title: Comprehensive identification and clustering of CLV3/ESR-related (CLE) genes in plants finds groups with potentially shared function.
abstract: CLV3/ESR (CLE) proteins are important signaling peptides in plants. The short CLE peptide (12-13 amino acids) is cleaved from a larger pre-propeptide and functions as an extracellular ligand. The CLE family is large and has resisted attempts at classification because the CLE domain is too short for reliable phylogenetic analysis and the pre-propeptide is too variable. We used a model-based search for CLE domains from 57 plant genomes and used the entire pre-propeptide for comprehensive clustering analysis. In total, 1628 CLE genes were identified in land plants, with none recognizable from green algae. These CLEs form 12 groups within which CLE domains are largely conserved and pre-propeptides can be aligned. Most clusters contain sequences from monocots, eudicots and Amborella trichopoda, with sequences from Picea abies, Selaginella moellendorffii and Physcomitrella patens scattered in some clusters. We easily identified previously known clusters involved in vascular differentiation and nodulation. In addition, we found a number of discrete groups whose function remains poorly characterized. Available data indicate that CLE proteins within a cluster are likely to share function, whereas those from different clusters play at least partially different roles. Our analysis provides a foundation for future evolutionary and functional studies.
authors.affiliation: Department of Biology, Washington University in St Louis, One Brookings Drive, St Louis, MO, 63130, USA.|Donald Danforth Plant Science Center, 975 North Warson Rd, St Louis, MO, 63132, USA.
authors.forename: David M
authors.initials: DM
authors.lastname: Goad
authors.affiliation: Donald Danforth Plant Science Center, 975 North Warson Rd, St Louis, MO, 63132, USA.
authors.forename: Chuanmei
authors.identifier: http://orcid.org/0000-0002-3026-7596
authors.initials: C
authors.lastname: Zhu
authors.affiliation: Donald Danforth Plant Science Center, 975 North Warson Rd, St Louis, MO, 63132, USA.
authors.forename: Elizabeth A
authors.initials: EA
authors.lastname: Kellogg
mesh_terms: D000595:Amino Acid Sequence; D016000:Cluster Analysis; D016384:Consensus Sequence; D017124:Conserved Sequence; D030541:Databases, Genetic; D017343:Genes, Plant; D010455:Peptides / Q000737:chemistry / Q000378:metabolism; D010944:Plants / Q000235:genetics*; D000072417:Protein Domains; D015203:Reproducibility of Results
chemical_list: D010455:Peptides
keywords: CLV3/ESR; clustering; hidden Markov model (HMM); meristem; nodulation; peptide hormone; peptide signaling; tracheary element differentiation inhibitory factor (TDIF)