ABSTRACT: Transcriptional Landscape and Regulatory Roles of Small Noncoding RNAs in the Oxidative Stress Response of the Haloarchaeon Haloferax volcanii
Project description:We demonstrate here the transcriptional landscape and functional roles of sRNAs specifically in the regulation of the oxidative stress response of the model haloarchaeon Haloferax volcanii. We sequenced 5 biological replicates of H. volcanii strain H53 under no challenge and oxidative stress (H2O2) conditions at mid-exponential phase (OD 0.4). Thousands of sRNAs, both intergenic and antisense, were discovered using strand-specific sRNA-seq, comprising around 30% of the transcriptome during non-challenged and oxidative stress conditions. Antisense sRNAs were found to overlap both 5’ and 3’ UTRs of mRNAs revealing a hybrid system between Eukarya (3’ UTR) and Bacteria (5’ UTR) sRNA-silencing systems, as well as targeting the coding sequence (CDS) of mRNAs, a unique system to Archaea. We identified hundreds of differentially expressed sRNAs in response to hydrogen peroxide induced oxidative stress in H. volcanii. A majority of these sRNAs are lowly expressed compared to mRNAs. The sRNAs could be classified in two populations based on expression patterns: those that are up-regulated and those that are down-regulated during oxidative stress. Targets of antisense sRNAs decreased in expression when sRNAs were up-regulated indicating that sRNAs are likely playing a negative regulatory role on mRNA targets at the transcript level. Target enrichment of sRNAs included mRNAs involved in transposons, chemotaxis signaling, peptidase activity, transcription factors, and secondary metabolite regulation.
Project description:Genome-wide identification of transcriptional start sites in the haloarchaeon Haloferax volcanii based on differential RNA-Seq (dRNA-Seq)
Project description:Purpose: The Haloferax volcanii ∆tfeB strain provided a unique opportunity to study a putative role of TFEβ in the regulation of gene expression. Results: The deletion of the tfeB gene in H. volcanii results in the aberrant expression of approximately one third of all genes, consistent with its function as a basal transcription initiation factor. Interestingly, tfeB deletion particularly affects foreign genes including a prophage region. Conclusions: Our results confirm the dual function of TFE as basal factor and regulator of transcription
Project description:Identification of global gene expression profiling when Haloferax volcanii H26 strain is grown in minimal medium supplemented with two nitrogen sources, 10 mM L-alanine and 10 mM ammonium chloride.
