Downstream deletion analysis of the lac promoter

CRISPR-RNAa: targeted activation of translation using dCas13 fusions to translation initiation factors

Tools for synthetically controlling gene expression are a cornerstone of genetic engineering. CRISPRi and CRISPRa technologies have been applied extensively for programmable modulation of gene transcription, but there are few such tools for targeted modulation of protein translation rates. Here, we employ CRISPR-Cas13 as a programmable activator of translation. We develop a novel variant of the catalytically-deactivated Cas13d enzyme dCasRx by fusing it to translation initiation factor IF3. We demonstrate dCasRx-IF3's ability to enhance expression 21.3-fold above dCasRx when both are targeted to the start of the 5' untranslated region of mRNA encoding red fluorescent protein in Escherichia coli. Activation of translation is location-dependent, and we show dCasRx-IF3 represses translation when targeted to the ribosomal binding site, rather than enhancing it. We provide evidence that dCasRx-IF3 targeting enhances mRNA stability relative to dCasRx, providing mechanistic insights into how this new tool functions to enhance gene expression. We also demonstrate targeted upregulation of native LacZ 2.6-fold, showing dCasRx-IF3's ability to enhance expression of endogenous genes. dCasRx-IF3 requires no additional host modification to influence gene expression. This work outlines a novel approach, CRISPR-RNAa, for post-transcriptional control of translation to activate gene expression.

Regulation of metabolism in Escherichia coli during growth on mixtures of the non-glucose sugars: arabinose, lactose, and xylose

Catabolite repression refers to the process where the metabolism of one sugar represses the genes involved in metabolizing another sugar. While glucose provides the canonical example, many other sugars are also known to induce catabolite repression. However, less is known about the mechanism for catabolite repression by these non-glucose sugars. In this work, we investigated the mechanism of catabolite repression in the bacterium Escherichia coli during growth on lactose, L-arabinose, and D-xylose. The metabolism of these sugars is regulated in a hierarchical manner, where lactose is the preferred sugar, followed by L-arabinose, and then D-xylose. Previously, the preferential utilization of L-arabinose over D-xylose was found to result from transcriptional crosstalk. However, others have proposed that cAMP governs the hierarchical regulation of many non-glucose sugars. We investigated whether lactose-induced repression of L-arabinose and D-xylose gene expression is due to transcriptional crosstalk or cAMP. Our results demonstrate that it is due to cAMP and not transcriptional crosstalk. In addition, we found that repression is reciprocal, where both L-arabinose and D-xylose also repress the lactose gene expression, albeit to a lesser extent and also through a mechanism involving cAMP. Collectively, the results further our understanding of metabolism during growth on multiple sugars.

Analysis of activator and repressor functions reveals the requirements for transcriptional control by LuxR, the master regulator of quorum sensing in Vibrio harveyi

LuxR-type transcription factors are the master regulators of quorum sensing in vibrios. LuxR proteins are unique members of the TetR superfamily of transcription factors because they activate and repress large regulons of genes. Here, we used chromatin immunoprecipitation and nucleotide sequencing (ChIP-seq) to identify LuxR binding sites in the Vibrio harveyi genome. Bioinformatics analyses showed that the LuxR consensus binding site at repressed promoters is a symmetric palindrome, whereas at activated promoters it is asymmetric and contains only half of the palindrome. Using a genetic screen, we isolated LuxR mutants that separated activation and repression functions at representative promoters. These LuxR mutants exhibit sequence-specific DNA binding defects that restrict activation or repression activity to subsets of target promoters. Altering the LuxR DNA binding site sequence to one more closely resembling the ideal LuxR consensus motif can restore in vivo function to a LuxR mutant. This study provides a mechanistic understanding of how a single protein can recognize a variety of binding sites to differentially regulate gene expression.

