Genomes and Genes
Experts and Doctors on saccharomyces cerevisiae proteins in Denver, Colorado, United States
Locale: Denver, Colorado, United States
Topic: saccharomyces cerevisiae proteins
- 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. ..
- 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. ..
- 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. ..
- 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...
- Anderson P, Lamba J, Aquilante C, Schuetz E, Fletcher C. Pharmacogenetic characteristics of indinavir, zidovudine, and lamivudine therapy in HIV-infected adults: a pilot study. J Acquir Immune Defic Syndr. 2006;42:441-9 pubmed..CYP3A5 expression was associated with faster indinavir oral clearance. These pilot data provide a scientific basis for more rational utilization of antiretroviral drugs. ..
- 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. ..
- 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. ..
- Matsunaga M, Jaehning J. A mutation in the yeast mitochondrial core RNA polymerase, Rpo41, confers defects in both specificity factor interaction and promoter utilization. J Biol Chem. 2004;279:2012-9 pubmed..The fact that mutation of Rpo41 results in selective transcription defects indicates that the core RNAP, like T7RNAP, plays an important role in promoter utilization. ..
- 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. ..
- 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. ..
- 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. ..
- Ferreira M, Cooper J. The fission yeast Taz1 protein protects chromosomes from Ku-dependent end-to-end fusions. Mol Cell. 2001;7:55-63 pubmed..Thus, Taz1 caps chromosome ends and provides the telomerespecific interaction that prevents Ku from treating telomeres as double-strand breaks. ..
- 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
- 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. ..
- Shi X, Chang M, Wolf A, Chang C, Frazer Abel A, Wade P, et al. Cdc73p and Paf1p are found in a novel RNA polymerase II-containing complex distinct from the Srbp-containing holoenzyme. Mol Cell Biol. 1997;17:1160-9 pubmed..Our analysis suggests that there are multiple RNA polymerase II-containing complexes involved in the expression of different classes of protein-coding genes. ..
- 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. ..
- 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. ..
- Adkins M, Howar S, Tyler J. Chromatin disassembly mediated by the histone chaperone Asf1 is essential for transcriptional activation of the yeast PHO5 and PHO8 genes. Mol Cell. 2004;14:657-66 pubmed..Finally, we show that nucleosomes are reassembled over the PHO5 promoter during repression. As such, nucleosome disassembly and reassembly are important mechanisms for transcriptional activation and repression, respectively. ..
- 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. ..
- 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
- 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. ..
- 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. ..
- 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
- 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
- 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. ..
- Cliften P, Jang S, Jaehning J. Identifying a core RNA polymerase surface critical for interactions with a sigma-like specificity factor. Mol Cell Biol. 2000;20:7013-23 pubmed
- 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. ..
- 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. ..
- 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. ..
- Sclafani R. Cdc7p-Dbf4p becomes famous in the cell cycle. J Cell Sci. 2000;113 ( Pt 12):2111-7 pubmed..Therefore, activation of Cdc7p is required for DNA replication. Given that Cdc7p-Dbf4 kinase is overexpressed in many neoplastic cells and tumors, it might be an important early biomarker during cancer progression. ..
- 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. ..
- 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. ..
- 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. ..
- Jones S, Alb J, Phillips S, Bankaitis V, Howell K. A phosphatidylinositol 3-kinase and phosphatidylinositol transfer protein act synergistically in formation of constitutive transport vesicles from the trans-Golgi network. J Biol Chem. 1998;273:10349-54 pubmed..These collective findings indicate that the PI 3-kinase and PITP synergize to form a pool of PI 3-phosphate that is essential for formation of exocytic vesicles from the hepatocyte TGN. ..
- 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. ..
- 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. ..
- 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. ..
- Sartorius C, Takimoto G, Richer J, Tung L, Horwitz K. Association of the Ku autoantigen/DNA-dependent protein kinase holoenzyme and poly(ADP-ribose) polymerase with the DNA binding domain of progesterone receptors. J Mol Endocrinol. 2000;24:165-82 pubmed..These data show that DNA-PK and DBD(PR) interact, that DBD(PR) is a phosphorylation substrate of DNA-PK, and suggest a potential role for DNA-PK in PR-mediated transcription. ..