- Volume 147, Issue 7, 2001
Volume 147, Issue 7, 2001
- Review Article
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- Biochemistry
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Separation and characterization of individual mycolic acids in representative mycobacteria
More LessTotal mycolic acid methyl ester fractions were isolated from 24 representatives of Mycobacterium tuberculosis, Mycobacterium bovis (including BCG), Mycobacterium microti, Mycobacterium kansasii and Mycobacterium avium. The total mycolate functional group composition was estimated from 1H-NMR spectra. Mycolates were separated into α-mycolates, methoxymycolates and ketomycolates and each class was further separated by argentation chromatography into mycolates with no double bonds, with one trans-double bond and with one cis-double bond. Mass spectrometry revealed the mycolate chain lengths and 1H-NMR the cis- and trans-double bond and cyclopropane ring content. The same species had similar mycolate profiles; the major type of each class had cis- or trans-cyclopropane rings and lacked double bonds. Minor proportions of possible unsaturated precursors of the cyclopropane mycolates were commonly encountered. Among unusual α-mycolates, many strains had tricyclopropyl components with chains extended by 6 to 8 carbons. Significantly, M. tuberculosis (Canetti) and M. avium had α-mycolates with a trans-double bond and cyclopropane ring, whose chain lengths suggested a relationship to possible precursors of oxygenated mycolates. The methoxy- and ketomycolates from a majority of M. tuberculosis strains had minor amounts of components with additional cyclopropane rings, some of whose chains were also extended by 6 to 8 carbons. These latter mycolates were major components in the attenuated M. tuberculosis H37Ra strain, whose mycolate profile was distinct from those of other strains of M. tuberculosis.
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A diffusible analogue of N 3-(4-methoxyfumaroyl)-l-2,3-diaminopropanoic acid with antifungal activity
More LessN 3-(4-Methoxyfumaroyl)-l-2,3-diaminopropanoic acid (FMDP), a specific and potent inactivator of glucosamine-6-phosphate (GlcN-6-P) synthase from Candida albicans, exhibits relatively poor anticandidal activity, with an MIC value amounting to 50 μg ml−1 (200 μM). Uptake of FMDP into C. albicans cells follows saturation kinetics and is sensitive to the action of metabolic inhibitors, thus indicating the active transport mechanism. However, the acetoxymethyl ester of FMDP penetrates the fungal cell membrane by free diffusion and is rapidly hydrolysed by C. albicans cytoplasmic enzymes to release the free FMDP. This mechanism gives rise to continuous accumulation of the enzyme inhibitor and results in higher antifungal activity of the FMDP ester (MIC=3·1 μg ml−1, 10 μM). These results show that the ‘pro-drug’ approach can be successfully applied for the enhancement of antifungal activity of glutamine analogues that inhibit GlcN-6-P synthase.
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- Biotechnology
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Expression control and specificity of the basic amino acid exporter LysE of Corynebacterium glutamicum
More LessLysE of Corynebacterium glutamicum belongs to a large new superfamily of translocators whose members are probably all involved in the export of small solutes. Here, the transcript initiation site of lysE, and its divergently transcribed regulator gene, lysG, are identified. Single-copy transcriptional fusions of lysE with lacZ, and titration experiments, show that LysG is the positive regulator of lysE expression enabling its up to 20-fold induction. This induction requires the presence of a coinducer, which is either intracellular L-lysine, or L-arginine. A competition experiment showed that LysE exports these two basic amino acids at comparable rates of about 0·75 nmol min−1 (mg dry wt)−1. Although L-histidine and L-citrulline also act as coinducers of lysE expression, these two amino acids are not exported by LysE. As is evident from the analysis of a lysEG deletion mutant, the physiological role of the lysEG system is to prevent bacteriostasis due to elevated L-lysine or L-arginine concentrations that arise during growth in the presence of peptides or in mutants possessing a deregulated biosynthesis pathway. C. glutamicum has additional export activities other than those of LysE for exporting L-histidine, L-citrulline and L-ornithine.
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Genetic and biochemical characterization of an enantioselective amidase from Agrobacterium tumefaciens strain d3
More LessThe NCBI accession number for the sequence reported in this paper is AF315580.
