Genomes and Genes
Experts and Doctors on saccharomyces cerevisiae proteins in Los Angeles, California, United States
Locale: Los Angeles, California, United States
Topic: saccharomyces cerevisiae proteins
- Shahbazian M, Zhang K, Grunstein M. Histone H2B ubiquitylation controls processive methylation but not monomethylation by Dot1 and Set1. Mol Cell. 2005;19:271-7 pubmed..Dot1 binding to chromatin occurs normally in the absence of H2B-K123 ubiquitylation, suggesting that ubiquitylation does not regulate enzyme recruitment but does regulate the processive activity of the histone methyltransferase. ..
- Fabrizio P, Gattazzo C, Battistella L, Wei M, Cheng C, McGrew K, et al. Sir2 blocks extreme life-span extension. Cell. 2005;123:655-67 pubmed..Our results demonstrate that effects of SIR2 on chronological life span are opposite to replicatve life span and suggest that the relevant activities of Sir2-like deacetylases may also be complex in higher eukaryotes. ..
- Porras Yakushi T, Whitelegge J, Clarke S. A novel SET domain methyltransferase in yeast: Rkm2-dependent trimethylation of ribosomal protein L12ab at lysine 10. J Biol Chem. 2006;281:35835-45 pubmed..These studies suggest that the remaining seven SET domain proteins may also be lysine methyltransferases. ..
- Niewmierzycka A, Clarke S. S-Adenosylmethionine-dependent methylation in Saccharomyces cerevisiae. Identification of a novel protein arginine methyltransferase. J Biol Chem. 1999;274:814-24 pubmed..Interestingly, Rmt2 has 27% sequence identity over 138 amino acids to the mammalian guanidinoacetate N-methyltransferase, an enzyme responsible for methylating the delta-nitrogen of the small molecule guanidinoacetate. ..
- Millar C, Kurdistani S, Grunstein M. Acetylation of yeast histone H4 lysine 16: a switch for protein interactions in heterochromatin and euchromatin. Cold Spring Harb Symp Quant Biol. 2004;69:193-200 pubmed
- Webb K, Zurita Lopez C, Al Hadid Q, Laganowsky A, Young B, Lipson R, et al. A novel 3-methylhistidine modification of yeast ribosomal protein Rpl3 is dependent upon the YIL110W methyltransferase. J Biol Chem. 2010;285:37598-606 pubmed publisher..This is the first report of a methylated histidine residue in yeast cells, and the first example of a gene required for protein histidine methylation in nature. ..
- Dowell N, Sperling A, Mason M, Johnson R. Chromatin-dependent binding of the S. cerevisiae HMGB protein Nhp6A affects nucleosome dynamics and transcription. Genes Dev. 2010;24:2031-42 pubmed publisher..We conclude that the chromatin environment, not DNA sequence recognition, localizes Nhp6A binding, and that Nhp6A stabilizes chromatin structure and coregulates transcription. ..
- Neves L, Douglass S, Spreafico R, Venkataramanan S, Kress T, Johnson T. The histone variant H2A.Z promotes efficient cotranscriptional splicing in S. cerevisiae. Genes Dev. 2017;31:702-717 pubmed publisher..Together, these data demonstrate that H2A.Z is required for efficient pre-mRNA splicing and indicate a role for H2A.Z in coordinating the kinetics of transcription elongation and splicing. ..
- Sayani S, Chanfreau G. Sequential RNA degradation pathways provide a fail-safe mechanism to limit the accumulation of unspliced transcripts in Saccharomyces cerevisiae. RNA. 2012;18:1563-72 pubmed publisher..The presence of these two sequential degradation pathways for unspliced pre-mRNAs underscores the importance of limiting their accumulation and might serve as a fail-safe mechanism to prevent the expression of these nonfunctional RNAs. ..
- Xie L, Ozeir M, Tang J, Chen J, Jaquinod S, Fontecave M, et al. Overexpression of the Coq8 kinase in Saccharomyces cerevisiae coq null mutants allows for accumulation of diagnostic intermediates of the coenzyme Q6 biosynthetic pathway. J Biol Chem. 2012;287:23571-81 pubmed publisher..The overexpression of Coq8 and the use of 4-hydroxybenzoic acid analogues represent innovative tools to elucidate the Q biosynthetic pathway. ..
- Daboussi L, Costaguta G, Payne G. Phosphoinositide-mediated clathrin adaptor progression at the trans-Golgi network. Nat Cell Biol. 2012;14:239-48 pubmed publisher..Gga2p binds directly to the TGN PtdIns(4)-kinase Pik1p and contributes to Pik1p recruitment. These results identify a PtdIns(4)P-based mechanism for regulating progressive assembly of adaptor-specific clathrin coats at the TGN. ..
