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Volume 155,
Issue 6,
2009
Volume 155, Issue 6, 2009
- Genes And Genomes
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Analysis of CRISPR in Streptococcus mutans suggests frequent occurrence of acquired immunity against infection by M102-like bacteriophages
More LessClustered regularly interspaced short palindromic repeats (CRISPR) consist of highly conserved direct repeats interspersed with variable spacer sequences. They can protect bacteria against invasion by foreign DNA elements. The genome sequence of Streptococcus mutans strain UA159 contains two CRISPR loci, designated CRISPR1 and CRISPR2. The aims of this study were to analyse the organization of CRISPR in further S. mutans strains and to investigate the importance of CRISPR in acquired immunity to M102-like phages. The sequences of CRISPR1 and CRISPR2 arrays were determined for 29 S. mutans strains from different persons. More than half of the CRISPR1 spacers and about 35 % of the CRISPR2 spacers showed sequence similarity with the genome sequence of M102, a virulent siphophage specific for S. mutans. Although only a few spacers matched the phage sequence completely, most of the mismatches had no effect on the amino acid sequences of the phage-encoded proteins. The results suggest that S. mutans is often attacked by M102-like bacteriophages, and that its acquisition of novel phage-derived CRISPR sequences goes along with the presence of S. mutans phages in the environment. Analysis of CRISPR1 of M102-resistant mutants of S. mutans OMZ 381 showed that some of them had acquired novel spacers, and the sequences of all but one of these matched the phage M102 genome sequence. This suggests that the acquisition of the spacers contributed to the resistance against phage infection. However, since not all resistant mutants had new spacers, and since the removal of the CRISPR1 array in one of the mutants and in wild-type strains did not lead to loss of resistance to infection by M102, the acquisition of resistance must be based on further elements as well.
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- Microbial Pathogenicity
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Survival of uropathogenic Escherichia coli in the murine urinary tract is dependent on OmpR
More LessUropathogenic Escherichia coli (UPEC) can grow in environments with significantly elevated osmolarities, such as murine and human urinary tracts. OmpR is the response regulator part of a two-component OmpR–EnvZ regulatory system that responds to osmotic stresses. To determine the role of OmpR in UPEC survival, a ΔompR mutant was created in the UPEC clinical isolate NU149. The ΔompR mutant had a growth defect compared with the wild-type strain under osmotic stress conditions; this defect was complemented by the full-length ompR gene on a plasmid, but not with a mutant OmpR with an alanine substitution for aspartic acid at the phosphorylation site at position 55. Furthermore, the ΔompR mutant displayed up to 2-log reduction in bacterial cell numbers in murine bladders and kidneys compared with wild-type bacteria after 5 days of infection. The ability of the bacteria to survive was restored to wild-type levels when the ΔompR mutant strain was complemented with wild-type ompR, but not when the alanine-substituted ompR gene was used. This study has fulfilled molecular Koch's postulates by showing the pivotal role OmpR plays in UPEC survival within the murine urinary tract.
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The OxyR homologue in Tannerella forsythia regulates expression of oxidative stress responses and biofilm formation
More LessTannerella forsythia is an anaerobic periodontal pathogen that encounters constant oxidative stress in the human oral cavity due to exposure to air and reactive oxidative species from coexisting dental plaque bacteria as well as leukocytes. In this study, we sought to characterize a T. forsythia ORF with close similarity to bacterial oxidative stress response sensor protein OxyR. To analyse the role of this OxyR homologue, a gene deletion mutant was constructed and characterized. Aerotolerance, survival after hydrogen peroxide challenge and transcription levels of known bacterial antioxidant genes were then determined. Since an association between oxidative stress and biofilm formation has been observed in bacterial systems, we also investigated the role of the OxyR protein in biofilm development by T. forsythia. Our results showed that aerotolerance, sensitivity to peroxide challenge and the expression of oxidative stress response genes were significantly reduced in the mutant as compared with the wild-type strain. Moreover, the results of biofilm analyses showed that, as compared with the wild-type strain, the oxyR mutant showed significantly less autoaggregation and a reduced ability to form mixed biofilms with Fusobacterium nucleatum. In conclusion, a gene annotated in the T. forsythia genome as an oxyR homologue was characterized. Our studies showed that the oxyR homologue in T. forsythia constitutively activates antioxidant genes involved in resistance to peroxides as well as oxygen stress (aerotolerance). In addition, the oxyR deletion attenuates biofilm formation in T. forsythia.
