Comparative Transcriptome Analysis for Metabolic Engineering

Transcriptome profiling allows massively parallel analysis of the dynamic expression of all genes and captures the cell physiology and regulatory mechanism in a holistic manner. Compared to other “omic” techniques, transcriptome is more tractable and sensitive. Transcriptomics has profoundly promoted development and applications of metabolic engineering by analysis of cell metabolism at a system level. Our recent effort was performed on a comparative transcriptome profiling between a riboflavin-producing Bacillus subtilis strain RH33 and the wild-type strain B . subtilis 168 to rationally identify new targets for improving riboflavin production. This transcriptome analysis-guided method improved the riboflavin titer by 32 � 3 %. Herein, we describe the detailed experimental protocols for predicting new engineering targets using comparative transcriptome analysis.