VGJ phi, a novel filamentous phage of Vibrio cholerae, integrates into the same chromosomal site as CTX phi

We describe a novel filamentous phage, designated VGJ phi, isolated from strain SG25-1 of Vibrio cholerae O139, which infects all O1 (classical and El Tor) and O139 strains tested. The sequence of the 7,542 nucleotides of the phage genome reveals that VGJ phi has a distinctive region of 775 nucleotides and a conserved region with an overall genomic organization similar to that of previously characterized filamentous phages, such as CTX phi of V. cholerae and Ff phages of Escherichia coli. The conserved region carries 10 open reading frames (ORFs) coding for products homologous to previously reported peptides of other filamentous phages, and the distinctive region carries one ORF whose product is not homologous to any known peptide. VGJ phi, like other filamentous phages, uses a type IV pilus to infect V. cholerae; in this case, the pilus is the mannose-sensitive hemagglutinin. VGJ phi-infected V. cholerae overexpresses the product of one ORF of the phage (ORF112), which is similar to single-stranded DNA binding proteins of other filamentous phages. Once inside a cell, VGJ phi is able to integrate its genome into the same chromosomal attB site as CTX phi, entering into a lysogenic state. Additionally, we found an attP structure in VGJ phi, which is also conserved in several lysogenic filamentous phages from different bacterial hosts. Finally, since different filamentous phages seem to integrate into the bacterial dif locus by a general mechanism, we propose a model in which repeated integration events with different phages might have contributed to the evolution of the CTX chromosomal region in V. cholerae El Tor.     

Novel type of specialized transduction for CTX phi or its satellite phage RS1 mediated by filamentous phage VGJ phi in Vibrio cholerae

The main virulence factor of Vibrio cholerae, the cholera toxin, is encoded by the ctxAB operon, which is contained in the genome of the lysogenic filamentous phage CTX phi. This phage transmits ctxAB genes between V. cholerae bacterial populations that express toxin-coregulated pilus (TCP), the CTX phi receptor. In investigating new forms of ctxAB transmission, we found that V. cholerae filamentous phage VGJ phi, which uses the mannose-sensitive hemagglutinin (MSHA) pilus as a receptor, transmits CTX phi or its satellite phage RS1 by an efficient and highly specific TCP-independent mechanism. This is a novel type of specialized transduction consisting in the site-specific cointegration of VGJ phi and CTX phi (or RS1) replicative forms to produce a single hybrid molecule, which generates a single-stranded DNA hybrid genome that is packaged into hybrid viral particles designated HybP phi (for the VGJ phi/CTX phi hybrid) and HybRS phi (for the VGJ phi/RS1 hybrid). The hybrid phages replicate by using the VGJ phi replicating functions and use the VGJ phi capsid, retaining the ability to infect via MSHA. The hybrid phages infect most tested strains more efficiently than CTX phi, even under in vitro optimal conditions for TCP expression. Infection and lysogenization with HybP phi revert the V. cholerae live attenuated vaccine strain 1333 to virulence. Our results reinforce that TCP is not indispensable for the acquisition of CTX phi. Thus, we discuss an alternative to the current accepted evolutionary model for the emergence of new toxigenic strains of V. cholerae and the importance of our findings for the development of an environmentally safer live attenuated cholera vaccine.     

Molecular analysis of VCA1008: a putative phosphoporin of Vibrio cholerae

The PhoB/PhoR-dependent response to inorganic phosphate (Pi)-starvation in Vibrio cholerae O1 includes the expression of vc0719 for the response regulator PhoB, vca0033 for an alkaline phosphatase and vca1008 for an outer membrane protein (OMP). Sequences with high identity to these genes have been found in the genome of clinical and environmental strains, suggesting that the Pi-starvation response in V. cholerae is well conserved. VCA1008, an uncharacterized OMP involved in V. cholerae pathogenicity, presents sequence similarity to porins of Gram-negative bacteria such as phosphoporin PhoE from Escherichia coli . A three-dimensional model shows that VCA1008 is a 16-stranded pore-forming β-barrel protein that shares three of the four conserved lysine residues responsible for PhoE anionic specificity with PhoE. VCA1008 β-barrel apparently forms trimers that collapse into monomers by heating. Properties such as heat modifiability and resistance to denaturation by sodium dodecyl sulfate at lower temperatures permitted us to suggest that VCA1008 is a classical porin, more precisely, a phosphoporin due to its Pi starvation-induced PhoB-dependent expression, demonstrated by electrophoretic mobility shift assay and promoter fusion- lacZ assays.     

