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PubMed1994

Participation of the bacteriophage Mu A protein and host factors in the initiation of Mu DNA synthesis in vitro.

During bacteriophage Mu transposition, strand transfer is catalyzed in the presence of phage-encoded A and B proteins and Escherichia coli HU protein, attaching Mu ends to target DNA and creating an intermediate in transposition. Bacteriophage Mu A protein, which remains tightly bound to the Mu ends in the native strand-transfer intermediate, blocked initiation of Mu DNA replication by a system of 8 host proteins (DnaB helicase, DnaC protein, DnaG primase, DNA polymerase III holoenzyme, DNA polymerase I, DNA gyrase, DNA ligase, and single-strand binding protein). This 8-protein system had all enzymatic activities to convert the deproteinized intermediate to a cointegrate; however, additional host factor(s) were required to replicate the native intermediate. While replication of the native intermediate absolutely required DnaB helicase, DnaC protein, and DNA polymerase III holoenzyme, the specific requirements were relaxed for the deproteinized intermediate. Other host factors were able to replace these specific factors. These results indicate that Mu A protein, in conjunction with additional host factor(s), acts to promote assembly of specific host replication proteins at the Mu replication fork. This process may alter the stable interaction of Mu A protein with the ends to allow initiation of Mu DNA synthesis.

Bacterial Proteins↗

PubMed2001

Compaction of single DNA molecules induced by binding of integration host factor (IHF).

We studied the interaction between the integration host factor (IHF), a major nucleoid-associated protein in bacteria, and single DNA molecules. Force-extension measurements of lambda DNA and an analysis of the Brownian motion of small beads tethered to a surface by single short DNA molecules, in equilibrium with an IHF solution, indicate that: (i) the DNA-IHF complex retains a random, although more compact, coiled configuration for zero or small values of the tension, (ii) IHF induces DNA compaction by binding to multiple DNA sites with low specificity, and (iii) with increasing tension on the DNA, the elastic properties of bare DNA are recovered. This behavior is consistent with the predictions of a statistical mechanical model describing how proteins bending DNA are driven off by an applied tension on the DNA molecule. Estimates of the amount of bound IHF in DNA-IHF complexes obtained from the model agree very well with independent measurements of this quantity obtained from the analysis of DNA-IHF crosslinking. Our findings support the long-held view that IHF and other histone-like proteins play an important role in shaping the long-scale structure of the bacterial nucleoid.

Bacterial Proteins↗

PubMed1994

The HimA and HimD subunits of integration host factor can specifically bind to DNA as homodimers.

Integration host factor (IHF) is a heterodimeric protein from Escherichia coli which specifically binds to an asymmetric consensus sequence. We have isolated the individual subunits of IHF, HimA and HimD, and show that an active IHF protein can be reconstituted from these subunits. The HimA and HimD polypeptides alone are capable of specifically recognizing the same ihf sequence. The mobilities of the protein-DNA complexes in a gel-retardation assay suggest that the proteins bind as homodimers. The stability of the HimD-DNA complex is approximately 100-fold lower than that of the IHF-DNA complex. The HimA-DNA complex is even less stable and is only observed when a large excess of HimA is used. This instability is possibly due to the inability of HimA to form stable homodimers. By domain swapping between HimA and HimD, we have constructed an IHF fusion protein which has the putative DNA-binding domains of only HimA. This fusion protein forms stable dimers and makes specific protein-DNA complexes with a high efficiency. A comparable fusion protein with only the DNA-binding domains of HimD forms less stable complexes, suggesting that sequence-specific contacts between IHF and the ihf consensus are mainly provided by the HimA subunit.

Amino Acid Sequence↗

PubMed1989

A protein factor which reduces the negative supercoiling requirement in the Mu DNA strand transfer reaction is Escherichia coli integration host factor.

