bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transformation‐associated recombination between diverged and homologous DNA repeats is induced by strand breaks
Authors: Larionov V. , Kouprina N. , Eldarov M. , Perkins E. , Porter G. , Resnick M. A. 
Published: May 2005

AbstractRearrangements within plasmid DNA are commonly observed during transformation of eukaryotic cells. One possible cause of rearrangements may be recombination between repeated sequences induced by some lesions in the plasmid. We have examined the mechanisms of transformation‐associated recombination in the yeast Saccharomyces cerevisiae using a plasmid system which allowed the effects of physical state and/or extent of homology on recombination to be studied. The plasmids contain homologous or diverged (19%) repeats of the URA3 genes (from S. cerevisiae or S. carlsbergensis) separated by the genetically detectable ADE2 colour marker. Recombination during transformation for covalently closed circular plasmids was over 100‐fold more frequent than during mitotic growth. The frequency of recombination is partly dependent on the method of transformation in that procedures involving lithium acetate or spheroplasting yield higher frequencies than electroporation. When present in the repeats, unique single‐strand breaks that are ligatable, as well as double‐strand breaks, lead to high levels of recombination between diverged and identical repeats. The transformation‐associated recombination between repeat DNAs is under the influence of the RAD52 and RAD1 genes.
Multipurpose vectors designed for the fast generation of N‐ or C‐terminal epitope‐tagged proteins
Authors: Cullin Christophe , Minvielle‐Sebastia Lionel 
Published: May 2005

AbstractIn this paper are described a set of new high‐copy‐number yeast vectors, which are specially designed for the conditional expression of epitope‐tagged proteins in vivo. One of the major advantages of these plasmids is that they allow polymerase chain reaction‐amplified open reading frames to be automatically fused in frame with the epitope‐coding sequence, avoiding longer procedures such as site‐directed mutagenesis. This heterologous construction can be realized either at the 5′‐end of the coding sequence, in the pYeF1 vector, or at its 3′‐end, in pYeF2, generating N‐ or C‐terminal tagged proteins, respectively. Moreover, to increase the usefulness of the method, derivatives of the two basic URA3‐borne pYeF1 and pYeF2 were constructed, carrying either the HIS3 or TRP1 gene as a marker of selection. These vectors could be of use for the purpose of functional analysis of the newly discovered genes resulting from the systematic sequencing of the yeast genome. Here, we present results showing the functional expression and the efficient immunoprecipitation of the epitope‐tagged Rna15 protein, which is involved in Saccharomyces cerevisiae mRNA stability.
Characterization of the KIN2 gene product in Saccharomyces cerevisiae and comparison between the kinase activities of p145KIN1 and p145KIN2
Authors: Donovan Mark , Romano Patrick , Tibbetts Michael , Hammond Charlotte I. 
Published: May 2005

AbstractWe have isolated two yeast genes, KIN1 and KIN2, by their homology to the protein kinase family of viral oncogenes. Previous studies have identified the yeast KIN1 gene product (pp145KIN1) as a 145 kilodalton (kDa) phosphoprotein with serine/threonine‐specific protein kinase activity. To identify and biochemically characterize the KIN2 gene product, antibodies were raised against a bacterial β‐galactosidase/KIN2 fusion polypeptide. In vivo, the KIN2 gene product is a 145 kDa phosphoprotein, pp145KIN2. In immune complexes, pp145KIN2 demonstrates serine/threonine protein kinase activity, transferring phosphate from [γ‐32P]ATP to either itself or the exogenously added substrates α‐casein, acid‐denatured enolase, or phosvitin. In vitro, kinase activity is dependent on either Mn2+ or Mg2+ ions. Both enzymes, pp145KIN1 and pp145KIN2, prefer ATP over GTP as their phosphoryl donor. Since a new class of yeast protein kinases has been identified which are serine/tyrosine‐specific, we analysed a wide range of substrates to see if any could be phosphorylated by pp145KIN1 or pp145KIN2 on tyrosine residues. Both enzymes phosphorylate α‐casein, acid‐denatured enolase, and phosvitin on serine and threonine residues. Neither enzyme could phosphorylate tyrosine residues even though good substrates for tyrosine‐specific kinases such as enolase, angiotensin II, and the synthetic polymer GLU80TYR20 were used. The biochemical analysis of KIN2 kinase activity shows remarkable similarity to that of its most closely related yeast kinase, KIN1. It remains to be seen if these two yeast protein kinases share any functional relationships or substrates in vivo.
Molecular cloning and analysis of the yeast flocculation geneFLO1
Authors: Watari Junji , Takata Yoshihiro , Ogawa Masahiro , Sahara Hirohisa , Koshino Shohei , Onnela Maija‐Leena , Airaksinen Ulla , Jaatinen Risto , Penttilä Merja , Keränen Sirkka 
Published: May 2005

