Genomes and Genes
Experts and Doctors on saccharomyces cerevisiae in California, United States
Locale: California, United States
Topic: saccharomyces cerevisiae
Publications172 found, 100 shown here
- Fasolo J, Sboner A, Sun M, Yu H, Chen R, Sharon D, et al. Diverse protein kinase interactions identified by protein microarrays reveal novel connections between cellular processes. Genes Dev. 2011;25:767-78 pubmed publisher..Our results further demonstrate that protein microarrays uncover a diverse set of interactions not observed previously. ..
- Kvitek D, Sherlock G. Reciprocal sign epistasis between frequently experimentally evolved adaptive mutations causes a rugged fitness landscape. PLoS Genet. 2011;7:e1002056 pubmed publisher..These results also provide a new interpretation on the classic Dobzhansky-Muller model of reproductive isolation and display some surprising parallels with mutations in genes often associated with tumors. ..
- Chen S, Novick P, Ferro Novick S. ER network formation requires a balance of the dynamin-like GTPase Sey1p and the Lunapark family member Lnp1p. Nat Cell Biol. 2012;14:707-16 pubmed publisher..In support of this proposal, we show that the collapsed, densely reticulated ER network in lnp1 ? cells is partially restored when the GTPase activity of Sey1p is abrogated. ..
- Pan Y, Sun M, Wohlschlegel J, Reed S. Cks1 enhances transcription efficiency at the GAL1 locus by linking the Paf1 complex to the 19S proteasome. Eukaryot Cell. 2013;12:1192-201 pubmed publisher..We further found that Cks1 in this capacity serves as an adaptor allowing Rtf1 to recruit 19S proteasome particles, shown to be required for efficient RNA production from some rapidly inducible genes such as GAL1...
- Albert F, Treusch S, Shockley A, Bloom J, Kruglyak L. Genetics of single-cell protein abundance variation in large yeast populations. Nature. 2014;506:494-7 pubmed publisher..The variants that underlie these hotspots have profound effects on the gene regulatory network and provide insights into genetic variation in cell physiology between yeast strains. ..
- Hattendorf D, Andreeva A, Gangar A, Brennwald P, Weis W. Structure of the yeast polarity protein Sro7 reveals a SNARE regulatory mechanism. Nature. 2007;446:567-71 pubmed..Sequence alignments indicate that lethal giant larvae and tomosyn have a two-beta-propeller fold similar to that of Sro7, but only tomosyn appears to retain the regulatory tail. ..
- Chittuluru J, Chaban Y, Monnet Saksouk J, Carrozza M, Sapountzi V, Selleck W, et al. Structure and nucleosome interaction of the yeast NuA4 and Piccolo-NuA4 histone acetyltransferase complexes. Nat Struct Mol Biol. 2011;18:1196-203 pubmed publisher..Taken together, these results provide an understanding of the NuA4 subunit organization and the NuA4-NCP interactions. ..
- Edwards A, Kane C, Young R, Kornberg R. Two dissociable subunits of yeast RNA polymerase II stimulate the initiation of transcription at a promoter in vitro. J Biol Chem. 1991;266:71-5 pubmed..These extracts were individually inactive, but a mixture would support promoter-directed initiation. The fourth and seventh largest subunits may, therefore, shuttle between polymerase molecules. ..
- Huang B, Mengersen A, Lee V. Molecular cloning of cDNA for caltractin, a basal body-associated Ca2+-binding protein: homology in its protein sequence with calmodulin and the yeast CDC31 gene product. J Cell Biol. 1988;107:133-40 pubmed..The association of these sequence-related calcium-binding proteins to microtubule-organizing centers of divergent structure suggests a potential conserved function for the proteins. ..
- Schwartz K, Richards K, Botstein D. BIM1 encodes a microtubule-binding protein in yeast. Mol Biol Cell. 1997;8:2677-91 pubmed..One of the human homologues, EB1, has been reported previously as binding APC, itself a microtubule-binding protein and the product of a gene implicated in the etiology of human colon cancer. ..
