Genome-wide dynamic transcriptional profiling in clostridium beijerinckii NCIMB 8052 using single-nucleotide resolution RNA-Seq

Abstract

BackgroundClostridium beijerinckii is 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 for C. beijerinckii.ResultsThe genome-wide transcriptional dynamics of C. beijerinckii NCIMB 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 the sol operon, exhibited highly-coordinated expression with the other sol genes. Out of the > 20 genes encoding alcohol dehydrogenase in C. 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 in C. beijerinckii 8052 demonstrated similar temporal expression patterns to those observed in B. subtilis and C. acetobutylicum, while sporulation sigma factor genes sigE and sigG exhibited accelerated and stronger expression in C. beijerinckii 8052, 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 further C. beijerinckii strain improvement employing system biology-based strategies and metabolic engineering approaches.

Development of a Gene Knockout System Using Mobile Group II Introns (Targetron) and Genetic Disruption of Acid Production Pathways in Clostridium beijerinckii

“…Turbo competent Escherichia coli cells (New England BioLabs Inc., Ipswich, MA) and TOP10 competent E. coli cells (Invitrogen, Grand Island, NY) were used for cloning and were grown aerobically at 37°C in LB medium supplemented with 100 g/ml of ampicillin or 50 g/ml of kanamycin as appropriate. C. beijerinckii 8052 was grown anaerobically at 35°C in tryptone-glucose-yeast extract (TGY) medium containing 30 g/liter of tryptone, 20 g/liter of glucose, 10 g/liter of yeast extract, and 1 g/liter of L-cysteine (20), supplemented with 25 g/ml of erythromycin as needed. All bacterial cultures, plasmids, and oligonucleotides used in this study are listed in Table S1 in the supplemental material.…”

Molecular Characterization of an NADPH-Dependent Acetoin Reductase/2,3-Butanediol Dehydrogenase from Clostridium beijerinckii NCIMB 8052

“…However, an acetoin dehydrogenase complex as found in C. magnum and B. subtilis is not present in C. beijerinckii. A recent genome-wide transcriptional analysis of C. beijerinckii by wholetranscriptome shotgun sequencing (RNA-Seq) technology revealed that CBEI_1464 is significantly expressed, especially during the solventogenic phase (51). This suggests that Cb-ACR might have a role in the formation of an alcohol.…”

Expression of different types of [FeFe]-hydrogenase genes in bacteria isolated from a population of a bio-hydrogen pilot-scale plant

“…Cbei_4110 was previously reported to be expressed in C. beijerinckii RZF-1108 [38] but surprisingly, in a recent genome-wide transcriptional analysis of C. beijerinckii NCIMB 8052, there is no mention of any hydrogenase genes expression levels [66].…”