Comparative genotyping of the Saccharomyces cerevisiae laboratory strains S288C and CEN.PK113-7D using oligonucleotide microarrays.

Abstract:

:To analyse the reliability and accuracy of genotype analysis with high-density oligonucleotide microarrays, this method and other experimental approaches were used to analyse genomic DNA of two popular Saccharomyces cerevisiae laboratory strains. S288C was used for systematic sequencing of 'the' S. cerevisiae genome; CEN.PK113-7D is a popular strain for physiological studies and functional genomics. Random amplified polymorphic DNA, electrophoretic karyotyping and microarray analysis all indicated a high level of sequence similarity between the two strains. In the microarray analysis, as few as 288 (4.5%) of the ca. 6300 represented yeast genes were identified that yielded significantly different hybridisation intensities between the two strains. These could be classified as amplified, absent, or with sequence polymorphism in CEN.PK113-7D compared to S288C. A detailed analysis focused on the subset of 25 genes called absent in CEN.PK113-7D. Among these absent genes, 17 were clustered together on five chromosomes, mainly in subtelomeric regions. Thorough analysis of these regions by polymerase chain reaction (PCR) and restriction fragment length polymorphism confirmed the absence of these genes in CEN.PK113-7D. Surprisingly, three of these regions were not smaller in CEN.PK113-7D chromosomes, indicating that they may harbour unidentified and potentially new sequences. In addition, eight genes called absent by the microarrays were scattered over the chromosomes. Using diagnostic PCR most of these genes were actually found to be present in CEN.PK113-7D, but after sequencing were found to differ significantly at the DNA level from S288C, explaining the poor hybridisation to the arrays. Our results indicate that DNA microarrays are a powerful tool for determining genotypic similarity between different yeast strains. However, to obtain meaningful information at the individual gene level, this method should be backed up by additional techniques.

journal_name

FEMS Yeast Res

journal_title

FEMS yeast research

authors

Daran-Lapujade P,Daran JM,Kötter P,Petit T,Piper MD,Pronk JT

doi

10.1016/S1567-1356(03)00156-9

keywords:

subject

Has Abstract

pub_date

2003-12-01 00:00:00

pages

259-69

issue

3

eissn

1567-1356

issn

1567-1364

pii

S1567135603001569

journal_volume

4

pub_type

杂志文章
  • The helicase CaHmi1p is required for wild-type mitochondrial DNA organization in Candida albicans.

    abstract::The mechanistic details of mtDNA maintenance in petite-negative yeasts have remained largely unexplored. We report here that the DNA helicase Hmi1p plays a crucial role in mtDNA stability in Candida albicans. Like its counterpart in Saccharomyces cerevisiae, Hmi1p in C. albicans (CaHmi1p) contains a C-terminal mitocho...

    journal_title:FEMS yeast research

    pub_type: 杂志文章

    doi:10.1111/j.1567-1364.2006.00132.x

    authors: Jõers P,Gerhold JM,Sedman T,Kuusk S,Sedman J

    更新日期:2007-01-01 00:00:00

  • Mating-type locus control of killer toxins from Kluyveromyces lactis and Pichia acaciae.

    abstract::Killer-toxin complexes produced by Kluyveromyces lactis and Pichia acaciae inhibit cell proliferation of Saccharomyces cerevisiae. Analysis of their actions in haploid MATalpha cells revealed that introduction of the opposite mating-type locus (MATa) significantly suppressed antizymosis. Together with resistance expre...

    journal_title:FEMS yeast research

    pub_type: 杂志文章

    doi:10.1111/j.1567-1364.2005.00006.x

    authors: Klassen R,Jablonowski D,Stark MJ,Schaffrath R,Meinhardt F

    更新日期:2006-05-01 00:00:00

  • Peer pressure: evolutionary responses to biotic pressures in wine yeasts.

    abstract::In the macroscopic world, ecological interactions between multiple species of fauna and flora are recognised as major role-players in the evolution of any particular species. By comparison, research on ecological interactions as a driver of evolutionary adaptation in microbial ecosystems has been neglected. The evolut...

    journal_title:FEMS yeast research

    pub_type: 杂志文章,评审

    doi:10.1093/femsyr/foz072

    authors: Conacher CG,Rossouw D,Bauer FFB

    更新日期:2019-11-01 00:00:00

  • Elucidating cellular mechanisms of Saccharomyces cerevisiae tolerant to combined lignocellulosic-derived inhibitors using high-throughput phenotyping and multiomics analyses.

