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Response of Saccharomyces cerevisiae to the stimulation of lipopolysaccharide.

Shen L, Li Y, Jiang L, Wang X - PLoS ONE (2014)

Bottom Line: In this study, we found that lipopolysaccharide-treated S. cerevisiae cells could be stained by methylene blue, but did not die.Significantly regulated genes (460 up-regulated genes and 135 down-regulated genes) in lipopolysaccharide-treated S. cerevisiae cells were analyzed on Gene Ontology, and used to establish physical protein-protein interaction network and protein phosphorylation network.Based on these analyses, most of the regulated genes in lipopolysaccharide-treated S. cerevisiae cells were related to cell wall, membrane, peroxisome and mitochondrion.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China; School of Biotechnology, Jiangnan University, Wuxi, China.

ABSTRACT
Lipopolysaccharide, known as endotoxin, can stimulate potent host immune responses through the complex of Toll-like-receptor 4 and myeloid differentiation protein 2; but its influence on Saccharomyces cerevisiae, a model organism for studying eukaryotes, is not clear. In this study, we found that lipopolysaccharide-treated S. cerevisiae cells could be stained by methylene blue, but did not die. Transcriptional profiling of the lipopolysaccharide-treated S. cerevisiae cells showed that 5745 genes were modulated: 2491 genes up-regulated and 3254 genes down-regulated. Significantly regulated genes (460 up-regulated genes and 135 down-regulated genes) in lipopolysaccharide-treated S. cerevisiae cells were analyzed on Gene Ontology, and used to establish physical protein-protein interaction network and protein phosphorylation network. Based on these analyses, most of the regulated genes in lipopolysaccharide-treated S. cerevisiae cells were related to cell wall, membrane, peroxisome and mitochondrion. Further experiments demonstrated that lipopolysaccharide stimulation caused the exposure of phosphatidylserine and the increase of mitochondrial membrane potential in S. cerevisiae cells, but levels of intracellular reactive oxygen species and metacaspase activation were not increased. This study demonstrated that lipopolysaccharide stimulation causes significant changes in S. cerevisiae cells, and the results would contribute to understand the response of eukaryotic cells to lipopolysaccharide stimulation.

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Related in: MedlinePlus

Protein phosphorylation network generated from the induced genes and the repressed genes, and its MCODE and CentiScaPe analyses.Green nodes indicate proteins encoded by the induced genes, while red nodes represent proteins encoded by the repressed genes. Deep colored nodes are associated to genes with /Log2R/ ≥1.0 while light colored nodes are associated to genes with 0.5≤ /Log2R/ ≤1.0. Yellow nodes indicate Atg1p and Tpk1p in Cluster1 and Cluster 2, respectively. Corresponding centrality values in betweeness and nodes degree were sub graphed according to the importance of selected nodes or bottlenecks. Edges represent interactions between proteins or nodes.
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pone-0104428-g005: Protein phosphorylation network generated from the induced genes and the repressed genes, and its MCODE and CentiScaPe analyses.Green nodes indicate proteins encoded by the induced genes, while red nodes represent proteins encoded by the repressed genes. Deep colored nodes are associated to genes with /Log2R/ ≥1.0 while light colored nodes are associated to genes with 0.5≤ /Log2R/ ≤1.0. Yellow nodes indicate Atg1p and Tpk1p in Cluster1 and Cluster 2, respectively. Corresponding centrality values in betweeness and nodes degree were sub graphed according to the importance of selected nodes or bottlenecks. Edges represent interactions between proteins or nodes.

Mentions: Since there are over 4,000 phosphorylation events involved in yeast [37], changes in protein phosphorylation (PP) network of S. cerevisiae BY4742 cells after exposure to LPS might provide new information on the mechanism. Therefore, the PP network was analyzed using more gene expression data (/Log2R/ ≥0.5) and cluster analysis was performed as before (Fig. 5). Two clusters (Cluster 1 and Cluster 2) were sub graphed, and their central bottlenecks were ATG1 and TPK1, respectively (Fig. 5). ATG1 encodes a kinase required for vesicle formation in autophagy and the cytoplasm-to-vacuole targeting pathway, while TPK1 encodes the catalytic subunit of the cAMP-dependent protein kinase that promotes vegetative growth in response to nutrients via the Ras-cAMP signaling pathway (SGD, Table S3). These two protein phosphorylation signaling pathways provide possible activated points during the cell exposure to LPS.


