scholarly journals Fitness effects ofcis-regulatory variants in theSaccharomyces cerevisiae TDH3promoter

2017 ◽  
Author(s):  
Fabien Duveau ◽  
William Toubiana ◽  
Patricia J. Wittkopp
Keyword(s):  
Gene Expression ◽  
Saccharomyces Cerevisiae ◽  
De Novo ◽  
Wild Type Allele ◽  
Wild Type ◽  
Fitness Effects ◽  
Regulatory Variants ◽  
Fitness Consequences ◽  
Regulatory Mutations ◽  
Affect Cell Growth

AbstractVariation in gene expression is widespread within and between species, but fitness consequences of this variation are generally unknown. Here we use mutations in theSaccharomyces cerevisiae TDH3promoter to assess how changes inTDH3expression affect cell growth. From these data, we predict the fitness consequences ofde novomutations and natural polymorphisms in theTDH3promoter. Nearly all mutations and polymorphisms in theTDH3promoter were found to have no significant effect on fitness in the environment assayed, suggesting that the wild type allele of this promoter is robust to the effects of most newcis-regulatory mutations.

scholarly journals De Novo Development of mtDNA Deletion Due to Decreased POLG and SSBP1 Expression in Humans

Genes ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 284
Author(s):  
Yeonmi Lee ◽  
Taeho Kim ◽  
Miju Lee ◽  
Seongjun So ◽  
Mustafa Zafer Karagozlu ◽  
...  
Keyword(s):  
Dna Polymerase ◽  
De Novo ◽  
Wild Type Allele ◽  
Wild Type ◽  
Factors Associated ◽  
Mtdna Deletions ◽  
Nuclear Factors ◽  
Mtdna Deletion ◽  
In The Wild ◽  
Mtdna Replication

Defects in the mitochondrial genome (mitochondrial DNA (mtDNA)) are associated with both congenital and acquired disorders in humans. Nuclear-encoded DNA polymerase subunit gamma (POLG) plays an important role in mtDNA replication, and proofreading and mutations in POLG have been linked with increased mtDNA deletions. SSBP1 is also a crucial gene for mtDNA replication. Here, we describe a patient diagnosed with Pearson syndrome with large mtDNA deletions that were not detected in the somatic cells of the mother. Exome sequencing was used to evaluate the nuclear factors associated with the patient and his family, which revealed a paternal POLG mutation (c.868C > T) and a maternal SSBP1 mutation (c.320G > A). The patient showed lower POLG and SSBP1 expression than his healthy brothers and the general population of a similar age. Notably, c.868C in the wild-type allele was highly methylated in the patient compared to the same site in both his healthy brothers. These results suggest that the co- deficient expression of POLG and SSBP1 genes could contribute to the development of mtDNA deletion.

scholarly journals Divergent MLS1 promoters lie on a fitness plateau for gene expression

2015 ◽  
Author(s):  
Andrew C Bergen ◽  
Gerilyn M Olsen ◽  
Justin C Fay
Keyword(s):  
Gene Expression ◽  
Saccharomyces Cerevisiae ◽  
Dynamic Response ◽  
Yeast Species ◽  
Glucose Repression ◽  
Gene Activation ◽  
Malate Synthase ◽  
Expression Divergence ◽  
Fitness Effects ◽  
Single Promoter

Qualitative patterns of gene activation and repression are often conserved despite an abundance of quantitative variation in expression levels within and between species. A major challenge to interpreting patterns of expression divergence is knowing which changes in gene expression affect fitness. To characterize the fitness effects of gene expression divergence we placed orthologous promoters from eight yeast species upstream of malate synthase (MLS1) in Saccharomyces cerevisiae. As expected, we found these promoters varied in their expression level under activated and repressed conditions as well as in their dynamic response following loss of glucose repression. Despite these differences, only a single promoter driving near basal levels of expression caused a detectable loss of fitness. We conclude that the MLS1 promoter lies on a fitness plateau whereby even large changes in gene expression can be tolerated without a substantial loss of fitness.

scholarly journals SPO71 Encodes a Developmental Stage-Specific Partner for Vps13 in Saccharomyces cerevisiae