- Gutierrez P, Wang T. Genomic instability induced by mutations in Saccharomyces cerevisiae POL1. Genetics. 2003;165:65-81 pubmed..Thus, mutations of POL1 can induce a variety of mutator phenotypes and can be a source of genomic instability in cells. ..
- Schmidt K, Kolodner R. Requirement of Rrm3 helicase for repair of spontaneous DNA lesions in cells lacking Srs2 or Sgs1 helicase. Mol Cell Biol. 2004;24:3213-26 pubmed..These observations identify Rrm3 as a new member of a network of pathways, involving Sgs1 and Srs2 helicases and Mus81 endonuclease, suggested to act during repair of stalled replication forks. ..
- Smolka M, Albuquerque C, Chen S, Schmidt K, Wei X, Kolodner R, et al. Dynamic changes in protein-protein interaction and protein phosphorylation probed with amine-reactive isotope tag. Mol Cell Proteomics. 2005;4:1358-69 pubmed
- Peng Z, Zhao Z, Nath N, Froula J, Clum A, Zhang T, et al. Generation of long insert pairs using a Cre-LoxP Inverse PCR approach. PLoS ONE. 2012;7:e29437 pubmed publisher..These libraries have demonstrated the ability to improve genome assemblies. The CLIP-PE methodology can be implemented with existing and future next-generation sequencing platforms. ..
- Lew D, Dulic V, Reed S. Isolation of three novel human cyclins by rescue of G1 cyclin (Cln) function in yeast. Cell. 1991;66:1197-206 pubmed..Cyclin C and E mRNAs accumulate periodically through the cell cycle, peaking at different times in G1. ..
- Martin G, Viskochil D, Bollag G, McCabe P, Crosier W, Haubruck H, et al. The GAP-related domain of the neurofibromatosis type 1 gene product interacts with ras p21. Cell. 1990;63:843-9 pubmed..However, its specific activity was about 30 times lower. These kinetic measurements suggest that NF1 may be a significant regulator of ras p21 activity, particularly at low ras p21 concentrations. ..
- Sweder K, Hanawalt P. The COOH terminus of suppressor of stem loop (SSL2/RAD25) in yeast is essential for overall genomic excision repair and transcription-coupled repair. J Biol Chem. 1994;269:1852-7 pubmed
- Ma X, Lu Q, Grunstein M. A search for proteins that interact genetically with histone H3 and H4 amino termini uncovers novel regulators of the Swe1 kinase in Saccharomyces cerevisiae. Genes Dev. 1996;10:1327-40 pubmed..We suggest that these cell cycle regulators function in a pathway upstream of both histones H3 and H4, thereby modulating histone function in the cell cycle. ..
- Henry N, Bushnell D, Kornberg R. A yeast transcriptional stimulatory protein similar to human PC4. J Biol Chem. 1996;271:21842-7 pubmed..The gene for the transcriptional stimulatory protein, termed TSP1, was cloned and found to be dispensable for yeast cell viability. The deduced amino acid sequence is similar to that of mammalian coactivator protein PC4. ..
- Fyrst H, Oskouian B, Kuypers F, Saba J. The PLB2 gene of Saccharomyces cerevisiae confers resistance to lysophosphatidylcholine and encodes a phospholipase B/lysophospholipase. Biochemistry. 1999;38:5864-71 pubmed..PLB2 gene expression was found to be maximal during exponential growth conditions and was decreased in late phase, in a manner similar to other genes involved in phospholipid metabolism. ..
- Li Y, Takagi Y, Jiang Y, Tokunaga M, Erdjument Bromage H, Tempst P, et al. A multiprotein complex that interacts with RNA polymerase II elongator. J Biol Chem. 2001;276:29628-31 pubmed..Preferential interaction of the Hap complex with free rather than RNA polymerase II-associated Elongator suggests a role in the regulation of Elongator activity. ..
- Nakagawa T, Kolodner R. The MER3 DNA helicase catalyzes the unwinding of holliday junctions. J Biol Chem. 2002;277:28019-24 pubmed..Possible roles for Holliday junction unwinding in meiotic crossover are discussed. ..
