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PubMed1976

Site-specific interaction of Qbeta host factor and ribosomal protein S1 with Qbeta and R17 bacteriophage RNAs.

We have studied the interaction of the host factor (HF) required for bacteriophage Qbeta RNA replication and of ribosomal protein S1, a subunit of Qbeta replicase, with Qbeta and R17 RNA. Both proteins bind to both Qbeta and R17 RNA; HF has a higher affinity than S1 for these phages RNAs. HF binds to a single site in R17 RNA located in the replicase cistron, and to two sites of Qbeta RNA, one of which is located approximately 60 nucleotides from the 6' end of Qbeta RNA. The three HF binding sites all have portions rich in adenylate residues; all are bound by HF when contained in oligonucleotides which are predicted to exist only in single-stranded form. S1 selects a single site in Qbeta RNA, also near the 6' end, but binds to a large number of sites in R17 RNA. These results suggest that HF and possibly S1, through their interaction with the 3'-terminal region of Qbeta RNA, are directly involved in the recognition of the 6' end of Qbeta RNA by Qbeta replicase. Under conditions where specific protein-R1M RNA complexes are formed, we have also tested host factor and S1 for cistron-specific interference with ribosome binding to R17 RNA. Although S1 and HF lower the efficiency of initiation complex formation as described previously, we detect no discrimination against any particular cistron. We therefore conclude that translational interference exhibited by the two proteins probably reflects simply their high affinity for RNA and certain defined polynucleotides.

Base Sequence↗

PubMed1997

Prevalence of melanocytic nevi and freckles in young Israeli males. Correlation with melanoma incidence in Jewish migrants: demographic and host factors.

The role of host and environmental factors in the pathogenesis of multiple melanocytic nevi, atypical nevi, and freckles was studied in 1989 in a random sample of 3,040 Israeli males aged 17 years. Multiple melanocytic nevi were significantly associated with family history of melanoma or multiple melanocytic nevi (odds ratio (OR) = 15.0), fair or lightly pigmented skin color (OR = 2.7 and 2.3, respectively), and affiliation to the high or heterogenous melanoma risk group, determined by the incidence rates of melanoma in Jewish migrants from corresponding origin (OR = 3.1 and 2.1, respectively). An environment-related effect may account for the increased multiple melanocytic nevi risk among second- (OR = 8.2) compared with first-generation, native-born recruits (OR = 3.0) from the high melanoma risk group whose families had been living in Israel the longest. Atypical nevi were associated with fair (OR = 6.1) and lightly pigmented (OR = 3.5) skin color, high and moderate sunburn susceptibility (OR = 4.7 and 2.5, respectively), and family history of melanoma or multiple melanocytic nevi (OR = 4.7). Freckles were significantly associated with sun-sensitive phenotype, family history of melanoma or multiple melanocytic nevi (OR = 1.5). Conservative (OR = 1.9) or nonreligious status (OR = 1.9), and high (OR = 2.4) or heterogenous melanoma risk groups (OR = 1.8). These findings indicate that environmental factors may modify the occurrence of multiple melanocytic nevi and freckles in genetically susceptible ethnic groups.

Adolescent↗

PubMed1992

Integration host factor activates the Ner-repressed early promoter of transposable Mu-like phage D108.

The lytic-lysogenic switch in transposable, Mu-like bacteriophage D108 is governed by two divergent and slightly overlapping transcription units originating from the Pe and Pc promoters. DNase I footprinting and in vivo mutational analysis suggest that lysogeny is maintained by c-repressor occupancy of the O2 operator, which precludes RNA polymerase from binding to Pe. Lytic development is controlled by the Ner repressor, which binds to a site symmetrically situated between the converging promoters and, in the absence of other factors, prevents RNA polymerase from binding to either Pc or Pe. DNase I protection and potassium permanganate hypersensitivity in the presence of integration host factor (IHF), which binds and alters the DNA structure upstream of Pe, revealed that RNA polymerase was able to bind Pe irrespective of the Ner.DNA-bound complex, and partially unwind the Pe "-10 region." Ner repression of Pe transcription in vitro was significantly more effective in the absence of IHF. Using a cloned D108 early region-lacZ fusion in IHF-deficient and -proficient backgrounds, we also demonstrate this host factor's affect on ner-repressed Pe in vivo, and generate a system for isolating mutants in the regulatory genes and sites controlling this genetic switch. D108 lytic growth is proposed to occur through IHF-mediated activation of the phage Ner-repressed early operon.

Amino Acid Sequence↗

PubMed1998

Integration host factor positively regulates cycJIH transcription.

