bluuebunny/crossref_metadata_2025_split huggingface dataset:
VII. Yeast sequencing reports. Physical, transcriptional and genetical mapping of a 24 kb DNA fragment located between the PMA1 and ATE1 loci on chromosome VII from Saccharomyces cerevisiae
Authors: Capieaux Etienne , Ulaszewski Stanislaw , Balzi Elisabetta , Goffeau André 
Published: May 2005

AbstractA physical map of a contiguous DNA fragment of 60 kb, extending from the centromere to TRP5 on the left arm of the chromosome VII of Saccharomyces cerevisiae, strain IL 125‐2B, was established. Within a 31 kb region from PMA1 towards TRP5, a total of 12 transcription products ranging from 0·6 to 3·6 kb were identified in cells grown exponentially on rich medium. Near 87% of the DNA investigated was transcribed and on average one transcript, of 2·3 kb average length, was detected every 2·7 kb of DNA. The physical and genetical distances between the markers CEN7, pma1, leu1, pdr1 and trp5 were compared. A recombination frequency of 1 cM corresponds to an average distance of 3·3 kb between alleles in this region of chromosome VII.
DNA insertions in the ‘silent’ regions of the 2 μm plasmid of Saccharomyces cerevisiae influence plasmid stability
Authors: Bijvoet J. F. M. , Van Der Zanden A. L. , Goosen N. , Brouwer J. , Van De Putte P. 
Published: May 2005

AbstractThe 2 μm plasmid of the yeast Saccharomyces cerevisiae is in principle a suitable vector for expression of foreign genes, due to high copy number and extreme stability. However, the cloning of genes into 2 μm often results in a reduced copy number and/or reduced stability. One reason for this observed instability could be that the inserts in general were made in one of the several open reading frames (ORFs) of the plasmid. Therefore we studied the effect on stability of insertions in the silent regions of 2 μm without interrupting any known essential regions or ORFs. Using the SnaBI site, a yeast‐integrating plasmid (Yip5) was introduced into the region between the ARS and STB locus in two possible orientations. The resulting plasmids could be stably maintained in the cells without the need for complementation by the wild‐type 2 μm plasmid. However, the stability of these plasmids in a cir° host was still one to two orders of magnitude lower (0·2% and 0·8% respectively) as reported for the wild‐type 2 μm (0·01%). Removal of 2 kb of the bacterial sequences from Yip5 did not increase stability. The stability was dependent on the orientation of the insert. We found that in the less stable orientation, transcription originating from the insert was running into the STB region.DNA inserted in the XmaIII site located outside the ORFs in the REP2/FLP intergenic region influenced both stability and copy number of the plasmid. These effects are strongly dependent on the size of the insert. Insertion of a 2 kb DNA fragment increased the copy number, probably through an effect on FLP expression.
Isolation and quantitation of M‐factor, a diffusible mating factor from the fission yeast Schizosaccharomyces pombe
Authors: Davey John 
Published: May 2005

AbstractAlthough there have been several reports demonstrating the existence of mating factors in the fission yeast Schizosaccharomyces pombe it has not been possible to isolate these factors as cell‐free preparations. Such an ability is the first requirement towards a molecular characterization of these factors and here I report the successful isolation of a mating factor from S. pombe. This factor, termed M‐factor, is released by cells of the cellular mating type M (Minus) and induces mating‐specific changes in P‐type cells. A reliable and accurate assay for the quantitation of the M‐factor, based upon changes in cell volume following exposure to the factor, is also described.
Multi‐functional DNA proteins in yeast: The factors GFI and GFII are identical to the ARS‐binding factor ABFI and the centromere‐binding factor CPF1 respectively
Authors: Dorsman J. C. , Gozdzicka‐Jozefiak A. , Van Heeswijk W. C. , Grivell L. A. 
Published: May 2005

