scholarly journals Splicing of a yeast intron containing an unusual 5' junction sequence.

1989 ◽  
Vol 9 (6) ◽  
pp. 2765-2770 ◽  
Author(s):  
M R Hodge ◽  
M G Cumsky
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Splice Junction ◽  
Protein Coding ◽  
Junction Sequence ◽  
Protein Coding Genes ◽  
Minor Fraction ◽  
A Minor ◽  
Mrna Precursor

The Saccharomyces cerevisiae COX5b gene contains a small intron that is unique in two respects. First, it interrupts the ATG codon that initiates translation of the COX5b product. Second, it contains a sequence at the 5' splice junction (5'-GCATGT-3') that differs from the highly conserved yeast hexanucleotide (5'-GTAPyGT-3') and from the 5'-GT found at the corresponding position in nearly all introns of eucaryotic protein-coding genes. We have analyzed both the transcripts derived from the COX5b gene and the splicing of its intron. We show here that an unspliced mRNA precursor constituted a minor fraction of the total COX5b message, even when the gene was overexpressed. We also show that both major transcripts derived from COX5b had been spliced. Our results suggest that at least in the case of COX5b, a 5'-GC can function as efficiently as the highly conserved 5'-GT in the splicing reaction.

Splicing of a yeast intron containing an unusual 5' junction sequence

1989 ◽  
Vol 9 (6) ◽  
pp. 2765-2770
Author(s):  
M R Hodge ◽  
M G Cumsky
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Splice Junction ◽  
Protein Coding ◽  
Junction Sequence ◽  
Protein Coding Genes ◽  
Minor Fraction ◽  
A Minor ◽  
Mrna Precursor

The Saccharomyces cerevisiae COX5b gene contains a small intron that is unique in two respects. First, it interrupts the ATG codon that initiates translation of the COX5b product. Second, it contains a sequence at the 5' splice junction (5'-GCATGT-3') that differs from the highly conserved yeast hexanucleotide (5'-GTAPyGT-3') and from the 5'-GT found at the corresponding position in nearly all introns of eucaryotic protein-coding genes. We have analyzed both the transcripts derived from the COX5b gene and the splicing of its intron. We show here that an unspliced mRNA precursor constituted a minor fraction of the total COX5b message, even when the gene was overexpressed. We also show that both major transcripts derived from COX5b had been spliced. Our results suggest that at least in the case of COX5b, a 5'-GC can function as efficiently as the highly conserved 5'-GT in the splicing reaction.

scholarly journals Analysis of thepdx-1(snz-1/sno-1) Region of theNeurospora crassaGenome: Correlation of Pyridoxine-Requiring Phenotypes With Mutations in Two Structural Genes

Genetics ◽  
2001 ◽  
Vol 157 (3) ◽  
pp. 1067-1075 ◽  
Author(s):  
Laura E Bean ◽  
William H Dvorachek ◽  
Edward L Braun ◽  
Allison Errett ◽  
Gregory S Saenz ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Stationary Phase ◽  
Neurospora Crassa ◽  
Vitamin B6 ◽  
Structural Genes ◽  
Protein Coding ◽  
Previous Conclusion ◽  
Protein Coding Genes ◽  
Shared Function ◽  
High Gene

AbstractWe report the analysis of a 36-kbp region of the Neurospora crassa genome, which contains homologs of two closely linked stationary phase genes, SNZ1 and SNO1, from Saccharomyces cerevisiae. Homologs of SNZ1 encode extremely highly conserved proteins that have been implicated in pyridoxine (vitamin B6) metabolism in the filamentous fungi Cercospora nicotianae and in Aspergillus nidulans. In N. crassa, SNZ and SNO homologs map to the region occupied by pdx-1 (pyridoxine requiring), a gene that has been known for several decades, but which was not sequenced previously. In this study, pyridoxine-requiring mutants of N. crassa were found to possess mutations that disrupt conserved regions in either the SNZ or SNO homolog. Previously, nearly all of these mutants were classified as pdx-1. However, one mutant with a disrupted SNO homolog was at one time designated pdx-2. It now appears appropriate to reserve the pdx-1 designation for the N. crassa SNZ homolog and pdx-2 for the SNO homolog. We further report annotation of the entire 36,030-bp region, which contains at least 12 protein coding genes, supporting a previous conclusion of high gene densities (12,000-13,000 total genes) for N. crassa. Among genes in this region other than SNZ and SNO homologs, there was no evidence of shared function. Four of the genes in this region appear to have been lost from the S. cerevisiae lineage.

