Unknown,Transcriptomics,Genomics,Proteomics

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Deciphering the transcriptional response mediated by the redox-sensing system HbpS-SenS-SenR from streptomycetes

ABSTRACT: Comparative analyses of the transcriptomes of the Streptomyces coelicolor A3(2) wild-type and the generated hbpSc-senSc-senRc (hsr) mutant under native and oxidative-stressing conditions allowed to identify differentially expressed genes, whose products may enhance the anti-oxidative defense of the bacterium. To obtain well-grown mycelia, spores of S. coelicolor (WT and hsr mutant) were inoculated in 10 ml R2 medium and grown as standing culture at 30C for 16 h and afterwards on a rotary shaker for 16 h after the addition of 90 ml R2 medium. The cultures were washed four times in minimal medium without supplement. The mycelia were suspended in 50 ml R2 medium and divided in two 25 ml-portions, one of which contained H2O2 (0.15 mM). Cultivation was continued at 30 C on a rotary shaker for two hours. Mycelia were harvested by centrifugation and the mycelia pellets were store at -80 C. Total RNA was isolated from two biological replicates. cDNA libraries of RNA from of S. coelicolor (WT and hsr mutant) were constructed using the TruSeq Stranded mRNA Library Prep Kit (Illumina,San Diego, CA, USA), and subsequently sequenced paired-end on an Illumina MiSeq system (San Diego, CA, USA) using 75 bp read length.

INSTRUMENT(S): Illumina MiSeq

ORGANISM(S): Streptomyces coelicolor

SUBMITTER: Anika Winkler

PROVIDER: E-MTAB-4833 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Rice blast is the most threatening disease to cultivated rice worldwide. Magnaporthe oryzae, its causal agent is likely to encounter environmental challenges during invasive growth in the host plants that require shifts in gene expression to establish a compatible interaction. Here, we tested the hypothesis that M. oryzae have similar gene expression patterns in planta, versus during in vitro stresses. Gene expression data was collected from in vitro experiments of heat shock, oxidative burst, and three different types of nutrient starvation. These data were compared to fungal gene expression during the invasive growth phase in compatible interactions on two grass hosts, rice and barley. We have identified 4,973 differentially expressed genes, from which 1,909 genes showed similar regulation patterns between at least one of the in vitro stresses and rice and/or barley. Hierarchical clustering of these 1,909 genes showed three major clusters in which growth in planta conditions closely grouped with the starving nutrient conditions. Out of these 1,909 genes, 55 and 129 genes were induced and repressed in all seven treatments, respectively. The functional categorization of those 55 induced genes revealed that most of them are either related to carbon metabolism, membrane proteins, or are involved in oxidoreduction reactions. The 129 repressed genes are putatively involved in vesicle trafficking, signal transduction, nitrogen metabolism, or molecular transport. These findings indicated that M. oryzae is likely coping with nutrient deprived environments in its hosts during the invasive growth stage about 72 hours post-inoculation, and not as much with host defense responses, or a temperature stress. Eight M. oryzae treatments: mycelia grown in liquid complete medium (set as the control); 72 hours post-incoulation (hpi) in rice leaves; 72 hours post-incoulation in barley leaves; mycelia under heat shock; mycelia under oxidative stress; mycelia under minimal medium; mycelia under nitrogen starvation; mycelia under carbon starvation. Three biological replicates had their total RNA pulled after RNA extraction. Dye-swaps used as technical replicates.

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Deciphering the transcriptional response mediated by the redox-sensing system HbpS-SenS-SenR from streptomycetes

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