Data_Sheet_2_Towards Understanding Afghanistan Pea Symbiotic Phenotype Through the Molecular Modeling of the Interaction Between LykX-Sym10 Receptor Heterodimer and Nod Factors.ZIP

The difference in symbiotic specificity between peas of Afghanistan and European phenotypes was investigated using molecular modeling. Considering segregating amino acid polymorphism, we examined interactions of pea LykX-Sym10 receptor heterodimers with four forms of Nodulation factor (NF) that varied in natural decorations (acetylation and length of the glucosamine chain). First, we showed the stability of the LykX-Sym10 dimer during molecular dynamics (MD) in solvent and in the presence of a membrane. Then, four NFs were separately docked to one European and two Afghanistan dimers, and the results of these interactions were in line with corresponding pea symbiotic phenotypes. The European variant of the LykX-Sym10 dimer effectively interacts with both acetylated and non-acetylated forms of NF, while the Afghanistan variants successfully interact with the acetylated form only. We additionally demonstrated that the length of the NF glucosamine chain contributes to controlling the effectiveness of the symbiotic interaction. The obtained results support a recent hypothesis that the LykX gene is a suitable candidate for the unidentified Sym2 allele, the determinant of pea specificity toward Rhizobium leguminosarum bv. viciae strains producing NFs with or without an acetylation decoration. The developed modeling methodology demonstrated its power in multiple searches for genetic determinants, when experimental detection of such determinants has proven extremely difficult.

本研究借助分子建模（molecular modeling）技术，探究了阿富汗表型与欧洲表型豌豆之间的共生特异性差异。基于分离氨基酸多态性（segregating amino acid polymorphism），我们分析了豌豆LykX-Sym10受体异二聚体（LykX-Sym10 receptor heterodimers）与四种经天然修饰的结瘤因子（Nodulation factor, NF）之间的相互作用——这四种结瘤因子的差异体现在乙酰化修饰及葡糖胺链长度两个维度。
首先，我们验证了LykX-Sym10二聚体在溶剂体系及膜环境中的分子动力学（molecular dynamics, MD）稳定性。随后，将四种结瘤因子分别与1个欧洲型二聚体及2个阿富汗型二聚体进行分子对接，所得相互作用结果与对应豌豆的共生表型高度契合。欧洲型LykX-Sym10二聚体可有效结合乙酰化与非乙酰化两种形式的结瘤因子，而阿富汗型二聚体仅能成功结合乙酰化形式的结瘤因子。
此外，我们证实结瘤因子的葡糖胺链长度可调控共生相互作用的有效性。本研究结果支持近期提出的假说：LykX基因可作为未被鉴定的Sym2等位基因（Sym2 allele）的候选基因，该等位基因是豌豆对产生带/不带乙酰化修饰结瘤因子的豌豆根瘤菌蚕豆生物型（Rhizobium leguminosarum bv. viciae）菌株具有宿主特异性的决定因子。本研究开发的建模方法在实验检测此类遗传决定因子（genetic determinants）极具挑战的场景下，展现出用于多维度筛选遗传决定因子的优异效能。