豆科植物百脉根(Lotus japonicus)的根瘤感受基因Nin与根瘤的早期发育有关。Nin的同源基因(Nin-like基因)功能上涉及氮代谢过程。从完成测序的豆科和非豆科植物基因组中获取Nin-like基因并进行系统发育分析。在此基础上, 追踪基因和蛋白质结构的歧异式样, 尝试建立结构歧异和功能分化的联系。通过比较, 新的Nin-like基因被鉴别。系统发育分析不仅重现了以前分辨的直系同源群(分支I、II和III), 且识别了它们之间的姐妹群关系。Nin-like基因的结构呈现多样性, 支持系统发育分析的结果。水稻OsNLP5基因缺乏内含子, 可能起源于基因返座事件。NIN-like蛋白结构域组织和功能位点在不同分支中存在差异, 提示它们的功能发生了分化。根瘤固氮植物NIN-like蛋白的GAF结构域中存在一个显著变异区, 三级建模分析显示这个变异区对应于百脉根非固氮NIN-like蛋白的一段保守构象, 这一变异可能使豆科植物具有根瘤固氮能力。研究结果为阐明Nin-like基因的功能提供了新的研究思路。
The nodule inception gene Nin is related to early stages of root nodule formation in the model plant Lotus japonicus. Functionally, its homologs, Nin-like genes, are also involved in N metabolism. In this study, Nin-like gene data were retrieved from completely sequencing genomes of legume and non-legume plants for investigating phylogeny to trace the divergence of genes and proteins and build relationships between structural divergence and functional differentiation. We revealed novel Nin-like genes; previously resolved orthologous groups were recovered and their sister relationships resolved. Nin-like genes showed a diversity of structures, which supports the results of phylogenetic and functional studies; OsNLP5 from Oryza sativa was found to be intronless, which probably originated from a gene retroposition event. We found discrepancies in domain organizations and functional sites among NIN-like proteins, which indicates possible functional differentiation. 3-D structural analysis revealed the occurrence of significant conformational changes in GAF domains of NIN-like proteins from nodule legume plants, which could become the basis of recruitment as nodule inception genes. Our findings will contribute to the design of further experimental studies.