Site-specific targeting of exogenous DNA into the genome of Candida albicans using the FLP recombinase

We have created a system that utilizes the FLP recombinase of Saccharomyces cerevisiae to reversibly introduce exogenous cloned DNA at defined locations into the Candida albicans genome. Recombination target (FRT) sites and the FLP gene can be introduced permanently at defined locations using homologous recombination. FLP recombinase is provided as needed through the regulated expression of its gene using the MAL2 promoter. Exogenous DNA is introduced on a cloning vector that is unable to replicate in C. albicans, and contains an FRT site and a selectable marker (URA3). Transformation by the lithium acetate or electroporation procedure is sufficient to obtain site-specific integration. This system permits rapid and precise excision of the introduced DNA when needed. It should facilitate studies on C. albicans genome structure and function, simplifying a wide range of chromosomal cloning applications, and generally enhancing the utility of C. albicans as a model organism for the study of fungal pathogenicity.

Dimorphism in fungal pathogens: Candida albicans and Ustilago maydis--similar inputs, different outputs

The ability to switch between a yeast-like form and a filamentous form is an extended characteristic among several fungi. In pathogenic fungi, this capacity has been correlated with virulence because along the infection process, dimorphic transitions are often required. Two well-known organisms for which dimorphism have been studied are the pathogenic fungi Candida albicans and Ustilago maydis, which infect mammals and corn, respectively. In both cases, several signal transduction pathways have been defined. Not surprisingly, these pathways are similar to the well-known pathways involved in the pseudohyphal differentiation that some Saccharomyces cerevisiae diploid strains show when nutrients are starved. However, in spite of similarities at the molecular level, strikingly, fungi use similar pathways to respond to environmental inputs, but with differing outcomes.

Evidence of an unusually long operator for the fur repressor in the aerobactin promoter of Escherichia coli

Production of the siderophore aerobactin in Escherichia coli is transcriptionally metalloregulated through the iron-dependent binding of the Fur (ferric uptake regulator) to a large region (>100 base pairs) within the cognate promoter in the pColV-K30 plasmid. We show in this article that such an unusually long operator results from the specific addition of degenerate repeats 5'-NAT(A/T)AT-3' and not from a fortuitous occupation of the DNA adjacent to the primary binding sites by an excess of the repressor. Furthermore, the protection pattern revealed by DNase I and hydroxyl radical footprinting reflected a side-by-side oligomerization of the protein along an extended DNA stretch. This type of DNA-protein interactions is more like those observed in some eukaryotic factors and nucleoid-associated proteins than typical of specific prokaryotic regulators.

Chromatin and transcription in Saccharomyces cerevisiae

A central problem in eukaryotic transcription is how proteins gain access to DNA packaged in nucleosomes. Research on the interplay between chromatin and transcription has progressed with the use of yeast genetics as a useful tool to characterize factors involved in this process. These factors have both positive and negative effects on the stability of nucleosomes, thereby controlling the role of chromatin in transcription in vivo. The negative effectors include the structural components of chromatin, the histones and non-histone chromatin associated proteins, as well as regulatory components like chromatin assembly factors and histone deacetylase complexes. The positive factors are involved in remodeling chromatin and several multiprotein complexes have been described: Swi/Snf, Srb/mediator and SAGA. The components of each of these complexes, as well as the functional relationships between them are covered by this review.

The IIANtr (PtsN) protein of Pseudomonas putida mediates the C source inhibition of the sigma54-dependent Pu promoter of the TOL plasmid

The gene cluster adjacent to the sequence of rpoN (encoding sigma factor sigma54) of Pseudomonas putida has been studied with respect to the C source regulation of the Pu promoter of the upper TOL (toluene catabolism) operon. The region includes four open reading frames (ORFs), two of which (named ptsN and ptsO genes) encode proteins similar to components of the phosphoenolpyruvate:sugar phosphotransferase system. Each of the four genes was disrupted with a nonpolar insertion, and the effects in the inhibition caused by glucose on Pu activity were inspected with a lacZ reporter system. Although cells lacking ORF102, ORF284, and ptsO did not display any evident phenotype under the conditions tested, the loss of ptsN, which encodes the IIANtr protein, made Pu unresponsive to repression by glucose. The ptsN mutant had rates of glucose/gluconate consumption identical to those of the wild type, thus ruling out indirect effects mediated by the transport of the carbohydrate. A site-directed ptsN mutant in which the conserved phospho-acceptor site His68 of IIANtr was replaced by an aspartic acid residue made Pu blind to the presence or absence of glucose, thus supporting the notion that phosphorylation of IIANtr mediates the C source inhibition of the promoter. These data substantiate the existence of a molecular pathway for co-regulation of some sigma54 promoters in which IIANtr is a key protein intermediate.

