Gene Expression Order Attributed to Genome Reduction and the Steady Cellular State in Escherichia coli

Transcriptomes not only reflect the growth status but also link to the genome in bacteria. To investigate if and how genome or cellular state changes contribute to the gene expression order, the growth profile-associated transcriptomes of an assortment of genetically differentiated Escherichia coli either exponentially growing under varied conditions or in response to environmental disturbance were analyzed. A total of 168 microarray data sets representing 56 transcriptome variations, were categorized by genome size (full length or reduced) and cellular state (steady or unsteady). At the genome-wide level, the power-law distribution of gene expression was found to be significantly disturbed by the genome size but not the cellular state. At the regulatory network level, more networks with improved coordination of growth rates were observed in genome reduction than at the steady state. At the single-gene level, both genome reduction and steady state increased the correlation of gene expression to growth rate, but the enriched gene categories with improved correlations were different. These findings not only illustrate the order of gene expression attributed to genome reduction and steady cellular state but also indicate that the accessory sequences acquired during genome evolution largely participated in the coordination of transcriptomes to growth fitness.