Long-range interaction between two promoters: activation of the leu-500 promoter by a distant upstream promoter

Collective polymerase dynamics emerge from DNA supercoiling during transcription

All biological processes ultimately come from physical interactions. The mechanical properties of DNA play a critical role in transcription. RNA polymerase can over or under twist DNA (referred to as DNA supercoiling) when it moves along a gene, resulting in mechanical stresses in DNA that impact its own motion and that of other polymerases. For example, when enough supercoiling accumulates, an isolated polymerase halts, and transcription stops. DNA supercoiling can also mediate nonlocal interactions between polymerases that shape gene expression fluctuations. Here, we construct a comprehensive model of transcription that captures how RNA polymerase motion changes the degree of DNA supercoiling, which in turn feeds back into the rate at which polymerases are recruited and move along the DNA. Surprisingly, our model predicts that a group of three or more polymerases move together at a constant velocity and sustain their motion (forming what we call a polymeton), whereas one or two polymerases would have halted. We further show that accounting for the impact of DNA supercoiling on both RNA polymerase recruitment and velocity recapitulates empirical observations of gene expression fluctuations. Finally, we propose a mechanical toggle switch whereby interactions between genes are mediated by DNA twisting as opposed to proteins. Understanding the mechanical regulation of gene expression provides new insights into how endogenous genes can interact and informs the design of new forms of engineered interactions.

DNA Supercoiling: an Ancestral Regulator of Gene Expression in Pathogenic Bacteria?

DNA supercoiling acts as a global and ancestral regulator of bacterial gene expression. In this review, we advocate that it plays a pivotal role in host-pathogen interactions by transducing environmental signals to the bacterial chromosome and coordinating its transcriptional response. We present available evidence that DNA supercoiling is modulated by environmental stress conditions relevant to the infection process according to ancestral mechanisms, in zoopathogens as well as phytopathogens. We review the results of transcriptomics studies obtained in widely distant bacterial species, showing that such structural transitions of the chromosome are associated to a complex transcriptional response affecting a large fraction of the genome. Mechanisms and computational models of the transcriptional regulation by DNA supercoiling are then discussed, involving both basal interactions of RNA Polymerase with promoter DNA, and more specific interactions with regulatory proteins. A final part is specifically focused on the regulation of virulence genes within pathogenicity islands of several pathogenic bacterial species.

Inhibition of the gyrA promoter by transcription-coupled DNA supercoiling in Escherichia coli

The E. coli gyrA promoter (P_gyrA) is a DNA supercoiling sensitive promoter, stimulated by relaxation of DNA templates, and inhibited by (−) DNA supercoiling in bacteria. However, whether P_gyrA can be inhibited by transient and localized transcription-coupled DNA supercoiling (TCDS) has not been fully examined. In this paper, using different DNA templates including the E. coli chromosome, we show that transient and localized TCDS strongly inhibits P_gyrA in E. coli. This result can be explained by a twin-supercoiled domain model of transcription in which (+) and (−) supercoiled domains are generated around the transcribing RNA polymerase. We also find that fluoroquinolones, such as ciprofloxacin, can substantially increase the expression of the firefly luciferase under the control of the P_gyrA coupled to a divergent IPTG-inducible promoter in the presence of IPTG. This stimulation of P_gyrA by fluoroquinolones can be also explained by the twin-supercoiled domain model of transcription. This unique property of TCDS may be configured into a high throughput-screening (HTS) assay to identify antimicrobial compounds targeting bacterial DNA gyrase.

Transient and dynamic DNA supercoiling potently stimulates the leu-500 promoter in Escherichia coli

The inactive prokaryotic leu-500 promoter (P_leu-500) contains a single A-to-G point mutation in the -10 region of the leucine operon promoter, which causes leucine auxotrophy. This promoter can be activated by (-) DNA supercoiling in Escherichia coli topA strains. However, whether this activation arises from global, permanent, or transient, dynamic supercoiling is still not fully understood. In this article, using a newly established in vivo system carrying a pair of divergently coupled promoters, i.e. an IPTG-inducible promoter and P_leu-500 that control the expression of lacZ and luc (the firefly luciferase gene), respectively, we demonstrate that transient, dynamic (-) DNA supercoiling provided by divergent transcription in both wild-type and topA strains can potently activate P_leu-500 We found that this activation depended on the promoter strength and the length of RNA transcripts, which are functional characteristics of transcription-coupled DNA supercoiling (TCDS) precisely predicted by the twin-supercoiled domain model of transcription in which a (+) supercoiled domain is produced ahead of the RNA polymerase and a (-) supercoiled domain behind it. We also demonstrate that TCDS can be generated on topologically open DNA molecules, i.e. linear DNA molecules, in Escherichia coli, suggesting that topological boundaries or barriers are not required for the production of TCDS in vivo This work demonstrates that transient, dynamic TCDS by RNA polymerases is a major chromosome remodeling force in E. coli and greatly influences the nearby, coupled promoters/transcription.

