bluuebunny/crossref_metadata_2025_split huggingface dataset:
Physical constitution of ribosomal genes in common strains of Saccharomyces cerevisiae
Authors: Rustchenko Elena P. , Sherman Fred 
Published: May 2005

AbstractSeveral recent investigations, employing restriction endonucleases that do not cleave within rDNA units, revealed that a number of laboratory strains of Saccharomyces cerevisiae apparently contain a single tandem array of approximately 50 to 200 rDNA units on each chromosome XII homolog. The number of these rDNA units varies from strain to strain, among subclones of the same strain, and after different conditions of growth. In contrast, the commonly‐used strain S288C and its derivatives contain two clusters on each chromosome XII homolog. Although the two clusters are stably maintained, the number of rDNA units within each cluster can vary as in strains with single clusters.
Isolation and partial purification of mannose‐specific agglutinin from brewer's yeast involved in flocculation
Authors: Straver Marika H. , Traas Vincent M. , Smit Gerrit , Kijne Jan W. 
Published: May 2005

AbstractYeast cell‐agglutinating activity, designated agglutinin (possible lectin), was isolated from cell walls of both non‐flocculent and flocculent brewer's yeast cells. Agglutinin‐mediated aggregation of yeast cells in a manner similar to flocculation with respect to specific mannose‐sensitivity, pH‐dependence and calcium‐dependence. Agglutinating activity was found to be heat‐stable and protease‐insensitive. Furthermore, addition of agglutinin to flocculent cells strongly stimulated the flocculation ability of the cells, whereas addition to non‐flocculent cells rendered these cells weakly flocculent.Agglutinin was found to be released from flocculent cells during the course of a flocculation assay, but not from non‐flocculent cells. Presence of mannose during the assay inhibited release of agglutinin. Our results suggest that (i) mannose‐specific agglutinin is continuously synthesized during growth of brewer's yeast cells, (ii) agglutinin is present in cell walls of non‐flocculent cells but is unable to bind its ligand on other cells, and (iii) the ability of yeast cells to flocculate in a flocculation assay depends, among other factors, on release of agglutinin from the cells. A 10‐kDa polypeptide might represent one form of agglutinin.
II. Yeast sequencing reports. A putative P‐type Cu2+‐transporting ATPase gene on chromosome II of Saccharomyces cerevisiae
Authors: Rad Massoud Ramezani , Kirchrath Lutz , Hollenberg Cornelis P. 
Published: May 2005

AbstractWe have sequenced a gene on the right arm near the telomere of chromosome II of Saccharomyces cerevisiae which codes for a putative P‐type cation‐transporting ATPase (PCA1). The gene codes for a 1216 amino acids protein. The PCA1 gene expresses a 3·5 kb message in both haploid and diploid cells when grown in glucose‐based rich medium YPD. The gene product is most similar at the C‐terminal region to a human copper‐transporting ATPase and Enterococcus hirae copper‐transporting ATPases and also an N‐terminal dithiol region that was proposed to be a ‘metal‐binding motif’. Cells lacking PCA1 display no obvious phenotype when tested under standard conditions; whereas they cease growth much earlier than the isogenic wild‐type cells in a minimal medium with high copper concentration. Overexpression of PCA1 under GAL1/10 promoter in yeast cells causes poor growth. We also show that yeast strains carrying PCA1 in multiple copies grow slower than isogenic wild‐type strains in a minimal synthetic medium containing 0·3 mM‐CuSO4. The sequence has been deposited in the EMBL data library under Accession Number Z29332.
Rapid protein extraction from Saccharomyces cerevisiae
Authors: Horvath Anton , Riezman Howard 
Published: May 2005

