Cloning and characterization of the key 4-coumarate CoA ligase genes in Boehmeria nivea

• Published in: South African journal of botany 2018-05, Vol.116, p.123-130
• Main Authors: Tang, Y.H., Liu, F., Mao, K.Q., Xing, H.C., Chen, J.R., Guo, Q.Q.
• Format: Article
• Language: English
• Subjects: 4-Coumarate CoA ligase; Bioinformatics analysis; Boehmeria nivea; Gene expression; Protein structure
• ISSN: 0254-6299; 1727-9321
• DOI: 10.1016/j.sajb.2018.02.398

The 4-coumarate CoA ligase (4CL) is an essential enzyme, in phenylpropanoid synthesis. Its function is responsible for the formation of the hydroxycinnamate-CoA thioester, precursors of lignin and flavonoids. In this study, we isolated three 4CL genes from the ramie, named as Bn4CL1, Bn4CL2 and Bn4CL3, and they were predicted to encode three proteins of 560, 547 and 539 amino acids respectively. These genes shared 80–92% identity with other plant 4CL homologous sequences that acquired in public databases. The amino acid sequence analysis showed that Bn4CLs contained most of the conserved active sites and two conserved motifs that called Box I and Box II of those kinds of enzymes, while Bn4CL3 has 2 bases were altered. Bn4CL1 and Bn4CL2 belong to the stable proteins and have no transmembrane region, while Bn4CL3 belong to unstable protein and has two transmembrane regions. The Bn4CL3 contains more serine amino acid residues than that in Bn4CL1 and Bn4CL2. The phylogenetic analysis suggested that the three homologous genes are in different classes that the Bn4CL1 and Bn4CL2 belonged to class I, and Bn4CL3 belonged to class II. The structural characteristics of Bn4CL proteins were analyzed by constructing the three-dimensional structure model. The results provided basic information to understand the structural characteristic of Bn4CLs. Expression patterns of the three Bn4CL genes in different developmental stages were analyzed. The expression level of Bn4CL3 was significantly different from the other two genes. In view of the above experimental results, we predicted that Bn4CL1 and Bn4CL2 may be involved in lignin synthesis in ramie, while Bn4CL3 may more likely be associated with flavonoid synthesis in ramie. The results pave the way for future work on the function of the Bn4CLs in phenylalanine metabolic pathway of ramie. •Bn4CL1, Bn4CL2 and Bn4CL3 genes were isolated from Boehmeria nivea.•The bioinformation of three genes were analysis.•The three dimensional model of three Bn4CLs were constructed.•The expression of Bn4CLs during different developmental stages in Boehmeria nivea were determined by RT-qPCR.