- Nelson R, Sawaya M, Balbirnie M, Madsen A, Riekel C, Grothe R, et al. Structure of the cross-beta spine of amyloid-like fibrils. Nature. 2005;435:773-8 pubmed..The structure illuminates the stability of amyloid fibrils, their self-seeding characteristic and their tendency to form polymorphic structures. ..
- Marbois B, Gin P, Faull K, Poon W, Lee P, Strahan J, et al. Coq3 and Coq4 define a polypeptide complex in yeast mitochondria for the biosynthesis of coenzyme Q. J Biol Chem. 2005;280:20231-8 pubmed..This study identifies Coq3p and Coq4p as defining members of a Q-biosynthetic Coq polypeptide complex. ..
- Szyjka S, Aparicio J, Viggiani C, Knott S, Xu W, Tavare S, et al. Rad53 regulates replication fork restart after DNA damage in Saccharomyces cerevisiae. Genes Dev. 2008;22:1906-20 pubmed publisher..We propose a model for regulation of replication fork progression through damaged DNA involving a cycle of Rad53 activation and deactivation that coordinates replication restart with DNA repair. ..
- Chan C, Schiestl R. Rad1, rad10 and rad52 mutations reduce the increase of microhomology length during radiation-induced microhomology-mediated illegitimate recombination in saccharomyces cerevisiae. Radiat Res. 2009;172:141-51 pubmed publisher..Taken together, these results suggest that radiation-induced microhomology-mediated recombination is under the same genetic control as the single-strand annealing apparatus that requires the RAD52, RAD1 and RAD10 genes. ..
- Gibson D, Bell S, Aparicio O. Cell cycle execution point analysis of ORC function and characterization of the checkpoint response to ORC inactivation in Saccharomyces cerevisiae. Genes Cells. 2006;11:557-73 pubmed..We discuss the potential significance of these overlapping checkpoints and the impact of our findings on previously postulated role(s) of ORCs in other cell cycle functions. ..
- Robinson N, Guo L, Imai J, Toh e A, Matsui Y, Tamanoi F. Rho3 of Saccharomyces cerevisiae, which regulates the actin cytoskeleton and exocytosis, is a GTPase which interacts with Myo2 and Exo70. Mol Cell Biol. 1999;19:3580-7 pubmed..These results provide a direct molecular basis for the action of Rho3 on exocytosis and the actin cytoskeleton. ..
- Singh M, Gonzales F, Cascio D, Heckmann N, Chanfreau G, Feigon J. Structure and functional studies of the CS domain of the essential H/ACA ribonucleoparticle assembly protein SHQ1. J Biol Chem. 2009;284:1906-16 pubmed publisher..These results show that the CS domain is essential for Shq1p function in H/ACA snoRNP biogenesis in vivo, possibly in an Hsp90-independent manner. ..
- Webb K, Al Hadid Q, Zurita Lopez C, Young B, Lipson R, Clarke S. The ribosomal l1 protuberance in yeast is methylated on a lysine residue catalyzed by a seven-beta-strand methyltransferase. J Biol Chem. 2011;286:18405-13 pubmed publisher..We propose that the YLR137W gene be given the standard name RKM5 (ribosomal lysine (K) methyltransferase 5). Orthologs of RKM5 are found only in fungal species, suggesting a role unique to their survival. ..
- Belogrudov G, Lee P, Jonassen T, Hsu A, Gin P, Clarke C. Yeast COQ4 encodes a mitochondrial protein required for coenzyme Q synthesis. Arch Biochem Biophys. 2001;392:48-58 pubmed..Y. Hsu, T. Q. Do, P. T. Lee, and C. F. Clarke, 2000, Biochim. Biophys. Acta 1484, 287-297). ..
- Webb K, Laganowsky A, Whitelegge J, Clarke S. Identification of two SET domain proteins required for methylation of lysine residues in yeast ribosomal protein Rpl42ab. J Biol Chem. 2008;283:35561-8 pubmed publisher..The top down approach was also used to reevaluate the methylation sites of Rpl12ab. We found that the yeast Rpl12ab protein is dimethylated at the N-terminal proline residue, trimethylated at Lys-3 by Rkm2, and monomethylated at Arg-66. ..
- Bensen E, Yeung B, Payne G. Ric1p and the Ypt6p GTPase function in a common pathway required for localization of trans-Golgi network membrane proteins. Mol Biol Cell. 2001;12:13-26 pubmed..Because Gos1p and Ykt6p interact with Sed5p, these results raise the possibility that TGN membrane protein localization requires Ric1p- and Ypt6p-dependent retrieval to the cis-Golgi network. ..
