Widespread Use of the Glu-tRNAGln Transamidation Pathway among Bacteria

Abstract

The expression of the Rhizobium meliloti glutamyl-tRNA synthetase gene in Escherichia coli under the control of a trc promoter results in a toxic effect upon isopropyl-beta-D-thiogalactopyranoside induction, which is probably caused by a misacylation activity. To further investigate this unexpected result, we looked at the pathway of Gln-tRNAGln formation in R. meliloti. No glutaminyl-tRNA synthetase activity has been found in R. meliloti crude extract, but we detected a specific aminotransferase activity that changes Glu-tRNAGln to Gln-tRNAGln. Our results show that R. meliloti, a member of the alpha-subdivision of the purple bacteria, is the first Gram-negative bacteria reported to use a transamidation pathway for Gln-tRNAGln synthesis. A phylogenetic analysis of the contemporary glutamyl-tRNA synthetase and glutaminyl-tRNA synthetase amino acid sequences reveals that a close evolutionary relationship exists between R. meliloti and yeast mitochondrial glutamyl-tRNA synthetases, which is consistent with an origin of mitochondria in the alpha-subdivision of Gram-negative purple bacteria. A 256-amino acid open reading frame closely related to bacterial glutamyl-tRNA synthetases, which probably originates from a glutamyl-tRNA synthetase gene duplication, was found in the 4-min region of the E. coli chromosome. We suggest that this open reading frame is a relic of an ancient transamidation pathway that occurred in an E. coli ancestor before the horizontal transfer of a eukaryotic glutaminyl-tRNA synthetase (Lamour, V., Quevillon, S., Diriong, S., N'Guyen, V. C., Lipinski, M., and Mirande, M.(1994) Proc. Natl. Acad. Sci. U. S. A. 91, 8670-8674) and that it favored its stable acquisition. From these observations, a revisited model for the evolution of the contemporary glutamyl-tRNA synthetases and glutaminyl-tRNA synthetases that differs from the generally accepted model for the evolution of aminoacyl-tRNA synthetases is proposed.

Glu-tRNA Gln amidotransferase: A novel heterotrimeric enzyme required for correct decoding of glutamine codons during translation

“…Based on the limited sampling of a number of organisms, we predicted (4) that the transamidation route occurs only in Gram-positive eubacteria, organelles, and Archaea. While this is generally true, there are a number of exceptions: mitochondria of Leishmania tarentolae possess the direct acylation pathway (29), whereas Rhizobium shows Glu-AdT activity (30). In addition, genomics suggest the occurrence of the transamidation genes in M. catarrhalis and N. gonorrhoeae.…”

Coevolution of an aminoacyl-tRNA synthetase with its tRNA substrates

“…Many bacteria [e.g., Sinorhizobium meliloti (3) or Chlamydia trachomatis (20)] have a single ND-GluRS and tRNA Gln isoacceptor without the augmented D-helix. The GluRS2-type enzyme is adapted to recognize only tRNA Gln lacking the augmented D-helix, a tRNA species also recognized by the canonical GlnRS.…”

“…However, this is true only for eukarya and some bacteria. Most of the other bacterial organisms (2,3), all known archaea (4,5), and eukaryotic organelles (6) lack the AARS specific for glutamine. In addition, a canonical asparaginyl-tRNA synthetase is missing from many archaeal and bacterial genomes (7), whereas a canonical cysteinyl-tRNA synthetase is not distinguishable in some methanogenic archaea (8).…”

An aminoacyl-tRNA synthetase-like protein encoded by the Escherichia coli yadB gene glutamylates specifically tRNA Asp

“…A phylogenetic study of GluRSs and glutaminyl-tRNA synthetases (GlnRSs), aaRSs from class Ib (7), including E. coli ORF256, suggests that this ORF is related to bacterial nondiscriminating GluRSs (ND-GluRSs), such as those of Rhizobium meliloti (8). The ND-GluRSs present in organisms that lack the GlnRS gene, like archaea and most bacteria, glutamylate both tRNA Glu and tRNA Gln (8)(9)(10)(11). The Glu-tRNA Gln product is then converted into Gln-tRNA Gln by a tRNA-dependent amidotransferase (7,12).…”