Genomes and Genes
Experts and Doctors on saccharomyces cerevisiae in Denver, Colorado, United States
Locale: Denver, Colorado, United States
Topic: saccharomyces cerevisiae
- Hollingsworth R, Sclafani R. DNA metabolism gene CDC7 from yeast encodes a serine (threonine) protein kinase. Proc Natl Acad Sci U S A. 1990;87:6272-6 pubmed..Because Cdc7 kinase acts downstream of Cdc28/cdc2 kinase function at "start," the transition from G1 to S phase in the cell cycle may be the result of a cascade of protein phosphorylation. ..
- Mueller C, Jaehning J. Ctr9, Rtf1, and Leo1 are components of the Paf1/RNA polymerase II complex. Mol Cell Biol. 2002;22:1971-80 pubmed..We suggest that lack of Paf1 results in a defective complex and a block in transcription, which is relieved by removal of Leo1 or Rtf1. ..
- Chang M, French Cornay D, Fan H, Klein H, Denis C, Jaehning J. A complex containing RNA polymerase II, Paf1p, Cdc73p, Hpr1p, and Ccr4p plays a role in protein kinase C signaling. Mol Cell Biol. 1999;19:1056-67 pubmed..Our observation that the Mpk1p kinase is fully active in a paf1Delta strain indicates that the Paf1p-Cdc73p complex may function downstream of the Pkc1p-Mpk1p cascade to regulate the expression of a subset of yeast genes. ..
- Fanger G, Widmann C, Porter A, Sather S, Johnson G, Vaillancourt R. 14-3-3 proteins interact with specific MEK kinases. J Biol Chem. 1998;273:3476-83 pubmed..With regard to MEKK1, -2 and -3, 14-3-3 proteins do not appear to directly influence activity, but rather function as "scaffolds" for protein-protein interactions. ..
- Mueller C, Porter S, Hoffman M, Jaehning J. The Paf1 complex has functions independent of actively transcribing RNA polymerase II. Mol Cell. 2004;14:447-56 pubmed..Therefore, the major functions of Paf1 can be independent of actively transcribing Pol II. ..
- Lange Carter C, Pleiman C, Gardner A, Blumer K, Johnson G. A divergence in the MAP kinase regulatory network defined by MEK kinase and Raf. Science. 1993;260:315-9 pubmed..Thus, MEKK and Raf converge at MEK in the protein kinase network mediating the activation of MAPKs by hormones, growth factors, and neurotransmitters. ..
- Pessoa Brandao L, Sclafani R. CDC7/DBF4 functions in the translesion synthesis branch of the RAD6 epistasis group in Saccharomyces cerevisiae. Genetics. 2004;167:1597-610 pubmed..Finally, activation of the DNA damage checkpoint and the resulting cell cycle delay is intact in cdc7Delta mcm5-bob1 cells, suggesting a direct role for CDC7 in DNA repair/damage tolerance. ..
- Spritz R. Multi-organellar disorders of pigmentation: intracellular traffic jams in mammals, flies and yeast. Trends Genet. 1999;15:337-40 pubmed..Recent discoveries show that several of these mutations directly affect components in the pathway of organelle-specific protein trafficking, and provide new insights into the relationships of these pathways in mammals, flies and yeast. ..
- Yao R, Zhang Z, An X, Bucci B, Perlstein D, Stubbe J, et al. Subcellular localization of yeast ribonucleotide reductase regulated by the DNA replication and damage checkpoint pathways. Proc Natl Acad Sci U S A. 2003;100:6628-33 pubmed..These results suggest a mechanism by which DNA damage checkpoint modulates RNR activity through the temporal and spatial regulation of its subunits. ..
- Cann J, Coombs R, Howlett G, Jacobsen M, Winzor D. Effects of molecular crowding on protein self-association: a potential source of error in sedimentation coefficients obtained by zonal ultracentrifugation in a sucrose gradient. Biochemistry. 1994;33:10185-90 pubmed..These features are illustrated by the results of computer-simulated sedimentation of reversibly dimerizing systems in a sucrose gradient, and by conventional sedimentation velocity experiments on yeast enolase. ..