Mutation in genes coding for glucose-induced degradation-deficient protein contribute to high malate production in yeast strains No. 28 and No. 77 used for industrial brewing of sake

2021 ◽  
Author(s):  
Hiroaki Negoro ◽  
Atsushi Kotaka ◽  
Hiroki Ishida
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Organic Acids ◽  
Nonsense Mutation ◽  
Yeast Strain ◽  
Homozygous Mutation ◽  
Alcohol Fermentation ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Yeast Strains

ABSTRACT Saccharomyces cerevisiae produces organic acids including malate during alcohol fermentation. Since malate contributes to the pleasant flavor of sake, high-malate-producing yeast strain No. 28 and No. 77 have been developed by the Brewing Society of Japan. In this study, the genes responsible for the high malate phenotype in these strains were investigated. We had found previously that the deletion of components of the glucose induced degradation-deficient (GID) complex led to high malate production in yeast. Upon examining GID protein-coding genes in yeast strain No. 28 and No. 77, a nonsense homozygous mutation of GID4 in strain No. 28, and of GID2 in strain No. 77, were identified as the cause of high malate production. Furthermore, complementary tests of these mutations indicated that the heterozygous nonsense mutation in GID2 was recessive. In contrast, the heterozygous nonsense mutation in GID4 was considered semi-dominant.

Differential regulation of the 70K heat shock gene and related genes in Saccharomyces cerevisiae

1984 ◽  
Vol 4 (8) ◽  
pp. 1454-1459
Author(s):  
M S Ellwood ◽  
E A Craig
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Heat Shock ◽  
Heat Shock Gene ◽  
Control Analysis ◽  
Coding Region ◽  
Protein Coding ◽  
Shock Gene ◽  
A Minor ◽  
Flanking Regions ◽  
Beta Galactosidase

Saccharomyces cerevisiae contains a family of genes related to Hsp70, the major heat shock gene of Drosophila melanogaster. The transcription of three of these genes, which show no conservation of sequences 5' to the protein-coding region, was analyzed. The 5' flanking regions from the three genes were fused to the Escherichia coli beta-galactosidase structural gene and introduced into yeasts on multicopy plasmids, putting the beta-galactosidase production under yeast promoter control. Analysis of beta-galactosidase mRNA and protein production in these transformed strains revealed that transcription from the three promoters is differentially regulated. The number of transcripts from one promoter is vastly increased for a brief period after heat shock, whereas mRNA from another declines. Transcripts from a third gene are slightly enhanced upon heat shock; however, multiple 5' ends of the mRNA are found, and a minor species increases in amount after heat shock. Transcription of these promoters in their native state on the chromosome appears to be modulated in the same manner.

Effects of mutations of GID protein–coding genes on malate production and enzyme expression profiles in Saccharomyces cerevisiae

2020 ◽  
Vol 104 (11) ◽  
pp. 4971-4983
Author(s):  
Hiroaki Negoro ◽  
Kengo Matsumura ◽  
Fumio Matsuda ◽  
Hiroshi Shimizu ◽  
Yoji Hata ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Expression Profiles ◽  
Enzyme Expression ◽  
Protein Coding ◽  
Protein Coding Genes

scholarly journals Landscape of the Dark Transcriptome Revealed through Re-mining Massive RNA-Seq Data

2019 ◽  
Author(s):  
Jing Li ◽  
Urminder Singh ◽  
Zebulun Arendsee ◽  
Eve Syrkin Wurtele
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Rna Seq ◽  
Protein Coding ◽  
Interactive Analysis ◽  
Protein Coding Genes ◽  
Yeast Data ◽  
Specific Proteins ◽  
Species Specific ◽  
Developmental Conditions ◽  
Expression Matrix

AbstractThe “dark transcriptome” can be considered the multitude of sequences that are transcribed but not annotated as genes. We evaluated expression of 6,692 annotated genes and 29,354 unannotated ORFs in the Saccharomyces cerevisiae genome across diverse environmental, genetic and developmental conditions (3,457 RNA-Seq samples). Over 48% of the transcribed ORFs have translation evidence. Phylostratigraphic analysis infers most of these transcribed ORFs would encode species-specific proteins (“orphan-ORFs”); hundreds have mean expression comparable to annotated genes. These data reveal unannotated ORFs most likely to be protein-coding genes. We partitioned a co-expression matrix by Markov Chain Clustering; the resultant clusters contain 2,468 orphan-ORFs. We provide the aggregated RNA-Seq yeast data with extensive metadata as a project in MetaOmGraph, a tool designed for interactive analysis and visualization. This approach enables reuse of public RNA-Seq data for exploratory discovery, providing a rich context for experimentalists to make novel, experimentally-testable hypotheses about candidate genes.

scholarly journals Differential regulation of the 70K heat shock gene and related genes in Saccharomyces cerevisiae.

