Genome-wide analysis of the Catalpa bungei caffeic acid O-methyltransferase (COMT) gene family: identification and expression profiles in normal, tension, and opposite wood.

Guanzheng Qu,Junhui Wang,Qiuxia Wang,Nan Wang,Donghua Han,Wenjun Ma,Zhi Wang,Guijuan Yang,Ying Liu,Kun Zhao,Nan Lu

doi:10.7717/peerj.6520

Abstract

Caffeic acid O-methyltransferase (COMT) is an important protein that participates in lignin synthesis and is associated with the ratio of G-/S-type lignin in plants. COMTs are associated with the wood properties of forest trees; however, little known about the COMT family in Catalpa bungei, a valuable timber tree species in China . We performed a comprehensive analysis of COMT genes in the C. bungei genome by describing the gene structure and phylogenetic relationships of each family member using bioinformatics-based methods. A total of 23 putative COMT genes were identified using the conserved domain sequences and amino acid sequences of COMTs from Arabidopsis thaliana and Populus trichocarpa as probes. Phylogenetic analysis showed that 23 CbuCOMTs can be divided into three groups based on their structural characteristics; five conserved domains were found in the COMT family. Promoter analysis indicated that the CbuCOMT promoters included various cis-acting elements related to growth and development. Real-time quantitative polymerase chain reaction (PCR) analysis showed differential expression among CbuCOMTs. CbuCOMT2, 7, 8, 9, 10, 12, 13, 14, 21, and 23 were mainly expressed in xylem. Only CbuCOMT23 was significantly downregulated in tension wood and upregulated in opposite wood compared to normal wood. Our study provides new information about the CbuCOMT gene family and will facilitate functional characterisation in further research.

Highlights

Caffeic acid O-methyltransferase (COMT, EC:2.1.1.68) is a lignin monomer-specific enzyme that catalyses O-methylation of the C5 hydroxyl moiety of suitably hydroxylatedHow to cite this article Lu N, Ma W, Han D, Liu Y, Wang Z, Wang N, Yang G, Qu G, Wang Q, Zhao K, Wang J. 2019
Sequence feature analysis of caffeic acid O-methyltransferase (COMT) genes suggested that CbuCOMT gene lengths varied from 1,132 bp (CbuCOMT 7) to 5,870 bp (CbuCOMT 22) and the lengths of open reading frames (ORFs) ranged from 579 bp (CbuCOMT 7) to 1,482 bp (CbuCOMT 22), with deduced amino acid sequence lengths varying from 193aa to 493aa (Table 1)
Phylogenetic analysis of the 23 CbuCOMT s indicated that the CbuCOMT genes could be classified into three groups: group I was composed of 12 CbuCOMT proteins; CbuCOMT 1, CbuCOMT 2, and CbuCOMT 19 belonged to an independent branch, group II; the remaining CbuCOMT genes comprised group III (Fig. 1)

Summary

Introduction

Caffeic acid O-methyltransferase (COMT, EC:2.1.1.68) is a lignin monomer-specific enzyme that catalyses O-methylation of the C5 hydroxyl moiety of suitably hydroxylatedHow to cite this article Lu N, Ma W, Han D, Liu Y, Wang Z, Wang N, Yang G, Qu G, Wang Q, Zhao K, Wang J. 2019. Trees often have their specific S/G ratio (S-type to G-type lignin monomers) in xylem (Cai et al, 2016); this ratio may be related to the mechanical properties of wood due to the different molecular structures of the monomers (Ozparpucu et al, 2018). Some recent studies have focused on the effects of altering the S/G lignin ratio using genetic engineering modification methods or oversuppression of COMT gene expression in plants such as Arabidopsis (Vanholme et al, 2010), wheat (Wang et al, 2018a; Wang et al, 2018b), Miscanthus sinensis (Yoo et al, 2018) and switchgrass (DeBruyn et al, 2017; Li et al, 2017)

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