Primary structure of the hip gene of Escherichia coli and of its product, the beta subunit of integration host factor

A novel stress response mechanism, triggered by indole, involved in quorum quenching enzyme MomL and iron-sulfur cluster in Muricauda olearia Th120

Indole, as a signal molecule, is involved in multiple physiological behavior including biofilm formation, antibiotic resistance and virulence. In this study, we demonstrated that indole was involved in iron deficient and H₂O₂ stress response in Muricauda olearia Th120. Transcriptome analysis showed that totally 206 genes were regulated by exogenous indole. Besides, momL-suf gene cluster, consisting of quorum quenching enzyme coding gene momL and iron-sulfur biosynthetic genes suf, were involved in indole-induced stress response pathway. The result indicated that indole not only up-regulated momL-suf gene cluster, but also enhanced the MomL secretion and the growth rates of MomL-bearing strains in H₂O₂ stress and iron deficient culture conditions. Co-incubation of M. olearia Th120 and Pectobacterium carotovorum subsp. carotovorum under H₂O₂ condition revealed that M. olearia Th120 bearing MomL possessed an increased competitive advantage, whereas its competitor had a reduced survival. The phenomenon that quorum quenching enzyme is triggered by stress factor has been rarely reported. The study also opens a new clue to explore the indole function towards quorum quenching factor in bacteria.

Replication Initiation in Bacteria

The initiation of chromosomal DNA replication starts at a replication origin, which in bacteria is a discrete locus that contains DNA sequence motifs recognized by an initiator protein whose role is to assemble the replication fork machinery at this site. In bacteria with a single chromosome, DnaA is the initiator and is highly conserved in all bacteria. As an adenine nucleotide binding protein, DnaA bound to ATP is active in the assembly of a DnaA oligomer onto these sites. Other proteins modulate DnaA oligomerization via their interaction with the N-terminal region of DnaA. Following the DnaA-dependent unwinding of an AT-rich region within the replication origin, DnaA then mediates the binding of DnaB, the replicative DNA helicase, in a complex with DnaC to form an intermediate named the prepriming complex. In the formation of this intermediate, the helicase is loaded onto the unwound region within the replication origin. As DnaC bound to DnaB inhibits its activity as a DNA helicase, DnaC must dissociate to activate DnaB. Apparently, the interaction of DnaB with primase (DnaG) and primer formation leads to the release of DnaC from DnaB, which is coordinated with or followed by translocation of DnaB to the junction of the replication fork. There, DnaB is able to coordinate its activity as a DNA helicase with the cellular replicase, DNA polymerase III holoenzyme, which uses the primers made by primase for leading strand DNA synthesis.

Aberrant community architecture and attenuated persistence of uropathogenic Escherichia coli in the absence of individual IHF subunits

Uropathogenic Escherichia coli (UPEC) utilizes a complex community-based developmental pathway for growth within superficial epithelial cells of the bladder during cystitis. Extracellular DNA (eDNA) is a common matrix component of organized bacterial communities. Integration host factor (IHF) is a heterodimeric protein that binds to double-stranded DNA and produces a hairpin bend. IHF-dependent DNA architectural changes act both intrabacterially and extrabacterially to regulate gene expression and community stability, respectively. We demonstrate that both IHF subunits are required for efficient colonization of the bladder, but are dispensable for early colonization of the kidney. The community architecture of the intracellular bacterial communities (IBCs) is quantitatively different in the absence of either IhfA or IhfB in the murine model for human urinary tract infection (UTI). Restoration of Type 1 pili by ectopic production does not restore colonization in the absence of IhfA, but partially compensates in the absence of IhfB. Furthermore, we describe a binding site for IHF that is upstream of the operon that encodes for the P-pilus. Taken together, these data suggest that both IHF and its constituent subunits (independent of the heterodimer), are able to participate in multiple aspects of the UPEC pathogenic lifestyle, and may have utility as a target for treatment of bacterial cystitis.

Regulation of fim genes in uropathogenic Escherichia coli

Uropathogenic Escherichia coli (UPEC) is the leading cause of urinary tract infections in women, causing significant morbidity and mortality in this population. Adherence to host epithelial cells is a pivotal step in the pathogenesis of UPEC. One of the most important virulence factors involved in mediating this attachment is the type 1 pilus (type 1 fimbria) encoded by a set of fim genes arranged in an operon. The expression of type 1 pili is controlled by a phenomenon known as phase variation, which reversibly switches between the expression of type 1 pili (Phase-ON) and loss of expression (Phase-OFF). Phase-ON cells have the promoter for the fimA structural gene on an invertible DNA element called fimS, which lines up to allow transcription, whereas transcription of the structural gene is silenced in Phase-OFF cells. The orientation of the fimS invertible element is controlled by two site-specific recombinases, FimB and FimE. Environmental conditions cause transcriptional and post-transcriptional changes in UPEC cells that affect the level of regulatory proteins, which in turn play vital roles in modulating this phase switching ability. The role of fim gene regulation in UPEC pathogenesis will be discussed.

Biofilms can be dispersed by focusing the immune system on a common family of bacterial nucleoid-associated proteins

Bacteria that cause chronic and/or recurrent diseases often rely on a biofilm lifestyle. The foundation of the biofilm structure is the extracellular polymeric substance (EPS) that acts as a barrier to both effectors of the immune system and antimicrobial agents. Recent work has highlighted extracellular DNA (eDNA) as a key component common to many pathogenic biofilms. Here, we show that the DNABII family of proteins, well known for their strong structural influences on intracellular DNA, was also critical for the integrity of the EPS matrix of biofilms that contain eDNA. In fact, antisera derived against a purified Escherichia coli DNABII family member rapidly disrupts the biofilm EPS formed by multiple human pathogens in vitro. In addition, when a member of this family of proteins was used as an immunogen in an animal model in which the bacteria had already formed a robust biofilm at the site of infection, the resultant targeted immune response strongly ameliorated this biofilm disease in vivo. Finally, this methodology to debulk the biofilm of EPS was shown to work synergistically with otherwise ineffective traditional anti-microbial approaches in vitro. We discuss the prospects for targeting DNABII family members as a potential universal strategy for treating biofilm diseases.

