Skip Navigation

Nucleic Acids Research 2005 33(13):4016-4022; doi:10.1093/nar/gki714
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (722K) Freely available
Right arrow Screen PDF (336K) Freely available
Right arrow Supplementary Material
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (11)
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Khachane, A. N.
Right arrow Articles by dos Santos, V. A. P. M.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Khachane, A. N.
Right arrow Articles by dos Santos, V. A. P. M.
Related Collections
Right arrow Computational methods
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Published online 19 July 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oupjournals.org

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.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Syst BiolHome page
M. E. Siddall, F. M. Fontanella, S. C. Watson, S. Kvist, and C. Erseus
Barcoding Bamboozled by Bacteria: Convergence to Metazoan Mitochondrial Primer Targets by Marine Microbes
Syst Biol, July 6, 2009; (2009) syp033v1.
[Full Text] [PDF]

Home page
 Appl. Environ. Microbiol.Home page
H. Kimura, J.-I. Ishibashi, H. Masuda, K. Kato, and S. Hanada
Selective Phylogenetic Analysis Targeting 16S rRNA Genes of Hyperthermophilic Archaea in the Deep-Subsurface Hot Biosphere
Appl. Envir. Microbiol., April 1, 2007; 73(7): 2110 - 2117.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
A. N. Khachane, K. N. Timmis, and V. A. P. Martins dos Santos
Dynamics of Reductive Genome Evolution in Mitochondria and Obligate Intracellular Microbes
Mol. Biol. Evol., February 1, 2007; 24(2): 449 - 456.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
Z. J. Lu, D. H. Turner, and D. H. Mathews
A set of nearest neighbor parameters for predicting the enthalpy change of RNA secondary structure formation
Nucleic Acids Res., October 18, 2006; 34(17): 4912 - 4924.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.