- Volume 154, Issue 2, 2008
Volume 154, Issue 2, 2008
- Review
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Advances in environmental genomics: towards an integrated view of micro-organisms and ecosystems
More LessMicrobial genome sequencing has, for the first time, made accessible all the components needed for both the elaboration and the functioning of a cell. Associated with other global methods such as protein and mRNA profiling, genomics has considerably extended our knowledge of physiological processes and their diversity not only in human, animal and plant pathogens but also in environmental isolates. At a higher level of complexity, the so-called meta approaches have recently shown great promise in investigating microbial communities, including uncultured micro-organisms. Combined with classical methods of physico-chemistry and microbiology, these endeavours should provide us with an integrated view of how micro-organisms adapt to particular ecological niches and participate in the dynamics of ecosystems.
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- Cell And Developmental Biology
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The chitobiose-binding protein, DasA, acts as a link between chitin utilization and morphogenesis in Streptomyces coelicolor
Streptomycetes are mycelial soil bacteria that undergo a developmental programme that leads to sporulating aerial hyphae. As soil-dwelling bacteria, streptomycetes rely primarily on natural polymers such as cellulose, xylan and chitin for the colonization of their environmental niche and therefore these polysaccharides may play a critical role in monitoring the global nutritional status of the environment. In this work we analysed the role of DasA, the sugar-binding component of the chitobiose ATP-binding cassette transport system, in informing the cell of environmental conditions, and its role in the onset of development and in ensuring correct sporulation. The chromosomal interruption of dasA resulted in a carbon-source-dependent vegetative arrest phenotype, and we identified a second DasR-dependent sugar transporter, in addition to the N-acetylglucosamine phosphotransferase system (PTSGlcNAc), that relates primary metabolism to development. Under conditions that allowed sporulation, highly aberrant spores with many prematurely produced germ tubes were observed. While GlcNAc locks streptomycetes in the vegetative state, a high extracellular concentration of the GlcNAc polymer chitin has no effect on development. The striking distinction is due to a difference in the transporters responsible for the import of GlcNAc, which enters via the PTS, and of chitin, which enters as the hydrolytic product chitobiose (GlcNAc2) through the DasABC transporter. A model explaining the role of these two essentially different transport systems in the control of development is provided.
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- Biochemistry And Molecular Biology
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Distinct functional domains of the Salmonella enterica WbaP transferase that is involved in the initiation reaction for synthesis of the O antigen subunit
WbaP is a membrane enzyme that initiates O antigen synthesis in Salmonella enterica by catalysing the transfer of galactose 1-phosphate (Gal-1-P) onto undecaprenyl phosphate (Und-P). WbaP possesses at least three predicted structural domains: an N-terminal region containing four transmembrane helices, a large central periplasmic loop, and a C-terminal domain containing the last transmembrane helix and a large cytoplasmic tail. In this work, we investigated the contribution of each region to WbaP function by constructing a series of mutant WbaP proteins and using them to complement O antigen synthesis in ΔwbaP mutants of S. enterica serovars Typhi and Typhimurium. Truncated forms of WbaP lacking the periplasmic loop exhibited altered chain-length distributions in O antigen polymerization, suggesting that this central domain is involved in modulating the chain-length distribution of the O polysaccharide. The N-terminal and periplasmic domains were dispensable for complementation of O antigen synthesis in vivo, suggesting that the C-terminal domain carries the sugar-phosphate transferase activity. However, despite the fact that they complemented the synthesis of O antigen in the ΔwbaP mutant in vivo, membrane extracts containing WbaP derivatives without the N-terminal domain failed to transfer radioactive Gal from UDP-Gal into a lipid-rich fraction. These results suggest that the N-terminal region of WbaP, which contains four transmembrane domains, is essential for the insertion or stability of the protein in the bacterial membrane. We propose that the domain structure of WbaP enables this protein not only to function in the transfer of Gal-1-P to Und-P but also to establish critical interactions with additional proteins required for the correct assembly of O antigen in S. enterica.
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The role of the Serratia marcescens SdeAB multidrug efflux pump and TolC homologue in fluoroquinolone resistance studied via gene-knockout mutagenesis
More LessSerratia marcescens is a prominent opportunistic nosocomial pathogen resistant to several classes of antibiotics. The major mechanism for fluoroquinolone resistance in various Gram-negative pathogens is active efflux. Our group previously identified SdeAB, a resistance-nodulation-cell division (RND) efflux pump complex, and a TolC-like outer-membrane protein (HasF), which together mediate energy-dependent fluoroquinolone efflux. In addition, a regulatory protein-encoding gene in the upstream region of sdeAB was identified (sdeR) and found to be 40 % homologous to MarA, an Escherichia coli transcriptional regulator. To provide conclusive evidence as to the role of these components in S. marcescens, sdeB, hasF and sdeR deletion mutants were constructed. Suicide vectors were created and introduced via triparental mating into S. marcescens UOC-67 (wild-type) and, for sdeB and hasF, T-861 (clinical isolate). We have analysed these genetically altered strains using minimal inhibitory concentration (MIC) assays for a wide range of compounds (fluoroquinolones, SDS, novobiocin, ethidium bromide and chloramphenicol). Intracellular accumulation of a variety of fluoroquinolones was measured fluorospectroscopically. The sdeB, hasF and sdeR knockout strains were consistently more susceptible to antibiotics than the parent strains, with the sdeB/hasF double knockout strain showing the highest susceptibility. A marked increase in fluoroquinolone (ciprofloxacin) accumulation was observed for strains deficient in either the sdeB or hasF genes when compared to the parental strains, with the highest ciprofloxacin accumulation observed for the sdeB/hasF double knockout. Antibiotic accumulation assays for the sdeB knockout mutant strains performed in the presence of carbonyl cyanide m-chlorophenylhydrazone (CCCP), a proton-motive-force inhibitor, demonstrated that SdeAB-mediated efflux is proton-motive-force dependent. Due to the comparable susceptibility of the sdeB and the hasF individual knockouts, we conclude that S. marcescens HasF is the sole outer-membrane component of the SdeAB pump. In addition, MIC data for sdeR-deficient and overexpressing strains confirm that SdeR is an activator of sdeAB and acts to enhance the overall multidrug resistance of S. marcescens.
