The role of the catalytic domain of <i>E. coli</i> GluRS in tRNA<sup>Gln</sup> discrimination

Dasgupta, Saumya; Saha, Rajesh; Dey, C.C.; Banerjee, Rajat; Roy, Siddhartha; Basu, Gautam

doi:10.1016/j.febslet.2009.05.041

Cited by 12 publications

(27 citation statements)

References 33 publications

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“…However, according to this model different bacterial phyla acquired different GluRS (C) independently, which is a very unlikely event. A more realistic model is where GluRS (C) was appended to GluRS (N) before bacterial phylum-divergence but because the acquired GluRS (C) was non-functional, it was lost and regained several times, probably via intra-bacterial HGT, before becoming functionally compatible with GluRS (N) in a synchronous way [26,27]. This model is compatible with Figure 4.…”

Section: Resultssupporting

confidence: 56%

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

Dasgupta

Basu

2014

BMC Evol Biol

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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.

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Section: Resultssupporting

confidence: 56%

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

Dasgupta

Basu

2014

BMC Evol Biol

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“…Certain bacterial D-GluRS enzymes are able to discriminate tRNA Glu from tRNA Gln at the acceptor stem. The catalytic domain of the E. coli D-GluRS alone is able to discriminate tRNA Glu from tRNA Gln (21). Discrimination of tRNA Gln from tRNA Glu isoacceptors by the Helicobacter pylori GluRS2 is also achieved by recognizing the acceptor stem, in particular the U 1 ∶A 72 base pair in tRNA Gln (23).…”

Section: Thermautotrohpicusmentioning

confidence: 97%

Rational design of an evolutionary precursor of glutaminyl-tRNA synthetase

O’Donoghue

Sheppard

Nureki

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

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The specificity of most aminoacyl-tRNA synthetases for an amino acid and cognate tRNA pair evolved before the divergence of the three domains of life. Glutaminyl-tRNA synthetase (GlnRS) evolved later and is derived from the archaeal-type nondiscriminating glutamyl-tRNA synthetase (GluRS), an enzyme with relaxed tRNA specificity capable of forming both Glu-tRNA Glu and Glu-tRNA Gln . The archaea lack GlnRS and use a specialized amidotransferase to convert Glu-tRNA Gln to Gln-tRNA Gln needed for protein synthesis. We show that the Methanothermobacter thermautotrophicus GluRS is active toward tRNA Glu and the two tRNA Gln isoacceptors the organism encodes, but with a significant catalytic preference for . The less active responds to the less common CAA codon for Gln. From a biochemical characterization of M. thermautotrophicus GluRS variants, we found that the evolution of tRNA specificity in GlnRS could be recapitulated by converting the M. thermautotrophicus GluRS to a tRNA Gln specific enzyme, solely through the addition of an acceptor stem loop present in bacterial GlnRS. One designed GluRS variant is also highly specific for the isoacceptor, which responds to the CAG codon, and shows no activity toward . Because it is now possible to eliminate particular codons from the genome of Escherichia coli , additional codons will become available for genetic code engineering. Isoacceptor-specific aminoacyl-tRNA synthetases will enable the reassignment of more open codons while preserving accurate encoding of the 20 canonical amino acids.

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“…Limited mutational studies have also been performed on GluRS1 and GluRS2 from Helicobacter pylori where GluRS1 stands for the canonical GluRS and GluRS2 corresponds to a non‐canonical version that only glutamylates tRNA Gln [10]. In addition to mutational studies, glutamylation efficiencies of a domain‐deleted or a domain‐swapped version of E. coli GluRS have also been reported – from our lab [11,12] and by Lapointe and co‐workers [13]. These studies show that the isolated N‐terminal catalytic domain of E. coli GluRS is still capable of glutamylating tRNA Glu , albeit with a reduced efficiency.…”

Section: Introductionmentioning

confidence: 95%

Structural and functional consequences of mutating a proteobacteria‐specific surface residue in the catalytic domain of Escherichia coli GluRS

2012

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Edited by Michael IbbaKeywords: Glutamyl-tRNA synthetase tRNA Glu Glutamylation Proteobacteria Phylum-specificity Escherichia coli a b s t r a c t Nucleotides whose mutations seriously affect glutamylation efficiency are experimentally known for Escherichia coli tRNA Glu . However, not much is known about functional hotspots on the complementary enzyme, glutamyl-tRNA synthetase (GluRS). From structural and functional studies on an Arg266Leu mutant of E. coli GluRS, we demonstrate that Arg266 is essential for efficient glutamylation of tRNA Glu . Consistent with this result, we found that Arg266 is a conserved signature of proteobacterial GluRS. In contrast, most non-proteobacterial GluRS contain Leu, and never Arg, at this position. Our results imply a unique strategy of glutamylation of tRNA Glu in proteobacteria under phylum-specific evolutionary compulsions.

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The role of the catalytic domain of E. coli GluRS in tRNA^Gln discrimination

Cited by 12 publications

References 33 publications

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

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

Rational design of an evolutionary precursor of glutaminyl-tRNA synthetase

Structural and functional consequences of mutating a proteobacteria‐specific surface residue in the catalytic domain of Escherichia coli GluRS

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The role of the catalytic domain of E. coli GluRS in tRNAGln discrimination

Cited by 12 publications

References 33 publications

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

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

Rational design of an evolutionary precursor of glutaminyl-tRNA synthetase

Structural and functional consequences of mutating a proteobacteria‐specific surface residue in the catalytic domain of Escherichia coli GluRS

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The role of the catalytic domain of E. coli GluRS in tRNA^Gln discrimination