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

Nawaz Z, Kakar KU, Saand MA, Shu QY - BMC Genomics (2014)

Bottom Line: 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.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.The various cis-acting regulatory elements in the upstream sequences may be responsible for responding to multiple stimuli, including hormonal, biotic and abiotic stresses.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou 310029, China. qyshu@zju.edu.cn.

ABSTRACT

Background: Cyclic 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.

Results: In 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.

Conclusions: There 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.

Show MeSH
Phylogenetic tree of OsCNGC and AtCNGC proteins. The multiple alignment was performed by ClustalX program. MEGA 6.0 was used to create the maximum likelihood (ML) under the Jones-Taylor-Thornton (JTT) model. The bootstrap values from 1000 resampling are given at each node. The rice CNGC genes identified in this study are shown in red circles and Arabidopsis CNGCs are shown in blue squares. Rice CNGC genes were designated according to their order in phylogeny.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
getmorefigures.php?uid=PMC4197254&req=5

Fig4: Phylogenetic tree of OsCNGC and AtCNGC proteins. The multiple alignment was performed by ClustalX program. MEGA 6.0 was used to create the maximum likelihood (ML) under the Jones-Taylor-Thornton (JTT) model. The bootstrap values from 1000 resampling are given at each node. The rice CNGC genes identified in this study are shown in red circles and Arabidopsis CNGCs are shown in blue squares. Rice CNGC genes were designated according to their order in phylogeny.

Mentions: To determine the phylogenic relationship of CNGC family between rice and Arabidopsis, a maximum likelihood (ML) phylogenetic tree was constructed using full-length amino acid sequences. Four groups, as described by Mäser et al. [18] were identified containing representative gene of both rice and Arabidopsis. All the Arabidopsis CNGC proteins were found to lie in groups similar to those identified previously [18]. Of the four groups, three groups (Group I, II and III) are monophyletic, while one group (IV) is sub-divided into two distinct clades, named group IV-A and IV-B (Figure 4). Group I comprises three members from rice CNGCs (OsCNGC1 to OsCNGC3) and six from Arabidopsis (AtCNGC1, 3, 10, 11, 12 and 13). Similarly, Group II contains three rice CNGCs (OsCNGC4 to OsCNGC6) and five AtCNGCs (AtCNGC5 to AtCNGC9). However, Group III embraces five in rice (OsCNGC7 to OsCNGC11) and five in Arabidopsis (AtCNGC14 to AtCNGC18), thus form the largest group, with 10 members. Two CNGCs from each rice (OsCNGC12 and OsCNGC13) and Arabidopsis (AtCNGC19 and AtCNGC20) were assigned to group IV-A, while, three rice CNGCs (OsCNGC14 to OsCNGC16) and two Arabidopsis CNGCs (AtCNGC2 and AtCNGC4) segregated into group IV-B (Figure 4). A separate phylogenetic tree was also generated from conserved CNBD domains sequences of all the CNGC proteins in rice and Arabidopsis, which resulted into similar clustering pattern.Figure 4


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

Nawaz Z, Kakar KU, Saand MA, Shu QY - BMC Genomics (2014)

Phylogenetic tree of OsCNGC and AtCNGC proteins. The multiple alignment was performed by ClustalX program. MEGA 6.0 was used to create the maximum likelihood (ML) under the Jones-Taylor-Thornton (JTT) model. The bootstrap values from 1000 resampling are given at each node. The rice CNGC genes identified in this study are shown in red circles and Arabidopsis CNGCs are shown in blue squares. Rice CNGC genes were designated according to their order in phylogeny.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4197254&req=5

Fig4: Phylogenetic tree of OsCNGC and AtCNGC proteins. The multiple alignment was performed by ClustalX program. MEGA 6.0 was used to create the maximum likelihood (ML) under the Jones-Taylor-Thornton (JTT) model. The bootstrap values from 1000 resampling are given at each node. The rice CNGC genes identified in this study are shown in red circles and Arabidopsis CNGCs are shown in blue squares. Rice CNGC genes were designated according to their order in phylogeny.
Mentions: To determine the phylogenic relationship of CNGC family between rice and Arabidopsis, a maximum likelihood (ML) phylogenetic tree was constructed using full-length amino acid sequences. Four groups, as described by Mäser et al. [18] were identified containing representative gene of both rice and Arabidopsis. All the Arabidopsis CNGC proteins were found to lie in groups similar to those identified previously [18]. Of the four groups, three groups (Group I, II and III) are monophyletic, while one group (IV) is sub-divided into two distinct clades, named group IV-A and IV-B (Figure 4). Group I comprises three members from rice CNGCs (OsCNGC1 to OsCNGC3) and six from Arabidopsis (AtCNGC1, 3, 10, 11, 12 and 13). Similarly, Group II contains three rice CNGCs (OsCNGC4 to OsCNGC6) and five AtCNGCs (AtCNGC5 to AtCNGC9). However, Group III embraces five in rice (OsCNGC7 to OsCNGC11) and five in Arabidopsis (AtCNGC14 to AtCNGC18), thus form the largest group, with 10 members. Two CNGCs from each rice (OsCNGC12 and OsCNGC13) and Arabidopsis (AtCNGC19 and AtCNGC20) were assigned to group IV-A, while, three rice CNGCs (OsCNGC14 to OsCNGC16) and two Arabidopsis CNGCs (AtCNGC2 and AtCNGC4) segregated into group IV-B (Figure 4). A separate phylogenetic tree was also generated from conserved CNBD domains sequences of all the CNGC proteins in rice and Arabidopsis, which resulted into similar clustering pattern.Figure 4

Bottom Line: 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.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.The various cis-acting regulatory elements in the upstream sequences may be responsible for responding to multiple stimuli, including hormonal, biotic and abiotic stresses.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou 310029, China. qyshu@zju.edu.cn.

ABSTRACT

Background: Cyclic 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.

Results: In 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.

Conclusions: There 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.

Show MeSH