SEARCH · PubMed Health

Results for “host factor”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 145 records · Page 8Linked to original sources

PubMed1994

Symmetry and asymmetry in the function of Escherichia coli integration host factor: implications for target identification by DNA-binding proteins.

BACKGROUND: Escherichia coli integration host factor (IHF) is a DNA-binding protein that participates in a wide variety of biochemical functions. In many of its activities, IHF appears to act as an architectural element, dramatically distorting the conformation of bound DNA. IHF is a dimer of non-identical subunits, each about 90 amino acids long. One dimer interacts specifically with a 30 base pair (bp) target, but well-conserved sequences are found in only half of this binding site. Thus, the IHF-DNA system has long been viewed as a paradigm of asymmetry in a protein-DNA interaction. RESULTS: We have isolated the subunits of IHF and show that either subunit is capable of specifically recognizing natural IHF-binding sites and supporting lambda site-specific recombination in vitro. Mobility shift and footprinting data indicate that the isolated subunits interact with DNA as homodimers. We also describe the design of symmetric duplexes to which heterodimeric and homodimeric IHFs can bind by recognizing specific sequences. CONCLUSIONS: Our in vitro manipulation of the IHF system demonstrates that binding and bending of target DNA can be accomplished symmetrically. The prevalence of asymmetry found for this system in nature suggests that additional selective forces may operate. We suggest that these follow from the disparity between the size of the DNA that IHF protects (30 bp) and the length of DNA that the protein can initially contact (10 bp). This disparity implies that an IHF target is recognized in stages and may dispose the part of the protein-DNA system used for initial recognition to evolve distinctly from the remainder of the interaction surface. We suggest that a limitation in the length of DNA that can be initially contacted is a general property of DNA-binding proteins. In that case, many proteins can be expected to identify complex targets by step-wise, rather than simultaneous, contact between sequence elements and DNA-binding domains.

Bacterial Proteins↗

PubMed2022

Genome-wide bidirectional CRISPR screens identify mucins as host factors modulating SARS-CoV-2 infection.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes a range of symptoms in infected individuals, from mild respiratory illness to acute respiratory distress syndrome. A systematic understanding of host factors influencing viral infection is critical to elucidate SARS-CoV-2-host interactions and the progression of Coronavirus disease 2019 (COVID-19). Here, we conducted genome-wide CRISPR knockout and activation screens in human lung epithelial cells with endogenous expression of the SARS-CoV-2 entry factors ACE2 and TMPRSS2. We uncovered proviral and antiviral factors across highly interconnected host pathways, including clathrin transport, inflammatory signaling, cell-cycle regulation, and transcriptional and epigenetic regulation. We further identified mucins, a family of high molecular weight glycoproteins, as a prominent viral restriction network that inhibits SARS-CoV-2 infection in vitro and in murine models. These mucins also inhibit infection of diverse respiratory viruses. This functional landscape of SARS-CoV-2 host factors provides a physiologically relevant starting point for new host-directed therapeutics and highlights airway mucins as a host defense mechanism.

Animals↗

PubMed1985

Implications for risk assessment of host factors causing large pharmacokinetic variations.

Normal human subjects vary widely in their capacity to eliminate many drugs and environmental chemicals. These variations range in magnitude from fourfold to fortyfold depending on the drug and the population studied. Pharmacogenetics deals with only one of many host factors responsible for these large pharmacokinetic differences. Age, sex, diet and exposure to other drugs and chemicals, including oral contraceptives, ethanol and cigarette smoking, can alter the genetically determined rate at which a particular subject eliminates drugs and environmental chemicals. These elimination rates, therefore, are dynamic and change even in the same subject with time and condition. Regulatory legislation has only recently begun to recognize this very broad spectrum of human susceptibility and the existence of multiple special subgroups of particularly sensitive subjects. In setting standards for environmental chemicals, EPA and NIOSH have attempted to protect the most sensitive humans and should be encouraged to continue this policy. For some drugs and environmental chemicals, the commonly used safety factor of 100 may be too low; for these chemicals large, interindividual pharmacokinetic variations produced by pharmacogenetic and other host factors may make a safety factor of 400 or 500 more adequate.

Environmental Pollutants↗

PubMed1993

Repression of the traM gene of plasmid R100 by its own product and integration host factor at one of the two promoters.

