Use of RNA arbitrarily primed-PCR fingerprinting to identify Vibrio cholerae genes differentially expressed in the host following infection

RNA fingerprinting analysis of Oenococcus oeni strains under wine conditions

Oenococcus oeni is a lactic acid bacterium of economic interest used in winemaking. This bacterium is the preferred species for malolactic fermentation (MLF) due its adaptability to the chemically harsh wine environment. MLF enhances the organoleptic properties and ensures deacidification of wines. The aim of this work was the transcriptional characterization of six O. oeni strains, four of them selected from distinct winemaking regions of Portugal, as candidates to malolactic starters, and two commercial malolactic starters. Using crossed assays with wines from different Portuguese winemaking regions, strain characteristic transcriptional patterns induced by each wine were analyzed based on Random Arbitrarily Primed PCR (RAP-PCR). The obtained results suggest that the starter strains showed more constrained and limited transcription profiles, whereas a high variation on the distribution of the transcription profiles was observed for the regional strains in each wine. According with our results, RAP-PCR is a useful technique for a preliminary investigation of strain behavior under different wine environmental conditions, which can be applied in field studies to monitor differential patterns of global gene expression and to select markers for the surveillance of malolactic starters performance in winemaking, as well as for quality and safety control.

Aga1, the first alpha-Galactosidase from the human bacteria Ruminococcus gnavus E1, efficiently transcribed in gut conditions

Differential gene expression analysis was performed in monoxenic mice colonized with Ruminococcus gnavus strain E1, a major endogenous member of the gut microbiota. RNA arbitrarily primed-PCR fingerprinting assays allowed to specifically detect the in vivo expression of the aga1 gene, which was further confirmed by RT-PCR. The aga1 gene encoded a protein of 744 residues with calculated molecular mass of 85,207 Da. Aga1 exhibited significant similarity with previously characterized α-Galactosidases of the GH 36 family. Purified recombinant protein demonstrated high catalytic activity (104 ± 7 U mg(-1)) and efficient p-nitrophenyl-α-d-galactopyranoside hydrolysis [k(cat)/K(m) = 35.115 ± 8.82 s(-1) mM(-1) at 55 °C and k(cat)/K(m) = 17.48 ± 4.25 s(-1) mM(-1) at 37 °C].

Inter-specific interactions between carbon-limited soil bacteria affect behavior and gene expression

Recent publications indicate that inter-specific interactions between soil bacteria may strongly affect the behavior of the strains involved, e.g., by increased production of antibiotics or extracellular enzymes. This may point at an enhanced competitive ability due to inter-specific triggering of gene expression. However, it is not known if such inter-specific interactions also occur during competition for carbon which is the normal situation in soil. Here, we report on competitive interactions between two taxonomically non-related bacterial strains, Pseudomonas sp. A21 and Pedobacter sp. V48, that were isolated from a dune soil. The strains showed strong effects on each other's behavior and gene expression patterns when growing together under carbon-limited conditions on agar. The most pronounced observed visual changes in mixed cultures as compared to monocultures were (1) strong inhibition of a bioindicator fungus, suggesting the production of a broad-spectrum antibiotic, and (2) the occurrence of gliding-like movement of Pedobacter cells. Two independent techniques, namely random arbitrary primed-PCR (RAP-PCR) and suppressive subtractive hybridization (SSH), identified in total 24 genes that had higher expression in mixed cultures compared to monocultures. Microbial interactions were clearly bidirectional, as differentially expressed genes were detected for both bacteria in mixed cultures. Sequence analysis of the differentially expressed genes indicated that several of them were most related to genes involved in motility and chemotaxis, secondary metabolite production and two-component signal transduction systems. The gene expression patterns suggest an interference competition strategy by the Pseudomonas strain and an escape/explorative strategy by the Pedobacter strain during confrontation with each other. Our results show that the bacterial strains can distinguish between intra- and inter-specific carbon competition.