Bacteria use the cell-cell communication process called quorum sensing to regulate collective behaviors. In vibrios, LuxR-type transcription factors control the quorum-sensing gene expression cascade. LuxR-type proteins are structural homologs of TetR-type transcription factors. LuxR proteins were assumed to function analogously to TetR proteins, which typically bind to a single conserved binding site to repress transcription of one or two genes. We find here that unlike TetR proteins, LuxR acts a global regulator, directly binding upstream of and controlling more than 100 genes. Again unlike TetR, LuxR functions as both an activator and a repressor, and these two activities can be separated by mutagenesis. Finally, the consensus binding motifs driving LuxR-activated and -repressed genes are distinct. This work shows that LuxR, although structurally similar to TetR, has evolved unique features enabling it to differentially control a large regulon of genes in response to quorum-sensing cues.

Accurate and simple sizing of primer extension products using a non-radioactive approach facilitates identification of transcription initiation sites

An improved method of non-radioactive identification of transcription start sites is presented in which the use of 7-deaza dGTP in the primer extension reaction allows the product to be directly aligned to cycle sequencing traces on an automated sequencer. This removes the documented need to apply corrections for mobility differences.

Increased resistance to beta-lactams in a Klebsiella pneumoniae strain: role of a deletion downstream of the Pribnow box in the blaSHV-1 promoter

Two hundred and five isolates of Klebsiella pneumoniae were collected from Nantes University Hospital in 2002. A new 30bp deletion was detected downstream of the -10 box of the SHV-1 promoter in a clinical K. pneumoniae isolate with a high amoxicillin/clavulanic acid minimum inhibitory concentration. Reverse transcription polymerase chain reaction revealed increased transcription of bla(SHV-1) mRNA. All conjugation mating assays failed. This new promoter was cloned upstream of the cat gene of the reporter plasmid pKK232-8 and compared with previously described bla(SHV-1) promoters. The deletion induced a 15-fold increase in promoter strength compared with the usual weak promoter. This study reports a new genetic event that increases bla(SHV-1) chromosomal gene expression, which may be of clinical relevance when associated with porin deficiency.

lacP1 promoter with an extended -10 motif. Pleiotropic effects of cyclic AMP protein at different steps of transcription initiation

The cyclic AMP receptor protein (CRP), which activates transcription from the wild-type lacP1 promoter and most of its mutants, represses productive RNA synthesis from a lacP1 promoter variant that contains an extended -10 element, although CRP enhances RNA polymerase binding as well as open complex formation in both promoters. Moreover, abortive RNA synthesis, which is already higher in the extended -10 variant compared with the parent promoter, was further enhanced by CRP. These results, together with the observed decrease in productive RNA synthesis, indicate that CRP, while facilitating the earlier steps of initiation, inhibits transcription from the extended -10 lacP1 by hindering promoter clearance. We propose that CRP decreases energetic barriers to RNA polymerase binding, isomerization, and abortive RNA synthesis but stabilizes the abortive RNA initiating complex, which results in increasing the activation energy of the transition state before the elongation complex. The results demonstrate for the first time that a DNA-binding regulatory protein acts as an activator or a repressor in different steps of the transcription initiation pathway because of the energetic differences of the intermediate complex in the same promoter.

Anaerobiosis, growth phase and Actinobacillus pleuropneumoniae RTX toxin production

Actinobacillus pleuropneumoniae is the causative agent of an economically significant form of porcine pleuropneumonia. This bacterium produces four distinct RTX toxins (ApxI-ApxIV) that play a key role in its pathogenesis, but further characterization of these hemolytic toxins is needed to identify the environmental signals and genes that affect their production during infection. In this report, we examined the effect of oxygen limitation on the production of ApxI and ApxII, the two RTX toxins that are produced by all highly virulent strains in North America. Batch cultures of ApxI- and ApxII-producing strains were grown in heart infusion broth supplemented with NAD, and samples were prepared throughout the growth curve. We compared batch cultures with normal oxygen levels to those that were maintained in an oxygen-depleted state. ApxI and ApxII hemolytic activity were nearly identical under both growth conditions. The level of toxin activity was confirmed by examination of extracellular ApxI concentrations and apxII mRNA levels. In addition, toxin activity examined on blood agar plates grown aerobically or anaerobically showed no significant difference. These results have important implications for the disease state where high-density growth is likely to result in local anaerobic or microaerophilic environments.

