The Cinnamyl Alcohol Dehydrogenase Gene Family in Melon (Cucumis melo L.): Bioinformatic Analysis and Expression Patterns

Abstract

Cinnamyl alcohol dehydrogenase (CAD) is a key enzyme in lignin biosynthesis. However, little was known about CADs in melon. Five CAD-like genes were identified in the genome of melons, namely CmCAD1 to CmCAD5. The signal peptides analysis and CAD proteins prediction showed no typical signal peptides were found in all CmCADs and CmCAD proteins may locate in the cytoplasm. Multiple alignments implied that some motifs may be responsible for the high specificity of these CAD proteins, and may be one of the key residues in the catalytic mechanism. The phylogenetic tree revealed seven groups of CAD and melon CAD genes fell into four main groups. CmCAD1 and CmCAD2 belonged to the bona fide CAD group, in which these CAD genes, as representative from angiosperms, were involved in lignin synthesis. Other CmCADs were distributed in group II, V and VII, respectively. Semi-quantitative PCR and real time qPCR revealed differential expression of CmCADs, and CmCAD5 was expressed in different vegetative tissues except mature leaves, with the highest expression in flower, while CmCAD2 and CmCAD5 were strongly expressed in flesh during development. Promoter analysis revealed several motifs of CAD genes involved in the gene expression modulated by various hormones. Treatment of abscisic acid (ABA) elevated the expression of CmCADs in flesh, whereas the transcript levels of CmCAD1 and CmCAD5 were induced by auxin (IAA); Ethylene induced the expression of CmCADs, while 1-MCP repressed the effect, apart from CmCAD4. Taken together, these data suggested that CmCAD4 may be a pseudogene and that all other CmCADs may be involved in the lignin biosynthesis induced by both abiotic and biotic stresses and in tissue-specific developmental lignification through a CAD genes family network, and CmCAD2 may be the main CAD enzymes for lignification of melon flesh and CmCAD5 may also function in flower development.

Characterization of Cinnamyl Alcohol Dehydrogenase gene family in lignifying tissues of Tectona grandis L.f.

“…Later, we found several conserved characteristics in teak proteins previously identified by Jin et al (Jin et al 2014) and Tang et al (Tang et al 2014a). TgCAD1 and TgCAD2 exhibited the Zn1 binding motif GHEx 2 Gx 5 Gx 2 V and the catalytic sites for zinc ion action (C47, H69 and C163 with TgCAD1 as reference) (Figure 2).…”

“…Elements of the secondary structure, domains and relevant residues, catalytic and structural sites were found following the annotations described by Tang et al (Tang et al 2014a), Jin et al (Jin et al 2014), Larroy et al (Larroy et al 2002) and Youn et al (Youn et al 2006 (Guo et al 2010) and Barakat et al (Barakat et al 2010), and groups (colored) were defined following the methods of Barakat et al . Secondary structure elements, important relevant residues, and catalytic and structural sites were found according to the methods described by Tang et al (Tang et al 2014a), Jin et al (Jin et al 2014), Larroy et al (Larroy et al 2002) and Youn et al (Youn et al 2006) annotations. Peptide signals and protein subcellular localization was performed following the method described by Jin et al (Jin et al 2014), using Signal IP4.1 program (http://www.cbs.dtu.dk/services/ SignalP/) and CELLO program v.2.5 (http://cello.life.nctu.edu.…”

“…Secondary structure elements, important relevant residues, and catalytic and structural sites were found according to the methods described by Tang et al (Tang et al 2014a), Jin et al (Jin et al 2014), Larroy et al (Larroy et al 2002) and Youn et al (Youn et al 2006) annotations. Peptide signals and protein subcellular localization was performed following the method described by Jin et al (Jin et al 2014), using Signal IP4.1 program (http://www.cbs.dtu.dk/services/ SignalP/) and CELLO program v.2.5 (http://cello.life.nctu.edu. tw/), respectively.…”

“…White star indicates key Phe299 residue for substrate specificity and black star indicates key Asp123 residue for substrate binding. Most of the alignment information was identified according to the results described by Jin et al (Jin et al 2014) and Tang et al (Tang et al 2014a). Figure 3 Phylogenetic tree of monocots, dicots and Tectona grandis CAD proteins.…”

“…Later, several CAD homologues were characterized by genomic sequencing, even obtaining complete gene families, such as Arabidopsis with 9 members (Kim et al 2004), rice with 12 CAD genes (Tobias and Chow 2005) and Populus with 15 members (Barakat et al 2009;Barakat et al 2010). Brachypodium (Bukh et al 2012), camellia, (Deng et al 2013) and melon (Jin et al 2014) also present several CAD genes described. Nearly, 80 CAD genes in 35 plants have been studied, usually existing in a multi-gene family and with differential expression during plant development and environmental conditions (Guo et al 2010;Tang et al 2014a).…”