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- Physiology And Biochemistry
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Phosphate and carbon source regulation of two PhoP-dependent glycerophosphodiester phosphodiesterase genes of Streptomyces coelicolor
More LessGlycerophosphodiesters are formed by deacylation of phospholipids. Streptomyces coelicolor and other soil-dwelling actinomycetes utilize glycerophosphodiesters as phosphate and carbon sources by the action of glycerophosphodiester phosphodiesterases (GDPDs). Seven genes encoding putative GDPDs occur in the S. coelicolor genome. Two of these genes, glpQ1 and glpQ2, encoding extracellular GDPDs, showed a PhoP-dependent upregulated profile in response to phosphate shiftdown. Expression studies using the luxAB genes as reporter confirmed the PhoP dependence of both glpQ1 and glpQ2. Footprinting analyses with pure GST-PhoP of the glpQ1 promoter revealed four protected direct repeat units (DRu). PhoP binding affinity to the glpQ2 promoter was lower and revealed a protected region containing five DRu. As expected for pho regulon genes, inorganic phosphate, and also glycerol 3-phosphate, inhibited the expression from both glpQ1 and glpQ2. The expression of glpQ1 was also repressed by serine and inositol but expression of glpQ2 was not. In contrast, glucose, fructose and glycerol increased expression of glpQ2 but not that of glpQ1. In summary, our results suggest an interaction of phosphate control mediated by PhoP and carbon source regulation of the glpQ1 and glpQ2 genes involving complex operator structures.
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polR, a pathway-specific transcriptional regulatory gene, positively controls polyoxin biosynthesis in Streptomyces cacaoi subsp. asoensis
The polyoxin (POL) biosynthetic gene cluster (pol) was recently cloned from Streptomyces cacaoi subsp. asoensis. A 3.3 kb DNA fragment carrying an obvious open reading frame (polR), whose deduced product shows sequence similarity to SanG of Streptomyces ansochromogenes and PimR of Streptomyces natalensis, was revealed within the pol gene cluster. Disruption of polR abolished POL production, which could be complemented by the integration of a single copy of polR into the chromosome of the non-producing mutant. The introduction of an extra copy of polR in the wild-type strain resulted in increased production of POLs. The transcription start point (tsp) of polR was determined by S1 mapping. Reverse transcriptase PCR experiments showed that PolR is required for the transcription of 18 structural genes in the pol gene cluster. Furthermore, we showed that polC and polB, the respective first genes of two putative operons (polC–polQ2 and polA–polB) consisting of 16 and 2 of these 18 genes, have similar promoter structures. Gel retardation assays indicated that PolR has specific DNA-binding activity for the promoter regions of polC and polB. Our data suggest that PolR acts in a positive manner to regulate POL production by activating the transcription of at least two putative operons in the pol gene cluster.
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Homocysteine editing and growth inhibition in Escherichia coli
More LessIn Escherichia coli homocysteine (Hcy) is metabolically converted to the thioester Hcy-thiolactone in ATP-consuming reactions catalysed by methionyl-, isoleucyl- and leucyl-tRNA synthetases. Here we show that growth inhibition caused by supplementation of E. coli cultures with Hcy is accompanied by greatly increased accumulation of Hcy-thiolactone. Energy dissipation for Hcy editing increases 100-fold in the presence of exogenous Hcy and reaches one mole of ATP unproductively dissipated for Hcy-thiolactone synthesis per each mole of ATP that is consumed for methionine activation. Inhibiting Hcy-thiolactone synthesis with isoleucine, leucine or methionine accelerates bacterial growth in Hcy-supplemented cultures. Growth rates in Hcy-inhibited cultures are inversely related to the accumulation of Hcy-thiolactone. We also show that the levels of protein N-linked Hcy modestly increase in E. coli cells in Hcy-supplemented cultures. The results suggest that Hcy editing restrains bacterial growth.
