- Volume 154, Issue 8, 2008
Volume 154, Issue 8, 2008
- Reviews
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Biocatalytic desulfurization (BDS) of petrodiesel fuels
More LessOil refineries are facing many challenges, including heavier crude oils, increased fuel quality standards, and a need to reduce air pollution emissions. Global society is stepping on the road to zero-sulfur fuel, with only differences in the starting point of sulfur level and rate reduction of sulfur content between different countries. Hydrodesulfurization (HDS) is the most common technology used by refineries to remove sulfur from intermediate streams. However, HDS has several disadvantages, in that it is energy intensive, costly to install and to operate, and does not work well on refractory organosulfur compounds. Recent research has therefore focused on improving HDS catalysts and processes and also on the development of alternative technologies. Among the new technologies one possible approach is biocatalytic desulfurization (BDS). The advantage of BDS is that it can be operated in conditions that require less energy and hydrogen. BDS operates at ambient temperature and pressure with high selectivity, resulting in decreased energy costs, low emission, and no generation of undesirable side products. Over the last two decades several research groups have attempted to isolate bacteria capable of efficient desulfurization of oil fractions. This review examines the developments in our knowledge of the application of bacteria in BDS processes, assesses the technical viability of this technology and examines its future challenges.
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Role of quorum sensing by Pseudomonas aeruginosa in microbial keratitis and cystic fibrosis
Pseudomonas aeruginosa is a ubiquitous bacterium that causes opportunistic infections in a range of host tissues and organs. Infections by P. aeruginosa are difficult to treat and hence there is interest in the development of effective therapeutics. One of the key mechanisms that P. aeruginosa uses to control the expression of many virulence factors is the N-acylated homoserine lactone (AHL) regulatory system. Hence, there is considerable interest in targeting this regulatory pathway to develop novel therapeutics for infection control. P. aeruginosa is the principal cause of microbial keratitis and of infections in cystic fibrosis (CF) sufferers, and AHL-dependent cell-to-cell signalling has been shown to be important for both infection types. However, keratitis tends to be an acute infection whereas infection of CF patients develops into a chronic, life-long infection. Thus, it is unclear whether AHL-regulated virulence plays the same role during these infections. This review presents a comparison of the role of AHL signalling in P. aeruginosa-mediated microbial keratitis and chronic lung infections of CF patients.
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- Biochemistry And Molecular Biology
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Identification of three cytotoxic early proteins of mycobacteriophage L5 leading to growth inhibition in Mycobacterium smegmatis
More LessMycobacteriophage L5 is a temperate phage with a broad host range among the fast- and slow-growing mycobacteria such as Mycobacterium smegmatis, Mycobacterium tuberculosis, Mycobacterium avium and Mycobacterium ulcerans. L5 switches off host protein synthesis during the early stage of lytic growth, as was previously shown by protein expression profiling. Also, lethal genetic elements have been identified in L5 based on the fact that transformants could not be obtained with these genes. Using an inducible mycobacterial shuttle vector, we have identified three ORFs within an early operon of mycobacteriophage L5 which encode gene products (gp) toxic to the host M. smegmatis when expressed. These ORFs, coding for gp77, gp78 and gp79, presumably function as shut-off genes during early stages of phage replication. There is evidence that cell division is affected by one of the proteins (gp79). The transcription of the cytotoxic polypeptides is directed by a promoter situated in ORF83 and transcription control is achieved through the phage repressor gp71, which is shown by co-expression of this protein. The findings presented here should provide useful tools for the molecular genetics of mycobacteria. Further analysis of these and other mycobacteriophage-derived toxic polypeptides, together with the identification of their cellular targets, might provide a tool for the rapid identification of promising drug targets in emerging and re-emerging mycobacterial pathogens.
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Partial redundancy in the synthesis of the d-arabinose incorporated in the cell wall arabinan of Corynebacterineae
The major cell wall carbohydrate of Corynebacterineae is arabinogalactan (AG), a branched polysaccharide that is essential for the physiology of these bacteria. Decaprenylphosphoryl-d-arabinose (DPA), the lipid donor of d-arabinofuranosyl residues of AG, is synthesized through a series of unique biosynthetic steps, the last one being the epimerization of decaprenylphosphoryl-β-d-ribose (DPR) into DPA, which is believed to proceed via a sequential oxidation–reduction mechanism. Two proteins from Mycobacterium tuberculosis (Rv3790 and Rv3791) have been shown to catalyse this epimerization in an in vitro system. The present study addressed the exact function of these proteins through the inactivation of the corresponding orthologues in Corynebacterium glutamicum (NCgl0187 and NCgl0186, respectively) and the analysis of their in vivo effects on AG biosynthesis. We showed that NCgl0187 is essential, whereas NCgl0186 is not. Deletion of NCgl0186 led to a mutant possessing an AG that contained half the arabinose and rhamnose, and less corynomycolates linked to AG but more trehalose mycolates, compared with the parental strain. A candidate gene that may encode a protein functionally similar to NCgl0186 was identified in both C. glutamicum (NCgl1429) and M. tuberculosis (Rv2073c). While the deletion of NCgl1429 had no effect on AG biosynthesis of the mutant, the gene could complement the mycolate defect of the AG of the NCgl0186 mutant, strongly supporting the concept that the two proteins play a similar function in vivo. Consistent with this, the NCgl1429 gene appeared to be essential in the NCgl0186-inactivated mutant. A detailed bioinformatics analysis showed that NCgl1429, NCgl0186, Rv3791 and Rv2073c could constitute, with 52 other proteins belonging to the actinomycetales, a group of closely related short-chain reductases/dehydrogenases (SDRs) with atypical motifs. We propose that the epimerization of DPR to DPA involves three enzymes that catalyse two distinct steps, each being essential for the viability of the bacterial cells.
