IDENTIFICATION OF PREFERENTIALLY EXPRESSED GENES IN ESCHERICHIA COLI CULTURES IN LATE STATIONARY PHASE

Abstract

<p><em>Escherichia coli </em>cells undergo many morphological and physiological changes to survive in late stationary phase due, in part, to the exhaustion of nutrients and accumulation of inhibitory metabolites. Previous microarray data in our lab provided the general profile of gene expression from exponential phase to 48 h of incubation. The goal of this study is to use qPCR to validate the preferentially expressed genes in late stationary phase determined by the microarray data. The expression of three genes (<em>hha, tomB </em>and <em>emrK</em>) with increased expression levels from 24 h to 48 h of incubation and another two RpoS-dependent genes (<em>bolA</em> and <em>osmY</em>) with decreased expression from 24 h to 48 h of incubation were chosen as the target genes. RNA was first extracted from exponential phase, early stationary phase, 24 h and 48 h bacterial cultures. Hot phenol-chloroform and a commercial kit were used to isolate RNA. All these methods recovered low RNA in late stationary phase. qPCR partly confirmed the previous microarray data. The expression of <em>hha</em>, <em>tomB</em> and <em>emrK</em> was validated to increase from 24 h to 48 h of incubation. The discordant results between qPCR and microarray data may be due to the low transcript abundance of target genes and genomic DNA contamination in RNA extracted from 48 h bacterial cultures.</p>