The Binding of Cyclic Adenosine Monophosphate Receptor to Deoxyribonucleic Acid

Enhancement by GTP of cAMP binding to hepatic nuclei and cytosol

In the present study we have demonstrated specific binding of 3H-labeled adenosine 3',5'-cyclic monophosphate (cAMP) to a nuclear extract from rat liver. GTP, GDP, and low concentrations of ATP and ADP increased nuclear binding of [3H]cAMP, and AMP inhibited [3H]cAMP binding. Photoaffinity labeling studies employing [32P]cAMP revealed four nuclear binding proteins [relative molecular weight (Mr) 36,000, 49,000, 54,000 and 57,000]. Unlabeled cAMP decreased [32P]cAMP binding to all four proteins, whereas GTP increased binding to the 57,000 protein. We also observed specific binding of [3H]cAMP in the liver cytosol, which was stimulated by GTP but not by ADP or ATP. Photoaffinity labeling studies of the cytosol in the absence of unlabeled nucleotides revealed three cAMP-binding proteins (Mr 36,000, 49,000, and 54,000). Unlabeled cAMP inhibited binding of [32P]cAMP to all three proteins, whereas in the presence of GTP there was binding of [32P]cAMP to a Mr 57,000 protein. Using DEAE-cellulose, we isolated from the nuclear extract and cytosol a cAMP-binding protein that responded to GTP with an increase in cAMP binding but was unaffected by GDP, ATP, ADP, and AMP. Guanosine imidodiphosphate did not affect cAMP binding, suggesting that the stimulatory effect of GTP may be mediated by phosphorylation. We speculate that alterations in intracellular GTP in vivo may modulate the binding of cAMP to a protein in the nucleus and cytosol.

Mechanism of CRP-mediated cya suppression in Escherichia coli

Escherichia coli strain NCR30 contains a cya lesion and a second-site cya suppressor mutation that lies in the crp gene. NCR30 shows a pleiotropic phenotypic reversion to the wild-type state in expressing many operons that require the cyclic AMP (cAMP)-cAMP receptor protein (CRP) complex for positive control. In vivo beta-galactosidase synthesis in NCR30 was sensitive to glucose-mediated repression, which was relieved not only by cAMP but also by cyclic GMP and cyclic CMP. The CRP isolated from NCR30 differed from the protein isolated from wild-type E. coli in many respects. The mutant protein bound cAMP with four to five times greater affinity than wild-type CRP. Protease digestion studies indicated that native NCR30 CRP exists in the cAMP-CRP complex-like conformation. The protein conferred a degree of cAMP independence on the in vitro synthesis of beta-galactosidase. In addition, the inherent positive control activity of the mutant protein in vitro was enhanced by those nucleotides that stimulate in vivo beta-galactosidase synthesis in NCR30. The results of this study supported the conclusion that the crp allele of NCR30 codes for a protein having altered effector specificity yet capable of promoting positive control over catabolite-sensitive operons in the absence of an effector molecule.

Autoregulation of the Escherichia coli crp gene: CRP is a transcriptional repressor for its own gene

The restriction fragments carrying the region preceding the Escherichia coli crp structural gene were transcribed. The 5' end of the crp mRNA was determined by RNAase partial digestion and S1 digestion methods. Thus the crp gene has been shown to possess a 167 bp leader. CRP-cAMP specifically prevents the crp transcription. In other words, the crp gene is regulated autogenously. DNAase foot-printing studies indicated that CRP-cAMP binds to the crp gene at positions +26 to +67. This region exhibits a striking sequence homology to the CRP-binding sites in other genes. CRP and RNA polymerase bind to the crp regulatory region simultaneously. These results suggest a different mechanism for transcriptional repression of the crp gene by CRP-cAMP from that of a typical operator-repressor model.