Growth phase mediated regulation of the Actinobacillus pleuropneumoniae ApxI and ApxII toxins

Actinobacillus pleuropneumoniae is the causative agent of porcine pleuropneumonia, a highly contagious and often fatal respiratory tract disease of pigs. The Apx toxins are primary virulence factors of this pathogen, with ApxI and ApxII being produced by all highly virulent strains in North America. Further characterization of these hemolytic toxins is needed to fully understand their role in disease and elucidate the environmental signals and genes that affect their production during infection. Many bacteria regulate genes in response to growth phase, and in this report we examined the effect of growth phase on ApxI and ApxII gene expression. Batch cultures of ApxI- and ApxII-producing strains were grown in heart infusion broth supplemented with beta-NAD, and samples were prepared throughout the growth curve. Maximal gene expression occurred in late exponential or early stationary phase, as indicated by a peak in apx mRNA concentration in Northern blot analysis. The amount of accumulated Apx protein and Apx hemolytic activity confirmed this increase in gene expression. These findings suggest a novel transcriptional regulatory mechanism that enhances Apx gene expression under in vitro conditions of high cell density and/or slow growth rate.

Genetic control of quorum-sensing signal turnover in Agrobacterium tumefaciens

A signal turnover system is an essential component of many genetic regulatory mechanisms. The best-known example is the ubiquitin-dependent protein degradation system that exists in many organisms. We found that Agrobacterium tumefaciens adopts a unique signal turnover system to control exiting from a quorum-sensing mode. A. tumefaciens regulates Ti plasmid conjugal transfer by a quorum-sensing signal, N-3-oxo-octanoyl homoserine lactone (3OC8HSL), also known as Agrobacterium autoinducer. By using Tn5 mutagenesis and a functional cloning approach, we identified two genes that are involved in switching from a conjugal quorum-sensing mode to a nonconjugal mode at the onset of stationary phase. First, we located attJ, which codes for an IclR-type suppressor that regulates the second gene attM. The latter encodes a homologue of N-acylhomoserine lactone (AHL)-lactonase. Mass spectrometry analysis shows that the enzyme encoded by attM is an AHL-lactonase that hydrolyzes the lactone ring of 3OC8HSL. In wild-type A. tumefaciens, attM expression is initially suppressed by AttJ but significantly elevated at the stationary phase accompanied a sharp decline in 3OC8HSL. DNA gel retardation analysis shows that AttJ specifically binds to the promoter that controls AHL-lactonase expression. Mutation of attJ resulted in constitutive production of AHL-lactonase that abolishes 3OC8HSL accumulation and Ti plasmid transfer. These data suggest that A. tumefaciens has a sophisticated multicomponent quorum-sensing signal turnover system, allowing the cell to sense a change in growth and adjust cellular activities accordingly.

Genetic determinants of tetracycline resistance in Vibrio harveyi

Isolates of Vibrio harveyi, a prawn pathogen, have demonstrated multiple antibiotic resistance to commonly used antimicrobial agents, such as oxytetracycline. In this paper, we describe the cloning and characterization of two tetracycline resistance determinants from V. harveyi strain M3.4L. The first resistance determinant, cloned as a 4,590-bp fragment, was identical to tetA and flanking sequences encoded on transposon Tn10 from Shigella flexneri. The second determinant, cloned as a 3,358-bp fragment in pATJ1, contains two open reading frames, designated tet35 and txr. tet35 encodes a 369-amino-acid protein that was predicted to have nine transmembrane regions. It is a novel protein which has no homology to any other drug resistance protein but has low levels of homology (28%) to Na(+)/H(+) antiporters. Transposon mutagenesis showed that tet35 and txr were required for tetracycline resistance in a heterologous Escherichia coli host. Tetracycline accumulation studies indicate that E. coli carrying tet35 and txr can function as an energy-dependent tetracycline efflux pump but is less efficient than TetA.

ohr, Encoding an organic hydroperoxide reductase, is an in vivo-induced gene in Actinobacillus pleuropneumoniae

