Transcription regulation by repressosome and by RNA polymerase contact

The transcriptional regulator GalR self-assembles to form highly regular tubular structures

The Gal repressor regulates transport and metabolism of D-galactose in Escherichia coli and can mediate DNA loop formation by forming a bridge between adjacent or distant sites. GalR forms insoluble aggregates at lower salt concentrations in vitro, which can be solubilized at higher salt concentrations. Here, we investigate the assembly and disassembly of GalR aggregates. We find that a sharp transition from aggregates to soluble species occurs between 200 and 400 mM NaCl, incompatible with a simple salting-in effect. The aggregates are highly ordered rod-like structures, highlighting a remarkable ability for organized self-assembly. Mutant studies reveal that aggregation is dependent on two separate interfaces of GalR. The highly ordered structures dissociate to smaller aggregates in the presence of D-galactose. We propose that these self-assembled structures may constitute galactose-tolerant polymers for chromosome compaction in stationary phase cells, in effect linking self-assembly with regulatory function.

Specific contacts of the -35 region of the galP1 promoter by RNA polymerase inhibit GalR-mediated DNA looping repression

The P1 promoter of the galactose operon in Escherichia coli is one of the best studied examples of ‘extended −10’ promoters. Recognition of the P1 promoter does not require specific contacts between RNA polymerase and its poor −35 element. To investigate whether specific recognition of the −35 element would affect the regulation of P1 by GalR, we mutagenized the −35 element of P1, isolated variants of the −35 element and studied the regulation of the mutant promoters by in vitro transcription assays and by mathematical modeling. The results show that the GalR-mediated DNA loop is less efficient in repressing P1 transcription when RNA polymerase binds to the −10 and −35 elements concomitantly. Our results suggest that promoters that lack specific −35 element recognition allow decoupling of local chromosome structure from transcription initiation.

Regulation of glutamate dehydrogenase expression in Pseudomonas putida results from its direct repression by NtrC under nitrogen-limiting conditions

Nitrogen-regulated genes in enterobacteria are positively controlled by the transcriptional activator of σ(N) -dependent promoters NtrC, either directly or indirectly, through the dual regulator Nac. Similar to enterobacteria, gdhA encoding glutamate dehydrogenase from Pseudomonas putida is one of the few genes that is induced by excess nitrogen. In P. putida, the binding of NtrC to the gdhA promoter region and in vitro transcription suggest that, unlike its enterobacterial homologue that is repressed by Nac, gdhA is directly repressed by NtrC. Footprinting analyses demonstrated that NtrC binds to four distinct sites in the gdhA promoter. NtrC dimers bind cooperatively, and those bound closer to the promoter interact with the dimers bound further upstream, thus producing a proposed repressor loop in the DNA. The formation of the higher-order complex and the repressor loop appears to be important for repression but not absolutely essential. Both the phosphorylated and the non-phosphorylated forms of NtrC efficiently repressed gdhA transcription in vitro and in vivo. Therefore, NtrC repression of gdhA under nitrogen-limiting conditions does not depend on the phosphorylation of the regulator; rather, it relies on an increase in the repressor concentration under these conditions.

Genetic flexibility of regulatory networks

Gene regulatory networks are based on simple building blocks such as promoters, transcription factors (TFs) and their binding sites on DNA. But how diverse are the functions that can be obtained by different arrangements of promoters and TF binding sites? In this work we constructed synthetic regulatory regions using promoter elements and binding sites of two noninteracting TFs, each sensing a single environmental input signal. We show that simply by combining these three kinds of elements, we can obtain 11 of the 16 Boolean logic gates that integrate two environmental signals in vivo. Further, we demonstrate how combination of logic gates can result in new logic functions. Our results suggest that simple elements of transcription regulation form a highly flexible toolbox that can generate diverse functions under natural selection.

DNA bending and looping in the transcriptional control of bacteriophage phi29

Recent studies on the regulation of phage phi29 gene expression reveal new ways to accomplish the processes required for the orderly gene expression in prokaryotic systems. These studies revealed a novel DNA-binding domain in the phage main transcriptional regulator and the nature and dynamics of the multimeric DNA-protein complex responsible for the switch from early to late gene expression. This review describes the features of the regulatory mechanism that leads to the simultaneous activation and repression of transcription, and discusses it in the context of the role of the topological modification of the DNA carried out by two phage-encoded proteins working synergistically with the DNA.

