Lac DNA, RNA polymerase and cyclic AMP receptor protein, cyclic AMP, lac repressor and inducer are the essential elements for controlled lac transcription

UV oxidation of cyclic AMP receptor protein, a global bacterial gene regulator, decreases DNA binding and cleaves DNA at specific sites

UV light is a widely-employed, and environmentally-sensitive bactericide but its mechanism of action is not fully defined. Proteins are major chromophores and targets for damage due to their abundance, but the role of proteins in inducing damage to bound DNA, and the effects on DNA-protein interactions is less well characterized. In E. coli (and other Gram-negative bacteria) the cyclic AMP receptor protein (CRP/CAP) regulates more than 500 genes. In this study we show that exposure of isolated dimeric CRP-cAMP to UV modifies specific Met, Trp, Tyr, and Pro side-chains, induces inter-protein Tyr63-Tyr41 cross-links, and decreases DNA binding via oxidation of Met114/Pro110 residues in close proximity at the CRP dimer interface. UV exposure also modifies DNA-bound cAMP-CRP, with this resulting in DNA cleavage at specific G/C residues within the sequence bound to CRP, but not at other G/C sites. Oxidation also increases CRP dissociation from DNA. The modifications at the CRP dimer interface, and the site-specific DNA strand cleavage are proposed to occur via oxidation of two species Met residues (Met114 and Met189, respectively) to reactive persulfoxides that damage neighbouring amino acids and DNA bases. These data suggest that modification to CRP, and bound DNA, contributes to UV sensitivity.

Novel insights from hybrid LacI/GalR proteins: family-wide functional attributes and biologically significant variation in transcription repression

LacI/GalR transcription regulators have extensive, non-conserved interfaces between their regulatory domains and the 18 amino acids that serve as ‘linkers’ to their DNA-binding domains. These non-conserved interfaces might contribute to functional differences between paralogs. Previously, two chimeras created by domain recombination displayed novel functional properties. Here, we present a synthetic protein family, which was created by joining the LacI DNA-binding domain/linker to seven additional regulatory domains. Despite ‘mismatched’ interfaces, chimeras maintained allosteric response to their cognate effectors. Therefore, allostery in many LacI/GalR proteins does not require interfaces with precisely matched interactions. Nevertheless, the chimeric interfaces were not silent to mutagenesis, and preliminary comparisons suggest that the chimeras provide an ideal context for systematically exploring functional contributions of non-conserved positions. DNA looping experiments revealed higher order (dimer–dimer) oligomerization in several chimeras, which might be possible for the natural paralogs. Finally, the biological significance of repression differences was determined by measuring bacterial growth rates on lactose minimal media. Unexpectedly, moderate and strong repressors showed an apparent induction phase, even though inducers were not provided; therefore, an unknown mechanism might contribute to regulation of the lac operon. Nevertheless, altered growth correlated with altered repression, which indicates that observed functional modifications are significant.

The study of guanosine 5'-diphosphate 3'-diphosphate-mediated transcription regulation in vitro using a coupled transcription-translation system

The effects of the "alarmone" guanosine 5'-diphosphate 3'-diphosphate (ppGpp) on regulation of the Salmonella typhimurium histindine operon and the Escherichia coli tRNA(leu) operon were analyzed in vitro using a DNA-dependent transcription-translation system, S-30. The expression of the hisG promoter is positively regulated by ppGpp, whereas that of the leuV promoter (of tRNA(1eu)) is negatively regulated by ppGpp. In an attempt to understand the global regulatory mechanism of ppGpp control, interrelationship between ppGpp-dependent activation and repression of gene expression was examined using these promoters as models. It has been traditionally supposed that the ppGpp-dependent regulation, at least for the activation, is by a passive mode of control: the activation of gene expression by ppGpp is a consequence of the repression of stable RNA gene expression in the condition of RNA polymerase limiting. To test this model, the ppGpp-dependent regulations of both an activable promoter (hisGp) and a repressible promoter (leuVp) were determined in vitro simultaneously using a mixed template setup. The rationale for this exercise was to see whether the ppGpp-dependent activation and repression are inversely correlated in the in vitro condition in which RNA polymerase is limiting. No correlation was observed. It was concluded that the ppGpp-dependent activation is independent of the repression. Moreover, it was proposed that ppGpp-dependent activation and repression are mediated by titratable factors, each of which operate independently.