TrwC-mediated site-specific recombination is controlled by host factors altering local DNA topology

R388 conjugative relaxase TrwC acts as a site-specific recombinase, promoting recombination between two cognate oriTs on double-stranded DNA substrates. The relaxosome component TrwA is also required for efficient recombination. In this work we present data on the in vivo control of this reaction by host proteins that affect local DNA topology. In the absence of TrwA, binding of integration host factor (IHF) to the oriT keeps the recombination levels low, probably by keeping the relaxosome complex, formed at recombination locus 1, in a "closed" conformation. In an IHF-deficient (IHF-) background, the formation of a transcript elongation complex at this locus still hampers recombination. A mutation abating the promoter sequence at locus 1, or repression of transcription by exposure to rifampin, lifts the inhibition imposed on recombination in an IHF- background. We also observe an increase in conjugation efficiency under these conditions. Relieving the inhibition imposed by these host factors allows efficient levels of recombination between short oriT loci in the absence of TrwA. The presence of TrwA counteracts these inhibitory effects. TrwA would then activate both recombination and conjugation by switching the conformation of the relaxosome to an "open" form that exposes single-stranded DNA at the nic site, promoting the initial TrwC nicking reaction.

Integration Host Factor is required for FarR repression of the farAB-encoded efflux pump of Neisseria gonorrhoeae

The farAB operon encodes an efflux pump system that mediates the resistance of Neisseria gonorrhoeae to antimicrobial long-chain fatty acids. We previously observed that expression of farAB is negatively regulated by the FarR repressor. In this study, we examined the molecular mechanism by which FarR represses expression of farAB. DNase I footprinting analysis, coupled with a deletion analysis of the farAB promoter region, indicated that FarR binds to three sites (termed sites A, B and C) within the DNA sequence upstream of farA; genetic analysis revealed, however, that site B is not required for FarR repression of farAB. This repression also required the presence of Integration Host Factor (IHF), which was found to bind to sequences located between FarR binding sites A and C. We determined that IHF binding to the farAB promoter region could inhibit transcription in vitro and that such binding induced a bending of the target DNA, which we propose to be important in regulating this operon. IHF binding to the promoter region was found to stabilize the binding of FarR to its binding sites A and C and as a consequence, enhanced repression of farAB expression mediated by FarR. We propose a model in which expression of the farAB-encoded efflux pump in N. gonorrhoeae is modulated by the DNA binding activities of FarR and IHF.

A suf operon requirement for Fe-S cluster assembly during iron starvation in Escherichia coli

The suf and isc operons of Escherichia coli have been implicated in Fe-S cluster assembly. However, it has been unclear why E. coli has two systems for Fe-S cluster biosynthesis. We have examined the regulatory characteristics and mutant phenotypes of both operons to discern if the two operons have redundant functions or if their cellular roles are divergent. Both operons are similarly induced by hydrogen peroxide and the iron chelator 2,2'-dipyridyl, although by different mechanisms. Regulation of the isc operon is mediated by IscR, whereas the suf operon requires OxyR and IHF for the response to oxidative stress and Fur for induction by iron starvation. Simultaneous deletion of iscS and most suf genes is synthetically lethal. However, although the suf and isc operons have overlapping functions, they act as distinct complexes because the SufS desulphurase alone cannot substitute for the IscS enzyme. In addition, suf deletion mutants are more sensitive to iron starvation than isc mutants, and the activity of the Fe-S enzyme gluconate dehydratase is diminished in the suf mutant during iron starvation. These findings are consistent with the model that the isc operon encodes the housekeeping Fe-S cluster assembly system in E. coli, whereas the suf operon is specifically adapted to synthesize Fe-S clusters when iron or sulphur metabolism is disrupted by iron starvation or oxidative stress.

Stable co-existence of separate replicons in Escherichia coli is dependent on once-per-cell-cycle initiation

DNA replication in most organisms is regulated such that all chromosomes are replicated once, and only once, per cell cycle. In rapidly growing Escherichia coli, replication of eight identical chromosomes is initiated essentially simultanously, each from the same origin, oriC. Plasmid-borne oriC sequences (minichromosomes) are also initiated in synchrony with the eight chromosomal origins. We demonstrate that specific inactivation of newly formed, hemimethylated origins (sequestration) was required for the stable co-existence of oriC-dependent replicons. Cells in which initiations were not confined to a short interval in the cell cycle (carrying mutations in sequestration or initiation genes or expressing excess initiator protein) could not support stable co-existence of several oriC-dependent replicons. The results show that such stable co-existence of oriC-dependent replicons is dependent on both a period of sequestration that is longer than the initiation interval and a reduction of the initiation potential during the sequestration period. These regulatory requirements are the same as those required to confine initiation of each replicon to once, and only once, per cell cycle.

Integration host factor interactions with Neisseria gene sequences: correlation between predicted binding sites and in vitro binding of Neisseria -derived IHF protein

Putative integration host factor (IHF) binding sites are frequently being identified in Neisseria gene sequences on the basis of similarity to a degenerate Escherichia coli -derived consensus binding sequence. In this report, three different Neisseria genetic systems that contain predicted IHF binding sites were assessed for IHF binding through gel retardation analysis. The results show a positive correlation between the identification of a predicted Neisseria IHF binding site and in vitro binding of Neisseria -derived IHF protein.

Direct atomic force microscopy visualization of integration host factor-induced DNA bending structure of the promoter regulatory region on the Pseudomonas TOL plasmid

Atomic force microscopy (AFM) was used to analyze DNA bending induced by integration host factor (IHF). The direct AFM visualization of IHF-DNA complexes on the OP1 promoter regulatory regions on the Pseudomonas TOL plasmid showed that there was no intrinsic DNA bend in the OP1 promoter region, but a sharp DNA bend was induced by binding of IHF to the region between the upstream regulatory sequence and the promoter sequence. The DNA bending angles were distributed with a mean bend angle of 123 degrees. The IHF-DNA complexes were shown to bend at the IHF binding site giving rise to an asymmetric structure. These results provide direct evidence that IHF is required functionally for activation of OP1 transcription and support the DNA-loop model that the sharp DNA bend induced by binding of IHF facilitates the contact between RNA polymerase bound by the promoter sequence and XylR protein attached to the upstream sequence in the OP1 promoter.