CTXphi and Vibrio cholerae: exploring a newly recognized type of phage-host cell relationship

The genes encoding cholera toxin, one of the principal virulence factors of the diarrhoeal pathogen Vibrio cholerae, are part of the genome of CTXphi, a filamentous bacteriophage. Thus, CTXphi has played a critical role in the evolution of the pathogenicity of V. cholerae. Unlike the well-studied F pilus-specific filamentous coliphages, CTXphi integrates site-specifically into its host chromosome and forms stable lysogens. Here we focus on the CTXphi life cycle and, in particular, on recent studies of the mechanism of CTXphi integration and the factors that govern lysogeny. These and other processes illustrate the remarkable dependence of CTXphi on host-encoded factors.     

Replication and integration of a Vibrio cholerae cryptic plasmid linked to the CTX prophage

We identified a 4.7 kb cryptic plasmid in all ctxAB ⁺ Vibrio cholerae strains we tested. An isolate of the V. cholerae classical biotype strain O395 that harbours the cryptic plasmid at high copy number was found. Hybridization analysis demonstrated that sequences highly related or identical to this plasmid exist in all toxigenic strains of V. cholerae but were notably absent in all non-toxigenic environmental isolates that lacked the genes for toxin-co-regulated pili and the filamentous CTX prophage. Accordingly, we have named the cryptic plasmid pTLC for toxin-linked cryptic. The complete nucleotide sequence of pTLC from the high-copy-number isolate was determined. The largest open reading frame in the plasmid is predicted to encode a protein similar to the replication initiation protein (pII) of Escherichia coli F-specific filamentous phages. The nucleotide sequence of pTLC also facilitated the structural characterization of the DNA homologous to pTLC in other strains of V. cholerae . pTLC-related DNA exists in these strains as both low-copy-number, covalently closed circular DNA and tandemly duplicated, chromosomally integrated DNA. Remarkably, the chromosomally integrated form of pTLC is adjacent to the CTX prophage. The strain distribution, chromosomal location and DNA sequence of pTLC suggests that it may be a genetic element that plays some role in the biology of CTXφ, perhaps facilitating either its acquisition or its replication.     

Molecular cloning of a gene coding for a Vibrio cholerae haemagglutinin

Recombinant plasmids encoding a Vibrio cholerae haemagglutinin were isolated from the highly virulent V. cholerae strain C5 by cosmid cloning. Both Escherichia coli HB101 containing the recombinant plasmids and V. cholerae C5 were able to agglutinate a variety of erythrocytes from human and animal origin; this haemagglutination was not inhibited by D-mannose or L-fucose. Subcloning of the recombinant cosmid DNA revealed that a 1.3 kb DNA fragment was sufficient for haemagglutinin production in E. coli HB101. Under direction of this 1.3 kb Vibrio DNA fragment, two proteins were made in E. coli minicells, of 27 and 10 kDa. Haemagglutinin-encoding sequences were not detected in every V. cholerae strain.     

Classification of hybrid and altered Vibrio cholerae strains by CTX prophage and RS1 element structure

Analysis of the CTX prophage and RS1 element in hybrid and altered Vibrio cholera O1 strains showed two classifiable groups. Group I strains contain a tandem repeat of classical CTX prophage on the small chromosome. Strains in this group either contain no element(s) or an additional CTX prophage or RS1 element(s) on the large chromosome. Group II strains harbor RS1 and CTX prophage, which has an E1 Tor type rstR and classical ctxB on the large chromosome.     

Isolation and characterization of a putative multidrug resistance pump from Vibrio cholerae

Multidrug-resistant strains of Vibrio cholerae (the causative agent of the diarrhoeal disease cholera) have recently been described. In an attempt to identify a homologue of the Escherichia coli TolC in V . cholerae , we isolated a DNA fragment (pVC) that enabled an E . coli tolC mutant to grow in the presence of 0.05% deoxycholate (DOC). However, other TolC defects were not complemented. Nucleotide sequence analysis of this fragment revealed the presence of two open reading frames (ORF1 and ORF2) separated by 9 bp and encoding 42.4 and 55.8 kDa proteins respectively. The translational products of these two ORFs correlated closely with the molecular weights of the predicted proteins. The deduced amino acid sequences of ORF1 and ORF2 showed a high degree of similarity with conserved regions of the E . coli efflux pump proteins, EmrA and EmrB. The presence of pVC2 within the E . coli efflux pump mutants defective in either the emrAB or the acrAB genes provided the mutants with resistance against several antibiotics. A V . cholerae isogenic mutant defective in ORF2 was constructed by gene replacement. Characterization of this mutant has shown it to be more sensitive to CCCP, PMA, PCP, nalidixic acid and DOC than the parent strain. These results suggest that ORF1 and ORF2 constitute an operon encoding two components of a putative multidrug resistance pump in V . cholerae . In addition, the presence of both structural and functional similarities between VceAB and EmrAB suggests that VceAB is a homologue of EmrAB.     

