Functionality of tRNAs encoded in a mobile genetic element from an acidophilic bacterium

Abstract

<p>The genome of the acidophilic, bioleaching bacterium <i>Acidithiobacillus ferrooxidans</i>, strain ATCC 23270, contains 95 predicted tRNA genes. Thirty-six of these genes (all 20 species) are clustered within an actively excising integrative-conjugative element (ICEA<i>fe</i>1). We speculated that these tRNA genes might have a role in adapting the bacterial tRNA pool to the codon usage of ICEA<i>fe</i>1 genes. To answer this question, we performed theoretical calculations of the global tRNA adaptation index to the entire <i>A. ferrooxidans</i> genome with and without the ICEA<i>fe</i>1 encoded tRNA genes. Based on these calculations, we observed that tRNAs encoded in ICEA<i>fe</i>1 negatively contribute to adapt the tRNA pool to the codon use in <i>A. ferrooxidans.</i> Although some of the tRNAs encoded in ICE<i>Afe</i>1 are functional in aminoacylation or protein synthesis, we found that they are expressed at low levels. These findings, along with the identification of a tRNA-like RNA encoded in the same cluster, led us to speculate that tRNA genes encoded in the mobile genetic element ICEA<i>fe</i>1 might have acquired mutations that would result in either inactivation or the acquisition of new functions.</p