We report the identification of integration host factor (IHF) as an additional element involved in the regulation of the cysJIH promoter of Salmonella typhimurium and Escherichia coli. An IHF-binding site was located in the regulatory region of the cysJIH promoter by using two methods, protection against DNase I digestion and hydroxyl radical cleavage. The positive influence of IHF on in vitro run-off transcription from the cysJIH promoter is shown. The in vivo observations suggest that IHF is necessary for full expression of cysJIH in stationary phase but not during exponential growth.

Bacterial Proteins↗

PubMed2004

Single-chain integration host factors as probes for high-precision nucleoprotein complex formation.

Integration host factor (IHF) is a heterodimeric, site-specific DNA-binding and DNA-bending protein from Escherichia coli. It is involved in high-precision DNA transactions where it serves as a key architectural component of specialized nucleoprotein structures (snups). We described recently a novel approach for protein engineering using a single polypeptide chain IHF, termed scIHF2, as a first example. ScIHF2 is made up of the alpha subunit of IHF which was inserted into the beta subunit at peptide bond Q39/G40 via two short linkers. The monomer behaves very similarly to the heterodimeric, parental IHF in biochemical and functional assays. Here, we describe an extension of this approach in which we shortened either one or both linkers by one amino acid, thereby generating three new variants termed scIHF1, 3, and 4. These variants exhibit distinct DNA-binding properties, different phenotypes in site-specific integrative and excisive recombination by phage lambda integrase in vitro, as well as in pSC101 replication assays in a DeltaIHF E. coli host. We also introduced a K45E substitution within the alpha domain of scIHF3 and based on electrophoretic mobility shift assays (EMSAs), argue that it significantly changes the DNA trajectory within the protein-DNA complex. Our results indicate that IHF's pleiotropic roles in DNA transactions inside E. coli require different types of high-precision DNA architectural activities. The scIHF variants described here will help to explore further how flexible these requirements are.

Amino Acid Sequence↗

PubMed1990

Prognosis in laryngeal carcinoma: host factors.

A personal series of 1171 patients with a laryngeal tumour seen in a 27-year period from 1962 to 1988 is reported. Of these patients, 763 were previously untreated and had a histologically proved squamous cell carcinoma. The interaction between the host factors (age, sex and general condition) and other tumour factors, and the effect of the host factors on survival were analysed. The maximum age incidence was the same in the two sexes but performance status (general condition) declined with increasing age. There was no relation between age and site or histological grade of the tumour. However, the incidence of T3-T4 tumours increased up to the seventh decade and then declined again. Age was not a significant predictor of survival when allowance was made for patients who were untreated, or who had died of intercurrent disease or a second primary tumour. Men were more likely to have a glottic tumour: these tumours presented at an earlier stage and were likely to be well differentiated, mainly because glottic T1 carcinoma is almost exclusively a male disease. When individual sites are examined the crude survival for supraglottic tumours in women is better than that in men because of a higher death rate from other diseases and other tumours in men. Sex had no other effect on survival. Good performance status was associated with lower T-stage but not quite significantly so. It was not associated with any other tumour parameters. Performance status significantly affected survival of treated patients, probably indicating that general condition affects the patient's ability to resist his tumour.

Adult↗

PubMed1995

Binding of Escherichia coli integration host factor (IHF) to the origin segment of p15A plasmid.

The integration host factor (IHF) is a sequence-specific, histone-like, multi-functional DNA-binding and -bending protein of Escherichia coli. Characterization and functional analysis of this protein has been carried out mainly in bacteriophage lambda and other mobile genetic elements. In this paper we report data concerning the binding of IHF protein to the plasmid orip15A region. IHF binds to the single site of the DNA fragment containing the orip15A, as shown by the gel mobility shift assays and footprinting experiment. On the basis of the ihf consensus sequences published, we have been able to identify one sequence of putative ihf site into the orip15A sequence with two mismatches in relation to the consensus sequence of Kur et al., 1989, Gene 81, 1-15. One ihf binding site was also found in the oriColE1 region sequence with three mismatches in relation to this consensus sequence.

Bacterial Proteins↗

PubMed1997

Integration host factor is a transcriptional cofactor of pilE in Neisseria gonorrhoeae.

Integration host factor (IHF) is a small, heterodimeric DNA-binding protein with pleiotropic function. IHF was purified to apparent homogeneity from Neisseria gonorrhoeae. Gel-retardation assays demonstrated binding of IHF to the pilE promoter region. The IHF-binding site was identified by DNase I protection assays and mapped proximal to three previously defined pilE promoters. Removal of the putative IHF-binding domain from pilE promoter DNA negated retardation of the DNA fragment when assessed by gel-shift analysis. Kleinschmidt electron microscopy showed pronounced kinking of pilE promoter DNA following incubation with IHF. Isogenic N. gonorrhoeae strains were constructed that contained either a wild-type pilE locus or a deleted pilE locus where the IHF-binding domain was removed. Primer-extension analysis and Northern blotting of total gonococcal RNA showed that in the absence of IHF binding at the pilE promoter, transcription was reduced 10-fold. Together, these data indicate that IHF is a transcriptional co-activator of pilE.