We have examined the supercoiling requirement for the in vitro Mu DNA strand transfer reaction and found that optimal efficiency requires a high level (sigma = -0.06) of donor plasmid superhelicity. At in vivo levels of supercoiling (sigma = -0.025) the reaction does not occur. Using an unreactive donor plasmid with a near physiological level of supercoiling, we identified an Escherichia coli protein factor which has the novel property of reducing the donor plasmid supercoiling requirement for the in vitro Mu DNA strand transfer reaction by 40%. This protein, which we named supercoiling relief factor was purified to near homogeneity and found to be identical to integration host factor (IHF), a protein known to induce site specific bends in DNA. The dramatic reduction in the supercoiling requirement was promoted by about 1.5 IHF dimers/donor substrate molecule. At these low levels of IHF, the HU requirement for the reaction was also reduced; a synergistic effect of the two proteins resulted in a greater than 10-fold stimulation of the reaction under appropriate conditions. Furthermore, at high concentrations of IHF, HU could be completely eliminated from the reaction.

Bacterial Proteins↗

PubMed1993

Bacteriuria, bacterial virulence and host factors in diabetic patients.

The prevalence of bacteriuria as well as bacterial virulence and host factors were studied in 514 diabetic outpatients and 405 nondiabetic controls. The prevalence of bacteriuria was not significantly higher in diabetic women (15/239, 6.3%) than in age-matched nondiabetic women (8/236, 3.4%). In diabetic and nondiabetic men, the prevalence was also similar but lower than in women. E. coli was found in 55% of urine cultures with significant growth from diabetic patients, while in 91% of positive cultures from nondiabetic controls. Most E. coli strains lacked ability of P-fimbriae-mediated adhesion and aerobactin-mediated iron uptake, indicating low bacterial virulence. Long-term metabolic control (HbA1c), prevalence of retinopathy, neuropathy and previous foot ulcers were similar in bacteriuric and nonbacteriuric diabetic patients, matched according to gender, age, and duration of diabetes. Renal function was also similar, though the frequency of proteinuria and elevated blood pressure tended to be higher in the bacteriuric than in the noninfected group. Eight-three percent of the bacteriuric patients reported previous urinary tract infections but only 61% of nonbacteriuric patients (p = 0.07). As compared to non-diabetic women, diabetic women reported significantly more previous urinary tract infections (p < 0.01). In conclusion, the prevalence of bacteriuria in diabetic outpatients was not significantly higher than in non-diabetic outpatients or healthy volunteers. No studied host factor was clearly associated with bacteriuria in diabetic patients, although proteinuria and hypertension tended to be more common. The infecting E. coli strains were of low virulence.

Adult↗

PubMed1998

Viral and host factors in the prediction of response to interferon-alpha therapy in chronic hepatitis C after long-term follow-up.

Acute infection with hepatitis C virus (HCV) develops into a chronic hepatitis in about 50-70% of patients. Treatment of these patients with interferon-alpha (IFN-alpha) results in a sustained long-term response in only 15-20% but causes numerous unwanted side-effects in a higher percentage of patients. The aim of our study was to define host or viral parameters that would allow identification of responders and non-responders to IFN-alpha prior to the onset of treatment. We studied a group of 87 patients suffering from chronic hepatitis C who were treated with IFN-alpha. After long-term follow-up, 18 patients (21%) showed a sustained response to IFN-alpha therapy (normalization of serum transaminases and loss of viral RNA from serum) for up to 7 years after therapy had ceased. By univariate and multivariate analyses, no host factors were found to be predictive of response to therapy. Neither the degree of inflammation or fibrosis in liver biopsy samples obtained before treatment nor immunogenetic factors (major histocompatibility complex II haplotype and tumour necrosis factor-alpha promoter polymorphism) were associated with response to therapy. In contrast, viral parameters showed a strong association with response to therapy. HCV genotype 3 was found significantly more frequently in responders (P = 0.034), and mean HCV RNA concentration was lower in responders (3.1 x 10(4)) than in non-responders (2.5 x 10(5)) (P = 0.01). By multivariate analysis, both HCV genotype and HCV RNA concentration were independent predictors of response to therapy. However, exact prediction of response to treatment for an individual patient was not possible on the basis of pretreatment viral RNA concentration or viral genotype. The best association with response to therapy was found to be clearance of HCV RNA from serum 3 months after the start of treatment (32 of 34 partial and sustained responders vs 0 of 53 non-responders; P = 0.001). In conclusion, determination of pretreatment viral factors, but not host factors, was significantly correlated with treatment response but did not give an accurate prediction for patients, whereas clearance of HCV RNA from serum after 3 months of therapy was predictive of response to therapy.