Molecular cloning, sequence and characterization of cjsT, a putative protease from Rickettsia rickettsii

The cloning and sequencing of a gene from Rickettsia rickettsii which confers haemolytic activity on Escherichia coli strain TB1 is described. The open reading frame of the haemolysis-promoting gene, cjsT, is 1041 bp and encodes a putative protein with a molecular mass of 33 825 Da. CjsT has high sequence similarity to several bacterial proteases, particularly type IV signal peptidases. Cell lysates from an E. coli clone containing cjsT in pUC19 (pJON1) exhibited greater protease activity in functional assays than found in E. coli containing pUC19 alone. Disruption of the cjsT gene by insertional inactivation with a kanamycin cassette reduced both the protease and haemolytic activities conferred by cjsT. The protease inhibitors antipain and diisopropylfluorophosphate (DFP) both reduced the proteolytic activity of pJON1. The mechanism by which the R. rickettsii cjsT promotes haemolysis in E. coli remains unclear.

Involvement of H-NS in transpositional recombination mediated by IS1

IS1, the smallest active transposable element in bacteria, encodes a transposase that promotes inter- and intramolecular transposition. Host-encoded factors, e.g., histone-like proteins HU and integration host factor (IHF), are involved in the transposition reactions of some bacterial transposable elements. Host factors involved in the IS1 transposition reaction, however, are not known. We show that a plasmid with an IS1 derivative that efficiently produces transposase did not generate miniplasmids, the products of intramolecular transposition, in mutants deficient in a nucleoid-associated DNA-binding protein, H-NS, but did generate them in mutants deficient in histone-like proteins HU, IHF, Fis, and StpA. Nor did IS1 transpose intermolecularly to the target plasmid in the H-NS-deficient mutant. The hns mutation did not affect transcription from the indigenous promoter of IS1 for the expression of the transposase gene. These findings show that transpositional recombination mediated by IS1 requires H-NS but does not require the HU, IHF, Fis, or StpA protein in vivo. Gel retardation assays of restriction fragments of IS1-carrying plasmid DNA showed that no sites were bound preferentially by H-NS within the IS1 sequence. The central domain of H-NS, which is involved in dimerization and/or oligomerization of the H-NS protein, was important for the intramolecular transposition of IS1, but the N- and C-terminal domains, which are involved in the repression of certain genes and DNA binding, respectively, were not. The SOS response induced by the IS1 transposase was absent in the H-NS-deficient mutant strain but was present in the wild-type strain. We discuss the possibility that H-NS promotes the formation of an active IS1 DNA-transposase complex in which the IS1 ends are cleaved to initiate transpositional recombination through interaction with IS1 transposase.

Identification of residues within two regions involved in self-association of viral histone-like protein p6 from phage theta29

Protein p6 of Bacillus subtilis phage theta29 is involved in the initiation of viral DNA replication and transcription by forming a multimeric nucleoprotein complex with the phage DNA. Based on this, together with its abundance and its capacity to bind to the whole viral genome, it has been proposed to be a viral histone-like protein. Protein p6 is in a monomer-dimer-oligomer equilibrium association. We have identified protein p6 mutants deficient in self-association by testing random mutants obtained by degenerated polymerase chain reaction in an in vivo assay for dimer formation. The mutations were mainly clustered in two regions located at the N terminus, and the central part of the protein. Site-directed single mutants, corresponding to those found in vivo, have been constructed and purified. Mutant p6A44V, located at the central part of the protein, showed an impaired dimer formation ability, and a reduced capacity to bind DNA and to activate the initiation of O29 DNA replication. Mutant p6I8T has at least 10-fold reduced self-association capacity, does not bind DNA nor activate O29 DNA initiation of replication. C-terminal deletion mutants showed an enhanced dimer formation capacity. The highly acidic tail, removed in these mutants, is proposed to modulate the protein p6 self-association.

A rhizobial homolog of IHF stimulates transcription of dctA in Rhizobium leguminosarum but not in Sinorhizobium meliloti

Sequence inspection identified several potential IHF binding sites adjacent to the Rhizobium leguminosarum dctA promoter. IHF protected the -30 to -76 region from DNase I digestion, but systematic error in quantitative assays suggested that this protein DNA interaction is complex. IHF stimulated DctD-mediated transcriptional activation from the R. leguminosarum dctA promoter both in vivo and in vitro. In contrast to R. leguminosarum dctA, the Sinorhizobium meliloti dctA promoter region was found to have a much weaker match to the consensus IHF binding site and a low affinity for IHF. Moreover, IHF had no effect on transcriptional activation from the S. meliloti dctA promoter in vitro. A base substitution was introduced into the IHF binding site of R. leguminosarum dtA that reduced the affinity of the promoter regulatory region for IHF by approximately 30-fold and resulted in an eight-fold decrease in transcriptional activation in both R. leguminosarum and S. meliloti. These data suggest that both rhizobial species have an IHF homolog that stimulates DctD-mediated transcriptional activation from the R. leguminosarum dctA promoter. Consistent with this hypothesis, a 12.5 kDa protein was identified from R. leguminosarum as a putative homolog of IHF subunit beta by immunoblotting and N-terminal sequence analysis.

Regulation of acetate metabolism by protein phosphorylation in enteric bacteria

Growth of enteric bacteria on acetate as the sole source of carbon and energy requires operation of a particular anaplerotic pathway known as the glyoxylate bypass. In this pathway, two specific enzymes, isocitrate lyase and malate synthase, are activated to divert isocitrate from the tricarboxylic acid cycle and prevent the quantitative loss of acetate carbons as carbon dioxide. Bacteria are thus supplied with the metabolic intermediates they need for synthesizing their cellular components. The channeling of isocitrate through the glyoxylate bypass is regulated via the phosphorylation/dephosphorylation of isocitrate dehydrogenase, the enzyme of the tricarboxylic acid cycle which competes for a common substrate with isocitrate lyase. When bacteria are grown on acetate, isocitrate dehydrogenase is phosphorylated and, concomitantly, its activity declines drastically. Conversely, when cells are cultured on a preferred carbon source, such as glucose, the enzyme is dephosphorylated and recovers full activity. Such reversible phosphorylation is mediated by an unusual bifunctional enzyme, isocitrate dehydrogenase kinase/phosphatase, which contains both modifying and demodifying activities on the same polypeptide. The genes coding for malate synthase, isocitrate lyase, and isocitrate dehydrogenase kinase/phosphatase are located in the same operon. Their expression is controlled by a complex dual mechanism that involves several transcriptional repressors and activators. Recent developments have brought new insights into the nature and mode of action of these different regulators. Also, significant advances have been made lately in our understanding of the control of enzyme activity by reversible phosphorylation. In general, analyzing the physiological behavior of bacteria on acetate provides a valuable approach for deciphering at the molecular level the mechanisms of cell adaptation to the environment.

