Genomes and Genes
Experts and Doctors on saccharomyces cerevisiae in Toronto, Ontario, Canada
Locale: Toronto, Ontario, Canada
Topic: saccharomyces cerevisiae
Publications177 found, 100 shown here
- Breitkreutz A, Boucher L, Breitkreutz B, Sultan M, Jurisica I, Tyers M. Phenotypic and transcriptional plasticity directed by a yeast mitogen-activated protein kinase network. Genetics. 2003;165:997-1015 pubmed..This systems-level robustness may also account for the observed diversity of signals that trigger invasive growth. ..
- Moffat J, Andrews B. Late-G1 cyclin-CDK activity is essential for control of cell morphogenesis in budding yeast. Nat Cell Biol. 2004;6:59-66 pubmed..We conclude that a burst of late G1 cyclin-CDK activity is essential for establishing cell polarity and development of the cleavage apparatus. ..
- Lau W, Baker L, Rubinstein J. Cryo-EM structure of the yeast ATP synthase. J Mol Biol. 2008;382:1256-64 pubmed publisher..This new map has allowed construction of a model of subunit arrangement in the F(O) motor of ATP synthase that dictates how dimerization of the complex via subunits e and g might occur. ..
- Lissina E, Young B, Urbanus M, Guan X, Lowenson J, Hoon S, et al. A systems biology approach reveals the role of a novel methyltransferase in response to chemical stress and lipid homeostasis. PLoS Genet. 2011;7:e1002332 pubmed publisher..This approach demonstrates the value of combining chemical genomics with other systems-based methods for characterizing proteins and elucidating previously unknown mechanisms of action of small molecule inhibitors. ..
- Bastajian N, Friesen H, Andrews B. Bck2 acts through the MADS box protein Mcm1 to activate cell-cycle-regulated genes in budding yeast. PLoS Genet. 2013;9:e1003507 pubmed publisher..Our data suggest that Yox1 and Bck2 may compete for access to the Mcm1-ECB scaffold to ensure appropriate activation of the initial suite of genes required for cell cycle commitment. ..
- Manolson M, Wu B, Proteau D, Taillon B, Roberts B, Hoyt M, et al. STV1 gene encodes functional homologue of 95-kDa yeast vacuolar H(+)-ATPase subunit Vph1p. J Biol Chem. 1994;269:14064-74 pubmed..The function of these 100-kDa homologues may be to target or regulate other common V-ATPase subunits for two distinct cellular locations. ..
- Kanellis P, Agyei R, Durocher D. Elg1 forms an alternative PCNA-interacting RFC complex required to maintain genome stability. Curr Biol. 2003;13:1583-95 pubmed..Collectively, these results reveal that Elg1 forms a novel and conserved alternative RFC complex. Furthermore, we propose that genome instability arises at high frequency in elg1 mutants due to a defect in Okazaki fragment maturation. ..
- Peng W, Krogan N, Richards D, Greenblatt J, Hughes T. ESF1 is required for 18S rRNA synthesis in Saccharomyces cerevisiae. Nucleic Acids Res. 2004;32:1993-9 pubmed..These data indicate that Esf1p plays a direct role in early pre-rRNA processing. ..
- Costanzo M, Nishikawa J, Tang X, Millman J, Schub O, Breitkreuz K, et al. CDK activity antagonizes Whi5, an inhibitor of G1/S transcription in yeast. Cell. 2004;117:899-913 pubmed..Elimination of CDK activity at the end of mitosis allows Whi5 to reenter the nucleus to again repress G1/S transcription. These findings harmonize G1/S control in eukaryotes. ..
- Aviv T, Lin Z, Ben Ari G, Smibert C, Sicheri F. Sequence-specific recognition of RNA hairpins by the SAM domain of Vts1p. Nat Struct Mol Biol. 2006;13:168-76 pubmed..Bioinformatic analysis of these mRNAs demonstrates that the RNA-binding specificity of Vts1p in vivo is probably more stringent than that of the isolated SAM domain in vitro. ..
