College of Horticulture, Henan Agricultural University, Zhengzhou, 450002, China.
Henan Key Laboratory of Fruit and Cucurbit Biology, Zhengzhou, 450002, China.
BMC Genomics. 2019 Nov 21;20(1):892. doi: 10.1186/s12864-019-6258-0.
Ubiquitin ligases (E3) are the enzymes in the ubiquitin/26S proteasome pathway responsible for targeting proteins to the degradation pathway and play major roles in multiple biological activities. However, the E3 family and their functions are yet to be identified in the fruit of peach.
In this study, genome-wide identification, classification and characterization of the E3 ligase genes within the genome of peach (Prunus persica) was carried out. In total, 765 E3 (PpE3) ligase genes were identified in the peach genome. The PpE3 ligase genes were divided into eight subfamilies according to the presence of known functional domains. The RBX subfamily was not detected in peach. The PpE3 ligase genes were not randomly distributed among the 8 chromosomes, with a greater concentration on the longer chromosomes. The primary mode of gene duplication of the PpE3 ligase genes was dispersed gene duplication (DSD). Four subgroups of the BTB subfamily never characterized before were newly identified in peach, namely BTBAND, BTBBL, BTBP and BTBAN. The expression patterns of the identified E3 ligase genes in two peach varieties that display different types of fruit softening (melting flesh, MF, and stony hard, SH) were analyzed at 4 different stages of ripening using Illumina technology. Among the 765 PpE3 ligase genes, 515 (67.3%) were expressed (FPKM > 1) in the fruit of either MF or SH during fruit ripening. In same-stage comparisons, 231 differentially expressed genes (DEGs) were identified between the two peach cultivars. The number of DEGs in each subfamily varied. Most DEGs were members of the BTB, F-box, U-box and RING subfamilies. PpE3 ligase genes predicted to be involved in ethylene, auxin, or ABA synthesis or signaling and DNA methylation were differentially regulated. Eight PpE3 ligase genes with possible roles in peach flesh texture and fruit ripening were discussed.
The results of this study provide useful information for further understanding the functional roles of the ubiquitin ligase genes in peach. The findings also provide the first clues that E3 ligase genes may function in the regulation of peach ripening.
泛素连接酶（E3）是泛素/26S 蛋白酶体途径中的酶，负责将蛋白质靶向降解途径，在多种生物活性中发挥重要作用。然而，E3 家族及其功能尚未在桃果实中得到鉴定。
本研究在桃（Prunus persica）基因组范围内进行了 E3 连接酶基因的全基因组鉴定、分类和特征分析。共鉴定出 765 个 E3（PpE3）连接酶基因。根据已知功能结构域的存在，将 PpE3 连接酶基因分为八个亚家族。RBX 亚家族在桃中未检测到。PpE3 连接酶基因在 8 条染色体上的分布不均匀，较长的染色体上分布较多。PpE3 连接酶基因的主要复制方式是分散基因复制（DSD）。在桃中，新鉴定了 4 个以前从未表征过的 BTB 亚家族亚组，即 BTBAND、BTBBL、BTBP 和 BTBAN。利用 Illumina 技术分析了在两个果实软化类型（肉质软化 MF 和石细胞硬 SH）不同的桃品种中，4 个不同成熟阶段的识别 E3 连接酶基因的表达模式。在 765 个 PpE3 连接酶基因中，515 个（67.3%）在 MF 或 SH 果实成熟过程中表达（FPKM > 1）。在同一阶段的比较中，在两个桃品种之间鉴定出 231 个差异表达基因（DEGs）。每个亚家族的 DEG 数量不同。大多数 DEGs 是 BTB、F-box、U-box 和 RING 亚家族的成员。预测参与乙烯、生长素或 ABA 合成或信号转导以及 DNA 甲基化的 PpE3 连接酶基因受到差异调控。讨论了 8 个可能参与桃果肉质地和果实成熟的 PpE3 连接酶基因。
本研究结果为进一步了解泛素连接酶基因在桃中的功能作用提供了有用信息。研究结果还首次表明，E3 连接酶基因可能在桃果实成熟调控中发挥作用。