AbstractGFI and GFII are abundant DNA‐binding proteins in the yeast Saccharomyces cerevisiae. Binding sites for GFI conform to the sequence 5′‐RTCRYNNNNNACG‐3′. This consensus can also accommodate the recognition sequence for the ARS1‐binding factor ABFI. Results of retardation‐competition assays, limited proteolysis experiments, molecular weight determinations based on denaturation–renaturation procedures and mobility shift assays of protein–DNA complexes formed in the presence of a monoclonal antibody raised against ABFI suggest strongly that GFI and ABFI are the same protein. Similarly, GFII appears to be identical to the centromere‐binding protein CPFI (alias CP1), since both proteins bind to the CDEI motif of yeast centromeres (5′‐RTCACRTG‐3′) and cannot be detected in a cpf1 disruption mutant yeast strain. In addition, based on denaturation–renaturation studies, both factors appear to have molecular weights in the same range of 53–62 kDa.
III. Yeast sequencing reports. The complete sequence of the unit YCR59, situated between CRY1 and MAT, reveals two long open reading frames, which cover 91% of the 10·1 kb segment
Authors: Jia Yankai , Slonimski Piotr P. , Herbert Christopher J. 
Published: May 2005

AbstractWe have entirely sequenced YCR59, which is a 10·1 kb segment of the right arm of chromosome III, and is a part of the clone E5F from the Newlon collection. The segment contains two long open reading frames (ORFs): YCR591 which starts in the adjacent fragment H9G (situated towards CRY1 and the centromere), and continues with 1833 codons in YCR59. The second ORF YCR592 is 1226 codons long and encoded entirely within YCR59. The two ORFs represent 91% of the total length of the segment. Excellent agreement in both location and length is found between the ORFs YCR591 and YCR592 and the transcripts 86 and 87 respectively in the Yoshikawa and Isono (1990) map of chromosome III. The two ORFs correspond to new genes and show no significant similarity with any known genes.
Cytochrome P450 lanosterol 14α‐demethylase (ERG11) and manganese superoxide dismutase (SOD1) are adjacent genes in Saccharomyces cerevisiae
Authors: Turi Thomas G. , Kalb Vernon F. , Loper John C. 
Published: May 2005

AbstractDNA sequencing and analysis of genomic DNA using the polymerase chain reaction were used to demonstrate that SOD1 and ERG11 are adjacent genes in Saccharomyces cerevisiae S288c and to establish the correct intergenic sequence of this segment on chromosome VIII.
Activity of promoter mutants of the yeast ribosomal RNA gene with and without the enhancer
Authors: Butlin Mike , Quincey Roger 
Published: May 2005

AbstractThe promoter and enhancer of the rRNA gene of Saccharomyces cerevisiae have been studied using a nuclease S1 protection assay to detect transcripts of an rRNA minigene in transformed yeast. Analysis of 5′ deletion mutants showed that DNA between − 163 bp and − 155 bp was important for promoter activity and that some DNA between − 155 bp and − 145 bp was essential. The importance of DNA far upstream from the initiation site was confirmed by showing that minigene expression was much reduced by linker scanner mutations clustered around − 148 bp, − 133 bp and − 100 bp, and was abolished by mutations clustered around − 118 bp. The enhancer for rRNA biosynthesis increased transcription from all of the five mutated promoters that were tested. The magnitude of the enhancer effects on weakly active promoters was two‐ to three‐fold less than on the wild‐type promoter. Expression of a minor transcript in a 5′ deletion to − 10 bp was substantially reduced by a mutation which altered two base pairs in the core sequence of the promoter‐proximal REB1 binding site.
Functional analysis of a conserved amino‐terminal region of HSP70 by site‐directed mutagenesis
Authors: Nicolet Charles M. , Craig Elizabeth A. 
Published: May 2005

AbstractHsp70 proteins have been highly conserved throughout evolution. As a first step in a structure–function analysis of hsp70, we constructed and analysed the consequences of mutations in a portion of the SSA1 gene, a member of the Saccharomyces cerevisiae HSP70 multigene family, that encodes a nearly invariant region near the amino terminus. Analysis of strains expressing SSA1 proteins with alterations at positions 8, 11 and 15 showed that these conserved residues within this region are critical for normal functioning of the protein. SSA1 protein containing either of two changes at position 15 was able to slightly complement the inviability of an ssa1ssa2ssa4 strain, but was inactive in other complementation assays. The other mutant proteins tested were unable to complement any tested phenotype. Effective interallelic complementation of several phenotypes was observed when a mutant protein substituted at position 8 was expressed in the same cell with either of two proteins carrying substitutions at position 15, suggesting that hsp70 acts as a multimer. Evidence from previous studies suggests that hsp70 proteins engage in ATP‐driven cycles of binding and release from peptides. The ability of the mutant proteins to bind ATP and a peptide was tested. The Ssa 1p carrying a substitution at position 8, which inhibits growth of cells carrying wild‐type SSA proteins, showed a defect in release from a peptide relative to wild type. Two mutations, one each at position 8 and 15, resulted in accumulation of phosphorylated isoforms which may be a normal, transient hsp70 intermediate.
The complete sequence of a 7·5 kb region of chromosome III from Saccharomyces cerevisiae that lies between CRY1 and MAT
Authors: Wicksteed Barton L. , Roberts A. Brett , Sagliocco Francis A. , Brown Alistair J. P. 
Published: May 2005