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Differential gene expression of Listeria monocytogenes during high hydrostatic pressure processing
More LessHigh hydrostatic pressure processing (HPP) is currently being used as a treatment for certain foods to control the presence of food-borne pathogens, such as Listeria monocytogenes. Genomic microarray analysis was performed to determine the effects of HPP on L. monocytogenes in order to understand how it responds to mechanical stress injury. Reverse transcriptase PCR analysis of tufA and rpoC indicated that the reduction of mRNA expression in HPP-treated cells was dependent on intensity and time of the treatment. Treatments of 400 and 600 MPa for 5 min on cells in the exponential growth phase, though leading to partial or complete cellular inactivation, still resulted in measurable relative differential gene expression. Gene set enrichment analysis indicated that HPP induced increased expression of genes associated with DNA repair mechanisms, transcription and translation protein complexes, the septal ring, the general protein translocase system, flagella assemblage and chemotaxis, and lipid and peptidoglycan biosynthetic pathways. On the other hand, HPP appears to suppress a wide range of energy production and conversion, carbohydrate metabolism and virulence-associated genes accompanied by strong suppression of the SigB and PrfA regulons. HPP also affected genes controlled by the pleotrophic regulator CodY. HPP-induced cellular damage appears to lead to increased expression of genes linked to sections of the cell previously shown in bacteria to be damaged or altered during HPP exposure and suppression of gene expression associated with cellular growth processes and virulence.
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Biosynthesis of osmoregulated periplasmic glucans in Escherichia coli: the membrane-bound and the soluble periplasmic phosphoglycerol transferases are encoded by the same gene
More LessIn Escherichia coli, osmoregulated periplasmic glucans (OPGs) are highly substituted by phosphoglycerol, phosphoethanolamine and succinyl residues. A two-step model was proposed to account for phosphoglycerol substitution: first, the membrane-bound phosphoglycerol transferase I transfers residues from membrane phosphatidylglycerol to nascent OPG molecules; second, the periplasmic phosphoglycerol transferase II swaps residues from one OPG molecule to another. Gene opgB was reported to encode phosphoglycerol transferase I. In this study, we demonstrate that the periplasmic enzyme II is a soluble form of the membrane-bound enzyme I. In addition, timing of OPG substitution was investigated. OPG substitution by succinyl residues occurs rapidly, probably during the backbone polymerization, whereas phosphoglycerol addition is a very progressive process. Thus, both phosphoglycerol transferase activities appear biologically necessary for complete OPG substitution.
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Modulation of DNA-binding activity of Mycobacterium tuberculosis HspR by chaperones
More LessIn Mycobacterium tuberculosis, hspR is the last gene of the dnaKJE operon. It encodes the repressor HspR, which regulates the expression from this operon by binding to a consensus upstream sequence known as HAIR (HspR-associated inverted repeats). Previous investigations in the related Gram-positive bacterium Streptomyces coelicolor have revealed that DnaK acts as a co-repressor for HspR. In this investigation, a similar situation was encountered using the corresponding mycobacterial pair. However, the novel feature unearthed in this study is that the mycobacterial GroELs, GroEL1 and GroEL2, considerably stimulate the HAIR-binding activity of the HspR-DnaK combination. That these GroELs play a role in the folding process was evident from the observation that when heat- or chemically denatured HspR was renatured, the protein gained optimal activity only if one of these GroEL class chaperones was present along with DnaK. The renaturation process was found to be dependent on ATP hydrolysis. The DnaK-dependent DNA-binding activity of HspR could also be stimulated by DnaJ, but GrpE, which is known to release DnaK-bound substrates, was found to be inhibitory. The results of this study suggest that protein folding plays a substantial role in the activation of HspR following heat shock and that DnaK may be involved in two ways – first, as a chaperone acting in concert with GroEL and/or DnaJ and second, as a co-repressor bound to HspR.
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The copper-dependent ACE1 transcription factor activates the transcription of the mco1 gene from the basidiomycete Phanerochaete chrysosporium
More LessWe have previously identified and functionally characterized the transcription factor ACE1 (Pc-ACE1) from Phanerochaete chrysosporium. In Saccharomyces cerevisiae, ACE1 activates the copper-dependent transcription of target genes through a DNA sequence element named ACE. However, the possible target gene(s) of Pc-ACE1 were unknown. An in silico search led to the identification of putative ACE elements in the promoter region of mco1, one of the four clustered genes encoding multicopper oxidases (MCOs) in P. chrysosporium. Since copper exerts an effect at the transcriptional level in MCOs from several organisms, in this work we analysed the effect of copper on transcript levels of the clustered MCO genes from P. chrysosporium, with the exception of the transcriptionally inactive mco3. Copper supplementation of cultures produced an increment in transcripts from genes mco1 and mco2, but not from mco4. Electrophoretic mobility-shift assays revealed that Pc-ACE1 binds specifically to a probe containing one of the putative ACE elements found in the promoter of mco1. In addition, using a cell-free transcription system, we showed that in the presence of cuprous ion, Pc-ACE1 induces activation of the promoter of mco1, but not that of mco2.