DNA linking number change induced by sequence-specific DNA-binding proteins

Sequence-specific DNA-binding proteins play a key role in many fundamental biological processes, such as transcription, DNA replication and recombination. Very often, these DNA-binding proteins introduce structural changes to the target DNA-binding sites including DNA bending, twisting or untwisting and wrapping, which in many cases induce a linking number change (ΔLk) to the DNA-binding site. Due to the lack of a feasible approach, ΔLk induced by sequence-specific DNA-binding proteins has not been fully explored. In this paper we successfully constructed a series of DNA plasmids that carry many tandem copies of a DNA-binding site for one sequence-specific DNA-binding protein, such as λ O, LacI, GalR, CRP and AraC. In this case, the protein-induced ΔLk was greatly amplified and can be measured experimentally. Indeed, not only were we able to simultaneously determine the protein-induced ΔLk and the DNA-binding constant for λ O and GalR, but also we demonstrated that the protein-induced ΔLk is an intrinsic property for these sequence-specific DNA-binding proteins. Our results also showed that protein-mediated DNA looping by AraC and LacI can induce a ΔLk to the plasmid DNA templates. Furthermore, we demonstrated that the protein-induced ΔLk does not correlate with the protein-induced DNA bending by the DNA-binding proteins.

Three-stage Regulation of the Amphibolic gal Operon: From Repressosome to GalR-free DNA

The gal operon of Escherichia coli is negatively regulated by the Gal repressosome, a higher order nucleoprotein complex containing a DNA loop that encompasses two gal promoters. In the repressosome structure, Gal repressor (GalR) dimers are bound to the two operator sites, flanking the promoter region, thus generating a DNA loop. The DNA loop is stabilized by binding of the architectural HU protein to the apex of the loop, and negative supercoiling. The gal promoters are also regulated in opposite directions by GalR without DNA looping. The repressosome-mediated as well as looping-independent transcription regulation of the two promoters is lifted in the presence of the inducer D-galactose. We tested the effect of D-galactose on various DNA-protein and protein-protein interactions of different regulatory complexes and on transcription repression in vitro. We found that the inducer breaks up the repressosome with clear intermediates in a concentration-dependent manner. The sequential disassembly generates different stages of regulation of the gal operon. The D-galactose-dependent switch from one stage of regulation to another satisfies the amphibolic requirement of the gal operon.

Mode of action of the Bordetella BvgA protein: transcriptional activation and repression of the Bordetella bronchiseptica bipA promoter

The Bordetella BvgAS signal transduction system controls the transition among at least three known phenotypic phases (Bvg+, Bvg(i), and Bvg-) and the expression of a number of genes which have distinct phase-specific expression profiles. This complex regulation of gene expression along the Bvg signaling continuum is best exemplified by the gene bipA, which is expressed at a low level in the Bvg+ phase, at a maximal level in the Bvg(i) phase, and at undetectable levels in the Bvg- phase. The bipA promoter has multiple BvgA binding sites which play distinct regulatory roles. We had previously speculated that the expression profile of bipA is a consequence of the differential occupancy of the various BvgA binding sites as a result of variation in the levels of phosphorylated BvgA (BvgA-P) inside the cell. In this report, we provide in vitro evidence for this model and show that bipA expression is activated at low concentrations of BvgA-P and is repressed at high concentrations. By using independent DNA binding assays, we demonstrate that under activating conditions there is a synergistic effect on the binding of BvgA and RNA polymerase (RNAP), leading to the formation of open complexes at the promoter. We further show that, under in vitro conditions, when bipA transcription is minimal, there is competition between the binding of RNAP and BvgA-P to the bipA promoter. Our results show that the BvgA binding site IR2 plays a central role in mediating this repression.

Estrogen action: revitalization of the chick oviduct model

Despite decades of investigation, the molecular pathways triggered by estrogen that lead to tissue-specific cell proliferation, differentiation and survival are only superficially understood. If we are to modulate the actions of estrogen selectively in these processes, continued investigation using biologically relevant models is essential. The chick oviduct emerged as an early model for investigating the mechanism of action of steroid hormones because of its exquisite responsiveness to them. Unfortunately, because of experimental limitations, this model has been neglected in the past decade. Reviving this model has become intellectually attractive and technically feasible.