AbstractWe report the sequence of a 7·5 kb region lying between the CRY1 and MAT loci of chromosome III from Saccharomyces cerevisiae. This region lies in the overlap between two major contigs used for the generation of the complete nucleotide sequence of this chromosome. Comparison of this sequence with those reported previously for this overlap [Thierry et al. (1990) Yeast 6, 521; Jia et al. (1991) Yeast 7, 413] reveals 38 nucleotide differences, 45% of which generate changes in the amino acid sequences of the four genes in this region (YCR591, YCR592, YCR521 and YCR522). These differences appear to reflect true sequence polymorphisms between the two yeast strains used to generate the clones used in the sequencing project. Three of the four genes in this region display weak homologies to proteins in the PIR database. Some properties of YCR521 are analogous to those of ribosomal protein genes. However, the functions of all four genes remain obscure.
A genomic sequence of the Schizosaccharomyces pombe 16 kDa vacuolar H+‐ATPase
Authors: Toyama Reiko , Goldstein David J. , Schlegel Richard , Dhar Ravi 
Published: May 2005

AbstractWe have isolated the gene encoding the 16 kDa vacuolar H+‐ATPase from Schizosaccharomyces pombe. On the basis of RNA splicing signals and amino acid sequence homology with other 16 kDa H+‐ATPases, the genomic DNA sequence indicated the 16 kDa protein is encoded by five exons. The C‐terminal 50 amino acids has more than 90% homology with vacuolar H+‐ATPases of mammalian cells.
Expression of recombinant platelet‐derived endothelial cell growth factor in the yeast Saccharomyces cerevisiae
Authors: Finnis Chris , Goodey Andrew , Coutrney Michael , Sleep Darrell 
Published: May 2005

AbstractA platelet‐derived endothelial cell growth factor cDNA has been cloned, sequenced and expressed using the Saccharomyces cerevesiae PRBI promoter. Soluble recombinant platelet‐derived endothelial cell growth factor constituted 0·5–1·0% of total soluble protein. Yeast soluble protein extracts containing recombinant platelet‐derived endothelial cell growth factor stimulate the growth of calf palmonary artery endothelial cells in vitro.
A putative serine/threonine protein kinase gene on chromosome III of Saccharomyces cerevisiae
Authors: Wilson Cathal , Frontali Laura , Bergantino Elisabetta , Carignani Giovanna , Lanfranchi Gerolamo , Valle Giorgio 
Published: May 2005

AbstractWe have sequenced a gene on chromosome III of Saccharomyces cerevisiae which codes for a putative serine/threonine protein kinase of 726 amino acids (calculated molecular weight 82 kDa). We have called this gene KIN82. The amino acid sequence of KIN82 is most similar to the cyclic nucleotide‐dependent protein kinase subfamily and the protein kinase C subfamily. Gene disruption of KIN82 did not produce any phenotype when tested under a variety of conditons. Reduced stringency hybridizations revealed the presence of another genomic sequence with high homology to the carboxy‐terminal catalytic domain of KIN82.
Inhibition of glycolysis by 2‐deoxygalactose in Saccharomyces cerevisiae
Authors: Lagunas Rosario , Moreno Eulalia 
Published: May 2005

AbstractThe enzymatic steps involved in the inhibition of glycolysis by 2‐deoxygalactose in Saccharomyces cerevisiae have been investigated. Yeast, incubated with 2‐deoxygalactose, accumulates up to 8 mM‐2‐deoxygalactose, 30 mM‐2‐deoxygalactose‐1‐phosphate and 0·25 mM‐UDP‐2‐deoxygalactose and UDP‐2‐dexyglucose. An inverse correlation between 2‐deoxygalactose‐1‐phosphate content and rate of glycolysis has been observed. The intracellular concentration of glycolytic intermediates and related metabolites point to the hexokinase and phosphofructokinase steps as the targets for the inhibition of glycolysis by 2‐deoxygalactose and rule out all other mechanisms that have been proposed to explain this inhibition.
Identification of RAD 16, a yeast excision repair gene homologous to the recombinational repair gene RAD 54 and to the SNF2 gene involved in transcriptioal activation
Authors: Schild David , Mortimer Robert K. , Glassner Brian J. , Carlson Marian , Laurent Brehon C. 
Published: May 2005