Selected phenotypes of ihf mutants of Escherichia coli

In attempts to identify subunit-specific phenotypes of ihf mutants we analyzed viability, thermoresistance and protein synthesis patterns in ihfA and ihfB mutants and their respective parental strains. Despite some detected differences in the two-dimensional protein patterns, no significant subunit-specific, physiological effects could be observed. Each mutant was less viable and less thermoresistant than the wild type strain. Moreover, in contrast to the wild type the mutants did not reduce global protein synthesis after prolonged culturing. Examination of expression of transcriptional fusions allowed us to demonstrate autoregulation of both genes by IHF. Additional IHF binding sites in the regulatory region of both ihf genes were footprinted.

Gene activation by the AraC protein can be inhibited by DNA looping between AraC and a LexA repressor that interacts with AraC: possible applications as a two-hybrid system

The Escherichia coli activator and repressor proteins AraC and LexA bind DNA as homodimers. Here we show that their heterodimerization through fused cognate dimerization domains results in repression of AraC-dependent gene activation by LexA. Repression also requires a LexA operator half-site located several helical turns downstream of the AraC operator. This requirement for a specific spatial organization of the operators suggests the formation of a DNA loop between operator-bound Ara/LexA heterodimers, and we propose that heterodimerization with the AraC hybrid provides co-operativity for operator binding and repression by the LexA hybrid. Consistent with a mechanism that involves DNA looping, repression increases when the E. coli DNA looping and transcriptional effector protein IHF binds between the AraC and LexA operators. Thus, we have combined the functions of three distinct transcriptional effector proteins to achieve a new mode of gene regulation by DNA looping, in which the activator protein is an essential part of the repressor complex. The flexibility of the DNA loop may facilitate this novel combinatorial arrangement of those proteins on the DNA. The requirement for protein interactions between the AraC and LexA hybrids for gene regulation suggests that this regulatory circuit may prove useful as an E. coli-based two-hybrid system.

Linkage map of Escherichia coli K-12, edition 10: the traditional map

This map is an update of the edition 9 map by Berlyn et al. (M. K. B. Berlyn, K. B. Low, and K. E. Rudd, p. 1715-1902, in F. C. Neidhardt et al., ed., Escherichia coli and Salmonella: cellular and molecular biology, 2nd ed., vol. 2, 1996). It uses coordinates established by the completed sequence, expressed as 100 minutes for the entire circular map, and adds new genes discovered and established since 1996 and eliminates those shown to correspond to other known genes. The latter are included as synonyms. An alphabetical list of genes showing map location, synonyms, the protein or RNA product of the gene, phenotypes of mutants, and reference citations is provided. In addition to genes known to correspond to gene sequences, other genes, often older, that are described by phenotype and older mapping techniques and that have not been correlated with sequences are included.

The ihf mRNA levels decline as Neisseria gonorrhoeae enters the stationary growth phase

Integration host factor (IHF) is a small heterodimeric DNA binding protein found in all Gram-negative bacteria and is implicated as a transcription cofactor of pilE in Neisseria gonorrhoeae (Hill, S.A., Samuels, D.S., Carlson, J.H., Wilson, J., Hogan, D., Lubke, L., Belland, R.J., 1997. Integration host factor is a transcriptional cofactor of pilE in Neisseria gonorrhoeae. Mol. Microbiol. 23, 649-656). The ihf genes (ihfA and ihfB) were cloned from N. gonorrhoeae through functional complementation of defined Escherichia coli ihf mutants for plating of phage lambda. The predicted aa sequences of each gonococcal IHF polypeptide showed extensive homology to other reported IHF polypeptide sequences. Northern blotting and primer extension analysis defined the tsp for each gene and indicated a disparity in ihfA and ihfB message levels over time, with ihfB mRNA being more abundant throughout the entire growth cycle. Furthermore, both the ihfA and ihfB message levels declined as cells entered the stationary growth phase. Overall, this study reveals several unique features of ihf transcription in the gonococcus which questions whether certain aspects if ihf transcriptional regulation are universally shared by all Gram-negative bacteria.

Nuclear magnetic resonance-based model of a TF1/HmU-DNA complex

Transcription factor 1 (TF1), a type II DNA-binding protein encoded by the Bacillus subtilis bacteriophage SPO1, has the capacity for sequence-selective DNA binding and a preference for 5-hydroxymethyl-2'-deoxyuridine (HmU)-containing DNA. In NMR studies of the TF1/HmU-DNA complex, intermolecular NOEs indicate that the flexible beta-ribbon and C-terminal alpha-helix are involved in the DNA-binding site of TF1, placing it in the beta-sheet category of DNA-binding proteins proposed to bind by wrapping two beta-ribbon "arms" around the DNA. Intermolecular and intramolecular NOEs were used to generate an energy-minimized model of the protein-DNA complex in which both DNA bending and protein structure changes are evident.

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

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

Association of the histone-like protein HBsu with the nucleoid of Bacillus subtilis

To investigate the physiological role of the essential histone-like protein of Bacillus subtilis (HBsu) in the nucleoid structure, a fusion to the green fluorescent protein (GFP) of Aequorea victoria was constructed. This purified fusion protein, HBsuGFP, showed a threefold-reduced affinity to DNA compared to unmodified HBsu; however, in gel mobility shift experiments HBsuGFP DNA-binding was greatly enhanced in the presence of low HBsu concentrations. Additional production of HBsu also had a positive effect on the retarded growth of a B. subtilis strain, PK9C8, which expresses only hbs-gfp (encoding HBsuGFP). HBsu seemed to influence not only growth but also nucleoid structure, as monitored by DNA staining and fluorescence microscopy. Without HBsu production, strain PK9C8 showed a relaxed nucleoid structure associated with HBsuGFP. However, a highly compact nucleoid structure that coincides with the fluorescence of the fusion protein was visualized when HBsu synthesis was induced. This provides the first evidence for in vivo association of HBsu in DNA packaging and its consequence on cell growth.

