State Key Laboratory of Subtropical Silviculture, SFGA Engineering Research Center for Dendrobium catenatum (D. officinale), Zhejiang A&F University, Lin'an, Hangzhou, 311300, Zhejiang, China.
Key Laboratory of Education Department of Hunan Province on Plant Genetics and Molecular Biology, Hunan Agricultural University, Changsha, 410128, China.
BMC Plant Biol. 2020 Jan 28;20(1):40. doi: 10.1186/s12870-020-2244-6.
Dendrobium catenatum, as a precious Chinese herbal medicine, is an epiphytic orchid plant, which grows on the trunks and cliffs and often faces up to diverse environmental stresses. SET DOMAIN GROUP (SDG) proteins act as histone lysine methyltransferases, which are involved in pleiotropic developmental events and stress responses through modifying chromatin structure and regulating gene transcription, but their roles in D. catenatum are unknown.
In this study, we identified 44 SDG proteins from D. catenatum genome. Subsequently, comprehensive analyses related to gene structure, protein domain organization, and phylogenetic relationship were performed to evaluate these D. catenatum SDG (DcSDG) proteins, along with the well-investigated homologs from the model plants Arabidopsis thaliana and Oryza sativa as well as the newly characterized 42 SDG proteins from a closely related orchid plant Phalaenopsis equestris. We showed DcSDG proteins can be grouped into eight distinct classes (I~VII and M), mostly consistent with the previous description. Based on the catalytic substrates of the reported SDG members mainly in Arabidopsis, Class I (E(z)-Like) is predicted to account for the deposition of H3K27me2/3, Class II (Ash-like) for H3K36me, Class III (Trx/ATX-like) for H3K4me2/3, Class M (ATXR3/7) for H3K4me, Class IV (Su (var)-like) for H3K27me1, Class V (Suv-like) for H3K9me, as well as class VI (S-ET) and class VII (RBCMT) for methylation of both histone and non-histone proteins. RNA-seq derived expression profiling showed that DcSDG proteins usually displayed wide but distinguished expressions in different tissues and organs. Finally, environmental stresses examination showed the expressions of DcASHR3, DcSUVR3, DcATXR4, DcATXR5b, and DcSDG49 are closely associated with drought-recovery treatment, the expression of DcSUVH5a, DcATXR5a and DcSUVR14a are significantly influenced by low temperature, and even 61% DcSDG genes are in response to heat shock.
This study systematically identifies and classifies SDG genes in orchid plant D. catenatum, indicates their functional divergence during the evolution, and discovers their broad roles in the developmental programs and stress responses. These results provide constructive clues for further functional investigation and epigenetic mechanism dissection of SET-containing proteins in orchids.
铁皮石斛作为一种珍贵的中草药，是一种附生或陆生的兰花植物，生长在树干和悬崖上，经常面临多种环境压力。SET 结构域组（SDG）蛋白作为组蛋白赖氨酸甲基转移酶，通过修饰染色质结构和调节基因转录，参与多种发育事件和应激反应，但它们在铁皮石斛中的作用尚不清楚。
在这项研究中，我们从铁皮石斛基因组中鉴定了 44 个 SDG 蛋白。随后，对这些铁皮石斛 SDG（DcSDG）蛋白进行了包括基因结构、蛋白质结构域组织和系统发育关系在内的综合分析，并与模式植物拟南芥和水稻的同源物以及最近从亲缘关系密切的兰花植物蝴蝶兰中鉴定的 42 个 SDG 蛋白进行了比较。我们表明，DcSDG 蛋白可以分为八个不同的类别（I~VII 和 M），这与之前的描述基本一致。基于报道的 SDG 成员的催化底物主要在拟南芥中，我们预测 I 类（E(z)-Like）蛋白负责沉积 H3K27me2/3，II 类（Ash-like）蛋白负责沉积 H3K36me，III 类（Trx/ATX-like）蛋白负责沉积 H3K4me2/3，M 类（ATXR3/7）蛋白负责沉积 H3K4me，IV 类（Su (var)-like）蛋白负责沉积 H3K27me1，V 类（Suv-like）蛋白负责沉积 H3K9me，而 VI 类（S-ET）和 VII 类（RBCMT）蛋白则负责组蛋白和非组蛋白的甲基化。RNA-seq 衍生的表达谱分析表明，DcSDG 蛋白在不同组织和器官中的表达通常很广泛，但有明显的差异。最后，环境胁迫检测表明，DcASHR3、DcSUVR3、DcATXR4、DcATXR5b 和 DcSDG49 的表达与干旱恢复处理密切相关，DcSUVH5a、DcATXR5a 和 DcSUVR14a 的表达受低温的显著影响，甚至 61%的 DcSDG 基因对热休克有反应。
本研究系统地鉴定和分类了兰花植物铁皮石斛中的 SDG 基因，表明它们在进化过程中的功能分化，并发现它们在发育程序和应激反应中具有广泛的作用。这些结果为进一步研究 SET 蛋白在兰花中的功能和表观遗传机制提供了有价值的线索。
