Identification and rescue of a tRNA wobble inosine deficiency causing intellectual disability disorder

Abstract

The deamination of adenosine to inosine at the wobble position of tRNA is an essential post-transcriptional RNA modification required for wobble decoding in bacteria and eukaryotes. In humans, the wobble inosine modification is catalyzed by the heterodimeric ADAT2/3 complex. Here, we describe novel pathogenic ADAT3 variants impairing adenosine deaminase activity through a distinct mechanism that can be corrected through expression of the heterodimeric ADAT2 subunit. The variants were identified in a family in which all three siblings exhibit intellectual disability linked to biallelic variants in the ADAT3 locus. The biallelic ADAT3 variants result in a missense variant converting alanine to valine at a conserved residue or the introduction of a premature stop codon in the deaminase domain. Fibroblast cells derived from two ID-affected individuals exhibit a reduction in tRNA wobble inosine levels and severely diminished adenosine tRNA deaminase activity. Notably, the ADAT3 variants exhibit impaired interaction with the ADAT2 subunit and alterations in ADAT2-dependent nuclear localization. Based upon these findings, we find that tRNA adenosine deaminase activity and wobble inosine modification can be rescued in patient cells by overexpression of the ADAT2 catalytic subunit. These results uncover a key role for the inactive ADAT3 deaminase domain in proper assembly with ADAT2 and demonstrate that ADAT2/3 nuclear import is required for maintaining proper levels of the wobble inosine modification in tRNA.

The structure of the mouse ADAT2/ADAT3 complex reveals the molecular basis for mammalian tRNA wobble adenosine-to-inosine deamination

“…Thus, our study provides the molecular basis for further investigating the involvement of ADAT in diseases ( 25–29 , 47 ). However, the mechanisms affected by the loss of tRNA wobble A-to-I modification in disease remain to be characterized.…”

The Importance of the Epi-Transcriptome in Translation Fidelity

“…I 37 is deaminated by ADAT1 and further modified by methylation (m 1 I 37 ) catalyzed by the tRNA methyltransferase TRM3 [ 48 ]. A deficiency of I 34 has been reported to affect human health, with patients presenting bi-allelic ADAT3 mutations displaying intellectual disability [ 49 ].…”

Methylated guanosine and uridine modifications inS. cerevisiaemRNAs modulate translation elongation

“…To date, over 150 different nucleoside chemical modifications have been identified within non-coding RNAs (ncRNA), and many are important, or even essential, for a myriad of cellular processes 1,3 . The significance of RNA modifications to cellular health is underscored by decades of observations implicating the mis-regulation of ncRNA modifying enzymes in cancer and other diseases [4][5][6][7][8][9] . Recent advances in next generation RNA sequencing (RNA-seq) [10][11][12][13][14][15][16][17][18][19] and liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) technologies [20][21][22][23][24] enabled the detection of chemical modifications in protein encoding messenger RNAs (mRNA).…”