- Riekhof W, Voelker D. Uptake and utilization of lyso-phosphatidylethanolamine by Saccharomyces cerevisiae. J Biol Chem. 2006;281:36588-96 pubmed
- Porter S, Washburn T, Chang M, Jaehning J. The yeast pafl-rNA polymerase II complex is required for full expression of a subset of cell cycle-regulated genes. Eukaryot Cell. 2002;1:830-42 pubmed..In addition, overexpression of either Swi4 or Mbp1 suppresses some paf1delta phenotypes. These data establish that the Paf1 complex plays an important role in the essential regulatory pathway controlled by SBF and MBF. ..
- Franzusoff A, Redding K, Crosby J, Fuller R, Schekman R. Localization of components involved in protein transport and processing through the yeast Golgi apparatus. J Cell Biol. 1991;112:27-37 pubmed..Colocalization of the two antigens, one implicated in protein transport through the Golgi apparatus and the other in processing within a late Golgi compartment, supports the conclusion that we have visualized the yeast Golgi apparatus. ..
- Cheever M, Sato T, de Beer T, Kutateladze T, Emr S, Overduin M. Phox domain interaction with PtdIns(3)P targets the Vam7 t-SNARE to vacuole membranes. Nat Cell Biol. 2001;3:613-8 pubmed..Conservation of key structural and binding site residues across the diverse PX family indicates a shared fold and phosphoinositide recognition function. ..
- Su J, Sclafani R. Molecular cloning and expression of the human deoxythymidylate kinase gene in yeast. Nucleic Acids Res. 1991;19:823-7 pubmed..The human enzyme activity has been investigated by expressing it in yeast. In this work, we demonstrate that the cloned human cDNA, when expressed in yeast, produces dTMP kinase activity. ..
- Betz J, Chang M, Washburn T, Porter S, Mueller C, Jaehning J. Phenotypic analysis of Paf1/RNA polymerase II complex mutations reveals connections to cell cycle regulation, protein synthesis, and lipid and nucleic acid metabolism. Mol Genet Genomics. 2002;268:272-85 pubmed..Conversely, the fact that mbp1 Delta and rlm1 Delta mutations do not enhance the phenotypes suggests that the Paf1 complex may function in the same regulatory pathway(s) with Mbp1 and Rlm1. ..
- Riekhof W, Wu J, Gijón M, Zarini S, Murphy R, Voelker D. Lysophosphatidylcholine metabolism in Saccharomyces cerevisiae: the role of P-type ATPases in transport and a broad specificity acyltransferase in acylation. J Biol Chem. 2007;282:36853-61 pubmed..These results establish a new pathway for the net synthesis of PtdCho in yeast and provide new tools for the study of PtdCho synthesis, transport, and remodeling...
- Redzic J, Bowler B. Role of hydrogen bond networks and dynamics in positive and negative cooperative stabilization of a protein. Biochemistry. 2005;44:2900-8 pubmed..9 +/-0.7 kcal/mol) that combined with cancellation of cooperative and anticooperative pairwise interactions produce apparent additivity for the stabilizing effects of the single mutations in the triple mutant variant. ..
- Fletcher R, Bishop B, Leon R, Sclafani R, Ogata C, Chen X. The structure and function of MCM from archaeal M. Thermoautotrophicum. Nat Struct Biol. 2003;10:160-7 pubmed..Yeast bypass experiments using MCM5 mutant proteins support the hypothesis for the bypass mechanism. ..
- Choi J, Augagneur Y, Ben Mamoun C, Voelker D. Identification of gene encoding Plasmodium knowlesi phosphatidylserine decarboxylase by genetic complementation in yeast and characterization of in vitro maturation of encoded enzyme. J Biol Chem. 2012;287:222-32 pubmed publisher..This study defines a new system for probing the function of Plasmodium genes by library-based genetic complementation and its usefulness in revealing new biochemical properties of encoded proteins...
- Choi J, Kumar V, Pachikara N, Garg A, Lawres L, Toh J, et al. Characterization of Plasmodium phosphatidylserine decarboxylase expressed in yeast and application for inhibitor screening. Mol Microbiol. 2016;99:999-1014 pubmed publisher..These results highlight the importance of 4-quinolinamines as a novel class of drugs targeting membrane biogenesis via inhibition of PSD activity. ..