- Kanazawa T, Zappaterra M, Hasegawa A, Wright A, Newman Smith E, Buttle K, et al. The C. elegans Opa1 homologue EAT-3 is essential for resistance to free radicals. PLoS Genet. 2008;4:e1000022 pubmed publisher..We conclude that free radicals contribute to the pathology of C. elegans eat-3 mutants. ..
- Ngo S, Chiang V, Ho E, Le L, Guo Z. Prion domain of yeast Ure2 protein adopts a completely disordered structure: a solid-support EPR study. PLoS ONE. 2012;7:e47248 pubmed publisher..A completely disordered Ure2p prion domain implies that the amyloid formation of Ure2p, and likely other Q/N-rich yeast prion proteins, is primarily driven by inter-molecular interactions. ..
- Jonassen T, Proft M, Randez Gil F, Schultz J, Marbois B, Entian K, et al. Yeast Clk-1 homologue (Coq7/Cat5) is a mitochondrial protein in coenzyme Q synthesis. J Biol Chem. 1998;273:3351-7 pubmed..elegans clk-1 mutants may relate to changes in the amount of ubiquinone, an essential electron transport component and a lipid soluble antioxidant. ..
- Barkovich R, Shtanko A, Shepherd J, Lee P, Myles D, Tzagoloff A, et al. Characterization of the COQ5 gene from Saccharomyces cerevisiae. Evidence for a C-methyltransferase in ubiquinone biosynthesis. J Biol Chem. 1997;272:9182-8 pubmed..These studies show that Coq5p is required for the C-methyltransferase step that converts 2-methoxy-6-polyprenyl-1, 4-benzoquinone to 2-methoxy-5-methyl-6-polyprenyl-1,4-benzoquinone. ..
- Wong B, Masse J, Yen Y, Giannikopoulos P, Feigon J, Johnson R, et al. Binding to cisplatin-modified DNA by the Saccharomyces cerevisiae HMGB protein Nhp6A. Biochemistry. 2002;41:5404-14 pubmed..In contrast, Deltanhp6a/b mutants are slightly more resistant to hydrogen peroxide and ultraviolet irradiation. Therefore, Nhp6A/Bp appears to directly or indirectly function in yeast to enhance cellular resistance to cisplatin. ..
- Li M, Baumeister P, Roy B, Phan T, Foti D, Luo S, et al. ATF6 as a transcription activator of the endoplasmic reticulum stress element: thapsigargin stress-induced changes and synergistic interactions with NF-Y and YY1. Mol Cell Biol. 2000;20:5096-106 pubmed..The requirement for a high-affinity NF-Y site for ATF6 but not human Ire1p activity suggests that they stimulate the ERSE through diverse pathways. ..
- Yang P, Rotondo G, Porras T, Legrain P, Chanfreau G. The Shq1p.Naf1p complex is required for box H/ACA small nucleolar ribonucleoprotein particle biogenesis. J Biol Chem. 2002;277:45235-42 pubmed..Shq1p and Naf1p form a complex, but they are not strongly associated with box H/ACA snoRNPs. We propose that Shq1p and Naf1p are involved in the early biogenesis steps of box H/ACA snoRNP assembly. ..
- Cho J, Hur J, Graniel J, Benzer S, Walker D. Expression of yeast NDI1 rescues a Drosophila complex I assembly defect. PLoS ONE. 2012;7:e50644 pubmed publisher..Our work shows that CG7598/dCIA30 is a functional homolog of Ndufaf1 and adds to the accumulating evidence that transgenic NDI1 expression is a viable therapy for disorders arising from complex I deficiency. ..
- Kurdistani S, Robyr D, Tavazoie S, Grunstein M. Genome-wide binding map of the histone deacetylase Rpd3 in yeast. Nat Genet. 2002;31:248-54 pubmed..Finally, we show that comparing the genome-wide pattern of Rpd3 binding with gene expression and histone acetylation in the rpd3 Delta mutant strain reveals new sites of Rpd3 function. ..
- Ramachander R, Kim C, Phillips M, Mackereth C, Thanos C, McIntosh L, et al. Oligomerization-dependent association of the SAM domains from Schizosaccharomyces pombe Byr2 and Ste4. J Biol Chem. 2002;277:39585-93 pubmed..The fact that high affinity binding occurs only with the addition of an oligomerization domain suggests that it may be necessary to include ancillary oligomerization modules when searching for binding partners of SAM domains. ..
