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:We tested a number of rRNA removal methods (Illumina RiboZero Plus, NEBNext, NEB Core Depletion Set with custom probes, siTools Panarchaea, siTools RiboPool) on 4 model halophile species: Halobacterium salinarum, Haloferax volcanii, Haloferax meditteranei, Haloarcula hispanica). It was found that methods using custom probes (NEB Core Depletion set with HVO probes, siTools RiboPool with HVO probes) efficiently remove rRNA in species they are targeted to, and that Panarchaea efficiently removes rRNA in all 4 tested species.
Project description:Eukaryotic genomes typically consist of multiple (linear) chromosomes that are replicated from multiple origins. Several hypothetical scenarios have been proposed to account for the evolution of multi-origin/multi-chromosome genomes, which are encountered in modern eukaryotes and archaea. Here we report an example of the generation of a new chromosome in the halophilic archaeon Haloferax volcanii through one of these scenarios: acquisition of new replication origins and splitting of an ancestral chromosome into two replication-competent chromosomes. The multi-origin main chromosome has split into two genome elements via homologous recombination. The newly generated elements possess all the features of bona fide chromosomes. To our knowledge, the spontaneous generation of a new chromosome in prokaryotes without horizontal gene transfer has not been reported previously.
Project description:For microbial cells, an appropriate response to changing environmental conditions is critical for viability. Transcription regulatory proteins, or transcription factors (TFs) sense environmental signals to change gene expression. However, it remains unclear how TFs and their corresponding gene regulatory networks are selected for over evolutionary time scales. The function of TFs and how they evolve are particularly understudied in archaeal organisms. Here we identified, characterized, and compared the function of the RosR transcription factor across three related species of hypersaline adapted model archaea. RosR was previously characterized as a global regulator of gene expression during oxidative stress in the species Halobacterium salinarum (HsRosR). Here we use functional genomics and quantitative phenotyping to demonstrate that, despite strong conservation of HsRosR across species, its function diverges substantially. Surprisingly, RosR in Haloferax volcanii and Haloferax mediterranei regulates genes whose products function in motility and the outer membrane, leading to significant defects in motility when rosR is deleted. Given weak conservation and degeneration in the RosR cis-regulatory sequence across species, we hypothesize that the RosR regulatory network is easily rewired during evolution across related species of archaea.
Project description:Transcriptional profiling of Haloferax mediterranei DF50 and M-NM-^TdeoR2 with induction by fructose comparing with the strains without this induction. Goal was to explore the effect of induction by fructose on Haloferax mediterranei. Total RNA from the Haloferax mediterranei DF50 and M-NM-^TdeoR2 with or without induction by fructose were used to generate target cDNA, and then hybridized to Haloferax mediterranei genome array genechips, representing about 3800 genes.
