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Bioinformatic analysis of the CLE signaling peptide family.

Oelkers K, Goffard N, Weiller GF, Gresshoff PM, Mathesius U, Frickey T - BMC Plant Biol. (2008)

Bottom Line: These peptides inhibit the activity of the root apical and lateral root meristems in a manner consistent with our functional predictions based on other CLE signaling peptides clustering in the same groups.Our analysis provides an identification and classification of a large number of novel potential CLE signaling peptides.The additional motifs we found could lead to future discovery of recognition sites for processing peptidases as well as predictions for receptor binding specificity.

View Article: PubMed Central - HTML - PubMed

Affiliation: School of Biochemistry and Molecular Biology, The Australian National University, Canberra, ACT, Australia. karsten.oelkers@anu.edu.au

ABSTRACT

Background: Plants encode a large number of leucine-rich repeat receptor-like kinases. Legumes encode several LRR-RLK linked to the process of root nodule formation, the ligands of which are unknown. To identify ligands for these receptors, we used a combination of profile hidden Markov models and position-specific iterative BLAST, allowing us to detect new members of the CLV3/ESR (CLE) protein family from publicly available sequence databases.

Results: We identified 114 new members of the CLE protein family from various plant species, as well as five protein sequences containing multiple CLE domains. We were able to cluster the CLE domain proteins into 13 distinct groups based on their pairwise similarities in the primary CLE motif. In addition, we identified secondary motifs that coincide with our sequence clusters. The groupings based on the CLE motifs correlate with known biological functions of CLE signaling peptides and are analogous to groupings based on phylogenetic analysis and ectopic overexpression studies. We tested the biological function of two of the predicted CLE signaling peptides in the legume Medicago truncatula. These peptides inhibit the activity of the root apical and lateral root meristems in a manner consistent with our functional predictions based on other CLE signaling peptides clustering in the same groups.

Conclusion: Our analysis provides an identification and classification of a large number of novel potential CLE signaling peptides. The additional motifs we found could lead to future discovery of recognition sites for processing peptidases as well as predictions for receptor binding specificity.

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Related in: MedlinePlus

Weblogo representation of the conservation pattern of residues in each group and for the entire protein family. The previously described main CLE motif of 12 amino acid length is marked with a black frame. Group specific residues are marked in black in the various groups. Invariant residues are marked in black in the bottommost logo. Conserved residues are marked grey. The size of the letter symbolizes the frequency of that residue in the group and at that position. A secondary motif was identified at around 50 amino acids upstream of the primary CLE motif in groups 1, 2, 8 and 13. Extensions of the motif are recognizable at both the C- and N-terminus. Bracketed figures indicate the number of sequences assigned to the respective group.
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Figure 3: Weblogo representation of the conservation pattern of residues in each group and for the entire protein family. The previously described main CLE motif of 12 amino acid length is marked with a black frame. Group specific residues are marked in black in the various groups. Invariant residues are marked in black in the bottommost logo. Conserved residues are marked grey. The size of the letter symbolizes the frequency of that residue in the group and at that position. A secondary motif was identified at around 50 amino acids upstream of the primary CLE motif in groups 1, 2, 8 and 13. Extensions of the motif are recognizable at both the C- and N-terminus. Bracketed figures indicate the number of sequences assigned to the respective group.

Mentions: After clustering, we analyzed the sequence similarity of the entire protein sequence to see whether the sequences grouped by their CLE motif had similar sequence regions outside the motif. We built sequence logos to visualize conserved residues within and outside the 12 amino acid CLE motif. Within the CLE motif, the sequence consensus over the whole family reveals that there are six residues which are almost invariant (Figure 3). These include R, P, G, P, P and H, of which the first two P residues were found to be hydroxylated [24]. Because of the central conserved position of G, we assigned G to the position zero and numbered the positions of the other amino acids relative to this G. There are two positions which have an equal probability of occurrence for N and D as well as for N and H. These conserved residues might provide a framework for the receptor interaction of the presumed ligands. Some rare variations in these conserved residues occur in position 0 (C instead of G in group 8 only) and position +1 (S instead of the predominant hydroxylated P in groups 6 and 12). Other positions in the domain are rather variable, such as positions -4 and -1. We were able to identify group-specific residues, i.e. residues that are responsible for the separation into distinct groups based on CLANS, which are highlighted in Figure 3.


