Independent component analysis of E. coli's transcriptome reveals the cellular processes which respond to heterologous gene expression

Heterologous gene expression to expand the native genetic capability of E. coli is the backbone of protein expression and metabolic engineering. The goal of this study was to determine how the identity of the heterologous gene expressed affected the host cell transcriptome. We generated a library of E. coli expressing 46 heterologous genes through an identical rhamnose inducible expression system and perform high throughput RNAseq as well as independent component analysis to elucidate the major variances in the transcriptome. We find that the major variations during heterologous gene expression can be divided into 5 main cellular responses: Fear vs greed, metal homeostasis, respiration, protein folding and amino acid and nucleotide metabolism. Overall design: RNAseq of 46 lines of heterologous gene expressing lines of E. coli using the same expression system