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Coupling between noise and plasticity in E. coli.

Singh GP - G3 (Bethesda) (2013)

Bottom Line: Using these data, I found significant positive correlation between noise and plasticity in E. coli.Many of these features are analogous to those found to influence noise-plasticity coupling in yeast.These results not only show the generality of noise-plasticity coupling across phylogenetically distant organisms but also suggest that its mechanism may be similar.

View Article: PubMed Central - PubMed

Affiliation: School of Biotechnology, KIIT University, Bhubaneswar 751024, Odisha, India.

ABSTRACT
Expression levels of genes vary not only between different environmental conditions ("plasticity") but also between genetically identical cells in constant environment ("noise"). Intriguingly, these two measures of gene expression variability correlate positively with each other in yeast. This coupling was found to be particularly strong for genes with specific promoter architecture (TATA box and high nucleosome occupancy) but weak for genes in which high noise may be detrimental (e.g., essential genes), suggesting that noise-plasticity coupling is an evolvable trait in yeast and may constrain evolution of gene expression and promoter usage. Recently, similar genome-wide data on noise and plasticity have become available for Escherichia coli, providing the opportunity to study noise-plasticity correlation and its mechanism in a prokaryote, which follows a fundamentally different mode of transcription regulation than a eukaryote such as yeast. Using these data, I found significant positive correlation between noise and plasticity in E. coli. Furthermore, this coupling was highly influenced by the following: level of expression; essentiality and dosage sensitivity of genes; regulation by specific nucleoid-associated proteins, transcription factors, and sigma factors; and involvement in stress response. Many of these features are analogous to those found to influence noise-plasticity coupling in yeast. These results not only show the generality of noise-plasticity coupling across phylogenetically distant organisms but also suggest that its mechanism may be similar.

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Related in: MedlinePlus

Noise–plasticity coupling for genes with different expression levels. (A) Spearman correlation coefficients between noise and plasticity are shown for genes divided into five equally populated nonoverlapping bins of genes according to their expression levels (e.g., extreme left bin has 20% of lowest expressing genes). *Bins with significant correlation (P < 0.01). (B) Noise and plasticity values are plotted for the highest expression bin. Correlation and P are shown in the inset.
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fig1: Noise–plasticity coupling for genes with different expression levels. (A) Spearman correlation coefficients between noise and plasticity are shown for genes divided into five equally populated nonoverlapping bins of genes according to their expression levels (e.g., extreme left bin has 20% of lowest expressing genes). *Bins with significant correlation (P < 0.01). (B) Noise and plasticity values are plotted for the highest expression bin. Correlation and P are shown in the inset.

Mentions: Next, I investigated whether level of expression might influence noise–plasticity coupling. Genes were placed into five equally sized nonoverlapping bins according to their expression level, and correlation between noise and plasticity was calculated for each bin. Genes with high mRNA expression levels showed high noise–plasticity coupling (genes with the top 20% expression show Spearman rho = 0.23; P = 7E−5; n = 291), whereas lowly expressed genes did not show significant coupling (Figure 1).


Coupling between noise and plasticity in E. coli.

Singh GP - G3 (Bethesda) (2013)

Noise–plasticity coupling for genes with different expression levels. (A) Spearman correlation coefficients between noise and plasticity are shown for genes divided into five equally populated nonoverlapping bins of genes according to their expression levels (e.g., extreme left bin has 20% of lowest expressing genes). *Bins with significant correlation (P < 0.01). (B) Noise and plasticity values are plotted for the highest expression bin. Correlation and P are shown in the inset.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3852374&req=5

fig1: Noise–plasticity coupling for genes with different expression levels. (A) Spearman correlation coefficients between noise and plasticity are shown for genes divided into five equally populated nonoverlapping bins of genes according to their expression levels (e.g., extreme left bin has 20% of lowest expressing genes). *Bins with significant correlation (P < 0.01). (B) Noise and plasticity values are plotted for the highest expression bin. Correlation and P are shown in the inset.
Mentions: Next, I investigated whether level of expression might influence noise–plasticity coupling. Genes were placed into five equally sized nonoverlapping bins according to their expression level, and correlation between noise and plasticity was calculated for each bin. Genes with high mRNA expression levels showed high noise–plasticity coupling (genes with the top 20% expression show Spearman rho = 0.23; P = 7E−5; n = 291), whereas lowly expressed genes did not show significant coupling (Figure 1).

Bottom Line: Using these data, I found significant positive correlation between noise and plasticity in E. coli.Many of these features are analogous to those found to influence noise-plasticity coupling in yeast.These results not only show the generality of noise-plasticity coupling across phylogenetically distant organisms but also suggest that its mechanism may be similar.

View Article: PubMed Central - PubMed

Affiliation: School of Biotechnology, KIIT University, Bhubaneswar 751024, Odisha, India.

ABSTRACT
Expression levels of genes vary not only between different environmental conditions ("plasticity") but also between genetically identical cells in constant environment ("noise"). Intriguingly, these two measures of gene expression variability correlate positively with each other in yeast. This coupling was found to be particularly strong for genes with specific promoter architecture (TATA box and high nucleosome occupancy) but weak for genes in which high noise may be detrimental (e.g., essential genes), suggesting that noise-plasticity coupling is an evolvable trait in yeast and may constrain evolution of gene expression and promoter usage. Recently, similar genome-wide data on noise and plasticity have become available for Escherichia coli, providing the opportunity to study noise-plasticity correlation and its mechanism in a prokaryote, which follows a fundamentally different mode of transcription regulation than a eukaryote such as yeast. Using these data, I found significant positive correlation between noise and plasticity in E. coli. Furthermore, this coupling was highly influenced by the following: level of expression; essentiality and dosage sensitivity of genes; regulation by specific nucleoid-associated proteins, transcription factors, and sigma factors; and involvement in stress response. Many of these features are analogous to those found to influence noise-plasticity coupling in yeast. These results not only show the generality of noise-plasticity coupling across phylogenetically distant organisms but also suggest that its mechanism may be similar.

Show MeSH
Related in: MedlinePlus