- Coulon S, Gaillard P, Chahwan C, McDonald W, Yates J, Russell P. Slx1-Slx4 are subunits of a structure-specific endonuclease that maintains ribosomal DNA in fission yeast. Mol Biol Cell. 2004;15:71-80 pubmed..pombe. We propose a model in which the Slx1-Slx4 complex is involved in the control of the expansion and contraction of the rDNA loci by initiating recombination events at stalled RFs. ..
- Parrish W, Stefan C, Emr S. PtdIns(3)P accumulation in triple lipid-phosphatase-deletion mutants triggers lethal hyperactivation of the Rho1p/Pkc1p cell-integrity MAP kinase pathway. J Cell Sci. 2005;118:5589-601 pubmed..Taken together, the results of this study indicated that aberrant Rho1p/Pkc1p signaling contributes to the lethal effects of PtdIns(3)P accumulation in cells deficient in PI 3-phosphatase activity. ..
- Para A, Farré E, Imaizumi T, Pruneda Paz J, Harmon F, Kay S. PRR3 Is a vascular regulator of TOC1 stability in the Arabidopsis circadian clock. Plant Cell. 2007;19:3462-73 pubmed
- Barber Singh J, Seo B, Nakamaru Ogiso E, Lau Y, Matsuno Yagi A, Yagi T. Neuroprotective effect of long-term NDI1 gene expression in a chronic mouse model of Parkinson disorder. Rejuvenation Res. 2009;12:259-67 pubmed publisher..The data presented in this study demonstrate a protective effect of the NDI1 gene in dopaminergic neurons, suggesting its therapeutic potential for Parkinson-like disorders. ..
- Olzmann J, Kopito R. Lipid droplet formation is dispensable for endoplasmic reticulum-associated degradation. J Biol Chem. 2011;286:27872-4 pubmed publisher..Our data demonstrate that lipid droplet formation is dispensable for the dislocation of a plant toxin and the degradation of both soluble and integral membrane glycoproteins...
- Stolc V, Shmygelska A, Griko Y. Adaptation of organisms by resonance of RNA transcription with the cellular redox cycle. PLoS ONE. 2011;6:e25270 pubmed publisher..This work demonstrates evidence for a universal, persistent and iterative feedback mechanism between the environment and heredity, whereby acquired variation between cell divisions can outweigh inherited variation. ..
- Webb K, Xu T, Park S, Yates J. Modified MuDPIT separation identified 4488 proteins in a system-wide analysis of quiescence in yeast. J Proteome Res. 2013;12:2177-84 pubmed publisher..In total, 4488 distinguishable protein families were identified in all cellular conditions tested. ..
- Toro T, Toth J, Petroski M. The cyclomodulin cycle inhibiting factor (CIF) alters cullin neddylation dynamics. J Biol Chem. 2013;288:14716-26 pubmed publisher..This leads to a dramatic change in the extent of activated cullin-RING ubiquitin ligases. ..
- Hennessy K, Lee A, Chen E, Botstein D. A group of interacting yeast DNA replication genes. Genes Dev. 1991;5:958-69 pubmed
- Schmidt K, Derry K, Kolodner R. Saccharomyces cerevisiae RRM3, a 5' to 3' DNA helicase, physically interacts with proliferating cell nuclear antigen. J Biol Chem. 2002;277:45331-7 pubmed..The results presented here suggest that the RRM3 helicase functions at the replication fork. ..
- Wendland B, Emr S. Pan1p, yeast eps15, functions as a multivalent adaptor that coordinates protein-protein interactions essential for endocytosis. J Cell Biol. 1998;141:71-84 pubmed..We suggest that Pan1p (and by extension eps15) serves as a multivalent adaptor around which dynamic interactions between structural and regulatory components of the endocytic pathway converge. ..
- Segal M, Bloom K, Reed S. Bud6 directs sequential microtubule interactions with the bud tip and bud neck during spindle morphogenesis in Saccharomyces cerevisiae. Mol Biol Cell. 2000;11:3689-702 pubmed..These data support a model whereby Bud6 sequentially cues microtubule capture events at the bud tip followed by capture events at the bud neck, necessary for correct spindle morphogenesis and polarity. ..