Plasmid R100 codes for the traM gene, which is required for DNA transfer and whose product has been shown to bind to the four sites, called sbmA to sbmD, upstream of traM. To determine whether the TraM protein regulates the expression of traM, we constructed the plasmids carrying various portions of the region upstream of the initiation codon ATG for traM, which was fused with lacZ in frame, and introduced them into the cells, which did or did not harbor another compatible plasmid carrying traM. We then assayed the beta-galactosidase (LacZ) activity to monitor the expression of the fusion genes and analyzed the traM-specific transcripts made in the cells. Two promoters for traM were identified and designated pM1 and pM2. Promoter pM2 lies upstream of pM1 and overlaps the sbmC-sbmD region. Promoter pM1 is constitutively expressed, while pM2 is much stronger but is repressed almost completely by the TraM protein and partially by integration host factor, whose binding site is near pM2. The traM gene is likely to be expressed from pM2 when the TraM protein is at low levels after dilution in the donor cell during cell growth or before its expression in the recipient cell which has just received R100 by conjugation. The expression from pM2 could maintain the amount of the TraM protein at a constant level needed to initiate DNA transfer at any time. Integration host factor, which can partially repress the traM gene, may play a role in forming an active complex with the TraM protein at the sbm region to facilitate DNA transfer.

Amino Acid Sequence↗

PubMed1997

The mouse homologue of the human transcription factor C1 (host cell factor). Conservation of forms and function.

The assembly of the herpes simplex virus (HSV) alpha/IE gene enhancer complex is determined by the interactions of the Oct-1 POU domain protein, the viral alphaTIF (alpha-trans-induction factor, VP16, ICP25, VMW65), and the C1 factor (host cell factor, HCF). A unique transcription factor, C1 consists of a family of polypeptides derived from a common precursor by site-specific proteolytic processing. To analyze the role of this factor in the determination of HSV lytic-latent infection, cDNAs and genomic DNAs encoding the mouse homologue have been isolated. This factor is nearly identical to the human protein, contains multiple consensus proteolytic processing sites, and functions efficiently in the assembly of a specific HSV enhancer complex. Interestingly, the differential expression of the C1 factors in both human and mouse tissues may be important for the determination of HSV tissue tropism in these two organisms.

Amino Acid Sequence↗

PubMed1990

Integration host factor affects expression of two genes at the conjugal transfer origin of plasmid R100.

Integration host factor (IHF) binds to two sites near the origin of transfer of the conjugative antibiotic resistance plasmid, R100. DNase I footprinting shows that one site is immediately adjacent to oriT and the gene X promoter, and another is adjacent to the traM promoter. A third site, known only from retardation gels, is near the traJ promoter. The relative promoter activities of genes X, traJ and traM are reduced in himA mutants (IHF-), as measured by chloramphenicol-resistance assays. Transcript analyses by Northern blots showed a reduction in size of the principal gene X and traJ transcripts in the absence of IHF.

Bacterial Proteins↗

PubMed1999

Replacement of integration host factor protein-induced DNA bending by flexible regions of DNA.

The Escherichia coli integration host factor (IHF) protein is required for site-specific recombination of bacteriophage lambda DNA. Previously, we had shown that alternative modules of static DNA curvature could partially replace IHF in recombination. Now we use regions of single-stranded DNA as a flexible tether to address whether the function of IHF in recombination is simply to reduce persistence length. Although we find that these modules clearly enhance recombination in the absence of IHF, they are not perfect replacements. In addition, evidence is presented that the efficacy of a flexibility swap is specific to a particular IHF site. This may indicate that additional functions beyond simple deformation of DNA are required of IHF. During the course of these experiments we discovered that these flexible sequences are still specific sites for IHF binding and function.

Bacterial Proteins↗

PubMed1990

Intrinsic bends and integration host factor binding at F plasmid oriT.

F plasmid oriT DNA extending from the F kilobase coordinate 66.7 (base pair [bp] 1 on the oriT sequence map) rightward to bp 527 was analyzed for intrinsic bends (by permutation assays) and for binding of integration host factor (IHF) (by gel retardation and DNase footprinting). Intrinsic bending of the 527-bp fragment (bend center approximately at bp 240) was represented as a composite of at least two components located near bp 170 and near bp 260. IHF bound primarily to a site extending from bp 165 to 195 and with lower affinity to a site extending from bp 287 to 319. The intrinsic curvature and sequences to which IHF binds (IHF is known to bend DNA) may play a structural role in oriT function.

Bacterial Proteins↗

PubMedDate not supplied

Host factors involved in the growth of microvirid phage alpha 3.

Host factors involed in the growth of microvirid phage alpha3 were determined using various replication mutants of Escherichia coli. The viral multiplication was dependent on functional products of dnaE, dnaF(NRDA), DNAG, and dnaZ genes. Host functions directed by dnaA, so-alled dnaH, dnaI, and dnaP genes were dispensable for the viral growth. In contrast with phiZ174 and G4, alpha3 would grow sufficiently In dnaB and dnaC(D) mutants. The viral growth was not significantly affected by host polAts, seg, and groPC mutations.

Coliphages↗

PubMed1988

Altered osmoregulation of ompF in integration host factor mutants of Escherichia coli.

