- Volume 148, Issue 5, 2002
Volume 148, Issue 5, 2002
- Mini-Review
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- Microbiology Comment
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- Research Paper
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Fine-scale genetic analyses reveal unexpected spatial-temporal heterogeneity in two natural populations of the commercial mushroom Agaricus bisporus
More LessThis study examined the fine-scale genetic variation of the commercial mushroom, Agaricus bisporus, over 2 years at two sites in France. One site was a meadow fertilized with horse manure and disturbed regularly by humans; the other was a Monterey cypress forest free of human disturbance. Altogether, 50 mushrooms were collected and analysed for mitochondrial and nuclear genetic variation marked by RFLPs and multilocus enzyme electrophoretic polymorphisms. Population samples from these two sites were genetically different and both sites contained high levels of genetic diversity. No identical genotypes were found at either site between the 2 years and there was little evidence for extensive vegetative clonality for this species. Contrary to expectations, very limited evidence of pseudohomothallic reproduction was found. Results from tests of Hardy–Weinberg equilibrium and genotypic equilibrium showed that outcrossing and recombination have played significant roles in both populations. The results demonstrated spatial-temporal genetic heterogeneity of A. bisporus in natural populations.
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Production of a monoclonal antibody specific to the genus Trichoderma and closely related fungi, and its use to detect Trichoderma spp. in naturally infested composts
More LessStudies of the interactions between hyperparasitic fungi and their hosts are severely hampered by the absence of methods that allow the unambiguous identification of individual genera in complex environments that contain mixed populations of fungi, such as soil or compost. This study details the development of a monoclonal antibody (MF2) that allows the detection and recovery of Trichoderma spp. in naturally infested composts, and the visualization of hyperparasitic strains of Trichoderma during antagonistic interactions with their hosts. Murine monoclonal antibody MF2, of immunoglobulin class M (IgM), was raised against a protein epitope of a glycoprotein antigen(s) specific for species of the genus Trichoderma and for the closely related fungi Gliocladium viride, Hypomyces chrysospermus, Sphaerostilbella spp. and Hypocrea spp. MF2 did not react with antigens from Gliocladium catenulatum, Gliocladium roseum, Nectria ochroleuca and Clonostachys spp., nor with a range of unrelated soil- and compost-borne fungi. Extracellular production of the MF2 antigen was constitutive. Western-blotting analysis showed that MF2 bound to a ladder of proteins with apparent molecular masses in the range 35–200 kDa. Immunofluorescence studies showed that MF2 bound strongly to the cell walls of hyphae and phialides and the intercalary and terminal chlamydospores of Trichoderma spp., whereas immunogold electron microscopy revealed strong binding of MF2 to the cell walls and septa of hyphae and to the cell walls of phialoconidia. In immunofluorescence studies of dual cultures of Trichoderma and Rhizoctonia solani, only the cell walls of the hyperparasite, which coiled around the host, were stained by MF2. The specificity of MF2 enabled the development of a combined baiting–ELISA technique for the detection of Trichoderma spp. in naturally infested composts. The specificity of this technique was confirmed by phylogenetic analysis based on sequences of the ITS1–5·8S–ITS2 rRNA-encoding regions of the isolates.
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Disruption in Candida albicans of the TPS2 gene encoding trehalose-6-phosphate phosphatase affects cell integrity and decreases infectivity
More LessThe EMBL accession number for the sequence reported in this paper is AJ242990.
The gene CaTPS2 encoding trehalose-6-phosphate (T6P) phosphatase from Candida albicans has been cloned and disrupted in this organism. The Catps2/Catps2 mutant did not accumulate trehalose but accumulated high levels of T6P. Disruption of the two copies of the CaTPS2 gene did not abolish growth even at 42 °C, but decreased the growth rate. In the stationary phase, the Catps2/Catps2 mutant aggregated, more than 50% of its cells became permeable to propidium iodide and a large amount of protein was found in the culture medium. Aggregation occurred only at pH values higher than 7 and was avoided by osmoprotectants; it was never observed during the exponential phase of growth. The mutant formed colonies with a smooth border on Spider medium. Mice inoculated with 1·5×106 c.f.u. of wild-type cells died after 8 days, while 80% of those inoculated with the same number of c.f.u. of the Catps2/Catps2 mutant survived for at least 1 month. Reintroduction of the wild-type CaTPS2 gene in the Catps2/Catps2 mutant abolished the phenotypes described. It is hypothesized that the accumulation of T6P interferes with the assembly of a normal cell wall.
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The ARO4 gene of Candida albicans encodes a tyrosine-sensitive DAHP synthase: evolution, functional conservation and phenotype of Aro3p-, Aro4p-deficient mutants
The GenBank accession number for the sequence reported in this paper is U53216.
The enzyme 3-deoxy-D-arabinoheptulosonate-7-phosphate (DAHP) synthase catalyses the first step in aromatic amino acid biosynthesis in prokaryotes, plants and fungi. Cells of Saccharomyces cerevisiae contain two catalytically redundant DAHP synthases, encoded by the genes ARO3 and ARO4, whose activities are feedback-inhibited by phenylalanine and tyrosine, respectively. ARO3/4 gene transcription is controlled by GCN4. The authors previously cloned an ARO3 gene orthologue from Candida albicans and found that: (1) it can complement an aro3 aro4 double mutation in S. cerevisiae, an effect inhibited by excess phenylalanine, and (2) a homozygous aro3-deletion mutant of C. albicans is phenotypically Aro+, suggesting the existence of another isozyme(s). They now report the identification and functional characterization of the C. albicans orthologue of S. cerevisiae Aro4p. The two Aro4p enzymes share 68% amino acid identity. Phylogenetic analysis places the fungal DAHP synthases in a cluster separate from prokaryotic orthologues and suggests that ARO3 and ARO4 arose from a single gene via a gene duplication event early in fungal evolution. C. albicans ARO4 mRNA is elevated upon amino acid starvation, consistent with the presence of three putative Gcn4p-responsive elements (GCREs) in the gene promoter sequence. C. albicans ARO4 complements an aro3 aro4 double mutation in S. cerevisiae, an effect inhibited by excess tyrosine. The authors engineered Δaro3/Δaro3 Δaro4/MET3p::ARO4 cells of C. albicans (with one wild-type copy of ARO4 placed under control of the repressible MET3 promoter) and found that they fail to grow in the absence of aromatic amino acids when ARO4 expression is repressed, and that this growth defect can be partially rescued by aromatic amino acids and certain aromatic amino acid pathway intermediates. It is concluded that, like S. cerevisiae, C. albicans contains two DAHP synthases required for the first step in the aromatic amino acid biosynthetic pathway.