AbstractWe have developed and evaluated an easy and rapid method for extraction of proteins from yeast cells for sodium dodecyl sulphate (SDS)–gel electrophoresis and Western blotting. The procedure comprises a centrifugation step to harvest the cells, addition of a sample buffer and heating, then another centrifugation step before applying the extracted proteins found in the supernatant to an SDS gel. It is applicable to the study of large numbers of samples in 1 day. This procedure is easier, quicker, and as efficient as procedures using base and 2‐mercaptoethanol, but somewhat less efficient than lysis with glass beads under certain conditions.
Yeast sequencing reports. Sequence of the AFG3 gene encoding a new member of the FtsH/Yme1/Tma subfamily of the AAA‐protein family
Authors: Guelin Emmanuel , Rep Martijn , Grivell Leslie A. 
Published: May 2005

AbstractA nuclear gene from Saccharomyces cerevisiae was cloned by genetic complementation of a temperature‐sensitive respiratory‐deficient mutant. DNA sequence analysis reveals that it encodes a protein with homology to Yme1, FtsH and Tma, proteins which belong to the AAA‐protein family (ÃPases associated with diverse cellular activities). The members of this family are involved in very different biological processes. Yme1p, a yeast mitochondrial protein, affects the rate of DNA escape from mitochondria to the nucleus and the Escherichia coli FtsH protein is apparently involved in the post‐translational processing of PBP3, a protein necessary for septation during cell division. This newly sequenced gene, which we have designated AFG3 for ÃPase family gene 3, encodes a putative mitochondrial protein of 760 amino acid residues that is closely related to FtsH, Tma (protein from Lactococcus lactis) and Yme1p with 58, 55 and 46% identity respectively. The sequence has been deposited in the EMBL data library under Accession Number X76643.
The in vivo activation of Saccharomyces cerevisiae plasma membrane H+‐ATPase by ethanol depends on the expression of the PMA1 gene, but not of the PMA2 gene
Authors: Monteiro G. A. , Sá‐Correia I. , Supply P. , Goffeau A. 
Published: May 2005

AbstractThe expression of the PMA1 and PMA2 genes during Saccharomyces cerevisiae growth in medium with glucose plus increasing concentrations of ethanol was monitored by using PMA1‐lacZ and PMA2‐lacZ fusions and Northern blot hybridizations of total RNA probed with PMA1 gene. The presence of sub‐lethal concentrations of ethanol enhanced the expression of PMA2 whereas it reduced the expression of PMA1. The inhibition of PMA1 expression by ethanol corresponded to a decrease in the content of plasma membrane ATPase as quantified by immunoassays. Although an apparent correspondence could exist between the increase of plasma membrane ATPase activity and the level of PMA2 expression, the maximal level of PMA2 expression remained about 200 times lower than PMA1. On the other hand, ethanol activated the plasma membrane H+‐ATPase activity from a strain expressing only the PMA1 ATPase but did not activate that from a strain expressing only the PMA2 ATPase. These results provide evidence that in the presence of ethanol it is the PMA1 ATPase which is activated, probably by a post‐translational mechanism and that the PMA2 ATPase is not involved.
The peroxisomal membrane proteins of Candida boidinii: Gene isolation and expression
Authors: Moreno Myrthala , Lark Richard , Campbell Kimberly L. , Goodman Joel M. 
Published: May 2005

