[Show abstract][Hide abstract] ABSTRACT: Several experimental methods exist to explore the microRNA (miRNA) regulome. These methods almost exclusively focus on multiple targets bound to a single, or perhaps a few miRNAs of interest. Here, we describe a microRNA capture affinity technology (miR-CATCH) which uses an affinity capture oligonucleotide to co-purify a single target messenger RNA (mRNA) together with all its endogenously bound miRNAs. This bench-top method is similar to RNA immunoprecipitation (RIP) and provides an experimental alternative to computational miRNA target prediction.
Full-text · Article · Jan 2015 · Methods in Molecular Biology
[Show abstract][Hide abstract] ABSTRACT: MicroRNAs (miRNAs) are small non-coding RNAs that regulate expression by translational repression or messenger RNA (mRNA) degradation. Although numerous bioinformatic prediction models exist to identify miRNA-mRNA interactions, experimental validation of bona fide interactions can be difficult and laborious. Few methods can comprehensively identify miRNAs that target a single mRNA. We have developed an experimental approach to search for miRNAs targeting any mRNA using a capture affinity assay involving a biotinylated DNA anti-sense oligonucleotide. This method identifies miRNAs targeting the full length of the mRNA. The method was tested using three separate mRNA targets: alpha-1 antitrypsin (AAT) mRNA, interleukin-8 mRNA and secretory leucoprotease inhibitor mRNA. AAT mRNA-specific and total miRNAs from three different cell lines (monocytic THP-1, bronchial epithelial 16HBE14o- and liver HepG2 cells) were profiled, and validation studies revealed that AAT mRNA-specific miRNAs functionally target the AAT mRNA in a cell-specific manner, providing the first evidence of innate miRNAs selectively targeting and modulating AAT mRNA expression. Interleukin-8 and secretory leucoprotease inhibitor mRNAs and their cognate miRNAs were also successfully captured using this approach. This is a simple and an efficient method to potentially identify miRNAs targeting sequences within the full length of a given mRNA transcript.
Full-text · Article · Jan 2013 · Nucleic Acids Research
[Show abstract][Hide abstract] ABSTRACT: Here we show that the Rns regulator of Escherichia coli dimerises in vivo and in vitro. Furthermore, we demonstrate that Rns forms aggregates in vitro and describe a methodology to ameliorate aggregation thus permitting the analysis of Rns by cross-linking.
[Show abstract][Hide abstract] ABSTRACT: In most cases, Escherichia coli exists as a harmless commensal organism, but it may on occasion cause intestinal and/or extraintestinal disease. Enterotoxigenic
E. coli (ETEC) is the predominant cause of E. coli-mediated diarrhea in the developing world and is responsible for a significant portion of pediatric deaths. In this study,
we determined the complete genomic sequence of E. coli H10407, a prototypical strain of enterotoxigenic E. coli, which reproducibly elicits diarrhea in human volunteer studies. We performed genomic and phylogenetic comparisons with other
E. coli strains, revealing that the chromosome is closely related to that of the nonpathogenic commensal strain E. coli HS and to those of the laboratory strains E. coli K-12 and C. Furthermore, these analyses demonstrated that there were no chromosomally encoded factors unique to any sequenced
ETEC strains. Comparison of the E. coli H10407 plasmids with those from several ETEC strains revealed that the plasmids had a mosaic structure but that several loci
were conserved among ETEC strains. This study provides a genetic context for the vast amount of experimental and epidemiological
data that have been published.
Full-text · Article · Nov 2010 · Journal of bacteriology
[Show abstract][Hide abstract] ABSTRACT: The pathogenesis of diarrhoeal disease due to human enterotoxigenic Escherichia coli absolutely requires the expression of fimbriae. The expression of CS1 fimbriae is positively regulated by the AraC-like protein Rns. AraC-like proteins are DNA-binding proteins that typically contain two helix-turn-helix (HTH) motifs. A program of pentapeptide insertion mutagenesis of the Rns protein was performed, and this revealed that both HTH motifs are required by Rns to positively regulate CS1 fimbrial gene expression. Intriguingly, a pentapeptide insertion after amino acid C102 reduced the ability of Rns to transactivate CS1 fimbrial expression. The structure of Rns in this vicinity (NACRS) was predicted to be disordered and thus might act as a flexible linker. This hypothesis was confirmed by deletion of this amino acid sequence from the Rns protein; a truncated protein that lacked this sequence was no longer functional. Strikingly, this sequence could be functionally substituted in vivo and in vitro by a flexible seven amino acid sequence from another E. coli AraC-like protein RhaS. Our data indicate that HTH motifs and a flexible sequence are required by Rns for maximal activation of fimbrial gene expression.
