bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sequence of a 17·1 kb DNA fragment from chromosome X of Saccharomyces cerevisiae includes the mitochondrial ribosomal protein L8
Authors: Vandenbol Micheline , Durand Patrick , Dion Caroline , Portetelle Daniel , Hilger Francois 
Published: May 2005

AbstractWe have sequenced a continuous segment of 17 137 bp on chromosome X. Sequence analysis of this stretch revealed 14 open reading frames (ORFs) at least 100 amino acids long. One gene, encoding the mitochondrial 60S ribosomal protein L8, had already been sequenced. Four ORF products show weak homologies with known protein sequences. The nine remaining ORF products have no homologies with sequences in data banks. The nucleotide sequence of the 17·1 kb fragment is available through the EMBL data library under Accession Number Z34288.
Nucleotide sequence and analysis of the centromeric region of yeast chromosome IX
Authors: Voss H. , Tamames J. , Teodoru C. , Valencia A. , Sensen C. , Wiemann S. , Schwager C. , Zimmermann J. , Sander C. , Ansorge W. 
Published: May 2005

AbstractWe have determined the nucleotide sequence of a cosmid (pIX338) containing the centromere region of yeast (Saccharomyces cerevisiae) chromosome IX. The complete nucleotide sequence of 33·8 kb was obtained by using an efficient directed sequencing strategy in combination with automated DNA sequencing on the A.L.F. DNA sequencer. Sequence analysis revealed the presence of 17 open reading frames (ORFs), four of them previously known yeast genes (sly12, pan1, sts1 and prl1), a tRNA gene and the centromere motif. Exhaustive database searches detected sequence homologues of known function for as many as 14 of the 17 ORFs. These include a mammalian tyrosine kinase substrate; the Escherichia coli cell cycle protein MinD; the human inositol polyphosphate‐5‐phosphatase (gene OCRL) involved in Lowe's syndrome, a developmental disorder; and helicases, for which the new yeast member defines a distinct DEAD/H‐box subfamily. A surprisingly large fraction of the ORFs (at least six out of 17) in the centromeric region are apparently involved in RNA or DNA binding.The nucleotide sequence reported here has been submitted to the EMBL data library under the accession number X79743.
Development and application of an in vivo system to study yeast ribosomal RNA biogenesis and function
Authors: Venema Jaap , Dirks‐Mulder Anita , Faber Alex W. , Raué Hendrik A. 
Published: May 2005

AbstractWe have developed a system for mutational analysis of Saccharomyces cerevisiae ribosomal RNA in vivo in which yeast cells can be made completely dependent on mutant rRNA and ribosomes by a simple switch in carbon source. The system is based on a yeast strain defective in RNA polymerase I (Pol I) transcription [Nogi et al. (1991). Proc. Natl. Acad. Sci. USA 88, 3962–3966]. This normally inviable strain was rescued by integration of multiple copies of the complete 37S pre‐rRNA operon under control of the inducible, Pol II‐transcribed GAL7 promoter into the rDNA repeat on chromosome XII. The resulting YJV100 strain can only grow on medium containing galactose as the carbon source. A second, episomal vector was constructed in which the rDNA unit was placed under control of the constitutive PGK1 promoter. YJV100 cells transformed with this vector are now also able to grow on glucose‐based medium making the cells completely dependent on plasmid‐encoded rRNA. We show that the Pol II‐transcribed pre‐rRNA is processed and assembled similarly to authentic Pol I‐synthesised pre‐rRNA, making this ‘in vivo Pol II system’ suitable for the detailed analysis of rRNA mutations, even highly deleterious ones, affecting ribosome biogenesis or function. A clear demonstration of this is our finding that an insertion into variable region V8 in 17S rRNA, previously judged to be neutral with respect to processing of 17S rRNA, its assembly into 40S subunits and the polysomal distribution of these subunits [Musters et al. (1989), Mol. Cell. Biol. 9, 551–559], is in fact a lethal mutation.
Vacuolar carboxypeptidase Y of Saccharomyces cerevisiae is glycosylated, sorted and matured in the fission yeast Schizosaccharomyces pombe
Authors: Simeon Angela , Egner Ralf , Gascon Santiago , Suarez‐Rendueles Paz 
Published: May 2005