- Kanellis P, Gagliardi M, Banath J, Szilard R, Nakada S, Galicia S, et al. A screen for suppressors of gross chromosomal rearrangements identifies a conserved role for PLP in preventing DNA lesions. PLoS Genet. 2007;3:e134 pubmed
- Tyers M. The cyclin-dependent kinase inhibitor p40SIC1 imposes the requirement for Cln G1 cyclin function at Start. Proc Natl Acad Sci U S A. 1996;93:7772-6 pubmed..The existence of this activity means that the B-type cyclin inhibitor p40SIC1 imposes the requirement for Cln function at Start. ..
- Nouraini S, Archambault J, Friesen J. Rpo26p, a subunit common to yeast RNA polymerases, is essential for the assembly of RNA polymerases I and II and for the stability of the largest subunits of these enzymes. Mol Cell Biol. 1996;16:5985-96 pubmed..Furthermore, A190p and Rpo21p continued to accumulate at low levels under these conditions. We suggest that Rpo26p is essential for the assembly of RNAPI and RNAPII and for the stability of the largest subunits of these enzymes. ..
- Xu D, Friesen J. Splicing factor slt11p and its involvement in formation of U2/U6 helix II in activation of the yeast spliceosome. Mol Cell Biol. 2001;21:1011-23 pubmed..These results suggest that the function of Slt11p is regulated by Slu7p in the spliceosome. ..
- Baetz K, Moffat J, Haynes J, Chang M, Andrews B. Transcriptional coregulation by the cell integrity mitogen-activated protein kinase Slt2 and the cell cycle regulator Swi4. Mol Cell Biol. 2001;21:6515-28 pubmed..Our results establish a new Slt2-dependent mode of Swi4 regulation and suggest roles for Swi4 beyond its prominent role in controlling cell cycle transcription. ..
- Friesen H, Murphy K, Breitkreutz A, Tyers M, Andrews B. Regulation of the yeast amphiphysin homologue Rvs167p by phosphorylation. Mol Biol Cell. 2003;14:3027-40 pubmed..Our results suggest that phosphorylation of Rvs167p by a cyclin-dependent kinase and by a MAP kinase is an important mechanism for regulating protein complexes involved in actin cytoskeleton function. ..
- Tsui K, Dubuis S, Gebbia M, Morse R, Barkai N, Tirosh I, et al. Evolution of nucleosome occupancy: conservation of global properties and divergence of gene-specific patterns. Mol Cell Biol. 2011;31:4348-55 pubmed publisher..Thus, while some evolutionary changes in nucleosome occupancy contribute to gene expression divergence, nucleosome occupancy often diverges extensively with apparently little impact on gene expression. ..
- Hughes T, de Boer C. Mapping yeast transcriptional networks. Genetics. 2013;195:9-36 pubmed publisher..We propose that the time is ripe for renewed systematic efforts toward a complete mapping of yeast transcriptional regulatory mechanisms. ..
- Subramanian M, Qiao W, Khanam N, Wilkins O, Der S, Lalich J, et al. Transcriptional regulation of the one-carbon metabolism regulon in Saccharomyces cerevisiae by Bas1p. Mol Microbiol. 2005;57:53-69 pubmed..The response of the promoter to glycine required an intact SHM2 gene but was restored in a shm2 strain by addition of formate to the medium. ..
- Chua G, Morris Q, Sopko R, Robinson M, Ryan O, Chan E, et al. Identifying transcription factor functions and targets by phenotypic activation. Proc Natl Acad Sci U S A. 2006;103:12045-50 pubmed..The general strategy outlined here presents a straightforward approach to discovery of TF activities and mapping targets that could be adapted to any organism with transgenic technology. ..
- Memarian N, Jessulat M, Alirezaie J, Mir Rashed N, Xu J, Zareie M, et al. Colony size measurement of the yeast gene deletion strains for functional genomics. BMC Bioinformatics. 2007;8:117 pubmed..GD offers significant improvement over the manual inspection method to detect relative yeast colony size differences. The speed and accuracy associated with GD makes it an ideal choice for large-scale functional genomics investigations. ..
