Expanding the repertoire of secretory peptides controlling root development with comparative genome analysis and functional assays

Abstract

HighlightComparative genome analysis combined with transcriptome mining identified secreted peptides possibly involved in root development. When applied on Arabidopsis roots, selected candidates affected growth or branching in specific ways.

Genome-Wide Identification of Medicago Peptides Involved in Macronutrient Responses and Nodulation

“…First, a homology search using representative proteins from established SSP families was performed. Second, HMMs of known or putative plant SSPs from the PlantSSP database (Ghorbani et al, 2015) were searched for matches. Third, to identify additional SSPs, short (less than 200 amino acids) and secreted (SignalP D-value .…”

“…The pipeline employed the MAKER software program with expression evidence from 64 in-house RNA-seq libraries of diverse tissue types and developmental stages, the M. truncatula EST Gene Index 11, and protein sequences from L. japonicus, Glycine max, and the Swiss-Prot manually curated protein database. SPADA was used to identify SSP gene models using HMMs from the PlantSSP database (Ghorbani et al, 2015) and the in-built HMMs of Cys-rich families, which facilitated the identification of sORFs. Finally, the sORF Finder program (Hanada et al, 2010) was run specifically on the Mt4.0 genome to identify sORF gene models from intergenic regions.…”

“…Furthermore, the PlantSSP database (http://bioinformatics. psb.ugent.be/webtools/PlantSSP/), based on 32 plant species, has been released, containing 39,135 small proteins (less than 200 amino acids) with predicted N-terminal signal peptides grouped into 4,681 families based on sequence homology of the C-terminal 50 amino acids (Ghorbani et al, 2015).…”

“…Moreover, only a tiny fraction of the known SSP-coding genes in M. truncatula have been connected to specific functions. There are 820 gene loci from 334 families in M. truncatula in the PlantSSP database (Ghorbani et al, 2015). However, the M. truncatula accessions are based on the previous Mt3.5 release, and no legumes were included in the initial HMM development, thus likely precluding legume-specific SSPs from identification.…”

The CLE gene family in Populus trichocarpa

“…1,8,9 The CLE genes have been found in many plant species, whereas the roles of most identified CLE genes remained to be elucidated. 2,[10][11][12][13][14][15] As the 2 most known members of CLE peptide family, AtCLV3 and AtCLE40 are key regulators in coordinating stem cell homeostasis in the SAM (Shoot Apical Meristem) and RAM (Root Apical Meristem), respectively. 1 Other than their functions in stem cell fate, it has been also revealed that the CLE peptides are important players in modulating various plant growth and developmental processes such as nodulation, [16][17][18] protoxylem formation, 19 embryogenesis and endosperm development, 20 phloem formation, 21 pollen growth, 22 and lateral root expansion.…”