National Engineering Research Center of Tree Breeding and Ecological Restoration, Institute of Tree Development and Genome Editing, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China.
Sci Rep. 2022 Oct 7;12(1):16805. doi: 10.1038/s41598-022-20800-9.
Cyclin-dependent kinases (CDKs) control the progression of the cell cycle. D-type cyclin (CYCD) is generally believed to form a complex with CDK and control the G1/S transition. In plants, CYCD and CDK gene families can be divided into 6 (D1-D7) and 7 (CDKA-CDKG) subclasses, respectively. Different subclasses in the CYCD and CDK families have different numbers, structures and functions. In some heterologous woody plants, the functions of these subclass family members remain unclear. In this study, 43 CYCD and 27 CDK gene family members were identified in the allodiploid Populus tomentosa Carr. Phylogenetic analysis suggested that these CYCDs and CDKs were divided into 6 and 7 subclasses, respectively, which were the same as other species. The analysis of protein properties, gene structure, motifs, domains, cis-acting elements and tissue-specific expression of all members of these CYCDs and CDKs showed that the differences between members of different subclasses varied widely, but members of the same subclass especially in the CDK gene family were very similar. These findings also demonstrated a strong correlation between CYCD and CDK gene family members in response to hormones and specific expression. The collinear analysis of P. tomentosa, Populus trichocarpa and Arabidopsis thaliana showed that the expansion patterns of CYCD and CDK gene families were predominantly whole genome duplications (WGD). The protein interaction prediction results of different subclasses of CYCD and CDKs showed that the interaction between different subclasses of CYCD and CDKs was significantly different. Our previous study found that transgenic PtoCYCD2;1 and PtoCYCD3;3 poplars exhibited opposite phenotypes. Y2H and BIFC results showed that the interaction between PtoCYCD2;1 and PtoCYCD3;3 was significantly different with CDKs. This finding might suggest that the functional differences of different CYCD subclasses in plant growth and development were closely related to the different interactions between CYCD and CDK. Our results provide a good idea and direction for the functional study of CYCD and CDK proteins in woody plants.
细胞周期蛋白依赖性激酶（CDKs）控制细胞周期的进程。D 型细胞周期蛋白（CYCD）通常与 CDK 形成复合物，控制 G1/S 期转换。在植物中，CYCD 和 CDK 基因家族可分别分为 6（D1-D7）和 7（CDKA-CDKG）亚类。CYCD 和 CDK 家族的不同亚类具有不同的数量、结构和功能。在一些异源木本植物中，这些亚类家族成员的功能仍不清楚。在这项研究中，在异源二倍体毛白杨中鉴定出 43 个 CYCD 和 27 个 CDK 基因家族成员。系统发育分析表明，这些 CYCD 和 CDK 分别分为 6 个和 7 个亚类，与其他物种相同。对所有这些 CYCD 和 CDK 家族成员的蛋白质特性、基因结构、基序、结构域、顺式作用元件和组织特异性表达进行分析表明，不同亚类成员之间的差异差异很大，但同一亚类的成员，尤其是 CDK 基因家族成员非常相似。这些发现还表明，CYCD 和 CDK 基因家族成员对激素和特定表达的反应之间存在很强的相关性。毛白杨、杨树和拟南芥的共线性分析表明，CYCD 和 CDK 基因家族的扩张模式主要是全基因组加倍（WGD）。不同亚类的 CYCD 和 CDK 的蛋白质相互作用预测结果表明，不同亚类的 CYCD 和 CDK 之间的相互作用存在显著差异。我们之前的研究发现，转 PtoCYCD2;1 和 PtoCYCD3;3 杨树的表型相反。Y2H 和 BIFC 结果表明，PtoCYCD2;1 和 PtoCYCD3;3 与 CDKs 的相互作用明显不同。这一发现可能表明，植物生长发育过程中不同 CYCD 亚类的功能差异与 CYCD 和 CDK 之间的不同相互作用密切相关。我们的研究结果为木本植物 CYCD 和 CDK 蛋白的功能研究提供了一个很好的思路和方向。
