Abstract 1517 Examining the effect of L-rhamnose metabolism on the transcriptome of Escherichia coli

Previous research in our lab has demonstrated that the metabolism of different sugars can alter the bacterial transcriptome to influence biofilm growth and composition. In this project, we seek to understand the effect of the sugar L-rhamnose on the transcriptome of E. coli str. PHL628. We cultivate swimming and biofilm cultures of E. coli str. PHL628, in both rich (LB) and minimal (M9) media, in glass flasks with glass wool. We incubate the flasks for 48 hours at different temperatures (28 °C and 37 °C), then harvest planktonic cells from the media and biofilm cells from the glass wool. Next, we extract and purify the RNA from these cells for transcriptomic analysis. Our lab has developed a bioinformatics workflow for quantifying, cleaning, aligning, and processing raw RNA-seq data - using this workflow, we are able to identify differentially regulated genes in planktonic and biofilm cells in the presence of L-rhamnose. Preliminary results collected with select genes using in-house qPCR suggest that the presence of L-rhamnose as the primary carbon source has a significant effect on the transcriptome of E. coli cells. For example, in rich media, we see that the presence of L-rhamnose inhibits the transcription of the gene csgA (involved in the formation and assembly of curli) by roughly 85% in planktonic cells at 28 °C, but increases the transcription of this gene by 920% in biofilm cells at the same temperature. We note significant correlation of upregulation of rhamnose transport and catabolism genes under all our experimental conditions where rhamnose is introduced, and differential gene expression of other catabolic and anabolic pathways. We expect that our results will shed light on the effect of L-rhamnose as an alternative source of carbon and energy for E. coli; as well as demonstrating how the metabolism of L-rhamnose influences E. coli biofilm formation and composition. We would like to thank Oberlin College, the Research Corporation for Science Advancement, and the National Science Foundation (MCB-2226953) for funding.