Transcriptional pattern of Escherichia coli ihfB (himD) gene expression

Integration host factor (IHF) is a small heterodimer containing subunits encoded by the unlinked ihfA (himA) and ihfB (himD, hip) genes. The transcriptional pattern of ihfB expression in the logarithmic and stationary growth phases was investigated. The ihfB gene is expressed as both monocistronic and polycistronic (hybridizing also to an internal rpsA probe) transcript. The intensity of the polycistronic transcripts, initiated upstream of rpsA, decreased sharply upon growth cessation. In contrast, expression of the monocistronic ihfB transcript strongly increased when cells entered stationary growth phase. The observed growth rate-dependent regulation of the transcription of these transcripts is in agreement with the previously published data about the regulation of the rpsA and ihfB promoters (Pedersen et al., 1984; Aviv et al., 1994).

Structure and function of the Pseudomonas putida integration host factor

Integration host factor (IHF) is a DNA-binding and -bending protein that has been found in a number of gram-negative bacteria. Here we describe the cloning, sequencing, and functional analysis of the genes coding for the two subunits of IHF from Pseudomonas putida. Both the ihfA and ihfB genes of P. putida code for 100-amino-acid-residue polypeptides that are 1 and 6 residues longer than the Escherichia coli IHF subunits, respectively. The P. putida ihfA and ihfB genes can effectively complement E. coli ihf mutants, suggesting that the P. putida IHF subunits can form functional heterodimers with the IHF subunits of E. coli. Analysis of the amino acid differences between the E. coli and P. putida protein sequences suggests that in the evolution of IHF, amino acid changes were mainly restricted to the N-terminal domains and to the extreme C termini. These changes do not interfere with dimer formation or with DNA recognition. We constructed a P. putida mutant strain carrying an ihfA gene knockout and demonstrated that IHF is essential for the expression of the P(U) promoter of the xyl operon of the upper pathway of toluene degradation. It was further shown that the ihfA P. putida mutant strain carrying the TOL plasmid was defective in the degradation of the aromatic model compound benzyl alcohol, proving the unique role of IHF in xyl operon promoter regulation.

Molecular characterization of adiY, a regulatory gene which affects expression of the biodegradative acid-induced arginine decarboxylase gene (adiA) of Escherichia coli

A transcriptional regulator gene, designated adiY, was found downstream of the biodegradative arginine decarboxylase (adiA) gene (previously known as adi) of Escherichia coli. The arginine decarboxylase system is maximally induced under conditions of acidic pH, anaerobiosis and rich medium, and AdiY was found to increase the expression of adiA. The DNA sequence of adiY encodes a protein of 253 amino acids. Primer extension analysis defined the promoter. The amino acid sequence of AdiY showed homology to the XylS/AraC family of transcriptional regulators, which includes EnvY and AppY. Studies suggested that sequences required for acid induction were also necessary to observe the stimulation by AdiY. An examination of the substitution of AdiY, AppY and EnvY showed that these three proteins can, to some extent, stimulate the other systems.

Serratia marcescens contains a heterodimeric HU protein like Escherichia coli and Salmonella typhimurium

Homologs of the dimeric HU protein of Escherichia coli can be found in every prokaryotic organism that has been analyzed. In this work, we demonstrate that Serratia marcescens synthesizes two distinct HU subunits, like E. coli and Salmonella typhimurium, suggesting that the heterodimeric HU protein could be a common feature of enteric bacteria. A phylogenetic analysis of the HU-type proteins (HU and IHF) is presented, and a scheme for the origin of the hup genes and the onset of HU heterodimericity is suggested.

Participation of the flank regions of the integration host factor protein in the specificity and stability of DNA binding

The heterodimeric integration host factor (IHF) protein is a site-specific DNA-binding protein from Escherichia coli that strongly bends the DNA. It has been proposed (Yang, C., and Nash, H.A. (1989) Cell 57, 869-880; Granston, A. E., and Nash, H. A. (1993) J. Mol. Biol 234, 45-59; Lee, E. C., Hales, L. M., Gumport, R. I., and Gardner, J. F. (1992) EMBO J. 11, 305-313) that the wrapping of the DNA around the protein is stabilized through interactions between the flanks of the protein and the DNA. In order to elucidate which domains of the IHF protein are involved in these interactions, we have constructed mutant proteins in which the C-terminal part of one of the subunits has been deleted. We observed that the C-terminal alpha 3 helix of HimD is involved in the stability of DNA binding, but not in the specificity. In contrast the corresponding alpha 3 helix of HimA is essential for the sequence specificity, since an IHF mutant lacking this domain only binds to the DNA in a non-specific way. The possible role of the two C-terminal alpha-helical structures in complex formation will be discussed. We also examined the properties of an IHF mutant that has an amino acid substitution between beta sheets beta 1 and beta 2 of the HimD subunit (R46H). The occupancy of the ihf site by the mutant and wild type proteins differ in the 3' part of the ihf site and as a result the bend introduced in the DNA by the mutant protein is less pronounced. We propose that the arginine 46 in the HimD subunit is in vicinity of the TTR region of the consensus and that through contacts within the minor groove the DNA bend introduced by IHF is stabilized.

Expression of the narX, narL, narP, and narQ genes of Escherichia coli K-12: regulation of the regulators

The products of four Escherichia coli genes (narX, narL, narQ, and narP) regulate anaerobic respiratory gene expression in response to nitrate and nitrite. We used lacZ gene and operon fusions to monitor the expression of these nar regulatory genes in response to different growth conditions. Maximal expression of the narXL operon required molybdate, nitrate, and integration host factor. Expression of the narP and narQ genes was weakly repressed by nitrate. The NarL and NarP proteins were required for full nitrate induction of narXL operon expression, whereas the nitrate repression of narP and narQ expression was mediated solely by the NarL protein. narXL operon expression was unaffected by anaerobiosis, whereas expression of narP and narQ was induced approximately fourfold. The Fnr and ArcA proteins were not required for this anaerobic induction.

