Studies of the distribution of Escherichia coli cAMP-receptor protein and RNA polymerase along the E. coli chromosome

The Escherichia coli cAMP receptor protein (CRP) is a factor that activates transcription at over 100 target promoters. At Class I CRP-dependent promoters, CRP binds immediately upstream of RNA polymerase and activates transcription by making direct contacts with the C-terminal domain of the RNA polymerase α subunit (αCTD). Since αCTD is also known to interact with DNA sequence elements (known as UP elements), we have constructed a series of semi-synthetic Class I CRP-dependent promoters, carrying both a consensus DNA-binding site for CRP and a UP element at different positions. We previously showed that, at these promoters, the CRP–αCTD interaction and the CRP–UP element interaction contribute independently and additively to transcription initiation. In this study, we show that the two halves of the UP element can function independently, and that, in the presence of the UP element, the best location for the DNA site for CRP is position -69.5. This suggests that, at Class I CRP-dependent promoters where the DNA site for CRP is located at position -61.5, the two αCTDs of RNA polymerase are not optimally positioned. Two experiments to test this hypothesis are presented.

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Determination of the rates of synthesis and degradation of adenosine 3′,5′-cyclic monophosphate in Escherichia coli CRP− and CRP+ strains

Canadian Journal of Biochemistry ◽

10.1139/o78-130 ◽

1978 ◽

Vol 56 (9) ◽

pp. 849-852 ◽

Cited By ~ 12

Author(s):

Ann D. E. Fraser ◽

Hiroshi Yamazaki

Keyword(s):

Escherichia Coli ◽

Receptor Protein ◽

Camp Receptor Protein ◽

Balanced Growth ◽

E Coli ◽

Cyclic Monophosphate ◽

Camp Receptor ◽

Extracellular Camp ◽

Synthesis And Degradation

We have developed a method for estimating the rates of synthesis and degradation of adenosine 3′,5′-cyclic monophosphate (cAMP) in Escherichia coli during balanced growth. Applying this method, we have found that an E. coli CRP− mutant 5333 (deficient for cAMP receptor protein) synthesizes cAMP about 25 times faster than does its CRP+ parent 1100. This accounts for the abnormally high intracellular and extracellular cAMP accumulation in 5333.

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Regulation of ytfK by cAMP-CRP Contributes to SpoT-Dependent Accumulation of (p)ppGpp in Response to Carbon Starvation YtfK Responds to Glucose Exhaustion

Frontiers in Microbiology ◽

10.3389/fmicb.2021.775164 ◽

2021 ◽

Vol 12 ◽

Author(s):

Laura Meyer ◽

Elsa Germain ◽

Etienne Maisonneuve

Keyword(s):

Escherichia Coli ◽

Cyclic Amp ◽

Catabolite Repression ◽

Stringent Response ◽

Receptor Protein ◽

Glucose Starvation ◽

Camp Receptor Protein ◽

E Coli ◽

Camp Receptor ◽

Glucose Availability

Guanosine penta- or tetraphosphate (known as (p)ppGpp) serves as second messenger to respond to nutrient downshift and other environmental stresses, a phenomenon called stringent response. Accumulation of (p)ppGpp promotes the coordinated inhibition of macromolecule synthesis, as well as the activation of stress response pathways to cope and adapt to harmful conditions. In Escherichia coli, the (p)ppGpp level is tightly regulated by two enzymes, the (p)ppGpp synthetase RelA and the bifunctional synthetase/hydrolase SpoT. We recently identified the small protein YtfK as a key regulator of SpoT-mediated activation of stringent response in E. coli. Here, we further characterized the regulation of ytfK. We observed that ytfK is subjected to catabolite repression and is positively regulated by the cyclic AMP (cAMP)-cAMP receptor protein (CRP) complex. Importantly, YtfK contributes to SpoT-dependent accumulation of (p)ppGpp and cell survival in response to glucose starvation. Therefore, regulation of ytfK by the cAMP-CRP appears important to adjust (p)ppGpp level and coordinate cellular metabolism in response to glucose availability.

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Asymmetric arrangement of two alpha subunits within Escherichia coli RNA polymerase Involvement of one alpha subunit in contact with cAMP receptor protein

Journal of Molecular Biology ◽

10.1016/0022-2836(94)90057-4 ◽

1994 ◽

Vol 236 (5) ◽

pp. 1283-1288 ◽

Cited By ~ 8

Author(s):

Chao Zou ◽

Nobuyuki Fujita ◽

Akira Ishihama

Keyword(s):

Escherichia Coli ◽

Rna Polymerase ◽

Alpha Subunit ◽

Receptor Protein ◽

Camp Receptor Protein ◽

Alpha Subunits ◽

Camp Receptor

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Mapping the cAMP receptor protein contact site on the ? subunit of Escherichia coli RNA polymerase

Molecular Microbiology ◽

10.1111/j.1365-2958.1992.tb01437.x ◽

1992 ◽

Vol 6 (18) ◽

pp. 2599-2605 ◽

Cited By ~ 56

Author(s):

Chao Zou ◽

Nobuyuki Fujita ◽

Kazuhiko Igarashi ◽

Akira Ishihama

Keyword(s):

Escherichia Coli ◽

Rna Polymerase ◽

Receptor Protein ◽

Camp Receptor Protein ◽

Contact Site ◽

Camp Receptor

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Spacing requirements for interactions between the C-terminal domain of the α subunit of Escherichia coli RNA polymerase and the cAMP receptor protein

Biochemical Journal ◽

10.1042/bj3300413 ◽

1998 ◽

Vol 330 (1) ◽

pp. 413-420 ◽

Cited By ~ 8

Author(s):

S. Georgina LLOYD ◽

J. W. Stephen BUSBY ◽

J. Nigel SAVERY

Keyword(s):

Escherichia Coli ◽

Rna Polymerase ◽

Binding Site ◽

Transcription Initiation ◽

Receptor Protein ◽

Camp Receptor Protein ◽

Α Subunit ◽

Synthetic Promoters ◽

Terminal Domain ◽

Camp Receptor

During transcription initiation at bacterial promoters, the C-terminal domain of the RNA polymerase α subunit (αCTD) can interact with DNA-sequence elements (known as UP elements) and with activator proteins. We have constructed a series of semi-synthetic promoters carrying both an UP element and a consensus DNA-binding site for the Escherichia coli cAMP receptor protein (CRP; a factor that activates transcription by making direct contacts with αCTD). At these promoters, the UP element was located at a variety of distances upstream of the CRP-binding site, which was fixed at position -41.5 bp upstream of the transcript start. At some positions, the UP element caused enhanced promoter activity whereas, at other positions, it had very little effect. In no case was the CRP-dependence of the promoter relieved. DNase I and hydroxyl-radical footprinting were used to study ternary RNA polymerase-CRP-promoter complexes formed at two of the most active of these promoters, and co-operativity between the binding of CRP and purified α subunits was studied. The footprints show that αCTD binds to the UP element as it is displaced upstream but that this displacement does not prevent αCTD from being contacted by CRP. Models to account for this are discussed.

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