AbstractCandida boidinii is a methylotrophic yeast in which several growth substrates can cause vigorous peroxisomal proliferation. While such diverse substrates as methanol, oleic acid and D‐alanine induce different peroxisomal metabolic pathways, membranes seem to contain common abundant peroxisomal membrane proteins (PMPs). These proteins have been termed PMP31, PMP32 and PMP47. The gene encoding PMP47 has been previously cloned and analysed. We now report the isolation of a second PMP47 gene (or allele) as well as PMP31 and PMP32. PMP47A and PMP47B share 95% sequence identity at the amino acid level. PMP31 and PMP32 each contain 256 amino acids and are highly similar (97% identity) in protein sequence. Both PMP31 and PMP32 are predicted to span the membrane once or twice. All abundant PMPs of C. boidinii are basic in charge; they all have predicted isoelectric points above 10. RNAs corresponding to the PMP47s and to PMPs31‐32 are strongly induced by methanol, oleic acid and D‐alanine. While the PMP47s probably encode substrate carriers, the functions of PMP31 and PMP32 from C. boidinii are still unknown. The GenBank Accession Numbers for PMP47B, PMP31, and PMP32 are L27998, L27999 and L28000, respectively. The 5′ untranslated sequence of PMP47A, accession number J05672, has been corrected.
II. Yeast sequencing reports. The sequence of a 22·4 kb DNA fragment from the left arm of yeast chromosome II reveals homologues to bacterial proline synthetase and murine α‐adaptin, as well as a new permease and a DNA‐binding protein
Authors: de Wergifosse Philippe , Jacques Bernard , Jonniaux Jean‐Luc , Purnelle Bénédicte , Goffeau André , Skala Jacek 
Published: May 2005

AbstractWe report the sequencing of a 22 470 bp DNA fragment from the left arm of Saccharomyces cerevisiae chromosome II. Thirteen open reading frames longer than 300 bp provisionally called YBL0520, YBL0401 to YBL0408 and YBL0410 to YBL0413 have been detected. Five genes were previously sequenced: COR1, encoding a core protein of the mitochondrial coenzyme QH2 cytochrome c reductase complex (Tzagaloff and Crivellone, 1986). PRS3, a proteasome subunit gene (Lee et al., 1992), ERD2, coding for a protein involved in the secretory pathway (Semeza et al., 1990), URA7, which encodes a CTP synthetase (Ozier‐Kalogeropoulos et al., 1991) and the gene for the ribosomal protein L16 (Pan et al., 1993). Among the others, YBL0406 shows striking homologies to FUR4 (Jund et al., 1988) and DAL4 (Yoo et al., 1992), the uracyl and allantoin permeases; YBL0520 is a DNA‐related protein, possibly involved in gene regulation; YBL0412 shares homologies with the mouse α‐adaptins A and C; and YBL0413 is homologous to a protein of Pseudomonas aeruginosa that is likely to be involved in proline biosynthesis. YBL0401, internal to YBL0520, is probably not expressed. The sequence has been deposited in the EMBL data library under accession number X78217
Development of a transformation system for the yeast Yamadazyma (Pichia) ohmeri
Authors: Piredda Sandrine , Gaillardin Claude 
Published: May 2005

AbstractThis communication describes the development of genetic tools for the yeast Yamadazyma ohmeri. Nystatin enrichment proved highly effective for isolating various auxotrophic strains, which were classified by complementation analysis. Biosynthetic genes encoding known biochemical functions were isolated by polymerase chain reaction, including YoLEU2 and YoURA3 that were sequenced. Using these homologous genes as selective markers, DNA transformation was accomplished by electroporation. Transformation with pBR322‐based plasmids, cut within the coding region of the homologous marker gene, yielded 20 to 50 stable transformants per μg of DNA. In about 80% of the cases, integration of plasmid DNA sequence occurred by homologous recombination of a single plasmid into the chromosome. Excision of the plasmid permitted gene replacement, as illustrated by the substitution of a wild‐type URA3 gene by an in vitro generated deletion.Sequences conferring extrachromosomal replication were isolated from Y. ohmeri DNA. Plasmids based on pBR322 carrying such an ARS and either selective markers transformed at 104/μg and were shown to replicate freely in Y. ohmeri at an approximate copy number of 40. Unexpectedly, we observed that BS‐SKR derivatives carrying either YoLEU2 or YoURA3 but no Y. ohmeri ARS also replicated extrachromosomally. Linearization of transforming plasmids within regions homologous or not to chromosomal sequences stimulated transformation frequencies up to four‐fold. The sequences are available for consultation under EMBL accession number Z35101 for YoLEU2 and Z35100 for YOURA3.
Kluyveromyces marxianus small DNA fragments contain both autonomous replicative and centromeric elements that also function in Kluyveromyces lactis
Authors: Iborra François , Ball Maria M. 
Published: May 2005

