Genome-wide analysis of the role of GlnR in Streptomyces venezuelae provides new insights into global nitrogen regulation in actinomycetes

<p>Abstract</p> <p>Background</p> <p>GlnR is an atypical response regulator found in actinomycetes that modulates the transcription of genes in response to changes in nitrogen availability. We applied a global <it>in vivo </it>approach to identify the GlnR regulon of <it>Streptomyces venezuelae</it>, which, unlike many actinomycetes, grows in a diffuse manner that is suitable for physiological studies. Conditions were defined that facilitated analysis of GlnR-dependent induction of gene expression in response to rapid nitrogen starvation. Microarray analysis identified global transcriptional differences between <it>glnR</it>⁺and <it>glnR </it>mutant strains under varying nitrogen conditions. To differentiate between direct and indirect regulatory effects of GlnR, chromatin immuno-precipitation (ChIP) using antibodies specific to a FLAG-tagged GlnR protein, coupled with microarray analysis (ChIP-chip), was used to identify GlnR binding sites throughout the <it>S. venezuelae </it>genome.</p> <p>Results</p> <p>GlnR bound to its target sites in both transcriptionally active and apparently inactive forms. Thirty-six GlnR binding sites were identified by ChIP-chip analysis allowing derivation of a consensus GlnR-binding site for <it>S. venezuelae</it>. GlnR-binding regions were associated with genes involved in primary nitrogen metabolism, secondary metabolism, the synthesis of catabolic enzymes and a number of transport-related functions.</p> <p>Conclusions</p> <p>The GlnR regulon of <it>S. venezuelae </it>is extensive and impacts on many facets of the organism's biology. GlnR can apparently bind to its target sites in both transcriptionally active and inactive forms.</p

Modulation of the oxidative stress in malaria infection by clotrimazole

Antimycotic clotrimazole (CTZ) has demonstrated remarkable activity against Plasmodium falciparum in vitro and in vivo. Hemoglobin degradation by Plasmodium parasites makes amino acids available for protein synthesis, inducing oxidative stress in infected cells and producing free heme. These events represent biochemical targets for potential antimalarials. In this study, we have tested the ability of CTZ to modify the oxidative status in Plasmodium berghei-infected erythrocytes. After hemolysis, activities of superoxide dismutase (SOD), catalase (CAT), glutathione cycle and NADPH+H+-producing dehydrogenases were investigated using UV-visible spectrophotometry. Thiobarbituric acid reactive substances (TBARS) were evaluated as a marker of lipid damage. Results showed that CTZ significantly decreased the overall activity of 6-phosphagluconate dehydrogenase (6PGD) compared to infected and non-treated cells; consequently, the glutathione cycle was inhibited, leaving the parasite vulnerable to the oxidative stress originating from hemoglobin degradation. As a compensatory response, CTZ prevented some loss of SOD and CAT activities in infected cells. The infection triggered lipid peroxidation in erythrocytes, which was decreased by CTZ. These results suggest the presence of a redox unbalance in cells treated with CTZ, discussing a possible effect of this compound disturbing the oxidative status in a Plasmodium berghei-infection.O antifúngico clotrimazol (CTZ) tem demonstrado notável atividade contra Plasmodium falciparum. A degradação da hemoglobina por Plasmodium para a obtenção dos aminoácidos necessários à síntese protéica induz estresse oxidativo em eritrócitos devido à liberação de hemos oxidantes. Estes eventos representam alvos bioquímicos para a produção de antimaláricos potenciais. Neste estudo, testamos a capacidade do CTZ para modificar o estado oxidativo em eritrócitos infectados com Plasmodium berghei. Depois da hemólise, as atividades da superóxido dismutase (SOD), catalase (CAT), desidrogenases produtoras de NADPH+H+ e do ciclo de glutationa (GSH) foram investigados. A produção das espécies reativas ao ácido tiobarbitúrico (TBARS) foi avaliada como marcador de dano lipídico. Os resultados mostraram que o CTZ diminuiu a atividade da 6-fosfogliconato desidrogenase (6PGD), em comparação com eritrócitos infectados e não tratados. Consequentemente, o ciclo da GSH foi inibido, tornando os parasitas vulneráveis ao estresse oxidativo resultante da degradação da hemoglobina. Como resposta compensatória, CTZ impediu a perda de atividade da SOD e CAT nas células infectadas. A infecção induz peroxidação lipídica nos eritrócitos, sendo esta diminuída pelo CTZ. Estes resultados sugerem a existência de desequilíbrio redox nas células tratadas com CTZ, interferindo, assim, com o estado oxidativo verificado durante a infecção malárica

Genome-wide transcriptomic analysis of the response to nitrogen limitation in Streptomyces coelicolor A3(2)

<p>Abstract</p> <p>Background</p> <p>The present study represents a genome-wide transcriptomic analysis of the response of the model streptomycete <it>Streptomyces coelicolor </it>A3(2) M145 to fermentor culture in Modified Evans Media limited, respectively, for nitrogen, phosphate and carbon undertaken as part of the ActinoGEN consortium to provide a publicly available reference microarray dataset.</p> <p>Findings</p> <p>A microarray dataset using samples from two replicate cultures for each nutrient limitation was generated. In this report our analysis has focused on the genes which are significantly differentially expressed, as determined by Rank Products Analysis, between samples from matched time points correlated by growth phase for the three pairs of differently limited culture datasets. With a few exceptions, genes are only significantly differentially expressed between the N6/N7 time points and their corresponding time points in the C and P-limited cultures, with the vast majority of the differentially expressed genes being more highly expressed in the N-limited cultures. Our analysis of these genes indicated expression of several members of the GlnR regulon are induced upon nitrogen limitation, as assayed for by [NH₄⁺] measurements, and we are able to identify several additional genes not present in the GlnR regulon whose expression is induced in response to nitrogen limitation. We also note SCO3327 which encodes a small protein (32 amino acid residues) unusually rich in the basic amino acids lysine (31.25%) and arginine (25%) is significantly differentially expressed in the nitrogen limited cultures. Additionally, we investigate the expression of known members of the GlnR regulon and the relationship between gene organization and expression for the SCO2486-SCO2487 and SCO5583-SCO5585 operons.</p> <p>Conclusions</p> <p>We provide a list of genes whose expression is differentially expressed in low nitrogen culture conditions, including a putative nitrogen storage protein encoded by SCO3327. Our list includes several genes whose expression patterns are similar to up-regulated members of the GlnR regulon and are induced in response to nitrogen limitation. These genes represent likely targets for future studies into the nitrogen starvation response in <it>Streptomyces coelicolor</it>.</p