An enantioselective amidase was purified to homogeneity from Agrobacterium tumefaciens d3. The enzyme has a molecular mass of about 490000 Da and is composed of identical subunits with a molecular mass of about 63000 Da. The purified enzyme converted racemic 2-phenylpropionamide to the corresponding S-acid with an enantiomeric excess (ee) value >95% at almost 50% conversion of the racemic amide. The purified enzyme was digested with trypsin and the amino acid sequences of the N terminus and different tryptic peptides determined. These amino acid sequences were used to clone the encoding gene. Finally, a 9330 bp DNA fragment was sequenced and the amidase gene identified. The deduced amino acid sequence showed homology to other enantioselective amidases from different bacterial genera. No indications of a structural coupling of the amidase gene with the genes for a nitrile hydratase could be found on the cloned DNA fragment. The amidase gene was encoded by an approximately 500 kb circular plasmid in A. tumefaciens d3. The amidase was heterologously expressed in Escherichia coli and, as well as 2-phenylpropionamide, was shown to hydrolyse α-chloro- and α-methoxyphenylacetamide and 2-methyl-3-phenylpropionamide highly enantioselectively. Some amino acids within a highly conserved region common amongst all known enantioselective amidases (‘amidase signature’) were changed by site-specific mutagenesis and significant changes in the relative activities with different amides observed.
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Analysis of the wee gene cluster responsible for the biosynthesis of the polymeric bioemulsifier from the oil-degrading strain Acinetobacter lwoffii RAG-1
More LessThe GenBank/EMBL accession number for the sequence analysis of the eight fragments determined in this work is AJ243431.
A cluster (27 kbp) of genes responsible for the biosynthesis of the amphipathic, polysaccharide bioemulsifier emulsan from the oil-degrading Acinetobacter lwoffii RAG-1 was isolated and characterized. The complete sequence of this cluster, termed wee, consisted of 20 ORFs. One set of 17 ORFs was transcribed in one direction, while a second set of three ORFs, 607 bp upstream of the first, was transcribed in the opposite direction. Mutations in either of the two regions caused defects in emulsan production, yielding specific activities of 5–14% of parental emulsifying activity. Putative functions could be assigned to proteins involved in production of nucleotide amino sugar precursors, transglycosylation, transacetylation, polymerization and transport. However, no JUMPstart or ops sequences, normally found associated with some polysaccharide biosynthetic gene clusters, were identified. Evidence is presented suggesting that the bioemulsifier may be a member of the group 1 or group 4 polysaccharides.
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- Development And Structure
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Secretion, interaction and assembly of two O-glycosylated cell wall antigens from Candida albicans
More LessThe mechanisms of incorporation of two antigens have been determined using a monoclonal antibody (3A10) raised against the material released from the mycelial cell wall by zymolyase digestion and retained on a concanavalin A column. One of the hybridomas secreted an IgG that reacted with two bands in Western blots. Indirect immunofluorescence showed that the antigens were located on the surfaces of mycelial cells, but within the cell walls of yeasts. These antigens were detected in a membrane preparation, in the SDS-soluble material and in the material released by a 1,3-β-glucanase and chitinase from the cell walls of yeast and mycelial cells. In the latter three samples, an additional high-molecular-mass, highly polydispersed band was also detected. Beta-elimination of each fraction resulted in the disappearance of all antigen bands, suggesting that they are highly O-glycosylated. In addition, the electrophoretic mobility of the high-molecular-mass, highly polydispersed bands increased after digestion with endoglycosidase H, indicating that they are also N-glycosylated. New antigen bands were released when remnants of the cell walls extracted with 1,3-β-glucanase or chitinase were digested with chitinase or 1,3-β-glucanase. These results are consistent with the notion that, after secretion, parts of the O-glycosylated antigen molecules are transferred to an N-glycosylated protein(s). This molecular complex, as well as the remaining original 70 and 80 kDa antigen molecules, next bind to 1,3-β-glucan or chitin, probably via 1,6-β-glucan, and, in an additional step, to chitin or 1,3-β-glucan. This process results in the final molecular product of each antigen, and their distribution in the cell walls.
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- Environmental Microbiology
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Repeated ruminal dosing of Ruminococcus spp. does not result in persistence, but changes in other microbial populations occur that can be measured with quantitative 16S-rRNA-based probes
Digestibility of fibre in ruminants may be improved by the introduction of highly fibrolytic strains of ruminal bacteria. This approach may be feasible if, for example, strains of Ruminococcus that are significantly more fibrolytic than the normal population of Ruminococcus are used for inoculation purposes. Introduced strains of bacteria, irrespective of ecosystem, often decline after inoculation, and in this study, highly fibrolytic strains of Ruminococcus were continuously dosed to ensure that measurements of fibre digestion were made in the presence of significant numbers of the introduced bacteria. During dosing the total culturable count increased significantly (P<0·05), but declined post-dosing. The level of dosed Ruminococcus, and total Ruminococcus, Fibrobacter succinogenes and eukaryotes measured by 16S rRNA probes increased significantly (P<0·05) during the dosing period, but also declined post-dosing. When in vitro nylon bag digestibility, feed intake or whole-tract digestibility was measured, no improvement could be measured.
