bluuebunny/crossref_metadata_2025_split huggingface dataset:
The In Vitro permeability of yeast peroxisomal membranes is caused by a 31 kDa integral membrane protein
Authors: Sulter G. J. , Harder W. , Verheyden K. , Mannaerts G. , Veenhuis M. 
Published: May 2005

AbstractA major 31 kDa integral peroxisomal membrane protein (PMP31) of Hansenula polymorpha was purified to homogeneity from isolated peroxisomal membranes by FPLC after solubilization by Triton X‐100. Biochemical analysis indicated that this protein, which showed cross‐reactivity with antibodies against the 31 kDa porin of the mitochondrial outer membrane of Saccharomyces cerevisiae, had pore‐forming properties. Firstly, proteoliposomes composed of asolectin and purified PMP31 showed selective permeability, determined as the [14C]sucrose/[3H]dextran leakage ratios. Furthermore, the generation of a ΔΨ by potassium diffusion gradients was negatively affected by the presence of PMP31 in asolectin liposomes. A similar effect was observed in proteoliposomes containing purified cytochrome c oxidase as a ΔΨ generating system. Control experiments confirmed that the observed leakage is significant and introduced by the incorporation of PMP31 protein. Selective sucrose leakage was abolished in samples pretreated with glutaraldehyde; an identical effect of glutaraldehyde was, however, not observed for the membrane potential measurements.
Vector YFRp1 allows transformant selection in Saccharomyces cerevisiae via resistance to formaldehyde
Authors: Wehner Eugen P. , Brendel Martin 
Published: May 2005

AbstractFormaldehyde (FA), a chemical with low toxic potential, is used as sole selective agent for transformation in the yeast Saccharomyces cerevisiae. Neither stable auxotrophic markers in recipient cells nor defined synthetic media are needed when multicopy vector YFRp1, containing the yeast SFA gene, is employed for yeast transformation. The SFA gene gives stability to the vector and its yeast (and other) passenger genes when transformants are propagated in complex media supplemented with 3–5 mM‐FA. Use of inexpensive FA and non‐synthetic, undefined media will lower the cost of yeast transformant propagation considerably and thus make feasible large‐volume industrial application of transformants containing YFRp1 derivatives.
CLG1, a new cyclin‐like gene of Saccharomyces cerevisiae
Authors: Matsumoto Yutaka , Wickner Reed B. 
Published: May 2005

AbstractA region of chromosome VII adjacent to SKI8 has a 453 amino acid open reading frame whose sequence has significant similarity to that of HCS26, a G1 cyclin. A disruption mutation of this open reading frame has no apparent phenotype under the conditions tested. ORFD, an open reading frame adjacent to the CDC48 gene, is even more similar to HCS26.
Transcriptional regulation by glucose of the yeast PMA1 gene encoding the plasma membrane H+‐ATPase
Authors: Rao Rajini , Drummond‐Barbosa Daniela , Slayman Carolyn W. 
Published: May 2005

AbstractThe yeast plasma membrane H+‐ATPase generates a membrane electrochemical gradient which is required for the secondary uptake of nutrients. Although the ATPase has previously been shown to be post‐translationally regulated in response to the availability of glucose, there has been no evidence to date for transcriptional regulation of the ATPase gene (PMA1). In this work, we have examined the pool of newly synthesized ATPase that accumulates in secretory vesicles en route to the cell surface in the temperature‐sensitive secretory mutant sec6‐4, and have observed changes in the level of ATPase polypeptide as a function of the glucose concentration in the growth medium. In parallel, there were rapid and reversible changes in the levels of ATPase mRNA. Finally, when cells were grown on a variety of carbon sources, the amount of ATPase polypeptide was proportional to the specific growth rate, suggesting that PMA1 expression is adjusted according to the metabolic state of the cell. These results complement the findings of Capieaux et al. (Capieaux, E., Vignais, M.‐L., Sentenac, A. and Goffeau, A. (1989). J. Biol. Chem. 264, 7437–7446), who show that the transcriptional factor TUF/RAP1 binds to upstream activating sequences in the PMA1 gene. Taken together, the results suggest a model in which transcriptional regulation of the ATPase gene by glucose is mediated by TUF/RAP1.
Synonymous codon usage in Kluyveromyces lactis
Authors: Lloyd Andrew T. , Sharp Paul M. 
Published: May 2005

