scholarly journals Experimental determination of codon usage‐dependent selective pressure on high copy‐number genes in Saccharomyces cerevisiae

Yeast ◽  
2018 ◽  
Author(s):  
Lyne Jossé ◽  
Tarun Singh ◽  
Tobias Haar
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Codon Usage ◽  
Experimental Determination ◽  
Copy Number ◽  
Selective Pressure ◽  
High Copy Number

scholarly journals Experimental determination of codon usage-dependent selective pressure on high copy-number genes in Saccharomyces cerevisiae

2018 ◽  
Author(s):  
Lyne Jossé ◽  
Tarun Singh ◽  
Tobias von der Haar
Keyword(s):  
Gene Expression ◽  
Saccharomyces Cerevisiae ◽  
Codon Usage ◽  
Copy Number ◽  
Molecular Mechanisms ◽  
Selective Pressure ◽  
Recombinant Protein Expression ◽  
High Expression ◽  
Expression Levels ◽  
Optimal Codon

AbstractOne of the central hypotheses in the theory of codon usage evolution is that in highly expressed genes particular codon usage patterns arise because they facilitate efficient gene expression and are thus selected for in evolution. Here we use plasmid copy number assays and growth rate measurements to explore details of the relationship between codon usage, gene expression level, and selective pressure in Saccharomyces cerevisiae. We find that when high expression levels are required optimal codon usage is beneficial and provides a fitness advantage, consistent with evolutionary theory. However, when high expression levels are not required, optimal codon usage is surprisingly and strongly selected against. We show that this selection acts at the level of protein synthesis, and we exclude a number of molecular mechanisms as the source for this negative selective pressure including nutrient and ribosome limitations and proteotoxicity effects. These findings inform our understanding of the evolution of codon usage bias, as well as the design of recombinant protein expression systems.

scholarly journals Introduction of extra telomeric DNA sequences into Saccharomyces cerevisiae results in telomere elongation.

1989 ◽  
Vol 9 (4) ◽  
pp. 1488-1497 ◽  
Author(s):  
K W Runge ◽  
V A Zakian
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Dna Sequences ◽  
Copy Number ◽  
Plasmid Copy Number ◽  
High Copy Number ◽  
Limiting Factor ◽  
Telomeric Dna ◽  
Base Pairs ◽  
Plasmid Copy ◽  
Telomere Elongation

The termini of Saccharomyces cerevisiae chromosomes consist of tracts of C1-3A (one to three cytosine and one adenine residue) sequences of approximately 450 base pairs in length. To gain insights into trans-acting factors at telomeres, high-copy-number linear and circular plasmids containing tracts of C1-3A sequences were introduced into S. cerevisiae. We devised a novel system to distinguish by color colonies that maintained the vector at 1 to 5, 20 to 50, and 100 to 400 copies per cell and used it to change the amount of telomeric DNA sequences per cell. An increase in the number of C1-3A sequences caused an increase in the length of telomeric C1-3A repeats that was proportional to plasmid copy number. Our data suggest that telomere growth is inhibited by a limiting factor(s) that specifically recognizes C1-3A sequences and that this factor can be effectively competed for by long tracts of C1-3A sequences at telomeres or on circular plasmids. Telomeres without this factor are exposed to processes that serve to lengthen chromosome ends.

sck1, a high copy number suppressor of defects in the cAMP-dependent protein kinase pathway in fission yeast, encodes a protein homologous to the Saccharomyces cerevisiae SCH9 kinase.

Genetics ◽  
1995 ◽  
Vol 140 (2) ◽  
pp. 457-467 ◽  
Author(s):  
M Jin ◽  
M Fujita ◽  
B M Culley ◽  
E Apolinario ◽  
M Yamamoto ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Protein Kinase ◽  
Adenylate Cyclase ◽  
Stationary Phase ◽  
Copy Number ◽  
Catalytic Subunit ◽  
High Copy Number ◽  
Dependent Protein Kinase ◽  
Camp Dependent Protein Kinase ◽  
Dependent Protein

Abstract Schizosaccharomyces pombe regulates intracellular cAMP levels, and thus cAMP-dependent protein kinase (PKA) activity, in response to changes in nutrient conditions. Mutations in any of eight git genes inhibit glucose repression of fbp1 transcription, alter the cell morphology, and cause a reduction in the growth rate. The eight git genes encode components of an adenylate cyclase activation pathway, adenylate cyclase itself, and the catalytic subunit of PKA. Three of these genes have been identified in other studies as regulators of meiosis. Here we show that the sck1 gene, cloned as a high copy number suppressor of a mutation in git3, is able to suppress the defects conferred by a mutation in any of these git genes. Sequence analysis suggests that sck1 encodes a protein most closely related to the Saccharomyces cerevisiae SCH9 protein kinase that had previously been identified as a high copy number suppressor of mutations in S. cerevisiae that reduce or eliminate PKA activity. Disruption of the sck1 gene causes a significant delay in exit from stationary phase when combined with a disruption of the pka1 (git6) gene encoding the catalytic subunit of PKA. However, the sck1 disruption by itself has little or no effect upon fbp1 transcription, meiosis, or exit from stationary phase, and does not enhance the constitutive fbp1 transcription observed in a pka1 mutant. Therefore, sck1 appears to function in a redundant fashion to pka1, but to varying degrees, in the pathways regulated by pka1.