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Cloning and characterization of a gene involved in triacylglycerol biosynthesis and identification of additional homologous genes in the oleaginous bacterium Rhodococcus opacus PD630
More LessThe oleaginous bacterium Rhodococus opacus strain PD630 serves as a model organism to investigate the metabolism of storage triacylglycerols (TAGs) in bacteria. The key enzyme catalysing the last step of TAG biosynthesis in bacteria is a promiscuous acyltransferase (Atf), exhibiting acyl-CoA acyltransferase activity to both diacylglycerols (DGAT activity) and fatty alcohols (wax ester synthase, WS activity). An 800 bp PCR product was obtained from chromosomal DNA of strain PD630 by using degenerate primers designed from conserved stretches of Atf proteins of Acinetobacter baylyi strain ADP1 and Mycobacterium smegmatis mc2155. The atf fragment was used as a probe on a strain PD630 gene library, resulting in the identification of a 3948 bp chromosomal DNA fragment containing the complete atf1 gene. An atf1 disruption mutant of strain PD630 exhibited a TAG-leaky phenotype and accumulated up to 50 % less fatty acids than the wild-type, with significantly reduced oleic acid content when cultivated in the presence of gluconate or oleic acid. Whereas DGAT activity was drastically reduced in comparison to the wild-type, WS activity remained almost unchanged in the mutant. RT-PCR analysis of gluconate-grown cells of strain PD630 showed that there is expression of atf1 under conditions of TAG synthesis. To identify additional Atfs in strain PD630, PCR employing non-degenerate primers deduced from Rhodococcus jostii RHA1 sequence data was used. This yielded nine additional atf-homologous genes exhibiting 88–99 % sequence identity to the corresponding strain RHA1 enzymes. Besides Atf1 only Atf2 exhibited high DGAT and/or WS activity when heterologously expressed in Escherichia coli.
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Interaction of the signal transduction protein GlnJ with the cellular targets AmtB1, GlnE and GlnD in Rhodospirillum rubrum: dependence on manganese, 2-oxoglutarate and the ADP/ATP ratio
More LessThe PII family of signal transduction proteins is widespread amongst the three domains of life, and its members have fundamental roles in the general control of nitrogen metabolism. These proteins exert their regulatory role by direct protein–protein interaction with a multitude of cellular targets. The interactions are dependent on the binding of metabolites such as ATP, ADP and 2-oxoglutarate (2-OG), and on whether or not the PII protein is modified. In the photosynthetic nitrogen-fixing bacterium Rhodospirillum rubrum three PII paralogues have been identified and termed GlnB, GlnJ and GlnK. In this report we analysed the interaction of GlnJ with known cellular targets such as the ammonium transporter AmtB1, the adenylyltransferase GlnE and the uridylyltransferase GlnD. Our results show that the interaction of GlnJ with cellular targets is regulated in vitro by the concentrations of manganese and 2-OG and the ADP : ATP ratio. Furthermore, we show here for the first time, to our knowledge, that in the interactions of GlnJ with the three different partners, the energy signal (ADP : ATP ratio) in fact overrides the carbon/nitrogen signal (2-OG). In addition, by generating specific amino acid substitutions in GlnJ we show that the interactions with different cellular targets are differentially affected, and the possible implications of these results are discussed. Our results are important to further the understanding of the regulatory role of PII proteins in R. rubrum, a photosynthetic bacterium in which the nitrogen fixation process and its intricate control mechanisms make the regulation of nitrogen metabolism even more complex than in other studied bacteria.
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Inactivation of the general transcription factor TnrA in Bacillus subtilis by proteolysis
More LessUnder conditions of nitrogen limitation, the general transcription factor TnrA in Bacillus subtilis activates the expression of genes involved in assimilation of various nitrogen sources. Previously, TnrA activity has been shown to be controlled by protein–protein interaction with glutamine synthetase, the key enzyme of ammonia assimilation. Furthermore, depending on ATP and 2-oxoglutarate levels, TnrA can bind to the GlnK–AmtB complex. Here, we report that upon transfer of nitrate-grown cells to combined nitrogen-depleted medium, TnrA is rapidly eliminated from the cells by proteolysis. As long as TnrA is membrane-bound through GlnK–AmtB interaction it seems to be protected from degradation. Upon removal of nitrogen sources, the localization of TnrA becomes cytosolic and degradation occurs. The proteolytic activity against TnrA was detected in the cytosolic fraction but not in the membrane, and its presence does not depend on the nitrogen regime of cell growth. The proteolytic degradation of TnrA as a response to complete nitrogen starvation might represent a novel mechanism of TnrA control in B. subtilis.
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Phosphate-dependent regulation of the low- and high-affinity transport systems in the model actinomycete Streptomyces coelicolor
More LessThe transport of inorganic phosphate (Pi) is essential for the growth of all organisms. The metabolism of soil-dwelling Streptomyces species, and their ability to produce antibiotics and other secondary metabolites, are strongly influenced by the availability of phosphate. The transcriptional regulation of the SCO4138 and SCO1845 genes of Streptomyces coelicolor was studied. These genes encode the two putative low-affinity Pi transporters PitH1 and PitH2, respectively. Expression of these genes and that of the high-affinity transport system pstSCAB follows a sequential pattern in response to phosphate deprivation, as shown by coupling their promoters to a luciferase reporter gene. Expression of pitH2, but not that of pap-pitH1 (a bicistronic transcript), is dependent upon the response regulator PhoP. PhoP binds to specific sequences consisting of direct repeats of 11 nt in the promoter of pitH2, but does not bind to the pap-pitH1 promoter, which lacks these direct repeats for PhoP recognition. The transcription start point of the pitH2 promoter was identified by primer extension analyses, and the structure of the regulatory sequences in the PhoP-protected DNA region was established. It consists of four central direct repeats flanked by two other less conserved repeats. A model for PhoP regulation of this promoter is proposed based on the four promoter DNA–PhoP complexes detected by electrophoretic mobility shift assays and footprinting studies.
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Molecular characterization of the basidiomycete isolate Nematoloma frowardii b19 and its manganese peroxidase places the fungus in the corticioid genus Phlebia
More LessThe basidiomycete isolate b19, originally identified by morphological characteristics of the fruiting body as Nematoloma frowardii, efficiently produces manganese peroxidase (MNP) and is used for degradation of natural, persistent aromatic polymers (lignin, humic acids and brown coal components). The N. frowardii MNP has shown good activity in conversion of xenobiotic compounds such as polycyclic hydrocarbons and trinitrotoluene. However, this biotechnologically promising fungus has not previously been studied at the molecular biology level. We show here that according to the molecular characterization of its main MNP isozyme, Nf b19 MNP2, and partial sequencing of its MNP3-, three lignin peroxidase- and two laccase-encoding genes, and the gene encoding the ribosomal SSU 18S RNA, that the fungus has a close phylogenetic relationship to the white-rot basidiomycete Phlebia radiata (Fr.). Ribosomal internal transcribed spacer (ITS) sequence (ITS1+5.8S+ITS2) phylogeny reclassifies Nf b19 as a possible representative of a new species of the genus Phlebia, nearest to the Phlebia acerina clade. The genus Phlebia belongs to a completely different family (Corticiaceae) and order (Aphyllophorales) within the phylum Basidiomycota than the genus Nematoloma, which is classified in the order Agaricales, family Strophariaceae. Our results thus indicate a need for systematic re-identification of the previously named N. frowardii isolate b19.