- Sopko R, Huang D, Smith J, Figeys D, Andrews B. Activation of the Cdc42p GTPase by cyclin-dependent protein kinases in budding yeast. EMBO J. 2007;26:4487-500 pubmed..Inhibition of GAPs by CDK phosphorylation may be a general mechanism to promote proper G1-phase progression. ..
- Catalano A, O Day D. Nucleoplasmic/nucleolar translocation and identification of a nuclear localization signal (NLS) in Dictyostelium BAF60a/SMARCD1 homologue Snf12. Histochem Cell Biol. 2012;138:515-30 pubmed publisher..Snf12 is the second Dictyostelium nucleolar protein for which its dynamics during mitosis have been investigated. ..
- Abdel Hamid H, Chin K, Moeder W, Shahinas D, Gupta D, Yoshioka K. A suppressor screen of the chimeric AtCNGC11/12 reveals residues important for intersubunit interactions of cyclic nucleotide-gated ion channels. Plant Physiol. 2013;162:1681-93 pubmed publisher..Taken together, we have identified two residues that are likely important for subunit interaction for plant CNGCs and likely for animal CNGCs as well. ..
- Gadsden M, McIntosh E, Game J, Wilson P, Haynes R. dUTP pyrophosphatase is an essential enzyme in Saccharomyces cerevisiae. EMBO J. 1993;12:4425-31 pubmed..These results are in general agreement with previous models in thymine-less death that implicate dUTP metabolism. They also suggest an alternative approach for chemotherapeutic drug design. ..
- Lee S, Hunte C, Malaney S, Robinson B. The N-terminus of the Qcr7 protein of the cytochrome bc(1) complex in S. cerevisiae may be involved in facilitating stability of the subcomplex with the Qcr8 protein and cytochrome b. Arch Biochem Biophys. 2001;393:215-21 pubmed..These results are interpreted in the light of the X-ray crystal structure of the yeast bc(1) complex. ..
- Nedea E, Nalbant D, Xia D, Theoharis N, Suter B, Richardson C, et al. The Glc7 phosphatase subunit of the cleavage and polyadenylation factor is essential for transcription termination on snoRNA genes. Mol Cell. 2008;29:577-87 pubmed publisher..Swd2 is also a subunit of the Set1c histone H3K4 methyltransferase complex and is required for its stability and optimal methyltransferase activity. ..
- Cutter A, Moses A. Polymorphism, divergence, and the role of recombination in Saccharomyces cerevisiae genome evolution. Mol Biol Evol. 2011;28:1745-54 pubmed publisher..We conclude that widespread natural selection across the yeast genome has left its imprint on segregating genetic variation, but that this signature is much weaker than in Drosophila and Caenorhabditis. ..
- Wallace I, Urbanus M, Luciani G, Burns A, Han M, Wang H, et al. Compound prioritization methods increase rates of chemical probe discovery in model organisms. Chem Biol. 2011;18:1273-83 pubmed publisher..As community resources, the ~7500 growth-inhibitory molecules have been made commercially available and the computational model and filter used are provided. ..
- Archambault J, Friesen J. Genetics of eukaryotic RNA polymerases I, II, and III. Microbiol Rev. 1993;57:703-24 pubmed
- Mrkobrada S, Boucher L, Ceccarelli D, Tyers M, Sicheri F. Structural and functional analysis of Saccharomyces cerevisiae Mob1. J Mol Biol. 2006;362:430-40 pubmed..The N-terminal region of Mob1 thus contains structural elements that are functionally important. ..
- Qiu L, Pashkova N, Walker J, Winistorfer S, Allali Hassani A, Akutsu M, et al. Structure and function of the PLAA/Ufd3-p97/Cdc48 complex. J Biol Chem. 2010;285:365-72 pubmed publisher..These data suggest that the p97-PLAA interaction is important for a subset of PLAA-dependent biological processes and provides a framework to better understand the role of these complex molecules in the ubiquitin system. ..
