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Evolutionary and structural perspectives of plant cyclic nucleotide-gated cation channels.

Zelman AK, Dawe A, Gehring C, Berkowitz GA - Front Plant Sci (2012)

Bottom Line: All eukaryote CNGC polypeptides have a cyclic nucleotide-binding domain and a calmodulin binding domain as well as a six transmembrane/one pore tertiary structure.Additionally, an amino acid motif that is only found in the phosphate binding cassette and hinge regions of plant CNGCs, and is present in all experimentally confirmed CNGCs but no other channels was identified.This CNGC-specific amino acid motif provides an additional diagnostic tool to identify plant CNGCs, and can increase confidence in the annotation of open reading frames in newly sequenced genomes as putative CNGCs.

View Article: PubMed Central - PubMed

Affiliation: Agricultural Biotechnology Laboratory, Department of Plant Science, University of Connecticut Storrs, CT, USA.

ABSTRACT
Ligand-gated cation channels are a frequent component of signaling cascades in eukaryotes. Eukaryotes contain numerous diverse gene families encoding ion channels, some of which are shared and some of which are unique to particular kingdoms. Among the many different types are cyclic nucleotide-gated channels (CNGCs). CNGCs are cation channels with varying degrees of ion conduction selectivity. They are implicated in numerous signaling pathways and permit diffusion of divalent and monovalent cations, including Ca(2+) and K(+). CNGCs are present in both plant and animal cells, typically in the plasma membrane; recent studies have also documented their presence in prokaryotes. All eukaryote CNGC polypeptides have a cyclic nucleotide-binding domain and a calmodulin binding domain as well as a six transmembrane/one pore tertiary structure. This review summarizes existing knowledge about the functional domains present in these cation-conducting channels, and considers the evidence indicating that plant and animal CNGCs evolved separately. Additionally, an amino acid motif that is only found in the phosphate binding cassette and hinge regions of plant CNGCs, and is present in all experimentally confirmed CNGCs but no other channels was identified. This CNGC-specific amino acid motif provides an additional diagnostic tool to identify plant CNGCs, and can increase confidence in the annotation of open reading frames in newly sequenced genomes as putative CNGCs. Conversely, the absence of the motif in some plant sequences currently identified as probable CNGCs may suggest that they are misannotated or protein fragments.

No MeSH data available.


Related in: MedlinePlus

Molecular phylogenetic history of the CNGC-specific conserved motif ([LI]-X(2)-[GS]-X-[FYIVS]-X-G-X(0,1)-[DE]-LL-X(8,25)-[SA]-X(9)-[VLIT]-E-X-F-X-[IL]) in A. thaliana. The analysis used the Maximum Likelihood method based on the JTT matrix-based model with a discrete gamma distribution [five categories (+G, parameter = 1.0852); Jones et al., 1992] in MEGA5 (Tamura et al., 2011) with 1000 bootstraps (Felsenstein, 1985). The initial heuristic trees were obtained automatically using the BioNJ method with MCL distance, unless the number of common sites was less than 100 or one quarter of the total number of sites, in which case the maximum parsimony method was used. The tree with the highest log likelihood (−771.1381) is shown, drawn to scale with branch lengths measured in the number of substitutions per site. All ambiguous positions were removed for each sequence pair with a total of 52 positions in the final dataset of 20 sequences.
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Figure 7: Molecular phylogenetic history of the CNGC-specific conserved motif ([LI]-X(2)-[GS]-X-[FYIVS]-X-G-X(0,1)-[DE]-LL-X(8,25)-[SA]-X(9)-[VLIT]-E-X-F-X-[IL]) in A. thaliana. The analysis used the Maximum Likelihood method based on the JTT matrix-based model with a discrete gamma distribution [five categories (+G, parameter = 1.0852); Jones et al., 1992] in MEGA5 (Tamura et al., 2011) with 1000 bootstraps (Felsenstein, 1985). The initial heuristic trees were obtained automatically using the BioNJ method with MCL distance, unless the number of common sites was less than 100 or one quarter of the total number of sites, in which case the maximum parsimony method was used. The tree with the highest log likelihood (−771.1381) is shown, drawn to scale with branch lengths measured in the number of substitutions per site. All ambiguous positions were removed for each sequence pair with a total of 52 positions in the final dataset of 20 sequences.