Differential regulation of interchromosomal copies of ToxR-induced genes

In Vibrio cholerae, ToxR transcriptionally activates a number of virulence genes in response to various environmental signals. In the present study, transcription profiling by macroarray was carried out with 13 pairs of genes, one copy of which is present in each chromosome under ToxR-inducing (pH 6.5, osmolarity 66 mmol/L, 30 degrees C) and ToxR-repressing (pH 8.5, osmolarity 300 mmol/L, 37 degrees C) conditions followed by high pH (8.5) and low pH (6.5) conditions to eliminate pH effect. The genes dacAII, tagEII, secDII, pmmI, pmmII, and immII showed increased expression in the ToxR-inducing conditions, but not at low pH, suggesting that the expression of these genes might be regulated by ToxR. The expression of pmmII, dacAII, tagEII, secDII, and immII genes decreased significantly in the toxR insertion mutant as determined by RT-PCR, whereas the expression of the chromosome I copy of pmm increased in toxR mutant compared with wild-type cells. Thus, the chromosome II copy of these genes, which show increased expression under ToxR-inducing conditions, are all regulated by ToxR in V. cholerae, whereas the chromosome I copy of pmm may be regulated by other factors under ToxR-inducing conditions.

Genomic instabilities in squamous cell carcinoma of head and neck from the Indian population

Intrinsic genomic instability of an incipient tumor cell drives the development of cancer. In colorectal cancer, an inverse relationship between microsatellite instability (MIN) and chromosomal instability (CIN) has been reported. The relationship between MIN and CIN in head and neck squamous cell carcinoma (HNSCC) is uncertain. In the present study, we examined these two types of instabilities in HNSCC using microsatellite markers and arbitrary primed PCR (APPCR) technique. HNSCC tumors showed high frequency of MIN and loss of heterozygosity (LOH). We observed that, in contrast to colorectal tumors, the frequency of LOH increased with the increase in MIN. There was no significant difference between MIN- and MIN+ groups of HNSCC tumors in the extent of overall genomic alterations; rather higher MIN+ tumors exhibited higher incidence of deletion. Thus, in sporadic HNSCC, both MIN and CIN pathways operate simultaneously to drive tumor formation.

In vivo induced clpB1 gene of Vibrio cholerae is involved in different stress responses and affects in vivo cholera toxin production

Previously in global transcription profile approach one of the cosmid clones of Vibrio cholerae containing the genes pnuC, icmF, and a fragment of clpB2 showed higher expression in V. cholerae grown inside rabbit intestine. In the present report, both the stress responsive clpB genes of V. cholerae O395 were cloned, clpB1 from chromosome I and clpB2 present in chromosome II. From the Northern blot hybridization it was observed that the level of transcription of clpB2 was very low which could be due to the weak promoter strength of clpB2 as predicted in silico. The deduced amino acid sequence showed that clpB1 possesses features typical of the ClpB ATPase family of stress response proteins. The clpB1 gene showed about three times higher expression under in vivo condition than in vitro. Increased expression of clpB1 gene was also observed at high temperature, high salt, and in the condition mimicking human intestine viz., 37 degrees C, pH 8.5, 300 mM NaCl, which is known to be the repressive condition for ToxR, the global transcriptional regulator of virulence in V. cholerae. The clpB1 insertion mutant showed increased sensitivity towards high temperature, oxidative stress, and acid pH. ClpB1 also conferred thermotolerance to V. cholerae. These effects could be reversed by complementation. Although clpB1 appeared not to be under the control of virulence regulatory cascade of V. cholerae, the CT production was reduced in clpB1 mutant when tested in vivo in an infant mice model.

Upregulation of human mitochondrial NADH dehydrogenase subunit 5 in intestinal epithelial cells is modulated byVibrio choleraepathogenesis

