Transcriptional regulation of the Staphylococcus aureus thioredoxin and thioredoxin reductase genes in response to oxygen and disulfide stress

Combining site-specific mutagenesis and seeding as a strategy to crystallize 'difficult' proteins: the case of Staphylococcus aureus thioredoxin

The P31T mutant of Staphylococcus aureus thioredoxin crystallizes spontaneously in space group P2(1)2(1)2(1), with unit-cell parameters a = 41.7, b = 49.5, c = 55.6 A. The crystals diffract to 2.2 A resolution. Isomorphous crystals of wild-type thioredoxin as well as of other point mutants only grow when seeded with the P31T mutant. These results suggest seeding as a valuable tool complementing surface engineering for proteins that are hard to crystallize.

Thioredoxin reductase is required for growth and regulates entry into culmination of Dictyostelium discoideum

The thioredoxin system, consisting of thioredoxin, thioredoxin reductase and NADPH, has been well established to be critical for the redox regulation of protein function and signalling. To investigate the role of thioredoxin reductase (Trr) in Dictyostelium discoideum, we generated mutant cells that underexpress or overexpress Trr. Trr-underexpressing cells exhibited severe defects in axenic growth and development. Trr-overexpressing (TrrOE) cells formed very tiny plaques on a bacterial lawn and had a lower rate of bacterial uptake. When developed in the dark, TrrOE cells exhibited a slugger phenotype, defined by a prolonged migrating slug stage. Like other slugger mutants, they were hypersensitive to ammonia, which has been known to inhibit culmination by raising the pH of intracellular acidic compartments. Interestingly, TrrOE cells showed defective acidification of intracellular compartments and decreased activity of vacuolar H+-ATPase which functions in the acidification of intracellular compartments. Moreover, biochemical studies revealed that the thioredoxin system can directly reduce the catalytic subunit of vacuolar H+-ATPase whose activity is regulated by reversible disulphide bond formation. Taken together, these results suggest that Dictyostelium Trr may be essential for growth and play a role in regulation of phagocytosis and culmination, possibly through the modulation of vacuolar H+-ATPase activity.

Spx is a global effector impacting stress tolerance and biofilm formation in Staphylococcus aureus

In Bacillus subtilis, Spx was recently characterized as a novel type of global regulator whose activity is regulated by the redox status of the cells. In the present study, we demonstrate that inactivation of Spx in the important pathogen Staphylococcus aureus renders the cells hypersensitive to a wide range of stress conditions including high and low temperature, high osmolarity, and hydrogen peroxide. Moreover, growth was restricted under nonstress conditions. Two-dimensional gel electrophoresis revealed that the proteome of the spx mutant differs substantially from the proteome of wild-type cells, supporting the finding that Spx is also a global regulator in S. aureus. More specifically, we demonstrated that Spx is required for transcription of trxB, encoding thioredoxin reductase, under all growth conditions examined. As trxB is essential in S. aureus, we speculate that the severely reduced trxB transcription could account for some of the growth defects of the spx mutant. Inactivation of spx also enhanced biofilm formation. S. aureus biofilm formation is associated with the production of the polysaccharide intercellular adhesin encoded by the ica operon. Interestingly, our data indicate that the augmented capacity of the spx mutant to form biofilms is due to Spx modulating the expression of icaR, encoding a repressor of the structural ica genes (icaABCD). In summary, we conclude that Spx fulfills an important role for growth, general stress protection, and biofilm formation in S. aureus.

Extracellular Matrix Proteome of Chickpea (Cicer arietinum L.) Illustrates Pathway Abundance, Novel Protein Functions and Evolutionary Perspect

The extracellular matrix (ECM) or cell wall is a dynamic system and serves as the first line mediator in cell signaling to perceive and transmit extra- and intercellular signals in many pathways. Although ECM is a conserved compartment ubiquitously present throughout evolution, a compositional variation does exist among different organisms. ECM proteins account for 10% of the ECM mass, however, comprise several hundreds of different molecules with diverse functions. To understand the function of ECM proteins, we have developed the cell wall proteome of a crop legume, chickpea (Cicer arietinum). This comprehensive overview of the proteome would provide a basis for future comparative proteomic efforts for this important crop. Proteomic analyses revealed new ECM proteins of unknown functions vis-à-vis the presence of many known cell wall proteins. In addition, we report here evidence for the presence of unexpected proteins with known biochemical activities, which have never been associated with ECM.