- Augustine A, Kragh M, Sarangi R, Fujii S, Liboiron B, Stoj C, et al. Spectroscopic studies of perturbed T1 Cu sites in the multicopper oxidases Saccharomyces cerevisiae Fet3p and Rhus vernicifera laccase: allosteric coupling between the T1 and trinuclear Cu sites. Biochemistry. 2008;47:2036-45 pubmed publisher..These changes in the side chain and backbone provide a possible mechanism for regulating intramolecular T1 to TNC ET in NI and partially reduced enzyme forms for efficient turnover. ..
- del Alamo M, Hogan D, Pechmann S, Albanèse V, Brown P, Frydman J. Defining the specificity of cotranslationally acting chaperones by systematic analysis of mRNAs associated with ribosome-nascent chain complexes. PLoS Biol. 2011;9:e1001100 pubmed publisher..The strategy we used should be generally applicable to mapping the specificity, interplay, and dynamics of the cotranslational protein homeostasis network. ..
- Cronin S, Khoury A, Ferry D, Hampton R. Regulation of HMG-CoA reductase degradation requires the P-type ATPase Cod1p/Spf1p. J Cell Biol. 2000;148:915-24 pubmed..The identification of Cod1p is especially intriguing in light of the role Ca(2+) plays in the regulated degradation of mammalian HMGR. ..
- Baskerville C, Segal M, Reed S. The protease activity of yeast separase (esp1) is required for anaphase spindle elongation independently of its role in cleavage of cohesin. Genetics. 2008;178:2361-72 pubmed publisher..Such a function is consistent with the previous observation that Esp1 localizes to the mitotic spindle during anaphase. ..
- Wagner M, Smolka M, de Bruin R, Zhou H, Wittenberg C, Dowdy S. Whi5 regulation by site specific CDK-phosphorylation in Saccharomyces cerevisiae. PLoS ONE. 2009;4:e4300 pubmed publisher..Although these four Whi5 CDK sites do not wholly determine Whi5 nuclear export, they do impact regulation of cell size. Taken together, these observations begin to dissect the regulatory role of specific phosphorylation sites on Whi5. ..
- Klass D, Scheibe M, Butter F, Hogan G, Mann M, Brown P. Quantitative proteomic analysis reveals concurrent RNA-protein interactions and identifies new RNA-binding proteins in Saccharomyces cerevisiae. Genome Res. 2013;23:1028-38 pubmed publisher..While existing methods can identify sets of RBPs that interact with common RNA targets, our approach can determine which of those interactions are concurrent-a crucial distinction for understanding post-transcriptional regulation. ..
- Hsiung Y, Chang H, Pellequer J, La Valle R, Lanker S, Wittenberg C. F-box protein Grr1 interacts with phosphorylated targets via the cationic surface of its leucine-rich repeat. Mol Cell Biol. 2001;21:2506-20 pubmed..We concluded that the cationic nature of the concave surface of the Grr1 LRR is critical for the recognition of phosphorylated targets of SCF(Grr1) but that other properties of Grr1 are required for its other functions. ..
- Varughese K, Madhusudan -, Zhou X, Whiteley J, Hoch J. Formation of a novel four-helix bundle and molecular recognition sites by dimerization of a response regulator phosphotransferase. Mol Cell. 1998;2:485-93 pubmed..It is apparent that different surfaces of response regulators may be involved in recognition of the protein partners to which they are paired. ..
- Amin N, Nguyen M, Oh S, Kolodner R. exo1-Dependent mutator mutations: model system for studying functional interactions in mismatch repair. Mol Cell Biol. 2001;21:5142-55 pubmed..These results support a model in which EXO1 plays a structural role in MMR and stabilizes multiprotein complexes containing a number of MMR proteins. A similar role is proposed for PCNA based on the data presented. ..