Adult↗

PubMedDate not supplied

Outcome in elderly injured patients: injury severity versus host factors.

To evaluate the differences between the outcome of elderly patients with severe injuries and that of their contemporaries with a less severe injury, we reviewed 42 severely injured elderly patients and compared them with 76 patients with a femoral neck fracture. We analysed the influence of injury severity and host factors (age, sex and pre-injury medical status) on outcome. The in-hospital mortality rate was 31 per cent in the severely injured patients and 3 per cent in those with a femoral neck fracture. Home was the main discharge destination in the severely injured elderly (34 per cent) and a nursing home in patients with a femoral neck fracture (65 per cent). Functional outcome 1 year after injury was better in the severely injured elderly group. Long-term survival was mainly determined by host factors and not by injury severity. Physicians and policy makers should be careful in predicting the outcome of elderly injured patients merely on the basis of injury severity, because host factors are of greater importance.

Age Factors↗

PubMed2004

Human APOBEC3F is another host factor that blocks human immunodeficiency virus type 1 replication.

Recently, APOBEC3G has been identified as a host factor that blocks retroviral replication. It introduces G to A hypermutations in newly synthesized minus strand viral cDNA at the step of reverse transcription in target cells. Here, we identified the human APOBEC3F protein as another host factor that blocks human immunodeficiency virus type 1 (HIV-1) replication. Similar to APOBEC3G, APOBEC3F also induced G to A hypermutations in HIV genomic DNA, and the viral Vif protein counteracted its activity. Thus, APOBEC family members might have evolved as a general defense mechanism of the body against retroviruses, retrotransposons, and other mobile genetic elements.

APOBEC-1 Deaminase↗

PubMed1984

In vitro regulation of phage lambda cII gene expression by Escherichia coli integration host factor.

The effect of Escherichia coli integration host factor (IHF) on phage lambda gene expression has been examined in a simplified DNA-directed in vitro system that measures the formation of the first dipeptide of the gene product. Plasmid pKC30cII, which contains the phage lambda genes N, cII and O, under control of the PL promoter, was used as template to study the expression of the first dipeptide of the gene products--i.e., fMet-Asp for N protein, fMet-Val for cII, and fMet-Thr for O. Purified IHF stimulates the DNA-directed synthesis of fMet-Val (cII) and fMet-Thr (O) 2-3-fold but has no effect on the synthesis of fMet-Asp (N). In this in vitro system, the stimulation by IHF of cII and O gene expression is at the level of transcription. Phage lambda repressor completely inhibits dipeptide synthesis in the presence or absence of IHF. The results are consistent with a role of IHF as a transcription antiterminator, perhaps functioning at or near the tR1 site preceding the cII gene.

Bacteriophage lambda↗

PubMed1997

Isolation and characterization of the integration host factor genes of Pasteurella haemolytica.

Using a bacteriophage lambda complementation system in Escherichia coli, we cloned genes encoding subunits of the heterodimeric DNA binding/bending protein, integration host factor, from the bovine pathogen, Pasteurella haemolytica. Complementation of ihfA and ihfB mutations in E. coli demonstrated that the P. haemolytica gene products form functional heterologous heterodimers. The ihfA and ihfB genes encode polypeptides predicted to be 99 and 93 amino acids long, respectively, and are very similar to integration host factor subunits from other Gram-negative bacteria, although phylogenetic analysis indicated that the P. haemolytica sequences are distantly related to those from other bacteria. Most significant amino acid differences were restricted to the amino-terminal domains of the predicted peptides.

Bacterial Proteins↗

PubMed1995

yst gene expression in Yersinia enterocolitica is positively regulated by a chromosomal region that is highly homologous to Escherichia coli host factor 1 gene (hfq).

