Experts and Doctors on saccharomyces cerevisiae in Pittsburgh, Pennsylvania, United States

Summary

Locale: Pittsburgh, Pennsylvania, United States
Topic: saccharomyces cerevisiae

Top Publications

  1. Ripmaster T, Vaughn G, Woolford J. DRS1 to DRS7, novel genes required for ribosome assembly and function in Saccharomyces cerevisiae. Mol Cell Biol. 1993;13:7901-12 pubmed
    ..Identification of gene products affecting ribosome assembly and function among the DNAs complementing the drs mutations validates the feasibility of this approach. ..
  2. Hrizo S, Gusarova V, Habiel D, Goeckeler J, Fisher E, Brodsky J. The Hsp110 molecular chaperone stabilizes apolipoprotein B from endoplasmic reticulum-associated degradation (ERAD). J Biol Chem. 2007;282:32665-75 pubmed
    ..This study indicates that chaperones within distinct complexes can play unique roles during ER-associated degradation (ERAD), establishes a role for Sse1/Hsp110 in ERAD, and identifies Hsp110 as a target to lower cholesterol. ..
  3. Zaks Makhina E, Li H, Grishin A, Salvador Recatala V, Levitan E. Specific and slow inhibition of the kir2.1 K+ channel by gambogic acid. J Biol Chem. 2009;284:15432-8 pubmed publisher
    ..1 and Kv2.1 from the Triton X-100-insoluble to the Triton X-100-soluble membrane fraction. Thus, GA changes the K+ channel membrane microenvironment resulting in potent, specific, and slow acting inhibition of Kir2.1 channels. ..
  4. Crisucci E, Arndt K. The Paf1 complex represses ARG1 transcription in Saccharomyces cerevisiae by promoting histone modifications. Eukaryot Cell. 2011;10:712-23 pubmed publisher
  5. Moehle C, Tizard R, Lemmon S, Smart J, Jones E. Protease B of the lysosomelike vacuole of the yeast Saccharomyces cerevisiae is homologous to the subtilisin family of serine proteases. Mol Cell Biol. 1987;7:4390-9 pubmed
  6. Patton Vogt J, Henry S. GIT1, a gene encoding a novel transporter for glycerophosphoinositol in Saccharomyces cerevisiae. Genetics. 1998;149:1707-15 pubmed
    ..Transport assays performed on a git1 mutant together with the above evidence indicate that the GIT1 gene encodes a permease involved in the uptake of GroPIns. ..
  7. Nakatsukasa K, Huyer G, Michaelis S, Brodsky J. Dissecting the ER-associated degradation of a misfolded polytopic membrane protein. Cell. 2008;132:101-12 pubmed publisher
    ..These data indicate that polytopic membrane proteins can be extracted from the ER, and define the point of action of chaperones and the requirement for Ufd2p during membrane protein quality control...
  8. Talkish J, Campbell I, Sahasranaman A, Jakovljevic J, Woolford J. Ribosome assembly factors Pwp1 and Nop12 are important for folding of 5.8S rRNA during ribosome biogenesis in Saccharomyces cerevisiae. Mol Cell Biol. 2014;34:1863-77 pubmed publisher
    ..8S rRNA. In the absence of Nop12 and Pwp1, rRNA helix 5 is not stably formed. Interestingly, the absence of Nop12 results in the formation of an alternative yet unproductive helix 5 when cells are grown at low temperatures. ..
  9. Ambroziak J, Henry S. INO2 and INO4 gene products, positive regulators of phospholipid biosynthesis in Saccharomyces cerevisiae, form a complex that binds to the INO1 promoter. J Biol Chem. 1994;269:15344-9 pubmed
    ..Immunoprecipitation experiments demonstrate that Ino2p and Ino4p interact in the absence of DNA. Ino2p and Ino4p are, thus, both necessary and sufficient for formation of a complex with the INO1 promoter. ..

More Information

Publications135 found, 100 shown here

  1. Paulovich A, Thompson J, Larkin J, Li Z, Woolford J. Molecular genetics of cryptopleurine resistance in Saccharomyces cerevisiae: expression of a ribosomal protein gene family. Genetics. 1993;135:719-30 pubmed
    ..Because CRY2 (and cry2) is expressed at lower levels than CRY1 (and cry1), the CryR phenotype of cry2 mutants is only expressed in strains containing a cry1-delta null allele. ..
  2. Talkish J, Zhang J, Jakovljevic J, Horsey E, Woolford J. Hierarchical recruitment into nascent ribosomes of assembly factors required for 27SB pre-rRNA processing in Saccharomyces cerevisiae. Nucleic Acids Res. 2012;40:8646-61 pubmed
    ..Inhibition of TOR kinase decreases association of Rpf2, Spb4, Nog1 and Nog2 with pre-ribosomes. ..