AbstractThe DNA sequence of the flocculation geneFLO1ofSaccharomyces cerevisiae, which is located on chromosome I (Watariet al., 1989) was determined. The sequence contains a large open reading frame (ORF) of 2586 bp and codes for a protein of 862 amino acids. However, further study (genomic Southern and polymerase chain reaction analyses) indicated that the gene we cloned was not the intactFLO1gene but a form with an approximately 2 kb deletion in the ORF region. The intactFLO1gene was then cloned and its nucleotide sequence determined. The sequence revealed that the ORF of the intact gene is composed of 4611 bp which code for a protein of 1537 amino acids. A remarkable feature of the putative Flo1 protein is that it contains four families of repeated sequences composed of 18, 2, 3 and 3 repeats and that it has a large number of serines and threonines. In the deletedFLO1form, a large part of these repeated sequences was missing. The N‐ and C‐terminal regions are hydrophobic and both contain a potential membrane‐spanning region, suggesting that the Flo1 protein is an integral membrane protein and a cell wall component.
XIII. Yeast sequencing reports. SED6 is identical to ERG6, and encodes a putative methyltransferase required for ergosterol synthesis
Authors: Hardwick Kevin G. , Pelham Hugh R. B. 
Published: May 2005

AbstractLuminal endoplasmic reticulum (ER) proteins carry a sorting signal that allows them to be retrieved from the Golgi apparatus by a specific receptor. In yeast, this receptor is encoded by the ERD2 gene. Although retrieval of ER proteins does not appear to be an essential process, cells lacking ERD2 do not grow. Several multicopy suppressors of this growth defect have been isolated. The sequence of one of these, SED6, is presented here. Its product contains motifs characteristic of methyltransferases, and it is identical to ERG6, the presumed structural gene for S‐adenosylmethionine:Δ24‐sterol‐C‐methyltransferase. The gene is located adjacent to PDR4, near the centromere of chromosome XIII.
Purification of properties of Saccharomyces cerevisiae cystathionine β‐synthase
Authors: Ono Bun‐Ichiro , Kijima Kazuyasu , Inoue Toyomi , Miyoshi Shin‐Ichi , Matsuda Akio , Shinoda Sumio 
Published: May 2005

AbstractCystathionine β‐synthase (β‐CTSase), which catalyses cystathionine synthesis from serine and homocysteine, was purified to homogeneity from Saccharomyces cerevisiae. The molecular mass of the enzyme was estimated to be 235 kDa by gel filtration and 55 kDa by sodium dodecyl sulphate–polyacrylamide gel electrophoresis, indicating that it is a homotetramer. The N‐terminal amino acid sequence of the enzyme perfectly coincided with that deduced from the nucleotide sequence of CYS4, except for the absence of initiation methionine. The purified β‐CTSase catalysed cysteine synthesis from serine (or O‐acetylserine) and H2S. From this finding, we discuss the multifunctional nature and evolutionary divergence of S‐metabolizing enzymes.
Yeast sequencing reports. Genes of the linear mitochondrial DNA of Williopsis mrakii: Coding sequences for a maturase‐like protein, a ribosomal protein VAR1 homologue, cytochrome oxidase subunit 2 and methionyl tRNA
Authors: Drissi Rachid , Sor Frederic , Nosek Jozef , Fukuhara Hiroshi 
Published: May 2005

AbstractThe mitochondrial DNA (mtDNA) in some yeasts has a linear structure with inverted terminal repeats closed by a single‐stranded loop. These mtDNAs have generally a constant gene order, beginning with a small ribosomal RNA gene at the right end and terminating with a cytochrome oxidase subunit 2 gene (COX2) at the left end, independently of the wide variation in genome size. In the mtDNAs from several species of the genus Williopsis, we found an additional open reading frame, ORF1, which was homologous to the Saccharomyces cerevisiae RF1 gene encoding a group I intron maturase‐like protein. ORF1 genes from W. mrakii and W. suaveolens were mapped and sequenced. Next to ORF1, COX2 and methionyl tRNA genes were present on the opposite strand. The same relative positions of genes in the mtDNAs so far examined suggests that the constancy of gene order is generally conserved also at the level of individual tRNA genes. We identified another open reading frame, ORF2, in W. mrakii mtDNA. It was mapped next to the cytochrome oxidase subunit 3 gene. Rich in adenine‐thymine bases, ORF2 appears to be a homologue of the VAR1 gene which codes for a small ribosomal subunit protein in S. cerevisiae mitochondria. Nucleotide sequences data have been deposited in the EmBL data library under the following Accession Numbers: X66594 (Apocytochrome b and ORF2 genes of W. mrakii), X66595 (ORF1, tRNA‐Met and COX2 genes of W. mrakii), X73415 (tRNA‐Met and COX2 genes of W. suaveolens), X73416 (ORF1 gene of W. suaveolens) and X73414 (tRNA‐Met and COX2 genes of P. jadinii).
V. Yeast sequencing reports. Identification of a gene encoding a new Ypt/Rab‐like monomeric G‐protein in Saccharomyces cerevisiae
Authors: Lai Margaret H. , Bard Martin , Kirsch Donald R. 
Published: May 2005