    abstract::A robust cell factory that can tolerate combined inhibitory lignocellulosic compounds is essential for the cost-effective lignocellulose-based production of second-generation bioethanol and other bulk chemicals. Following high-throughput phenotyping of a yeast genomic overexpression library, we identified a Saccharomy...

    journal_title:FEMS yeast research

    pub_type: 杂志文章

    doi:10.1093/femsyr/foy106

    authors: Unrean P,Gätgens J,Klein B,Noack S,Champreda V

    更新日期:2018-12-01 00:00:00

  • Pkc1 and actin polymerisation activities play a role in ribosomal gene repression associated with secretion impairment caused by oxidative stress.

    abstract::In Saccharomyces cerevisiae, the cell integrity pathway plays a role in the oxidative stress response. In this study, we show that the Pkc1 protein mediates oxidative signalling by helping to downregulate ribosomal gene expression when cells are exposed to hydrogen peroxide. An active actin cytoskeleton is required fo...

    journal_title:FEMS yeast research

    pub_type: 杂志文章

    doi:10.1111/j.1567-1364.2011.00754.x

    authors: Mitjana FV,Petkova MI,Pujol-Carrion N,de la Torre-Ruiz MA

    更新日期:2011-12-01 00:00:00

  • Multilocus sequence typing confirms synonymy but highlights differences between Candida albicans and Candida stellatoidea.

    abstract::We used multi-locus sequence typing (MLST) to investigate 35 yeast isolates representing the two genome-sequenced strains plus the type strain of Candida albicans, four isolates originally identified as Candida stellatoidea type I and 28 representing type strains of other species now regarded as synonymous with C. alb...

    journal_title:FEMS yeast research

    pub_type: 杂志文章

    doi:10.1111/j.1567-1364.2008.00392.x

    authors: Jacobsen MD,Boekhout T,Odds FC

    更新日期:2008-08-01 00:00:00

  • Relocalization of DNA lesions to the nuclear pore complex.

    abstract::Early screens in yeast for mutations exhibiting sensitivity to DNA damage identified nuclear pore components, but their role in DNA repair was not well understood. Over the last decade, studies have revealed that several types of persistent DNA lesions relocate to either the nuclear pore complex (NPC) or nuclear envel...

    journal_title:FEMS yeast research

    pub_type: 杂志文章,评审

    doi:10.1093/femsyr/fow095

    authors: Freudenreich CH,Su XA

    更新日期:2016-12-01 00:00:00

  • Adaptive response to the antimalarial drug artesunate in yeast involves Pdr1p/Pdr3p-mediated transcriptional activation of the resistance determinants TPO1 and PDR5.

    abstract::The expression of the transcription regulator Pdr1p and its target genes PDR5 and TPO1 is required for Saccharomyces cerevisiae adaptation and resistance to artesunate, a promising antimalarial drug, also active against tumour cells and viruses. PDR5 and TPO1 encode plasma membrane multidrug transporters of the ATP-bi...

    journal_title:FEMS yeast research

    pub_type: 杂志文章

    doi:10.1111/j.1567-1364.2006.00095.x

    authors: Alenquer M,Tenreiro S,Sá-Correia I

    更新日期:2006-12-01 00:00:00

  • Rapid detection of yeast rRNA genes with primed in situ (PRINS) labeling.

    abstract::In yeast, rRNA genes can be detected with the FISH technique using rRNA gene probes. This technique yields reliable, reproducible and precise results, but is time-consuming. Here, the primed in situ DNA synthesis (PRINS) procedure has been optimized for rapid detection of yeast rRNA genes. PRINS, which is as sensitive...

    journal_title:FEMS yeast research

    pub_type: 杂志文章

    doi:10.1111/j.1567-1364.2009.00499.x

    authors: Wnuk M,Lewinska A,Bugno M,Bartosz G,Slota E

    更新日期:2009-06-01 00:00:00

  • The putative transcription factor CaMaf1 controls the sensitivity to lithium and rapamycin and represses RNA polymerase III transcription in Candida albicans.

    abstract::Maf1 is a repressor of RNA polymerase (Pol) III transcription for tRNA. Nutrient deprivation and environmental stress repress Pol III transcription through Maf1 in Saccharomyces cerevisiae. The sole Candida albicans homolog CaMaf1 is a protein of 380 amino acids with conserved domains and motifs of the eukaryotic Maf1...

    journal_title:FEMS yeast research

    pub_type: 杂志文章

    doi:10.1093/femsyr/foy068

    authors: Asghar F,Yan H,Jiang L

    更新日期:2018-09-01 00:00:00

  • Activation of a peroxisomal Pichia pastoris D-amino acid oxidase, which uses d-alanine as a preferred substrate, depends on pyruvate carboxylase.

