Genomes and Genes
Experts and Doctors on saccharomyces cerevisiae in San Diego, California, United States
Locale: San Diego, California, United States
Topic: saccharomyces cerevisiae
- Deckert M, Elly C, Altman A, Liu Y. Coordinated regulation of the tyrosine phosphorylation of Cbl by Fyn and Syk tyrosine kinases. J Biol Chem. 1998;273:8867-74 pubmed..These findings implicate Fyn as an adaptor protein that facilitates the interaction between Syk and Cbl, and suggest that Src and Syk family PTKs coordinately regulate the tyrosine phosphorylation of Cbl. ..
- Bicknell A, Tourtellotte J, Niwa M. Late phase of the endoplasmic reticulum stress response pathway is regulated by Hog1 MAP kinase. J Biol Chem. 2010;285:17545-55 pubmed publisher..From its cytoplasmic location, Hog1 contributes to the activation of autophagy by enhancing the stability of Atg8, a critical autophagy protein. Thus, Hog1 coordinates a multifaceted response to persistent ER stress. ..
- Putnam C, Kolodner R. Pathways and Mechanisms that Prevent Genome Instability in Saccharomyces cerevisiae. Genetics. 2017;206:1187-1225 pubmed publisher..Integrated models for the formation and suppression of GCRs are discussed. ..
- Katzmann D, Sarkar S, Chu T, Audhya A, Emr S. Multivesicular body sorting: ubiquitin ligase Rsp5 is required for the modification and sorting of carboxypeptidase S. Mol Biol Cell. 2004;15:468-80 pubmed..Thus, both Rsp5 and Fab1 play distinct and essential roles in the targeting of biosynthetic MVB cargoes. However, whereas Rsp5 seems to be responsible for cargo ubiquitination, the precise role for Fab1 remains to be elucidated. ..
- Berger K, Yaffe M. Prohibitin family members interact genetically with mitochondrial inheritance components in Saccharomyces cerevisiae. Mol Cell Biol. 1998;18:4043-52 pubmed..These results provide the first evidence of a role for prohibitin in mitochondrial inheritance and in the regulation of mitochondrial morphology. ..
- Rieder S, Emr S. Overview of subcellular fractionation procedures for the yeast Saccharomyces cerevisiae. Curr Protoc Cell Biol. 2001;Chapter 3:Unit 3.7 pubmed publisher..Topics include yeast cell lysate preparation, differential velocity centrifugation, density gradient centrifugation, and the analysis of subcellular fractions. ..
- Stefan C, Audhya A, Emr S. The yeast synaptojanin-like proteins control the cellular distribution of phosphatidylinositol (4,5)-bisphosphate. Mol Biol Cell. 2002;13:542-57 pubmed..Taken together, our results demonstrate that the yeast synaptojanins control the localization of PtdIns(4,5)P(2) in vivo and provide further evidence for the compartmentalization of different PI species. ..
- Rehling P, Skaletz Rorowski A, Girzalsky W, Voorn Brouwer T, Franse M, Distel B, et al. Pex8p, an intraperoxisomal peroxin of Saccharomyces cerevisiae required for protein transport into peroxisomes binds the PTS1 receptor pex5p. J Biol Chem. 2000;275:3593-602 pubmed..In pex8Delta cells, the PTS1 and PTS2 receptor still associate with membrane bound components of the protein import machinery, supporting the assumption that the Pex8p function in protein translocation follows the docking event. ..
- Ferry M, Razinkov I, Hasty J. Microfluidics for synthetic biology: from design to execution. Methods Enzymol. 2011;497:295-372 pubmed publisher..Finally, the procedures for conducting Escherichia coli and S. cerevisiae microchemostat experiments are addressed. ..
- Farre J, Burkenroad A, Burnett S, Subramani S. Phosphorylation of mitophagy and pexophagy receptors coordinates their interaction with Atg8 and Atg11. EMBO Rep. 2013;14:441-9 pubmed publisher..We present a common model for the phosphoregulation of selective autophagy receptors...
- Kassavetis G, Kumar A, Ramirez E, Geiduschek E. Functional and structural organization of Brf, the TFIIB-related component of the RNA polymerase III transcription initiation complex. Mol Cell Biol. 1998;18:5587-99 pubmed..The constraints established by these analyses specify a global model of the functional segments of Brf and how they fit into the structure of the TFIIIB-DNA complex. ..