Bacterial pathogen gene regulation: a DNA-structure-centred view of a protein-dominated domain

The mechanisms used by bacterial pathogens to regulate the expression of their genes, especially their virulence genes, have been the subject of intense investigation for several decades. Whole genome sequencing projects, together with more targeted studies, have identified hundreds of DNA-binding proteins that contribute to the patterns of gene expression observed during infection as well as providing important insights into the nature of the gene products whose expression is being controlled by these proteins. Themes that have emerged include the importance of horizontal gene transfer to the evolution of pathogens, the need to impose regulatory discipline upon these imported genes and the important roles played by factors normally associated with the organization of genome architecture as regulatory principles in the control of virulence gene expression. Among these architectural elements is the structure of DNA itself, its variable nature at a topological rather than just at a base-sequence level and its ability to play an active (as well as a passive) part in the gene regulation process.

DNA supercoiling is a fundamental regulatory principle in the control of bacterial gene expression

Although it has become routine to consider DNA in terms of its role as a carrier of genetic information, it is also an important contributor to the control of gene expression. This regulatory principle arises from its structural properties. DNA is maintained in an underwound state in most bacterial cells and this has important implications both for DNA storage in the nucleoid and for the expression of genetic information. Underwinding of the DNA through reduction in its linking number potentially imparts energy to the duplex that is available to drive DNA transactions, such as transcription, replication and recombination. The topological state of DNA also influences its affinity for some DNA binding proteins, especially in DNA sequences that have a high A + T base content. The underwinding of DNA by the ATP-dependent topoisomerase DNA gyrase creates a continuum between metabolic flux, DNA topology and gene expression that underpins the global response of the genome to changes in the intracellular and external environments. These connections describe a fundamental and generalised mechanism affecting global gene expression that underlies the specific control of transcription operating through conventional transcription factors. This mechanism also provides a basal level of control for genes acquired by horizontal DNA transfer, assisting microbial evolution, including the evolution of pathogenic bacteria.

DNA supercoiling is a fundamental regulatory principle in the control of bacterial gene expression

Although it has become routine to consider DNA in terms of its role as a carrier of genetic information, it is also an important contributor to the control of gene expression. This regulatory principle arises from its structural properties. DNA is maintained in an underwound state in most bacterial cells and this has important implications both for DNA storage in the nucleoid and for the expression of genetic information. Underwinding of the DNA through reduction in its linking number potentially imparts energy to the duplex that is available to drive DNA transactions, such as transcription, replication and recombination. The topological state of DNA also influences its affinity for some DNA binding proteins, especially in DNA sequences that have a high A + T base content. The underwinding of DNA by the ATP-dependent topoisomerase DNA gyrase creates a continuum between metabolic flux, DNA topology and gene expression that underpins the global response of the genome to changes in the intracellular and external environments. These connections describe a fundamental and generalised mechanism affecting global gene expression that underlies the specific control of transcription operating through conventional transcription factors. This mechanism also provides a basal level of control for genes acquired by horizontal DNA transfer, assisting microbial evolution, including the evolution of pathogenic bacteria.

Biosynthesis and Regulation of the Branched-Chain Amino Acids†

This review focuses on more recent studies concerning the systems biology of branched-chain amino acid biosynthesis, that is, the pathway-specific and global metabolic and genetic regulatory networks that enable the cell to adjust branched-chain amino acid synthesis rates to changing nutritional and environmental conditions. It begins with an overview of the enzymatic steps and metabolic regulatory mechanisms of the pathways and descriptions of the genetic regulatory mechanisms of the individual operons of the isoleucine-leucine-valine (ilv) regulon. This is followed by more-detailed discussions of recent evidence that global control mechanisms that coordinate the expression of the operons of this regulon with one another and the growth conditions of the cell are mediated by changes in DNA supercoiling that occur in response to changes in cellular energy charge levels that, in turn, are modulated by nutrient and environmental signals. Since the parallel pathways for isoleucine and valine biosynthesis are catalyzed by a single set of enzymes, and because the AHAS-catalyzed reaction is the first step specific for valine biosynthesis but the second step of isoleucine biosynthesis, valine inhibition of a single enzyme for this enzymatic step might compromise the cell for isoleucine or result in the accumulation of toxic intermediates. The operon-specific regulatory mechanisms of the operons of the ilv regulon are discussed in the review followed by a consideration and brief review of global regulatory proteins such as integration host factor (IHF), Lrp, and CAP (CRP) that affect the expression of these operons.

The Subtleties and Contrasts of the LeuO Regulator in Salmonella Typhi: Implications in the Immune Response

Salmonella are facultative intracellular pathogens. Salmonella infection occurs mainly by expression of two Salmonella pathogenicity Islands (SPI-1 and SPI-2). SPI-1 encodes transcriptional factors that participate in the expression of virulence factors encoded in the island. However, there are transcriptional factors encoded outside the island that also participate in the expression of SPI-1-encoded genes. Upon infection, bacteria are capable of avoiding the host immune response with several strategies that involve several virulence factors under the control of transcriptional regulators. Interestingly, LeuO a transcriptional global regulator which is encoded outside of any SPI, is proposed to be part of a complex regulatory network that involves expression of several genes that help bacteria to survive stress conditions and, also, induces the expression of porins that have been shown to be immunogens and can thus be considered as antigenic candidates for acellular vaccines. Hence, the understanding of the LeuO regulon implies a role of bacterial genetic regulation in determining the host immune response.

