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Integration Host Factors (1):
Recent article
Integration Host Factors
Abstract
The results of previous investigations indicate that age and gender may influence the strength of the human host's immune response to infection of the central nervous system with the larvae of Taenia solium. Most of the relevant research on such neurocysticercosis (NCC) has, however, been conducted...
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PMID: 19695154
PDF is available here.
PDF is available here.
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Abstract
We demonstrate that IHF influences the morphology of DNA condensed by polyamines in vitro. In the absence of IHF, spermidine and spermine condense DNA primarily into toroidal structures, whereas in the presence of IHF, polyamines condense DNA primarily into rodlike structures. Computer simulations o...
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PMID: 19132923
PDF is available here.
PDF is available here.
Journal of Bacteriology (190)21 2008
Abstract
We have exploited mutational analysis and biochemistry to investigate the actions of IHF and Fis at these sites. We show that the effects of IHF and Fis are position dependent and that IHF II functions independently of IHF I and Fis I. Using in vitro assays, we report that IHF and Fis repress transc...
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PMID: 18757534
PDF is available here.
PDF is available here.
Abstract
We demonstrate that IHF affects transcription from bacteriophage lambdapR promoter and the ptac promoter located on plasmids that contain IHF-binding sites. The IHF consensus sites are abundant and they can bind the IHF protein as shown in in vitro studies. The SeqA protein has a role in the complex...
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PMID: 18590762
PDF is available here.
PDF is available here.
Physical Review Letters (101)3 2008
Abstract
We present a model of nonspecific cooperative binding of proteins to DNA in which the binding of isolated proteins generates local bends but binding of proteins at neighboring sites on DNA straightens the polymer. We solve the statistical mechanical problem and calculate the effective persistence le...
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PMID: 18764298
PDF is available here.
PDF is available here.
Journal of Clinical Oncology (26)20 2008
Abstract
Microbiology (154)Pt 7 2008
Abstract
We present in vitro and in vivo studies to demonstrate the involvement of FIS protein in this catabolic repression. DNase I footprinting experiments show that FIS binds to multiple sites within the Pg promoter. FIS-site I overlaps the CRP-binding site. By using an electromobility shift assay, we dem...
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PMID: 18599842
PDF is available here.
PDF is available here.
Abstract
We have found that protection by simvastatin includes the inhibition of host cell invasion by Staphylococcus aureus, the most common etiologic agent of sepsis. Inhibition was due in part to depletion of isoprenoid intermediates within the cholesterol biosynthesis pathway and led to the cytosolic acc...
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PMID: 18388257
PDF is available here.
PDF is available here.
Journal of Bacteriology (190)13 2008
Abstract
We report that the global regulator integration host factor (IHF) positively affects virulence gene expression in V. cholerae. Inactivation of ihfA and ihfB, the genes encoding the IHF subunits, decreased the expression levels of the two main virulence factors tcpA and ctx and prevented toxin-coregu...
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PMID: 18456804
PDF is available here.
PDF is available here.
Journal of Biological Chemistry (283)24 2008
Abstract
We used the prototype arterivirus, equine arteritis virus (EAV), to gain insight into the structure and function of the replication/transcription complex (RTC) of nidoviruses. RTCs were isolated from EAV-infected cells, and their activity was studied using a newly developed in vitro assay for viral...
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PMID: 18411274
PDF is available here.
PDF is available here.
Journal of Physical Chemistry B (112)19 2008
Abstract
We have carried out measurements of DNA bending/unbending dynamics on a cognate DNA substrate in complex with integration host factor (IHF), an architectural protein from E. coli that bends its cognate site by approximately 180 degrees . We use a laser temperature jump to perturb the IHF-DNA complex...
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PMID: 18461910
PDF is available here.
PDF is available here.
Biochemistry (Washington) (47)12 2008
Abstract
We have employed Raman difference spectroscopy and gel mobility assays to characterize the molecular mechanisms underlying such differences in DNA recognition. Parallel studies of solution complexes of IHF and HU with the same DNA nonadecamer (5' --> 3' sequence: TC TAAGTAGTTGATTCATA, where the phag...
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PMID: 18302340
PDF is available here.
PDF is available here.
