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.2018;9(4):205-224.
doi: 10.1080/21541264.2018.1467718. Epub 2018 May 30.

Aminoacyl-tRNA synthetase evolution and sectoring of the genetic code

Affiliations

Aminoacyl-tRNA synthetase evolution and sectoring of the genetic code

Daewoo Pak et al. Transcription.2018.

Abstract

The genetic code sectored via tRNA charging errors, and the code progressed toward closure and universality because of evolution of aminoacyl-tRNA synthetase (aaRS) fidelity and translational fidelity mechanisms. Class I and class II aaRS folds are identified as homologs. From sequence alignments, a structurally conserved Zn-binding domain common to class I and class II aaRS was identified. A model for the class I and class II aaRS alternate folding pathways is posited. Five mechanisms toward code closure are highlighted: 1) aaRS proofreading to remove mischarged amino acids from tRNA; 2) accurate aaRS active site specification of amino acid substrates; 3) aaRS-tRNA anticodon recognition; 4) conformational coupling proofreading of the anticodon-codon interaction; and 5) deamination of tRNA wobble adenine to inosine. In tRNA anticodons there is strong wobble sequence preference that results in a broader spectrum of contacts to synonymous mRNA codon wobble bases. Adenine is excluded from the anticodon wobble position of tRNA unless it is modified to inosine. Uracil is generally preferred to cytosine in the tRNA anticodon wobble position. Because of wobble ambiguity when tRNA reads mRNA, the maximal coding capacity of the three nucleotide code read by tRNA is 31 amino acids + stops.

Keywords: The last universal common cellular ancestor; aminoacyl-tRNA synthetases; anticodon wobble preference; class I and class II aaRS homology; cloverleaf tRNA; standard genetic code; synonymous anticodons; tRNA wobble inosine.

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Figures

Figure 1.
Figure 1.
Pyrococcus furiosis (Pfu) aaRS enzymes were searched using NCBI Blast tools for nearest homologs inPfu. In some cases,Staphylothermus marinus (Sma) (archaea) andEscherichia coli (Eco) (bacteria) homologs are identified. AlaX is one of a set of tRNAAla editing enzymes inPfu.
Figure 2.
Figure 2.
Similarity of class I and class II aaRS enzymes is indicated. A partial sequence alignment of GlyRS-IIA, ValRS-IA and IleRS-IA enzymes is shown demonstrating sequence similarity of a shared Zn-binding motif and GlyRS-IIA Motif 2 with IleRS-IA KMSKS motif. Red shading indicates identity comparing class I and class II aaRS. Yellow shading indicates similarity comparing class I and class II aaRS. Green shading is used to highlight Zn-binding motifs. Cyan shading indicates active site β-sheets (sss). Magenta shading indicates 3 β-sheets in GlyRS-IIA expected to block class I folding by a class II aaRS. Gray shading indicates β1-β3 of the shared Zn-binding domain. The entire alignment is shown in Supplementary Figure 1. The schematic diagram shows howPfu GlyRS-IIA andSma IleRS-IA align (gray lines highlight some similarities).Pae)Pyrobaculum aerophilum;Sso)Sulfolobus solfataricus.
Figure 3.
Figure 3.
A homology model (Supplementary File 1) ofPyrococcus furiosis GlyRS-IIA was constructed by homology threading to human GlyRS-IIA (PDB 4KQE). The homology model (powder blue), PDB 4KQE [28] (white) and related PDB 4QEI [27] (magenta) were overlaid. Although human (Hs) GlyRS-IIA lacks Zn binding, the shape of the loops is maintained.
Figure 4.
Figure 4.
A structurally conserved Zn-binding motif among class I and class II aaRS enzymes. Similar orientations ofTth ValRS-IA (green),Pfu GlyRS-IIA (magenta) and human GlyRS-IIA (white) are shown.
Figure 5.
Figure 5.
Incompatibility of class I and class II aaRS folding patterns. An overlay of the shared Zn-binding motif of GlyRS-IIA (secondary structure representation) and ValRS-IA (green) demonstrates a clash by three antiparallel GlyRS-IIA β-sheets with the N-terminal ValRS-IA Zn-binding domain. A ValRS-IA active site β-sheet (LVLEG) is yellow. LVLEG corresponds toPfu GlyRS-IIA β-sheet KAYL in the 3 antiparallel β-sheet cluster surrounding the shared Zn-binding motif.
Figure 6.
Figure 6.
Codon-anticodon tables. Proofreading by aaRS enzymes in archaea is confined to the left half of the codon-anticodon table. Gray shading indicates editing by aaRS enzymes. Red shading indicates anticodons that are disallowed or strongly underrepresented. Green shading indicates adenosine→inosine conversion in bacteria and eukaryotes (tRNAArg (ACG→ICG)). Yellow shading indicates adenosine→inosine conversion in eukaryotes (very rarely, these modifications are found in some bacteria) [19].
Figure 7.
Figure 7.
Anticodon wobble preferences comparing synonymous ANN and GNN tRNA anticodons. * indicates A→I conversion. Synonymous anticodons: Ser1 (AAA vs GAA), Ser2 (ACU vs GCU).
Figure 8.
Figure 8.
Anticodon wobble preferences comparing synonymous UNN and CNN tRNA anticodons. Synonymous anticodons: Leu1 (UAA vs CAA), Leu2 (UAG vs CAG), Arg1 (UCG vs CCG), Arg2 (UCU vs CCU).
Figure 9.
Figure 9.
A representation that combines purine and pyrimidine anticodon wobble preference data. The down arrow indicates Ile (UAU) utilization in eukaryotes. The black lines indicate interesting differences comparing Arg anticodons in bacteria and eukarya.
Figure 10.
Figure 10.
Consequences of apparent limiting of tRNAArg (CCG) in eukarya and tRNAArg (UCG) in bacteria. Ac for anticodon.
Figure 11.
Figure 11.
An approximate sequence of events for the requirement of different mechanisms for discrimination of tRNA identities by aaRS enzymes and the evolution of ribosome fidelity. Green text indicates aaRS proofreading (in archaea).
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