Cholera still remains an important global predicament especially in India and other developing countries. Vibrio cholerae, the etiologic agent of cholera, colonizes the small intestine and produces an enterotoxin that is largely responsible for the watery diarrheal symptoms of the disease. Using RNA arbitrarily primed PCR, ND5 a mitochondria encoded subunit of complex I of the mitochondrial respiratory chain was found to be upregulated in the human intestinal epithelial cell line Int407 following exposure to V. cholerae. The upregulation of ND5 was not observed when Int407 was infected with Escherichia coli strains. Incubation with heat-killed V. cholerae or cholera toxin or culture supernatant also showed no such upregulation indicating the involvement of live bacteria in the process. Infection of the monolayer with aflagellate non-motile mutant of V. cholerae O395 showed a very significant (59-fold) downregulation of ND5. In contrast, a remarkable upregulation of ND5 expression (200-fold) was observed in a hyperadherent icmF insertion mutant with reduced motility. V. cholerae cheY4 null mutant defective in adherence and motility also resulted in significantly reduced levels of ND5 expression while mutant with the cheY4 gene duplicated showing increased adherence and motility resulted in increased expression of ND5. These results clearly indicate that both motility and adherence to intestinal epithelial cells are possible triggering factors contributing to ND5 mRNA expression by V. cholerae. Interestingly infection with insertion mutant in the gene coding for ToxR, the master regulator of virulence in V. cholerae resulted in significant downregulation of ND5 expression. However, infection with ctxA or toxT insertion mutants did not show any significant changes in ND5 expression compared to wild-type. Almost no expression of ND5 was observed in case of mutation in the gene coding for OmpU, a ToxR activated protein. Thus, infection of Int407 with virulence mutant strains of V. cholerae revealed that the ND5 expression is modulated by the virulence of V. cholerae in a ToxT independent manner. Although no difference in the mitochondrial copy number could be detected between infected and uninfected cells, the modulation of the expression of other mitochondrial genes were also observed. Incidentally, upon V. cholerae infection, complex I activity was found to increase about 3-folds after 6 h. This is the first report of alteration in mitochondrial gene expression upon infection of a non-invasive enteric bacterium like V. cholerae showing its modulation with adherence, motility and virulence of the organism.

Lipopolysaccharides of Vibrio cholerae

An account of our up to date knowledge of the genetics of biosynthesis of Vibrio cholerae lipopolysaccharide (LPS) is presented in this review. While not much information is available in the literature on the genetics of biosynthesis of lipid A of V. cholerae, the available information on the characteristics and proposed functions of the corepolysaccharide (core-PS) biosynthetic genes is discussed. The genetic organizations encoding the O-antigen polysaccharides (O-PS) of V. cholerae of serogroups O1 and O139, the disease causing ones, have been described along with the putative functions of the different constituent genes. The O-PS biosynthetic genes of some non-O1, non-O139 serogroups, particularly the serogroups O37 and O22, and their putative functions have also been discussed briefly. In view of the importance of the serogroup O139, the origination of the O139 strain and the possible donor of the corresponding O-PS gene cluster have been analyzed with a view to having knowledge of (i) the mode of evolution of different serogroups and (ii) the possible emergence of pathogenic strain(s) belonging to non-O1, non-O139 serogroups. The unsolved problems in this area of research and their probable impact on the production of an effective cholera vaccine have been outlined in conclusion.

Identification of differential gene expression in bacteria associated with coral black band disease by using RNA-arbitrarily primed PCR

RNA-arbitrarily primed PCR techniques have been applied for the first time to identify differential gene expression in black band disease (BBD), a virulent coral infection that affects reef ecosystems worldwide. The gene activity for the BBD mat on infected surfaces of the brain coral Diploria strigosa was compared with that for portions of the BBD mat that were removed from the coral and suspended nearby in the seawater column. The results obtained indicate that three genes (DD 95-2, DD 95-4, and DD 99-9) were up-regulated in the BBD bacterial mat on the coral surface compared to the transcript base levels observed in the BBD mat suspended in seawater. Clone DD 95-4 has homology with known amino acid ABC transporter systems in bacteria, while clone DD 99-9 exhibits homology with chlorophyll A apoprotein A1 in cyanobacteria. This protein is essential in the final conformation of photosystem I P700. DD 95-2, the only gene that was fully repressed in the BBD mat samples suspended in seawater, exhibited homology with the AraC-type DNA binding domain-containing proteins. These transcriptional activators coordinate the expression of genes essential for virulence in many species of gram-negative bacteria.

Identification of Porphyromonas gingivalis genes specifically expressed in human gingival epithelial cells by using differential display reverse transcription-PCR

