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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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Related in: MedlinePlus

The rice CNGC-specific motif spans the putative PBC and the hinge within the CNBD of the 16 OsCNGCs. The diagram at the top represents three regions of plant CNGCs: the six transmembrane domains (TM), a CNBD containing a PBC and the hinge, and CaMBD. The rice CNGC-specific amino acid motif is shown below the cartoon. In the square brackets “[]” are the amino acids allowed in this position of the motif, “X” represents any amino acid and the round brackets “()” indicate the number of amino acids. Below is the alignment of CNBD domains of 16 rice CNGCs. Residues in white highlighted in blue indicate 100% identity among the 16 rice CNGCs.
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Fig3: The rice CNGC-specific motif spans the putative PBC and the hinge within the CNBD of the 16 OsCNGCs. The diagram at the top represents three regions of plant CNGCs: the six transmembrane domains (TM), a CNBD containing a PBC and the hinge, and CaMBD. The rice CNGC-specific amino acid motif is shown below the cartoon. In the square brackets “[]” are the amino acids allowed in this position of the motif, “X” represents any amino acid and the round brackets “()” indicate the number of amino acids. Below is the alignment of CNBD domains of 16 rice CNGCs. Residues in white highlighted in blue indicate 100% identity among the 16 rice CNGCs.

Mentions: As mentioned earlier, an essential structural feature of plant CNGCs is their CNBD, a direct binding site for cAMP/cGMP to modify the channel opening [59]. The most conserved feature of CNBD domain is the PBC that makes direct contact with cAMP [60], and the hinge region, essential for the capping of cAMP by the C-helix of the CNBD [61]. No plant CNGC-specific motifs had been reported until Zelman et al. [21] aligned the PBC and hinge regions for 20 AtCNGC proteins, from which the following consensus motif was derived: ([21]-X(2)-[GS]-X-[FYIVS]-X-G-X(0,1)-[DE]-LL-X(8,25)-[1]-X(9)-[VLIT]-E-X-F-[62]). Similarly we aligned the CNBD region of rice CNGCs (Individually and with Arabidopsis CNGCs) and identified a putative PBC and a hinge (Figure 3; Additional file 7). We identified a conserved (100%) glycine (G), acidic residue glutamate (E) followed by two aliphatic leucines (L) and aromatic tryptophan (W) inside the PBCs (Figure 3). We also detected that the putative hinge also comprises a conserved (100%) aromatic phenylalanine (F), aliphatic alanine (A) and leucines (L) (Figure 3). A neutral residue, threonine (T) was also found to be conserved (100%) near the hinge region. We successively built a stringent motif: (LI-X(2)-[GS]-X-[FV]-X-G-[DE]-ELL-X-W-X(12,22)-SA-X(2)-T-X(7)-[EQ]-AF-X-L) that recognizes the 16 rice CNGCs specifically. The rice PBC and hinge regions differed from the conserved residues of Arabidopsis. For example, residues E, W and T within PBCs, and residues A and L in hinges were found be conserved at 100% in rice CNGCs only. The diversity of motif patterns between the rice and Arabidopsis indicate the functional divergence across the species and individual groups.Figure 3


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)

The rice CNGC-specific motif spans the putative PBC and the hinge within the CNBD of the 16 OsCNGCs. The diagram at the top represents three regions of plant CNGCs: the six transmembrane domains (TM), a CNBD containing a PBC and the hinge, and CaMBD. The rice CNGC-specific amino acid motif is shown below the cartoon. In the square brackets “[]” are the amino acids allowed in this position of the motif, “X” represents any amino acid and the round brackets “()” indicate the number of amino acids. Below is the alignment of CNBD domains of 16 rice CNGCs. Residues in white highlighted in blue indicate 100% identity among the 16 rice CNGCs.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig3: The rice CNGC-specific motif spans the putative PBC and the hinge within the CNBD of the 16 OsCNGCs. The diagram at the top represents three regions of plant CNGCs: the six transmembrane domains (TM), a CNBD containing a PBC and the hinge, and CaMBD. The rice CNGC-specific amino acid motif is shown below the cartoon. In the square brackets “[]” are the amino acids allowed in this position of the motif, “X” represents any amino acid and the round brackets “()” indicate the number of amino acids. Below is the alignment of CNBD domains of 16 rice CNGCs. Residues in white highlighted in blue indicate 100% identity among the 16 rice CNGCs.
Mentions: As mentioned earlier, an essential structural feature of plant CNGCs is their CNBD, a direct binding site for cAMP/cGMP to modify the channel opening [59]. The most conserved feature of CNBD domain is the PBC that makes direct contact with cAMP [60], and the hinge region, essential for the capping of cAMP by the C-helix of the CNBD [61]. No plant CNGC-specific motifs had been reported until Zelman et al. [21] aligned the PBC and hinge regions for 20 AtCNGC proteins, from which the following consensus motif was derived: ([21]-X(2)-[GS]-X-[FYIVS]-X-G-X(0,1)-[DE]-LL-X(8,25)-[1]-X(9)-[VLIT]-E-X-F-[62]). Similarly we aligned the CNBD region of rice CNGCs (Individually and with Arabidopsis CNGCs) and identified a putative PBC and a hinge (Figure 3; Additional file 7). We identified a conserved (100%) glycine (G), acidic residue glutamate (E) followed by two aliphatic leucines (L) and aromatic tryptophan (W) inside the PBCs (Figure 3). We also detected that the putative hinge also comprises a conserved (100%) aromatic phenylalanine (F), aliphatic alanine (A) and leucines (L) (Figure 3). A neutral residue, threonine (T) was also found to be conserved (100%) near the hinge region. We successively built a stringent motif: (LI-X(2)-[GS]-X-[FV]-X-G-[DE]-ELL-X-W-X(12,22)-SA-X(2)-T-X(7)-[EQ]-AF-X-L) that recognizes the 16 rice CNGCs specifically. The rice PBC and hinge regions differed from the conserved residues of Arabidopsis. For example, residues E, W and T within PBCs, and residues A and L in hinges were found be conserved at 100% in rice CNGCs only. The diversity of motif patterns between the rice and Arabidopsis indicate the functional divergence across the species and individual groups.Figure 3

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
Related in: MedlinePlus