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Volume 272, Number 24, Issue of June 13, 1997 pp. 15516-15520
©1997 by The American Society for Biochemistry and Molecular Biology, Inc.

Processing of the rne Transcript by an RNase E-independent Amino Acid-dependent Mechanism

(Received for publication, November 27, 1996, and in revised form, March 8, 1997)

Wei-Meng Woo ^§ and Sue Lin-Chao

From the  Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, Taiwan 115 and the ^§ Institute of Biochemistry, National Yang-Ming University, Taipei, Taiwan 112, Republic of China

RNase E is encoded by the rne (also known as ams or hmp) gene and is the principal enzyme that controls the chemical decay of bulk mRNA in Escherichia coli. Earlier work has shown that RNase E degrades its own mRNA, autoregulating production of the RNase E protein. Here we show that in cells lacking RNase E activity, the 3.6-kilobase rne gene transcript is cleaved site specifically at two locations near its center by a novel endonuclease whose activity is modulated by the presence or absence of amino acids in the culture medium. These cleavages produce a 2-kilobase RNase E-sensitive RNA fragment corresponding to the 3 half of the transcript. Using primer extension and RNase protection analysis, we mapped RNase E-independent cleavages to sites 1558 and 1576 nucleotides from the 5 end of the rne transcript (coordinates 1738 and 1747 of the rne gene). Our results indicate the existence of a previously unknown RNase E-independent mechanism for degradation of rne transcripts and further demonstrate that this mechanism responds to changes in cell growth conditions.

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