Phenotypic switching in Candida albicans is controlled by a SIR2 gene

We report the cloning of a gene from the human fungal pathogen Candida albicans with sequence and functional similarity to the Saccharomyces cerevisiae SIR2 gene. Deletion of the gene in C. albicans produces a dramatic phenotype: variant colony morphologies arise at frequencies as high as 1 in 10. The morphologies resemble those described previously as part of a phenotypic switching system proposed to contribute to pathogenesis. Deletion of SIR2 also produces a high frequency of karyotypic changes. These and other results are consistent with a model whereby Sir2 controls phenotypic switching and chromosome stability in C.albicans by organizing chromatin structure.

Binding of the fur (ferric uptake regulator) repressor of Escherichia coli to arrays of the GATAAT sequence

The mode of DNA binding of the Fur (ferric uptake regulator) repressor which controls transcription of iron-responsive genes in Escherichia coli, has been re-examined. Using as a reference the known sites at the promoter of the aerobactin operon of Escherichia coli, we have compared in detail the patterns of interaction between the purified Fur protein and natural or synthetic DNA targets. DNase I and hydroxyl radical footprinting, as well as missing-T assays, consistently revealed that functional Fur sites are composed of a minimum of three repeats of the hexameric motif GATAAT rather than by a palindromic 19 bp target sequence. Extended binding sites, constructed by stepwise addition of one or two direct repeats of the same sequence, were occupied co-operatively by Fur with the same pattern of interactions as those observed with the core of three repeats. This indicated that functional sites with a range of affinities can be formed by the addition of discrete GATAAT extensions to a minimal recognition sequence. The fashion in which Fur binds its target, virtually unknown in prokaryotic transcriptional regulators, accounts for the observed helical wrapping of the protein around the DNA helix.

The C-terminal domain of Sin1 interacts with the SWI-SNF complex in yeast

In the yeast Saccharomyces cerevisiae, the SWI-SNF complex has been proposed to antagonize the repressive effects of chromatin by disrupting nucleosomes. The SIN genes were identified as suppressors of defects in the SWI-SNF complex, and the SIN1 gene encodes an HMG1-like protein that has been proposed to be a component of chromatin. Specific mutations (sin mutations) in both histone H3 and H4 genes produce the same phenotypic effects as do mutations in the SIN1 gene. In this study, we demonstrate that Sin1 and the H3 and H4 histones interact genetically and that the C terminus of Sin1 physically associates with components of the SWI-SNF complex. In addition, we demonstrate that this interaction is blocked in the full-length Sin1 protein by the N-terminal half of the protein. Based on these and additional results, we propose that Sin1 acts as a regulatable bridge between the SWI-SNF complex and the nucleosome.

Coordinated repression in vitro of the divergent fepA-fes promoters of Escherichia coli by the iron uptake regulation (Fur) protein

The mechanism involved in transcriptional repression of the fepA-fes divergent promoters of Escherichia coli by the Fur (ferric uptake regulation) protein has been examined in vitro. This DNA region includes a suboptimal and single Fur-binding site with two divergent and overlapped -35/-10 hexamers. Comparison of transcription patterns generated with runoff experiments in either the presence or the absence of heparin showed that access of the RNA polymerase to the principal -35/-10 hexamers was fully prevented by Fur-Mn2+ bound to its target site within the divergent promoter region. Neither RNA polymerase bound to the fes and fepA promoters could be displaced by Fur-Mn2+, nor could the bound repressor be outcompeted by an excess of the enzyme. However, the repressor blocked reinitiation as soon as the polymerase moved away from the fes promoter during transcription. The spatial distribution of regulatory elements within the DNA region allowed the simultaneous binding of the RNA polymerase to the fes and fepA promoters and their coordinate regulation regardless of their different transcriptional activities. Comparisons with other iron-regulated systems support a general mechanism for Fur-controlled promoters that implies a direct competition between the polymerase and the regulator for overlapping target sites in the DNA.