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Uptake of l-nicotine and of 6-hydroxy-l-nicotine by Arthrobacter nicotinovorans and by Escherichia coli is mediated by facilitated diffusion and not by passive diffusion or active transport
More LessThe mechanism by which l-nicotine is taken up by bacteria that are able to grow on it is unknown. Nicotine degradation by Arthrobacter nicotinovorans, a Gram-positive soil bacterium, is linked to the presence of the catabolic megaplasmid pAO1. l-[14C]Nicotine uptake assays with A. nicotinovorans showed transport of nicotine across the cell membrane to be energy-independent and saturable with a K m of 6.2±0.1 μM and a V max of 0.70±0.08 μmol min−1 (mg protein)−1. This is in accord with a mechanism of facilitated diffusion, driven by the nicotine concentration gradient. Nicotine uptake was coupled to its intracellular degradation, and an A. nicotinovorans strain unable to degrade nicotine (pAO1−) showed no nicotine import. However, when the nicotine dehydrogenase genes were expressed in this strain, import of l-[14C]nicotine took place. A. nicotinovorans pAO1− and Escherichia coli were also unable to import 6-hydroxy-l-nicotine, but expression of the 6-hydroxy-l-nicotine oxidase gene allowed both bacteria to take up this compound. l-Nicotine uptake was inhibited by d-nicotine, 6-hydroxy-l-nicotine and 2-amino-l-nicotine, which may indicate transport of these nicotine derivatives by a common permease. Attempts to correlate nicotine uptake with pAO1 genes possessing similarity to amino acid transporters failed. In contrast to the situation at the blood–brain barrier, nicotine transport across the cell membrane by these bacteria was not by passive diffusion or active transport but by facilitated diffusion.
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The relevance of carbon dioxide metabolism in Streptococcus thermophilus
Streptococcus thermophilus is a major component of dairy starter cultures used for the manufacture of yoghurt and cheese. In this study, the CO2 metabolism of S. thermophilus DSM 20617T, grown in either a N2 atmosphere or an enriched CO2 atmosphere, was analysed using both genetic and proteomic approaches. Growth experiments performed in a chemically defined medium revealed that CO2 depletion resulted in bacterial arginine, aspartate and uracil auxotrophy. Moreover, CO2 depletion governed a significant change in cell morphology, and a high reduction in biomass production. A comparative proteomic analysis revealed that cells of S. thermophilus showed a different degree of energy status depending on the CO2 availability. In agreement with proteomic data, cells grown under N2 showed a significantly higher milk acidification rate compared with those grown in an enriched CO2 atmosphere. Experiments carried out on S. thermophilus wild-type and its derivative mutant, which was inactivated in the phosphoenolpyruvate carboxylase and carbamoyl-phosphate synthase activities responsible for fixing CO2 to organic molecules, suggested that the anaplerotic reactions governed by these enzymes have a central role in bacterial metabolism. Our results reveal the capnophilic nature of this micro-organism, underlining the essential role of CO2 in S. thermophilus physiology, and suggesting potential applications in dairy fermentation processes.
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Contributions of two UDP-glucose dehydrogenases to viability and polymyxin B resistance of Burkholderia cenocepacia
Burkholderia cenocepacia is highly resistant to antimicrobial peptides and we hypothesized that the conversion of UDP-glucose to UDP-glucuronic acid, a reaction catalysed by the enzyme UDP-glucose dehydrogenase (Ugd) would be important for this resistance. The genome of B. cenocepacia contains three predicted ugd genes: ugdBCAL2946 , ugdBCAM0855 and ugdBCAM2034 , all of which were individually inactivated. Only inactivation of ugdBCAL2946 resulted in increased sensitivity to polymyxin B and this sensitivity could be overcome when either ugdBCAL2946 or ugdBCAM0855 but not ugdBCAM2034 was expressed from plasmids. The growth of a conditional ugdBCAL2946 mutant, created in the ΔugdBCAM0855 background, was significantly impaired under non-permissive conditions. Growth could be rescued by either ugdBCAL2946 or ugdBCAM0855 expressed in trans, but not by ugdBCAM2034 . Biochemical analysis of the purified, recombinant forms of UgdBCAL2946 and UgdBCAM0855 revealed that they are soluble homodimers with similar in vitro Ugd activity and comparable kinetic constants for their substrates UDP-glucose and NAD+. Purified UgdBCAM2034 showed no in vitro Ugd activity. Real-time PCR analysis showed that the expression of ugdBCAL2946 was 5.4- and 135-fold greater than that of ugdBCAM0855 and ugdBCAM2034 , respectively. Together, these data indicate that the combined activity of UgdBCAL2946 and UgdBCAM0855 is essential for the survival of B. cenocepacia but only the most highly expressed ugd gene, ugdBCAL2946 , is required for polymyxin B resistance.
