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.

Codon replacement in the PGK1 gene of Saccharomyces cerevisiae: experimental approach to study the role of biased codon usage in gene expression

1987 ◽  
Vol 7 (8) ◽  
pp. 2914-2924
Author(s):  
A Hoekema ◽  
R A Kastelein ◽  
M Vasser ◽  
H A de Boer
Keyword(s):  
Gene Expression ◽  
Saccharomyces Cerevisiae ◽  
Steady State ◽  
Codon Usage ◽  
Experimental Approach ◽  
Mrna Translation ◽  
Yeast Cells ◽  
Expression Level ◽  
Start Codon ◽  
Mrna Levels

The coding sequences of genes in the yeast Saccharomyces cerevisiae show a preference for 25 of the 61 possible coding triplets. The degree of this biased codon usage in each gene is positively correlated to its expression level. Highly expressed genes use these 25 major codons almost exclusively. As an experimental approach to studying biased codon usage and its possible role in modulating gene expression, systematic codon replacements were carried out in the highly expressed PGK1 gene. The expression of phosphoglycerate kinase (PGK) was studied both on a high-copy-number plasmid and as a single copy gene integrated into the chromosome. Replacing an increasing number (up to 39% of all codons) of major codons with synonymous minor ones at the 5' end of the coding sequence caused a dramatic decline of the expression level. The PGK protein levels dropped 10-fold. The steady-state mRNA levels also declined, but to a lesser extent (threefold). Our data indicate that this reduction in mRNA levels was due to destabilization caused by impaired translation elongation at the minor codons. By preventing translation of the PGK mRNAs by the introduction of a stop codon 3' and adjacent to the start codon, the steady-state mRNA levels decreased dramatically. We conclude that efficient mRNA translation is required for maintaining mRNA stability in S. cerevisiae. These findings have important implications for the study of the expression of heterologous genes in yeast cells.

scholarly journals Elucidation of molecular mechanisms of flower form development in tree peony ( Paeonia suffriticosa ) through comparative transcriptome analysis of floral parts

2019 ◽  
Author(s):  
Jiuxing Lu ◽  
Yun Zheng ◽  
Haoning Wang ◽  
Zheng Wang ◽  
Yonghua Li ◽  
...  
Keyword(s):  
Woody Plants ◽  
Molecular Mechanisms ◽  
High Expression ◽  
Limited Information ◽  
Mads Box ◽  
Mads Box Genes ◽  
Tree Peony ◽  
Expression Levels ◽  
Key Genes ◽  
Flower Form

Abstract Background: Tree peony (Paeonia suffruticasa) is an economically, medicinally ornamentally important woody flowering woody plants in East Asia and is a common also ornamental shrub in Europe and North America. It is well known and prized for their beautiful flowers in many different forms. Samen petalody has been shown to be the most effective way to modify flower forms. However, there is limited information on the molecular mechanisms of stamen petalody and flower form formation in tree peony.Results: In this study, RNA sequencing was used to assemble and annotate the unigenes in the tree peony to identify the critical genes related to flower parts formation and verify the key genes in different flower forms of tree peony cultivar. A total of 76,007 high quality unigenes were assembled and 30,505 were successfully annotated. A total of 1,833 TFs were identified in our study, among them 16 MADS-box genes were found and characterized. Six key genes were selected to verity their functions in stamen petalody. AG and SEP showed high expression level in carpals and sepals separately both in stamen petalody group and non-stamen petalody groups. PI and AP3 showed high expression levels in inter-petals in stamen petalody groups than in staments in non-stamen petalody.Conclusion: Sixteen MADS-box genes were identified for the first time in tree peony through RNA-seq method. We identified six key genes based on their differential expression levels in different flower parts. These six key genes represented all categories in the ABCDE model to verify the functions in stamen petalody. PI and AP3 were verified to likely play important roles in regulating stamen petalody in tree peony. Our study has helped establish the flower development model in tree peony, identified key molecular mechanisms in the development of different flower forms, and provided valuable information in improving genetic diversity of tree peony and many other woody plants.