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Aspartyl protease from Trichoderma harzianum CECT 2413: cloning and characterization
More LessThe GenBank/EMBL/DDBJ accession number for the sequence reported in this paper is AJ276388.
A gene that encodes an extracellular aspartyl protease from Trichoderma harzianum CECT 2413, papA, has been isolated and characterized. Based on several conserved regions of other fungal acid proteases, primers were designed to amplify a probe that was used to isolate the papA gene from a genomic library of T. harzianum. papA was an intronless ORF which encoded a polypeptide of 404 aa, including a prepropeptide at the N-terminal region formed by one putative signal peptide, a second peptide which could be cleaved to activate the enzyme and the active protease of calculated 36·7 kDa and pI 4·35. Northern experiments indicated that papA gene was pH regulated, repressed by ammonium, glucose and glycerol, and induced by organic nitrogen sources. The promoter possessed potential AreA, PacC and MYC sites for nitrogen, pH and mycoparasitism regulation respectively, but lacked potential CreA sites for carbon regulation. IEF and zymograms indicated that PAPA was a pepstatin-sensitive aspartyl protease of pI 4·5. Transformants from T. harzianum CECT 2413 cultivated in yeast extract-supplemented medium overexpressed papA and had a fourfold increase in protease activity compared to the wild-type, while transformants that overexpressed the β-1,6-glucanase gene bgn16.2 and papA had an additional 30% increase in β-1,6-glucanase activity compared to bgn16.2 single transformants. Overexpression of both genes in ammonium-supplemented medium did not result in higher levels of PAPA and/or BGN16.2 proteins. These results indicated that both PAPA and β-1,6-glucanase undergo proteolysis in ammonium-supplemented medium but PAPA is not responsible for β-1,6-glucanase degradation.
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Mutational analysis of K28 preprotoxin processing in the yeast Saccharomyces cerevisiae
More LessK28 killer strains of Saccharomyces cerevisiae are permanently infected with a cytoplasmic persisting dsRNA virus encoding a secreted α/β heterodimeric protein toxin that kills sensitive cells by cell-cycle arrest and inhibition of DNA synthesis. In vivo processing of the 345 aa toxin precursor (preprotoxin; pptox) involves multiple internal and carboxy-terminal cleavage events by the prohormone convertases Kex2p and Kex1p. By site-directed mutagenesis of the preprotoxin gene and phenotypic analysis of its in vivo effects it is now demonstrated that secretion of a biological active virus toxin requires signal peptidase cleavage after Gly36 and Kex2p-mediated processing at the α subunit N terminus (after Glu-Arg49), the α subunit C terminus (after Ser-Arg149) and at the β subunit N terminus (after Lys-Arg245). The mature C terminus of the β subunit is trimmed by Kex1p, which removes the terminal Arg345 residue, thus uncovering the toxin’s endoplasmic reticulum targeting signal (HDEL) which – in a sensitive target cell – is essential for retrograde toxin transport. Interestingly, both toxin subunits are covalently linked by a single disulfide bond between α-Cys56 and β-Cys340, and expression of a mutant toxin in which β-Cys340 had been replaced by Ser340 resulted in the secretion of a non-toxic α/β heterodimer that is blocked in retrograde transport and incapable of entering the yeast cell cytosol, indicating that one important in vivo function of β-Cys340 might be to ensure accessibility of the toxin’s β subunit C terminus to the HDEL receptor of the target cell.
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Transglutaminase activity is involved in Saccharomyces cerevisiae wall construction
More LessTransglutaminase activity, which forms the interpeptidic cross-link N ϵ-(γ-glutamyl)-lysine, was demonstrated in cell-free extracts of Saccharomyces cerevisiae by incorporation of [14C]lysine into an exogenous acceptor, N,N′-dimethylcasein. Higher levels of the activity were present in the cell wall, which also contained endogenous acceptors. The enzyme activity in the wall was inhibited by cystamine, a known inhibitor of transglutaminase, and by EDTA, indicating a cation-dependent activity. After the endogenous wall acceptors were labelled radioactively by transglutaminase, extraction with SDS solubilized about 50% of the total radioactivity, while Zymolyase and chitinase each released a further 3%. The proteins solubilized by SDS had molecular masses less than 50 kDa, whereas the material released by Zymolyase or chitinase had molecular masses greater than 180 kDa, suggesting a precursor–product relationship. Cystamine inhibited the growth of several strains of S. cerevisiae. Treated cells showed increased sensitivity to Zymolyase and appeared as protoplasts, indicating gross alterations in the cell wall. These data suggest that transglutaminase may be involved in the formation of covalent cross-links between wall proteins during wall construction.
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Repression of chsB expression reveals the functional importance of class IV chitin synthase gene chsD in hyphal growth and conidiation of Aspergillus nidulans
The GenBank accession number for the the new version of the chsD nucleotide sequence is D83246.
The functions of two previously identified chitin synthase genes in Aspergillus nidulans, chsB and chsD, were analysed. First, a conditional chsB mutant was constructed in which the expression of chsB is under the control of a repressible promoter, the alcA promoter, of A. nidulans. Under repressing conditions, the mutant grew slowly and produced highly branched hyphae, supporting the idea that chsB is involved in normal hyphal growth. The involvement of chsB in conidiation was also demonstrated. Next, double mutants of chsB and chsD were constructed, in which chsB was placed under the control of the alcA promoter and chsD was replaced with the argB gene of A. nidulans. These double mutants grew more slowly than the chsB single mutant under high-osmolarity conditions. The hyphae of the double mutant appeared to be more disorganized than those of the chsB single mutant. It was also found that ChsD was functionally implicated in conidiation when the expression of chsB was limited. These results indicate the importance of the ChsD function in the absence of chsB expression. The roles of ChsB and ChsD in hyphal growth and in conidiation were supported by the analysis of the spatial expression patterns of chsB and chsD, using lacZ of Escherichia coli as a reporter gene.
