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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.

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Robustness of extrinsic noise to different levels of iron deprivation. (A) Representative scatter plot of fluorescence intensities of CFP and YFP reporters fused to different copies of the pLac promoter in the same cell, measured at different DTPA concentrations: 0 µM (blue), 25 µM (green), 88 µM (red) and 125 µM (violet). Intensities were normalized both by cell volume and by the mean over the population. (B) Extrinsic noise  as a function of DTPA concentration (4). The data represent averages over two independent experimental runs, each consisting of ∼1300 cells. Error bars represent standard errors.
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gkt184-F4: Robustness of extrinsic noise to different levels of iron deprivation. (A) Representative scatter plot of fluorescence intensities of CFP and YFP reporters fused to different copies of the pLac promoter in the same cell, measured at different DTPA concentrations: 0 µM (blue), 25 µM (green), 88 µM (red) and 125 µM (violet). Intensities were normalized both by cell volume and by the mean over the population. (B) Extrinsic noise as a function of DTPA concentration (4). The data represent averages over two independent experimental runs, each consisting of ∼1300 cells. Error bars represent standard errors.

Mentions: To test whether global extrinsic fluctuations are directly affected by iron deprivation, we studied cell-to-cell variations in the expression of a gene outside the iron homeostasis network. We show in Figure 4A a scatter plot of normalized fluorescence levels of CFP and YFP reporters measured in the same individual cells for different DTPA concentrations in a representative experimental run. The reporters were expressed from two identical Lac promoters in the chromosome (4). There is considerable overlap between the clusters of points corresponding to different DTPA concentrations. Given that extrinsic noise is measured by the extent of the clusters along the main diagonal, this suggests a low sensitivity of extrinsic noise on iron deprivation. This is confirmed by calculating the extrinsic noise for each DTPA concentration (Figure 4B), following previous methods (4). We note that also the means of both CFP and YFP themselves are rather insensitive to changes in DTPA concentration (Supplementary Figure S8), as expected for genes outside the iron homeostasis network. One can account for this insensitivity by the balance between a reduction in the number of global factors, such as RNA polymerases and ribosomes (28), and the slower cell growth rate observed in our experiments (Supplementary Figure S2).Figure 4.


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)

Robustness of extrinsic noise to different levels of iron deprivation. (A) Representative scatter plot of fluorescence intensities of CFP and YFP reporters fused to different copies of the pLac promoter in the same cell, measured at different DTPA concentrations: 0 µM (blue), 25 µM (green), 88 µM (red) and 125 µM (violet). Intensities were normalized both by cell volume and by the mean over the population. (B) Extrinsic noise  as a function of DTPA concentration (4). The data represent averages over two independent experimental runs, each consisting of ∼1300 cells. Error bars represent standard errors.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

gkt184-F4: Robustness of extrinsic noise to different levels of iron deprivation. (A) Representative scatter plot of fluorescence intensities of CFP and YFP reporters fused to different copies of the pLac promoter in the same cell, measured at different DTPA concentrations: 0 µM (blue), 25 µM (green), 88 µM (red) and 125 µM (violet). Intensities were normalized both by cell volume and by the mean over the population. (B) Extrinsic noise as a function of DTPA concentration (4). The data represent averages over two independent experimental runs, each consisting of ∼1300 cells. Error bars represent standard errors.
Mentions: To test whether global extrinsic fluctuations are directly affected by iron deprivation, we studied cell-to-cell variations in the expression of a gene outside the iron homeostasis network. We show in Figure 4A a scatter plot of normalized fluorescence levels of CFP and YFP reporters measured in the same individual cells for different DTPA concentrations in a representative experimental run. The reporters were expressed from two identical Lac promoters in the chromosome (4). There is considerable overlap between the clusters of points corresponding to different DTPA concentrations. Given that extrinsic noise is measured by the extent of the clusters along the main diagonal, this suggests a low sensitivity of extrinsic noise on iron deprivation. This is confirmed by calculating the extrinsic noise for each DTPA concentration (Figure 4B), following previous methods (4). We note that also the means of both CFP and YFP themselves are rather insensitive to changes in DTPA concentration (Supplementary Figure S8), as expected for genes outside the iron homeostasis network. One can account for this insensitivity by the balance between a reduction in the number of global factors, such as RNA polymerases and ribosomes (28), and the slower cell growth rate observed in our experiments (Supplementary Figure S2).Figure 4.

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