  3. Guerriero C, Weiberth K, Brodsky J. Hsp70 targets a cytoplasmic quality control substrate to the San1p ubiquitin ligase. J Biol Chem. 2013;288:18506-20 pubmed publisher
    ..These results emphasize the diverse action of molecular chaperones during CytoQC. ..
  4. Chen Y, Stabryla L, Wei N. Improved Acetic Acid Resistance in Saccharomyces cerevisiae by Overexpression of the WHI2 Gene Identified through Inverse Metabolic Engineering. Appl Environ Microbiol. 2016;82:2156-2166 pubmed publisher
    ..These results improve our understanding of the yeast response to acetic acid stress and provide a new strategy to breed acetic acid-resistant yeast strains for renewable biofuel production. ..
  5. Bailis A, Lopes J, Kohlwein S, Henry S. Cis and trans regulatory elements required for regulation of the CHO1 gene of Saccharomyces cerevisiae. Nucleic Acids Res. 1992;20:1411-8 pubmed
  6. Roy J, Kim K, Maddock J, Anthony J, Woolford J. The final stages of spliceosome maturation require Spp2p that can interact with the DEAH box protein Prp2p and promote step 1 of splicing. RNA. 1995;1:375-90 pubmed
    ..These results suggest that Spp2p interacts with Prp2p in the spliceosome prior to the first cleavage-ligation reaction. Spp2p is the first protein that has been found to interact with a DEAD/H box splicing factor. ..
  7. Naik R, Jones E. The PBN1 gene of Saccharomyces cerevisiae: an essential gene that is required for the post-translational processing of the protease B precursor. Genetics. 1998;149:1277-92 pubmed
    ..Based on these results, we propose that one of the functions of Pbn1p is to aid in the autocatalytic processing of Prb1p. ..
  8. Sheldon K, Mauger D, Arndt K. A Requirement for the Saccharomyces cerevisiae Paf1 complex in snoRNA 3' end formation. Mol Cell. 2005;20:225-36 pubmed
    ..Our results reveal a posttranscriptional function for the Paf1 complex, which appears unrelated to its role in histone methylation. ..
  9. Elbing K, Rubenstein E, McCartney R, Schmidt M. Subunits of the Snf1 kinase heterotrimer show interdependence for association and activity. J Biol Chem. 2006;281:26170-80 pubmed
  10. Preston R, Manolson M, Becherer K, Weidenhammer E, Kirkpatrick D, Wright R, et al. Isolation and characterization of PEP3, a gene required for vacuolar biogenesis in Saccharomyces cerevisiae. Mol Cell Biol. 1991;11:5801-12 pubmed
    ..Sequence identity established that PEP3 and VPS18 (J. S. Robinson, T. R. Graham, and S. D. Emr, Mol. Cell. Biol. 11:5813-5824, 1991) are the same gene. ..
  11. Rotenberg M, Moritz M, Woolford J. Depletion of Saccharomyces cerevisiae ribosomal protein L16 causes a decrease in 60S ribosomal subunits and formation of half-mer polyribosomes. Genes Dev. 1988;2:160-72 pubmed
    ..43S preinitiation complexes accumulate in half-mer polyribosomes in the absence of sufficient 60S subunits. We postulate that the slow-growth phenotype of rpl16 mutants results from the perturbation of initiation of protein synthesis. ..
  12. Deng C, Saunders W. RIM4 encodes a meiotic activator required for early events of meiosis in Saccharomyces cerevisiae. Mol Genet Genomics. 2001;266:497-504 pubmed
    ..These results suggest that RIM4 is epistatic to IME2, and is required for multiple steps during sporulation. In agreement with this interpretation, overexpression of RIM4 induces low levels of sporulation in rich medium. ..
  13. Wang H, Jiang Y. The Tap42-protein phosphatase type 2A catalytic subunit complex is required for cell cycle-dependent distribution of actin in yeast. Mol Cell Biol. 2003;23:3116-25 pubmed
    ..In addition, we provide evidence that PP2A activity plays a negative role in controlling the actin cytoskeleton and, possibly, in regulation of the G(2)/M transition of the cell cycle. ..
  14. Zhang Y, McCartney R, Chandrashekarappa D, Mangat S, Schmidt M. Reg1 protein regulates phosphorylation of all three Snf1 isoforms but preferentially associates with the Gal83 isoform. Eukaryot Cell. 2011;10:1628-36 pubmed publisher
    ..Taken together, these data indicate that the ability of Reg1 to promote the dephosphorylation of Snf1 is not directly related to the strength of its association with the Snf1 complex. ..
  15. Senutovitch N, Stanfield R, Bhattacharyya S, Rule G, Wilson I, Armitage B, et al. A variable light domain fluorogen activating protein homodimerizes to activate dimethylindole red. Biochemistry. 2012;51:2471-85 pubmed publisher
  16. Moritz M, Paulovich A, Tsay Y, Woolford J. Depletion of yeast ribosomal proteins L16 or rp59 disrupts ribosome assembly. J Cell Biol. 1990;111:2261-74 pubmed
    ..The implications of these findings for control of ribosome assembly and the order of assembly of ribosomal proteins into the ribosome are discussed. ..