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Cloning of feather-degrading minor extracellular protease from Bacillus cereus DCUW: dissection of the structural domains
More LessBacterial extracellular proteases play an important role in cell survival and cell–cell communication. A high-molecular-mass minor extracellular protease (Vpr) from a feather-degrading bacterium, Bacillus cereus DCUW, has been reported by our laboratory. In the present study, we cloned and expressed Vpr in Escherichia coli. Complete nucleotide sequencing of this gene predicted that the protease is a member of the serine protease family, and smart domain analysis revealed that the protease consists of an N-terminal signal sequence for secretion, a subtilisin_N sequence that is a signature for N-terminal processing, a catalytic S_8 peptidase domain, and finally a long C-terminal protease-associated (PA) region containing nine intrinsically disordered subdomains. Four truncated constructs of the Vpr protease were cloned and expressed in E. coli. We found that the catalytic domain (amino acid residues 172–583) is sufficient for protease activity. Maturation of the Vpr protease needed both N-terminal and C-terminal processing. We have demonstrated that the oligomerization property is associated with the C-terminal protease-associated domain and also shown that the substrate-binding specificity to raw feather resides in this domain.
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Raman spectroscopic typing reveals the presence of carotenoids in Mycoplasma pneumoniae
Raman spectroscopy has previously been demonstrated to be a highly useful methodology for the identification and/or typing of micro-organisms. In this study, we set out to evaluate whether this technology could also be applied as a tool to discriminate between isolates of Mycoplasma pneumoniae, which is generally considered to be a genetically highly uniform species. In this evaluation, a total of 104 strains of M. pneumoniae were analysed, including two reference strains (strains M129 and FH), and 102 clinical isolates, which were isolated between 1973 and 2005 and originated from various countries. By Raman spectral analysis (Raman typing) of this strain collection, we were able to reproducibly distinguish six different clusters of strains. An unequivocal correlation between Raman typing and P1 genotyping, which is based on sequence differences in the P1 (or MPN141) gene of M. pneumoniae, was not observed. In the two major Raman clusters that we identified (clusters 3 and 6, which together harboured 81 % of the strains), the different P1 subtypes were similarly distributed, and ∼76 % isolates were of subtype 1, ∼20 % of subtype 2 and ∼5 % of variant 2a. Nevertheless, a relatively high prevalence of P1 subtype 2 strains was found in clusters 2 and 5 (100 %), as well as in cluster 1 (75 %) and cluster 4 (71 %); these clusters, however, harboured a small number of strains. Only two of the strains (2 %) could not be typed correctly. Interestingly, analysis of the Raman spectra revealed the presence of carotenoids in M. pneumoniae. This finding is in line with the identification of M. pneumoniae genes that have similarity with genes involved in a biochemical pathway leading to carotenoid synthesis, i.e. the 2-C-methyl-d-erythritol 4-phosphate (MEP) pathway. Therefore, we hypothesize that M. pneumoniae hosts an MEP-like pathway for carotenoid synthesis. We conclude that Raman spectroscopy is a convenient tool for discriminating between M. pneumoniae strains, and that it presents a promising supplement to the current methods for typing of this bacterium.
