Transcription profiling of butanol producer Clostridium beijerinckii NRRL B-598 using RNA-Seq
Abstract
Thinning supplies of natural resources increase attention to sustainable microbial production of bio-based fuels. The strain Clostridium beijerinckii NRRL B-598 is a relatively well-described butanol producer regarding its genotype and phenotype under various conditions. However, a link between these two levels, lying in the description of the gene regulation mechanisms, is missing for this strain, due to the lack of transcriptomic data. In this paper, we present a transcription profile of the strain over the whole fermentation using an RNA-Seq dataset covering six time-points with the current highest dynamic range among solventogenic clostridia. We investigated the accuracy of the genome sequence and particular genome elements, including pseudogenes and prophages. While some pseudogenes were highly expressed, all three identified prophages remained silent. Furthermore, we identified major changes in the transcriptional activity of genes using differential expression analysis between adjacent time-points. We identified functional groups of these significantly regulated genes and together with fermentation and cultivation kinetics captured using liquid chromatography and flow cytometry, we identified basic changes in the metabol...Continue Reading
References
Phages and the evolution of bacterial pathogens: from genomic rearrangements to lysogenic conversion
featureCounts: an efficient general purpose program for assigning sequence reads to genomic features
Complete genome sequence of Clostridium pasteurianum NRRL B-598, a non-type strain producing butanol
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