AbstractThe nature and variation of synonymous codon usage in 47 open reading frames from Kluyveromyces lactis have been investigated. Using multivariate statistical analysis, a single major trend among K. lactis genes was identified that differentiates among genes by expression level: highly expressed genes have high codon usage bias, while genes of low expression level have low bias. A relatively minor secondary trend differentiates among genes according to G+C content at silent sites. In these respects, K. lactis is similar to both Saccharomyces cerevisiae and Candida albicans, and the same ‘optimal’ codons appear to be selected in highly expressed genes in all three species. In addition, silent sites in K. lactis and S. cerevisiae have similar G+C contents, but in C. albicans genes they are more A+T‐rich. Thus, in all essential features, codon usage in K. lactis is very similar to that in S. cerevisiae, even though silent sites in genes compared between these two species have undergone sufficient mutation to be saturated with changes. We conclude that the factors influencing overall codon usage, namely mutational biases and the abundances of particular tRNAs, have not diverged between the two species. Nevertheless, in a few cases, codon usage differs between homologous genes from K. lactis and S. cerevisae. The strength of codon usage bias in cytochrome c genes differs considerably, presumably because of different expression patterns in the two species. Two other, linked, genes have very different G+C content at silent sites in the two species, which may be a reflection of their chromosomal locations. Correspondence analysis was used to identify two open reading frames with highly atypical codon usage that are probably not genes.
The DNA sequence analysis of the HAP4–LAP4 region on chromosome XI of Saccharomyces cerevisiae suggests the presence of a second aspartate aminotransferase gene in yeast
Authors: Chéret Geneviève , Pallier Chantal , Valens Michèle , Daignan‐Fornier Bertrand , Fukuhara Hiroshi , Bolotin‐Fukuhara Monique , Sor Frédéric 
Published: May 2005

AbstractThe nucleotide sequence of a 19 000 base pair region from the left arm of chromosome XI of Saccharomyces cerevisiae has been determined and analysed. It covers the HAP4–GFA1–LAP4 loci already described. As expected HAP4, GFA1 and LAP4 genes have been found and six new open reading frames (ORFs) with a coding capacity of more than 100 amino acid residues have been identified. One of them (YKL461) shows a high degree of identity with an aspartate aminotransferase gene. This raises the question of a second aspartate aminotransferase gene in yeast. A second ORF (YKL462) shows features compatible with a membranous localization. The other ORFs do not show a similarity with any known gene. A member of the highly repetitive ‘CAT’ DNA sequence is present.
Transport of hexoses in yeast. Re‐examination of the sugar phosphorylation hypothesis with a new experimental approach
Authors: Nevado Julián , Navarro MA Asunción , Heredia Claudio F. 
Published: May 2005

AbstractThe constitutive transport of hexoses in yeast has been re‐examined with a new radioactive experimental approach devised to distinguish between association or independence of the transport step with phosphorylation of the sugar substrate. The approach takes advantage of the fact that the label of [2‐3H]mannose disappears once it has been phosphorylated by the yeast, due to its conversion to fructose‐6‐phosphate. Our results with wild‐type yeast and this fermentable sugar support the view that the transport of hexoses in yeast does not involve phosphorylation of the substrate. Other features of the transport process have been examined using this experimental procedure and are also reported.
A homologous cell‐free system for studying protein translocation across the endoplasmic reticulum membrane in fission yeast
Authors: Brennwald Patrick , Wise Jo Ann 
Published: May 2005

AbstractWe report the development of a homologous in vitro assay system for analysing translocation of proteins across the endoplasmic reticulum (ER) membrane of the fission yeast Schizosaccharomyces pombe. Our protocol for preparing an S. pombe extract capable of translating natural messenger RNAs was modified from a procedure previously used for Saccharomyces cerevisiae, in which cells are lysed in a bead‐beater. However, we were unable to prepare fission yeast microsomes active in protein translocation using existing budding yeast protocols. Instead, our most efficient preparations were isolated by fractionating spheroplasts, followed by extensive washing and size exclusion chromatography of the crude membranes. Translocation of two ER‐targeted proteins, pre‐acid phosphatase from S. pombe and prepro‐α‐factor from S. cerevisiae, was monitored using two distinct assays. First, evidence that a fraction of both proteins was sequestered within membrane‐enclosed vesicles was provided by resistance to exogenously added protease. Second, the protected fraction of each protein was converted to a higher molecular weight, glycosylated form; attachment of carbohydrate to the translocated proteins was confirmed by their ability to bind Concanavalin A–Sepharose. Finally, we examined whether proteins could be translocated across fission yeast microsomal membranes after their synthesis was complete. Our results indicate that S. cerevisiae prepro‐α‐factor can be post‐translationally imported into the fission yeast ER, while S. pombe pre‐acid phosphatase crosses the membrane only by a co‐translational mechanism.
XI. Yeast sequencing reports. Sequence analysis of a 10 kb fragment of yeast chromosome XI identifies the SMY1 locus and reveals sequences related to a pre‐mRNA splicing factor and vacuolar ATPase subunit C plus a number of unidentified open reading frames
Authors: James Carolyn M. , Gent Manda E. , Indge Keith J. , Oliver Stephen G. 
Published: May 2005

