Transcriptome analysis using RNA-Seq reveals complex acid responsive mechanisms in 3-hydroxypropionic aicd producing strains of E. coli

RNA-Seq analysis was conducted at different growth phases of the cell cycle as well as various fermentation conditions. The genes encoding RNA polymerase were down-regulated in SH0012 compared to its mother strain, suggesting reprogramming of cells for survival in new environments. The micro-aerobic fermentation caused down-regulation of transporter proteins and 3-HP non-producing fermentation caused up-regulation of phage shock proteins and lipoproteins. Additionally, the clustering analyses revealed that there is a mode of temporal regulation of biological pathways during organic acid production. RNA transcriptome profiling of 6 samples: SH0012 (20h), SH0012 (30h), SH0012 (40h), SH0012 (no rpm change), SH0012 (no vitamin B12), SH0003 (30h, control strain)