Porphyromonas gingivalis, one of the causative agents of adult periodontitis, can invade and survive within host epithelial cells. The molecular mechanisms by which P. gingivalis induces uptake and adapts to an intracellular environment are not fully understood. In this study, we have investigated the genetic responses of P. gingivalis internalized within human gingival epithelial cells (GECs) in order to identify factors involved in invasion and survival. We compared the differential display of arbitrarily PCR-amplified gene transcripts in P. gingivalis recovered from GECs with the display of transcripts in P. gingivalis control cultures. Over 20 potential differentially expressed transcripts were identified. Among these, pepO, encoding an endopeptidase, and genes encoding an ATP-binding cassette (ABC) transporter and a cation-transporting ATPase were upregulated in GECs. To investigate the functionality of these gene products, mutants were generated by insertional inactivation. Compared to the parental strain, mutants of each gene showed a significant reduction in their invasion capabilities. In addition, GEC cytoskeletal responses to the mutants were distinct from those induced by the parent. In contrast, adhesion of the mutant strains to GECs was not affected by lack of expression of the gene products. These results suggest that PepO, a cation-transporting ATPase, and an ABC transporter are required for the intracellular lifestyle of P. gingivalis.

Differential expression of Desulfovibrio vulgaris genes in response to Cu(II) and Hg(II) toxicity

The response of Desulfovibrio vulgaris to Cu(II) and Hg(II) was characterized. Both metals increased the lag phase, and Cu(II) reduced cell yield at concentrations as low as 50 microM. mRNA expression was analyzed using random arbitrarily primed PCR, differential display, and quantitative PCR. Both Cu(II) and Hg(II) (50 micro M) caused upregulation of mRNA expression for an ATP binding protein (ORF2004) and an ATPase (ORF856) with four- to sixfold increases for Hg(II) and 1.4- to 3-fold increases with Cu(II). These results suggest that D. vulgaris uses an ATP-dependent mechanism for adapting to toxic metals in the environment.

A search for virulence genes of Haemophilus parasuis using differential display RT-PCR

Although Haemophilus parasuis is an important bacterial pathogen of swine, little is known about its pathogenesis or why some strains seem to be more virulent than others. Therefore, we used differential display reverse transcription-polymerase chain reaction (DDRT-PCR) to search for virulence-associated genes in a pathogenic serotype 5 strain, H. parasuis 1185. Gene expression was evaluated following growth in conditions chosen to begin to approximate those found in the upper respiratory tract and those encountered by the organism during acute infection. Seven different differentially expressed gene fragments were identified in cells grown at 40 degrees C in both the presence and absence of swine serum. Based on the deduced amino acid sequences, the most strongly up-regulated genes were homologs of fadD (a fatty acyl-CoA synthetase), apaH (diadenosine tetraphosphatase), pstI (enzyme I of the phosphoenolpyruvate-protein phosphotransferase system), and cysK (cysteine synthetase). Homologs of Std (Na(+)- and Cl(-)-dependent ion transporter), HSPG (a mammalian basement membrane-specific heparin sulphate core protein precursor) and PntB (pyridine nucleotide transhydrogenase) were also up-regulated, but to a much lower extent. Sequences homologous to all of the differentially expressed genes were detected in the reference strains of all 15 H. parasuis serotypes. This is the first report of a global search for virulence factors of H. parasuis.

DegS is necessary for virulence and is among extraintestinal Escherichia coli genes induced in murine peritonitis

Extraintestinal Escherichia coli strains cause meningitis, sepsis, urinary tract infection, and other infections outside the bowel. We examined here extraintestinal E. coli strain CFT073 by differential fluorescence induction. Pools of CFT073 clones carrying a CFT073 genomic fragment library in a promoterless gfp vector were inoculated intraperitoneally into mice; bacteria were recovered by lavage 6 h later and then subjected to fluorescence-activated cell sorting. Eleven promoters were found to be active in the mouse but not in Luria-Bertani (LB) broth culture. Three are linked to genes for enterobactin, aerobactin, and yersiniabactin. Three others are linked to the metabolic genes metA, gltB, and sucA, and another was linked to iha, a possible adhesin. Three lie before open reading frames of unknown function. One promoter is associated with degS, an inner membrane protease. Mutants of the in vivo-induced loci were tested in competition with the wild type in mouse peritonitis. Of the mutants tested, only CFT073 degS was found to be attenuated in peritoneal and in urinary tract infection, with virulence restored by complementation. CFT073 degS shows growth similar to that of the wild type at 37 degrees C but is impaired at 43 degrees C or in 3% ethanol LB broth at 37 degrees C. Compared to the wild type, the mutant shows similar serum survival, motility, hemolysis, erythrocyte agglutination, and tolerance to oxidative stress. It also has the same lipopolysaccharide appearance on a silver-stained gel. The basis for the virulence attenuation is unclear, but because DegS is needed for sigma(E) activity, our findings implicate sigma(E) and its regulon in E. coli extraintestinal pathogenesis.

