Elucidating a newly discovered selective agent operating in bacterial genomes

描述(申请人提供)：细菌的基因组碱基组成差异很大，不同物种之间的差异从14%到75%G+C，这导致了对其起源、其持久性及其对细菌适合性的影响的许多猜测。已经提出了几种适应性的解释，然而，最有说服力和被广泛接受的观点是，50多年前首次提出的观点是，这种变异是中性的，是由分类群之间潜在突变模式的差异造成的。最近通过全面的序列比较反驳了这一观点，确定突变普遍偏向A+T，即使在基因组G+C含量较高的细菌中也是如此，这表明自然选择在决定碱基组成中发挥了作用。此外，初步实验表明，表达富含GC基因的细菌比表达富含AT基因的细菌显示出更高的生长率，这再次表明，在突变偏向A+T的基因组中，选择有利于更高的基因G+C。为什么以及如何在基因的碱基组成上进行选择是未知的，而且已知的对同义位点或基因和蛋白质表达施加限制的过程都不能解释有利于高G+C的选择力量。提出的工作的目标是确定(I)这种新发现的选择过程的来源，(Ii)其作用的普遍性，以及(Iii)通过什么机制 它在运作。这些目标将通过四个目标来实现，第一个目标是使用合成基因结构，旨在识别促进选择性差异的基因的关键组成特征。在第二个目标中，这些基因结构将在不同的细菌群中测试它们的选择效果，这些细菌群的突变模式和总体基因组碱基组成不同。结果将揭示选择是否作用于所有细菌共同的细胞过程。第三个目标将研究天然基因碱基组成变异的影响，以确定对基因G+C的选择性作用力在多大程度上与生理相关，并影响在基因组中驻留了数百万年的基因。虽然序列比较和适合度分析都为检测过去的选择行为提供了可靠的方法，但它们提供的关于其实际原因的信息很少。因此，最终目标将应用一种灵敏的、全基因组的方法来研究基因转录本和核糖体之间的相互作用，以阐明成分选择的机制基础。总之，这些研究将解决细菌进化中的一个长期问题，并增加我们对塑造细菌基因组的分子进化过程的理解。

DESCRIPTION (provided by applicant): The wide variation in the genomic base compositions of bacteria, which ranges among species from 14% to 75% G+C, has led to much speculation as to its origin, its persistence and its implications for bacterial fitness. Several adaptive explanations have been proposed~ however, the most persuasive and widely held view, first posited over 50 years ago, is that this variation is neutral, caused by differences among taxa in the underlying pattern of mutations. This view was recently countered through comprehensive sequence comparisons, which determined that mutations are universally biased towards A+T, even in bacteria with high genomic G+C contents, indicating a role of natural selection in determining base composition. Moreover, preliminary experiments revealed that bacteria expressing GC-rich versions of genes display higher growth rates than those expressing the identical protein from AT-rich versions, again showing that selection favors higher genic G+C in a genome where mutations are biased towards A+T. Why and how selection operates on the base composition of genes is unknown~ and none of the processes known to exert constraints on synonymous sites, or on gene and protein expression, can explain the selective force favoring high G+C. The goals of the proposed work are to determine (i) the source of this newly discovered selective process, (ii) the universality of its action, and (iii) the mechanism by which it operates. These goals will be accomplished in four Aims, the first of which employs synthetic gene constructs that are designed to identify the key compositional features of genes that foster the selective differences. In the second Aim, these gene constructs will be tested for their selective effects in bacterial groups that differ with respect to their mutational patterns and overall genomic base compositions~ results will reveal if selection acts on a cellular process that is common to all bacteria. The third Aim will examine effects of base compositional variation in native genes to determine the extent to which the selective force on genic G+C is physiologically relevant and has affected genes that have resided in a genome for millions of years. Although sequence comparisons and fitness assays both offer robust methods for detecting the past action of selection, they provide little information about its actual causes. Therefore, the final Aim will apply a sensitive, genome-wide approach for studying the interactions between gene transcripts and ribosomes to elucidate the mechanistic basis of compositional selection. Together, these studies will resolve a longstanding question in bacterial evolution and increase our understanding of the molecular evolutionary processes that shape bacterial genomes.