  17. Patton Vogt J, Griac P, Sreenivas A, Bruno V, Dowd S, Swede M, et al. Role of the yeast phosphatidylinositol/phosphatidylcholine transfer protein (Sec14p) in phosphatidylcholine turnover and INO1 regulation. J Biol Chem. 1997;272:20873-83 pubmed
  18. Almaguer C, Fisher E, Patton Vogt J. Posttranscriptional regulation of Git1p, the glycerophosphoinositol/glycerophosphocholine transporter of Saccharomyces cerevisiae. Curr Genet. 2006;50:367-75 pubmed
    ..In addition, the results indicate that the Git1p substrates (and alternate phosphate sources) GroPIns and GroPCho behave distinctly from P(i) in their ability to affect GIT1 expression. ..
  19. Hainer S, Pruneski J, Mitchell R, Monteverde R, Martens J. Intergenic transcription causes repression by directing nucleosome assembly. Genes Dev. 2011;25:29-40 pubmed publisher
    ..Our results raise the possibility that transcription of ncDNA may contribute to nucleosome positioning on a genome-wide scale where, in some cases, it negatively impacts protein-DNA interactions. ..
  20. Amrich C, Davis C, Rogal W, Shirra M, Heroux A, Gardner R, et al. Cdc73 subunit of Paf1 complex contains C-terminal Ras-like domain that promotes association of Paf1 complex with chromatin. J Biol Chem. 2012;287:10863-75 pubmed publisher
    ..We conclude that the Cdc73 C-domain probably constitutes a protein interaction surface that functions with Rtf1 in coupling the Paf1 complex to the RNA polymerase II elongation machinery. ..
  21. Preston G, Brodsky J. The evolving role of ubiquitin modification in endoplasmic reticulum-associated degradation. Biochem J. 2017;474:445-469 pubmed publisher
    ..Here, we summarize these data and provide an overview of questions driving this field of research. ..
  22. Liu Q, Gabriel S, Roinick K, Ward R, Arndt K. Analysis of TFIIA function In vivo: evidence for a role in TATA-binding protein recruitment and gene-specific activation. Mol Cell Biol. 1999;19:8673-85 pubmed
  23. Guerrero Santoro J, Yang L, Stallcup M, DeFranco D. Distinct LIM domains of Hic-5/ARA55 are required for nuclear matrix targeting and glucocorticoid receptor binding and coactivation. J Cell Biochem. 2004;92:810-9 pubmed
    ..Thus, as suggested from previous analysis of LIM domain-containing proteins, separate but highly related LIM domains serve distinct functions...
  24. Pruneski J, Hainer S, Petrov K, Martens J. The Paf1 complex represses SER3 transcription in Saccharomyces cerevisiae by facilitating intergenic transcription-dependent nucleosome occupancy of the SER3 promoter. Eukaryot Cell. 2011;10:1283-94 pubmed publisher
    ..Taken together, our results suggest that Paf1 and Ctr9 repress SER3 by maintaining SRG1 transcription-dependent nucleosome occupancy. ..
  25. O Donnell B, Mackie T, Subramanya A, Brodsky J. Endoplasmic reticulum-associated degradation of the renal potassium channel, ROMK, leads to type II Bartter syndrome. J Biol Chem. 2017;292:12813-12827 pubmed publisher
  26. Diao J. Crystal structure of a super leucine zipper, an extended two-stranded super long coiled coil. Protein Sci. 2010;19:319-26 pubmed publisher
    ..Analysis of the formation mechanism of the super long coiled coil may help understand and design self-assembling protein fibers. ..
  27. Yan G, Lai Y, Jiang Y. TOR under stress: targeting TORC1 by Rho1 GTPase. Cell Cycle. 2012;11:3384-8 pubmed publisher
    ..This novel crosstalk extends the signaling network of Rho1 into many TORC1-dependent processes and sheds light on how yeast cells coordinate polarized spatial expansion with mass increase. ..
  28. Sun C, Woolford J. The yeast NOP4 gene product is an essential nucleolar protein required for pre-rRNA processing and accumulation of 60S ribosomal subunits. EMBO J. 1994;13:3127-35 pubmed
    ..Nop4 protein depletion results in diminished accumulation of 60S ribosomal subunits, assignable to a defect in ribosome biogenesis arising from a lack of production of mature 25S rRNA from 27S precursor rRNA. ..
  29. Schmidt M, McCartney R, Zhang X, Tillman T, Solimeo H, Wolfl S, et al. Std1 and Mth1 proteins interact with the glucose sensors to control glucose-regulated gene expression in Saccharomyces cerevisiae. Mol Cell Biol. 1999;19:4561-71 pubmed
    ..Finally, studies with green fluorescent protein fusions indicate that Std1 is localized to the cell periphery and the cell nucleus, supporting the idea that it may transduce signals from the plasma membrane to the nucleus. ..
