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. 2015 Feb 6:6:21.
doi: 10.3389/fgene.2015.00021. eCollection 2015.

Structural modeling of tissue-specific mitochondrial alanyl-tRNA synthetase (AARS2) defects predicts differential effects on aminoacylation

Liliya Euro  1 , Svetlana Konovalova  1 , Jorge Asin-Cayuela  2 , Már Tulinius  3 , Helen Griffin  4 , Rita Horvath  4 , Robert W Taylor  5 , Patrick F Chinnery  4 , Ulrike Schara  6 , David R Thorburn  7 , Anu Suomalainen  8 , Joseph Chihade  9 , Henna Tyynismaa  10
Affiliations

Structural modeling of tissue-specific mitochondrial alanyl-tRNA synthetase (AARS2) defects predicts differential effects on aminoacylation

Liliya Euro et al. Front Genet. .

Abstract

The accuracy of mitochondrial protein synthesis is dependent on the coordinated action of nuclear-encoded mitochondrial aminoacyl-tRNA synthetases (mtARSs) and the mitochondrial DNA-encoded tRNAs. The recent advances in whole-exome sequencing have revealed the importance of the mtARS proteins for mitochondrial pathophysiology since nearly every nuclear gene for mtARS (out of 19) is now recognized as a disease gene for mitochondrial disease. Typically, defects in each mtARS have been identified in one tissue-specific disease, most commonly affecting the brain, or in one syndrome. However, mutations in the AARS2 gene for mitochondrial alanyl-tRNA synthetase (mtAlaRS) have been reported both in patients with infantile-onset cardiomyopathy and in patients with childhood to adulthood-onset leukoencephalopathy. We present here an investigation of the effects of the described mutations on the structure of the synthetase, in an effort to understand the tissue-specific outcomes of the different mutations. The mtAlaRS differs from the other mtARSs because in addition to the aminoacylation domain, it has a conserved editing domain for deacylating tRNAs that have been mischarged with incorrect amino acids. We show that the cardiomyopathy phenotype results from a single allele, causing an amino acid change R592W in the editing domain of AARS2, whereas the leukodystrophy mutations are located in other domains of the synthetase. Nevertheless, our structural analysis predicts that all mutations reduce the aminoacylation activity of the synthetase, because all mtAlaRS domains contribute to tRNA binding for aminoacylation. According to our model, the cardiomyopathy mutations severely compromise aminoacylation whereas partial activity is retained by the mutation combinations found in the leukodystrophy patients. These predictions provide a hypothesis for the molecular basis of the distinct tissue-specific phenotypic outcomes.

Keywords: alanyl-tRNA synthetase; aminoacyl-tRNA synthetases; mitochondrial disease; structural modeling; tissue-specificity.