Journal of Molecular Biology (377)1 2008
Abstract
We have investigated the thermodynamics of binding the 34-base pair (bp) H' DNA sequence to the Escherichia coli DNA-remodeling protein integration host factor (IHF). Isothermal titration calorimetry and fluorescence resonance energy transfer are applied to determine effects of salt concentration [K...
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PMID: 18237740
PDF is available here.
PDF is available here.
Journal of Molecular Biology (376)4 2008
Abstract
We demonstrate that a second 'host' protein, histone-like nucleoid structuring protein (H-NS), acts as an anti-channeling factor to limit self-destructive intramolecular transposition events in vitro. Evidence that H-NS competes with IHF for binding to the Tn10 transpososome to block channeling and...
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PMID: 18191147
PDF is available here.
PDF is available here.
BMC Microbiology (8)1 2008
Abstract
StyR-P and IHF compete for binding to the URE region. PstyA full activity in inducing conditions is achieved when StyR-P and IHF bind to site STY2 and to the URE, respectively. Under catabolite repression conditions, StyR-P binds the STY1 site, replacing IHF at the URE region. StyR-P bound to both S...
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PMID: 18547423
PDF is available here.
PDF is available here.
Journal of Bacteriology (189)24 2007
TrwC-mediated site-specific recombination is controlled by host factors altering local DNA topology.
Abstract
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...
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PMID: 17921309
PDF is available here.
PDF is available here.
Biophysical Journal (93)9 2007
Abstract
Molecular beacon detection of equilibrium cyclization (MBEC) is a novel, high sensitivity technique that can allow DNA-protein complex formation to be studied under diverse conditions in a cost effective and rapid manner that can be adapted to high throughput screening. To demonstrate the ease and u...
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PMID: 17631534
PDF is available here.
PDF is available here.
Journal of Biological Chemistry (282)40 2007
Hierarchical delivery of an essential host colonization factor in enteropathogenic Escherichia coli.
Abstract
We demonstrate that the enteropathogenic Escherichia coli (EPEC) chaperone CesT interacts with a variety of known and putative type III effector proteins. Using pull-down and secretion assays, a degenerate CesT binding domain was identified within multiple type III effectors. Domain exchange experim...
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PMID: 17681945
PDF is available here.
PDF is available here.
Abstract
A 1-year prospective cohort study of all episodes of Escherichia coli bacteraemia in two French university hospitals was conducted to assess simultaneously the influence of host and bacterial determinants on the initial severity and outcome of E. coli sepsis. Clinical data (community-acquired/nosoco...
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PMID: 17617183
PDF is available here.
PDF is available here.
Abstract
We follow, here, the production of SeV particles upon regular virus infection. We find that neither Alix suppression nor dominant negative-VPS4A expression, applied separately or in combination, affects physical or infectious virion production. This contrasts with the observed decrease of SV5 virion...
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PMID: 17467023
PDF is available here.
PDF is available here.
Biophysical Chemistry (128)2-3 2007
Abstract
We show that both specific bending and non-specific compaction alter LacI-mediated looping of DNA. Our results highlight the subtle regulatory roles that proteins, which confer structure upon DNA, might have in controlling DNA transcription and other processes in which the conformation of DNA determ...
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PMID: 17543441
PDF is available here.
PDF is available here.
Molecular Microbiology (65)2 2007
Abstract
We reported that cAMP receptor protein (CRP) activates acs transcription by binding tandem DNA sites located upstream of the major acsP2 promoter and that the nucleoid protein IHF (integration host factor) binds three specific sites located just upstream. In vivo, the sequence that includes these IH...
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PMID: 17630973
PDF is available here.
PDF is available here.
FEMS Microbiology Letters (271)1 2007
Abstract
These results point to an as yet undisclosed function of IHF in the regulation of R. etli nifA expression....
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PMID: 17403047
PDF is available here.
PDF is available here.
Journal of Bacteriology (189)10 2007
Abstract
We describe our efforts to more precisely define the role of sbyA and ihfA by examining the effects of multiple base substitutions at sbyA and ihfA on binding and plasmid mobilization. While we observed significant decreases in in vitro DNA-binding affinities, we saw little effect on plasmid mobiliz...