- Amin N, Tuffo K, Holm C. Dominant mutations in three different subunits of replication factor C suppress replication defects in yeast PCNA mutants. Genetics. 1999;153:1617-28 pubmed..Biochemical analysis of the wild type and mutant PCNA and RFC3 proteins shows that mutant RFC3p enhances the production of long DNA products in pol delta-dependent DNA synthesis, which is consistent with an increase in processivity. ..
- Gardner R, Shearer A, Hampton R. In vivo action of the HRD ubiquitin ligase complex: mechanisms of endoplasmic reticulum quality control and sterol regulation. Mol Cell Biol. 2001;21:4276-91 pubmed..Thus, it appears that the physiologically regulated, HRD-dependent degradation of HMGR is effected by a programmed structural transition from a stable protein to a quality control substrate. ..
- Darsow T, Burd C, Emr S. Acidic di-leucine motif essential for AP-3-dependent sorting and restriction of the functional specificity of the Vam3p vacuolar t-SNARE. J Cell Biol. 1998;142:913-22 pubmed..Regulated transport of cargoes such as Vam3p through the AP-3-dependent pathway may play an important role in maintaining the unique composition, function, and morphology of the vacuole. ..
- Darsow T, Katzmann D, Cowles C, Emr S. Vps41p function in the alkaline phosphatase pathway requires homo-oligomerization and interaction with AP-3 through two distinct domains. Mol Biol Cell. 2001;12:37-51 pubmed..These data indicate that a homo-oligomeric form of Vps41p is required for the formation of ALP containing vesicles at the Golgi complex via interactions with AP-3. ..
- Deckert M, Tartare Deckert S, Hernandez J, Rottapel R, Altman A. Adaptor function for the Syk kinases-interacting protein 3BP2 in IL-2 gene activation. Immunity. 1998;9:595-605 pubmed..Thus, 3BP2 is an important adaptor that may couple activated Zap-70/Syk to a LAT-containing signaling complex involved in TCR-mediated gene transcription. ..
- Geiduschek E, Kassavetis G. Transcription: adjusting to adversity by regulating RNA polymerase. Curr Biol. 2006;16:R849-51 pubmed
- Lukasiewicz R, Velazquez Dones A, Huynh N, Hagopian J, Fu X, Adams J, et al. Structurally unique yeast and mammalian serine-arginine protein kinases catalyze evolutionarily conserved phosphorylation reactions. J Biol Chem. 2007;282:23036-43 pubmed..Thus, there are physical attributes of SR and SR-like substrates that dictate the mechanism of phosphorylation, whereas the ability to processively phosphorylate substrates is inherent to SR protein kinases. ..
- Ishiguro A, Kassavetis G, Geiduschek E. Essential roles of Bdp1, a subunit of RNA polymerase III initiation factor TFIIIB, in transcription and tRNA processing. Mol Cell Biol. 2002;22:3264-75 pubmed..Physical interaction of RNase P with Bdp1 was demonstrated by coimmunoprecipitation and pull-down assays. ..
- Fekkes P, Shepard K, Yaffe M. Gag3p, an outer membrane protein required for fission of mitochondrial tubules. J Cell Biol. 2000;151:333-40 pubmed..These results indicate that Gag3p plays a distinct role on the mitochondrial surface to mediate the fission of mitochondrial tubules. ..
- Hossain M, Chung C, Pradhan S, Johnson T. The yeast cap binding complex modulates transcription factor recruitment and establishes proper histone H3K36 trimethylation during active transcription. Mol Cell Biol. 2013;33:785-99 pubmed publisher..This work provides evidence for an emerging model that RNA processing factors can modulate the recruitment of transcription factors and influence histone modification during elongation. ..
- Herrgard M, Swainston N, Dobson P, Dunn W, Arga K, Arvas M, et al. A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Nat Biotechnol. 2008;26:1155-60 pubmed publisher..org/yeastnet). It can be maintained as a resource that serves as a common denominator for studying the systems biology of yeast. Similar strategies should benefit communities studying genome-scale metabolic networks of other organisms. ..
