Genomes and Genes
Experts and Doctors on saccharomyces cerevisiae proteins in Nashville, Tennessee, United States
Locale: Nashville, Tennessee, United States
Topic: saccharomyces cerevisiae proteins
- Klebanow E, Poon D, Zhou S, Weil P. Cloning and characterization of an essential Saccharomyces cerevisiae gene, TAF40, which encodes yTAFII40, an RNA polymerase II-specific TATA-binding protein-associated factor. J Biol Chem. 1997;272:9436-42 pubmed..By these criteria yTAF40 appears to encode a bona fide RNA polymerase II-specific TAF, and thus the protein that it encodes has been termed yTAFII40. ..
- Ohi R, Feoktistova A, McCann S, Valentine V, Look A, Lipsick J, et al. Myb-related Schizosaccharomyces pombe cdc5p is structurally and functionally conserved in eukaryotes. Mol Cell Biol. 1998;18:4097-108 pubmed..Collectively, these results suggest that Cdc5 family members participate in a novel pathway to regulate G2/M progression. ..
- Fang H, Panzner S, Mullins C, Hartmann E, Green N. The homologue of mammalian SPC12 is important for efficient signal peptidase activity in Saccharomyces cerevisiae. J Biol Chem. 1996;271:16460-5 pubmed..Through both genetic and biochemical criteria, Spc1p appears, however, to be important for efficient signal peptidase activity. ..
- Flick J, Thorner J. An essential function of a phosphoinositide-specific phospholipase C is relieved by inhibition of a cyclin-dependent protein kinase in the yeast Saccharomyces cerevisiae. Genetics. 1998;148:33-47 pubmed..Unlike single mutants, plc1delta pho81delta and plc1delta spl2delta double mutants were unable to grow on synthetic complete medium, but were able to grow on rich medium. ..
- DeGregori J, Russ A, von Melchner H, Rayburn H, Priyaranjan P, Jenkins N, et al. A murine homolog of the yeast RNA1 gene is required for postimplantation development. Genes Dev. 1994;8:265-76 pubmed..These similarities suggest that Fug1 may be required for developmental changes in RNA processing or chromatin structure prior to gastrulation. ..
- Kanter D, Kaplan D. Sld2 binds to origin single-stranded DNA and stimulates DNA annealing. Nucleic Acids Res. 2011;39:2580-92 pubmed publisher..Sld2-stimulated annealing may be important for maintaining genome stability during the initiation of DNA replication. ..
- Gumbs O, Campbell A, Weil P. High-affinity DNA binding by a Mot1p-TBP complex: implications for TAF-independent transcription. EMBO J. 2003;22:3131-41 pubmed..We propose that this altered TBP-DNA recognition is integral to Mot1p's ability to regulate transcription, and further postulate that the Mot1p-TBP complex delivers TBP to TAF-independent mRNA encoding genes. ..
- Zhang Y, Rodesch C, Broadie K. Living synaptic vesicle marker: synaptotagmin-GFP. Genesis. 2002;34:142-5 pubmed
- Fang H, Mullins C, Green N. In addition to SEC11, a newly identified gene, SPC3, is essential for signal peptidase activity in the yeast endoplasmic reticulum. J Biol Chem. 1997;272:13152-8 pubmed..Here we report the cloning of the SPC3 gene encoding the homolog to mammalian signal peptidase subunit SPC22/23. We find that Spc3p is also required for cell growth and signal peptidase activity within the yeast endoplasmic reticulum. ..
- Bruck I, Kaplan D. GINS and Sld3 compete with one another for Mcm2-7 and Cdc45 binding. J Biol Chem. 2011;286:14157-67 pubmed publisher..Our results are consistent with a model wherein GINS trades places with Sld3 at a replication origin, contributing to the activation of the replication fork helicase. ..
- Dawson T, Lazarus M, Hetzer M, Wente S. ER membrane-bending proteins are necessary for de novo nuclear pore formation. J Cell Biol. 2009;184:659-75 pubmed publisher..We hypothesize that these ER membrane-bending proteins mediate early NPC assembly steps...