A-tract clusters may facilitate DNA packaging in bacterial nucleoid

Molecular mechanisms of bacterial chromosome packaging are still unclear, as bacteria lack nucleosomes or other apparent basic elements of DNA compaction. Among the factors facilitating DNA condensation may be a propensity of the DNA molecule for folding due to its intrinsic curvature. As suggested previously, the sequence correlations in genome reflect such a propensity [Trifonov and Sussman (1980) Proc. Natl Acad. Sci. USA, 77, 3816-3820]. To further elaborate this concept, we analyzed positioning of A-tracts (the sequence motifs introducing the most pronounced DNA curvature) in the Escherichia coli genome. First, we observed that the A-tracts are over-represented and distributed 'quasi-regularly' throughout the genome, including both the coding and intergenic sequences. Second, there is a 10-12 bp periodicity in the A-tract positioning indicating that the A-tracts are phased with respect to the DNA helical repeat. Third, the phased A-tracts are organized in approximately 100 bp long clusters. The latter feature was revealed with the help of a novel approach based on the Fourier series expansion of the A-tract distance autocorrelation function. Since the A-tracts introduce local bends of the DNA duplex and these bends accumulate when properly phased, the observed clusters would facilitate DNA looping. Also, such clusters may serve as binding sites for the nucleoid-associated proteins that have affinities for curved DNA (such as HU, H-NS, Hfq and CbpA). Therefore, we suggest that the approximately 100 bp long clusters of the phased A-tracts constitute the 'structural code' for DNA compaction by providing the long-range intrinsic curvature and increasing stability of the DNA complexes with architectural proteins.

Gal repressor-operator-HU ternary complex: pathway of repressosome formation

DNA transaction reactions require formation of nucleoprotein complexes that involve multifaceted DNA-protein and protein-protein interactions. Genetic and biochemical studies suggested that the higher order Gal repressosome structure, which governs the transcription of two tandem galpromoters in Escherichia coli, involves sequence-specific binding of GalR repressor dimers to two operators, O(E) and O(I), located 113 bp apart, binding of GalR to the sequence-nonspecific DNA binding protein HU, interaction of HU with an architecturally critical DNA site between the two operators, and interaction between two DNA-bound GalR dimers generating a loop of the intervening DNA segment. In this paper, we demonstrate and determine the thermodynamic parameters of several of these interactions, GalR dimer-O(E), GalR tetramerization, HU-GalR, and HU-GalR-O(E) interactions, by analytical ultracentrifugation, fluorescence anisotropy, and fluorescence resonance energy transfer. The physiological significance of several of these interactions was confirmed by the finding that a mutant HU, which is unable to form the repressosome in vivo and in vitro, failed to show the HU-GalR interaction. The results help to construct a pathway of Gal repressosome assembly.

Archaeal transcriptional regulation – variation on a bacterial theme?

There is now an increasing body of data available on the DNA-binding properties of several putative transcriptional regulators in the Archaeal domain of life. The evidence points to simple models of promoter occlusion or facilitated recruitment of basal machinery for repressors and activators, respectively. However, little is known about the co-factor requirements, in vivo mechanisms and targets of many of these regulators. It is anticipated that the application of post-genomic technologies will begin to shed light on this fascinating area.

Sir2 and the Acetyltransferase, Pat, Regulate the Archaeal Chromatin Protein, Alba

The DNA binding affinity of Alba, a chromatin protein of the archaeon Sulfolobus solfataricus P2, is regulated by acetylation of lysine 16. Here we identify an acetyltransferase that specifically acetylates Alba on this residue. The effect of acetylation is to lower the affinity of Alba for DNA. Remarkably, the acetyltransferase is conserved not only in archaea but also in bacteria where it appears to play a role in metabolic regulation. Therefore, our data suggest that S. solfataricus has co-opted this bacterial regulatory system to generate a rudimentary form of chromatin regulation.

