Genome-wide annotation and characterization of CLAVATA/ESR (CLE) peptide hormones of soybean (Glycine max) and common bean (Phaseolus vulgaris), and their orthologues of Arabidopsis thaliana.

April H Hastwell,Peter M Gresshoff,Brett J Ferguson

doi:10.1093/jxb/erv351

Abstract

CLE peptides are key regulators of cell proliferation and differentiation in plant shoots, roots, vasculature, and legume nodules. They are C-terminally encoded peptides that are post-translationally cleaved and modified from their corresponding pre-propeptides to produce a final ligand that is 12-13 amino acids in length. In this study, an array of bionformatic and comparative genomic approaches was used to identify and characterize the complete family of CLE peptide-encoding genes in two of the world's most important crop species, soybean and common bean. In total, there are 84 CLE peptide-encoding genes in soybean (considerably more than the 32 present in Arabidopsis), including three pseudogenes and two multi-CLE domain genes having six putative CLE domains each. In addition, 44 CLE peptide-encoding genes were identified in common bean. In silico characterization was used to establish all soybean homeologous pairs, and to identify corresponding gene orthologues present in common bean and Arabidopsis. The soybean CLE pre-propeptide family was further analysed and separated into seven distinct groups based on structure, with groupings strongly associated with the CLE domain sequence and function. These groups provide evolutionary insight into the CLE peptide families of soybean, common bean, and Arabidopsis, and represent a novel tool that can aid in the functional characterization of the peptides. Transcriptional evidence was also used to provide further insight into the location and function of all CLE peptide-encoding members currently available in gene atlases for the three species. Taken together, this in-depth analysis helped to identify and categorize the complete CLE peptide families of soybean and common bean, established gene orthologues within the two legume species, and Arabidopsis, and provided a platform to help compare, contrast, and identify the function of critical CLE peptide hormones in plant development.

Highlights

CLAVATA/embryo surrounding region (ESR) peptide hor- modified signal molecules involved in the regulation and mones (CLE peptides) are a group of post-translationally differentiation of meristematic plant tissues
BLAST queries were based on all known soybean CLE genes, and some Arabidopsis genes, and involved searching with both pre-propeptide and CLE domain sequences to enhance the likelihood of detecting all CLE peptide-encoding genes in the two genomes
CLE peptides are widely recognized as important contributors to plant signalling and development; a lot remains to be understood about these critical signal molecules

Summary

Introduction

CLAVATA/embryo surrounding region (ESR) peptide hor- modified signal molecules involved in the regulation and mones (CLE peptides) are a group of post-translationally differentiation of meristematic plant tissues Been shown to control cell divisions in the shoot apical meristem (SAM), root apical meristem (RAM), vasculature, and legume nodules (Matsubayashi, 2014; Ferguson and Mathesius, 2014; Grienenberger and Fletcher, 2015; Hastwell et al, 2015) They arise from a structurally conserved gene family and are named after the first identified CLE peptide (AtCLV3 in Arabidopsis thaliana; Fletcher et al, 1999), and the structurally and functionally similar, but unrelated, ESR peptides (first identified in Zea mays; Opsahl-Ferstad et al, 1997; Cock and McCormick, 2001). One gene identified in Arabidopsis (AtCLE18) contains both a CLE and a CLEL domain (Meng et al, 2012)

Methods

Results

Conclusion