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Journal of Bacteriology, May 2000, p. 2422-2427, Vol. 182, No. 9
0021-9193/00/$04.00+0
Copyright © 2000, American Society for Microbiology. All rights reserved.

Action of RNase II and Polynucleotide Phosphorylase against RNAs Containing Stem-Loops of Defined Structure

Catherine Spickler and George A. Mackie*

Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3

Received 11 January 2000/Accepted 16 February 2000

The 3'right-arrow5' exoribonucleases, RNase II and polynucleotide phosphorylase (PNPase), play an essential role in degrading fragments of mRNA generated by prior cleavages by endonucleases. We have assessed the ability of small RNA substrates containing defined stem-loop structures and variable 3' extensions to impede the exonucleolytic activity of these enzymes. We find that stem-loops containing five G-C base pairs do not block either enzyme; in contrast, more stable stem-loops of 7, 9, or 11 bp block the processive action of both enzymes. Under conditions where enzyme activity is limiting, both enzymes stall and dissociate from their substrates six to nine residues, on average, from the base of a stable stem-loop structure. Our data provide a clear mechanistic explanation for the previous observation that RNase II and PNPase behave as functionally redundant.

* Corresponding author. Mailing address: Department of Biochemistry & Molecular Biology, University of British Columbia, D.H. Copp Building, 2146 Health Sciences Mall, Vancouver, British Columbia, Canada V6T 1Z3. Phone: (604) 822-2792. Fax: (604) 822-5227. E-mail: gamackie{at}interchange.ubc.ca.

Journal of Bacteriology, May 2000, p. 2422-2427, Vol. 182, No. 9
0021-9193/00/$04.00+0
Copyright © 2000, American Society for Microbiology. All rights reserved.


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