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PMID: 17351033
PDF is available here.
PDF is available here.
Gastroenterology (132)4 2007
Abstract
We propose a model in which Hp has evolved a mechanism to use at least 2 tyrosine kinases, Abl and Src, for CagA phosphorylation and subsequent actin-cytoskeletal rearrangements leading to cell scattering and elongation....
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PMID: 17408661
PDF is available here.
PDF is available here.
Journal of Bacteriology (189)8 2007
Abstract
We examined the mechanisms that control transcription of fnr to increase our understanding of how FNR protein levels are regulated. Under anaerobic conditions, one mechanism that controls fnr expression is negative autoregulation by the active [4Fe-4S] form of FNR. Through DNase I footprinting and i...
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PMID: 17293415
PDF is available here.
PDF is available here.
Journal of Molecular Biology (367)3 2007
Abstract
We show that this switch can be employed to control the efficiency of site-specific recombination catalyzed by lambda integrase. Introduction of acidic residues at the protein-DNA interface holds potential for the design of metal-mediated switches for the investigation of functional relationships....
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PMID: 17276457
PDF is available here.
PDF is available here.
Molecular Microbiology (63)4 2007
Abstract
Conjugative DNA transfer is a highly conserved process for the direct transfer of DNA from a donor to a recipient. The conjugative initiator proteins are key players in the DNA processing reactions that initiate DNA transfer - they introduce a site- and strand-specific break in the DNA backbone via...
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PMID: 17238924
PDF is available here.
PDF is available here.
Molecular Microbiology (63)4 2007
Abstract
These results support a refined model for how two potentially key indicators of host inflammation, Neu(5)Ac and GlcNAc, regulate type 1 fimbriation....
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PMID: 17238917
PDF is available here.
PDF is available here.
Journal of Molecular Biology (365)4 2007
Abstract
We report binding affinities for AHU and the DNA in the cocrystal structures. The binding free energies for formation of these AHU-DNA complexes range from approximately 10-14.5 kcal/mol, representing K(d) values in the nanomolar to low picomolar range, and a maximum stabilization of at least approx...
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PMID: 17097674
PDF is available here.
PDF is available here.
BMC Microbiology (7)1 2007
Abstract
Crp and a more local regulator, ArgR, directly control gltBDF transcription, both acting negatively. Crp-cAMP binds a sequence centered at -65.5 relative to the transcript start. Mutation of conserved nucleotides in the Crp binding site abolishes the Crp-dependent repression. ArgR also binds to the...
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PMID: 17233899
PDF is available here.
PDF is available here.
BMC Genomics (8) 2007
Abstract
Using features that have been previously experimentally verified in the alpha-Proteobacterium Caulobacter crescentus, the origin of DNA replication (ori) regions were identified in silico for Wolbachia strains and eleven other related bacteria belonging to Ehrlichia, Anaplasma, and Rickettsia genera...
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PMID: 17584494
PDF is available here.
PDF is available here.
Nucleic Acids Research (35)12 2007
Abstract
We test DNA looping in bacterial strains lacking the nucleoid proteins HU, IHF or H-NS. We confirm that deletion of HU inhibits looping and that quantitative modeling suggests residual looping in the induced operon. Deletion of IHF has little effect. Remarkably, DNA looping is strongly enhanced in t...
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PMID: 17553830
PDF is available here.
PDF is available here.
Nucleic Acids Research (35)6 2007
Abstract
We showed that DNA flexibility compensates for structural characteristics of the four consensus recognition elements associated with specific binding (Aeling et al., J. Biol. Chem. 281, 39236-39248, 2006). If elements are missing, high-affinity binding occurs only if DNA deformation energy is low. I...
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PMID: 17324943
PDF is available here.
PDF is available here.
Abstract
Journal of Biological Chemistry (281)51 2006
Abstract
We assessed the contributions of pre-formed and protein-induced DNA conformations to the energetics of IHF binding. Binding energies determined experimentally were compared with energies predicted for the IHF-induced deformation of the DNA helix (DNA deformation energy) in the IHF-DNA complex. Combi...
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PMID: 17035240
PDF is available here.
PDF is available here.