[Show abstract][Hide abstract] ABSTRACT: Dysregulation of airway inflammation contributes to lung disease in cystic fibrosis (CF). Inflammation is mediated by inflammatory cytokines, including IL-8, which illustrates an increase in biological half-life and proinflammatory activity when bound to glycosaminoglycans (GAGs). The aim of this project was to compare IL-8 and IL-18 for their relative stability, activity, and interaction with GAGs, including chondroitin sulfate, hyaluronic acid, and heparan sulfate, present in high quantities in the lungs of patients with CF. Bronchoalveolar lavage fluid was collected from patients with CF (n = 28), non-CF controls (n = 14), and patients with chronic obstructive pulmonary disease (n = 12). Increased levels of IL-8 and reduced concentrations of IL-18 were detected in bronchial samples obtained from CF individuals. The low level of IL-18 was not a defect in IL-18 production, as the pro- and mature forms of the molecule were expressed and produced by CF epithelial cells and monocytes. There was, however, a marked competition between IL-8 and IL-18 for binding to GAGs. A pronounced loss of IL-18 binding capacity occurred in the presence of IL-8, which displaced IL-18 from these anionic-matrices, rendering the cytokine susceptible to proteolytic degradation by neutrophil elastase. As a biological consequence of IL-18 degradation, reduced levels of IL-2 were secreted by Jurkat T lymphocytes. In conclusion, a novel mechanism has been identified highlighting the potential of IL-8 to determine the fate of other inflammatory molecules, such as IL-18, within the inflammatory milieu of the CF lung.
Full-text · Article · Dec 2009 · The Journal of Immunology
[Show abstract][Hide abstract] ABSTRACT: Heparan sulphate proteoglycans are major components of the mammalian cell membrane. Here we show that PagN of Salmonella enterica serovar Typhimurium utilizes heparinated proteoglycan to successfully invade mammalian cells. Mutants defective in the production of the outer membrane protein PagN displayed similar levels of invasiveness of glycosylation-deficient pgsA-745 cells in comparison with wild-type Salmonella. Furthermore, pgsA-745 cells were invaded c. 400-fold less efficiently than CHO-K1 cells by Escherichia coli expressing PagN. PagN is likely to interact with heparinated proteoglycan as heparin could inhibit PagN-mediated invasion in a dose-dependent manner. Finally, we show, by deletion analysis, that all four extracellular loops of PagN are crucial for invasion of mammalian cells.
[Show abstract][Hide abstract] ABSTRACT: The pagN gene of Salmonella enterica serovar Typhimurium is a PhoP-regulated gene that is up-regulated during growth within macrophages and in vivo in murine models of infection. The PagN protein displays similarity to the Hek and Tia invasins/adhesins of Escherichia coli. Thus far no function has been ascribed to the PagN protein.
Here we show that the outer membrane located PagN protein mediates agglutination of red blood cells and that this can be masked by LPS. When expressed in Escherichia coli the PagN protein supports adhesion to and invasion of mammalian cells in a manner that is dependent on cytoskeletal rearrangements. S. enterica sv Typhimurium pagN mutants display a reduction in adhesion to and invasion of epithelial cells. Finally, we demonstrate that over-expression of PagN in a SPI-1 mutant can partially compensate for the lack of a functional invasasome.
PagN is an outer membrane protein that may contribute to the virulence of S. Typhimurium. This protein is a haemagglutinin and contributes to the adherence to mammalian cells. In addition, PagN can mediate high-level invasion of CHO-K1 cells. Previously,pagN mutants have been shown to be less competitive in vivo and thus this may be due to their lessened ability to interact with mammalian cells. Finally PagN can be added to an ever-growing repertoire of factors that contribute to the pathogenesis of Salmonella.
[Show abstract][Hide abstract] ABSTRACT: Escherichia coli is the principal gram-negative causative agent of sepsis and meningitis in neonates. The pathogenesis of meningitis due to
E. coli K1 involves mucosal colonization, transcytosis of epithelial cells, survival in the bloodstream, and eventually invasion
of the meninges. The last two aspects have been well characterized at a molecular level. Less is known about the early stages
of pathogenesis, i.e., adhesion to and invasion of epithelial cells. We have previously reported that the Hek protein causes
autoaggregation and can mediate adherence to and invasion of epithelial cells. Here, we report that Hek-mediated adherence
is dependent on binding to glycosoaminoglycan, in particular, heparin. The ability to hemagglutinate, autoaggregate, adhere,
and invade is contingent on a putative 25-amino-acid loop that is exposed to the outside of the bacterial cells.