- Denis V, Cyert M. Molecular analysis reveals localization of Saccharomyces cerevisiae protein kinase C to sites of polarized growth and Pkc1p targeting to the nucleus and mitotic spindle. Eukaryot Cell. 2005;4:36-45 pubmed..This novel nuclear and spindle localization of Pkc1p may provide a molecular explanation for previous observations that suggest a role for Pkc1p in regulating microtubule function. ..
- Lin H, Li L, Jia X, Ward D, Kaplan J. Genetic and biochemical analysis of high iron toxicity in yeast: iron toxicity is due to the accumulation of cytosolic iron and occurs under both aerobic and anaerobic conditions. J Biol Chem. 2011;286:3851-62 pubmed publisher..Deletion of TSA1, which encodes a peroxiredoxin, exacerbated iron toxicity in ?ccc1 cells under both aerobic and anaerobic conditions, suggesting a unique role for Tsa1 in iron toxicity. ..
- Kim H, Raphael A, LADOW E, McGurk L, Weber R, Trojanowski J, et al. Therapeutic modulation of eIF2? phosphorylation rescues TDP-43 toxicity in amyotrophic lateral sclerosis disease models. Nat Genet. 2014;46:152-60 pubmed publisher..These findings indicate that the dysfunction induced by prolonged stress granule formation might contribute directly to ALS and that compounds that mitigate this process may represent a novel therapeutic approach. ..
- Jiang B, Cyert M. Identification of a novel region critical for calcineurin function in vivo and in vitro. J Biol Chem. 1999;274:18543-51 pubmed
- Cairns B, Henry N, Kornberg R. TFG/TAF30/ANC1, a component of the yeast SWI/SNF complex that is similar to the leukemogenic proteins ENL and AF-9. Mol Cell Biol. 1996;16:3308-16 pubmed..These results suggest that ENL and AF-9 proteins interact with the SNF5 component of the human SWI/SNF complex and raise the possibility that the SWI/SNF complex is involved in acute leukemia. ..
- Tsuruta H, Paddon C, Eng D, Lenihan J, Horning T, Anthony L, et al. High-level production of amorpha-4,11-diene, a precursor of the antimalarial agent artemisinin, in Escherichia coli. PLoS ONE. 2009;4:e4489 pubmed publisher..Production of >25 g/L amorpha-4,11-diene by fermentation followed by chemical conversion to artemisinin may allow for development of a process to provide an alternative source of artemisinin to be incorporated into ACTs. ..
- Lama J, Trono D. Human immunodeficiency virus type 1 matrix protein interacts with cellular protein HO3. J Virol. 1998;72:1671-6 pubmed..The stimulating effect of HO3 was independent from the presence of Envelope, Vpr, or Vpu. Taken together, these results suggest that HO3, through its recognition of MA, plays a role in the life cycle of HIV-1. ..
- Shibagaki N, Grossman A. Binding of cysteine synthase to the STAS domain of sulfate transporter and its regulatory consequences. J Biol Chem. 2010;285:25094-102 pubmed publisher..These observations suggest a regulatory model in which interactions between SULTR1;2 and OASTL coordinate internalization of SO(4)(2-) with the energetic/metabolic state of plant root cells. ..
- Miyamoto A, Cui X, Naumovski L, Cleary M. Helix-loop-helix proteins LYL1 and E2a form heterodimeric complexes with distinctive DNA-binding properties in hematolymphoid cells. Mol Cell Biol. 1996;16:2394-401 pubmed
- Namsaraev E, Berg P. Characterization of strand exchange activity of yeast Rad51 protein. Mol Cell Biol. 1997;17:5359-68 pubmed..Joint molecules formed via the 5' end are processed by branch migration in the 3'-to-5' direction with respect to ssDNA, and joint molecules formed with a 3' end are processed in the opposite direction. ..
- Gerber A, Herschlag D, Brown P. Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast. PLoS Biol. 2004;2:E79 pubmed
- Sayre M, Tschochner H, Kornberg R. Reconstitution of transcription with five purified initiation factors and RNA polymerase II from Saccharomyces cerevisiae. J Biol Chem. 1992;267:23376-82 pubmed..TFIIA failed to substitute for any purified factor or to stimulate transcription with the complete set of factors, indicating that its function in crude extracts is primarily as an anti-inhibitor. ..