- Vinci C, Clarke S. Yeast, plants, worms, and flies use a methyltransferase to metabolize age-damaged (R,S)-AdoMet, but what do mammals do?. Rejuvenation Res. 2010;13:362-4 pubmed publisher..We find no evidence for the enzymatic breakdown of (R,S)-AdoMet in these extracts. Thus, mammals may metabolize (R,S)-AdoMet using a different strategy than other organisms. ..
- Chanfreau G. Conservation of RNase III processing pathways and specificity in hemiascomycetes. Eukaryot Cell. 2003;2:901-9 pubmed..This analysis shows that RNase III processing signals and RNase III cleavage specificity are conserved in most Hemiascomycetes species but probably not in the evolutionarily more distant species Y. lipolytica. ..
- Bernard D, Quevillon Cheruel S, Merchant S, Guiard B, Hamel P. Cyc2p, a membrane-bound flavoprotein involved in the maturation of mitochondrial c-type cytochromes. J Biol Chem. 2005;280:39852-9 pubmed..We postulate that, in vivo, Cyc2p interacts with CCHL and is involved in the reduction of heme prior to its ligation to apocytochrome c by CCHL. ..
- Gabunilas J, Chanfreau G. Splicing-Mediated Autoregulation Modulates Rpl22p Expression in Saccharomyces cerevisiae. PLoS Genet. 2016;12:e1005999 pubmed publisher..These results demonstrate an autoregulatory mechanism that fine-tunes the expression of the Rpl22 protein and by extension Rpl22p paralog composition according to the cellular demands for ribosome biogenesis. ..
- Ngo S, Gu L, Guo Z. Hierarchical organization in the amyloid core of yeast prion protein Ure2. J Biol Chem. 2011;286:29691-9 pubmed publisher..The hierarchical organization in the amyloid core may be a structural origin for polymorphism in fibrils and prion strains. ..
- Cabrera G, Godt D, Fang P, Couderc J, Laski F. Expression pattern of Gal4 enhancer trap insertions into the bric à brac locus generated by P element replacement. Genesis. 2002;34:62-5 pubmed
- Petrossian T, Clarke S. Multiple Motif Scanning to identify methyltransferases from the yeast proteome. Mol Cell Proteomics. 2009;8:1516-26 pubmed publisher..chem.ucla.edu/files/MotifSetup.Zip). Finally hidden Markov model profile clustering analysis was used to subgroup Class I methyltransferases into groups that reflect their methyl-accepting substrate specificity. ..
- Knott S, Viggiani C, Tavare S, Aparicio O. Genome-wide replication profiles indicate an expansive role for Rpd3L in regulating replication initiation timing or efficiency, and reveal genomic loci of Rpd3 function in Saccharomyces cerevisiae. Genes Dev. 2009;23:1077-90 pubmed publisher..Our results also reveal a novel and complementary genomic map of Rpd3L- and Rpd3S-regulated chromosomal loci. ..
- Somasundaram T, Bhat S. Developmentally dictated expression of heat shock factors: exclusive expression of HSF4 in the postnatal lens and its specific interaction with alphaB-crystallin heat shock promoter. J Biol Chem. 2004;279:44497-503 pubmed
- Szyjka S, Viggiani C, Aparicio O. Mrc1 is required for normal progression of replication forks throughout chromatin in S. cerevisiae. Mol Cell. 2005;19:691-7 pubmed..These findings elucidate a central role for Mrc1 in normal replisome function, which is distinct from its role as a checkpoint mediator, but nevertheless critical to genome stability. ..
- Gin P, Clarke C. Genetic evidence for a multi-subunit complex in coenzyme Q biosynthesis in yeast and the role of the Coq1 hexaprenyl diphosphate synthase. J Biol Chem. 2005;280:2676-81 pubmed..These data suggest that the lipid product of Coq1p or a Q-intermediate derived from polyprenyl diphosphate is involved in stabilizing the Coq3, Coq4, and Coq6 polypeptides. ..
- Sam M, Henras A, Chanfreau G. A conserved major groove antideterminant for Saccharomyces cerevisiae RNase III recognition. Biochemistry. 2005;44:4181-7 pubmed..cerevisiae RNase III activity, and suggest a rationale for their apparent counter selection in RNA processing sites. ..
- Wang B, Feng L, Hu Y, Huang S, Reynolds C, Wu L, et al. The essential role of Saccharomyces cerevisiae CDC6 nucleotide-binding site in cell growth, DNA synthesis, and Orc1 association. J Biol Chem. 1999;274:8291-8 pubmed..Our results suggest that a proper molecular interaction between Orc1 and Cdc6 depends on the functional ATP-binding of Cdc6, which may be a prerequisite step to assemble the operational replicative complex at the G1/S transition. ..