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Closely related Prochlorococcus genotypes show remarkably different depth distributions in two oceanic regions as revealed by in situ hybridization using 16S rRNA-targeted oligonucleotides
The GenBank accession numbers for the sequences reported in this paper are AF311217 (RCC278, EQPAC1), AF311218 (RCC277, NATL1MIT), AF311219 (RCC280, NATL2B), AF311220 (RCC264, TAK9803-2), AF311291 (WH7803), AF311292 (WH8018) and AF311293 (WH8103).
An in situ hybridization method was applied to the identification of marine cyanobacteria assignable to the genus Prochlorococcus using horseradish-peroxidase-labelled 16S rRNA-targeted oligonucleotide probes in combination with tyramide signal amplification (TSA). With this method very bright signals were obtained, in contrast to hybridizations with oligonucleotides monolabelled with fluorochromes, which failed to give positive signals. Genotype-specific oligonucleotides for high light (HL)- and low light (LL)-adapted members of this genus were identified by 16S rRNA sequence analyses and their specificities confirmed in whole-cell hybridizations with cultured strains of Prochlorococcus marinus Chisholm et al., 1992 R8 , Prochlorococcus sp. and Synechococcus sp. In situ hybridization of these genotype-specific probes to field samples from stratified water bodies collected in the North Atlantic Ocean and the Red Sea allowed a rapid assessment of the abundance and spatial distribution of HL- and LL-adapted Prochlorococcus. In both oceanic regions the LL-adapted Prochlorococcus populations were localized in deeper water whereas the HL-adapted Prochlorococcus populations were not only distinct in each region but also exhibited strikingly different depth distributions, HLI being confined to shallow water in the North Atlantic, in contrast to HLII, which was present throughout the water column in the Red Sea.
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- Genetics And Molecular Biology
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Use of a halobacterial bgaH reporter gene to analyse the regulation of gene expression in halophilic archaea
More LessThe bgaH reading frame encoding a β-galactosidase of ‘Haloferax alicantei’ was used as a reporter gene to investigate three different promoter regions derived from gvpA genes of Haloferax mediterranei (mc-gvpA) and Halobacterium salinarum (c-gvpA and p-gvpA) in Haloferax volcanii transformants. The fusion of bgaH at the start codon of each gvpA reading frame (A1–bgaH fusion genes) caused translational problems in some cases. Transformants containing constructs with fusions further downstream in the gvpA reading frame (A–bgaH) produced β-galactosidase, and colonies on agar plates turned blue when sprayed with X-Gal. The β-galactosidase activities quantified by standard ONPG assays correlated well with the mRNA data determined with transformants containing the respective gvpA genes: the cA–bgaH fusion gene was completely inactive, the mcA–bgaH transformants showed low amounts of products, whereas the pA–bgaH fusion gene was constitutively expressed in the respective transformants. The transcription of each A–bgaH gene was activated by the homologous transcriptional activator protein GvpE. The cGvpE, pGvpE and mcGvpE proteins were able to activate the promoter of pA–bgaH and mcA–bgaH, whereas the promoter of cA–bgaH was only activated by cGvpE. Among the three GvpE proteins tested, cGvpE appeared to be the strongest transcriptional activator.
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Differential regulation of laccase gene expression in Pleurotus sajor-caju
More LessThe GenBank accession numbers for the sequences determined in this work are AF297525–AF297528.
Four laccase isozyme genes, Psc lac1, 2, 3 and 4 have been cloned from the edible mushroom, Pleurotus sajor-caju. The genes display a high degree of homology with other basidiomycete laccases (55–99%) at the amino acid level. Of the laccase genes isolated, Psc lac1 and 4 displayed the highest degree of similarity (85% at the amino acid level), while Psc lac3 showed the highest degree of divergence, exhibiting only 52–57% amino acid similarity to the other Pl. sajor-caju laccase gene sequences. Laccase activity in Pl. sajor-caju is affected by nutrient nitrogen and carbon, and by the addition of copper and manganese to the growth medium. In addition, 2,5-xylidine, ferulic acid, veratric acid and 1-hydroxybenzotriazole induced laccase activity in the fungus. Induction of individual laccase isozyme genes by carbon, nitrogen, copper, manganese and the two aromatic compounds, 2,5-xylidine and ferulic acid, occured at the level of gene transcription. While Psc lac3 transcript levels appeared to be constitutively expressed, transcript levels for the other laccase isozyme genes, lac1, 2 and 4, were differentially regulated under the conditions tested.