Mentions: To date, no CNGC-specific motifs have been reported, however, Jackson et al. (2007) aligned different animal CNGCs, and in particular their PBC and hinge regions from which the following consensus motif can be derived: FGE-[IT]-[CIA]-LL-X(3,4)-[RK]-R-X-A-SV-X(11)-[SH]-[VRA]-[FY]-[HNQ]-X-[LV]-[LA] (the animal CNGC hinge sequence spans from the conserved serine (S) to the C-terminus of the motif). We noted that such a motif does not occur in plants but hypothesized that some of the functionally critical residues might be conserved. We therefore aligned A. thaliana CNGCs and identified putative PBCs and hinges. Within the putative PBCs we identified a conserved phenylalanine (F), a stabilizing glycine (G) and an acidic residue (either D or E) followed by two aliphatic leucines (L). We also observed that the putative hinge also contains an E, F, and one aliphatic residue much like in the animal CNGCs. The plant CNGC hinge occurs in between the CNBD and CaMBD regions (Figure 4C). We subsequently built a stringent motif ([LI]-X(2)-[GS]-X-[FYIVS]-X-G-X(0,1)-[DE]-LL-X(8,25)-[SA]-X(9)-[VLIT]-E-X-F-X-[IL]) that recognizes 20 A. thaliana CNGC proteins and no other sequences in A. thaliana. This subsequence includes the hinge domain and PBC (Figure 5). This conserved sequence differs from the animal CNBD; it occurs in between the CNBD and CaMBD while in animals the hinge occurs within the CNBD itself. Additionally it lacks, for example, the conserved proline (P) that was shown to affect gating in animal CNGCs (Jackson et al., 2007). Possible functional similarities may derive from the correspondence between the F in the center of the hinge in A. thaliana CNGCs and the F/Y in a bovine and a catfish CNGC (Young and Krougliak, 2004). The animal PBC region differs from the A. thaliana PBC conserved residues as well (Young and Krougliak, 2004). A scan of UniProt (Swiss-Prot/TrEMBL, The UniProt Consortium, 2012) including splice variants and excluding fragments using the ScanProSite tool2 (Sigrist et al., 2010) further revealed that the motif is restricted to land plants. Notably, the three predicted algal CNGC sequences from Chlamydomonas reinhardtii (Verret et al., 2010) lacked the motif. CNGC-related sequences matched against the 20 A. thaliana CNGCs using BLASTP (E-value <0.01) in UniProt for rice (Oryza sativa var. japonica) and the pin-cushion spikemoss (Selaginella moellendorffii) were then extracted, along with all hits for A. thaliana. Duplicates were removed and the remaining 53 sequences checked for the motif, before being used to construct a cladogram (Figure 6). The genes included in this cladogram are listed in Table A1 in Appendix. In this cladogram it can be seen that the majority of the rice and A. thaliana sequences tend to group together intraspecifically, suggesting numerous gene duplication events. The sequences across all three species partition into two clusters: a larger, more diverse cluster containing the bulk of the CNGC gene family, and a smaller cluster containing CNGC2, 4, 19, and 20. Of particular interest is that the only sequences to contain a conserved alanine (A) in place of the more frequent S in the motif are all from rice (denoted by blue diamonds) and all group together closely with CNGC19 and 20. The cladogram shown in Figure 7 is based upon only the conserved CNGC-specific motif. This phylogeny has striking congruence to previously published cladograms generated from aligning the full-length A. thaliana CNGC gene sequences (Mäser et al., 2001; Talke et al., 2003; Ward et al., 2009), as well as alignments of the pore domain amino acid sequences and the CNDB domain amino acid sequences (Kaplan et al., 2007). This supports the idea that the motif is informative for identifying and comparing putative CNGCs in other plants. Figure 7 also suggests that mutations in the motif have occurred concurrently with the branching of the CNGC gene family.