AbstractTwo fragments containing both an autonomous replicating sequence (ARS) and a centromere have been isolated and sequenced from the yeast Kluyveromyces marxianus. The ARS and centromeric core sequences are only 500 bp apart, but ARS activity could be separated from the centromeric sequences.Centromeric sequences are organized in a similar way to those of budding yeasts: two well‐conserved elements: CDEI (5′ TCACGTG 3′) and CDEIII (5′ TNTTCCGAAAGTWAAA 3′), are separated by a 165 bp AT‐rich (± 90%) CDEII element whose length is twice that of Saccharomyces cerevisiae CDEII but almost identical to that of K. lactis.The ARS‐core consensus sequence (5′ TTTATTGTT 3′) is also similar to that of K. lactis. Both ARS and centromeric elements function in this strain, albeit inefficiently, but not in S. cerevisiae.A third ARS‐containing fragment with a different organization has been isolated and sequenced.The nucleotide sequences of DNA fragments reported in this paper will appear in the EMB data library under the accession numbers: Z31562, Z31563, Z31564.
Yeast sequencing reports. CAN1, a gene encoding a permease for basic amino acids in Candida albicans
Authors: Sychrová Hana , Souciet Jean‐Luc 
Published: May 2005

AbstractThe first gene coding for an amino‐acid permease of Candida albicans was sequenced. The DNA fragment complementing the lysine‐permease deficiency was 3385 bp long. An open reading frame of 1713 nucleotides was found encoding a protein of 571 amino acids, with a calculated molecular weight of 63 343. Analysis of the deduced primary structure revealed ten membrane spanning regions and three potential N‐glycosylation sites. The protein sequence is strongly homologous to both permeases for basic amino acids (Can1 and Lyp1) of Saccharomyces cerevisiae. C‐terminal part of another ORF (105 aa), highly homologous to the gene HAL2 of S. cerevisiae, was found 133 bp downstream, and in tail‐to‐tail orientation to the permease gene. The sequence data will appear in the EMBL/GenBank/DDBJ Nucleotide Sequence Data Libraries under the accession number X76689.
IV. Yeast sequencing reports. Sequence of the PHO2‐POL3 (CDC2) region of chromosome IV of Saccharomyces cerevisiae
Authors: Simon Michel , Bénit Paule , Vassal Anne , Dubois Céline , Faye Gérard 
Published: May 2005

AbstractThe nucleotide sequence of a 5 kb EcoRI‐NcoI fragment of chromosome IV, contiguous to gene POL3 (CDC2), has been determined. It contains three open reading frames: QRI1, QRI2 and QRI7. Two of them are essential genes. QRI7 is homologous to the Escherichia coli orfx gene. Accession number to EMBL/Genbank Data Library is X79380.
X. Yeast sequencing reports. Sequence analysis of a 40·2 kb DNA fragment located near the left telomere of yeast chromosome X
Authors: Vandenbol Micheline , Durand Patrick , Bolle Paul‐Andre , Dion Caroline , Portetelle Daniel , Hilger Francois 
Published: May 2005

AbstractWe have sequenced on both strands a 40,257 bp fragment located near the left telomere of chromosome X of Saccharomyces cerevisiae.The sequenced segment contains 21 open reading frames (ORFs) at least 100 amino acids long. Five of the ORFs correspond to known amino acid sequences: two hypothetical proteins in the subtelomeric Y′ repeat region of 65·4 and 12·8 KDa, the cytochrome B pre‐mRNA processing CBP1 protein, the mitochondrial nuclease NUC1 and the CRT1 protein. Of the 16 remaining ORFs, eight show highest homologies with the S. cerevisiae hexose transporters family (two ORFs), the yeast α‐glucosidase (two ORFs), the yeast PEP1 precursor, the Escherichia coli galactoside O‐acetyltransferase, the S. cerevisiae 137·7 KDa protein located in the Y′ region and a protein of unknown function of Schizosaccharomyces pombe. Finally, eight of the ORFs exhibit no significant similarity with any amino acid sequences described in data banks.DNA sequence comparison has revealed the presence of different repeated elements characteristic of yeast chromosome ends.Disruption studies have been performed on two ORFs encoding putative proteins of unknown function.The sequence has been entered in the EMBL Data Library under Accession Number Z34098.
A deviation from the universal genetic code in Candida maltosa and consequences for heterologous expression of cytochromes P450 52A4 and 52A5 in Saccharomyces cerevisiae
Authors: Zimmer Thomas , Schunck Wolf‐Hagen 
Published: May 2005

