Genome-Wide Identification and Expression Analyses of the 4-Coumarate: CoA Ligase (4CL) Gene Family in Eucommia ulmoides

Abstract

4-Coumarate: coenzyme A ligase (4CL) is an important rate-limiting enzyme in phenylpropanoid metabolism that plays an important role in the biosynthesis of phenylpropanoid, flavonoid, lignin and other secondary metabolites in plants. However, the family members and functions have not been identified in Eucommia ulmoides (E. ulmoides). In this study, 35 Eu4CLs were identified in the E. ulmoides genome, and the gene structure, conserved domain, evolutionary relationship and expression pattern were comprehensively analyzed. The results show that 35 Eu4CLs were assembled into three subgroups according to the classification in Arabidopsis, where Eu4CLs in the same subgroup had similar gene structures and conserved protein motifs. Putative cis-element analysis of Eu4CL promoter regions uncovered numerous elements related to the response of stress and plant hormones. Expression patterns showed that Eu4CL4/5/13/34 expression levels were positively related to chlorogenic acid content in different periods, which indicate that the synthesis of chlorogenic acid in E. ulmoides was regulated by multiple genes, and the genes regulating the synthesis of chlorogenic acid in different tissues were different. In addition, nine selected Eu4CL genes showed different expression patterns under cold, WeJA (methyl jasmonate), and ethylene by quantitative reverse transcription-PCR (qRT-PCR) assay, suggesting that Eu4CL genes not only play an important role in the synthesis of chlorogenic acid, but also plays an important role in the process of biotic and abiotic stress. Taken together, these findings provide theoretical reference for further exploring the molecular characteristics and biological functions of Eu4CL genes.

Genome-wide identification analysis of the 4-Coumarate: CoA ligase (4CL) gene family expression profiles in Juglans regia and its wild relatives J. Mandshurica resistance and salt stress

“…We identified a total of 36 and 31 4CL gene members in J. regia and J. mandshurica, respectively. The large variation in the number of 4CL genes in different species [35][36][37][38][39] may be related to the gene duplication events experienced by different species during evolution. WGD is the most common gene duplication pattern, and WGD events may enhance the adaptability of species to their environment [77].…”

“…The same phenomenons were observed in most species of 4CL gene families. For example, the number of exons in Md4CL [39] and Eu4CL gene families [37] also ranged from 1 to 23. An increment in the number of introns in genes may be better than harm to the plant.…”

“…The 4CL genes have been extensively genome-wide identification studied in plant species, with 13 At4CL genes identified in Arabidopsis thaliana, 14 Os4CL genes in rice [35], 29 Pbr4CL genes in Pyrus bretschneideri [36], 35 Eu4CL genes in Eucommia ulmoides [37], 12 Pg4CL genes in Punica granatum [38] and 12 Md4CL genes in apple [39]. Since 4CL genes are generally regulated in the process of plant response stresses, the studies of the regulatory mechanism and expression level of 4CL genes are important for plant molecular biology [40][41][42].…”

Genome-Wide Identification and Expression Analysis of the 4-Coumarate: CoA Ligase Gene Family in Solanum tuberosum

“…In this study, the St4CL5 subcellular localization assay was performed. The 4CL proteins are predominantly distributed in bio-membrane system of plant cell [ 59 ], but Peucedanum praeruptorum Dunn Pp4CL1 and Pp4CL10, which have different functions compared to other Pp4CL family genes, are localized to the cytosol [ 60 ]. Recent results of subcellular localization of Cs4CL1 and Cs4CL2 in Camellia sinensis have shown that Cs4CL1 and Cs4CL2 were also mainly distributed in the cytosol [ 8 ].…”

Potential regulatory genes of light induced anthocyanin accumulation in sweet cherry identified by combining transcriptome and metabolome analysis

“…In previous studies, promoter sequences of the potato 4CL gene family members all contain photoresponsive elements. UV stress can promote the up-regulation of St4CL6 and St4CL8 but inhibit the expression of St4CL5 ( Zhong et al., 2022 ). Studies in tea tree also showed that the promoters of two 4CL genes, Cs4CL1 and Cs4CL2 , contained 9 kinds of light response elements, and Cs4CL2 was induced by UV-B ( Li et al., 2022b ).…”