- Chen J, Lu L, Ohi M, Creamer K, English C, Partridge J, et al. Cdk1 phosphorylation of the kinetochore protein Nsk1 prevents error-prone chromosome segregation. J Cell Biol. 2011;195:583-93 pubmed publisher..Our findings establish new roles for Cdk1 and the Nsk1-Dlc1 complex in regulating the k-MT interface and chromosome segregation. ..
- Singh M, Bland C, Weil P. Molecular and genetic characterization of a Taf1p domain essential for yeast TFIID assembly. Mol Cell Biol. 2004;24:4929-42 pubmed..These data are consistent with the hypothesis that Taf1p subserves a critical scaffold function within the TFIID complex. The significance of these data with regard to TFIID structure and function is discussed. ..
- Durst K, Lutterbach B, Kummalue T, Friedman A, Hiebert S. The inv(16) fusion protein associates with corepressors via a smooth muscle myosin heavy-chain domain. Mol Cell Biol. 2003;23:607-19 pubmed..inv(16)-mediated repression is sensitive to HDAC inhibitors. We propose a model whereby the inv(16) fusion protein associates with AML1 to convert AML1 into a constitutive transcriptional repressor. ..
- Gould K, Burns C, Feoktistova A, Hu C, Pasion S, Forsburg S. Fission yeast cdc24(+) encodes a novel replication factor required for chromosome integrity. Genetics. 1998;149:1221-33 pubmed..An S. pombe homolog of the replicative DNA helicase DNA2 of S. cerevisiae suppresses cdc24. These results suggest that Cdc24p plays a role in the progression of normal DNA replication and is required to maintain genomic integrity. ..
- Bolger T, Folkmann A, Tran E, Wente S. The mRNA export factor Gle1 and inositol hexakisphosphate regulate distinct stages of translation. Cell. 2008;134:624-33 pubmed publisher..However, Gle1 also independently mediates initiation. Thus, Gle1 is uniquely positioned to coordinate the mRNA export and translation mechanisms. These results directly impact models for perturbation of Gle1 function in pathophysiology. ..
- Olsen D, Jordan B, Chen D, Wek R, Cavener D. Isolation of the gene encoding the Drosophila melanogaster homolog of the Saccharomyces cerevisiae GCN2 eIF-2alpha kinase. Genetics. 1998;149:1495-509 pubmed..Drosophila and other higher eukaryotes. Despite these differences, the presence of GCN2 in Drosophila suggests at least partial conservation from yeast to multicellular organisms of the mechanisms responding to amino acid deprivation. ..
- Gall W, Geething N, Hua Z, Ingram M, Liu K, Chen S, et al. Drs2p-dependent formation of exocytic clathrin-coated vesicles in vivo. Curr Biol. 2002;12:1623-7 pubmed..These data provide the first in vivo evidence for an integral membrane protein requirement in forming CCVs. ..
- Ren L, McLean J, Hazbun T, Fields S, VANDER KOOI C, Ohi M, et al. Systematic two-hybrid and comparative proteomic analyses reveal novel yeast pre-mRNA splicing factors connected to Prp19. PLoS ONE. 2011;6:e16719 pubmed publisher..Our multi-faceted approach has revealed new low abundance splicing factors connected to NTC function, provides evidence for distinct Prp19 containing complexes, and underscores the role of the Prp19 WD40 domain as a splicing scaffold...
- Ji H, Platts M, Dharamsi L, Friedman K. Regulation of telomere length by an N-terminal region of the yeast telomerase reverse transcriptase. Mol Cell Biol. 2005;25:9103-14 pubmed..Taken together, these data suggest that specific amino acids within region I of the catalytic subunit of yeast telomerase play a previously unanticipated role in the response to Tel1p regulation at the telomere. ..
- Bai Y, Perez G, Beechem J, Weil P. Structure-function analysis of TAF130: identification and characterization of a high-affinity TATA-binding protein interaction domain in the N terminus of yeast TAF(II)130. Mol Cell Biol. 1997;17:3081-93 pubmed..Moreover, we found that the N-terminal domain of yTAF(II)130 actively dissociated TBP from TATA box-containing DNA. ..