- Schumacher M, Choi J, Voelker D. Phosphatidylserine transport to the mitochondria is regulated by ubiquitination. J Biol Chem. 2002;277:51033-42 pubmed..These data provide compelling evidence that interorganelle PtdSer traffic is regulated by ubiquitination. ..
- Sclafani R, Tecklenburg M, Pierce A. The mcm5-bob1 bypass of Cdc7p/Dbf4p in DNA replication depends on both Cdk1-independent and Cdk1-dependent steps in Saccharomyces cerevisiae. Genetics. 2002;161:47-57 pubmed..Thus Cdc7p and Cdk1p kinases catalyze the initiation of DNA replication at several distinct steps, of which only a subset is bypassed by the mcm5-bob1 mutation. ..
- Matsunaga M, Jaehning J. Intrinsic promoter recognition by a "core" RNA polymerase. J Biol Chem. 2004;279:44239-42 pubmed..The requirement for Mtf1 on closed but not open templates indicates that Mtf1 facilitates melting but not recognition of promoters. ..
- Porter S, Penheiter K, Jaehning J. Separation of the Saccharomyces cerevisiae Paf1 complex from RNA polymerase II results in changes in its subnuclear localization. Eukaryot Cell. 2005;4:209-20 pubmed..Instead, we speculate that the change in localization may reflect a link between the Paf1C and newly synthesized mRNAs as they exit the nucleus. ..
- Deitz S, Rambourg A, Kepes F, Franzusoff A. Sec7p directs the transitions required for yeast Golgi biogenesis. Traffic. 2000;1:172-83 pubmed
- Goodman S, Axtell K, Bindoff L, Beard S, Gill R, Frerman F. Molecular cloning and expression of a cDNA encoding human electron transfer flavoprotein-ubiquinone oxidoreductase. Eur J Biochem. 1994;219:277-86 pubmed..The detergent-solubilized protein transfers electrons from ETF to the ubiquinone homolog, Q1, indicating that both the FAD and iron-sulfur cluster are properly inserted into the heterologously expressed protein. ..
- Jackson A, Pahl P, Harrison K, Rosamond J, Sclafani R. Cell cycle regulation of the yeast Cdc7 protein kinase by association with the Dbf4 protein. Mol Cell Biol. 1993;13:2899-908 pubmed
- Shellman Y, Svee E, Sclafani R, Langan T. Identification and characterization of individual cyclin-dependent kinase complexes from Saccharomyces cerevisiae. Yeast. 1999;15:295-309 pubmed..These procedures provide the basis for the analysis of regulatory, enzymatic and functional properties of individual Cdc28p kinase complexes. ..
- Dohrmann P, Oshiro G, Tecklenburg M, Sclafani R. RAD53 regulates DBF4 independently of checkpoint function in Saccharomyces cerevisiae. Genetics. 1999;151:965-77 pubmed..These results suggest that two different functions of the cell cycle, initiation of DNA replication and the checkpoint function, can be coordinately regulated through the common intermediate RAD53. ..
- Ghosh K, Dill K. Cellular proteomes have broad distributions of protein stability. Biophys J. 2010;99:3996-4002 pubmed publisher..In addition, it predicts the dependence of cellular growth rates on temperature. This approach may be useful for studying physical forces in biological evolution and the role of climate change on biology. ..
- Trotter P, Pedretti J, Voelker D. Phosphatidylserine decarboxylase from Saccharomyces cerevisiae. Isolation of mutants, cloning of the gene, and creation of a null allele. J Biol Chem. 1993;268:21416-24 pubmed..Analysis of lipid synthesis and enzyme activity in null mutants indicates that there are two PSD genes. ..
- Hunger S, Li S, Fall M, Naumovski L, Cleary M. The proto-oncogene HLF and the related basic leucine zipper protein TEF display highly similar DNA-binding and transcriptional regulatory properties. Blood. 1996;87:4607-17 pubmed..Thus, TEF and HLF share indistinguishable DNA-binding and transcriptional regulatory properties, whose alteration in leukemia may be pathogenetically important. ..