AbstractA Saccharomyces cerevisiae sequence cloned by serendipity was found to encode a protein that is a new member of the Ypt/Rab monomeric G‐protein family. This sequence shows high homology to the yeast genes SEC4 and YPT1 and, like SEC4 and YPT1, is essential for viability. The sequence was localized to chromosome V based upon hybridization to pulse‐field gel‐separated yeast chromosomes. The sequence has been deposited in the GenBank data library under Accession Number L17070.
XII. Yeast sequencing reports. Sequence, mapping and disruption of CCC1, a gene that cross‐complements the Ca2+‐sensitive phenotype of csg1 mutants
Authors: Fu Dadin , Beeler Troy , Dunn Teresa 
Published: May 2005

AbstractWe have isolated, sequenced, mapped and disrupted a novel gene, CCC1, from Saccharomyces cerevisiae. This gene displays non‐allelic complementation of the Ca2+‐sensitive phenotype conferred by the csg1 mutation. The ability of this gene, in two copies per cell, to reverse the csg1 defect suggests it may have a role in regulating Ca2+ homeostasis. The sequence of CCC1 indicates that it encodes a 322 amino acid, membrane‐associated protein. The CCC1 gene is located on the right arm of chromosome XII. The sequence has been deposited in the GenBank data library under Accession Number L24112.
XIV. Yeast sequencing reports. Organization of the centromeric region of chromosome XIV in Saccharomyces cerevisiae
Authors: Lalo Dominique , Stettler Sophie , Mariotte Sylvie , Gendreau Emmanuel , Thuriaux Pierre 
Published: May 2005

AbstractA 15·1 kb fragment of the yeast genome was allocated to the centromeric region of chromosome XIV by genetic mapping. It contained six bona fide genes, RPC34, FUN34, CIT1 (Suissa et al., 1984), RLP7, PET8 and MRP7 (Fearon and Mason, 1988) and two large open reading frames, DOM34 and TOM34, RPC34 and RLP7 define strictly essential functions, whereas CIT1, PET8 and MRP7 encode mitochondrial proteins. The PET8 product belongs to a family of mitochondrial carrier proteins. FUN34 encodes a putative transmembraneous protein that is non‐essential as judged from the normal growth of the fun34‐::L̈K18 (URA3) allele, even on respirable substrates. TOM34 codes for a putative RNA binding protein, and DOM34 defines a hypothetical polypeptide of 35 kDa, with no significant homology to known proteins. The region under study also contains two divergently transcribed tDNAs, separated only by a chimeric transposable element. This tight tDNA linkage pattern is commonly encountered in yeast, and a general hypothesis is proposed for its emergence on the Saccharomyces cerevisiae genome. RPC34, RLP7, PET8 and MRP7 are unique on the yeast genome, but the remaining genes belong to an extant centromeric duplication between chromosome III and XIV. The sequences have been deposited in the EMBL/GenBank data libraries under Accession Numbers L11277, L19167, M11344, M22116, V02536, X00782 and X63746.
Chemical synthesis of the M‐factor mating pheromone from Schizosaccharomyces pombe
Authors: Wang Shu‐Hua , Xue Chu‐Biao , Nielsen Olaf , Davey John , Naider Fred 
Published: May 2005

AbstractConjugation in the fission yeast Schizosaccharomyces pombe is controlled by the reciprocal action of mating pheromones. We recently showed that M‐factor, the pheromone released by cells of the cellular mating type Minus, is a nonapeptide in which the C‐terminal cysteine residue is carboxyl‐methylated and S‐alkylated, probably with a farnesyl residue (Davey, 1992): Tyr‐Thr‐Pro‐Lys‐Val‐Pro‐Tyr‐Met‐Cys(S‐farnesyl)‐OCH3. Here we describe the chemical synthesis of this modified peptide and show that it exhibits all of the properties of the native pheromone. These results confirm the structure of the M‐factor while the production of relatively large amounts of pure pheromone will be invaluable for studying the mating response in this yeast.
The frequency of oligopurine. Oligopyrimidine and other two‐base tracts in yeast chromosome III
Authors: Yagil G. 
Published: May 2005