- Powell D, Weaver C, Jennings J, McAfee K, He Y, Weil P, et al. Cluster analysis of mass spectrometry data reveals a novel component of SAGA. Mol Cell Biol. 2004;24:7249-59 pubmed..Our data suggest that the role of SGF11 in transcription is independent of SAGA's histone acetyltransferase activity but may involve Ubp8p recruitment to or stabilization in SAGA. ..
- Podust V, Tiwari N, Stephan S, Fanning E. Replication factor C disengages from proliferating cell nuclear antigen (PCNA) upon sliding clamp formation, and PCNA itself tethers DNA polymerase delta to DNA. J Biol Chem. 1998;273:31992-9 pubmed..The readdition of RF-C to the isolated PCNA.DNA complex did not further stimulate pol delta DNA synthesis. We conclude that pol delta holoenzyme consists of PCNA and pol delta core and that RF-C serves only to load PCNA clamp. ..
- Ohi M, Vander Kooi C, Rosenberg J, Chazin W, Gould K. Structural insights into the U-box, a domain associated with multi-ubiquitination. Nat Struct Biol. 2003;10:250-5 pubmed..These comparative structural and functional analyses imply that the U-box and its associated ubiquitin ligase activity are critical for Prp19p function in vivo. ..
- Browne C, Samir P, Fites J, Villarreal S, Link A. The yeast eukaryotic translation initiation factor 2B translation initiation complex interacts with the fatty acid synthesis enzyme YBR159W and endoplasmic reticulum membranes. Mol Cell Biol. 2013;33:1041-56 pubmed publisher..We show that a ybr159w? yeast strain and other strains with null mutations in the VLCFA pathway cause eIF2B to appear as numerous foci throughout the cytoplasm. ..
- Tasto J, Morrell J, Gould K. An anillin homologue, Mid2p, acts during fission yeast cytokinesis to organize the septin ring and promote cell separation. J Cell Biol. 2003;160:1093-103 pubmed..These results suggest that Mid2p influences septin ring organization at the site of cell division and its turnover might normally be required to permit septin ring disassembly. ..
- Ho H, MacGurn J, Emr S. Deubiquitinating enzymes Ubp2 and Ubp15 regulate endocytosis by limiting ubiquitination and degradation of ARTs. Mol Biol Cell. 2017;28:1271-1283 pubmed publisher..Our results uncover a novel function for DUBs in the endocytic pathway by which Ubp2 and Ubp15 positively regulate the ART-Rsp5 network. ..
- Delpire E. The mammalian family of sterile 20p-like protein kinases. Pflugers Arch. 2009;458:953-67 pubmed publisher..A number of molecular details involved in the activation of the kinases are discussed including autophosphorylation, substrate recognition, autoinhibition, dimerization, and substrate binding. ..
- Liu K, Surendhran K, Nothwehr S, Graham T. P4-ATPase requirement for AP-1/clathrin function in protein transport from the trans-Golgi network and early endosomes. Mol Biol Cell. 2008;19:3526-35 pubmed publisher..These results imply that Drs2p acts independently of coat recruitment to facilitate AP-1/clathrin-coated vesicle budding from the TGN. ..
- Garbett K, Tripathi M, Cencki B, Layer J, Weil P. Yeast TFIID serves as a coactivator for Rap1p by direct protein-protein interaction. Mol Cell Biol. 2007;27:297-311 pubmed..We conclude that Rap1p and TFIID directly interact and that this interaction contributes importantly to RP gene transcription. ..
- Burns C, Ohi R, Krainer A, Gould K. Evidence that Myb-related CDC5 proteins are required for pre-mRNA splicing. Proc Natl Acad Sci U S A. 1999;96:13789-94 pubmed..These data provide evidence that eukaryotic cells require CDC5 proteins for pre-mRNA splicing. ..
