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Inherent characteristics of gene expression for buffering environmental changes without the corresponding transcriptional regulations

View Article: PubMed Central - PubMed

ABSTRACT

Gene expression patterning is crucial for environmental nutritional responses such as the nitrogen response in Escherichia coli. The nitrogen response is primarily regulated by the expression of glutamine synthetase (GS), which catalyzes the sole reaction of glutamine formation, by cis-logic regulatory circuits. Here, by removing the entire corresponding operator and promoter regions required for the control of GS, we constructed an E. coli strain that enables the detection of the basal GS gene expression, which is expressed from a plain promoter unrelated to the nitrogen response, and measured by co-transcribed GFP expression, an indicator of GS expression. Using strain cultures, we found that the GS expression level was able to shift inversely against the change of the environmental glutamine concentration. As a control experiment, we repeated similar experiments with another strain in which the GS regulatory region remained intact and the GFP gene following the plain promoter was introduced into a different chromosomal site. For this strain, we found that the GFP expression level did not shift in accordance with the environmental glutamine concentration. These results showed that GS expression from the plain promoter exhibited a responsive ability to buffer environmental changes, whereas the GS expression shift did not correlate with the specific characteristics of the plain promoter and GFP expression. This study identifies the inherent characteristics of basal gene expression in response to environmental changes, facilitating a deeper understanding of cellular design principles.

No MeSH data available.


Shift in the GFP concentration distribution observed during the upshift and downshift of the glutamine concentration. Strains OSU8 (A), OSU7 (B), and OSU9 (C) were cultured for serial-transfer cultures. In each experiment, the glutamine concentration was changed in a transition between 0 mM (gray curve) and 5 mM (black curve). Arrows indicate the direction of the distribution shift. The GFP concentration values are in arbitrary units (a.u.).
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f5-2_63: Shift in the GFP concentration distribution observed during the upshift and downshift of the glutamine concentration. Strains OSU8 (A), OSU7 (B), and OSU9 (C) were cultured for serial-transfer cultures. In each experiment, the glutamine concentration was changed in a transition between 0 mM (gray curve) and 5 mM (black curve). Arrows indicate the direction of the distribution shift. The GFP concentration values are in arbitrary units (a.u.).

Mentions: Through the acclimation described above, we prepared the cells used for the environmental glutamine transition experiments. The frozen acclimated cell stocks were inoculated and subjected to the serial-transfer cultures. We confirmed that the cells reached a plateau in the specific growth rate, and, at the fifth subculture, the medium was exchanged to either upshift (from 0 mM to 5 mM glutamine) or down-shift the glutamine concentration (from 5 mM to 0 mM glutamine). During the serial-transfer cultures, we traced the time-series data of the values from the flow cytometry and the specific growth rate (Fig. 4). After the upshift of the glutamine concentration from 0 mM to 5 mM, the specific growth rate exhibited a gradual increase and reached a plateau at the fourteenth subculture, whereas the GFP concentration in cells exhibited a gradual decrease and reached a plateau at the fourteenth subculture (Fig. 4A). Among the serial-transfer cultures, the fifth and nineteenth subcultures were evaluated with cell-cell variation (Fig. 5A; Glutamine Upshift). The shape of the distribution of the GFP concentration in cells did not change; rather, its average value shifted. These results indicate that the level of GS expression decreased in response to the increased environmental glutamine concentration, even without regulation by the corresponding transcriptional mechanisms.


Inherent characteristics of gene expression for buffering environmental changes without the corresponding transcriptional regulations
Shift in the GFP concentration distribution observed during the upshift and downshift of the glutamine concentration. Strains OSU8 (A), OSU7 (B), and OSU9 (C) were cultured for serial-transfer cultures. In each experiment, the glutamine concentration was changed in a transition between 0 mM (gray curve) and 5 mM (black curve). Arrows indicate the direction of the distribution shift. The GFP concentration values are in arbitrary units (a.u.).
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Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC5036647&req=5

f5-2_63: Shift in the GFP concentration distribution observed during the upshift and downshift of the glutamine concentration. Strains OSU8 (A), OSU7 (B), and OSU9 (C) were cultured for serial-transfer cultures. In each experiment, the glutamine concentration was changed in a transition between 0 mM (gray curve) and 5 mM (black curve). Arrows indicate the direction of the distribution shift. The GFP concentration values are in arbitrary units (a.u.).
Mentions: Through the acclimation described above, we prepared the cells used for the environmental glutamine transition experiments. The frozen acclimated cell stocks were inoculated and subjected to the serial-transfer cultures. We confirmed that the cells reached a plateau in the specific growth rate, and, at the fifth subculture, the medium was exchanged to either upshift (from 0 mM to 5 mM glutamine) or down-shift the glutamine concentration (from 5 mM to 0 mM glutamine). During the serial-transfer cultures, we traced the time-series data of the values from the flow cytometry and the specific growth rate (Fig. 4). After the upshift of the glutamine concentration from 0 mM to 5 mM, the specific growth rate exhibited a gradual increase and reached a plateau at the fourteenth subculture, whereas the GFP concentration in cells exhibited a gradual decrease and reached a plateau at the fourteenth subculture (Fig. 4A). Among the serial-transfer cultures, the fifth and nineteenth subcultures were evaluated with cell-cell variation (Fig. 5A; Glutamine Upshift). The shape of the distribution of the GFP concentration in cells did not change; rather, its average value shifted. These results indicate that the level of GS expression decreased in response to the increased environmental glutamine concentration, even without regulation by the corresponding transcriptional mechanisms.

View Article: PubMed Central - PubMed

ABSTRACT

Gene expression patterning is crucial for environmental nutritional responses such as the nitrogen response in Escherichia coli. The nitrogen response is primarily regulated by the expression of glutamine synthetase (GS), which catalyzes the sole reaction of glutamine formation, by cis-logic regulatory circuits. Here, by removing the entire corresponding operator and promoter regions required for the control of GS, we constructed an E. coli strain that enables the detection of the basal GS gene expression, which is expressed from a plain promoter unrelated to the nitrogen response, and measured by co-transcribed GFP expression, an indicator of GS expression. Using strain cultures, we found that the GS expression level was able to shift inversely against the change of the environmental glutamine concentration. As a control experiment, we repeated similar experiments with another strain in which the GS regulatory region remained intact and the GFP gene following the plain promoter was introduced into a different chromosomal site. For this strain, we found that the GFP expression level did not shift in accordance with the environmental glutamine concentration. These results showed that GS expression from the plain promoter exhibited a responsive ability to buffer environmental changes, whereas the GS expression shift did not correlate with the specific characteristics of the plain promoter and GFP expression. This study identifies the inherent characteristics of basal gene expression in response to environmental changes, facilitating a deeper understanding of cellular design principles.

No MeSH data available.