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1.
Nucleic Acids Res ; 32(Database issue): D258-61, 2004 Jan 01.
Article in English | MEDLINE | ID: mdl-14681407

ABSTRACT

The Gene Ontology (GO) project (http://www. geneontology.org/) provides structured, controlled vocabularies and classifications that cover several domains of molecular and cellular biology and are freely available for community use in the annotation of genes, gene products and sequences. Many model organism databases and genome annotation groups use the GO and contribute their annotation sets to the GO resource. The GO database integrates the vocabularies and contributed annotations and provides full access to this information in several formats. Members of the GO Consortium continually work collectively, involving outside experts as needed, to expand and update the GO vocabularies. The GO Web resource also provides access to extensive documentation about the GO project and links to applications that use GO data for functional analyses.


Subject(s)
Databases, Genetic , Genes , Terminology as Topic , Animals , Bibliographies as Topic , Electronic Mail , Genomics , Humans , Information Storage and Retrieval , Internet , Molecular Biology , Proteins/classification , Proteins/genetics , Software
2.
Nucleic Acids Res ; 29(1): 75-9, 2001 Jan 01.
Article in English | MEDLINE | ID: mdl-11125054

ABSTRACT

The BioKnowledge Library is a relational database and web site (http://www.proteome.com) composed of protein-specific information collected from the scientific literature. Each Protein Report on the web site summarizes and displays published information about a single protein, including its biochemical function, role in the cell and in the whole organism, localization, mutant phenotype and genetic interactions, regulation, domains and motifs, interactions with other proteins and other relevant data. This report describes four species-specific volumes of the BioKnowledge Library, concerned with the model organisms Saccharomyces cerevisiae (YPD), Schizosaccharomyces pombe (PombePD) and Caenorhabditis elegans (WormPD), and with the fungal pathogen Candida albicans (CalPD). Protein Reports of each species are unified in format, easily searchable and extensively cross-referenced between species. The relevance of these comprehensively curated resources to analysis of proteins in other species is discussed, and is illustrated by a survey of model organism proteins that have similarity to human proteins involved in disease.


Subject(s)
Databases, Factual , Proteome , Animals , Caenorhabditis elegans/genetics , Candida albicans/genetics , Computational Biology , Genomics , Information Services , Internet , Saccharomyces cerevisiae/genetics , Schizosaccharomyces/genetics
3.
Mol Cell Biol ; 19(11): 7705-11, 1999 Nov.
Article in English | MEDLINE | ID: mdl-10523659

ABSTRACT

The pheromone response in the yeast Saccharomyces cerevisiae is mediated by a heterotrimeric G protein. The Gbetagamma subunit (a complex of Ste4p and Ste18p) is associated with both internal and plasma membranes, and a portion is not stably associated with either membrane fraction. Like Ras, Ste18p contains a farnesyl-directing CaaX box motif (C-terminal residues 107 to 110) and a cysteine residue (Cys 106) that is a potential site for palmitoylation. Mutant Ste18p containing serine at position 106 (mutation ste18-C106S) migrated more rapidly than wild-type Ste18p during sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). The electrophoretic mobility of wild-type Ste18p (but not the mutant Ste18p) was sensitive to hydroxylamine treatment, consistent with palmitoyl modification at Cys 106. Furthermore, immunoprecipitation of the Gbetagamma complex from cells cultured in the presence of [(3)H]palmitic acid resulted in two radioactive species on nonreducing SDS-PAGE gels, with molecular weights corresponding to Ggamma and Gbetagamma. Substitution of serine for either Cys 107 or Cys 106 resulted in the failure of Gbetagamma to associate with membranes. The Cys 107 substitution also resulted in reduced steady-state accumulation of Ste18p, suggesting that the stability of Ste18p requires modification at Cys 107. All of the mutant forms of Ste18p formed complexes with Ste4p, as assessed by coimmunoprecipitation. We conclude that tight membrane attachment of the wild-type Gbetagamma depends on palmitoylation at Cys 106 and prenylation at Cys 107 of Ste18p.


