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Novel roles of cAMP receptor protein (CRP) in regulation of transport and metabolism of carbon sources.

Shimada T, Fujita N, Yamamoto K, Ishihama A - PLoS ONE (2011)

Bottom Line: Using the newly developed Genomic SELEX screening system of transcription factor-binding sequences, however, we have identified a total of at least 254 CRP-binding sites.Based on the functions of novel target genes, we conclude that CRP plays a key regulatory role in the whole processes from the selective transport of carbon sources, the glycolysis-gluconeogenesis switching to the metabolisms downstream of glycolysis, including tricarboxylic acid (TCA) cycle, pyruvate dehydrogenase (PDH) pathway and aerobic respiration.One unique regulation mode is that a single and the same CRP molecule bound within intergenic regions often regulates both of divergently transcribed operons.

View Article: PubMed Central - PubMed

Affiliation: Department of Frontier Bioscience, Hosei University, Koganei, Tokyo, Japan.

ABSTRACT
CRP (cAMP receptor protein), the global regulator of genes for carbon source utilization in the absence of glucose, is the best-studied prokaryotic transcription factor. A total of 195 target promoters on the Escherichia coli genome have been proposed to be under the control of cAMP-bound CRP. Using the newly developed Genomic SELEX screening system of transcription factor-binding sequences, however, we have identified a total of at least 254 CRP-binding sites. Based on their location on the E. coli genome, we predict a total of at least 183 novel regulation target operons, altogether with the 195 hitherto known targets, reaching to the minimum of 378 promoters as the regulation targets of cAMP-CRP. All the promoters selected from the newly identified targets and examined by using the lacZ reporter assay were found to be under the control of CRP, indicating that the Genomic SELEX screening allowed to identify the CRP targets with high accuracy. Based on the functions of novel target genes, we conclude that CRP plays a key regulatory role in the whole processes from the selective transport of carbon sources, the glycolysis-gluconeogenesis switching to the metabolisms downstream of glycolysis, including tricarboxylic acid (TCA) cycle, pyruvate dehydrogenase (PDH) pathway and aerobic respiration. One unique regulation mode is that a single and the same CRP molecule bound within intergenic regions often regulates both of divergently transcribed operons.

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Regulatory roles of CRP.Upper panel: The genes under the control of CRP are indicated under either purple background (the genes for sugar transport systems) or blue background (the genes for metabolic enzymes). CRP regulates the majority of genes for three pathways of sugar transport (MFS, PTS and ABC). The number in boxes represent in the order from left to right: The number of CRP target genes listed in Regulon DB (white); the number of genes identified to be regulated by CRP in this study (green); the number of genes predicted to be under the control of CRP in this study (yellow); the total number of genes under the control of CRP (orange). The numbers shown in parenthesis represent total number of genes constituting the respective transport systems, including those not regulated by CRP. Lower panel: Most of the genes for the enzymes involved in glycolysis are controlled by Cra [30] while only three genes, fbaA, gapA and pgk, had been identified as the regulation targets of CRP (shown in while under blue background). In this study, we identified a number of novel targets of CRP (shown in green under blue background). Furthermore a number of the genes involved in the metabolism downstream of glycolysis including PDH pathway and aerobic respiration were found to be the targets of CRP regulation. The number of target 0.5 represents such a particular case as fbaB<CRP>yegT (see Table S3), in which one (fbaB) of the divergent promoters is known under the control of CRP but possible regulation of the opposite promoter (yegT) by CRP can not be ruled out.
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pone-0020081-g005: Regulatory roles of CRP.Upper panel: The genes under the control of CRP are indicated under either purple background (the genes for sugar transport systems) or blue background (the genes for metabolic enzymes). CRP regulates the majority of genes for three pathways of sugar transport (MFS, PTS and ABC). The number in boxes represent in the order from left to right: The number of CRP target genes listed in Regulon DB (white); the number of genes identified to be regulated by CRP in this study (green); the number of genes predicted to be under the control of CRP in this study (yellow); the total number of genes under the control of CRP (orange). The numbers shown in parenthesis represent total number of genes constituting the respective transport systems, including those not regulated by CRP. Lower panel: Most of the genes for the enzymes involved in glycolysis are controlled by Cra [30] while only three genes, fbaA, gapA and pgk, had been identified as the regulation targets of CRP (shown in while under blue background). In this study, we identified a number of novel targets of CRP (shown in green under blue background). Furthermore a number of the genes involved in the metabolism downstream of glycolysis including PDH pathway and aerobic respiration were found to be the targets of CRP regulation. The number of target 0.5 represents such a particular case as fbaB<CRP>yegT (see Table S3), in which one (fbaB) of the divergent promoters is known under the control of CRP but possible regulation of the opposite promoter (yegT) by CRP can not be ruled out.

Mentions: E. coli contains a set of substrate-specific transport systems, which are classified on the basis of molecular composition into PTS (phosphoenolpuruvate: sugar phosphotransferase) [46]–[48], ABC (ATP-binding cassette transporter) [49], MFS systems (major facilitator superfamily) [50] and several unclassified transporters. A total of 25 PTS members have been identified in E. coli [46]–[48] (Fig. 5). After Genomic SELEX screening, some additional PTS system genes for sugar transport were found to belong the CRP regulon, including fruBKA for fructose [51], [52], manXYZ for mannose transport [47], ptsG for glucose transport [47], mtlAD for mannitol transport [47] and ptsH encoding HPr component of PTS [47]. Transcription of fruAB, ptsH and pstG was confirmed to be down-regulated in the crp mutant (see Fig. 3). As a result, almost all the genes for transport of carbon sources are now identified to be under the direct control of cAMP-CRP.


