Human tRNAs with inosine 34 are essential to efficiently translate eukarya-specific low-complexity proteins

The modification of adenosine to inosine at the wobble position (I34) of tRNA anticodons is an abundant and essential feature of eukaryotic tRNAs. The expansion of inosine-containing tRNAs in eukaryotes followed the transformation of the homodimeric bacterial enzyme TadA, which generates I34 in tRNAArg and tRNALeu, into the heterodimeric eukaryotic enzyme ADAT, which modifies up to eight different tRNAs. The emergence of ADAT and its larger set of substrates, strongly influenced the tRNA composition and codon usage of eukaryotic genomes. However, the selective advantages that drove the expansion of I34-tRNAs remain unknown. Here we investigate the functional relevance of I34-tRNAs in human cells and show that a full complement of these tRNAs is necessary for the translation of low-complexity protein domains enriched in amino acids cognate for I34-tRNAs. The coding sequences for these domains require codons translated by I34-tRNAs, in detriment of synonymous codons that use other tRNAs. I34-tRNA-dependent low-complexity proteins are enriched in functional categories related to cell adhesion, and depletion in I34-tRNAs leads to cellular phenotypes consistent with these roles. We show that the distribution of these low-complexity proteins mirrors the distribution of I34-tRNAs in the phylogenetic tree.

转运RNA（transfer RNA, tRNA）反密码子摆动位点（wobble position，I34）处，腺苷（adenosine）向肌苷（inosine）的修饰，是真核生物tRNA的一类普遍且必需的特征。真核生物中含肌苷的tRNA的扩增，源于同源二聚体细菌酶TadA向异源二聚体真核酶ADAT的演化：前者仅能在精氨酸转运RNA（tRNAArg）和亮氨酸转运RNA（tRNALeu）上催化I34位点修饰，后者则可修饰多达8种不同的tRNA。ADAT的出现及其更广泛的底物谱，极大地重塑了真核基因组的tRNA组成与密码子使用偏好。然而，驱动I34-tRNAs扩增的选择优势机制至今仍未阐明。本研究针对人类细胞中I34-tRNAs的功能相关性展开探究，结果显示，完整的I34-tRNA组分对于富集I34-tRNA对应氨基酸的低复杂度蛋白质结构域的翻译过程不可或缺。此类结构域的编码序列必须依赖由I34-tRNAs解码的密码子，而非采用依赖其他tRNA的同义密码子。依赖I34-tRNAs的低复杂度蛋白质，在与细胞黏附相关的功能类别中显著富集；而I34-tRNAs的缺失会导致与上述功能相符的细胞表型异常。本研究还发现，此类低复杂度蛋白质的系统发育分布与I34-tRNAs的系统发育分布高度一致。