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Evolutionary responses to codon usage of horizontally transferred genes in Pseudomonas aeruginosa: gene retention, amelioration and compensatory evolution
Microbial Genomics ( IF 3.9 ) Pub Date : 2021-06-24 , DOI: 10.1099/mgen.0.000587
Martijn Callens 1 , Celine Scornavacca 2 , Stéphanie Bedhomme 1
Affiliation  

Prokaryote genome evolution is characterized by the frequent gain of genes through horizontal gene transfer (HGT). For a gene, being horizontally transferred can represent a strong change in its genomic and physiological context. If the codon usage of a transferred gene deviates from that of the receiving organism, the fitness benefits it provides can be reduced due to a mismatch with the expression machinery. Consequently, transferred genes with a deviating codon usage can be selected against or elicit evolutionary responses that enhance their integration, such as gene amelioration and compensatory evolution. Within bacterial species, the extent and relative importance of these different mechanisms has never been considered altogether. In this study, a phylogeny-based method was used to investigate the occurrence of these different evolutionary responses in Pseudomonas aeruginosa . Selection on codon usage of genes acquired through HGT was observed over evolutionary time, with the overall codon usage converging towards that of the core genome. Gene amelioration, through the accumulation of synonymous mutations after HGT, did not seem to systematically affect transferred genes. This pattern therefore seemed to be mainly driven by selective retention of transferred genes with an initial codon usage similar to that of the core genes. Additionally, variation in the copy number of tRNA genes was often associated with the acquisition of genes for which the observed variation could enhance their expression. This provides evidence that compensatory evolution might be an important mechanism for the integration of horizontally transferred genes.

中文翻译:

铜绿假单胞菌中水平转移基因密码子使用的进化反应:基因保留、改善和补偿进化

原核生物基因组进化的特点是通过水平基因转移(HGT)频繁获得基因。对于一个基因来说,水平转移可以代表其基因组和生理背景的强烈变化。如果转移基因的密码子使用与接收生物体的密码子使用不同,则由于与表达机制的不匹配,其提供的适应性益处可能会减少。因此,具有不同密码子使用的转移基因可以被选择以对抗或引发增强其整合的进化反应,例如基因改善和补偿进化。在细菌物种中,这些不同机制的程度和相对重要性从未被完全考虑过。在本研究中,使用基于系统发育的方法来研究铜绿假单胞菌中这些不同进化反应的发生。在进化过程中观察到通过 HGT 获得的基因密码子使用的选择,总体密码子使用向核心基因组的密码子使用趋同。通过 HGT 后同义突变的积累进行的基因改善似乎并没有系统地影响转移的基因。因此,这种模式似乎主要是由选择性保留所转移的基因驱动的,其初始密码子使用与核心基因相似。此外,tRNA 基因拷贝数的变化通常与观察到的变化可以增强其表达的基因的获得有关。这提供了证据表明补偿进化可能是水平转移基因整合的重要机制。
更新日期:2021-06-25
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