AbstractVacuolar carboxypeptidase Y of Saccharomyces cerevisiae (CPYsc) has been expressed in a Schizosaccharomyces pombe strain devoid of the endogenous equivalent peptidase, employing a 2 μ derived plasmid. Immunoblot analysis revealed that CPYsc produced in the fission yeast has a higher molecular mass than mature CPYsc produced by the budding yeast. CPYsc is glycosylated when expressed in S. pombe and uses four N‐linked glycosylation sites as shown by endoglycosidase H digestion. Carbohydrate removal leads to a protein moiety which is indistinguishable in size from deglycosylated CPYsc produced by S. cerevisiae. CPYsc isolated from S. pombe soluble extracts is enzymatically active and thus is presumed to undergo correct proteolytic maturation. Subcellular fractionation experiments showed a cofractionation of CPYsc with the S. pombe endoproteinases PrA and PrB, suggesting that the protein is correctly sorted to the vacuole and that these peptidases might be responsible for zymogen activation.
Induced expression of bacterial β‐glucosidase activity in saccharomyces
Authors: Adam Ana C. , Rubio‐Texeira Marta , Polaina Julio 
Published: May 2005

AbstractThe bglA gene which encodes a β‐glucosidase from Bacillus polymyxa, has been expressed in Saccharomyces cerevisiae under control of the yeast CYC‐GAL promoter. Strains have been constructed which carry the gene in different locations: in a multicopy plasmid, a single integration at the URA3 locus, or multiple integrations at the RDN1 locus. Integrative transformation at RDN1 yielded genetically stable clones with a high level of β‐glucosidase activity. Coordinated overexpression of the GAL4 inducer protein further increased the level of enzyme activity, although eventually caused the lysis of the cultures. Diploid, triploid and tetraploid strains derived from the transformants with multiple integrations were constructed and expression of β‐glucosidase activity in different conditions of growth was assayed. While per‐cell activity increased with ploidy, specific activity was about the same in strains of equivalent genotype regardless of ploidy. Genetically stable and regulated expression in Saccharomyces of β‐glucosidase activity is interesting for the development of strains able to ferment β‐glycosidic sugars (i.e. cellobiose and lactose). From another point of view, the bglA product proved to be a convenient reporter enzyme to monitor heterologous gene expression.
Saccharomyces cerevisiae mRNA 3′ end forming signals are also involved in transcription termination
Authors: Russo Patrick 
Published: May 2005

AbstractPreviously, a 38‐base‐pair (bp) region in the 3′ untranslated portion of the Saccharomyces cerevisiae iso‐1‐cytochrome c gene, was shown to be required for both normal CYC1 mRNA 3′ end formation (Zaret and Sherman, 1982), and efficient transcription termination (Russo and Sherman, 1989). In another study, specific sequences such as TATATA, TACATA, and TAGTAGTA were shown to be involved in mRNA 3′ end formation in S. cerevisiae (Russo et al., 1991). In this report, an in vivo plasmid stability assay has been utilized to show that these and related sequences are also involved in transcription termination, at varying efficiencies, and in an orientation‐dependent manner. For example: the sequence TATATA appeared to terminate transcription almost as efficiently as the original wild type 38‐bp region; whereas, the sequences TAGATATATGTAA and TACATA were less efficient, and TTTTTTTATA had little, if any, transcription termination function. In contrast, none of these sequences appeared to terminate transcription in the reverse orientation. Therefore, it appears that certain sequence signals capable of promoting mRNA 3′ end formation in yeast, are also directly involved in transcription termination.
Sequence and analysis of 24 kb on chromosome II of Saccharomyces cerevisiae
Authors: Aljinovic Gordana , Pohl Thomas M. 
Published: May 2005

AbstractIn the course of the European yeast genome sequencing project, we determined 23,920 bp of a continuous chromosome II right arm sequence. Analysis of data revealed 13 open reading frames (ORFs), three of which corresponded to previously identified genes; two tRNA genes and one repetitive element. One ORF showed considerable homology (46%) to a hypothetical chromosome III gene; another, putatively very hydrophobic gene product, was 30% identical to the heat‐shock protein HSP30. Two ORFs were homologous to human genes. The complete sequence was submitted to the EMBL data bank under the Accession Number Z46260 Authorin submission ‘3’.
Mutations sensitizing yeast cells to the start inhibitor nalidixic acid
Authors: Prendergast John A. , Singer Richard A. , Rowley Neil , Rowley Adele , Johnston Gerald C. , Danos Maria , Kennedy Brian , Gaber Richard F. 
Published: May 2005

