bluuebunny/crossref_metadata_2025_split huggingface dataset:
Stuctural and putative regulatory sequences of Kluyveromyces ribosomal protein genes
Authors: Bergkamp‐Steffens G. Karin , Hoekstra Ruurdtje , Planta Rudi J. 
Published: May 2005

AbstractThe transcription of the majority of the ribosomal protein (rp) genes of Saccharmoyces cerevisiae is activated by cis‐acting elements, designated RPG boxes, which specifically bind the multifunctional protein RAPI in vitro.To investigate to what extent this global system of tanscription regulation has been conserved, we have isolated a number of rp genes of the related yeast species Kluyveromyces lactis and Kluyveromyces marxianus, whose counterparts in Saccharomyces are controlled by RAPI. The coding regions of these genes showed a sequence similarity of about 90% when compared to their Saccharomyces counterparts. In contrast, little or no sequence similarity was found between the upstream regions and the intervening sequences of Kluyveromyces and Saccharomyces homologs. However, the occurrence and the position of the introns is conserved. The sequence data also show that the physical linkage that exists in S. cerevisiae between the rp genes encoding RP59 (CRY1), S24 and L46 is conserved in Kluyveromyces. Northern analysis demonstrated that each of the isolated Kluyveromyces genes is transcriptionally active.By sequence comparison we idetified a number of conseerved sequences in the upstream region of each of the Kluyveromyces rp genes, which we designated the X, Z and RPGK boxes. The last one is highly similar, though not identical, to the S. cerevisiae RPG box.Functional analysis of the intergenic region between the genes encoding Kluyveromyces ribosomal proteins S24 and L46 showed that the RPGK box (+Z box) functions as a transcriptional activator, while the X box acts as a trascriptional repressor. Band‐shift assays confirmed the existence of a RAP1‐like protein in Kluyveromyces that binds to the RPGK box but not to the S. cerevisiae RPG box. In contrast, S. cerevisiae RAP1 did recognize the RPGK box.
Parameters affecting the frequencies of transformation and co‐transfromation with synthetic oligonucleotides in yeast
Authors: Yamamoto Tetsuro , Moerschell Richard P. , Wakem Paul , Ferguson David , Sherman Fred 
Published: May 2005

AbstractFactors influencing the direct transformation of the yeast Saccharomyces cerevisiae with synthetic oligonucleotides were investigated by selecting for cyc1 transformants that contained at least partially fuctional iso‐1‐cytochrome c. Aproximately 3 × 104 transformanrs, constituting 0·1% of the cells, were obtained by using 1 mg of oligonucleotide in the reaction mixture. Carrier, such as heterogenous oligonucleotides, enhanced transformation frequencies. Transformation frequencies were dramatically reduced if the oligonucleotides had a large number of mismatches or had terminally located mismatches. Transformation with oligonucleotides, but not with linearized double‐strand plasmid, was efficient in a rad52− strain, ssuggesting that the pathway for transformation with oligonucleotides is different from that with linearized double‐strand plasmid. We describe a procedure of co‐transformation with two oligonucleotides, one correcting the cyc1 defect of the target allele in the host strain, and the other producing a desired amono acid alteration elsewhere in the iso‐1‐cytochrome c molecule; approximately 20% of the transformants obtained by co‐transformation contained these desired second alterations.
Structure and expression of the ABF1‐regulated ribosomal protein S33 gene in Kluyveromyces
Authors: Hoekstra Ruurdtje , Ferreira Pedro Moradas , Bootsman Theo C. , Mager Willem H. , Plnata Rudi J. 
Published: May 2005

AbstractThe abundant multifuctional protein ABF1 of Saccharomyces cerevisiae binds to the upstream region of several genes, including some ribosomal protein genes like the one encoding protein S33. Deletion of th ABF1‐binding sequence lowers the transcription of these genes three‐ to more than ten‐fold.We have isolated the S33 genes of two related yeast species. Kluyveromyces lactis and Kluveromyces marxianus. Comparison of the nucleotide sequences of these S33 genes with their counterpart form S. Cerevisiae shows a strong sequence similarity covering the whole of the coding regions. In contrast, little or no sequence similarly is found in the 5′‐flanking regions of the three genes. Also the trailer regions differ considerably in both length and sequence from one species to another.An ABF1‐binding site is present in the upstream region of the S33 gene of K. marxianus. Retardation analyses showed that this sequences is able to bind a protein present in Kluyveromyces cells with a molecular mass somewhat lower than that of S. cerevisiae ABF1. Functional analyses, using a β‐glucuronidase reporter system, showed that the ABF1‐binding site is indeed involved in transcription activation of the K. marxianus S33 gene in Kluyveromyces DNA and Northern blots did not show a signal.These results indicate that S. cerevisiae and Kluyveromyces contain functionally related but structurally dissimilar ABF1‐type proteins.
Mapping the putative RNA helicase genes by sequence overlaping
Authors: Chang Tien‐Hsien , Baum Bobby 
Published: May 2005

