The Ubiquitin-Conjugating Enzyme Gene Family in Longan (Dimocarpus longan Lour.): Genome-Wide Identification and Gene Expression during Flower Induction and Abiotic Stress Responses

Dengwei Jue, Xuelian Sang, Liqin Liu, Bo Shu, Yicheng Wang, Jianghui Xie, Chengming Liu, Shengyou Shi
2018 Molecules  
Ubiquitin-conjugating enzymes (E2s or UBC enzymes) play vital roles in plant development and combat various biotic and abiotic stresses. Longan (Dimocarpus longan Lour.) is an important fruit tree in the subtropical region of Southeast Asia and Australia; however the characteristics of the UBC gene family in longan remain unknown. In this study, 40 D. longan UBC genes (DlUBCs), which were classified into 15 groups, were identified in the longan genome. An RNA-seq based analysis showed that
more » ... is showed that DlUBCs showed distinct expression in nine longan tissues. Genome-wide RNA-seq and qRT-PCR based gene expression analysis revealed that 11 DlUBCs were up-or down-regualted in the cultivar "Sijimi" (SJ), suggesting that these genes may be important for flower induction. Finally, qRT-PCR analysis showed that the mRNA levels of 13 DlUBCs under SA (salicylic acid) treatment, seven under methyl jasmonate (MeJA) treatment, 27 under heat treatment, and 16 under cold treatment were upor down-regulated, respectively. These results indicated that the DlUBCs may play important roles in responses to abiotic stresses. Taken together, our results provide a comprehensive insight into the organization, phylogeny, and expression patterns of the longan UBC genes, and therefore contribute to the greater understanding of their biological roles in longan. Molecules 2018, 23, 662 2 of 18 are degraded by the 26S proteasome. In the ubiquitylation system, substrate specificity is mainly determined by E2 and E3 enzymes. The E2 enzymes contain a conserved catalytic domain called the UBC domain, which comprises approximately 140-200 amino acids [4] . In addition to the core E2 domain, many detected isoforms contain various N-and C-terminal extensions that are proposed to influence target recognition and localization [5] . Based on the UBC domain and the N-and C-terminal extensions, E2 proteins are divided into four classes. Class I E2s only contain the UBC domain; class II E2s contain the UBC domain and the N-terminal extensions; class III E2s contain the UBC domain and the C-terminal extensions; and class IV E2s contain the UBC domain and both N-and C-terminal extensions [4, 6] . The UBC protein family is very different from the ancestral eukaryotes that possess fewer members (e.g., ≤20 in algae), to the multicellular plants and animals that possess more diverse proteins (e.g., ≥70 in banana and maize) [7, 8] . In addition, the ubiquitin-like conjugating enzymes (UBLs), which include the related ubiquitin-(RUB) conjugating enzymes and the SUMO-conjugating enzymes, as well as the ubiquitin-conjugating enzyme variants (UEVs), were also found among the E2 classes. For example, a total of 48 UBC domain-containing proteins have been identified in Arabidopsis [9], of which three have thioester-linked UBLs, two are RUB-conjugating enzymes (RCE1, At4g36800 and RCE2, At2g18600), and one is a SUMO-conjugating enzyme (AtSCE1, At3g57870). Eight other UBC proteins lack the Cys active site and are referred to as ubiquitin-conjugating enzyme variants (UEVs) that are not active by themselves, leaving 37 potential E2s [10]. Plant UBC proteins play an important role in regulating plant growth, development, and many abiotic stress reactions. For example, the Arabidopsis ubiquitin-conjugating gene AtUBC13 has been implicated in epidermal cell differentiation and iron deficiency responses [11, 12] . AtUBC32 is an ERAD (endoplasmic reticulum-associated protein degradation) component that functions in brassinosteroid-mediated salt stress tolerance [13] . AtUBC22 is required for female gametophyte development and is likely to be involved in Lys11-linked ubiquitination [14] . A tomato UBC13-type homologous protein, FNI3, is involved in the regulation of Fen-mediated immunity [15] , and the tomato-specific E2 regulates fruit ripening [16] . The virus induced gene silencing of a Triticum aestivum ubiquitin-conjugating enzyme 4 (TaU4) gene expressed in wheat leaves results in delayed development of disease symptoms, and reduced Septoria growth and reproduction [17] . Flowering is a crucial developmental process in the life cycle of plants [18] . The molecular and genetic basis of flowering is well studied in the model plant Arabidopsis [19] [20] [21] . In Arabidopsis, five major flowering pathways have been identified, including the photoperiod pathway, the vernalization pathway, the autonomous pathway, the GA pathway, and the aging pathway [22] . These pathways mediate responses to various stimuli, such as light, age, circadian clock, photoperiod, temperature, abiotic stresses, and hormones. Several genes such as CONSTANS (CO), FLOWERING LOCUS T (FT), SUPPRESSOR OF OVEREXPRESSION OF CO1 (SOC1), and FLOWERING LOCUS C FLC) are key components in flowering signal pathways [23]. In addition, a number of transcription factor (TF) family genes, such as MADS-domain TFs [24], NACs [25], MYBs [26], DREBs [27], WRKYs [28] and ASMTs [29] are involved in flowering regulation. Ubiqitination appears to play a role in most phases of floral development [11] . The RING-finger E3 ligase CONSTITUTIVE PHOTOMORPHOGENIC1 (COP1) is a central regulator of light-dependent physiological processes such as photomorphogenesis, circadian oscillation, and floral transition, and is also involved in ambient temperature-dependent flowering [30] [31] [32] . The light/dark-dependent localization of COP1 is regulated by E2 COP10 through non-K48-linked polyubiquitin, as well as by derubylation by CSN, which is emerging as a regulator of SCF E3 ligase activity [33] . In Arabidopsis, AtUBC1/AtUBC2 act together with the E3s HUB1/HUB2 in H2B ubiquitylation, which is involved in the activation of floral repressor genes [34] . However, little is known about the function of E2s in flower induction, especially in fruit trees. Longan (Dimocarpus longan Lour.) is an important subtropical fruit tree belonging to the family Sapindaceae, which is grown in many subtropical and tropical countries, with the majority of its
doi:10.3390/molecules23030662 pmid:29543725 fatcat:pgnc3tflbnfypoxtxyqhy2lrse