Actinobacillus pleuropneumoniae is the causative agent of porcine pleuropneumonia, a disease characterized by pulmonary necrosis and hemorrhage caused in part by neutrophil degranulation. In an effort to understand the pathogenesis of this disease, we have developed an in vivo expression technology (IVET) system to identify genes that are specifically up-regulated during infection. One of the genes that we have identified as being induced in vivo is ohr, encoding organic hydroperoxide reductase, an enzyme that could play a role in detoxification of organic hydroperoxides generated during infection. Among the 12 serotypes of A. pleuropneumoniae, ohr was found in only serotypes 1, 9, and 11. This distribution correlated with increased resistance to cumene hydroperoxide, an organic hydroperoxide, but not to hydrogen peroxide or to paraquat, a superoxide generator. Functional assays of Ohr activity demonstrated that A. pleuropneumoniae serotype 1 cultures, but not serotype 5 cultures, were able to degrade cumene hydroperoxide. In A. pleuropneumoniae serotype 1, expression of ohr was induced by cumene hydroperoxide, but not by either hydrogen peroxide or paraquat. In contrast, an ohr gene from serotype 1 cloned into A. pleuropneumoniae serotype 5 was not induced by cumene hydroperoxide or by other forms of oxidative stress, suggesting the presence of a serotype-specific positive regulator of ohr in A. pleuropneumoniae serotype 1.

PNPase autocontrols its expression by degrading a double-stranded structure in the pnp mRNA leader

Polynucleotide phosphorylase synthesis is autocontrolled at a post-transcriptional level in an RNase III-dependent mechanism. RNase III cleaves a long stem-loop in the pnp leader, which triggers pnp mRNA instability, resulting in a decrease in the synthesis of polynucleotide phosphorylase. The staggered cleavage by RNase III removes the upper part of the stem-loop structure, creating a duplex with a short 3' extension. Mutations or high temperatures, which destabilize the cleaved stem-loop, decrease expression of pnp, while mutations that stabilize the stem increase expression. We propose that the dangling 3' end of the duplex created by RNase III constitutes a target for polynucleotide phosphorylase, which binds to and degrades the upstream half of this duplex, hence inducing pnp mRNA instability. Consistent with this interpretation, a pnp mRNA starting at the downstream RNase III processing site exhibits a very low level of expression, regardless of the presence of polynucleotide phosphorylase. Moreover, using an in vitro synthesized pnp leader transcript, it is shown that polynucleotide phosphorylase is able to digest the duplex formed after RNase III cleavage.

Identification of an Actinobacillus pleuropneumoniae consensus promoter structure

Actinobacillus pleuropneumoniae promoter-containing clones were isolated from a genomic DNA library constructed in our lVET promoter trap vector pTF86. The promoter-containing clones were identified by their ability to drive expression of the promoterless luxAB genes of Vibrio harveyi. The degree of expression was quantifiable, and only high-expression or "hot" promoters were used for this study. Nine clones were sequenced, and their transcriptional start sites were determined by primer extension. The sequences upstream of the start site were aligned, and a consensus promoter structure for A. pleuropneumoniae was identified. The consensus promoter sequence for A. pleuropneumoniae was found to be TATAAT and TTG/AAA, centered approximately 10 and 35 bp upstream of the transcriptional start site, respectively. A comparison of the A. pleuropneumoniae consensus with other prokaryotic consensus promoters showed that the A. pleuropneumoniae consensus promoter is similar to that found in other eubacteria in terms of sequence, with an identical -10 element and a similar but truncated -35 element. However, the A. pleuropneumoniae consensus promoter is unique in the spacing between the -10 and -35 elements. The promoter spacing was analyzed by site-directed mutagenesis, which demonstrated that optimal spacing for an A. pleuropneumoniae promoter is shorter than the spacing identified for Escherichia coli and Bacillus subtilis promoters.