AbstractWe report the DNA sequence analysis of a region on the left arm of chromosome XI of Saccharomyces cerevisiae extending over 10 kb. The region contains five open reading frames (ORFs) of greater than 100 amino acids which do not show significant overlap with other ORFs. YKL408 contains a sequence with strong similarity to the RNA helicase pre‐mRNA splicing factors PRP2, PRP16 and PRP22 (Burgess et al., 1990; Company et al., 1991; Ruby et al., 1991). YKL409 corresponds to the gene SMY1, the sequence of which was previously reported by Lillie and Brown (1992). YKL410 is identical to ATPase subunit C (Beltran et al., 1992) except for an N‐terminal extension. YKL406 and YKL407 show no significant identity with any sequences in the databases searched. The sequence has been entered in the EMBL Data Library under Accession Number X75560.
Sequence comparison of the ARG4 chromosomal regions from the two related yeasts, Saccharomyces cerevisiae and Saccharomyces douglasii
Authors: Adjiri Adouda , Chanet Roland , Mezard Christine , Fabre Francis 
Published: May 2005

AbstractA 3·6 kb DNA fragment from Saccharomyces douglasii, containing the ARG4 gene, has been cloned, sequenced and compared to the corresponding region from Saccharomyces cerevisiae. The organization of this region is identical in both yeasts. It contains besides the ARG4 gene, another complete open reading frame (ORF) (YSD83) and a third incomplete one (DED81). The ARG4 and the YSD83 coding regions differ from their S. cerevisiae homologs by 8.1% and 12·5%, respectively, of base substitutions. The encoded proteins have evolved differently: amino acid replacements are significantly less frequent in Arg4 (2·8%) than in Ysc83 (12·4%) and most of the changes in Arg4 are conservative, which is not the case for Ysc83. The non‐coding regions are less conserved, with small AT‐rich insertions/deletions and 20% base substitutions. However, the level of divergence is smaller in the aligned sequences of these regions than in silent sites of the ORFs, probably revealing a higher degree of constraints. The Gcn4 binding site and the region where meiotic double‐strand breaks occur, are fully conserved. The data confirm that these two yeasts are evolutionarily closely related and that comparisons of their sequences might reveal conserved protein and DNA domains not expected to be found in sequence comparisons between more diverged organisms.
Purification of yeast histones competent for nucleosome assembly in vitro
Authors: Fukuma Mariko , Hiraoka Yoshiki , Sakurai Hiroshi , Fukasawa Toshio 
Published: May 2005

AbstractWe have developed a procedure to purify nucleosomal assembly‐competent histones as a mixture of H2A, H2B, H3 and H4 from isolated nuclei of the yeast Saccharomyces cerevisiae with a purity of 70–80%. The mixture contained each of the histone subunits approximately at the equi‐molar ratio. Plasmid pBR322 DNA was assembled into nucleosomes with the purified yeast histones in the presence of nucleoplasmin from unfertilized eggs of the frog Xenopus laevis. The efficiency of assembly of yeast histones was comparable to that of core histones purified from HeLa cells. The length of DNA fragment wrapping around a core histone particle and the molar ratio of histone components in an assembled nucleosome particle were estimated to be 150 ± 10 bp long and H2A:H2B:H3:H4 = 1·0:0·9:0·9:1·0, respectively.
XIIXVI. Yeast sequencing reports. Mapping and sequencing of two yeast genes belonging to the ATP‐binding cassette superfamily
Authors: Dean Michael , Allikmets Rando , Gerrard Bernard , Stewart Claudia , Kistler Amy , Shafer Brenda , Michaelis Susan , Strathern Jeff 
Published: May 2005

AbstractATP‐binding cassette (ABC) transporters share significant sequence identity within their ATP‐binding domains. Degenerate oligonucleotides based on highly conserved portions of the ATP‐binding domain genes were used to clone portions of two members of the ABC gene superfamily from Saccharomyces cerevisiae DNA. These genes were designated MDL1 and MDL2 (for multidrug resistance‐like). Each MDL gene is predicted to encode a single set of transmembrane domains and a single ATP‐binding domain, thus the MDL gene products are ‘half‐molecule’ ABC proteins. The two genes were mapped to precise regions on chromosomes XII and XVI and show a considerable similarity to the mammalian P‐glycoprotein/multidrug resistance (MDR) and peptide transporter (TAP) genes. Preliminary analysis of null mutants constructed by gene replacement has indicated that the MDL genes are not essential for viability of yeast. The sequences have been deposited in the GenBank data library under Accession Numbers L16958 (Locus YSCBCSA) and L16959 (Locus YSCBCSB).
Genetic evidence for a functional interaction between Saccharomyces cerevisiae CDC24 and CDC42
Authors: Ziman Michael , Johnson Douglas I. 
Published: May 2005