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Bacterial Ohr and OsmC paralogues define two protein families with distinct functions and patterns of expression
Xanthomonas campestris Ohr (a protein involved in organic peroxide protection) and Escherichia coli OsmC (an osmotically inducible protein of unknown function) are related proteins. Database searches and phylogenetic analyses reveal that Ohr and OsmC homologues cluster into two related subfamilies of proteins widely distributed in both Gram-negative and Gram-positive bacteria. To determine if these two subfamilies are functionally distinct, ohr and osmC in Pseudomonas aeruginosa (a bacterium with one representative from each subfamily) were analysed. Only ohr mutants are hypersensitive to organic peroxide, and this phenotype can be restored by complementation with ohr but not osmC. In addition, expression of ohr was highly induced only by organic peroxides, and not by other oxidants or stresses. In contrast, osmC was induced by ethanol and osmotic stress. A similar pattern of regulation was observed for Ohr and OsmC homologues in the Gram-positive bacterium Deinococcus radiodurans, though uninduced expression was much higher and induction lower in this species. These data clearly support the conclusion that Ohr and OsmC define two functionally distinct subfamilies with distinct patterns of regulation.
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YkrB is the main peptide deformylase in Bacillus subtilis, a eubacterium containing two functional peptide deformylases
More LessPeptide deformylation is an essential process in eubacteria. The peptide deformylase Def has been suggested to be an attractive target for antibacterial drug discovery. Some eubacteria including medically important pathogens possess two def-like genes. Until now, the functionality of both genes has been tested only in Staphylococcus aureus with the result that one gene copy was functional. Here, expression of two functional def-like gene products in Bacillus subtilis is demonstrated. Besides the def gene, which is chromosomally located close to the formyltransferase gene fmt and which was overexpressed and biochemically tested previously, B. subtilis possesses a second def-like gene, called ykrB. The encoded protein is 32% identical to the def gene product. It was shown that either def or ykrB had to be present for growth of B. subtilis in rich medium (each was individually dispensable). Studies with a def/ykrB double deletion strain with xylose-inducible ykrB copy demonstrated that, besides def, the gene ykrB is a second cellular target of deformylase inhibitors such as the antibiotic actinonin. The gene products exhibited similar enzymic properties, exemplified by similar inhibition efficacy of actinonin in biochemical assays. Antibiotic susceptibility tests with different deletion strains and Northern analyses indicated that YkrB is probably the predominant deformylase in B. subtilis. It was shown that duplication of the deformylase function does not lead to an increased actinonin-resistance frequency in comparison to B. subtilis mutants carrying only one deformylase gene.
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A Bacillus amyloliquefaciens ChbB protein binds β- and α-chitin and has homologues in related strains
More LessThe GenBank/NCIB accession number for the sequence reported in this paper is AF181997.
A small (19·8 kDa) protein was identified in Bacillus amyloliquefaciens ALKO 2718 cultures during growth in the presence of yeast extract and chitin, but not with glucose. The protein targets β-chitin best, then α-chitin, but barely any other polysaccharide. This described chitin-binding protein (ChbB) is the first of its type from a Bacillus strain and cross-reacts with antibodies raised against the Streptomyces α-chitin-binding protein CHB1. Using reverse genetics, the chromosomal chbB gene of strain ALKO 2718 was identified, cloned and sequenced. ChbB shares several motifs with the α-chitin-binding proteins CHB1 and CHB2 of Streptomyces and CBP21 of Serratia marcescens predominantly targeting β-chitin. Synthesis was repressed by glucose and the presence of cre boxes suggests catabolite control. Using PCR, Southern hybridization and anti-ChbB antibodies, the presence of a chbB gene, as well as of a ChbB protein homologue, was ascertained in several tested B. amyloliquefaciens strains, but not in Bacillus subtilis 168. Contrary to B. subtilis 168, all B. amyloliquefaciens strains secreted varying amounts of enzymic activity, degrading carboxymethyl chitin coupled with Remazol brilliant violet.
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Identification of genes involved in the activation of the Bacillus thuringiensis inhA metalloprotease gene at the onset of sporulation
More LessThe GenBank/EMBL/DDBJ accession number for the sequence reported in this paper is AF287346.
The immune inhibitor A (InhA) metalloprotease from Bacillus thuringiensis specifically cleaves antibacterial proteins produced by the insect host, suggesting that it may contribute to the overall virulence of B. thuringiensis. The transcriptional regulation of the inhA gene in both B. thuringiensis and Bacillus subtilis was investigated. Using a transcriptional inhA′–lacZ fusion, it was shown that inhA expression is activated at the onset of sporulation. However, the transcriptional start site of inhA is similar to σA-dependent promoters, and deletion of the sporulation-specific sigma factors σF or σE had no effect on inhA expression in B. subtilis. The DNA region upstream from inhA contains two genes encoding polypeptides similar to the SinI and SinR regulators of B. subtilis. SinR is a DNA-binding protein regulating gene expression and SinI inhibits SinR activity. Overexpression of the sin genes affects the expression of the inhA′–lacZ transcriptional fusion in B. thuringiensis: early induction of inhA expression was observed when sinI was overexpressed, whereas inhA expression was reduced in a strain overexpressing sinR, suggesting that inhA transcription is repressed, directly or indirectly, by SinR. inhA transcription was greatly reduced in B. thuringiensis and B. subtilis spo0A mutants. Analysis of the inhA′–lacZ expression in abrB and abrB–spo0A mutants of B. subtilis indicates that the Spo0A-dependent regulation of inhA expression depends on AbrB, which is known to regulate expression of transition state and sporulation genes in B. subtilis.