In vitro protein folding by ribosomes from Escherichia coli, wheat germ and rat liver: the role of the 50S particle and its 23S rRNA

Ribosomes from a number of prokaryotic and eukaryotic sources (e.g. Escherichia coli, wheat germ and rat liver) can refold a number of enzymes which are denatured with guanidine/HC1 prior to incubation with ribosomes. In this report, we present our observations on the refolding of denatured lactate dehydrogenase from rabbit muscle and glucose-6-phosphate dehydrogenase from baker's yeast by ribosomes from E. coli, wheat germ and rat liver. The protein-folding activity of E. coli ribosomes was found to be present in 50S particles and in 23S rRNA. The 30S particle or 16S rRNA did not show any protein-folding activity. The protein-folding activity of 23S rRNA may depend on its tertiary conformation. Loss of tertiary structure, by incubation with low concentrations of EDTA, inhibited the protein-folding activity of 23S rRNA. This low concentration of EDTA had no effect on folding of the denatured enzymes by themselves.

Refolding of denatured lactate dehydrogenase by Escherichia coli ribosomes

Escherichia coli ribosomes were used to refold denatured lactate dehydrogenase from porcine muscle. This activity of ribosomes, unlike most of the chaperons, did not require the presence of ATP. The molar concentration of ribosomes required for this refolding was comparable with that of the enzyme. Restoration of the enzyme activity was demonstrated using assays for both the forward and backward reactions. Binding of the denatured enzyme to ribosomes and its refolding were fairly rapid processes as revealed by the time course of the reaction and inhibition of folding when the denatured enzyme was allowed to refold spontaneously for short times before the addition of ribosomes. This protein-folding activity was detected in 70 S ribosomes as well as its RNA, in 50 S particles and in 23 S rRNA. However, 30 S particles failed to refold the enzyme.

Control of gal transcription through DNA looping: inhibition of the initial transcribing complex

Involvement of DNA looping between two spatially separated gal operators, OE and OI, in repression of the gal operon has been demonstrated in vivo. An in vitro transcription assay using a minicircle DNA containing the gal promoter region with lac operators was employed to elucidate the molecular mechanism of repression. Wild-type lac repressors (LacI+ protein molecules), which are capable of associating into a tetramer and forming a DNA loop, repressed transcription from promoter sites P1 and P2, whereas a non-looping lac repressor mutant (LacI(adi)) failed to show normal repression of both of the gal promoters. Thus a DNA loop is also required for repression of transcription in vitro. Repression mediated by DNA looping resulted in the inhibition of the synthesis of complete as well as aborted transcripts, demonstrating that the repressive action was on the formation or activity of the initial transcribing complex. Under similar conditions, the gal repressor (GalR protein) did not repress the gal promoters effectively, apparently because it failed to loop DNA containing gal operators in the purified system. The component(s) or conditions that aid GalR in DNA looping remain to be identified.

lac repressor acts by modifying the initial transcribing complex so that it cannot leave the promoter

RNA polymerase engaged in the joint complex with the lac repressor at the lac UV5 promoter cannot escape into elongation but generates abortive RNA oligomers. The joint complex actively transcribes a few initial base pairs in a reaction unusually sensitive to a decrease in the substrate concentration. The joint complex, however, fails to traverse a point in the initial transcribed sequence that normally requires a high concentration of the elongating substrate. Thus, the repressor acts by augmenting a natural high "kNTP" site (pause site) embedded in the promoter. A lethal RNA polymerase mutation that mimics the effect of the repressor leads to an analogous block of promoter clearance and shortened abortive product pattern on several promoters, reflecting the widespread occurrence of high kNTP sites in promoters.

Identification and characterization of transcription termination sites in the Escherichia coli lacZ gene

The Escherichia coli lacZ gene contains a series of latent transcriptional terminators that are responsible for the polar effects of certain mutations. We demonstrate, using gel electrophoretic size analyses and nuclease S1 mapping procedures, that RNA polymerase terminates RNA synthesis in the vicinity of five positions 180, 220, 379, 421 and 463 base-pairs downstream from the start point during transcription of lacZ DNA in vitro in the presence of rho factor. Termination at all but the 421 position depends on rho factor. In the in vitro assays with 0.05 M-KCl and excess rho (36 nM), the terminators are moderately effective, having efficiencies that range from about 8% at the 180 base-pair site to 56% at the 463 base-pair site. These termination stop points correspond to five of the 11 transcriptional pause sites between 180 and 463 base-pairs. Several stop points also correspond to 3' end points of lacZ mRNA isolated from cells containing the strongly polar lacZ-U118 mutation and from cells starved for serine, thus confirming that these latent terminators are responsible for the polar effect and demonstrating that they also function under a condition of physiological stress that prevents the transcription from being translated properly. Two other potential termination factors, NusA protein and cyclic AMP receptor protein have no effect in vitro on the efficiency of termination at the five lacZ sites.

