Using model organism Saccharomyces cerevisiae to evaluate the effects of ELF-MF and RF-EMF exposure on global gene expression

2012 ◽  
Vol 33 (7) ◽  
pp. 550-560 ◽  
Author(s):  
Guangdi Chen ◽  
Deqiang Lu ◽  
Huai Chiang ◽  
Dariusz Leszczynski ◽  
Zhengping Xu
Keyword(s):  
Gene Expression ◽  
Saccharomyces Cerevisiae ◽  
Model Organism ◽  
Global Gene Expression

scholarly journals Molecular Basis for Anaerobic Growth of Saccharomyces cerevisiae on Xylose, Investigated by Global Gene Expression and Metabolic Flux Analysis

2004 ◽  
Vol 70 (4) ◽  
pp. 2307-2317 ◽  
Author(s):  
Marco Sonderegger ◽  
Marie Jeppsson ◽  
Bärbel Hahn-Hägerdal ◽  
Uwe Sauer
Keyword(s):  
Gene Expression ◽  
Saccharomyces Cerevisiae ◽  
Metabolic Flux Analysis ◽  
Metabolic Flux ◽  
Global Gene Expression ◽  
Anaerobic Growth ◽  
Flux Analysis ◽  
Atp Production ◽  
Redox Imbalance ◽  
Chemostat Cultures

ABSTRACT Yeast xylose metabolism is generally considered to be restricted to respirative conditions because the two-step oxidoreductase reactions from xylose to xylulose impose an anaerobic redox imbalance. We have recently developed, however, a Saccharomyces cerevisiae strain that is at present the only known yeast capable of anaerobic growth on xylose alone. Using transcriptome analysis of aerobic chemostat cultures grown on xylose-glucose mixtures and xylose alone, as well as a combination of global gene expression and metabolic flux analysis of anaerobic chemostat cultures grown on xylose-glucose mixtures, we identified the distinguishing characteristics of this unique phenotype. First, the transcript levels and metabolic fluxes throughout central carbon metabolism were significantly higher than those in the parent strain, and they were most pronounced in the xylose-specific, pentose phosphate, and glycerol pathways. Second, differential expression of many genes involved in redox metabolism indicates that increased cytosolic NADPH formation and NADH consumption enable a higher flux through the two-step oxidoreductase reaction of xylose to xylulose in the mutant. Redox balancing is apparently still a problem in this strain, since anaerobic growth on xylose could be improved further by providing acetoin as an external NADH sink. This improved growth was accompanied by an increased ATP production rate and was not accompanied by higher rates of xylose uptake or cytosolic NADPH production. We concluded that anaerobic growth of the yeast on xylose is ultimately limited by the rate of ATP production and not by the redox balance per se, although the redox imbalance, in turn, limits ATP production.

scholarly journals Intestinal DCs global gene expression dynamics affected by recombinant baker’s yeasts saccharomyces cerevisiae

2019 ◽  
Author(s):  
Baoquan Han ◽  
Tingting Zhang ◽  
Xinyi Li ◽  
Rui Zhao ◽  
Wei Ge ◽  
...  
Keyword(s):  
Gene Expression ◽  
Saccharomyces Cerevisiae ◽  
Inflammatory Response ◽  
Budding Yeast ◽  
Global Gene Expression ◽  
Transcriptome Profile ◽  
Delivery Vehicle ◽  
Gene Delivery Vehicle ◽  
Gene Expression Dynamics

Abstract Background The baker’s yeast, saccharomyces cerevisiae, has been widely used throughout our daily life in diverse aspects for thousands of years. The saccharomyces cerevisiae was found to specifically target the dendritic cells (DCs) in mammalian with a manner of antigen-receptor interaction as described previously. It is necessary to investigate the effect of the baker’s yeasts on global gene expression dynamics of intestinal DCs and explore the possibilities of using baker’s yeast as gene delivery vehicle to modulate animal’s immune functions Results with a murine oral delivery model in vivo, we confirmed the feasibility of using budding yeast as gene delivery vehicle to the intestinal DCs using the Western blots. We then examined the transcriptome profile of the mouse intestinal DCs upon yeast stimulus. The enrichment analysis of unique transcripts indicated the beneficial role of yeast in modulating the DC-mediated adaptive immunity. Compared with previous study, we also found that a large fraction of the regulated genes is coincident with the response induced by other fungus, suggesting that the budding yeast induces a similar tailored unique genetic re-programming of DCs. Another analysis of transcriptome profile indicated that expression of β-catenin gene significantly changes DCs gene expression related to inflammatory response and cell adhesion. Conclusions Here, we defined the role of budding yeast on global gene expression of intestinal DCs, and confirmed the important role of β-catenin gene on the DCs-related inflammatory response, which provides a framework for the development of mucosa yeast-based DNA vaccine.