scholarly journals Codon usage is an important determinant of gene expression levels largely through its effects on transcription

2016 ◽  
Vol 113 (41) ◽  
pp. E6117-E6125 ◽  
Author(s):  
Zhipeng Zhou ◽  
Yunkun Dang ◽  
Mian Zhou ◽  
Lin Li ◽  
Chien-hung Yu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Codon Usage ◽  
Important Determinant ◽  
Mrna Translation ◽  
Mrna Levels ◽  
Protein Coding ◽  
Expression Levels ◽  
Highly Expressed Genes ◽  
The Impact ◽  
Gene Expression Levels

Codon usage biases are found in all eukaryotic and prokaryotic genomes, and preferred codons are more frequently used in highly expressed genes. The effects of codon usage on gene expression were previously thought to be mainly mediated by its impacts on translation. Here, we show that codon usage strongly correlates with both protein and mRNA levels genome-wide in the filamentous fungus Neurospora. Gene codon optimization also results in strong up-regulation of protein and RNA levels, suggesting that codon usage is an important determinant of gene expression. Surprisingly, we found that the impact of codon usage on gene expression results mainly from effects on transcription and is largely independent of mRNA translation and mRNA stability. Furthermore, we show that histone H3 lysine 9 trimethylation is one of the mechanisms responsible for the codon usage-mediated transcriptional silencing of some genes with nonoptimal codons. Together, these results uncovered an unexpected important role of codon usage in ORF sequences in determining transcription levels and suggest that codon biases are an adaptation of protein coding sequences to both transcription and translation machineries. Therefore, synonymous codons not only specify protein sequences and translation dynamics, but also help determine gene expression levels.

Identification of Aberrantly Regulated Genes through Comparison of Genome-Wide Expression Profiles and Karyotype in Hyperdiploid >50 Chromosomes Pediatric Acute Lymphoblastic Leukemia.

Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 420-420
Author(s):  
Christian Flotho ◽  
Susana C. Raimondi ◽  
James R. Downing
Keyword(s):  
Gene Expression ◽  
Copy Number ◽  
Expression Profiles ◽  
Chromosome 21 ◽  
Small Subset ◽  
Specific Gene ◽  
Expression Levels ◽  
Number Of Genes ◽  
The Mean ◽  
Gene Expression Levels

Abstract We have demonstrated that expression profiling of leukemic blasts can accurately identify the known prognostic subtypes of ALL, including T-ALL, E2A-PBX1, TEL-AML1, MLL rearrangements, BCR-ABL, and hyperdiploid >50 chromosomes (HD>50). Interestingly, almost 70% of the genes that defined HD>50 ALL localized to chromosome 21 or X. To further explore the relationship between gene expression and chromosome dosage, we compared the expression profiles obtained using the Affymetrix U133A&B microarrays of 17 HD>50 ALLs to 78 diploid or pseudodiploid ALLs. Our analysis demonstrated that the average expression level for all genes on a chromosome could be used to predict chromosome copy numbers. Specifically, the copy number for each chromosome calculated by gene expression profiling predicted the numerical chromosomal abnormalities detected by standard cytogenetics. For chromosomes that were trisomic in HD>50 ALL, the mean chromosome-specific gene expression level was increased approximately 1.5-fold compared to that observed in diploid or pseudodiploid ALL cases. Similarly, for chromosome 21 and X, the mean chromosome-specific gene expression levels were increased approximately 2-fold, consistent with a duplication of the active X chromosome and tetrasomy of chromosome 21, a finding verified by standard cytogenetics in >90% of the HD>50 cases. These finding indicate that the aberrant gene expression levels seen in HD>50 ALL primarily reflect gene dosages. Importantly, we did not observe any clustering of aberrantly expressed genes across the duplicated chromosomes, making regional gain or loss of genomic material unlikely. Paradoxically, however, a more detailed analysis revealed a small but statistically significant number of genes on the trisomic/tetrasomic chromosomes whose expression levels were markedly reduced when compared to that seen in diploid or pseudodiploid leukemic samples. Using the Statistical Analysis of Microarrays (SAM) algorithm we identified 20 genes whose expression was reduced >2-fold despite having an increase in copy number. Interestingly, included within this group are several known tumor suppressors, including AKAP12, which is specifically silenced by methylation in fos-transformed cells, and IGF2R and IGFBP7, negative regulators of insulin-like growth factor signaling. In addition to the silencing of a small subset of genes, we also identified 21 genes on these chromosomes whose expression levels were markedly higher (>3-fold) than would be predicted solely based on copy number. Although the mechanism responsible for their increased expression remains unknown, included in this group are four genes involved in signal transduction (IL3RA, IL13RA1, SNX9, and GASP) and a novel cytokine, C17, whose expression is normally limited to CD34+ hematopoietic progenitors. Taken together, these data suggest that aberrant growth in HD>50 ALL is in part driven by increased expression of a large number of genes secondary to chromosome duplications, coupled with a further enhanced expression of a limited number of growth promoting genes, and the specific silencing of a small subset of negative growth regulatory genes. Understanding the mechanisms responsible for the non-dosage related changes in gene expression should provide important insights into the pathology of HD>50 ALL.

