tRNA in codon usage

项目概要： 密码子使用是每个基因和每个基因组的特定特征，并影响每个生物体的适应性。在 由于遗传密码的简并性，蛋白质可以使用不同的同义词集合以多种方式编码。 密码子，其在速度或质量上不相等地翻译。同义词之间的每个密码子选择 需要提供具有匹配反密码子的tRNA。密码子-反密码子配对的质量 相互作用不仅取决于密码子的tRNA水平，还取决于表观遗传修饰。 转录后合成的tRNA。虽然大多数研究都集中在丰富的 tRNA作为密码子使用和细胞适应性的决定因素，对转录后修饰知之甚少。 在过去的5年里，我的实验室一直致力于合成人β-内酰胺酶的37位鸟嘌呤的N1-甲基化， tRNA中的m1 G37，在蛋白质合成过程中维持阅读框所需。m1 G37缺失- tRNA导致核糖体+1-移位的积累，导致蛋白质合成的过早终止， 最终导致细胞死亡。我们工作的一个关键发现是，虽然m1 G37是翻译所有四个密码子所必需的， 对于脯氨酸（Pro），其对于CC[C/U]密码子的翻译是必需的。因为Pro是蛋白质中唯一的氨基酸 合成，这一发现提供了有趣和重要的新生物学，其中m1 G37-tRNA提供了一个全球性的 控制CC[C/U]富集基因表达的机制。在下一个研究领域，我们将重点关注 的m1 G37依赖的差异翻译CC[CU]作为一个模型来阐明的原则， tRNA的供需比决定了细胞的适应性。本文首先分析了E.杆菌 作为全基因组蛋白质合成的报告者。我们将测试所阐明的原则的预测能力， 确定人类蛋白质组。我们还将讨论m1 G甲基化的作用，当放置在9位时， 致病性线粒体tRNA（mt-tRNA），在线粒体疾病的发展。通过探索 我们开发的独特方法和概念框架，我们将解决这些关键差距 并促进我们对人类健康和疾病中密码子使用的理解。

PROJECT SUMMARY: Codon usage is a specific feature of each gene and each genome and impacts the fitness of each organism. In the degeneracy of the genetic code, proteins can be coded in multiple ways using different sets of synonymous codons, which are not translated equally in speed or quality. Each codon choice between the synonyms makes a demand for the supply of the tRNA with the matching anticodon. The quality of a codon-anticodon pairing interaction is determined not only by the level of the tRNA for the codon, but also by the epigenetic modifications to the tRNA that are synthesized post-transcriptionally. While most studies have focused on the abundance of tRNA as a determinant of codon usage and cell fitness, less is known about post-transcriptional modifications. In the past 5 years, my lab has focused on the N1-methylation of the guanine at position 37 that synthesizes m1G37 in tRNAs, which is required for reading-frame maintenance during protein synthesis. Loss of m1G37- tRNAs leads to accumulation of ribosomal +1-shifts, resulting in pre-mature termination of protein synthesis and ultimately cell death. A key finding of our work is that, while m1G37 is required for translation of all four codons for proline (Pro), it is essential for translation of CC[C/U] codons. Because Pro is a unique amino acid in protein synthesis, this finding offers interesting and important new biology, in which m1G37-tRNAs provide a global mechanism to control the expression of CC[C/U]-enriched genes. In the next frontier of research, we will focus on the m1G37-dependent differential translation of CC[CU] as a model to elucidate the principles by which the supply-to-demand ratio of tRNAs governs cell fitness. We will start by analysis of the balanced growth of E. coli as a reporter for genome-wide protein synthesis. We will test the predictive power of the elucidated principles in determining the human proteome. We will also address the role of m1G methylation, when placed at position 9 of a pathogenic mitochondrial tRNA (mt-tRNA), in the development of the mitochondrial disorder. By exploring the unique methodologies and conceptual frameworks that we have developed, we will address these key gaps in the field and advance our understanding of codon usage in human health and disease.