High A + T content conserved in DNA sequences upstream of leuABCD in Escherichia coli and Salmonella typhimurium

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.

Reconstructed Ancestral Enzymes Impose a Fitness Cost upon Modern Bacteria Despite Exhibiting Favourable Biochemical Properties

Ancestral sequence reconstruction has been widely used to study historical enzyme evolution, both from biochemical and cellular perspectives. Two properties of reconstructed ancestral proteins/enzymes are commonly reported--high thermostability and high catalytic activity--compared with their contemporaries. Increased protein stability is associated with lower aggregation rates, higher soluble protein abundance and a greater capacity to evolve, and therefore, these proteins could be considered "superior" to their contemporary counterparts. In this study, we investigate the relationship between the favourable in vitro biochemical properties of reconstructed ancestral enzymes and the organismal fitness they confer in vivo. We have previously reconstructed several ancestors of the enzyme LeuB, which is essential for leucine biosynthesis. Our initial fitness experiments revealed that overexpression of ANC4, a reconstructed LeuB that exhibits high stability and activity, was only able to partially rescue the growth of a ΔleuB strain, and that a strain complemented with this enzyme was outcompeted by strains carrying one of its descendants. When we expanded our study to include five reconstructed LeuBs and one contemporary, we found that neither in vitro protein stability nor the catalytic rate was correlated with fitness. Instead, fitness showed a strong, negative correlation with estimated evolutionary age (based on phylogenetic relationships). Our findings suggest that, for reconstructed ancestral enzymes, superior in vitro properties do not translate into organismal fitness in vivo. The molecular basis of the relationship between fitness and the inferred age of ancestral LeuB enzymes is unknown, but may be related to the reconstruction process. We also hypothesise that the ancestral enzymes may be incompatible with the other, contemporary enzymes of the metabolic network.

Regulation of Salmonella enterica pathogenicity island 1 (SPI-1) by the LysR-type regulator LeuO

LeuO is a quiescent LysR-type regulator belonging to the H-NS regulon. Activation of leuO transcription represses expression of pathogenicity island 1 (SPI-1) in Salmonella enterica serovar Typhimurium and inhibits invasion of epithelial cells. Loss of HilE suppresses LeuO-mediated downregulation of SPI-1. Activation of leuO transcription reduces the level of HilD protein, and loss of HilE restores the wild type HilD level. Hence, LeuO-mediated downregulation of SPI-1 may involve inhibition of HilD activity by HilE, a view consistent with the fact that HilE is a HilD inhibitor. In vivo analyses using β-galactosidase fusions indicate that LeuO activates hilE transcription. In vitro analyses by slot blotting, electrophoretic mobility shift analysis and DNase I footprinting show that LeuO binds the hilE promoter region. Although residual SPI-1 repression by LeuO is observed in the absence of HilE, the LeuO-HilE-HilD 'pathway' appears to be the major mechanism. Because both leuO and SPI-1 are repressed by H-NS, activation of leuO transcription may provide a backup mechanism for SPI-1 repression under conditions that impair H-NS-mediated silencing.

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.

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.

Characterization of the gltF gene product of Escherichia coli

The glt operon of Escherichia coli comprises the structural genes for the glutamate synthase subunits (gltB and gltD) and gltF, whose product was previously suggested to have regulatory functions. The A/T-rich region between gltD and gltF contains a weak promoter and a translation initiation site for gltF. The GltF protein is preceded by a signal peptide, which is cleaved off during export into the periplasmic space. A gltF::Km(R) insertion mutant was constructed and shown here to have no detectable phenotype with respect to amino acid utilization or ammonium transport. Thus, GltF is apparently not involved in regulation of nitrogen catabolism.

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.

Activation of gene expression by a novel DNA structural transmission mechanism that requires supercoiling-induced DNA duplex destabilization in an upstream activating sequence

We have previously demonstrated that integration host factor (IHF)-mediated activation of transcription from the ilvPG promoter of Escherichia coli requires a supercoiled DNA template and occurs in the absence of specific interactions between IHF and RNA polymerase. In this report, we describe a novel, supercoiling-dependent, DNA structural transmission mechanism for this activation. We provide theoretical evidence for a supercoiling-induced DNA duplex destabilized (SIDD) structure in the A + T-rich, ilvPG regulatory region between base pair positions +1 and -160. We show that the region of this SIDD sequence immediately upstream of an IHF binding site centered at base pair position -92 is, in fact, destabilized by superhelical stress and that this duplex destabilization is inhibited by IHF binding. Thus, in the presence of IHF, the negative superhelical twist normally absorbed by this DNA structure in the promoter distal half of the SIDD sequence is transferred to the downstream portion of the SIDD sequence containing the ilvPG promoter site. This IHF-mediated translocation of superhelical energy facilitates duplex destabilization in the -10 region of the downstream ilvPG promoter and activates transcription by increasing the rate of open complex formation.