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- Biodiversity And Evolution
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Variable length tandem repeat polyglutamine sequences in the flexible tether region of the Tsr chemotaxis receptor of Escherichia coli
More LessMethyl-accepting chemotaxis proteins (MCPs) are receptors that play an important role in bacterial chemotaxis. Methylation of Tsr, the MCP that mediates chemotaxis towards serine in Escherichia coli, is thought to be facilitated by binding of the methyltransferase to a flexible tether region at the C-terminal end of Tsr. This study analysed natural length variants of the tether that occur in E. coli due to genetic instability in tandem repeat DNA sequences that code for glutaminyl (Q) residues, creating polyQ sequences of variable lengths in the tether region. The tsr gene of E. coli K-12 (strain MG1655) codes for 4Q at the beginning of its 35 aa tether region. The tether varies in length from 35 to 47 residues among pathogenic and non-pathogenic strains of Escherichia, Shigella spp., Salmonella, Yersinia and Photorhabdus. Among previous sequences, Escherichia and Shigella mostly have 4Q and 7Q variants, and one strain (E. coli HS) has 10Q. In E. coli isolated from 50 humans and 75 animals (dogs, cats, horses, birds, etc.), polyQ up to 13Q (44 aa tether) were identified (6 strains); relative frequencies were 7Q (∼77 % of the total) >4Q (14 %) >13Q (5 %) >10Q (4 %). Phylogenetic analysis revealed that E. coli strains with 10Q or 13Q largely fell within two clusters. Serine chemotaxis was not significantly different among 7Q, 10Q and 13Q strains, and was comparable to chemotaxis in the frequently studied K-12 strain. These results are consistent with models indicating that polyQ sequences from 7Q to13Q are flexible, and that longer tethers, within this range, would not change the precision of adaptation mediated by methylation. Studies of this naturally variable polyQ region in E. coli may also have relevance to mechanisms that mediate polyQ instability in human genetic diseases.
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16S rDNA and 16S–23S internal transcribed spacer sequence analyses reveal inter- and intraspecific Acidithiobacillus phylogeny
More LessIn order to contribute to our understanding of Acidithiobacillus taxonomy, we determined 16S rDNA sequences and the 16S–23S internally transcribed spacer (ITS) sequence of 35 Chinese Acidithiobacillus isolates and three reference strains representing three validly described species and used them to construct phylogenetic trees. The two phylogenetic trees were roughly similar topologically, and Acidithiobacillus strains were assigned to eight phylogenetic groups. In addition, the results of phylogenetic analysis were consistent with those obtained by randomly amplified polymorphic DNA (RAPD) cluster analysis. Compared with a phylogenetic tree based on the 16S rRNA sequences, the ITS tree showed more clearly the inter- and intraspecific genealogical relationships of the genus Acidithiobacillus. Similarity values of the ITSs varied from 60.5 % to 84.7 % between representative strains of different species, and the maximum level of ITS divergence between strains belonging to the same species was 13 %. Coupling phylogenetic analysis and phenotypic characteristics, we concluded that at least each of the three Acidithiobacillus ferrooxidans phylogenetic groups should be considered a separate subspecies, and that five sulfur-oxidizing Chinese Acidithiobacillus-like isolates represent one or two new species of the genus Acidithiobacillus. The ITS may be a potential target for the development of fluorescent in situ hybridization probes for more accurately detecting distinct ecotypes of Acidithiobacillus strains and other closely related sulfur-oxidizing bacteria.
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Phylogenetic analysis of Clostridium botulinum type A by multi-locus sequence typing
More LessThe genus Clostridium comprises a heterogeneous group of organisms for which the phylogeny and evolutionary relationships are poorly understood. The elucidation of these evolutionary relationships necessitates the use of experimental methods that can distinguish Clostridium lineages that are time and cost effective, and can be accurately and reproducibly employed in different laboratories. Multi-locus sequence typing (MLST) has been successfully used as a reproducible and discriminating system in the study of eukaryotic and prokaryotic evolutionary biology, and for strain typing of various bacteria. In this study, MLST was applied to evaluate the evolutionary lineages in the serotype A group of Clostridium botulinum. C. botulinum type A has recently been shown to produce multiple subtypes, suggesting that it is not monophyletic as previously reported, but comprises distinct lineages. For MLST analysis, we initially evaluated 14 housekeeping genes (gapdh, tuf, sod, oppB, hsp60, dnaE, aroE, pta, 23S rDNA, aceK, rpoB, 16S rDNA, mdh and recA) for amplification and sequence analysis. In the first phase of the analysis, 30 C. botulinum type A strains producing botulinum neurotoxin subtypes A1–A4 were examined. Results of this pilot study suggested that seven of the genes (mdh, aceK, rpoB, aroE, hsp60, oppB and recA) could be used for elucidation of evolutionary lineages and strain typing. These seven housekeeping genes were successfully applied for the elucidation of lineages for 73 C. botulinum type A strains, which resulted in 24 distinct sequence types. This strategy should be applicable to phylogenetic studies and typing of other C. botulinum serotypes and Clostridium species.