  30. Coury L, Hiller M, Mathai J, Jones E, Zeidel M, Brodsky J. Water transport across yeast vacuolar and plasma membrane-targeted secretory vesicles occurs by passive diffusion. J Bacteriol. 1999;181:4437-40 pubmed
    ..However, spheroplasts prepared from the strain overexpressing Fps1p showed enhanced glycerol uptake, suggesting that Fps1p becomes active only upon insertion in the plasma membrane. ..
  31. Buck T, Kolb A, Boyd C, Kleyman T, Brodsky J. The endoplasmic reticulum-associated degradation of the epithelial sodium channel requires a unique complement of molecular chaperones. Mol Biol Cell. 2010;21:1047-58 pubmed publisher
    ..Our data indicate that Hsp40s can act independently of Hsp70 to select substrates for ERAD. ..
  32. Tran J, Tomsic L, Brodsky J. A Cdc48p-associated factor modulates endoplasmic reticulum-associated degradation, cell stress, and ubiquitinated protein homeostasis. J Biol Chem. 2011;286:5744-55 pubmed publisher
    ..These data suggest that Ydr049p acts in parallel with Cdc48p partners to modulate ERAD and other cellular activities. ..
  33. Gamalinda M, Ohmayer U, Jakovljevic J, Kumcuoglu B, Woolford J, Mbom B, et al. A hierarchical model for assembly of eukaryotic 60S ribosomal subunit domains. Genes Dev. 2014;28:198-210 pubmed publisher
    ..Our results reveal striking differences and similarities between assembly of bacterial and eukaryotic large ribosomal subunits, providing insights into how these RNA-protein particles evolved. ..
  34. Fewell S, Woolford J. Ribosomal protein S14 of Saccharomyces cerevisiae regulates its expression by binding to RPS14B pre-mRNA and to 18S rRNA. Mol Cell Biol. 1999;19:826-34 pubmed
  35. Ahner A, Nakatsukasa K, Zhang H, Frizzell R, Brodsky J. Small heat-shock proteins select deltaF508-CFTR for endoplasmic reticulum-associated degradation. Mol Biol Cell. 2007;18:806-14 pubmed
  36. Qi Y, Klein Seetharaman J, Bar Joseph Z. A mixture of feature experts approach for protein-protein interaction prediction. BMC Bioinformatics. 2007;8 Suppl 10:S6 pubmed publisher
    ..Our method improved upon the best previous methods for this task. In addition, the weighting of the experts provides means to evaluate the prediction based on the high scoring features. ..
  37. Curtis R, Kim S, Woolford J, Xu W, Xing E. Structured association analysis leads to insight into Saccharomyces cerevisiae gene regulation by finding multiple contributing eQTL hotspots associated with functional gene modules. BMC Genomics. 2013;14:196 pubmed publisher
  38. Brodsky J, Werner E, Dubas M, Goeckeler J, Kruse K, McCracken A. The requirement for molecular chaperones during endoplasmic reticulum-associated protein degradation demonstrates that protein export and import are mechanistically distinct. J Biol Chem. 1999;274:3453-60 pubmed
    ..We found that pro-alpha factor and A1PiZ were degraded normally, indicating further that import and export are distinct and that other cytosolic factors may pull polypeptides from the ER. ..
  39. Wang H, Wang X, Jiang Y. Interaction with Tap42 is required for the essential function of Sit4 and type 2A phosphatases. Mol Biol Cell. 2003;14:4342-51 pubmed
    ..In addition, we showed that Tap42 is able to interact with two other 2A-like phosphatases, Pph3 and Ppg1. ..
  40. Delfino F, Shaffer J, Smithgall T. The KRAB-associated co-repressor KAP-1 is a coiled-coil binding partner, substrate and activator of the c-Fes protein tyrosine kinase. Biochem J. 2006;399:141-50 pubmed
    ..Association of endogenous Fes and KAP-1 was also observed in HL-60 myeloid leukaemia cells. Together, these data identify a novel Fes-KAP-1 interaction, and suggest a dual role for KAP-1 as both a Fes activator and downstream effector. ..
  41. Grishin A, Li H, Levitan E, Zaks Makhina E. Identification of gamma-aminobutyric acid receptor-interacting factor 1 (TRAK2) as a trafficking factor for the K+ channel Kir2.1. J Biol Chem. 2006;281:30104-11 pubmed
    ..Yeast two-hybrid assays showed that an N-terminal region of GRIF-1 interacts with a C-terminal region of Kir2.1. These results indicate that GRIF-1 binds to Kir2.1 and facilitates trafficking of this channel to the cell surface. ..