Yersinia enterocolitica produces heat-stable enterotoxin (Y-ST) as one of its virulence factors. The yst gene, however, frequently and spontaneously becomes inactive (silent) during storage, which is accompanied by concurrent changes in some biological properties such as colony morphology, growth rate, carbon fermentation and ornithine decarboxylase activity. Northern blot analysis revealed that the level of mRNA for yst was repressed. To investigate the regulatory region, we transformed a yst-silent strain with a chromosomal gene library of Y-ST producing an isogenic counterpart. Out of 3604 clones, one clone resumed the Y-ST production and concurrently other biological properties. An open reading frame in this clone was designated as yrp, yersinia regulator for pleiotropic phenotype. Deduced from the nucleotide sequence, Yrp was a small protein of I01 amino acids with no similarity with any regulatory factor described, but showed high homology with an Escherichia coli host factor 1 required for Q beta-replicase, and with an Azorhizobium caulinodans NrfA required for the expression of nifA. The yrp gene mutation caused decreased negative supercoiling of plasmids, as did hfq. The yrp gene could similarly complement Y-ST production in two other silent strains of Y. enterocolitica. In all three silent strains examined, we found various mutations in the yrp region.

Amino Acid Sequence↗

PubMed1988

Gamma delta transposase and integration host factor bind cooperatively at both ends of gamma delta.

gamma delta, a prokaryotic transposon, encodes a transposase that is essential for its transposition. We show here, by DNase I protection experiments, that purified gamma delta transposase binds at the transposon's inverted repeats (IRs). Immediately adjacent to each transposase binding site (and within gamma delta DNA) we have identified a binding site for an additional protein factor, the Escherichia coli-encoded integration host factor (IHF). The binding of transposase and IHF to these adjacent sites is mutually cooperative. An IHF binding-site was also found in the original target DNA, just outside one of the ends of gamma delta. The affinity of IHF for this flanking site is reduced by transposase. These results demonstrate that gamma delta transposase binds at the IRs of gamma delta, and suggest that IHF may be involved in forming a transposase-DNA complex and/or influencing the target site selection during the transposition of gamma delta.

Adenosine Triphosphate↗

PubMed1992

Stabilization of bacteriophage Mu repressor-operator complexes by the Escherichia coli integration host factor protein.

All of the previously described effects of integration host factor (IHF) on bacteriophage Mu development have supported the view that IHF favours transposition-replication over the alternative state of lysogenic phage growth. In this report we show that, consistent with a model in which Mu repressor binding to its operators requires a particular topology of the operator DNA, IHF stimulates repressor binding to the O1 and O2 operators and enhances Mu repression. IHF would thus be one of the keys, besides supercoiling and the H-NS protein, that lock the operator region into the appropriate topological conformation for high-affinity binding not only of the phage transposase but also of the phage repressor.

Bacterial Proteins↗

PubMed1990

Integration host factor stimulates the phage lambda pL promoter.

Escherichia coli integration host factor (IHF) is a small dimeric protein that binds to a specific DNA consensus sequence and produces DNA bending. Transcription from the bacteriophage lambda pL promoter is stimulated three- to fourfold by IHF both in vivo and in vitro. IHF binds with high-affinity to two tandem sites located just upstream from the pL promoter and enhances the formation of RNA polymerase-promoter closed complexes. The rate of isomerization to open complex is not influenced by IHF. IHF may stimulate recognition of pL by one or more of several mechanisms: (1) by bending DNA; (2) by making protein-protein contacts with RNA polymerase; or (3) by occluding a competing promoter upstream from pL.

Bacterial Proteins↗

PubMed2003

Integration host factor: putting a twist on protein-DNA recognition.

Integration host factor (IHF) is a DNA-bending protein that recognizes its cognate sites through indirect readout. Previous studies have shown that binding of wild-type (WT)-IHF is disrupted by a T to A mutation at the center position of a conserved TTR motif in its binding site, and that substitution of betaGlu44 with Ala prevented IHF from discriminating between A and T at this position. We have determined the crystal structures and relative binding affinities for all combinations of WT-IHF and IHF-betaGlu44Ala bound to the WT and mutant DNAs. Comparison of these structures reveals that DNA twist plays a major role in DNA recognition by IHF, and that this geometric parameter is dependent on the dinucleotide step and not on the bound IHF variant.

Amino Acid Substitution↗

PubMed1993

Function of IHF in lambda DNA packaging. I. Identification of the strong binding site for integration host factor and the locus for intrinsic bending in cosB.

