 2009;10:353 pubmed publisher