- Smirnova E, Shurland D, Ryazantsev S, van der Bliek A. A human dynamin-related protein controls the distribution of mitochondria. J Cell Biol. 1998;143:351-8 pubmed..The function of this new dynamin-related protein in organelle morphology represents a novel role for a member of the dynamin family of proteins. ..
- Porras Yakushi T, Whitelegge J, Miranda T, Clarke S. A novel SET domain methyltransferase modifies ribosomal protein Rpl23ab in yeast. J Biol Chem. 2005;280:34590-8 pubmed..These results show that SET domain methyltransferases can be involved in translational roles as well as in the previously described transcriptional roles. ..
- Wei M, Fabrizio P, Hu J, Ge H, Cheng C, Li L, et al. Life span extension by calorie restriction depends on Rim15 and transcription factors downstream of Ras/PKA, Tor, and Sch9. PLoS Genet. 2008;4:e13 pubmed publisher..Notably, the anti-aging effect caused by the inactivation of both pathways is much more potent than that caused by CR. ..
- 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. ..
- Vinci C, Clarke S. Recognition of age-damaged (R,S)-adenosyl-L-methionine by two methyltransferases in the yeast Saccharomyces cerevisiae. J Biol Chem. 2007;282:8604-12 pubmed..Such activity may function to prevent the accumulation of (R,S)-AdoMet in these organisms. ..
- Young B, Weiss D, Zurita Lopez C, Webb K, Clarke S, McBride A. Identification of methylated proteins in the yeast small ribosomal subunit: a role for SPOUT methyltransferases in protein arginine methylation. Biochemistry. 2012;51:5091-104 pubmed publisher..The discovery of these three novel sites of protein modification within the small ribosomal subunit will now allow for an analysis of their functional roles in translation and possibly other cellular processes. ..
- Courey A, Jia S. Transcriptional repression: the long and the short of it. Genes Dev. 2001;15:2786-96 pubmed
- Yen Y, Wong B, Johnson R. Determinants of DNA binding and bending by the Saccharomyces cerevisiae high mobility group protein NHP6A that are important for its biological activities. Role of the unique N terminus and putative intercalating methionine. J Biol Chem. 1998;273:4424-35 pubmed..Methionine 29, which may intercalate into DNA, is essential for NHP6A-induced microcircle formation of 75-bp but not 98-bp fragments in vitro, and for full growth complementation of Deltanhp6a/b mutants in vivo. ..
- Fabrizio P, Liou L, Moy V, Diaspro A, Valentine J, Gralla E, et al. SOD2 functions downstream of Sch9 to extend longevity in yeast. Genetics. 2003;163:35-46 pubmed..cerevisiae to superoxide dismutases and suggest that the induction of other stress-resistance genes regulated by Msn2/4 and Rim15 is required for maximum longevity extension. ..
- MacLellan W, Xiao G, Abdellatif M, Schneider M. A novel Rb- and p300-binding protein inhibits transactivation by MyoD. Mol Cell Biol. 2000;20:8903-15 pubmed..Inhibition of MyoD may be explained by EID-1's ability to bind and inhibit p300's histone acetylase activity, an essential MyoD coactivator. Thus, EID-1 binds both Rb and p300 and is a novel repressor of MyoD function. ..
- Rundlett S, Carmen A, Suka N, Turner B, Grunstein M. Transcriptional repression by UME6 involves deacetylation of lysine 5 of histone H4 by RPD3. Nature. 1998;392:831-5 pubmed..As increased acetylation of this residue is not merely a consequence of gene transcription, acetylation of this site may be essential for regulating gene activity. ..
- Suka N, Luo K, Grunstein M. Sir2p and Sas2p opposingly regulate acetylation of yeast histone H4 lysine16 and spreading of heterochromatin. Nat Genet. 2002;32:378-83 pubmed..These data indicate that opposing effects of Sir2p and Sas2p on acetylation of H4-Lys16 maintain the boundary at telomeric heterochromatin. ..
- Day G, Mosteller R, Broek D. Distinct subclasses of small GTPases interact with guanine nucleotide exchange factors in a similar manner. Mol Cell Biol. 1998;18:7444-54 pubmed..This finding suggests that GTPases of the Ras superfamily each may share common features of GEF-mediated guanine nucleotide exchange even though the GEFs for each of the Ras subfamilies appear evolutionarily unrelated. ..