Flexibility in repression and cooperativity by KorB of broad host range IncP-1 plasmid RK2

KorB, encoded by plasmid RK2, belongs to the ParB family of active partitioning proteins. It binds to 12 operators on the RK2 genome and was previously known to repress promoters immediately adjacent to operators O(B)1, O(B)10 and O(B)12 (proximal) or up to 154 bp away (distal) from O(B)2, O(B)9 and O(B)11. To achieve strong repression, KorB requires a cooperative interaction with one of two other plasmid-encoded repressors, KorA or TrbA. Reporter gene assays were used in this study to test whether the additional KorB operators may influence transcription and to test how KorB acts at a distance. The distance between O(B)9 and trbBp could be increased to 1.6kb with little reduction in repression or cooperativity with TrbA. KorB was also able to repress the promoter and cooperate with TrbA when the O(B) site was placed downstream of trbBp. This suggested a potential regulatory role for O(B) sites located a long way from any known promoter on RK2. O(B)4, 1.9kb upstream of traGp, was shown to mediate TrbA-potentiated KorB repression of this promoter, but no effect on traJp upstream of O(B)4 was observed, which may be due to the roadblocking or topological influence of the nucleoprotein complex formed at the adjacent transfer origin, oriT. Repression and cooperativity were alleviated significantly when a lac operator was inserted between O(B)9 and trbBp in the context of a LacI+ host, a standard test for spreading of a DNA-binding protein. On the other hand, a standard test for DNA looping, movement of the operator to the opposite face of the DNA helix from the natural binding site, did not significantly affect KorB repression or cooperativity with TrbA and KorA over relatively short distances. While these results are more consistent with spreading as the mechanism by which KorB reaches its target, previous estimates of KorB molecules per cell are not consistent with there being enough to spread up to 1kb from each O(B). A plausible model is therefore that KorB can do both, spreading over relatively short distances and looping over longer distances.

GalR represses galP1 by inhibiting the rate-determining open complex formation through RNA polymerase contact: a GalR negative control mutant

GalR represses the galP1 promoter by a DNA looping-independent mechanism. Equilibrium binding of GalR and RNA polymerase to DNA, and real-time kinetics of base-pair distortion (isomerization) showed that the equilibrium dissociation constant of RNA polymerase-P1 closed complexes is largely unaffected in the presence of saturating GalR, indicating that mutual antagonism (steric hindrance) of the regulator and the RNA polymerase does not occur at this promoter. In fluorescence kinetics with 2-AP labeled P1 DNA, GalR inhibited the slower of the two-step base-pair distortion process. We isolated a negative control GalR mutant, S29R, which while bound to the operator DNA was incapable of repression of P1. Based on these results and previous demonstration that repression requires the C-terminal domain of the alpha subunit (alpha-CTD) of RNA polymerase, we propose that GalR establishes contact with alpha-CTD at the last resolved isomerization intermediate, forming a kinetic trap.

Analysis in vitro and in vivo of the transcriptional regulator CrgA of Neisseria meningitidis upon contact with target cells

Contact between CrgA, a LysR-like regulatory protein in Neisseria meningitidis, and DNA is involved in the repression of several bacterial genes upon contact with epithelial cells. We used a defined in vitro system containing crgA promoter, purified RNA polymerase (RNAP) and purified CrgA protein to demonstrate that CrgA was directly responsible for this transcriptional repression. Interaction between the C-terminal domain of CrgA and the RNAP led to the production of short abortive transcripts, suggesting that CrgA may act by preventing RNAP from clearing the promoter. We probed the regulation by CrgA of its own production by analysing CrgA-DNA contacts during cell-bacteria interaction by assaying in vivo protection against dimethyl sulphate (DMS) methylation. Comparison of DMS footprints in vitro and in vivo suggested that CrgA repressed transcription through specific base contacts, probably in the major groove of the DNA double helix, resulting in DNA looping. Upon contact with target cells, CrgA was released from the DNA, allowing transcription of the target gene to proceed to elongation and facilitating tight control of the expression of genes regulated by CrgA.