- Terry L, Wente S. Nuclear mRNA export requires specific FG nucleoporins for translocation through the nuclear pore complex. J Cell Biol. 2007;178:1121-32 pubmed..These results pinpoint distinct steps in the mRNA export mechanism that regulate NPC translocation efficiency. ..
- Miller A, Suntharalingam M, Johnson S, Audhya A, Emr S, Wente S. Cytoplasmic inositol hexakisphosphate production is sufficient for mediating the Gle1-mRNA export pathway. J Biol Chem. 2004;279:51022-32 pubmed..Additionally, the cytoplasmic production of IP6 by plasma membrane-anchored Ipk1 rescued a gle1-2 ipk1-4 synthetic lethal mutant. Thus, cytoplasmic IP6 production is sufficient for mediating the Gle1-mRNA export pathway. ..
- Bartholomew C, Hardy C. p21-activated kinases Cla4 and Ste20 regulate vacuole inheritance in Saccharomyces cerevisiae. Eukaryot Cell. 2009;8:560-72 pubmed publisher..We propose that Cla4 and Ste20 are bud-specific proteins that play roles in both segregation structure resolution and the degradation of Vac17. ..
- McDonald W, Ohi R, Smelkova N, Frendewey D, Gould K. Myb-related fission yeast cdc5p is a component of a 40S snRNP-containing complex and is essential for pre-mRNA splicing. Mol Cell Biol. 1999;19:5352-62 pubmed..These data raise the possibility that the cdc5p complex is an intermediate in the assembly or disassembly of an active S. pombe spliceosome. ..
- Alcázar Román A, Tran E, Guo S, Wente S. Inositol hexakisphosphate and Gle1 activate the DEAD-box protein Dbp5 for nuclear mRNA export. Nat Cell Biol. 2006;8:711-6 pubmed..We now propose that Dbp5 activation at NPCs requires Gle1 and InsP6. This would facilitate spatial control of the remodelling of mRNP protein composition during directional transport and provide energy to power transport cycles. ..
- Natarajan P, Liu K, Patil D, Sciorra V, Jackson C, Graham T. Regulation of a Golgi flippase by phosphoinositides and an ArfGEF. Nat Cell Biol. 2009;11:1421-6 pubmed publisher..These interactions suggest the presence of a coincidence detection system used to activate phospholipid translocation at sites of vesicle formation. ..
- Wang J, STAFFORD J, Granner D. SRC-1 and GRIP1 coactivate transcription with hepatocyte nuclear factor 4. J Biol Chem. 1998;273:30847-30850 pubmed..Thus, HNF4 is involved in the regulation of glucose homeostasis at several levels and along with the SRC-1, GRIP1, and p300 may play an important role in the pathophysiology of non-insulin-dependent diabetes mellitus. ..
- Chim N, Gall W, Xiao J, Harris M, Graham T, Krezel A. Solution structure of the ubiquitin-binding domain in Swa2p from Saccharomyces cerevisiae. Proteins. 2004;54:784-93 pubmed..We propose that Swa2p is a multifunctional protein capable of recognizing several proteins through its protein-protein recognition domains. ..
- Mordes D, Nam E, Cortez D. Dpb11 activates the Mec1-Ddc2 complex. Proc Natl Acad Sci U S A. 2008;105:18730-4 pubmed publisher..Thus, Dpb11 is a functional ortholog of human TopBP1, and the Mec1/ATR activation mechanism is conserved from yeast to humans. ..
- Sammons M, Samir P, Link A. Saccharomyces cerevisiae Gis2 interacts with the translation machinery and is orthogonal to myotonic dystrophy type 2 protein ZNF9. Biochem Biophys Res Commun. 2011;406:13-9 pubmed publisher..These data suggest that Gis2 is functionally orthologous to ZNF9 and acts as a cap-independent translation factor...
- Lee Y, Naider F, Becker J. Interacting residues in an activated state of a G protein-coupled receptor. J Biol Chem. 2006;281:2263-72 pubmed..The information gained from this study should contribute to an understanding of the conformational differences between resting and active states in GPCRs. ..