2013 ◽  
Vol 12 (11) ◽  
pp. 1530-1537 ◽  
Author(s):  
Jae-Sook Park ◽  
Yuuya Okumura ◽  
Hiroyuki Tachikawa ◽  
Aaron M. Neiman
Keyword(s):  
Saccharomyces Cerevisiae ◽  
De Novo ◽  
Ectopic Expression ◽  
Membrane Vesicles ◽  
Specific Gene ◽  
Wild Type ◽  
Protein Mutation ◽  
Prospore Membrane ◽  
In The Wild ◽  
Membrane Morphogenesis

ABSTRACT The creation of haploid gametes in yeast, termed spores, requires the de novo formation of membranes within the cytoplasm. These membranes, called prospore membranes, enclose the daughter nuclei generated by meiosis. Proper growth and closure of prospore membranes require the highly conserved Vps13 protein. Mutation of SPO71 , a meiosis-specific gene first identified as defective in spore formation, was found to display defects in membrane morphogenesis very similar to those seen in vps13 Δ cells. Specifically, prospore membranes are smaller than in the wild type, they fail to close, and membrane vesicles are present within the prospore membrane lumen. As in vps13 Δ cells, the levels of phophatidylinositol-4-phosphate are reduced in the prospore membranes of spo71 Δ cells. SPO71 is required for the translocation of Vps13 from the endosome to the prospore membrane, and ectopic expression of SPO71 in vegetative cells results in mislocalization of Vps13. Finally, the two proteins can be coprecipitated from sporulating cells. We propose that Spo71 is a sporulation-specific partner for Vps13 and that they act in concert to regulate prospore membrane morphogenesis.

Comparison of Clinical and Biologic Significance of WT1 Mutations in Populations of Older (≥60 years[y]) and Younger (<60 y) Adult Patients (Pts) with Cytogenetically Normal (CN) De Novo Acute Myeloid Leukemia (AML): a Cancer and Leukemia Group B (CALGB) Study.

Blood ◽  
2009 ◽  
Vol 114 (22) ◽  
pp. 326-326
Author(s):  
Heiko Becker ◽  
Guido Marcucci ◽  
Kati Maharry ◽  
Michael D. Radmacher ◽  
Krzysztof Mrózek ◽  
...  
Keyword(s):  
Gene Expression ◽  
De Novo ◽  
Age Groups ◽  
Stem Cell Marker ◽  
Treatment Intensity ◽  
Prognostic Impact ◽  
Wild Type ◽  
Age Related ◽  
Exon 9 ◽  
Wt1 Mutation