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Characterization of the Escherichia coli K-12 ydhYVWXUT operon: regulation by FNR, NarL and NarP
In Escherichia coli K-12 the expression of many genes is controlled by the oxygen-responsive transcription factor FNR and the nitrate- and nitrite-responsive two-component systems NarXL and NarPQ. Here, the ydhY gene is shown to be the first gene of a six-gene operon (ydhYVWXUT) that encodes proteins predicted to be components of an oxidoreductase. Mapping the ydhY–T transcript start and site-directed mutagenesis confirmed that the ydhY–T genes are transcribed from an FNR-dependent class II promoter and showed that the FNR site is centred at −42.5. In the presence of nitrate or nitrite, NarXL and NarPQ repressed ydhY–T expression. Analysis of the DNA sequence of the ydhY promoter region (PydhY) revealed the presence of four heptameric sequences similar to NarL/P binding sites centred at −42, −16, +6 and +15. The latter heptamers are arranged as a 7-2-7 inverted repeat, which is required for recognition by NarP. Accordingly, NarP protected the 7-2-7 region in DNase I footprints, and mutation of either heptamer +6 or heptamer +15 impaired nitrite-mediated repression, whereas mutation of heptamer −42 and heptamer −16 did not affect the response to nitrite. The NarL protein also protected the 7-2-7 region, but in contrast to NarP, the NarL footprint extended further upstream to encompass the −16 heptamer. The extended NarL footprint was consistent with the presence of multiple NarL–PydhY complexes in gel retardation assays. Mutation of heptamer −42, which is located within the FNR binding site, or heptamer +6 (but not heptamers −16 or +15) impaired nitrate-mediated repression. Thus, although the region of the ydhY–T promoter containing the −16 and +15 heptamers was recognized by NarL in vitro, mutation of these heptamers did not affect NarL-mediated repression in vivo.
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- Biodiversity And Evolution
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Genomic comparison of the O-antigen biosynthesis gene clusters of Escherichia coli O55 strains belonging to three distinct lineages
Typical enteropathogenic Escherichia coli (EPEC) O55 : H7 is regarded as the closest relative of enterohaemorrhagic E. coli (EHEC) O157 : H7. Both serotypes usually express the γ1 intimin subclass and trigger actin polymerization by the Tir-TccP pathway. However, atypical O55 : H7 strains capable of triggering actin polymerization via the Tir-Nck pathway have recently been identified. In this study, we investigated the genotypic differences and phylogenetic relationships between typical and atypical O55 : H7 strains. We show that the atypical O55 : H7 strains, which express the θ intimin subclass and lack both tccP and tccP2, belong to an E. coli lineage distinct from the typical O55 : H7 and from the EPEC O55 : H6, which also uses the Tir-Nck actin polymerization pathway. We conducted genomic comparisons of the chromosomal regions covering the O-antigen gene cluster and its flanking regions between the three O55 lineages by RFLP analysis of PCR products and DNA sequencing analysis of about 65 kb chromosomal regions. This unexpectedly revealed that horizontal transfer of large fragments (≥40 kb) encoding the O55-antigen gene cluster and part of the neighbouring colanic acid gene cluster was involved in the emergence of the three O55 E. coli lineages. The data provide new insights into the mechanisms involved in the generation of a wide variety of O-serotypes in Gram-negative bacteria.
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- Genes And Genomes
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Two-component systems of the myxobacteria: structure, diversity and evolutionary relationships
More LessTwo-component systems (TCSs) are a large family of signalling pathways characterized by the successive transfer of phosphoryl groups between the histidine and aspartate residues of paired histidine kinase and response regulator proteins. With the availability of genome sequences for four genera of myxobacteria it has become possible to assess the genomic complements of myxobacterial TCS genes and to characterize features of their organization and evolutionary heritage. In this study we have compiled lists of the TCS genes within myxobacterial genomes and characterized their domain architecture, gene organization and evolutionary relationships. In order to provide an appropriate context for our conclusions, where possible we have compared myxobacterial TCSs with those found in 316 other completely sequenced bacteria. Myxobacteria have the largest number of TCSs of any organisms. An unusually low proportion of TCS genes are paired in myxobacterial genomes, and myxobacterial histidine kinases also seem to sense internal signals to an unusual degree. Phylogenetic evidence has allowed us to suggest homologous relationships of proteins across the myxobacteria, and it appears that myxobacterial TCS evolution has been dominated by duplications, gene rearrangements and changes in sensory domain complements. The systematic classification of the TCS proteins of the myxobacteria presented here should also provide a framework for future experimental studies on two-component regulation in these organisms.
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Evidence for the horizontal transfer of an integrase gene from a fusellovirus to a pRN-like plasmid within a single strain of Sulfolobus and the implications for plasmid survival
More LessA fusellovirus SSV4 and a pRN-like plasmid pXZ1 were co-isolated from a single strain of Sulfolobus. In contrast to the previously characterized virus–plasmid hybrids pSSVx and pSSVi, which can coexist intracellulary with a fusellovirus, pXZ1 is not packaged into viral particles and shows no viral infectivity. The virus and plasmid carry genomes of 15 135 and 6970 bp, respectively. For SSV4, 33 predicted ORFs are compactly organized with a strong preference for UGA stop codons, three-quarters of which overlap with either the Shine–Dalgarno motif or the start codon of the following gene. pXZ1 carries seven ORFs, three of which encode an atypical RepA, a PlrA and a CopG protein. A fourth ORF exhibits a high nucleotide sequence identity to the SSV4 integrase gene, which suggests that it has been transferred to the plasmid from SSV4. A single point mutation within an otherwise identical 500 bp region of the integrase gene occurs in the viral attachment site (attP), which corresponds to the anticodon region of the targeted tRNA gene in the host chromosome. This point mutation confers on pXZ1 the ability to integrate into the tRNAGlu[CUC] gene, which differs from the integration site of SSV4, tRNAGlu[UUC]. SSV4 and pXZ1 were also shown experimentally to integrate into separate sites on the host chromosome. This is believed to be the first report of a pRN plasmid sharing its natural host with a fusellovirus and carrying a highly similar integrase gene.