Caspase-9: A Candidate Susceptibility Factor for Murine Alkylator-Induced Leukemia.

Blood ◽  
2009 ◽  
Vol 114 (22) ◽  
pp. 1273-1273
Author(s):  
Yedda Li ◽  
Patrick Cahan ◽  
Masayo Izumi ◽  
Timothy Graubert
Keyword(s):  
Gene Expression ◽  
Progenitor Cells ◽  
Copy Number ◽  
Genetic Factors ◽  
The Novel ◽  
Caspase 9 ◽  
Hematopoietic Stem ◽  
Exon 2 ◽  
Expression Levels ◽  
Induced Apoptosis

Abstract Abstract 1273 Poster Board I-295 Therapy-related acute myeloid leukemia (tAML) is caused by exposure to chemotherapies and radiotherapies and has a poor prognosis. To better understand the genetic factors involved in secondary leukemogenesis, we studied alkylator-induced leukemias in murine models. We performed genome-wide mRNA profiling and found that differential expression of apoptosis-related genes was correlated with strain-dependent differences in tAML susceptibility. To identify genetic variants associated with these gene expression changes, we examined copy number variants (CNVs), differences in the DNA copy number of genomic regions greater than one kilobase in length, across 20 different inbred murine genomes. Our studies indicate that CNVs are a major contributor to natural variation among inbred laboratory mouse strains, and our array-based expression data show that the presence of certain CNVs correlates with differences in apoptotic gene expression. One CNV identified on murine chromosome 4 is correlated with altered Caspase-9 (Casp9) expression levels in murine hematopoietic stem/progenitor cells. Casp9 is a gene downstream from extrinsic and intrinsic death-inducing signals crucial for the initiation of cellular apoptosis, and we propose that it may be an important factor that influences tAML susceptibility. Sequencing the CNV region confirmed in two tAML susceptible strains (DBA/2J and PL/J) the presence of a 1,705 bp CNV loss in Casp9 intron 6. In these strains, Casp9 expression is undetectable in flow sorted kit+/lineage- (KL) hematopoietic stem/progenitor cells as measured by microarray profiling, and confirmed in independent samples by qRT-PCR using assays targeting Casp9 exons 2-3 or exons 8-9. Full-length Casp9 cDNA clones could be isolated from mRNA libraries prepared from KL cells, but 35% of the transcripts isolated from DBA/2J and PL/J mice were a novel isoform lacking exon 2 that results in a frameshift and an early stop codon in exon 4. This premature translation termination codon is predicted to trigger nonsense-mediated mRNA decay, leading to the degradation of the novel isoform and thus preventing its translation. This mechanism may account for the low Casp9 expression levels in DBA/2J and PL/J mice. In addition, Casp9 cDNA sequencing also identified an unusually high SNP density in exon 2 for the full-length isoforms in these strains. At least two of the six SNPs result in the formation of putative exonic splice enhancers (ESE), sequences that enhance the splicing of the exon in which they reside. The presence of these novel ESEs could explain the excision of exon 2 and the creation of the novel Casp9 isoform in DBA/2J and PL/J mice. We hypothesize that cells with relatively low Casp9 expression would be more resistant to alkylator-induced apoptosis. Cells that fail to undergo apoptosis after genotoxic stress may be more likely to accumulate mutations and initiate leukemias. Preliminary data from flow cytometric apoptosis assays (by Annexin V staining) in flow sorted KL bone marrow cells after treatment with ENU, an alkylating agent, suggest that PL/J cells may be more resistant to ENU-induced apoptosis, compared to C57BL/6J cells with normal Casp9 expression (5.3±1.4% vs. 9.7±1.8% post-ENU AnnexinV+ cells, respectively). These results suggest that differences in Casp9 expression levels may play a role in influencing individual susceptibility to tAML, and that inherited genetic factors may explain the observed expression differences. Ultimately, our understanding of the role that genetics plays in determining susceptibility to secondary leukemias may allow us to define a process by which individuals who are more susceptible can be successfully identified and screened from potential treatments that are known to induce these cancers. Disclosures No relevant conflicts of interest to declare.