Novel roles of cAMP receptor protein (CRP) in regulation of transport and metabolism of carbon sources.

Shimada T, Fujita N, Yamamoto K, Ishihama A - PLoS ONE (2011)

Regulatory roles of CRP.Upper panel: The genes under the control of CRP are indicated under either purple background (the genes for sugar transport systems) or blue background (the genes for metabolic enzymes). CRP regulates the majority of genes for three pathways of sugar transport (MFS, PTS and ABC). The number in boxes represent in the order from left to right: The number of CRP target genes listed in Regulon DB (white); the number of genes identified to be regulated by CRP in this study (green); the number of genes predicted to be under the control of CRP in this study (yellow); the total number of genes under the control of CRP (orange). The numbers shown in parenthesis represent total number of genes constituting the respective transport systems, including those not regulated by CRP. Lower panel: Most of the genes for the enzymes involved in glycolysis are controlled by Cra [30] while only three genes, fbaA, gapA and pgk, had been identified as the regulation targets of CRP (shown in while under blue background). In this study, we identified a number of novel targets of CRP (shown in green under blue background). Furthermore a number of the genes involved in the metabolism downstream of glycolysis including PDH pathway and aerobic respiration were found to be the targets of CRP regulation. The number of target 0.5 represents such a particular case as fbaB<CRP>yegT (see Table S3), in which one (fbaB) of the divergent promoters is known under the control of CRP but possible regulation of the opposite promoter (yegT) by CRP can not be ruled out.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3105977&req=5

pone-0020081-g005: Regulatory roles of CRP.Upper panel: The genes under the control of CRP are indicated under either purple background (the genes for sugar transport systems) or blue background (the genes for metabolic enzymes). CRP regulates the majority of genes for three pathways of sugar transport (MFS, PTS and ABC). The number in boxes represent in the order from left to right: The number of CRP target genes listed in Regulon DB (white); the number of genes identified to be regulated by CRP in this study (green); the number of genes predicted to be under the control of CRP in this study (yellow); the total number of genes under the control of CRP (orange). The numbers shown in parenthesis represent total number of genes constituting the respective transport systems, including those not regulated by CRP. Lower panel: Most of the genes for the enzymes involved in glycolysis are controlled by Cra [30] while only three genes, fbaA, gapA and pgk, had been identified as the regulation targets of CRP (shown in while under blue background). In this study, we identified a number of novel targets of CRP (shown in green under blue background). Furthermore a number of the genes involved in the metabolism downstream of glycolysis including PDH pathway and aerobic respiration were found to be the targets of CRP regulation. The number of target 0.5 represents such a particular case as fbaB<CRP>yegT (see Table S3), in which one (fbaB) of the divergent promoters is known under the control of CRP but possible regulation of the opposite promoter (yegT) by CRP can not be ruled out.
Mentions: E. coli contains a set of substrate-specific transport systems, which are classified on the basis of molecular composition into PTS (phosphoenolpuruvate: sugar phosphotransferase) [46]–[48], ABC (ATP-binding cassette transporter) [49], MFS systems (major facilitator superfamily) [50] and several unclassified transporters. A total of 25 PTS members have been identified in E. coli [46]–[48] (Fig. 5). After Genomic SELEX screening, some additional PTS system genes for sugar transport were found to belong the CRP regulon, including fruBKA for fructose [51], [52], manXYZ for mannose transport [47], ptsG for glucose transport [47], mtlAD for mannitol transport [47] and ptsH encoding HPr component of PTS [47]. Transcription of fruAB, ptsH and pstG was confirmed to be down-regulated in the crp mutant (see Fig. 3). As a result, almost all the genes for transport of carbon sources are now identified to be under the direct control of cAMP-CRP.

Bottom Line: Using the newly developed Genomic SELEX screening system of transcription factor-binding sequences, however, we have identified a total of at least 254 CRP-binding sites.Based on the functions of novel target genes, we conclude that CRP plays a key regulatory role in the whole processes from the selective transport of carbon sources, the glycolysis-gluconeogenesis switching to the metabolisms downstream of glycolysis, including tricarboxylic acid (TCA) cycle, pyruvate dehydrogenase (PDH) pathway and aerobic respiration.One unique regulation mode is that a single and the same CRP molecule bound within intergenic regions often regulates both of divergently transcribed operons.

View Article: PubMed Central - PubMed

Affiliation: Department of Frontier Bioscience, Hosei University, Koganei, Tokyo, Japan.

ABSTRACT
CRP (cAMP receptor protein), the global regulator of genes for carbon source utilization in the absence of glucose, is the best-studied prokaryotic transcription factor. A total of 195 target promoters on the Escherichia coli genome have been proposed to be under the control of cAMP-bound CRP. Using the newly developed Genomic SELEX screening system of transcription factor-binding sequences, however, we have identified a total of at least 254 CRP-binding sites. Based on their location on the E. coli genome, we predict a total of at least 183 novel regulation target operons, altogether with the 195 hitherto known targets, reaching to the minimum of 378 promoters as the regulation targets of cAMP-CRP. All the promoters selected from the newly identified targets and examined by using the lacZ reporter assay were found to be under the control of CRP, indicating that the Genomic SELEX screening allowed to identify the CRP targets with high accuracy. Based on the functions of novel target genes, we conclude that CRP plays a key regulatory role in the whole processes from the selective transport of carbon sources, the glycolysis-gluconeogenesis switching to the metabolisms downstream of glycolysis, including tricarboxylic acid (TCA) cycle, pyruvate dehydrogenase (PDH) pathway and aerobic respiration. One unique regulation mode is that a single and the same CRP molecule bound within intergenic regions often regulates both of divergently transcribed operons.

Show MeSH
Related in: MedlinePlus