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The copper resistance operon copAB from Xanthomonas axonopodis pathovar citri: gene inactivation results in copper sensitivity
Xanthomonas axonopodis pv. citri (Xac) causes citrus canker and the completion of the Xac genome sequence has opened up the possibility of investigating basic cellular mechanisms at the genomic level. Copper compounds have been extensively used in agriculture to control plant diseases. The copA and copB genes, identified by annotation of the Xac genome, encode homologues of proteins involved in copper resistance. A gene expression assay by Northern blotting revealed that copA and copB are expressed as a unique transcript specifically induced by copper. Synthesis of the gene products was also induced by copper, reaching a maximum level at 4 h after addition of copper to the culture medium. CopA was a cytosolic protein and CopB was detected in the cytoplasmic membrane. The gene encoding CopA was disrupted by the insertion of a transposon, leading to mutant strains that were unable to grow in culture medium containing copper, even at the lowest CuSO4 concentration tested (0.25 mM), whereas the wild-type strain was able to grow in the presence of 1 mM copper. Cell suspensions of the wild-type and mutant strains in different copper concentrations were inoculated in lemon leaves to analyse their ability to induce citrus canker symptoms. Cells of mutant strains showed higher sensitivity than the wild-type strain in the presence of copper, i.e. they were not able to induce citrus canker symptoms at high copper concentrations and exhibited a more retarded growth in planta.
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Regulation of Pseudomonas aeruginosa ptxR by Vfr
More LessPseudomonas aeruginosa PtxR enhances the expression of the exotoxin A gene toxA. The expression of ptxR itself, which occurs from two promoters (P1 and P2), is not completely understood. We have recently demonstrated that the ptxR upstream region contains potential binding sites for multiple regulators, including the virulence factor regulator Vfr. In this study, we identified within the ptxR upstream region, a 25 bp sequence to which Vfr specifically binds. The sequence is located 20–44 (32.5) bp 5′ of the ptxR P2 promoter, and overlaps a potential binding site for the iron-starvation sigma factor PvdS. We also show that, throughout the growth cycle, deletion of vfr reduces ptxR expression from the P2 promoter in the P. aeruginosa strain PAO1 by four- to eightfold, but does not affect ptxR expression from P1. Further, loss of Vfr eliminates the PtxR-induced enhancement in the synthesis of exotoxin A and the metalloproteinase LasB. Our results suggest that Vfr modulates toxA and lasB expression in PAO1 through PtxR. A model defining the relationships between these different genes is presented.
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A subset of mucosa-associated Escherichia coli isolates from patients with colon cancer, but not Crohn's disease, share pathogenicity islands with urinary pathogenic E. coli
Adherent and invasive mucosa-associated Escherichia coli have been implicated in the pathogenesis of colon cancer and inflammatory bowel diseases. It has been reported that such isolates share features of extraintestinal E. coli (ExPEC) and particularly uropathogenic E. coli (UPEC). We used suppression subtractive hybridization (SSH) to subtract the genome of E. coli K-12 from that of a colon cancer mucosal E. coli isolate. Of the subtracted sequences, 53 % were present in the genomes of one or more of three sequenced UPEC strains but absent from the genome of an enterohaemorrhagic E. coli (EHEC) strain. Of the subtracted sequences, 80 % matched at least one UPEC genome, whereas only 4 % were absent from the UPEC genomes but present in the genome of the EHEC strain. A further genomic subtraction against the UPEC strain 536 enriched for sequences matching mobile genetic elements, other ExPEC strains, and other UPEC strains or commensals, rather than strains associated with gastrointestinal disease. We analysed the distribution of selected subtracted sequences and UPEC-associated pathogenicity islands (PAIs) amongst a panel of mucosa-associated E. coli isolated from colonoscopic biopsies of patients with colon cancer, patients with Crohn's disease and controls. This enabled us to identify a group of isolates from colon cancer (30–40 %) carrying multiple genes previously categorized as UPEC-specific and implicated in virulence.
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Functional analysis of a Campylobacter jejuni alkaline phosphatase secreted via the Tat export machinery
Bacterial alkaline phosphatases (PhoA) hydrolyse phosphate-containing substrates to provide the preferred phosphorus source inorganic phosphate (Pi). Campylobacter jejuni does not contain a typical PhoA homologue but contains a phosphatase that is regulated by the two-component system PhosS/PhosR. Here we describe the characterization of the enzyme, its secretion pathway and its function in the bacterium's biology. Phosphatase assays showed that the enzyme utilizes exclusively phosphomonoesters as a substrate, requires Ca2+ for its activity, and displays maximum activity at a pH of 10. Gene disruption revealed that it is the sole alkaline phosphatase in C. jejuni. The protein contained a twin-arginine motif (RR) at its N terminus, typical of substrates of the Tat secretion system. Substitution of the twin-arginine residues showed that they are essential for enzyme activity. C. jejuni genome analysis indicated the presence of four ubiquitously expressed Tat components that may form a functional Tat secretion system as well as 11 putative Tat substrates, including the alkaline phosphatase (PhoACj) and the nitrate reductase NapA. Inactivation of tatC caused defects in both PhoACj and NapA activity as well as a reduction in bacterial growth that were all restored by complementation in trans with an intact tatC copy. The atypical overall features of the PhoACj compared to Escherichia coli PhoA support the existence in prokaryotes of a separate group of Tat-dependent alkaline phosphatases, classified as the PhoX family.
