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Transcriptome analysis of Enterococcus faecalis in response to alkaline stress.

Ran S, Liu B, Jiang W, Sun Z, Liang J - Front Microbiol (2015)

Bottom Line: The transcriptome sequencing results revealed that 613 genes were differentially expressed (DEGs) for E. faecalis grown in pH 10 medium; 211 genes were found to be differentially up-regulated and 402 genes differentially down-regulated.The results presented here reveal that cultivation of E. faecalis in alkaline stress has a profound impact on its transcriptome.The observed regulation of genes and pathways revealed that E. faecalis reduced its carbohydrate and amino acid metabolism and increased nucleotide synthesis to adapt and grow in alkaline stress.

View Article: PubMed Central - PubMed

Affiliation: Shanghai Key Laboratory of Stomatology, Department of Endodontics and Operative Dentistry, School of Medicine, Ninth People's Hospital, Shanghai Jiao Tong University Shanghai, China.

ABSTRACT
Enterococcus faecalis is the most commonly isolated species from endodontic failure root canals; its persistence in treated root canals has been attributed to its ability to resist high pH stress. The goal of this study was to characterize the E. faecalis transcriptome and to identify candidate genes for response and resistance to alkaline stress using Illumina HiSeq 2000 sequencing. We found that E. faecalis could survive and form biofilms in a pH 10 environment and that alkaline stress had a great impact on the transcription of many genes in the E. faecalis genome. The transcriptome sequencing results revealed that 613 genes were differentially expressed (DEGs) for E. faecalis grown in pH 10 medium; 211 genes were found to be differentially up-regulated and 402 genes differentially down-regulated. Many of the down-regulated genes found are involved in cell energy production and metabolism and carbohydrate and amino acid metabolism, and the up-regulated genes are mostly related to nucleotide transport and metabolism. The results presented here reveal that cultivation of E. faecalis in alkaline stress has a profound impact on its transcriptome. The observed regulation of genes and pathways revealed that E. faecalis reduced its carbohydrate and amino acid metabolism and increased nucleotide synthesis to adapt and grow in alkaline stress. A number of the regulated genes may be useful candidates for the development of new therapeutic approaches for the treatment of E. faecalis infections.

No MeSH data available.


Related in: MedlinePlus

Differentially expressed genes of E. faecalis cultured in pH 10 media. Red dots indicate differentially expressed genes. Black-colored dots were not considered as significantly differentially expressed. In the figure of the MA plot, the X-axis shows the average count of reads per million reads based on a log2 scale, and the Y-axis shows the fold-change values between the control and alkaline group based on a log2 scale. In the figure of a volcano plot, the X-axis shows the fold-change values between the control and alkaline groups based on a log2 scale, and the Y-axis shows the FDR value of differentially expressed genes based on a -log10 scale.
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Figure 4: Differentially expressed genes of E. faecalis cultured in pH 10 media. Red dots indicate differentially expressed genes. Black-colored dots were not considered as significantly differentially expressed. In the figure of the MA plot, the X-axis shows the average count of reads per million reads based on a log2 scale, and the Y-axis shows the fold-change values between the control and alkaline group based on a log2 scale. In the figure of a volcano plot, the X-axis shows the fold-change values between the control and alkaline groups based on a log2 scale, and the Y-axis shows the FDR value of differentially expressed genes based on a -log10 scale.

Mentions: Primary sequence analysis and annotations of all of the unigenes provided us with a great deal of useful information to understand the transcriptome and to further define the DEGs that are induced by alkaline stress. The transcriptome sequencing results revealed 613 genes that were differentially expressed (DEGs) for E. faecalis grown in pH 10 medium (Figure 4). Among these DEGs, 211 genes were found to be differentially up-regulated genes (DUGs), and 402 genes were identified as differentially down-regulated genes (DDGs). The data, including the gene ID, gene length, FRKM in the control and pH 10 groups, log2FC1 (pH 10/Control), FDR, up- or down-regulation (pH 10/control) and annotation of all of the DEGs are provided in Table S3.