Mutations in chromatin components suppress a defect of Gcn5 protein in Saccharomyces cerevisiae

The yeast GCN5 gene encodes the catalytic subunit of a nuclear histone acetyltransferase and is part of a high-molecular-weight complex involved in transcriptional regulation. In this paper we show that full activation of the HO promoter in vivo requires the Gcn5 protein and that defects in this protein can be suppressed by deletion of the RPD3 gene, which encodes a histone deacetylase. These results suggest an interplay between acetylation and deacetylation of histones in the regulation of the HO gene. We also show that mutations in either the H4 or the H3 histone gene, as well as mutations in the SIN1 gene, which encodes an HMG1-like protein, strongly suppress the defects produced by the gcn5 mutant. These results suggest a hierarchy of action in the process of chromatin remodeling.

Metalloregulation in vitro of the aerobactin promoter of Escherichia coli by the Fur (ferric uptake regulation) protein

The mechanism of transcriptional repression of the aerobactin operon of Escherichia coli by the Fe2+-responsive Fur (ferric uptake regulation) protein has been investigated. In the presence of a divalent metal, such as Mn2+, the Fur protein sequentially occupies two defined sites at the aerobactin promoter region, followed by a looser occupation of upstream DNA sequences. However, binding to the primary target site suffices for the entire repression effect. Comparison of transcription patterns generated with run-off experiments in the presence and absence of heparin showed that access of the RNA polymerase to the principal -35/-10 hexamers of the promoter region was fully prevented by Fur-Mn2+ bound to its primary site. Similarly, promoter-bound RNA polymerase could not be competed out from the DNA even in the presence of a large Fur-Mn2+ excess, although the repressor could immediately bind its target sequence at the region as soon as RNA polymerase moved away from the promoter during transcription. The high affinities of either protein for the promoter produce, in practice, a first-come, first-served effect that helps the system to respond instantly to changes in the iron status of the cells.

Clues and consequences of DNA bending in transcription

This review attempts to substantiate the notion that nonlinear DNA structures allow prokaryotic cells to evolve complex signal integration devices that, to some extent, parallel the transduction cascades employed by higher organisms to control cell growth and differentiation. Regulatory cascades allow the possibility of inserting additional checks, either positive or negative, in every step of the process. In this context, the major consequence of DNA bending in transcription is that promoter geometry becomes a key regulatory element. By using DNA bending, bacteria afford multiple metabolic control levels simply through alteration of promoter architecture, so that positive signals favor an optimal constellation of protein-protein and protein-DNA contacts required for activation. Additional effects of regulated DNA bending in prokaryotic promoters include the amplification and translation of small physiological signals into major transcriptional responses and the control of promoter specificity for cognate regulators.

Coactivation in vitro of the sigma54-dependent promoter Pu of the TOL plasmid of Pseudomonas putida by HU and the mammalian HMG-1 protein

The mechanism by which the prokaryotic histone-like protein HU replaces the integration host factor (IHF) in the coactivation of the sigma54-dependent promoter Pu of Pseudomonas putida has been investigated. By using a preactivated form of the cognate activator protein XylR, we show that the functional replacement of IHF with HU previously suggested in vivo can be faithfully reproduced in vitro with purified components. Furthermore, the coactivation effect of IHF on Pu could be mimicked not only by HU but also by the mammalian nonhistone chromatin protein HMG-1 and could be bypassed by intrinsically curved DNA. These results suggest that either of two different mechanisms (generation of a site-specific static DNA bend or a general flexibilization of the promoter region) gives rise to the same structural effect of stimulating transcription from Pu through changes in promoter architecture.

Genetic evidence of separate repressor and activator activities of the XylR regulator of the TOL plasmid, pWW0, of Pseudomonas putida

The XylR protein encoded by pWW0, the TOL (toluene biodegradation) plasmid of Pseudomonas putida, activates at a distance the transcription of Pu and Ps, which are the two sigma(54)-dependent promoters of the plasmid, but it also downregulates its own sigma(70)-promoter, Pr, which divergently overlaps the upstream activating sites of Ps. All regulatory elements that control Pr activity have been faithfully reproduced in Escherichia coli, and the basis of the autoregulation of XylR transcription has been examined by monitoring the activity in vivo of different combinations of mutant proteins and promoters in rpoN+ and rpoN-genetic backgrounds. By using Ps/Pr regions bearing deleted or offset binding sites for XylR and the sigma(54)-containing RNA polymerase, we could show that formation of a nucleoprotein complex involving the polymerase bound to the divergent promoter Ps is not required for downregulation of Pr. Mutant XylR proteins, G268N and A311V (mutated within the NTP-binding region of XylR) or R453H (affected in multimerization), which are unable to activate sigma(54)-dependent transcription from Ps, were indistinguishable from the wild-type XylR in their ability to repress a reporter Pr-lacZ fusion. Autoregulation of XylR is therefore due exclusively to the binding of the protein to its target sites at the Pr promoter. This allows one to define sensu stricto XylR as a transcriptional repressor, independently of its activator role in other promoters.