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The temperature-adaptive fatty acid content in Bacillus simplex strains from ‘Evolution Canyon’, Israel
More LessExploring the evolutionary response of Bacillus simplex strains to the slope-specific habitats of ‘Evolution Canyon’ I and II, Israel, we report here on presumably adaptive differences in fatty acid (FA) content that correlate with one particular feature of the habitats, temperature difference. These two canyons represent similar ecological sites, separated by 40 km, in which the orientation of the sun yields a strong sun-exposed and hot ‘African’ south-facing slope versus a rather cooler and mesic-lush ‘European’ north-facing slope within a distance of only 50–400 m. Among 131 strains, which are identical in their 16S sequences, those assigned genetically to the ‘African’ ecotypes express phenotypically generally more high-temperature-tolerance-providing iso-branched FAs than strains assigned to the ‘European’ ecotypes when grown at 20 °C, 28 °C and 40 °C. Conversely, ‘European’ lineages express larger amounts of low-temperature-tolerance-providing anteiso-branched and non-saturated FAs when grown at the same temperatures. Moreover, ‘African’ ecotypes show a stronger adjustment of their high- and low-temperature-tolerance-providing FAs in response to low temperatures, which suggests that, as a result of temperature adaptation, ‘African’ and ‘European’ ecotypes have evolved different reaction norms within their phenotypic plasticity response. Thus, bacterial adaptive microevolution may include such multigenic and highly complex organs as the bacterial cell membrane. The results contribute to our understanding of the speciation process among the ‘Evolution Canyon’ B. simplex ecotypes.
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- Genes And Genomes
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Unmarked insertional mutagenesis in the bovine pathogen Mycoplasma mycoides subsp. mycoides SC: characterization of a lppQ mutant
Mycoplasma mycoides subspecies mycoides small colony (SC) is the aetiologic agent of contagious bovine pleuropneumonia (CBPP), a respiratory disease causing important losses in cattle production. The publication of the genome sequence of M. mycoides subsp. mycoides SC should facilitate the identification of putative virulence factors. However, real progress in the study of molecular mechanisms of pathogenicity also requires efficient molecular tools for gene inactivation. In the present study, we have developed a transposon-based approach for the random mutagenesis of M. mycoides subsp. mycoides SC. A PCR-based screening assay enabled the characterization of several mutants with knockouts of genes potentially involved in pathogenicity. The initial transposon was further improved by combining it with the transposon γδ TnpR/res recombination system to allow the production of unmarked mutations. Using this approach, we isolated a mutant free of antibiotic-resistance genes, in which the gene encoding the main lipoprotein LppQ was disrupted. The mutant was found to express only residual amounts of the truncated N-terminal end of LppQ. This approach opens the way to study virulence factors and pathogen–host interactions of M. mycoides subsp. mycoides SC and to develop new, genetically defined vaccine strains.
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The RecBCD and SbcCD DNases suppress homology-facilitated illegitimate recombination during natural transformation of Acinetobacter baylyi
More LessDuring natural transformation of Acinetobacter baylyi, the genomic integration of foreign (non-homologous) DNA is possible when the DNA contains a single segment homologous to the recipient genome (anchor) through homologous recombination in the anchor facilitating illegitimate recombination in the neighbouring foreign DNA (homology-facilitated illegitimate recombination; HFIR). DNA integration by HFIR occurs about 10 000 times less frequently than fully homologous recombination, but at least 100 000-fold more frequently than integration in the absence of any homology. We investigated the influence of the RecBCD enzyme (DNase/helicase) and SbcCD DNase (DNA-structure-specific single-strand endonuclease and exonuclease) on HFIR. In a recBCD null mutant the acquisition of foreign DNA was elevated 11-fold relative to wild-type cells by a 6.9-fold increased HFIR frequency and by the integration of longer stretches of foreign DNA in each event. In an sbcCD null mutant, the foreign DNA acquisition was 4.5-fold higher than in the wild-type, while homologous transformation with large DNA molecules was unaffected and increased 3.2-fold with small DNA fragments. The sbcCD mutation partially suppressed the high UV sensitivity and low viability of the recBCD mutant and also decreased its foreign DNA acquisition by HFIR to the lower level of the sbcCD mutant. We propose that suppression of HFIR results from the elimination of double-stranded intermediates of the HFIR process during transformation by RecBCD, and by SbcCD interfering with branched molecules. Our results provide evidence that the homologous recombination enzymes RecBCD and SbcCD control the level of foreign DNA acquisition by HFIR.
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Analysis of base excision and nucleotide excision repair in Candida albicans
More LessCandida albicans, clinically the most important human fungal pathogen, rapidly develops resistance to antifungal drugs. The acquisition of resistance has been linked to various types of genome changes. As part of an ongoing study of this problem, we investigated mutation, genome stability and drug resistance acquisition in C. albicans strains with deletions in the base excision repair (BER) genes NTG1, APN1 and OGG1, and in the nucleotide excision repair (NER) genes RAD2 and RAD10. The BER mutants did not exhibit any change in their susceptibility to DNA-damaging agents, but the NER mutants were extremely sensitive to UV-induced DNA damage. We did not observe any significant change in mutation, genome stability and antifungal drug sensitivity in the mutant strains we tested. However, we detected a number of intriguing phenotypic differences between strains bearing deletions in equivalent C. albicans and Saccharomyces cerevisiae BER and NER genes, which may be related to differences in the life cycles of these two fungi.
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Improved annotation of conjugated bile acid hydrolase superfamily members in Gram-positive bacteria
More LessMost Gram-positive bacteria inhabiting the gastrointestinal tract are capable of hydrolysing bile salts. Bile salt hydrolysis is thought to play an important role in various biological processes in the host. Therefore, correct annotation of bacterial bile salt hydrolases (Bsh) in public databases (EC 3.5.1.24) is of importance, especially for lactobacilli, which are considered to play a major role in bile salt hydrolysis in vivo. In the present study, all enzymes listed in public databases that belong to the Bsh family and the closely related penicillin V acylase (Pva; EC 3.5.1.11) family were compared with the sequences annotated as Bsh in Lactobacillus plantarum WCFS1, as an example. In Gram-positive bacteria, a clear distinction was made between the two families using sequence alignment, phylogenetic clustering, and protein homology modelling. Biochemical and structural data on experimentally verified Bsh and Pva enzymes were used for validation of function prediction. Hidden Markov models were constructed from the sequence alignments to enable a more accurate prediction of Bsh-encoding genes, and their distinction from those encoding members of the Pva family. Many Pva-related sequences appeared to be annotated incorrectly as Bsh in public databases. This refinement in the annotation of Bsh family members influences the prediction of the function of bsh-like genes in species of the genus Lactobacillus, and it is discussed in detail.
