PRJNA273734
Mapping the Clostridium acetobutylicum transcriptome under butanol and butyrate stresses using strand-specific RNA-seq data
The C. acetobutylicum genome annotation cab me markedly improved by integrating bioinformatic predictions with Illumina-based strand-specific deep RNA sequencing (RNA-seq) data. Samples were acquired under low, medium and high butanol or butyrate stress, with unstressed conditions as control, across exponential and transition-phase time points to assess the cell’s transcriptome as it responds to metabolite stress in various physiological states represented by the aforementioned culture conditions. Reference assembly and curation were used to identify transcript boundaries, operon organization, and regulatory regions. This combined approach minimized false positive errors from the highly sensitive sequencing technique. Transcript boundaries from several canonical transcripts were determined to the exact base pair. This dataset was used to generate the first strand-specific transcriptome assembly in a Clostridium organism. The data were also used for comparative analysis against corresponding proteome data in order to assess more complex regulation of genes and programs involving post-transcriptional regulation.