ATP binding to the sigma 54-dependent activator XylR triggers a protein multimerization cycle catalyzed by UAS DNA

The events that take place at the prokaryotic enhancer of the Pu promoter of Pseudomonas putida prior to the engagement of the sigma 54-RNA polymerase (sigma 54-RNAP) have been studied in vitro. ATP hydrolysis by XylR, the cognate regulator of the system, is preceded by the multimerization of XylR at the enhancer, which is itself triggered by the sole allosteric effect of ATP binding to the protein. Since ADP is unable to support multimerization, ATP hydrolysis might be followed by a return to the nonmultimerized state. This notion is supported further by the properties of mutant proteins that seem to be frozen, in either the nonmultimerized or the multimerized state, respectively. These results support a cyclic mechanism of ATP-dependent association/dissociation of XylR at the promoter UAS that precedes any involvement of the polymerase in transcription initiation.

VTR expression cassettes for engineering conditional phenotypes in Pseudomonas: activity of the Pu promoter of the TOL plasmid under limiting concentrations of the XylR activator protein

A simplified procedure to construct recombinant Pseudomonas putida (Pp) and related bacteria, which transcribe conditionally specific genes inserted into their chromosome in response to lac inducers such as IPTG, has been developed. The method is based on the so-called VTR expression cassettes. These are three small (1.98-kb) DNA segments engineered as NotI restriction fragments that include a lacIq gene along with the hybrid trp/lac promoter, Ptrc, followed by an optimised translation initiation region with a leading ATG and a multiple cloning site in each of the three reading frames. This arrangement allows the chromosomal insertion of the conditionally expressed genes of interest through its transfer to any of the mini-Tn5 transposon vectors available. VTR cassettes permit construction of specialized strains that are instrumental to address, by genetic means, otherwise intractable regulatory problems observed in biodegradative pathways of Pp. In this context, the VTR system was employed to examine the effect of the intracellular concentration of XylR, the main regulator of the TOL (toluene biodegradation) plasmid pWW0, on the exponential silencing of the promoter of the upper operon, Pu. Increasing concentrations of XylR resulted in more intense induction of the system that, however, remained silent during fast cell growth regardless of activator levels.

Physical and functional analysis of the prokaryotic enhancer of the sigma 54-promoters of the TOL plasmid of Pseudomonas putida

The physical and the functional organization of the upstream cis-acting sequence that controls at a distance the transcriptional activity of Pu and Ps, the two sigma 54-dependent promoters of the TOL (toluene/xylene biodegradation) operons of Pseudomonas putida, have been determined. DNase I and hydroxyl radical footprinting of the promoters with the purified and pre-activated enhancer-binding protein XylR clearly indicated the presence of two distinct binding sites (proximal and distal) that were occupied independently and did not share an evident sequence similarity. However, alignment of the sequence on the basis of the cleavage protection patterns, along with those produced on Po, a third XylR-responsive promoter of a phenol degradation operon, generated a consensus sequence 5'-TTGATCAATTGATCAA-3' having greater similarity to the proximal than to the distal boxes. To verify that this consensus was the sequence recognized by XylR, we footprinted in vitro a synthetic site, the results indicating that it was strongly bound by the activator with the predicted pattern of interactions. The mode of protection indicated that XylR recognized the sequence as a palindrome and not as a tandem repeat, interacting with it on one side of the DNA helix. In vivo experiments involving directed deletions through the entire 5' region of the Pu promoter confirmed that the proximal XylR-binding sequence suffices for promoter activity. In vivo data also suggested that XylR binding to the upstream sequences promoted the assembly of the oligomeric form of the activator that is competent for transcription initiation.

