scholarly journals Extrachromosomal elements cause a reduced division potential in nib 1 strains of Saccharomyces cerevisiae.

Genetics ◽  
1989 ◽  
Vol 122 (4) ◽  
pp. 749-757
Author(s):  
R Sweeney ◽  
V A Zakian
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Open Reading Frames ◽  
Simultaneous Presence ◽  
Extrachromosomal Elements ◽  
Severe Reduction ◽  
Extrachromosomal Element ◽  
Generalized Sensitivity ◽  
Reading Frames

Abstract The nib 1 allele of yeast confers a sensitivity to an endogenous plasmid, 2 mu DNA, in that nib 1 strains bearing 2 mu DNA (cir+) exhibit a reduction in division potential. In the present study, the reduction in division potential characteristic of nib 1 cir+ strains is shown to be dependent on the simultaneous presence of both the A and the D open reading frames of 2 mu DNA as well as on the presence of an unidentified extrachromosomal element other than 2 mu DNA. Furthermore, in nib 1 strains, an uncharacterized extrachromosomal element can cause a less severe reduction of division potential in the absence of intact 2 mu DNA. Thus, the nib 1 allele may confer a generalized sensitivity to extrachromosomal elements.

Divergent overlapping transcripts at the PET122 locus in Saccharomyces cerevisiae

1990 ◽  
Vol 10 (6) ◽  
pp. 3027-3035
Author(s):  
J D Ohmen ◽  
K A Burke ◽  
J E McEwen
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Nucleotide Sequence ◽  
Cytochrome C Oxidase ◽  
Genomic Dna ◽  
Transcription Unit ◽  
Open Reading Frames ◽  
Base Pairs ◽  
Opposite Strand ◽  
Overlapping Transcripts ◽  
Reading Frames

PET122 is one of three nuclear genes specifically required for translation of the mitochondrial mRNA for cytochrome c oxidase subunit III in Saccharomyces cerevisiae. The nucleotide sequence of 2,862 base pairs (bp) of yeast genomic DNA encompassing the PET122 locus shows very close spacing between the PET122 gene (254 codons) and two unidentified open reading frames, termed ORF2 and ORF3. ORF2 is encoded by the same strand of DNA as PET122 and is located 53 bp downstream of PET122, while ORF3 is encoded on the opposite strand and is located 215 bp upstream of PET122. Five transcripts, with sizes of 2.9, 2.3, 2.1, 1.5, and 1.4 kilobases (kb), are produced from this locus. The 2.1- and 1.4-kb transcripts encode ORF3, the 1.5-kb transcript encodes ORF2, and the 2.9- and 2.3-kb transcripts encode PET122. A particularly interesting feature of the ORF3-PET122-ORF2 transcription unit is a 535-base overlap between the 2.3-kb PET122 transcript produced from one strand and a 2.1-kb ORF3 transcript produced from the opposite strand. Similarly, the 2.9-kb PET122 transcript overlaps the 2.1-kb ORF3 transcript by more than 900 bases and the 1.5-kb ORF3 transcript by at least 200 bases. Hence, these pairs of transcripts are antisense to one another and have the potential to regulate, in an interdependent fashion, the posttranscriptional expression of ORF3 and PET122.

scholarly journals Regulation of transcription by Saccharomyces cerevisiae 14-3-3 proteins

2004 ◽  
Vol 382 (3) ◽  
pp. 867-875 ◽  
Author(s):  
Astrid BRUCKMANN ◽  
H. Yde STEENSMA ◽  
M. Joost TEIXEIRA de MATTOS ◽  
G. Paul H. van HEUSDEN
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Stress Response ◽  
Open Reading Frames ◽  
Ergosterol Biosynthesis ◽  
Temperature Sensitive ◽  
Regulation Of Transcription ◽  
Mrna Levels ◽  
Transcription Analysis ◽  
A Genome ◽  
Reading Frames