- McNeil J, Flynn J, Tsao N, Monschau N, Stahmann K, Haynes R, et al. Glycine metabolism in Candida albicans: characterization of the serine hydroxymethyltransferase (SHM1, SHM2) and threonine aldolase (GLY1) genes. Yeast. 2000;16:167-75 pubmed..cerevisiae. GenBank Accession Nos of the C. albicans SHM1 and SHM2 are AF009965 and AF009966, respectively. Accession No. for C. albicans GLY1 is AF009967. ..
- Lalor D, Schnyder T, Saridakis V, Pilloff D, Dong A, Tang H, et al. Structural and functional analysis of a truncated form of Saccharomyces cerevisiae ATP sulfurylase: C-terminal domain essential for oligomer formation but not for activity. Protein Eng. 2003;16:1071-9 pubmed..Careful inspection and modeling revealed that the groove is sufficiently deep and wide, as well as properly positioned, to act as a substrate channel between the ATP sulfurylase and APS kinase-like domains of the enzyme. ..
- Hepworth S, Friesen H, Segall J. NDT80 and the meiotic recombination checkpoint regulate expression of middle sporulation-specific genes in Saccharomyces cerevisiae. Mol Cell Biol. 1998;18:5750-61 pubmed..Thus, middle genes are expressed only on completion of meiotic recombination and subsequent generation of an active form of Ndt80p. ..
- Donaldson I, Friesen J. Zinc stoichiometry of yeast RNA polymerase II and characterization of mutations in the zinc-binding domain of the largest subunit. J Biol Chem. 2000;275:13780-8 pubmed..Core activity of the mutant enzyme was reduced 20-fold. We conclude that mutations in the zinc-binding domain can reduce core activity without altering the association of any of the subunits required for this activity. ..
- Zhang C, Roberts T, Yang J, Desai R, Brown G. Suppression of genomic instability by SLX5 and SLX8 in Saccharomyces cerevisiae. DNA Repair (Amst). 2006;5:336-46 pubmed..This suggested that Slx8 and Slx8 played limited roles in stabilizing, restarting, or resolving transiently stalled replication forks, but were critical for preventing the accumulation of DNA damage during normal cell cycle progression. ..
- Helsen C, Glover J. A new perspective on Hsp104-mediated propagation and curing of the yeast prion [PSI (+) ]. Prion. 2012;6:234-9 pubmed publisher..In light of this finding, we present a modified model of Hsp104-mediated [PSI (+) ] propagation and curing that requires only partial remodeling of Sup35 assembled into amyloid fibrils. ..
- Robbins N, Collins C, Morhayim J, Cowen L. Metabolic control of antifungal drug resistance. Fungal Genet Biol. 2010;47:81-93 pubmed publisher..Compromising a global regulator that couples growth and metabolism to environmental cues, Tor kinase, provides a powerful strategy to abrogate drug resistance of S. cerevisiae and Candida albicans with broad therapeutic potential. ..
- Ryan O, Shapiro R, Kurat C, Mayhew D, Baryshnikova A, Chin B, et al. Global gene deletion analysis exploring yeast filamentous growth. Science. 2012;337:1353-6 pubmed publisher..cerevisiae and C. albicans. ..
- Lagosky P, Taylor G, Haynes R. Molecular characterization of the Saccharomyces cerevisiae dihydrofolate reductase gene (DFR1). Nucleic Acids Res. 1987;15:10355-71 pubmed..cerevisiae are located within the 5'-noncoding region with respect to the open reading frame. The DNA fragment containing these sequences has been shown to be necessary for DFR1 gene expression in both S. cerevisiae and E. coli. ..
- Grigull J, Mnaimneh S, Pootoolal J, Robinson M, Hughes T. Genome-wide analysis of mRNA stability using transcription inhibitors and microarrays reveals posttranscriptional control of ribosome biogenesis factors. Mol Cell Biol. 2004;24:5534-47 pubmed..Our results indicate that the abundance of ribosome biogenesis factors is controlled at the level of mRNA stability. ..