In vitro activities of an N-terminal truncated form of XylR, a sigma 54-dependent transcriptional activator of Pseudomonas putida

A truncated derivative of the XylR protein, which is able to constitutively activate the sigma 54-dependent Pu promoter of the TOL (toluene biodegradation) plasmid of Pseudomonas putida, has been purified to homogeneity and its various activities have been separately examined, in vitro. The truncated regulator XylR delta A was deleted of the signal reception N-terminal module present in wild-type XylR, but retained its central activation domain and the DNA binding segment, located at its C terminus. XylR delta A bound to the region -120 to -190 bp upstream of the transcription initiation site of the Pu promoter, where previous analyses have located the XylR target site. XylR delta A showed an intrinsic ATPase activity that was strongly stimulated by DNA containing the native upstream activation sequences of Pu. Both ATPase activity and ATP binding were abolished in mutant G268N in which the Walker A domain of the central module was altered. Mutant R453H lacked ATPase activity but retained the nucleotide-binding ability of the parental protein. XylR delta A was able to activate transcription in vitro with sigma 54-RNA polymerase alone, although its activity was enhanced up to 20-fold in the presence of the integration host factor protein. The requirements for activation of the Pu promoter in vitro are consistent with the view that DNA-facilitated oligomerization of the regulator for an enhanced ATPase activity is the critical event that precedes transcription initiation at sigma 54-dependent promoters. Furthermore, additional co-regulation elements seem to adjust promoter activity in vivo to the physiological status of the cells.

Identification of the repressor subdomain within the signal reception module of the prokaryotic enhancer-binding protein XylR of Pseudomonas putida

In the presence of m-xylene, the protein XylR encoded by the TOL plasmid of Pseudomonas putida, activates the final sigma54-dependent promoter Pu. Early activation stages involve the release of the intramolecular repression caused by the signal reception N-terminal (A domain) of XylR on the central module of the protein. A genetic approach has been followed to locate the specific segment within A domain of XylR that is directly responsible for its down-regulation in the absence of inducer, as compared to that involved in effector (m-xylene) binding. For this, a reporter Escherichia coli strain carrying a monocopy transcriptional fusion of Pu to lacZ was transformed with a collection of plasmids encoding equivalent truncated varieties of XylR, consisting of nested and internal deletions throughout the entire A domain. Examination of the resulting phenotypes allowed the assignment of the A domain region near the central activation domain, as the portion of the protein responsible for the specific repression of XylR activity in the absence of m-xylene.

Regulatory noise in prokaryotic promoters: how bacteria learn to respond to novel environmental signals

Various features of the regulation of pathways for biodegradation of recalcitrant compounds by Pseudomonas provide insights into the mechanisms by which operons evolve to acquire conditionally active promoters that permit the corresponding genes to be transcribed only when required. The "regulatory noise hypothesis' proposes that transcriptional control systems develop responsiveness to new signals due to the leakiness and lack of specificity of preexisting promoters and regulators. When needed, these may become more specific through suppression of undesirable signals and further fine-tuning of the recruited proteins to interact with distinct chemicals. This hypothesis is supported by the sophisticated regulation of sigma 54-dependent promoters of the TOL (toluene biodegradation) operons, which can be activated to various degrees by heterologous proteins. Such "illegitimate' activation is suppressed by bent DNA structures, either static or protein induced, between promoter core elements. Therefore, not only the regulators but also the DNA sequences participate in the process that gives rise to novel specificities.

Involvement of sigma 54 in exponential silencing of the Pseudomonas putida TOL plasmid Pu promoter

The sigma 54-dependent Pu promoter of the TOL plasmid pWW0 of Pseudomonas putida becomes activated by the prokaryotic enhancer-binding XyIR protein when cells encounter m-xylene in the medium. However, even in the presence of the aromatic inducer, Pu activity is silenced in vivo during rapid exponential growth of the cells in rich medium. Various elements known to be involved in the control of the transcriptional activity of the promoter were examined to ascertain the mechanism by which expression of Pu is limited during the exponential phase of growth. A truncated and fully constitutive XyIR derivative deleted of its signal-reception N-terminal domain was found to be subjected to the same exponential silencing as the wild-type XyIR when exposed to m-xylene. This indicated that the phenomenon is not due to a late activation of XyIR by the aromatic effector. A Pu variant in which the integration host factor (IHF)-binding site had been functionally replaced by a statically curved DNA segment showed the same induction pattern, thus ruling out variations in the intracellular levels of IHF changes during growth as the element responsible for the inactivity of Pu in rapidly growing cells. On the contrary, overproduction of the sigma 54 factor allowed Pu expression during exponential phase. As sigma 54 protein levels remained approximately constant during growth, the exponential silencing of Pu could be caused ultimately by changes in the activity of the factor itself. This effect may not be exclusive to Pu, but could be a general co-regulation mechanism in sigma 54-dependent promoters that connects transcription of a specific set of genes with the general physiological status of the cells.