Identification of related genes in phages phi 80 and P22 whose products are inhibitory for phage growth in Escherichia coli IHF mutants

Bacteriophage lambda grows in both IHF+ and IHF- host strains, but the lambdoid phage phi 80 and hybrid phage lambda (QSRrha+)80 fail to grow in IHF- host strains. We have identified a gene, rha, in the phi80 region of the lambda(QSRrha+)80 genome whose product, Rha, inhibits phage growth in an IHF- host. A search of the GenBank database identified a homolog of rha, ORF201, a previously identified gene in phage P22, which similarly inhibits phage growth in IHF- hosts. Both rha and ORF201 contain two possible translation start sites and two IHF binding site consensus sequences flanking the translation start sites. Mutations allowing lambda (QSRrha+)80 and P22 to grow in IHF- hosts map in rha and ORF201, respectively. We present evidence suggesting that, in an IHF+ host, lambda(QSRrha+)80 expresses Rha only late in infection but in an IHF- host the phage expresses Rha at low levels early in infection and at levels higher than those in an IHF+ host late in infection. We suspect that the deregulation of rha expression and, by analogy, ORF201 expression, is responsible for the failure of phi80, lambda(QSRrha+)80, and P22 to grow in IHF mutants.

IHF- and RpoN-dependent regulation of hydrogenase expression in Bradyrhizobium japonicum

Sequence analysis of the Bradyrhizobium japonicum hydrogenase promoter regulatory region indicated the presence of a -24/-12 type promoter, which is recognized by RpoN, and a potential integration host factor (IHF)-binding site. B. japonicum rpoN1-/rpoN2- double mutants were deficient in hydrogen-uptake activity. Using plasmid-borne hup-lacZ fusions, it was shown that the rpoN mutants were also deficient in nickel-dependent transcriptional regulation of hydrogenase. Gel-shift assays of the hydrogenase promoter regulatory region showed that purified IHF from Escherichia coli binds to a 210 bp fragment. DNase footprint analysis revealed a protected region of 31 bp between bases -44 and -75 from the transcription start site. Western analysis with B. japonicum soluble extract and antibodies against E. coli IHF gave two bands equivalent to molecular masses of 12 and 14 kDa approximately. When the IHF-binding area is mutated on a plasmid-borne hup-lacZ fusion, nickel-dependent transcriptional regulation of hydrogenase is still observed, but the transcriptional rates are clearly less than in the parent hup-lacZ fusion plasmid. Like the results with nickel, regulation of hydrogenase by other transcriptional regulators (hydrogen and oxygen) still occurs, but at a diminished level in the IHF-binding-area-mutated construct.

Cloning and sequence analyses of the genes coding for the integration host factor (IHF) and HU proteins of Pseudomonas aeruginosa

Histone-like proteins, such as HU and the integration host factor (IHF), are small, dimeric, DNA-bending proteins which play a role in maintaining constrained DNA structures and hence in regulating gene expression. Two different strategies were used to isolate the genes coding for Pseudomonas aeruginosa (Pa) HU and IHF, two proteins that we have previously isolated from a mucoid strain. By use of a PCR-based technique with oligodeoxyribonucleotides (oligos) designed from the N-terminal amino acid (aa) sequences of HU and the beta-subunit of IHF, and Southern blot analyses, hupB and himD, encoding HU and IHF beta, respectively, have been cloned. The himA gene of Pa, encoding the alpha-subunit of IHF, was isolated using himA of Escherichia coli (Ec) as a probe in Southern blot analyses. The deduced hupB product (90 aa, 9 kDa) is 79% identical to HU beta and 61% to HU alpha of Ec. The predicted products of himA (100 aa, 11.5 kDa) and of himD (94 aa, 10.6 kDa) share 77 and 70% identity with IHF alpha and IHF beta of Ec, respectively. The promoter region of himD contains an IHF consensus sequence, as is the case for Ec himD.

Expression of the genes coding for the Escherichia coli integration host factor are controlled by growth phase, rpoS, ppGpp and by autoregulation

Transcriptional control of the himA and the himD/hip genes coding for the two subunits of the integration host factor (IHF) was investigated. The promoters for the two genes were identified by the use of primer extension and S1 analysis. Expression from both promoters was found to increase as the cells enter stationary phase. Mutation in rpoS, known to be induced upon entry to stationary phase, dramatically reduced the growth-phase response of the himA P4 promoter but had only a small effect on the induction of the himD/hip promoter. The increased activity of both promoters required the presence of the relA and spoT genes, suggesting that ppGpp plays a major role in the response to stationary phase. An artificial increase in ppGpp in exponentially growing cells induced a rapid increase in himA P4 and himD/hip mRNA levels. Experiments with a mutant defective in rpoS showed that the response of the himA P4 promoter to high ppGpp levels was greatly reduced while that of himD/hip was only slightly affected. Therefore, it seems that different mechanisms involving RpoS and ppGpp regulate the growth-phase response of the two promoters. We propose that the effect of ppGpp on himA P4 is mediated via RpoS whereas the himD/hip promoter is affected by ppGpp independently of RpoS. Expression of the himD/hip and himA genes was found to be subject to negative autoregulation. IHF-binding sites, implicated in autoregulation, were found to overlap both the himD/hip and himA P4 promoters. An additional IHF-binding site was found upstream of the himD/hip promoter. All three sites show low binding affinity to IHF suggesting that autoregulation can take place only after sufficiently high levels of IHF accumulate in the cell.

Role of the AGA/AGG codons, the rarest codons in global gene expression in Escherichia coli

AGA and AGG codons for arginine are the least used codons in Escherichia coli. Previous findings have shown that these codons are used preferentially within the first 25 codons in E. coli genes. More than 100 genes having a single AGA/AGG codon within the first 25 codons were identified to be associated with various essential cellular functions. The lacZ gene, containing 5 AGG codons after the tenth codon from the initiation codon, was constructed as a model system. The production of beta-galactosidase was inhibited almost completely during the stationary phase, whereas the production of the control beta-galactosidase without AGG codons was not. The inhibitory effect by the 5 AGG codons was substantially suppressed either by coexpressing the argU gene for tRNA(ArgUCU/CCU) or by moving the 5 AGG codons by > 50 codons away from the initiation codon. In addition, the production of a number of proteins resolved by two-dimensional gel electrophoresis was enhanced significantly during the stationary phase in the cells harboring a plasmid containing argU. At least one of them was identified as the hns product encoded by an ORF having an AGA codon at the nineteenth position. On the basis of these results, it is proposed that the expression of a group of essential genes for various cellular functions that have a single AGA/AGG codon very close to the initiation codon are globally regulated by the availability of the least abundant tRNA(ArgUCU/CCU). A model for this regulation is proposed.