- On T, Xiong X, Pu S, Turinsky A, Gong Y, Emili A, et al. The evolutionary landscape of the chromatin modification machinery reveals lineage specific gains, expansions, and losses. Proteins. 2010;78:2075-89 pubmed publisher..As such, in addition to informing on the evolution of CM as a system, this study provides a set of comparative genomic approaches that can be generally applied to any biological systems. ..
- Makhnevych T, Wong P, Pogoutse O, Vizeacoumar F, Greenblatt J, Emili A, et al. Hsp110 is required for spindle length control. J Cell Biol. 2012;198:623-36 pubmed publisher..These data suggest a model whereby the Hsp70-Hsp110 chaperone complex antagonizes Cin8 plus-end motility and prevents premature spindle elongation in S phase. ..
- Ho Y, Costanzo M, Moore L, Kobayashi R, Andrews B. Regulation of transcription at the Saccharomyces cerevisiae start transition by Stb1, a Swi6-binding protein. Mol Cell Biol. 1999;19:5267-78 pubmed..Our results suggest a role for STB1 in controlling the timing of Start transcription that is revealed in the absence of the G(1) regulator CLN3, and they implicate Stb1 as an in vivo target of G(1)-specific cyclin-dependent kinases. ..
- Zou J, Friesen H, Larson J, Huang D, Cox M, Tatchell K, et al. Regulation of cell polarity through phosphorylation of Bni4 by Pho85 G1 cyclin-dependent kinases in Saccharomyces cerevisiae. Mol Biol Cell. 2009;20:3239-50 pubmed publisher..Our data suggest that misregulated Bni4 may bind in an uncontrolled manner to an essential component that resides at the bud neck, causing catastrophic morphogenesis defects. ..
- Costanzo M, Baryshnikova A, Bellay J, Kim Y, Spear E, Sevier C, et al. The genetic landscape of a cell. Science. 2010;327:425-31 pubmed publisher..We also demonstrate that extensive and unbiased mapping of the genetic landscape provides a key for interpretation of chemical-genetic interactions and drug target identification. ..
- Yeung M, Durocher D. Srs2 enables checkpoint recovery by promoting disassembly of DNA damage foci from chromatin. DNA Repair (Amst). 2011;10:1213-22 pubmed publisher..A failure to remove Rad51 causes persistence of ssDNA and the checkpoint signal. Therefore, we conclude that cells initiate recovery when the DNA structures that elicit the checkpoint are eliminated. ..
- Zhao R, Reithmeier R. Expression and characterization of the anion transporter homologue YNL275w in Saccharomyces cerevisiae. Am J Physiol Cell Physiol. 2001;281:C33-45 pubmed..These results suggest that the yeast gene YNL275w encodes a nonglycosylated anion transport protein, localized to the plasma membrane...
- Krogan N, Greenblatt J. Characterization of a six-subunit holo-elongator complex required for the regulated expression of a group of genes in Saccharomyces cerevisiae. Mol Cell Biol. 2001;21:8203-12 pubmed..cerevisiae genes in vivo. ..
- Vizeacoumar F, van Dyk N, S Vizeacoumar F, Cheung V, Li J, Sydorskyy Y, et al. Integrating high-throughput genetic interaction mapping and high-content screening to explore yeast spindle morphogenesis. J Cell Biol. 2010;188:69-81 pubmed publisher..Although we focused on spindle disassembly in a proof-of-principle study, our integrated HCS-SGA method can be applied to virtually any pathway, making it a powerful means for identifying specific cellular functions. ..
- Shabtai D, Giaever G, Nislow C. An algorithm for chemical genomic profiling that minimizes batch effects: bucket evaluations. BMC Bioinformatics. 2012;13:245 pubmed publisher..We created software and a user interface for using BE, which is publically available. ..
- Snow B, Hall R, Krumins A, Brothers G, Bouchard D, Brothers C, et al. GTPase activating specificity of RGS12 and binding specificity of an alternatively spliced PDZ (PSD-95/Dlg/ZO-1) domain. J Biol Chem. 1998;273:17749-55 pubmed..The presence of an alternatively spliced PDZ domain within RGS12 suggests a mechanism by which RGS proteins may target specific G-protein-coupled receptor systems for desensitization. ..
