RNA-seq transcriptome data could help identify strong promoters useful for biotechnology

Strong promoters are typically favoured to help drive the expression of genes in biotechnology applications such as metabolic engineering and biocatalysis. But, how do we find them? One possible approach lies in the use of RNA-seq transcriptome data. Specifically, highly expressed genes profiled in RNA-seq would likely have a strong promoter driving high gene expression activity. The converse may not be true as some genes are not expressed under particular conditions. Although RNA-seq transcriptome data could suggest strong promoters for use in biotechnology, experimental characterization remains necessary to gain a better understanding of the promoter such as its regulatory mode. For example, given the prevalence of genes encapsulated in the glucose regulon, presence of glucose-dependent carbon catabolite repression effect on the promoter needs to be characterized as mixed substrate fermentation involving glucose is gaining importance in biotechnology. In this respect, glucose-dependent carbon catabolite repression would result in repression of transcriptional activity on the promoter, leading to poor gene transcription and expression. Finally, it is important to note that promoters profiled by RNA-seq transcriptome are likely to be useful in the species of origin and cannot be easily transferred to another species such as the synthetic T7 promoter. Collectively, strong promoters are frequently needed in biotechnology to drive high expression of genes, but the field of biocatalysis and metabolic engineering still relies on a few well-characterized strong synthetic promoters such as T7 promoter. RNA-seq transcriptome of biotechnology workhorse such as Escherichia coli could open the path to identifying strong promoters as they are likely the ones driving high expression of genes. However, proper characterization of such promoters is necessary to identify those vulnerable to glucose-dependent carbon catabolite repression.