- Casey A, Dawson T, Chen J, Friederichs J, Jaspersen S, Wente S. Integrity and function of the Saccharomyces cerevisiae spindle pole body depends on connections between the membrane proteins Ndc1, Rtn1, and Yop1. Genetics. 2012;192:441-55 pubmed publisher..We propose that NPC and SPB biogenesis are altered in cells lacking Rtn1 and Yop1 due to competition between these complexes for Ndc1, an essential common component of both NPCs and SPBs...
- Natarajan P, Wang J, Hua Z, Graham T. Drs2p-coupled aminophospholipid translocase activity in yeast Golgi membranes and relationship to in vivo function. Proc Natl Acad Sci U S A. 2004;101:10614-9 pubmed..Therefore, whereas NBD-PS is a preferred substrate for Drs2p in vitro, endogenous PS is not an obligatory substrate in vivo for the role Drs2p plays in protein transport...
- Baldridge R, Graham T. Two-gate mechanism for phospholipid selection and transport by type IV P-type ATPases. Proc Natl Acad Sci U S A. 2013;110:E358-67 pubmed publisher..This work describes a unique transport mechanism for a P-type ATPase and provides insight into how integral membrane proteins can recognize and transport phospholipid substrate across a lipid bilayer...
- Ohi M, Gould K. Characterization of interactions among the Cef1p-Prp19p-associated splicing complex. RNA. 2002;8:798-815 pubmed..Further, our data indicate that a mutation in the U-box of Prp19p disrupts these numerous protein interactions causing Cef1p degradation and Ntc instability. ..
- Bruck I, Kanter D, Kaplan D. Enabling association of the GINS protein tetramer with the mini chromosome maintenance (Mcm)2-7 protein complex by phosphorylated Sld2 protein and single-stranded origin DNA. J Biol Chem. 2011;286:36414-26 pubmed publisher..Furthermore, origin ssDNA may stimulate the formation of the CMG complex by alleviating inhibitory interactions between Sld2 with Mcm2-7. ..
- AlcÃ¡zar RomÃ¡n A, Bolger T, Wente S. Control of mRNA export and translation termination by inositol hexakisphosphate requires specific interaction with Gle1. J Biol Chem. 2010;285:16683-92 pubmed publisher..We conclude that Gle1 specifically binds IP(6) and that this interaction is required for the full potentiation of Dbp5 ATPase activity during both mRNA export and translation termination. ..
- Zhou X, Sebastian T, Graham T. Auto-inhibition of Drs2p, a yeast phospholipid flippase, by its carboxyl-terminal tail. J Biol Chem. 2013;288:31807-15 pubmed publisher..This work provides the first direct evidence, in a purified system, that a phospholipid flippase is subject to auto-inhibition by its C-terminal tail, which can be relieved by a phosphoinositide to stimulate flippase activity. ..
- Chen S, Wang J, Muthusamy B, Liu K, Zare S, Andersen R, et al. Roles for the Drs2p-Cdc50p complex in protein transport and phosphatidylserine asymmetry of the yeast plasma membrane. Traffic. 2006;7:1503-17 pubmed
- Burns C, Ohi R, Mehta S, O TOOLE E, Winey M, Clark T, et al. Removal of a single alpha-tubulin gene intron suppresses cell cycle arrest phenotypes of splicing factor mutations in Saccharomyces cerevisiae. Mol Cell Biol. 2002;22:801-15 pubmed
- Kirchner J, Sanders S, Klebanow E, Weil P. Molecular genetic dissection of TAF25, an essential yeast gene encoding a subunit shared by TFIID and SAGA multiprotein transcription factors. Mol Cell Biol. 2001;21:6668-80 pubmed..The results of these analyses show that TAF25p is comprised of multiple mutable elements which contribute importantly to RNA polymerase II-mediated mRNA gene transcription. ..
- Gall W, Higginbotham M, Chen C, Ingram M, Cyr D, Graham T. The auxilin-like phosphoprotein Swa2p is required for clathrin function in yeast. Curr Biol. 2000;10:1349-58 pubmed..They suggest that Swa2p is the yeast ortholog of auxilin and has a role in disassembling clathrin, not only in uncoating clathrin-coated vesicles but perhaps in preventing unproductive clathrin assembly in vivo. ..
