Genome-wide comparison of two RNA-stabilizing reagents for transcriptional profiling of peripheral blood

Abstract

AbstractBackgroundClostridium beijerinckiiis a prominent solvent-producing microbe that has great potential for biofuel and chemical industries. Although transcriptional analysis is essential to understand gene functions and regulation and thus elucidate proper strategies for further strain improvement, limited information is available on the genome-wide transcriptional analysis forC. beijerinckii.ResultsThe genome-wide transcriptional dynamics ofC. beijerinckiiNCIMB 8052 over a batch fermentation process was investigated using high-throughput RNA-Seq technology. The gene expression profiles indicated that the glycolysis genes were highly expressed throughout the fermentation, with comparatively more active expression during acidogenesis phase. The expression of acid formation genes was down-regulated at the onset of solvent formation, in accordance with the metabolic pathway shift from acidogenesis to solventogenesis. The acetone formation gene (adc), as a part of thesoloperon, exhibited highly-coordinated expression with the othersolgenes. Out of the > 20 genes encoding alcohol dehydrogenase inC. beijerinckii, Cbei_1722 and Cbei_2181 were highly up-regulated at the onset of solventogenesis, corresponding to their key roles in primary alcohol production. Most sporulation genes inC. beijerinckii8052 demonstrated similar temporal expression patterns to those observed inB. subtilisandC. acetobutylicum, while sporulation sigma factor genessigEandsigGexhibited accelerated and stronger expression inC. beijerinckii8052, which is consistent with the more rapid forespore and endspore development in this strain. Global expression patterns for specific gene functional classes were examined using self-organizing map analysis. The genes associated with specific functional classes demonstrated global expression profiles corresponding to the cell physiological variation and metabolic pathway switch.ConclusionsThe results from this work provided insights for furtherC. beijerinckiistrain improvement employing system biology-based strategies and metabolic engineering approaches.