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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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Effects of iron deprivation on mean protein concentration of RyhB targets. Mean intracellular concentrations  of SodB-CFP (full circles) and FumA-YFP (empty circles), normalized by their values at 0 µM DTPA as a function of DTPA concentration. The data for FumA-YFP have also been normalized (crosses) by the ratio of fluorescence density of cells bearing promoter fusion plasmids with either PsodB–YFP or PfumA–YFP (Supplementary Figure S5). Data points represent an average over three independent experimental runs, and error bars represent standard errors.
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gkt184-F2: Effects of iron deprivation on mean protein concentration of RyhB targets. Mean intracellular concentrations of SodB-CFP (full circles) and FumA-YFP (empty circles), normalized by their values at 0 µM DTPA as a function of DTPA concentration. The data for FumA-YFP have also been normalized (crosses) by the ratio of fluorescence density of cells bearing promoter fusion plasmids with either PsodB–YFP or PfumA–YFP (Supplementary Figure S5). Data points represent an average over three independent experimental runs, and error bars represent standard errors.

Mentions: We show in Figure 1 histograms of protein concentrations of SodB-CFP and FumA-YFP (CFP and YFP: cyan and yellow fluorescent protein respectively) measured in the same individual cells (Supplementary Figure S1), grown under different levels of iron deprivation that allow cells to maintain logarithmic cell growth, although with a reduced growth rate (Supplementary Figure S2). As E. coli cells exposed to sudden low-iron conditions exhibit oscillations in the expression of RyhB and other Fur-controlled genes that die out six to seven generations later (25), fluorescence levels were measured 3.5 h after exposing cells to different concentrations of the cell-impermeable iron chelator DTPA (Supplementary Figure S3). The yield of both fluorescently labeled proteins decreased as iron is decreased, as illustrated by a plot of the mean protein concentration , normalized by the mean value when no DTPA is added (Figure 2). is equal to 350 ± 50 nM and 130 ± 13 nM for SodB-CFP and FumA-YFP, respectively; the corresponding numbers of mRNA molecules [4.9 ± 0.6 and 1.2 ± 0.2 (mean ± standard error from seven experiments)] as measured by smFISH (single-molecule fluorescence in situ hybridization) techniques are much smaller (Supplementary Figure S4).Figure 1.


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)

Effects of iron deprivation on mean protein concentration of RyhB targets. Mean intracellular concentrations  of SodB-CFP (full circles) and FumA-YFP (empty circles), normalized by their values at 0 µM DTPA as a function of DTPA concentration. The data for FumA-YFP have also been normalized (crosses) by the ratio of fluorescence density of cells bearing promoter fusion plasmids with either PsodB–YFP or PfumA–YFP (Supplementary Figure S5). Data points represent an average over three independent experimental runs, and error bars represent standard errors.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

gkt184-F2: Effects of iron deprivation on mean protein concentration of RyhB targets. Mean intracellular concentrations of SodB-CFP (full circles) and FumA-YFP (empty circles), normalized by their values at 0 µM DTPA as a function of DTPA concentration. The data for FumA-YFP have also been normalized (crosses) by the ratio of fluorescence density of cells bearing promoter fusion plasmids with either PsodB–YFP or PfumA–YFP (Supplementary Figure S5). Data points represent an average over three independent experimental runs, and error bars represent standard errors.
Mentions: We show in Figure 1 histograms of protein concentrations of SodB-CFP and FumA-YFP (CFP and YFP: cyan and yellow fluorescent protein respectively) measured in the same individual cells (Supplementary Figure S1), grown under different levels of iron deprivation that allow cells to maintain logarithmic cell growth, although with a reduced growth rate (Supplementary Figure S2). As E. coli cells exposed to sudden low-iron conditions exhibit oscillations in the expression of RyhB and other Fur-controlled genes that die out six to seven generations later (25), fluorescence levels were measured 3.5 h after exposing cells to different concentrations of the cell-impermeable iron chelator DTPA (Supplementary Figure S3). The yield of both fluorescently labeled proteins decreased as iron is decreased, as illustrated by a plot of the mean protein concentration , normalized by the mean value when no DTPA is added (Figure 2). is equal to 350 ± 50 nM and 130 ± 13 nM for SodB-CFP and FumA-YFP, respectively; the corresponding numbers of mRNA molecules [4.9 ± 0.6 and 1.2 ± 0.2 (mean ± standard error from seven experiments)] as measured by smFISH (single-molecule fluorescence in situ hybridization) techniques are much smaller (Supplementary Figure S4).Figure 1.

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