Limits...
Effects of post-transcriptional regulation on phenotypic noise in Escherichia coli.

Arbel-Goren R, Tal A, Friedlander T, Meshner S, Costantino N, Court DL, Stavans J - Nucleic Acids Res. (2013)

Bottom Line: Cell-to-cell variations in protein abundance, called noise, give rise to phenotypic variability between isogenic cells.Studies of noise have focused on stochasticity introduced at transcription, yet the effects of post-transcriptional regulatory processes on noise remain unknown.Extrinsic noise provides the dominant contribution to the total protein noise over the total range of RyhB production rates.

View Article: PubMed Central - PubMed

Affiliation: Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel.

ABSTRACT
Cell-to-cell variations in protein abundance, called noise, give rise to phenotypic variability between isogenic cells. Studies of noise have focused on stochasticity introduced at transcription, yet the effects of post-transcriptional regulatory processes on noise remain unknown. We study the effects of RyhB, a small-RNA of Escherichia coli produced on iron stress, on the phenotypic variability of two of its downregulated target proteins, using dual chromosomal fusions to fluorescent reporters and measurements in live individual cells. The total noise of each of the target proteins is remarkably constant over a wide range of RyhB production rates despite cells being in stress. In fact, coordinate downregulation of the two target proteins by RyhB reduces the correlation between their levels. Hence, an increase in phenotypic variability under stress is achieved by decoupling the expression of different target proteins in the same cell, rather than by an increase in the total noise of each. Extrinsic noise provides the dominant contribution to the total protein noise over the total range of RyhB production rates. Stochastic simulations reproduce qualitatively key features of our observations and show that a feed-forward loop formed by transcriptional extrinsic noise, an sRNA and its target genes exhibits strong noise filtration capabilities.

Show MeSH

Related in: MedlinePlus

Correlation between the expressions of two RyhB targets for different levels of iron deprivation. (A) Scatter plot of SodB-CFP and FumA-YFP concentrations measured in the same individual cells, for different concentrations of DTPA chelator: 0 µM (violet), 25 µM (red), 88 µM (green) and 125 µM (blue) in a representative experiment. (B) Pearson correlation coefficient ρ between SodB-CFP and FumA-YFP concentrations measured within the same cells as a function of the geometric mean of SodB-CFP and FumA-YFP concentrations (), corresponding to the data shown in Figure 3. Error bars represent standard errors computed from 10 000 bootstrap samples. The straight line, a linear fit to the data serving as a guide to the eye, highlights the decreasing trend of ρ with increasing RyhB production. The data were obtained in four independent experiments, each carried out under the same conditions as in Figure 1.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3643596&req=5

gkt184-F5: Correlation between the expressions of two RyhB targets for different levels of iron deprivation. (A) Scatter plot of SodB-CFP and FumA-YFP concentrations measured in the same individual cells, for different concentrations of DTPA chelator: 0 µM (violet), 25 µM (red), 88 µM (green) and 125 µM (blue) in a representative experiment. (B) Pearson correlation coefficient ρ between SodB-CFP and FumA-YFP concentrations measured within the same cells as a function of the geometric mean of SodB-CFP and FumA-YFP concentrations (), corresponding to the data shown in Figure 3. Error bars represent standard errors computed from 10 000 bootstrap samples. The straight line, a linear fit to the data serving as a guide to the eye, highlights the decreasing trend of ρ with increasing RyhB production. The data were obtained in four independent experiments, each carried out under the same conditions as in Figure 1.

Mentions: Evidence for RyhB-mediated cross-talk between two RyhB targets has been reported in a study using plasmids that allow independent expression of RyhB and of one of its target genes from inducible promoters (20). To study the effects of extrinsic noise sources on cross-talk, we quantified the extent of correlation between SodB-CFP and FumA-YFP concentrations when expressed in single copy from their native locations. Scatter plots of SodB-CFP and FumA-YFP concentrations measured in the same cells for different concentrations of DTPA are shown in Figure 5A. The clusters of points contract as the DTPA concentration is increased, whereas the slopes of the main diagonals become progressively smaller (Figure 5A).Figure 5.