Bacterial Proteins↗

PubMed1995

The specific binding of Escherichia coli integration host factor involves both major and minor grooves of DNA.

The integration host factor (IHF) of Escherichia coli is a small, sequence-specific DNA-binding protein. The specific and nonspecific binding constants of IHF were estimated by gel-retardation assays. The equilibrium association constant of IHF for the H' site in lambda attP is 6.8 x 10(8) M-1 (Kd = 1.5 nM), and the nonspecific binding constant is 5.8 x 10(5) M-1 (Kd = 1.7 microM), giving a selectivity of approximately 1,000-fold for a specific site over random sequences. To study the molecular determinants specifying IHF binding, we used a series of 41 oligonucleotides containing adenine analogues that modified the surfaces of the major and minor grooves of the DNA. Many of the analogue substitutions within the previously defined consensus region caused decreased binding. Replacement with various analogues outside the consensus domain had little effect. Quantifying the binding constants for those sites with reduced affinities indicated an interaction with the minor groove within the consensus sequence. The binding constants of sites with 2-aminopurine and an inosine substitution within the same region suggest that IHF may also interact with the major groove. Thus, the specific interaction of IHF with its H' site likely involves interactions with both the minor and major grooves of the DNA.

2-Aminopurine↗

PubMed1994

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.

Bacterial Proteins↗

PubMed2000

Host factors that influence the behaviour of bacterial pathogens in vivo.

Interest is increasing in how bacteria behave and produce virulence determinants within the infected host. There are three aspects of this process; observations on the bacteria themselves, recognition of host factors that affect them and investigation of metabolic interactions between the two. The first aspect is relatively easy to investigate and attracts much interest. The second and third are difficult to work on and hence understudied. The review aims to stimulate interest in them by indicating methods of investigation and describing some successful studies. After discussing host factors that determine growth in vivo consideration is given to factors that influence the production of the determinants of mucosal colonization, penetration, interference with host defence and damage to the host. The final section deals with the influence of host-derived cytidine 5'-monophospho-N-acetyl neuraminic acid and lactate on the pathogenicity of gonococci, meningococci and Haemophilus influenzae.

Cytidine Monophosphate N-Acetylneuraminic Acid↗

PubMed1989

Integration host factor (IHF) stimulates binding of the gpNu1 subunit of lambda terminase to cos DNA.

The lambda terminase enzyme binds to the cohesive end sites (cos) of multimeric replicating lambda DNA and introduces staggered nicks to regenerate the 12 bp single-stranded cohesive ends of the mature phage genome. In vitro this endonucleolytic cleavage requires spermidine, magnesium ions, ATP and a host factor. One of the E. coli proteins which can fulfill this latter requirement is Integration Host Factor (IHF). IHF and the gpNu1 subunit of terminase can bind simultaneously to their own specific binding sites at cos. DNase I footprinting experiments suggest that IHF may promote gpNu1 binding. Although no specific gpNu1 binding to the left side of cos can be detected, this DNA segment does play a specific role since a cos fragment that does not include the left side or whose left side is replaced by non-cos sequences, is unable to bind gpNu1 unless either spermidine or IHF is present. Binding studies on the right side of cos using individual or combinations of gpNu1 binding sites I, II and III indicate that binding at sites I and II is not optimal unless site III is present.

Attachment Sites, Microbiological↗

PubMed1977

Host factor for coliphage Q beta RNA replication: presence in procaryotes and association with the 30S ribosomal subunit in Escherichia coli.

The Host Factor required for in vitro coliphage Q beta RNA replication, a heat-stable RNA binding protein present in uninfected Escherichia coli, has been detected by both immunological and functional tests in Acinetobacter calcoaceticus, Klebsiella pneumoniae, Pseudomonas aeruginosa and Pseudomonas putida. It was not detectable by these criteria in Bacillus stearothermophilus, Bacillus subtilis, Caulobacter crescentus, Micrococcus lysodeikticus, Rhodopseudomonas capsulata or Saccharomyces cerevisiae. In Escherichia coli the Host Factor protein has been shown to be associated with ribosomes. It is demonstrated here that this association is specific for the 30S ribosomal subunit.

Acinetobacter↗

PubMed1984

Host factors in metastasis: immunostimulatory action of retinoids.