- Su J, Erikson E, Maller J. Cloning and characterization of a novel serine/threonine protein kinase expressed in early Xenopus embryos. J Biol Chem. 1996;271:14430-7 pubmed..An immunoprecipitate of oocyte/egg extracts with anti-XEEK1 serum contains a protein of approximately 155 kDa that may be a substrate and/or a regulatory component of the kinase. ..
- Bin L, Nielson L, Liu X, Mason R, Shu H. Identification of uteroglobin-related protein 1 and macrophage scavenger receptor with collagenous structure as a lung-specific ligand-receptor pair. J Immunol. 2003;171:924-30 pubmed..Our findings suggest that UGRP1-MARCO is a ligand-receptor pair that is probably involved in inflammation and pathogen clearance in the lung. ..
- Leon R, Tecklenburg M, Sclafani R. Functional conservation of beta-hairpin DNA binding domains in the Mcm protein of Methanobacterium thermoautotrophicum and the Mcm5 protein of Saccharomyces cerevisiae. Genetics. 2008;179:1757-68 pubmed publisher..Therefore, in addition to its known regulatory role, Mcm5 protein has a positive role in origin binding, which requires coordination by all six Mcm2-7 subunits in the hexamer. ..
- Cliften P, Park J, Davis B, Jang S, Jaehning J. Identification of three regions essential for interaction between a sigma-like factor and core RNA polymerase. Genes Dev. 1997;11:2897-909 pubmed..Our results demonstrate that interactions between sigma-like specificity factors and core RNA polymerases require multiple regions from both components of the holoenzymes. ..
- Roberts B, Ying C, Gautier J, Maller J. DNA replication in vertebrates requires a homolog of the Cdc7 protein kinase. Proc Natl Acad Sci U S A. 1999;96:2800-4 pubmed
- Storey M, Clay K, Kutateladze T, Murphy R, Overduin M, Voelker D. Phosphatidylethanolamine has an essential role in Saccharomyces cerevisiae that is independent of its ability to form hexagonal phase structures. J Biol Chem. 2001;276:48539-48 pubmed..The essential function of the PtdEtn in the presence of propanolamine does not appear to be the formation of hexagonal phase lipid, insofar as PtdPrn readily forms hexagonal phase structures detectable by (31)P NMR. ..
- Garrington T, Johnson G. Organization and regulation of mitogen-activated protein kinase signaling pathways. Curr Opin Cell Biol. 1999;11:211-8 pubmed..As new MAPK members are defined, determining their organization in kinase modules will be critical in understanding their select role in cellular regulation. ..
- Oshiro G, Owens J, Shellman Y, Sclafani R, Li J. Cell cycle control of Cdc7p kinase activity through regulation of Dbf4p stability. Mol Cell Biol. 1999;19:4888-96 pubmed..Thus, the regulation of Dbf4p levels through the control of Dbf4p degradation has an important role in the regulation of Cdc7p kinase activity during the cell cycle. ..
- Schroeder S, Schwer B, Shuman S, Bentley D. Dynamic association of capping enzymes with transcribing RNA polymerase II. Genes Dev. 2000;14:2435-40 pubmed..CTD phosphorylation and dephosphorylation therefore control the association of capping enzymes with pol II as it transcribes a gene. ..
- Wu W, Routt S, Bankaitis V, Voelker D. A new gene involved in the transport-dependent metabolism of phosphatidylserine, PSTB2/PDR17, shares sequence similarity with the gene encoding the phosphatidylinositol/phosphatidylcholine transfer protein, SEC14. J Biol Chem. 2000;275:14446-56 pubmed
- Sun W, Vincent S, Settleman J, Johnson G. MEK kinase 2 binds and activates protein kinase C-related kinase 2. Bifurcation of kinase regulatory pathways at the level of an MAPK kinase kinase. J Biol Chem. 2000;275:24421-8 pubmed..MEKK2 activation of PRK2 is independent of MEKK2 regulation of the c-Jun NH(2)-terminal kinase pathway. MEKK2 activation of PRK2 results in a bifurcation of signaling for the dual control of MAPK pathways and PRK2 regulated responses. ..