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.

Flagellar flhA, flhB and flhE genes, organized in an operon, cluster upstream from the inv locus in Yersinia enterocolitica

The inv gene of Yersinia enterocolitica codes for invasin, a member of the invasin/intimin-like protein family, which mediates the internalization of the bacterium into cultured epithelial cells. The putative inclusion of inv into a pathogenicity island was tested by investigating its flanking sequences. Indeed, the enteropathogenic Escherichia coli (EPEC) intimin, a member of the same family of proteins, is encoded by eaeA, a gene which belongs to a pathogenicity island. An ORF located upstream from inv was of particular interest since it appeared homologous both to the flagellar flhA gene and to sepA, an EPEC gene lying inside the same pathogenicity island as eaeA. A mutant in this ORF was non-motile and non-flagellated while its invasion phenotype remained unaffected. These data indicated that the ORF corresponded to the flhA gene of Y. enterocolitica. Subsequently, the flhB and flhE genes, located respectively upstream and downstream from flhA, were identified. The three flh genes appear to be transcribed from a single operon called flhB, according to the nomenclature used for Salmonella typhimurium. Intergenic sequence between flhE and inv includes a grey hole, with no recognizable function. Downstream from inv, we have detected the flagellar flgM operon as already reported. Finally, the incongruous localization of inv amidst the flagellar cluster is discussed; while transposition could explain this phenomenon, no trace of such an event was detected.

DNA supercoiling and transcription: topological coupling of promoters

DNA supercoiling is a consequence of the double-stranded nature of DNA. When a linear DNA molecule is ligated into a covalently closed circle, the two strands become intertwined like the links of a chain, and will remain so unless one of the strands is broken. The number of times one strand is linked with the other is described by a fundamental property of DNA supercoiling, the linking number (Lk).

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

The leu-500 mutation can be suppressed in S. typhimurium topA. Previous studies have demonstrated that the plasmid-borne leu-500 minimal promoter cannot be activated in topA mutants unless adjacent (< 250 bp) transcription occurs away from the leu-500 promoter (short-range promoter interaction). To search for a potential upstream promoter responsible for activation of leu-500 in the chromosomal context, we have identified the ilvlH promoter, located 1.9 kb upstream of leu-500 (long-range promoter interaction). Different from short-range promoter interaction, which is abolished by DNA sequence insertions, the long-range promoter interaction is mediated by the intervening DNA sequence. These studies suggest that the long-range interaction between a pair of divergently arrayed promoters is probably mediated by a complex process involving relay of DNA supercoiling by the DNA sequence located between the two promoters.

Activity of a plasmid-borne leu-500 promoter depends on the transcription and translation of an adjacent gene

leu-500 is a chromosomal promoter mutation in Salmonella typhimurium that normally causes the promoter to be inactive in the initiation of RNA synthesis. But in a strain that has mutations in topA, the gene encoding DNA topoisomerase I, the mutant promoter becomes active. We show that the leu-500 promoter can function on a plasmid when it is adjacent to the tetracycline-resistance gene tetA. Activation of the leu-500 promoter requires that the tetA gene is transcribed and translated and that the host cell is topA. We propose that the A----G mutation in the -10 region of the leu-500 promoter is compensated by local negative supercoiling arising from transcription of the tetA gene, which may reach elevated levels in a topA background, provided that diffusional dissipation is reduced due to anchoring of the TetA peptide in the membrane. This is a clear example of the modulation of the activity of a promoter by the activity of another promoter in cis, when they can be coupled through the topology of the template.

A functional leuABCD operon is required for leucine synthesis by the tyrosine-repressible transaminase in Escherichia coli K-12

In Escherichia coli K-12, two enzymes, encoded by ilvE and tyrB, catalyze the amination of 2-ketoisocaproate (2-KIC) to form leucine. Although leucine-requiring derivatives of an ilvE strain that are unable to grow on 2-KIC were expected to have mutations only in tyrB, mapping studies showed that one such mutation was tightly linked to the leu operon (at 1.5 min), not to tyrB (at 92 min). Chromosomal fragments cloned because they complemented this mutation were found to complement leu mutations, and vice versa, but none of these fragments complemented a tyrB mutation. The Tn5 insertion and flanking host DNA from this anomalous mutant was cloned in vivo, using Mu dII4042, and an in vivo procedure was developed to isolate deletion derivatives of Tn5-containing plasmids. These deletion plasmids were used to determine the DNA sequences flanking the transposon. The data showed that Tn5 was inserted between bp 122 and 132 in the leu leader. In addition, other ilvE leu double mutants were found to be unable to grow on 2-KIC in place of leucine. The accumulation of 2-ketoisovalerate in ilvE leu double mutants was shown to interfere with 2-KIC amination by the tyrB-encoded transaminase and also by the aspC- and avtA-encoded transaminases (which are able to catalyze this reaction in vivo when the corresponding genes are present on multicopy plasmids).