AbstractAn ‘electroinic’ gene mapping procedure based on computer‐aided search for overlapping gene sequences was used to identify adjacent genes and localize several putative RNA helicase genes to different chromosomes. PRP28 and AMD1 genes map to the right arm of chromosome IV netxt to sup2, which encodes a tyrsine tRNA PRP16, previouslymapped to chromosome XI, is tightly linked to MRP − L20. PRP22 is adjacent to PRE1, whose chromosomal location is currently unknown. The utility of this aproach in yeast gene mapping is evaluated.
XI. Yeast sequencing reports. The sequence of a 12kb fragment on the left arm of yeast chromosome XI reveals five new open reading frames, including a zinc finger protein and a homolog of the UDP‐glucose pyrophosphorylase from potato
Authors: Purnelle Bénédicte , Skala Jacek , Van Dyack Luc , Goffeau André 
Published: May 2005

AbstractWe report the sequence of a 12 299 bp DNA fragment from the left arm of Saccharomyces cerevisiae chromosome XI. This fragment is located between the genetic loci mif2 and mak11. We have detected five new open reading frames (ORFs) longer than 300 bp provisionally called YKL248 to YKL252. One of them, YKL248 encodes a homolog of the UDP‐glucose pyrophosphorylase from potato. The product of YKL251 contains the consensus for zinc binding proteins, similar to those of a number of fungal transcriptional activators. The three other ORFs do not show significant homology to known protein.
The allantoin and uracil permease gene sequences of Saccharomyces cerevisiae are nearly identical
Authors: Yoo Hyang Sook , Cunningham Thomas S. , Cooper Terrance G. 
Published: May 2005

AbstractWe have determined the structure of the allantoin permease (DAL4) gene of Saccharomyces cerevisiae. The gene patatively encodes a hydrophobic protein with a Mr of 71 755. It possesses the alternating hydrophobic–hydrophilic regions similar to those found in many other integral membrane proteins. The most striking feature of the allantoin permease component encoded by DAL4 is its striking similarity to the uracil permease component encoded by FUR4 Although data available indicate that these proteins do not share any overlap of function, their predicted protein sequences are 68% identical, 81% similar, and their DNA sequences are 70% identical. The upstream regulatory region of DAL4 contains all lof the characterized cis‐acting elements previously reported for inducible allantoin pathway genes: six sequences homologous to UAS NTR, the element responsible for nitrogen catabolite repression‐sensitive activation of allantoin pathway gene expression, and two sequences homologous to the cis‐acting element responsible for inducere‐responsiveness of the allantoin pathway genes, UIS. The finding of these homologous sequences predicted to exist on the basis of DAL4's expression characteristics, supports and strengthens the suggestion that these elements mediate the functions we have we have previously ascribed to them.
DNA transformations of Candida tropicalis with replicating and integrative vectors
Authors: Sanglard Dominiqaue , Fiechter Armin 
Published: May 2005

AbstractThe alkane‐assimilating yeast Candida tropicalis was used as a host for DNA transformations. A stable ade2 mutant (Ha900) obtained by UV‐mutagenesis was used as a recipient for different vectors carrying selectable markers. A first vector, pMK 16, that was developed for the transformation of C. albicans and caries an ADE2 gene marker and a Canadida autonomously replicating sequence (CARS) element promoting autonomous replication, was compatible for transforming Ha900. Two transformant types were observed: (i) pink transformants which easily lose pMK 16 under non‐selective growth conditions; (ii) white transformants, in which the same plasmid exhibited a higher mitotic stability. In both cases pMK 16 could be rescued from these cells in Escherichia coli. A second vector, pADE2, containing the isolated C. tropicalis ADE2, gene was used to transform Ha900. This vector integrated in the yeast genome at homologous sites of the ade2 locus. Different integration types were observed at one or both ade2 alleles in single or in tandem repeats.
V. Yeast mapping reports. Genetic and physical mapping of the WBP1 locus close to CENV
Authors: Heesen Stephan Te , Aebi Markus 
Published: May 2005