The amino-terminal domain of the prokaryotic enhancer-binding protein XylR is a specific intramolecular repressor

The mechanism under which the signal-reception amino-terminal portion (A domain) of the prokaryotic enhancer-binding protein XylR controls the activity of the regulator has been investigated through complementation tests in vivo, in which the various protein segments were produced as independent polypeptides. Separate expression of the A domain repressed the otherwise constitutive activity of a truncated derivative of XylR deleted of its A domain (XylR delta A). Such inhibition was not released by m-xylene, the natural inducer of the system. Repression caused by the A domain was specific for XylR because it did not affect activation of the sigma 54 promoter PnifH by a derivative of its cognate regulator, NifA, deleted of its own A domain. The A domain was also unable to repress the activity of a NifA-XylR hybrid protein resulting from fusing two-thirds of the central domain of NifA to the carboxyl-terminal third of XylR, which includes its DNA-binding domain. The inhibitory effect caused by the A domain of XylR on XylR delta A seems, therefore, to result from specific interactions in trans between the two truncated proteins and not from mere hindering of an activating surface.

Integration host factor suppresses promiscuous activation of the sigma 54-dependent promoter Pu of Pseudomonas putida

In the presence of m-xylene, the Pu promoter of the TOL plasmid of Pseudomonas putida is activated by the prokaryotic enhancer-binding protein XylR. The intervening DNA segment between the upstream activating sequences (UASs) and those for RNA polymerase binding contains an integration host factor (IHF) attachment site that is required for full transcriptional activity. In the absence of IHF, the Pu promoter can be cross-activated by other members of the sigma 54-dependent family of regulatory proteins. Such illegitimate activation does not require the binding of the heterologous regulators to DNA and it is suppressed by bent DNA structures, either static or protein induced, between the promoter core elements (UAS and RNA polymerase recognition sequence). The role of IHF in some sigma 54 promoters is, therefore, not only a structural aid for assembling a correct promoter geometry but also that of an active suppressor (restrictor) of promiscuous activation by heterologous regulators for increased promoter specificity.

The sigma 54-dependent promoter Ps of the TOL plasmid of Pseudomonas putida requires HU for transcriptional activation in vivo by XylR

In the presence of toluene and xylenes, the sigma 54-dependent Ps promoter of the TOL (toluene biodegradation) plasmid pWW0 of Pseudomonas putida is activated at a distance by the XylR protein, of the NtrC family of transcriptional regulators. Since contacts between XylR bound to upstream activating sites and the RNA polymerase require the looping out of the intervening DNA segment, the intrinsic curvature, the bendability of the corresponding sequence, and the spatial effects of protein-induced DNA bending have an influence on promoter activity. Unlike other sigma 54-dependent promoters, Ps does not require the structural aid of the integration host factor to assemble a specific promoter geometry required for transcriptional initiation. In vivo analysis of transcriptional activity in various genetic backgrounds suggests, instead, that the looping out of intervening DNA sequences in Ps would result from the exacerbation of a preexisting static bend within the region, assisted by the histone-like protein HU.

Activation of the transcriptional regulator XylR of Pseudomonas putida by release of repression between functional domains

In the presence of toluene, xylenes and other structural analogues, the regulatory protein XylR, of the family of transcriptional regulators which act in concert with the sigma 54 factor, activate the promoter Pu of the TOL (toluene degradation) plasmid pWWO of Pseudomonas putida. Amino acid changes Val-219-Asp and Ala-220-Pro, introducing a proline kink at the hinge region between the N-terminal A domain and the central portion of XylR, resulted in a semi-constitutive phenotype which mimicked the activating effect of aromatic inducers. This phenotype was further exacerbated by inserting extra amino acid residues within the same inter-domain region. A truncated XylR protein devoid of the signal-receiving, amino-terminal portion of the protein stimulated the cognate promoter Pu at high levels independently of inducer addition, both in Escherichia coli and in Pseudomonas putida. Replacement of the amino-terminal domain by a heterologous peptide derived from the MS2 virus polymerase resulted in a hybrid protein still able to bind DNA to the same extent in vivo as XylR, but unable to stimulate transcription. These data indicate that a key event in the activation of XylR by toluene/xylenes is the release of the repression caused by the A domain of the protein on surfaces located at the central domain of the regulator.