Bioinformatic analysis of the CLE signaling peptide family.

Oelkers K, Goffard N, Weiller GF, Gresshoff PM, Mathesius U, Frickey T - BMC Plant Biol. (2008)

Weblogo representation of the conservation pattern of residues in each group and for the entire protein family. The previously described main CLE motif of 12 amino acid length is marked with a black frame. Group specific residues are marked in black in the various groups. Invariant residues are marked in black in the bottommost logo. Conserved residues are marked grey. The size of the letter symbolizes the frequency of that residue in the group and at that position. A secondary motif was identified at around 50 amino acids upstream of the primary CLE motif in groups 1, 2, 8 and 13. Extensions of the motif are recognizable at both the C- and N-terminus. Bracketed figures indicate the number of sequences assigned to the respective group.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2254619&req=5

Figure 3: Weblogo representation of the conservation pattern of residues in each group and for the entire protein family. The previously described main CLE motif of 12 amino acid length is marked with a black frame. Group specific residues are marked in black in the various groups. Invariant residues are marked in black in the bottommost logo. Conserved residues are marked grey. The size of the letter symbolizes the frequency of that residue in the group and at that position. A secondary motif was identified at around 50 amino acids upstream of the primary CLE motif in groups 1, 2, 8 and 13. Extensions of the motif are recognizable at both the C- and N-terminus. Bracketed figures indicate the number of sequences assigned to the respective group.
Mentions: After clustering, we analyzed the sequence similarity of the entire protein sequence to see whether the sequences grouped by their CLE motif had similar sequence regions outside the motif. We built sequence logos to visualize conserved residues within and outside the 12 amino acid CLE motif. Within the CLE motif, the sequence consensus over the whole family reveals that there are six residues which are almost invariant (Figure 3). These include R, P, G, P, P and H, of which the first two P residues were found to be hydroxylated [24]. Because of the central conserved position of G, we assigned G to the position zero and numbered the positions of the other amino acids relative to this G. There are two positions which have an equal probability of occurrence for N and D as well as for N and H. These conserved residues might provide a framework for the receptor interaction of the presumed ligands. Some rare variations in these conserved residues occur in position 0 (C instead of G in group 8 only) and position +1 (S instead of the predominant hydroxylated P in groups 6 and 12). Other positions in the domain are rather variable, such as positions -4 and -1. We were able to identify group-specific residues, i.e. residues that are responsible for the separation into distinct groups based on CLANS, which are highlighted in Figure 3.

Bottom Line: These peptides inhibit the activity of the root apical and lateral root meristems in a manner consistent with our functional predictions based on other CLE signaling peptides clustering in the same groups.Our analysis provides an identification and classification of a large number of novel potential CLE signaling peptides.The additional motifs we found could lead to future discovery of recognition sites for processing peptidases as well as predictions for receptor binding specificity.

View Article: PubMed Central - HTML - PubMed

Affiliation: School of Biochemistry and Molecular Biology, The Australian National University, Canberra, ACT, Australia. karsten.oelkers@anu.edu.au

ABSTRACT

Background: Plants encode a large number of leucine-rich repeat receptor-like kinases. Legumes encode several LRR-RLK linked to the process of root nodule formation, the ligands of which are unknown. To identify ligands for these receptors, we used a combination of profile hidden Markov models and position-specific iterative BLAST, allowing us to detect new members of the CLV3/ESR (CLE) protein family from publicly available sequence databases.

Results: We identified 114 new members of the CLE protein family from various plant species, as well as five protein sequences containing multiple CLE domains. We were able to cluster the CLE domain proteins into 13 distinct groups based on their pairwise similarities in the primary CLE motif. In addition, we identified secondary motifs that coincide with our sequence clusters. The groupings based on the CLE motifs correlate with known biological functions of CLE signaling peptides and are analogous to groupings based on phylogenetic analysis and ectopic overexpression studies. We tested the biological function of two of the predicted CLE signaling peptides in the legume Medicago truncatula. These peptides inhibit the activity of the root apical and lateral root meristems in a manner consistent with our functional predictions based on other CLE signaling peptides clustering in the same groups.

Conclusion: Our analysis provides an identification and classification of a large number of novel potential CLE signaling peptides. The additional motifs we found could lead to future discovery of recognition sites for processing peptidases as well as predictions for receptor binding specificity.

Show MeSH
Related in: MedlinePlus