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Two novel metal-independent long-chain alkyl alcohol dehydrogenases from Geobacillus thermodenitrificans NG80-2
More LessTwo alkyl alcohol dehydrogenase (ADH) genes from the long-chain alkane-degrading strain Geobacillus thermodenitrificans NG80-2 were characterized in vitro. ADH1 and ADH2 were prepared heterologously in Escherichia coli as a homooctameric and a homodimeric protein, respectively. Both ADHs can oxidize a broad range of alkyl alcohols up to at least C30, as well as 1,3-propanediol and acetaldehyde. ADH1 also oxidizes glycerol, and ADH2 oxidizes isopropyl alcohol, isoamylol, acetone, octanal and decanal. The best substrate is ethanol for ADH1 and 1-octanol for ADH2. For both ADHs, the optimum assay condition is at 60 °C and pH 8.0, and both NAD and NADP can be used as the cofactor. Sequence analysis reveals that ADH1 and ADH2 belong to the Fe-containing/activated long-chain ADHs. However, the two enzymes contain neither Fe nor other metals, and Fe is not required for the activity, suggesting a new type of ADH. The ADHs characterized here are potentially useful in crude oil bioremediation and other bioconversion processes.
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Kinetic characterization of the soluble butane monooxygenase from Thauera butanivorans, formerly ‘Pseudomonas butanovora’
More LessSoluble butane monooxygenase (sBMO), a three-component di-iron monooxygenase complex expressed by the C2–C9 alkane-utilizing bacterium Thauera butanivorans, was kinetically characterized by measuring substrate specificities for C1–C5 alkanes and product inhibition profiles. sBMO has high sequence homology with soluble methane monooxygenase (sMMO) and shares a similar substrate range, including gaseous and liquid alkanes, aromatics, alkenes and halogenated xenobiotics. Results indicated that butane was the preferred substrate (defined by k cat : K m ratios). Relative rates of oxidation for C1–C5 alkanes differed minimally, implying that substrate specificity is heavily influenced by differences in substrate K m values. The low micromolar K m for linear C2–C5 alkanes and the millimolar K m for methane demonstrate that sBMO is two to three orders of magnitude more specific for physiologically relevant substrates of T. butanivorans. Methanol, the product of methane oxidation and also a substrate itself, was found to have similar K m and k cat values to those of methane. This inability to kinetically discriminate between the C1 alkane and C1 alcohol is observed as a steady-state concentration of methanol during the two-step oxidation of methane to formaldehyde by sBMO. Unlike methanol, alcohols with chain length C2–C5 do not compete effectively with their respective alkane substrates. Results from product inhibition experiments suggest that the geometry of the active site is optimized for linear molecules four to five carbons in length and is influenced by the regulatory protein component B (butane monooxygenase regulatory component; BMOB). The data suggest that alkane oxidation by sBMO is highly specialized for the turnover of C3–C5 alkanes and the release of their respective alcohol products. Additionally, sBMO is particularly efficient at preventing methane oxidation during growth on linear alkanes ≥C2, despite its high sequence homology with sMMO. These results represent, to the best of our knowledge, the first kinetic in vitro characterization of the closest known homologue of sMMO.
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pH controls both transcription and post-translational processing of the protease BcACP1 in the phytopathogenic fungus Botrytis cinerea
During pathogenesis, the ascomycete Botrytis cinerea secretes a range of cell-wall-degrading enzymes such as polygalacturonases, glucanases and proteases. We report the identification of a new member of the G1 family of proteases, BcACP1, which is secreted by B. cinerea during infection. The production of BcACP1 correlates with the acidification of the plant tissue, and transcriptional analysis of the Bcacp1 gene showed that it is only expressed under acidic growth conditions. Using a transcriptional reporter system, we showed that pH regulation of Bcacp1 is not mediated by the canonical PacC transcription factor binding site. Like other G1 proteases, BcACP1 is produced as a pro-enzyme. Trapping of the zymogen form allowed investigation of its maturation process. Evidence is presented for an autocatalytic proteolysis of the enzyme that is triggered by acidic pH. Environmental pH therefore controls Bcacp1 production at both the transcriptional and post-translational level.
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- Corrigenda
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