  42. Needham P, Mikoluk K, Dhakarwal P, Khadem S, Snyder A, Subramanya A, et al. The thiazide-sensitive NaCl cotransporter is targeted for chaperone-dependent endoplasmic reticulum-associated degradation. J Biol Chem. 2011;286:43611-21 pubmed publisher
    ..Together, these results provide the first survey of components involved in the ERAD of a mammalian SLC12 cation chloride cotransporter and provide a framework for future studies on NCC ER quality control. ..
  43. Ripmaster T, Vaughn G, Woolford J. A putative ATP-dependent RNA helicase involved in Saccharomyces cerevisiae ribosome assembly. Proc Natl Acad Sci U S A. 1992;89:11131-5 pubmed
    ..These results suggest that, as in pre-mRNA splicing, RNA helicase activities are involved in ribosomal RNA processing. ..
  44. Braun M, Costa P, Crisucci E, Arndt K. Identification of Rkr1, a nuclear RING domain protein with functional connections to chromatin modification in Saccharomyces cerevisiae. Mol Cell Biol. 2007;27:2800-11 pubmed
    ..Taken together, our results identify a new participant in a protein ubiquitylation pathway within the nucleus that acts to modulate chromatin function and transcription. ..
  45. Trible R, Emert Sedlak L, Wales T, Ayyavoo V, Engen J, Smithgall T. Allosteric loss-of-function mutations in HIV-1 Nef from a long-term non-progressor. J Mol Biol. 2007;374:121-9 pubmed
    ..These findings show that residues at a distance from the SH3 domain binding site influence Nef interactions allosterically with a key effector protein linked to AIDS progression. ..
  46. Rubenstein E, McCartney R, Zhang C, Shokat K, Shirra M, Arndt K, et al. Access denied: Snf1 activation loop phosphorylation is controlled by availability of the phosphorylated threonine 210 to the PP1 phosphatase. J Biol Chem. 2008;283:222-30 pubmed
    ..Glucose-mediated regulation of Snf1 activation loop dephosphorylation is controlled by changes in the ability of the Snf1 activation loop to act as a substrate for Glc7. ..
  47. Ganster R, McCartney R, Schmidt M. Identification of a calcineurin-independent pathway required for sodium ion stress response in Saccharomyces cerevisiae. Genetics. 1998;150:31-42 pubmed
    ..Taken together, our data demonstrate that response to ion stress requires the participation of both calcineurin-dependent and -independent pathways. ..
  48. Ouyang Q, Ruiz Noriega M, Henry S. The REG1 gene product is required for repression of INO1 and other inositol-sensitive upstream activating sequence-containing genes of yeast. Genetics. 1999;152:89-100 pubmed
    ..A deletion mutation in the OPI1 negative regulator was incapable of suppressing ino4-8. The relative roles of the OPI1 and REG1 gene products in control of INO1 expression are discussed. ..
  49. Almaguer C, Mantella D, Perez E, Patton Vogt J. Inositol and phosphate regulate GIT1 transcription and glycerophosphoinositol incorporation in Saccharomyces cerevisiae. Eukaryot Cell. 2003;2:729-36 pubmed
  50. Subramanian S, Woolford C, Drill E, Lu M, Jones E. Pbn1p: an essential endoplasmic reticulum membrane protein required for protein processing in the endoplasmic reticulum of budding yeast. Proc Natl Acad Sci U S A. 2006;103:939-44 pubmed
    ..These results suggest that Pbn1p is required for proper folding and/or the stability of a subset of proteins in the ER. Thus, Pbn1p is an essential chaperone-like protein in the ER of yeast. ..
  51. Mayekar M, Gardner R, Arndt K. The recruitment of the Saccharomyces cerevisiae Paf1 complex to active genes requires a domain of Rtf1 that directly interacts with the Spt4-Spt5 complex. Mol Cell Biol. 2013;33:3259-73 pubmed publisher
    ..Collectively, our results provide molecular insight into a key attachment point between Paf1C and the RNA polymerase II elongation machinery...
  52. Preston R, Reinagel P, Jones E. Genes required for vacuolar acidity in Saccharomyces cerevisiae. Genetics. 1992;131:551-8 pubmed
    ..Strains that contained representative mutant alleles of the 17 previously described PEP genes were assayed for vacuolar pH; mutations in seven of the PEP genes (including PEP3, PEP5, PEP6 and PEP7) caused loss of vacuolar acidity. ..
  53. Becherer K, Rieder S, Emr S, Jones E. Novel syntaxin homologue, Pep12p, required for the sorting of lumenal hydrolases to the lysosome-like vacuole in yeast. Mol Biol Cell. 1996;7:579-94 pubmed
    ..These observations suggest that Pep12p may mediate the docking of Golgi-derived transport vesicles at the endosome. ..
  54. Zeng X, Kahana J, Silver P, Morphew M, McIntosh J, Fitch I, et al. Slk19p is a centromere protein that functions to stabilize mitotic spindles. J Cell Biol. 1999;146:415-25 pubmed
    ..Thus, these proteins seem to play overlapping roles in stabilizing spindle structure while acting from opposite ends of the microtubules. ..