- Barton J, Bleskan J, Patterson D. Isolation of a human cDNA encoding amidophosphoribosyltransferase and functional complementation of a CHO Ade-A mutant deficient in this activity. Somat Cell Mol Genet. 1991;17:311-22 pubmed..This observation, along with the functionality of the cDNA in both yeast and CHO cells deficient in PRAT activity, suggests the isolated cDNA is full length. ..
- Trotter P, Voelker D. Identification of a non-mitochondrial phosphatidylserine decarboxylase activity (PSD2) in the yeast Saccharomyces cerevisiae. J Biol Chem. 1995;270:6062-70 pubmed..Unlike the PSD1 activity, the PSD2 enzyme activity does not localize to the mitochondria, but to a low density subcellular compartment with fractionation properties similar to both vacuoles and Golgi...
- Riekhof W, Wu J, Jones J, Voelker D. Identification and characterization of the major lysophosphatidylethanolamine acyltransferase in Saccharomyces cerevisiae. J Biol Chem. 2007;282:28344-52 pubmed..Ale1p catalytic activity has a pH optimum between pH 7 and 7.5 and a strong preference for unsaturated acyl-CoA substrates. ..
- Beernink H, Miller K, Deshpande A, Bucher P, Cooper J. Telomere maintenance in fission yeast requires an Est1 ortholog. Curr Biol. 2003;13:575-80 pubmed
- Penheiter K, Washburn T, Porter S, Hoffman M, Jaehning J. A posttranscriptional role for the yeast Paf1-RNA polymerase II complex is revealed by identification of primary targets. Mol Cell. 2005;20:213-23 pubmed..Therefore, although the Paf1C is associated with Pol II at initiation and during elongation, these critical Paf1-dependent changes in transcript abundance are due to alterations in posttranscriptional processing. ..
- Qadri I, Conaway J, Conaway R, Schaack J, Siddiqui A. Hepatitis B virus transactivator protein, HBx, associates with the components of TFIIH and stimulates the DNA helicase activity of TFIIH. Proc Natl Acad Sci U S A. 1996;93:10578-83 pubmed..Furthermore, the DNA helicase activity of purified TFIIH from rat liver and, individually, the ERCC2 component of TFIIH is stimulated in the presence of HBx. These observations suggest a role for HBx in transcription and DNA repair. ..
- Hovland P, Tecklenberg M, Sclafani R. Overexpression of the protein kinase Pak1 suppresses yeast DNA polymerase mutations. Mol Gen Genet. 1997;256:45-53 pubmed..Overexpression of PAK1 does not enhance the expression of the POL1 gene. Pak1 may function by modifying and partially stabilizing thermolabile DNA polymerases, perhaps during DNA repair, because pak1 mutant cells are caffeine sensitive. ..
- Wolf J, Nicks M, Deitz S, van Tuinen E, Franzusoff A. An N-end rule destabilization mutant reveals pre-Golgi requirements for Sec7p in yeast membrane traffic. Biochem Biophys Res Commun. 1998;243:191-8 pubmed..Immuno-EM of sec7 revealed exaggeration of ER and Golgi membranes with protein accumulation in these exaggerated structures, suggesting that these regions may represent staging areas for cargo sorting and vesicle assembly. ..
- Pahl P, Berger R, Hart I, Chae H, Rhee S, Patterson D. Localization of TDPX1, a human homologue of the yeast thioredoxin-dependent peroxide reductase gene (TPX), to chromosome 13q12. Genomics. 1995;26:602-6 pubmed..Oxygen radical metabolism has been hypothesized to be important for cancer, muscular dystrophy, and other disorders, so TDPX1 should be considered a candidate gene for these diseases. ..
- Shellman Y, Schauer I, Oshiro G, Dohrmann P, Sclafani R. Oligomers of the Cdc7/Dbf4 protein kinase exist in the yeast cell. Mol Gen Genet. 1998;259:429-36 pubmed..Oligomers of Cdc7 protein may exist for the purpose of allosteric regulation or to allow phosphorylation of multiple substrate protein molecules. ..
- Franzusoff A, Lauzé E, Howell K. Immuno-isolation of Sec7p-coated transport vesicles from the yeast secretory pathway. Nature. 1992;355:173-5 pubmed..This Sec7p-containing coat structure is proposed to be essential for vesicle budding at multiple stages in the yeast secretory pathway. ..