Subject(s)
Cell Compartmentation , GTP-Binding Protein beta Subunits , GTP-Binding Protein gamma Subunits , Heterotrimeric GTP-Binding Proteins/metabolism , Membrane Proteins/metabolism , Protein Processing, Post-Translational , Saccharomyces cerevisiae Proteins , Fatty Acids, Unsaturated/metabolism , Heterotrimeric GTP-Binding Proteins/genetics , Mutation , Palmitic Acid/metabolism , Palmitic Acids , Protein Prenylation , Saccharomyces cerevisiae , Substrate Specificity
4.
J Biol Chem ; 272(1): 240-8, 1997 Jan 03.
Article in English | MEDLINE | ID: mdl-8995254

ABSTRACT

Genetic evidence suggests that the yeast STE4 and STE18 genes encode G beta and G gamma subunits, respectively, that the G betagamma complex plays a positive role in the pheromone response pathway, and that its activity is subject to negative regulation by the G alpha subunit (product of the GPA1 gene) and to positive regulation by cell-surface pheromone receptors. However, as yet there is no direct biochemical evidence for a G betagamma protein complex associated with the plasma membrane. We found that the products of the STE4 and STE18 genes are stably associated with plasma membrane as well as with internal membranes and that 30% of the protein pool is not tightly associated with either membrane fraction. A slower-migrating, presumably phosphorylated, form of Ste4p is enriched in the non-membrane fraction. The Ste4p and Ste18p proteins that had been extracted from plasma membranes with detergent were found to co-sediment as an 8 S particle under low salt conditions and as a 6 S particle in the presence of 0.25 M NaCl; the Ste18p in these fractions was precipitated with anti-Ste4p antiserum. Under the conditions of our assay, Gpa1p was not associated with either particle. The levels of Ste4p and Ste18p accumulation in mutant cells provided additional evidence for a G betagamma complex. Ste18p failed to accumulate in ste4 mutant cells, and Ste4p showed reduced levels of accumulation and an increased rate of turnover in ste18 mutant cells. The gpa1 mutant blocked stable association of Ste4p with the plasma membrane, and the ste18 mutant blocked stable association of Ste4p with both plasma membranes and internal membranes. The membrane distribution of Ste4p was unaffected by the ste2 mutation or by down-regulation of the cell-surface receptors. These results indicate that at least 40% of Ste4p and Ste18p are part of a G betagamma complex at the plasma membrane and that stable association of this complex with the plasma membrane requires the presence of G alpha.


Subject(s)
GTP-Binding Protein alpha Subunits , GTP-Binding Protein beta Subunits , GTP-Binding Protein gamma Subunits , GTP-Binding Proteins/physiology , Heterotrimeric GTP-Binding Proteins , Saccharomyces cerevisiae Proteins , Saccharomyces cerevisiae/physiology , Transcription Factors , Cell Compartmentation , Cell Membrane/metabolism , Centrifugation, Density Gradient , Endocytosis , Fungal Proteins/chemistry , Fungal Proteins/physiology , GTP-Binding Protein alpha Subunits, Gq-G11 , GTP-Binding Proteins/chemistry , Macromolecular Substances , Mating Factor , Osmolar Concentration , Peptides/physiology , Protein Binding , Receptors, Mating Factor , Receptors, Peptide/physiology , Signal Transduction , Solubility
5.
Mol Cell Biol ; 8(11): 4608-15, 1988 Nov.
Article in English | MEDLINE | ID: mdl-2850465

ABSTRACT

The his4-912 delta mutation is an insertion of the long terminal repeat (delta) of the yeast retrotransposon Ty into the HIS4 promoter region, such that the delta is 97 base pairs upstream of the HIS4 transcription initiation site. Strains carrying the his4-912 delta allele are His- at 23 degrees C; this phenotype can be reversed either by growth at 37 degrees C or by mutations in trans-acting SPT genes. Under conditions in which his4-912 delta confers a His- phenotype. HIS4 transcription initiates at the delta initiation site, rather than at the HIS4 initiation site, producing a longer, nonfunctional transcript. Under conditions in which the strain is His+, transcription initiates at the wild-type HIS4 initiation site. To understand how transcription is balanced between the delta and HIS4 promoters, we have selected for cis-acting suppressors of his4-912 delta. Two classes defined by six independent mutations restore synthesis of a functional HIS4 transcript. The first class is an A-to-G base change 1 base upstream of the proposed delta TATA sequence. These mutants do not synthesize the delta-initiated transcript; instead, they synthesize only the wild-type HIS4 transcript. The second class of mutations alters base pairs surrounding the functional HIS4 TATA sequence. The two strongest His+ mutants of this class synthesize the wild-type HIS4 transcript at levels consistent with their His+ phenotype. Surprisingly, these two mutants also have a reduced level of the delta-initiated transcript relative to the his4-912 delta parent. Analysis of these mutants indicates that the level of transcription from one promoter can affect the level of transcription from the other promoter and suggests that delta and HIS4 transcription signals compete for initiation of transcription from each site.


Subject(s)
Genes, Fungal , Promoter Regions, Genetic , Saccharomyces cerevisiae/genetics , Base Sequence , DNA Transposable Elements , DNA, Fungal/genetics , Histidine/metabolism , Mutation , Repetitive Sequences, Nucleic Acid , Saccharomyces cerevisiae/metabolism , Temperature , Transcription, Genetic
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