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The Bacillus subtilis and Bacillus halodurans Aspartyl-tRNA Synthetases Retain Recognition of tRNAAsn

Nair, Nilendra, Raff, Hannah, Islam, Mohammed Tarek, Feen, Melanie, Garofalo, Denise M., Sheppard, Kelly
Journal of Molecular Biology 2016 v.428 pp. 618-630
Bacillus halodurans, Bacillus subtilis, aspartate-tRNA ligase, bacteria, biosynthesis, genes, genetic code, phylogeny, transfer RNA
Synthesis of asparaginyl-tRNA (Asn-tRNAAsn) in bacteria can be formed either by directly ligating Asn to tRNAAsn using an asparaginyl-tRNA synthetase (AsnRS) or by synthesizing Asn on the tRNA. In the latter two-step indirect pathway, a non-discriminating aspartyl-tRNA synthetase (ND-AspRS) attaches Asp to tRNAAsn and the amidotransferase GatCAB transamidates the Asp to Asn on the tRNA. GatCAB can be similarly used for Gln-tRNAGln formation. Most bacteria are predicted to use only one route for Asn-tRNAAsn formation. Given that Bacillus halodurans and Bacillus subtilis encode AsnRS for Asn-tRNAAsn formation and Asn synthetases to synthesize Asn and GatCAB for Gln-tRNAGln synthesis, their AspRS enzymes were thought to be specific for tRNAAsp. However, we demonstrate that the AspRSs are non-discriminating and can be used with GatCAB to synthesize Asn. The results explain why B. subtilis with its Asn synthetase genes knocked out is still an Asn prototroph. Our phylogenetic analysis suggests that this may be common among Firmicutes and 30% of all bacteria. In addition, the phylogeny revealed that discrimination toward tRNAAsp by AspRS has evolved independently multiple times. The retention of the indirect pathway in B. subtilis and B. halodurans likely reflects the ancient link between Asn biosynthesis and its use in translation that enabled Asn to be added to the genetic code.