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Adaptation in bacterial flagellar and motility systems: from regulon members to 'foraging'-like behavior in E. coli.

Zhao K, Liu M, Burgess RR - Nucleic Acids Res. (2007)

Bottom Line: Bacterial flagellar motility and chemotaxis help cells to reach the most favorable environments and to successfully compete with other micro-organisms in response to external stimuli.To define the physiological role of these two regulators, we carried out transcription profiling experiments to identify, on a genome-wide basis, genes under the control of these two regulators.In addition, the synchronized pattern of increasing CRP activity causing increasing FlhDC expression with decreasing carbon source quality, together with the apparent coupling of motility activity with the activation of motility and chemotaxis genes in poor quality carbon sources, highlights the importance of CRP activation in allowing E. coli to devote progressively more of its limited reserves to search out better conditions.

View Article: PubMed Central - PubMed

Affiliation: McArdle Laboratory for Cancer Research, Department of Genetics, University of Wisconsin, Madison, WI 53706, USA.

ABSTRACT
Bacterial flagellar motility and chemotaxis help cells to reach the most favorable environments and to successfully compete with other micro-organisms in response to external stimuli. Escherichia coli is a motile gram-negative bacterium, and the flagellar regulon in E. coli is controlled by a master regulator FlhDC as well as a second regulator, flagellum-specific sigma factor, sigma(F). To define the physiological role of these two regulators, we carried out transcription profiling experiments to identify, on a genome-wide basis, genes under the control of these two regulators. In addition, the synchronized pattern of increasing CRP activity causing increasing FlhDC expression with decreasing carbon source quality, together with the apparent coupling of motility activity with the activation of motility and chemotaxis genes in poor quality carbon sources, highlights the importance of CRP activation in allowing E. coli to devote progressively more of its limited reserves to search out better conditions. In adaptation to a variety of carbon sources, the motile bacteria carry out tactical responses by increasing flagellar operation but restricting costly flagellar synthesis, indicating its capability of strategically using the precious energy in nutrient-poor environments for maximizing survival.

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In vitro transcription assays to test the transcription by σF holoenzyme of the DNA fragments carrying putative promoter element(s). (A) SDS–PAGE gel shows purified core RNA polymerase and σF as well as MultiMark Standard. In vitro transcription assays are performed using purified σF-associated holoenzyme with DNA fragments from the upstream sequence of candidate σF-dependent genes. The upstream sequence of grpE served as a negative control. Error bars represent standard deviation in three different experiments. (B) Potential σF consensus-binding sites of each gene are predicted and aligned by computer program. Previously known σF two-block promoter element consensus is shown below.
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Figure 4: In vitro transcription assays to test the transcription by σF holoenzyme of the DNA fragments carrying putative promoter element(s). (A) SDS–PAGE gel shows purified core RNA polymerase and σF as well as MultiMark Standard. In vitro transcription assays are performed using purified σF-associated holoenzyme with DNA fragments from the upstream sequence of candidate σF-dependent genes. The upstream sequence of grpE served as a negative control. Error bars represent standard deviation in three different experiments. (B) Potential σF consensus-binding sites of each gene are predicted and aligned by computer program. Previously known σF two-block promoter element consensus is shown below.

Mentions: We chose the top 10 genes in Table 2 for in vitro transcription assays because no experiment has been performed so far to test if these genes can be directly transcribed by σF-associated holoenzyme. The upstream sequence of grpE gene, encoding a heat shock protein, was chosen as a negative control for the in vitro transcription assay because transcription of this gene is dependent on σ32 and is not a σF-dependent gene (35). In vitro transcription assay results (Figure 4A) show that most of these 10 genes can be directly transcribed by σF holoenzyme. Note both modA and modB genes are in one operon. The modB gene can be co-transcribed by σF-dependent promoter located in the upstream region of the modA gene. Results from promoter region consensus analysis using the algorithms BioProspector (36) and HMMER (37) revealed σF holoenzyme-binding sites in the upstream regulatory sequences of these genes (Figure 4B). Note that several of these genes have two putative promoters. Based solely on the negative results from our in vitro transcription assay, we are not sure if the hemL gene belongs to the σF regulon. While these possible two-block DNA consensus sequences might provide the primary interaction with holoenzyme, additional transcriptional activators such as FIS and CRP might be utilized to strengthen the promoter–holoenzyme interaction in vivo which are not available in our in vitro transcription assay. Due to the virulence role of pathogenic bacteria flagella system in adhesion, biofilm formation and colonization of host organisms and in secretion of virulence determinants to host (38–40), the homologous counterparts of the newly identified genes presented here might be potentially associated with these functions, especially with that of the pathogenicity island SPI-1 TTSS (type three secretion system) which appears to be most commonly found in pathogenic bacteria.Figure 4.