Growth phase variation of integration host factor level in Escherichia coli

We have measured the intracellular abundance of integration host factor (IHF), a site-specific, heterodimeric DNA-binding protein, in exponential- and stationary-phase cultures of Escherichia coli K-12. Western immunoblot analysis showed that cultures that had been growing exponentially for several generations contained 0.5 to 1.0 ng of IHF subunits per microgram of total protein and that this increased to 5 to 6 ng/microgram in late-stationary-phase cultures. IHF is about one-third to one-half as abundant in exponentially growing cells as HU, a structurally related protein that binds DNA with little or no site specificity. Wild-type IHF is metabolically stable, but deletion mutations that eliminated one subunit reduced the abundance of the other when cells enter stationary phase. We attribute this reduction to the loss of stabilizing interactions between subunits. A mutation that inactivates IHF function but not subunit interaction increased IHF abundance, consistent with results of previous work showing that IHF synthesis is negatively autoregulated. We estimate that steady-state exponential-phase cultures contain about 8,500 to 17,000 IHF dimers per cell, a surprisingly large number for a site-specific DNA-binding protein with a limited number of specific sites. Nevertheless, small reductions in IHF abundance had significant effects on several IHF-dependent functions, suggesting that the wild-type exponential phase level is not in large excess of the minimum required for occupancy of physiologically important IHF-binding sites.

Interaction of Fis protein with DNA: bending and specificity of binding

The Escherichia coli Fis protein is a dimeric DNA-binding protein whose specific binding sites share a weak consensus sequence. Use of the gel retardation technique indicates that binding of Fis on a linear DNA fragment leads to the formation of a ladder of defined retarded complexes, independently of the presence of a specific site. This non-specific binding of Fis is consistent with a model where equivalent low-affinity sites on a given fragment would be bound randomly and independently of each other by consecutive Fis dimers. Evidence is presented that non-specific binding of Fis can, however, induce an apparent site-specific conformational change in the DNA. This observation is discussed in terms of a model in which each Fis:DNA complex detected in gel retardation experiments actually represents a dynamic equilibrium of a fixed number of Fis dimers distributed on the fragment.

On the role of the Escherichia coli integration host factor (IHF) in repression at a distance of the pyrimidine specific promoter P1 of the carAB operon

Binding of integration host factor to its target site, centered around nucleotide -305 upstream of the transcription startpoint, exerts antagonistic effects on the expression of P1, the upstream pyrimidine specific promoter of the E coli and S typhimurium carAB operons. IHF stimulates P1 promoter activity in minimal medium, but also increases the repressibility of this promoter by pyrimidines. We present evidence strongly suggesting that IHF exerts these effects by modulating the binding of another pyrimidine specific regulatory molecule, probably the product of gene carP. The carAB control region contains a GATC Dam methylation site, 106 bp upstream of the P1 transcription startpoint, which can be protected in vivo against methylation. This protection requires at least the regulatory carP gene product and a high pyrimidine nucleotide pool and, as shown here, the integration host factor. Whether CarP directly binds to this site or exerts its protective effect indirectly is not yet known. In the absence of IHF (himA) or in mutants affected in the IHF target site this protection is strongly impaired, suggesting that IHF positively influences the formation or the stability of the protective protein-DNA complex some 200 bp downstream. Furthermore, we have demonstrated that the distance separating the IHF and GATC Dam methylase target sites is crucial for the in vivo protection and for pyrimidine mediated regulation of P1 promoter expression. Indeed, shortening this distance by 6 bp, and more surprisingly also by 11 bp, results in a severe reduction of the degree of in vivo protection of the GATC site against methylation and concomitantly of the repressibility by pyrimidines of P1 promoter activity. The absence of both these effects in a double, deletion-duplication, mutant resulting in a net increase of the intervening sequence by 1 bp, clearly demonstrates that these effects are not due to the disruption of an important regulatory site, but must be attributed to variations in the distance separating different protein binding sites.

Histones, HMG, HU, IHF: Même combat

In this review article we present a compilation of the proteins homologous to Escherichia coli HU: the HU-like family. Two of these, HU and IHF from E coli have been extensively characterized genetically and biochemically. Due to their DNA binding activities, these proteins confer a condensed shape to the chromosome and regulate the transcription of selected sets of its genes. The parallel between the dual function of the HU-like proteins and the roles described for eukaryotic histone and HMG proteins is striking, especially in the view that they are evolutionary unrelated.

Identification of the integration host factor genes of Erwinia chrysanthemi 3937

Two Erwinia chrysanthemi homologues of the himA and himD genes of Escherichia coli which encode the integration host factor (IHF) were cloned, sequenced and compared to their homolog in other enterobacteria (EMBL accession nos X74749 and X74750). Both genes were inactivated by the insertion of an antibiotic resistance cassette, allowing for the isolation of IHF- mutants of E chrysanthemi.

Genetic and biochemical analysis of IHF/HU hybrid proteins

Integration host factor (IHF) is a small heterodimeric DNA-binding protein of E coli composed of two subunits, alpha and beta, encoded by the himA and hip genes, respectively. IHF binds to DNA at a consensus sequence and bends DNA. HU protein, encoded by the hupA and hupB genes, is similar to IHF except that it does not bind to a specific DNA sequence. To investigate the protein determinants for IHF specificity we exchanged progressively longer segments from the C-terminus of Hip with those of HupA, and followed the activity in vivo and in vitro of four such IHF/HU hybrids. Replacement of 11 residues from the C-terminal alpha helix of Hip by the complementary eight residues of HupA (hybrid 1), had only minor effects on the DNA binding activity of the protein. As progressively longer segments of Hip were replaced by HupA, a precipitous decrease in IHF activity was observed. The hybrid with the longest substitution, hybrid 4, was totally inactive in vivo and could not be purified. None of the hybrid proteins could complement HU activity. Comparing the activities of hybrid 1, hybrid 2 and IHF point mutants, led us to conclude that the structural integrity of the C-terminal alpha helix and its spatial position, but not its amino acid sequence, are important for DNA binding specificity. We favor the hypothesis that alpha helices 3 of both IHF subunits interact with the body of IHF so as to anchor the arms. This interaction stabilizes the arms to permit DNA binding specificity. Thus the C-termini of IHF influence, in an indirect way, the recognition of specific sites on DNA.