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A chromosomal region surrounding the ompD porin gene marks a genetic difference between Salmonella typhi and the majority of Salmonella serovars
More LessIn this work it is shown that the majority of Salmonella serovars most frequently associated with the systemic infection of vertebrate hosts produce a major outer-membrane porin, OmpD. However, OmpD is absent from the outer-membrane protein profiles of Salmonella typhi strain Ty2 and 26 clinical isolates of S. typhi examined by SDS-PAGE. To determine whether the ompD gene is present in S. typhi, primers internal to the ompD coding sequence were used to amplify the gene by PCR. With the exception of S. typhi strains, the ompD gene was amplified from the genomes of all Salmonella serovars tested. Consistently, a specific ompD probe did not hybridize with DNA isolated from the S. typhi strains. Taken together, these results demonstrate that S. typhi does not produce OmpD due to the absence of the ompD gene. Furthermore, it was investigated whether the deletion of ompD extended to smvA. This gene is adjacent to ompD in the Salmonella typhimurium chromosome and encodes a protein involved in the resistance to methyl viologen, a superoxide-generating agent. Although PCR failed to amplify the smvA gene from the S. typhi strain Ty2 genome, it was possible to amplify it from the chromosome of the clinical strains. On the other hand, hybridization analyses showed that the smvA gene is present in all the S. typhi strains tested. In contrast to the other Salmonella serovars, S. typhi strain Ty2 and the clinical isolates showed sensitivity to methyl viologen, suggesting that smvA gene is inactive in S. typhi. In conclusion, the ompD–smvA region is variable in structure among Salmonella serovars. It is hypothesized that the absence of ompD may suggest a role in host specificity.
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The double mechanism of incompatibility between λ plasmids and Escherichia coli dnaA(ts) host cells
For plasmids derived from bacteriophage λ, the initiation of bidirectional DNA replication from oriλ depends on the stimulation of transcription from the p R promoter by the host replication initiator protein DnaA. Certain Escherichia coli dnaA(ts) mutants cannot be transformed by wild-type λ plasmids even at the temperature permissive to cell growth. This plasmid–host incompatibility appeared to be due to inefficient stimulation of transcription from the p R promoter by the mutant DnaA protein. This paper shows that there is a second mechanism for the incompatibility between λ plasmids and dnaA(ts) hosts, exemplified in this study by the dnaA46 mutant. This is based on the competition between the λ P protein and the host DnaA and DnaC proteins for DnaB helicase. Both mechanisms must be operative for the incompatibility.
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Ralstonia metallidurans CH34 RpoN sigma factor and the control of nitrogen metabolism and biphenyl utilization
More LessThe GenBank accession number for the sequence determined in this work is AJ131690.
Ralstonia metallidurans CH34 can use biphenyl as carbon and energy source when provided with the catabolic transposon Tn4371. Previous results suggested that this property was dependent on the RNA polymerase subunit σ54. The authors sequenced the CH34 rpoN gene and flanking DNA and isolated a CH34 rpoN-deficient strain. Analysis of the sequence revealed a set of features conserved in all rpoN genes and flanking DNA regions previously analysed in other bacterial species. Nevertheless, despite this conservation, CH34 differed even from the closely related strain R. eutropha H16 by one particular ORF. The rpoN null mutation did not affect expression of the Tn4371 bph operon although it did alter the ability of the Tn4371 host strain to grow on biphenyl. The CH34 rpoN mutant had lost the capacity for autotrophic growth and for responding to poor nitrogen sources by a decrease in urease and proline oxidase activity. CH34 RNA polymerase σ54 thus positively controls autotrophy as well as nitrogen metabolism but only indirectly affects Tn4371-directed biphenyl utilization.
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Overexpression of a dominant-negative allele of YPT1 inhibits growth and aspartyl protease secretion in Candida albicans
More LessThe GenBank accession number for the C. albicans YPT1 sequence reported in this paper is AF330211.