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The ‘primitive’ microaerophile Giardia intestinalis (syn. lamblia, duodenalis) has specialized membranes with electron transport and membrane-potential-generating functions
Here it is shown that the flagellated protozoon Giardia intestinalis, commonly regarded as an early branching eukaryote because of its lack of mitochondria, has membraneous structures that partition the cationic, membrane-potential-sensitive fluorophore rhodamine 123. This organism also reduces a tetrazolium fluorogen at discrete plasma-membrane-associated sites. That these functions occur in distinctive specialized membrane systems supports the growing evidence that G. intestinalis may not be primitive, but is derived from an aerobic, mitochondria-containing flagellate.
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Enteropathogenic Escherichia coli translocate Tir and form an intimin–Tir intimate attachment to red blood cell membranes
More LessType III secretion allows bacteria to inject effector proteins into host cells. In enteropathogenic Escherichia coli (EPEC) the type III secreted protein, Tir, is translocated to the host-cell plasma membrane where it functions as a receptor for the bacterial adhesin intimin, leading to intimate bacterial attachment and ‘attaching and effacing’ (A/E) lesion formation. To study EPEC type III secretion the interaction of EPEC with monolayers of red blood cells (RBCs) has been exploited and in a recent study [Shaw, R. K., Daniell, S., Ebel, F., Frankel, G. & Knutton, S. (2001 R33 ). Cell Microbiol 3, 213–222] it was shown that EPEC induced haemolysis of RBCs and translocation of EspD, a putative pore-forming type III secreted protein in the RBC membrane. Here it is demonstrated that EPEC are able to translocate and correctly insert Tir into the RBC membrane and produce an intimin–Tir intimate bacterial attachment, identical to that seen in A/E lesions. Following translocation Tir did not undergo any change in apparent molecular mass or become tyrosine-phosphorylated and there was no focusing of RBC cytoskeletal actin beneath intimately adherent bacteria, and no pedestal formation. This study, employing an RBC model of infection, has demonstrated that Tir translocation can be separated from host-cell-mediated Tir modifications; the data show that the EPEC type III protein translocation apparatus is sufficient to deliver and correctly insert Tir into host-cell membranes independent of eukaryotic cell functions.
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Sample sequencing of a selected region of the genome of Erwinia carotovora subsp. atroseptica reveals candidate phytopathogenicity genes and allows comparison with Escherichia coli
The GenBank accession numbers for the 424 sequences determined in this work are BH614193 to BH614616.
Genome sequencing is making a profound impact on microbiology. Currently, however, only one plant pathogen genome sequence is publicly available and no genome-sequencing project has been initiated for any species of the genus Erwinia, which includes several important plant pathogens. This paper describes a targeted sample sequencing approach to study the genome of Erwinia carotovora subsp. atroseptica (Eca), a major soft-rot pathogen of potato. A large insert DNA (approx. 115 kb) library of Eca was constructed using a bacterial artificial chromosome (BAC) vector. Hybridization and end-sequence data revealed two overlapping BAC clones that span an entire hrp gene cluster. Random subcloning and one-fold sequence coverage (>200 kb) across these BACs identified 25 (89%) of 28 hrp genes predicted from the orthologous hrp cluster of Erwinia amylovora. Regions flanking the hrp cluster contained orthologues of known or putative pathogenicity operons from other Erwinia species, including dspEF (E. amylovora), hecAB and pecSM (E. chrysanthemi), sequences similar to genes from the plant pathogen Xylella fastidiosa, including haemagglutinin-like genes, and sequences similar to genes involved in rhizobacterium–plant interactions. Approximately 10% of the sequences showed strongest nucleotide similarities to genes in the closely related model bacterium and animal pathogen Escherichia coli. However, the positions of some of these genes were different in the two genomes. Approximately 30% of sequences showed no significant similarity to any database entries. A physical map was made across the genomic region spanning the hrp cluster by hybridization to the BAC library and to digested BAC clones, and by PCR between sequence contigs. A multiple genome coverage BAC library and one-fold sample sequencing are an effective combination for extracting useful information from important regions of the Eca genome, providing a wealth of candidate novel pathogenicity genes for functional analyses. Other genomic regions could be similarly targeted.
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Direct quantitative differentiation between Prevotella intermedia and Prevotella nigrescens in clinical specimens
More LessThis paper describes a quantitative fluorescent in situ hybridization (FISH) assay for the differential identification of Prevotella intermedia and Prevotella nigrescens in clinical samples, and compares its performance with less discriminatory culture and quantitative immunofluorescence (IF) assays. Fluorescence-labelled oligonucleotide probes directed to specific 16S rRNA sequences of P. intermedia, P. nigrescens, Prevotella pallens and Prevotella denticola were hybridized under stringent conditions with cultured reference strains or plaque samples from deep periodontal pockets. Probe specificity was defined with strains from multiple oral Prevotella species. The lower detection level of the assays was approximately 3×103 target cells per ml of plaque-sample suspension. P. intermedia, P. nigrescens, P. pallens and P. denticola were detected in plaques with prevalences of 69, 67, 0 and 28%, respectively. On average, 3·9×106 P. intermedia, 3·1×106 P. nigrescens and 5·6×105 P. denticola cells were counted per positive sample. All three species were found almost exclusively in dense mixed aggregates. Quantitative FISH data agreed satisfactorily with corresponding IF data (r=0·711). Both FISH and IF enumerations of the sum of P. intermedia and P. nigrescens markedly exceeded the c.f.u. counts of black-pigmented colonies in Porphyromonas gingivalis-free cultured subgingival plaques. The results demonstrate the validity of this new assay. Unlike established IF, culture, PCR or checkerboard DNA hybridization assays, this FISH assay differentiates quantitatively between P. intermedia and P. nigrescens, provides visual accuracy control, and offers insights into the spatial distribution of the target cells within a clinical sample.
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Evidence of intermolecular recombination between extrachromosomal DNAs in phytoplasma: a trigger for the biological diversity of phytoplasma? b
bThe GenBank accession numbers for EcOYW and EcOYM are AB076262 and AB076263, respectively.