14-3-3 proteins form a family of highly conserved eukaryotic proteins involved in a wide variety of cellular processes, including signalling, apoptosis, cell-cycle control and transcriptional regulation. More than 150 binding partners have been found for these proteins. The yeast Saccharomyces cerevisiae has two genes encoding 14-3-3 proteins, BMH1 and BMH2. A bmh1 bmh2 double mutant is unviable in most laboratory strains. Previously, we constructed a temperature-sensitive bmh2 mutant and showed that mutations in RTG3 and SIN4, both encoding transcriptional regulators, can suppress the temperature-sensitive phenotype of this mutant, suggesting an inhibitory role of the 14-3-3 proteins in Rtg3-dependent transcription [van Heusden and Steensma (2001) Yeast 18, 1479–1491]. In the present paper, we report a genome-wide transcription analysis of a temperature-sensitive bmh2 mutant. Steady-state mRNA levels of 60 open reading frames were increased more than 2.0-fold in the bmh2 mutant, whereas those of 78 open reading frames were decreased more than 2.0-fold. In agreement with our genetic experiments, six genes known to be regulated by Rtg3 showed elevated mRNA levels in the mutant. In addition, several genes with other cellular functions, including those involved in gluconeogenesis, ergosterol biosynthesis and stress response, had altered mRNA levels in the mutant. Our data show that the yeast 14-3-3 proteins negatively regulate Rtg3-dependent transcription, stimulate the transcription of genes involved in ergosterol metabolism and in stress response and are involved in transcription regulation of multiple other genes.

scholarly journals Translation of Small Open Reading Frames within Unannotated RNA Transcripts in Saccharomyces cerevisiae

Cell Reports ◽  
2014 ◽  
Vol 7 (6) ◽  
pp. 1858-1866 ◽  
Author(s):  
Jenna E. Smith ◽  
Juan R. Alvarez-Dominguez ◽  
Nicholas Kline ◽  
Nathan J. Huynh ◽  
Sarah Geisler ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Open Reading Frames ◽  
Rna Transcripts ◽  
Reading Frames ◽  
Small Open Reading Frames

scholarly journals Translation Initiation from Conserved Non-AUG Codons Provides Additional Layers of Regulation and Coding Capacity

mBio ◽  
2017 ◽  
Vol 8 (3) ◽  
Author(s):  
Ivaylo P. Ivanov ◽  
Jiajie Wei ◽  
Stephen Z. Caster ◽  
Kristina M. Smith ◽  
Audrey M. Michel ◽  
...  
Keyword(s):  
Gene Expression ◽  
Saccharomyces Cerevisiae ◽  
Amino Acid ◽  
Neurospora Crassa ◽  
Open Reading Frames ◽  
Reading Frame ◽  
Coding Sequence ◽  
Cell Extracts ◽  
Upstream Open Reading Frames ◽  
Reading Frames

ABSTRACT Neurospora crassa cpc-1 and Saccharomyces cerevisiae GCN4 are homologs specifying transcription activators that drive the transcriptional response to amino acid limitation. The cpc-1 mRNA contains two upstream open reading frames (uORFs) in its >700-nucleotide (nt) 5′ leader, and its expression is controlled at the level of translation in response to amino acid starvation. We used N. crassa cell extracts and obtained data indicating that cpc-1 uORF1 and uORF2 are functionally analogous to GCN4 uORF1 and uORF4, respectively, in controlling translation. We also found that the 5′ region upstream of the main coding sequence of the cpc-1 mRNA extends for more than 700 nucleotides without any in-frame stop codon. For 100 cpc-1 homologs from Pezizomycotina and from selected Basidiomycota, 5′ conserved extensions of the CPC1 reading frame are also observed. Multiple non-AUG near-cognate codons (NCCs) in the CPC1 reading frame upstream of uORF2, some deeply conserved, could potentially initiate translation. At least four NCCs initiated translation in vitro . In vivo data were consistent with initiation at NCCs to produce N-terminally extended N. crassa CPC1 isoforms. The pivotal role played by CPC1, combined with its translational regulation by uORFs and NCC utilization, underscores the emerging significance of noncanonical initiation events in controlling gene expression. IMPORTANCE There is a deepening and widening appreciation of the diverse roles of translation in controlling gene expression. A central fungal transcription factor, the best-studied example of which is Saccharomyces cerevisiae GCN4, is crucial for the response to amino acid limitation. Two upstream open reading frames (uORFs) in the GCN4 mRNA are critical for controlling GCN4 synthesis. We observed that two uORFs in the corresponding Neurospora crassa cpc-1 mRNA appear functionally analogous to the GCN4 uORFs. We also discovered that, surprisingly, unlike GCN4, the CPC1 coding sequence extends far upstream from the presumed AUG start codon with no other in-frame AUG codons. Similar extensions were seen in homologs from many filamentous fungi. We observed that multiple non-AUG near-cognate codons (NCCs) in this extended reading frame, some conserved, initiated translation to produce longer forms of CPC1, underscoring the significance of noncanonical initiation in controlling gene expression.

