Bioinformatic analysis of the CLE signaling peptide family

Oelkers, Karsten, Goffard, Nicolas, Weiller, Georg F., Gresshoff, Peter M., Mathesius, Ulrike and Frickey, Tancred (2008) Bioinformatic analysis of the CLE signaling peptide family. BMC Plant Biology, 8 1: 1-15. doi:10.1186/1471-2229-8-1


Author Oelkers, Karsten
Goffard, Nicolas
Weiller, Georg F.
Gresshoff, Peter M.
Mathesius, Ulrike
Frickey, Tancred
Title Bioinformatic analysis of the CLE signaling peptide family
Journal name BMC Plant Biology   Check publisher's open access policy
ISSN 1471-2229
Publication date 2008-01-03
Year available 2008
Sub-type Article (original research)
DOI 10.1186/1471-2229-8-1
Open Access Status DOI
Volume 8
Issue 1
Start page 1
End page 15
Total pages 15
Place of publication London, United Kingdom
Publisher BioMed Central
Collection year 2009
Language eng
Subject 820507 Wheat
060702 Plant Cell and Molecular Biology
Formatted 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.
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ
Additional Notes Article # 1

Document type: Journal Article
Sub-type: Article (original research)
Collections: 2009 Higher Education Research Data Collection
School of Biological Sciences Publications
 
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Created: Fri, 14 Nov 2008, 14:19:35 EST by Gail Walter on behalf of School of Biological Sciences