AbstractWe demonstrate that serine instead of leucine is specified by the CUG codon in the yeast Candida maltosa. Evidence for this deviation from the universal genetic code was obtained by means of in vitro translation experiments. Depending on the cell‐free system used, either serine, in the C. maltosa system, or leucine, in the control with the conventional wheat germ system, was found to be incorporated into the translation products of artificial CUG‐containing mRNAs. Moreover, we were able to transfer the non‐universal decoding of CUG to the wheat germ system by adding a tRNA fraction isolated from C. maltosa. This finding indicates the presence in C. maltosa of an unusual serine tRNA that recognizes CUG. As a consequence of the altered genetic code, expression in Saccharomyces cerevisiae of C. maltosa cytochrome P450 genes required an exchange of their CTG triplets by TCT encoding serine in order to produce the authentic proteins. In contrast, heterologous expression of the original C. maltosa genes resulted in the formation of still active but unstable enzymes probably subject to selective proteolysis in the host cells.
Construction of a set of convenient saccharomyces cerevisiae strains that are isogenic to S288C
Authors: Winston Fred , Dollard Catherine , Ricupero‐Hovasse Stephanie L. 
Published: May 2005

AbstractA set of GAL2+ yeast strains that are isogenic to strain S288C have been constructed. They contain non‐reverting mutations in genes commonly used for selection for recombinant plasmids. Strains from this collection are being used for the European Union Yeast Genome Sequencing Programme. Representative strains from this collection have been deposited with the ATCC.
Sequence and functional analysis of a 7·2 kb fragment of Saccharomyces cerevisiae chromosome II including GAL7 and GAL10 and a new essential open reading frame
Authors: Schaaff‐Gerstenschläger Ine , Schindwolf Thomas , Lehnert Wolfgang , Rose Matthias , Zimmermann Friedrich K. 
Published: May 2005

AbstractThe nucleotide sequence of a fragment of 7200 base pairs of Saccharomyces cerevisiae chromosome II has been determined. The sequence contains three open reading frames (ORFs). Two genes for galactose metabolism, GAL7 and part of the GAL10 coding region, are localized on the fragment. Comparison to the previously published sequence data showed several differences, leading to changes in the amino acid sequences of GAL7 and GAL10.One new ORF, YBR0224, was detected, coding for a protein with 918 amino acids. Comparison to the DNA and protein data bases showed no significant homologies. The protein has some interesting features pointing to a function involved in transcription regulation: a leucine zipper motif, a highly acidic region, possibly involved in transcription activation and a putative nuclear localization signal. Deletion analysis showed that the gene is essential when deleted in strain W303. Spores could germinate and form microcolonies, but efforts to propagate the colonies failed. Deletion of this gene in a different genetic background (strain M5) led to very poor‐growing mutant strains with cells showing aberrant cellular morphologies.The nucleotide sequence of the fragment has been deposited in the EMBL‐database under the Accession Number X81324.
Perfect state of Rhodomyces dendrorhous (Phaffia rhodozyma)
Authors: Golubev Wladyslav I. 
Published: May 2005

