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Journal of Bacteriology, October 2009, p. 6157-6166, Vol. 191, No. 19
0021-9193/09/$08.00+0     doi:10.1128/JB.00699-09
Copyright © 2009, American Society for Microbiology. All Rights Reserved.

Significant Bias against the ACA Triplet in the tmRNA Sequence of Escherichia coli K-12 {triangledown} ,{dagger}

Sarah Baik,1,{ddagger} Koichi Inoue,1,{ddagger} Ming Ouyang,2 and Masayori Inouye1*

Department of Biochemistry, Robert Wood Johnson Medical School, 675 Hoes Lane, Piscataway, New Jersey 08854,1 Computer Engineering and Computer Science Department, University of Louisville, Louisville, Kentucky 402922

Received 28 May 2009/ Accepted 21 July 2009

The toxin MazF in Escherichia coli cleaves single-stranded RNAs specifically at ACA sequences. MazF overexpression virtually eliminates all cellular mRNAs to completely block protein synthesis. However, protein synthesis can continue on an mRNA that is devoid of ACA triplets. The finding that ribosomal RNAs remain intact in the face of complete translation arrest suggested a purpose for such preservation. We therefore examined the sequences of all transcribed RNAs to determine if there was any statistically significant bias against ACA. While ACA motifs are absent from tmRNA, 4.5S RNA, and seven of the eight 5S rRNAs, statistical analysis revealed that only for tmRNA was the absence nonrandom. The introduction of single-strand ACAs makes tmRNA highly susceptible to MazF cleavage. Furthermore, analysis of tmRNA sequences from 442 bacteria showed that the discrimination against ACA in tmRNAs was seen mostly in enterobacteria. We propose that the unusual bias against ACA in tmRNA may have coevolved with the acquisition of MazF.

* Corresponding author. Mailing address: Department of Biochemistry, Robert Wood Johnson Medical School, 675 Hoes Lane, Piscataway, NJ 08854. Phone: (732) 235-4115. Fax: (732) 235-4559. E-mail: inouye{at}umdnj.edu

{triangledown} Published ahead of print on 24 July 2009.

{dagger} Supplemental material for this article may be found at http://jb.asm.org/.

{ddagger} S.B. and K.I. contributed equally to the work.

Journal of Bacteriology, October 2009, p. 6157-6166, Vol. 191, No. 19
0021-9193/09/$08.00+0     doi:10.1128/JB.00699-09
Copyright © 2009, American Society for Microbiology. All Rights Reserved.





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