AbstractThe RAD54 gene of Saccharomyces cerevisiae is involved in the recombinational repair of DNA damage. The predicted amino acid sequence of the RAD54 protein shows significant homologies with the yeast SNF2 protein, which is required for the transcriptioal activation of a number of diversely regulated genes. These proteins are 31% identical in a 492‐amino acid region that includes presumed nucleotide and Mg2+ binding sites. We noted previously that the SNF2 protein also shares homology with a partial open reading frame (ORF) that was reported with the sequence of an adjacent gene. This ORF also shares homology with the RAD54 protein. To test whether this ORF is involved in transcriptional activation or DNA repair, yeast strains deleted for part of it have been isolated. These strains do not show a Snf‐like phenotyp, but they are UV sensitive. This gene has been identified as RAD 16, a gene involved in the excision repair of DNA damage. Analysis of the rad16 deletion mutations indicates that RAD16 encodes a nonessential function and is not absolutely required for excision repair. Outside the region of homology to RAD54 and SNF2, the predicted RAD16 protein contains a novel cysteine‐rich motif that may bind zinc and that has been found recently in eleven other proteins, including the yeast RAD18 protein. The homologies between RAD16, RAD54 and SNF2 are also shared by several additional, recently isolated yeast and Drosophila genes.
Saccharomyces cerevisiae contains a homolog of human fkbp‐13, a membrane‐associated fk506/rapamycin binding protein
Authors: Partaledis Judith A. , Fleming Mark A. , Harding Matthew W. , Berlin Vivian 
Published: May 2005

AbstractFKB2 encodes a homolog of human FKBP‐13, a membrane‐associated binding protein for the immunosuppressants FK506 and rapamycin. FKB2 is located on the right arm of chromosome IV and contains an open reading frame of 135 amino acids, of which the first 17 residues comprise a putative hydrophobic leader peptide. Yeast FKBP‐13 is homologous to human FKBP‐13 (52% amino acid identity) and to FKBP‐12, the major cytosolic receptor for FK506. In the alignment of FKBP‐13 and FKBP‐12 sequences, there are 28 invariant residues. Among these conserved residues are those that comprise the drug binding and peptidyl‐prolyl cis‐trans isomerase active site of FKBP‐12. The phylogenetic conservation of the FKBP family suggests that the proteins are involved in a basic cellular function.
Efficient electropulse transformation of intact Candida maltosa cells by different homologous vector plusmids
Authors: Kasüske Anette , Wedler Holger , Schulze Steffen , Becher Dietmar 
Published: May 2005

AbstractConditions for efficient and quick transformation by electroporation were developed in Candida maltosa. To investigate the efficiency of transformation with integrative as well as with autonomously replicating plasmids, a series of vectors was constructed for homologous transformation of the species. Transformants were obtained with different plasmids as covalently closed circular molecules and as linearized DNA. The influence of recipient strain and plasmid type as well as of cell number and parameters of the supplied electrical pulse on the transformation efficiency have been investigated. A maximum of 7000 transformants per 100ng of plasmid DNA was reached. The efficiency of transformation was compared with that of the LiCl method.
Disruption and mapping of IDI1, the gene for isopentenyl diphosphate isomerase in Saccharomyces cerevisiae
Authors: Mayer Matthias P. , Hahn Frederick M. , Stillman David J. , Poulter C. Dale 
Published: May 2005

AbstractIsopontenyl diphosphate isomerase catalyses an essential activation step in the isoprene biosynthetic pathwasy. The Saccharomyces cerevisiae gene for isomerase, IDI1, was recently isolated and characterized (Anderson et al. J. Biol. Chem. 1989aa, 264, 19169–19175). Wild‐type IDI1 was disrupted with a LEU2 marker, and the resulting DNA was used to transform a yeast leucine auxotroph. Southern blots of EcoRI fragments of chromosomal DNA from the diploid strain showed the expected fragments for intact and disrupted IDI1. Dissection and analysis of tetrads demonstrated that IDI1 is an essential single‐copy gene. A CHEF gel and clone grid filter analysis, followed by chromosomal mapping indicated that the gene is located on chromosome that the gene is located on the chromosome XVI approximately 55 kb contromere proximal to PEP4.
Yeast sequencing reports. Sequence of the genes encoding subunits A and B of the vacuolar H+‐ATPase of Schizosaccharomyces pombe
Authors: Ghislain Michel , Bowman Emma Jean 
Published: May 2005