Osmoregulation of the porin protein OmpF was strongly altered in integration host factor (IHF) mutants. These mutants produced approximately 15-fold more OmpF than did the parent strain when grown in media of intermediate osmolarity. At high osmolarity IHF mutants continued to produce considerable amounts of OmpF, although this protein was undetectable in the parent grown under these conditions. Experiments with an ompF-lacZ chromosomal fusion strain suggested that these changes in osmoregulation in large part involve alterations in transcriptional activity of the ompF promoter. These results add to the growing list of genes whose expression is modified in IHF mutants.

Bacterial Outer Membrane Proteins↗

PubMed1992

Stimulation of the phage lambda pL promoter by integration host factor requires the carboxy terminus of the alpha-subunit of RNA polymerase.

Escherichia coli integration host factor (IHF) binds with high affinity to two tandem IHF consensus sequences located upstream from the pL promoter of bacteriophage lambda. IHF was shown to stimulate transcription initiation from the pL promoter by increasing close complex formation (KB). We show here, by the use of reconstituted mutant RNA polymerases, that the C-terminal portion of the alpha subunit of RNA polymerase plays an essential role in the stimulation of transcription by IHF. Our results are in agreement with the hypothesis that IHF, like the cAMP-CRP activator, increases the affinity of RNA polymerase to the promoter by protein-protein interaction.

Bacterial Proteins↗

PubMed1997

What are the host factors that place an individual at risk for Helicobacter pylori-associated disease?

Helicobacter pylori infection is associated with duodenal and gastric ulcer disease, gastric cancer, and gastric mucosa-associated lymphoid tissue lymphoma. Although more than half the world's population harbors H. pylori, only a proportion will develop clinically significant disease. The specific clinical outcome of an individual can be examined as the modulation of host factors by H. pylori infection. Host acid-secretory status and sensitivity to gastrin can be modulated by H. pylori infection. Once H. pylori has established itself in the stomach, virtually everyone develops gastritis, and variations in gastritis patterns have been associated with different gastric acid responses to H. pylori infection. The patterns of gastritis are important because they seem to determine disease outcome. Blood group antigens have been implicated in studies of ulcer disease. Receptors to Lewis antigens in gastric mucosa indicate that host mucosal factors influence H. pylori attachment. Conversely, H. pylori strains express Lewis antigen-like molecules, suggesting an autoimmune component for some H. pylori-associated diseases. HLA genotypes may influence the host response to H. pylori infection, and those of H. pylori-infected individuals have been correlated with histological features. The clinical outcome of H. pylori infection is most likely a result of complex interactions among host, bacterial, and environmental factors. The mechanisms by which these diverse factors influence the pathogenesis of different clinical outcomes remain under investigation.

Animals↗

PubMedDate not supplied

A rapid purification procedure of recombinant integration host factor from Escherichia coli.

A rapid procedure for the large-scale isolation of recombinant integration host factor (IHF) protein from Escherichia coli is presented. The protein was overproduced in the E. coli K5746 strain, whose construction has already been described. The procedure consists of a mild extraction of protein and fractionation by ammonium sulfate. A single-step affinity chromatography on heparin-Sepharose provided very pure IHF protein. A Mono-S FPLC column was used to highly concentrate the pure IHF for crystallization trials. Attempts to crystallize IHF produced small stable crystals that have a large number of molecules in the asymmetric unit and to date diffract poorly. Further attempts to crystallize IHF under other conditions as well as in a complex with the putative DNA binding site are underway.

Ammonium Sulfate↗

PubMed1991

HU and integration host factor function as auxiliary proteins in cleavage of phage lambda cohesive ends by terminase.

HU and integration host factor (IHF) are small, basic heterodimeric DNA-binding proteins which participate in transcription initiation, DNA replication, and recombination. We constructed isogenic Escherichia coli strains in which HU, IHF, or both proteins were absent. Bacteriophage lambda did not grow in hosts lacking both HU and IHF. Phage DNA replication and late gene transcription were normal in the double mutants, but packaging of lambda DNA was defective. Mature phage DNA molecules were absent, indicating that terminase was unable to linearize lambda DNA. Phage variants carrying a small substitution near cos or the ohm1 mutation in the terminase gene, Nul, formed plaques on HU- IHF- strains. We propose that HU or IHF is required to establish the higher-order DNA-protein structure at cos that is the substrate for lambda terminase.

Bacterial Proteins↗

PubMed1996

Integration host factor alleviates the H-NS-mediated repression of the early promoter of bacteriophage Mu.