AbstractThe WBP1 locus, encoding an essential component of the N‐oligosaccharyl transferase, was mapped both genetically and physically. The gene is located on chromosome V between CENV and gcn4. The distance from CENV sequences is 2 kb.
Physical localization of the flocculation gene FLO1 on chromosome I of Saccharomyces cerevisiae
Authors: Teunissen Aloys W. R. H. , Van Den Berg Johan A. , Steensma H. Yde 
Published: May 2005

AbstractThe genetics of flocculation in the yeast Saccharomyces cerevisiae are poorly understood despite the importance of this property for strains used in industry. To be able to study the regulation of flocculation in yeast, one of the genes involved, FLO1, has been partially cloned. The identity of the gene was confirmed by the non‐flocculent phenotype of cells in which the C‐terminal part of the gene had been replaced by the URA3 gene. Southern blots and genetic crosses showed that the URA3 gene had integrated at the expected position on chromosome I. A region of approximately 2 kb in the middle of the FLO1 gene was consistently deleted during propagation in Escherichia coli and could not be isolated. Plasmids containing the incomplete gene, however, were still able to cause weak flocculation in a nonflocculent strain. The 3′ end of the FLO1 gene was localized at approximately 24 kb from the right end of chromosome I, 20 kb centromere‐proximal to PHO11. Most of the newly isolated chromosome I sequences also hybridized to chromosome VIII DNA, thus extending the homology between the right end of chromosome I and chromosome VIII to approximately 28 kb.
A yeast antiviral protein, SKI8, shares a repeated amino acid sequence pattern with β‐subunits of G proteins and several other proteins
Authors: Matsumoto Yutaka , Sarkar Gobinda , Sommer Steve S. , Wickner Reed B. 
Published: May 2005

AbstractSKI8 is a yeast antiviral gene, essential for controlling the propagation of M double‐stranded RNA (dsRNA) and thus for preventing virus‐induced cytopathology. Our DNA sequence of SKI8 shows that it encodes a 397 amino acid protein containing two copies of a 31 amino acid repeat pattern first identified in mammalian β‐transducin and Cdc4p of yeast. There are also four copies of this repeat in yeast Mak11p, necessary for M dsRNA propagation, and three copies in the putative product of the Dictyostelium AAC3 gene. Analysis of 36 cases of the repeat unit shows they have a consensus predicted structure: N–helix–sheet–turn–sheet–turn–sheet–helix–C.
Yeast flocculation: Flocculation onset and receptor availability
Authors: Stratford Malcolm 
Published: May 2005

AbstractFlocculent strains of brewing yeast grow and ferment as single cells and flocculate in the stationary phase of growth. The switch from single‐celled yeast growth to multi‐celled aggregation, flocculation onset, is of critical importance to the brewing industry. Yeast flocculation involves adhesion of surface‐lectins on flocculent cells to carbohydrate receptors on neighbouring cell‐walls. The presence of carbohydrate receptors, outer‐chain mannan side‐branches, was monitored throughout growth of flocculent and non‐flocculent strains of Saccharomyces cerevisiae, with particular attention to the growth phases where flocculation is normally developed. Receptors were probed by coflocculation with flocculent strains and by aggregation with concanavalin A, a lectin shown to use the same receptors as flocculation.While considerable variation was found in coflocculation and concanavalin A aggregation between strains, little or no change in receptor availability was found throughout the growth of all yeast strains. Yeast cells could easily be coflocculated at any growth stage. It was concluded that receptor availability is not involved in the process of flocculation onset.
The VPH2 gene encodes a 25 kDa protein required for activity of the yeast vacuolar H+‐ATPase
Authors: Bachhawat Anand K. , Manolson Morris F. , Murdock Deborah G. , Garman J. David , Jones Elizabeth W. 
Published: May 2005