Turn of promotor DNA by cAMP receptor protein characterized by bead model simulation of rotational diffusion

The rotation diffusion of DNA double helices and their complexes with the cAMP receptor protein (CRP) has been simulated by bead models, in order to derive information on their structure in solution by comparison with results obtained from dichroism decay measurements. Straight DNA double helices are simulated by linear, rigid strings of overlapping beads. The radius of the beads and the length of the string are increased simultaneously by the same increments from initial outer dimensions derived from crystallographic data to final values, which are fitted to experimental rotation time constants observed for short DNA fragments (less than 100 bp). The final values reflect the solvated structure with the same 'solvation layer' added in all three dimensions. The protein is simulated by overlapping beads, which are assembled to a structure very similar to that found by x-ray crystallography. Complexes of the protein with DNA are formed with the centres of palindromic DNA sites at the centre of the two helix-turn-helix-motifs of the protein with some overlap of the two components. Simulation of the experimental data obtained for CRP complexes with specific DNA in the presence of cAMP requires strong bending of the double helices. According to our simulation the DNA is almost completely wrapped around the protein both in the complexes with a 62 bp fragment containing the standard CRP site and with a 80 bp fragment containing the second binding site of the lac operon. Simulations of the data obtained for a 203 bp fragment with both binding sites suggest that the two bound CRP proteins are in contact with each other and that the DNA is wrapped around the two protein dimers. A stereochemical model is suggested with a tetrahedral arrangement of the four protein subunits, which provides the advantage that two binding sites of the protein formed by two subunits each are located favorable for tight contacts to two binding sites on bent DNA, provided that the DNA sites are separated by an integer number of helix turns. In summary, the simulations demonstrate strong bending, which can be reflected by an arc radius in the range around 50 A. According to these data the overall bending angle of our longest DNA fragment is approximately 180 degrees, and thus the protruding ends are sufficiently close to each other such that RNA polymerase, for example, could contact both helical segments.

Generation of deletions in the 3'-flanking sequences of the Escherichia coli crp gene that induce cyclic AMP suppressor functions

The crp structural gene and its 3'-flanking sequences were subcloned into M13mp8, and in vitro deletions were constructed in both the 5' and 3' ends of the gene by using Bal 31 nuclease. Deletions ranged in size from 24 to 250 base pairs at the 5' end of crp. Sixteen deletions generated at the 3' end of the gene ranged in size from 133 to 675 base pairs. The majority of deletions extended into the crp structural gene. Another class of deletions, i.e., delta crp-4, delta crp-17, and delta crp-2, had endpoints extending in the 3'-flanking sequences external to the crp structural gene. Deletions were subcloned into pBR322 and transformed into the Escherichia coli cya crp deletion strain NCR438. Transformants containing plasmid pBM4 with the delta crp4 mutation, a deletion of 133 base pairs, were cyclic AMP independent. Strain NCR440 harboring this plasmid expressed beta-galactosidase and threonine dehydratase activities and fermented lactose, ribose, arabinose, and xylose in the absence of exogenous cyclic AMP. The delta crp-4 mutation also caused strain NCR440 to be hypersensitive to exogenous cyclic AMP. The cylic AMP receptor protein expressed in maxicells from pBM4 carrying the delta crp-4 mutation comigrated with the wild-type protein on electrophoretic gels. The delta crp-4 mutation demonstrates that sequences distal to the crp structural gene can mediate cyclic AMP suppressor functions.

