Characterization of the activating region of Escherichia coli catabolite gene activator protein (CAP) II. Role at class I and class II CAP-dependent promoters

Zhou, Yuhong; Merkel, Tod J.; Ebright, Richard H.

doi:10.1016/0022-2836(94)90035-3

Cited by 98 publications

(88 citation statements)

References 31 publications

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“…The linker connecting the N-and C-terminal domains of ␣ is sufficiently flexible to allow the CTD to move freely at least 30 bp along the promoter DNA. This is supported by previous reports that a single CRP site can be shifted from Ϫ61.5 to around Ϫ90, with retention of transcription activation (25) and with retention of the same critical determinants of CRP (26). NMR studies also indicate the presence of a flexible linker of at least 13 residues between the N-and C-terminal domains (27).…”

Section: Resultssupporting

confidence: 85%

Positioning of two alpha subunit carboxy-terminal domains of RNA polymerase at promoters by two transcription factors

Murakami

Owens

Belyaeva

et al. 1997

Proc. Natl. Acad. Sci. U.S.A.

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Interactions between the cAMP receptor protein (CRP) and the carboxy-terminal regulatory domain (CTD) of Escherichia coli RNA polymerase ␣ subunit were analyzed at promoters carrying tandem DNA sites for CRP binding using a chemical nuclease covalently attached to ␣. Each CRP dimer was found to direct the positioning of one of the two ␣ subunit CTDs. Thus, the function of RNA polymerase may be subject to regulation through protein-protein interactions between the two ␣ subunits and two different species of transcription factors.The RNA polymerase holoenzyme of Escherichia coli is composed of core enzyme with subunit structure ␣ 2 ␤␤Ј, responsible for RNA polymerization, and one of multiple species of subunit, responsible for promoter recognition. Promoter selectivity of the holoenzyme is modulated by direct or indirect interaction with many transcription factors, resulting in switching of the global pattern of gene transcription according to the environment. The best-characterized target on the RNA polymerase involved in molecular communication with transcription factors is the ␣ subunit carboxy-terminal domain (CTD) that contains the contact sites for class I transcription factors. The ␣ subunit, consisting of 329 amino acid residues, is composed of two structural domains, each responsible for distinct functions (1-3) and each forming independent structural domains connected by a protease-sensitive flexible linker (4-6). The amino (N)-terminal domain from residues 20 to 235 plays a key role in RNA polymerase assembly by providing the contact surface for ␣ dimerization and binding of ␤ and ␤Ј subunits (7-10), whereas the CTD from residues 235 to 329 plays a regulatory role by providing the contact surfaces for trans-acting protein factors and cis-acting DNA elements (11)(12)(13)(14).Whereas the regulation of many E. coli promoters involves a single factor, some promoters are regulated by two or more transcription factors, and such coregulation systems involving multiple species of transcription factors can couple gene expression to diverse environmental conditions. Knowledge of the molecular mechanism of prokaryotic transcription regulation involving more than two factors would contribute much to understanding of the events carried out in eukaryotes, because the regulation of gene transcription in eukaryotes generally involves the action of multiple transcription factors. To gain insight into this problem, we analyzed interactions between RNA polymerase and cAMP receptor protein (CRP) dimers on promoters carrying tandem CRP-binding sites at various positions relative to the transcription start site. A set of promoters was constructed carrying one DNA site for CRP centered at position Ϫ41.5 upstream from the transcription start point and a second DNA site for CRP located further upstream (refs. 15

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Section: Resultssupporting

confidence: 85%

Positioning of two alpha subunit carboxy-terminal domains of RNA polymerase at promoters by two transcription factors

Murakami

Owens

Belyaeva

et al. 1997

Proc. Natl. Acad. Sci. U.S.A.

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“…This observation is consistent with data obtained for other promoters, such as mtr regulated by TyrR (18), the TOL plasmid P m promoter (17), and the rha promoter of E. coli (15). Subsequently, we used a series of point mutants exhibiting alanine substitutions (19,20). TodT-dependent transcription from P todX was significantly affected in a background in which ␣-CTDL289A or ␣-CTDK291A mutants were overproduced, because activity decreased by Ϸ40% with respect to the wild type.…”

Section: Ihf Binds To Ptodx In Vitrosupporting

confidence: 87%

The TodS–TodT two-component regulatory system recognizes a wide range of effectors and works with DNA-bending proteins