Interaction of the chick oviduct progesterone receptor with deoxyribonucleic acid

The purified DNA binding component (receptor A) of the chick oviduct progesterone receptor has been analyzed for its ability to bind to the cloned ovalbumin gene and to plasmid DNA of various structural compositions. The rapid equilibrium filter adsorption assay of Riggs et al. [Riggs, A. D., Suzuki, H., & Bourgeois, S. (1970) J. Mol. Biol. 48, 67] has been used to demonstrate high affinity binding of the protein to DNA (Kdiss = 10(-10) M at 50 mM KCl, pH 7.2). Studies of association rates are consistent with equilibrium measurements (t 1/2 = 40-80 min). Association of purified receptor with DNA and the kinetics of the interaction have been verified independently by velocity sedimentation techniques. Direct binding assays were performed with the ovalbumin structural gene (cDNA), the entire natural ovalbumin gene containing seven intervening sequences, and various ovalbumin gene fragments coding for the 5' end of the nuclear precursor RNA, intron-exon junctions, and the 3'-noncoding region of the gene. No DNA-sequence specificity was identified for the binding of the receptor protein to any region of ovalbumin gene DNA. In contrast, the structural integrity of the DNA template greatly affected receptor binding. The poorest affinity was to supercoiled DNA and to blunt end, linear duplex gene fragments. The receptor bound saturably to DNA containing limited nicks but became nonsaturable as nicks were increased. Binding of the protein to double-stranded DNA increased susceptibility of the DNA to digestion by the enzyme S1, a single strand specific nuclease. On the basis of preferential receptor binding to single-stranded DNA, a possible mechanism involving DNA helix destabilization is discussed.

Purification of glutamine synthetase from a variety of bacteria

We have developed two procedures which allow the very rapid purification of glutamine synthetase (GS) from a diverse variety of bacteria. The first procedure, based upon differential sedimentation, depends upon the association of GS with deoxyribonucleic acid in cell extracts. The second procedure, derived from the method of C. Gross et al (J. Bacteriol. 128:382-389, 1976) for purifying ribonucleic acid polymerase by polyethylene glycol (PEG) precipitation, enabled us to obtain high yields of GS from either small or large quantities of cells. We used the PEG procedure to purify GS from Klebsiella aerogenes, K. pneumoniae, Escherichia coli, Salmonella typhimurium, Rhizobium sp. strain 32H1, R. meliloti, Azotobacter vinelandii, Pseudomonas putida, Caulobacter crescentus, and Rhodopseudomonas capsulata. The purity of the GS obtained, judged by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, was high, and in many instances only a single protein band was detected.

Binding of CRP to DNA-dependent RNA polymerase from E. coli: modulation by cAMP of the interactions with free and DNA-bound holo and core enzyme

The regulatory protein CRP (or CAP) from E. coli is shown to display two distinct patterns of binding interactions with DNA-dependent RNA polymerase. The free core enzyme, and both the core and the holo polymerase when bound to single-stranded DNA, can bind CRP in a cAMP-independent association reaction. Instead, the binding of CRP to free holoenzyme and to holo or core polymerase bound to native DNA was undetectable in the absence of cAMP. The specific ligand of CRP (cAMP) strengthens distinctively this class of interactions. In no case could any release of sigma-factor be demonstrated. Estimates of the dissociation constants were obtained for the various binding reactions which were investigated under quasi-physiological ionic conditions. These, together with the known values of the in vivo concentrations of CRP and RNA polymerase, suggest that the interactions described may have a functional significance.

Intracellular location of catabolite activator protein of Escherichia coli

The catabolite activator protein was assayed in extracts from the minicell-producing Escherichia coli strain P678-54. The level of catabolite activator protein was found to be the same in both parent cells and purified minicells, regardless of whether the bacteria were grown on glucose (which leads to low intracellular cyclic adenosine monophosphate levels) or on glycerol-yeast extract or LB broth (which lead to high cyclic adenosine monophosphate concentrations in the cell). Thus, at any given time most catabolite activator protein molecules are found in the cytoplasm. The implications of this for the mechanism of catabolite activator protein action at catabolite-sensitive operons are discussed.

Glucocorticoid regulation of mouse mammary tumor virus gene expression

Glucocorticoid hormones act rapidly and specifically to stimulate the synthesis of mouse mammary tumor virus RNA in a variety of mouse mammary tumor cells and infected heterologous cells. The increase in viral RNA production appears to be mediated by receptor proteins and requires the presence of basal levels of viral RNA. Infection of heterologous cells with MMTV may alter host cell responses to glucocorticoids; in addition, production of unintegrated viral DNA in these cells has provided reagents required for studying the structure and function of the viral DNA itself. The advent of new techniques for genetic manipulation of eukaryotic cells and for isolation of large amounts of specific DNA sequences should now permit detailed analyses of steroid hormone action in this system.

