College of Life Sciences, Capital Normal University, Beijing 100048, China.
BMC Evol Biol. 2014 Jun 9;14:124. doi: 10.1186/1471-2148-14-124.
The caleosin genes encode proteins with a single conserved EF hand calcium-binding domain and comprise small gene families found in a wide range of plant species. These proteins may be involved in many cellular and biological processes coupled closely to the synthesis, degradation, or stability of oil bodies. Although previous studies of this protein family have been reported for Arabidopsis and other species, understanding of the evolution of the caleosin gene family in plants remains inadequate.
In this study, comparative genomic analysis was performed to investigate the phylogenetic relationships, evolutionary history, functional divergence, positive selection, and coevolution of caleosins. First, 84 caleosin genes were identified from five main lineages that included 15 species. Phylogenetic analysis placed these caleosins into five distinct subfamilies (sub I-V), including two subfamilies that have not been previously identified. Among these subfamilies, sub II coincided with the distinct P-caleosin isoform recently identified in the pollen oil bodies of lily; caleosin genes from the same lineage tended to be clustered together in the phylogenetic tree. A special motif was determined to be related with the classification of caleosins, which may have resulted from a deletion in sub I and sub III occurring after the evolutionary divergence of monocot and dicot species. Additionally, several segmentally and tandem-duplicated gene pairs were identified from seven species, and further analysis revealed that caleosins of different species did not share a common expansion model. The ages of each pair of duplications were calculated, and most were consistent with the time of genome-wide duplication events in each species. Functional divergence analysis showed that changes in functional constraints have occurred between subfamilies I/IV, II/IV, and II/V, and some critical amino acid sites were identified during the functional divergence. Additional analyses revealed that caleosins were under positive selection during evolution, and seven candidate amino acid sites (70R, 74G, 88 L, 89G, 100 K, 106A, 107S) for positive selection were identified. Interestingly, the critical amino acid residues of functional divergence and positive selection were mainly located in C-terminal domain. Finally, three groups of coevolved amino acid sites were identified. Among these coevolved sites, seven from group 2 were located in the Ca2+-binding region of crucial importance.
In this study, the evolutionary and expansion patterns of the caleosin gene family were predicted, and a series of amino acid sites relevant to their functional divergence, adaptive evolution, and coevolution were identified. These findings provide data to facilitate further functional analysis of caleosin gene families in the plant lineage.
钙调素蛋白基因编码具有单个保守 EF 手钙结合域的蛋白质，包含在广泛的植物物种中发现的小基因家族。这些蛋白质可能参与许多与油体的合成、降解或稳定性密切相关的细胞和生物学过程。尽管先前已经对拟南芥和其他物种的这种蛋白质家族进行了研究，但对植物中钙调素基因家族的进化仍了解不足。
本研究通过比较基因组分析，研究了钙调素的系统发育关系、进化历史、功能分化、正选择和共进化。首先，从包括 15 个物种的五个主要谱系中鉴定出 84 个钙调素基因。系统发育分析将这些钙调素分为五个不同的亚家族（亚 I-V），包括两个以前未鉴定的亚家族。在这些亚家族中，亚 II 与最近在百合花粉油体中鉴定出的独特 P-钙调素同工型相吻合；来自同一谱系的钙调素基因在系统发育树中倾向于聚集在一起。确定了一个特殊的基序与钙调素的分类有关，这可能是由于单子叶植物和双子叶植物进化分化后亚 I 和亚 III 发生缺失所致。此外，从七个物种中鉴定出几个片段和串联重复的基因对，进一步分析表明不同物种的钙调素没有共同的扩展模型。计算了每对重复的年龄，并且大多数与每个物种的全基因组复制事件的时间一致。功能分化分析表明，亚家族 I/IV、II/IV 和 II/V 之间发生了功能约束的变化，并且在功能分化过程中鉴定出了一些关键氨基酸位点。进一步的分析表明，钙调素在进化过程中受到正选择，鉴定出 7 个候选氨基酸位点（70R、74G、88L、89G、100K、106A、107S）受到正选择。有趣的是，功能分化和正选择的关键氨基酸残基主要位于 C 端结构域。最后，鉴定出三组共进化的氨基酸位点。在这些共进化的位点中，来自组 2 的七个位于至关重要的 Ca2+结合区域。
本研究预测了钙调素基因家族的进化和扩展模式，并鉴定出一系列与功能分化、适应性进化和共进化相关的关键氨基酸位点。这些发现为进一步分析植物谱系中钙调素基因家族的功能提供了数据。
