The impact of RNase E C-terminal truncation mutant compared with wildtype RNase E on whole transcriptome expression profile of E. coli soft-agar plate culture

RNase E is involved in the post-transcriptional gene regulation of a broad spectrom of RNA species involving in different biological processes. Frequently RNase E cooperates with other protein components to form a RNA degradosome to regulate gene expression. Here, we aim to study the impact of RNA degradosome formation on E. coli gene expression by comparing the whole transcriptiome isolate from wildtype Rne strain and Rne C-terminal truncated strain that deleting the RNA degradosome binding domain. We choose to study the bacterial growth conditions in soft-agar culture because it is a condition more silimar to that in the gut of warm-blooded organism compared to merely liquid culture condition.Here we found different groups of transcript that was affected by Rne C-termianl truncation mutant. Altogether, our data give insight into the complex regulation of RNase E/RNA degradosome in transcripts involved in different biological processes of soft-agar growing system. Overall design: To understand the impact of RNase E on gene expression, we compared wildtype strain MG1655 with RNase E C-terminal deletion strain Rned500. RNA samples were isolated from bacterial culture grown on 0.35% soft-agar LB plate after 24 h incubation.