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Journal of Bacteriology, November 1998, p. 5968-5977, Vol. 180, No. 22
0021-9193/98/$04.00+0
Copyright © 1998, American Society for Microbiology. All rights reserved.

Decay of ermC mRNA in a Polynucleotide Phosphorylase Mutant of Bacillus subtilis

David H. Bechhofer* and Wei Wang

Department of Biochemistry, Mount Sinai School of Medicine of the City University of New York, New York, New York 10029

Received 13 August 1998/Accepted 15 September 1998

ermC mRNA decay was examined in a mutant of Bacillus subtilis that has a deleted pnpA gene (coding for polynucleotide phosphorylase). 5'-proximal RNA fragments less than 400 nucleotides in length were abundant in the pnpA strain but barely detectable in the wild type. On the other hand, the patterns of 3'-proximal RNA fragments were similar in the wild-type and pnpA strains. Northern blot analysis with different probes showed that the 5' end of the decay intermediates was the native ermC 5' end. For one prominent ermC RNA fragment, in particular, it was shown that formation of its 3' end was directly related to the presence of a stalled ribosome. 5'-proximal decay intermediates were also detected for transcripts encoded by the yybF gene. These results suggest that PNPase activity, which may be less sensitive to structures or sequences that block exonucleolytic decay, is required for efficient decay of specific mRNA fragments. However, it was shown that even PNPase activity could be blocked in vivo at a particular RNA structure.

* Corresponding author. Mailing address: Department of Biochemistry, Mount Sinai School of Medicine of the City University of New York, New York, NY 10029. Phone: (212) 241-5628. Fax: (212) 996-7214. E-mail: dbechho{at}smtplink.mssm.edu.

Journal of Bacteriology, November 1998, p. 5968-5977, Vol. 180, No. 22
0021-9193/98/$04.00+0
Copyright © 1998, American Society for Microbiology. All rights reserved.


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