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J. Bacteriol. doi:10.1128/JB.00559-07
Copyright (c) 2007, American Society for Microbiology and/or the Listed Authors/Institutions. All Rights Reserved.

Global analysis of mRNA decay in Halobacterium salinarum NRC-1 at single-gene resolution using DNA microarrays

Institut für Mikrobiologie und Molekularbiologie, Justus-Liebig-Universität, Heinrich-Buff-Ring 26-32, D-35392 Giessen, Germany; Institut für Molekulare Biowissenschaften, Biozentrum Niederursel, Johann Wolfgang Goethe-Universität, Max-von-Laue Str. 9, D-60438 Frankfurt, Germany

^* To whom correspondence should be addressed. Email: Gabriele.Klug{at}mikro.bio.uni-giessen.de.

	Abstract

RNA degradation is an important factor in the regulation of gene expression. It allows organisms to quickly respond to changing environmental conditions by adapting the expression of individual genes. The stability of individual mRNAs within an organism varies considerably, contributing to differential amounts of proteins expressed. In this study we used DNA microarrays to analyze mRNA degradation in exponentially growing cultures of the extremely halophilic euryarchaeon Halobacterium salinarum NRC-1 on a global level. We determined mRNA half-lives for 1717 open reading frames (ORFs), 620 of which are part of known or predicted operons. Under the tested conditions transcript stabilities ranged from 5 to over 18 min with 79% of the evaluated mRNAs showing half-lives between 8 and 12 min. The overall mean half-life was 10 min which is considerably longer than the ones found in the other prokaryotes investigated so far. As previously observed in Escherichia coli and Saccharomyces cerevisiae we could not detect a significant correlation between transcript length and transcript stability but there was a relationship between gene function and transcript stability. Genes that are known or predicted to be transcribed in operons exhibited similar mRNA half-lives.

These results provide first insight in mRNA turn-over in an euryarchaeon. Moreover our model organism Halobacterium salinarum NRC-1 is one of just two archaea sequenced to date, which are missing the core-subunits of the archaeal exosome. This complex orthologous to the RNA degrading exosome of eukarya is found in all other archaeal genomes sequenced so far.