The Salmonella enterica serovar Typhi LeuO global regulator forms tetramers: residues involved in oligomerization, DNA binding, and transcriptional regulation

LeuO is a LysR-type transcriptional regulator (LTTR) that has been described to be a global regulator in Escherichia coli and Salmonella enterica, since it positively and negatively regulates the expression of genes involved in multiple biological processes. LeuO is comprised of an N-terminal DNA-binding domain (DBD) with a winged helix-turn-helix (wHTH) motif and of a long linker helix (LH) involved in dimerization that connects the DBD with the C-terminal effector-binding domain (EBD) or regulatory domain (RD; which comprises subdomains RD-I and RD-II). Here we show that the oligomeric structure of LeuO is a tetramer that binds with high affinity to DNA. A collection of single amino acid substitutions in the LeuO DBD indicated that this region is involved in oligomerization, in positive and negative regulation, as well as in DNA binding. Mutants with point mutations in the central and C-terminal regions of RD-I were affected in transcriptional activation. Deletion of the RD-II and RD-I C-terminal subdomains affected not only oligomerization but also DNA interaction, showing that they are involved in positive and negative regulation. Together, these data demonstrate that not only the C terminus but also the DBD of LeuO is involved in oligomer formation; therefore, each LeuO domain appears to act synergistically to maintain its regulatory functions in Salmonella enterica serovar Typhi.

Transcription-coupled DNA supercoiling in defined protein systems and in E. coli topA mutant strains

Transcription by RNA polymerases can stimulate (-) DNA supercoiling both in vitro and in Escherichia coli topA strains. This phenomenon has been successfully explained by a "twin-supercoiled-domain" model of transcription in which (+) supercoils are produced in front of the transcribing RNA polymerase and (-) supercoils behind it. Previously, it has been shown that certain sequence-specific DNA-binding proteins potently stimulate transcription-coupled DNA supercoiling (TCDS) in an in vitro protein system. These results are consistent with a topological barrier model where certain nucleoprotein complexes can form topological barriers that impede the diffusion and merger of independent chromosomal supercoil domains. Indeed, recent biochemical and single-molecule results demonstrated the existence of nucleoprotein-based DNA topological barriers, which are capable of dividing a DNA molecule into different topological domains. Additionally, recent in vivo studies showed that a transcriptional ensemble (including the transcribing RNA polymerase and the RNA transcript) alone is sufficient to cause a change in local DNA superhelicity. This topological change in local chromosome structure should have a great impact on the conformation and function of critical DNA sequence elements, such as promoters and DNA replication origins. In this article, we will also review recent progress by which TCDS is a critical stimulating force to activate transcription initiation from weak promoters, such as the Salmonella typhimurium leu-500 promoter.

Regulation of the yjjQ-bglJ operon, encoding LuxR-type transcription factors, and the divergent yjjP gene by H-NS and LeuO

The yjjQ and bglJ genes encode LuxR-type transcription factors conserved in several enterobacterial species. YjjQ is a potential virulence factor in avian pathogenic Escherichia coli. BglJ counteracts the silencing of the bgl (beta-glucoside) operon by H-NS in E. coli K-12. Here we show that yjjQ and bglJ form an operon carried by E. coli K-12, whose expression is repressed by the histone-like nucleoid structuring (H-NS) protein. The LysR-type transcription factor LeuO counteracts this repression. Furthermore, the yjjP gene, encoding a membrane protein of unknown function and located upstream in divergent orientation to the yjjQ-bglJ operon, is likewise repressed by H-NS. Mapping of the promoters as well as the H-NS and LeuO binding sites within the 555-bp intergenic region revealed that H-NS binds to the center of the AT-rich regulatory region and distal to the divergent promoters. LeuO sites map to the center and to positions distal to the yjjQ promoters, while one LeuO binding site overlaps with the divergent yjjP promoter. This latter LeuO site is required for full derepression of the yjjQ promoters. The arrangement of regulatory sites suggests that LeuO restructures the nucleoprotein complex formed by H-NS. Furthermore, the data support the conclusion that LeuO, whose expression is likewise repressed by H-NS and which is a virulence factor in Salmonella enterica, is a master regulator that among other loci, also controls the yjjQ-bglJ operon and thus indirectly the presumptive targets of YjjQ and BglJ.

