<scp>D</scp>‐Amino acids and <scp>D</scp>‐Tyr‐tRNA<sup>Tyr</sup> deacylase: stereospecificity of the translation machine revisited

Yang, Hong-Bo; Zheng, Gen; Peng, Xiaozhong; Qiang, Boqin; Yuan, Jing

doi:10.1016/s0014-5793(03)00858-5

Cited by 39 publications

(32 citation statements)

References 44 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Strain BD630 but not strain NAFM5 exhibits hyper-susceptibility to D-amino acids such as D-tyrosine and D-serine. D-Aminoacyl-tRNA deacylase degrades aminoacyl-tRNAs charged with D-amino acids to prevent mis-incorporation of D-amino acids into proteins (Yang et al, 2003) and a mutant devoid of this enzyme becomes sensitive to D-amino acids (Soutourina et al, 2000). A possible explanation for the apparent sensitivity of B. subtilis 168 to different D-amino acids is that this strain lacks D-amino acid deacylase activity.…”

Section: Discussionmentioning

confidence: 99%

Roles and regulation of the glutamate racemase isogenes, racE and yrpC, in Bacillus subtilis

2004

View full text Add to dashboard Cite

Roles and regulation of the glutamate racemase isogenes, racE and yrpC, in Bacillus subtilis Many bacteria, including Escherichia coli, have a unique gene that encodes glutamate racemase. This enzyme catalyses the formation of D-glutamate, which is necessary for cell wall peptidoglycan synthesis. However, Bacillus subtilis has two glutamate racemase genes, named racE and yrpC. Since racE appears to be indispensable for growth in rich medium, the role of yrpC in D-amino acid synthesis is vague. Experiments with racE-and yrpC-knockout mutants confirmed that racE is essential for growth in rich medium but showed that this gene was dispensable for growth in minimal medium, where yrpC executes the anaplerotic role of racE. LacZ fusion assays demonstrated that racE was expressed in both types of media but yrpC was expressed only in minimal medium, which accounted for the absence of yrpC function in rich medium. Neither racE nor yrpC was required for B. subtilis cells to synthesize poly-c-DL-glutamate (c-PGA), a capsule polypeptide of D-and L-glutamate linked through a c-carboxylamide bond. Wild-type cells degraded the capsule during the late stationary phase without accumulating the degradation products, D-glutamate and L-glutamate, in the medium. In contrast, racE or yrpC mutant cells accumulated significant amounts of D-but not L-glutamate. Exogenous D-glutamate utilization was somewhat defective in the mutants and the double mutation of racE and yrpC severely impaired D-amino acid utilization. Thus, both racemase genes appear necessary to complete the catabolism of exogenous D-glutamate generated from c-PGA.

show abstract

Section: Discussionmentioning

confidence: 99%

Roles and regulation of the glutamate racemase isogenes, racE and yrpC, in Bacillus subtilis

2004

View full text Add to dashboard Cite

show abstract

“…D-TyrtRNA deacylase was originally identified on the basis of its ability to specifically remove D-Tyr from mischarged tRNA Tyr but has since been shown to deacylate tRNAs mischarged with other Damino acids (12). Thus, for simplicity, we will henceforth refer to this enzyme as D-aminoacyl-tRNA deacylase (13). If, as we hypothesize, the effects of D-amino acids are largely due to their misincorporation into protein, then repairing the mutant deacylase gene ought to confer resistance to the inhibitory effects of D-amino acids on growth and biofilm formation.…”

Section: Methodsmentioning

confidence: 99%

D-Amino Acids Indirectly Inhibit Biofilm Formation in Bacillus subtilis by Interfering with Protein Synthesis