Recombination among bacterial extrachromosomal DNAs (EC-DNAs) plays a major evolutionary role by creating genetic diversity, and provides the potential for rapid adaptation to new environmental conditions. Previously, a 7 kbp EC-DNA, EcOYW1, with a geminivirus-like rolling-circle-replication protein (Rep) gene was isolated and characterized from an original wild-type line (OY-W) of onion yellows (OY) phytoplasma, an endocellular cell-wall-less prokaryote that inhabits the cytoplasm of both plant and insect cells. EcOYW1, found in OY-W, was not present in a mild-symptom line (OY-M) derived from OY-W. A 4 kbp EC-DNA, pOYW, was also isolated and characterized from OY-W, and its pLS1-plasmid-like rep gene was expressed. This paper describes the isolation and sequencing of an EC-DNA of 5560 nt, EcOYW2, from OY-W, and its counterpart EC-DNA of 5025 nt, EcOYM, from OY-M. EcOYW2 and EcOYM contained seven and six ORFs, respectively. They both encoded a geminivirus-like Rep and a putative single-stranded-DNA-binding protein (SSB). Southern blot analysis indicated that no more EC-DNAs with a rep gene exist in either OY-W or OY-M, which means that the complete set of EC-DNAs has been cloned from the OY-W and OY-M lines of OY phytoplasmas. Sequence analysis revealed that both EcOYW2 and EcOYM have chimeric structures of previously characterized EcOYW1 and pOYW, suggesting that they have a recombinational origin. This is the first evidence of intermolecular recombination between EC-DNAs in phytoplasma. The possible implications of these findings in increasing the biological diversity of phytoplasma are discussed.
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Identification of novel sulfur-containing bacterial polyesters: biosynthesis of poly(3-hydroxy-S-propyl-ω-thioalkanoates) containing thioether linkages in the side chains
More LessThis study describes the biosynthesis of novel sulfur-containing polyhydroxyalkanoates (PHAs), which consist exclusively of hydroxypropylthioalkanoic acid containing thioether groups in the side chains. In addition, the utilization of alkylthioalkanoic acids (=thia fatty acids) by various bacteria was investigated. Based on feedings with propylthiooctanoic acid (PTO) or propylthiohexanoic acid, the metabolically engineered PHA-negative mutant PHB−4 of Ralstonia eutropha, which harbours plasmid pBBR1::phaC1 expressing the PHA synthase of Pseudomonas mendocina, synthesized two novel poly(3-hydroxy-S-propyl-ω-thioalkanoic) acids [poly(3HPTA)s]. A terpolyester consisting of 3-hydroxypropylthiobutyric acid (3HPTB), 3-hydroxypropylthiohexanoic acid (3HPTHx) and 3-hydroxypropyl- thiooctanoic acid (3HPTO) was synthesized from PTO, whereas a co-polyester of 3HPTB and 3HPTHx was synthesized from propylthiohexanoic acid. Fed-batch fermentation of R. eutropha PHB−4(pBBR1::phaC1) on PTO was done on a 26-litre scale, providing a cell density of 7·3 g l−1, from which 45 g of the novel poly(3HPTB-co-3HPTHx-co-3HPTO) were isolated. The chemical structures of the poly(3HPTA)s were identified by gas chromatography/mass spectrometry, elemental sulfur analysis, partial pyrolysis and detailed mass spectrometric analysis, exhibiting 3HPTB, 3HPTHx and 3HPTO as constituents. These novel, hitherto undescribed, constituents of PHAs were randomly distributed in the co-polyesters.
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Identification of phenyldecanoic acid as a constituent of triacylglycerols and wax ester produced by Rhodococcus opacus PD630
Phenyldecane supported growth and lipid accumulation of Rhodococcus opacus PD630 during cultivation under nitrogen-limiting conditions. The results of this study suggested that the hydrocarbon phenyldecane was degraded by monoterminal oxidation, followed by β-oxidation of the alkyl side-chain to phenylacetic acid, and by an additional degradative route for the oxidation of the latter to intermediates of the central metabolism. α-Oxidation of phenyldecanoic acid also occurred to some extent. Phenyldecanoic acid, the monoterminal oxidation product, was also utilized for the biosynthesis of a novel wax ester and novel triacylglycerols. The formation of the wax ester phenyldecylphenyldecanoate probably resulted from the condensation of phenyldecanoic acid and phenyldecanol, which were produced as metabolites during the catabolism of phenyldecane. Two types of triacylglycerol were detected in phenyldecane-grown cells of strain PD630. Triacylglycerols containing only odd- and even-numbered aliphatic fatty acids, as well as triacylglycerols in which one fatty acid was replaced by a phenyldecanoic acid residue, occurred. Other phenyl intermediates, such as phenylacetic acid, phenylpropionic acid, 4-hydroxyphenylpropionic acid, protocatechuate and homogentisic acid, were excreted into the medium during cultivation on phenyldecane. On the basis of the results obtained, pathways for the catabolism and assimilation of phenyldecane by R. opacus PD630 are discussed.
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Characterization of the hom–thrC–thrB cluster in aminoethoxyvinylglycine-producing Streptomyces sp. NRRL 5331
More LessThe GenBank accession number for the sequence reported in this paper is AJ312095.
Three genes from the aminoethoxyvinylglycine (AVG)-producing Streptomyces sp. NRRL 5331 involved in threonine biosynthesis, hom, thrB and thrC, encoding homoserine dehydrogenase (HDH), homoserine kinase (HK) and threonine synthase (TS), respectively, have been cloned and sequenced. The hom and thrC genes appear to be organized in a bicistronic operon as deduced by disruption experiments. The thrB gene, however, is transcribed as a monocistronic transcript. The encoded proteins are quite similar to the HDH, HK and TS proteins from other bacterial species. The overall organization of these three genes, in the order hom–thrC–thrB, differs from that in other bacteria and is similar to that reported in the Streptomyces coelicolor genome sequence. This is the first time in which the gene cluster for the three last steps of threonine biosynthesis has been characterized from a streptomycete. Disruption of thrC indicated that threonine is not a direct precursor for AVG biosynthesis in Streptomyces sp. NRRL 5331 and suggested that the branching point of the aspartic acid-derived biosynthetic route of this metabolite should lie earlier on the threonine biosynthetic route.