Analysis of pleiotropic transcriptional profiles: a case study of DNA gyrase inhibition

Genetic and environmental perturbations often result in complex transcriptional responses involving multiple genes and regulons. In order to understand the nature of a response, one has to account for the contribution of the downstream effects to the formation of a response. Such analysis can be carried out within a statistical framework in which the individual effects are independently collected and then combined within a linear model. Here, we modeled the contribution of DNA replication, supercoiling, and repair to the transcriptional response of inhibition of the Escherichia coli gyrase. By representing the gyrase inhibition as a true pleiotropic phenomenon, we were able to demonstrate that: (1) DNA replication is required for the formation of spatial transcriptional domains; (2) the transcriptional response to the gyrase inhibition is coordinated between at least two modules involved in DNA maintenance, relaxation and damage response; (3) the genes whose transcriptional response to the gyrase inhibition does not depend on the main relaxation activity of the cell can be classified on the basis of a GC excess in their upstream and coding sequences; and (4) relaxation by topoisomerase I dominates the transcriptional response, followed by the effects of replication and RecA. We functionally tested the effect of the interaction between relaxation and repair activities, and found support for the model derived from the microarray data. We conclude that modeling compound transcriptional profiles as a combination of downstream transcriptional effects allows for a more realistic, accurate, and meaningful representation of the transcriptional activity of a genome.

Pleiotropism—a movement, or reaction, in multiple directions: although it was initially used specifically to describe the effect of a single genetic mutation on multiple characters in the offspring, the transcriptional responses of cells are often best described in terms of pleiotropy, when a single input affects multiple components inside the cell. This, in turn, presents a dilemma with the analysis and interpretation of the observed effects: which effects are directly due to the input itself and which are not? How are the effects related to each other and which are more important? And finally, can the overall transcriptional response be summarized as a combination of the effects? There is, however, a problem with recording the effects when they occur almost simultaneously in the same organism. The authors approached this by recording the effects independently, using mutants that could generate all of the effects of interest but one, and then estimating the effects and their interactions from a multivariate linear model. The authors applied this method to explain the transcriptional response of Escherichia coli to a quinolone antibacterial, a relative of Cipro (ciprofloxacin hydrochloride), and discovered unexpected interactions between DNA maintenance modules in the cell.

DNA supercoiling and bacterial gene expression

DNA in bacterial cells is maintained in a negatively supercoiled state. This contributes to the organization of the bacterial nucleoid and also influences the global gene expression pattern in the cell through modulatory effects on transcription. Supercoiling arises as a result of changes to the linking number of the relaxed double-stranded DNA molecule and is set and reset by the action of DNA topoisomerases. This process is subject to a multitude of influences that are usually summarized as environmental stress. Responsiveness of linking number change to stress offers the promise of a mechanism for the wholesale adjustment of the transcription programme of the cell as the bacterium experiences different environments. Recent data from DNA microarray experiments support this proposition. The emerging picture is one of DNA supercoiling acting at or near the apex of a regulatory hierarchy where it collaborates with nucleoid-associated proteins and transcription factors to determine the gene expression profile of the cell.

LeuO protein delimits the transcriptionally active and repressive domains on the bacterial chromosome

LeuO protein relieves bacterial gene silencer AT8-mediated transcriptional repression as part of a promoter relay mechanism found in the ilvIH-leuO-leuABCD gene cluster. The gene silencing activity has recently been characterized as a nucleoprotein filament initiated at the gene silencer. In this gene locus, the nucleoprotein filament cis-spreads toward the target leuO promoter and results in the repression of the leuO gene. Although the cis-spreading nature of the transcriptionally repressive nucleoprotein filament has been revealed, the mechanism underlying LeuO-mediated gene silencing relief remains unknown. We have demonstrated here that LeuO functions analogously to the eukaryotic boundary element that delimits the transcriptionally active and repressive domains on the chromosome by blocking the cis-spreading pathway of the transcriptionally repressive heterochromatin. Given that one LeuO-binding site is positioned between the gene silencer and the target promoter, the simultaneous presence of a second LeuO-binding site synergistically enhances the blockade, resulting in a cooperative increase in LeuO-mediated gene silencing relief. A known DNA loop-forming protein, the lac repressor (LacI), was used to confirm that cooperative protein binding via DNA looping is responsible for the blocking synergy. Indeed, a distal LeuO site located downstream cooperates with the LeuO sites located upstream of the leuO gene, resulting in synergistic relief for the repressed leuO gene via looping out the intervening DNA between LeuO sites in the ilvIH-leuO-leuABCD gene cluster.

A cis-spreading nucleoprotein filament is responsible for the gene silencing activity found in the promoter relay mechanism

Transcription-generated DNA supercoiling plays a decisive role in a promoter relay mechanism for the coordinated expression of genes in the Salmonella typhimurium ilvIH-leuO-leuABCD gene cluster. A similar mechanism also operates to control expression of the genes in the Escherichia coli ilvIH-leuO-leuABCD gene cluster. However, the mechanism underlying the DNA supercoiling effect remained elusive. A bacterial gene silencer AT8 was found to be important for the repression state of the leuO gene as part of the promoter relay mechanism. In this communication, we demonstrated that the gene silencer AT8 is a nucleation site for recruiting histone-like nucleoid structuring protein to form a cis-spreading nucleoprotein filament that is responsible for silencing of the leuO gene. With a DNA geometric similarity rather than a DNA sequence specificity, the E. coli gene silencer EAT6 was capable of replacing the histone-like nucleoid structuring protein nucleation function of the S. typhimurium gene silencer AT8 for the leuO gene silencing. The interchangeability between DNA geometrical elements for supporting the silencing activity in the region is consistent with a previous finding that a neighboring transcription activity determines the outcome of the gene silencing activity. The geometric requirement, which was revealed for this silencing activity, explains the decisive role of transcription-generated DNA supercoiling found in the promoter relay mechanism.