- Macpherson N, Measday V, Moore L, Andrews B. A yeast taf17 mutant requires the Swi6 transcriptional activator for viability and shows defects in cell cycle-regulated transcription. Genetics. 2000;154:1561-76 pubmed..The cell cycle and transcriptional defects caused by taf17(slm7-1) are consistent with the role of TAF(II)s as modulators of transcriptional activation and may reflect a role for TAF17 in regulating activation by SBF and MBF. ..
- Gonzalez C, Proudfoot M, Brown G, Korniyenko Y, Mori H, Savchenko A, et al. Molecular basis of formaldehyde detoxification. Characterization of two S-formylglutathione hydrolases from Escherichia coli, FrmB and YeiG. J Biol Chem. 2006;281:14514-22 pubmed..Thus, FrmB and YeiG are S-formylglutathione hydrolases with a Ser-His-Asp catalytic triad involved in the detoxification of formaldehyde in E. coli. ..
- He Z, Wong J, Maniar H, Brill S, Ingles C. Assessing the requirements for nucleotide excision repair proteins of Saccharomyces cerevisiae in an in vitro system. J Biol Chem. 1996;271:28243-9 pubmed..These data indicate that Rpa is an essential component of the NER machinery in S. cerevisiae as it is in mammalian cells. ..
- Lin A, Wang S, Nguyen T, Shire K, Frappier L. The EBNA1 protein of Epstein-Barr virus functionally interacts with Brd4. J Virol. 2008;82:12009-19 pubmed publisher..The results indicate that EBNA1 can functionally interact with Brd4 in native and heterologous systems and that this interaction facilitates transcriptional activation by EBNA1 from the FR element. ..
- Stark C, Su T, Breitkreutz A, Lourenco P, Dahabieh M, Breitkreutz B, et al. PhosphoGRID: a database of experimentally verified in vivo protein phosphorylation sites from the budding yeast Saccharomyces cerevisiae. Database (Oxford). 2010;2010:bap026 pubmed publisher..Database URL: http://phosphogrid.org/ ..
- Snider J, Kittanakom S, Damjanovic D, Curak J, Wong V, Stagljar I. Detecting interactions with membrane proteins using a membrane two-hybrid assay in yeast. Nat Protoc. 2010;5:1281-93 pubmed publisher..In this article, we describe a protocol for MYTH bait generation, validation and library screening. The entire MYTH procedure can generally be completed in 4-6 weeks. ..
- Maicas E, Shago M, Friesen J. Translation of the Saccharomyces cerevisiae tcm1 gene in the absence of a 5'-untranslated leader. Nucleic Acids Res. 1990;18:5823-8 pubmed..We conclude that the 5'-untranslated leader of the yeast tcm1 gene is not essential for accurate translation initiation, but enhances its efficiency. ..
- Lipshitz H, Smibert C. Mechanisms of RNA localization and translational regulation. Curr Opin Genet Dev. 2000;10:476-88 pubmed..Cis-acting sequences and trans-acting factors that function in translational repression have been identified along with factors involved in relief of translational repression at the site of localization. ..
- Kwan J, Warner N, Maini J, Chan Tung K, Zakaria H, Pawson T, et al. Saccharomyces cerevisiae Ste50 binds the MAPKKK Ste11 through a head-to-tail SAM domain interaction. J Mol Biol. 2006;356:142-54 pubmed..Yeast bearing mutations that prevented the heterotypic Ste11-Ste50 association in vitro presented signaling defects in the mating and high-osmolarity growth pathways. ..
- Tritchler D, Parkhomenko E, Beyene J. Filtering genes for cluster and network analysis. BMC Bioinformatics. 2009;10:193 pubmed publisher..coli and S. cerevisiae regulatory networks. The methods introduced apply very generally, to any similarity matrix describing gene expression. One of the proposed methods, SUMCOV, performed well for all models simulated. ..
