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Uri Gophna

Publications and source records attributed to Uri Gophna.

18 recordsLinked to original sources
PubMed2026

Short-Term Success, Long-Term Failure: Strain Turnover and Virulence Re-Emergence May Drive Relapse in Pouchitis.

BACKGROUND & AIMS: Pouchitis, de-novo small intestinal inflammation is the most common complication developing in patients with ulcerative colitis after total large bowel resection and ileal pouch-anal anastomosis (IPAA) reconstruction. While the first line treatment is antibiotics, the microbial properties underlying flare, remission, and relapse remain vague. We aimed to investigate how antibiotic treatment drives microbial shifts that underlie remission and contribute to relapse. METHODS: Patients after IPAA were prospectively recruited during clinical flare (active pouchitis defined by the pouchitis disease activity index) and received a two-week course of metronidazole with either ciprofloxacin or doxycycline. Longitudinal follow up was conducted during a year. Clinical data were recorded, and fecal samples were obtained during consequent flares, recovery, and relapses. Microbial gene repertoire, strains, and resistance to antibiotics were determined. Metagenomic sequencing was integrated with whole-genome sequencing of Escherichia coli isolates, providing strain-specific virulence and antibiotic resistance profiles. RESULTS: Patients (n=21) recruited provided 130 samples over one-year follow-up. Both antibiotic regimens induced rapid but transient clinical improvement, reflected by a decrease in fecal calprotectin (728 to 265 &#x3bc;g/g, p<.05), and a marked reduction in bacterial exotoxin genes (p<.05), yet both parameters rebounded by 6 weeks post-treatment. Antibiotic resistance gene abundance significantly increased during treatment (p<.05), without expansion of resistance gene diversity, indicating that pre-existing resistant strains increased. CONCLUSIONS: Antibiotic-induced remission in pouchitis likely results from a temporary suppression of exotoxin-producing bacteria, enabling resistant, low-virulence strains to transiently dominate; The fact that harmful strains quickly rebound after treatment cessation highlights the need for targeted approaches to achieve sustained microbial control.

Inflammatory bowel disease↗
PubMed2006

Differences between tissue-associated intestinal microfloras of patients with Crohn's disease and ulcerative colitis.

A leading hypothesis for the role of bacteria in inflammatory bowel diseases is that an imbalance in normal gut flora is a prerequisite for inflammation. Testing this hypothesis requires comparisons between the microbiota compositions of ulcerative colitis and Crohn's disease patients and those of healthy individuals. In this study, we obtained biopsy samples from patients with Crohn's disease and ulcerative colitis and from healthy controls. Bacterial DNA was extracted from the tissue samples, amplified using universal bacterial 16S rRNA gene primers, and cloned into a plasmid vector. Insert-containing colonies were picked for high-throughput sequencing, and sequence data were analyzed, yielding species-level phylogenetic data. The clone libraries yielded 3,305 sequenced clones, representing 151 operational taxonomical units. There was no significant difference between floras from inflamed and healthy tissues from within the same individual. Proteobacteria were significantly (P = 0.0007) increased in Crohn's disease patients, as were Bacteroidetes (P < 0.0001), while Clostridia were decreased in that group (P < 0.0001) in comparison with the healthy and ulcerative colitis groups, which displayed no significant differences. Thus, the bacterial flora composition of Crohn's patients appears to be significantly altered from that of healthy controls, unlike that of ulcerative colitis patients. Imbalance in flora in Crohn's disease is probably not sufficient to cause inflammation, since microbiotas from inflamed and noninflamed tissues were of similar compositions within the same individual.

Adult↗
PubMed2006

Ancient lateral gene transfer in the evolution of Bdellovibrio bacteriovorus.

The recently sequenced genome of the predatory delta-proteobacterium Bdellovibrio bacteriovorus provides many insights into its metabolism and evolution. Because its genes are reasonably uniform in G+C content, it was suggested that B. bacteriovorus actively resists recombination with foreign DNA and horizontal transfer of DNA from other bacteria. To investigate this further, we carried out a variety of phylogenetic and comparative genomics analyses using data from >200 microbial genomes, including several published delta-proteobacteria. Although there might be little evidence for the extensive recent transfer of genes, we demonstrate that ancient lateral gene acquisition has shaped the B. bacteriovorus genome to a great extent.