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Figures

FIGURE 1
FIGURE 1
Patient haplotypes around the AARS2 mutation. The haplotype of the Swedish patient shows recombination 165 kilobases upstream of the mutation site.
FIGURE 2
FIGURE 2
AARS2 mutations. The compound heterozygous mutations found in patients with cardiomyopathy or leukodystrophy are illustrated. Truncating mutations that are predicted to destabilize the entire synthetase are marked with dotted lines. The thicker arrows demonstrate recurring mutations. The AARS2 mutation leading to the R592W amino acid change has been the only one identified in a homozygous state.
FIGURE 3
FIGURE 3
Sequence alignment between human mtAlaRS and AlaRS from A. fulgidus (3WQY). The alignment was extracted from multiple sequence alignment of AlaRS homologs from eukaryotes and prokaryotes using BioEdit software. The aminoacylation domain is marked with dark gray bar, the editing domain with cyan, and the C-terminal domain with magenta bars. Identical/similar amino acid residues in the same position are marked with colored boxes.
FIGURE 4
FIGURE 4
Overview of the modeled structure of human AlaRS. Aminoacylation subdomain (24–312 aa) is in silver, tRNA recognition subdomain (313–477 aa) of aminoacylation domain is in green, linker (“safety belt” – 478–529 aa) between tRNA recognition and editing domain is presented as solvent interpolated charge surface, β-barrel (530–621 aa) and editing core (622–783 aa) subdomains of editing domain are in pink and cyan, respectively. C-Ala domain or C-terminal domain is predicted to have helical (784–874 aa in magenta) and globular (875–985 aa in yellow) subdomains. R480 and R482 from the linker are predicted to stabilize bound tRNA within the aminoacylation domain. Backbone of docked tRNA is shown in dark gray. Docked alanyl-adenylate in the aminoacylation site is shown as stick model with carbon atoms labeled with magenta. Part of β-barrel subdomain (592–604 aa) of the editing domain proposed to interact with the linker is marked with purple (see text).
FIGURE 5
FIGURE 5
Analysis of the contact surface between linker (“safety belt”) and β-barrel of the editing domain in A. fulgidus AlaRS structure (3WQY), which was used as template for modeling. (A) Superimposed chains A “closed” form (blue) and B “open” form (pink). Fragments encompassing residues K474–D589 are shown. For superimposition T582–V613 fragment was used as tether. (B) Residues from the linker (“safety belt”) interacting with the surface exposed residues on the β-barrel in “closed” conformation. Carbon atoms of interacting amino acid residues are in blue. (C) The position of the same residues in “open” conformation (carbon atoms in magenta). Hydrophobic interactions are marked with magenta dashed lines, electrostatic interactions with orange dashed lines.
FIGURE 6
FIGURE 6
Analysis of the contact surface between linker (“safety belt”) and β-barrel of the editing domain in modeled human mitochondrial AlaRS. (A) Superimposed chains A “closed” form (green) and B “open” form (yellow). Fragments encompassing residues G468-D621 are shown. For superimposition Q615–L646 fragment was used as tether. (B) Interacting residues from the linker (”safety belt”) and surface exposed residues on the β-barrel in ”closed” conformation (shown in khaki). (C) Interacting residue in the “open” conformation (in orange). Hydrophobic interactions are marked with magenta dashed lines. Fragment L494–Q505 conserved between mitochondrial AlaRS homologs is marked with red.
FIGURE 7
FIGURE 7
Mapping and function predictions of AARS2 mutations associated with cardiomyopathy and leukodystrophy. Domains are color-coded as in Figure 4. Structural loss-of-function mutations are marked in black, mutations affecting substrate binding and resulting in severe reduction in aminoacylation activity are in red, and mutations resulting in moderate decrease of aminoacylation activity are in orange.
FIGURE 8
FIGURE 8
Classification of mutations based on structural predictions. The lines between mutation categories connect the compound heterozygous mutations identified in individual cardiomyopathy patients (with red lines), and leukodystrophy patients (with blue lines). The three categories at the top are predicted to have a severe effect on the aminoacylation function of the synthetase, whereas the mutations in the lower category are predicted to retain partial catalytic activity.
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References

    1. Ahola S., Isohanni P., Euro L., Brilhante V., Palotie A., Pihko H., et al. (2014). Mitochondrial EFTs defects in juvenile-onset Leigh disease, ataxia, neuropathy, and optic atrophy. Neurology 83 743–751 10.1212/WNL.0000000000000716 - DOI - PMC - PubMed
    1. Bayat V., Thiffault I., Jaiswal M., Tetreault M., Donti T., Sasarman F., et al. (2012). Mutations in the mitochondrial methionyl-tRNA synthetase cause a neurodegenerative phenotype in flies and a recessive ataxia (ARSAL) in humans. PLoS Biol. 10:e1001288 10.1371/journal.pbio.1001288 - DOI - PMC - PubMed
    1. Beebe K., Ribas De Pouplana L., Schimmel P. (2003). Elucidation of tRNA-dependent editing by a class II tRNA synthetase and significance for cell viability. EMBO J. 22 668–675 10.1093/emboj/cdg065 - DOI - PMC - PubMed
    1. Belostotsky R., Ben-Shalom E., Rinat C., Becker-Cohen R., Feinstein S., Zeligson S., et al. (2011). Mutations in the mitochondrial seryl-tRNA synthetase cause hyperuricemia, pulmonary hypertension, renal failure in infancy and alkalosis, HUPRA syndrome. Am. J. Hum. Genet. 88 193–200 10.1016/j.ajhg.2010.12.010 - DOI - PMC - PubMed
    1. Calvo S. E., Compton A. G., Hershman S. G., Lim S. C., Lieber D. S., Tucker E. J., et al. (2012). Molecular diagnosis of infantile mitochondrial disease with targeted next-generation sequencing. Sci. Transl. Med. 4:118ra10 10.1126/scitranslmed.3003310 - DOI - PMC - PubMed

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