Lacal

Büsch

Guazzaroni

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

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The TodS and TodT proteins form a previously unrecognized and highly specific two-component regulatory system in which the TodS sensor protein contains two input domains, each of which are coupled to a histidine kinase domain. This system regulates the expression of the genes involved in the degradation of toluene, benzene, and ethylbenzene through the toluene dioxygenase pathway. In contrast to the narrow substrate range of this catabolic pathway, the TodS effector profile is broad. TodS has basal autophosphorylation activity in vitro, which is enhanced by the presence of effectors. Toluene binds to TodS with high affinity (K d ‫؍‬ 684 ؎ 13 nM) and 1:1 stoichiometry. The analysis of the truncated variants of TodS reveals that toluene binds to the N-terminal input domain (K d ‫؍‬ 2.3 ؎ 0.1 M) but not to the C-terminal half. TodS transphosphorylates TodT, which binds to two highly similar DNA binding sites at base pairs ؊107 and ؊85 of the promoter. Integration host factor (IHF) plays a crucial role in the activation process and binds between the upstream TodT boxes and the ؊10 hexamer region. In an IHF-deficient background, expression from the tod promoter drops 8-fold. In vitro transcription assays confirmed the role determined in vivo for TodS, TodT, and IHF. A functional model is presented in which IHF favors the contact between the TodT activator, bound further upstream, and the ␣-subunit of RNA polymerase bound to the downstream promoter element. Once these contacts are established, the tod operon is efficiently transcribed.Pseudomonas ͉ sensor kinase ͉ toluene dioxygenase ͉ transcriptional regulator M any Pseudomonas putida strains are able to use benzene, toluene, and ethylbenzene as the sole carbon and energy source through the toluene dioxygenase (TOD) pathway (1). In this pathway, the aromatic hydrocarbons are oxidized to their corresponding substituted catechols, which are further metabolized to Krebs cycle intermediates (1, 2). The catabolic genes of the TOD pathway form the operon todXFC1C2BADEGIH, which is transcribed from a single promoter called P todX , located upstream from the todX gene (1-3). The todST genes are found downstream and form an independent operon that is expressed constitutively (2, 3).TodS and TodT have been proposed to form a two-component regulatory system (TCS) that regulates the tod catabolic operon in P. putida F1 (3). TodT shows all of the characteristics of a response regulator, whereas sequence-based domain predictions indicate that the 108-kDa TodS belongs to a family of sensor histidine kinases that have not been studied at the biochemical level. TodS is predicted to comprise two supradomains, each containing a PAS͞PAC sensory domain and a histidine kinase domain. The supradomains are separated by the receiver domain of a response regulator. In contrast to other histidine kinases, TodS apparently lacks transmembrane regions (3). The mode of action of this previously unrecognized type of histidine kinase has yet to be established. On the basis of moderate sequence simil...

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“…Biochemical and genetic results indicate that the interaction between CAP and αCTD is mediated by "activating region 1" of the downstream subunit of CAP (AR1; blue in Fig 3a [31,32,33,34,35]) and the "287 determinant" of αCTD (yellow in Fig 3a [36]). Biochemical and genetic results further indicate that the interaction between αCTD and DNA is mediated by the "265 determinant" of αCTD (red in Fig 3a [36,37,38]) and the DNA minor groove [39].…”

Section: Transcription Activation At Class I Cap-dependent Promotersmentioning

confidence: 99%

Catabolite activator protein: DNA binding and transcription activation

Lawson

Swigon

Murakami

et al. 2004

Current Opinion in Structural Biology

291

322

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Recent structures of Escherichia coli catabolite activator protein (CAP) in complex with DNA, and in complex with RNA polymerase α subunit C-terminal domain (αCTD) and DNA, have yielded insights into how CAP binds DNA and activates transcription. Comparison of multiple structures of CAP-DNA complexes has revealed contributions of direct readout and indirect readout to DNA binding by CAP. The structure of the CAP-αCTD-DNA complex has provided the first structural description of interactions between a transcription activator and its functional target within the general transcription machinery. Using the structure of the CAP-αCTD-DNA complex, the structure of an RNAP-DNA complex, and restraints from biophysical, biochemical, and genetic experiments, it has been possible to construct detailed three-dimensional models of intact Class I and Class II transcription activation complexes.

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Characterization of the activating region of Escherichia coli catabolite gene activator protein (CAP) II. Role at class I and class II CAP-dependent promoters

Cited by 98 publications

References 31 publications

Positioning of two alpha subunit carboxy-terminal domains of RNA polymerase at promoters by two transcription factors

Positioning of two alpha subunit carboxy-terminal domains of RNA polymerase at promoters by two transcription factors

The TodS–TodT two-component regulatory system recognizes a wide range of effectors and works with DNA-bending proteins

Catabolite activator protein: DNA binding and transcription activation

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