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J. Biol. Chem., Vol. 282, Issue 28, 20238-20244, July 13, 2007

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Initiation of decay of Bacillus subtilis trp leader RNA^*

From the Department of Pharmacology and Biological Chemistry, Mount Sinai School of Medicine of New York University, New York, New York 10029

Transcription termination in the leader region of the Bacillus subtilis trp operon is regulated by binding of the 11-mer TRAP complex to nascent trp RNA, which results in formation of a terminator structure. Rapid decay of trp leader RNA, which is required to release the TRAP complex and maintain a sufficient supply of free TRAP, is mediated by polynucleotide phosphorylase (PNPase). Using purified B. subtilis PNPase, we showed that, when TRAP was present, PNPase binding to the 3' end of trp leader RNA and PNPase digestion of trp leader RNA from the 3' end were inefficient. These results suggested that initiation of trp leader RNA may begin with an endonuclease cleavage upstream of the transcription terminator structure. Such cleavage was observed in vivo. Mutagenesis of nucleotides at the cleavage site abolished processing and resulted in a 4-fold increase in trp leader RNA half-life. This is the first mapping of a decay-initiating endonuclease cleavage site on a native B. subtilis RNA.

Received for publication, March 30, 2007 , and in revised form, May 15, 2007.

^* This work was supported by United States Public Health Service Grant GM48804 from the National Institutes of Health. The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

¹ To whom correspondence should be addressed: Box 1603, 1 Gustave L. Levy Place, New York, NY 10029-6574. Tel.: 212-241-5628; Fax: 212-996-7214; E-mail: david.bechhofer{at}mssm.edu.

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				G. Deikus, C. Condon, and D. H. Bechhofer Role of Bacillus subtilis RNase J1 Endonuclease and 5'-Exonuclease Activities in trp Leader RNA Turnover J. Biol. Chem., June 20, 2008; 283(25): 17158 - 17167. [Abstract] [Full Text] [PDF]