- Colwill K, Pawson T, Andrews B, Prasad J, Manley J, Bell J, et al. The Clk/Sty protein kinase phosphorylates SR splicing factors and regulates their intranuclear distribution. EMBO J. 1996;15:265-75 pubmed..Overexpression of the active Clk/Sty kinase caused a redistribution of SR proteins within the nucleus. These results suggest that Clk/Sty kinase directly regulates the activity and compartmentalization of SR splicing factors. ..
- Tedford K, Kim S, Sa D, Stevens K, Tyers M. Regulation of the mating pheromone and invasive growth responses in yeast by two MAP kinase substrates. Curr Biol. 1997;7:228-38 pubmed..cerevisiae by directly inhibiting Ste12. Activation of Fus3 or Kss1 may cause phosphorylation-dependent release of Ste12 from Rst1/Rst2 and thereby activate Ste12-dependent transcription. ..
- Botuyan M, Koth C, Mer G, Chakrabartty A, Conaway J, Conaway R, et al. Binding of elongin A or a von Hippel-Lindau peptide stabilizes the structure of yeast elongin C. Proc Natl Acad Sci U S A. 1999;96:9033-8 pubmed..These results suggest a structural basis for the interaction of an F-box-containing protein with a SKP1 homologue and the modulation of this interaction by the tumor suppressor VHL. ..
- Tang X, Orlicky S, Lin Z, Willems A, Neculai D, Ceccarelli D, et al. Suprafacial orientation of the SCFCdc4 dimer accommodates multiple geometries for substrate ubiquitination. Cell. 2007;129:1165-76 pubmed..This spatial variability may accommodate diverse acceptor lysine geometries in both substrates and the elongating ubiquitin chain and thereby increase catalytic efficiency. ..
- Baxter J, Moeder W, Urquhart W, Shahinas D, Chin K, Christendat D, et al. Identification of a functionally essential amino acid for Arabidopsis cyclic nucleotide gated ion channels using the chimeric AtCNGC11/12 gene. Plant J. 2008;56:457-69 pubmed publisher..This suggests that AtCNGC11/12 suppressors could be a useful tool for discovering important residues not only for plant CNGCs but also for CNGCs in general. ..
- Murdoch T, Xu W, Stempak J, Landers C, Targan S, Rotter J, et al. Pattern recognition receptor and autophagy gene variants are associated with development of antimicrobial antibodies in Crohn's disease. Inflamm Bowel Dis. 2012;18:1743-8 pubmed publisher..In particular, the additive effect of NOD2 3020insC and ATG16L1 T300A suggests a role for autophagy in development of ASCA. ..
- Tkach J, Yimit A, Lee A, Riffle M, Costanzo M, Jaschob D, et al. Dissecting DNA damage response pathways by analysing protein localization and abundance changes during DNA replication stress. Nat Cell Biol. 2012;14:966-76 pubmed publisher..This method identifies response pathways that were not detected in genetic and protein interaction screens, and can be readily applied to any form of chemical or genetic stress to reveal cellular response pathways. ..
- Ochotny N, Van Vliet A, Chan N, Yao Y, Morel M, Kartner N, et al. Effects of human a3 and a4 mutations that result in osteopetrosis and distal renal tubular acidosis on yeast V-ATPase expression and activity. J Biol Chem. 2006;281:26102-11 pubmed..That a4 W520L affects both Vo and V1 subunits is a unique phenotype for any V-ATPase subunit mutation and supports the concerted pathway for V-ATPase assembly in vivo. ..
- Meglei G, McQuibban G. The dynamin-related protein Mgm1p assembles into oligomers and hydrolyzes GTP to function in mitochondrial membrane fusion. Biochemistry. 2009;48:1774-84 pubmed publisher..Together, these data indicate that Mgm1p mediates fusion through oligomerization, GTP hydrolysis, and lipid binding in a manner similar to those of other dynamin mechanoenzymes. ..