Oxidative stress and heat-shock responses in Desulfovibrio vulgaris by genome-wide transcriptomic analysis

Sulfate-reducing bacteria such as Desulfovibrio vulgaris have developed a set of responses that allow them to survive in hostile environments. To obtain further knowledge of the protective mechanisms employed by D. vulgaris in response to oxidative stress and heat shock, we performed a genome-wide transcriptomic analysis to determine the cellular responses to both stimuli. The results showed that 130 genes were responsive to oxidative stress, while 427 genes were responsive to heat-shock. Functional analyses suggested that the genes regulated were involved in a variety of cellular functions. Amino acid biosynthetic pathways were induced by both oxidative stress and heat shock treatments, while fatty acid metabolism, purine and cofactor biosynthesis were induced by heat shock only. The rubrerythrin gene (rbr) was up-regulated in response to oxidative stress, suggesting an important role for this protein in the oxidative damage resistance response in D. vulgaris. In addition, thioredoxin reductase (trxB) was also responsive to oxidative stress, suggesting that the thiol-specific redox system might also be involved in oxidative protection in this organism. In contrast, the expression of rubredoxin oxidoreductase (rbo), superoxide dismutase (sodB) and catalase (katA) genes were not regulated in response to oxidative stress. Comparison of cellular responses to oxidative stress and heat-shock allowed the identification of 66 genes that showed a similar drastic response to both environmental perturbations, implying that these genes might be part of the general stress response (GSR) network in D. vulgaris. This hypothesis was further supported by the identification of a conserved motif upstream of these stress-responsive genes.

The sigmaB regulon in Staphylococcus aureus and its regulation

The Staphylococcus aureus genome codes for a sigma factor that shows close sequence similarity to the alternative sigma factor sigmaB of Bacillus subtilis. However, of the proteins controlling the activity of sigmaB in B. subtilis only RsbU, RsbV, and RsbW are encoded in the staphylococcal genome. Therefore, the regulation of the sigmaB activity must differ between these two bacterial species. The present study was designed (i) to describe the sigmaB regulon and (ii) to identify stimuli leading to an activation of sigmaB-dependent transcription. All conditions under which sigmaB was activated in S. aureus (heat shock, addition of MnCl2 or NaCl, alkaline shock) required the presence of RsbU, a positive regulator of sigmaB. In contrast to B. subtilis, a drop in the cellular ATP level caused by the addition of carbonyl cyanide m-chlorophenylhydrazone did not lead to an activation of sigmaB in S. aureus. Moreover, ethanol, a strong inductor of sigmaB activity in B. subtilis, also failed to induce sigmaB in S. aureus. Expression of sigB and sigmaB-dependent genes was enhanced following entry into stationary phase of cells grown in complex medium (LB medium). Our DNA microarray data indicated that 122 genes are positively regulated by sigmaB under alkaline stress conditions. Interestingly, only 12% of these genes have an orthologue in the B. subtilis sigmaB regulon, suggesting that the function of the sigmaB regulon in S. aureus is different from that in B. subtilis. We could show that sigmaB of S. aureus, in contrast to B. subtilis, may have a function in more basic cellular processes such as cell envelope composition, membrane transport processes and intermediary metabolism. sigmaB-dependent genes identified by the DNA microarray approach were subjected to detailed transcriptional analyses using primer extension and Northern blot techniques. These analyses confirmed our DNA microarray data and furthermore revealed different regulatory groups of sigmaB-dependent genes.

DNA microarray analysis of anaerobic Methanosarcina barkeri reveals responses to heat shock and air exposure

Methanosarcina barkeri is a methanogenic archaeon that can digest cellulose and other polysaccharides to produce methane. It can only grow under strictly anoxic conditions, but which can survive air exposure. To obtain further knowledge of cellular changes occurring in M. barkeri in response to air exposure and other environmental stresses, we constructed the first oligonucleotide microarray for M. barkeri and used it to investigate the global transcriptomic responses of M. barkeri to air exposure and heat shock at 45 degrees C for 1 h. The results showed that various house-keeping genes, such as genes involved in DNA replication recombination and repair, energy production and conversion, and protein turnover were regulated by environmental stimuli. In response to air exposure, up-regulation of a large number of transposase encoding genes was observed. However, no differential expression of genes encoding superoxide dismutase, catalase, nonspecific peroxidases or thioredoxin reductase was observed in response to air exposure, implying that no significant level of reactive oxygen species has been formed under air exposure. In response to heat shock, both Hsp70 (DnaK-DnaJ-GrpE chaperone system) the Hsp60 (GroEL) systems were up-regulated, suggesting that they may play an important role in protein biogenesis in M. barkeri during heat stress.