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- Pathogens And Pathogenicity
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Carnitine acetyltransferases are required for growth on non-fermentable carbon sources but not for pathogenesis in Candida albicans
More LessCarbon starvation is a significant stress encountered by the opportunistic fungal pathogen Candida albicans, and mutations in several pathways required to assimilate non-fermentable carbon sources attenuate virulence. These pathways – β-oxidation, the glyoxylate cycle and gluconeogenesis – are compartmentalized in the fungal cell between the peroxisome, mitochondria and cytosol; thus, the cell must transport key intermediates between these organelles. Transport of acetyl-CoA, a particularly important intermediate of carbon metabolism, is catalysed by membrane-associated carnitine acetyltransferases (CATs). We report here the characterization of the three predicted CAT genes in C. albicans, CTN1, CTN2 and CTN3. Strains lacking CTN1 or CTN2 were unable to grow on ethanol or acetate as sole carbon source; additionally, citrate was utilized poorly (Δctn2) or not at all (Δctn1) and the Δctn2 mutant failed to grow on fatty acids as well. In contrast, deletion of CTN3 had no observable phenotype. All three genes were upregulated in the presence of non-fermentable carbon sources and after macrophage phagocytosis. CTN1 and CTN3 were able to complement the corresponding Saccharomyces cerevisiae Δyat1 and Δyat2 mutants. However, these mutants had no obvious attenuation in virulence in a mouse model of disseminated candidiasis, in contrast to other carbon metabolism mutants. These findings extend our understanding of nutrient stress in vivo and in vitro and the contribution of metabolic pathways to virulence in C. albicans.
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Hypoxic conditions and iron restriction affect the cell-wall proteome of Candida albicans grown under vagina-simulative conditions
Proteins that are covalently linked to the skeletal polysaccharides of the cell wall of Candida albicans play a major role in the colonization of the vaginal mucosal surface, which may result in vaginitis. Here we report on the variability of the cell-wall proteome of C. albicans as a function of the ambient O2 concentration and iron availability. For these studies, cells were cultured at 37 °C in vagina-simulative medium and aerated with a gas mixture consisting of 6 % (v/v) CO2, 0.01–7 % (v/v) O2 and N2, reflecting the gas composition in the vaginal environment. Under these conditions, the cells grew exclusively in the non-hyphal form, with the relative growth rate being halved at ∼0.02 % (v/v) O2. Using tandem MS and immunoblot analysis, we identified 15 covalently linked glycosylphosphatidylinositol (GPI) proteins in isolated walls (Als1, Als3, Cht2, Crh11, Ecm33, Hwp1, Pga4, Pga10, Phr2, Rbt5, Rhd3, Sod4, Ssr1, Ywp1, Utr2) and 4 covalently linked non-GPI proteins (MP65, Pir1, Sim1/Sun42, Tos1). Five of them (Als3, Hwp1, Sim1, Tos1, Utr2) were absent in cells grown in rich medium. Immunoblot analysis revealed that restricted O2 availability resulted in higher levels of the non-GPI protein Pir1, a putative β-1,3-glucan cross-linking protein, and of the GPI-proteins Hwp1, an adhesion protein, and Pga10 and Rbt5, which are involved in iron acquisition. Addition of the iron chelator ferrozine at saturating levels of O2 resulted in higher cell wall levels of Hwp1 and Rbt5, suggesting that the responses to hypoxic conditions and iron restriction are related.
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Genotyping reveals a wide heterogeneity of Tropheryma whipplei
Tropheryma whipplei, the causative agent of Whipple's disease, is associated with various clinical manifestations as well as an asymptomatic carrier status, and it exhibits genetic heterogeneity. However, relationships that may exist between environmental and clinical strains are unknown. Herein, we developed an efficient genotyping system based on four highly variable genomic sequences (HVGSs) selected on the basis of genome comparison. We analysed 39 samples from 39 patients with Whipple's disease and 10 samples from 10 asymptomatic carriers. Twenty-six classic gastrointestinal Whipple's disease associated with additional manifestations, six relapses of classic Whipple's disease (three gastrointestinal and three neurological relapses), and seven isolated infections due to T. whipplei without digestive involvement (five endocarditis, one spondylodiscitis and one neurological infection) were included in the study. We identified 24 HVGS genotypes among 39 T. whipplei DNA samples from the patients and 10 T. whipplei DNA samples from the asymptomatic carriers. No significant correlation between HVGS genotypes and clinical manifestations of Whipple's disease, or asymptomatic carriers, was found for the 49 samples tested. Our observations revealed a high genetic diversity of T. whipplei strains that is apparently independent of geographical distribution and unrelated to bacterial pathogenicity. Genotyping in Whipple's disease may, however, be useful in epidemiological studies.