Two different modes of transcription repression of the Escherichia coli acetate operon by IclR

IclR is a repressor for the Escherichia coli aceBAK operon, which encodes isocitrate lyase (aceB), malate synthase (aceA) and isocitrate dehydroge-nase kinase/phosphorylase (aceK) in the glyoxylate bypass. IclR also represses the expression of iclR in an autogenous manner. DNase I footprinting and in vitro transcription assays indicated that IclR binds to an IclR box (-21 to +14), which overlaps the iclR promoter and thus competes with the RNA polymerase for DNA binding, leading to transcription repression. In the case of the aceBAK operon, IclR binds to IclR box II between -52 and -19 of the aceB promoter and interferes with binding of the RNA polymerase to this promoter. A secondary IclR binding site (IclR box I) was identified between -125 and -99 of the aceB promoter. IclR binds to this IclR box I even after formation of the aceB promoter open complex and, moreover, induces disassembly of the open complex, leading to repression of aceB transcription. In parallel, the location of the C-terminal domain of the RNA polymerase alpha subunit (alphaCTD) on DNA is shifted close to the IclR box I, indicating that direct interaction between the alphaCTD and the IclR box I-associated IclR caused the repression.

Holding it together: chromatin in the Archaea

Recently, several advances have been made in the understanding of the form and function of archaeal chromatin. Remarkable parallels can be drawn between the structure and modification of chromatin components in the archaeal and the eukaryotic domains of life. Indeed, it now appears that key components of the hugely complex eukaryotic chromatin regulatory machinery were established before the divergence of the archaeal and eukaryotic lineages.

Differential regulation of the Bordetella bipA gene: distinct roles for different BvgA binding sites

The BvgAS signal transduction system of Bordetella controls an entire spectrum of gene expression states in response to differences in environmental conditions. In particular, the Bordetella Bvg-intermediate-phase gene bipA displays a complex regulatory pattern in response to various concentrations of modulators. Expression of bipA is low in the absence of modulating signals, maximal at intermediate concentrations of modulators, and near background levels at high concentrations of modulators. bipA is regulated at the transcriptional level, and the bipA promoter contains multiple BvgA binding sites present both upstream and downstream of the transcriptional initiation site. In vivo transcriptional analyses, utilizing several mutant promoter fusions to the reporter enzyme beta-galactosidase, suggest that the upstream binding site IR1 is essential for expression and that the downstream binding sites IR2 and IR3 are involved in transcriptional repression. Mutations of IR2 or IR3 convert the expression profile of bipA from that of a Bvg-intermediate-specific-phase gene to that of a Bvg(+)-phase gene. To gain insight into the mechanism responsible for differential bipA regulation, DNase I protection studies were conducted with various mutant promoters. These analyses suggest that IR1 and IR2 function as core binding sites and are the primary determinants for the phosphorylation-induced oligomerization of BvgA to the adjacent regions.

Protein-protein and protein-DNA interactions of sigma70 region 4 involved in transcription activation by lambdacI

The cI protein of bacteriophage lambda (lambdacI) activates transcription from promoter P(RM) through an acidic patch on the surface of its DNA-binding domain. Genetic evidence suggests that this acidic patch stimulates transcription from P(RM) through contact with the C-terminal domain (region 4) of the sigma(70) subunit of Escherichia coli RNA polymerase. Here, we identify two basic residues in region 4 of sigma(70) that are critical for lambdacI-mediated activation of transcription from P(RM). On the basis of structural modeling, we propose that one of these sigma(70) residues, K593, facilitates the interaction between lambdacI and region 4 of sigma(70) by inducing a bend in the DNA upstream of the -35 element, whereas the other, R588, interacts directly with a critical acidic residue within the activating patch of lambdacI. Residue R588 of sigma(70) has been shown to play an important role in promoter recognition; our findings suggest that the R588 side-chain has a dual function at P(RM), facilitating the interaction of region 4 with the promoter -35 element and participating directly in the protein-protein interaction with lambdacI.

The phi29 transcriptional regulator contacts the nucleoid protein p6 to organize a repression complex

The nucleoid protein p6 of Bacillus subtilis phage phi29 binds to DNA, recognizing a structural feature rather than a specific sequence. Upon binding to the viral DNA ends, p6 generates an extended nucleoprotein complex that activates the initiation of phi29 DNA replication. Protein p6 also participates in transcription regulation, repressing the early C2 promoter and assisting the viral regulatory protein p4 in controlling the switch from early to late transcription. Proteins p6 and p4 bind cooperatively to an approximately 200 bp DNA region located between the late A3 and the early A2c promoters, generating an extended nucleoprotein complex that helps to repress the early A2c promoter and to activate the late A3 promoter. We show that stable assembly of this complex requires interaction between protein p6 and the C-terminus of protein p4. Therefore, at this DNA region, stable polymerization of protein p6 relies on p4-specified signals in addition to the structural features of the DNA. Protein p4 would define the phase and boundaries of the p6-DNA complex.