Thioredoxins in bacteria: functions in oxidative stress response and regulation of thioredoxin genes

Thioredoxins fulfill a number of different important cellular functions in all living organisms. In bacteria, thioredoxin genes are often regulated by external factors. In turn, thioredoxins influence the expression of many other genes. The multiple and important functions of thioredoxins in cells necessitate to appropriately adjust their level. This review outlines different strategies that have evolved for the regulation of bacterial thioredoxin genes. It also summarizes effects of thioredoxins on gene regulation and presents a recent model for a redox-dependent gene regulation that is mediated by thioredoxins.

Predicted highly expressed genes in Nocardia farcinica and the implication for its primary metabolism and nocardial virulence

Nocardia farcinica is a Gram positive, filamentous bacterium, and is considered an opportunistic pathogen. In this study, the highly expressed genes in N. farcinica were predicted using the codon adaptation index (CAI) as a numerical estimator of gene expressivity. Using ribosomal protein (RP) genes as references, the top approximately approximately 10% of the genes were predicted to be the predicted highly expressed (PHX) genes in N. farcinica using a CAI cutoff of greater than 0.73. Consistent with earlier analysis of Streptomyces genomes, most of the PHX genes in N. farcinica were involved in various 'house-keeping' functions important for cell growth. However, 15 genes putatively involved in nocardial virulence were predicted as PHX genes in N. farcinica, which included genes encoding four Mce proteins, cyclopropane fatty acid synthase which is involved in the modification of cell wall which may be important for nocardia virulence, polyketide synthase PKS13 for mycolic acid synthesis and a non-ribosomal peptide synthetase involved in biosynthesis of a mycobactin-related siderophore. In addition, multiple genes involved in defense against reactive oxygen species (ROS) produced by the phagocyte were predicted with high expressivity, which included alkylhydroperoxide reductase (ahpC), catalase (katG), superoxide dismutase (sodF), thioredoxin, thioredoxin reductase, glutathione peroxidase, and peptide methionine sulfoxide reductase, suggesting that combating against ROS is essential for survival of N. farcinica in host cells. The study also showed that the distribution of PHX genes in the N. farcinica circular chromosome was uneven, with more PHX genes located in the regions close to replication initiation site. The results provided the first estimates of global gene expression patterns in N. farcinica, which will be useful in guiding experimental design for further investigations.

Thioredoxin reductase is essential for viability in the fungal pathogen Cryptococcus neoformans

Thioredoxin reductase (TRR1) is an important component of the thioredoxin oxidative stress resistance pathway. Here we show that it is induced during oxidative and nitrosative stress and is preferentially localized to the mitochondria in Cryptococcus neoformans. The C. neoformans TRR1 gene encodes the low-molecular-weight isoform of the thioredoxin reductase enzyme, which shares little homology with that of its mammalian host. By replacing the endogenous TRR1 promoter with an inducible copper transporter promoter, we showed that Trr1 appears to be essential for viability of this pathogenic fungus, making it a potential antifungal target.

Functional analysis of sigH expression in Corynebacterium glutamicum

The sigH gene of Corynebacterium glutamicum encodes ECF sigma factor sigmaH. The gene apparently plays an important role in other stress responses as well as heat stress response. In this study, we found that deleting the sigH gene made C. glutamicum cells sensitive to the thiol-specific oxidant diamide. In the sigH mutant strain, the activity of thioredoxin reductase markedly decreased, suggesting that the trxB gene encoding thioredoxin reductase is probably under the control of sigmaH. The expression of sigH was stimulated in the stationary growth phase and modulated by diamide. In addition, the SigH protein was required for the expression of its own gene. These data indicate that the sigH gene of C. glutamicum stimulates and regulates its own expression in the stationary growth phase in response to environmental stimuli, and participates in the expression of other genes which are important for survival following heat and oxidative stress response.

