Molecular evolution of the major outer-membrane protein gene (oprF) of Pseudomonas
Molecular evolution of the major outer-membrane protein gene (oprF) of Pseudomonas
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DOI：
10.1099/mic.0.28656-0
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发表时间：
2006-04-01
期刊：
影响因子：
2.8
通讯作者：
Barray, S
中科院分区：
文献类型：
--
作者：
Bodilis, J;Barray, S
假单胞菌的主要外膜蛋白OprF具有多种功能。它是一种非特异性的孔蛋白，在维持细胞形态、在低渗透压环境中生长以及与各种载体或分子的黏附中发挥作用。OprF作为疫苗成分的实用性、其在抗菌素耐药性中的作用以及其孔蛋白功能已被广泛研究。作者之前已经展示了OprF和16S rIDNA系统发育之间的重要差异：荧光假单胞菌分离物分成两个完全独立的簇，可能根据它们的生态位。本研究进一步探讨了oprF基因的进化史。对密码子第三位G+C含量、同义密码子使用(密码子适应指数)和基因组背景的研究表明，没有证据表明水平转移或基因重复。同样，不一致的稳健似然检验表明，oprF系统发育和物种系统发育之间没有显著的不一致。此外，不同簇之间的非同义突变与同义突变(K-a/K-S)的比率很高，特别是在含有荧光假单胞菌分离株的两个簇之间，这突显了oprF基因历史上进化限制的重要修改。由于OprF是已知的多效性蛋白质，进化限制的修改可能是由于与生态指纹相关的隐藏功能的变化造成的。最后，放松的限制和/或间歇性的积极进化，特别是对于一些荧光假单胞菌菌株，可能会导致系统发育重建人工制品。
The major outer-membrane protein of Pseudomonas, OprF, is multifunctional. It is a non-specific porin that plays a role in maintenance of cell shape, in growth in a low-osmolarity environment, and in adhesion to various supports or molecules. OprF has been studied extensively for its utility as a vaccine component, its role in antimicrobial drug resistance, and its porin function. The authors have previously shown important differences between the OprF and 16S rIDNA phylogenies: Pseudomonas fluorescens isolates split into two quite separate clusters, probably according to their ecological niche. In this study, the evolutionary history of the oprF gene was investigated further. The study of G + C content at the third codon position, synonymous codon usage (codon adaptation index, CAI) and genomic context showed no evidence of horizontal transfer or gene duplication. Similarly, a robust likelihood test of incongruence showed no significant incongruence between the oprF phylogeny and the species phylogeny. In addition, the ratio of nonsynonymous mutations to synonymous mutations (K-a/K-s) is high between the different clusters, especially between the two clusters containing P. fluorescens isolates, highlighting important modifications in evolutionary constraints during the history of the oprF gene. Since OprF is known as a pleiotropic protein, modifications in evolutionary constraints could have resulted from variations in cryptic functions, correlated with the ecological fingerprint. Finally, relaxed constraints and/or episodic positive evolution, especially for some P. fluorescens strains, could have led to a phylogeny reconstruction artifact.