Multiple molecules of integration host factor (IHF) at a single DNA binding site, the bacteriophage lambda cos I1 site

Integration host factor (IHF) is an E coli protein that binds DNA sequence-specifically and serves as a cofactor in many intracellular processes including lambda DNA packaging. In gel shift experiments, cos DNA, a DNA fragment containing the recognition signal for lambda DNA packaging, forms multiple protein-DNA complexes when combined with pure IHF. Copper(II)-1,10 orthophenanthroline footprinting of individual IHF-cos DNA complexes shows that multiple complex formation does not result from IHF binding to successive sites on the cos DNA fragment. Instead, the footprinting of DNA from two IHF-cos complexes shows protection at one site alone. DNA in the first complex is only partially protected from nucleolytic cleavage, while DNA in the second, slower-moving, complex is completely protected at the same binding site. Quantitative Western blotting experiments determined the relative stoichiometry of IHF to DNA in the two complexes. The results confirm that two molecules of IHF bind at a single site in the cos fragment. This site, cos I1, has two matches to the IHF consensus sequence, but the two matches overlap by eight of thirteen nucleotides. A search of the DNA sequence around cos, using an expanded IHF consensus sequence, has revealed additional, low-affinity consensus matches, contiguous to these. The extent of the copper(II)-1,10 orthophenanthroline footprint and the stoichiometry of the IHF-cos I1 complexes suggest that either two molecules of IHF bind to overlapping sites, or IHF binds to a site of low affinity contiguous to a strong site. Application of a thermodynamic model to the results of gel shift experiments with IHF and cos DNA suggests that multiple complex formation requires cooperative interaction between the two IHF binding sites.

Integration host factor binds to a unique class of complex repetitive extragenic DNA sequences in Escherichia coli

Interspersed repeated DNA sequences are characteristic features of both prokaryotic and eukaryotic genomes. REP sequences are defined as conserved repetitive extragenic palindromic sequences and are found in Escherichia coli, Salmonella typhimurium and other closely related enteric bacteria. These REP sequences may participate in the folding of the bacterial chromosome. In this work we describe a unique class of 28 conserved complex REP clusters, about 100bp long, in which two inverted REPs are separated by a singular integration host factor (IHF) recognition sequence. We term these sequences RIP (for repetitive IHF-binding palindromic) elements and demonstrate that IHF binds to them specifically. It is estimated that there are about 70 RIP elements in E. coli. Our analysis shows that the RIP elements are evenly distributed around the bacterial chromosome. The possible function of the RIP element is discussed.

Purification of the integration host factor homolog of Rhodobacter capsulatus: cloning and sequencing of the hip gene, which encodes the beta subunit

We describe a method for rapid purification of the integration host factor (IHF) homolog of Rhodobacter capsulatus that has allowed us to obtain microgram quantities of highly purified protein. R. capsulatus IHF is an alpha beta heterodimer similar to IHF of Escherichia coli. We have cloned and sequenced the hip gene, which encodes the beta subunit. The deduced amino acid sequence (10.7 kDa) has 46% identity with the beta subunit of IHF from E. coli. In gel electrophoretic mobility shift DNA binding assays, R. capsulatus IHF was able to form a stable complex in a site-specific manner with a DNA fragment isolated from the promoter of the structural hupSL operon, which contains the IHF-binding site. The mutated IHF protein isolated from the Hup- mutant IR4, which is mutated in the himA gene (coding for the alpha subunit), gave a shifted band of greater mobility, and DNase I footprinting analysis has shown that the mutated IHF interacts with the DNA fragment from the hupSL promoter region differently from the way that the wild-type IHF does.

Integration host factor is required for anaerobic pyruvate induction of pfl operon expression in Escherichia coli

The expression of the pyruvate formate-lyase gene (pfl) is induced by anaerobic growth, and this is increased further by growth in pyruvate. Previous work has shown that anaerobic induction is strongly dependent on the activator FNR and partially dependent on a second transcription factor, ArcA, while pyruvate induction only required FNR. Anaerobic and pyruvate regulation both require the presence of a 5' nontranslated regulatory sequence which spans approximately 500 bp of DNA. A mobility shift assay was developed to identify proteins that bind to this regulatory region. Several binding activities were separated by heparin agarose chromatography, and one of these activities was characterized and shown to be integration host factor (IHF). Mobility shift and DNase I footprinting experiments defined a single IHF binding site in the pfl promoter-regulatory region. With pfl-lacZ fusions, it could be shown that introduction of a himD mutation abolished pyruvate-dependent induction of anaerobic expression in vivo. The same result was observed when the pfl IHF binding site was mutated. In addition, the partial anaerobic induction of expression found in an fnr strain was completely blocked in an fnr himD double mutant and in an fnr IHF binding site double mutant. Taken together, these data suggest that IHF is necessary for both pyruvate induction and the anaerobic induction mediated by ArcA.

Propagation of phage Mu in IHF-deficient Escherichia coli in the absence of the H-NS histone-like protein

Integration host factor (IHF) is known to be required for the expression of early genes and formation of the transpososome of mutator phage Mu. Prophage Mucts62 was stably maintained at 30 degrees C and proliferated effectively after thermal induction at 42 degrees C in an Escherichia coli mutant defective in the histone-like H-NS and IHF proteins. No IHF activity was detected in cells lacking H-NS and IHF; cells could not be transformed with plasmid pCL1920, which is based on the pSC101 replicon whose replication requires IHF. No difference in the superhelical densities of the reporter plasmid was detected in the H-NS, IHF null mutant and parental cells. From these results it is concluded that IHF is not essential for Mu development. These results also suggest that H-NS may function as a silencer for Pe operon expression and that IHF overcomes the inhibitory effect of H-NS.