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Intrinsic curvature associated with the coordinately regulated anthrax toxin gene promoters
More LessThe current model for virulence gene regulation in Bacillus anthracis involves several trans-acting factors, the most important of which appears to be the anthrax toxin activator encoded by the atxA gene. AtxA is a positive regulator of the toxin genes pagA, cya and lef, and of a number of other plasmid- and chromosome-encoded genes. The AtxA protein (56 kDa) possesses a predicted winged-helix DNA-binding domain and phosphotransferase system-regulated domains, but the mechanism for positive regulation of AtxA target genes is not known. Sequence similarities in the promoter regions of AtxA-regulated genes are not apparent, and recombinant AtxA binds DNA with a high affinity in a non-specific manner. We hypothesized that the toxin genes possess common structural features or cis-acting elements that are required for positive regulation. We employed deletion analyses to determine the minimal sequences required for atxA-mediated toxin gene expression. In silico modelling and in vitro experiments using double-stranded DNA corresponding to the toxin gene promoter regions indicated significant curvature associated with these regions. These findings suggest that the structural topology of the DNA plays an important role in the control of anthrax toxin gene expression.
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- Pathogens And Pathogenicity
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High-cell-density regulation of the Pseudomonas aeruginosa type III secretion system: implications for tryptophan catabolites
The Pseudomonas aeruginosa type III secretion system (T3SS) is known to be a very important virulence factor in acute human infections, but it is less important in maintaining chronic infections in which T3SS genes are downregulated. In vitro, the activation of T3SS expression involves a positive activating loop that acts on the transcriptional regulator ExsA. We have observed that in vivo T3SS expression is cell density-dependent in a manner that does not need known quorum-sensing (QS) signals. In addition, stationary-phase culture supernatants added to exponential-phase growing strains can inhibit T3SS expression. The analysis of transposon insertion mutants showed that the production of such T3SS-inhibiting signals might depend on tryptophan synthase and hence tryptophan, which is the precursor of signalling molecules such as indole-3-acetic acid (IAA), kynurenine and Pseudomonas quinolone signal (PQS). Commercially available tryptophan-derived molecules were tested for their role in the regulation of T3SS expression. At millimolar concentrations, IAA, 1-naphthalacetic acid (NAA) and 3-hydroxykynurenine inhibited T3SS expression. Inactivation of the tryptophan dioxygenase-encoding kynA gene resulted in a decrease in the T3SS-inhibiting activity of supernatants. These observations suggest that tryptophan catabolites are involved in the downregulation of T3SS expression in the transition from a low- to a high-cell-density state.
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Genetic analysis of genes involved in dipeptide metabolism and cytotoxicity in Pseudomonas aeruginosa PAO1
More LessThe dipeptide transport operon in bacteria comprises genes for the transport and metabolism of amino acids and dipeptides, as well as haem and haem precursors such as aminolaevulinic acid. Such nutrient and mineral sources are vital for bacteria to survive in and colonize a range of niches. In silico analysis of the dipeptide transport systems in sequenced Pseudomonas species identified the presence of two genes in P. aeruginosa strains that were absent in other sequenced pseudomonads. These genes encode a putative metallopeptidase, PA4498, and a putative transcriptional regulator, PA4499. Proteomic profiling of wild-type PAO1 and a PA4499 mutant strain indicated that PA4499 negatively regulated the putative peptidase, PA4498. Transcriptional fusion analysis verified that expression of PA4498 (mdpA, metallo-dipeptidase aeruginosa) was negatively regulated by the downstream putative transcriptional regulator PA4499 (psdR, Pseudomonas dipeptide regulator). Transcriptional fusion analysis also showed that the dppABCDF operon was under the negative control of psdR. Functional genomic analysis of mdpA indicated that it is required for the metabolism of a range of dipeptides and that it contributes to the cytotoxicity of PAO1 on an epithelial cell line.
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Contribution of the stereospecific methionine sulphoxide reductases MsrA and MsrB to oxidative and nitrosative stress resistance in the food-borne pathogen Campylobacter jejuni
More LessThe microaerophilic food-borne pathogen Campylobacter jejuni is exposed to highly variable oxygen concentrations during its life cycle and employs a variety of protection mechanisms to resist oxidative stress. However, not all of the enzymes that mediate such protection have yet been identified. Two genes in strain NCTC 11168, Cj0637c and Cj1112c, are predicted to encode unrelated methionine sulphoxide reductases, which may repair oxidized methionine residues in proteins and thus contribute to oxidative stress defence. Cj0637 and Cj1112 were overexpressed, purified and shown by a coupled thioredoxin–thioredoxin reductase–NADPH assay to catalyse the stereospecific reduction of the S and R diastereoisomers, respectively, of the model compound methyl p-tolyl sulphoxide. Cj0637 is thus identified as MsrA and Cj1112 as MsrB. The contribution of these enzymes to oxidative and nitrosative stress resistance in C. jejuni was assessed by phenotypic analysis of a set of isogenic msrA, msrB and msrA/B insertion mutants. As RT-PCR data suggested a polar effect on Cj1111c in the msrB mutant, an msrB/msrB+ merodiploid complementation strain was also constructed. The msrA/B strain was severely growth inhibited under standard microaerobic conditions, whereas the msrA and msrB strains grew normally. Agar plate disc diffusion assays showed that all mutants displayed increased sensitivity to hydrogen peroxide, organic peroxide, superoxide, and nitrosative and disulphide stress, but quantitative cell viability assays showed that the msrA/B double mutant was markedly more sensitive to both oxidative and nitrosative stress. All of the stress-sensitivity phenotypes observed for the msrB mutant were restored to wild-type in the msrB/msrB+ merodiploid. It is concluded that MsrA and MsrB make a significant contribution to the protection of C. jejuni against oxidative and nitrosative stress.
