Codon usage bias is a universal feature of all genomes and plays an important role in regulating protein expression levels. Modification of adenosine to inosine at the tRNA anticodon wobble position (I34) by adenosine deaminases (ADATs) is observed in all eukaryotes and has been proposed to explain the correlation between codon usage and tRNA pool. However, how the tRNA pool is affected by I34 modification to influence codon usage-dependent gene expression is unclear. Using Neurospora crassa as a model system, by combining molecular, biochemical and bioinformatics analyses, we show that silencing of adat2 expression severely impaired the I34 modification levels for the ADAT-related tRNAs, resulting in major ADAT-related tRNA profile changes and reprogramming of translation elongation kinetics on ADAT-related codons. adat2 silencing also caused genome-wide codon usage-biased ribosome pausing on mRNAs and proteome landscape changes, leading to selective translational repression or induction of different mRNAs. The induced expression of CPC-1, the Neurospora ortholog of yeast GCN4p, mediates the transcriptional response after adat2 silencing and amino acid starvation. Together, our results demonstrate that the tRNA I34 modification by ADAT plays a major role in driving codon usage-biased translation to shape proteome landscape.

密码子使用偏倚是所有基因组的普遍特征，并且在调节蛋白质表达水平中起重要作用。在所有真核生物中均观察到腺苷脱氨酶（ADAT）将tRNA反密码子摆动位置（I34）的腺苷修饰为肌苷，并已被提议用于解释密码子使用与tRNA库之间的相关性。然而，尚不清楚I34修饰如何影响tRNA库以影响依赖密码子使用的基因表达。使用Neurospora crassa作为模型系统，通过分子，生化和生物信息学分析相结合，我们证明了adat2的沉默表达严重损害ADAT相关tRNA的I34修饰水平，导致主要ADAT相关tRNA谱变化和ADAT相关密码子翻译延伸动力学的重新编程。adat2沉默还引起全基因组使用密码子偏向核糖体的mRNA和蛋白质组景观变化的暂停，导致选择性翻译抑制或诱导不同的mRNA。酵母GCN4p的Neurospora直系同源基因CPC-1的诱导表达介导adat2沉默和氨基酸饥饿后的转录反应。在一起，我们的结果表明，ADAT对tRNA I34的修饰在驱动偏向密码子使用的翻译以形成蛋白质组格局方面起着重要作用。