Bdellovibrio↗
PubMed2005

The formation of Escherichia coli curli amyloid fibrils is mediated by prion-like peptide repeats.

Amyloid fibril formation is the hallmark of major human maladies including Alzheimer's disease, type II diabetes, and prion diseases. Prion-like phenomena were also observed in yeast. Although not evolutionarily related, one similarity between the animal PrP and the yeast Sup35 prion proteins is the occurrence of short peptide repeats that are assumed to play a key role in the assembly of the amyloid structures. It was recently demonstrated that typical amyloid fibril formation is associated with biofilm formation by Escherichia coli. Here, we note the functional and structural similarity between oligopeptide repeats of the major curli protein and those of animal and yeast prions. We demonstrate that synthetic peptides corresponding to the repeats form fibrillar structures. Furthermore, conjugation of beta-breaker elements to the prion-like repeat significantly inhibits amyloid formation and cell invasion of curli-expressing bacteria. This implies a functional role of the repeat in the self-assembly of the fibrils. Since mammal prion, yeast prion, and curli protein are evolutionarily distinct, the conserved peptide repeats most likely define an optimized self-association motif that was independently evolved by diverse systems.

Amino Acid Sequence↗
PubMed2005

Complex histories of genes encoding 3-hydroxy-3-methylglutaryl-CoenzymeA reductase.

The mevalonate pathway for the synthesis of isoprenoids can be found in organisms from all domains of life. It has been previously demonstrated that the first gene specific to that pathway, which encodes the enzyme 3-hydroxy-3-methylglutaryl-CoenzymeA reductase (HMGR), has been transferred between domains by lateral gene transfer on several occasions. Here we look within the domain Bacteria at lateral acquisition of HMGR, whether as a single gene or as part of a mevalonate pathway cluster. We observe a complex history of multiple transfer events probably reflecting the fact that HMGR could be beneficial in a variety of physiological and genetic contexts. We demonstrate that even in Vibrio species, where HMGR is not clustered with other genes to form an operon or a metabolic cluster, it is under strong purifying selection.

Bacteria↗
PubMed2005

Evolutionary plasticity of methionine biosynthesis.

Methionine is an essential cellular constituent, the initiator of protein synthesis and a precursor in many metabolic activities, such as methylation and formylation. Here we investigate the genomic distribution of the methionine biosynthetic pathway and analyze its evolutionary history by reconstructing the phylogeny of its enzymatic components. We demonstrate the evolutionary complexity of methionine synthesis and describe the various mechanisms that have shaped this biosynthetic pathway: gene duplication, functional reassignment, lateral acquisition and gene loss. Lateral gene transfer within and between domains and gene recruitment have played an important role in the evolution of this pathway, especially in its first and third enzymatic steps--homoserine activation and homocysteine methylation. These analyses are also the basis of predictions regarding methionine synthesis in Archaea, where the pathway is yet to be characterized. This study illustrates how diverse molecular solutions can fulfill a conserved function in living beings.

Arabidopsis↗
PubMed2005

The lpf operon of invasive Escherichia coli.

Extraintestinal pathogenic Escherichia coli (ExPEC) strains have been shown to code for several virulence factors involved in adherence to host tissues. Here we show the existence of an additional adherence gene cluster, coding for long polar fimbriae--LPF--in several strains of serotype O78 from septicemia and newborn meningitis. The complete gene cluster was sequenced in strain 789 (lpf789), where it is located between the genes glmS and pstS, and contains four ORFs, lpfA to lpfD. The lpf operon is expressed and is important for adherence to epithelial cells. The lpf operon was found only in four of the ExPEC strains tested and is likely to have been acquired by horizontal gene transfer.

Bacterial Adhesion↗
PubMed2005

Virulence factors of septicemic Escherichia coli strains.

Extraintestinal pathogenic Escherichia coli strains (ExPEC) are the cause of a diverse spectrum of invasive human and animal infections, often leading to septicemia. This review deals with the virulence genes of septicemic ExPEC strains. We discuss the meaning of a virulence gene and survey the genomic, genetic and physiological studies on these strains. Apparently, there are a few virulence factors, which are conserved in the septicemic strains, implying that they are essential for the infection. For the other virulence-related genes a high level of diversity is observed, demonstrating that all stages of the infection can be mediated by a number of alternative virulence factors. The variable profile of virulence genes in septicemic E. coli strains, as well as a prevalence of mobility-related sequences point out the existence of a "mix and match" combinatorial system.