scholarly journals RSC1 and RSC2 Are Required for Expression of Mid-Late Sporulation-Specific Genes in Saccharomyces cerevisiae

2004 ◽  
Vol 3 (4) ◽  
pp. 910-918 ◽  
Author(s):  
David Bungard ◽  
Michelle Reed ◽  
Edward Winter
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Copy Number ◽  
Spore Wall ◽  
Spore Formation ◽  
Mitogen Activated Protein Kinase ◽  
High Copy Number ◽  
Chromatin Remodeling Complex ◽  
Mitogen Activated Protein ◽  
Combined Action ◽  
Key Steps

ABSTRACT Rsc1 and Rsc2 are alternative bromodomain-containing subunits of the ATP-dependent RSC chromatin remodeling complex in Saccharomyces cerevisiae. Smk1 is a sporulation-specific mitogen-activated protein kinase homolog that is required for the postmeiotic events of spore formation. In this study we show that RSC1 and RSC2 are haploinsufficient for spore formation in a smk1 hypomorph. Moreover, diploids lacking Rsc1 or Rsc2 show a subset of smk1-like phenotypes. High-copy-number RSC1 plasmids do not suppress rsc2-Δ/rsc2-Δ sporulation defects, and high-copy-number RSC2 plasmids do not suppress rsc1-Δ/rsc1-Δ sporulation defects. Mid-late sporulation-specific genes, which are normally expressed while key steps in spore assembly occur and which include genes that are required for spore wall formation, are not expressed in cells lacking Rsc1 or Rsc2. We speculate that the combined action of Rsc1 and Rsc2 at mid-late promoters is specifically required for the proper expression of this uniquely timed set of genes. Our data suggest that Smk1 and Rsc1/2 define parallel pathways that converge to provide signaling information and the expression of gene products, respectively, that are required for spore morphogenesis.

High-copy-number integration into the ribosomal DNA of Saccharomyces cerevisiae: a new vector for high-level expression

Gene ◽  
1989 ◽  
Vol 79 (2) ◽  
pp. 199-206 ◽  
Author(s):  
Teresa S. Lopes ◽  
Jacobus Klootwijk ◽  
Annemarie E. Veenstra ◽  
Paul C. van der Aar ◽  
Harm van Heerikhuizen ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Ribosomal Dna ◽  
Copy Number ◽  
High Copy Number ◽  
High Level Expression ◽  
High Level

scholarly journals A Novel Plasmid-Based Microarray Screen Identifies Suppressors of rrp6Δ in Saccharomyces cerevisiae

2006 ◽  
Vol 27 (3) ◽  
pp. 1044-1055 ◽  
Author(s):  
Katharine Abruzzi ◽  
Sylvia Denome ◽  
Jens Raabjerg Olsen ◽  
Jannie Assenholt ◽  
Line Lindegaard Haaning ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Copy Number ◽  
High Copy Number ◽  
The Novel ◽  
Genetic Screens ◽  
Gene Encoding ◽  
Mrna Metabolism ◽  
High Copy Number Plasmid ◽  
Nuclear Exosome ◽  
Microarray Analyses

ABSTRACT Genetic screens in Saccharomyces cerevisiae provide novel information about interacting genes and pathways. We screened for high-copy-number suppressors of a strain with the gene encoding the nuclear exosome component Rrp6p deleted, with either a traditional plate screen for suppressors of rrp6Δ temperature sensitivity or a novel microarray enhancer/suppressor screening (MES) strategy. MES combines DNA microarray technology with high-copy-number plasmid expression in liquid media. The plate screen and MES identified overlapping, but also different, suppressor genes. Only MES identified the novel mRNP protein Nab6p and the tRNA transporter Los1p, which could not have been identified in a traditional plate screen; both genes are toxic when overexpressed in rrp6Δ strains at 37°C. Nab6p binds poly(A)+ RNA, and the functions of Nab6p and Los1p suggest that mRNA metabolism and/or protein synthesis are growth rate limiting in rrp6Δ strains. Microarray analyses of gene expression in rrp6Δ strains and a number of suppressor strains support this hypothesis.

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