  55. Trible R, Emert Sedlak L, Smithgall T. HIV-1 Nef selectively activates Src family kinases Hck, Lyn, and c-Src through direct SH3 domain interaction. J Biol Chem. 2006;281:27029-38 pubmed
    ..These data show that Nef selectively activates Hck, Lyn, and c-Src among SFKs, identifying these kinases as proximal effectors of Nef signaling and potential targets for anti-HIV drug discovery. ..
  56. Crisucci E, Arndt K. Paf1 restricts Gcn4 occupancy and antisense transcription at the ARG1 promoter. Mol Cell Biol. 2012;32:1150-63 pubmed publisher
    ..This promoter-associated antisense transcription positively correlates with ARG1 sense transcription. Finally, our results indicate that Paf1 represses other genes through mechanisms similar to those used at the ARG1 gene. ..
  57. Wong E, Cao W, Vörös J, Merchant M, Modis Y, Hackney D, et al. P(I) Release Limits the Intrinsic and RNA-Stimulated ATPase Cycles of DEAD-Box Protein 5 (Dbp5). J Mol Biol. 2016;428:492-508 pubmed publisher
  58. Fisher E, Almaguer C, Holic R, Griac P, Patton Vogt J. Glycerophosphocholine-dependent growth requires Gde1p (YPL110c) and Git1p in Saccharomyces cerevisiae. J Biol Chem. 2005;280:36110-7 pubmed
    ..In contrast to glycerophosphocholine, glycerophosphoinositol metabolism is unaffected by deletion of YPL110c. The open reading frame YPL110c has been termed GDE1. ..
  59. Piro A, Mayekar M, Warner M, Davis C, Arndt K. Small region of Rtf1 protein can substitute for complete Paf1 complex in facilitating global histone H2B ubiquitylation in yeast. Proc Natl Acad Sci U S A. 2012;109:10837-42 pubmed publisher
    ..Finally, the Rtf1 HMDs from other species can function in yeast. Our findings suggest a direct and conserved role for Paf1C in coupling histone modifications to transcription elongation. ..
  60. Gelling C, Dawes I, Perlmutter D, Fisher E, Brodsky J. The endosomal protein-sorting receptor sortilin has a role in trafficking ?-1 antitrypsin. Genetics. 2012;192:889-903 pubmed publisher
    ..This study represents the first genome-wide screen for factors that modulate ATZ secretion and has led to the identification of a gene that may modify disease severity or presentation in individuals with ATZ-associated liver disease. ..
  61. Kinzy T, Ripmaster T, Woolford J. Multiple genes encode the translation elongation factor EF-1 gamma in Saccharomyces cerevisiae. Nucleic Acids Res. 1994;22:2703-7 pubmed
    ..Low-stringency genomic Southern hybridization analysis indicates there may be additional yeast genes related to TEF3 and TEF4. ..
  62. Langlands K, Yin X, Anand G, Prochownik E. Differential interactions of Id proteins with basic-helix-loop-helix transcription factors. J Biol Chem. 1997;272:19785-93 pubmed
    ..The Id proteins thus display a signature range of interactions with all of their potential dimerization partners and may play a role in myogenesis which is distinct from that in hematopoiesis. ..
  63. Delfino F, Stevenson H, Smithgall T. A growth-suppressive function for the c-fes protein-tyrosine kinase in colorectal cancer. J Biol Chem. 2006;281:8829-35 pubmed
    ..Together, our findings strongly implicate the c-Fes protein-tyrosine kinase as a tumor suppressor rather than a dominant oncogene in colorectal cancer. ..
  64. Yan G, Lai Y, Jiang Y. The TOR complex 1 is a direct target of Rho1 GTPase. Mol Cell. 2012;45:743-53 pubmed publisher
    ..Our findings demonstrate that TORC1 acts both upstream and downstream of Rho1 GTPase, unveiling a mechanism that integrates stress and nutrient signals to coordinate Rho1-mediated spatial expansion and TORC1-dependent mass increase. ..
  65. Maddock J, Weidenhammer E, Adams C, Lunz R, Woolford J. Extragenic suppressors of Saccharomyces cerevisiae prp4 mutations identify a negative regulator of PRP genes. Genetics. 1994;136:833-47 pubmed
    ..SPP41 was cloned and sequenced and found to be essential. spp43 is allelic to the previously identified suppressor srn1, which encodes a negative regulator of gene expression. ..
  66. Sun C, Woolford J. The yeast nucleolar protein Nop4p contains four RNA recognition motifs necessary for ribosome biogenesis. J Biol Chem. 1997;272:25345-52 pubmed
    ..Deletion of both acidic motifs is lethal but replacement of most of the acidic residues with alanine has no apparent phenotype. These acidic residues may serve as spacers or tethers to separate the RRMs. ..
