Functional and promoter analysis of conserved gene coexpression network of 4-Coumarate 3-hydroxylase in Brachypodium distachyon and Glycine max

Lignin is a Heterogeneous phenolic polymer in secondrary cell wall in vasculer plants that has important roles in cell wall strength and resilience to biotic and abiotic stresses [1,2,3]. C3H is one of three cytocorome P450s involved in lignin biosynthetic pathway that converts p-coumaric shikimate to 5-O-caffeoyl shikimic acid [4]. Here, functional and promoter analysis of conserved gene coexpression network (CGCN) of 4-Coumarate 3-hydroxylase in Brachypodium distachyon and Glycine max were carried out. several DNA repair and cellulose synthase genes were observed in CGCNs. The results were indicative common cis-elements between C3H and the coexpressed genes in each plant. Lignin is made up of guaiacyl (G), syringyl (S) and p-hydroxyphenyl (H). C3H (4-coumarate 3-hydroxylase), a cytochorome P450, is an enzyme that is involved in early steps of lignin biosynthesis [5,6]. Gene coexpression network (GCN) for C3H was predicted via PlaNet and Phytozome for B. distachyon and Phytozome for Glycine max. CGCN was established through comparison of the two gene coexpression networks of the two plants. Functional analysis performed in Phytomine tool of Phytozome. Plantpan 2.0 was implemented to look for the co-occurrence of transcription factor binding sited (TFBS) in the promoter sequences of the coexpressed genes to further confirm what was obtained in GCN. G. max with 2 and B. distachyon with 1 C3H genes, respectively. showed to have 15 and 19 coexpressed genes, respectively. In between coexpressed genes, several monolignol biosynthetic genes, i.e., CCR, 4CL, CAD, COMT were noted in CGCN. Additionally, several DNA repair and cellulose synthase genes were observed in CGCNs. The role of cytocorome p450 in response to UV was previously reported [7], that can explain the cooccurence of DNA repair genes in this network. The co-occurance of transcription factor binding sites (TFBSs), i.e., common cis-elements was also analyzed in each plant between C3H and the coexpressed genes. The results were indicative of the presence of such elements.

Keywords:

Lignin biosynthesis , Transcription factor binding site , Gene coexpressed network , 4-Coumarate 3-hydroxylase