Cloning and molecular characterization of csm mutations allowing expression of catabolite-repressible operons in the absence of exogenous cyclic AMP

The cyclic AMP (cAMP) suppressor mutation (csm) of Escherichia coli has been cloned from strain NCR30 in the HindIII-EcoRI site of pBR322. This mutation has been mapped in or near the crp gene. Wild-type crp DNA hybridized to recombinant plasmids pGM5 and pGM25 containing the cloned csm mutation. These recombinant plasmids encoded a protein product of identical molecular weight and charge as that of the wild-type cAMP receptor protein. Transformants of cya crp deletion strains harboring pBM5 or pGM25 exhibited phenotypic characteristics common to strain NCR30. These included the expression of catabolite-repressible enzymes, such as arabinose isomerase, tryptophanase, beta-galactosidase, and threonine deaminase; the expression of chemotactic and motility genes; cAMP sensitivity; and the accumulation of toxic levels of methylglyoxal. DNA sequence analysis indicated that the Csm suppressor phenotype was attributable to the insertion of a guanosine residue 17 base pairs downstream from the termination codon of the crp structural gene. The guanosine insertion is located in the stem region of the presumed transcriptional termination loop. This stem region contained a unique BssHII restriction site which was used to construct an in vitro deletion in the wild-type crp insert in plasmid pHA7. The resulting plasmid, pGM459, renders transformants having a phenotype common to that conferred by the chromosomal or cloned csm mutation. Our results indicate a novel role for the 3' flanking region of the crp structural gene in the expression of the cAMP receptor protein.

A nuclear-Overhauser-enhancement study of the solution structure of a double-stranded DNA undecamer comprising a portion of the specific target site for the cyclic-AMP-receptor protein in the gal operon. Sequential resonance assignment

A 500-MHz 1H-NMR study on a double-stranded non-self-complementary DNA undecamer comprising a portion of the specific target site for the cyclic AMP receptor protein in the gal operon is presented. Using pre-steady-state nuclear Overhauser effect (NOE) measurements, all exchangeable imino, non-exchangeable base, methyl, and H1', H2' and H2" sugar proton resonances are assigned in a sequential manner. In addition, some of the H3' sugar proton resonances are also assigned and some of the exchangeable amino proton resonances identified. The relative magnitudes of the intranucleotide and internucleotide NOEs are indicative of a right-handed B-type conformation for the duplex undecamer in solution.

The effect of glucose on cellobiose uptake and beta-D-glucosidase activity in Streptomyces granaticolor

Glucose inhibits the inducible synthesis of beta-D-glucosidase in Streptomyces granaticolor. Neither cAMP nor cGMP influence the inhibitory effect of glucose. Glucose also inhibits the inducible synthesis of the cellobiose uptake system but has no effect on its activity. This may be the mechanism underlying glucose inhibition of induction of beta-D-glucosidase in S. granaticolor.

The characterization and purification of DNA binding proteins present within herpes simplex virus infected cells using monoclonal antibodies

Hybridomas secreting monoclonal antibodies against herpes simplex virus (HSV) DNA binding proteins (DBP) have been produced. Five HSV DBP have been characterized according to molecular weight, affinity for DNA, kinetic class and localization within the infected cell. By preparing an immunoadsorbent column from antibody TI8, its specific DBP was purified to apparent homogeneity. The purified DBP retained the ability to bind to DNA.

Seminal plasmin, an antimicrobial protein from bull semen, inhibits gene expression in E. coli

RNA synthesis in Escherichia coli was immediately inhibited after addition of seminal plasmin, an antimicrobial protein from bull semen. RNA synthesis progressively decreased within 12 min and then ceased completely. In contrast, protein synthesis was not affected within the first 12 min, but thereafter became progressively inhibited. Inhibition of RNA synthesis by seminal plasmin in E. coli interfered with induction of beta-galactosidase by isopropyl-beta-D-thiogalactoside (IPTG). This implied inhibition of beta-galactosidase mRNA synthesis by seminal plasmin in vivo. The sensitivities of total in vivo RNA synthesis and beta-galactosidase mRNA synthesis against seminal plasmin were found to be similar. Seminal plasmin had no effect on the uptake of the inducer IPTG by E. coli cells.

A nuclear Overhauser enhancement study on the imino proton resonances of a DNA pentadecamer comprising the specific target site of the cyclic AMP receptor protein in the ara BAD operon

A 500 MHz 1H-NMR study on a synthetic DNA pentadecamer comprising the specific target site of the cAMP receptor protein in the ara BAD operon is presented. Using pre-steady state NOE measurements, unambiguous assignments of all the imino proton resonances and associated adenine (H2) resonances are obtained. From the NOE data interbase pair interproton distances involving the imino and adenine (H2) protons are determined. It is shown that these distances are very similar to those expected for classical B DNA (RMS difference of 0.5 A), but are significantly different from those expected for classical A DNA (RMS difference of 1.1 A).