- Richardson H, Lew D, Henze M, Sugimoto K, Reed S. Cyclin-B homologs in Saccharomyces cerevisiae function in S phase and in G2. Genes Dev. 1992;6:2021-34 pubmed..Taken together, these analyses suggest that CLB1 and CLB2 are crucial for mitotic induction, whereas CLB3 and CLB4 might participate additionally in DNA replication and spindle assembly. ..
- Sachs A, Davis R. The poly(A) binding protein is required for poly(A) shortening and 60S ribosomal subunit-dependent translation initiation. Cell. 1989;58:857-67 pubmed..These data suggest that the 60S subunit mediates the PAB requirement of translation initiation, thereby ensuring that only intact poly(A)+ mRNA will be translated efficiently in vivo. ..
- Feaver W, Henry N, Bushnell D, Sayre M, Brickner J, Gileadi O, et al. Yeast TFIIE. Cloning, expression, and homology to vertebrate proteins. J Biol Chem. 1994;269:27549-53 pubmed..The deduced amino acid sequences of the TFA1 and TFA2 gene products were homologous to those of the large and small subunits of human TFIIE, respectively, identifying factor a as the yeast homolog of TFIIE. ..
- Wang C, Morales A, Schimmel P. Functional redundancy in the nonspecific RNA binding domain of a class I tRNA synthetase. J Biol Chem. 2000;275:17180-6 pubmed..Further experiments suggest that this redundancy is not used to dock two molecules of RNA but rather to enhance the overall affinity for a single RNA molecule. ..
- Boustany L, Cyert M. Calcineurin-dependent regulation of Crz1p nuclear export requires Msn5p and a conserved calcineurin docking site. Genes Dev. 2002;16:608-19 pubmed..Therefore, in yeast as in mammals, a docking site is required to target calcineurin to its substrate such that it can dephosphorylate it efficiently. ..
- Kirchner J, Salazar E, Lamerdin J, Montgomery M, Carrano A, Weber C. Cloning and molecular characterization of the Chinese hamster ERCC2 nucleotide excision repair gene. Genomics. 1994;23:592-9 pubmed..There is no apparent TAATA box. No consensus polyadenylation sequence (AATAAA or its variants) was found within 663 bases 3' of the translation termination codon. ..
- Amberg D, Zahner J, Mulholland J, Pringle J, Botstein D. Aip3p/Bud6p, a yeast actin-interacting protein that is involved in morphogenesis and the selection of bipolar budding sites. Mol Biol Cell. 1997;8:729-53 pubmed..Surprisingly, the localization of Aip3p does not appear to require either polarized actin or the septin proteins of the neck filaments. ..
- Hays S, Firmenich A, Massey P, Banerjee R, Berg P. Studies of the interaction between Rad52 protein and the yeast single-stranded DNA binding protein RPA. Mol Cell Biol. 1998;18:4400-6 pubmed..Given the location of the mutations in the DNA binding domain of Rad52, a model incorporating the role of DNA in the protein-protein interactions involved in the repair of DNA double-strand breaks is presented. ..
- Yam A, Albanèse V, Lin H, Frydman J. Hsp110 cooperates with different cytosolic HSP70 systems in a pathway for de novo folding. J Biol Chem. 2005;280:41252-61 pubmed..It, thus, appears that Hsp110 is an important regulator of Hsp70-substrate interactions. Based on our data, we propose that Hsp110 cooperates with the SSB and SSA Hsp70 subfamilies, which act sequentially during de novo folding. ..
- Green E, Mas G, Young N, Garcia B, Gozani O. Methylation of H4 lysines 5, 8 and 12 by yeast Set5 calibrates chromatin stress responses. Nat Struct Mol Biol. 2012;19:361-3 pubmed publisher..Set5's enzymatic activity functions together with the global chromatin-modifying complexes COMPASS and NuA4 to regulate cell growth and stress responses. ..
