Evolutionary insights about bacterial GlxRS from whole genome analyses: is GluRS2 a chimera?

Abstract

BackgroundEvolutionary histories of glutamyl-tRNA synthetase (GluRS) and glutaminyl-tRNA synthetase (GlnRS) in bacteria are convoluted. After the divergence of eubacteria and eukarya, bacterial GluRS glutamylated both tRNAGln and tRNAGlu until GlnRS appeared by horizontal gene transfer (HGT) from eukaryotes or a duplicate copy of GluRS (GluRS2) that only glutamylates tRNAGln appeared. The current understanding is based on limited sequence data and not always compatible with available experimental results. In particular, the origin of GluRS2 is poorly understood.ResultsA large database of bacterial GluRS, GlnRS, tRNAGln and the trimeric aminoacyl-tRNA-dependent amidotransferase (gatCAB), constructed from whole genomes by functionally annotating and classifying these enzymes according to their mutual presence and absence in the genome, was analyzed. Phylogenetic analyses showed that the catalytic and the anticodon-binding domains of functional GluRS2 (as in Helicobacter pylori) were independently acquired from evolutionarily distant hosts by HGT. Non-functional GluRS2 (as in Thermotoga maritima), on the other hand, was found to contain an anticodon-binding domain appended to a gene-duplicated catalytic domain. Several genomes were found to possess both GluRS2 and GlnRS, even though they share the common function of aminoacylating tRNAGln. GlnRS was widely distributed among bacterial phyla and although phylogenetic analyses confirmed the origin of most bacterial GlnRS to be through a single HGT from eukarya, many GlnRS sequences also appeared with evolutionarily distant phyla in phylogenetic tree. A GlnRS pseudogene could be identified in Sorangium cellulosum.ConclusionsOur analysis broadens the current understanding of bacterial GlxRS evolution and highlights the idiosyncratic evolution of GluRS2. Specifically we show that: i) GluRS2 is a chimera of mismatching catalytic and anticodon-binding domains, ii) the appearance of GlnRS and GluRS2 in a single bacterial genome indicating that the evolutionary histories of the two enzymes are distinct, iii) GlnRS is more widespread in bacteria than is believed, iv) bacterial GlnRS appeared both by HGT from eukarya and intra-bacterial HGT, v) presence of GlnRS pseudogene shows that many bacteria could not retain the newly acquired eukaryal GlnRS. The functional annotation of GluRS, without recourse to experiments, performed in this work, demonstrates the inherent and unique advantages of using whole genome over isolated sequence databases.

Ancestral Reconstruction of a Pre-LUCA Aminoacyl-tRNA Synthetase Ancestor Supports the Late Addition of Trp to the Genetic Code

“…This is not without precedent, as a partial HGT within halobacterial LeuRS and GluRS has also been reported in previous analyses. In both cases, the recombined regions were also shown to be involved in tRNA recognition (Dasgupta and Basu 2014;Fang et al 2014).…”

Dispensability of zinc and the putative zinc-binding domain in bacterial glutamyl-tRNA synthetase

“…We have experimentally studied a number of Ec -GluRS pZBD -chimeric constructs, with and without a ZB-motif, to understand the functional role of Zn 2+ . In addition, as part of our ongoing work on sequence analysis of a large database of bacterial GluRS from whole genome sequences [ 14 ], we have examined the occurrence of pZBD and ZB-motifs in GluRS across different bacterial phyla in conjunction with analyses of available GluRS structures. We show that a number of extant bacterial GluRS lack a pZBD .…”

Preliminary X-ray crystallographic analysis of an engineered glutamyl-tRNA synthetase fromEscherichia coli

“…The core function of glutamyl-tRNA synthetase (GluRS) is to glutamylate tRNA Glu (Kern et al, 1979;Breton et al, 1986), but not all bacterial GluRS restrict their tRNA-glutamylation to only the cognate tRNA (tRNA Glu ) (Lapointe et al, 1986;Lamour et al, 1994;Dasgupta & Basu, 2014). In bacteria such as Escherichia coli and Thermus thermophilus that possess glutaminyl-tRNA synthetase (GlnRS), the cognate aminoacylating enzyme for tRNA Gln , GluRS exclusively glutamylates tRNA Glu (Kern et al, 1979;Dasgupta et al, 2009;Becker & Kern, 1998).…”

“…The diverse tRNA Glx specificities of bacterial GluRS call for structure-function correlation studies that will yield a clear understanding of the mechanisms that control the GluRS-tRNA Glx interaction in bacteria. Because the precise nature of the GluRS-tRNA Glx interaction in bacteria is phylum-specific (Dasgupta et al, 2012;Dasgupta & Basu, 2014), biochemical work performed on the GluRS-tRNA Glx interaction in a bacterium from one phylum may not be compatible with the GluRS structure from a bacterium belonging to a distant phylum.…”

“…In addition, crystal structures of GluRS from Burkholderia thailandensis (PDB entry 4g6z; Baugh et al, 2013) and Borrelia burgdorferi (PDB entry 4gri; T. E. Edwards and M. C. Clifton, unpublished work) are also available. Based on the occurrences of GlnRS in their genomes (Dasgupta & Basu, 2014), the GluRS in B. thailandensis (a GlnRScontaining bacterium) and B. burgdorferi (a GlnRS-lacking bacterium) are expected to be tRNA Gln -discriminatory and tRNA Glnnondiscriminatory, respectively. Figs.…”