Adhesins, Escherichia coli↗
PubMed2005

A degenerate type III secretion system from septicemic Escherichia coli contributes to pathogenesis.

The type III secretion system (T3SS) is an important virulence factor used by several gram-negative bacteria to deliver effector proteins which subvert host cellular processes. Enterohemorrhagic Escherichia coli O157 has a well-defined T3SS involved in attachment and effacement (ETT1) and critical for virulence. A gene cluster potentially encoding an additional T3SS (ETT2), which resembles the SPI-1 system in Salmonella enterica, was found in its genome sequence. The ETT2 gene cluster has since been found in many E. coli strains, but its in vivo role is not known. Many of the ETT2 gene clusters carry mutations and deletions, raising the possibility that they are not functional. Here we show the existence in septicemic E. coli strains of an ETT2 gene cluster, ETT2(sepsis), which, although degenerate, contributes to pathogenesis. ETT2(sepsis) has several premature stop codons and a large (5 kb) deletion, which is conserved in 11 E. coli strains from cases of septicemia and newborn meningitis. A null mutant constructed to remove genes coding for the putative inner membrane ring of the secretion complex exhibited significantly reduced virulence. These results are the first demonstration of the importance of ETT2 for pathogenesis.

Animals↗
PubMed2005

Weighted genome trees: refinements and applications.

There are many ways to group completed genome sequences in hierarchical patterns (trees) reflecting relationships between their genes. Such groupings help us organize biological information and bear crucially on underlying processes of genome and organismal evolution. Genome trees make use of all comparable genes but can variously weight the contributions of these genes according to similarity, congruent patterns of similarity, or prevalence among genomes. Here we explore such possible weighting strategies, in an analysis of 142 prokaryotic and 5 eukaryotic genomes. We demonstrate that alternate weighting strategies have different advantages, and we propose that each may have its specific uses in systematic or evolutionary biology. Comparisons of results obtained with different methods can provide further clues to major events and processes in genome evolution.

Animals↗
PubMed2005

Extensive gene diversity in septicemic Escherichia coli strains.

Extraintestinal pathogenic Escherichia coli strains (ExPEC) are the cause of a diverse spectrum of invasive infections in humans and animals, and these infections often lead to septicemia. Strains of serogroups O2 and O78 of E. coli are involved in human urinary tract infections and newborn meningitis and also constitute the major serotypes involved in avian colisepticemia. In the present study we compared the unique genomic sequences of two such septicemic strains, strains O2-1772 and O78-9, obtained by suppression subtractive hybridization. Evaluation of the degree of similarity between these two strains, which cause the same disease, revealed a high degree of diversity, with only a few shared genes. Subsequently, additional strains of each serogroup of human and animal origin were screened by PCR, and the results provided further evidence for the existence of a high degree of genome plasticity. These results were unexpected, in view of data showing that the two O157:H7 strains that have been sequenced are nearly identical in terms of virulence factors. Furthermore, the data obtained for the septicemic strains suggest that each step in the infection can be mediated by a number of alternative virulence factors, indicating the existence of a mix-and-match combinatorial system. Although whole-genome comparisons of E. coli strains causing different diseases have shown great differences in gene contents, we show that such differences exist even within strains that cause the same disease and that target the same host tissues. Moreover, in addition to the high level of genome plasticity, we show that the large pool of virulence genes in the septicemic strains is independent of the host, implying a high degree of zoonotic risk.

Animals↗
PubMed2004

OmpA of a septicemic Escherichia coli O78--secretion and convergent evolution.

