Analysis of transcriptomes of the free-living \emph{Escherichia coli} K-12 MG1655 and their biofilms

A. D. Kaznadzey ; A. I. Dakhnovets ; T. A. Bessonova ; M. N. Tutukina

Matematičeskaâ biologiâ i bioinformatika, Tome 19 (2024) no. 2, pp. 646-657.

Résumé

Biofilm formation can lead to multiple problems – for example, biofilms formed by the pathogenic Escherichia coli strains cause chronic urinary tract infections and gastroenteritis that can hardly be treated with antibiotics. Despite obvious priority, the key regulators and signals leading to a switch of bacterial lifestyle from free-living to attachment and biofilm formation are still not fully known. Here, an analysis was made to compare transcriptomes of the E. coli K-12 MG1655 cells growing in standard laboratory conditions and in conditions close to that inside a host organism. It was shown that upon cell transition from the free-living lifestyle to biofilms a huge rearrangement of their carbon metabolism occurred, and a key role belonged to hexuronate metabolism. At the same time, 6S RNA SsrS was dramatically overexpressed. In the second part, differential expression of genes in the E. coli K-12 MG1655 cells growing in the biofilm-forming conditions upon deletion of the yjjM gene coding for one of hexuronate regulators, YjjM (LgoR), was analysed. During this work, an analysis pipeline was optimized to allow trimming of randomly attached adaptors. The data obtained clearly indicate that small regulatory RNAs, including SsrS, play a key role in the biofilm formation by E. coli K-12, along with the YjjM protein. It was also revealed that YjjM might regulate the processes of protein biosynthesis, mRNA stabilization and antiphage defense. These observations clearly need further investigation.