Evolutionary and structural perspectives of plant cyclic nucleotide-gated cation channels.

Zelman AK, Dawe A, Gehring C, Berkowitz GA - Front Plant Sci (2012)

Molecular phylogenetic history of the CNGC-specific conserved motif ([LI]-X(2)-[GS]-X-[FYIVS]-X-G-X(0,1)-[DE]-LL-X(8,25)-[SA]-X(9)-[VLIT]-E-X-F-X-[IL]) in A. thaliana. The analysis used the Maximum Likelihood method based on the JTT matrix-based model with a discrete gamma distribution [five categories (+G, parameter = 1.0852); Jones et al., 1992] in MEGA5 (Tamura et al., 2011) with 1000 bootstraps (Felsenstein, 1985). The initial heuristic trees were obtained automatically using the BioNJ method with MCL distance, unless the number of common sites was less than 100 or one quarter of the total number of sites, in which case the maximum parsimony method was used. The tree with the highest log likelihood (−771.1381) is shown, drawn to scale with branch lengths measured in the number of substitutions per site. All ambiguous positions were removed for each sequence pair with a total of 52 positions in the final dataset of 20 sequences.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3362136&req=5

Figure 7: Molecular phylogenetic history of the CNGC-specific conserved motif ([LI]-X(2)-[GS]-X-[FYIVS]-X-G-X(0,1)-[DE]-LL-X(8,25)-[SA]-X(9)-[VLIT]-E-X-F-X-[IL]) in A. thaliana. The analysis used the Maximum Likelihood method based on the JTT matrix-based model with a discrete gamma distribution [five categories (+G, parameter = 1.0852); Jones et al., 1992] in MEGA5 (Tamura et al., 2011) with 1000 bootstraps (Felsenstein, 1985). The initial heuristic trees were obtained automatically using the BioNJ method with MCL distance, unless the number of common sites was less than 100 or one quarter of the total number of sites, in which case the maximum parsimony method was used. The tree with the highest log likelihood (−771.1381) is shown, drawn to scale with branch lengths measured in the number of substitutions per site. All ambiguous positions were removed for each sequence pair with a total of 52 positions in the final dataset of 20 sequences.
Mentions: To date, no CNGC-specific motifs have been reported, however, Jackson et al. (2007) aligned different animal CNGCs, and in particular their PBC and hinge regions from which the following consensus motif can be derived: FGE-[IT]-[CIA]-LL-X(3,4)-[RK]-R-X-A-SV-X(11)-[SH]-[VRA]-[FY]-[HNQ]-X-[LV]-[LA] (the animal CNGC hinge sequence spans from the conserved serine (S) to the C-terminus of the motif). We noted that such a motif does not occur in plants but hypothesized that some of the functionally critical residues might be conserved. We therefore aligned A. thaliana CNGCs and identified putative PBCs and hinges. Within the putative PBCs we identified a conserved phenylalanine (F), a stabilizing glycine (G) and an acidic residue (either D or E) followed by two aliphatic leucines (L). We also observed that the putative hinge also contains an E, F, and one aliphatic residue much like in the animal CNGCs. The plant CNGC hinge occurs in between the CNBD and CaMBD regions (Figure 4C). We subsequently built a stringent motif ([LI]-X(2)-[GS]-X-[FYIVS]-X-G-X(0,1)-[DE]-LL-X(8,25)-[SA]-X(9)-[VLIT]-E-X-F-X-[IL]) that recognizes 20 A. thaliana CNGC proteins and no other sequences in A. thaliana. This subsequence includes the hinge domain and PBC (Figure 5). This conserved sequence differs from the animal CNBD; it occurs in between the CNBD and CaMBD while in animals the hinge occurs within the CNBD itself. Additionally it lacks, for example, the conserved proline (P) that was shown to affect gating in animal CNGCs (Jackson et al., 2007). Possible functional similarities may derive from the correspondence between the F in the center of the hinge in A. thaliana CNGCs and the F/Y in a bovine and a catfish CNGC (Young and Krougliak, 2004). The animal PBC region differs from the A. thaliana PBC conserved residues as well (Young and Krougliak, 2004). A scan of UniProt (Swiss-Prot/TrEMBL, The UniProt Consortium, 2012) including splice variants and excluding fragments using the ScanProSite tool2 (Sigrist et al., 2010) further revealed that the motif is restricted to land plants. Notably, the three predicted algal CNGC sequences from Chlamydomonas reinhardtii (Verret et al., 2010) lacked the motif. CNGC-related sequences matched against the 20 A. thaliana CNGCs using BLASTP (E-value <0.01) in UniProt for rice (Oryza sativa var. japonica) and the pin-cushion spikemoss (Selaginella moellendorffii) were then extracted, along with all hits for A. thaliana. Duplicates were removed and the remaining 53 sequences checked for the motif, before being used to construct a cladogram (Figure 6). The genes included in this cladogram are listed in Table A1 in Appendix. In this cladogram it can be seen that the majority of the rice and A. thaliana sequences tend to group together intraspecifically, suggesting numerous gene duplication events. The sequences across all three species partition into two clusters: a larger, more diverse cluster containing the bulk of the CNGC gene family, and a smaller cluster containing CNGC2, 4, 19, and 20. Of particular interest is that the only sequences to contain a conserved alanine (A) in place of the more frequent S in the motif are all from rice (denoted by blue diamonds) and all group together closely with CNGC19 and 20. The cladogram shown in Figure 7 is based upon only the conserved CNGC-specific motif. This phylogeny has striking congruence to previously published cladograms generated from aligning the full-length A. thaliana CNGC gene sequences (Mäser et al., 2001; Talke et al., 2003; Ward et al., 2009), as well as alignments of the pore domain amino acid sequences and the CNDB domain amino acid sequences (Kaplan et al., 2007). This supports the idea that the motif is informative for identifying and comparing putative CNGCs in other plants. Figure 7 also suggests that mutations in the motif have occurred concurrently with the branching of the CNGC gene family.