DNA supercoiling and transcription control: a model from the study of suppression of the leu-500 mutation in Salmonella typhimurium topA- strains

DNA supercoiling is known to modulate gene expression. The functional relationship between DNA supercoiling and transcription initiation has been established genetically and biochemically. The molecular mechanism whereby DNA supercoiling regulates gene expression remains unclear however. Quite commonly, the same gene responds to the same DNA supercoiling change differently when the gene is positioned at different locations. Such strong positional effects on gene expression suggest that rather than the overall DNA supercoiling change, the variation of DNA supercoiling at a local site might be important for transcription control. We have started to understand the local DNA supercoiling dynamic on the chromosome. As a primary source of local DNA supercoiling fluctuation, transcription-driven DNA supercoiling is important in determining the chromosome supercoiling dynamic and theoretically, therefore, for transcription control as well. Indeed, by studying the coordinated expression of genes in the ilvIH-leuO-leuABCD gene cluster, we found that transcription-driven DNA supercoiling governs the expression of a group of functionally related genes in a sequential manner. Based on the findings in this model system, we put forward the possible mechanisms whereby DNA supercoiling plays its role in transcription control.

LeuO-mediated transcriptional derepression

To understand the coordination of gene expression in the Salmonella typhimurium ilvIH-leuO-leuABCD gene cluster, we had previously identified a 72-bp AT-rich (78% A+T) DNA sequence element, AT4, which was capable of silencing transcription in a promoter nonspecific manner. LeuO protein provided in trans relieved (derepressed) AT4-mediated gene silencing (transcriptional repression), but underlying mechanisms remained unclear. In the present communication, the 72-bp DNA sequence element is further dissected into two functional elements, AT7 and AT8. LeuO binds to the 25-bp AT7, which lies closest to the leuO promoter in the AT4 DNA. After deletion of the AT7 DNA sequence responsible for LeuO binding from AT4, the remaining 47-bp AT-rich (85% A+T) DNA sequence, termed AT8, retains the full bi-directional gene-silencing activity, which is no longer relieved by LeuO. LeuO-mediated transcriptional derepression is restored when the LeuO binding site, AT7, is placed within close proximity to the gene silencer AT8. As a pair of functionally coupled transcription elements, the presence of an equal copy number of AT7 and AT8 within proximity is important for the transcription control. The characterization provides clues for future elucidation of the molecular details whereby LeuO negates the gene-silencing activity.

Distant cis-active sequences and sialic acid control the expression of fimB in Escherichia coli K-12

The phase variation of type 1 fimbriation in Escherichia coli is controlled by the inversion of a 314 bp element of DNA, determined by FimB (switching in both directions) or FimE (switching from the ON-to-OFF orientation predominantly), and influenced by auxiliary factors IHF, Lrp and H-NS. The fimB gene is separated from the divergently transcribed yjhATS operon by a large (1.4 kbp) intergenic region of unknown function. Here, we show that fimB expression is regulated by multiple cis-active sequences that lie far upstream (>600 bp) of the transcription start sites for the recombinase gene. Two regions characterized further (regions 1 and 2) show sequence identity, and each coincides with a methylation-protected Dam (5'-GATC) site. Regions 1 and 2 apparently control fimB expression by an antirepression mechanism that involves additional sequences proximal to yjhA. Region 1 encompasses a 27 bp DNA sequence conserved upstream of genes known (nanAT ) or suspected (yjhBC) to be involved in sialic acid metabolism, and we show that FimB expression and recombination are suppressed by N-acetylneuraminic acid. We propose that E. coli recognizes the amino sugars as a harbinger of potential host defence activation, and suppresses the expression of type 1 fimbriae in response.

A 72-base pair AT-rich DNA sequence element functions as a bacterial gene silencer

We have previously demonstrated that sequential activation of the bacterial ilvIH-leuO-leuABCD gene cluster involves a promoter-relay mechanism. In the current study, we show that the final activation of the leuABCD operon is through a transcriptional derepression mechanism. The leuABCD operon is transcriptionally repressed by the presence of a 318-base pair AT-rich upstream element. LeuO is required for derepressing the repressed leuABCD operon. Deletion analysis of the repressive effect of the 318-bp element has led to the identification of a 72-bp AT-rich (78% A+T) DNA sequence element, AT4, which is capable of silencing a number of unrelated promoters in addition to the leuABCD promoter. AT4-mediated gene silencing is orientation-independent and occurs within a distance of 300 base pairs. Furthermore, an increased gene-silencing effect was observed with a tandemly repeated AT4 dimer. The possible mechanism of AT4-mediated gene silencing in bacteria is discussed.