Abstract Abstract 326 Mutations of the Wilms tumor (WT1) gene are found in ∼10% of younger (<60 years[y]) adult pts with de novo CN-AML and impact adversely on their outcome. The clinical significance of WT1 mutations has not yet been evaluated in older (≥60 y) CN-AML pts. Therefore, we analyzed frequency and clinical impact of WT1 mutations in the context of other molecular markers in a relatively large cohort of 243 pts ≥60 y (range, 60-83 y) with de novo CN-AML treated intensively on upfront cytarabine/daunorubicin-based CALGB protocols. Included pts were those with material available for analysis of WT1 mutation status and that of a panel of other validated molecular prognosticators including NPM1, FLT3 (ie, FLT3-ITD, FLT3-TKD) and CEBPA mutations, BAALC and ERG expression levels. Mutations in WT1 “hot spots” (exons 7 and 9) were assessed by DHPLC and sequencing. The results were compared with the findings in younger (18-59 y) CALGB pts (n=207) characterized molecularly in a similar fashion. Gene expression profiles in both populations were assessed centrally using Affymetrix U133 plus 2.0 microchip. Among the 243 older pts, 16 (7%) had WT1 mutations. Of those, 14 had single WT1 mutations in exon 7 [frameshift (n=8), nonsense (n=1), and missense (n=1)] or in exon 9 [missense (n=4)]; 1 pt had 2 frameshift mutations in exon 7, and 1 had 1 frameshift mutation in exon 7 and 1 missense mutation in exon 9. Compared with older WT1 wild-type pts, older WT1 mutated pts more often had FLT3-ITD (P<.001) and had lower hemoglobin (P=.01), and higher WBC (P=.03) and % blood blasts (P=.03). WT1 mutated pts had a trend for lower complete remission (CR) rates (50% v 70%, P=.16) and shorter OS (P=.08; Figure 1), but similar disease-free survival (DFS; P=.59; Figure 2) compared with WT1 wild-type pts. The frequency of WT1 mutations tended to be lower in older than younger pts (7% v 12%, P=.07). Mutation types and pretreatment clinical and molecular characteristics associated with WT1 mutations were similar between the two age groups. Despite differences in treatment intensity, there were no significant differences in younger v older WT1 mutated pts with regard to CR rates (P=.18), or OS (P=.68; Figure 1) or DFS (P=.66; Figure 2) durations. In contrast, younger WT1 wild-type pts had significantly higher CR rates (P<.001), and longer OS (P<.001; Figure 1) and DFS (P<.001; Figure 2) than older WT1 wild-type pts. Although associated with WT1 mutations in both the younger (P=.02) and older age groups, FLT3-ITD had no impact on CR rates (P=.28), or OS (P=.15) or DFS (P=.21) durations of all WT1 mutated pts after controlling for age-related treatment intensity. To provide insights into the molecular features associated with WT1 mutations we analyzed the whole cohort (younger and older) for genes differentially expressed (ie, P≤.001) between WT1 mutated and WT1 wild-type pts. A signature comprising 110 named genes was derived. Among the 71 upregulated genes in WT1 mutated pts, were those encoding the leukemia stem cell marker CD96 and the leukemia fusion protein partners PML and MLL. The most upregulated gene (6.2 fold) was GTSF1, which, like WT1, may be involved in germ cell development. Among the 39 genes downregulated in WT1 mutated pts, were those encoding SNRPN and SNURF, involved in pre-mRNA processing, and the insulin receptor and IRS2, upstream effectors of the PI3K/AKT pathway. In conclusion, WT1 mutations in older CN-AML pts are less frequent than in younger pts. While WT1 mutations independently associate with shorter OS and DFS in younger CN-AML pts, in older CN-AML pts they are only associated with trends for a worse CR rate and shorter OS. This difference appears due to the poor outcome of the older compared to younger WT1 wild-type pts, which reduced the prognostic impact of WT1 mutations in the former. Nevertheless, the outcome of pts with WT1 mutations is equally poor in older and younger pts regardless of differences in treatment, thereby suggesting that WT1 mutated CN-AML may constitute a distinct biologic entity across age groups. The unique gene expression signature associated with WT1 mutations could provide useful insights into WT1 mutation-driven leukemogenic mechanisms across age-related groups, and help in devising novel molecular targeted therapeutic approaches for this subtype of CN-AML. Disclosures: No relevant conflicts of interest to declare.

scholarly journals Perturbations of transcription and gene expression-associated processes alter distribution of cell size values in Saccharomyces cerevisiae

2018 ◽  
Author(s):  
Nairita Maitra ◽  
Jayamani Anandhakumar ◽  
Heidi M. Blank ◽  
Craig D. Kaplan ◽  
Michael Polymenis
Keyword(s):  
Gene Expression ◽  
Saccharomyces Cerevisiae ◽  
Rna Polymerase Ii ◽  
Cell Size ◽  
Gamma Distribution ◽  
Single Gene ◽  
Growth Conditions ◽  
Wild Type ◽  
Pol Ii ◽  
Diploid Cells

ABSTRACTThe question of what determines whether cells are big or small has been the focus of many studies because it is thought that such determinants underpin the coupling of cell growth with cell division. In contrast, what determines the overall pattern of how cell size is distributed within a population of wild type or mutant cells has received little attention. Knowing how cell size varies around a characteristic pattern could shed light on the processes that generate such a pattern and provide a criterion to identify its genetic basis. Here, we show that cell size values of wild type Saccharomyces cerevisiae cells fit a gamma distribution, in haploid and diploid cells, and under different growth conditions. To identify genes that influence this pattern, we analyzed the cell size distributions of all single-gene deletion strains in Saccharomyces cerevisiae. We found that yeast strains which deviate the most from the gamma distribution are enriched for those lacking gene products functioning in gene expression, especially those in transcription or transcription-linked processes. We also show that cell size is increased in mutants carrying altered activity substitutions in Rpo21p/Rpb1, the largest subunit of RNA polymerase II (Pol II). Lastly, the size distribution of cells carrying extreme altered activity Pol II substitutions deviated from the expected gamma distribution. Our results are consistent with the idea that genetic defects in widely acting transcription factors or Pol II itself compromise both cell size homeostasis and how the size of individual cells is distributed in a population.

scholarly journals The Saccharomyces cerevisiae MUM2 Gene Interacts With the DNA Replication Machinery and Is Required for Meiotic Levels of Double Strand Breaks

