Identification and Analysis of E2 Gene Family in Pepper（Capsicum annuum L.）

doi:10.13560/j.cnki.biotech.bull.1985.2024-0044

Abstract

Abstract:

【Objective】 Ubiquitin-binding enzyme E2（UBC）is an important transit enzyme in the ubiquitin-proteasomal pathway that transfers ubiquitin to target proteins, which is involved in plant growth and development and many stresses. The E2 gene family members were identified from the whole genome of pepper, and the expression patterns of related genes were analyzed, which provided a theoretical basis for subsequent research.【Method】 Based on the genome-wide information of pepper, the E2 family was identified by bioinformatics. The basic physio-chemical properties, subcellular localization, chromosomal localization, gene structure and phylogenetic analysis, cis-acting elements, abiotic stress response, tissue and organ expression patterns, and protein-protein interaction network of the family members were systematically analyzed. 【Result】 There were 48 members in the E2 gene family, which were unevenly distributed on 11 chromosomes, and its encoded proteins were mainly localized in the extracellular and nucleus. After comparative evolutionary analysis of pepper, tomato and Arabidopsis thaliana, they were divided into the Group I-Group XIII subfamily, which had similar conserved protein motifs and gene structures. A total of 26 proteins were found to interact. The cis-element analysis showed that the promoter region of CaUBC gene contained a large number of light-responsive and hormone-responsive elements, and there were a variety of cis-acting elements related to growth, development and stress resistance in the upstream 2 000 bp region. CaUBC was involved in the stress, under different abiotic stresses and hormone treatments, they were divided into three categories, among which the third type of genes were highly expressed in high temperature environment; different expressions showed in tissues and organs, among which the expression of CaUBC38 in fruits changed significantly. RT-qPCR analysis showed that the relative expression was the highest at 50 d and the lowest at 10 d. 【Conclusion】 The 48 members of E2（CaUBC）gene family are systematically identified from the pepper genome. The expression characteristics of CaUBC family members during its growth, development, and abiotic stress responses are revealed.

Key words: Capsicum annuum L., E2 gene family, ubiquitin-proteasome system, bioinformatics, expression analysis, abiotic pressure, tissues and organs

CHANG Xue-rui, WANG Tian-tian, WANG Jing. Identification and Analysis of E2 Gene Family in Pepper（Capsicum annuum L.）[J]. Biotechnology Bulletin, 2024, 40(6): 238-250.

Figures/Tables 9

Table 1 Primers required for RT-qPCR for E2 family gene expression analysis

基因名称 Gene name	上游引物Forward primer（5'-3'）	下游引物Reverse primer（5'-3'）
CaUBC3	AGCGGAGGTAGAGGAAGAGG	GCCACCCTCATAAGGTGTTC
CaUBC8	GCTGGTGGTGTTTTCCAAGT	GCTTCGAGCCATTGATTCAT
CaUBC18	TGCAGGTGGTGTTTTTCAAG	CGAGCCACCGATTCATATTT
CaUBC21	ATAGCCCCTATGCAGGAGGT	CAAGTGGATCGTCTGGGTTT
CaUBC23	CCCAATAAGCCACCAACAGT	ACTGAACATCCGAGCTGCTT
CaUBC38	GCGGAAAGTCCTTATCATGG	GATCAACAGGACCTGCCATT
β-Actin	CCACCTCTTCACTCTCTGCTCT	ACTAGGAAAAACAGCCCTTGGT

Fig. 1 Distribution of E2 gene family on chromosome in pepper（Capsicum annuum L.）

Fig. 2 Phylogenetic tree of UBC protein in C. annuum L.（48），A. thaliana L.（36）and S. lycopersicum L.（52） At: Arabidopsis thaliana L.; Sl: Solanum lycopersicum L.; Ca: Capsicum annuum L.

Fig. 3 Structure distribution patterns of 48 CaUBC genes

Fig. 4 Cis-acting elements of the pepper E2 family

Fig. 5 Analysis of the protein interaction network of the E2 family The nodes in the protein interaction network indicate all proteins produced by a protein-coding locus, and the nodes of different colors indicate different degrees of interaction, and the intensity of interaction increases with the deepening of the color of the lines between nodes, and the thinner lines indicate that the interaction between proteins is weaker

Fig. 6 Expression profile of CaUBC genes under different treatments

Fig. 7 Expression profiles of CaUBC genes in different organs F1-F9: After the appearance of flower buds. G1-G11: Fruits at 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, and 60 d after pollination. ST1 and ST2: Fruits at 10 and 15 d after pollination. S3-S11: Fruits at 20, 25, 30, 35, 40, 45, 50, 55, and 60 d after pollination. T3-T11: Fruits at 20, 25, 30, 35, 40, 45, 50, 55 and 60 d after pollination. L1-L9: 2, 5, 10, 15, 20, 25, 30, 40, 50 and 60 d after the emergence of new leaves. The same below

Fig. 8 Relative expressions of eight representative genes of E2 gene family in pepper A: Relative expression of CaUBC38 during fruit development; relative expression of CaUBC8 during flower development; relative expression of CaUBC3/18 under heat stress.B: CaUBC8/21/23/38 under heat stress

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