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cDNA cloning confirms the polyadenylation of RNA decay intermediates in Streptomyces coelicolor
More LessIn Escherichia coli the poly(A) tails of messenger and rRNAs are a major determinant of RNA stability. These tails are formed primarily by poly(A) polymerase I (PAP I) in wild-type strains or by polynucleotide phosphorylase (PNPase) in PAP I-deficient strains. In Streptomyces coelicolor it has been shown that mycelial RNAs display biochemical characteristics consistent with the presence of poly(A) tails. To confirm the occurrence of polyadenylation, rRNA and mRNA transcripts from S. coelicolor were isolated by oligo(dT)-dependent RT-PCR followed by cDNA cloning. One of the clones obtained was polyadenylated at a site corresponding to the mature 3′ terminus of 16S rRNA, while two 23S rRNA cDNA clones were polyadenylated at precursor processing sites. Other clones identified polyadenylation sites internal to the coding regions of both 16S and 23S rRNAs, and redD and actII-orf4 mRNAs. While most rRNA cDNA clones displayed adenosine homopolymer tails, the poly(A) tails of three rRNAs and all the redD and actII-orf4 clones consisted of a variety of heteropolymers. These results suggest that the enzyme primarily responsible for polyadenylation in S. coelicolor is PNPase rather than a PAP I homologue.
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The clavulanic acid biosynthetic cluster of Streptomyces clavuligerus: genetic organization of the region upstream of the car gene
The GenBank accession number for the 12162 bp sequence reported in this paper is AY034175.
The genetic organization of the region upstream of the car gene of the clavulanic acid biosynthetic gene cluster of Streptomyces clavuligerus has been determined. Sequence analysis of a 12·1 kb region revealed the presence of 10 ORFs whose putative functions, according to database searches, are discussed. Three co-transcriptional units are proposed: ORF10–11, ORF12–13 and ORF15–16–17–18. Potential transcriptional terminators were identified downstream of ORF11 (fd) and ORF15. Targeted disruption of ORF10 (cyp) gave rise to transformants unable to produce clavulanic acid, but with a considerably higher production of cephamycin C. Transformants inactivated at ORF14 had a remarkably lower production of clavulanic acid and similar production of cephamycin C. Significant improvements of clavulanic acid production, associated with a drop in cephamycin C biosynthesis, were obtained with transformants of S. clavuligerus harbouring multiple copies of plasmids carrying different constructions from the ORF10–14 region. This information can be used to guide strain improvement programs, blending random mutagenesis and molecular cloning, to optimize the yield of clavulanic acid.
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An essential virulence protein of Brucella abortus, VirB4, requires an intact nucleoside-triphosphate-binding domain
More LessBrucella abortus is a facultative intracellular bacterium capable of surviving inside macrophages. The VirB complex, which is highly similar to conjugative DNA transfer apparatuses, is required for intracellular replication. A conserved NTP-binding domain in VirB4 suggests that one or both proteins couple energy by NTP hydrolysis to transport of putative effector molecule(s). Here it is shown that a mutant strain of B. abortus that contains an in-frame deletion in virB4 is unable to replicate in macrophages and survives in mice. Intracellular replication and virulence in mice are fully restored by expressing virB4 in trans, indicating that VirB4 is essential for intracellular replication and virulence in mice. An alteration within the NTP-binding region of VirB4 by site-directed mutagenesis abolished complementation of a virB4 mutant, demonstrating that an intact NTP-binding domain is critical for VirB4 function. Intracellular replication was inhibited in wild-type B. abortus after introducing a plasmid expressing a mutant VirB4 altered in the NTP-binding region. The dominant negative phenotype suggests that VirB4 either functions as a multimer or interacts with some other component(s) necessary for intracellular replication. Wild-type B. abortus-containing phagosomes lack the glycoprotein LAMP-1, which is an indicator of the normal endocytic pathway. Mutant strains were found in phagosomes that co-localized with LAMP-1, indicating that VirB4 containing the intact NTP-binding region is essential for evasion of fusion with lysosomes.
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Isogenic mutants of the cag pathogenicity island of Helicobacter pylori in the mouse model of infection: effects on colonization efficiency
More LessStrains of Helicobacter pylori that contain the cag pathogenicity island (cag PAI) are associated with increased virulence and severe clinical outcomes. To evaluate the role of the cag island in infection, isogenic null mutations were generated in two clinical isolates (SS1 and Iris1) with distinct genetic backgrounds. When tested for their ability to establish infection in the stomach of CD1/SPF mice, at the early phase of infection, strains in which cagE, ORF528, ORF527 or ORF525 were inactivated showed a reduced capacity to initiate colonization compared to the wild-type strain. Strains with a mutation in the ORF524 gene were more efficient than the other mutants, but still less efficient than the wild-type strain. Mutation in the effector protein, CagA, which is injected into host cells and tyrosine-phosphorylated, did not change the colonization efficiency. In conclusion, all cag genes analysed, with the exception of the effector protein, CagA, influenced the early phase of colonization in the mouse model of infection. These results suggest that the structure of the H. pylori secretion apparatus itself is involved in this process.
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Yersinia enterocolitica YopQ: strain-dependent cytosolic accumulation and post-translational secretion
More LessThe GenBank/EMBL accession numbers for the sequences reported in this paper are AJ421529 [yopQ gene fragment from Y. enterocolitica WA-314 (O:8)] and AJ421530 [yopQ gene fragment from Y. enterocolitica Y-108-P (O:3)].
YopQ in Yersinia enterocolitica (YopK in Yersinia pseudotuberculosis) is a type III secreted protein required for virulence of yersiniae. In this study YopQ expression, secretion and nucleotide sequences of the corresponding yopQ gene from different yersinia strains were analysed. The cytosolic accumulation differed significantly among serotypes of Y. enterocolitica. These differences might be attributable to variations in the nucleotide sequence and their consequences on mRNA secondary structure. An mRNA signal hypothesis has been proposed for YopQ, predicting the coupling of translation and secretion via an mRNA signal. This hypothesis claims a strictly co-translational secretion of YopQ without its intracellular accumulation. The presence of YopQ in the cytosol, even with a closed secretion apparatus, is demonstrated. Moreover, post-translational secretion of YopQ could be demonstrated. These findings do not support the mRNA signal hypothesis for co-translational secretion.