Integration host factor (IHF), which is a histone-like protein, has been shown to positively regulate transcription in two different ways. It can either help the formation of a complex between a transcription factor and RNA polymerase or it can itself activate RNA polymerase without the involvement of other transcription factors. In this study, we present a third mechanism for IHF-stimulated gene expression, by counteracting the repression by another histone-like protein, H-NS. The early (Pe) promoter of bacteriophage Mu is specifically inhibited by H-NS, both in vivo and in vitro. For this inhibition, H-NS binds to a large DNA region overlapping the Pe promoter. Binding of IHF to a binding site just upstream of Pe alleviates the H-NS-mediated repression of transcription. This same ihf site is also involved in the direct activation of Pe by IHF. In contrast to the direct activation by IHF, however, the alleviating effect of IHF appears not to be dependent on the relevant position of the ihf site on the DNA helix, and it also does not require the presence of the C-terminal domain of the alpha subunit of RNA polymerase. Footprint analysis shows that binding of IHF to the ihf site destabilizes the interaction of H-NS with the DNA, not only in the IHF-binding region but also in the DNA regions flanking the ihf site. These results suggest that IHF disrupts a higher-order nucleoprotein complex that is formed by H-NS and the DNA.

Bacterial Outer Membrane Proteins↗

PubMed2001

The leucine-rich repeat domain can determine effective interaction between RPS2 and other host factors in arabidopsis RPS2-mediated disease resistance.

Like many other plant disease resistance genes, Arabidopsis thaliana RPS2 encodes a product with nucleotide-binding site (NBS) and leucine-rich repeat (LRR) domains. This study explored the hypothesized interaction of RPS2 with other host factors that may be required for perception of Pseudomonas syringae pathogens that express avrRpt2 and/or for the subsequent induction of plant defense responses. Crosses between Arabidopsis ecotypes Col-0 (resistant) and Po-1 (susceptible) revealed segregation of more than one gene that controls resistance to P. syringae that express avrRpt2. Many F(2) and F(3) progeny exhibited intermediate resistance phenotypes. In addition to RPS2, at least one additional genetic interval associated with this defense response was identified and mapped using quantitative genetic methods. Further genetic and molecular genetic complementation experiments with cloned RPS2 alleles revealed that the Po-1 allele of RPS2 can function in a Col-0 genetic background, but not in a Po-1 background. The other resistance-determining genes of Po-1 can function, however, as they successfully conferred resistance in combination with the Col-0 allele of RPS2. Domain-swap experiments revealed that in RPS2, a polymorphism at six amino acids in the LRR region is responsible for this allele-specific ability to function with other host factors.

Alleles↗

PubMed1996

A 38-kDa host factor interacts with functionally important motifs within the Autographa californica multinucleocapsid nuclear polyhedrosis virus homologous region (hr1) DNA sequence.

We recently demonstrated that the Autographa californica multinucleocapsid nuclear polyhedrosis virus homologous region (hr1) enhances transcription from the viral polyhedrin promoter and also functions as a putative origin of replication (ori). Hr1, carrying five 28-base pair core palindrome units, has also been mapped with respect to its enhancer and ori functions (Habib, S., Pandey, S., Chatterji, U., Burma, S., Ahmad, R., Jain, A., and Hasnain, S. E. (1996) DNA Cell Biol. 15, 737-747). A 38-kDa host factor termed hr1-binding protein (hr1-BP) binds with high specificity and affinity (Kd approximately 6.5 x 10(-11) M) to functionally important motifs within hr1. The core palindrome as well as sequences immediately flanking it are required for this interaction. Divalent cations are not essential, and ionic interactions play only a minor role in complex formation. hr1-BP binds through the minor groove of the double helix to multiple sites within hr1, and binding occurs as a function of the number of modules within hr1. Phosphorylation of hr1-BP is important for host factor-hr1 interaction. Hr1-BP differs in several respects from the other host factor, polyhedrin promoter-binding protein, described previously (Burma, S., Mukherjee, B., Jain, A., Habib, S., and Hasnain, S. E. (1994) J. Biol. Chem. 269, 2750-2757). When hr1-BP was sequestered out, in vivo, by a plasmid carrying hr1 alone, the hr1-mediated enhancement of reporter expression was abolished, demonstrating that the binding of hr1-BP may be crucial for the enhancer activity of the dual function hr1 element.

Base Sequence↗

PubMed1984

E. coli integration host factor binds to specific sites in DNA.

E. coli integration host factor (IHF) both participates directly in phage lambda site-specific recombination and regulates the expression of phage and bacterial genes. Using protection from nuclease and chemical attack as an assay, we examined the interaction of IHF with DNA. We found that IHF is a specific DNA binding protein that interacts with three distinct segments of attP, the recombination site carried by phage lambda. We also found that specific IHF binding sites are located in non-att DNA. Several non-att IHF binding sites that we have identified are adjacent to genes whose expression is altered in IHF mutants. From comparison of the sequences protected by IHF, we suggest that the critical determinant in specific IHF-DNA interaction is contained in the sequence T.PyAA...PuTTGaT.A.PuTT...PyAACtA.

Bacteriophage lambda↗