Nucleic Acids Research Advance Access originally published online on October 25, 2006
Nucleic Acids Research 2006 34(20):5923-5931; doi:10.1093/nar/gkl763
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Nucleic Acids Research, 2006, Vol. 34, No. 20 5923-5931
© 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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RNA polyadenylation and degradation in different Archaea; roles of the exosome and RNase R
Department of Biology, Technion–Israel Institute of Technology Haifa 32000, Israel
*To whom correspondence should be addressed. Tel: +972 4 8293171; Fax: +972 4 8295587; Email: gadis{at}tx.technion.ac.il
Received July 18, 2006. Revised September 25, 2006. Accepted September 26, 2006.
Polyadenylation is a process common to almost all organisms. In eukaryotes, stable poly(A)-tails, important for mRNA stability and translation initiation, are added to the 3' ends of most mRNAs. Contrarily, polyadenylation can stimulate RNA degradation, a phenomenon witnessed in prokaryotes, organelles and recently, for nucleus-encoded RNA as well. Polyadenylation takes place in hyperthermophilic archaea and is mediated by the archaeal exosome, but no RNA polyadenylation was detected in halophiles. Here, we analyzed polyadenylation in the third archaea group, the methanogens, in which some members contain genes encoding the exosome but others lack these genes. Polyadenylation was found in the methanogen, Methanopyrus kandleri, containing the exosome genes, but not in members which lack these genes. To explore how RNA is degraded in the absence of the exosome and without polyadenylation, we searched for the exoribonuclease that is involved in this process. No homologous proteins for any other known exoribonuclease were detected in this group. However, the halophilic archaea contain a gene homologous to the exoribonuclease RNase R. This ribonuclease is not able to degrade structured RNA better than PNPase. RNase R, which appears to be the only exoribonucleases in Haloferax volcanii, was found to be essential for viability.
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