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Expression of the Helicobacter pylori adhesin SabA is controlled via phase variation and the ArsRS signal transduction system
Adaptation to the acidic microenvironment, and adherence to mucosal epithelium, are essential for persistent colonization of the human stomach by Helicobacter pylori. The expression of SabA, an adhesin implicated in the ability of H. pylori to adhere to the host gastric epithelium, can be modulated by phase variation via slipped-strand mispairing in repetitive nucleotide tracts located in both the promoter region and the coding region. This study demonstrates the occurrence of phase variation at the sabA locus within individual strains of H. pylori, and among multiple isolates from a single patient. In addition, transcription of sabA is repressed by the acid-responsive ArsRS two-component signal transduction system in vitro. Our results demonstrate that isogenic inactivation of the arsS (jhp0151/HP0165) histidine kinase locus results in a 10-fold SabA-dependent increase in adherence to gastric epithelial cells in strain J99 (contains an in-frame sabA allele), but not in strain 26695 (out-of-frame sabA allele). The combination of transcriptional regulation of the sabA locus by the ArsRS two-component signal-transduction system and the generation of subpopulations harbouring alternate sabA alleles by slipped-strand mispairing during chromosomal replication could permit H. pylori to rapidly adapt to varying microenvironments or host immune responses. As a pathogen with a paucity of regulatory proteins, this dual regulation indicates that SabA expression is a tightly regulated process in H. pylori infection.
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Germination of spores of Clostridium difficile strains, including isolates from a hospital outbreak of Clostridium difficile-associated disease (CDAD)
More LessClostridium difficile is an emerging nosocomial pathogen and one of the major causes of antibiotic-associated diarrhoea. Cases of Clostridium difficile-associated disease (CDAD) are likely initiated by the ingestion of dormant C. difficile spores, which then germinate, outgrow and rapidly proliferate to cause gastrointestinal (GI) infections. To understand the initial stages of CDAD pathogenesis, we have characterized the germination of spores from a collection of C. difficile strains, including some clinical isolates obtained from a CDAD outbreak (CDAD isolates). Spores of one laboratory strain and five CDAD isolates did not germinate with amino acids, but did germinate on a nutrient-rich medium. However, bile salts had little effect on spore germination, either alone or in a nutrient-rich medium. These spores also germinated with KCl, as well as the non-nutrient germinants dodecylamine and a 1 : 1 chelate of Ca2+ and dipicolinic acid. An unexpected finding was that spores of most of the C. difficile strains also germinated with inorganic phosphate (Pi) with a pH optimum of 6. The in vitro germination of spores of CDAD strains with KCl and Pi, two molecules present at significant levels in the GI tract, suggests that C. difficile spores germinate in the human body by sensing Pi in the early segments of the duodenum and KCl in the colon.
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The DegU orphan response regulator of Listeria monocytogenes autorepresses its own synthesis and is required for bacterial motility, virulence and biofilm formation
The Gram-positive intracellular pathogen Listeria monocytogenes is endowed with 17 sets of genes encoding two-component systems. L. monocytogenes is closely related to the Gram-positive model bacterium Bacillus subtilis, in which we have shown previously that the DegS/DegU system plays a central role in controlling stationary phase adaptive responses, including degradative enzyme synthesis and competence. Although an orthologue of the DegU response regulator is present in L. monocytogenes, the gene encoding the cognate DegS kinase is conspicuously absent. We have inactivated the degU gene of L. monocytogenes and shown that DegU negatively regulates its own synthesis. Direct binding of L. monocytogenes DegU to its own promoter region was shown in vitro by gel mobility shift and DNase I footprinting experiments. DegU was also shown to bind upstream from the motB operon, which also encodes the GmaR anti-repressor of flagellar synthesis. In contrast to the situation in B. subtilis, DegU was shown to be essential for flagellar synthesis and bacterial motility in L. monocytogenes and is cotranscribed with the yviA gene located downstream. We also show that DegU is required for growth at high temperatures, adherence to plastic surfaces and the formation of efficient biofilms by L. monocytogenes. DegU plays a role in virulence of L. monocytogenes as well: in a murine intravenous infection model, an 11-fold increase in LD50 was observed for the degU mutant. Taken together, our results indicate that despite the lack of the DegS kinase, DegU is fully functional as an orphan response regulator, and plays a central role in controlling several crucial adaptive responses in L. monocytogenes.
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agr function in clinical Staphylococcus aureus isolates
The accessory gene regulator (agr) of Staphylococcus aureus is a global regulator of the staphylococcal virulon, which includes secreted virulence factors and surface proteins. The agr locus is important for virulence in a variety of animal models of infection, and has been assumed by inference to have a major role in human infection. Although most human clinical S. aureus isolates are agr +, there have been several reports of agr-defective mutants isolated from infected patients. Since it is well known that the agr locus is genetically labile in vitro, we have addressed the question of whether the reported agr-defective mutants were involved in the infection or could have arisen during post-isolation handling. We obtained a series of new staphylococcal isolates from local clinical infections and handled these with special care to avoid post-isolation mutations. Among these isolates, we found a number of strains with non-haemolytic phenotypes owing to mutations in the agr locus, and others with mutations elsewhere. We have also obtained isolates in which the population was continuously heterogeneous with respect to agr functionality, with agr + and agr− variants having otherwise indistinguishable chromosomal backgrounds. This finding suggested that the agr− variants arose by mutation during the course of the infection. Our results indicate that while most clinical isolates are haemolytic and agr +, non-haemolytic and agr− strains are found in S. aureus infections, and that agr + and agr− variants may have a cooperative interaction in certain types of infections.
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Shuttle expression plasmids for genetic studies in Streptococcus mutans
More LessA set of shuttle plasmids containing four different constitutive promoters was generated to facilitate overexpression of foreign and native genes in streptococci, such as Streptococcus mutans. The four promoters that were chosen were: P ami , P spac , P 23 and P veg . These promoters are active in many Gram-positive bacteria, and allow various levels of gene expression depending on the host bacterium. Shuttle plasmids were constructed based on two types of broad-host-range replication origins: a rolling-circle replicon (pSH71) and a theta replicon (pAMβ1). Shuttle plasmids derived from the pAMβ1 replicon were generated to avoid the structural and segregational stability problems associated with rolling-circle replication, since these problems may be encountered during large gene cloning. In a complementation assay, we used one such plasmid to express a gene in trans to show the utility of these plasmids. In addition, a series of plasmids was generated for the expression of recombinant proteins with an N-terminal 6×His tag or a C-terminal Strep-tag fusion, and, using a gene derived from S. mutans, we showed a high level of recombinant protein expression in S. mutans and Streptococcus pyogenes. Since these plasmids contain broad-host-range replication origins, and because the selected promoters are functional in many bacteria, they can be used for gene expression studies, such as complementation and recombinant protein expression.