Response of Saccharomyces cerevisiae to the stimulation of lipopolysaccharide.

Shen L, Li Y, Jiang L, Wang X - PLoS ONE (2014)

Protein phosphorylation network generated from the induced genes and the repressed genes, and its MCODE and CentiScaPe analyses.Green nodes indicate proteins encoded by the induced genes, while red nodes represent proteins encoded by the repressed genes. Deep colored nodes are associated to genes with /Log2R/ ≥1.0 while light colored nodes are associated to genes with 0.5≤ /Log2R/ ≤1.0. Yellow nodes indicate Atg1p and Tpk1p in Cluster1 and Cluster 2, respectively. Corresponding centrality values in betweeness and nodes degree were sub graphed according to the importance of selected nodes or bottlenecks. Edges represent interactions between proteins or nodes.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4126697&req=5

pone-0104428-g005: Protein phosphorylation network generated from the induced genes and the repressed genes, and its MCODE and CentiScaPe analyses.Green nodes indicate proteins encoded by the induced genes, while red nodes represent proteins encoded by the repressed genes. Deep colored nodes are associated to genes with /Log2R/ ≥1.0 while light colored nodes are associated to genes with 0.5≤ /Log2R/ ≤1.0. Yellow nodes indicate Atg1p and Tpk1p in Cluster1 and Cluster 2, respectively. Corresponding centrality values in betweeness and nodes degree were sub graphed according to the importance of selected nodes or bottlenecks. Edges represent interactions between proteins or nodes.
Mentions: Since there are over 4,000 phosphorylation events involved in yeast [37], changes in protein phosphorylation (PP) network of S. cerevisiae BY4742 cells after exposure to LPS might provide new information on the mechanism. Therefore, the PP network was analyzed using more gene expression data (/Log2R/ ≥0.5) and cluster analysis was performed as before (Fig. 5). Two clusters (Cluster 1 and Cluster 2) were sub graphed, and their central bottlenecks were ATG1 and TPK1, respectively (Fig. 5). ATG1 encodes a kinase required for vesicle formation in autophagy and the cytoplasm-to-vacuole targeting pathway, while TPK1 encodes the catalytic subunit of the cAMP-dependent protein kinase that promotes vegetative growth in response to nutrients via the Ras-cAMP signaling pathway (SGD, Table S3). These two protein phosphorylation signaling pathways provide possible activated points during the cell exposure to LPS.

Bottom Line: In this study, we found that lipopolysaccharide-treated S. cerevisiae cells could be stained by methylene blue, but did not die.Significantly regulated genes (460 up-regulated genes and 135 down-regulated genes) in lipopolysaccharide-treated S. cerevisiae cells were analyzed on Gene Ontology, and used to establish physical protein-protein interaction network and protein phosphorylation network.Based on these analyses, most of the regulated genes in lipopolysaccharide-treated S. cerevisiae cells were related to cell wall, membrane, peroxisome and mitochondrion.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China; School of Biotechnology, Jiangnan University, Wuxi, China.

ABSTRACT
Lipopolysaccharide, known as endotoxin, can stimulate potent host immune responses through the complex of Toll-like-receptor 4 and myeloid differentiation protein 2; but its influence on Saccharomyces cerevisiae, a model organism for studying eukaryotes, is not clear. In this study, we found that lipopolysaccharide-treated S. cerevisiae cells could be stained by methylene blue, but did not die. Transcriptional profiling of the lipopolysaccharide-treated S. cerevisiae cells showed that 5745 genes were modulated: 2491 genes up-regulated and 3254 genes down-regulated. Significantly regulated genes (460 up-regulated genes and 135 down-regulated genes) in lipopolysaccharide-treated S. cerevisiae cells were analyzed on Gene Ontology, and used to establish physical protein-protein interaction network and protein phosphorylation network. Based on these analyses, most of the regulated genes in lipopolysaccharide-treated S. cerevisiae cells were related to cell wall, membrane, peroxisome and mitochondrion. Further experiments demonstrated that lipopolysaccharide stimulation caused the exposure of phosphatidylserine and the increase of mitochondrial membrane potential in S. cerevisiae cells, but levels of intracellular reactive oxygen species and metacaspase activation were not increased. This study demonstrated that lipopolysaccharide stimulation causes significant changes in S. cerevisiae cells, and the results would contribute to understand the response of eukaryotic cells to lipopolysaccharide stimulation.

Show MeSH
Related in: MedlinePlus