- Rudge S, Sciorra V, Iwamoto M, Zhou C, Strahl T, Morris A, et al. Roles of phosphoinositides and of Spo14p (phospholipase D)-generated phosphatidic acid during yeast sporulation. Mol Biol Cell. 2004;15:207-18 pubmed
- Yeakley J, Tronchere H, Olesen J, Dyck J, Wang H, Fu X. Phosphorylation regulates in vivo interaction and molecular targeting of serine/arginine-rich pre-mRNA splicing factors. J Cell Biol. 1999;145:447-55 pubmed
- Garza R, Sato B, Hampton R. In vitro analysis of Hrd1p-mediated retrotranslocation of its multispanning membrane substrate 3-hydroxy-3-methylglutaryl (HMG)-CoA reductase. J Biol Chem. 2009;284:14710-22 pubmed publisher..These studies directly demonstrate polytopic membrane protein retrotranslocation during ERAD and delineate avenues for mechanistic understanding of this general process. ..
- Fisk H, Yaffe M. Mutational analysis of Mdm1p function in nuclear and mitochondrial inheritance. J Cell Biol. 1997;138:485-94 pubmed..These results support a model of Mdm1p function in which a network comprised of multimeric assemblies of the protein mediates two distinct cellular processes. ..
- Putnam C, Hayes T, Kolodner R. Specific pathways prevent duplication-mediated genome rearrangements. Nature. 2009;460:984-9 pubmed publisher..This explains how extensive genome instability is prevented in eukaryotic cells whose genomes contain numerous divergent repeated sequences...
- Kennedy E, Ghosh G, Pillus L. Identification of functionally distinct regions that mediate biological activity of the protein kinase a homolog Tpk2. J Biol Chem. 2008;283:1084-93 pubmed..Because many of these map outside the conserved core, this approach should be broadly useful in identifying new, more kinase-specific therapeutic targets. ..
- Ruault M, Pillus L. Chromatin-modifiying enzymes are essential when the Saccharomyces cerevisiae morphogenesis checkpoint is constitutively activated. Genetics. 2006;174:1135-49 pubmed..A catalytically dead Hsl7p retained wild-type interactions, implying that modification of histone H3 or H4 N termini by Gcn5p, Esa1p, Rpd3p, and Set1p, but not by Hsl7p, was needed to bypass the morphogenesis checkpoint. ..
- Clizbe D, Owens M, Masuda K, Shackelford J, Krisans S. IDI2, a second isopentenyl diphosphate isomerase in mammals. J Biol Chem. 2007;282:6668-76 pubmed..8 microm IPP. Both isozymes, IDI1 and IDI2 are localized to the peroxisome by a PTS1-dependent pathway. Finally, our data suggest that IDI2 is regulated independently from IDI1, by a mechanism that may involve PPARalpha. ..
- Kassavetis G, Han S, Naji S, Geiduschek E. The role of transcription initiation factor IIIB subunits in promoter opening probed by photochemical cross-linking. J Biol Chem. 2003;278:17912-7 pubmed..In contrast, promoter opening-defective TFIIIB mutants generate significant changes of cross-linking of polymerase subunits. The weight of this evidence argues in favor of an indirect mode of action of TFIIIB in promoter opening. ..
- Pazin M, Hermann J, Kadonaga J. Promoter structure and transcriptional activation with chromatin templates assembled in vitro. A single Gal4-VP16 dimer binds to chromatin or to DNA with comparable affinity. J Biol Chem. 1998;273:34653-60 pubmed
- Lee S, Parent C, Insall R, Firtel R. A novel Ras-interacting protein required for chemotaxis and cyclic adenosine monophosphate signal relay in Dictyostelium. Mol Biol Cell. 1999;10:2829-45 pubmed
- Merrill B, Holm C. A requirement for recombinational repair in Saccharomyces cerevisiae is caused by DNA replication defects of mec1 mutants. Genetics. 1999;153:595-605 pubmed..Taken together, these data suggest that the RAD52 recombinational repair pathway is required to prevent or repair double-stranded DNA breaks caused by defective DNA replication in mec1-srf mutants. ..