Genetics ◽  
2001 ◽  
Vol 157 (3) ◽  
pp. 1179-1189 ◽  
Author(s):  
Luther Davis ◽  
Maria Barbera ◽  
Amanda McDonnell ◽  
Katherine McIntyre ◽  
Rolf Sternglanz ◽  
...  
Keyword(s):  
Gene Expression ◽  
Saccharomyces Cerevisiae ◽  
Dna Replication ◽  
Dna Synthesis ◽  
Origin Recognition Complex ◽  
Wild Type ◽  
Replication Machinery ◽  
Synthesis Inhibitor ◽  
Strand Breaks ◽  
Meiotic Gene

Abstract The Saccharomyces cerevisiae MUM2 gene is essential for meiotic, but not mitotic, DNA replication and thus sporulation. Genetic interactions between MUM2 and a component of the origin recognition complex and polymerase α-primase suggest that MUM2 influences the function of the DNA replication machinery. Early meiotic gene expression is induced to a much greater extent in mum2 cells than in meiotic cells treated with the DNA synthesis inhibitor hydroxyurea. This result indicates that the mum2 meiotic arrest is downstream of the arrest induced by hydroxyurea and suggests that DNA synthesis is initiated in the mutant. Genetic analyses indicate that the recombination that occurs in mum2 mutants is dependent on the normal recombination machinery and on synaptonemal complex components and therefore is not a consequence of lesions created by incompletely replicated DNA. Both meiotic ectopic and allelic recombination are similarly reduced in the mum2 mutant, and the levels are consistent with the levels of meiosis-specific DSBs that are generated. Cytological analyses of mum2 mutants show that chromosome pairing and synapsis occur, although at reduced levels compared to wild type. Given the near-wild-type levels of meiotic gene expression, pairing, and synapsis, we suggest that the reduction in DNA replication is directly responsible for the reduced level of DSBs and meiotic recombination.

scholarly journals Improving 3-methylphenol (m-cresol) production in yeast via in vivo glycosylation or methylation

2020 ◽  
Vol 20 (8) ◽  
Author(s):  
Julia Hitschler ◽  
Eckhard Boles
Keyword(s):  
Saccharomyces Cerevisiae ◽  
De Novo ◽  
Wild Type ◽  
Biotechnological Production ◽  
Yeast Saccharomyces Cerevisiae ◽  
In Situ Extraction ◽  
Methylsalicylic Acid Synthase ◽  
In The Wild

ABSTRACT Heterologous expression of 6-methylsalicylic acid synthase (MSAS) together with 6-MSA decarboxylase enables de novo production of the platform chemical and antiseptic additive 3-methylphenol (3-MP) in the yeast Saccharomyces cerevisiae. However, toxicity of 3-MP prevents higher production levels. In this study, we evaluated in vivo detoxification strategies to overcome limitations of 3-MP production. An orcinol-O-methyltransferase from Chinese rose hybrids (OOMT2) was expressed in the 3-MP producing yeast strain to convert 3-MP to 3-methylanisole (3-MA). Together with in situ extraction by dodecane of the highly volatile 3-MA this resulted in up to 211 mg/L 3-MA (1.7 mM) accumulation. Expression of a UDP-glycosyltransferase (UGT72B27) from Vitis vinifera led to the synthesis of up to 533 mg/L 3-MP as glucoside (4.9 mM). Conversion of 3-MP to 3-MA and 3-MP glucoside was not complete. Finally, deletion of phosphoglucose isomerase PGI1 together with methylation or glycosylation and feeding a fructose/glucose mixture to redirect carbon fluxes resulted in strongly increased product titers, with up to 897 mg/L 3-MA/3-MP (9 mM) and 873 mg/L 3-MP/3-MP as glucoside (8.1 mM) compared to less than 313 mg/L (2.9 mM) product titers in the wild type controls. The results show that methylation or glycosylation are promising tools to overcome limitations in further enhancing the biotechnological production of 3-MP.

scholarly journals tRNA thiolation links translation to stress responses in Saccharomyces cerevisiae

2015 ◽  
Vol 26 (2) ◽  
pp. 270-282 ◽  
Author(s):  
Jadyn R. Damon ◽  
David Pincus ◽  
Hidde L. Ploegh
Keyword(s):  
Gene Expression ◽  
Saccharomyces Cerevisiae ◽  
Endoplasmic Reticulum ◽  
Elevated Temperature ◽  
Heat Shock ◽  
Stress Responses ◽  
Wild Type ◽  
Trna Modifications ◽  
Shock Response ◽  
Tightly Coupled