BCL6 Overexpression – Regulated By AhR/ARNT and Wild-Type MEF2B – Drives Expression of Germinal Center Markers MYBL1 and LMO2

Blood ◽  
2014 ◽  
Vol 124 (21) ◽  
pp. 865-865
Author(s):  
Hilmar Quentmeier ◽  
Jie Ding ◽  
Willy Dirks ◽  
Stefan Ehrentraut ◽  
Robert Geffers ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Line ◽  
Differentially Expressed Genes ◽  
Germinal Center ◽  
Copy Number ◽  
Specific Gene ◽  
Wild Type ◽  
Expression Levels ◽  
Numerical Aberrations ◽  
Bcl6 Expression

Abstract The evolution of tumor clones and the clonal architecture of tumors can be followed by the analysis of clone-specific mutations. The diffuse large B-cell lymphoma (DLBCL)-derived cell line U-2932 comprises two subclones (R1 and R2). Immunoglobulin gene hypermutation analysis showed that R1 and R2 represent subclones of the original tumor. Thus, the two U-2932 subclones seemed to be ideal to study the cellular consequences of clonal evolution. Both clones were derived from a presumptive mother clone with genomic BCL2 amplification, which acquired distinct sets of secondary rearrangements leading alternatively to the overexpression of BCL6 (R1) and MYC (R2) in the respective daughter clones. R2 carries t(8;14) a classical activating rearrangement of MYC in B-cells. R1 did not show any of the typical BCL6 translocations responsible for aberrant BCL6 expression. We applied a whole genome array to find out whether numerical aberrations might explain BCL6 expression in R1 and to investigate if subclone-specific gene expression might be attributable to numerical aberrations in general. More than 200 genes showed >10 fold expression differences between R1 and R2. Statistical analysis of results from copy number aberration and expression data analysis revealed that for 58/221 of the differentially expressed genes, numerical differences between the two subclones effectively predict differences in gene expression (sensitivity 0.64; specificity 0.94; accuracy 0.78). Thus, for a sizeable minority of genes numerical aberrations provided an explanation for the differences in gene expression between the U-2932 subclones. However, BCL6 was none of these genes. Thus, we searched for an alternative explanation for the R1-restricted overexpression of this germinal center oncogene. MEF2B point mutations occur in 11% of DLBCL contributing to the genesis of BCL6 positive lymphomas. The U-2932 subclones did not carry MEF2B mutations. Interestingly however, expression levels of MEF2B paralleled those of BCL6 in the U-2932 subclones. Knockdown experiments showed that wild-type MEF2B controlled BCL6 transcription. To test whether MEF2B and BCL6 showed coordinated expression in general, we analyzed the expression and the mutational status of these genes in 23 DLBCL cell lines. Confirming a positive correlation, independence of MEF2B and BCL6 expression levels could be rejected with a p-value according to Fisher´s exact test of 0.0001 against a level of significance of 0.05 (sensitivity 0.92, specificity 0.9, accuracy 0.91). The MEF2B promoter carries binding sites of the AhR/ARNT transcriptional complex. AhR inhibition and ARNT knockdown experiments with the U-2932 subclones revealed that MEF2B is a downstream target of AhR/ARNT signalling. A positive correlation between AhR and MEF2B expression levels could be shown for the majority of 23 DLBCL