Widespread Distribution of Cell Defense against d-Aminoacyl-tRNAs

Several l-aminoacyl-tRNA synthetases can transfer a d-amino acid onto their cognate tRNA(s). This harmful reaction is counteracted by the enzyme d-aminoacyl-tRNA deacylase. Two distinct deacylases were already identified in bacteria (DTD1) and in archaea (DTD2), respectively. Evidence was given that DTD1 homologs also exist in nearly all eukaryotes, whereas DTD2 homologs occur in plants. On the other hand, several bacteria, including most cyanobacteria, lack genes encoding a DTD1 homolog. Here we show that Synechocystis sp. PCC6803 produces a third type of deacylase (DTD3). Inactivation of the corresponding gene (dtd3) renders the growth of Synechocystis sp. hypersensitive to the presence of d-tyrosine. Based on the available genomes, DTD3-like proteins are predicted to occur in all cyanobacteria. Moreover, one or several dtd3-like genes can be recognized in all cellular types, arguing in favor of the nearubiquity of an enzymatic function involved in the defense of translational systems against invasion by d-amino acids.Although they are detected in various living organisms (reviewed in Ref. 1), d-amino acids are thought not to be incorporated into proteins, because of the stereospecificity of aminoacyl-tRNA synthetases and of the translational machinery, including EF-Tu and the ribosome (2). However, the discrimination between l- and d-amino acids by aminoacyl-tRNA synthetases is not equal to 100%. Significant d-aminoacylation of their cognate tRNAs by Escherichia coli tyrosyl-, tryptophanyl-, aspartyl-, lysyl-, and histidyl-tRNA synthetases has been characterized in vitro (3–9). Recently, using a bacterium, transfer of d-tyrosine onto tRNA^Tyr was shown to occur in vivo (10).With such misacylation reactions, the resulting d-aminoacyl-tRNAs form a pool of metabolically inactive molecules, at best. At worst, d-aminoacylated tRNAs infiltrate the protein synthesis machinery. Although the latter harmful possibility has not yet been firmly established, several cells were shown to possess a d-tyrosyl-tRNA deacylase, or DTD, that should help them counteract the accumulation of d-aminoacyl-tRNAs. This enzyme shows a broad specificity, being able to remove various d-aminoacyl moieties from the 3′-end of a tRNA (4–6, 11). Such a function makes the deacylase a member of the family of enzymes capable of editing in trans mis-aminoacylated tRNAs. This family includes several homologs of aminoacyl-tRNA synthetase editing domains (12), as well as peptidyl-tRNA hydrolase (13, 14).Two distinct deacylases have already been discovered. The first one, called DTD1, is predicted to occur in most bacteria and eukaryotes (see d-amino acids, including d-tyrosine (6). In fact, in an E. coli Δdtd strain grown in the presence of 2.4 mm d-tyrosine, as much as 40% of the cellular tRNA^Tyr pool becomes esterified with d-tyrosine (10).

TABLE 1

Distribution of DTD1 and DTD2 homologs in various phylogenetic groupsHomologs of DTD1 and DTD2 were searched for using a genomic Blast analysis against complete genomes in the NCBI Database (www.ncbi.nlm.nih.gov). Values in the table are number of species. For instance, E. coli is counted only once in γ-proteobacteria despite the fact that several E. coli strains have been sequenced.

	DTD1	DTD2	DTD1 + DTD2	None
Bacteria
Acidobacteria	2	0	0	0
Actinobacteria	27	0	0	8
Aquificae	1	0	0	0
Bacteroidetes/Chlorobi	12	0	0	5
Chlamydiae	1	0	0	6
Chloroflexi	4	0	0	0
Cyanobacteria	5	0	0	16
Deinococcus/Thermus	4	0	0	0
Firmicutes
Bacillales	19	0	0	0
Clostridia	19	0	0	0
Lactobacillales	23	0	0	0
Mollicutes	0	0	0	15
Fusobacteria/Planctomycetes	2	0	0	0
Proteobacteria
α	6	0	0	55
β	24	0	0	11
γ	80	0	0	8
δ	15	0	0	0
ε	1	0	0	12
Spirochaetes	0	0	0	7
Thermotogae	5	0	0	0
Archaea
Crenarchaeota	0	13	0	0
Euryarchaeota	1	26	0	2
Nanoarchaeota	0	0	0	1
Eukaryota
Dictyosteliida	1	0	0	0
Fungi/Metazoa
Fungi	13	0	0	1
Metazoa	19	0	0	0
Kinetoplastida	3	0	0	0
Viridiplantae	4	4	4	0

Open in a separate windowHomologs of dtd/DTD1 are not found in the available archaeal genomes except that of Methanosphaera stadtmanae. A search for deacylase activity in Sulfolobus solfataricus and Pyrococcus abyssi led to the detection of another enzyme (DTD2), completely different from the DTD1 protein (15). Importing dtd2 into E. coli functionally compensates for dtd deprivation. As shown in 16).Several cells contain neither dtd nor dtd2 homologs (d-tyrosyl-tRNA deacylase (DTD3). This protein, encoded by dtd3, behaves as a metalloenzyme. Sensitivity of the growth of Synechocystis to external d-tyrosine is strongly exacerbated by the disruption of dtd3. Moreover, expression of the Synechocystis DTD3 in a Δdtd E. coli strain, from a plasmid, restores the resistance of the bacterium to d-tyrosine. Finally, using the available genomes, we examined the occurrence of DTD3 in the living world. The prevalence of DTD3-like proteins is surprisingly high. It suggests that the defense of protein synthesis against d-amino acids is universal.