OmpA is an important constituent of the outer membrane of Gram-negative bacteria. OmpA is involved in a variety of host-bacteria interactions, including crossing of the blood-brain barrier by E. coli strains causing newborn meningitis, and elicits a significant response by the immune system of the host. The bactericidal effect of neutrophil elastase (NE) is also attributed to degradation of the bacterial OmpA. Here we examined the OmpA of septicemic E. coli 078 strains and show that two surface-exposed loops are conserved among invasive strains of E. coli and other pathogenic Enterobacteriaceae. In addition, there is evidence for convergent evolution, implying the existence of selective pressure. Our results also indicate that large quantities of OmpA are secreted into the medium during all phases of growth, where it is present both in secreted vesicles and as a soluble secreted protein. We assume that secreted OmpA can play a role in protection of bacteria from NE by competitive inhibition. Support for this assumption was obtained from experiments indicating that addition of exogenous, purified OmpA reduces killing of bacteria by NE.

Amino Acid Sequence↗
PubMed2003

Bacterial type III secretion systems are ancient and evolved by multiple horizontal-transfer events.

Type III secretion systems (TTSS) are unique bacterial mechanisms that mediate elaborate interactions with their hosts. The fact that several of the TTSS proteins are closely related to flagellar export proteins has led to the suggestion that TTSS had evolved from flagella. Here we reconstruct the evolutionary history of four conserved type III secretion proteins and their phylogenetic relationships with flagellar paralogs. Our analysis indicates that the TTSS and the flagellar export mechanism share a common ancestor, but have evolved independently from one another. The suggestion that TTSS genes have evolved from genes encoding flagellar proteins is effectively refuted. A comparison of the species tree, as deduced from 16S rDNA sequences, to the protein phylogenetic trees has led to the identification of several major lateral transfer events involving clusters of TTSS genes. It is hypothesized that horizontal gene transfer has occurred much earlier and more frequently than previously inferred for TTSS genes and is, consequently, a major force shaping the evolution of species that harbor type III secretion systems.

Bacteria↗
PubMed2003

Multilocus sequence typing (MLST) of Escherichia coli O78 strains.

Strains of Escherichia coli serotype O78 are associated with many diseases, including invasive infections, in humans and farm animals. The clonal relationship between strains from different hosts is therefore important for assessing the risk of zoonotic infections. Here we propose a multilocus sequence typing scheme for E. coli, based on six housekeeping genes. Preliminary, but significant, results indicate that clonal division in E. coli O78 strains is host independent, and closely related clones reside in different hosts. There was a positive correlation between virulence and clonal origin.

Acyltransferases↗
PubMed2003

Virulence and the heat shock response.

The major adaptive response to elevation in temperature is the heat shock response that involves the induction of many proteins--called heat shock proteins. These include chaperones, proteases, alternative sigma factors and other regulatory and structural proteins. The heat shock response is also turned on by other stress conditions, such as oxidative stress or pH changes. Bacterial entry into the host organism involves a significant environmental change, which is expected to induce the heat shock response. Indeed, some of the heat shock proteins are themselves virulence factors while others affect pathogenesis indirectly, by increasing bacterial resistance to host defenses or regulating virulence genes. The cross talk between heat shock and virulence genes is discussed.

Animals↗
PubMed2003

A novel ColV plasmid encoding type IV pili.

Many septicaemic Escherichia coli strains harbour ColV virulence plasmids. This paper describes pO78V, a conjugative ColV plasmid from an avian pathogenic E. coli strain that encodes type IV pili in addition to other virulence-related genes and tetracycline resistance. Plasmid location of type IV pili genes was demonstrated using Southern hybridization and expression of the pili was demonstrated using RT-PCR and phage sensitivity assays. This is a first report of a ColV plasmid encoding type IV pili. Plasmid pO78V is a mosaic plasmid containing replicons and other genes typical to both IncI1 and IncFII groups. As type IV pili of Gram-negative bacteria are involved in several stages of infection, their presence on a ColV virulence plasmid could expand the repertoire of pathogenesis-related genes.

Animals↗
PubMed2002

Role of fibronectin in curli-mediated internalization.

Curli fibers of Escherichia coli mediate internalization of bacteria by eukaryotic cells. As curli fibers bind fibronectin with high affinity, the role of fibronectin in the uptake process was studied. The experiments presented here support the involvement of fibronectin in internalization of bacteria. Furthermore, a peptide containing the RGD motif, responsible for interaction of fibronectin with cellular integrins, can strongly inhibit curli-mediated internalization. The ability of curli fibers to bind fibronectin can therefore be linked to virulence.

Bacterial Proteins↗