LeuO expression in response to starvation for branched-chain amino acids

The recently identified role of LeuO in the regulation of transcription has prompted us to search for the specific function(s) of LeuO in bacterial physiology. The cryptic nature of expression of leuO has previously limited such analysis. A conditional leuO expression was found when bacteria enter stationary phase and was shown to be guanosine 3',5'-bispyrophosphate-dependent. Multiple physiological events, including the stringent response, are induced upon the increase of the bacterial stress signal, guanosine 3',5'-bispyrophosphate. In this study, we tested whether LeuO was directly involved in the bacterial stringent response. LeuO was shown to be indispensable for growth resumption following a 2-h growth arrest caused by starvation for branched-chain amino acids in an E. coli K-12 relA1 strain. This result supports a functional role for LeuO in the bacterial stringent response.

ppGpp-dependent leuO expression in bacteria under stress

Despite the known potential transcription regulatory role of leuO gene product, LeuO, the condition when leuO expresses during bacterial growth cycle remains unclear. Mechanistically, leuO expression was shown to be part of promoter relay mechanism, however, the factor(s) responsible for the regulation of leuO expression is not known. Combining Northern and Western results, we demonstrate in the present communication that leuO expression is normally low and enhanced when bacteria are in transition from exponential growth to stationary phase. The stationary phase-associated leuO expression is ppGpp dependent and rpoS (sigma(s) factor) independent.

Activation and silencing of leu-500 promoter by transcription-induced DNA supercoiling in the Salmonella chromosome

The notion that transcription can generate supercoils in the DNA template largely stems from work with small circular plasmids. In the present work, we tested this model in the bacterial chromosome using a supercoiling-sensitive promoter as a functional sensor of superhelicity changes. The leu-500 promoter of Salmonella typhimurium is a mutant and inactive variant of the leucine operon promoter that regains activity if negative DNA supercoiling rises above normal levels, typically as a result of mutations affecting DNA topoisomerase I (topA mutants). Activation of the leu-500 promoter was analysed in topA mutant cells harbouring transcriptionally inducible tet or cat gene cassettes inserted in the region upstream from the leu operon. Some insertions inhibited leu-500 promoter activation in the absence of inducer. This effect is dramatic in the interval between 1.7 kb and 0.6 kb from the leu operon, suggesting that the insertions physically interfere with the mechanism responsible for activation. Superimposed on these effects, transcription of the inserted gene stimulated or inhibited leu-500 promoter activity depending on whether this gene was oriented divergently from the leu operon or in the same direction respectively. Interestingly, transcription-mediated inhibition of leu-500 promoter was observed with inserts as far as 5 kb from the leu operon, and it could be relieved by the introduction of a strong gyrase site between the inserted element and the leu-500 promoter. These results are consistent with the idea that transcriptionally generated positive and negative supercoils can diffuse along chromosomal DNA and, depending on their topological sign, elicit opposite responses from the leu-500 promoter.

Effects of local transcription and H-NS on inversion of the fim switch of Escherichia coli

The fim switch of Escherichia coli is responsible for phase-variable expression of type 1 fimbriae. Switching in the ON-to-OFF and OFF-to-ON directions is promoted by the FimB recombinase, while the FimE recombinase directs switching predominantly in the ON-to-OFF direction. The effects of local promoter activity and the H-NS nucleoid-associated protein on inversion of the switch were assessed. In contrast to FimB-mediated inversion, inversion of the switch by the FimE recombinase was unaffected by the H-NS status of the cell. Transcription towards the switch from within a translationally inactivated fimE gene was found to bias the switch strongly in the OFF direction, creating a FimE+-like phenotype in the absence of the FimE protein. This biasing was H-NS dependent and was also contingent on transcription from within the switch. These data show that local transcription and a nucleoid-associated protein both contribute to the modulation of a site-specific recombination event on the bacterial chromosome.

Large-scale effects of transcriptional DNA supercoiling in vivo

The scale of negative DNA supercoiling generated by transcription in Top(+) Escherichia coli cells was assessed from the efficiency of cruciform formation upstream of a regulated promoter. An increase in negative supercoiling upon promoter induction led to cruciform formation, which was quantitatively measured by chemical probing of intracellular DNA. By placing a cruciform-forming sequence at varying distances from the promoter, we found that the half-dissociation length of transcription supercoiling wave is approximately 800 bp. This is the first proof that transcription can affect DNA structure on such a remarkably large scale in vivo. Moreover, cooperative binding of the cI repressor to the upstream promoter DNA did not preclude efficient diffusion of transcriptional supercoiling. Finally, our plasmids appeared to contain discrete domains of DNA supercoiling, defined by the features and relative orientation of different promoters.

Characterization of mdcR, a regulatory gene of the malonate catabolic system in Klebsiella pneumoniae

The Klebsiella pneumoniae mdcR gene, which encodes a LysR-type regulator, was overexpressed in Escherichia coli. Purified MdcR was found to bind specifically to the control region of either the malonate decarboxylase (mdc) genes or mdcR. We have also demonstrated that MdcR is an activator of the expression of the mdc genes, whereas it represses the transcription of the putative control region of mdcR, PmdcR, indicating a negative autoregulatory control.

