Cyclic nucleotide-gated ion channel gene family in rice, identification, characterization and experimental analysis of expression response to plant hormones, biotic and abiotic stresses.

Zarqa Nawaz,Qing-Yao Shu,Mumtaz A Saand,Kaleem Ullah Kakar

doi:10.1186/1471-2164-15-853

Abstract

BackgroundCyclic nucleotide-gated channels (CNGCs) are Ca2+-permeable cation transport channels, which are present in both animal and plant systems. They have been implicated in the uptake of both essential and toxic cations, Ca2+ signaling, pathogen defense, and thermotolerance in plants. To date there has not been a genome-wide overview of the CNGC gene family in any economically important crop, including rice (Oryza sativa L.). There is an urgent need for a thorough genome-wide analysis and experimental verification of this gene family in rice.ResultsIn this study, a total of 16 full length rice CNGC genes distributed on chromosomes 1–6, 9 and 12, were identified by employing comprehensive bioinformatics analyses. Based on phylogeny, the family of OsCNGCs was classified into four major groups (I-IV) and two sub-groups (IV-A and IV- B). Likewise, the CNGCs from all plant lineages clustered into four groups (I-IV), where group II was conserved in all land plants. Gene duplication analysis revealed that both chromosomal segmentation (OsCNGC1 and 2, 10 and 11, 15 and 16) and tandem duplications (OsCNGC1 and 2) significantly contributed to the expansion of this gene family. Motif composition and protein sequence analysis revealed that the CNGC specific domain “cyclic nucleotide-binding domain (CNBD)” comprises a “phosphate binding cassette” (PBC) and a “hinge” region that is highly conserved among the OsCNGCs. In addition, OsCNGC proteins also contain various other functional motifs and post-translational modification sites. We successively built a stringent motif: (LI-X(2)-[GS]-X-[FV]-X-G-[1]-ELL-X-W-X(12,22)-SA-X(2)-T-X(7)-[EQ]-AF-X-L) that recognizes the rice CNGCs specifically. Prediction of cis-acting regulatory elements in 5′ upstream sequences and expression analyses through quantitative qPCR demonstrated that OsCNGC genes were highly responsive to multiple stimuli including hormonal (abscisic acid, indoleacetic acid, kinetin and ethylene), biotic (Pseudomonas fuscovaginae and Xanthomonas oryzae pv. oryzae) and abiotic (cold) stress.ConclusionsThere are 16 CNGC genes in rice, which were probably expanded through chromosomal segmentation and tandem duplications and comprise a PBC and a “hinge” region in the CNBD domain, featured by a stringent motif. The various cis-acting regulatory elements in the upstream sequences may be responsible for responding to multiple stimuli, including hormonal, biotic and abiotic stresses.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-853) contains supplementary material, which is available to authorized users.

Highlights

Cyclic nucleotide-gated channels (CNGCs) are Ca2+-permeable cation transport channels, which are present in both animal and plant systems
Identification of CNGC genes in rice genome To obtain a complete overview of CNGC gene family in rice, we conducted a genome-wide analysis by using various bioinformatics resources
The deduced protein sequences of all the 17 putative genes were further analyzed to confirm the presence of Cyclic nucleotide-binding domain (CNBD)/Cyclic NucleotideMonophosphate Binding Domain, Cap Family Effector Domain (CAP_ED), RmlC-like jelly roll fold (RmlC), and ion transport domains

Summary

Introduction

Cyclic nucleotide-gated channels (CNGCs) are Ca2+-permeable cation transport channels, which are present in both animal and plant systems. CNGCs, functionally defined as ligand-gated protein channels, are nonselective cation channels, gated by the direct binding of cyclic nucleotides, and are present in both animals and plants system [9,10,11,12]. A large family of CNGCs composed of 20 members have been identified in Arabidopsis genome [8] which are classified into four groups (groups I–IV) and two subgroups “IV-A and IV-B” [18] These CNGCs are characterized by general structural resemblance to animal CNGCs [8], having a predicted structure of six transmembrane domains (S1–S6) with a pore domain (P loop) between S5 and S6, C-terminal Cyclic nucleotide-binding domain (CNBD) and CaM-binding domains (CaMBD) [8,13,19,20]. Physiological processes in which these signaling molecules are believed to be involved include various developmental processes, photomorphogenesis and tolerance to salt stress [27,28], gibberellic acid-induced signaling in barley [29] and phytochrome signaling [30]

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