Investigations on stimulation of lac transcription in vivo in Escherichia coli by cAMP analogues. Biological activities and structure-activity correlations

The ability of 24 systematically modified analogues of adenosine 3',5'-monophosphate (cAMP) to enhance the synthesis of beta-galactosidase in glucose-repressed Escherichia coli strains KNBL 1001 and cpd- Crookes has been investigated. The properties of the analogues in comparison with cAMP are, with only two exceptions, alike in both strains. Two analogues, 7-deazaadenosine 3',5'-monophosphate (i.e. tubercidin 3',5'-monophosphate) and (Rp)-adenosine 3',5'-monothionophosphate, exhibit higher biological activity than cAMP. The latter analogue is 50-fold more active in both strains. Three analogues showed activities comparable to cAMP, four analogues were less active and 12 analogues were unable to antagonize catabolite repression. Structure-activity correlations showed that the 2'OH-, 3'O-, 5'O-, the negative charge and the 6-amino group cannot be modified without losing biological activity in vivo, while the N-1 and N-7 in adenine are not essential. The interaction with the catabolite gene activator protein is stereoselective for an unmodified axial exocyclic oxygen. The results are compared to those obtained with cAMP analogues in E. coli in vitro and those obtained with the same analogues in protein-kinase systems and Dictyostelium species. The model of McKay et al. [McKay, D.B., Weber, J.T. and Steitz, T.A. (1982) J. Biol. Chem. 257, 9518-9524] proposed for distinct chemical interactions of cAMP with the catabolite gene activator protein is discussed and supplemented by additional hydrogen bond interactions.

Specific DNA binding of the cyclic AMP receptor protein to a synthetic oligodeoxyribonucleotide. A circular dichroism study

The interaction of the cAMP receptor protein (CRP) of Escherichia coli with a synthetic DNA undecamer (11 mer) comprising a portion of the specific target site in the gal operon and containing 8 basepairs out of the 10 basepair concensus making up specific CRP sites, has been studied by circular dichroism spectroscopy. The binding constants for the interaction of CRP with the 11 mer in the presence and absence of cAMP have been determined, and it is shown that CRP, both in the presence and absence of cAMP, induces a B-C transition in the conformation of the 11 mer.

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.

The cAMP-binding domains of the regulatory subunit of cAMP-dependent protein kinase and the catabolite gene activator protein are homologous

Comparison of the recently determined amino acid sequences of the regulatory subunit of cAMP-dependent protein kinase (RII) from bovine cardiac muscle and the Escherichia coli catabolite gene activator protein (CAP) shows significant homology. This homology extends over most of the amino-terminal domain in CAP and is particularly good for the region of the beta-roll structure. The RII sequence contains two adjacent and internally homologous regions, both of which have high resemblance to the cAMP-binding domain in CAP. This suggests that the protein kinase regulatory subunit contains two cAMP-binding domains in the carboxyl-terminal region, each having a beta-roll structure similar to that in CAP. The cAMP molecule is expected to bind to the RII within a pocket formed by residues from the beta-roll, as is the case with CAP. One cAMP molecule would interact with residues from about 163 to 220, and the other cAMP would interact with amino acids in the stretch 285-350 of the RII protein kinase sequence. As the carboxyl-terminal domain of CAP shows homologies to the DNA-binding domains of other regulatory proteins, the protein appears to be of modular construction: a DNA-binding domain joined to a cAMP-binding domain.

Cyclic AMP may not be involved in catabolite repression in Saccharomyes cerevisiae: evidence from mutants capable of utilizing it as an adenine source

Mutants able to utilize 5'-AMP or cyclic AMP as the adenine source were isolated from an ade6 ade10 double mutant by ethyl methane sulfonate mutagenesis. A single amp1 mutation, primarily selected on 5'-AMP medium, confers the phenotype for utilization of exogenous 5'-AMP as the adenine source. From the ade6 ade10 amp1 triple mutant, a mutant able to utilize cyclic AMP was isolated, and the mutant phenotype was proven to be due to the simultaneous occurrence of triple mutations designated as cam1, cam2, and cam3. The cam3 mutation, but not cam1 or cam2, also confers the phenotype for utilizing 5'-AMP, the same phenotype as the amp1 mutation. All of these mutations are recessive to the respective wild-type counterparts. Cells having the ade6 ade10 amp1 cam1 cam2 cam3 genotype showed significant ability to take up exogenous cyclic AMP, whereas no differences were observed in cyclic AMP phosphodiesterase activity in comparison with that of the original strains used in the mutant isolation. Since glucose severely repressed galactokinase synthesis in the constitutive GAL81 mutant having the ade6 ade10 amp1 cam1 cam2 cam3 genotype, irrespective of the presence or absence of cyclic AMP in the medium, it was suggested that cyclic AMP is not involved in the mechanism of catabolite repression in Saccharomyces cerevisiae. It does, however, have a stimulative effect on the galactokinase synthesis in the GAL81 mutant in the absence of glucose.