- Ji H, Adkins C, Cartwright B, Friedman K. Yeast Est2p affects telomere length by influencing association of Rap1p with telomeric chromatin. Mol Cell Biol. 2008;28:2380-90 pubmed publisher..Taken together, these results suggest that Est2p can directly or indirectly influence the binding of Rap1p to telomeric DNA, implicating telomerase in roles both upstream and downstream of Rap1p in telomere length homeostasis...
- Luo W, Fang H, Green N. Substrate specificity of inner membrane peptidase in yeast mitochondria. Mol Genet Genomics. 2006;275:431-6 pubmed..These results suggest, surprisingly, G-3-P dehydrogenase has switched from Imp1p in yeast to Imp2p in mammals. ..
- Gerbasi V, Weaver C, Hill S, Friedman D, Link A. Yeast Asc1p and mammalian RACK1 are functionally orthologous core 40S ribosomal proteins that repress gene expression. Mol Cell Biol. 2004;24:8276-87 pubmed..Our data suggest that one of Asc1p's or RACK1's functions is to repress gene expression. ..
- Singleton C. Identification and characterization of the thiamine transporter gene of Saccharomyces cerevisiae. Gene. 1997;199:111-21 pubmed..The level of transporter mRNA was found to be rapidly and dramatically reduced by the addition of thiamine to the growth medium. ..
- Liang H, VanValkenburgh C, Chen X, Mullins C, Van Kaer L, Green N, et al. Genetic complementation in yeast reveals functional similarities between the catalytic subunits of mammalian signal peptidase complex. J Biol Chem. 2003;278:50932-9 pubmed..These data, thus, support a model that SPC18 and SPC21 are functionally and structurally similar to each other. ..
- Zhou X, Graham T. Reconstitution of phospholipid translocase activity with purified Drs2p, a type-IV P-type ATPase from budding yeast. Proc Natl Acad Sci U S A. 2009;106:16586-91 pubmed publisher..These data demonstrate for the first time the reconstitution of a flippase activity with a purified P4-ATPase. ..
- Baldridge R, Xu P, Graham T. Type IV P-type ATPases distinguish mono- versus diacyl phosphatidylserine using a cytofacial exit gate in the membrane domain. J Biol Chem. 2013;288:19516-27 pubmed publisher..These studies indicate that Dnf1 poorly recognizes diacylated phospholipid and define key substitutions enabling recognition of endogenous PS. ..
- Baldridge R, Graham T. Identification of residues defining phospholipid flippase substrate specificity of type IV P-type ATPases. Proc Natl Acad Sci U S A. 2012;109:E290-8 pubmed publisher..Modeling of residues involved in substrate selection suggests a novel P-type ATPase transport pathway at the protein/lipid interface and a potential solution to the giant substrate problem...
- Ryan K, McCaffery J, Wente S. The Ran GTPase cycle is required for yeast nuclear pore complex assembly. J Cell Biol. 2003;160:1041-53 pubmed..We propose a model wherein a Ran-mediated vesicular fusion step is required for NPC assembly into intact nuclear envelopes. ..
- Piechotta K, Lu J, Delpire E. Cation chloride cotransporters interact with the stress-related kinases Ste20-related proline-alanine-rich kinase (SPAK) and oxidative stress response 1 (OSR1). J Biol Chem. 2002;277:50812-9 pubmed..We conclude that several cation chloride co-transporters interact with SPAK and/or OSR1, and we hypothesize that this interaction might play a role during the initiation of the cellular stress response. ..
- Wanzek K, Schwindt E, Capra J, Paeschke K. Mms1 binds to G-rich regions in Saccharomyces cerevisiae and influences replication and genome stability. Nucleic Acids Res. 2017;45:7796-7806 pubmed publisher..Based on these data we propose a mechanistic model in which Mms1 binds to specific G-rich/G4 motif located on the lagging strand template for DNA replication and supports Pif1 function, DNA replication and genome integrity. ..