Transcriptome analysis of Enterococcus faecalis in response to alkaline stress.

Ran S, Liu B, Jiang W, Sun Z, Liang J - Front Microbiol (2015)

Differentially expressed genes of E. faecalis cultured in pH 10 media. Red dots indicate differentially expressed genes. Black-colored dots were not considered as significantly differentially expressed. In the figure of the MA plot, the X-axis shows the average count of reads per million reads based on a log2 scale, and the Y-axis shows the fold-change values between the control and alkaline group based on a log2 scale. In the figure of a volcano plot, the X-axis shows the fold-change values between the control and alkaline groups based on a log2 scale, and the Y-axis shows the FDR value of differentially expressed genes based on a -log10 scale.
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Related In: Results  -  Collection

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Figure 4: Differentially expressed genes of E. faecalis cultured in pH 10 media. Red dots indicate differentially expressed genes. Black-colored dots were not considered as significantly differentially expressed. In the figure of the MA plot, the X-axis shows the average count of reads per million reads based on a log2 scale, and the Y-axis shows the fold-change values between the control and alkaline group based on a log2 scale. In the figure of a volcano plot, the X-axis shows the fold-change values between the control and alkaline groups based on a log2 scale, and the Y-axis shows the FDR value of differentially expressed genes based on a -log10 scale.
Mentions: Primary sequence analysis and annotations of all of the unigenes provided us with a great deal of useful information to understand the transcriptome and to further define the DEGs that are induced by alkaline stress. The transcriptome sequencing results revealed 613 genes that were differentially expressed (DEGs) for E. faecalis grown in pH 10 medium (Figure 4). Among these DEGs, 211 genes were found to be differentially up-regulated genes (DUGs), and 402 genes were identified as differentially down-regulated genes (DDGs). The data, including the gene ID, gene length, FRKM in the control and pH 10 groups, log2FC1 (pH 10/Control), FDR, up- or down-regulation (pH 10/control) and annotation of all of the DEGs are provided in Table S3.

Bottom Line: The transcriptome sequencing results revealed that 613 genes were differentially expressed (DEGs) for E. faecalis grown in pH 10 medium; 211 genes were found to be differentially up-regulated and 402 genes differentially down-regulated.The results presented here reveal that cultivation of E. faecalis in alkaline stress has a profound impact on its transcriptome.The observed regulation of genes and pathways revealed that E. faecalis reduced its carbohydrate and amino acid metabolism and increased nucleotide synthesis to adapt and grow in alkaline stress.

View Article: PubMed Central - PubMed

Affiliation: Shanghai Key Laboratory of Stomatology, Department of Endodontics and Operative Dentistry, School of Medicine, Ninth People's Hospital, Shanghai Jiao Tong University Shanghai, China.

ABSTRACT
Enterococcus faecalis is the most commonly isolated species from endodontic failure root canals; its persistence in treated root canals has been attributed to its ability to resist high pH stress. The goal of this study was to characterize the E. faecalis transcriptome and to identify candidate genes for response and resistance to alkaline stress using Illumina HiSeq 2000 sequencing. We found that E. faecalis could survive and form biofilms in a pH 10 environment and that alkaline stress had a great impact on the transcription of many genes in the E. faecalis genome. The transcriptome sequencing results revealed that 613 genes were differentially expressed (DEGs) for E. faecalis grown in pH 10 medium; 211 genes were found to be differentially up-regulated and 402 genes differentially down-regulated. Many of the down-regulated genes found are involved in cell energy production and metabolism and carbohydrate and amino acid metabolism, and the up-regulated genes are mostly related to nucleotide transport and metabolism. The results presented here reveal that cultivation of E. faecalis in alkaline stress has a profound impact on its transcriptome. The observed regulation of genes and pathways revealed that E. faecalis reduced its carbohydrate and amino acid metabolism and increased nucleotide synthesis to adapt and grow in alkaline stress. A number of the regulated genes may be useful candidates for the development of new therapeutic approaches for the treatment of E. faecalis infections.

No MeSH data available.


Related in: MedlinePlus