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Nucleic Acids Research 2005 33(13):4016-4022; doi:10.1093/nar/gki714
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Published online 19 July 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
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Article

Uracil content of 16S rRNA of thermophilic and psychrophilic prokaryotes correlates inversely with their optimal growth temperatures

Amit N. Khachane, Kenneth N. Timmis and Vítor A. P. Martins dos Santos*

Division of Microbiology, GBF—German Research Centre for Biotechnology Braunschweig, Germany

*To whom correspondence should be addressed at Division of Microbiology, GBF—German Research Centre for Biotechnology, Mascheroder Weg 1, D-38124 Braunschweig, Germany. Tel: +49(0) 531 6181 422; Fax: +49(0) 531 6181 411; Email: vds{at}gbf.de

Received April 29, 2005. Revised June 30, 2005. Accepted June 30, 2005.

We report here the finding of a highly significant inverse correlation of the uracil content of 16S rRNA and the optimum growth temperature (Topt) of cultured thermophilic and psychrophilic prokaryotes. This correlation was significantly different from the weaker correlations between the contents of other nucleotides and Topt. Analysis of the 16S rRNA secondary structure regions revealed a fall in the A:U base-pair content in step with the increase in Topt that was much steeper than that of mismatched base-pairs, which are thermodynamically less stable. These findings indicate that the 16S rRNA sequences of thermophiles and psychrophiles are under a strong thermo-adaptive pressure, and that structure–function constraints play a crucial role in determining their 16S rRNA nucleotide composition. The derived relationship between uracil content and Topt was used to develop an algorithm to predict the Topt values of uncultured prokaryotes lacking cultured close relatives and belonging to the phyla predominantly containing thermophiles. This algorithm may be useful in guiding the design of cultivation conditions for hitherto uncultured microbes.


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