Negative regulation of IS2 transposition by the cyclic AMP (cAMP)-cAMP receptor protein complex

Three sequences similar to that of the consensus binding sequence of the cyclic AMP (cAMP)-cAMP receptor protein (CRP) complex were found in the major IS2 promoter region. Experiments were performed to determine whether the cAMP-CRP complex plays a role in the regulation of IS2 transposition. In the gel retardation assay, the cAMP-CRP complex was found to be able to bind the major IS2 promoter. A DNA footprinting assay confirmed that the cAMP-CRP complex binds to the sequences mentioned above. With an IS2 promoter-luciferase gene fusion construct, the cAMP-CRP complex was shown to inhibit transcription from the major IS2 promoter. IS2 was found to transpose at a frequency approximately 200-fold higher in an Escherichia coli host defective for CRP or adenyl cyclase than in a wild-type host. These results suggest that the cAMP-CRP complex is a negative regulator of IS2 transposition.

Alanine catabolism in Klebsiella aerogenes: molecular characterization of the dadAB operon and its regulation by the nitrogen assimilation control protein

Klebsiella aerogenes strains with reduced levels of D-amino acid dehydrogenase not only fail to use alanine as a growth substrate but also become sensitive to alanine in minimal media supplemented with glucose and ammonium. The inability of these mutant strains to catabolize the alanine provided in the medium interferes with both pathways of glutamate production. Alanine derepresses the nitrogen regulatory system (Ntr), which in turn represses glutamate dehydrogenase, one pathway of glutamate production. Alanine also inhibits the enzyme glutamine synthetase, the first enzyme in the other pathway of glutamate production. Therefore, in the presence of alanine, strains with mutations in dadA (the gene that codes for a subunit of the dehydrogenase) exhibit a glutamate auxotrophy when ammonium is the sole source of nitrogen. The alanine catabolic operon of Klebsiella aerogenes, dadAB, was cloned, and its DNA sequence was determined. The clone complemented the alanine defects of dadA strains. The operon has a high similarity to the dadAB operon of Salmonella typhimurium and the dadAX operon of Escherichia coli, each of which codes for the smaller subunit of D-amino acid dehydrogenase and the catabolic alanine racemase. Unlike the cases for E. coli and S. typhimurium, the dad operon of K. aerogenes is activated by the Ntr system, mediated in this case by the nitrogen assimilation control protein (NAC). A sequence matching the DNA consensus for NAC-binding sites is located centered at position -44 with respect to the start of transcription. The promoter of this operon also contains consensus binding sites for the catabolite activator protein and the leucine-responsive regulatory protein.

The -45 region of the Escherichia coli lac promoter: CAP-dependent and CAP-independent transcription

The lactose (lac) operon promoter is positively regulated by the catabolite gene activator-cyclic AMP complex (CAP) that binds to the DNA located 61.5 bp upstream of the transcription start site. Between the CAP binding site and the core promoter sequence is a 13-bp sequence (from -38 to -50 [the -45 region]). The possible roles of the -45 region in determining the CAP-independent level of lac expression and in the CAP activation process were studied by isolating and characterizing random multisite mutations. Only a small percentage of mutants have dramatic effects on lac promoter activity. Among the mutations that did affect expression, a 26-fold range in lac promoter activity in vivo was observed in the CAP-independent activity. The highest level of CAP-independent lac expression (13-fold the level of the wild-type lac promoter) correlated with changes in the -40 to -45 sequence and required an intact RNA polymerase alpha subunit for in vitro expression, as expected for an upstream DNA recognition element. Mutant promoters varied in their ability to be stimulated by CAP in vivo, with levels ranging from 2-fold to the wild-type level of 22-fold. Only a change of twofold in responsiveness to CAP could be attributed to direct DNA sequence effects. The -40 to -45 sequence-dependent enhancement of promoter activity and CAP stimulation of promoter activity did not act additively. The mutant promoters also displayed other characteristics, such as the activation of nascent promoter-like activities overlapping lac P1 and, in one case, replicon-dependent changes in promoter activity.