AbstractAfter mother–daughter cell conjugation, formation of long holobasidia with terminal basidiospores was observed without mycelium production in Rhodomyces dendrorhous (including the type strain of Phaffia rhodozyma) on polyol‐containing media. Basidiospores are not forcibly discharged and germinate by budding. A new genus Xanthophyllomyces (Filobasidiaceae, Tremellales) with a species, X. dendrorhous, is proposed for the telemorphic state of R. dendrorhous.
Characterization of a glycerol/H+ symport in the halotolerant yeast Pichia sorbitophila
Authors: Lages Fernanda , Lucas Cândida 
Published: May 2005

AbstractPichia sorbitophila is a halotolerant yeast capable of surviving to extracellular NaCl concentrations up to 4 M in mineral medium when glucose or glycerol are the only carbon and energy sources. Evidence is presented here that glycerol, the main compatible solute this yeast accumulates so as to maintain osmotic balance, is actively co‐transported with protons. This transport system was shown to be constitutive, not needing induction by either glycerol or salt, and was not repressible by glucose. In glucose‐ or glycerol‐grown cells, a simple diffusion was detectable, and iterative calculations were performed to calculate kinetic parameters, in the presence and in the absence of NaCl. At 25°C, pH 5·0, in glucose‐grown cells these were: Km = 0·81 ± 0·11 mM and Vmax = 634·2 ± 164·8 μmol h−1 per g (glycerol); Km = 1·28 ± 0·60 mM and Vmax = 558·6 · 100·6 μmol h−1 per g (protons). Correspondent stoichiometry was approximately 1, either for these conditions or in the presence of 1 M‐NaCl. An increase in acumulation capacity was evident when different concentrations of NaCl were present. This capacity was shown to be dependent on ΔpH and membrane potential, consistently with an electrogenic character. We suggest that the main role of this system is in osmoregulation, by keeping glycerol accumulated inside the cells, compensating for leakage, due to its liposoluble character.
Characterization of Schizosaccharomyces pombe his1 and his5 cDNAs
Authors: Erickson F. Les , Hannig Ernest M. 
Published: May 2005

AbstractWe have isolated Schizosaccharomyces pombe cDNAs corresponding to the genes his1+ and his5+. The his1 cDNA was isolated by functional complementation of the His− phenotype in a his1‐29 gcn3 Saccharomyces cerevisiae strain, while the his5 cDNA was isolated as a suppressor of the 3‐amino‐1,2,4‐triazole (3‐AT) sensitivity in a gcn3 S. cerevisiae strain. his1 and his5 are each present in single copy in haploid S. pombe. As is the case with S. cerevisiae, we have found that the growth of wild‐type strains of S. pombe is sensitive to 3‐AT, an inhibitor of imidazoleglycerol‐phosphate dehydratase. This enzyme is encoded by the HIS3 gene in S. cerevisiae and the his5+ gene in S. pombe. Treatment of S. pombe cells with 3‐AT leads to a small increase in the level of the his5 transcript, but no effect is seen on the level of the his1 transcript. This is in contrast to larger increases in transcription of amino acid biosynthetic genes, regulated by the general amino acid control, seen previously in similarly treated cultures of S. cerevisiae. These results suggest that there are likely to be some differences in the regulation of amino acid biosynthesis between these two yeasts.Sequences reported here have been deposited with GenBank as U07830 (his1) and U07831 (his5).
Localization of a protein a‐tagged kex2 protein to the vacuole of Saccharomyces cerevisiae allows rapid purification of vacuolar membranes
Authors: Bryant Nia J. , Boyd Alan 
Published: May 2005

AbstractWe have previously reported an immunoisolation procedure which allows purification of Kex2p‐containing Golgi membranes from lysed yeast cells. In order to evaluate the use of tagging procedures in organelle isolation we set out to isolate the same Golgi membrane fraction using a version of the Kex2 protease that had been affinity‐tagged at its C‐terminus. This protein is found to be localized in the vacuole, providing the basis of a method for the affinity‐purification of vacuolar membranes.