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Induction of Aggregatibacter actinomycetemcomitans leukotoxin expression by IS1301 and orfA
More LessMost Aggregatibacter actinomycetemcomitans strains express relatively low levels of leukotoxin, encoded by the orfA–ltxCABD operon. However, several strains isolated from patients with localized aggressive periodontitis are hyperleukotoxic and transcribe the ltx operon at high levels. These strains possess a copy of IS1301 in the ltx promoter and previous studies have suggested that the presence of the insertion sequence increases ltx transcription by uncoupling a cis-acting negative regulator of ltx expression from the basal elements of the ltx promoter. However, we now report that replacing IS1301 with an equal length of random sequence has little effect on transcriptional activity of the ltx promoter, suggesting that the physical displacement of the negative regulatory element does not contribute to the hyperleukotoxic phenotype of IS1301-containing strains. Instead, we show that a −10-like element upstream of the transposase ORF of IS1301 is required for increased transcriptional activity of the ltx promoter. Site-specific mutation of the −10 sequence, or reversing the orientation of IS1301 relative to the basal ltx promoter elements, reduced transcriptional activity to levels exhibited by the native ltx promoter. However, no increase in transcription was observed when IS1301 was recombinantly inserted into a ltx promoter that contained a truncated copy of orfA, suggesting that an intact orfA may also be required for IS1301-mediated induction of ltxCABD. Therefore, to determine if orfA functions as a regulator of ltx expression, three independent ltx-promoter–lacZ-reporter constructs containing frameshift mutations in orfA were analysed. Each exhibited significantly lower expression of β-galactosidase than the control reporter with intact orfA. In addition, OrfA protein was shown, by mobility shift electrophoresis, to interact with the ltx promoter at or downstream of the −35 sequence. These results suggest that a potential transposase promoter and the OrfA polypeptide may modulate leukotoxin expression in hyperleukotoxic A. actinomycetemcomitans strains containing IS1301.
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Expression and immunogenicity of six putative variable surface proteins in Mycoplasma mycoides subsp. mycoides SC
More LessVariable surface protein Vmm and five Vmm-type proteins from Mycoplasma mycoides subsp. mycoides SC were analysed to determine whether these proteins are expressed in vivo in animals affected by contagious bovine pleuropneumonia (CBPP) and in vitro. Recombinant versions of these proteins were constructed and expressed in Escherichia coli after mutation of the TGA Trp codons to TGG. These proteins were then analysed by dot and Western blotting with sera from CBPP-affected cattle. Furthermore, affinity-purified polyclonal antibodies to the recombinant proteins were used in Western and colony blotting to look for expression of the putative Vmm-type proteins in cultured M. mycoides SC. This study demonstrates that immunoglobulins in CBPP sera recognize all putative Vmm-type proteins tested, indicating that these proteins or their homologues are expressed by mycoplasmas during natural infections. Vmm and one of the putative Vmm-type proteins showed variable expression in vitro.
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Identification of the Staphylococcus aureus MSCRAMM clumping factor B (ClfB) binding site in the αC-domain of human fibrinogen
More LessClumping factor B (ClfB) of Staphylococcus aureus binds to cytokeratin 10 and to fibrinogen. In this study the binding site in human fibrinogen was localized to a short region within the C terminus of the Aα-chain. ClfB only bound to the Aα-chain of fibrinogen in a ligand-affinity blot and in solid-phase assays with purified recombinant fibrinogen chains. A variant of fibrinogen with wild-type Bβ- and γ-chains but with a deletion that lacked the C-terminal residues from 252–610 of the Aα-chain did not support adherence of S. aureus Newman expressing ClfB. A series of truncated mutants of the recombinant Aα-chain were tested for their ability to support adherence of S. aureus Newman ClfB+, which allowed the binding site to be localized to a short segment of the unfolded flexible repeated sequence within the C terminus of the Aα-chain. This was confirmed by two amino acid substititions within repeat 5 of the recombinant Aα-chain which did not support adherence of Newman ClfB+. Lactococcus lactis expressing ClfB mutants with amino acid substitutions (N256 and Q235) located in the putative ligand-binding trench between domains N2 and N3 of the A-domain were defective in adherence to immobilized fibrinogen and cytokeratin 10, suggesting that both ligands bind to the same or overlapping regions.
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Membrane localization and topology of the Yersinia pestis YscJ lipoprotein
More LessThe localization and membrane topology of the Yersinia pestis YscJ lipoprotein, an essential component of the type III secretion apparatus, was investigated. YscJ was demonstrated to be an inner membrane (IM) lipoprotein that is anchored to the periplasmic face of the IM via an N-terminal lipid moiety and via a C-terminal transmembrane (TM) domain. Localization of the N-terminal lipid moiety to the IM occurred regardless of the amino-acid residues found in the +2 or +3 positions. IM localization was dependent upon an intact N-terminal domain (amino acids +1 to +61), suggesting that this region plays a role in YscJ localization. In contrast, the YscJ C-terminal domain and TM domain were not required for IM localization. N-terminal sequence analysis demonstrated that a significant proportion of membrane-localized YscJ lacks N-acylation, the final modification required for Lol-dependent transport of a lipoprotein to the OM. Interestingly, attachment of the N-terminus to the IM was required for YscJ function; however, the YscJ secretion signal and lipo-box could be functionally replaced by the first TM domain of the YscV protein, suggesting that the mechanism of attachment to the IM was not critical.