Staphylococcus aureus NfrA (SA0367) is a flavin mononucleotide-dependent NADPH oxidase involved in oxidative stress response

The NfrA protein, a putative essential oxidoreductase in the soil bacterium Bacillus subtilis, is induced under heat shock and oxidative stress conditions. In order to characterize the function of an homologous NfrA protein in Staphylococcus aureus, an nfrA deletion strain was constructed, the protein was purified, the enzymatic activity was determined, and the transcriptional regulation was investigated. The experiments revealed that NfrA is not essential in S. aureus. The purified protein oxidized NADPH but not NADH, producing NADP in the presence of flavin mononucleotide, suggesting that NfrA is an NADPH oxidase in S. aureus. In addition, the NfrA enzyme showed nitroreductase activity and weak disulfide reductase activity. Transcription was strongly induced by ethanol, diamide, and nitrofurantoin. Hydrogen peroxide induced nfrA transcription only at high concentrations. The expression of nfrA was independent of the alternative sigma factor sigma(B). Furthermore, the transcriptional start site was determined, which allowed identification of a PerR box homologous sequence upstream of the nfrA promoter. The observations presented here suggest that NfrA is a nonessential NADPH oxidoreductase which may play a role in the oxidative stress response of S. aureus, especially in keeping thiol-disulfide stress in balance.

Roles of thioredoxin reductase during the aerobic life of Lactococcus lactis

Thiol-disulfide bond balance is generally maintained in bacteria by thioredoxin reductase-thioredoxin and/or glutathione-glutaredoxin systems. Some gram-positive bacteria, including Lactococcus lactis, do not produce glutathione, and the thioredoxin system is presumed to be essential. We constructed an L. lactis trxB1 mutant. The mutant was obtained under anaerobic conditions in the presence of dithiothreitol (DTT). Unexpectedly, the trxB1 mutant was viable without DTT and under aerated static conditions, thus disproving the essentiality of this system. Aerobic growth of the trxB1 mutant did not require glutathione, also ruling out the need for this redox maintenance system. Proteomic analyses showed that known oxidative stress defense proteins are induced in the trxB1 mutant. Two additional effects of trxB1 were not previously reported in other bacteria: (i) induction of proteins involved in fatty acid or menaquinone biosynthesis, indicating that membrane synthesis is part of the cellular response to a redox imbalance, and (ii) alteration of the isoforms of the glycolytic enzyme glyceraldehyde-3-phosphate dehydrogenase (GapB). We determined that the two GapB isoforms in L. lactis differed by the oxidation state of catalytic-site cysteine C152. Unexpectedly, a decrease specific to the oxidized, inactive form was observed in the trxB1 mutant, possibly because of proteolysis of oxidized GapB. This study showed that thioredoxin reductase is not essential in L. lactis and that its inactivation triggers induction of several mechanisms acting at the membrane and metabolic levels. The existence of a novel redox function that compensates for trxB1 deficiency is suggested.

How thioredoxin can reduce a buried disulphide bond

We present a study of the interaction between thioredoxin and the model enzyme pI258 arsenate reductase (ArsC) from Staphylococcus aureus. ArsC catalyses the reduction of arsenate to arsenite. Three redox active cysteine residues (Cys10, Cys82 and Cys89) are involved. After a single catalytic arsenate reduction event, oxidized ArsC exposes a disulphide bridge between Cys82 and Cys89 on a looped-out redox helix. Thioredoxin converts oxidized ArsC back towards its initial reduced state. In the absence of a reducing environment, the active-site P-loop of ArsC is blocked by the formation of a second disulphide bridge (Cys10-Cys15). While fully reduced ArsC can be recovered by exposing this double oxidized ArsC to thioredoxin, the P-loop disulphide bridge is itself inaccessible to thioredoxin. To reduce this buried Cys10-Cys15 disulphide-bridge in double oxidized ArsC, an intra-molecular Cys10-Cys82 disulphide switch connects the thioredoxin mediated inter-protein thiol-disulphide transfer to the buried disulphide. In the initial step of the reduction mechanism, thioredoxin appears to be selective for oxidized ArsC that requires the redox helix to be looped out for its interaction. The formation of a buried disulphide bridge in the active-site might function as protection against irreversible oxidation of the nucleophilic cysteine, a characteristic that has also been observed in the structurally similar low molecular weight tyrosine phosphatase.