Involvement of in vivo induced cheY-4 gene of Vibrio cholerae in motility, early adherence to intestinal epithelial cells and regulation of virulence factors

Using a global transcription profile approach cheY-4 of Vibrio cholerae was identified as an in vivo induced gene. In the present study, duplication of the gene in the chromosome resulted in increased motility, increased chemotactic response towards isolated intestinal mucus layer and stronger adhesion to human intestinal epithelial cell line at an early phase of infection compared to wild type and a null mutant strain. In contrast to the cheY-4 null mutant, duplication of cheY-4 gene resulted in increased expression of ctxAB and tcpA, the two major virulence genes of V. cholerae.

Involvement of in vivo induced icmF gene of Vibrio cholerae in motility, adherence to epithelial cells, and conjugation frequency

Previously, using global transcription profile approach icmF gene of Vibrio cholerae was identified as an in vivo induced gene. In the present study, the icmF gene of V. cholerae O395 was cloned, sequenced, and used to construct an icmF insertion mutant. This IcmF is homologous to Legionella pneumophila IcmF, belonging to the icm cassette responsible for macrophage killing and intracellular survival of the organism. The icmF insertion mutant exhibited reduced motility and increased adherence to human intestinal epithelial cells. The presence of ATP-GTP-binding site suggests further a possible role of IcmF as a signaling molecule. Triparental-mating assay, with the mutant as a recipient, showed higher conjugation frequency than wild type. We propose that the increased adherence to epithelial cell line and increased conjugation frequency of the mutant result from some sort of cell surface reorganization.

RNA arbitrarily primed PCR survey of genes regulated by ToxR in the deep-sea bacterium Photobacterium profundum strain SS9

We are currently investigating the role of ToxR-mediated gene regulation in Photobacterium profundum strain SS9. SS9 is a moderately piezophilic ("pressure loving") psychrotolerant marine bacterium belonging to the family Vibrionaceae. In Vibrio cholerae, ToxR is a transmembrane DNA binding protein involved in mediating virulence gene expression in response to various environmental signals. A homolog to V. cholerae ToxR that is necessary for pressure-responsive gene expression of two outer membrane protein-encoding genes was previously found in SS9. To search for additional genes regulated by ToxR in SS9, we have used RNA arbitrarily primed PCR (RAP-PCR) with wild-type and toxR mutant strains of SS9. Seven ToxR-activated transcripts and one ToxR-repressed transcript were identified in this analysis. The cDNAs corresponding to these partial transcripts were cloned and sequenced, and ToxR regulation of their genes was verified. The products of these genes are all predicted to fall into one or both of two functional categories, those whose products alter membrane structure and/or those that are part of a starvation response. The transcript levels of all eight newly identified genes were also characterized as a function of hydrostatic pressure. Various patterns of pressure regulation were observed, indicating that ToxR activation or repression cannot be used to predict the influence of pressure on gene expression in SS9. These results provide further information on the nature of the ToxR regulon in SS9 and indicate that RAP-PCR is a useful approach for the discovery of new genes under the control of global regulatory transcription factors.

Lessons to be learned from studying Vibrio cholerae in model systems

A response to The complete genome sequence of Vibrio cholerae: a tale of two chromosomes and of two lifestyles, by Gary K Schoolnik and Fitnat H Yildiz, Genome Biology 2000 1:reviews1016.1-1016.3.

Comparison of global transcription responses allows identification of Vibrio cholerae genes differentially expressed following infection

Comparison of global transcription profiles of Vibrio cholerae grown in vitro and in vivo revealed that 20% of the genome was repressed and about 5% was induced under in vivo conditions. Hybridization with the cloned genes revealed that the virulence genes ctx, toxR, toxT and tcpA were induced under in vivo conditions. Dissection of two in vivo induced cosmids identified another set of three genes homologous to che Y1 involved in motility and chemotaxis, pnuC encoding the major component of the nicotinamide mononucleotide transport system and icmF belonging to a cassette involved in multiplication inside host cells. These results demonstrate that the global transcription profile approach might be a powerful method for identification of differentially expressed transcripts under in vivo conditions.