Abstract
We sought to dissect the complex formation process into its component binding and bending reaction steps, using stopped-flow fluorimetry to observe changes in resonance energy transfer between DNA-bound dyes, which in turn reflect distance changes upon bending. Different DNA substrates that are like...
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PMID: 17116862
PDF is available here.
PDF is available here.
Abstract
We use a nanosecond laser temperature-jump apparatus to probe, with submillisecond time resolution, the kinetics of bending/unbending of a DNA substrate bound to integration host factor (IHF), an architectural protein from Escherichia coli. The kinetics are monitored with time-resolved FRET, with th...
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PMID: 17124171
PDF is available here.
PDF is available here.
Abstract
These results strongly suggest that the expression of the nifB promoter of H. seropedicae is dependent on the NifA and RpoN proteins and that the IHF protein stimulates NifA activation of nifB promoter....
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PMID: 17473889
PDF is available here.
PDF is available here.
Molecular Microbiology (62)6 2006
Abstract
We show here that all five known DnaA boxes can be deleted from the plasmid origin provided the origin is extended by about 120 bp. The additional DNA provides an IHF site and most likely a weak DnaA binding site, because replacing the putative site with an authentic DnaA box enhanced plasmid replic...
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PMID: 17087773
PDF is available here.
PDF is available here.
Journal of Bacteriology (188)21 2006
Abstract
We show that IHF binding to one of these sites, located at position -127 with respect to the nrf promoter, has a positive effect on nrf promoter activity. This activation is dependent on the face of the DNA helix, independent of IHF binding at other locations, and found only when NarL/NarP are not b...
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PMID: 16936015
PDF is available here.
PDF is available here.
Abstract
I classifications, including a depressive disorder, and her parents participated in a year-long, multimodal intervention that included mood-focused psychoeducation and coaching designed to impact on her, her family, school, and community systems. Self-report, clinician-driven, and ecologically valid...
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PMID: 17163224
PDF is available here.
PDF is available here.
Abstract
We demonstrated that co-transfection of a plasmid expressing phiC31 integrase with a plasmid containing the transgene and attB increased the frequency of transgene expression in rabbit synovial fibroblasts and primary human RA synoviocytes. Plasmid rescue and DNA sequence analysis of plasmid-chromos...
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PMID: 16779871
PDF is available here.
PDF is available here.
FEMS Microbiology Letters (261)1 2006
Abstract
CsgD is a master regulator of multicellular behaviour in Salmonella enterica serovar Typhimurium. Expression of CsgD is highly regulated on the transcriptional level. A nucleo-protein complex had been defined where the global regulators OmpR and integration host factor (IHF) bind up- and downstream...
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PMID: 16842367
PDF is available here.
PDF is available here.
Journal of Bacteriology (188)16 2006
Abstract
We tested whether integration host factor (IHF) or Fis, two host-encoded nucleoid proteins, are required for transfer of SXT, a Vibrio cholerae-derived ICE that can be transmitted to many gram-negative species. Fis did not influence the transfer of SXT to or from V. cholerae. In contrast, IHF proved...
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PMID: 16885438
PDF is available here.
PDF is available here.
Molecular Microbiology (61)1 2006
Abstract
We isolated an ORE-III-binding factor that positively regulates the suf operon in response to various oxidants. MALDI-TOF mass analysis identified it with IscR, known to serve as a repressor of the iscRSUA gene expression under anaerobic condition as a [2Fe-2S]-bound form. The iscR null mutation abo...
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PMID: 16824106
PDF is available here.
PDF is available here.
Molecular Microbiology (60)6 2006
Abstract
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...
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PMID: 16796676
PDF is available here.
PDF is available here.
Abstract
We reviewed the latest evidences about the effects of H pylori infection on gastric carcinogenesis, classified into epidemiology, dynamics of gastric mucosal changes, DNA damages, virulence factors, host factors, and source of gastric malignancy. Through the considerable progress made in research in...
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PMID: 16718758
PDF is available here.
PDF is available here.
Journal of Bacteriology (188)9 2006
Abstract
We focus on the linker regions that impose the distribution of target sites for DNA-binding proteins involved in pyrimidine- and purine-specific repression of the upstream promoter P1. We introduced deletions and insertions, and combinations thereof, in four linkers connecting the binding sites for...