To investigate the pre-Golgi secretion pathway in the pathogenic yeast Candida albicans, we cloned the C. albicans homologue of the Saccharomyces cerevisiae protein secretion gene YPT1. The C. albicans YPT1 ORF contained a 624 bp intronless ORF encoding a deduced protein of 207 aa and 2·3 kDa. This deduced protein was 77% identical to S. cerevisiae Ypt1 protein (Ypt1p) and it contained GTP-binding domains that are conserved among all known ras-like GTPases. Multicopy plasmids containing C. albicans YPT1 complemented the temperature-sensitive S. cerevisiae ypt1 (A136D) mutation. One chromosomal YPT1 allele in C. albicans CAI4 was readily disrupted by homologous gene targeting, but attempts to disrupt the second allele yielded no viable null mutants. Since this suggested that C. albicans YPT1 may be essential, a mutant ypt1 allele was constructed encoding the amino acid substitution analogous to the N121I substitution in a known trans-dominant inhibitor of S. cerevisiae Ypt1p. Next, a GAL1-regulated plasmid was used to express the mutant ypt1(N121I) allele in C. albicans CAI4. Ten of 11 transformants tested grew normally in glucose and poorly in galactose, and plasmid curing restored growth to wild-type levels. When these transformants were incubated in galactose, secretion of aspartyl proteinase (Sap) was inhibited and membrane-bound secretory vesicles accumulated intracellularly. These results imply that C. albicans YPT1 is required for growth and protein secretion, and they confirm the feasibility of using inducible dominant-negative alleles to define the functions of essential genes in C. albicans.
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- Genomics
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Physical and genetic map of the Clostridium saccharobutylicum (formerly Clostridium acetobutylicum) NCP 262 chromosome
More LessA physical and genetic map of the Clostridium saccharobutylicum NCP 262 chromosome was constructed. The order of macrorestriction fragments was determined by analysing fragments generated after single and double digestion with the restriction enzymes BssHII, I-CeuI, Sse8387I, RsrII and SfiI and separation by PFGE. The I-CeuI backbone of C. saccharobutylicum was constructed by indirect end-labelling with rrs- and 3′ rrl-specific probes located on either side of the I-CeuI site in the rrn operon, and reciprocal separation of BssHII and I-CeuI digestion products by two-dimensional PFGE. The positions of BssHII fragments on the physical map were determined using a library of linking clones containing BssHII cleavage sites. The size of the circular genome was estimated to be 5·3 Mb with a mean resolution of approximately 140 kb. The chromosome of C. saccharobutylicum contains 12 rrn operons, located on 46% of the chromosome, which are transcribed divergently from the deduced origin of replication. The genetic map was constructed by determining the location of 28 genes involved in house-keeping, heat-shock response, sporulation, electron transfer and acid- and solvent-formation. Comparison of the C. saccharobutylicum genetic map with those of the spore-forming bacteria Bacillus subtilis, Clostridium acetobutylicum, Clostridium perfringens and Clostridium beijerinckii indicated C. saccharobutylicum to be most similar to the latter two Clostridium species, with the order of the genes within the gyrAB and recA loci being conserved.
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- Pathogenicity And Medical Microbiology
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Mosaic structure of Shiga-toxin-2-encoding phages isolated from Escherichia coli O157:H7 indicates frequent gene exchange between lambdoid phage genomes
More LessShiga-toxin-2 (stx 2)-encoding bacteriophages were isolated from Norwegian Escherichia coli O157:H7 isolates of cattle and human origin. The phages were characterized by restriction enzyme analysis, hybridization with probes for toxin genes and selected phage DNA such as the P gene, integrase gene and IS1203, and by PCR studies and partial sequencing of selected DNA regions in the integrase to stx 2 region of the phages. The stx 2-phage-containing bacteria from which inducible phages were detected produced similar amounts of toxin, as shown by a Vero cell assay. The results indicate that the population of stx 2-carrying phages is heterogeneous, although the phages from epidemiologically linked E. coli O157:H7 isolates were similar. There appears to have been frequent recombination of stx 2 phages with other lambdoid phages.
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Different adhesins for type IV collagen on Candida albicans: identification of a lectin-like adhesin recognizing the 7S(IV) domain
More LessAdherence of the opportunistic pathogen Candida albicans to basement membrane (BM) proteins is considered a crucial step in the development of candidiasis. In this study the interactions of C. albicans yeast cells with the three main domains of type IV collagen, a major BM glycoprotein, were analysed. C. albicans adhered to the three immobilized domains by different mechanisms. Adhesion to the N-terminal cross-linking domain (7S) required the presence of divalent cations, whereas interaction with the central collagenous domain (CC) was cation-independent. Recognition of the C-terminal non-collagenous domain (NC1) was partially cation-dependent. Binding inhibition assays with the corresponding domains in soluble form showed that these interactions were specific. Both Ca2+ and Mg2+ promoted adhesion to the 7S domain and the interaction was completely abolished by EDTA. Treatment of the 7S domain, or its subunits, with N-glycosidase F reduced yeast binding by approximately 70%. Moreover, several sugars known to be part of the N-linked oligosaccharide chains of collagen IV inhibited adhesion to immobilized 7S; N-acetylglucosamine, L-fucose and methylmannoside caused a similar inhibition whereas N-acetyllactosamine was a more effective inhibitor. In contrast, glucose, galactose, lactose or heparan sulfate did not affect yeast binding. Combinations of the inhibitory sugars at suboptimal inhibition concentrations did not reduce C. albicans adhesion more than the individual sugars, pointing to a single lectin as responsible for the interaction. These results taken together show that C. albicans utilizes several adhesins for interacting with type IV collagen, and that at least one of them is a lectin which recognizes the 7S(IV) oligosaccharide residues as its receptor.