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Invasion by Neisseria meningitidis varies widely between clones and among nasopharyngeal mucosae derived from adult human hosts
Colonization of the human nasopharynx is a feature of some species of Neisseria, and is a prerequisite of invasive meningococcal disease. The likelihood of colonization by Neisseria meningitidis varies widely between humans, and very few develop invasive disease. Explants of nasal mucosa derived from adult patients with non-allergic nasal obstruction were infected experimentally with Neisseria spp. At intervals over 18 h incubation, washed explants were homogenized, and viable bacteria were counted. To estimate bacterial invasion of mucosa, explants were exposed to 0·25% sodium taurocholate for 30 s prior to homogenization. N. meningitidis was recovered from the mucosa and the organism invaded and replicated within the tissue, in contrast to N. lactamica and N. animalis (n=9, P<0·008). N. meningitidis isolates of clones ET-5, ET-37 and lineage III were recovered from and invaded tissue, but strains of clones A4, A:subgroup I, A:subgroup III and A:subgroup IV-1 did not invade (n=6). To measure host variation, survival of N. meningitidis within nasal mucosa of 40 different human donors was measured. Intra-class correlation of replicates was 0·97, but the coefficient of variation of recovered viable counts was 1335% after 4 h and 77% after 18 h incubation. It is concluded that the distinctive colonization and disease potential of Neisseria spp. may be partly a consequence of their ability to invade and survive within human nasopharyngeal mucosa, but that this is influenced greatly by genetic or environmental factors operating on the host mucosa. This is consistent with the unpredictable epidemiology of meningococcal disease.
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Quorum sensing in Campylobacter jejuni: detection of a luxS encoded signalling molecule
More LessThe expression of a wide variety of physiological functions in many bacterial species is modulated by quorum sensing, a population-dependent signalling mechanism that involves the production and detection of extracellular signalling molecules. The genome sequence of Campylobacter jejuni NCTC 11168 contains a gene encoding an orthologue of LuxS, which is required for autoinducer-2 (AI-2) production in other bacterial species, but does not contain genes predicted to encode any known acyl-homoserine lactone synthetase. This study demonstrates that C. jejuni produces functional AI-2 activity through the ability of cell-free extracts to specifically induce bioluminescence in Vibrio harveyi BB170, a reporter strain for quorum-sensing system 2. Production of this signalling compound was shown to be dependent upon the product of the C. jejuni luxS gene (Cj1198). While the luxS mutant showed comparable growth rate, resistance to oxidative stress and ability to invade Caco-2 cell monolayers to the parental strain, it exhibited decreased motility haloes in semisolid media, suggesting a role for quorum sensing in the regulation of motility.
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In vivo characterization of the psa genes from Streptococcus pneumoniae in multiple models of infection
More LessDifferential fluorescence induction technology was used to identify promoters of Streptococcus pneumoniae genes that are expressed during lung infection of the mouse. Among the promoter clones that were identified multiple times was the psa promoter, which drives expression of the psaBCA operon. These genes have been identified previously and shown to encode a manganese permease system as well as play a role in the virulence of this organism. Mutations in psaB, psaC or psaA result in growth limitation in low manganese. The expression of the psa operon was examined in vivo and the virulence of deletion mutants of psaB, psaC, psaA and psaBCA was assessed in four different animal models of infection. The psa promoter was induced more than ten-fold in vivo using an intraperitoneal chamber implant model. The psaB, psaC and psaA mutants were completely attenuated in systemic, respiratory tract and otitis media infections. In addition, these mutants were unable to grow in an implanted peritoneal chamber, but growth was restored by the addition of manganese to the chambers.
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tRNA gene clusters at the 3′ end of rRNA operons are specific to virulent subgroups of Streptococcus agalactiae strains, as demonstrated by molecular differential analysis at the population level
More LessThe GenBank accession numbers for the sequences reported in this paper are AF302130 (for the 2·4 kb amplified fragment) and AF302131 (for the 2·6 kb amplified fragment).
The aim of this work was to characterize a 2·4 kb randomly amplified polymorphic DNA (RAPD) fragment described as a marker for a phylogenetic group of Streptococcus agalactiae strains significantly associated with neonatal meningitis. This fragment was analysed by cloning and sequencing, and showed that two types of tRNA gene cluster flank the 3′ end of the rRNA operons in S. agalactiae strains. Both types of tRNA gene cluster act as markers for phylogenetic subgroups of strains within the species. One type could be used to distinguish two of the three virulent intraspecies subgroups to which most of the S. agalactiae strains able to invade the central nervous system of neonates belong. This raises the possibility that there is a link between these tRNA genes and the virulence of the bacterium. Based on this analysis, PCR primers were designed to determine whether S. agalactiae strains are likely to belong to lineages of organisms in which most of the highly virulent strains isolated from cerebrospinal fluid cluster. In addition, this work demonstrated that RAPD can be used to detect novel particularities within intraspecies variants of pathogens.
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Group A streptococcal RofA-type global regulators exhibit a strain-specific genomic presence and regulation pattern
More LessRofA-like protein (RALP) type regulators have been shown to exist in different forms in group A streptococci (GAS) and to regulate the expression of important bacterial adhesins. This study shows that the vast majority of strains from different GAS M serotypes carried a rofA virulence regulator gene in their genome and that this gene could be detected in combination with other RALP genes and RALP-dependent adhesin genes in a strain-specific manner. The gene encoding the Nra regulator was predominantly found in opacity factor (OF)-negative serotypes. When analysing a rofA mutant in a serotype M2 strain, the strain specificity was also found in the positive and negative regulatory functions of RALP genes as well as in the type and number of virulence genes and functions controlled by the RALP genes. Of 17 virulence-associated genes tested, only one, the putative streptolysin S gene, was observed to be derepressed in RALP mutants of three different GAS serotype strains. This strain-specific variability of RALP regulon sizes is associated with different patterns of host cell attachment and internalization. In addition, RofA2 was shown to control expression of the ribosomal protein gene rpsL. As a consequence, it was demonstrated for the first time in streptococci that aminoglycoside resistance mediated by rpsL expression is apparently controlled by a virulence gene regulator.
