title: The Bacillus subtilis and Bacillus halodurans Aspartyl-tRNA Synthetases Retain Recognition of tRNA(Asn).
abstract: Synthesis of asparaginyl-tRNA (Asn-tRNA(Asn)) in bacteria can be formed either by directly ligating Asn to tRNA(Asn) 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 tRNA(Asn) and the amidotransferase GatCAB transamidates the Asp to Asn on the tRNA. GatCAB can be similarly used for Gln-tRNA(Gln) formation. Most bacteria are predicted to use only one route for Asn-tRNA(Asn) formation. Given that Bacillus halodurans and Bacillus subtilis encode AsnRS for Asn-tRNA(Asn) formation and Asn synthetases to synthesize Asn and GatCAB for Gln-tRNA(Gln) synthesis, their AspRS enzymes were thought to be specific for tRNA(Asp). 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 tRNA(Asp) 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.
authors.affiliation: Chemistry Department, Skidmore College, Saratoga Springs, NY 12866, USA.
authors.forename: Nilendra
authors.initials: N
authors.lastname: Nair
authors.affiliation: Chemistry Department, Skidmore College, Saratoga Springs, NY 12866, USA.
authors.forename: Hannah
authors.initials: H
authors.lastname: Raff
authors.affiliation: Chemistry Department, Skidmore College, Saratoga Springs, NY 12866, USA.
authors.forename: Mohammed Tarek
authors.initials: MT
authors.lastname: Islam
authors.affiliation: Chemistry Department, Skidmore College, Saratoga Springs, NY 12866, USA.
authors.forename: Melanie
authors.initials: M
authors.lastname: Feen
authors.affiliation: Chemistry Department, Skidmore College, Saratoga Springs, NY 12866, USA.
authors.forename: Denise M
authors.initials: DM
authors.lastname: Garofalo
authors.affiliation: Chemistry Department, Skidmore College, Saratoga Springs, NY 12866, USA. Electronic address: ksheppar@skidmore.edu.
authors.forename: Kelly
authors.initials: K
authors.lastname: Sheppard
mesh_terms: D001216:Asparagine / Q000378:metabolism*; D001226:Aspartate-tRNA Ligase / Q000378:metabolism*; D001407:Bacillus / Q000201:enzymology* / Q000378:metabolism; D001412:Bacillus subtilis / Q000201:enzymology / Q000378:metabolism; D012346:RNA, Transfer, Amino Acyl / Q000378:metabolism*; D012348:RNA, Transfer, Asn / Q000378:metabolism*; D013379:Substrate Specificity
chemical_list: D012346:RNA, Transfer, Amino Acyl; D012348:RNA, Transfer, Asn; D001216:Asparagine; D001226:Aspartate-tRNA Ligase; C029194:asparaginyl-tRNA synthetase
keywords: AspRS; GatCAB; asparagine biosynthesis; tRNA-dependent biosynthesis