Transcriptome Analysis of Germinating Cyst-Like Dormant Cells of Escherichia coli K-12

The transcriptome of Escherichia coli cells germinated from the dormant forms of this bacterium (cyst-like cells, CLCs) was investigated for the first time. Upon E. coli CLC germination, the specific RNA content increased 129-fold, from 0.26 to 33 fg/cell, i.e., it became 9.5 times higher than in a cell of an exponentially growing culture (3.5 fg/cell). This is consistent with the hypothesis of “transcriptional bursting” that enables the bacteria to rapidly test (“explore”) a new environment. The complete gene reading (expression) pools of germinating CLCs were characterized. Based on these data, their differential expression was estimated using the calculation algorithm that takes account of the average mRNA amount in a single cell. It was revealed that 4042 out of 4102 genes (98.5% of the genome) increased their activity at least twofold upon E. coli CLC germination, with the activity of 105 genes increasing at least 1000-fold. These genes have been suggested to perform important functions in the germination process. They include the genes responsible for membrane receptors and transport systems; for the membrane structure; insertases; metabolic enzymes and protein synthesis systems; toxin/antitoxin systems; as well as for DNA replication, recombination, and repair. This work introduces, for the first time, the notion of genes active in each cell of the population. Our calculations demonstrate that not every gene contained in the transcript pool of the whole population produces transcripts in each cell within the population. Each cell of the dormant and germinating E. coli populations contains the transcripts of 21 and 14% of the genes, respectively, which reflects the heterogeneity (biodiversity) of population cells with respect to this trait.