AbstractCdc24p and Cdc42p are involved in the control of cell polarity during the Saccharomyces cerevisiae cell cycle. Cdc42p is a member of the Ras superfamily of GTPases and Cdc24p displays limited amino‐acid sequence similarity with the Dbl proto‐oncoprotein, which acts to stimulate guanine‐nucleotide exchange on human Cdc42p. We have performed several genetic experiments to test whether Cdc24p and Cdc42p interact within the cell. First, overexpression of Cdc24p suppressed the dominant‐negative cdc42D118A allele. Second, overexpression of wild‐type CDC24 and CDC42 genes together was a lethal event resulting in a morphological phenotype of large, round, unbudded cells, indicating a loss of cell polarity. Third, a cdc24ts cdc42ts double mutant exhibited a synthetic‐lethal phenotype at the semi‐permissive temperature of 30°C. These data suggest that Cdc24p and Cdc42p interact within the cell and that Cdc24p may be involved in the regulation of Cdc42p activity.
X–XI. Yeast mapping reports. The use of random‐breakage mapping to locate the genes APN1 and YUH1 in the Saccharomyces genome, and to determine gene order near the left end of chromosome XI
Authors: Game John , Bell Maren , Ramotar Dindial , Miller Harvey 
Published: May 2005

AbstractWe have used the previously described technique of random‐breakage mapping to locate the two yeast genes APN1 and YUH1. The APN1 locus is located ∼235 kb from the left telomere of chromosome XI, and shows weak (∼53 cM) genetic linkage to ura1. The YUH1 locus is located ∼140 kb from the right telomere of chromosome X, and genetically maps 3·6 cM distal to cdc11. In addition, we show by random‐breakage mapping that TRP3 is located ∼45 kb from the left telomere of chromosome XI, whereas FAS1 is ∼110 kb from the same telomere. This supports a gene order on the left distal portion of chromosome XI that agrees with other physical reports but is inverted with respect to Edition 11 of the published genetic map. This report confirms that random‐breakage mapping is a rapid and convenient method of locating cloned genes.
Transfer RNA profiling: A new method for the identification of pathogenic Candida species
Authors: Santos Manuel A. S. , El‐Adlouni Chakib , Cox Alison D. , Luz José M. , Keith Gerard , Tuite Mick F. 
Published: May 2005

AbstractA new molecular taxonomic method applicable to the identification of medically important Candida species and other yeast species has been developed. It is based on the electrophoretic pattern of total tRNA samples (a ‘tRNA profile’) isolated from Candida species and generated using high‐resolution semi‐denaturing urea‐polyacrylamide gel electrophoresis and methylene blue staining. Species‐specific tRNA profiles for the species. C. albicans, C. tropicalis, C. parapsilosis, C. guilliermondii, C. glabrata and Pichia guilliermondii were obtained. Detailed studies with the major human pathogen of the Candida genus, C. albicans, demonstrated that the tRNA profile for a given species was both reproducible and strain‐independent; seven different C. albicans strains generated identical tRNA profiles. Minor strain‐specific heterogeneities in the tRNA profiles of C. guilliermondii and C. parapsilosis were detected, but in neither case did they significantly alter the species‐specific diagnostic tRNA profile. The potential of this method in clarifying taxonomic anomalies was demonstrated by the finding that Type I and Type II strains of C. stellatoidea generate very different tRNA profiles, with that of a Type II strain being identical to the C. albicans tRNA profile. This method offers a number of advantages over current electrophoretic karyotype methods for species identification, both within the Candida genus and with yeast species in general.
IV. Yeast sequencing reports. A Saccharomyces cerevisiae gene encoding a potential adenine phosphoribosyltransferase
Authors: Yuryev Anton , Corden Jeffry L. 
Published: May 2005