Co-regulation by bent DNA. Functional substitutions of the integration host factor site at sigma 54-dependent promoter Pu of the upper-TOL operon by intrinsically curved sequences

The role of integration host factor (IHF) in the regulation of the sigma 54-dependent promoter Pu of the TOL plasmid of Pseudomonas putida has been examined. We have selected in vivo insertions of intrinsically curved DNA that restore the responsiveness of an IHF-binding site deletion variant of Pu to the cognate activator of the system, XylR. We found five Pu derivatives which had inserted a core sequence with 6 phased [A]6 tracts, flanked by different lengths of DNA at the location of the former IHF site. They displayed 40-100% of the activity of Pu, were independent of IHF, and maintained the overall geometry of the wild-type promoter. The induction patterns of Pu, compared to those of hybrid promoters, were virtually indistinguishable. This supports the notion that, in native conditions, IHF co-regulates the system by providing a structural aid for promoter architecture and not by interacting directly with the RNA polymerase, as it has been suggested with other known IHF-dependent promoters.

Correlation between DNA bending and transcriptional activation at a plasmid promoter

Plasmid pLS1 replicates in both Gram-positive and Gram-negative bacteria. One of the elements controlling plasmid replication is an antisense RNA (ctRNA II), transcribed from promoter PctII, which should be expressed in all the hosts where the plasmid replicates. We show here that expression from PctII and the presence of curved DNA regions located upstream of this promoter are related. DNA fragments containing these upstream regions exhibit anomalous electrophoretic mobility, and their presence increases in vivo and in vitro transcription, apparently with an independence of any activator protein. RNA polymerase is able to bend a DNA fragment containing PctII, suggesting that an increase in the RNA polymerase-DNA contacts is an important step in transcription initiation. Furthermore, the upstream activating region could be substituted by targets of unrelated DNA-bending proteins. This finding supports the role of curved DNA as a transcriptional modulator.

Promoters responsive to DNA bending: a common theme in prokaryotic gene expression

The early notion of DNA as a passive target for regulatory proteins has given way to the realization that higher-order DNA structures and DNA-protein complexes are at the basis of many molecular processes, including control of promoter activity. Protein binding may direct the bending of an otherwise linear DNA, exacerbate the angle of an intrinsic bend, or assist the directional flexibility of certain sequences within prokaryotic promoters. The important, sometimes essential role of intrinsic or protein-induced DNA bending in transcriptional regulation has become evident in virtually every system examined. As discussed throughout this article, not every function of DNA bends is understood, but their presence has been detected in a wide variety of bacterial promoters subjected to positive or negative control. Nonlinear DNA structures facilitate and even determine proximal and distal DNA-protein and protein-protein contacts involved in the various steps leading to transcription initiation.

Protein-induced bending as a transcriptional switch

The question of whether protein-induced DNA bending can act as a switch factor when placed upstream of an array of promoters located in tandem was investigated in vivo. The catabolite activating protein binding site of the fur operon was replaced by the binding site of the RepA repressor protein, which is able to bend DNA immediately after binding. Appropriately phased induced bending could act as a transcriptional switch factor in vivo.

A genetic system to study the in vivo role of transcriptional regulators in Escherichia coli

A genetic system for studying in vivo the interactions between a transcriptional regulatory protein and its target DNA has been developed for Escherichia coli. It is composed of two compatible plasmids: one high-copy-number promoter-probe vector, and one low-copy-number vector in which the gene encoding the desired protein is cloned under the control of an inducible promoter. The system was successfully tested for its specificity and for dosage analysis by using a combination of the plasmid pLS1-encoded RepA repressor and its target DNA.

The RepA repressor can act as a transcriptional activator by inducing DNA bends

We have shown that a transcriptional repressor protein can regulate promoter activity via DNA bending by using the pLS1 plasmid promoter PII (which has intrinsic curvature upstream of its -35 box) and the plasmid-encoded repressor protein RepA (which strongly bends DNA). Substitution of the curved region for a straight DNA fragment containing the RepA target resulted in increased (or decreased) gene expression when RepA was supplied in trans: enhanced gene expression was evident when the target of RepA and the promoter were on the same face of the DNA helix; repression was found when they were on opposite faces of the DNA. In vitro activation of transcription from PII was observed when supercoiled DNA was used as template, but not with linear molecules. We propose that promoter activity can be regulated by the proper positioning (in or out of phase) of an induced DNA bend with the RNA polymerase recognition sites.