Molecular cloning and nucleotide sequencing of the gene for E. coli cAMP receptor protein

The crp gene of E. coli, which codes for cAMP receptor protein (CRP), has been cloned in the plasmid pBR322 on the basis of a genetic complementation. One of the recombinant plasmids, pHA1, was shown to direct the synthesis of CRP in a cell-free system. The location of the crp gene was determined by constructing subclones carrying various portions of pHA1. The nucleotide sequence of the crp gene has been determined. The coding region consists of 627 base pairs (bp), which specify a protein of 209 amino acids. The predicted amino acid sequence from the DNA sequence is consistent with the amino acid sequence partially known and the amino acid composition of CRP. After the coding region, there is a G-C rich inverted repeat sequence followed by a run of Ts, which could be a terminator of the crp gene. A possible promoter sequence was found about 180 bp upstream from the initiation codon and was shown to act as a promoter in vitro and in vivo. There are two dyad symmetry regions in a 167 bp leader sequence.

Effect of catabolite repression on the mer operon

The plasmid-determined mer operon, which provides resistance to inorganic mercury compounds, was subject to a 2.5-fold decrease in expression when glucose was administered at the same time as the inducer HgCl2. This glucose-mediated transient repression of the operon was overcome by the addition of cyclic AMP. Permanent catabolite repression of the operon was observed in the 1.6- to 1.9-fold decrease in expression in mutants lacking either adenyl cyclase (cya) or the catabolite activator protein (crp). The effect of the cya mutation on mer expression could be overcome by the addition of cyclic AMP at the time of induction, In addition to these effects on the whole cells of a wild-type strains, we examined the effect of catabolite repression on the expression of the mercuric ion [Hg(II)] reductase enzyme, assayable in cell extracts, and on the Hg(II) uptake system, assayable in a mutant strain which lacked reductase activity. There was a two- to threefold effect of repression on the Hg(II) reductase enzyme assayable in vitro after induction under catabolite repressing conditions (either with glucose or in the crp and cya mutants). We did not find a similar repressing effect on the induction of the Hg(II) uptake system, which is also determined by the mer operon.

Catabolite repression of different inducible enzymes in Escherichia coli and the effect of cAMP

Simultaneous induction of two enzymes sensitive to catabolite repression does not lead to an additive decrease of the specific activity of the two. Exogenously added cAMP increases the specific activity of catabolically repressed enzymes, irrespective of whether the enzyme is induced separately or simultaneously with another enzyme. In the presence of 12 different substrates metabolized by inducible enzymes glucose does not bring about catabolite repression. Synthesis of cAMP is identical with that occurring under conditions when glucose brings about catabolite repression.

Mechanism for transcriptional action of cyclic AMP in Escherichia coli: entry into DNA to disrupt DNA secondary structure

Binding analysis with purified bacterial receptor distinguishes two structural domains in cyclic AMP (cAMP). The first, the cyclic phosphate and furanose, constitutes a binding domain. This region is bound tightly to the receptor. The rest of cAMP is not bound; the adenine moiety of cAMP is exposed. Unlike binding, activity of cAMP requires the adenine moiety. To be active, cAMP must have in domain II the base adenine--specifically, its Watson--Crick atoms N-1 and N-6. Analysis of indoleacetic acid, a compound able to replace cAMP at the L-arabinose operon, indicates a similar distinction between binding and active domains. To be active, the indole must have substitution (carboxyl or amide) electronically comparable to the cAMP N-1 and N-6. On this basis, we propose a detailed mechanism for action of cAMP (or indoleacetic acid) in Escherichia coli. We propose that the exposed adenine of cAMP enters into the DNA. The adenine's N-1 and N-6 form hydrogen bonds to a thymine in DNA. This interaction destabilizes the DNA. It enhances transcription. Marked similarities indicate an identical mechanism for the steroid hormones in eukaryotes.