scholarly journals Acute condensin depletion causes genome decompaction without altering the level of global gene expression in Saccharomyces cerevisiae

2017 ◽  
Author(s):  
Matthew Robert Paul ◽  
Tovah Elise Markowitz ◽  
Andreas Hochwagen ◽  
Sevinç Ercan
Keyword(s):  
Gene Expression ◽  
Saccharomyces Cerevisiae ◽  
Genome Organization ◽  
Large Scale ◽  
Global Gene Expression ◽  
Higher Order ◽  
Gene Clustering ◽  
Global Changes ◽  
Chromatin Compaction ◽  
And Function

AbstractCondensins are broadly conserved chromosome organizers that function in chromatin compaction and transcriptional regulation, but to what extent these two functions are linked has remained unclear. Here, we analyzed the effect of condensin inactivation on genome compaction and global gene expression in the yeast Saccharomyces cerevisiae. Spike-in-controlled 3C-seq analysis revealed that acute condensin inactivation leads to a global decrease in close-range chromosomal interactions as well as more specific losses of homotypic tRNA gene clustering. In addition, a condensin-rich topologically associated domain between the ribosomal DNA and the centromere on chromosome XII is lost upon condensin inactivation. Unexpectedly, these large-scale changes in chromosome architecture are not associated with global changes in transcript levels as determined by spike-in-controlled mRNA-seq analysis. Our data suggest that the global transcriptional program of S. cerevisiae is resistant to condensin inactivation and the associated profound changes in genome organization.Significance StatementGene expression occurs in the context of higher-order chromatin organization, which helps compact the genome within the spatial constraints of the nucleus. To what extent higher-order chromatin compaction affects gene expression remains unknown. Here, we show that gene expression and genome compaction can be uncoupled in the single-celled model eukaryote Saccharomyces cerevisiae. Inactivation of the conserved condensin complex, which also organizes the human genome, leads to broad genome decompaction in this organism. Unexpectedly, this reorganization has no immediate effect on the transcriptome. These findings indicate that the global gene expression program is robust to large-scale changes in genome architecture in yeast, shedding important new light on the evolution and function of genome organization in gene regulation.

scholarly journals Condensin Depletion Causes Genome Decompaction Without Altering the Level of Global Gene Expression in Saccharomyces cerevisiae

Genetics ◽  
2018 ◽  
Vol 210 (1) ◽  
pp. 331-344 ◽  
Author(s):  
Matthew Robert Paul ◽  
Tovah Elise Markowitz ◽  
Andreas Hochwagen ◽  
Sevinç Ercan
Keyword(s):  
Gene Expression ◽  
Saccharomyces Cerevisiae ◽  
Global Gene Expression

scholarly journals Pervasive and Dynamic Transcription Initiation in Saccharomyces cerevisiae

2018 ◽  
Author(s):  
Zhaolian Lu ◽  
Zhenguo Lin
Keyword(s):  
Gene Expression ◽  
Saccharomyces Cerevisiae ◽  
Transcription Initiation ◽  
Core Promoter ◽  
Model Organism ◽  
Start Codon ◽  
Yeast Genome ◽  
Core Promoters ◽  
Nucleotide Resolution ◽  
Yeast Genes