Operator-bound GalR dimers close DNA loops by direct interaction: tetramerization and inducer binding

The assembly of the Gal repressosome, a higher order nucleoprotein complex that represses transcription of the gal operon in Escherichia coli, involves the formation of a DNA loop encompassing the promoter segment. GalR dimers bound to two spatially separated operators, O(E) and O(I), specifically interact with the histone-like protein HU and close the loop in supercoiled DNA. We isolated and characterized a GalR mutant containing an amino acid substitution (R282L) that can repress transcription in the absence of HU and supercoiled DNA both in vivo and in vitro. Repression involves the same DNA looping; deletion of either O(E) or O(I) makes the mutant GalR ineffective in repression. This and other results suggest that the R282L substitution increases the normal affinity between two DNA-bound GalR dimers, allowing looping. We conclude that GalR dimers interact directly and do not use HU as an adaptor in loop closure; HU and DNA supercoiling act in concert to stabilize the GalR tetramer. The stronger GalR-GalR interaction also made the gal transcription non-inducible, suggesting that the inducer binding acts by modulating tetramerization.

Mechanism for the switch of phi29 DNA early to late transcription by regulatory protein p4 and histone-like protein p6

Bacteriophage phi29 gene expression takes place from four major promoters, three of them (A2b, A2c and A3) clustered within 219 bp at a central region of the genome. Transcription regulation of these promoters involves both a highly specific DNA-binding protein (p4) and a low specificity DNA-binding protein (p6) functionally related to prokaryotic histone-like proteins. Protein p6 forms extended oligomeric arrays along the phage DNA. In contrast, protein p4 binds specifically upstream of late promoter A3 and early promoter A2c. We have analysed the concomitant binding of p6 and p4 and found that the proteins cooperate with each other in the binding to the central region of the genome, resulting in a ternary p4-p6-DNA complex that affects local DNA topology. Through this complex, protein p6 exerts a direct role in the repression of promoter A2c, impeding unwinding of the DNA strands needed for open complex formation. In contrast, protein p6 functions by reinforcing the positioning of protein p4 in the repression of promoter A2b and activation of promoter A3, thereby facilitating p4-mediated transcription regulation.

Structural basis for SRY-dependent 46-X,Y sex reversal: modulation of DNA bending by a naturally occurring point mutation

The HMG-box domain of the human male sex-determining factor SRY, hSRY(HMG) (comprising residues 57-140 of the full-length sequence), binds DNA sequence-specifically in the minor groove, resulting in substantial DNA bending. The majority of point mutations resulting in 46X,Y sex reversal are located within this domain. One clinical de novo mutation, M64I in the full-length hSRY sequence, which corresponds to M9I in the present hSRY(HMG) construct, acts principally by reducing the extent of DNA bending. To elucidate the structural consequences of the M9I mutation, we have solved the 3D solution structures of wild-type and M9I hSRY(HMG) complexed to a DNA 14mer by NMR, including the use of residual dipolar couplings to derive long-range orientational information. We show that the average bend angle (derived from an ensemble of 400 simulated annealing structures for each complex) is reduced by approximately 13 degrees from 54(+/-2) degrees in the wild-type complex to 41(+/-2) degrees in the M9I complex. The difference in DNA bending can be localized directly to changes in roll and tilt angles in the ApA base-pair step involved in interactions with residue 9 and partial intercalation of Ile13. The larger bend angle in the wild-type complex arises as a direct consequence of steric repulsion of the sugar of the second adenine by the bulky S(delta) atom of Met9, whose position is fixed by a hydrogen bond with the guanidino group of Arg17. In the M9I mutant, this hydrogen bond can no longer occur, and the less bulky C(gamma)m methyl group of Ile9 braces the sugar moieties of the two adenine residues, thereby decreasing the roll and tilt angles at the ApA step by approximately 8 degrees and approximately 5 degrees, respectively, and resulting in an overall difference in bend angle of approximately 13 degrees between the two complexes. To our knowledge, this is one of the first examples where the effects of a clinical mutation involving a protein-DNA complex have been visualized at the atomic level.