Integration host factor (IHF) plays an accessory role in lambda DNA packaging. IHF affects the interaction of the lambda DNA packaging protein, terminase, with cos, the site on lambda DNA at which terminase binds and introduces staggered nicks to generate cohesive ends of mature lambda chromosomes. cos includes cosB, the terminase binding site and cosN, the adjacent nicking site. cosB includes multiple binding sites for gpNu1, the small subunit of terminase, and an IHF binding site, I1. I1 contains two overlapping sequences, called I1A and I1B, that closely match the consensus sequence for IHF binding sites. The I1A sequence was determined to be the site of IHF binding by hydroxyl radical footprinting experiments. Comparison of the pattern of IHF-induced enhancements and diminishments at I1 with published patterns for IHF binding sites at the lambda attachment site identifies I1A as the IHF binding site at I1. The conclusion that I1A is the IHF binding site was confirmed by studies with DNA mutant in I1A. The I1A- mutation, consisting of three adjacent base-pair changes in I1A, abolished IHF binding. In contrast to the I1A- mutation, a mutation in I1B, also consisting of three adjacent base-pair changes, caused a reduction in the affinity of IHF for I1A, and caused a reduction in the magnitude of the net intrinsic bending of cos lambda.

Bacterial Proteins↗

PubMed2002

Host factors limiting monogenean infections: a case study.

Comprehensive field data on polystomatid monogeneans record low prevalence and intensity of infection and suggest that worm burdens in this group are strongly regulated: thus, in the majority of Polystoma species infecting anuran amphibians mean abundance is typically less than one parasite/host. There is circumstantial evidence that the dominant control is attributable to host factors which over-ride variations in transmission success. This review provides a brief summary of information on Pseudodiplorchis americanus, a parasite of the desert toad, Scaphiopus couchii, and then focuses in detail on the spectrum of factors regulating infrapopulations of Protopolystoma xenopodis, a parasite of the aquatic Xenopus laevis. Infection levels of adult worms and their contribution to transmission are regulated by external environmental factors (especially temperature), by host factors (including behaviour and population density), and by a range of parasite factors including intra- and inter-specific competitive interactions and variations in intrinsic characters, especially survivorship and reproductive output. In addition to these factors whose primary effect is to modulate transmission rates, there is a major attrition in parasite numbers between invasion and maturity (3 months post-infection). Long-term laboratory experiments on the Xenopus laevis/Protopolystoma xenopodis interaction demonstrate a powerful acquired immune response. Primary infection is characterised by a high prevalence of established adult worms but the success of subsequent challenge infection is greatly reduced, leading to low prevalence and extended pre-patent period. In the small proportion of hosts supporting a second infection of adult parasites, surviving burdens are small (one to two worms/host) and show reduced egg production. These results provide an explanation for the low burdens encountered in field studies: a majority of adult X. laevis in natural populations are likely to exhibit strong, relatively long-term, post-infection immunity after the loss of a previous infection.

Amphibians↗

PubMed2001

Evaluation of the role of heterogeneous nuclear ribonucleoprotein A1 as a host factor in murine coronavirus discontinuous transcription and genome replication.

Viruses with RNA genomes often capture and redirect host cell components to assist in mechanisms particular to RNA-dependent RNA synthesis. The nidoviruses are an order of positive-stranded RNA viruses, comprising coronaviruses and arteriviruses, that employ a unique strategy of discontinuous transcription, producing a series of subgenomic mRNAs linking a 5' leader to distal portions of the genome. For the prototype coronavirus mouse hepatitis virus (MHV), heterogeneous nuclear ribonucleoprotein (hnRNP) A1 has been shown to be able to bind in vitro to the negative strand of the intergenic sequence, a cis-acting element found in the leader RNA and preceding each downstream ORF in the genome. hnRNP A1 thus has been proposed as a host factor in MHV transcription. To test this hypothesis genetically, we initially constructed MHV mutants with a very high-affinity hnRNP A1 binding site inserted in place of, or adjacent to, an intergenic sequence in the MHV genome. This inserted hnRNP A1 binding site was not able to functionally replace, or enhance transcription from, the intergenic sequence. This finding led us to test more directly the role of hnRNP A1 by analysis of MHV replication and RNA synthesis in a murine cell line that does not express this protein. The cellular absence of hnRNP A1 had no detectable effect on the production of infectious virus, the synthesis of genomic RNA, or the quantity or quality of subgenomic mRNAs. These results strongly suggest that hnRNP A1 is not a required host factor for MHV discontinuous transcription or genome replication.

Animals↗