Purification and crystallization of CII: an unstable transcription activator from phage lambda

The CII protein of the temperate bacteriophage lambda is a transcriptional activator involved in the lysis-lysogeny switch of the phage. It is an unstable protein of 97 amino acids and is known to exist as a tetramer in the native state. The cII gene has been cloned and expressed in Escherichia coli using a T7 promoter based over-expression system. The recombinant CII protein has been purified to homogeneity by ammonium sulfate fractionation followed by two steps of ion-exchange chromatography. The purified protein crystallized at pH 8.2 in hanging-drop vapor diffusion method at 293 K. The crystals diffract to a resolution of 2.8 A and belong to the space group C222 with unit-cell parameters a = 64.10, b = 106.95 and c = 120.16 A.

A novel RNA polymerase binding site upstream of the galactose promoter in Escherichia coli exhibits promoter-like activity

RNA polymerase is known to bind and utilize the overlapping promoters P1 and P2 in Escherichia coli galactose operon. We have identified an additional specific site upstream of P2, where RNA polymerase binds in a heparin-resistant manner. Binding of polymerase to this site, termed P3, occurs simultaneous to its binding at P1/P2. We have located this P3 site by DNase I footprinting. A 63 base pair region centered around position - 100 with respect to galP1 is protected by polymerase. Interestingly, a Pribnow box TATAAT is present within this protected region (-103 to -108). We have shown that transcription occurs from P3 in vitro. Primer extension analysis provides direct evidence that P3 is transcribed in vivo. The start site of transcription has been mapped at -96 position relative to galP1. beta-galactosidase assays with different gal promoter constructs reveal that while P3 alone functions as a weak in vivo promoter, it has a synergistic effect on transcription from the gal operon, since deletion of P3 or specifically mutating its -10 region result in a substantial reduction in the gal promoter activity.

Functional roles of the two cyclic AMP-dependent forms of cyclic AMP receptor protein from Escherichia coli

The cyclic AMP receptor protein activates transcription in Escherichia coli, only when complexed with cyclic AMP. The cyclic AMP receptor protein-cyclic AMP complex formed at low concentrations of cyclic AMP has a different conformation from either cyclic AMP receptor protein alone or its complex with cyclic AMP formed at high cyclic AMP concentrations. Various biophysical data suggest that the latter complex resembles free cyclic AMP receptor protein. We have examined the conformational and biological properties of cyclic AMP receptor protein as a function of cyclic AMP concentrations, using the gal operon of E. coli. A biphasic behavior is observed. It is shown that only the complex formed at lower concentrations of cyclic AMP is the transcriptionally active form. This difference between the complexes at different levels of cyclic AMP arises from a decreased ability of the cyclic AMP receptor protein-cyclic AMP complex at high cyclic AMP concentrations to bind to DNA at specific sites.

Repression and activation of transcription by Gal and Lac repressors: involvement of alpha subunit of RNA polymerase

Gal or Lac repressor binding to an upstream DNA segment, in the absence of DNA looping, represses the P1 promoter located on the same face and activates the P2 promoter situated on the opposite face of the DNA helix in the gal operon. Both inhibition and stimulation of transcription requires the physical presence of the C-terminal domain of the alpha subunit of RNA polymerase although the latter is not required for transcription itself. We propose that Gal and Lac repressors inhibit or stimulate transcription initiation by disabling or stimulating RNA polymerase activity at a post-binding step by directly or indirectly altering the C-terminal alpha domain to an unfavorable state at P1 or a more favorable state at P2, respectively.

Transcription regulation by inflexibility of promoter DNA in a looped complex

The gal operon of Escherichia coli is negatively regulated by repressor binding to bipartite operators separated by 11 helical turns of DNA. Synergistic binding of repressor to separate sites on DNA results in looping, with the intervening DNA as a topologically closed domain containing the two promoters. A closed DNA loop of 11 helical turns, which is in-flexible to torsional changes, disables the promoters either by resisting DNA unwinding needed for open complex formation or by impeding the processive DNA contacts by an RNA polymerase in flux during transcription initiation. Interaction between two proteins bound to different sites on DNA modulating the activity of the intervening segment toward other proteins by allostery may be a common mechanism of regulation in DNA-multiprotein complexes.

Interaction of synthetic analogues of distamycin with poly(dA-dT): role of the conjugated N-methylpyrrole system

Two synthetic analogues of distamycin (Dst), PPA and PAP, containing a saturated beta-alanine moiety substituting for an N-methylpyrrole chromophore were studied for their interactions with the double-stranded alternating copolymer poly(dA-dT).poly(dA-dt) [abbreviated as poly(dA-dT)], with UV absorption and circular dichroism (CD) spectroscopy. The distinctive feature of these analogues is the difference in the extents of extended conjugation due to contiguous pyrrole rings: it decreases in the order Dst greater than PPA greater than PAP. Both these analogues bind to poly(dA-dT) in a way similar to Dst, as suggested from the observed red shift in the UV spectra of the ligands upon complexation and the appearance of induced Cotton effects (in the 290-350-nm region) in the CD spectra of the complexes. A comparative study of (i) the spectral features of the complexes between these ligands, Dst and netrospin (Nt) and poly(dA-dT), and (ii) the binding parameters for the association with the polynucleotide suggests that the number and relative positions of the pyrrole moieties influence the spectral features and thermodynamic stabilities of the complexes, and the latter show a progressive decrease in the order Dst greater than Nt greater than PPA greater than PAP. Implications of these results vis-à-vis the molecular basis of Dst-DNA interaction are discussed.

Interaction of synthetic analogs of distamycin with DNA. Role of the conjugated N-methylpyrrole system in specificity of binding

Interaction of two synthetic analogs of distamycin (Dst), PPA and PAP, containing a saturated beta-alanine moiety replacing one N-methylpyrrole ring, with different polynucleotides and natural DNAs were studied using UV and CD spectroscopy. The results indicate that, similar to Dst, these analogs bind to DNA via the minor groove with a specificity towards AT-base pairs. It may be proposed that pyrrole chromophores in Dst probably do not play a role in the AT-base selectivity exhibited by Dst.