AbstractThe nucleotide sequence of a Saccharomyces cerevisiae gene encoding a potential adenine phosphoribosyltransferase (APRT) has been determined. The protein encoded by this gene shows a high degree of similarity with APRTs from a variety of other species. The S. cerevisiae gene, named APT2, has been mapped to chromosome IV. The sequence has been deposited in the GenBank data library under Accession Number L14434.
IV. XV. Yeast mapping reports. RPL44 and RPL44′, encoding acidic ribosomal phosphoproteins YP2α(l44) and YP1β(l44′), are adjacent to rig and STF1 on Saccharomyces cerevisiae chromosomes XV and IV respectively
Authors: Rodriguez‐Gabriel M. A. , Zambrano R. , Ballesta J. P. G. 
Published: May 2005

AbstractThe RPL44′ gene from Saccharomyces cerevisiae encoding the ribosomal protein YP1β(L44′) has been found to be linked to the STF1 gene, encoding a stabilizing factor of the F1F0‐ATPase inhibitor protein from mitochondria. Evidence of this linkage comes from results obtained from Northern hybridization using a DNA probe that contains a complementary region to the 5′ end of the mRNA of RPL44′. Similarly, a data bank search has shown that RPL44, encoding ribosomal protein YP2α(L44) is linked to the rig gene that encodes ribosomal protein S21.
Phosphoribosylpyrophosphate synthetase (PRS): A new gene family in Saccharomyces cerevisiae
Authors: Carter Andrew T. , Narbad Arjan , Pearson Bruce M. , Beck Karl‐Friedrich , Baum Bobby , Logghe Marc , Contreras Roland , Schweizer Michael 
Published: May 2005

AbstractSaccharomyces cerevisiae contains at least four PRS genes, all of which have been cloned and sequenced. Each of the four derived amino acid sequences have more than 60% similarity to the corresponding polypeptides of man, rat, Escherichia coli and Salmonella typhimurium. The PRS1 gene maps on chromosome XI, PRS2 on chromosome V, PRS3 on chromosome VIII and PRS4 on chromosome II. One member of this gene family, PRS1, contains a region of non‐homology (NHR) shown by cDNA cloning and sequencing not to be an intron. The results presented here suggest that the presence of this NHR is not detrimental to the function of the gene. To date the possibility of protein splicing can be neither proven nor disputed. The sequences submitted to the EMBL data library are available under the following accession numbers: PRS1 (X70069), PRS2 (X74414) and PRS3 (X74415).
nmt2 of fission yeast: A second thiamine‐repressible gene co‐ordinately regulated with nmt1
Authors: Manetti Andrea G. O. , Rosetto Marco , Maundrell Kinsey G. 
Published: May 2005

AbstractWe previously described a screen for thiamine‐repressible genes in Schizosaccharomyces pombe and reported on one such gene, nmt1, required for thiamine biosynthesis. Here we describe a second gene, nmt2, recovered in the same screen. Disruption of nmt2 also resulted in thiamine auxotrophy, indicating a role for the nmt2 gene product in thiamine biosynthesis. Both genes are highly transcribed in minimal medium and repressed in medium containing thiamine, and nuclear ‘run‐on’ experiments confirm that expression in both cases is controlled by the rate of transcription initiation. The virtually identical kinetics of induction and repression suggest that the two genes are co‐ordinately regulated. Sequence comparison of the two promoters reveals a canonical TATA box, downstream of which is a perfectly conserved 11 bp element. Transcript mapping experiments show that transcription initiation of both genes is centred on this element.
X. Yeast sequencing reports. The sequence of a 36 kb segment on the left arm of yeast chromosome X identifies 24 open reading frames including NUC1, PRP21 (SPP91), CDC6, CRY2, the gene for S24, a homologue to the aconitase gene ACO1 and two homologues to chromosome III genes
Authors: Purnelle Bénédicte , Coster Françoise , Goffeau André 
Published: May 2005

AbstractA 36 kb fragment from the left arm of chromosome X, located at about 50 kb from the telomere, was sequenced and analysed. The segment contains a new putative ARS, a new tRNA for threonine, remnants of a solo delta and 24 open reading frames (ORFs) numbered from J0310 to J0355. Six of them, NUC1, PRP21 (also called SPP91), CDC6, CRY2, the gene encoding the ribosomal protein S24 and the gene coding for a hypothetical protein of 599 amino acids, have been sequenced previously. Three ORFs show high homology to the yeast gene ACO1 encoding mitochondrial aconitase and to the chromosome III genes YCR34W and YCR37C of unknown function. Three other ORFs show lower but significant homology: a first one to UNP, a gene related to the tre‐2 oncogene from mouse and to the gene coding for the yeast deubiquitinating enzyme DOA2; a second one to SLY41, a suppressor of the functional loss of YPT1 and a third one to the gene encoding the proline utilization activator PUT3.The complete nucleotide sequence of 36 016 bp was submitted to the EMBL database (accession number X77688).