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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

Multidomain CLE sequences. The potential multidomain CLE signaling peptides CLE75, CLE76, CLE68, CLE31 and CLE30 are represented. The figure is a scaled representation of the domain organization. The relative positions of the first amino acid of the motifs are specified.
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Figure 1: Multidomain CLE sequences. The potential multidomain CLE signaling peptides CLE75, CLE76, CLE68, CLE31 and CLE30 are represented. The figure is a scaled representation of the domain organization. The relative positions of the first amino acid of the motifs are specified.

Mentions: A general characteristic of the CLE family is that members contain a single conserved domain. Surprisingly, we found five sequences (CLE75, CLE76, CLE68, CLE30, CLE31) from three plant species which contained multiple CLE motifs (Table 2). The sequences encoding CLE75 and CLE76 had one entry each in the O. sativa genome, originating from two different genomic loci on chromosome 5. CLE68 had one entry in the M. truncatula genome. CLE30 and CLE31 from T. aestivum were identified by Cock and McCormick and originate from the T. aestivum EST database [5]. In all five cases, the conserved CLE motifs within one protein sequence are very similar to one another and carry the same variations within the CLE motif. CLE68 from M. truncatula is an exception, as the third domain is different from the first two domains in the protein sequence. In all cases, the CLE domains are regularly arranged, with the first domain occurring after 50–75 amino acids, which is typical for standard CLE members, and further domains occurring at intervals of approximately 30 amino acids (Figure 1). Again, CLE68 from M. truncatula forms an exception with a larger gap between the first and the second domain. The sequences positioned in between consecutive CLE motifs are similar to one another, indicating a fusion of tandem duplications of the gene or a mis-annotation of the genome or EST entry.


Bioinformatic analysis of the CLE signaling peptide family.

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

Multidomain CLE sequences. The potential multidomain CLE signaling peptides CLE75, CLE76, CLE68, CLE31 and CLE30 are represented. The figure is a scaled representation of the domain organization. The relative positions of the first amino acid of the motifs are specified.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 1: Multidomain CLE sequences. The potential multidomain CLE signaling peptides CLE75, CLE76, CLE68, CLE31 and CLE30 are represented. The figure is a scaled representation of the domain organization. The relative positions of the first amino acid of the motifs are specified.
Mentions: A general characteristic of the CLE family is that members contain a single conserved domain. Surprisingly, we found five sequences (CLE75, CLE76, CLE68, CLE30, CLE31) from three plant species which contained multiple CLE motifs (Table 2). The sequences encoding CLE75 and CLE76 had one entry each in the O. sativa genome, originating from two different genomic loci on chromosome 5. CLE68 had one entry in the M. truncatula genome. CLE30 and CLE31 from T. aestivum were identified by Cock and McCormick and originate from the T. aestivum EST database [5]. In all five cases, the conserved CLE motifs within one protein sequence are very similar to one another and carry the same variations within the CLE motif. CLE68 from M. truncatula is an exception, as the third domain is different from the first two domains in the protein sequence. In all cases, the CLE domains are regularly arranged, with the first domain occurring after 50–75 amino acids, which is typical for standard CLE members, and further domains occurring at intervals of approximately 30 amino acids (Figure 1). Again, CLE68 from M. truncatula forms an exception with a larger gap between the first and the second domain. The sequences positioned in between consecutive CLE motifs are similar to one another, indicating a fusion of tandem duplications of the gene or a mis-annotation of the genome or EST entry.

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