Suppression of leu-500 mutation in topA+ Salmonella typhimurium strains. The promoter relay at work

Suppression of leu-500 mutation in Salmonella typhimurium topA- strains has been one of the most fascinating examples for the DNA supercoiling effect on transcription initiation control. Previous studies have indicated possible involvement of transcription-driven DNA supercoiling in the activation of the leu-500 promoter in topA- strains. Our recent studies have shown that ilvIH transcription activity located 1.9 kilobase pairs upstream is the initial supercoiling signal for leu-500 activation via a promoter relay mechanism. In the present communication, we show that the ilvIH transcription activity-initiated promoter relay can result in leu-500 activation in topA+ strains. In addition, suppression of the chromosomal leu-500 mutation correlates with the transcription activities of ilvIH and leuO rather than the TopA level in the topA+ strain. It appears that the leu-500 suppression in a topA- strain is due to the constant ilvIH transcription activity.

Gyrase and Topo IV modulate chromosome domain size in vivo

In bacteria, DNA supercoil movement is restricted to subchromosomal regions or 'domains.' To elucidate the nature of domain boundaries, we analysed reaction kinetics for gammadelta site-specific resolution in six chromosomal intervals ranging in size from 14 to 90 kb. In stationary cultures of Salmonella typhimurium, resolution kinetics were rapid for both short and long intervals, suggesting that random stationary barriers occur with a 30% probability at approximately 80 kb intervals along DNA. To test the biochemical nature of domain barriers, a genetic screen was used to look for mutants with small domains. Rare temperature-sensitive alleles of DNA gyrase and Topo IV (the two essential type II topoisomerases) had more supercoil barriers than wild-type strains in all growth states. The most severe gyrase mutants were found to have twice as many barriers in growing cells as wild type throughout a 90 kb interval of the chromosome. We propose that knots and tangles in duplex DNA restrain supercoil diffusion in living bacteria.

Topoisomerase I of Helicobacter pylori: juxtaposition with a flagellin gene (flaB) and functional requirement of a fourth zinc finger motif

Cloning and nucleotide sequence analysis showed that in Helicobacter pylori the gene encoding topoisomerase I (topA) lies about 170 nucleotides upstream from flaB, a gene encoding one of the two flagellin proteins that is required for virulence. The topA and flaB genes are divergently transcribed. The orientation and spatial relationship between flaB and topA are remarkably conserved among strains of a bacterium in which genomic rearrangements are common. The deduced amino acid sequence of topoisomerase I revealed four zinc finger motifs, one more than has been reported previously for the Escherichia coli homologue. The additional motif, which is near the C-terminus of the protein, appears to be essential for function since mutations in that region are lethal. These data show that TopA proteins can be divided into several classes on the basis of zinc finger motifs and raise the interesting possibility that the H. pylori enzyme has local topological effects focussed on a flagellin gene.

A promoter relay mechanism for sequential gene activation

The effect of DNA supercoiling on gene expression is dependent not only on specific genes but also on the sequence context of the genes. This position-dependent supercoiling effect on gene activation is best illustrated in the study of the suppression of the leu-500 mutation of the leuABCD operon in a Salmonella typhimurium topA mutant. In this communication, we report a novel promoter relay mechanism whereby several genes are sequentially expressed in a position-dependent manner: the ilvIH promoter (pilvIH) activates a cryptic leuO promoter (pleuO) located between the two divergently arrayed ilvIH and leu-500 promoters. Both the cis-acting pleuO activity and the trans-acting LeuO protein are necessary for subsequent activation of the leu-500 promoter (pleu-500). Furthermore, pleuO can be functionally replaced with the inducible tac promoter (ptac) for leu-500 activation, suggesting that transcription-driven DNA supercoiling underlies the relay mechanism. This is the first example of several related genes communicating via a promoter relay mechanism for their coordinated expression.

Long-range effects in a supercoiled DNA domain generated by transcription in vitro

The translocation of a transcription complex can transiently introduce positive and negative superhelical windings into the template DNA. To gain further insight into this dynamic DNA supercoiling mechanism and its possible involvement in biological processes, we employed an in vitro system in which site-specific recombination by gammadelta resolvase is topologically coupled to transcription-induced negative supercoiling. Our kinetic experiments suggest that recombination is closely linked to the process of supercoiling by transcription. We utilized the known high speed at which two resolvase-bound recombination sites can pair to form a synaptic complex in kinetic experiments with DNA substrates containing three recombination sites. Our data provide evidence for the existence of a transient gradient of negative supercoiling. Such a gradient seems to be predominantly a consequence of DNA double helix rotation behind a translocating RNA polymerase and originates within a broad region up to two kilobase-pairs upstream of the transcriptional start site. We further demonstrate that the topological coupling between transcription and recombination is not affected when the DNA-bending protein integration host factor from E. coli is bound to multiple sites within the phage lambda attachment region. We discuss implications of our in vitro findings with respect to possible in vivo functions of the dynamic nature of transcription-induced supercoiling.

