Genome-wide identification and functional analysis of the cyclic nucleotide-gated channel gene family in Chinese cabbage

Abstract

Cyclic nucleotide-gated channels (CNGCs) are a class of nonselective cationic channels that are widely found in animals and plants. Plant CNGCs participate in numerous biological functions that vary from development to stress tolerance. Most CNGC genes have been identified in plant genomes, but no such comprehensive study has yet been conducted on Chinese cabbage. In this study, thirty BrCNGC genes were identified, divided into five groups, and used for evolutionary analysis. We assigned names of all individual CNGC members on the basis of phylogenetic relationship with A. thaliana CNGCs. All BrCNGC genes were randomly distributed on chromosomes, and the A08 chromosome did not carry any CNGC gene. The CNGC genes of Chinese cabbage and A. thaliana from the same group displayed similar conserved motifs and gene structures. Especially the closer the homology, the higher the similarity. Quantitative expression analysis showed that most of the CNGC genes were expressed under four stresses, indicating that they play a key role in the stress response of Chinese cabbage. Expression patterns of 12 BrCNGC in the roots, stems, leaves, flowers, and siliques showed that BrCNGC8 and BrCNGC16 were specifically expressed only in flowers but not in other parts. This study lays a theoretical foundation for future research on the function of the CNGC gene family in Chinese cabbage.

The Complex Story of Plant Cyclic Nucleotide-Gated Channels

“…Prior to this, the need for four CNGC subunits to combine to make a channel had been assumed by analogy with animal and bacterial channels, then supported by molecular modelling [ 78 ] (see Section 4 on channel structure). The range of subunit interactions found to date shows that they are not limited to co-members of the five phylogenetic groups within the family (I, II, III, IV-A and IV-B; Figure 1 [ 16 , 17 , 18 , 19 , 21 , 22 , 23 , 79 ]) but can occur across groups. Therefore, CNGC–CNGC interactions are isoform specific but are not restricted to closely related CNGC isoforms.…”

“…Transcriptomic data indicate that many CNGCs (23 of 35 in N. tabacum [ 18 ]) are expressed throughout the plant. Expression levels, however, vary greatly, suggesting that many CNGCs have tissue-specific or cell-specific functions [ 4 , 18 , 21 , 22 , 23 , 44 , 47 ]. Expression of an individual CNGC can vary with development and growth conditions.…”

“…For example, leaf expression of AtCNGC3 increases with leaf age and lessens when the plant is grown in soil rather than on an agar plate [ 40 ]. CNGC promotors have been found to contain elements associated with responses to abscisic acid, auxin, ethylene, gibberellin, salicylic acid and methyl-jasmonate [ 17 , 18 , 19 , 20 , 21 ], and CNGC transcript levels are highly sensitive to abiotic and biotic stressors [ 17 , 18 , 19 , 20 , 22 , 23 , 79 ]. Notably, it has also been found that Ziziphus jujube CNGC2 expression is rapidly induced by application of cAMP to callus [ 79 ], potentially providing a mechanism for priming signalling pathways involving ZjCNGC2.…”

“…Most research into CNGC contribution to signalling has focused on the 20 cngc loss-of-function mutants in Arabidopsis thaliana (summarised in Table 1 ) and on the functional characteristics of homotetrameric CNGCs in heterologous expression systems such as Escherichia coli , yeast, Xenopus oocytes and HEK293 cells. The 20 AtCNGC gene sequences [ 16 ] have been used to predict that Glycine max has 39 [ 17 ], Hordeum vulgare has 9 [ 7 ], Nicotiana tabacum has 35 [ 18 ], Oryza sativa has 16 [ 19 ], Triticum aestivum has 47 [ 20 ], Zea mays has 12 [ 21 ], Brassica oleracea has 26 [ 22 ] and Brassica rapa has 30 CNGCs [ 23 ]. Advances made with Arabidopsis may well have implications for crop species.…”

CRISPR/Cas9-Mediated Mutagenesis of MdCNGC2 in Apple Callus and VIGS-Mediated Silencing of MdCNGC2 in Fruits Improve Resistance to Botryosphaeria dothidea

“…In the C-terminal, there is a cyclic nucleotide-binding domain comprising three α-helices and two β-sheets ( Zagotta and Siegelbaum, 1996 ). At present, CNGCs have been identified in many plant species, such as Arabidopsis ( Ma et al, 2009 ), rice ( Nawaz et al, 2014 ), tomato ( Saand et al, 2015 ), and cabbage ( Li et al, 2019 ). Plant CNGCs play important roles in plant development, the maintenance of intracellular Ca 2+ homeostasis, and immune defense against pathogenic microorganisms ( Duszyn et al, 2019 ).…”