Ecology and genetic structure of a northern temperate Vibrio cholerae population related to toxigenic isolates

Although Vibrio cholerae is an important human pathogen, little is known about its populations in regions where the organism is endemic but where cholera disease is rare. A total of 31 independent isolates confirmed as V. cholerae were collected from water, sediment, and oysters in 2008 and 2009 from the Great Bay Estuary (GBE) in New Hampshire, a location where the organism has never been detected. Environmental analyses suggested that abundance correlates most strongly with rainfall events, as determined from data averaged over several days prior to collection. Phenotyping, genotyping, and multilocus sequence analysis (MLSA) revealed a highly diverse endemic population, with clones recurring in both years. Certain isolates were closely related to toxigenic O1 strains, yet no virulence genes were detected. Multiple statistical tests revealed evidence of recombination among strains that contributed to allelic diversity equally as mutation. This relatively isolated population discovered on the northern limit of detection for V. cholerae can serve as a model of natural population dynamics that augments predictive models for disease emergence.     

The genome polymorphism of Vibrio cholerae ctxAB(-) strains, containing the proximal part of the CTX element

The comparative analysis of the hybridization patterns of DNA restricts for 20 V. cholerae, groups 01 and non-01 (non-0139), containing the incomplete CTX element (ctxAB-) was carried out with the use of probes, complementary to the genes of the proximal part of the virulence cassettle and flanking its RS1 sequences. This group was found to be heterogeneous both in the number of copies of "truncated" CTX prophage and their localizations in the genome, as well as in the position of the sites of restriction endonucleases HindlII and BglII. Among 17 clinically noncholerigenic isolates, 5 etiologically dangerous clones were found, each of them characterized by the definite time and place of isolation. At least one of them proved to be the causative agent of the local outbreak of diarrheal diseases in Uzbekistan.     

Molecular cloning and characterization of a unique beta-glucosidase from Vibrio cholerae

We have recently reported the molecular cloning of a gene, gspK, in Vibrio cholerae that encodes a specific glucosamine kinase. We describe here the identification of bglA, a gene contiguous to gspK in a presumptive large chitin catabolic operon. BglA was molecularly cloned into Escherichia coli, and the protein BglA was overexpressed and purified to apparent homogeneity. BglA is 65 kDa (574 amino acids) with an N-terminal amino acid sequence predicted by the gene sequence, suggesting that the enzyme is cytoplasmic. The purified enzyme exhibited optimal activity with p-nitrophenyl beta-glucoside, cellobiose, and higher oligosaccharides of cellulose. No other glucosides or glycosides tested were hydrolyzed, including Glc-Glc disaccharides where the linkage is beta 1-->2, beta 1-->3, and beta 1-->6, respectively. The predicted BglA sequence bears little similarity to other proteins in the data banks. The Henrissat algorithm places BglA sequence in Family 9 of the glycosidases, suggesting it is an endoglucanase. However, the results summarized above suggested that BglA is an exoenzyme yielding Glc at each cleavage step. To resolve this apparent discrepancy, detailed kinetic studies were conducted with cellotetraose. Only exoglucanase activity was detected. The function of this enzyme in V. cholerae remains to be determined, especially because our strain of this organism does not utilize cellobiose.     

Occurrence and distribution of plankton-associated and free-living toxigenic Vibrio cholerae in a tropical estuary of a cholera endemic zone