Identification of the cpdA gene encoding cyclic 3',5'-adenosine monophosphate phosphodiesterase in Escherichia coli

We have identified a gene, cpdA, located at 66.2 min of the chromosome of Escherichia coli that encodes cyclic 3',5'-adenosine monophosphate phosphodiesterase (cAMP phosphodiesterase, EC). The expression of beta-galactosidase, which is a product of the lacZ gene, was repressed in cells that harbored multiple copies of the plasmid carrying the cpdA gene. Northern blotting showed that the transcription of the lacZ gene was inhibited in these cells. Multiple copies of the cpdA gene decreased the intracellular concentration of cAMP, which is a positive regulator for transcription of the lacZ gene. We found that the purified CpdA protein repressed in vitro transcription from the lacP1 promoter by decreasing cAMP. In addition, we showed that the CpdA protein hydrolyzed cAMP to 5'-adenosine monophosphate and that its activity was activated by iron. Our results suggested that regulation of intracellular concentration of cAMP is dependent not only on synthesis of cAMP but also on hydrolysis of cAMP by cAMP phosphodiesterase.

Activation of the Escherichia coli lacZ promoter by the Klebsiella aerogenes nitrogen assimilation control protein (NAC), a LysR family transcription factor

A chimeric promoter with the nitrogen assimilation control protein binding site from hutUp of Klebsiella aerogenes fused to the lacZ core promoter from Escherichia coli was built and cloned in a lacZ reporter plasmid. This construct showed a 14-fold increase of beta-galactosidase activity upon nitrogen limitation. Primer extension experiments showed that the nitrogen assimilation control protein activates lacZp1 in a position-dependent manner.

Start site selection at lacUV5 promoter affected by the sequence context around the initiation sites

The effects of single base pair substitutions at the initiation sites of lacUV5 promoter on the transcription start site selection by E. coli RNA polymerase were systematically studied. Transcription start sites were mapped by sizing the cytosine-specifically terminated transcripts produced in vitro by using a chain terminator 3'-deoxycytidine 5'-triphosphate (3'-dCTP) in transcription reactions. Transcription of a prototype lacUV5 promoter initiated with three purines (-1G, +1A and +2A; +1 representing the predominant start site) located 6-8 bp downstream from the Pribnow box. All the substitutions affected the start site selection, resulting in a change in the number of start sites (from 3 to 2 or 1) and/or a shift of the major start site (to -1 or +2). None of the variants started outside the 3-bp region and at the positions substituted by a pyrimidine. Purine-to-pyrimidine changes suppressed not only initiation at the substituted position but also, in some cases, at the other purine position. Purine-to-purine changes also shifted the major start site or suppressed the initiation at other sites. Changes at -2 and +5 also affected the start site selection. Thus, the sequence context around the initiation sites of lacUV5 promoter strongly influences the selection of initiating nucleotides by E. coli RNA polymerase.

Functional analysis of the tdcABC promoter of Escherichia coli: roles of TdcA and TdcR

The efficient expression of the tdc operon of Escherichia coli requires the products of two regulatory genes, tdcR and tdcA. We have identified the transcription site of tdcR by primer extension mapping and established the translation start site of TdcR by mutational analysis of its reading frame. In a tdcR tdcABC deletion strain, tdcR+ promoted high-level LacZ expression from a lambda tdcAB-lacZ lysogen and mutations introduced in tdcR resulted in a greater than sixfold decrease in LacZ level. In-frame deletions of tdcA also reduced LacZ expression, and chromosomal and plasmid-borne tdcA+ increased the LacZ level in tdcA mutant lysogens. Interestingly, multicopy tdcA+ plasmids introduced into tdcR mutant strains completely restored tdc expression. In separate experiments we found that mutations in the tdc promoter DNA around positions -70, -140, and -175 greatly reduced tdc expression relative to that for the wild-type promoter and the tdcP mutation around -175 prevented multicopy tdcA+ from rescuing tdcR mutants. Furthermore, competition experiments revealed that a wild-type promoter fragment encompassing the -175 region cloned into a plasmid reduced tdc expression by titrating TdcA in vivo, and this effect was reversed with excess TdcA. These results suggest that in tdcR+ cells TdcR interacts with tdcP and/or TdcA to enhance tdc transcription whereas in tdcR mutant cells a new tdcP-TdcA complex around -175 in the native promoter bypasses the requirement for TdcR. On the basis of the accumulated data summarized here and elsewhere we propose that multiple transcription factors enhance tdc operon expression by bending and looping of the promoter DNA to form an active transcription complex.

