Horizontal transfer of drug-resistant aminoacyl-transfer-RNA synthetases of anthrax and Gram-positive pathogens

Abstract

The screening of new antibiotics against several bacterial strains often reveals unexpected occurrences of natural drug resistance. Two examples of this involve specific inhibitors of Staphylococcus aureus isoleucyl-transfer-RNA synthetase 1 (IleRS1) and, more recently, Streptococcus pneumoniae methionyl-tRNA synthetase 1 (MetRS1). In both cases, resistance is due to the presence of a second gene that encodes another synthetase (IleRS2 or MetRS2). Here, we show that both S. pneumoniae MetRS2 and S. aureus IleRS2 have closely related homologues in the Gram-positive bacterium Bacillus anthracis, the causative agent of anthrax. Furthermore, similar to drug-resistant pathogens, strains of B. anthracis and its closest relative, B. cereus, also have wild-type ileS1 and metS1 genes. Clostridium perfringens, the causative agent of gangrene, also has two metS genes, whereas Oceanobacillus iheyensis isolated from deep-sea sediments has a single ileS2-type gene. This study shows the importance of understanding complex evolutionary networks of ancient horizontal gene transfer for the development of novel antibiotics.

Figure 1

Alignments of horizontally transferred aminoacyl-transfer-RNA synthetases from anthrax and Gram-positive cocci. (A) Isoleucyl-transefer-RNA synthetases (IleRS2s) from Bacillus anthracis (Baan_ileS2) and Staphylococcus aureus (Stau_ileS2), which is resistant to the antibiotic mupirocin. Identical residues are shaded. (B) Methionyl-tRNA synthetases (MetRS2s) from B. anthracis (Baan_metS2) and Streptococcus pneumoniae (Stpn_metS2), which is resistant to MetRS inhibitory compounds. Letters above the alignments indicate the positions of the HIGH and KMSKS signature motifs of class I tRNA synthetases.

Figure 2

Phylogeny of isoleucyl-transfer-RNA synthetase protein sequences. Those species with genes for both isoleucyl-transfer-RNA synthetase 1 (IleRS1) and IleRS2 (Staphylococcus aureus, Pseudomonas flurorescens, Bacillus anthracis and B. cereus) are indicated in light and dark blue, respectively. Eukaryotic (green), archaeal (red) and bacterial (black) species are also indicated. Trees were constructed using the neighbour-joining (NJ) method (http://evolution.genetics.washington.edu/phylip.html). Numbers along the branches show the percentage occurrence of nodes in 1,000 bootstrap replicates of NJ (numbers in plain text) and maximum parsimony (MP; italicized numbers) analyses (Swofford, 1999) or greater than 50% of 1,000 maximum likelihood (ML; Strimmer and von Hasseler, 1996) quartet puzzling steps (numbers in parentheses). Asterisks represent support for nodes in more than 70% of NJ and MP bootstrap replications and 60% of ML puzzling steps. Scale bar, 0.1 estimated amino-acid substitutions per site.

Figure 3

Phylogeny of methionyl-transfer-RNA synthetase protein sequences. Species with genes for both methionyl-transfer-RNA synthetase 1 (MetRS1) and MetRS2 (Streptococcus pneumoniae, Bacillus anthracis, B. cereus and Clostridium perfringens) are indicated (in light and dark blue, respectively). Phylogenetic-tree reconstruction methods and nomenclature are given in the legend to Fig. 2. For some eukaryotic species, mitochondria-targeted (mt.) or chloroplast-targeted (chl.) MetRS isoforms have been identified. Scale bar, 0.1 estimated amino-acid substitutions per site.