Cholera epidemics are thought to be influenced by changes in populations of estuarine Vibrio cholerae. We investigated the abundance and distribution of this bacterium, as ??free-living?? (<20???m fraction) and associated with microphytoplankton (>20???m) or zooplankton (>60???m), in the Karnaphuli estuary of Bangladesh during pre- and post-monsoon seasons. Cultivable Vibrio populations were ~10²?C10⁴ colony forming units (CFU) ml^?1 in the high saline zone (19?C23 practical salinity unit, PSU) and declined in freshwater (<10¹?CFU?ml^?1). Culture independent detection of toxigenic V. cholerae O1 and O139 serogroups revealed a higher abundance of ??free-living?? (10⁴?C10⁵ cells?l^?1) than those attached to plankton (10¹?C10³ cells?l^?1). However, ??free-living?? O1 and O139 cells were sometimes absent in the medium saline and freshwater areas (0.0?C11 practical salinity unit [PSU]). In contrast, plankton samples always harbored these serogroups despite changes in salinity and other physico-chemical properties. Microphytoplankton and zooplankton were dominated by diatoms and blue-green algae, and copepods and rotifers, respectively. Toxigenic V. cholerae abundance did not correlate with plankton abundance or species but had a positive correlation with chitin in the <20???m fraction, where suspended particulate matter (SPM), V. cholerae and chitin concentrations were highest. C:N ratios indicated that organic matter in SPM originated predominantly from plankton. The differential occurrence of ??free-living?? and attached V. cholerae suggests a pivotal function of plankton in V. cholerae spreading into freshwater areas. The probable association of this pathogen with organisms and particles in the nanoplankton (<20???m) fraction requires validation of the concept of the ??free living?? state of V. cholerae in aquatic habitats.     

Role of iron ions in the production of hemolysin by toxigenic and nontoxigenic Vibrio cholerae of different serogroups

The hemolytic activity of ctx- and ctx+ V. cholerae, serogroups eltor and O39, in a medium free of FeCl3 was studied. During the cultivation in this medium, the strains of both V. cholerae serogroups proved to be capable of lysing sheep red blood cells in the Graig test, irrespective of the presence of ctx genes. The cultivation of V. cholerae ctx+ strains of both serogroups under such conditions facilitated the production of hemolysin with the same spectrum of lytic activity as hemolysin produced by ctx- strains.     

Genetic diversity of toxigenic and nontoxigenic Vibrio cholerae serogroups O1 and O139 revealed by array-based comparative genomic hybridization

Toxigenic serogroups O1 and O139 of Vibrio cholerae may cause cholera epidemics or pandemics. Nontoxigenic strains within these serogroups also exist in the environment, and also some may cause sporadic cases of disease. Herein, we investigate the genomic diversity among toxigenic and nontoxigenic O1 and O139 strains by comparative genomic microarray hybridization with the genome of El Tor strain N16961 as a base. Conservation of the toxigenic O1 El Tor and O139 strains is found as previously reported, whereas accumulation of genome changes was documented in toxigenic El Tor strains isolated within the 40 years of the seventh pandemic. High phylogenetic diversity in nontoxigenic O1 and O139 strains is observed, and most of the genes absent from nontoxigenic strains are clustered together in the N16961 genome. By comparing these toxigenic and nontoxigenic strains, we observed that the small chromosome of V. cholerae is quite conservative and stable, outside of the superintegron region. In contrast to the general stability of the genome, the superintegron demonstrates pronounced divergence among toxigenic and nontoxigenic strains. Additionally, sequence variation in virulence-related genes is found in nontoxigenic El Tor strains, and we speculate that these intermediate strains may have pathogenic potential should they acquire CTX prophage alleles and other gene clusters. This genome-wide comparison of toxigenic and nontoxigenic V. cholerae strains may promote understanding of clonal differentiation of V. cholerae and contribute to an understanding of the origins and clonal selection of epidemic strains.     

Identification of distinct messenger RNAs for nuclear lamin C and a putative precursor of nuclear lamin A

The lamins are the major components of the nuclear matrix and are known as lamins A, B, and C with Mr 72,000, 68,000, and 62,000 when analysed by SDS PAGE. These three polypeptides are very similar, as determined by polypeptide mapping and immunological reactivity. Lamins A and C are so homologous that a precursor-product relationship has been proposed. Using an antiserum against nuclear matrix proteins that specifically immunoprecipitates the three lamins, we examined their synthesis in the rabbit reticulocytes lysate. Four bands of Mr 62,000, 68,000, 70,000, and 74,000 were specifically immunoprecipitated when polysomes or polyadenylated RNA were translated in vitro. By two-dimensional gel electrophoresis, the 68,000- and the 62,000-mol-wt proteins were identified as lamins B and C, respectively, and the 74,000-mol-wt polypeptide had properties of a precursor of lamin A. The mRNAs of lamin C and of the putative precursor of lamin A were completely separated by gel electrophoresis under denaturing conditions, and their respective sizes were determined. These results suggest that lamin A is not a precursor of lamin C.