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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.

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Expression profiles of OsCNGC genes in 4 weeks old rice leaves. The expression patterns of OsCNGC genes under hormonal (ABA, ETH, IAA, and KN), biotic (Xoo and P. fuscovaginae) and abiotic (cold) stresses are depicted in figure. Gene expression was perforemd by qPCR, 4 h after each treatment and non-treated CK. The Y-axis indicates the relative experssion levels (in folds) of treated versus untreated (control) for each gene and X axis shows OsCNGC genes. The error bars were calculated based on three biological repliactes using standard deviation. *significant difference at p < 0.05, **means very significant difference p < 0.01.
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Fig6: Expression profiles of OsCNGC genes in 4 weeks old rice leaves. The expression patterns of OsCNGC genes under hormonal (ABA, ETH, IAA, and KN), biotic (Xoo and P. fuscovaginae) and abiotic (cold) stresses are depicted in figure. Gene expression was perforemd by qPCR, 4 h after each treatment and non-treated CK. The Y-axis indicates the relative experssion levels (in folds) of treated versus untreated (control) for each gene and X axis shows OsCNGC genes. The error bars were calculated based on three biological repliactes using standard deviation. *significant difference at p < 0.05, **means very significant difference p < 0.01.

Mentions: By using quantitative real-time PCR (qPCR) analysis, the expression level of OsCNGC genes was investigated in leaves of the rice cultivar Nipponbare (O. sativa L. ssp. japonica). The results indicated there were tremendous variations among the OsCNGC genes (Figure 6). OsCNGC8 and 13 were highly expressed and had transcripts abundances of 441 and 518 times that of OsCNGC5, while OsCNGC11 had the lowest transcripts abundances (Figure 6).Figure 6


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)

Expression profiles of OsCNGC genes in 4 weeks old rice leaves. The expression patterns of OsCNGC genes under hormonal (ABA, ETH, IAA, and KN), biotic (Xoo and P. fuscovaginae) and abiotic (cold) stresses are depicted in figure. Gene expression was perforemd by qPCR, 4 h after each treatment and non-treated CK. The Y-axis indicates the relative experssion levels (in folds) of treated versus untreated (control) for each gene and X axis shows OsCNGC genes. The error bars were calculated based on three biological repliactes using standard deviation. *significant difference at p < 0.05, **means very significant difference p < 0.01.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig6: Expression profiles of OsCNGC genes in 4 weeks old rice leaves. The expression patterns of OsCNGC genes under hormonal (ABA, ETH, IAA, and KN), biotic (Xoo and P. fuscovaginae) and abiotic (cold) stresses are depicted in figure. Gene expression was perforemd by qPCR, 4 h after each treatment and non-treated CK. The Y-axis indicates the relative experssion levels (in folds) of treated versus untreated (control) for each gene and X axis shows OsCNGC genes. The error bars were calculated based on three biological repliactes using standard deviation. *significant difference at p < 0.05, **means very significant difference p < 0.01.
Mentions: By using quantitative real-time PCR (qPCR) analysis, the expression level of OsCNGC genes was investigated in leaves of the rice cultivar Nipponbare (O. sativa L. ssp. japonica). The results indicated there were tremendous variations among the OsCNGC genes (Figure 6). OsCNGC8 and 13 were highly expressed and had transcripts abundances of 441 and 518 times that of OsCNGC5, while OsCNGC11 had the lowest transcripts abundances (Figure 6).Figure 6

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