The relationship between mRNA half-life and gene function in the yeast Saccharomyces cerevisiae

Gene ◽  
1995 ◽  
Vol 166 (1) ◽  
pp. 145-149 ◽  
Author(s):  
Joyce Moore ◽  
Howard T. Jacobs ◽  
Kim Kaiser
2021 ◽  
Vol 118 (51) ◽  
pp. e2026362118
Author(s):  
Ajeet K. Sharma ◽  
Johannes Venezian ◽  
Ayala Shiber ◽  
Günter Kramer ◽  
Bernd Bukau ◽  
...  

The presence of a single cluster of nonoptimal codons was found to decrease a transcript’s half-life through the interaction of the ribosome-associated quality control machinery with stalled ribosomes in Saccharomyces cerevisiae. The impact of multiple nonoptimal codon clusters on a transcript’s half-life, however, is unknown. Using a kinetic model, we predict that inserting a second nonoptimal cluster near the 5′ end can lead to synergistic effects that increase a messenger RNA’s (mRNA’s) half-life in S. cerevisiae. Specifically, the 5′ end cluster suppresses the formation of ribosome queues, reducing the interaction of ribosome-associated quality control factors with stalled ribosomes. We experimentally validate this prediction by introducing two nonoptimal clusters into three different genes and find that their mRNA half-life increases up to fourfold. The model also predicts that in the presence of two clusters, the cluster closest to the 5′ end is the primary determinant of mRNA half-life. These results suggest the “translational ramp,” in which nonoptimal codons are located near the start codon and increase translational efficiency, may have the additional biological benefit of allowing downstream slow-codon clusters to be present without decreasing mRNA half-life. These results indicate that codon usage bias plays a more nuanced role in controlling cellular protein levels than previously thought.


2006 ◽  
Vol 17 (1) ◽  
pp. 213-226 ◽  
Author(s):  
Cory D. Dunn ◽  
Marina S. Lee ◽  
Forrest A. Spencer ◽  
Robert E. Jensen

Unlike many other organisms, the yeast Saccharomyces cerevisiae can tolerate the loss of mitochondrial DNA (mtDNA). Although a few proteins have been identified that are required for yeast cell viability without mtDNA, the mechanism of mtDNA-independent growth is not completely understood. To probe the relationship between the mitochondrial genome and cell viability, we conducted a microarray-based, genomewide screen for mitochondrial DNA-dependent yeast mutants. Among the several genes that we discovered is MGR1, which encodes a novel subunit of the i-AAA protease complex located in the mitochondrial inner membrane. mgr1Δ mutants retain some i-AAA protease activity, yet mitochondria lacking Mgr1p contain a misassembled i-AAA protease and are defective for turnover of mitochondrial inner membrane proteins. Our results highlight the importance of the i-AAA complex and proteolysis at the inner membrane in cells lacking mitochondrial DNA.


Genetics ◽  
1979 ◽  
Vol 92 (2) ◽  
pp. 397-408
Author(s):  
Christopher W Lawrence ◽  
Roshan B Christensen

ABSTRACT The role of the REV3 gene function in UV-induced mutagensis in the yeast Saccharomyces cerevisiae has been examined by determining the reversion of 12 well-defined cycl mutations in diploid strains homozygous for the rev3—1 or rev3—3 allele. The 12 cycl alleles include one ochre, one amber, four initiation, two proline missense, and four frameshift mutations. We find that the rev3 mutations reduce the frequency of UV-induced reversion of all of the cycl alleles, though different classes of alleles respond to a different extent. These results imply that the REV3 gene function is required for the production of a wide variety of mutational events, though probably not all, and show that each of the three REV loci have different mutational phenotypes. Such diverse phenotypes are not predicted by the unitary model for bacterial mutagenesis (CAILLET-FAUQUET, DEFAIS and RADMAN 1977; WITKIN 1976), suggesting that this is at best an incomplete description of eukaryotic mutagenesis.


Genetics ◽  
2000 ◽  
Vol 155 (1) ◽  
pp. 43-55
Author(s):  
Cordell R DeMattei ◽  
Colleen P Davis ◽  
James B Konopka

Abstract Mating pheromone receptors activate a G protein signal pathway that leads to the conjugation of the yeast Saccharomyces cerevisiae. This pathway also induces the production of Afr1p, a protein that negatively regulates pheromone receptor signaling and is required to form pointed projections of new growth that become the site of cell fusion during mating. Afr1p lacks strong similarity to any well-characterized proteins to help predict how it acts. Therefore, we investigated the relationship between the different functions of Afr1p by isolating and characterizing seven mutants that were defective in regulating pheromone signaling. The AFR1 mutants were also defective when expressed as fusions to STE2, the α-factor receptor, indicating that the mutant Afr1 proteins are defective in function and not in co-localizing with receptors. The mutant genes contained four distinct point mutations that all occurred between codons 254 and 263, identifying a region that is critical for AFR1 function. Consistent with this, we found that the corresponding region is very highly conserved in the Afr1p homologs from the yeasts S. uvarum and S. douglasii. In contrast, there were no detectable effects on pheromone signaling caused by deletion or overexpression of YER158c, an open reading frame with overall sequence similarity to Afr1p that lacks this essential region. Interestingly, all of the AFR1 mutants showed a defect in their ability to form mating projections that was proportional to their defect in regulating pheromone signaling. This suggests that both functions may be due to the same action of Afr1p. Thus, these studies identify a specific region of Afr1p that is critical for its function in both signaling and morphogenesis.


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