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The binding of Tritrichomonas foetus to immobilized laminin-1 and its role in the cytotoxicity exerted by the parasite
The recognition and binding of pathogens to extracellular matrix glycoproteins may determine the outcome of infective processes. The interaction between the bovine urogenital parasite Tritrichomonas foetus and the major basal membrane glycoprotein laminin-1 (LMN-1) was investigated. The chemical nature of parasite molecules involved in the attachment of T. foetus to immobilized LMN-1 and the influence of LMN-1 in the toxicity exerted by the parasite to HeLa cells was studied. Attachment of T. foetus to LMN-1 resulted in notable morphological alterations of the parasite, which became amoeboid. T. foetus recognized LMN-1 through specific amino acid sequences (AG73, C16, A208 and A13) in the LMN-1 molecule, and the protein nature of the parasite molecules involved in the recognition was demonstrated by dot-blot analyses. Such molecular recognition was cation-dependent and five LMN-1-binding molecules (220, 200, 130, 125 and 80 kDa) were identified in T. foetus. Binding of T. foetus to LMN-1 rendered the parasite toxic to HeLa cell monolayers. Thus, LMN-1 appears to provide signalling cues that mediate important cell functions in T. foetus concerning its interaction with host cells.
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Characterization of genes differentially expressed within macrophages by virulent and attenuated Mycobacterium tuberculosis identifies candidate genes involved in intracellular growth
More LessTo identify genes involved in the intracellular survival of Mycobacterium tuberculosis we compared the transcriptomes of virulent (H37Rv) and attenuated (H37Ra) strains during their interaction with murine bone-marrow-derived macrophages. Expression profiling was accomplished via the bacterial artificial chromosome fingerprint array (BACFA) technique. Genes identified with BACFA, and confirmed via qPCR to be upregulated in the attenuated H37Ra at 168 h post-infection, were frdB, frdC and frdD. Genes upregulated in the virulent H37Rv were pks2, aceE and Rv1571. Further qPCR analysis of these genes at 4 and 96 h post-infection revealed that the frd operon (encoding the fumarate reductase enzyme complex) is expressed at higher levels in the virulent H37Rv at earlier time points while the expression of aceE and pks2 is higher in the virulent strain throughout the course of infection. Assessment of frd transcripts in oxygen-limited cultures of M. tuberculosis H37Ra and H37Rv showed that the attenuated strain displayed a lag in frdA and frdB expression at the onset of microaerophilic culture, when compared to microaerophilic cultures of H37Rv and aerated cultures of H37Ra. Lastly, treatment of intracellular bacteria with a putative inhibitor of fumarate reductase resulted in a significant reduction of bacterial growth.
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Plant host and sugar alcohol induced exopolysaccharide biosynthesis in the Burkholderia cepacia complex
The species that presently constitute the Burkholderia cepacia complex (Bcc) have multiple roles; they include soil and water saprophytes, bioremediators, and plant, animal and human pathogens. Since the first description of pathogenicity in the Bcc was based on sour skin rot of onion bulbs, this study returned to this plant host to investigate the onion-associated phenotype of the Bcc. Many Bcc isolates, which were previously considered to be non-mucoid, produced copious amounts of exopolysaccharide (EPS) when onion tissue was provided as the sole nutrient. EPS production was not species-specific, was observed in isolates from both clinical and environmental sources, and did not correlate with the ability to cause maceration of onion tissue. Chemical analysis suggested that the onion components responsible for EPS induction were primarily the carbohydrates sucrose, fructose and fructans. Additional sugars were investigated, and all alcohol sugars tested were able to induce EPS production, in particular mannitol and glucitol. To investigate the molecular basis for EPS biosynthesis, we focused on the highly conserved bce gene cluster thought to be involved in cepacian biosynthesis. We demonstrated induction of the bce gene cluster by mannitol, and found a clear correlation between the inability of representatives of the Burkholderia cenocepacia ET12 lineage to produce EPS and the presence of an 11 bp deletion within the bceB gene, which encodes a glycosyltransferase. Insertional inactivation of bceB in Burkholderia ambifaria AMMD results in loss of EPS production on sugar alcohol media. These novel and surprising insights into EPS biosynthesis highlight the metabolic potential of the Bcc and show that a potential virulence factor may not be detected by routine laboratory culture. Our results also highlight a potential hazard in the use of inhaled mannitol as an osmolyte to improve mucociliary clearance in individuals with cystic fibrosis.
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Differential expression of the polysialyl capsule during blood-to-brain transit of neuropathogenic Escherichia coli K1
More LessEscherichia coli K1 isolates synthesize a polysialic acid (polySia) capsule, are components of the adult gastrointestinal microbiota and may cause lethal bacteraemia and meningitis if acquired maternally by newborn infants. We used a neonatal rat pup K1 infection model to establish that prompt administration of a selective capsule depolymerase reverses the bacteraemic state and prevents death of almost all pups. In untreated animals, bacteria colonize the gastrointestinal tract and gain entry to the blood compartment, where they express the non-O-acetylated form of polySia. The bacteria invade the major organs of the host; histological and histochemical analysis of brain sections revealed that at least some bacteria enter the central nervous system through the blood–cerebrospinal fluid barrier at the choroid plexus prior to colonization of the meninges. Once in this location, they cease expression of polySia. The unexpected abrogation of polySia, a factor associated with the pathogenesis of meningitis and essential for transit through the blood, suggests that the neuropathogen dispenses with its protective capsule once it has colonized protected niches. Thus, systemic infections due to encapsulated pathogens may be resolved by capsule depolymerization only if the enzyme modifies the bacteria whilst they are in the blood compartment.
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- Physiology
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Plasminogen-dependent proteolytic activity in Bifidobacterium lactis
Bifidobacteria represent one of the most important health-promoting bacterial groups of the intestinal microbiota. The binding of plasminogen to species of Bifidobacterium has been recently reported. To further explore the interaction between bifidobacteria and plasminogen, we investigated the role of Bifidobacterium lactis BI07 plasminogen-dependent proteolytic activity in the degradation of host-specific substrates. Our experimental data demonstrate that the recruitment of plasminogen on the bacterial cell surface and its subsequent conversion into plasmin by host-derived plasminogen activators provide B. lactis BI07 with a surface-associated plasmin activity effective in degradation of physiological substrates such as extracellular matrix, fibronectin and fibrinogen. The ability of bifidobacteria to intervene in the host plasminogen/plasmin system may contribute to facilitating colonization of the host gastrointestinal tract.
