Project description:Sulfolobus acidocaldarius is an obligate aerobe that grows in hot and acidic environments. S. acidocaldarius have been reported to grow on a variety of organic compounds as carbon and energy sources. However, little is known about systemic elucidation of carbon utilization for biomass formation and energy metabolism in S. acidocaldarius. In this analysis, the effect of glucose on genome-wide transcriptional profiling in S. acidocaldarius DSM 639 was investigated by RNA-Seq technology.
Project description:Analysis of transcriptional response to UV irradiation in two related crenarchaea, Sulfolobus solfataricus and Sulfolobus acidocaldarius.
Project description:To elucidate the glycerol catabolism in glycerol-adapted S. acidocaldarius MW00G the carbon source dependent global transcriptional response to glycerol compared to D-xylose the transcriptome was analyzed via RNA-Seq. Growth experiments with the S. acidocaldarius MW00G werewas performed in triplicates at 76°C and 120 rpm under constant shaking using (Innova®44, (New Brunswick, Germany) in the presence 10 mM glycerol, 20 mM glycerol or 40 mM glycerol as sole carbon and energy source. For comparison the same strain was cultivated with 0.2 % (w/v) D-xylose. RNA isolation, library preparation, and next-generation cDNA sequencing RNA was isolated using Zymo Direct-zol RNA Miniprep kit following manufactures instructions. The RNA quality was checked by Trinean Xpose (Gentbrugge, Belgium) and the Agilent RNA Nano 6000 kit using an Agilent 2100 Bioanalyzer (Agilent Technologies, Böblingen, Germany). Pan-Archaea riboPOOL kit from siTOOLs Biotech was used to remove the rRNA. TruSeq Stranded mRNA Library Prep Kit from Illumina was applied to prepare the cDNA libraries. The cDNAs were sequenced paired end on an Illumina NextSeq 500 system (San Diego, CA, USA) using 74 bp read length mid output. The paired-end cDNA reads were mapped to the Sulfolobus acidocaldarius DSM 639/MW001 genome sequence (accession number CP000077.1) using bowtie2 v2.2.7. with default settings for paired-end read mapping. All mapped sequence data were converted from SAM to BAM format with SAMtools v1.3 and imported to the software ReadXplorer v.2.2.