Structure of catabolite gene activator protein at 2.9 A resolution suggests binding to left-handed B-DNA

The 2.9 A resolution crystal structure of Escherichia coli catabolite gene activator protein (CAP) complexed with cyclic AMP reveals two distinct structural domains separated by a cleft. The smaller carboxy-terminal domain is presumed to bind DNA while the amino-terminal domain is seen to bind cyclic AMP. Model building studies suggest that CAP binds to left-handed B-type DNA, contracting its major groove via two alpha-helices. It is possible that the CAP conversion of right- to left-handed DNA in a closed supercoil, is what activates transcription by RNA polymerase.

Hydrogenase genes

For a variety of reasons, including the potential industrial applications of hydrogenase, we are interested in the isolation and analysis of hydrogenase genes. In a program focusing on the hydrogen bacterium A. eutrophus H1 and E. coli, we have developed a preliminary concept of the interaction of hydrogenase in cellular metabolism, constructed mutants deficient in hydrogenase activity, and begun the isolation of hydrogenase genes utilizing the technology allowing the in vitro manipulation of DNA. We hope to pursue this project to its ultimate goal: the analysis of the molecular mechanisms involved in the control of expression of these genes and the development of the ability to manipulate the production of hydrogenase.

The phage promoter responsible for the expression of the inserted beta-galactosidase gene in bacteriophage lambda plac5

The lac transducing phage, lambda plac5, carries a segment of the E. coli lac operon on the left side of the b2 region of the lambda phage. In the absence of additional cyclic AMP, beta-galactosidase can only be expressed from the phage promoter, and the expression of the inserted lac promoter is suppressed. This phage promoter responsible for beta-galactosidase synthesis is shown to be under the control of the cI and N gene products; however, the repressive action of the cro gene product at high multiplicity of infection is not observed although some turn off at very late time is detected. To pin down this phage promoter, results described in this communication and those described elsewhere can rule out the promoter PI, PR, P'R, and the promoter PL also looks rather unlikely. No firm identification of this phage promoter has been made, but the promoter(s) in the b2 region (the b2 promoter) is proposed. The phage promoter responsible for beta-galacrosidase synthesis is shown to be a weak promoter, requires the Q gene product or one (or more) of the late gene products for activation, and the time of expression is very late.

Molecular cloning of the gene for the beta-lactamase of Bacillus licheniformis and its expression in Escherichia coli

The structural gene, pen, for the beta-lactamase of B. licheniformis has been cloned into a lambda vector and shown to be expressed at a low rate in E. coli. The cloned pen gene appears to be expressed from a promoter within the fragment of B. licheniformia DNA, since its rate of expression is not affected by the presence of the phage repressor, the absence of the phage's positive-control functions, or the position or orientation of the gene within the phage genome.

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.

Is cyclic guanosine 3',5'-monophosphate a cell cycle regulator?

Transient increases in the intracellular level of cyclic guanosine 3',5'-monophosphate have been observed at a periodicity of one generation time in two spoT strains of Escherichia coli and in Bacillus licheniformis.

Metabolite gene regulation: imidazole and imidazole derivatives which circumvent cyclic adenosine 3',5'-monophosphate in induction of the Escherichia coli L-arabinose operon

Imidazole, histidine, histamine, histidinol phosphate, urocanic acid, or imidazolepropionic acid were shown to induce the L-arabinose operon in the absence of cyclic adenosine 3',5'-monophosphate. Induction was quantitated by measuring the increased differential rate of synthesis of L-arabinose isomerase in Escherichia coli strains which carried a deletion of the adenyl cyclase gene. The crp gene product (cyclic adenosine 3',5'-monophosphate receptor protein) and the araC gene product (P2) were essential for induction of the L-arabinose operon by imidazole and its derivatives. These compounds were unable to circumvent the cyclic adenosine 3',5'-monophosphate in the induction of the lactose or the maltose operons. The L-arabinose regulon was catabolite repressed upon the addition of glucose to a strain carrying an adenyl cyclase deletion growing in the presence of L-arabinose with imidazole. These results demonstrated that several imidazole derivatives may be involved in metabolite gene regulation (23).