Reciprocal Translocations in Saccharomyces cerevisiae Formed by Nonhomologous End Joining

Genetics ◽  
2004 ◽  
Vol 166 (2) ◽  
pp. 741-751 ◽  
Author(s):  
Xin Yu ◽  
Abram Gabriel
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Chromosomal Rearrangements ◽  
Double Strand Breaks ◽  
Open Reading Frames ◽  
Nonhomologous End Joining ◽  
Wild Type ◽  
End Joining ◽  
Reciprocal Translocations ◽  
Strand Breaks ◽  
Reading Frames

Abstract Reciprocal translocations are common in cancer cells, but their creation is poorly understood. We have developed an assay system in Saccharomyces cerevisiae to study reciprocal translocation formation in the absence of homology. We induce two specific double-strand breaks (DSBs) simultaneously on separate chromosomes with HO endonuclease and analyze the subsequent chromosomal rearrangements among surviving cells. Under these conditions, reciprocal translocations via nonhomologous end joining (NHEJ) occur at frequencies of ∼2-7 × 10-5/cell exposed to the DSBs. Yku80p is a component of the cell’s NHEJ machinery. In its absence, reciprocal translocations still occur, but the junctions are associated with deletions and extended overlapping sequences. After induction of a single DSB, translocations and inversions are recovered in wild-type and rad52 strains. In these rearrangements, a nonrandom assortment of sites have fused to the DSB, and their junctions show typical signs of NHEJ. The sites tend to be between open reading frames or within Ty1 LTRs. In some cases the translocation partner is formed by a break at a cryptic HO recognition site. Our results demonstrate that NHEJ-mediated reciprocal translocations can form in S. cerevisiae as a consequence of DSB repair.

Sequencing of chromosome I from Saccharomyces cerevisiae: analysis of a 32 kb region between the LTE1 and SPO7 genes

Genome ◽  
1993 ◽  
Vol 36 (1) ◽  
pp. 32-42 ◽  
Author(s):  
B. F. Francis Ouellette ◽  
Michael W. Clark ◽  
Teresa Keng ◽  
Reg K. Storms ◽  
Wuwei Zhong ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Functional Analysis ◽  
Genome Analysis ◽  
Open Reading Frames ◽  
Average Spacing ◽  
Coding Regions ◽  
Significant Homology ◽  
Yeast Chromosome ◽  
Chromosome I ◽  
Reading Frames

The DNA sequencing and preliminary functional analysis of a 32 kb section of yeast chromosome I has been completed. This region lies on the left arm of the chromosome between the LTE1 and SPO7 genes and contains 14 open reading frames (ORFs) positioned closely together, with an average spacing of approximately 350 nucleotides between coding regions. Three of these ORFs correspond to previously identified genes, a further three show significant homology with other proteins, while the remaining eight ORFs share no significant homology to genes in the databases.Key words: chromosome I, genome analysis, Saccharomyces cerevisiae, yeast.

scholarly journals Divergent overlapping transcripts at the PET122 locus in Saccharomyces cerevisiae.

1990 ◽  
Vol 10 (6) ◽  
pp. 3027-3035 ◽  
Author(s):  
J D Ohmen ◽  
K A Burke ◽  
J E McEwen
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Nucleotide Sequence ◽  
Cytochrome C Oxidase ◽  
Genomic Dna ◽  
Transcription Unit ◽  
Open Reading Frames ◽  
Base Pairs ◽  
Opposite Strand ◽  
Overlapping Transcripts ◽  
Reading Frames

PET122 is one of three nuclear genes specifically required for translation of the mitochondrial mRNA for cytochrome c oxidase subunit III in Saccharomyces cerevisiae. The nucleotide sequence of 2,862 base pairs (bp) of yeast genomic DNA encompassing the PET122 locus shows very close spacing between the PET122 gene (254 codons) and two unidentified open reading frames, termed ORF2 and ORF3. ORF2 is encoded by the same strand of DNA as PET122 and is located 53 bp downstream of PET122, while ORF3 is encoded on the opposite strand and is located 215 bp upstream of PET122. Five transcripts, with sizes of 2.9, 2.3, 2.1, 1.5, and 1.4 kilobases (kb), are produced from this locus. The 2.1- and 1.4-kb transcripts encode ORF3, the 1.5-kb transcript encodes ORF2, and the 2.9- and 2.3-kb transcripts encode PET122. A particularly interesting feature of the ORF3-PET122-ORF2 transcription unit is a 535-base overlap between the 2.3-kb PET122 transcript produced from one strand and a 2.1-kb ORF3 transcript produced from the opposite strand. Similarly, the 2.9-kb PET122 transcript overlaps the 2.1-kb ORF3 transcript by more than 900 bases and the 1.5-kb ORF3 transcript by at least 200 bases. Hence, these pairs of transcripts are antisense to one another and have the potential to regulate, in an interdependent fashion, the posttranscriptional expression of ORF3 and PET122.

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