The Escherichia coli YadB Gene Product Reveals a Novel Aminoacyl-tRNA Synthetase Like Activity

Campanacci, Valérie; Dubois, Daniel Y.; Becker, Hubert Dominique; Kern, Daniel; Spinelli, S.; Valencia, C. Alexander; Pagot, Fabienne; Salomoni, Aurelia; Grisel, Sacha; Vincentelli, Renaud; Bignon, Christophe; Lapointe, Jacques; Giegé, Richard; Cambillau, Christian

doi:10.1016/j.jmb.2004.01.027

Cited by 47 publications

(54 citation statements)

References 49 publications

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“…2A); however, in contrast to GluRS, YadB can carry out this process in the absence of tRNA (a similar finding was published very recently, ref. 22). This observation is consistent with the fact that the amino acid-binding site is conserved in GluRS and YadB, but the lack of the anticodon binding domain in YadB should prohibit the major conformational rearrangements observed in the active site of the T. thermophilus GluRS upon tRNA binding (19 YadB Transfers Glutamate to tRNA Asp .…”

Section: Resultsmentioning

confidence: 99%

A truncated aminoacyl–tRNA synthetase modifies RNA

Salazar

Ambrogelly

Crain

et al. 2004

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

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Aminoacyl-tRNA synthetases are modular enzymes composed of a central active site domain to which additional functional domains were appended in the course of evolution. Analysis of bacterial genome sequences revealed the presence of many shorter aminoacyl-tRNA synthetase paralogs. Here we report the characterization of a well conserved glutamyl-tRNA synthetase (GluRS) paralog (YadB in Escherichia coli) that is present in the genomes of >40 species of proteobacteria, cyanobacteria, and actinobacteria. The E. coli yadB gene encodes a truncated GluRS that lacks the C-terminal third of the protein and, consequently, the anticodon binding domain. Generation of a yadB disruption showed the gene to be dispensable for E. coli growth in rich and minimal media. Unlike GluRS, the YadB protein was able to activate glutamate in presence of ATP in a tRNA-independent fashion and to transfer glutamate onto tRNA Asp . Neither tRNA Glu nor tRNA Gln were substrates. In contrast to canonical aminoacyl-tRNA, glutamate was not esterified to the 3 -terminal adenosine of tRNA Asp . Instead, it was attached to the 2-amino-5-(4,5-dihydroxy-2-cyclopenten-1-yl) moiety of queuosine, the modified nucleoside occupying the first anticodon position of tRNA Asp . Glutamyl-queuosine, like canonical Glu-tRNA, was hydrolyzed by mild alkaline treatment. Analysis of tRNA isolated under acidic conditions showed that this novel modification is present in normal E. coli tRNA; presumably it previously escaped detection as the standard conditions of tRNA isolation include an alkaline deacylation step that also causes hydrolysis of glutamyl-queuosine. Thus, this aminoacyl-tRNA synthetase fragment contributes to standard nucleotide modification of tRNA.

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Section: Resultsmentioning

confidence: 99%

A truncated aminoacyl–tRNA synthetase modifies RNA

Salazar

Ambrogelly

Crain

et al. 2004

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

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“…In particular, the functional and evolutionary importance of these free standing synthetase-like modules is of great interest. Although some of these single-domain homologs have been shown to carry out functions unrelated to tRNA charging (35,36) others, such as YbaK and PrdX, have clearly been shown to possess aminoacylation or editing activity (22,23,25,28,29,31,37). Free-standing editing proteins found in nature appear to have evolved alternate mechanisms to function as efficient and specific editing modules in trans (23,28,29,31).…”

Section: Discussionmentioning

confidence: 99%

Restoring species-specific posttransfer editing activity to a synthetase with a defunct editing domain

SternJohn

Hati

Siliciano

et al. 2007

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

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In contrast, the isolated INS domain displays only weak editing activity and lacks tRNA sequence specificity. These results emphasize the modular nature of synthetase editing active sites and demonstrate how in evolution, a weak editing activity can be converted to a more robust state through fusion to the body of a synthetase. In this manner, a single editing module can be distributed to different synthetases, and simultaneously acquire specificity and enhanced activity.Prolyl-tRNA synthetase ͉ Saccharomyces cerevisiae

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“…Recent studies confirmed YadB as a structural analogue of the catalytic core of GluRS that has retained the ability to activate glutamate (11), albeit without the need for tRNA binding that characterizes GluRS (12). Closer examination revealed that YadB does not attach activated glutamate to either tRNA Gln or tRNA Glu (11), but instead to tRNA Asp (9,13). Although the latter report by Dubois et al (13) in this issue of PNAS provided unequivocal evidence for the surprising aminoacylation of tRNA Asp , it left unanswered the more vexing question of what function, if any, this apparent heterologous aminoacylation serves in vivo.…”

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confidence: 97%

“…That particular hypothesis postulated that the ancestor of YadB was a GluRS able to attach glutamate to the noncognate substrate tRNA Gln . Recent studies confirmed YadB as a structural analogue of the catalytic core of GluRS that has retained the ability to activate glutamate (11), albeit without the need for tRNA binding that characterizes GluRS (12). Closer examination revealed that YadB does not attach activated glutamate to either tRNA Gln or tRNA Glu (11), but instead to tRNA Asp (9,13).…”

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confidence: 99%

“…The ability of YadB to aminoacylate a modified base in the anticodon creates a special structural challenge: how is the tRNA anticodon accommodated in the YadB active site? The recently solved crystal structure of YadB provides some indirect insight, in as much as tRNA Glu could not be docked onto YadB despite its high homology to GluRS (11). Furthermore, YadB contains a distinctly modified version of a zinc cluster used by GluRS for tRNA Glu acceptor stem recognition.…”

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confidence: 99%

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