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Analysis of a novel spore antigen in Bacillus anthracis that contributes to spore opsonization
More LessThe significance of Bacillus anthracis as an agent of bioterrorism has been well established. An understanding of both the pathogenesis and the host response is required to elucidate approaches to more rapidly detect and effectively prevent or treat anthrax. Current vaccine strategies are focused primarily on production of antibodies against the protective antigen components of the anthrax toxins, which are secreted by the bacilli. A better understanding of the dynamic morphology of the dormant and germinating spore and its interaction with the host immune system could be important in developing an optimally efficacious anthrax vaccine. A spore-associated protein was identified that was specific to the Bacillus cereus group of bacteria and referred to as spore opsonization-associated antigen A (SoaA). Immuno-electron microscopy localized this protein to the area of the cortex beneath the coat of the dormant spore. Although our data suggested that SoaA was found below the coat layers of the ungerminated spore, SoaA was involved in the interaction of spores with macrophages shortly after infection. To investigate further the specific properties of the SoaA protein, the soaA gene was inactivated in the B. anthracis Ames strain. The SoaA protein in the Ames strain of B. anthracis increased the phagocytic uptake of the spores in the presence of anti-spore antibodies. Unlike the wild-type strain, the mutant soaA : : Kan strain was not readily opsonized by anti-spore antibodies. While the mutant spores retained characteristic resistance properties in vitro and virulence in vivo, the soaA : : Kan mutant strain was significantly less suited for survival in vivo when competed against the wild-type Ames strain.
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The formation and structure of Escherichia coli K-12 haemolysin E pores
Some enteric bacteria synthesize a pore-forming toxin, HlyE, which is cytolytic and cytotoxic to host cells. Measurement of HlyE binding to erythrocyte ghosts and the kinetics of HlyE-mediated erythrocyte lysis suggests that interaction with target membranes is not the rate-limiting step in the formation of HlyE pores, but that there is a temperature-dependent lag phase before a functional pore is formed. Circular dichroism and fluorescence energy transfer analyses show that HlyE protomers retain an α-helical structure when oligomerized to form a pore consisting of parallel HlyE protomers. Comparison of the proteolytic sensitivities of the water-soluble and oligomeric forms of HlyE identifies inner and outer surfaces of the pore. This new information has been used to constrain a model of the HlyE pore, which allows a more detailed interpretation of previous low-resolution 3D reconstructions and suggests a novel mechanism for insertion of HlyE into target membranes.
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Burkholderia cenocepacia requires RpoE for growth under stress conditions and delay of phagolysosomal fusion in macrophages
More LessBurkholderia cenocepacia is an opportunistic pathogen causing serious infections in patients with cystic fibrosis. The widespread distribution of this bacterium in the environment suggests that it must adapt to stress to be able to survive. We identified in B. cenocepacia K56-2 a gene predicted to encode RpoE, the extra-cytoplasmic stress response regulator. The rpoE gene is the first gene of a predicted operon encoding proteins homologous to RseA, RseB, MucD and a protein of unknown function. The genomic organization and the co-transcription of these genes were confirmed by PCR and RT-PCR. The mucD and rpoE genes were mutated, giving rise to B. cenocepacia RSF24 and RSF25, respectively. While mutant RSF24 did not demonstrate any growth defects under the conditions tested, RSF25 was compromised for growth under temperature (44 °C) and osmotic stress (426 mM NaCl). Expression of RpoE in trans could complement the osmotic growth defect but exacerbated temperature sensitivity in both RSF25 and wild-type K56-2. Inactivation of rpoE altered the bacterial cell surface, as indicated by increased binding of the fluorescent dye calcofluor white and by an altered outer-membrane protein profile. These cell surface changes were restored by complementation with a plasmid encoding rpoE. Macrophage infections in which bacterial colocalization with fluorescent dextran was examined demonstrated that the rpoE mutant could not delay the fusion of B. cenocepacia-containing vacuoles with lysosomes, in contrast to the parental strain K56-2. These data show that B. cenocepacia rpoE is required for bacterial growth under certain stress conditions and for the ability of intracellular bacteria to delay phagolysosomal fusion in macrophages.
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A novel oxidized low-density lipoprotein-binding protein from Pseudomonas aeruginosa
A novel protein, PA0122, has been identified in Pseudomonas aeruginosa and shown to bind to oxidized low-density lipoprotein (Ox-LDL). The PA0122 gene was recognized based on gene expression pattern differences between two strains of P. aeruginosa isolated from the sputum of an individual with cystic fibrosis (CF). There was an approximately eightfold increase in PA0122 expression in the non-mucoid strain 383, compared to that in the mucoid strain 2192. Quantitative real-time RT-PCR (qRT-PCR) supported PA0122 transcript expression differences between strains 383 and 2192 and revealed growth-phase dependence, with the highest level of expression at early stationary phase (OD600 1.5). PA0122 encodes a 136 aa ‘conserved hypothetical’ protein that has similarity to Aspergillus fumigatus Asp-haemolysin, which is an Ox-LDL-binding protein, and possessed a motif that is homologous to the fungal aegerolysin family of proteins. Antibodies produced to purified recombinant PA0122 recognized a 16 kDa protein band in cell lysates as well as in the supernatant fractions of strain 383. The PA0122 protein expression pattern was growth phase-dependent, with maximal production observed at OD600 1.5 that was consistent with the PA0122 transcript expression profile. Subcellular fractionation studies revealed differences in the localization of PA0122 between strains 383 and 2192. In 383, PA0122 was observed in the cytoplasm and in membrane fractions. In 2192, PA0122 was found in the cytoplasm but was not detected in membrane fractions. Surface plasmon resonance revealed that recombinant PA0122 binds with high affinity to Ox-LDL and to its major subcomponent, lysophosphatidylcholine, but not to non-oxidized LDL.
