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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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PPPI networks generated from the induced genes (A) and the repressed genes (B).Green nodes indicate proteins encoded by the induced genes, while red nodes represent proteins encoded by the repressed genes. Red lines indicate the interactions among proteins encoded by differentially expressed genes.
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pone-0104428-g004: PPPI networks generated from the induced genes (A) and the repressed genes (B).Green nodes indicate proteins encoded by the induced genes, while red nodes represent proteins encoded by the repressed genes. Red lines indicate the interactions among proteins encoded by differentially expressed genes.

Mentions: To understand how LPS stimulation affects biological processes in S. cerevisiae BY4742, two PPPI networks were retrieved from SGD using the transcriptome data: one associated to the 460 induced genes (367 genes were picked up) and the other associated to the 135 repressed genes (108 genes were picked up) (Fig. 4). The induced genes-associated network contains 2,651 nodes and 5,107 connectors (Fig. 4A), and the repressed genes-associated network contains 1,653 nodes and 3,660 connectors (Fig. 4B). Nodes represent proteins encoded by the corresponding genes in the network, and connectors are introduced to represent interactions among the proteins encoded by the differentially expressed genes. Clusters present in both PPPI networks were identified and retrieved using MCODE, and subjected to GO analysis; there were 8 clusters extracted from the induced genes-associated network (Table S1) and 11 clusters obtained from the repressed genes-associated network (Table S2). Moreover, there were 23 biological processes associated to more than 10 clusters (Table 1), including response to stress, signal transduction, chromosome, transcription, ribosome biogenesis, enzyme regulator activity and cell cycle. This suggests that LPS stimulation caused a series of responses in different biological processes from chromosome segregation to protein modification process. To identify nodes and the consequent biological processes that have a relevant important position in the overall network architecture, the centrality analysis of both networks and their clusters were performed using CentiScaPe; there were 26 and 27 bottlenecks, the key nodes with high values of nodes degree and betweeness, identified from the induced and repressed genes-associated networks, respectively (Table S3).


Response of Saccharomyces cerevisiae to the stimulation of lipopolysaccharide.

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

PPPI networks generated from the induced genes (A) and the repressed genes (B).Green nodes indicate proteins encoded by the induced genes, while red nodes represent proteins encoded by the repressed genes. Red lines indicate the interactions among proteins encoded by differentially expressed genes.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0104428-g004: PPPI networks generated from the induced genes (A) and the repressed genes (B).Green nodes indicate proteins encoded by the induced genes, while red nodes represent proteins encoded by the repressed genes. Red lines indicate the interactions among proteins encoded by differentially expressed genes.
Mentions: To understand how LPS stimulation affects biological processes in S. cerevisiae BY4742, two PPPI networks were retrieved from SGD using the transcriptome data: one associated to the 460 induced genes (367 genes were picked up) and the other associated to the 135 repressed genes (108 genes were picked up) (Fig. 4). The induced genes-associated network contains 2,651 nodes and 5,107 connectors (Fig. 4A), and the repressed genes-associated network contains 1,653 nodes and 3,660 connectors (Fig. 4B). Nodes represent proteins encoded by the corresponding genes in the network, and connectors are introduced to represent interactions among the proteins encoded by the differentially expressed genes. Clusters present in both PPPI networks were identified and retrieved using MCODE, and subjected to GO analysis; there were 8 clusters extracted from the induced genes-associated network (Table S1) and 11 clusters obtained from the repressed genes-associated network (Table S2). Moreover, there were 23 biological processes associated to more than 10 clusters (Table 1), including response to stress, signal transduction, chromosome, transcription, ribosome biogenesis, enzyme regulator activity and cell cycle. This suggests that LPS stimulation caused a series of responses in different biological processes from chromosome segregation to protein modification process. To identify nodes and the consequent biological processes that have a relevant important position in the overall network architecture, the centrality analysis of both networks and their clusters were performed using CentiScaPe; there were 26 and 27 bottlenecks, the key nodes with high values of nodes degree and betweeness, identified from the induced and repressed genes-associated networks, respectively (Table S3).

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