Arginine-rich RNA binding domain and protein scaffold domain of RNase E are important for degradation of RNAI but not for that of the Rep mRNA of the ColE2 plasmid.

Expression of the replication initiator protein (Rep) of the ColE2 plasmid is controlled by antisense RNA (RNAI). Therefore alterations in processes and/or rates of degradation of these two RNAs would affect the Rep expression. Here, we have shown that the arginine-rich RNA binding domain (ARRBD) of RNase E is important for the initial endoribonucleolytic cleavage of RNAI but dispensable for the endoribonucleolytic cleavages of the Rep mRNA. We have also shown that the protein scaffold domain of RNase E is important for successive exoribonucleolytic degradation of RNAI, suggesting involvement of RhlB, but dispensable for that of the Rep mRNA. Such differences in the initiation and successive steps of degradation between RNAI and the Rep mRNA might be important in determining their individual degradation efficiencies required for a quick response to the changes in the plasmid copy number.

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