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The yejABEF operon of Salmonella confers resistance to antimicrobial peptides and contributes to its virulence
More LessPathogenic micro-organisms have evolved many strategies to counteract the antimicrobial peptides (AMPs) that they encounter upon entry into host systems. These strategies play vital roles in the virulence of pathogenic micro-organisms. The Salmonella enterica serovar Typhimurium genome has a gene cluster consisting of yejA, yejB, yejE and yejF genes, which encode a putative ATP-binding cassette (ABC) transporter. Our study shows that these genes constitute an operon. We deleted the yejF gene, which encodes the ATPase component of the putative ABC transporter. The ΔyejF strain showed increased sensitivity to protamine, melittin, polymyxin B, human defensin (HBD)-1 and HBD-2, and was compromised in its capacity to proliferate inside activated macrophages and epithelial cells. Inside Intestine 407 cells, Salmonella was found to co-localize with human defensins HD-5 and HBD-1; this suggests that the ability to counteract AMPs in the intracellular milieu is important for Salmonella. In a murine typhoid model, the ΔyejF strain displayed decreased virulence when infected intragastrically. These findings suggest that the putative transporter encoded by the yejABEF operon is involved in counteracting AMPs, and that it contributes to the virulence of Salmonella.
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- Physiology
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Ethanol tolerance of sugar transport, and the rectification of stuck wine fermentations
The incomplete consumption of sugar resulting from stuck wine fermentation is associated with important economic losses. One of the solutions to this serious problem consists of reinoculating the brew with a yeast starter culture that is both alcohol tolerant and a vigorous fructose fermenter. The present work aimed to select yeast strains capable of restarting stuck wine fermentations, and identify key parameters that contribute to the efficiency of the strains. Commercial and non-commercial Saccharomyces wine strains were tested, as well as strains of the fermentative non-Saccharomyces species Zygosaccharomyces bailii and Torulaspora delbrueckii. Although the latter species were shown to be more resistant to a combination of ethanol- and acetic-acid-induced cell death, commercial Saccharomyces cerevisiae strains were the most efficient fructose consumers in medium simulating a stuck fermentation. Stationary-phase S. cerevisiae cells performed better than inocula prepared from exponentially growing cultures, which correlates with the higher resistance to ethanol of non-growing populations. Stationary-phase cells pre-adapted to ethanol did not improve fructose consumption rates; this was in contrast to exponential-phase cells that benefited from prior incubation in ethanol-containing medium. Notably, a correlation was observed between yeast fructose consumption capacity and glucose (or fructose) transport. Our results challenge the current belief that ethanol tolerance, expressed in terms of cell viability, is a reliable criterion for the selection of yeast strains to restart stuck fermentations. Instead, this capacity seems to be based on sugar transport and its resistance to ethanol. In an attempt to further improve cell viability in the presence of high ethanol concentrations, hybrid strains of T. delbrueckii and S. cerevisiae were produced, and they showed high potential as restarter strains. The present work opens perspectives for the application of innovative strategies in the wine-making industry.
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- Plant-Microbe Interactions
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Functional analyses of heterotrimeric G protein Gα and Gβ subunits in Gibberella zeae
More LessThe homothallic ascomycete fungus Gibberella zeae (anamorph: Fusarium graminearum) is a major toxigenic plant pathogen that causes head blight disease on small-grain cereals. The fungus produces the mycotoxins deoxynivalenol (DON) and zearalenone (ZEA) in infected hosts, posing a threat to human and animal health. Despite its agricultural and toxicological importance, the molecular mechanisms underlying its growth, development and virulence remain largely unknown. To better understand such mechanisms, we studied the heterotrimeric G proteins of G. zeae, which are known to control crucial signalling pathways that regulate various cellular and developmental responses in fungi. Three putative Gα subunits, GzGPA1, GzGPA2 and GzGPA3, and one Gβ subunit, GzGPB1, were identified in the F. graminearum genome. Deletion of GzGPA1, a homologue of the Aspergillus nidulans Gα gene fadA, resulted in female sterility and enhanced DON and ZEA production, suggesting that GzGPA1 is required for normal sexual reproduction and repression of toxin biosynthesis. The production of DON and ZEA was also enhanced in the GzGPB1 mutant, suggesting that both Gα GzGPA1 and Gβ GzGPB1 negatively control mycotoxin production. Deletion of GzGPA2, which encodes a Gα protein similar to A. nidulans GanB, caused reduced pathogenicity and increased chitin accumulation in the cell wall, implying that GzGPA2 has multiple functions. Our study shows that G. zeae heterotrimeric G protein subunits can regulate vegetative growth, sexual development, toxin production and pathogenicity.
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The alternative sigma factor AlgT, but not alginate synthesis, promotes in planta multiplication of Pseudomonas syringae pv. glycinea
More LessThe phytopathogen Pseudomonas syringae pv. glycinea produces the exopolysaccharide (EPS) alginate, which is thought to function in epiphytic fitness and virulence. A key regulator for alginate biosynthesis in Pseudomonas aeruginosa and P. syringae is the alternative sigma factor AlgT (σ 22). In this study, the contribution of alginate synthesis and AlgT to in planta epiphytic fitness and virulence of P. syringae was examined. Alginate biosynthesis mutants were generated for the P. syringae pv. glycinea strains PG4180 and PG4180.muc, representing a comprehensive set of alginate- and AlgT-positive or -negative derivatives. Analysis of in vitro and in planta phenotypes revealed that AlgT strongly promoted in planta growth, survival and symptom development, but decreased the ability to grow in vitro. In contrast, alginate biosynthesis had only marginal impact. Quantitative in vitro and in planta gene expression analyses for alginate biosynthesis and algT were carried out at two temperatures in AlgT-negative and -positive backgrounds. algT as well as algD gene expression was AlgT-dependent, plant-inducible and temperature-dependent, with higher expression at 18 compared to 28 °C; however, no temperature dependence was observed in vitro. Our data suggest that AlgT may act as a global regulator for virulence and in planta fitness traits of P. syringae independent of its role in EPS biosynthesis.
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Volumes and issues
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Volume 170 (2024)
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