Adaptation in bacterial flagellar and motility systems: from regulon members to 'foraging'-like behavior in E. coli.

Zhao K, Liu M, Burgess RR - Nucleic Acids Res. (2007)

In vitro transcription assays to test the transcription by σF holoenzyme of the DNA fragments carrying putative promoter element(s). (A) SDS–PAGE gel shows purified core RNA polymerase and σF as well as MultiMark Standard. In vitro transcription assays are performed using purified σF-associated holoenzyme with DNA fragments from the upstream sequence of candidate σF-dependent genes. The upstream sequence of grpE served as a negative control. Error bars represent standard deviation in three different experiments. (B) Potential σF consensus-binding sites of each gene are predicted and aligned by computer program. Previously known σF two-block promoter element consensus is shown below.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC1935009&req=5

Figure 4: In vitro transcription assays to test the transcription by σF holoenzyme of the DNA fragments carrying putative promoter element(s). (A) SDS–PAGE gel shows purified core RNA polymerase and σF as well as MultiMark Standard. In vitro transcription assays are performed using purified σF-associated holoenzyme with DNA fragments from the upstream sequence of candidate σF-dependent genes. The upstream sequence of grpE served as a negative control. Error bars represent standard deviation in three different experiments. (B) Potential σF consensus-binding sites of each gene are predicted and aligned by computer program. Previously known σF two-block promoter element consensus is shown below.
Mentions: We chose the top 10 genes in Table 2 for in vitro transcription assays because no experiment has been performed so far to test if these genes can be directly transcribed by σF-associated holoenzyme. The upstream sequence of grpE gene, encoding a heat shock protein, was chosen as a negative control for the in vitro transcription assay because transcription of this gene is dependent on σ32 and is not a σF-dependent gene (35). In vitro transcription assay results (Figure 4A) show that most of these 10 genes can be directly transcribed by σF holoenzyme. Note both modA and modB genes are in one operon. The modB gene can be co-transcribed by σF-dependent promoter located in the upstream region of the modA gene. Results from promoter region consensus analysis using the algorithms BioProspector (36) and HMMER (37) revealed σF holoenzyme-binding sites in the upstream regulatory sequences of these genes (Figure 4B). Note that several of these genes have two putative promoters. Based solely on the negative results from our in vitro transcription assay, we are not sure if the hemL gene belongs to the σF regulon. While these possible two-block DNA consensus sequences might provide the primary interaction with holoenzyme, additional transcriptional activators such as FIS and CRP might be utilized to strengthen the promoter–holoenzyme interaction in vivo which are not available in our in vitro transcription assay. Due to the virulence role of pathogenic bacteria flagella system in adhesion, biofilm formation and colonization of host organisms and in secretion of virulence determinants to host (38–40), the homologous counterparts of the newly identified genes presented here might be potentially associated with these functions, especially with that of the pathogenicity island SPI-1 TTSS (type three secretion system) which appears to be most commonly found in pathogenic bacteria.Figure 4.

Bottom Line: Bacterial flagellar motility and chemotaxis help cells to reach the most favorable environments and to successfully compete with other micro-organisms in response to external stimuli.To define the physiological role of these two regulators, we carried out transcription profiling experiments to identify, on a genome-wide basis, genes under the control of these two regulators.In addition, the synchronized pattern of increasing CRP activity causing increasing FlhDC expression with decreasing carbon source quality, together with the apparent coupling of motility activity with the activation of motility and chemotaxis genes in poor quality carbon sources, highlights the importance of CRP activation in allowing E. coli to devote progressively more of its limited reserves to search out better conditions.

View Article: PubMed Central - PubMed

Affiliation: McArdle Laboratory for Cancer Research, Department of Genetics, University of Wisconsin, Madison, WI 53706, USA.

ABSTRACT
Bacterial flagellar motility and chemotaxis help cells to reach the most favorable environments and to successfully compete with other micro-organisms in response to external stimuli. Escherichia coli is a motile gram-negative bacterium, and the flagellar regulon in E. coli is controlled by a master regulator FlhDC as well as a second regulator, flagellum-specific sigma factor, sigma(F). To define the physiological role of these two regulators, we carried out transcription profiling experiments to identify, on a genome-wide basis, genes under the control of these two regulators. In addition, the synchronized pattern of increasing CRP activity causing increasing FlhDC expression with decreasing carbon source quality, together with the apparent coupling of motility activity with the activation of motility and chemotaxis genes in poor quality carbon sources, highlights the importance of CRP activation in allowing E. coli to devote progressively more of its limited reserves to search out better conditions. In adaptation to a variety of carbon sources, the motile bacteria carry out tactical responses by increasing flagellar operation but restricting costly flagellar synthesis, indicating its capability of strategically using the precious energy in nutrient-poor environments for maximizing survival.

Show MeSH
Related in: MedlinePlus