AbstractTranscription initiation is finely regulated to ensure the proper expression and function of these genes. The regulated transcription initiation in response to various environmental cues in the model organism Saccharomyces cerevisiae has not been systematically investigated. In this study, we generated quantitative maps of transcription start site (TSS) at a single-nucleotide resolution for S. cerevisiae grown in nine different conditions using no-amplification non-tagging Cap analysis of gene expression (nAnT-iCAGE) sequencing. Based on 337 million uniquely mapped CAGE tags, we mapped ~1 million well-supported TSSs, suggesting highly pervasive transcription initiation in the compact genome of yeast. The comprehensive TSS maps allowed us to identify core promoters for ~96% verified protein-coding genes and to revise the predicted translation start codon for 183 genes. We found that 56% of yeast genes have at least two core promoters and alternative usage of different core promoters in a gene is widespread in response to changing environments. More importantly, most core promoter shifts are coupled with differential gene expression, indicating that core promoter shift might play an important role in controlling transcriptional activity of yeast genes. Based on their dynamic activities, we divided yeast core promoters as constitutive core promoters (55%) and inducible core promoters (45%). The two classes of core promoters exhibit distinctive patterns in transcriptional abundance, chromatin structure, promoter shape, and sequence context. In summary, the quantitative TSS maps generated by this study improved the annotation of yeast genome, and revealed a highly pervasive and dynamic nature of transcription initiation in yeast.

scholarly journals NORF5/HUG1 Is a Component of theMEC1-Mediated Checkpoint Response to DNA Damage and Replication Arrest in Saccharomyces cerevisiae

1999 ◽  
Vol 19 (10) ◽  
pp. 7041-7049 ◽  
Author(s):  
Munira A. Basrai ◽  
Victor E. Velculescu ◽  
Kenneth W. Kinzler ◽  
Philip Hieter
Keyword(s):  
Gene Expression ◽  
Saccharomyces Cerevisiae ◽  
Dna Damage ◽  
Global Gene Expression ◽  
Open Reading Frames ◽  
Ataxia Telangiectasia Mutated ◽  
Checkpoint Response ◽  
Replication Arrest ◽  
Checkpoint Pathway ◽  
Radiation Induced

ABSTRACT Analysis of global gene expression in Saccharomyces cerevisiae by the serial analysis of gene expression technique has permitted the identification of at least 302 previously unidentified transcripts from nonannotated open reading frames (NORFs). Transcription of one of these, NORF5/HUG1 (hydroxyurea and UV and gamma radiation induced), is induced by DNA damage, and this induction requires MEC1, a homolog of the ataxia telangiectasia mutated (ATM) gene. DNA damage-specific induction of HUG1, which is independent of the cell cycle stage, is due to the alleviation of repression by the Crt1p-Ssn6p-Tup1p complex. Overexpression of HUG1 is lethal in combination with a mec1 mutation in the presence of DNA damage or replication arrest, whereas a deletion of HUG1 rescues the lethality due to a mec1 null allele. HUG1 is the first example of a NORF with important biological functional properties and defines a novel component of the MEC1checkpoint pathway.

scholarly journals Extended Archaeal Histone-Based Chromatin Structure Regulates Global Gene Expression in Thermococcus kodakarensis

2021 ◽  
Vol 12 ◽  
Author(s):  
Travis J. Sanders ◽  
Fahad Ullah ◽  
Alexandra M. Gehring ◽  
Brett W. Burkhart ◽  
Robert L. Vickerman ◽  
...  
Keyword(s):  
Gene Expression ◽  
Chromatin Structure ◽  
Regulation Of Gene Expression ◽  
Model Organism ◽  
Global Gene Expression ◽  
Single Amino Acid ◽  
Post Translational Modification ◽  
Histone Proteins ◽  
Thermococcus Kodakarensis ◽  
Archaeal Histone

Histone proteins compact and organize DNA resulting in a dynamic chromatin architecture impacting DNA accessibility and ultimately gene expression. Eukaryotic chromatin landscapes are structured through histone protein variants, epigenetic marks, the activities of chromatin-remodeling complexes, and post-translational modification of histone proteins. In most Archaea, histone-based chromatin structure is dominated by the helical polymerization of histone proteins wrapping DNA into a repetitive and closely gyred configuration. The formation of the archaeal-histone chromatin-superhelix is a regulatory force of adaptive gene expression and is likely critical for regulation of gene expression in all histone-encoding Archaea. Single amino acid substitutions in archaeal histones that block formation of tightly packed chromatin structures have profound effects on cellular fitness, but the underlying gene expression changes resultant from an altered chromatin landscape have not been resolved. Using the model organism Thermococcus kodakarensis, we genetically alter the chromatin landscape and quantify the resultant changes in gene expression, including unanticipated and significant impacts on provirus transcription. Global transcriptome changes resultant from varying chromatin landscapes reveal the regulatory importance of higher-order histone-based chromatin architectures in regulating archaeal gene expression.

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