AbstractThe regulatory step Start in the cell cycle of the budding yeast Saccharomyces cerevisiae is inhibited by nalidixic acid (Nal). To study this inhibition, mutations were identified that alter the sensitivity of yeast cells to Nal. Nal‐sensitive mutations were sought because the inhibitory effects of Nal on wild‐type cells are only transient, and wild‐type cells naturally become refractory to Nal. Three complementation groups of Nal‐sensitive mutations were found. Mutations in the first complementation group were shown to reside in the ARO7 gene, encoding chorismate mutase; tyrosine and phenylalanine synthesis was inhibited by Nal in these aro7 mutants, whereas wild‐type chorismate mutase was unaffected. These aro7 alleles demonstrate ‘recruitment’, by mutation, of an innately indifferent protein to an inhibitor‐sensitive form. The Nal‐sensitive aro7 mutant cells were used to show that the resumption of Nal‐inhibited nuclear activity and cell proliferation takes place while cytoplasmic Nal persists at concentrations inhibitory for the mutant chorismate mutase. Mutations in the second complementation group, nss2 (Nal‐supersensitive), increased intracellular Nal concentrations, and may simply alter the permeability of cells to Nal. The third complementation group was found to be the ERG6 gene, previously suggested to encode the ergosterol biosynthetic enzyme sterol methyltransferase. Mutation or deletion of the ERG6 gene had little effect on the inhibition of Start by Nal, but prevented recovery from this inhibition. Mutation of ERG3, encoding another ergosterol biosynthetic enzyme, also caused Nal sensitivity, suggesting that plasma membrane sterol composition, and plasma membrane function, mediates recovery from Nal‐mediated inhibition of Start.
The peculiarities of the interaction of radiation and hyperthermia in Saccharomyces cerevisiae irradiated with various dose rates
Authors: Petin Vladislav G. , Zhurakovskaya Galina P. 
Published: May 2005

AbstractIn experiments with yeast cells it was shown that the synergistic effect of a simultaneous action of ionizing radiation and hyperthermia was a function of dose rate. It was demonstrated that, with increasing dose rate to obtain maximum synergistic effect, the temperature at which radiation is delivered should be elevated. Possible explanation of this effect is discussed.
Automatic intron detection in nuclear DNA sequences of Saccharomyces cerevisiae
Authors: Kalogeropoulos Angelos 
Published: May 2005

AbstractThe goal of the present work is the construction of software (EXPLORA) which automatically detects Open Reading Frames (ORF), intron‐containing or not, in the nuclear sequences of the yeast Saccharomyces cerevisiae. In order to detect introns within (or preceding) ORFs, one must define precise rules of how an intron is identified. These rules are described here. The software is able to detect correctly an intron‐associated ORF in at least 88% of cases. We tested all yeast nuclear entries of the EMBL database with the software, and found, in addition to the known intron‐associated ORFs, some others which may include an intron. Finally the software was applied to the DNA sequences of chromosomes III and XI, in which it detected eight new intron‐associated ORFs.
Identification and initial characterization of the cytosolic protein Ycr77p
Authors: Rodriguez‐Cousino Nieves , Lill Roland , Neupert Walter , Court Deborah A. 
Published: May 2005

AbstractThe nucleotide sequence of yeast chromosome III encompassing the previously described open reading frames (ORFs) YCR80w, YCR77c and YCR78c (Oliver et al., 1992) has been updated. In the corrected sequence, these ORFs are replaced by two new ORFs, YCR80w (453 bp) and YCR77c (2391 bp). In addition, the orientation of Ycr79c is reversed to give ORF Ycr79w, which has an unaltered nt sequence. The predicted translation products do not exhibit significant homology to known proteins. ORF Ycr77p encodes an 88 kDa, cytosolic protein. A fraction of the protein is associated with small membranous structures in a salt‐sensitive fashion. Initial characterization revealed that the protein is not essential for yeast viability, growth on non‐fermentable carbon sources, mating and sporulation. The chromosome III DNA sequence that was used for the analysis has the Accession Number X59720 in the GenBank/EMBL database.
The maintenance of self‐replicating plasmids in Saccharomyces cerevisiae: Mathematical modelling, computer simulations and experimental tests
Authors: Van Der Sand Sueli T. , Greenhalf William , Gardner David C. J. , Oliver Stephen G. 
Published: May 2005