The binding of lac repressor and the catabolite gene activator protein to halogen-substituted analogues of poly[d(A-T)]

We have measured the binding of two regulatory proteins to the complete halogen-substituted series of poly[d(A-T)] analogues. Both the lac repressor and the catabolite gene activator protein were found to bind more strongly to all of the halogen-substituted DNAs than they do to poly[d(A-T)]. For both proteins, the order of binding preference is poly[d(A-ioU)] is greater than poly[d(A-brU)] is greater than or equal to poly[d(A-clU)] is greater than poly[d(A-flU)] is greater than poly[d(A-T)]. Quantitative data on the binding of these proteins to poly[d(A-U)] is also given. The significance of these results for the mechanism of protein-DNA interaction is discussed. This is the first report that an activator protein binds more strongly to a halogen-substituted DNA; we discuss this result with regard to the mechanism of action of bromodeoxyruidine and other halogen-substituted base analogues on the inhibition and induction of differentiation in eucaryotic cells.

Cyclic adenosine monophosphate receptor: effect of cyclic AMP analogues on DNA binding and proteolytic inactivation

The cyclic AMP receptor protein of Escherichia coli in the presence of cyclic AMP undergoes a conformational change resulting in an increased affinity for DNA and an increased susceptibility to attack by proteolytic enzymes resulting in loss of DNA binding capacity. Of several cyclic nucleotides tested only cyclic AMP and cyclic tubercidin monophosphate are able to effect the conformational transition in cyclic AMP receptor protein, prerequisite to proteolytic inactivation or DNA binding. Other analogues such as cyclic GMP or cyclic IMP which are competitive inhibitors of cyclic AMP do not support DNA binding or proteolytic inactivation.

The interaction of estradiol-receptor protein with the genome: an argument for the existence of undetected specific sites

In extracts from rat and calf uterus, the steroid hormone 17 beta-estradiol stimulates the binding of its specific receptor protein to DNA. This interaction appears to be of low affinity (half of the estradiol-activated, 5S receptor bound at 300-400 mug/ml DNA) and nonspecific with respect to DNA base sequence. No binding to double-stranded RNA is observed. These findings are consistent with several in vivo observations. In particular, when the cytoplasmic receptor protein binds hormone, it migrates to the cell nucleus to an extent consistent with its affinity for DNA in vitro, and this in vivo nuclear binding is uniform and nonsaturable in the testable range (to greater than 3 times 10-4 sites per cell). The level of biological response appears to parallel the hormone dose up to these high levels of receptor binding. How are these observations to be reconciled with the prevalent view of steroid receptors as gene control proteins regulating transcription at specific loci on the genome? Our model is based on an analogy with the DNA binding properties of the E. coli lac repressor protein. We believe that the estradiol receptor exerts its effect by binding to a small number of high affinity sites on the genome, while also having a finite low affinity for nonspecific DNA sequences. These nonspecific loci, because of their vast number, completely mask the presence of the high affinity sites. We estimate that up to 10-3 specific sites, with affinities in the range 10- minus 8 minus 10- minus 10 M, could exist without being detected by bulk binding assays currently in use. However, alternative approaches should allow detection of these sites, and some of these are suggested.

Developmental modulation of deoxyribonucleic acid-binding proteins of Bacillus subtilis during sporulation stages

The isolation of deoxyribonucleic acid (DNA)-binding proteins from various stages of growth and sporulation of Bacillus subtilis is described. After adsorption and elution from phosphocellulose, the proteins were fractionated according to their ability to adsorb to denatured calf thymus DNA-cellulose or native B. subtilis DNA-cellulose. The proteins were analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and purification was monitored by a nitrocellulose filter binding assay. Approximately 1% of the proteins in the crude extract adsorbed to denatured calf thymus DNA-cellulose and 0.1% adsorbed to native B. subtilis DNA-cellulose. Each class of proteins varied qualitatively and quantitatively as sporulation proceeded. Several proteins from the exponential phase of growth that bound to denatured DNA were lost by T(0), whereas at T(5) new polypeptides appeared. Fewer changes in the profile of proteins with affinity for native DNA were observed between exponential phase and T(0); however, the dominant species in these eluates were clearly different.