AbstractStrains bearing the vph2 mutation are defective in vacuolar acidification. The VPH2 gene was isolated from a genomic DNA library by complementation of the zinc‐sensitive phenotype of the mutant. Deletion analysis localized the complementing activity to a 1·2 kb DNA fragment. Sequence analysis of this fragment revealed the presence of a single open reading frame that encoded a protein of 215 amino acids. Computer analysis indicated that the protein, which has a predicted molecular mass of 25 286 Daltons, has two distinct membrane‐spanning domains. Biochemical studies indicated that strains bearing the vph2 mutation have greatly reduced levels of vacuolar proton pumping and ATPase activity and that the nucleotide binding subunits of the multimeric vacuolar H+‐ATPase failed to be correctly targeted to the vacuolar membrane. The vph2 mutant fails to grow on YEP glycerol medium and on media containing 100 mM‐CaCl2 or 4 mM‐ZnCl2 or buffered to pH 7·5, a phenotype observed in strains carrying deletions in the genes encoding several vacuolar H+‐ATPase subunits. The VPH2 gene is identical to the VMA12 gene (T. Stevens and Y. Anraku, personal communication).
Peroxisomal amine oxidase of Hansenula polymorpha does not require its SRL‐containing C‐terminal sequence for targeting
Authors: Faber Klaas Nico , Haima Peter , De Hoop Meltsje Janke , Harder Wim , Veenhuis Marten , Ab Geert 
Published: May 2005

AbstractAmine oxidase (AMO) is a peroxisomal matrix protein of Hansenula polymorpha, which is induced during growth of the yeast in media containing primary amines as a sole nitrogen source. The deduced amino acid sequence of the protein contains an SRL sequence at nine amino acids from the C‐terminus. In this study, we have examined the possible role of the SRL motif in sorting of AMO to peroxisomes by mutating the corresponding gene sequence. For this purpose, we have developed a DNA construct that is specifically integrated into the AMO locus of the H. polymorpha genome, placing the mutant gene under the control of the endogenous AMO promoter and eliminating expression of the wild‐type gene. Analysis of a stable transformant, containing the desired gene configuration, showed that mutation of the C‐terminal sequence neither interfered with correct targeting of the protein into the peroxisome nor displayed significant effects on its activity. From this, it was concluded that the SRL‐containing C‐terminus is not essential for peroxisomal targeting of AMO in H. polymorpha.
Yeast flocculation: Lectin synthesis and activation
Authors: Stratford Malcolm , Carter Andrew T. 
Published: May 2005

AbstractYeast flocculation involves binding of surface lectins to carbohydrate receptors on neighbouring cell walls. Brewing strains of Saccharomyces cerevisiae normally become flocculent in the stationary phase of growth. This paper presents evidence that lectins are synthesized in exponential phase, inserted into the cell wall, and activated later at the time of flocculation onset.Cycloheximide failed to prevent flocculation unless it was added in early growth; with later additions progressively larger degrees of flocculation occurred. Flocculation onset was delayed by cycloheximide but was otherwise cycloheximide insensitive. Preflocculent cells could be artificially activated to full flocculation by heat. Artificial activation of samples from growing yeast cultures confirmed the progressive synthesis of lectins throughout exponential growth. Pronase E treatment of whole cells prior to heating prevented any activation of flocculation.It was concluded that lectins were synthesized continuously from an early stage of growth and rapidly inserted into the cell wall (accessible by pronase E), where they remained inactive for up to 14 h, before being activated at flocculation onset by an as‐yet unknown mechanism. It was found that lectin synthesis and activation occurred in all brewing strains tested.
Carbon source induces growth of stationary phase yeast cells, independent of carbon source metabolism
Authors: Granot David , Snyder Michael 
Published: May 2005

AbstractNutrients regulate the proliferation of many eukaryotic cells: in the absence of sufficient nutrients vegetatively growing cells will enter stationary (G0 like) phase; in the presence of sufficient nutrients non‐proliferative cells will begin growth. Previously we have shown that glucose is the critical nutrient which stimulates a variety of growth‐related events in the yeast Saccharomyces cerevisiae (Granot and Snyder, 1991). This paper describes six new aspects of the induction of cell growth events by nutrients in S. cerevisiae. First, all carbon sources tested, both fermentable and non‐fermentable, induce growth‐related events in stationary phase cells, suggesting that the carbon source is the critical nutrient which stimulates growth. Second, the continuous presence of glucose is not necessary for the induction of growth events, but rather a short ‘pulse’ of glucose followed by an incubation period in water will induce growth events. Third, growth stimulation by glucose occurs in the absence of the SNF3 high affinity glucose transporter. Fourth, growth stimulation occurs independent of carbon source phosphorylation and carbon source metabolism. Fifth, growth induction by carbon source does not require protein synthesis or extracellular calcium. Sixth, following stimulation by carbon source, the cells remain induced for more than 2 h after removal of the carbon source. We suggest a general model in which different carbon sources act as signals to induce the earliest growth events during or following its entry into the cell and that these growth events do not depend upon metabolism of the carbon source.
The NUM1 yeast gene: Length polymorphism and physiological aspects of mutant phenotype
Authors: Revardel Emmanuelle , Aigle Michel 
Published: May 2005