- Hennessy K, Clark C, Botstein D. Subcellular localization of yeast CDC46 varies with the cell cycle. Genes Dev. 1990;4:2252-63 pubmed..This partitioning of proteins in a cell cycle-dependent manner illustrates a general means of regulating events that must occur only once in each cycle, such as DNA initiation. ..
- Chen J, Evans R. A transcriptional co-repressor that interacts with nuclear hormone receptors. Nature. 1995;377:454-7 pubmed..Together, our results identify a new class of cofactors which may be important mediators of hormone action. ..
- Sato T, Darsow T, Emr S. Vam7p, a SNAP-25-like molecule, and Vam3p, a syntaxin homolog, function together in yeast vacuolar protein trafficking. Mol Cell Biol. 1998;18:5308-19 pubmed
- Gary J, Wurmser A, Bonangelino C, Weisman L, Emr S. Fab1p is essential for PtdIns(3)P 5-kinase activity and the maintenance of vacuolar size and membrane homeostasis. J Cell Biol. 1998;143:65-79 pubmed..We propose that Fab1p and Vac7p are components of a signal transduction pathway which functions to regulate the efflux or turnover of vacuolar membranes through the regulated production of PtdIns(3,5)P2. ..
- Naitow H, Canady M, Lin T, Wickner R, Johnson J. Purification, crystallization, and preliminary X-ray analysis of L-A: a dsRNA yeast virus. J Struct Biol. 2001;135:1-7 pubmed..7 A, b = 403.3 A, c = 572.5 A, beta = 90.3 degrees with two virus particles in the unit cell. The particle orientation was determined with the rotation function and the particle center was estimated on the basis of packing considerations...
- Takagi Y, Masuda C, Chang W, Komori H, Wang D, Hunter T, et al. Ubiquitin ligase activity of TFIIH and the transcriptional response to DNA damage. Mol Cell. 2005;18:237-43 pubmed..Rather, it correlates with reduced transcriptional induction of genes involved in DNA repair, suggesting that the E3 Ub ligase activity of TFIIH mediates the transcriptional response to DNA damage. ..
- Carroll S, Hampton R. Usa1p is required for optimal function and regulation of the Hrd1p endoplasmic reticulum-associated degradation ubiquitin ligase. J Biol Chem. 2010;285:5146-56 pubmed publisher..Many of the described actions of Usa1p are distinct from those of Der1p, which is recruited to the HRD complex by Usa1p. Thus, this novel, conserved factor is broadly involved in the function and regulation of the HRD pathway of ERAD. ..
- Masters B, Stohl L, Clayton D. Yeast mitochondrial RNA polymerase is homologous to those encoded by bacteriophages T3 and T7. Cell. 1987;51:89-99 pubmed..Interestingly, the mitochondrial enzyme is highly homologous to the DNA-directed RNA polymerases of bacteriophages T3 and T7, especially in regions most highly conserved between the T3 and T7 enzymes themselves...
- Deiters A, Cropp T, Mukherji M, Chin J, Anderson J, Schultz P. Adding amino acids with novel reactivity to the genetic code of Saccharomyces cerevisiae. J Am Chem Soc. 2003;125:11782-3 pubmed..As an example, we have shown that proteins containing these amino acids can be efficiently bioconjugated with small organic molecules by a [3 + 2] cycloaddition reaction that is mild enough for the manipulation of biological samples. ..
- de Bruin R, McDonald W, Kalashnikova T, Yates J, Wittenberg C. Cln3 activates G1-specific transcription via phosphorylation of the SBF bound repressor Whi5. Cell. 2004;117:887-98 pubmed..Like mammalian Rb, Whi5 is a G1-specific transcriptional repressor antagonized by CDK. ..
- Stambuk B, Dunn B, Alves S, Duval E, Sherlock G. Industrial fuel ethanol yeasts contain adaptive copy number changes in genes involved in vitamin B1 and B6 biosynthesis. Genome Res. 2009;19:2271-8 pubmed publisher..These genetic changes have likely been adaptive and selected for in the industrial environment, and may be required for the efficient utilization of biomass-derived sugars from other renewable feedstocks. ..