- Mittag T, Marsh J, Grishaev A, Orlicky S, Lin H, Sicheri F, et al. Structure/function implications in a dynamic complex of the intrinsically disordered Sic1 with the Cdc4 subunit of an SCF ubiquitin ligase. Structure. 2010;18:494-506 pubmed publisher..These results provide a physical picture of a protein that is predominantly disordered in both its free and bound states, enabling aspects of its structure/function relationship to be elucidated. ..
- Tsui K, Durbic T, Gebbia M, Nislow C. Genomic approaches for determining nucleosome occupancy in yeast. Methods Mol Biol. 2012;833:389-411 pubmed publisher..Here, we describe the use of genome-wide approaches to determining nucleosome occupancy in yeast. ..
- Lam M, Snider J, Rehal M, Wong V, Aboualizadeh F, Drecun L, et al. A Comprehensive Membrane Interactome Mapping of Sho1p Reveals Fps1p as a Novel Key Player in the Regulation of the HOG Pathway in S. cerevisiae. J Mol Biol. 2015;427:2088-103 pubmed publisher..This study represents the largest membrane interactome analysis of Sho1p to date and complements past studies on the HOG pathway by increasing our understanding of Sho1p regulation. ..
- Davidson M, Katou Y, Keszthelyi A, Sing T, Xia T, Ou J, et al. Endogenous DNA replication stress results in expansion of dNTP pools and a mutator phenotype. EMBO J. 2012;31:895-907 pubmed publisher..Together, our data point to a vicious circle in which mutations in gatekeeper genes give rise to genomic instability during S phase, inducing expansion of the dNTP pool, which in turn results in high levels of spontaneous mutagenesis. ..
- Sukhai M, Prabha S, Hurren R, Rutledge A, Lee A, Sriskanthadevan S, et al. Lysosomal disruption preferentially targets acute myeloid leukemia cells and progenitors. J Clin Invest. 2013;123:315-28 pubmed publisher..These results demonstrate that lysosomal disruption preferentially targets AML cells and AML progenitor cells, providing a rationale for testing lysosomal disruption as a novel therapeutic strategy for AML. ..
- Roberts T, Kobor M, Bastin Shanower S, Ii M, Horte S, Gin J, et al. Slx4 regulates DNA damage checkpoint-dependent phosphorylation of the BRCT domain protein Rtt107/Esc4. Mol Biol Cell. 2006;17:539-48 pubmed
- Ghavidel A, Kislinger T, Pogoutse O, Sopko R, Jurisica I, Emili A. Impaired tRNA nuclear export links DNA damage and cell-cycle checkpoint. Cell. 2007;131:915-26 pubmed
- Dixon S, Costanzo M, Baryshnikova A, Andrews B, Boone C. Systematic mapping of genetic interaction networks. Annu Rev Genet. 2009;43:601-25 pubmed publisher..Together, our emerging knowledge of the genetic wiring diagrams of eukaryotic and prokaryotic cells is providing a new understanding of the relationship between genotype and phenotype. ..
- Davierwala A, Haynes J, Li Z, Brost R, Robinson M, Yu L, et al. The synthetic genetic interaction spectrum of essential genes. Nat Genet. 2005;37:1147-52 pubmed
- Lam M, Urban Grimal D, Bugnicourt A, Greenblatt J, Haguenauer Tsapis R, Emili A. Interaction of the deubiquitinating enzyme Ubp2 and the e3 ligase Rsp5 is required for transporter/receptor sorting in the multivesicular body pathway. PLoS ONE. 2009;4:e4259 pubmed publisher..Taken together, our data suggest a previously overlooked role for Ubp2 as a positive regulator of Rsp5-mediated membrane protein trafficking subsequent to endocytosis. ..
- Zhang W, Durocher D. De novo telomere formation is suppressed by the Mec1-dependent inhibition of Cdc13 accumulation at DNA breaks. Genes Dev. 2010;24:502-15 pubmed publisher..These studies therefore identify a mechanism by which the ATR family of kinases enforces genome integrity, and a process that underscores the contribution of Cdc13 to the fate of DNA ends. ..