Nucleic Acids Research Advance Access originally published online on October 12, 2006
Nucleic Acids Research 2006 34(19):5695-5704; doi:10.1093/nar/gkl684
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Nucleic Acids Research, 2006, Vol. 34, No. 19 5695-5704
© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
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The majority of Escherichia coli mRNAs undergo post-transcriptional modification in exponentially growing cells
Department of Genetics, University of Georgia Athens, GA 30602, USA
*To whom correspondence should be addressed. Tel: +1 706 542 8000; Fax: +1 706 542 3910; Email: skushner{at}uga.edu
Received May 18, 2006. Revised September 5, 2006. Accepted September 6, 2006.
Polyadenylation of RNAs by poly(A) polymerase I (PAP I) in Escherichia coli plays a significant role in mRNA decay and general RNA quality control. However, many important features of this system, including the prevalence of polyadenylated mRNAs in the bacterium, are still poorly understood. By comparing the transcriptomes of wild-type and pcnB deletion strains using macroarray analysis, we demonstrate that >90% of E.coli open reading frames (ORFs) transcribed during exponential growth undergo some degree of polyadenylation by PAP I, either as full-length transcripts or decay intermediates. Detailed analysis of over 240 transcripts suggests that Rho-independent transcription terminators serve as polyadenylation signals. Conversely, mRNAs terminated in a Rho-dependent fashion are probably not substrates for PAP I, but can be modified by the addition of long polynucleotide tails through the biosynthetic activity of polynucleotide phosphorylase (PNPase). Furthermore, real-time PCR analysis indicates that the extent of polyadenylation of individual full-length transcripts such as lpp and ompA varies significantly in wild-type cells. The data presented here demonstrates that polyadenylation in E.coli occurs much more frequently than previously envisioned.
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