AbstractWe have isolated a mutant (rvs272) of the yeast (Saccharomyces cerevisiae) that displays an altered phenotype in stationary phase. It shows a high proportion of large‐budded cells with two non‐segregated nuclei staying in the mother cell. This phenotype is also expressed in various conditions when cells are synchronized, energy depleted or treated with the antimitotic drug benomyl. The RVS272 gene has been identified as the NUM1 gene already described. This gene presents a 192 bp tandemly repeated motif and we show that the number of repeats can vary from 1 to about 24 among different strains, without apparently affecting the function of the encoded protein. We suggest that this protein could be involved in polymerization catalysis and/or stabilization of microtubules.
The yal017 gene on the left arm of chromosome I of Saccharomyces cerevisiae encodes a putative serine/threonine protein kinase
Authors: Clark Michael W. , Zhong Wu Wei , Ouellette B. F. Francis , Bussey Howard , Keng Teresa , Storms Reginald K. , Barton Arnold , Kaback David B. 
Published: May 2005

AbstractThe DNA sequence of a region between the LTE1 and CYS3 genes on the left arm of chromosome I from Saccharomyces cerevisiae contains an open reading frame (ORF), YAL017, corresponding to the 5·0 kb FUN31 (Function Unknown Now) transcribed region. The predicted protein from this ORF contains 1358 amino acid residues with a molecular weight of 152 531, and an identifiable serine/threonine protein kinase catalytic domain. When compared with other yeast protein kinases, the Ya1017p kinase most resembles the SNF1 serine/threonine protein kinase which is involved in regulating sucrose fermentation genes. The Ya1017p kinase shows highest amino acid identities with two mammalian carcinoma‐related serine/threonine protein kinases; PIM‐1, which shows induced expression in T‐cell lymphomas; and p78A1, whose expression is lost in human pancreatic carcinomas. Gene disruption of YAL017 indicates that it is non‐essential for growth on glucose.
Identification of a gene encoding a novel zinc finger protein in Saccharomyces cerevisiae
Authors: Breitwieser Wolfgang , Schuster Tillman , Price Clive 
Published: May 2005

AbstractIn the course of a comprehensive genomic screen for cell cycle regulated genes in the yeast Saccharomyces cerevisiae (Price et al., 1991) we identified and characterized a transcriptional unit encoding a putative zinc finger protein named FZF1 (EMBL accession number: X67787). This gene encodes a protein containing five zinc fingers of the Cys2His2 class, three of which are positioned in tandem at the N‐terminus. The fourth and fifth finger follow after an interruption of 61 and 66 amino acids, respectively. While FZF1 is constitutively expressed at a very low level, its deletion is not essential for growth. Its similarity with known transcription factors, however, suggests that the FZF1 gene product may serve as a transcription factor in yeast.
Alteration of cell population structure due to cell lysis in Saccharomyces cerevisiae cells overexpressing the GAL4 gene
Authors: Martegani Enzo , Brambilla Luca , Porro Danilo , Ranzi Bianca Maria , Alberghina Lilia 
Published: May 2005

AbstractTransformed Saccharomyces cerevisiae cells overexpressing the Escherichia coli LacZ gene and the transcriptional activator GAL4, release in the external medium a fraction (from 2 to 10%) of the total β‐galactosidase activity (Porro et al., 1992b). It is known that this abnormal release of a cytoplasmic protein is related to a partial cell lysis of the yeast population, which is likely to be caused by the overexpression of the transcriptional activator GAL4.In the present paper we have characterized the GAL4‐induced cell lysis phenomenon. The expression of the GAL4 gene causes morphological modifications and alteration of the cell size distribution. The cell lysis is independent of the expression of the heterologous LacZ gene and occurs in a specific subpopulation of cells (the parent cells) independently of the genealogical age, growth phase conditions and cell cycle progression. Lysis is preceded by a loss of the plasma membrane integrity as indicated by the uptake of ethidium bromide in unfixed cells.Computer analysis of simulated protein distributions indicates that cell lysis takes place in a sizeable aliquot (about 50%) of the parent cells, therefore profoundly altering the age structure of the population.