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- Physiology And Growth
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Trehalose is required for the acquisition of tolerance to a variety of stresses in the filamentous fungus Aspergillus nidulans
The GenBank accession number for the sequence reported in this paper is AF043230.
Trehalose is a non-reducing disaccharide found at high concentrations in Aspergillus nidulans conidia and rapidly degraded upon induction of conidial germination. Furthermore, trehalose is accumulated in response to a heat shock or to an oxidative shock. The authors have characterized the A. nidulans tpsA gene encoding trehalose-6-phosphate synthase, which catalyses the first step in trehalose biosynthesis. Expression of tpsA in a Saccharomyces cerevisiae tps1 mutant revealed that the tpsA gene product is a functional equivalent of the yeast Tps1 trehalose-6-phosphate synthase. The A. nidulans tpsA-null mutant does not produce trehalose during conidiation or in response to various stress conditions. While germlings of the tpsA mutant show an increased sensitivity to moderate stress conditions (growth at 45 °C or in the presence of 2 mM H2O2), they display a response to severe stress (60 min at 50 °C or in the presence of 100 mM H2O2) similar to that of wild-type germlings. Furthermore, conidia of the tpsA mutant show a rapid loss of viability upon storage. These results are consistent with a role of trehalose in the acquisition of stress tolerance. Inactivation of the tpsA gene also results in increased steady-state levels of sugar phosphates but does not prevent growth on rapidly metabolizable carbon sources (glucose, fructose) as seen in Saccharomyces cerevisiae. This suggests that trehalose 6-phosphate is a physiological inhibitor of hexokinase but that this control is not essential for proper glycolytic flux in A. nidulans. Interestingly, tpsA transcription is not induced in response to heat shock or during conidiation, indicating that trehalose accumulation is probably due to a post-translational activation process of the trehalose 6-phosphate synthase.
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The acid-stress response in Lactobacillus sanfranciscensis CB1
More LessLactobacillus sanfranciscensis CB1, an important sourdough lactic acid bacterium, can withstand low pH after initial exposure to sublethal acidic conditions. The sensitivity to low pH varied according to the type of acid used. Treatment of Lb. sanfranciscensis CB1 with chloramphenicol during acid adaptation almost completely eliminated the protective effect, suggesting that induction of protein synthesis was required for the acid-tolerance response. Two constitutively acid-tolerant mutants, CB1-5R and CB1-7R, were isolated using natural selection techniques after sequential exposure to lactic acid (pH 3·2). Two-dimensional gel electrophoresis analysis of protein expression by non-adapted, acid-adapted and acid-tolerant mutant cells of Lb. sanfranciscensis showed changes in the levels of 63 proteins. While some of the modifications were common to the acid-adapted and acid-tolerant mutant cells, several differences, especially regarding the induced proteins, were determined. The two mutants showed a very similar level of protein expression. Antibodies were used to identify heat-shock proteins DnaJ, DnaK, GroES and GrpE. Only GrpE showed an increased level of expression in the acid-adapted and acid-tolerant mutants as compared with non-adapted cells. The N-terminal sequence was determined for two proteins, one induced in both the acid-adapted and mutant cells and the other showing the highest induction factor of those proteins specifically induced in the acid-adapted cells. This second protein has 60% identity with the N-terminal portion of YhaH, a transmembrane protein of Bacillus subtilis, which has 54 and 47% homology with stress proteins identified in Listeria monocytogenes and Bacillus halodurans. The constitutively acid-tolerant mutants showed other different phenotypic features compared to the parental strain: (i) the aminopeptidase activity of CB1-5R decreased and that of CB1-7R markedly increased, especially in acid conditions; (ii) the growth in culture medium at 10 °C and in the presence of 5% NaCl was greater (the same was found for acid-adapted cells); and (iii) the acidification rate during sourdough fermentation in acid conditions was faster and greater.