cell lines tested (sensitivity 0.61, specificity 1.0, accuracy 0.78). These results indicate that the AhR/ARNT-induced expression of wild-type MEF2B might be an independent regulator for BCL6 expression in DLBCL, besides canonical BCL6 translocations, BCL6 promoter hypermutation and MEF2B mutations. To find out the extent to which BCL6 contributed to the subclone-specific gene expression in the U-2932 subclones, we ectopically expressed BCL6 in subclone R2: 48/221 differentially expressed genes were affected. Interestingly, 28/48 genes were upregulated by BCL6 inducing the germinal center markers MYBL1 and LMO2, although BCL6 is believed to act as a transcriptional repressor. In summary, the two subclones of the DLBCL cell line U-2932 faithfully model tumor heterogeneity. Significant expression differences were shown for 221 genes, more than half of which were attributable to genomic copy number differences or to clone-specific expression of the signal transducer AhR and the oncogene BCL6. Moreover, we could show that BCL6 overexpression – regulated by AhR/ARNT and wild-type MEF2B – drives expression of subclone-specific germinal center markers MYBL1 and LMO2 in the DLBCL cell line U-2932. Disclosures No relevant conflicts of interest to declare.

Insights into Responses to Extreme Environmental Conditions in Humans from Studies on Saccharomyces cerevisiae

2015 ◽  
Vol 65 (6) ◽  
pp. 444
Author(s):  
Ramesh C. Meena ◽  
Amitabha Chakrabarti
Keyword(s):  
Gene Expression ◽  
Saccharomyces Cerevisiae ◽  
Stress Response ◽  
Gene Expression Data ◽  
Molecular Mechanisms ◽  
Multiple Stressors ◽  
Expression Data ◽  
Environmental Stress Response ◽  
Yeast Saccharomyces Cerevisiae ◽  
Pathways Analysis

<p>The versatility of the yeast experimental model has aided in innumerable ways in the understanding of fundamental cellular functions and has also contributed towards the elucidation of molecular mechanisms underlying several pathological conditions in humans. Genome-wide expression, functional, localization and interaction studies on the yeast Saccharomyces cerevisiae exposed to various stressors have made profound contributions towards the understanding of stress response pathways. Analysis of gene expression data from S. cerevisiae cells indicate that the expression of a common set of genes is altered upon exposure to all the stress conditions examined. This common response to multiple stressors is known as the Environmental stress response. Knowledge gained from studies on the yeast model has now become helpful in understanding stress response pathways and associated disease conditions in humans. Cross-species microarray experiments and analysis of data with ever improving computational methods has led to a better comparison of gene expression data between diverse organisms that include yeast and humans.</p>

scholarly journals Post-Therapy Measurable Residual Disease Monitoring in Peripheral Blood Using Overexpressed Genes in Childhood Acute Myeloid Leukemia

Blood ◽  
2018 ◽  
Vol 132 (Supplement 1) ◽  
pp. 1480-1480
Author(s):  
Anne-Sofie Skou ◽  
Kristian Juul-Dam ◽  
Maria Hansen ◽  
Anni Aggerholm ◽  
Birgitte Lausen ◽  
...  
Keyword(s):  
Gene Expression ◽  
Residual Disease ◽  
Disease Recurrence ◽  
High Expression ◽  
Specific Reference ◽  
Healthy Children ◽  
Expression Levels ◽  
Childhood Aml ◽  
Post Therapy

