Saksena Saksham, Forbes Kwame, Rajan Nipun, Giles David
College of Arts and Sciences, Vanderbilt University, 2201 West End Ave., Nashville, TN, 37235, USA.
College of Science and Mathematics, The University of the Virgin Islands, 2 John Brewers Bay, St. Thomas, USVI, 00802-9990, USA.
Biochem Biophys Rep. 2023 Jul 4;35:101504. doi: 10.1016/j.bbrep.2023.101504. eCollection 2023 Sep.
The incorporation of exogenous fatty acids into the cell membrane yields structural modifications that directly influence membrane phospholipid composition and indirectly contribute to virulence. FadL and FadD are responsible for importing and activating exogenous fatty acids, while acyltransferases (PlsB, PlsC, PlsX, PlsY) incorporate fatty acids into the cell membrane. Many Gammaproteobacteria species possess multiple homologs of these proteins involved in exogenous fatty acid metabolism, suggesting the evolutionary acquisition and maintenance of this transport pathway.
This study developed phylogenetic trees based on amino acid and nucleotide sequences of homologs of FadL, FadD, PlsB, PlsC, PlsX, and PlsY via Mr. Bayes and RAxML algorithms. We also explored the operon arrangement of genes encoding for FadL. Additionally, FadL homologs were modeled via SWISS-MODEL, validated and refined by SAVES, Galaxy Refine, and GROMACS, and docked with fatty acids via AutoDock Vina. Resulting affinities were analyzed by 2-way ANOVA test and Tukey's post-hoc test.
Our phylogenetic trees revealed grouping based on operon structure, original homolog blasted from, and order of the homolog, suggesting a more ancestral origin of the multiple homolog phenomena. Our molecular docking simulations indicated a similar binding pattern for the fatty acids between the different FadL homologs.
Our study is the first to illustrate the phylogeny of these proteins and to investigate the binding of various FadL homologs across orders with fatty acids. This study helps unravel the mystery surrounding these proteins and presents topics for future research.
将外源脂肪酸掺入细胞膜会产生结构修饰，这些修饰直接影响膜磷脂组成，并间接促进毒力。FadL和FadD负责导入和激活外源脂肪酸，而酰基转移酶（PlsB、PlsC、PlsX、PlsY）则将脂肪酸掺入细胞膜。许多γ-变形菌物种拥有参与外源脂肪酸代谢的这些蛋白质的多个同源物，这表明该转运途径在进化过程中被获得并得以维持。
本研究通过Mr. Bayes和RAxML算法，基于FadL、FadD、PlsB、PlsC、PlsX和PlsY同源物的氨基酸和核苷酸序列构建了系统发育树。我们还探究了编码FadL的基因的操纵子排列。此外，通过SWISS-MODEL对FadL同源物进行建模，经SAVES、Galaxy Refine和GROMACS验证和优化，并通过AutoDock Vina与脂肪酸进行对接。通过双向方差分析和Tukey事后检验分析所得亲和力。
我们的系统发育树显示，基于操纵子结构、最初比对的同源物以及同源物的顺序进行分组，这表明多重同源物现象有更古老的起源。我们的分子对接模拟表明，不同FadL同源物之间的脂肪酸结合模式相似。
我们的研究首次阐明了这些蛋白质的系统发育，并研究了不同目之间各种FadL同源物与脂肪酸的结合情况。这项研究有助于揭开围绕这些蛋白质的谜团，并提出未来研究的课题。
