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Gene regulation by H-NS as a function of growth conditions depends on chromosomal position in Escherichia coli.

Brambilla E, Sclavi B - G3 (Bethesda) (2015)

Bottom Line: Cellular adaptation to changing environmental conditions requires the coordinated regulation of expression of large sets of genes by global regulatory factors such as nucleoid associated proteins.Our results show that the activity of the Phns promoter depends on whether it is placed within the AT-rich regions of the genome that are known to be bound preferentially by H-NS.Genomic position can thus play a significant role in the adaptation of the cells to environmental changes, providing a fitness advantage that can explain the selection of a gene's position during evolution.

View Article: PubMed Central - PubMed

Affiliation: LBPA, UMR 8113 du CNRS, Ecole Normale Supérieure de Cachan, Cachan, France School of Engineering and Science, Jacobs University Bremen, Bremen, Germany.

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Change in OD and YFP concentration obtained from the plate reader measurements. The average protein concentration as a function of time is shown from technical triplicates within a single experiment, which is one of three independent experiments. The dashed lines represent the change in OD, whereas the continuous lines the change in YFP concentration. (A) The growth phase dependence of YFP concentration depends on the growth rate. At fast growth (glu04caa05), there is no accumulation of the protein while entering in stationary phase, whereas at slow growth (caa02), the amount of protein per unit of OD increases as cells approach to stationary phase. The data shown here are for the reporter in the LM position at 30°. This change in YFP concentration as a function of the growth medium doesn’t depend on the chromosomal position of the insertion. (B) YFP concentration depends on the chromosomal position of the gene. In the same growth conditions (caa02 at 30°), the amount of protein concentration is greater for insertions near the origin of replication (as expected due to gene copy number). However, in this growth medium the concentration is considerably lower for the strains with the insertion in the left terminus (LT, white squares) and right origin (RO, black triangles), than the ones in the right terminus (RT, black squares) and left origin (LO, white triangles), respectively, even though they are equally distant from the origin and thus with the same gene copy number. LM, left medium; LO, left origin; LT, left terminus; OD, optical density; RM, right medium; RO, right origin; RT, right terminus; YFP, yellow fluorescent protein.
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fig2: Change in OD and YFP concentration obtained from the plate reader measurements. The average protein concentration as a function of time is shown from technical triplicates within a single experiment, which is one of three independent experiments. The dashed lines represent the change in OD, whereas the continuous lines the change in YFP concentration. (A) The growth phase dependence of YFP concentration depends on the growth rate. At fast growth (glu04caa05), there is no accumulation of the protein while entering in stationary phase, whereas at slow growth (caa02), the amount of protein per unit of OD increases as cells approach to stationary phase. The data shown here are for the reporter in the LM position at 30°. This change in YFP concentration as a function of the growth medium doesn’t depend on the chromosomal position of the insertion. (B) YFP concentration depends on the chromosomal position of the gene. In the same growth conditions (caa02 at 30°), the amount of protein concentration is greater for insertions near the origin of replication (as expected due to gene copy number). However, in this growth medium the concentration is considerably lower for the strains with the insertion in the left terminus (LT, white squares) and right origin (RO, black triangles), than the ones in the right terminus (RT, black squares) and left origin (LO, white triangles), respectively, even though they are equally distant from the origin and thus with the same gene copy number. LM, left medium; LO, left origin; LT, left terminus; OD, optical density; RM, right medium; RO, right origin; RT, right terminus; YFP, yellow fluorescent protein.

Mentions: Schematic representation of the Phns promoter and of the insertions in the E. coli chromosome. (A) The boxes indicate the binding sites for different proteins in the Phns promoter region (black for FIS, gray for H-NS, white for CspA) as derived from the literature (La Teana et al. 1991; Ueguchi et al. 1993; Falconi et al. 1996). Stars indicate the H-NS high-affinity DNA binding sites (Lang et al. 2007). The -10, -35 regions and the transcription starting site, +1, also are annotated. (B) The promoter-yfp unit is flanked by two T1 terminators from the E. coli rrnB coding sequence. (C) Representation of the six different mirror sites on the E. coli chromosome in which the yfp gene was inserted under the control of the Phns promoter next to the gene conferring resistance to chloramphenicol. The symbols used here are the ones used to indicate these positions in Figure 2B, Figure 5 and Supporting Information, Figure S6. Details about the insertion positions can be found in Table 1. CspA, Cold shock protein A; FIS, factor for inversion stimulation; H-NS, histone-like nucleoid-structuring protein.


Gene regulation by H-NS as a function of growth conditions depends on chromosomal position in Escherichia coli.