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Characterization of an autostimulatory substance produced by Escherichia coli
More LessThe recovery of dilute populations of stationary phase cells of Escherichia coli was studied using an automatic growth analyser. The addition of 30% supernatant from 2-d-old stationary phase cells of the organism reproducibly shortened the apparent lag times by 22–57·5%, depending on the age of the inoculum. True lag times, as determined by colony counts, of stationary phase cells were reduced by supernatant addition by 41–62%. The growth-stimulating substance was characterized and partly purified from supernatants: the active material was shown to be dialysable, heat-stable, acid- and alkali-stable and protease-resistant. Extraction with ethyl acetate or ion-exchange resins was not successful, but the active material could be quantitatively extracted with ethanol after saturation with salt. It is concluded that the active substance is a small, non-proteinaceous, non-ionic organic molecule. Separation of extracts by HPLC indicated that the stimulatory substance is weakly hydrophobic and has retention times similar to those of uracil. So far, however, the exact chemical identity of the active substance has not been elucidated.
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- Systematics And Evolution
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Comparison of cell-wall polysaccharides from Nectria cinnabarina with those from the group of Nectria with Sesquicillium anamorphs
More LessAlkali-extractable and water-soluble polysaccharides were purified from cell walls of five species of Sesquicillium or its teleomorphs, Nectria lasiacidis and Nectria impariphialis, and from Nectria cinnabarina, the type species of Nectria, a heterogeneous genus that belongs to the Hypocreales. Methylation and NMR analyses for determination of linkage types and structure were performed and indicated differences between the polysaccharides purified during the present study and those isolated from other nectrioid fungi, namely the presence of 5-O-substituted galactofuranose (→5)-Galf-(1→) in the main chain together with 2,6-di-O-substituted galactofuranose (→2,6)-Galf-(1→) residues in Sesquicillium buxi and Sesquicillium pseudosetosum. The polysaccharide from N. impariphialis was similar to those obtained from the above species, although an additional residue of 6-O-substituted glucopyranose (→6)-Glcp-(1→), was detected in some side chains. In N. lasiacidis and Sesquicillium candelabrum the polysaccharide contained an additional branching point of 5,6-di-O-substituted galactofuranose (→5,6)-Galf-(1→) linked to terminal N-acetylglucosamine GlcNAc-(1→). These chains were linked to a small mannan core. All these polysaccharides showed major differences to the polysaccharide of N. cinnabarina, which was formed by a main chain of (1→6)-β-linked galactofuranose units almost fully branched at positions 2-O by either single residues of glucopyranose or acidic chains containing glucuronic acid and mannose.
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The cryptic ushA gene (ushA c) in natural isolates of Salmonella enterica (serotype Typhimurium) has been inactivated by a single missense mutation
The GenBank accession numbers for the sequences determined in this work are AF188721–AF188732.
Two mutational mechanisms, both supported by experimental studies, have been proposed for the evolution of new or improved enzyme specificities in bacteria. One mechanism involves point mutation(s) in a gene conferring novel substrate specificity with partial or complete loss of the original (wild-type) activity of the encoded product. The second mechanism involves gene duplication followed by silencing (inactivation) of one of these duplicates. Some of these ‘silent genes’ may still be transcribed and translated but produce greatly reduced levels of functional protein; gene silencing, in this context, is distinct from the more common associations with bacterial partitioning sequences, and with genes which are no longer transcribed or translated. Whereas most Salmonella enterica strains are ushA +, encoding an active 5′-nucleotidase (UDP-sugar hydrolase), some natural isolates, including most genetically related strains of serotype Typhimurium, have an ushA allele (designated ushA c) which produces a protein with, comparatively, very low 5′-nucleotidase activity. Previous sequence analysis of cloned ushA c and ushA + genes from serotype Typhimurium strain LT2 and Escherichia coli, respectively, did not reveal any changes which might account for the significantly different 5′-nucleotidase activities. The mechanism responsible for this reduced activity of UshAc has hitherto not been known. Sequence analysis of Salmonella ushA + and ushA c alleles indicated that the relative inactivity of UshAc may be due to one, or more, of four amino acid substitutions. One of these changes (S139Y) is in a sequence motif that is conserved in 5′-nucleotidases across a range of diverse prokaryotic and eukaryotic species. Site-directed mutagenesis confirmed that a Tyr substitution of Ser-139 in Salmonella UshA+ was solely responsible for loss of 5′-nucleotidase activity. It is concluded that the corresponding single missense mutation is the cause of the UshAc phenotype. This is the first reported instance of gene inactivation in natural isolates of bacteria via a missense mutation. These results support a model of evolution of new enzymes involving a ‘silent gene’ which produces an inactive, or relatively inactive, product, and are also consistent with the evolution of a novel, but unknown, enzyme specificity by a single amino acid change.
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