  67. McCartney R, Schmidt M. Regulation of Snf1 kinase. Activation requires phosphorylation of threonine 210 by an upstream kinase as well as a distinct step mediated by the Snf4 subunit. J Biol Chem. 2001;276:36460-6 pubmed
    ..Our data indicate that activation of the Snf1 kinase complex involves two steps, one that requires a distinct upstream kinase and one that is mediated by the gamma subunit of the kinase itself. ..
  68. Harnpicharnchai P, Jakovljevic J, Horsey E, Miles T, Roman J, Rout M, et al. Composition and functional characterization of yeast 66S ribosome assembly intermediates. Mol Cell. 2001;8:505-15 pubmed
    ..These results demonstrate that proteomic approaches in concert with genetic tools provide powerful means to purify and characterize ribosome assembly intermediates. ..
  69. Elbing K, McCartney R, Schmidt M. Purification and characterization of the three Snf1-activating kinases of Saccharomyces cerevisiae. Biochem J. 2006;393:797-805 pubmed
    ..Finally, we showed that the Snf1 kinase domain isolated from bacteria as a GST fusion protein can be activated in vitro and shows substrate specificity in the absence of its beta and gamma subunits. ..
  70. Rubenstein E, McCartney R, Schmidt M. Regulatory domains of Snf1-activating kinases determine pathway specificity. Eukaryot Cell. 2006;5:620-7 pubmed
  71. Bochman M, Schwacha A. Differences in the single-stranded DNA binding activities of MCM2-7 and MCM467: MCM2 and MCM5 define a slow ATP-dependent step. J Biol Chem. 2007;282:33795-804 pubmed
    ..We propose that the DNA binding differences between MCM2-7 and MCM467 correspond to a conformational change at the MCM2/5 active site with putative regulatory significance. ..
  72. Subramanian S, Woolford C, Desai J, Lanni F, Mitchell A. cis- and trans-acting localization determinants of pH response regulator Rim13 in Saccharomyces cerevisiae. Eukaryot Cell. 2012;11:1201-9 pubmed publisher
    ..The ancestor lost the coding region for its MIT domain through a 5' rearrangement and acquired the coding region for the Saccharomyces-specific functional equivalent through a 3' rearrangement. ..
  73. Last R, Maddock J, Woolford J. Evidence for related functions of the RNA genes of Saccharomyces cerevisiae. Genetics. 1987;117:619-31 pubmed
    ..These results suggest that the SRN2 and RNA2 gene products have related functions, as do the RNA3 and RNA4 gene products. ..
  74. Webb G, Hoedt M, Poole L, Jones E. Genetic interactions between a pep7 mutation and the PEP12 and VPS45 genes: evidence for a novel SNARE component in transport between the Saccharomyces cerevisiae Golgi complex and endosome. Genetics. 1997;147:467-78 pubmed
  75. Koldamova R, Lefterov I, Gadjeva V, Lazo J. Essential binding and functional domains of human bleomycin hydrolase. Biochemistry. 1998;37:2282-90 pubmed
    ..Thus, the C-terminus of hBH has two independent roles controlling both the catalytic activity and oligomerization of hBH. ..
  76. Mu Z, Yin X, Prochownik E. Pag, a putative tumor suppressor, interacts with the Myc Box II domain of c-Myc and selectively alters its biological function and target gene expression. J Biol Chem. 2002;277:43175-84 pubmed
    ..These features, along with the previously identified interaction with c-Abl, provide support for the idea that Pag functions as a tumor suppressor. ..
  77. Miles T, Jakovljevic J, Horsey E, Harnpicharnchai P, Tang L, Woolford J. Ytm1, Nop7, and Erb1 form a complex necessary for maturation of yeast 66S preribosomes. Mol Cell Biol. 2005;25:10419-32 pubmed
    ..Mutations in the WD40 motifs of Ytm1 disrupt binding to Erb1, destabilize the heterotrimer, and delay pre-rRNA processing and nuclear export of preribosomes. Nevertheless, 66S preribosomes lacking Ytm1 remain otherwise intact. ..
  78. Wright C, Fewell S, Sullivan M, Pipas J, Watkins S, Brodsky J. The Hsp40 molecular chaperone Ydj1p, along with the protein kinase C pathway, affects cell-wall integrity in the yeast Saccharomyces cerevisiae. Genetics. 2007;175:1649-64 pubmed
    ..Together, these data provide the first direct link between cytoplasmic chaperone function and cell-wall integrity and suggest that chaperones orchestrate the complex biogenesis of this structure. ..
  79. Guo S, Shen X, Yan G, Ma D, Bai X, Li S, et al. A MAP kinase dependent feedback mechanism controls Rho1 GTPase and actin distribution in yeast. PLoS ONE. 2009;4:e6089 pubmed publisher
    ..It is also required for terminating Rho1 activity toward the Pkc1-MAPK pathway and for repolarizing actin cytoskeleton and restoring growth after the stressed cells become adapted. ..
