Poly(A)- and poly(U)-specific RNA 3' tail shortening by E. coli ribonuclease E

Area of Science:

• Molecular Biology
• Enzymology
• RNA Metabolism

Background:

• Ribonuclease E (RNase E) is a key enzyme in Escherichia coli.
• RNase E plays critical roles in rRNA processing, mRNA degradation, and plasmid replication.
• Its endoribonuclease activity on single-stranded RNA is well-established.

Purpose of the Study:

• To investigate previously undetected activities of RNase E.
• To characterize the enzyme's role in RNA tail processing.
• To elucidate RNase E's contribution to RNA decay control.

Main Methods:

• Biochemical assays to detect and characterize RNase E activity.
• Analysis of RNA processing and degradation products.
• Site-specific cleavage studies on RNA molecules with varying 3' tails.

Main Results:

• RNase E exhibits a novel activity: shortening of 3' poly(A) and poly(U) homopolymer tails on RNA.
• This tail shortening leaves specific remnant nucleotides (6-adenylate or 1-uridylate).
• The activity resides in the amino-terminal region and is independent of cofactors.
• A 3'-terminal phosphate group inhibits poly(A) tail removal and primary transcript cleavage.

Conclusions:

• RNase E possesses a previously unrecognized function in shortening 3' RNA homopolymer tails.
• The enzyme's ability to modify tail length is linked to its endonucleolytic cleavage activity.
• These findings suggest a novel mechanism for RNase E-mediated control over global RNA decay pathways.