Many host factors contribute to the death of cells shed from cancers and with many immunogenic tumors immune control is decisive in determining the incidence of metastasis. Although an aromatic analogue of retinoic acid did not affect the growth of nonimmunogenic carcinomas or sarcomas it slowed the tumor growth of immunogenic cancers but only if they were grown in immunocompetent hosts. A working hypothesis is that retinoids enhance the magnitude of a T-cell dependant host response to the tumor and it is this that causes the inhibition of growth. If the animals are rendered incapable of evoking a T-cell response then retinoids are unable to influence tumor growth.

Animals↗

PubMed1991

Integration host factor of Escherichia coli reverses the inhibition of R6K plasmid replication by pi initiator protein.

Integration host factor (IHF) protein is the only host-encoded protein known to bind and to affect replication of the gamma origin of Escherichia coli plasmid R6K. We examined the ability of R6K origins to replicate in cells lacking either of the two subunits of IHF. As shown previously, the gamma origin cannot replicate in IHF-deficient cells. However, this inability to replicate was relieved under the following conditions: underproduction of the wild-type pi replication protein of R6K or production of normal levels of mutant pi proteins which exhibit relaxed replication control. The copy number of plasmids containing the primary R6K origins (alpha and beta) is substantially reduced in IHF-deficient bacteria. Furthermore, replication of these plasmids is completely inhibited if the IHF-deficient strains contain a helper plasmid producing additional wild-type pi protein. IHF protein has previously been shown to bind to two sites within the gamma origin. These sites flank a central repeat segment which binds pi protein. We propose a model in which IHF binding to its sites reduces the replication inhibitor activity of pi protein at all three R6K origins.

Bacterial Proteins↗

PubMed1994

Mutants of Escherichia coli integration host factor: DNA-binding and recombination properties.

Integration host factor (IHF) is a protein encoded by Escherichia coli, which was first discovered as a requirement for bacteriophage lambda site-specific recombination. In this study, we characterized mutants of IHF for their ability to bind to various IHF binding sites in vivo and to promote recombination of lambda in vitro. DNA-binding in vivo was monitored using the challenge-phage system. If IHF binds to its DNA-binding site that has been placed into the P(ant) region of bacteriophage P22, it acts as a repressor of the ant (antirepressor) gene, leading to the formation of lysogens of Salmonella typhimurium. If IHF cannot bind to its site, antirepressor is made leading to cell lysis. Challenge phages containing chimeras of different lambda IHF binding sites were constructed to test the contribution to the binding of a dA+dT-rich region, found in the sequence of the H' site but not in the H' site. In one case, the binding of mutant IHF proteins was enhanced by the presence of the dA+dT-rich region, indicating that IHF may be affected by neighboring bases and local DNA structure when it binds to its site. A subset of the mutant proteins retained the ability to form a looped attL complex in vivo, representing part of a higher-order protein-DNA complex (the 'intasome'). Additionally, this same subset of proteins also promoted the integration and excision of bacteriophage lambda in vitro. Thus, these mutant proteins not only retain their DNA-bending ability but make any protein-protein contacts necessary to form a recombination-proficient intasome.

Bacterial Proteins↗

PubMed1990

Integration host factor bends the DNA in the Escherichia coli ilvBN promoter region.

Integration host factor (IHF) of Escherichia coli is a site-specific DNA binding protein involved in a wide variety of physiological activities in E. coli and its phages and plasmids. We have previously found that IHF binds specifically to a site just upstream from the ilvBN promoter and strongly decreases transcriptional pausing and termination in the ilvBN leader. In this work we show by gel retardation analysis that IHF binds to bent ilvBN DNA and greatly enhances the bend located within or near the IHF binding site. These data are consistent with the hypothesis that IHF-induced alterations in the conformation of ilvBN promoter-leader DNA is a key to its antitermination activity in this system.

Bacterial Proteins↗

PubMed1995

In vivo interaction of the Escherichia coli integration host factor with its specific binding sites.

The histone-like protein integration host factor (IHF) of Escherichia coli binds to specific binding sites on the chromosome or on mobile genetic elements, and is involved in many cellular processes. We have analyzed the interaction of IHF with five different binding sites in vitro and in vivo using UV laser footprinting, a technique that probes the immediate environment and conformation of a segment of DNA. Using this generally applicable technique we can directly compare the binding modes and interaction strengths of a DNA binding protein in its physiological environment within the cell to measurements performed in vitro. We conclude that the interactions between IHF and its specific binding sites are identical in vitro and in vivo. The footprinting signal is consistent with the model of IHF-binding to DNA proposed by Yang and Nash (1989). The occupancy of binding sites varies with the concentration of IHF in the cell and allows to estimate the concentration of free IHF protein in the cell.

Amino Acid Sequence↗