AbstractThe genes coding subunits A (vma1) and B (vma2) of the vacuolar H+‐ATPase from Schizosaccharomyces pombe were cloned by hybridization to cDNAs of the homologous genes in Neurospora crasa. Both genes are interrupted by introns, two in vma1 and four in vma2. Positions of introns do not appear to be conserved when compared to those of N. crassa. The subunit A gene encodes a single product of 619 amino acids and is not interrupted by the coding sequence for a second product as found for Saccharomyces cerevisiae (Kane, P.K., Yamashiro, C.T., Wolczyk, D.F., Neff, N., Goebl, M., and Stevens, T.H. (1990). Science 250, 651–657).
DIT101 (CSD2, CAL1), a cell cycle‐regulated yeast gene required for synthesis of chitin in cell walls and chitosan in spore walls
Authors: Pammer Manuela , Briza Peter , Ellinger Adolf , Schuster Tillman , Stucka Rolf , Feldmann H. , Breitenbach Michael 
Published: May 2005

AbstractA mutant screen has been designed to isolate mutants in Saccharomyces cerevisiae deficient in spore wall dityrosine. As shown by electron microscopy, most of the mutant spores lacked only the outermost, dityrosine‐rich layer of the spore wall. Mutant dit101, however, was additionally lacking the chitosan layer of the spore wall. Chemical measurements showed that this mutant does not synthesize chitosan during sporulation. The mutant spores were viable but sensitive to lytic enzymes (glusulase or zymolyase). Unlike most of the dit‐mutants, dit101 did show a distinctive phenotype in vegetative cells: they grew normally but contained very little chitin and were therefore resistant to the toxic chitin‐binding dye, Calcofluor White. The cells showed barely detectable staining of the walls with Calcofluor White or primulin. The decrease in the amount of chitin in vegetative cells and the absence of chitosan in spores suggested that the mutant dit101 could be defective in a chitin synthase. Indeed, a genomic yeast clone harboring the gene, CSD2, sharing significant sequence similarity with yeast chitin synthases I and II (C. E. Bulawa (1992), Mol. Cell. Biol. 12, 1764–1776), complemented our mutant and was shown to correspond to the chromosomal locus of dit101. Thus, the mutations dit101 and csd2 (and probably also call; M. H. Valdivieso et al., (1991), J. Cell Biol. 114, 101–109) were shown to be allelic. The gene was mapped to chromosome II and was located about 3 kb distal of FAL1. Using this DNA clone, a transcript of about 3500–4000 nucleotides was detected. Comparing RNA isolated from vegetative cells and from sporulating cells at different times throughout the sporulation process, no significant differences in DIT101 transcript levels could be detected indicating absence of sporulation‐specific transcriptional regulation. However, the amount of DIT101 transcript changed significantly at different stages of the mitotic cell cycle, peaking after septum formation, but before cytokinesis. As most of the chitin synthesis of vegetative cells occurs at this stage of the cell division cycle, chitin synthesis mediated by DIT101 could be primarily regulated at the level of transcription in vegetatively growing cells.
In Saccharomyces cerevisiae, protein secretion into the growth medium depends on environmental factors
Authors: Rossini Dominique , Porro Danilo , Brambilla Luca , Venturini Marina , Ranzi Bianca Maria , Vanoni Marco , Alberghina Lilia 
Published: May 2005

AbstractIn the budding yeast Saccharomyces cerevisiae the cell wall, mainly composed of mannoproteins and glucans, constitutes a barrier to protein excretion in the growth medium. In this paper we have studied the effects of different environmental parameters on excretion of Escherichia coli β‐galactosidase obtained by exploiting the glucoamylase II signal sequence. Excretion of the unglycosylated β‐galactosidase was detectable only in cells grown in rich medium, was affected by temperature (36°C > 30°C >> 24°C) and slightly stimulated by reducing agents. On the contrary, glycosylated proteins, such as α‐galactosidase and glucoamylase II, were excreted to a good extent under all tested conditions of medium composition, growth temperature and pH. These data indicate that optimization of environmental parameters may help the excretion of heterologous proteins, offering advantages for protein purification.