AbstractThe TRACTS program was employed to map the occurrence of base tracts composed of only two bases in Saccharomyces cerevisiae chromosome III. The observed frequencies were compared with those expected in random DNA. A vast excess of long base tracts of the three possible two‐base combinations, namely, purine, pyrimidine (R.Y), keto imino (K.M) and weak;strong (W;S, mainly A,T rich), was documented. The observed excess places yeast in the same category as other eukaryote and organelle genomes analysed. The excess of the two‐base tracts was considerably larger in the 1/3 of the chromosome not coding for a protein, in particular proximal to coding initiation and termination sites, but was observed for coding regions as well. A functional role for the excessive tracts, possibly as unwinding centers of particular genes, is proposed. Multiple occurrence of long two‐base tracts is offered as another diagnostic to determine whether an open reading frame (ORF), or an ORF subregion, is an actually translated gene region.
Transcription regulation of ribosomal protein genes at different growth rates in continuous cultures of Kluyveromyces yeasts
Authors: Hoekstra R. , Groeneveld Ph. , van Verseveld H. W. , Stouthamer A. H. , Planta R. J. 
Published: May 2005

AbstractWe have investigated the relationship between the growth rate of two Kluyveromyces strains that differ in their maximum growth rate, namely K. lactis (μmax = 0·5 h−1) and K. marxianus (μmax = 1·1 h−1), and the transcription rate of ribosomal protein (rp) genes in these strains. The growth rate of either strain was varied by culturing the cells in a chemostat under conditions of glucose limitation at different dilution rates. Although the steady‐state levels of transcription of the rp‐genes of both Kluyveromyces strains were tightly coupled to the cellular growth rate, no clear relationship between the level of rp‐gene transcription and the amount of in vitro binding of the RAP1‐ and ABF1‐like proteins to the promoters of these rp‐genes was observed.Upon a sudden increase in the growth rate of a steady‐state culture, the transcription of rp‐genes of K. lactis showed a different response from that in K. marxianus. Whereas a substantial overexpression of the K. lactis rp‐genes was found during at least 4–5 h, the level of expression of the K. marxianus rp‐genes was almost immediately adjusted to the new growth rate.
XI. Yeast sequencing reports. The yeast YKL741 gene situated on the left arm of chromosome XI codes for a homologue of the human ALD protein
Authors: Bossier Peter , Fernandes Lisete , Vilela Cristina , Rodrigues‐Pousada Claudina 
Published: May 2005

AbstractThe yeast gene YKL741 is situated on the left arm of chromosome XI, 12 kb closer to the centromere with respect to the previously localized PAS1 gene. The new yeast gene codes for a homologue of the human ALD protein (ALD: adrenoleukodystrophy). The similarity between the YKL741 protein and the ALD protein is very high in the C‐terminal half, which contains an ATP‐binding cassette characteristic of the ABC family of transporters. Additionally the YKL741 protein shows some similarity to the ALD protein in the N‐terminal half in three putative transmembrane spanning domains. The sequence has been deposited in the EMBL data library under Accession Number X76133 SC YKL.
Specific identification of Candida albicans by hybridization with oligonucleotides derived from ribosomal DNA internal spacers
Authors: Botelho Ana R. , Planta Rudi J. 
Published: May 2005

AbstractIn order to develop DNA probes for rapid, sensitive and specific detection of the pathogenic yeast species Candida albicans, we carried out comparative sequence analysis of the two internal transcribed spacer regions (ITS1 and ITS2) of the ribosomal DNA (rDNA) units of C. albicans and the closely related pathogenic species C. tropicalis. While overall sequence similarity between the two species was considerable (65–75%), both ITS1 and ITS2 were found to contain distinct regions with sufficient sequence divergence to make them suitable as specific target sites for the identification of C. albicans. On the basis of these results one ITS1‐derived (ANAB1) and two ITS2‐derived (ANAB2 and ANAB3) oligonucleotides were selected, chemically synthesized, and used as hybridization probes. Their specificity and reliability were evaluated in dot‐blot hybridization experiments with total genomic DNA from 13 strains of medically important Candida species, six strains of other yeast genera associated with man and animals, and ten strains previously identified as C. albicans by phenotypic criteria. Under well‐defined hybridization conditions the three probes hybridized exclusively with DNA derived from strains belonging to the species C. albicans, thus demonstrating their potential clinical usefulness. The failure of four of the (presumed) C. albicans strains to show hybridization to the ITS probes sheds doubt upon their taxonomic classification, which is reinforced by other phenotypic aspects of these strains.
XIII. Yeast mapping reports. MTF1, encoding the yeast mitochondrial RNA polymerase specificity factor, is located on chromosome XIII
Authors: Ulery Terrie L. , Jaehning Judith A. 
Published: May 2005