AbstractA distributive model has been constructed to describe the maintenance of the native 2 μm and 2 μm‐based plasmids in the yeast Saccharomyces cerevisiae. This model includes elements which represent the influence of selection, segregation, replication and amplification on plasmid stability. A computer program has been written in TURBO PASCAL to implement the model and a number of simulation experiments have been carried out. These simulations permitted the choice of a form of the model which is compatible with the available experimental evidence. The form chosen involves an amplification system in which the RAF gene product binds to the Rep1/Rep2 dimer to prevent the latter acting to repress the activity of the FLP gene. At the same time an upper limit (or ‘ceiling’) was imposed on the number of plasmid molecules able to replicate. Maternal bias was accommodated by ‘tagging’ a small proportion of molecules for inheritance by the mother nucleus and these tags being removed (or ‘cleared’) by the Rep1/Rep2 dimers. This final form of the model makes specific predictions about the stability of 2 μm and YEp plasmids in yeast populations and about the distribution of plasmid copy number between cells in such populations. The predictions on stability have been subjected to experimental test and results provide good support for the model.
High‐Resolution cosmid mapping of the left arm of Saccharomyces cerevisiae chromosome XII; A first step towards an ordered sequencing approach
Authors: Scholler Patrik , Schwarz Sandra , Hoheisel Jörg D. 
Published: May 2005

AbstractFor the sequencing of the left arm of chromosome XII of Saccharomyces cerevisiae, we fine‐mapped the entire 450 kb fragment between the ribosomal DNA (rDNA) and the left telomere. Total yeast DNA in agarose blocks was digested with I‐PpoI, which exclusively cuts once in each repeat unit of the rDNA. The resulting fragment was isolated from pulsed‐field gels, together with the equally sized chromosome IX. A cosmid library of some 30‐fold chromosome coverage was generated from this material, with the cloning efficiency being around 20 000 clones per microgram genomic DNA. The chromosome XII and IX specific clones were identified by complementary hybridizations with the respective chromosomes. For the left arm of chromosome XII, a contiguous cosmid array (contig) with an average map resolution better than 9 kb was generated by clone hybridization procedures. The ordered library serves as a tool for the physical mapping of genetic markers. Also, a minimal set of 15 clones was selected that covers the entire fragment. This subset forms the basis for the generation of a template map of much higher resolution for a directed sequencing of the left arm of chromosome XII.
Mapping of the ACC1/FAS3 gene to the right arm of chromosome XIV of Saccharomyces cerevisiae
Authors: Guerra Cesar E. , Klein Hannah L. 
Published: May 2005

AbstractThe ACC1/FAS3 gene has been mapped to the right arm of chromosome XIV by both genetic and physical methods. The gene is closely linked to RNA2 and is allelic to the ABP2 gene of chromosome XIV.
Characterization of the glyceraldehyde‐3‐phosphate dehydrogenase gene family from Kluyveromyces marxianus—polymerase chain reaction–single‐strand conformation polymorphism as a tool for the study of multigenic families
Authors: Fernandes P. A. , Sena‐Esteves M. , Moradas‐Ferreira P. 
Published: May 2005

AbstractThree glyceraldehyde‐3‐phosphate dehydrogenase (GAPDH) genes from Kluyveromyces marxianus were identified and characterized. The coding region of two of them (GAP2 and GAP3) is very similar (99·6% homology). The other gene (GAP1) is only 86% homologous to GAP2 or GAP3 and is responsible for the expression of Gap1p. This protein is extremely homologous to the K. marxianus cell wall protein p37, presumably involved in flocculation. However, no leader sequence could be detected in this gene. The identification of the three genes was possible with the use of polymerase chain reaction–single‐strand conformation polymorphism (PCRSSCP), as it permits us to overcome the difficulties caused by the high homology amongst the genes. Expression of the GAPDH genes under different carbon sources (glucose or ethanol) was assessed either by Northern blot or reverse transcription–PCRSSCP analysis, revealing that genes GAP1 and GAP2, but not GAP3, are transcribed. The results also indicate that the transcription of the gene encoding the cell wall protein p37 (Gap1p) is not dependent on the carbon source, in contrast with the expression of the gene GAP2, which is affected in cells growing in a glucose‐depleted medium.
The S1, S2 and SGA1 ancestral genes for the STA glucoamylase genes all map to chromosome IX in Saccharomyces cerevisiae
Authors: Lambrechts Marius G. , Pretorius Isak S. , Marmur Julius , Sollitti Paul 
Published: May 2005