Bottom Line: All eukaryote CNGC polypeptides have a cyclic nucleotide-binding domain and a calmodulin binding domain as well as a six transmembrane/one pore tertiary structure.Additionally, an amino acid motif that is only found in the phosphate binding cassette and hinge regions of plant CNGCs, and is present in all experimentally confirmed CNGCs but no other channels was identified.This CNGC-specific amino acid motif provides an additional diagnostic tool to identify plant CNGCs, and can increase confidence in the annotation of open reading frames in newly sequenced genomes as putative CNGCs.

View Article: PubMed Central - PubMed

Affiliation: Agricultural Biotechnology Laboratory, Department of Plant Science, University of Connecticut Storrs, CT, USA.

ABSTRACT
Ligand-gated cation channels are a frequent component of signaling cascades in eukaryotes. Eukaryotes contain numerous diverse gene families encoding ion channels, some of which are shared and some of which are unique to particular kingdoms. Among the many different types are cyclic nucleotide-gated channels (CNGCs). CNGCs are cation channels with varying degrees of ion conduction selectivity. They are implicated in numerous signaling pathways and permit diffusion of divalent and monovalent cations, including Ca(2+) and K(+). CNGCs are present in both plant and animal cells, typically in the plasma membrane; recent studies have also documented their presence in prokaryotes. All eukaryote CNGC polypeptides have a cyclic nucleotide-binding domain and a calmodulin binding domain as well as a six transmembrane/one pore tertiary structure. This review summarizes existing knowledge about the functional domains present in these cation-conducting channels, and considers the evidence indicating that plant and animal CNGCs evolved separately. Additionally, an amino acid motif that is only found in the phosphate binding cassette and hinge regions of plant CNGCs, and is present in all experimentally confirmed CNGCs but no other channels was identified. This CNGC-specific amino acid motif provides an additional diagnostic tool to identify plant CNGCs, and can increase confidence in the annotation of open reading frames in newly sequenced genomes as putative CNGCs. Conversely, the absence of the motif in some plant sequences currently identified as probable CNGCs may suggest that they are misannotated or protein fragments.

No MeSH data available.


Related in: MedlinePlus