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Polar accumulation of the metabolic sensory histidine kinases DcuS and CitA in Escherichia coli
Signal transduction in prokaryotes is frequently accomplished by two-component regulatory systems in which a histidine protein kinase is the sensory component. Many of these sensory kinases control metabolic processes that do not show an obvious requirement for inhomogeneous distribution within bacterial cells. Here, the sensory kinases DcuS and CitA, two histidine kinases of Escherichia coli, were investigated. Both are membrane-integral and involved in the regulation of carboxylate metabolism. The two-component sensors were fused with yellow fluorescent protein (YFP) and live images of immobilized cells were obtained by confocal laser fluorescence microscopy. The fluorescence of the fusion proteins was concentrated at the poles of the cells, indicating polar accumulation of the sensory kinases. For quantitative evaluation, line profiles of the imaged fluorescence intensities were generated; these revealed that the fluorescence intensity of the polar bright spots was 2.3–8.5 times higher than that of the cytoplasm. With respect to the cylindrical part of the membrane, the values were lower by about 40 %. The polar accumulation was comparable to that of methyl-accepting chemotaxis proteins (MCPs) and MCP-related proteins. The degree of DcuS–YFP localization was independent of the presence of MCP and the expression level of dcuS–yfp (or DcuS concentration). The presence of effector (fumarate or citrate, respectively) increased the polar accumulation by more than 20 %. Cell fractionation demonstrated that polar accumulation was not related to inclusion body formation. Therefore, sensory kinases DcuS and CitA, which regulate metabolic processes without obvious polar function, exhibit polar accumulation.
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d-Lactate metabolism and the obligate requirement for CO2 during growth on nitrite by the facultative lithoautotroph Nitrobacter hamburgensis
More LessNitrobacter hamburgensis X14 is a facultative lithoautotroph that conserves energy from the oxidation of nitrite () and fixes carbon dioxide (CO2) as its sole source of carbon. The availability of the N. hamburgensis X14 genome sequence initiated a re-examination of its mixotrophic and organotrophic potential, as genes encoding three flavin-dependent oxidases were identified that may function to oxidize lactate, providing energy and carbon for growth. The response of N. hamburgensis to d- and l-lactate in the presence (mixotrophy) and absence (organotrophy) of was examined. l-Lactate did not support organotrophic growth or stimulate mixotrophic growth. In contrast, d-lactate enhanced the growth rate and yield of N. hamburgensis in the presence of , and served as the sole carbon and energy source for growth in the absence of with ammonium as the sole nitrogen source. Lithoautotrophically grown cells immediately consumed d-lactate, suggesting that a lactate metabolic pathway is constitutively expressed. Nevertheless, a physiological adaptation to lactate occurred, as d-lactate-grown cells consumed and assimilated lactate at a faster rate than -grown cells, and the d-lactate-dependent O2 uptake rate was significantly greater in cells grown either organotrophically or mixotrophically compared with cells grown lithoautotrophically. Although d-lactate was assimilated and metabolized to CO2 in the presence or absence of , exposure to atmospheric CO2 or the addition of 0.75 mM sodium carbonate was required for mixotrophic growth and for optimum organotrophic growth on d-lactate.
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Nsf1/Ypl230w participates in transcriptional activation during non-fermentative growth and in response to salt stress in Saccharomyces cerevisiae
More LessIn Saccharomyces cerevisiae, fermentable carbon sources such as glucose and fructose are preferred and elicit glucose repression of genes needed to metabolize non-fermentable carbon sources such as glycerol, ethanol and acetate. Different sets of transcription factors are needed to adjust to specific carbon conditions. For example, Mig1 and Mig2 repress the transcription of gluconeogenic and respiratory genes in the presence of abundant glucose, while the transcriptional activation of these genes depends on transcription factors such as Adr1 and Cat8. Here we show that Ypl230w, which we renamed to Nsf1 (nutrient and stress factor 1), is expressed and localizes to the nucleus under non-fermentable carbon conditions to activate gene transcription. Specifically, the transcriptional activation of ACS1, CIT2 and IDH1 is shown to be partially dependent on intact NSF1. Similarly, the transcriptional activation of ENA1 is impaired in the nsf1Δ mutant in response to high concentrations of NaCl, implying that NSF1 is also needed for the yeast response to sodium stress. The carbon- and NaCl-mediated transcriptional activation of ENA1 is dependent on Nsf1. This finding implies that the yeast response to non-fermentable carbon and salt stress is at least partially dependent on NSF1.
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- Plant-Microbe Interactions
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Microarray profiling of host-extract-induced genes and characterization of the type VI secretion cluster in the potato pathogen Pectobacterium atrosepticum
Pectobacterium atrosepticum is a Gram-negative plant-pathogenic bacterium that rots potato stems and tubers. Microarray analysis was used to identify genes that were differentially expressed when host extracts were added to the growth medium. Potato extracts downregulated the expression of ribosomal genes and genes related to uptake and metabolism of nutrients, and upregulated genes needed for nitrate or phosphonate use. Some of the observed changes in gene expression in host-extract-induced cultures are similar to those during attachment of the bacterium to host tissues. Other responses indicated defence against toxic metabolites in the extract. Tuber extract induced a large gene cluster having homology to type VI secretion genes shown to be virulence determinants in many, but not all, animal and human pathogens. Two of the genes in the type VI cluster were found to be expressed during infection in potato tubers and stems, and mutants with knockouts of the corresponding genes had increased virulence on potato. One of the type VI secretion mutants was further characterized and found to grow to higher cell density in culture in the presence of host extract and to produce slightly more extracellular tissue-macerating enzymes than the wild-type strain. Analysis of secreted proteins showed that this type VI mutant was affected in the production of haemolysin-coregulated proteins (Hcps), which have been suggested to be secreted by the type VI pathway in other bacteria. The results suggest that the type VI secretion system of P. atrosepticum is needed for secretion of Hcps but not for virulence on its host plant, potato.
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Volumes and issues
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