Alanyl-tRNA synthetase from Escherichia coli, Bombyx mori and Ratus ratus. Existence of common structural features

OUP accepted manuscript

Unlike many other aminoacyl-tRNA synthetases, alanyl-tRNA synthetase (AlaRS) retains a conserved prototype structure throughout biology. While Caenorhabditis elegans cytoplasmic AlaRS (CeAlaRS_c) retains the prototype structure, its mitochondrial counterpart (CeAlaRS_m) contains only a residual C-terminal domain (C-Ala). We demonstrated herein that the C-Ala domain from CeAlaRS_c robustly binds both tRNA and DNA. It bound different tRNAs but preferred tRNA^Ala. Deletion of this domain from CeAlaRS_c sharply reduced its aminoacylation activity, while fusion of this domain to CeAlaRS_m selectively and distinctly enhanced its aminoacylation activity toward the elbow-containing (or L-shaped) tRNA^Ala. Phylogenetic analysis showed that CeAlaRS_m once possessed the C-Ala domain but later lost most of it during evolution, perhaps in response to the deletion of the T-arm (part of the elbow) from its cognate tRNA. This study underscores the evolutionary gain of C-Ala for docking AlaRS to the L-shaped tRNA^Ala.

Effects of substrate and inhibitor binding on proteolysis of isoleucyl-tRNA synthetase from Staphylococcus aureus

Binding of ligands to isoleucyl-tRNA synthetase (IleRS; E) from Staphylococcus aureus was investigated through effects on proteolytic digestion. Approximately 50-fold higher concentrations of protease (trypsin or chymotrypsin) were required to inactivate IleRS after incubation with substrates and formation of the E. Ile-AMP intermediate compared with free E. Binding of pseudomonic acid A (PS-A) or isoleucynol adenylate (Ile-ol-AMP) also induced resistance to proteolysis and altered the patterns of IleRS cleavage fragments in an inhibitor-class specific manner. The determinants for PS-A binding were investigated via proteolysis of E.[3H]PS-A. Limited proteolysis of E.[3H]PS-A (excising residues 186-407) could be achieved without significant loss of bound inhibitor, eliminating this region as contributing to inhibitor binding. Assays were developed which allowed IleRS proteolysis to be readily followed using fluorescence polarization. Inhibitor-protected IleRS was labeled with fluorescein isothiocyanate with only a small effect upon catalytic activity (Fl-IleRS). The (pseudo) kinetics of proteolytic cleavage of Fl-IleRS could be measured at low nanomolar Fl-IleRS concentrations in 96/384-well microtiter plates, allowing real-time monitoring of dose-dependent protection from proteolysis. Thus, inhibitor (and substrate) binding could be reproducibly assessed in the absence of measurements of catalytic acitvity. This could potentially form the basis of novel screening assays for ligands to other proteins.

Human alanyl-tRNA synthetase: conservation in evolution of catalytic core and microhelix recognition

The class II Escherichia coli and human alanyl-tRNA synthetases cross-acylate their respective tRNAs and require, for aminoacylation, an acceptor helix G3:U70 base pair that is conserved in evolution. We report here the primary structure and expression in the yeast Pichia of an active human alanyl-tRNA synthetase. The N-terminal 498 amino acids of the 968-residue polypeptide have substantial (41%) identity with the E. coli protein. A closely related region encompasses the class-defining domain of the E. coli enzyme and includes the part needed for recognition of the acceptor helix. As a result, previously reported mutagenesis, modeling, domain organization, and biochemical characterization on the E. coli protein appear valid as a template for the human protein. In particular, we show that both the E. coli enzyme and the human enzyme purified from Pichia aminoacylate 9-base pair RNA duplexes whose sequences are based on the acceptor stems of either E. coli or human alanine tRNAs. In contrast, the sequences of the two enzymes completely diverge in an internal portion of the C-terminal half that is essential for tetramer formation by the E. coli enzyme, but that is dispensable for microhelix aminoacylation. This divergence correlates with the expressed human enzyme behaving as a monomer. Thus, the region of close sequence similarity may be a consequence of strong selective pressure to conserve the acceptor helix G3:U70 base pair as an RNA signal for alanine.

Mammalian tryptophanyl-tRNA synthetases

Aminoacyl-tRNA synthetases of higher organisms are far less studied compared to their prokaryotic and unicellular eukaryotic counterparts. However, many aminoacyl-tRNA synthetases from multi-cellular organisms exhibit certain features not yet described for the same enzymes of bacteria or yeast. Tryptophanyl-tRNA synthetases (TrpRS) are among the most thoroughly studied mammalian enzymes of this group. TrpRS are Zn(2+)-dependent, dimeric, class I aminoacyl-tRNA synthetases with known amino acid sequence for four different mammalian orders. TrpRS is not associated in a stable multi-synthetase complex, although it exhibits a long N-terminal extension absent from bacterial TrpRS. The human gene encoding TrpRS belongs to the interferon-responsive gene family and TrpRS activity drastically increases after interferon gamma induction. For unknown reasons TrpRS is overproduced in pancreas of Ruminantia. Other data on TrpRS available so far are summarized and briefly discussed here.