Full-text · Article · Apr 2008 · Infection and immunity
[Show abstract][Hide abstract] ABSTRACT: The OmpA outer membrane protein of Escherichia coli and other enterobacteria is a multifaceted protein. This protein is expressed to very high levels and ompA is tightly regulated at the posttranscriptional level. It can function as an adhesin and invasin, participate in biofilm formation, act as both an immune target and evasin, and serves as a receptor for several bacteriophages. Many of these properties are due to four short protein loops that emanate from the protein to the outside of the cell. Herein it is described how the structure of this protein relates to its many functions.
[Show abstract][Hide abstract] ABSTRACT: Escherichia coli is the principal gram-negative causative agent of sepsis and meningitis in neonates. The pathogenesis of meningitis due to E. coli K1 involves mucosal colonization, transcytosis of epithelial cells, survival in the blood stream and eventually invasion of the meninges. The latter two aspects have been well characterized at a molecular level in the last decade. Less is known about the early stages of pathogenesis, i.e. adhesion to and invasion of gastrointestinal cells. Here, the characterization of the Hek protein is reported, which is expressed by neonatal meningitic E. coli (NMEC) and is localized to the outer membrane. It is demonstrated that this protein can cause agglutination of red blood cells and can mediate autoaggregation. Escherichia coli expressing this protein can adhere to and invade epithelial cells. So far, this is the first outer membrane protein in NMEC to be directly implicated in epithelial cell invasion.
Full-text · Article · May 2007 · FEMS Microbiology Letters
[Show abstract][Hide abstract] ABSTRACT: Site-specific recombinases of the integrase family usually require cofactors to impart directionality in the recombination
reactions that they catalyze. The FimB integrase inverts the Escherichia coli fim switch (fimS) in the on-to-off and off-to-on directions with approximately equal efficiency. Inhibiting DNA gyrase with novobiocin caused
inversion to become biased in the off-to-on direction. This directionality was not due to differential DNA topological distortion
of fimS in the on and off phases by the activity of its resident PfimA promoter. Instead, the leucine-responsive regulatory (Lrp) protein was found to determine switching outcomes. Knocking out
the lrp gene or abolishing Lrp binding sites 1 and 2 within fimS completely reversed the response of the switch to DNA relaxation. Inactivation of either Lrp site alone resulted in mild
on-to-off bias, showing that they act together to influence the response of the switch to changes in DNA supercoiling. Thus,
Lrp is not merely an architectural element organizing the fim invertasome, it collaborates with DNA supercoiling to determine the directionality of the DNA inversion event.
Full-text · Article · Sep 2006 · Journal of Bacteriology
[Show abstract][Hide abstract] ABSTRACT: Cystic fibrosis (CF) is a genetic disease characterized by severe neutrophil-dominated airway inflammation. An important cause of inflammation in CF is Pseudomonas aeruginosa infection. We have evaluated the importance of a number of P. aeruginosa components, namely lipopeptides, LPS, and unmethylated CpG DNA, as proinflammatory stimuli in CF by characterizing the expression and functional activity of their cognate receptors, TLR2/6 or TLR2/1, TLR4, and TLR9, respectively, in a human tracheal epithelial line, CFTE29o(-), which is homozygous for the DeltaF508 CF transmembrane conductance regulator mutation. We also characterized TLR expression and function in a non-CF airway epithelial cell line 16HBE14o(-). Using RT-PCR, we demonstrated TLR mRNA expression. TLR cell surface expression was assessed by fluorescence microscopy. Lipopeptides, LPS, and unmethylated CpG DNA induced IL-8 and IL-6 protein production in a time- and dose-dependent manner. The CF and non-CF cell lines were largely similar in their TLR expression and relative TLR responses. ICAM-1 expression was also up-regulated in CFTE29o(-) cells following stimulation with each agonist. CF bronchoalveolar lavage fluid, which contains LPS, bacterial DNA, and neutrophil elastase (a neutrophil-derived protease that can activate TLR4), up-regulated an NF-kappaB-linked reporter gene and increased IL-8 protein production in CFTE29o(-) cells. This effect was abrogated by expression of dominant-negative versions of MyD88 or Mal, key signal transducers for TLRs, thereby implicating them as potential anti-inflammatory agents for CF.