Brambilla E, Sclavi B - G3 (Bethesda) (2015)

Change in OD and YFP concentration obtained from the plate reader measurements. The average protein concentration as a function of time is shown from technical triplicates within a single experiment, which is one of three independent experiments. The dashed lines represent the change in OD, whereas the continuous lines the change in YFP concentration. (A) The growth phase dependence of YFP concentration depends on the growth rate. At fast growth (glu04caa05), there is no accumulation of the protein while entering in stationary phase, whereas at slow growth (caa02), the amount of protein per unit of OD increases as cells approach to stationary phase. The data shown here are for the reporter in the LM position at 30°. This change in YFP concentration as a function of the growth medium doesn’t depend on the chromosomal position of the insertion. (B) YFP concentration depends on the chromosomal position of the gene. In the same growth conditions (caa02 at 30°), the amount of protein concentration is greater for insertions near the origin of replication (as expected due to gene copy number). However, in this growth medium the concentration is considerably lower for the strains with the insertion in the left terminus (LT, white squares) and right origin (RO, black triangles), than the ones in the right terminus (RT, black squares) and left origin (LO, white triangles), respectively, even though they are equally distant from the origin and thus with the same gene copy number. LM, left medium; LO, left origin; LT, left terminus; OD, optical density; RM, right medium; RO, right origin; RT, right terminus; YFP, yellow fluorescent protein.
© Copyright Policy - open-access
Related In: Results  -  Collection

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Show All Figures
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fig2: Change in OD and YFP concentration obtained from the plate reader measurements. The average protein concentration as a function of time is shown from technical triplicates within a single experiment, which is one of three independent experiments. The dashed lines represent the change in OD, whereas the continuous lines the change in YFP concentration. (A) The growth phase dependence of YFP concentration depends on the growth rate. At fast growth (glu04caa05), there is no accumulation of the protein while entering in stationary phase, whereas at slow growth (caa02), the amount of protein per unit of OD increases as cells approach to stationary phase. The data shown here are for the reporter in the LM position at 30°. This change in YFP concentration as a function of the growth medium doesn’t depend on the chromosomal position of the insertion. (B) YFP concentration depends on the chromosomal position of the gene. In the same growth conditions (caa02 at 30°), the amount of protein concentration is greater for insertions near the origin of replication (as expected due to gene copy number). However, in this growth medium the concentration is considerably lower for the strains with the insertion in the left terminus (LT, white squares) and right origin (RO, black triangles), than the ones in the right terminus (RT, black squares) and left origin (LO, white triangles), respectively, even though they are equally distant from the origin and thus with the same gene copy number. LM, left medium; LO, left origin; LT, left terminus; OD, optical density; RM, right medium; RO, right origin; RT, right terminus; YFP, yellow fluorescent protein.
Mentions: Schematic representation of the Phns promoter and of the insertions in the E. coli chromosome. (A) The boxes indicate the binding sites for different proteins in the Phns promoter region (black for FIS, gray for H-NS, white for CspA) as derived from the literature (La Teana et al. 1991; Ueguchi et al. 1993; Falconi et al. 1996). Stars indicate the H-NS high-affinity DNA binding sites (Lang et al. 2007). The -10, -35 regions and the transcription starting site, +1, also are annotated. (B) The promoter-yfp unit is flanked by two T1 terminators from the E. coli rrnB coding sequence. (C) Representation of the six different mirror sites on the E. coli chromosome in which the yfp gene was inserted under the control of the Phns promoter next to the gene conferring resistance to chloramphenicol. The symbols used here are the ones used to indicate these positions in Figure 2B, Figure 5 and Supporting Information, Figure S6. Details about the insertion positions can be found in Table 1. CspA, Cold shock protein A; FIS, factor for inversion stimulation; H-NS, histone-like nucleoid-structuring protein.

Bottom Line: Cellular adaptation to changing environmental conditions requires the coordinated regulation of expression of large sets of genes by global regulatory factors such as nucleoid associated proteins.Our results show that the activity of the Phns promoter depends on whether it is placed within the AT-rich regions of the genome that are known to be bound preferentially by H-NS.Genomic position can thus play a significant role in the adaptation of the cells to environmental changes, providing a fitness advantage that can explain the selection of a gene's position during evolution.

View Article: PubMed Central - PubMed

Affiliation: LBPA, UMR 8113 du CNRS, Ecole Normale Supérieure de Cachan, Cachan, France School of Engineering and Science, Jacobs University Bremen, Bremen, Germany.

Show MeSH
Related in: MedlinePlus