Leiman¹,

May²,

Lebar³

et al. 2013

Journal of Bacteriology

190

139

View full text Add to dashboard Cite

The soil bacterium Bacillus subtilis forms biofilms on surfaces and at air-liquid interfaces. It was previously reported that these biofilms disassemble late in their life cycle and that conditioned medium from late-stage biofilms inhibits biofilm formation. Such medium contained a mixture of D-leucine, D-methionine, D-tryptophan, and D-tyrosine and was reported to inhibit biofilm formation via the incorporation of these D-amino acids into the cell wall. Here, we show that L-amino acids were able to specifically reverse the inhibitory effects of their cognate D-amino acids. We also show that D-amino acids inhibited growth and the expression of biofilm matrix genes at concentrations that inhibit biofilm formation. Finally, we report that the strain routinely used to study biofilm formation has a mutation in the gene (dtd) encoding D-tyrosyl-tRNA deacylase, an enzyme that prevents the misincorporation of D-amino acids into protein in B. subtilis. When we repaired the dtd gene, B. subtilis became resistant to the biofilm-inhibitory effects of D-amino acids without losing the ability to incorporate at least one noncanonical D-amino acid, D-tryptophan, into the peptidoglycan peptide side chain. We conclude that the susceptibility of B. subtilis to the biofilm-inhibitory effects of D-amino acids is largely, if not entirely, due to their toxic effects on protein synthesis.

show abstract

“…Consistent with the notion that charging with D-amino acids can occur in vivo, the modern cellular machinery has avariety of mechanisms in place to prevent it. These include deacylases that remove D-amino acids from incorrectly charged tRNAs before they reach the ribosome (Soutourina et al 2000;Yang et al 2003). In addition, many aminoacyl tRNA synthetases have an editing domain.…”

Section: Chirality and The Ribosomementioning

confidence: 99%

Origin and Evolution of the Ribosome

Fox¹

2010

Cold Spring Harbor Perspectives in Biology

216

186

View full text Add to dashboard Cite

The modern ribosome was largely formed at the time of the last common ancestor, LUCA. Hence its earliest origins likely lie in the RNA world. Central to its development were RNAs that spawned the modern tRNAs and a symmetrical region deep within the large ribosomal RNA, (rRNA), where the peptidyl transferase reaction occurs. To understand pre-LUCA developments, it is argued that events that are coupled in time are especially useful if one can infer a likely order in which they occurred. Using such timing events, the relative age of various proteins and individual regions within the large rRNA are inferred. An examination of the properties of modern ribosomes strongly suggests that the initial peptides made by the primitive ribosomes were likely enriched for L-amino acids, but did not completely exclude D-amino acids. This has implications for the nature of peptides made by the first ribosomes. From the perspective of ribosome origins, the immediate question regarding coding is when did it arise rather than how did the assignments evolve. The modern ribosome is very dynamic with tRNAs moving in and out and the mRNA moving relative to the ribosome. These movements may have become possible as a result of the addition of a template to hold the tRNAs. That template would subsequently become the mRNA, thereby allowing the evolution of the code and making an RNA genome useful. Finally, a highly speculative timeline of major events in ribosome history is presented and possible future directions discussed.

show abstract

D‐Amino acids and D‐Tyr‐tRNA^Tyr deacylase: stereospecificity of the translation machine revisited

Cited by 39 publications

References 44 publications

Roles and regulation of the glutamate racemase isogenes, racE and yrpC, in Bacillus subtilis

Roles and regulation of the glutamate racemase isogenes, racE and yrpC, in Bacillus subtilis

D-Amino Acids Indirectly Inhibit Biofilm Formation in Bacillus subtilis by Interfering with Protein Synthesis

Origin and Evolution of the Ribosome

Contact Info

Product

Resources

About

D‐Amino acids and D‐Tyr‐tRNATyr deacylase: stereospecificity of the translation machine revisited

Cited by 39 publications

References 44 publications

Roles and regulation of the glutamate racemase isogenes, racE and yrpC, in Bacillus subtilis

Roles and regulation of the glutamate racemase isogenes, racE and yrpC, in Bacillus subtilis

D-Amino Acids Indirectly Inhibit Biofilm Formation in Bacillus subtilis by Interfering with Protein Synthesis

Origin and Evolution of the Ribosome

Contact Info

Product

Resources

About

D‐Amino acids and D‐Tyr‐tRNA^Tyr deacylase: stereospecificity of the translation machine revisited