•Many bacteria are missing asparaginyl-tRNA and/or glutaminyl-tRNA synthetase.•Asn-tRNAAsn and Gln-tRNAGln are produced in a two-step, indirect pathway.•GatCAB uses an unusually hydrophilic ammonia tunnel to transport ammonia between active sites.•A large complex called the Asn-transamidosome sequesters Asp-tRNAAsn from the ribosome.•Indirect tRNA aminoacylation can induce beneficial mistranslation under stress.The fact that most bacteria do not contain a full set of aminoacyl-tRNA synthetases (aaRS) is often underappreciated. In the absence of asparaginyl-tRNA and/or glutaminyl-tRNA synthetase (AsnRS and GlnRS), Asn-tRNAAsn and/or Gln-tRNAGln are produced by an indirect tRNA aminoacylation pathway that relies on misacylation of these two tRNAs by two different misacylating aaRSs, followed by transamidation by an amidotransferase (GatCAB in bacteria). This review highlights the central importance of indirect tRNA aminoacylation to accurate protein translation, mechanistic peculiarities that appear to be unique to this system, and the newly recognized connection between indirect tRNA aminoacylation and mistranslation as a strategy used by bacteria to respond to environmental stressors like antibiotics.Download high-res image (80KB)Download full-size image

•The soluble domains of Gpi823-306 and Gaa150-343 form a stable, discrete complex.•The Gpi823-306:Gaa150-343 complex adopts an α2β2 stoichiometry.•The Gaa150-343 monomer and homodimer were not observed in the absence of Gpi823-306.•Truncation of a conserved face of Gaa150-343 did not disrupt assembly of the Gpi823-306:Gaa150-343 complex.Glycosylphosphatidylinositol transamidase (GPI-T) catalyzes the post-translational addition of the GPI anchor to the C-terminus of some proteins. In most eukaryotes, Gpi8, the active site subunit of GPI-T, is part of a hetero-pentameric complex containing Gpi16, Gaa1, Gpi17, and Gab1. Gpi8, Gaa1, and Gpi16 co-purify as a heterotrimer from Saccharomyces cerevisiae, suggesting that they form the core of the GPI-T. Details about the assembly and organization of these subunits have been slow to emerge. We have previously shown that the soluble domain of S. cerevisiae Gpi8 (Gpi823-306) assembles as a homodimer, similar to the caspases with which it shares weak sequence homology (Meitzler, J. L. et al., 2007). Here we present the characterization of a complex between the soluble domains of Gpi8 and Gaa1. The complex between GST-Gpi823-306 (α) and His6-Gaa150-343 (β) was characterized by native gel analysis and size exclusion chromatography (SEC) and results are most consistent with an α2β2 stoichiometry. These results demonstrate that Gpi8 and Gaa1 interact specifically without a requirement for other subunits, bring us closer to determining the stoichiometry of the core subunits of GPI-T, and lend further credence to the hypothesis that these three subunits assemble into a dimer of a trimer.Download high-res image (222KB)Download full-size image

The Helicobacter pylori (Hp) Asp-tRNAAsn/Glu-tRNAGln amidotransferase (AdT) plays important roles in indirect aminoacylation and translational fidelity. AdT has two active sites, in two separate subunits. Kinetic studies have suggested that interdomain communication occurs between these subunits; however, this mechanism is not well understood. To explore domain–domain communication in AdT, we adapted an assay and optimized it to kinetically characterize the kinase activity of Hp AdT. This assay was applied to the analysis of a series of point mutations at conserved positions throughout the putative AdT ammonia tunnel that connects the two active sites. Several mutations that caused significant decreases in AdT’s kinase activity (reduced by 55–75%) were identified. Mutations at Thr149 (37 Å distal to the GatB kinase active site) and Lys89 (located at the interface of GatA and GatB) were detrimental to AdT’s kinase activity, suggesting that these mutations have disrupted interdomain communication between the two active sites. Models of wild-type AdT, a valine mutation at Thr149, and an arginine mutation at Lys89 were subjected to molecular dynamics simulations. A comparison of wild-type, T149V, and K89R AdT simulation results unmasks 59 common residues that are likely involved in connecting the two active sites.

Many eukaryotic proteins are modified with a glycosylphosphatidylinositol (GPI) anchor at their C-termini. This post-translational modification causes these proteins to be noncovalently tethered to the plasma membrane. The synthesis of truncated GPI anchor analogues is reported; these compounds were designed for use as soluble substrates for GPI transamidase (GPI-T), the enzyme that appends the GPI anchor onto proteins.

Elongation factor Tu (EF-Tu) binds and loads elongating aminoacyl-tRNAs (aa-tRNAs) onto the ribosome for protein biosynthesis. Many bacteria biosynthesize Gln-tRNAGln and Asn-tRNAAsn by an indirect, two-step pathway that relies on the misacylated tRNAs Glu-tRNAGln and Asp-tRNAAsn as intermediates. Previous thermodynamic and experimental analyses have demonstrated that Thermus thermophilus EF-Tu does not bind Asp-tRNAAsn and predicted a similar discriminatory response against Glu-tRNAGln [Asahara, H., and Uhlenbeck, O. (2005) Biochemistry 46, 6194−6200; Roy, H., et al. (2007) Nucleic Acids Res. 35, 3420−3430]. By discriminating against these misacylated tRNAS, EF-Tu plays a direct role in preventing misincorporation of aspartate and glutamate into proteins at asparagine and glutamine codons. Here we report the characterization of two different mesophilic EF-Tu orthologs, one from Escherichia coli, a bacterium that does not utilize either Glu-tRNAGln or Asp-tRNAAsn, and the second from Helicobacter pylori, an organism in which both misacylated tRNAs are essential. Both EF-Tu orthologs discriminate against these misacylated tRNAs, confirming the prediction that Glu-tRNAGln, like Asp-tRNAAsn, will not form a complex with EF-Tu. These results also demonstrate that the capacity of EF-Tu to discriminate against both of these aminoacyl-tRNAs is conserved even in bacteria like E. coli that do not generate either misacylated tRNA.