Nucleotide pool-sensitive selection of the transcriptional start site in vivo at the Salmonella typhimurium pyrC and pyrD promoters

Expression of the Salmonella typhimurium pyrC and pyrD genes is regulated in response to fluctuations in the intracellular CTP/GTP pool ratio. The repressive mechanism involves the formation of a stable secondary structure (hairpin) at the 5' ends of the transcripts that precludes translational initiation by sequestering sequences required for ribosomal binding. The potential for hairpin formation is controlled through CTP/GTP-modulated selection of the transcriptional start site. Substitution of nucleotides in the region of transcriptional initiation has revealed that selection of the transcriptional start point in vivo depends on the nucleotide context within the initiation region and the nucleoside triphosphate pool ratios. For maximal control in response to CTP/GTP pool ratios, the wild-type CCGG start site motif appears to be optimal. Changing the -35 region in the pyrC promoter to the consensus sequence, or replacement of the pyrC promoter with the lac promoter from Escherichia coli, has served to illustrate that the ability of the RNA polymerase to select the initiation site in response to the intracellular nucleoside triphosphate pools is not promoter specific but is determined by the kinetic properties of the initiating RNA polymerase during the formation of the first phosphodiester bond of the transcript.

Synergistic activation of transcription by Escherichia coli cAMP receptor protein

Activation of gene expression in eukaryotes generally involves the action of multiple transcription factors that function synergistically when bound near a particular target gene. Such effects have been suggested to occur because multiple activators can interact simultaneously with one or more components of the basal transcription machinery. In prokaryotes, examples of synergistic effects on transcription are much more limited and can often be explained by cooperative DNA binding. Here we show that the Escherichia coli cAMP receptor protein (CRP) functions synergistically to activate transcription from a derivative of the lac promoter that bears a second CRP-binding site upstream of the natural binding site. We present evidence indicating that cooperative DNA binding of two CRP dimers does not account for the magnitude of the observed cooperative activation. We suggest, instead, that the two dimers stimulate transcription directly by contacting two distinct surfaces of RNA polymerase simultaneously. Thus, synergistic activation by CRP may provide a relatively simple model for examining the molecular basis of such effects in higher organisms.

The lactose operon-controlling elements: a complex paradigm

The lactose-controlling elements have been considered to be the simple paradigm of a cis-acting genetic regulatory system, containing a promoter whose activity is modulated by an operator and a catabolite gene activator protein (CAP)-binding site. The reality is considerably more complex. We now know that transcription is negatively regulated as a result of the repressor binding to three binding sites: the operator, a secondary repressor-binding site within the lacZ gene and a tertiary repressor-binding site upstream near lacI. In addition to the promoter, the lac-controlling elements contain five promoter-like elements. The physiological role, if any, of these promoter-like elements is not clear, although three of them can be activated by single base pair changes to give high levels of in vivo expression. Finally, the positive activator protein CAP has been found to bind to a secondary site which is coincident with the operator. No role has been identified for this secondary CAP-DNA complex.

Catabolite gene activator protein activation of lac transcription

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Escherichia coli catabolite gene activator protein mutants defective in positive control of lac operon transcription

We isolated three Escherichia coli catabolite gene activator protein mutants that are defective in the positive control of transcription initiation from the lac operon promoter region yet retain negative control of transcription from other promoters. One mutant has a substitution of valine for glutamate at residue 72, which lies in the cyclic AMP binding domain and contacts cyclic AMP. The other two mutants have substitutions of asparagine and cysteine for glycine 162, which lies in a surface-exposed turn of the DNA-binding domain. Surprisingly, although all three mutants can repress the lacP2/P3 promoters through the catabolite gene activator protein target site of lac, none displays strong dominance over the ability of wild-type catabolite gene activator protein to stimulate the lacP1 promoter.