Project description:Archaeal viruses display unusually high genetic and morphologic diversity. The Sulfolobus islandicus Rod Shaped Virus 2 (SIRV2) is a model to study virus-host interactions in Archaea. It is a lytic virus that exploits a unique egress mechanism based on formation of remarkable pyramidal structures on the host cell envelope. The hyperthermophilic Sulfolobus islandicus LAL14/1 is the natural host for SIRV2. RNA was isolated at 0,1,2,3,5,7 and 9 hours after SIRV2 infection of two S.islandicus cultures and analysed with whole transcriptome sequencing (RNAseq). As a control RNA was isolated at the same time points from two uninfected cultures.
Project description:Transcriptome sequencing was carried out on an Illumina HiSeq platform to investigate CRISPR-Cas and DNA repair systems by Csa3b in Sulfolobus islandicus Rey15A. We compared the differently expressed genes in Sulfolobus islandicus Rey15A strain with csa3a overexpression vs. Sulfolobus islandicus Rey15A strain carrying an empty expression vector,We find thatcmr-α (SiRe_0890 ~ SiRe_0895) and cmr-β (SiRe_0597 ~ SiRe_0603)、the DNA double strand break (DSB)repair genes, including nurA, rad50, mre11, and herA (SiRe_0061 ~ SiRe_0064), as well as two subunits of DNA polymerase II (SiRe_0615 and SiRe_0617) that function in DNA repair, were significantly up-regulated. Our data indicated that the Csa3b regulator couples transcriptional activation of cmr genes, DNA repair genes.
Project description:Transcriptome sequencing was carried out on an Illumina HiSeq platform to investigate the activation of CRISPR-Cas and DNA repair systems by Csa3a in Sulfolobus islandicus Rey15A. We compared the differently expressed genes in Sulfolobus islandicus Rey15A strain with csa3a overexpression vs. Sulfolobus islandicus Rey15A strain carrying an empty expression vector, cas1 deletion strain with csa3a overexpression vs. cas1 deletion strain carrying an empty expression vector, as well as interference-deficient strain with csa3a overexpression vs. interference-deficient strain carrying an empty expression vector. We find that cas genes (SiRe_0760, SiRe_0761, SiRe_0762, SiRe_0763), nucleotidyltransferase domain of DNA polymerase beta (SiRe_0459), chromosome segregation protein (SMC)-related ATPase (SiRe_0649), SMC-related protein (SiRe_1142) and three HerA helicases involved in DNA double break repair (encoded by SiRe_0064 and SiRe_0095 of nurA-herA operons, and SiRe_1857) were significantly up-regulated. Our data indicated that the Csa3a regulator couples transcriptional activation of spacer acquisition genes, CRISPR RNA transcription, DNA repair and genome stability genes.
Project description:A whole transcriptome study was performed on Sulfolobus islandicus REY15A actively undergoing CRISPR spacer acquisition from the crenarchaeal monocaudavirus STSV2 in rich (TYS) and basal (SCV) media over a 6 day period. Spacer acquisition preceded strong host growth retardation, and changes in viral transcript abundance and virus copy numbers showed significant differences between the two media. Results showed that rich medium favoured CRISPR-Cas immunity generation.
Project description:Analysis of transcriptional response to UV irradiation in two related crenarchaea, Sulfolobus solfataricus and Sulfolobus acidocaldarius.
Project description:This is ChIPseq result of FadR, which is the only TetR family regulator presented in Sulfolobus acidocaldarius. The aim of the study is to gain insights into the function of TetR regulator by analyzing its whole genome binding sites.
Project description:Sulfolobus solfataricus P2 was grown aerobically, with O2 concentrations ranging from 1.5 to 26 % (v/v; gas phase). To gain some insight in control of the respiratory system, transcriptomes of the strain cultivated in different O2 concentrations (1.5 % vs 21 %, 1.5 % vs 26 %) were compared using a DNA microarray approach.
Project description:The Leucine-responsive Regulatory Protein (Lrp) family is a widespread family of regulatory transcription factors in prokaryotes. BarR is an Lrp-like transcription factor in the model archaeon Sulfolobus acidocaldarius that activates the expression of a -alanine aminotransferase gene, which is involved in -alanine degradation. In contrast to classical Lrp-like transcription factors, BarR is not responsive to any of the -amino acids but interacts specifically with -alanine. Besides the juxtaposed -alanine aminotransferase gene, other regulatory targets of BarR have not yet been identified although -alanine is the precursor of coenzyme A and thus an important central metabolite. The aim of this study is to extend the knowledge of the DNA-binding characteristics of BarR and of its corresponding regulon from a local to a genome-wide perspective.
Project description:Sulfolobus solfataricus P2 was grown aerobically, with O2 concentrations ranging from 1.5 to 26 % (v/v; gas phase). To gain some insight in control of the respiratory system, transcriptomes of the strain cultivated in different O2 concentrations (1.5 % vs 21 %, 1.5 % vs 26 %) were compared using a DNA microarray approach. Two-condition experiments: 1.5% O2 vs two other O2 concentrations (21 or 26% O2). Biological replicates independently grown. One replicate per array. Dye swaps.