- ..Here, I summarize our current understanding of the dynamic remodeling of the NE during the cell cycle. ..
- Kvitek D, Sherlock G. Whole genome, whole population sequencing reveals that loss of signaling networks is the major adaptive strategy in a constant environment. PLoS Genet. 2013;9:e1003972 pubmed publisher..Our results are a clear example of the myopic nature of evolution: a loss of environmental sensitivity in a constant environment is adaptive in the short term, but maladaptive should the environment change. ..
- Cismowski M, Laff G, Solomon M, Reed S. KIN28 encodes a C-terminal domain kinase that controls mRNA transcription in Saccharomyces cerevisiae but lacks cyclin-dependent kinase-activating kinase (CAK) activity. Mol Cell Biol. 1995;15:2983-92 pubmed..We conclude that Kin28 is a strong candidate for the physiological CTD kinase of S. cerevisiae and that Kin28 function is required for mRNA transcription. ..
- Svejstrup J, Feaver W, Lapointe J, Kornberg R. RNA polymerase transcription factor IIH holoenzyme from yeast. J Biol Chem. 1994;269:28044-8 pubmed..By contrast, core TFIIH is inert in both C-terminal repeat domain kinase and reconstituted transcription assays. ..
- Parisi M, Xu B, Clayton D. A human mitochondrial transcriptional activator can functionally replace a yeast mitochondrial HMG-box protein both in vivo and in vitro. Mol Cell Biol. 1993;13:1951-61 pubmed..Both human and yeast proteins affect yeast mitochondrial transcription initiation in vitro, suggesting that the two proteins may have a common role in this fundamental process. ..
- Das Gupta R, Kolodner R. Novel dominant mutations in Saccharomyces cerevisiae MSH6. Nat Genet. 2000;24:53-6 pubmed..Our work suggests that such mutations may underlie some cases of inherited cancer susceptibility similar to those caused by MSH2 mutations. ..
- Matsuyama S, Llopis J, Deveraux Q, Tsien R, Reed J. Changes in intramitochondrial and cytosolic pH: early events that modulate caspase activation during apoptosis. Nat Cell Biol. 2000;2:318-25 pubmed..These findings indicate that mitochondria-mediated alteration of intracellular pH may be an early event that regulates caspase activation in the mitochondrial pathway for apoptosis. ..
- Lorch Y, Beve J, Gustafsson C, Myers L, Kornberg R. Mediator-nucleosome interaction. Mol Cell. 2000;6:197-201 pubmed..Sequence alignment shows significant similarity of Nut1 to the GCN5-related N-acetyltransferase superfamily. Finally, recombinant Nut1 exhibits HAT activity in an in-gel assay. ..
- Kai M, Wang T. Checkpoint activation regulates mutagenic translesion synthesis. Genes Dev. 2003;17:64-76 pubmed..Moreover, association of DinB with chromatin is dependent on functional Rad17, and DinB physically interacts with the checkpoint-clamp components Hus1 and Rad1. Thus, translesion synthesis is a part of the checkpoint response. ..
- Ma H, Han B, Guaderrama M, Aslanian A, Yates J, Hunter T, et al. Psy2 targets the PP4 family phosphatase Pph3 to dephosphorylate Mth1 and repress glucose transporter gene expression. Mol Cell Biol. 2014;34:452-63 pubmed publisher..We conclude that the Pph3-Psy2 phosphatase modulates Mth1 activity to facilitate precise regulation of HXT gene expression by glucose...
- Zhou J, Saba J. Identification of the first mammalian sphingosine phosphate lyase gene and its functional expression in yeast. Biochem Biophys Res Commun. 1998;242:502-7 pubmed..Chromosomal localization mapped this SPL gene to Chromosome 10 at 32 cM. Here, we report the identification of the first mammalian sphingosine phosphate lyase gene. ..
- Alory C, Balch W. Molecular basis for Rab prenylation. J Cell Biol. 2000;150:89-103 pubmed