Full-text · Article · Mar 2005 · The Journal of Immunology
[Show abstract][Hide abstract] ABSTRACT: The FimB protein is a site-specific recombinase that inverts thefimS genetic switch in Escherichia coli. Based on amino acid sequence analysis alone, FimB has been assigned to the integrase family of tyrosine recombinases. We
show that amino acid substitutions at positions R47, H141, R144, and Y176, corresponding to highly conserved members of the
catalytic motif of integrase proteins, render FimB incapable of inverting the fimS element in vivo. The arginine substitutions reduced the ability of FimB to bind tofimS in vivo or in vitro, while the substitution R144Q resulted in a protein unable to bind independently to the half sites located
at the left end of fimS in phase-on bacteria. These data confirm that FimB is an integrase and suggest that residue R144 has a role in binding to
a specific component of the fimswitch.
Preview · Article · Jun 2000 · Journal of Bacteriology
[Show abstract][Hide abstract] ABSTRACT: Phase variable expression of type 1 fimbriae in Escherichia coli arises from a site-specific recombination event that inverts a short segment of chromosomal DNA carrying the promoter for transcription of the gene encoding the fimbrial subunit protein. Two integrase-like recombinases are involved in switching. The FimB recombinase inverts the DNA segment in either orientation, whereas the FimE protein inverts it predominantly in the ON-to-OFF direction. In this paper, we report the isolation of a FimE mutant protein that has enhanced bidirectional switching activity. This protein has an arginine-to-lysine substitution at position 59, and this confers a FimB-like switching character on FimE without altering its ability to bind to DNA. The arginine was not a member of the arginine-histidine-arginine-tyrosine catalytic tetrad that is common to all integrase-like recombinases. The catalytic tetrad members of FimE were identified at positions 41, 136, 139 and 171 and shown to be essential for FimE function. In addition, other amino acid residues that make important contributions to the DNA binding activity of FimE or its ON-to-OFF inversion efficiency were identified.
Preview · Article · Jan 2000 · Molecular Microbiology
[Show abstract][Hide abstract] ABSTRACT: The Rns protein of enterotoxigenic Escherichia coli (ETEC) and the VirF protein of Shigella flexneri are members of the AraC family of transcription regulators. Rns is required for positive activation of the CS1 fimbrial genes, while VirF is a positive regulator of an invasion gene regulon. The amino acid sequences of the proteins are 36% identical, and both proteins activate transcription in response to increases in temperature. Here, we show that Rns is capable of complementing fully a null mutation in the S. flexneri virF gene. However, the VirF protein cannot replace Rns as an activator of CS1 gene expression in ETEC. This failure is not due to the absence from ETEC of a co-factor required by VirF since it also occurs when the CS1 system is moved into an S. flexneri genetic background. Nor is it a function of growth medium composition or a failure in virF gene expression. Instead, these findings point to important differences in the mechanisms by which these related transcription factors regulate gene expression in Gram-negative pathogens.
[Show abstract][Hide abstract] ABSTRACT: Fimbriae are wiry (2 to 4 nm diam.) or rod-shaped (6 to 8 nm diam.), fibre-like structures on the surfaces of bacteria which mediate attachment to host cells. Much has been learned in recent years about the biogenesis, structure and regulation of expression of these adhesive organelles in Gram-negative bacteria. Analyses of the genetic determinants encoding the biogenesis of fimbriae has revealed that the adhesive interaction of fimbriae can be mediated by major subunits (CFA/I and CS1 fimbriae) or minor subunits (P, S, and type 1 fimbriae), with the adhesin being located either at the tip of the fimbria or along the length of the fimbrial shaft. Minor subunits can also act as adapters, anchors, initiators or elongators. Post-translational glycosylation of the type 4 pilins of Neisseria gonorrhoeae, Neisseria meningitidis and Pseudomonas aeruginosa has been demonstrated. The structures of the PapD chaperone of Escherichia coli and of N. gonorrhoeae type 4 fimbrin have been resolved at 2.0-2.6 A. Rod-shaped fimbriae should not be thought of as being rigid inflexible structures but rather as dynamic structures which can undergo transition from a helicoidal to a fibrillar conformation to provide a degree of elasticity and plasticity to the fimbriae so that they can resist shear forces, rather like a bungee cord. At least four mechanisms have been identified in the assembly of fimbriae from fimbrin subunits, namely the chaperone-usher pathway (e.g., P-fimbriae of uropathogenic E. coli), the general secretion assembly pathway (e.g., type 4 fimbriae or N-methylphenylalanine fimbriae of P. aeruginosa, the extracellular nucleation-precipitation pathway (e.g., curli of E. coli) and the CFA/I, CS1 and CS2 fimbrial pathway.
Preview · Article · Jan 1997 · FEMS Immunology & Medical Microbiology