scholarly journals Genome-Wide Transcriptional Analysis of Aerobic and Anaerobic Chemostat Cultures of Saccharomyces cerevisiae

1999 ◽  
Vol 181 (24) ◽  
pp. 7409-7413 ◽  
Author(s):  
J. J. M. ter Linde ◽  
H. Liang ◽  
R. W. Davis ◽  
H. Y. Steensma ◽  
J. P. van Dijken ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Dna Microarrays ◽  
Growth Parameter ◽  
Open Reading Frames ◽  
Transcriptional Analysis ◽  
Anaerobic Conditions ◽  
Chemostat Cultivation ◽  
Transcript Levels ◽  
Genome Wide ◽  
Transcriptional Adaptation

ABSTRACT The yeast Saccharomyces cerevisiae is unique among eukaryotes in exhibiting fast growth in both the presence and the complete absence of oxygen. Genome-wide transcriptional adaptation to aerobiosis and anaerobiosis was studied in assays using DNA microarrays. This technique was combined with chemostat cultivation, which allows controlled variation of a single growth parameter under defined conditions and at a fixed specific growth rate. Of the 6,171 open reading frames investigated, 5,738 (93%) yielded detectable transcript levels under either aerobic or anaerobic conditions; 140 genes showed a >3-fold-higher transcription level under anaerobic conditions. Under aerobic conditions, transcript levels of 219 genes were >3-fold higher than under anaerobic conditions.

scholarly journals Genome-Wide Screen for Oxalate-Sensitive Mutants of Saccharomyces cerevisiae

2007 ◽  
Vol 73 (18) ◽  
pp. 5919-5927 ◽  
Author(s):  
V. Cheng ◽  
H. U. Stotz ◽  
K. Hippchen ◽  
A. T. Bakalinsky
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Oxalic Acid ◽  
Indirect Evidence ◽  
Open Reading Frames ◽  
Monocarboxylate Transporter ◽  
Genome Wide ◽  
Self Tolerance ◽  
Important Virulence Factor ◽  
Endosomal Transport ◽  
Yeast Genes

ABSTRACT Oxalic acid is an important virulence factor produced by phytopathogenic filamentous fungi. In order to discover yeast genes whose orthologs in the pathogen may confer self-tolerance and whose plant orthologs may protect the host, a Saccharomyces cerevisiae deletion library consisting of 4,827 haploid mutants harboring deletions in nonessential genes was screened for growth inhibition and survival in a rich medium containing 30 mM oxalic acid at pH 3. A total of 31 mutants were identified that had significantly lower cell yields in oxalate medium than in an oxalate-free medium. About 35% of these mutants had not previously been detected in published screens for sensitivity to sorbic or citric acid. Mutants impaired in endosomal transport, the rgp1Δ, ric1Δ, snf7Δ, vps16Δ, vps20Δ, and vps51Δ mutants, were significantly overrepresented relative to their frequency among all verified yeast open reading frames. Oxalate exposure to a subset of five mutants, the drs2Δ, vps16Δ, vps51Δ, ric1Δ, and rib4Δ mutants, was lethal. With the exception of the rib4Δ mutant, all of these mutants are impaired in vesicle-mediated transport. Indirect evidence is provided suggesting that the sensitivity of the rib4Δ mutant, a riboflavin auxotroph, is due to oxalate-mediated interference with riboflavin uptake by the putative monocarboxylate transporter Mch5.

scholarly journals Genome-wide Analysis of Pre-mRNA Splicing

2004 ◽  
Vol 279 (50) ◽  
pp. 52437-52446 ◽  
Author(s):  
Aparna K. Sapra ◽  
Yoav Arava ◽  
Piyush Khandelia ◽  
Usha Vijayraghavan
Keyword(s):  
Splice Site ◽  
Dna Microarrays ◽  
Expression Profiles ◽  
Open Reading Frames ◽  
Specific Factor ◽  
Splicing Factors ◽  
Critical Function ◽  
Genome Wide

Removal of pre-mRNA introns is an essential step in eukaryotic genome interpretation. The spliceosome, a ribonucleoprotein performs this critical function; however, precise roles for many of its proteins remain unknown. Genome-wide consequences triggered by the loss of a specific factor can elucidate its function in splicing and its impact on other cellular processes. We have employed splicing-sensitive DNA microarrays, with yeast open reading frames and intron sequences, to detect changes in splicing efficiency and global expression. Comparison of expression profiles, for intron-containing transcripts, among mutants of two second-step factors, Prp17 and Prp22, reveals their unique and shared effects on global splicing. This analysis enabled the identification of substrates dependent on Prp17. We find a significant Prp17 role in splicing of introns which are longer than 200nts and note its dispensability when introns have a ≤13-nucleotide spacing between their branch point nucleotide and 3 ′ splice site.In vitrosplicing of substrates with varying branch nucleotide to 3 ′ splice site distances supports the differential Prp17 dependencies inferred from thein vivoanalysis. Furthermore, we tested the predicted dispensability of Prp17 for splicing short introns in the evolutionarily distant yeast,Schizosaccharomyces pombe, where the genome contains predominantly short introns. SpPrp17 was non-essential at all growth temperatures implying that functional evolution of splicing factors is integrated with genome evolution. Together our studies point to a role for budding yeast Prp17 in splicing of subsets of introns and have predictive value for deciphering the functions of splicing factors in gene expression and regulation in other eukaryotes.

scholarly journals 5-Fluorouracil Enhances Exosome-Dependent Accumulation of Polyadenylated rRNAs

2004 ◽  
Vol 24 (24) ◽  
pp. 10766-10776 ◽  
Author(s):  
Feng Fang ◽  
Jason Hoskins ◽  
J. Scott Butler
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Dna Synthesis ◽  
General Result ◽  
Rna Processing ◽  
Ribosome Biogenesis ◽  
Dna Microarrays ◽  
Rrna Processing ◽  
Genome Wide ◽  
Genes Encoding ◽  
Nuclear Exosome

ABSTRACT The antimetabolite 5-fluorouracil (5FU) is a widely used chemotherapeutic for the treatment of solid tumors. Although 5FU slows DNA synthesis by inhibiting the ability of thymidylate synthetase to produce dTMP, the drug also has significant effects on RNA metabolism. Recent genome-wide assays for 5FU-induced haploinsufficiency in Saccharomyces cerevisiae identified genes encoding components of the RNA processing exosome as potential targets of the drug. In this report, we used DNA microarrays to analyze the effect of 5FU on the yeast transcriptome and found that the drug causes the accumulation of polyadenylated fragments of the 27S rRNA precursor and that defects in the nuclear exoribonuclease Rrp6p enhance this effect. The size distribution of these RNAs and their sensitivity to Rrp6p suggest that they are normally degraded by the nuclear exosome and a 5′-3′ exoribonuclease. Consistent with this hypothesis, 5FU inhibits the growth of RRP6 mutants with defects in the degradation function of the enzyme and it interferes with the degradation of an rRNA precursor. The detection of poly(A)+ pre-RNAs in strains defective in various steps in ribosome biogenesis suggests that the production of poly(A)+ pre-rRNAs may be a general result of defects in rRNA processing. These findings suggest that 5FU inhibits an exosome-dependent surveillance pathway that degrades polyadenylated precursor rRNAs.

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