    abstract::d-Amino acid oxidase (DAO) is an important flavo-enzyme that catalyzes the oxidative deamination of d-amino acids into the corresponding alpha-keto acid, ammonia and H(2)O(2). We identified two amino acid oxidases in the methylotrophic yeast Pichia pastoris: Dao1p, which preferentially uses d-alanine as a substrate, a...

    journal_title:FEMS yeast research

    pub_type: 杂志文章

    doi:10.1111/j.1567-1364.2010.00647.x

    authors: Klompmaker SH,Kilic A,Baerends RJ,Veenhuis M,van der Klei IJ

    更新日期:2010-09-01 00:00:00

  • Discrete roles of trehalose and Hsp104 in inhibition of protein aggregation in yeast cells.

    abstract::Heat shock response (HSR) is an important element of cellular homeostasis. In yeast, HSR comprises of the heat shock proteins (Hsps) and the osmolytes trehalose and glycerol. The respective roles of trehalose and Hsp104 in regulating protein aggregation remain ambiguous. We report that trehalose and Hsp104 are importa...

    journal_title:FEMS yeast research

    pub_type: 杂志文章

    doi:10.1093/femsyr/foy058

    authors: Sethi R,Iyer SS,Das E,Roy I

    更新日期:2018-09-01 00:00:00

  • Impact of glutathione metabolism on zinc homeostasis in Saccharomyces cerevisiae.

    abstract::Zinc is a crucial mineral for all organisms as it is an essential cofactor for the proper function of a plethora of proteins and depletion of zinc causes oxidative stress. Glutathione is the major redox buffering agent in the cell and therefore important for mitigation of the adverse effects of oxidative stress. In ma...

    journal_title:FEMS yeast research

    pub_type: 杂志文章

    doi:10.1093/femsyr/fox028

    authors: Steiger MG,Patzschke A,Holz C,Lang C,Causon T,Hann S,Mattanovich D,Sauer M

    更新日期:2017-06-01 00:00:00

  • Dynamic 13C-labeling experiments prove important differences in protein turnover rate between two Saccharomyces cerevisiae strains.

    abstract::We developed a method for the quantification of protein turnover rates using (13)C-labeled substrates combined with the analysis of the labeling patterns of proteinogenic amino acids. Using this method, the specific amino acid turnover rates between proteins and the pool of free amino acids were determined for eight d...

    journal_title:FEMS yeast research

    pub_type: 杂志文章

    doi:10.1111/j.1567-1364.2012.00823.x

    authors: Hong KK,Hou J,Shoaie S,Nielsen J,Bordel S

    更新日期:2012-11-01 00:00:00

  • Phenotypic evaluation and characterization of 21 industrial Saccharomyces cerevisiae yeast strains.

    abstract::Microorganisms have been studied and used extensively to produce value-added fuels and chemicals. Yeasts, specifically Saccharomyces cerevisiae, receive industrial attention because of their well-known ability to ferment glucose and produce ethanol. Thousands of natural or genetically modified S. cerevisiae have been ...

    journal_title:FEMS yeast research

    pub_type: 杂志文章

    doi:10.1093/femsyr/foy001

    authors: Kong II,Turner TL,Kim H,Kim SR,Jin YS

    更新日期:2018-02-01 00:00:00

  • Development of a genetic transformation toolkit for Brettanomyces bruxellensis.

    abstract::Brettanomyces bruxellensis is usually considered a spoilage microorganism, responsible for significant economic losses during the production of fermented beverages such as wine, beer and cider, though for some styles of beer its influence is essential. In recent years, the competitiveness of this yeast in bioethanol p...

    journal_title:FEMS yeast research

    pub_type: 杂志文章

    doi:10.1093/femsyr/foy070

    authors: Varela C,Lleixà J,Curtin C,Borneman A

    更新日期:2018-11-01 00:00:00

  • Characterisation of glucose transport in Saccharomyces cerevisiae with plasma membrane vesicles (countertransport) and intact cells (initial uptake) with single Hxt1, Hxt2, Hxt3, Hxt4, Hxt6, Hxt7 or Gal2 transporters.

    abstract::The yeast glucose transporters Hxt1, Hxt2, Hxt3, Hxt4, Hxt6, Hxt7 and Gal2, individually expressed in an hxt1-7 null mutant strain, demonstrate the phenomenon of countertransport. Thus, these transporters, which are the most important glucose transporters in Saccharomyces cerevisiae, are facilitated diffusion transpor...

