Effect of different N-terminal catalytic activity of RNase E compared to full-length 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 different enzymes such as RNA degradosome components in the post-transcriptional regulation. As the regulation as a whole RNA degradosome is complicated and might differ case by case, we would like to seperate the effect of catalytic activity of RNase E per se and the effect of RNA degradosome. On the other hand, the physiology of bacterial growth in liquid culture is different from that on swmming plate culture. In real growing enviromnent, in which E. coli grows in the gut of warm-blooded organism, is a condition more like in soft-agar system instead of liquid culture that commonly adapted in laboratory study. To study the regulatory role of RNase E per se and RNA degradosmoe in gene regualtion of soft-agar culture, we used two different length of N-terminal RNase E which give different catalytic acitvity and compared theire effect of the transcriptome expressional level of strain with full-length RNase E.Here we found different groups of transcript that was regulated by merely RNase E catalytic acitivity, effect of RNA degradosome, or both. 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 separate the effect of RNA degradosome (which assemble on the C-terminal part of RNase E), we compared RNase E C-terminal deletion strain with plasmid ectopically expressing full-length RNase E to that expressing only N-termianl of RNase E protein. To further differentiate whether RNase E catalytic activity also have regulatory role on individual transcript, we compare the effect of Rne600 (encodes 1-599 aa of N-terminal RNase E, have membrane binding domain and has higher catalytic activity) to that of Rne500 (encodes 1-499 aa of N-terminal RNase E, does not have membrane binding domain and has lower catalytic activity). RNA samples were isolated from bacterial culture grown on 0.35% soft-agar LB plate after 24 h incubation.