Mechanism of action of codon pair bias

密码子对偏倚的作用机制

基本信息

批准号：
8158728
负责人：
BRUCE Bruce FUTCHER
金额：
$ 23.5万
依托单位：
STATE UNIVERSITY NEW YORK STONY BROOK
依托单位国家：
美国
项目类别：
财政年份：
2011
资助国家：
美国
起止时间：
2011-08-01 至 2015-04-30
项目状态：
已结题

项目摘要

DESCRIPTION (provided by applicant): Because an amino acid can be encoded by as many as six codons, there are many different ways to encode any particular protein. Biases exist in the way codons are used. One well- known bias is the codon bias, which is simply that some codons are used more than others. Less well-known is that there is also a "codon pair bias", such that some codons "prefer" to be adjacent to certain other codons. This codon pair bias is completely separate and independent from the codon bias. Recently, we have found that when viruses are re-coded to have a bad codon pair bias, the viruses are attenuated, in extreme cases to inviability. It appears that attenuation of a virus via a bad codon pair bias can be used to make a live, attenuated vaccine. However, while the procedure works, nothing whatever is known about the mechanim by which codon pair bias causes attenuation, and this lack of knowledge is slowing the work with viral vaccines. In this proposal, we will investigate, for the first time, the mechanism of attenuation by bad codon pair bias. This will be done in yeast, where we have recently shown there are strong codon pair bias effects. We will confirm the effects of codon pair bias in yeast using two codon pair de-optimized synthetic yeast genes, dHIS3 and dLYS2. We will test the idea that bad codon pair bias slows translation using polysome profiling and ribosome density mapping. We will test the idea that bad codon pair bias causes inaccurate translation and protein degradation by turning off proteasomal degradation, and also using other methods. We have already selected yeast mutants that are apparently less sensitive than wild-type to codon pair bias, and we will characterize these mutants and identify the mutant genes. Finally we will do a high- throughput study of (initially) 22,000 different encodings of HIS3 to correlate particular encodings with the strength of gene function. Our long term goal is to understand the mechanism of attenuation by bad codon pair bias to facilitate the development of live, attenuated viral vaccines, and also to facilitate the tuning of gene expression. PUBLIC HEALTH RELEVANCE: One way to make an anti-viral vaccine is to mutate the virus to weaken it, then use this weakened virus as a vaccine (e.g., FluMist, a live Flu vaccine). However there are many difficulties in doing this. Recently we have found a new method, codon pair de-optimization, for this purpose. Although the method works, we do not know why it works. Here, we will study the mechanism of attenuation by codon pair de-optimization.

描述（由申请人提供）：由于氨基酸可以由多达六个密码子编码，因此有许多不同的方法可以编码任何特定的蛋白质。偏见以使用密码子的方式存在。一个众所周知的偏见是密码子偏见，这仅仅是某些密码子比其他密码子更多。鲜为人知的是，还有一个“密码子对偏置”，因此某些密码子“更喜欢”与某些其他密码子相邻。该密码子对偏置是完全独立的，并且与密码子偏置无关。最近，我们发现，当病毒被重新编码以具有不良的密码子对偏置时，在极端情况下，病毒会减弱。看来通过不良密码子对偏置的病毒衰减可用于生产现场衰减的疫苗。但是，尽管该过程有效，但对密码子对偏置引起衰减的机械的了解一无所知，缺乏知识正在减缓病毒疫苗的工作。在此提案中，我们将首次研究不良密码子对偏差的衰减机制。这将在酵母中完成，我们最近显示有强大的密码子对偏置效应。我们将使用两个密码子对脱离合成酵母基因DHIS3和DLYS2确认酵母中密码子对偏置的影响。我们将测试使用多核体分析和核糖体密度映射减慢翻译的不良密码子偏置的想法。我们将测试不良密码子对偏置通过关闭蛋白酶体降解以及使用其他方法而导致不准确的翻译和蛋白质降解的想法。我们已经选择了显然对密码子对偏置敏感的酵母突变体，我们将表征这些突变体并鉴定突变基因。最后，我们将对His3的22,000个不同编码进行高吞吐量研究，以将特定的编码与基因功能的强度相关联。我们的长期目标是了解不良密码子对衰减的机理，以促进活体，病毒疫苗的发展，并促进基因表达的调整。公共卫生相关性：制造抗病毒疫苗的一种方法是突变病毒以削弱该病毒，然后将这种弱的病毒用作疫苗（例如Flumist，一种活流感疫苗）。但是，这样做有很多困难。最近，为此，我们发现了一种新方法，即密码子对脱位。尽管该方法有效，但我们不知道为什么它有效。在这里，我们将研究密码子对降低的衰减机制。