Environmental shaping of ribosomal RNA nucleotide composition

Ribosomal RNA (rRNA) is one of the most important macromolecules in the cell. It is well established that high-temperature environmental conditions destabilize rRNA, leading to a selection for G+C-rich stabilizing structures. Our knowledge about the nucleotide composition effect of other environmental conditions, however, is limited. In the present work, I addressed this by correlating the rRNA nucleotide composition to known environmental habitats for bacteria. The bacterial phyla Firmicutes, Actinobacteria, and Proteobacteria were chosen for in-depth analyses due to the abundance of information available in the databases. Major differences in nucleotide composition were identified between these phyla. In addition to the G+C-->A+T gradients, a main gradient of G+A-->C+T was identified for Firmicutes, while a G+T-->A+C gradient was identified for Actinobacteria. With respect to correlation to environmental conditions, the Firmicutes showed a main structure of high G+C being correlated to thermophilic conditions, high A+T to anaerobic conditions, and high C+T to halophilic conditions. The main patterns detected for Firmicutes can be explained by structural stability for high G+C, chemical instability of G under aerobic conditions, and structural stability by purine/pyrimidine skew for halophilic conditions. On the contrary, the correlations for Actinobacteria cannot easily be explained by chemical and/or structural stability. This may indicate interference with factors not included in my work. Finally, I found a main correlation between high A+T and endosymbiosis for Proteobacteria. High A+T probably reflects adaptation to cell internal growth. Further support for environmentally driven nucleotide composition shaping was found and that polyphyletic bacteria were associated with the same environment/nucleotide correlations. My conclusion is that environmental conditions and habitats have a major effect on rRNA nucleotide composition but that the effects may differ between the bacterial phyla.