Distal enhancer regulation by promoter derepression in topologically constrained DNA in vitro

Long-range promoter-enhancer interactions are a crucial regulatory feature of many eukaryotic genes yet little is known about the mechanisms involved. Using cloned chicken betaA-globin genes, either individually or within the natural chromosomal locus, enhancer-dependent transcription is achieved in vitro at a distance of 2 kb with developmentally staged erythroid extracts. This occurs by promoter derepression and is critically dependent upon DNA topology. In the presence of the enhancer, genes must exist in a supercoiled conformation to be actively transcribed, whereas relaxed or linear templates are inactive. Distal protein-protein interactions in vitro may be favored on supercoiled DNA because of topological constraints. In this system, enhancers act primarily to increase the probability of rapid and efficient transcription complex formation and initiation. Repressor and activator proteins binding within the promoter, including erythroid-specific GATA-1, mediate this process.

An HMG I/Y-containing repressor complex and supercoiled DNA topology are critical for long-range enhancer-dependent transcription in vitro

The 3' enhancer of the T cell receptor alpha-chain (TCR alpha) gene directs the tissue- and stage-specific expression and V(D)J recombination of this gene locus. Using an in vitro system that reproduces TCR alpha enhancer activity efficiently, we show that long-range promoter-enhancer regulation requires a T cell-specific repressor complex and is sensitive to DNA topology. In this system, the enhancer functions to derepress the promoter on supercoiled, but not relaxed, templates. We find that the TCR alpha promoter is inactivated by a repressor complex that contains the architectural protein HMG I/Y. In the absence of this repressor complex, expression of the TCR alpha gene is completely independent of the 3' enhancer and DNA topology. The interaction of the T cell-restricted protein LEF-1 with the TCR alpha enhancer is required for promoter derepression. In this system, the TCR alpha enhancer increases the number of active promoters rather than the rate of transcription. Thus, long-range enhancers function in a distinct manner from promoters and provide the regulatory link between repressors, DNA topology, and gene activity.

Discoordinate gene expression of gyrA and gyrB in response to DNA gyrase inhibition in Escherichia coli

The intracellular level of DNA supercoiling is regulated in Escherichia coli by a homeostatic control mechanism that includes DNA gyrase and topoisomerase I gene expression. Despite several biochemical and genetical evidence that supports the existence of a homeostatic regulation mechanism, there are only few studies focusing gyrA and gyrB gene expression in connection to the mechanism involved in the regulation of DNA supercoiling in vivo. To study DNA gyrase gene expression and to be able to isolate mutants with altered expression of DNA gyrase, we constructed a new chromosomal reporter system based on two translational fusions of gyrA and gyrB to lacZ Using this stable monitor system in a robust wild type, we simultaneously studied the influence of several inhibitors of DNA gyrase (quinolones and coumarins) on gyrA and gyrB gene expression as well as on the intracellular level of DNA supercoiling. Surprisingly, we found a delayed and differential response of gyrA and gyrB gene expression following inhibition of DNA gyrase by quinolones or coumarins. Whereas both groups of drugs were able to increase the expression of gyrA, the gyrB gene expression was only induced by the coumarins. Although the action of the quinolones was able to alter DNA supercoiling, we never observed any induction of gyrB from the chromosome. These results revealed that the gene expressio of gyrA appears to be more sensitive to alterations in DNA supercoiling than the gyrB gene expression and suggest that probably additional regulatory mechanisms on the post-translational level might be involved in the regulation of DNA supercoiling and DNA gyrase gene expression.

Long-distance effect of downstream transcription on activity of the supercoiling-sensitive leu-500 promoter in a topA mutant of Salmonella typhimurium

Expression of the lacZ gene from the supercoiling-sensitive leu-500 promoter on a plasmid in topA mutant cells was stimulated by activating a divergently oriented Tac promoter, 400 bp upstream from leu-500. The stimulation was approximately threefold regardless of whether the Tac promoter drove the expression of the tet gene, whose product is membrane bound, or of the cat gene, whose product is cytosolic. Putting a second copy of the Tac promoter downstream from lacZ, approximately 3,000 bp from leu-500 in the same orientation as the latter, resulted in 30-fold increase in lacZ expression upon isopropyl-beta-D-thiogalactopyranoside induction. Again, these effects were independent of the nature of the gene upstream from leu-500 (tet or cat). With both tet- and cat-harboring constructs, activation of the two Tac promoter copies caused plasmid DNA to become hypernegatively supercoiled in topA mutant cells. Thus, neither leu-500 activation nor hypernegative plasmid DNA supercoiling appears to require membrane anchoring of DNA in this system. Replacing the downstream copy of Tac with a constitutive promoter resulted in high-level lacZ expression even when the upstream copy was repressed. Under these conditions, no hypernegative DNA supercoiling was observed, indicating that the activity of plasmid-borne leu-500 in topA mutant cells does not necessarily correlate with the linking deficit of plasmid DNA. The response of the leu-500-lacZ fusion to downstream transcription provides a sensitive assay for transcriptional supercoiling in bacteria.