Coevolution of an Aminoacyl-tRNA Synthetase with Its tRNA Substrates

• Published in: Proceedings of the National Academy of Sciences - PNAS 2003-11, Vol.100 (24), p.13863-13868
• Main Authors: Salazar, Juan C., Ahel, Ivan, Orellana, Omar, Tumbula-Hansen, Debra, Krieger, Robert, Daniels, Lacy, Söll, Dieter
• Format: Article
• Language: English
• Subjects: Acidithiobacillus - enzymology; Acidithiobacillus - genetics; Acidithiobacillus ferrooxidans; Amino acids; Amino Acyl-tRNA Synthetases - genetics; Amino Acyl-tRNA Synthetases - metabolism; Bacteria; Base Sequence; Biochemistry; Biological Sciences; DNA; Enzyme substrates; Enzymes; Evolution, Molecular; Gels; Gene Duplication; Gene Transfer, Horizontal; Genes, Bacterial; Genomes; Helicobacter pylori; Helicobacter pylori - enzymology; Helicobacter pylori - genetics; Molecular Sequence Data; Nucleic Acid Conformation; Nucleotides; Phylogeny; Ribonucleic acid; RNA; RNA, Bacterial - chemistry; RNA, Bacterial - genetics; RNA, Bacterial - metabolism; RNA, Transfer, Gln - chemistry; RNA, Transfer, Gln - genetics; RNA, Transfer, Gln - metabolism; RNA, Transfer, Glu - chemistry; RNA, Transfer, Glu - genetics; RNA, Transfer, Glu - metabolism; Substrate Specificity; Transfer RNA; tRNA Gln; tRNA Glu
• ISSN: 0027-8424; 1091-6490
• DOI: 10.1073/pnas.1936123100

Glutamyl-tRNA synthetases (GluRSs) occur in two types, the discriminating and the nondiscriminating enzymes. They differ in their choice of substrates and use either tRNAGluor both tRNAGluand tRNAGln. Although most organisms encode only one GluRS, a number of bacteria encode two different GluRS proteins; yet, the tRNA specificity of these enzymes and the reason for such gene duplications are unknown. A database search revealed duplicated GluRS genes in >20 bacterial species, suggesting that this phenomenon is not unusual in the bacterial domain. To determine the tRNA preferences of GluRS, we chose the duplicated enzyme sets from Helicobacter pylori and Acidithiobacillus ferrooxidans. H. pylori contains one tRNAGluand one tRNAGluspecies, whereas A. ferrooxidans possesses two of each. We show that the duplicated GluRS proteins are enzyme pairs with complementary tRNA specificities. The H. pylori GluRS1 acylated only tRNAGlu, whereas GluRS2 was specific solely for tRNAGln. The A. ferrooxidans GluRS2 preferentially charged TRNAUUG Gln. Conversely, A. ferrooxidans GluRS1 glutamylated both tRNAGluisoacceptors and the tRNACUG Glnspecies. These three tRNA species have two structural elements in common, the augmented D-helix and a deletion of nucleotide 47. It appears that the discriminating or nondiscriminating natures of different GluRS enzymes have been derived by the coevolution of protein and tRNA structure. The coexistence of the two GluRS enzymes in one organism may lay the groundwork for the acquisition of the canonical glutaminyl-tRNA synthetase by lateral gene transfer from eukaryotes.