  80. Godin S, Wier A, Kabbinavar F, Bratton Palmer D, Ghodke H, Van Houten B, et al. The Shu complex interacts with Rad51 through the Rad51 paralogues Rad55-Rad57 to mediate error-free recombination. Nucleic Acids Res. 2013;41:4525-34 pubmed publisher
    ..Our data suggest a model in which Csm2-Psy3 recruit the Shu complex to HR substrates, where it interacts with Rad51 through Rad55-Rad57 to stimulate Rad51 filament assembly and stability, promoting error-free repair. ..
  81. Nath N, McCartney R, Schmidt M. Purification and characterization of Snf1 kinase complexes containing a defined Beta subunit composition. J Biol Chem. 2002;277:50403-8 pubmed
    ..Our studies indicate that the reduced activity of Snf1-Snf4-Sip1 kinase is due to low level of Sip1 accumulation rather than a limited ability of the Sip1 form of the enzyme to direct phosphorylation of specific substrates. ..
  82. Sumrada R, Cooper T. Isolation of the CAR1 gene from Saccharomyces cerevisiae and analysis of its expression. Mol Cell Biol. 1982;2:1514-23 pubmed
    ..Therefore, they remain consistent with our earlier suggestion that arginase production is probably controlled at the level of gene expression. ..
  83. Subramanian S, Woolford C, Jones E. The Sec1/Munc18 protein, Vps33p, functions at the endosome and the vacuole of Saccharomyces cerevisiae. Mol Biol Cell. 2004;15:2593-605 pubmed
    ..This is the first report demonstrating the involvement of a single syntaxin with two SM proteins at the same organelle. ..
  84. Goeckeler J, Brodsky J. Molecular chaperones and substrate ubiquitination control the efficiency of endoplasmic reticulum-associated degradation. Diabetes Obes Metab. 2010;12 Suppl 2:32-8 pubmed publisher
    ..We will also indicate links between ERAD and disease and emphasize future research avenues. ..
  85. Tomson B, Davis C, Warner M, Arndt K. Identification of a role for histone H2B ubiquitylation in noncoding RNA 3'-end formation through mutational analysis of Rtf1 in Saccharomyces cerevisiae. Genetics. 2011;188:273-89 pubmed publisher
  86. Kinzy T, Woolford J. Increased expression of Saccharomyces cerevisiae translation elongation factor 1 alpha bypasses the lethality of a TEF5 null allele encoding elongation factor 1 beta. Genetics. 1995;141:481-9 pubmed
    ..These phenotypes indicate that translation and cell growth are highly sensitive to changes in EF-1alpha and EF-1beta activity. ..
  87. Shirra M, Patton Vogt J, Ulrich A, Liuta Tehlivets O, Kohlwein S, Henry S, et al. Inhibition of acetyl coenzyme A carboxylase activity restores expression of the INO1 gene in a snf1 mutant strain of Saccharomyces cerevisiae. Mol Cell Biol. 2001;21:5710-22 pubmed
  88. Enyenihi A, Saunders W. Large-scale functional genomic analysis of sporulation and meiosis in Saccharomyces cerevisiae. Genetics. 2003;163:47-54 pubmed
    ..The set of genes identified in this phenotypic screen shows only limited overlap with those identified by expression-based studies. ..
  89. Nath N, McCartney R, Schmidt M. Yeast Pak1 kinase associates with and activates Snf1. Mol Cell Biol. 2003;23:3909-17 pubmed
    ..The closest mammalian homologue of yeast Pak1 kinase, calcium-calmodulin-dependent protein kinase kinase beta, may play a similar role in mammalian nutrient stress signaling. ..
  90. Chang H, Jesch S, Gaspar M, Henry S. Role of the unfolded protein response pathway in secretory stress and regulation of INO1 expression in Saccharomyces cerevisiae. Genetics. 2004;168:1899-913 pubmed
    ..Indeed, many of the Sec(-) mutants that had elevated UPR expression at semipermissive growth temperatures failed to achieve wild-type levels of INO1 expression under these same conditions. ..
  91. Zhang J, Harnpicharnchai P, Jakovljevic J, Tang L, Guo Y, Oeffinger M, et al. Assembly factors Rpf2 and Rrs1 recruit 5S rRNA and ribosomal proteins rpL5 and rpL11 into nascent ribosomes. Genes Dev. 2007;21:2580-92 pubmed
    ..Consequently, the abortive 66S pre-rRNPs are prematurely released from the nucleolus to the nucleoplasm, and cannot be exported to the cytoplasm. ..
  92. Bochman M, Bell S, Schwacha A. Subunit organization of Mcm2-7 and the unequal role of active sites in ATP hydrolysis and viability. Mol Cell Biol. 2008;28:5865-73 pubmed publisher
    ..Our conclusions predict a structural discontinuity between Mcm2 and Mcm5 and demonstrate that in contrast to other hexameric helicases, the six Mcm2-7 active sites are functionally distinct. ..