AbstractThe polymorphic extracellular glucoamylase‐encoding genes STA1 (chr. IV), STA2 (chr. II) and STA3 (chr. XIV), from Saccharomyces cerevisiae var. diastaticus probably evolved by genomic rearrangement of DNA regions (S1, S2 and SGA1) present in S. cerevisiae, and subsequent translocation to unlinked regions of chromosomal regions. S1, encoding a homologue to the threonine/serine‐rich domain of STA glucoamylases (GAI‐III), mapped to the right arm of chromosome IX. S2, encoding the hydrophobic leader peptide of GAI‐III, was also mapped on the right arm of chromosome IX, next to S1, close to DAL81. The SGA1 sporulation‐specific, intracellular glucoamylase‐encoding gene is located on the left arm of chromosome IX, 32 kb proximal of HIS5.
A 37·5 kb region of yeast chromosome X includes the SME1, MEF2, GSH1 and CSD3 genes, a TCP‐1‐related gene, an open reading frame similar to the DAL80 gene, and a tRNAArg
Authors: Rasmussen Søren W. 
Published: May 2005

AbstractThe complete DNA sequence of cosmid clone p59 comprising 37,549 bp derived from chromsome X was determined from an ordered set of subclones. The sequence contains 14 open reading frames (ORFs) containing at least 100 consecutive sense codons. Four of the ORFs represent already known and sequenced yeast genes: B645 is identical to the SME1 gene encoding a protein kinase, required for induction of meiosis in yeast, D819 represents the MEF2 gene probably encoding a second mitochondrial elongation factor‐like protein, D678 is identical to the yeast GSH1 gene encoding γ‐glutamylcysteine synthetase and B746 is identical to the CSD3 gene, which plays an as yet unidentified role in chitin biosynthesis and/or its regulation. The deduced amino acid sequence of A550 is 63% identical to the Ccη subunit of a murine TCP‐1‐containing chaperonin and more than 35% identical to thermophilic factor 55 from Sulfolobus shibatae, as well as to a number of proteins belonging to the chaperonin TCP‐1 family. Open reading frame F551 exhibits homology to two regions of the DAL80 gene located on yeast chromosome XI encoding a pleiotropic negative regulatory protein. In addition, extensive homology was detected in three regions including parts of ORFs A560, B746/CSD3 and the incomplete ORF C852 to three consecutive ORFs of unknown function in the middle of the right arm of chromosome XI. Finally, the sequence contained a tRNAArg3 (AGC) gene. The nucleotide sequence data reported in this paper have been deposited in the EMBL and GenBank databases under the accession number X85021.
II. Yeast sequencing reports. Sequence analysis of a 78·6 kb segment of the left end of Saccharomyces cerevisiae chromosome II
Authors: Obermaier Brigitte , Gassenhuber Johann , Piravandi Ester , Domdey Horst 
Published: May 2005

AbstractWe report the sequence analysis of a 78,601 bp DNA segment on the left arm of chromosome II of Saccharomyces cerevisiae. This 78·6 kb segment spans the region from the start of a subtelomeric Y′ element up to the ILS1 gene. It contains 49 open reading frames (ORFs) with more than 100 amino acids length including 14 internal and five overlapping ORFs. The gene density, excluding the internal ORFs, was calculated as one ORF per 2·2 kb. Eight ORFs (PKC1, TyA, TyB, ATP1, ROX3, RPL17a, PET112 and ILS1) correspond to previously characterized genes. ORF YBL0718 was identified as CDC27; YBL0706 as TEL1. Four other ORFs show strong similarities to already known genes. The gene product of YBL0838 is 60% identical to the ribosomal protein RPL32 from rat, mouse and man. YBL0701 encodes a protein with significant similarity to the initiation factor eIF2 associated p67 glycoprotein from rat. Eight ORFs were disrupted and the resulting yeast strains analysed with respect to their phenotype. The sequence has been deposited in the EMBL Nucleotide Sequence Database under the Accession Number X79489.
Yeast sequencing reports. Sequence analysis of the ADE2 gene coding for phosphoribosylaminoimidazole carboxylase in schwanniomyces occidentalis
Authors: Gourdon Pierre , Janatova Ivana , Meilhoc Eliane , Klein Ronald D. , Costaglioli Patricia , Masson Jean Michel 
Published: May 2005

AbstractWe have determined the nucleotide sequence of a 3·3 kb fragment containing the gene (ADE2) encoding phosphoribosylaminoimidazole carboxylase (AIRC) from the yeast Schwanniomyces occidentalis. Translation of a 1671 bp open reading frame predicts a protein of 557 amino acids which has significant homology to AIRC from Saccharomyces cerevisiae and Schizosaccharomyces pombe. The 5′ untranslated region of the S. occidentalis gene contains a sequence corresponding to the consensus binding site of the S. cerevisiae transcription regulatory proteins GCN4, BAS1 and BAS2. The ADE2 gene nucleotide sequence has received the GenBank Accession Number U23210.