    journal_title:FEMS yeast research

    pub_type: 杂志文章

    doi:10.1111/j.1567-1364.2002.tb00121.x

    authors: Maier A,Völker B,Boles E,Fuhrmann GF

    更新日期:2002-12-01 00:00:00

  • Characterization of a biofilm-like extracellular matrix in FLO1-expressing Saccharomyces cerevisiae cells.

    abstract::Like bacteria, fungi growing in biofilms are often embedded in a so-called extracellular matrix (ECM), a complex and species-specific mixture of compounds secreted by cells in the biofilm. The precise physiological role of this ECM and its importance for the stress and drug resistance that is so characteristic of biof...

    journal_title:FEMS yeast research

    pub_type: 杂志文章

    doi:10.1111/j.1567-1364.2009.00482.x

    authors: Beauvais A,Loussert C,Prevost MC,Verstrepen K,Latgé JP

    更新日期:2009-05-01 00:00:00

  • Identification and characterization of Csh3 as an SH3 protein that interacts with fission yeast Cap1.

    abstract::Schizosaccharomyces pombe Cap1 has been identified as the (adenylyl) cyclase-associated protein. Cap1 was able to bind Cap1 itself and actin. Cap1 localized at the growing tip, and this localization was dependent on the Cap1 P2 region. In a two-hybrid screening using cap1 as bait, we isolated csh3, which encodes a pro...

    journal_title:FEMS yeast research

    pub_type: 杂志文章

    doi:10.1093/femsyr/fov097

    authors: Yamamoto T,Kobayashi-Ooka Y,Zhou GL,Kawamukai M

    更新日期:2015-12-01 00:00:00

  • A respiratory-deficient mutation associated with high salt sensitivity in Kluyveromyces lactis.

    abstract::A salt-sensitive mutant of Kluyveromyces lactis was isolated that was unable to grow in high-salt media. This mutant was also respiratory-deficient and temperature-sensitive for growth. The mutation mapped in a single nuclear gene that is the ortholog of BCS1 of Saccharomyces cerevisiae. The BCS1 product is a mitochon...

    journal_title:FEMS yeast research

    pub_type: 杂志文章

    doi:10.1111/j.1567-1364.2006.00148.x

    authors: Goffrini P

    更新日期:2007-03-01 00:00:00

  • Molecular genetic identification of Saccharomyces sensu stricto strains from African sorghum beer.

    abstract::Genetic relationships of 24 phenotypically different strains isolated from sorghum beer in West Africa and the type cultures of the Saccharomyces sensu stricto species were investigated by universally primed polymerase chain reaction (PCR) analysis, microsatellite fingerprinting and PCR-restriction fragment length pol...

    journal_title:FEMS yeast research

    pub_type: 杂志文章

    doi:10.1016/S1567-1356(02)00191-5

    authors: Naumova ES,Korshunova IV,Jespersen L,Naumov GI

    更新日期:2003-04-01 00:00:00

  • Five new combinations in the yeast genus Zygofabospora Kudriavzev emend. G. Naumov (pro parte Kluyveromyces) based on genetic data.

    abstract::The rDNA sequencing data obtained during the last 5 years in several laboratories clearly demonstrate that within the heterogeneous genus Kluyveromyces there is a group of highly related species, which we refer to as the genus Zygofabospora Kudriavzev 1960 emend. G. Naumov 2002. This genus includes four hybridizing sp...

    journal_title:FEMS yeast research

    pub_type: 杂志文章

    doi:10.1111/j.1567-1364.2002.tb00067.x

    authors: Naumov GI,Naumova ES

    更新日期:2002-03-01 00:00:00

  • The genome sequence of the wine yeast VIN7 reveals an allotriploid hybrid genome with Saccharomyces cerevisiae and Saccharomyces kudriavzevii origins.

    abstract::The vast majority of wine fermentations are performed principally by Saccharomyces cerevisiae. However, there are a growing number of instances in which other species of Saccharomyces play a predominant role. Interestingly, the presence of these other yeast species generally occurs via the formation of interspecific h...

    journal_title:FEMS yeast research

    pub_type: 杂志文章

    doi:10.1111/j.1567-1364.2011.00773.x

    authors: Borneman AR,Desany BA,Riches D,Affourtit JP,Forgan AH,Pretorius IS,Egholm M,Chambers PJ

    更新日期:2012-02-01 00:00:00

  • Mitochondrial genome from the facultative anaerobe and petite-positive yeast Dekkera bruxellensis contains the NADH dehydrogenase subunit genes.

