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Functional analysis of the molecular interactions of TATA box-containing genes and essential genes.

Bae SH, Han HW, Moon J - PLoS ONE (2015)

Bottom Line: In a previous study, we demonstrated that there are striking differences among four gene sets defined by the presence of TATA box (TATA-containing) and essentiality (TATA-less) with respect to number of associated transcription factors, amino acid usage, and functional annotation.As expected, genes in TEPs and EEPs exhibited opposite results in terms of functional category, transcriptional regulation, codon adaptation index, and network properties, suggesting the possibility that the bipolar patterns in these pathways also contribute to the regulation of the stress response and to cell survival.Our findings provide the novel insight that significant enrichment of TATA-binding or TATA-less genes defines pathways as stress-responsive or growth-related.

View Article: PubMed Central - PubMed

Affiliation: College of Life Science, Department of Bioengineering, CHA University, Seoul, Korea; General Research Institute, Gangnam CHA General Hospital, Seoul, Korea.

ABSTRACT
Genes can be divided into TATA-containing genes and TATA-less genes according to the presence of TATA box elements at promoter regions. TATA-containing genes tend to be stress-responsive, whereas many TATA-less genes are known to be related to cell growth or "housekeeping" functions. In a previous study, we demonstrated that there are striking differences among four gene sets defined by the presence of TATA box (TATA-containing) and essentiality (TATA-less) with respect to number of associated transcription factors, amino acid usage, and functional annotation. Extending this research in yeast, we identified KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways that are statistically enriched in TATA-containing or TATA-less genes and evaluated the possibility that the enriched pathways are related to stress or growth as reflected by the individual functions of the genes involved. According to their enrichment for either of these two gene sets, we sorted KEGG pathways into TATA-containing-gene-enriched pathways (TEPs) and essential-gene-enriched pathways (EEPs). As expected, genes in TEPs and EEPs exhibited opposite results in terms of functional category, transcriptional regulation, codon adaptation index, and network properties, suggesting the possibility that the bipolar patterns in these pathways also contribute to the regulation of the stress response and to cell survival. Our findings provide the novel insight that significant enrichment of TATA-binding or TATA-less genes defines pathways as stress-responsive or growth-related.

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Enrichment of metabolic pathways and enzyme.(a) There is a marked difference in the enriched metabolic pathways between TATA and essential genes. (b) Oxidoreductases are enriched in the enzyme set (197 enzymes) of the TEPs, whereas transferases are enriched in the enzyme set (124) of the EEPs. The red dashed lines correspond to the negative log transformation of an adjusted p-value of 0.05.
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pone.0120848.g006: Enrichment of metabolic pathways and enzyme.(a) There is a marked difference in the enriched metabolic pathways between TATA and essential genes. (b) Oxidoreductases are enriched in the enzyme set (197 enzymes) of the TEPs, whereas transferases are enriched in the enzyme set (124) of the EEPs. The red dashed lines correspond to the negative log transformation of an adjusted p-value of 0.05.

Mentions: The marked difference in the enriched metabolic pathways with which the two sets of genes are associated (Fig. 6a) raises the question of whether the genes in the two groups encode specific enzymes. To facilitate the categorization of enzymatic reactions, we divided the enzymes encoded by genes of TEPs and EEPs into six classes that describe their general functions: oxidoreductases, transferases, hydrolases, lyases, isomerases and ligases. As expected, oxidoreductases catalyzing the transfer of electrons were enriched in the enzyme set of TEPs (P < 0.01), whereas transferases were enriched in EEPs (P < 0.05) (Fig. 6b).


Functional analysis of the molecular interactions of TATA box-containing genes and essential genes.

Bae SH, Han HW, Moon J - PLoS ONE (2015)

Enrichment of metabolic pathways and enzyme.(a) There is a marked difference in the enriched metabolic pathways between TATA and essential genes. (b) Oxidoreductases are enriched in the enzyme set (197 enzymes) of the TEPs, whereas transferases are enriched in the enzyme set (124) of the EEPs. The red dashed lines correspond to the negative log transformation of an adjusted p-value of 0.05.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4366266&req=5

pone.0120848.g006: Enrichment of metabolic pathways and enzyme.(a) There is a marked difference in the enriched metabolic pathways between TATA and essential genes. (b) Oxidoreductases are enriched in the enzyme set (197 enzymes) of the TEPs, whereas transferases are enriched in the enzyme set (124) of the EEPs. The red dashed lines correspond to the negative log transformation of an adjusted p-value of 0.05.
Mentions: The marked difference in the enriched metabolic pathways with which the two sets of genes are associated (Fig. 6a) raises the question of whether the genes in the two groups encode specific enzymes. To facilitate the categorization of enzymatic reactions, we divided the enzymes encoded by genes of TEPs and EEPs into six classes that describe their general functions: oxidoreductases, transferases, hydrolases, lyases, isomerases and ligases. As expected, oxidoreductases catalyzing the transfer of electrons were enriched in the enzyme set of TEPs (P < 0.01), whereas transferases were enriched in EEPs (P < 0.05) (Fig. 6b).

Bottom Line: In a previous study, we demonstrated that there are striking differences among four gene sets defined by the presence of TATA box (TATA-containing) and essentiality (TATA-less) with respect to number of associated transcription factors, amino acid usage, and functional annotation.As expected, genes in TEPs and EEPs exhibited opposite results in terms of functional category, transcriptional regulation, codon adaptation index, and network properties, suggesting the possibility that the bipolar patterns in these pathways also contribute to the regulation of the stress response and to cell survival.Our findings provide the novel insight that significant enrichment of TATA-binding or TATA-less genes defines pathways as stress-responsive or growth-related.

View Article: PubMed Central - PubMed

Affiliation: College of Life Science, Department of Bioengineering, CHA University, Seoul, Korea; General Research Institute, Gangnam CHA General Hospital, Seoul, Korea.

ABSTRACT
Genes can be divided into TATA-containing genes and TATA-less genes according to the presence of TATA box elements at promoter regions. TATA-containing genes tend to be stress-responsive, whereas many TATA-less genes are known to be related to cell growth or "housekeeping" functions. In a previous study, we demonstrated that there are striking differences among four gene sets defined by the presence of TATA box (TATA-containing) and essentiality (TATA-less) with respect to number of associated transcription factors, amino acid usage, and functional annotation. Extending this research in yeast, we identified KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways that are statistically enriched in TATA-containing or TATA-less genes and evaluated the possibility that the enriched pathways are related to stress or growth as reflected by the individual functions of the genes involved. According to their enrichment for either of these two gene sets, we sorted KEGG pathways into TATA-containing-gene-enriched pathways (TEPs) and essential-gene-enriched pathways (EEPs). As expected, genes in TEPs and EEPs exhibited opposite results in terms of functional category, transcriptional regulation, codon adaptation index, and network properties, suggesting the possibility that the bipolar patterns in these pathways also contribute to the regulation of the stress response and to cell survival. Our findings provide the novel insight that significant enrichment of TATA-binding or TATA-less genes defines pathways as stress-responsive or growth-related.

Show MeSH
Related in: MedlinePlus