Repression of bacteriophage phi 29 early promoter C2 by viral protein p6 is due to impairment of closed complex

Bacillus subtilis phage phi 29 encodes a very abundant protein, p6, which is a non sequence-specific DNA-binding protein. Protein p6 has the potential to bind cooperatively to the phage genome, forming a nucleoprotein complex in which the DNA adopts a right-handed toroidal conformation winding around a protein core. The formation of this complex at the right end of the phage genome where the early promoter C2 is located affects local topology, which may contribute to the promoter repression, although the underlying molecular mechanism of this repression is not presently known. In this study, we analyzed the effect of the p6 nucleoprotein complex on the formation of transcription complexes at the C2 promoter. The results obtained indicate that the nucleoprotein complex does not occlude promoter C2 to RNA polymerase because both proteins can bind to the same DNA molecule. Protein p6 binds along the fragment including the sequence adjacent to the bound polymerase, altering the structure of the transcriptional complex and affecting specifically the stability of the closed complex. The findings presented might help to answer some of the open questions about the concerted molecular mechanisms of histone-like proteins as transcriptional silencers.

Repression of transcription initiation at 434 P(R) by 434 repressor: effects on transition of a closed to an open promoter complex

The lambdoid bacteriophage repressors function both as transcription activators and repressors. Regulation of transcription at the adjacent, but divergent promoters, P(RM) and P(R), determines the phage's choice between the lytic and lysogenic development pathways. Here, we demonstrate that 434 repressor bound at 434 O(R)1 alone is not sufficient to repress transcription from 434 P(R,) but that 434 repressor bound at 434 O(R)2 alone is necessary and sufficient to repress P(R )transcription. This is different from what occurs in the related bacteriophage lambda, in which binding of lambda repressor to either lambdaO(R)1 or lambdaO(R)2 represses transcription from lambdaP(R). The combined results of gel mobility shift and KMnO(4) footprinting assays show that while 434 repressor binding to 434 O(R)2 does not preclude RNA polymerase binding at the P(R) promoter, it does prevent it from forming open complexes at this promoter. The RNA polymerase-P(R) complexes that form in the presence of repressor are heparin-resistant and the DNA is not melted. This observation indicates that 434 repressor bound at 434 O(R)2 inhibits transcription initiation at the P(R) promoter by "locking" the RNA polymerase-P(R) complex into an inactive state instead of "blocking" the access of RNA polymerase to promoter DNA.

Mechanisms of transcriptional repression

Transcriptional repressors are usually viewed as proteins that bind to promoters in a way that impedes subsequent binding of RNA polymerase. Although this repression mechanism is found at several promoters, there is a growing list of repressors that inhibit transcription initiation in other ways. For example, several repressors allow the simultaneous binding of RNA polymerase to the promoter, but interfere with subsequent events of the initiation process, eventually inhibiting transcription initiation. The recent increase in the number of repressors for which the repression mechanism has been characterized in detail has shown an amazing variety of strategies to repress transcription initiation. It is not surprising to find that the repression mechanism used is usually exquisitely adapted to the characteristics of the promoter and of the repressor involved.

The bacterial DNA-binding protein H-NS represses ribosomal RNA transcription by trapping RNA polymerase in the initiation complex