Local DNA topology and gene expression: the case of the leu-500 promoter

Many promoters are sensitive to DNA supercoiling, and it is becoming apparent that this may play an important role in gene regulation. The twin supercoiled-domain hypothesis (Liu and Wang, 1987) proposes that transcription can lead to local variation in supercoiling. The mutant leu-500 promoter has presented a long-standing problem to the understanding of the control of promoter function by DNA supercoiling. This promoter is activated by mutations in the gene encoding topoisomerase I, but is apparently unaffected by mutations in the genes encoding DNA gyrase. We propose a model to explain the anomalous regulation of this promoter, based on the twin supercoiled-domain model. This allows us to account for the unusual properties of the leu-500 promoter, and confirms the biological importance of the twin supercoiled-domain model. We suggest that such topological coupling between promoters may be general, leading to co-operativity and anti-co-operativity between divergent promoter pairs.

DNA sequence and translational product of a new nodulation-regulatory locus: syrM has sequence similarity to NodD proteins

Rhizobium meliloti nodulation (nod) genes are expressed when activated by trans-acting proteins in the NodD family. The nodD1 and nodD2 gene products activate nod promoters when cells are exposed to plant-synthesized signal molecules. Alternatively, the same nod promoters are activated by the nodD3 gene when nodD3 is carried in trans along with a closely linked global regulatory locus, syrM (symbiotic regulator) (J. T. Mulligan and S. R. Long, Genetics 122:7-18, 1989). In this article we report the nucleotide sequence of a 2.6-kilobase SphI fragment from R. meliloti SU47 containing syrM. Expression from this locus was confirmed by using in vitro transcription-translation assays. The open reading frame encoded a protein of either 33 or 36 kilodaltons whose sequence shows similarity to NodD regulatory proteins.

pBR322-derived multicopy plasmids harboring large inserts are often dimers in Escherichia coli K-12

pBR322-related plasmids that are 2.3 to 5.1 kb were found predominantly as monomers, while plasmids that are 7.7 to 15.2 kb were found predominantly as dimers in rec+ cells of Escherichia coli K-12.

A large family of bacterial activator proteins

At least nine different bacterial proteins belong to the LysR family. The gene sequence for one of these proteins is presented here. Six others (Escherichia coli LysR, IlvY, CysB; Salmonella typhimurium MetR; Rhizobium NodD; and Enterobacter cloacae AmpR) are known to activate other genes. Based on sequence alignments, each member of this family is predicted to have a helix-turn-helix DNA binding motif near its amino terminus. The combined evidence indicates that all nine proteins are related by common ancestry, are similarly folded, and are not detectably related to other known bacterial regulatory proteins. The DNA database searching procedure and other methods used in this study should be useful in detecting other groups of related proteins.

Pseudomonas aeruginosa infection in cystic fibrosis: nucleotide sequence and transcriptional regulation of the algD gene

Pulmonary infection by mucoid, alginate producing, Pseudomonas aeruginosa is a major complication in patients suffering from cystic fibrosis (CF). To analyze the mechanisms leading to the emergence of mucoid P. aeruginosa in CF lungs, control of the algD gene coding for GDPmannose dehydrogenase was studied. Transcriptional activation of algD was shown to be necessary for alginate production. Sequencing of algD and its promoter revealed multiple direct repeats upstream of the transcription start and throughout the promoter region. Using the algD-xy1E transcriptional fusion the algD promoter was demonstrated to be under positive control by the algR gene. This gene has previously been shown to undergo antibiotic promoted chromosomal amplification resulting in the emergence of the mucoid phenotype. These findings provide a basis for better understanding the control of mucoidy in P. aeruginosa.

Effect of the deletion of upstream DNA sequences on expression from the ilvGp2 promoter of the ilvGMEDA operon of Escherichia coli K-12

Transcription in vitro of the regulatory region of the ilvGMEDA operon yields two attenuated RNAs initiated from the tandem promoters ilvGp1 and ilvGp2. Both S1 nuclease analysis and the fusion of ilvGp1 to galK indicate that transcription is not initiated in vivo from ilvGp1. However deletion of DNA sequences 150 to 100 bp upstream of ilvGp2 drastically reduces expression in vivo from ilvGp2. Both the distance separating ilvGp2 from the upstream DNA sequences and their relative orientation to each other on the DNA helix affect expression from ilvGp2. Deletion of DNA sequences approximately 400 bp upstream of ilvGp2 increases expression in vivo from this promoter. Analysis of products of transcription in vitro indicates that the effects observed in vivo are probably not due to DNA conformation or interactions of RNA polymerase.