Journal of Molecular Evolution

, Volume 65, Issue 6, pp 687–696 | Cite as

Intragenomic 16S rDNA Divergence in Haloarcula marismortui Is an Adaptation to Different Temperatures

  • A. López-López
  • S. Benlloch
  • M. Bonfá
  • F. Rodríguez-Valera
  • A. Mira


The halophilic archaeon Haloarcula marismortui contains three ribosomal RNA operons, designated rrnA, rrnB, and rrnC. Operons A and C are virtually identical, whereas operon B presents a high divergence in nucleotide sequence, having up to 135 nucleotide polymorphisms among the three 16S, 23S, and 5S ribosomal RNA genes. Quantitative PCR and structural analyses have been performed to elucidate whether the presence of this intragenomic heterogeneity could be an adaptation to the variable environmental conditions in the natural habitat of H. marismortui. Variation in salt concentration did not affect expression but variation in incubation temperature did produce significant changes, with operon B displaying an expression level four times higher than the other two together at 50°C and three times lower at 15°C. We show that the putative promoter region of operon B is also different. In addition, the predicted secondary structure of these genes indicated that they have distinct stabilities at different temperatures and a mutant strain lacking operon B grew slower at high temperatures. This study supports the idea that divergent rRNA genes can be adaptive, with different variants being functional under different environmental conditions (e.g., temperature). The same phenomenon could take place in other halophiles or thermophiles with intragenomic rDNA heterogeneity, where the use of 16S rDNA as a phylogenetic marker and indicator of biodiversity should be used with caution.


Genome evolution Ribosomal operons Concerted evolution Thermal adaptation Extremophile Thermophile Paralogues Thermal stability Phylogenetic marker Real-time PCR 



This work was funded by the MIRACLE (EVK3-2002-00087) and GEMINI (QLK3-CT-2002-02056) projects of the European Commission. A.M. is funded by a Ramón y Cajal contract from the Ministry of Science and Technology and M.B. by Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES, Brazil). We thank P. B. Moore for kindly providing the mutant strains DT29, DT38, and DT41.


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Copyright information

© Springer Science+Business Media, LLC 2007

Authors and Affiliations

  • A. López-López
    • 1
    • 3
  • S. Benlloch
    • 2
  • M. Bonfá
    • 1
  • F. Rodríguez-Valera
    • 1
  • A. Mira
    • 1
  1. 1.Evolutionary Genomics Group, División de MicrobiologíaUniversidad Miguel HernándezSan Juan de AlicanteSpain
  2. 2.Unidad de InvestigaciónHospital General Universitario de AlicanteSan Juan de AlicanteSpain
  3. 3.Instituto Mediterraneo de Estudios AvanzadosCSICMallorcaSpain

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