Kunming Institute of Botany, Institute of Tibetan Plateau Research at Kunming, Chinese Academy of sciences, Kunming, Yunnan, 650204, China.
BMC Plant Biol. 2010 Jun 18;10:117. doi: 10.1186/1471-2229-10-117.
The Phospholipase D (PLD) family plays an important role in the regulation of cellular processes in plants, including abscisic acid signaling, programmed cell death, root hair patterning, root growth, freezing tolerance and other stress responses. PLD genes constitute an important gene family in higher plants. However, until now our knowledge concerning the PLD gene family members and their evolutionary relationship in woody plants such as Poplar and Grape has been limited.
In this study, we have provided a genome-wide analysis of the PLD gene family in Poplar and Grape. Eighteen and eleven members of the PLD gene family were identified in Poplar and Grape respectively. Phylogenetic and gene structure analyses showed that the PLD gene family can be divided into 6 subgroups: alpha, beta/gamma, delta, epsilon, zeta, and phi, and that the 6 PLD subgroups originated from 4 original ancestors through a series of gene duplications. Interestingly, the majority of the PLD genes from both Poplar (76.5%, 13/17) and Grape (90.9%, 10/11) clustered closely together in the phylogenetic tree to the extent that their evolutionary relationship appears more tightly linked to each other, at least in terms of the PLD gene family, than it does to either Arabidopsis or rice. Five pairs of duplicated PLD genes were identified in Poplar, more than those in Grape, suggesting that frequent gene duplications occurred after these species diverged, resulting in a rapid expansion of the PLD gene family in Poplar. The majority of the gene duplications in Poplar were caused by segmental duplication and were distinct from those in Arabidopsis, rice and Grape. Additionally, the gene duplications in Poplar were estimated to have occurred from 11.31 to 13.76 million years ago, which are later than those that occurred in the other three plant species. Adaptive evolution analysis showed that positive selection contributed to the evolution of the PXPH- and SP-PLDs, whereas purifying selection has driven the evolution of C2-PLDs that contain a C2 domain in their N-terminal. Analyses have shown that the C2-PLDs generally contain 23 motifs, more than 17 motifs in PXPH-PLDs that contain PX and PH domains in N-terminal. Among these identified motifs, eight, (6, 8, 5, 4, 3, 14, 1 and 19) were shared by both the C2- and PXPH-PLD subfamilies, implying that they may be necessary for PLD function. Five of these shared motifs are located in the central region of the proteins, thus strongly suggesting that this region containing a HKD domain (named after three conserved H, K and D residues) plays a key role in the lipase activity of the PLDs.
As a first step towards genome wide analyses of the PLD genes in woody plants, our results provide valuable information for increasing our understanding of the function and evolution of the PLD gene family in higher plants.
磷脂酶 D (PLD) 家族在植物细胞过程的调节中起着重要作用，包括脱落酸信号转导、程序性细胞死亡、根毛模式形成、根生长、耐冻性和其他应激反应。PLD 基因构成高等植物中重要的基因家族。然而，直到现在，我们对杨树和葡萄等木本植物中的 PLD 基因家族成员及其进化关系的了解还很有限。
在这项研究中，我们对杨树和葡萄中的 PLD 基因家族进行了全基因组分析。分别在杨树和葡萄中鉴定出 18 个和 11 个 PLD 基因家族成员。系统发育和基因结构分析表明，PLD 基因家族可分为 6 个亚组：alpha、beta/gamma、delta、epsilon、zeta 和 phi，这 6 个 PLD 亚组起源于 4 个原始祖先，通过一系列基因复制。有趣的是，来自杨树（76.5%，13/17）和葡萄（90.9%，10/11）的大多数 PLD 基因在系统发育树上紧密聚集在一起，以至于它们的进化关系似乎比与拟南芥或水稻更紧密地联系在一起，至少在 PLD 基因家族方面是这样。在杨树中鉴定出 5 对复制的 PLD 基因，多于葡萄，表明这些物种分化后频繁发生基因复制，导致杨树 PLD 基因家族快速扩张。杨树中大多数基因复制是由片段复制引起的，与拟南芥、水稻和葡萄中的基因复制不同。此外，杨树中的基因复制估计发生在 1131 万至 1376 万年前，晚于其他三个植物物种。适应性进化分析表明，正选择导致 PXPH 和 SP-PLDs 的进化，而纯化选择导致含有 N 端 C2 结构域的 C2-PLDs 的进化。分析表明，C2-PLDs 通常包含 23 个基序，比 N 端含有 PX 和 PH 结构域的 PXPH-PLDs 多 17 个基序。在这些鉴定出的基序中，有 8 个（6、8、5、4、3、14、1 和 19）存在于 C2-PLD 和 PXPH-PLD 亚家族中，这表明它们可能是 PLD 功能所必需的。其中 5 个共享基序位于蛋白质的中心区域，因此强烈表明包含 HKD 结构域（以三个保守的 H、K 和 D 残基命名）的该区域在 PLD 的脂肪酶活性中起着关键作用。
作为对木本植物中 PLD 基因进行全基因组分析的第一步，我们的结果为增加对高等植物中 PLD 基因家族功能和进化的理解提供了有价值的信息。
