Analysis of tRNA gene evolution in bacterial genomes

转移RNA （tRNA）基因是最重要和最古老的基因之一。大量的研究涉及tRNA序列鉴定、结构预测和身份元件。然而，在全基因组范围内，tRNA基因在数量、组织和功能特异性方面的进化知之甚少。更好地了解tRNA库进化有望揭示许多与蛋白质表达相关的重要问题，如tRNA拷贝数与蛋白质合成之间的联系，遗传密码的进化和tRNA功能转移。此外，由于tRNA基因分散在整个基因组中，它们代表了一个有趣的基因子集，可以用来研究改变基因组的主要进化事件。最近，我们推测了50株芽孢杆菌中tRNA基因的进化历史。我们观察到芽孢杆菌基因组中的tRNA基因主要受到重复和缺失的影响。我们还观察到在复制轴（起点或终点）周围发生了大的反转。最有趣和令人惊讶的结果来自于对芽孢杆菌和大肠杆菌中不同类型事件发生率的比较。在芽孢杆菌中推断的平均重复率比大肠杆菌研究报告的重复率低24倍，而平均损失和反转率都低12倍。这些比率极低，表明在芽孢杆菌中tRNA基因库有很强的选择压力。我的研究项目的目标是在其他细菌中进行类似的分析。随着越来越多的细菌基因组被完全测序，有越来越多有趣的细菌属可以分析：例如李斯特菌，沙门氏菌，葡萄球菌，链球菌和弧菌。将其他属的进化与从芽孢杆菌和大肠杆菌中推断出来的进化进行比较，将有助于了解某些属是否在tRNA基因的数量和组织方面明显比其他属更稳定，以及这种稳定性与这些不同细菌的生活环境之间是否存在关联。然而，与芽孢杆菌相比，大多数新测序的细菌属表现出非常高的分化水平，因此需要开发新的算法方法来推断这些基因组中tRNA基因的进化史。特别是，考虑重叠事件的方法和考虑序列、基因组背景和结构信息的方法将被用于两个基因组的比较，然后将被优化和推广到计算整个系统发育背景下的最小进化距离。

Transfer RNA (tRNA) genes are among the most important and ancient genes. A large number of studies have addressed tRNA sequence identification, structure prediction and identity elements. However, little is known about the evolution of tRNA genes in terms of number, organization and functional specificity on a genome-wide scale. Having a better understanding of tRNA repertoire evolution is expected to shed light on many important questions related to protein expression, such as the link between tRNA copy number and protein synthesis, the evolution of the genetic code and tRNA functional shift. Moreover, since tRNA genes are dispersed throughout the genome, they represent an interesting subset of genes to study the major evolutionary events that have transformed the genomes. Recently, we inferred the evolutionary history of the tRNA genes in 50 Bacillus strains. We observed that the tRNA genes in Bacillus genomes are mostly affected by duplications and deletions. We also observed large inversions occurring around the axes of replication (origin or terminus). The most interesting and surprising result came from the comparison of the rates of the different types of events in Bacillus and E. coli. The average rate of duplications inferred in Bacillus was 24 times lower than the one that was reported in the E. coli study, while the average rates of losses and inversions were both 12 times lower. These rates were extremely low, suggesting a strong selective pressure acting on tRNA gene repertoires in Bacillus. The goal of my research program is to conduct similar analyses in other bacteria. With the ever-increasing number of bacterial genomes being completely sequenced, there are more and more interesting bacterial genera to analyze: Listeria, Salmonella, Staphylococcus, Streptococcus and Vibrio for example. Comparing the evolution of those other genera with what was inferred in Bacillus and E. coli would help understand if certain genera are clearly more stable than others in terms of the number and the organization of tRNA genes, and if there is a correlation between this stability and the living environment of those different bacteria. However, as most of these newly sequenced bacterial genera exhibit a very high level of divergence compared to Bacillus, new algorithmic methods need to be developed to infer evolutionary histories of tRNA genes in those genomes. In particular, methods taking into account overlapping events and methods considering sequence, genomic context and structural information will be developed for the comparison of two genomes, then will be optimized and generalized to calculate the minimum evolutionary distance in the context of a whole phylogeny.