Effects of post-transcriptional regulation on phenotypic noise in Escherichia coli.

Arbel-Goren R, Tal A, Friedlander T, Meshner S, Costantino N, Court DL, Stavans J - Nucleic Acids Res. (2013)

Correlation between the expressions of two RyhB targets for different levels of iron deprivation. (A) Scatter plot of SodB-CFP and FumA-YFP concentrations measured in the same individual cells, for different concentrations of DTPA chelator: 0 µM (violet), 25 µM (red), 88 µM (green) and 125 µM (blue) in a representative experiment. (B) Pearson correlation coefficient ρ between SodB-CFP and FumA-YFP concentrations measured within the same cells as a function of the geometric mean of SodB-CFP and FumA-YFP concentrations (), corresponding to the data shown in Figure 3. Error bars represent standard errors computed from 10 000 bootstrap samples. The straight line, a linear fit to the data serving as a guide to the eye, highlights the decreasing trend of ρ with increasing RyhB production. The data were obtained in four independent experiments, each carried out under the same conditions as in Figure 1.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3643596&req=5

gkt184-F5: Correlation between the expressions of two RyhB targets for different levels of iron deprivation. (A) Scatter plot of SodB-CFP and FumA-YFP concentrations measured in the same individual cells, for different concentrations of DTPA chelator: 0 µM (violet), 25 µM (red), 88 µM (green) and 125 µM (blue) in a representative experiment. (B) Pearson correlation coefficient ρ between SodB-CFP and FumA-YFP concentrations measured within the same cells as a function of the geometric mean of SodB-CFP and FumA-YFP concentrations (), corresponding to the data shown in Figure 3. Error bars represent standard errors computed from 10 000 bootstrap samples. The straight line, a linear fit to the data serving as a guide to the eye, highlights the decreasing trend of ρ with increasing RyhB production. The data were obtained in four independent experiments, each carried out under the same conditions as in Figure 1.
Mentions: Evidence for RyhB-mediated cross-talk between two RyhB targets has been reported in a study using plasmids that allow independent expression of RyhB and of one of its target genes from inducible promoters (20). To study the effects of extrinsic noise sources on cross-talk, we quantified the extent of correlation between SodB-CFP and FumA-YFP concentrations when expressed in single copy from their native locations. Scatter plots of SodB-CFP and FumA-YFP concentrations measured in the same cells for different concentrations of DTPA are shown in Figure 5A. The clusters of points contract as the DTPA concentration is increased, whereas the slopes of the main diagonals become progressively smaller (Figure 5A).Figure 5.

Bottom Line: Cell-to-cell variations in protein abundance, called noise, give rise to phenotypic variability between isogenic cells.Studies of noise have focused on stochasticity introduced at transcription, yet the effects of post-transcriptional regulatory processes on noise remain unknown.Extrinsic noise provides the dominant contribution to the total protein noise over the total range of RyhB production rates.

View Article: PubMed Central - PubMed

Affiliation: Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel.

ABSTRACT
Cell-to-cell variations in protein abundance, called noise, give rise to phenotypic variability between isogenic cells. Studies of noise have focused on stochasticity introduced at transcription, yet the effects of post-transcriptional regulatory processes on noise remain unknown. We study the effects of RyhB, a small-RNA of Escherichia coli produced on iron stress, on the phenotypic variability of two of its downregulated target proteins, using dual chromosomal fusions to fluorescent reporters and measurements in live individual cells. The total noise of each of the target proteins is remarkably constant over a wide range of RyhB production rates despite cells being in stress. In fact, coordinate downregulation of the two target proteins by RyhB reduces the correlation between their levels. Hence, an increase in phenotypic variability under stress is achieved by decoupling the expression of different target proteins in the same cell, rather than by an increase in the total noise of each. Extrinsic noise provides the dominant contribution to the total protein noise over the total range of RyhB production rates. Stochastic simulations reproduce qualitatively key features of our observations and show that a feed-forward loop formed by transcriptional extrinsic noise, an sRNA and its target genes exhibits strong noise filtration capabilities.

Show MeSH
Related in: MedlinePlus