The molecular topography of RNA polymerase-promoter interaction

Ultraviolet irradiation forms covalent crosslinks between E. coli RNA polymerase and the lac UV5 promoter substituted with bromouracil in the place of thymine. I have determined the polymerase subunit and the base within the promoter sequence that are joined to each other in two such crosslinks. The sigma and beta subunits of RNA polymerase, respectively, are crosslinked to the third base upstream (-3) and the second base downstream (+3) from the starting point of transcription (+1). Both bases are on the nontemplate strand of the promoter DNA. The location of the beta subunit suggests that it forms at least part of the catalytic site of the enzyme. The disposition of sigma suggests that this subunit plays a direct role in unwinding the DNA at the promoter. The sigma crosslink is close to the "Pribnow Box," which is centered about 10 bases upstream from the RNA start site, contains a striking homology between promoters and is the locus of many promoter mutations.

Effect of cyclic guanosine 3',5'-monophosphate on nitrogen fixation in Rhizobium japonicum

The addition of exogenous cyclic guanosine 3',5'-monophosphate (cGMP) at a concentration of 0.1 mM to a free-living culture of Rhizobium japonicum 3I1b110 was found to completely inhibit the expression of nitrogenase activity and markedly inhibit the expression of hydrogenase and nitrate reductase activities. The effect was specific for cGMP. Experiments on the in vivo incorporation of radioactive methionine and subsequent analysis of the labeled proteins on polyacrylamide gels showed that the biosynthesis of nitrogenase polypeptides was inhibited. It appears that the time of addition of cGMP is important since the effect was only seen during the early stages of nif gene expression. The intracellular level of cGMP was found to respond to physiological changes in the cell, and there was a fall in cGMP concentrations when nitrogenase was induced. Microaerophilic-aerobic shift experiments showed that intracellular levels increased from 0.25 pmol/mg of cell protein under microaerophilic conditions to 2.6 pmol/mg of cell protein under aerobic conditions, suggesting that the cellular pool size of cGMP may be under redox control.

Effects of 8-substituted analogs of cyclic adenosine 3',5'-monophosphate on in vivo and in vitro syntheses of beta-galactosidase in Escherichia coli

Several 8-substituted alkylthio and alkylamino cyclic adenosine 3',5'-monophosphate (cAMP) derivatives were tested for their ability to stimulate beta-galactosidase synthesis in Estherichia coli in vivo and in vitro and to inhibit the cAMP phosphodiesterase activity of E. coli. Stimulation of beta-galactosidease synthesis in vivo by cAMP derivatives decreased with increasing length of the unbranched carbon chain of the substituent. On the other hand, the stimulation in vitro was increased as the carbon chain elongated. The 8-decylthio- and 8-dodecylthio-cAMP compounds stimulated beta-galactosidase synthesis almost eight-fold compared with cAMP, whereas 8-undecyl-, 8-dodectyl-, and 8-tridecylamino-cAMP stimulated beta-galactosidase synthesis about threefold. However, in in vitro experiments with a phosphodiesterase-deficient strain of E. coli, the Crooks strain, the stimulatory effects of the derivatives disappeared, except for 8-dodecylthio cAMP which stimulated beta-galactosidase about 1.4- to 1.6-fold. All derivatives were quite resistant to hydrolysis by phosphodiesterase. Most derivatives competitively inhibited the hydrolysis of cAMP by phosphodiesterase.

Regulation of the biosynthesis of cytochrome P-450 in brewer's yeast. Role of cyclic AMP

The drug metabolising enzyme cytochrome P-450 has been studied in great detail in mammalian systems and its presence in microorganisms is also well established. However, neither its function nor its means of control in brewer's yeast, Saccharomyces cerevisiae, has been investigated. We demonstrate here using yeast protoplasts that it is the intracellular concentration of cyclic AMP which controls, by repression, the de novo synthesis of the enzyme, and also that cyclic AMP concentrations are in turn inversely related to the concentration of glucose in the yeast growth medium.

Coenzyme B12-dependent diol dehydratase: regulation of apoenzyme synthesis in Klebsiella pneumoniae (Aerobacter aerogenes) ATCC 8724

Immunochemical studies demonstrated that Klebsiella pneumoniae (Aerobacter aerogenes) ATCC 8724 produces only a single diol dehydratase whether grown on glycerol or on 1,2-propanediol. The enzyme was subject to induction by 1,2-diols and to catabolite repression reversed by cyclic AMP.