AbstractMTF1 is a nuclear gene that encodes the promoter recognition factor of the yeast mitochondrial RNA polymerase. The MTF1 gene was physically mapped to chromosome XIII. Genetic mapping data indicate that the gene is closely linked to RNA1.
Mating in the heterothallic haploid yeast Clavispora opuntiae, with special reference to mating type imbalances in local populations
Authors: Lachance Marc‐André , Nair Pradeep , Lo Patrick 
Published: May 2005

AbstractMating was studied in the haploid, heterothallic yeast Clavispora opuntiae to assess the importance of nutritional, genetic, and other factors that may favour mating and recombination. Local populations of this yeast generally exhibit dramatic inequalities in mating type distributions, suggesting that mating is rare in nature even though most isolates mate freely in the laboratory. The absence of assimilable nitrogen is prerequisite to mating competence, presumably by causing G1 arrest. Maximum mating competence is found in cells entering stationary phase in nitrogen‐limited media. Unlike the vast majority of mating yeasts, C. opuntiae does not appear to produce diffusible mating factors (sex pheromones), and mating‐competent cells do not undergo sexual agglutination. Pairwise cell contact appears to be the only signal that triggers the sexual process in this case. In order to determine if mating type imbalances in nature are caused by reduced fertility of ‘consanguine’ crosses, meiotic recombination was measured in pairs of strains that varied in their genetic distances as indicated by restriction mapping. That hypothesis was rejected, as recombination efficiency decreased with increasing genetic distance. We conclude that the rarity of mating in local populations is exacerbated by the stringent physical (pairwise cell contact) and nutritional (nitrogen depletion) conditions that will allow mating to proceed. Parallels are drawn with mating patterns observed in Clavispora lusitaniae.
The peroxisomal targeting signal of 3‐oxoacyl‐coA thiolase from Saccharomyces cerevisiae
Authors: Erdmann Ralf 
Published: May 2005

AbstractAll peroxisomal 3‐oxoacyl‐CoA thiolases identified so far do not contain the previously identified tripeptide peroxisomal targeting signal at their carboxy‐termini. For the two rat thiolases it was shown that their peroxisomal targeting signals are localized within the amino‐terminal region of the proteins and are cleaved upon import. This report demonstrates that the N‐terminal region of the peroxisomal 3‐oxoacyl‐CoA thiolase from Saccharomyces cerevisiae is essential for its peroxisomal targeting, and that the N‐terminal 16 amino acids of yeast thiolase are sufficient to target the otherwise cytosolic small subunit of ribulose‐1,5‐bisphosphate carboxylase to peroxisomes for import.
XIV. Yeast sequencing reports. Nucleotide sequence analysis of an 8887 bp region of the left arm of yeast chromosome XIV, encompassing the centromere sequence
Authors: Verhasselt Peter , Aert Rita , Voet Marleen , Volckaert Guido 
Published: May 2005

AbstractThe nucleotide sequencing of 8887 bp of the left arm of chromsome XIV is described. The sequence includes the centromeric region. Both strands were sequenced with an average redundancy of 5·09 per base pair. The overall G+C content is 37·3% (39·2% for putative coding regions versus 32·5% for non‐coding regions). Six open reading frames (ORFs) greater than 100 amino acids were detected, all of which are completely confined to the 8·9 kbp region. Codon frequencies of the six ORFs agree with codon usage in Saccharomyces cerevisiae and all show the characteristics of low‐level expressed genes. Comparison of the translated sequences with protein sequences in data bases suggests the presence of two ORFs (N2014 and N2007) encoding ribosomal proteins, the latter of which is the previously sequenced MRP7 gene. Another ORF (N2012) could encode a membrane‐associated protein since it contains secretory signal sequence and two presumed transmembrane helices. This protein might be involved in mitochondrial energy transfer. ORF N2016 is immediately adjacent to the centromere, suggesting that it corresponds to the SPO1 gene, which is very tightly linked to the centromere at the left arm side of chromosome XIV (Mortimer et al., 1989). The sequence has been deposited in the EMBL, GenBank and DDBJ Nucleotide Sequence Databases under the Accession Number X77114.