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PMID: 16621816
PDF is available here.
PDF is available here.
Biochemistry (Washington) (45)16 2006
Abstract
We proposed a novel DNA binding mode that predicts significant bending of duplex DNA by gpNu1 (de Beer et al. (2002) Mol. Cell 9, 981-991). We further proposed that gpNu1 and IHF cooperatively bind and bend viral DNA to regulate the assembly of the packaging motor. Here, we characterize cooperative...
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PMID: 16618107
PDF is available here.
PDF is available here.
Archives of Microbiology (185)3 2006
Abstract
We show that inactivation of IHF in vivo abolishes the sigma (S)-dependent transcription initiation of the pst operon, indicating that both -13C residue and IHF are required to confer on pst the ability to be transcribed by Esigma (S). Introduction of a -13C residue in the promoter region of phoA, a...
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PMID: 16404567
PDF is available here.
PDF is available here.
Molecular Microbiology (59)6 2006
Abstract
Our data reveal a new connection between IHF and the expression of genes required by the bacterium to undergo the physiological changes associated with the transition from exponential growth to stationary phase. When a mutant lacking IHF entered stationary phase, it displayed downregulated expressio...
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PMID: 16553887
PDF is available here.
PDF is available here.
Molecular Microbiology (59)6 2006
Abstract
We constructed a chimaeric recombination site (resF) which allows Hbsu to be substituted by IHF, binding specifically between site I (the crossover site) and site II. Two Sin dimers and one IHF dimer can bind together to the closely adjoining sites in resF, forming folded complexes. The precise posi...
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PMID: 16553879
PDF is available here.
PDF is available here.
Science progress (89)Pt 3-4 2006
Abstract
DNA in bacterial cells is maintained in a negatively supercoiled state. This contributes to the organization of the bacterial nucleoid and also influences the global gene expression pattern in the cell through modulatory effects on transcription. Supercoiling arises as a result of changes to the lin...
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PMID: 17338437
PDF is available here.
PDF is available here.
Abstract
Phage Mu is the most efficient transposable element known, its high efficiency being conferred by an enhancer DNA element. Transposition is the end result of a series of well choreographed steps that juxtapose the enhancer and the two Mu ends within a nucleoprotein complex called the 'transpososome....
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PMID: 17092824
PDF is available here.
PDF is available here.
Abstract
Tn10 is a bacterial transposon that transposes through a non-replicative mechanism. This mode of DNA transposition is widely used in bacteria and is also used by "DNA-based" transposons in eukaryotes. Tn10 has served as a paradigm for this mode of transposition and continues to provide novel insight...
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PMID: 17092825
PDF is available here.
PDF is available here.
Abstract
The FIS protein (factor for inversion stimulation) is known to activate the transcription of rRNA and tRNA operons in Escherichia coli. In this report the growth behaviour of a fis bacterium was studied under steady-state conditions and in competition experiments with a wild-type bacterium in a chemo...
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PMID: 1468620
PDF is available here.
PDF is available here.
Nucleic Acids Research (34)16 2006
Association of nucleoid proteins with coding and non-coding segments of the Escherichia coli genome.
Abstract
We have exploited chromatin immunoprecipitation and high-density microarrays to study the binding of three such proteins, FIS, H-NS and IHF, across the E.coli genome in vivo. Our results show that the distribution of these proteins is biased to intergenic parts of the genome, and that the binding pr...
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PMID: 16963779
PDF is available here.
PDF is available here.
Genes & Development (19)18 2005
Abstract
We demonstrate here that H-NS promotes Tn10 transposition by binding directly to the transposition complex (or transpososome). We present evidence that, upon binding, H-NS induces the unfolding of the Tn10 transpososome and helps to maintain the transpososome in an unfolded state. This ensures that...
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PMID: 16166383
PDF is available here.
PDF is available here.
Abstract
We suggest that the cellular levels of phosphorylated StyR, as determined by StyS sensor kinase activity, and the interplay of this molecule with IHF modulate the activity of the promoter in different growth conditions....
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PMID: 16151132
PDF is available here.
PDF is available here.