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The genetic structure of Escherichia coli populations in primary and secondary habitats
More LessEscherichia coli were recovered from the members of two two-person households and their associated septic tanks. The E. coli were isolated using selective and non-selective isolation techniques, characterized using the method of multi-locus enzyme electrophoresis and screened for the presence of virulence factors associated with extra-intestinal disease by using PCR. The growth rate–temperature relationships of strains from the two habitats were also determined. Temporal variation explained 25% of the observed electrophoretic type (ET) diversity in the humans. Among-host variation accounted for 29% of the observed allelic diversity. In one household, ET diversity of the E. coli population in the septic tank was significantly lower than ET diversity in the humans providing the inputs to the septic tank. Molecular analysis of variance revealed that, on average, strains recovered from the septic tank of this household were genetically distinct from strains recovered from the humans providing the faecal inputs to the septic tank. Further, the growth rate–temperature response of strains differed between strains isolated from the septic tank and strains isolated from the humans. Septic tank isolates grew better at low temperatures than strains isolated from humans, but more slowly at high temperatures compared to the human isolates. By contrast, no real differences in ET diversity, allelic diversity, or the growth charcteristics of strains could be detected between strains from the humans and strains from the septic tank of the other household. The results of this study suggest there are strains of E. coli that are better ‘adapted’ to conditions found in the external environment compared to strains isolated from the gastrointestinal habitat. Further, the finding that the numerically dominant clones and clonal diversity in secondary habitats can differ substantially from those found in the source populations will confound efforts to identify the sources of faecal pollution in the environment.
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Intraspecific diversity of Brevibacterium linens, Corynebacterium glutamicum and Rhodococcus erythropolis based on partial 16S rDNA sequence analysis and Fourier-transform infrared (FT-IR) spectroscopy
More LessThe GenBank accession numbers for the 16S rDNA gene sequences reported in this paper are AY017065 to AY017067, AY017069 to AY017087, and AF426135 to AF426143 for Brevibacterium linens; AY017088 to AY017091, AY017093 to AY017104, AY017107 to AY017111, and AF426144 to AF426149 for Corynebacterium glutamicum; and AY017113 to AY017126, AY017128 to AY017138, and AF426150 to AF426153 for Rhodococcus erythropolis.
The intraspecific diversity of 31 strains of Brevibacterium linens, 27 strains of Corynebacterium glutamicum and 29 strains of Rhodococcus erythropolis was determined by partial 16S rDNA sequence analysis and Fourier-transform infrared (FT-IR) spectroscopy. As a prerequisite for the analyses, 27 strains derived from culture collections which had carried invalid or wrong species designations were reclassified in accordance with polyphasic taxonomical data. FT-IR spectroscopy proved to be a rapid and reliable method for screening for similar isolates and for identifying these actinomycetes at the species level. Two main conclusions emerged from the analyses. (1) Comparison of intraspecific 16S rDNA similarities suggested that R. erythropolis strains have a very low diversity, B. linens displays high diversity and C. glutamicum occupies an intermediate position. (2) No correlation of FT-IR spectral similarity and 16S rDNA sequence similarity below the species level (i.e. between strains of one species) was observed. Therefore, diversification of 16S rDNA sequences and microevolutionary change of the cellular components detected by FT-IR spectroscopy appear to be de-coupled.
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The cell surface protein Ag43 facilitates phage infection of Escherichia coli in the presence of bile salts and carbohydrates
It was found that infection of Escherichia coli by bacteriophage λ is inhibited in the presence of certain bile salts and carbohydrates when cells are in the ’OFF’ state for production of the phase-variable cell surface protein antigen 43 (Ag43). The inhibition of phage growth was found to be due to a significant impairment in the process of phage adsorption. Expression of the gene encoding Ag43 (agn43) from a plasmid or inactivation of the oxyR gene (encoding an activator of genes important for defence against oxidative stress) suppressed this inhibition. A mutation, rpoA341, in the gene encoding the α subunit of RNA polymerase also facilitated phage adsorption in the presence of bile salts and carbohydrates. The rpoA341 mutation promoted efficient production of Ag43 in a genetic background that would otherwise be in the ’OFF’ phase for expression of the agn43 gene. Analysis of a reporter gene fusion demonstrated that the promoter for the agn43 gene was more active in the rpoA341 mutant than in the otherwise isogenic rpoA + strain. The combined inhibitory action of bile salts and carbohydrates on phage adsorption and the abolition of this inhibition by production of Ag43 was not restricted to λ, as a similar phenomenon was observed for the coliphages P1 and T4.
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Regulation of bacterial motility in response to low pH in Escherichia coli: the role of H-NS protein
The effect of detrimental conditions on bacterial motility in Escherichia coli was investigated. Expression profiling of mutant E. coli strains by DNA arrays and analysis of phenotypic traits demonstrated that motility and low-pH resistance are coordinately regulated. Analysis of transcriptional fusions suggests that bacterial motility in response to an acidic environment is mediated via the control by H-NS of flhDC expression. Moreover, the results suggested that the presence of an extended mRNA 5′ end and DNA topology are required in this process. Finally, the presence of a similar regulatory region in several Gram-negative bacteria implies that this mechanism is largely conserved.
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The regulation of Enzyme IIAGlc expression controls adenylate cyclase activity in Escherichia coli
More LessDuring the last few years, several genes, such as pap, bgl and flhDC, have been shown to be coregulated by the histone-like nucleoid-structuring (H-NS) protein and the cyclic AMP-catabolite activator protein (cAMP/CAP) complex, suggesting an interaction between both systems in the control of some cellular functions. In this study, the possible effect of H-NS on the cAMP level was investigated. In a CAP-deficient strain, the presence of an hns mutation results in a strong reduction in the amount of cAMP, due to a decrease in adenylate cyclase activity. This is caused by the reduced expression of crr, which encodes the Enzyme IIAGlc of the phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS), from its specific P2 promoter. This leads to a twofold reduction in the global amount of Enzyme IIAGlc, the adenylate cyclase activator, responsible for the decrease in adenylate cyclase activity observed in the hns crp strain.
