Molecular evolution and optimization of the translation machinery

翻译是基因分型和表型分型之间的关键环节。准确和有效的翻译、起始和延伸对于包括病毒在内的生物体的成功至关重要。我将在这个项目中解决的研究问题包括：1.翻译起始：在酵母等模式生物中，5‘非编码区应该具有哪些序列特征来提高翻译起始(以核糖体密度衡量)的效率？翻译起始因子和Poly(A)结合蛋白的变化如何影响5‘非编码区翻译相关基序的进化？5‘非编码区中调节翻译起始的基序是什么？在哪里？2.翻译延长：许多实验研究监测了将同义密码子替换为最喜欢或最不喜欢的密码子后的翻译效率。为什么这些实验经常有相互矛盾的结果，例如，一些实验发现使用优化的密码子显著提高了蛋白质产量，而另一些实验则没有发现任何改善？这些研究忽略了翻译起始，然而密码子优化只有在翻译起始有效的情况下才能提高蛋白质产量。我们假设，那些发现优化密码子没有改善蛋白质生产的研究涉及翻译起始效率低或一般的mRNAs，并将使用最近获得的核糖体加载数据来验证这一假说。3.用于研究翻译的生物信息学工具：我们应该如何开发和改进生物信息学工具，以便更好地量化调控基序(目前主要通过位置权重矩阵和隐马尔可夫模型的特征)和密码子使用偏向(例如，密码子适应指数、有效密码子数量等)。为了便于对翻译的起始、延伸和终止的研究？例如，目前的密码子使用偏倚指数不能校正背景核苷酸频率，也不能区分突变和选择的影响。我们的研究将有助于制药行业从事蛋白质生产。

Translation is the key link between genotype and phenotype. Accurate and efficient translation initiation and elongation are essential for the success of living organisms including viruses. Research questions I will address in this project include:1. Translation initiation: What sequence features should the 5' UTR have to increase the efficiency of translation initiation (measured by ribosomal density) in model organisms such as the yeast? How do translation-related motifs in 5' UTR evolve in response to changes in translation initiation factors and poly(A) binding protein? What and where are the motifs in 5' UTR that modulate translation initiation?2. Translation elongation: Many experimental studies have monitored translation efficiency after replacing synonymous codons either to the most preferred or the least preferred codons. Why do these experiments often have contradictory results, e.g., some finding dramatically improved protein production with optimized codons and some finding no improvement? These studies ignored translation initiation, yet codon optimization can lead to improved protein production only when translation initiation is efficient. We hypothesize that those studies finding no improved protein production with optimized codons involve mRNAs of low or mediocre translation initiation efficiency and will test the hypothesis by using ribosomal loading data available recently. 3. Bioinformatics tools for study translation: How should we develop and improve bioinformatic tools for better quantification of regulatory motifs (currently characterized mainly by position weight matrix and profiles from hidden Markov models) and codon usage bias (e.g., codon adaptation index, effective number of codons, etc.) in order to facilitate studies on translation initiation, elongation and termination? For example, current codon usage bias indices do not correct for background nucleotide frequencies and do not distinguish the effect of mutation and selection.Our research will contribute to pharmaceutical industry engaged in protein production.