Elsevier

Methods

Volume 113, 15 January 2017, Pages 139-151
Methods

Predicting the pathogenicity of aminoacyl-tRNA synthetase mutations

https://doi.org/10.1016/j.ymeth.2016.11.013Get rights and content

Highlights

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    Aminoacyl-tRNA synthetases (ARSs) are essential and ligate tRNA to amino acids.

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    Genes encoding ARSs are associated with a spectrum of human inherited diseases.

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    Implicating an ARS allele in genetic disease requires strong genetic evidence.

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    Most ARS mutations implicated in human disease cause impaired enzyme function.

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    Functional studies should be cautiously employed to assess ARS mutations.

Abstract

Aminoacyl-tRNA synthetases (ARSs) are ubiquitously expressed, essential enzymes responsible for charging tRNA with cognate amino acids—the first step in protein synthesis. ARSs are required for protein translation in the cytoplasm and mitochondria of all cells. Surprisingly, mutations in 28 of the 37 nuclear-encoded human ARS genes have been linked to a variety of recessive and dominant tissue-specific disorders. Current data indicate that impaired enzyme function is a robust predictor of the pathogenicity of ARS mutations. However, experimental model systems that distinguish between pathogenic and non-pathogenic ARS variants are required for implicating newly identified ARS mutations in disease. Here, we outline strategies to assist in predicting the pathogenicity of ARS variants and urge cautious evaluation of genetic and functional data prior to linking an ARS mutation to a human disease phenotype.

Section snippets

Mutations in nuclear-encoded ARS enzymes cause human inherited disease

Aminoacyl-tRNA synthetases (ARSs) are ubiquitously expressed, essential enzymes that charge tRNA molecules with cognate amino acids in the cytoplasm and mitochondria. The human nuclear genome harbors 37 ARS loci: 17 that encode a cytoplasmic enzyme, 17 that encode a mitochondrial enzyme, and three that encode a bi-functional enzyme that charges tRNA for both cytoplasmic and mitochondrial protein translation [1]. One of the more interesting, albeit perplexing, findings in ARS research is that

Linkage analysis

To identify a genetic locus involved in Mendelian disease pathogenesis, investigators must first ensure that the phenotype of interest is both monogenetic (i.e., caused by a single gene) and measurable [17]. When feasible, generating a pedigree that illustrates the familial structure and phenotypic information for each individual allows for interrogation of the inheritance pattern (e.g., dominant, recessive, or X-linked). Clinical data must be carefully collected to ensure that factors such as

Functional studies to predict the pathogenicity of ARS variants

Linkage, statistical, and validation studies are required for implicating a mutation in any Mendelian disease. However, functional studies can also be used to assist in predicting, but not proving, pathogenicity. These studies are most useful when the functional consequences of a newly identified variant can be compared to the functional consequences of variants that have been implicated in disease via strong genetic data (e.g., R329H AARS). As mentioned, mutations in genes encoding ARS enzymes

Models to study the mechanism of ARS mutations in human disease

The functional strategies outlined above are useful for predicting the pathogenicity of newly identified ARS variants. Interestingly, the majority of previous studies employing these approaches revealed loss-of-function effects for ARS mutations implicated in recessive and dominant disease phenotypes. A loss-of-function effect is clearly the predominant hypothesis for the molecular pathology of ARS-associated recessive diseases, which is supported by functional analyses and the types of alleles

Moving forward: New disease-associated ARS loci and alleles

It is important to emphasize that building a strong genetic argument is essential for implicating any newly identified ARS locus or allele in human Mendelian disease. Specifically, the mode of inheritance (autosomal recessive or autosomal dominant; all ARS loci are encoded on autosomes) must be considered in the context of factors such as the disease prevalence, the frequency of the implicated variant in control populations, and the genotypes of individuals in control populations that carry the

Funding

L.B.G. was supported by the NIH Cellular and Molecular Biology Training Grant (GM007315), the NIH Medical Scientist Training Grant (GM07863), and an NIH F30 NRSA (NS092238). A.A.B is supported by grants from the Muscular Dystrophy Association (MDA382300) and the National Institute of Neurological Disorders and Stroke (NS094678). A.A. is supported by grants from the Muscular Dystrophy Association (MDA294479) and the National Institute of General Medical Sciences (GM118647).

Acknowledgments

We would like to thank all of the patients and their families for agreeing to participate in the studies reviewed here; each of our colleagues for contributing to our current knowledge of ARS-associated disease; and Rebecca Meyer for critical evaluation of the manuscript.

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