- Lamonte G, Almaliti J, Bibo Verdugo B, Keller L, Zou B, Yang J, et al. Development of a Potent Inhibitor of the Plasmodium Proteasome with Reduced Mammalian Toxicity. J Med Chem. 2017;60:6721-6732 pubmed publisher..This study describes a promising new class of antimalarial compound based on the carmaphycin B scaffold, as well as several chemical structural features that serve to enhance antimalarial specificity. ..
- Miklos G, Rubin G. The role of the genome project in determining gene function: insights from model organisms. Cell. 1996;86:521-9 pubmed
- Peterson M, Emr S. The class C Vps complex functions at multiple stages of the vacuolar transport pathway. Traffic. 2001;2:476-86 pubmed..Collectively, these results indicate that the Class C Vps complex plays essential roles in the processes of membrane docking and fusion at both the Golgi-to-endosome and endosome-to-vacuole stages of transport. ..
- Chen S, Zhou H. Reconstitution of Rad53 activation by Mec1 through adaptor protein Mrc1. J Biol Chem. 2009;284:18593-604 pubmed publisher..Further, the conserved C-terminal domain of Mrc1 was found to be required for Rad53 activation. These results thus provide insights into the role of the adaptor protein Mrc1 in activating Rad53 in the DNA replication checkpoint. ..
- Allen Soltero S, Martinez S, Putnam C, Kolodner R. A saccharomyces cerevisiae RNase H2 interaction network functions to suppress genome instability. Mol Cell Biol. 2014;34:1521-34 pubmed publisher..This analysis suggests that cells with RNase H2 defects have increased levels of DNA damage and depend on other pathways of DNA metabolism to overcome the deleterious effects of this DNA damage. ..
- Casteel D, Zhuang S, Gudi T, Tang J, Vuica M, Desiderio S, et al. cGMP-dependent protein kinase I beta physically and functionally interacts with the transcriptional regulator TFII-I. J Biol Chem. 2002;277:32003-14 pubmed..Binding of G-kinase to TFII-I may position the kinase to phosphorylate and regulate TFII-I and/or factors that interact with TFII-I at the serum-response element. ..
- Fisk H, Yaffe M. A role for ubiquitination in mitochondrial inheritance in Saccharomyces cerevisiae. J Cell Biol. 1999;145:1199-208 pubmed..These results indicate that protein ubiquitination mediated by Rsp5p plays an essential role in mitochondrial inheritance, and reveal a novel function for protein ubiquitination. ..
- Gaynor E, Mondesert G, Grimme S, Reed S, Orlean P, Emr S. MCD4 encodes a conserved endoplasmic reticulum membrane protein essential for glycosylphosphatidylinositol anchor synthesis in yeast. Mol Biol Cell. 1999;10:627-48 pubmed..A putative role for Mcd4p as participating in the modification of GPI anchors with side chain phosphoethanolamine is also discussed. ..
- Foti M, Audhya A, Emr S. Sac1 lipid phosphatase and Stt4 phosphatidylinositol 4-kinase regulate a pool of phosphatidylinositol 4-phosphate that functions in the control of the actin cytoskeleton and vacuole morphology. Mol Biol Cell. 2001;12:2396-411 pubmed..Regulation of this PtdIns(4)P pool appears to be crucial for the maintenance of vacuole morphology, regulation of lipid storage, Golgi function, and actin cytoskeleton organization. ..
- Darsow T, Rieder S, Emr S. A multispecificity syntaxin homologue, Vam3p, essential for autophagic and biosynthetic protein transport to the vacuole. J Cell Biol. 1997;138:517-29 pubmed..This result indicated that SNAREs alone do not define the specificity of vesicle docking reactions. ..
- Kassavetis G, Driscoll R, Geiduschek E. Mapping the principal interaction site of the Brf1 and Bdp1 subunits of Saccharomyces cerevisiae TFIIIB. J Biol Chem. 2006;281:14321-9 pubmed
- Portnoy V, Bezdan D, Zengler K. Adaptive laboratory evolution--harnessing the power of biology for metabolic engineering. Curr Opin Biotechnol. 2011;22:590-4 pubmed publisher..This review will focus on current applications of ALE as a tool for metabolic engineering and discuss advancements and achievements that have been made in this field. ..