Plasmid pLS1-encoded RepA protein regulates transcription from repAB promoter by binding to a DNA sequence containing a 13-base pair symmetric element

The repA gene product of the promiscuous plasmid pLS1 is a 45-amino acid repressor protein. The plasmid initiator of replication protein, RepB, is encoded by the repB gene which is situated downstream of repA. The results presented here demonstrate that both genes constitute a transcriptional unit. We show that the repA gene product inhibits transcription from the repAB promoter both in vitro and in vivo. By hydroxyl radical footprinting on both DNA strands, we show that RepA binds specifically to a plasmid region in which a 13-base pair element, showing a 2-fold rotational symmetry, is located. Within this symmetric element lies the -35 region of the repAB promoter. RepA binds into successive major grooves along one face of the DNA helix. The general architecture of RepA and of its interactions with DNA resembles that of the Cro repressor proteins of bacteriophages lambda and 434. We propose that RepA regulates the plasmid copy number by binding to its own promoter, thus controlling the synthesis of the plasmid initiator of replication protein.

Induced bending of plasmid pLS1 DNA by the plasmid-encoded protein RepA

The broad host range streptococcal plasmid pLS1 encodes for a 5.1-kDa repressor protein, RepA. This protein has affinity for DNA (linear or supercoiled) and is translated from the same mRNA as the replication initiator protein RepB. By gel retardation assays, we observed that RepA shows specificity for binding to the plasmid HinfID fragment, which includes the target of the protein. The target of RepA within the plasmid DNA molecule has been located around the plasmid single site ApaLI. This site is included in a region that contains the promoter for the repA and repB genes and is contiguous to the plasmid ori(+). A complex sequence-directed DNA curvature is observed in this region of pLS1. Upon addition of RepA to plasmid linear DNA or to circularly permuted restriction fragments, this intrinsic curvature was greatly enhanced. Thus, a strong RepA-induced bending could be located in the vicinity of the ApaLI site. Visualization of the bent DNA was achieved by electron microscopy of complexes between RepA and plasmid DNA fragments containing the RepA target.

Purification and characterization of RepA, a protein involved in the copy number control of plasmid pLS1

The promiscuous streptococcal plasmid pLS1 encodes for the 5.1 kDa RepA protein, involved in the regulation of the plasmid copy number. Synthesis of RepA was observed both in Bacillus subtilis minicells and in an Escherichia coli expression system. From this system, the protein has been purified and it appears to be a dimer of identical subunits. The amino acid sequence of RepA has been determined. RepA shows the alpha helix-turn-alpha helix motif typical of many DNA-binding proteins and it shares homology with a number of repressors, specially with the TrfB repressor encoded by the broad-host-range plasmid RK2. DNase I footprinting revealed that the RepA target is located in the region of the promoter for the repA and repB genes. Trans-complementation analysis showed that in vivo, RepA behaves as a repressor by regulating the plasmid copy number. We propose that the regulatory role of RepA is by limitation of the synthesis of the initiator protein RepB.

Three regions in the DNA of plasmid pLS1 show sequence-directed static bending

Three regions showing abnormal electrophoretic mobility, which is an indication of the existence of bends in DNA, have been observed in the DNA of plasmid pLS1. These loci have been characterized by assays designed to detect sequence-directed bending in DNA (temperature-dependence migration and two dimensional electrophoresis). The first region (locus B-1) was located within a fragment that contains a proposed inhibitor countertranscribed RNA (RNAII). The second locus (B-2) contains the plasmid plus origin of replication and the third region (locus B-3) was located in the vicinity of a putative antisense RNA (RNAI) of unknown function. The centres of the first two bent DNA regions were located by circular permutation assays at nucleotides 882 (locus B-1) and 634 (locus B-2). The bend centre of locus B-1 was found to be upstream of the promoter for the putative antisense RNAII. The centre of curvature in locus B-2 was located in the vicinity of the putative promoter of the replication proteins RepA and RepB and of a sequence that has three 11-bp direct repeats. The DNA sequence at this region showed the existence of A.T tracts, with an internal repeat of 10 to 11 base pairs, for five helix turns. A complex curvature in the DNA of pLS1 at locus B-2 that may have a regulatory role in plasmid replication is postulated.