Abstract Background: Even though children with acute myeloid leukemia (AML) receive a very intensive chemotherapy and most achieve a complete remission (CR) ~30% of patients suffer from relapse. Post-treatment monitoring of measurable residual disease (MRD) can allow detection of a re-emerging leukemic clone several months before clinical relapse, and studies are in progress that aim at treating children with a molecular relapse. Specific genetic aberrations can be used for disease monitoring after therapy completion, but even though oncogenic fusion transcripts are more common in childhood than adult AML, NPM1 mutation is much rarer and consequently MRD measurements based on these aberrations are clinically applicable in only ~40% of childhood AML patients. Thus, a considerable fraction of patients do not have a suitable leukemia-specific molecular MRD target, but genes with an abnormally high expression in the leukemic cells might be candidate MRD targets in those patients. WT1 overexpression in childhood AML is well described, and if distinctly overexpressed at diagnosis, serves as a suitable MRD target in a large proportion of patients. Gene expression profiling has identified several other genes with an abnormally high expression in the leukemic blasts compared to normal hematopoietic cells. We investigated the applicability of 4 leukemia-associated genes (PRAME, GAGED2, ST18, SPAG6) as targets for early detection of relapse in peripheral blood (PB) in a Danish cohort of childhood AML patients, defined child-specific reference values of gene expression based on a large material of PB and BM samples from hematologically healthy children, and investigated gene expression levels under the presence of infection. Methods: We investigated the expression of 4 leukemia-associated genes (PRAME, GAGED2, ST18, SPAG6) in hematologically healthy children (n=53) and during suspected infection in febrile but otherwise healthy children (n=90). Gene expression in de novo AML at diagnosis (n=50) and during follow-up (n=20) was compared with child-specific reference values. We defined the 95th percentile of expression levels in hematologically healthy children as the upper limit of normal expression. RT-qPCR analyses were performed in compliance with EAC protocols and due to concordant qPCR efficiencies the ΔΔCq method for relative quantification could be applied. Results: At AML diagnosis, 64% had high expression of at least 1 of the 4 genes defined as >20-fold overexpression compared to hematologically healthy children. Nine out of 10 patients (90%) without established molecular MRD targets or high WT1 expression had high expression of at least 1 of the 4 genes. All 7 children with t(9;11) had GAGED2>1000-fold overexpressed. Gene expression was quantified in 99 PB samples (163 RT-qPCR analyses) during follow-up in 20 patients with distinct overexpression at diagnosis. All 10 patients with PB sampling performed within 100 days of disease recurrence displayed expression above normal by a median of 1.6 months (range 0.5-6 months) before hematological relapse. Patients with CBF-AML had a significantly longer interval between molecular relapse and hematological relapse than patients with non-CBF-AML (2.5 months (range 0.8-6 months) vs. 0.9 months (range 0.5-2 months), p=0.047). One patient with PB sampling performed only once at 119 days prior to hematological relapse did not show any molecular evidence of disease recurrence before hematological relapse. Only 1 of 96 (1%) post-therapy follow-up analyses performed in 9 patients in continuous CR for >5 years after diagnosis had expression above normal. In this case, a 9-year-old girl in continuous CR had an increase in ST18 expression, however the increase was transient and returned to normal level in the following samples. We found no clinically relevant influence of fever on gene expression levels, except for GAGED2, where 21% of febrile children had expression above normal. Conclusions: Sequential post-therapy monitoring of overexpressed genes in PB can predict relapse in childhood AML patients and facilitates molecular MRD monitoring in 90% of patients without a leukemia-specific target or WT1 overexpression. Frequent PB sampling (every 4-6 weeks) is necessary to detect an upcoming relapse, however in the post-treatment follow-up setting PB serves as an attractive and easily accessible source of preference compared to BM aspiration. Disclosures No relevant conflicts of interest to declare.

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