    abstract::The progenitor of the Dekkera/Brettanomyces clade separated from the Saccharomyces/Kluyveromyces clade over 200 million years ago. However, within both clades, several lineages developed similar physiological traits. Both Saccharomyces cerevisiae and Dekkera bruxellensis are facultative anaerobes; in the presence of e...

    journal_title:FEMS yeast research

    pub_type: 杂志文章

    doi:10.1111/j.1567-1364.2010.00644.x

    authors: Procházka E,Poláková S,Piskur J,Sulo P

    更新日期:2010-08-01 00:00:00

  • Genetic variants of Malassezia pachydermatis from canine skin: body distribution and phospholipase activity.

    abstract::Malassezia pachydermatis isolates (n=185) from skin sites from dogs (n=30) were characterized genetically and biochemically following in vitro culture. Two regions in the chitin synthase-2 gene (chs-2) and the first internal transcribed spacer (ITS-1) of nuclear ribosomal DNA were sequenced, and the phospholipase acti...

    journal_title:FEMS yeast research

    pub_type: 杂志文章

    doi:10.1111/j.1567-1364.2008.00358.x

    authors: Cafarchia C,Gasser RB,Latrofa MS,Parisi A,Campbell BE,Otranto D

    更新日期:2008-05-01 00:00:00

  • Production of glycosylated thermostable Providencia rettgeri penicillin G amidase in Pichia pastoris.

    abstract::Penicillin G amidase from Providencia rettgeri is a heterodimer of 92 kDa. We have previously expressed the Pr. rettgeri pac gene coding for this enzyme in Saccharomyces cerevisiae, and now we report the expression and characterization in the methylotrophic yeast Pichia pastoris. The recombinant catalytically active e...

    journal_title:FEMS yeast research

    pub_type: 杂志文章

    doi:10.1111/j.1567-1364.2002.tb00045.x

    authors: Sevo M,Degrassi G,Skoko N,Venturi V,Ljubijankić G

    更新日期:2002-01-01 00:00:00

  • Metabolically engineered methylotrophic yeast cells and enzymes as sensor biorecognition elements.

    abstract::An extended definition of the term metabolic engineering is given and its successful use in the construction of biorecognition elements of sensors is demonstrated. It is shown that genetic and chemical modifications of methylotrophic yeast cells provide directed changes in their physiological responses towards methano...

    journal_title:FEMS yeast research

    pub_type: 杂志文章

    doi:10.1016/S1567-1356(02)00124-1

    authors: Gonchar M,Maidan M,Korpan Y,Sibirny V,Kotylak Z,Sibirny A

    更新日期:2002-08-01 00:00:00

  • Genetic engineering of brewing yeast to reduce the content of ethanol in beer.

    abstract::The GPD1 gene encoding the glycerol-3-phosphate dehydrogenase was overexpressed in an industrial lager brewing yeast (Saccharomyces cerevisiae ssp. carlsbergensis) to reduce the content of ethanol in beer. The amount of glycerol produced by the GPD1-overexpressing yeast in fermentation experiments simulating brewing c...

    journal_title:FEMS yeast research

    pub_type: 杂志文章

    doi:10.1111/j.1567-1364.2002.tb00087.x

    authors: Nevoigt E,Pilger R,Mast-Gerlach E,Schmidt U,Freihammer S,Eschenbrenner M,Garbe L,Stahl U

    更新日期:2002-05-01 00:00:00

  • Vaccines based on whole recombinant Saccharomyces cerevisiae cells.

    abstract::The ultimate goal of therapeutic vaccines is to activate and exploit the patient's own immune system to vigorously and dynamically seek and eradicate established malignant or virally infected cells. Therapeutic vaccines also offer the potential for preventing disease recurrence. Saccharomyces cerevisiae-based vaccines...

    journal_title:FEMS yeast research

    pub_type: 杂志文章,评审

    doi:10.1111/j.1567-1364.2010.00665.x

    authors: Ardiani A,Higgins JP,Hodge JW

    更新日期:2010-12-01 00:00:00

  • CRIMEtoYHU: a new web tool to develop yeast-based functional assays for characterizing cancer-associated missense variants.

    abstract::Evaluation of the functional impact of cancer-associated missense variants is more difficult than for protein-truncating mutations and consequently standard guidelines for the interpretation of sequence variants have been recently proposed. A number of algorithms and software products were developed to predict the imp...

    journal_title:FEMS yeast research

    pub_type: 杂志文章

    doi:10.1093/femsyr/fox078

    authors: Mercatanti A,Lodovichi S,Cervelli T,Galli A

    更新日期:2017-12-01 00:00:00