Although tRNA modifications have been well catalogued, the precise functions of many modifications and their roles in mediating gene expression are still being elucidated. Whereas tRNA modifications were long assumed to be constitutive, it is now apparent that the modification status of tRNAs changes in response to different environmental conditions. The URM1 pathway is required for thiolation of the cytoplasmic tRNAs tGluUUC, tGlnUUG, and tLysUUU in Saccharomyces cerevisiae. We demonstrate that URM1 pathway mutants have impaired translation, which results in increased basal activation of the Hsf1-mediated heat shock response; we also find that tRNA thiolation levels in wild-type cells decrease when cells are grown at elevated temperature. We show that defects in tRNA thiolation can be conditionally advantageous, conferring resistance to endoplasmic reticulum stress. URM1 pathway proteins are unstable and hence are more sensitive to changes in the translational capacity of cells, which is decreased in cells experiencing stresses. We propose a model in which a stress-induced decrease in translation results in decreased levels of URM1 pathway components, which results in decreased tRNA thiolation levels, which further serves to decrease translation. This mechanism ensures that tRNA thiolation and translation are tightly coupled and coregulated according to need.

A large internal deletion converts yeast LEU3 to a constitutive transcriptional activator

1989 ◽  
Vol 9 (9) ◽  
pp. 4056-4060
Author(s):  
P Friden ◽  
C Reynolds ◽  
P Schimmel
Keyword(s):  
Gene Expression ◽  
Saccharomyces Cerevisiae ◽  
Amino Acid ◽  
Transcriptional Activator ◽  
Large Block ◽  
Wild Type ◽  
Internal Deletion ◽  
Dense Cluster

LEU3 of Saccharomyces cerevisiae encodes an 886-amino-acid polypeptide that activates transcription of at least five genes by binding to an upstream decanucleotide sequence. This activation is dependent on the inducer alpha-isopropylmalate, the synthesis of which is repressed by leucine. We created a 285-amino-acid LEU3 derivative by removing a large block of internal sequences, including a dense cluster of acidic residues. This deletion protein bound to the decanucleotide sequence in vitro and activated gene expression in vivo. In contrast to wild-type LEU3, the truncated LEU3 protein was an effective transcriptional activator when alpha-isopropylmalate synthesis was repressed by leucine.

scholarly journals Saccharomyces cerevisiae Transcription Elongation Mutants Are Defective in PUR5 Induction in Response to Nucleotide Depletion

2000 ◽  
Vol 20 (20) ◽  
pp. 7427-7437 ◽  
Author(s):  
Randal J. Shaw ◽  
Daniel Reines
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Rna Polymerase Ii ◽  
De Novo ◽  
Transcription Elongation ◽  
Elongation Factor ◽  
Normal Growth ◽  
Luciferase Reporter ◽  
Wild Type ◽  
Luciferase Reporter Gene ◽  
Pol Ii

ABSTRACT IMP dehydrogenase (IMPDH) is the rate-limiting enzyme in the de novo synthesis of guanine nucleotides. It is a target of therapeutically useful drugs and is implicated in the regulation of cell growth rate. In the yeast Saccharomyces cerevisiae, mutations in components of the RNA polymerase II (Pol II) transcription elongation machinery confer increased sensitivity to a drug that inhibits IMPDH, 6-azauracil (6AU), by a mechanism that is poorly understood. This phenotype is thought to reflect the need for an optimally functioning transcription machinery under conditions of lowered intracellular GTP levels. Here we show that in response to the application of IMPDH inhibitors such as 6AU, wild-type yeast strains induce transcription of PUR5, one of four genes encoding IMPDH-related enzymes. Yeast elongation mutants sensitive to 6AU, such as those with a disrupted gene encoding elongation factor SII or those containing amino acid substitutions in Pol II subunits, are defective inPUR5 induction. The inability to fully inducePUR5 correlates with mutations that effect transcription elongation since 6AU-sensitive strains deleted for genes not related to transcription elongation are competent to induce PUR5. DNA encompassing the PUR5 promoter and 5′ untranslated region supports 6AU induction of a luciferase reporter gene in wild-type cells. Thus, yeast sense and respond to nucleotide depletion via a mechanism of transcriptional induction that restores nucleotides to levels required for normal growth. An optimally functioning elongation machinery is critical for this response.

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