Project description:The gasotransmitter hydrogen sulfide (H2S), produced by transsulfuration pathway, in recent years has been recognized as a biological mediator playing important role under normal conditions and in various pathologies both in eukaryotes and prokaryotes. The transsulfuration pathway (TSP) includes the conversion of homocysteine to cysteine following the breakdown of methionine. In Drosophila melanogaster and other eukaryotes H2S is produced by cystathionine B-synthase (CBS), cystathionine y-lyase (CSE), and 3-mercaptopyruvate sulftransferase (MST). In the experiments reported here we were able exploring CRISPR technique to obtain single and double deletions of these three major genes responsible for H2S production. In most cases the deletion of one studied gene does not result in the compensatory induction of two other genes responsible for H2S production. Transcriptomic studies demonstrated that the deletions of the above genes alter the genome expression to different degree with more pronounced effect exerted by deletions of CBS gene. Furthermore, the double deletion of both CBS and CSE resulted in cumulative effect on the transcription in the resulted strains. Overall, we found that the obtained deletions affected numerous genes involved in various biological pathways. Characteristically, genes involved in oxidative reduction process, stress-response genes, house-keeping genes, genes participating in olfactory and reproduction were among the most affected. Furthermore, characteristic differences in the response to the deletions of the studied genes were apparently organ specific and have clear-cut gender character. Importantly, the deletions altered global methylation and chromatin state of the experimental strains by increasing the level of inactive chromatin of the genome. Single and double deletions of the three genes responsible for the production of H2S helped to understand new aspects of biological significance of this vital physiological mediator.

Project description:Mutations in the cysB, sconB and sconC genes affect sulfur metabolism in Aspergillus nidulans in different ways. Mutation of cysB blocks synthesis of cysteine by the main pathway leaving only the less effective alternative route. Mutations of sconB or sconC affect subunits of the SCF ubiquitin ligase complex, a negative controller of METR transcription factor, resulting in specific activation of a number of sulfur assimilation and metabolism genes, ultimately leading to elevated levels of cysteine and glutathione in scon mutants. We compared transcriptomes of these three mutants with that of a wild type strain finding that expression of a few hundred genes is altered at least twofold indicating a major reorganization of cellular metabolism. Despite the different effects of the cysB and scon mutations on sulfur metabolism they affect expression of overlapping sets of genes. We identified categories of the Functional Catalogue assigned to the differentially expressed genes and selected categories most enriched among the up- and down-regulated gene groups. Besides those involved in sulfur metabolism, many up-regulated genes are related to stress responses. The two-component signal transduction system is most enriched in genes up-regulated in the cysB, sconB and sconC mutants. This category contains histidine kinases that sense and transduce environmental signals to a cascade of protein kinases. Genes encoding heat shock proteins are also up-regulated, as are genes of the glutamate degradation pathway. The latter, also known as the GABA shunt, is induced by oxidative stress. A large group of up-regulated genes are involved in carbohydrate and energy metabolism, including genes coding for enzymes of trehalose and glycerol synthesis. Genes coding for enzymes of alcohol fermentation, which are induced in response to anaerobic stress, are also up-regulated in the mutants studied. The altered expression of the carbohydrate metabolism genes is accompanied by changes in sugar accumulation in mycelia and conidia of the mutants. Among the down-regulated genes the most numerous are those encoding membrane proteins and enzymes involved in secondary metabolism, including the penicillin biosynthesis cluster. Genes coding for lysozyme are down-regulated too. As secondary metabolites often inhibit growth of other organisms, lowered expression of genes responsible for their synthesis suggests a decreased response to biotic stress in the mutants studied. Comparison of transcriptomes of the filamentous fungus Aspergillus nidulans strains bearing mutations in the cysB, sconB or sconC genes, affecting sulfur metabolism in different ways, with that of the wild type (WT) strain. Three biological replicates of WT vs cysB and WT vs sconC comparisons were performed and four biological replicates of WT vs sconB comparison were done. Each biological replicate had two technical replicates with dye swapping. A total of twenty individual hybridizations were made.

Project description:Mutations in the cysB, sconB and sconC genes affect sulfur metabolism in Aspergillus nidulans in different ways. Mutation of cysB blocks synthesis of cysteine by the main pathway leaving only the less effective alternative route. Mutations of sconB or sconC affect subunits of the SCF ubiquitin ligase complex, a negative controller of METR transcription factor, resulting in specific activation of a number of sulfur assimilation and metabolism genes, ultimately leading to elevated levels of cysteine and glutathione in scon mutants. We compared transcriptomes of these three mutants with that of a wild type strain finding that expression of a few hundred genes is altered at least twofold indicating a major reorganization of cellular metabolism. Despite the different effects of the cysB and scon mutations on sulfur metabolism they affect expression of overlapping sets of genes. We identified categories of the Functional Catalogue assigned to the differentially expressed genes and selected categories most enriched among the up- and down-regulated gene groups. Besides those involved in sulfur metabolism, many up-regulated genes are related to stress responses. The two-component signal transduction system is most enriched in genes up-regulated in the cysB, sconB and sconC mutants. This category contains histidine kinases that sense and transduce environmental signals to a cascade of protein kinases. Genes encoding heat shock proteins are also up-regulated, as are genes of the glutamate degradation pathway. The latter, also known as the GABA shunt, is induced by oxidative stress. A large group of up-regulated genes are involved in carbohydrate and energy metabolism, including genes coding for enzymes of trehalose and glycerol synthesis. Genes coding for enzymes of alcohol fermentation, which are induced in response to anaerobic stress, are also up-regulated in the mutants studied. The altered expression of the carbohydrate metabolism genes is accompanied by changes in sugar accumulation in mycelia and conidia of the mutants. Among the down-regulated genes the most numerous are those encoding membrane proteins and enzymes involved in secondary metabolism, including the penicillin biosynthesis cluster. Genes coding for lysozyme are down-regulated too. As secondary metabolites often inhibit growth of other organisms, lowered expression of genes responsible for their synthesis suggests a decreased response to biotic stress in the mutants studied.

			Action	DRS
	SRR18674367.fastq.gz	Fastqsanger.gz
	SRR18674368.fastq.gz	Fastqsanger.gz
	SRR18674369.fastq.gz	Fastqsanger.gz
	SRR18674370.fastq.gz	Fastqsanger.gz
	SRR18674371.fastq.gz	Fastqsanger.gz

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Transcriptome data on gene expression in Drosophila strains with deletions of sulfur metabolism genes: CBS and CSE

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