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Effect of vfr mutation on global gene expression and catabolite repression control of Pseudomonas aeruginosa
Vfr of Pseudomonas aeruginosa is 91% similar to the cAMP receptor protein (CRP) of Escherichia coli. Based on the high degree of sequence homology between the two proteins, the question arose whether Vfr had a global regulatory effect on gene expression for P. aeruginosa as CRP did for E. coli. This report provides two-dimensional polyacrylamide gel electrophoretic evidence that Vfr is a global regulator of gene expression in P. aeruginosa. In a vfr101::aacC1 null mutant, at least 43 protein spots were absent or decreased when compared to the proteome pattern of the parent strain. In contrast, 17 protein spots were absent or decreased in the parent strain when compared to the vfr101::aacC1 mutant. Thus, a mutation in vfr affected production of at least 60 proteins in P. aeruginosa. In addition, the question whether Vfr and CRP shared similar mechanistic characteristics was addressed. To ascertain whether Vfr, like CRP, can bind cAMP, Vfr and CRP were purified to homogeneity and their apparent dissociation constants (K d) for binding to cAMP were determined. The K d values were 1·6 μM for Vfr and 0·4 μM for CRP, suggesting that these proteins have a similar affinity for cAMP. Previously the authors had demonstrated that Vfr could complement a crp mutation and modulate catabolite repression in E. coli. This study presents evidence that Vfr binds to the E. coli lac promoter and that this binding requires the presence of cAMP. Finally, the possible involvement of Vfr in catabolite repression control in P. aeruginosa was investigated. It was found that succinate repressed production of mannitol dehydrogenase, glucose-6-phosphate dehydrogenase, amidase and urocanase both in the parent and in two vfr null mutants. This implied that catabolite repression control was not affected by the vfr null mutation. In support of this, the cloned vfr gene failed to complement a mutation in the P. aeruginosa crc gene. Thus, although Vfr is structurally similar to CRP, and is a global regulator of gene expression in P. aeruginosa, Vfr is not required for catabolite repression control in this bacterium.
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Use of an arrayed promoter-probe library for the identification of macrophage-regulated genes in Mycobacterium tuberculosis
More LessThe survival of Mycobacterium tuberculosis within the human host after infection, especially within macrophages, is likely to require the activation of a number of mycobacterial genes. To identify such genes, a promoter-probe library was constructed in which fragments of M. tuberculosis H37Rv DNA were inserted upstream of a lacZ reporter gene, using an Escherichia coli–mycobacterial shuttle vector. Mycobacterium bovis Bacille Calmette–Guérin (BCG) was subsequently transformed with this library and 4800 BCG clones were arrayed in a 96-well microtitre format, enabling the testing of individual clones for promoter activity under a variety of conditions. From preliminary screening, 41 clones were selected that exhibited upregulation of lacZ expression when subjected to acidified sodium nitrite. Subsequent sequence analyses identified 26 of these clones as containing potential promoters. After measuring lacZ expression in BCG clones recovered from a THP-1 macrophage cell line, three genes were selected for assessment of their expression in M. tuberculosis during macrophage infection, by real-time RT-PCR. Two of these genes, Rv1265 (with unknown function) and Rv2711 (encoding the iron-dependent repressor protein IdeR), showed evidence of being upregulated within macrophages.
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Formation and resuscitation of ‘non-culturable’ cells of Rhodococcus rhodochrous and Mycobacterium tuberculosis in prolonged stationary phase
More LessAfter growth of Rhodococcus rhodochrous in Sauton’s medium, and further incubation for about 60 h in stationary phase, there was a transient (up to 5 log) decrease in the c.f.u. count, whereas the total count remained similar to its initial value. At the point of minimal viability, the most probable number (MPN) count was 10 times greater than the c.f.u. count. This difference was further magnified by 3–4 logs (giving values close to the total count) by incorporating supernatant taken from growing cultures. A small protein similar to Rpf (resuscitation-promoting factor of Micrococcus luteus) appeared to be responsible for some of the activity in the culture supernatant. The formation of ‘non-culturable’ cells of the ‘Academia’ strain of Mycobacterium tuberculosis was similarly observed following growth in Sauton’s medium containing Tween 80 in sealed culture vessels, and further incubation for an extended stationary phase. This resulted in the formation, 4–5 months post-inoculation, of a homogeneous population of ostensibly ‘non-culturable’ cells (zero c.f.u.). Remarkably, the MPN count for these cultures was 105 organisms ml−1, and this value was further increased by one log using supernatant from an actively growing culture. Populations of ‘non-culturable’ cells of Mycobacterium tuberculosis were also obtained by the filtration of ‘clumpy’ cultures, which were grown in the absence of Tween 80. These small cells could only be grown in liquid medium (MPN) and their viability was enhanced by the addition of culture supernatant or Rpf. The ‘non-culturable’ cells that accumulated during prolonged stationary phase in both the R. rhodochrous and the Mycobacterium tuberculosis cultures were small ovoid and coccoid forms with an intact permeability barrier, but with undetectable respiratory activity. The authors consider these non-culturable bacteria to be dormant. The observed activity of culture supernatants and Rpf with ‘non-culturable’ bacterial suspensions invites the speculation that one, or more, of the cognate Mycobacterium tuberculosis Rpf-like molecule(s) could be involved in mechanisms of latency and reactivation of tuberculosis in vivo.
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Regulatory interactions between the Pho and σB-dependent general stress regulons of Bacillus subtilis
More LessWhen Bacillus subtilis is subjected to phosphate starvation, the Pho and σB-dependent general stress regulons are activated to elicit, respectively, specific and non-specific responses to this nutrient-limitation stress. A set of isogenic mutants, with a β-galactosidase reporter gene transcriptionally fused to the inactivated target gene, was used to identify genes of unknown function that are induced or repressed under phosphate limitation. Nine phosphate-starvation-induced (psi) genes were identified: yhaX, yhbH, ykoL and yttP were regulated by the PhoP–PhoR two-component system responsible for controlling the expression of genes in the Pho regulon, while ywmG (renamed csbD), yheK, ykzA, ysnF and yvgO were dependent on the alternative sigma factor σB, which controls the expression of the general stress genes. Genes yhaX and yhbH are unique members of the Pho regulon, since they are phosphate-starvation induced via PhoP–PhoR from a sporulation-specific σE promoter or a promoter that requires the product of a σE-dependent gene. Null mutations in key regulatory genes phoR and sigB showed that the Pho and σB-dependent general stress regulons of Bacillus subtilis interact to modulate the levels at which each are activated.
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