1984 ◽  
Vol 4 (8) ◽  
pp. 1454-1459 ◽  
Author(s):  
M S Ellwood ◽  
E A Craig
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Heat Shock ◽  
Heat Shock Gene ◽  
Control Analysis ◽  
Coding Region ◽  
Protein Coding ◽  
Shock Gene ◽  
A Minor ◽  
Flanking Regions ◽  
Beta Galactosidase

Saccharomyces cerevisiae contains a family of genes related to Hsp70, the major heat shock gene of Drosophila melanogaster. The transcription of three of these genes, which show no conservation of sequences 5' to the protein-coding region, was analyzed. The 5' flanking regions from the three genes were fused to the Escherichia coli beta-galactosidase structural gene and introduced into yeasts on multicopy plasmids, putting the beta-galactosidase production under yeast promoter control. Analysis of beta-galactosidase mRNA and protein production in these transformed strains revealed that transcription from the three promoters is differentially regulated. The number of transcripts from one promoter is vastly increased for a brief period after heat shock, whereas mRNA from another declines. Transcripts from a third gene are slightly enhanced upon heat shock; however, multiple 5' ends of the mRNA are found, and a minor species increases in amount after heat shock. Transcription of these promoters in their native state on the chromosome appears to be modulated in the same manner.

scholarly journals Interactions of Sen1, Nrd1, and Nab3 with Multiple Phosphorylated Forms of the Rpb1 C-Terminal Domain in Saccharomyces cerevisiae

2012 ◽  
Vol 11 (4) ◽  
pp. 417-429 ◽  
Author(s):  
Karen Chinchilla ◽  
Juan B. Rodriguez-Molina ◽  
Doris Ursic ◽  
Jonathan S. Finkel ◽  
Aseem Z. Ansari ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Rna Polymerase Ii ◽  
Protein Interactions ◽  
Noncoding Rna ◽  
Protein Protein Interactions ◽  
Coding Region ◽  
Protein Coding ◽  
Content Type ◽  
Protein Coding Genes ◽  
Terminal Domain

ABSTRACT The Saccharomyces cerevisiae SEN1 gene codes for a nuclear, ATP-dependent helicase which is embedded in a complex network of protein-protein interactions. Pleiotropic phenotypes of mutations in SEN1 suggest that Sen1 functions in many nuclear processes, including transcription termination, DNA repair, and RNA processing. Sen1, along with termination factors Nrd1 and Nab3, is required for the termination of noncoding RNA transcripts, but Sen1 is associated during transcription with coding and noncoding genes. Sen1 and Nrd1 both interact directly with Nab3, as well as with the C-terminal domain (CTD) of Rpb1, the largest subunit of RNA polymerase II. It has been proposed that Sen1, Nab3, and Nrd1 form a complex that associates with Rpb1 through an interaction between Nrd1 and the Ser 5 -phosphorylated (Ser 5 -P) CTD. To further study the relationship between the termination factors and Rpb1, we used two-hybrid analysis and immunoprecipitation to characterize sen1-R302W , a mutation that impairs an interaction between Sen1 and the Ser 2 -phosphorylated CTD. Chromatin immunoprecipitation indicates that the impairment of the interaction between Sen1 and Ser 2 -P causes the reduced occupancy of mutant Sen1 across the entire length of noncoding genes. For protein-coding genes, mutant Sen1 occupancy is reduced early and late in transcription but is similar to that of the wild type across most of the coding region. The combined data suggest a handoff model in which proteins differentially transfer from the Ser 5 - to the Ser 2 -phosphorylated CTD to promote the termination of noncoding transcripts or other cotranscriptional events for protein-coding genes.

scholarly journals Draft Genome Sequence of Saccharomyces cerevisiae Barra Grande (BG-1), a Brazilian Industrial Bioethanol-Producing Strain

2017 ◽  
Vol 5 (13) ◽  
Author(s):  
Natalia Coutouné ◽  
Aline Tieppo Nogueira Mulato ◽  
Diego Mauricio Riaño-Pachón ◽  
Juliana Velasco de Castro Oliveira
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Genome Sequence ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Bioethanol Production ◽  
Industrial Strain ◽  
Protein Coding ◽  
Content Type ◽  
Protein Coding Genes

ABSTRACT Here, we present the draft genome sequence of Saccharomyces cerevisiae BG-1, a Brazilian industrial strain widely used for bioethanol production from sugarcane. The 11.7-Mb genome sequence consists of 216 scaffolds and harbors 5,607 predicted protein-coding genes.

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