The interaction of the bacterial regulatory protein H-NS with RNA polymerase and the ribosomal RNA P1 promoter was analyzed to better understand the mechanism of H-NS-dependent transcriptional repression. We could show that initial binding of RNA polymerase to the promoter was not inhibited by the simultaneous interaction of H-NS, although H-NS binding sites extend into the core promoter region. Binding of sigma(70)-saturated RNA polymerase and H-NS to the promoter DNA occurs cooperatively and results in a stable complex of slower gel electrophoretic mobility as compared to complexes formed with the single proteins. The presence of the upstream curved H-NS binding site contributes strongly to the cooperative RNA polymerase-promoter interaction. By KMnO(4) modification of single-stranded template nucleotides we could show that open complex formation at the rrnB P1 promoter was not inhibited by H-NS binding. An increased KMnO(4) reactivity of several positions within the open complex rather supports the view that open complex formation is stimulated in presence of H-NS. Moreover, subtle changes in the modification pattern indicate that the open complex formed in the presence of H-NS are structurally distinct from the H-NS-free complex. In vitro transcriptional analysis of the abortive and productive yields revealed that the formation of transcription products longer than three nucleotides is dramatically reduced in the presence of H-NS, while the amount of shorter abortive products remained unaffected. Together the results demonstrate that H-NS inhibits transcription at the rrnB P1 promoter not by interfering with initial RNA polymerase binding but by blocking chain elongation steps subsequent to the first (two) phosphodiester bond formations. The mechanism of H-NS dependent repression at rRNA promoters can thus be explained as a trap which inhibits substrate NTP incorporation beyond template position +3 into the initial transcribing complex.

Transcriptional silencing in bacteria

Transcriptional silencing and repression are modes of negative control of gene expression that differ in specificity. Repressors, when present at promoter-specific binding sites, interfere locally with RNA polymerase function. Silencing proteins act by covering a continuous region of DNA, compete with a broader spectrum of proteins and are non-specific with respect to the promoters affected. Studies of transcriptional silencing promise an entrée to relatively unexplored areas of prokaryotic biology.

Identification of a boundary domain adjacent to the potent human cytomegalovirus enhancer that represses transcription of the divergent UL127 promoter

Transcriptional repression within a complex modular promoter may play a key role in determining the action of enhancer elements. In human cytomegalovirus, the major immediate-early promoter (MIEP) locus contains a highly potent and complex modular enhancer. Evidence is presented suggesting that sequences of the MIEP between nucleotide positions -556 and -673 function to prevent transcription activation by enhancer elements from the UL127 open reading frame divergent promoter. Transient transfection assays of reporter plasmids revealed repressor sequences located between nucleotides -556 and -638. The ability of these sequences to confer repression in the context of an infection was shown using recombinant viruses generated from a bacterial artificial chromosome containing an infectious human cytomegalovirus genome. In addition to repressor sequences between -556 and -638, infection experiments using recombinant virus mutants indicated that sequences between -638 and -673 also contribute to repression of the UL127 promoter. On the basis of in vitro transcription and transient transfection assays, we further show that interposed viral repressor sequences completely inhibit enhancer-mediated activation of not only the homologous but also heterologous promoters. These and other experiments suggest that repression involves an interaction of host-encoded regulatory factors with defined promoter sequences that have the property of proximally interfering with upstream enhancer elements in a chromatin-independent manner. Altogether, our findings establish the presence of a boundary domain that efficiently blocks enhancer-promoter interactions, thus explaining how the enhancer can work to selectively activate the MIEP.

GalR mutants defective in repressosome formation

Transcription repression of the galactose operon of Escherichia coli requires (1) the binding of the GalR repressor to tandem operators flanking the promoters, (2) the binding of histone-like protein, HU, to a site between the GalR-binding sites, and (3) negatively supercoiled DNA. Under these conditions, protein-protein interactions mediate the formation of a nucleoprotein complex in the form of a DNA loop, which we have termed a repressosome. To analyze the structure of the repressosome, we have screened and isolated galR mutants in which single amino acid substitutions in GalR lead to defects in loop formation while the protein's operator-binding activity is retained. The mutant proteins were purified and their properties confirmed in vitro. We verified that in the case of the two stronger mutations, the proteins had secondary structures that were identical to that of wild-type GalR as reflected by circular dichroism spectroscopy. Homology-based modeling of GalR by use of the crystal structures of PurR and LacI has enabled us to place the three sites of mutation in a structural context. They occur in the carboxy-terminal subdomain of the GalR core, are surface exposed, and, therefore, may be involved in protein-protein interactions. On the basis of our model of GalR and its structural alignment with LacI and PurR, we have identified additional residues, the substitution of which leads to a specific defect in repression by looping. The effects of the mutations are the same in the presence of HMG-17, a eukaryotic protein unrelated to HU, which can also mediate GalR-dependent repression of the gal promoter. This observation suggests that the mutations define sites of GalR-GalR interaction rather than HU-GalR interaction in the repressosome.