A Comprehensive Analysis of RALF Proteins in Green Plants Suggests There Are Two Distinct Functional Groups

Abstract

Rapid Alkalinization Factors (RALFs) are small, cysteine-rich peptides known to be involved in various aspects of plant development and growth. Although RALF peptides have been identified within many species, a single wide-ranging phylogenetic analysis of the family across the plant kingdom has not yet been undertaken. Here, we identified RALF proteins from 51 plant species that represent a variety of land plant lineages. The inferred evolutionary history of the 795 identified RALFs suggests that the family has diverged into four major clades. We found that much of the variation across the family exists within the mature peptide region, suggesting clade-specific functional diversification. Clades I, II, and III contain the features that have been identified as important for RALF activity, including the RRXL cleavage site and the YISY motif required for receptor binding. In contrast, members of clades IV that represent a third of the total dataset, is highly diverged and lacks these features that are typical of RALFs. Members of clade IV also exhibit distinct expression patterns and physico-chemical properties. These differences suggest a functional divergence of clades and consequently, we propose that the peptides within clade IV are not true RALFs, but are more accurately described as RALF-related peptides. Expansion of this RALF–related clade in the Brassicaceae is responsible for the large number of RALF genes that have been previously described in Arabidopsis thaliana. Future experimental work will help to establish the nature of the relationship between the true RALFs and the RALF-related peptides, and whether they function in a similar manner.

Induced expression of the Fragaria × ananassa Rapid alkalinization factor‐33‐like gene decreases anthracnose ontogenic resistance of unripe strawberry fruit stages

“…). According to Campell and Turner () RALF sequence classifications FaRALF33‐like belongs to the clade I subfamily of RALF peptides, since its mature form contains the YISY, YYNC and CRC motifs typical of this clade (Supplementary Fig. ).…”

“…RALF peptides have been linked to several physiological and developmental processes, including cell expansion (Haruta et al , ), lateral root development (Murphy et al , ), root hair growth (Wu et al , ), pollen tube elongation (Covey et al , ), nodulation in legumes (Djordjevic et al , ) and stress (Atkinson et al , ). In silico analysis of the Arabidopsis thaliana genome identified 37 genes belonging to the RALF family, named RALF1 to RALF37 (Olsen et al , ), and the homologues identified in other species have been named according to their similarities to the members of the A. thaliana family (Campbell and Turner, ). The RALF pleiotropic role indicates that these peptides are key players in plant development.…”

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

“…Hierarchical clustering has grouped the CLE genes into four groups (I-IV), labeled on the right. 2017), and RALF (Campbell and Turner, 2017) families. However, the extensive, manual curation performed in this study ensured high confidence in all known SSP families and the corresponding HMMs, which will enable high-quality annotation of a broad range of SSP families in other plant species.…”

Regulation of plant peptide hormones and growth factors by post‐translational modification

“…). Subsequently more than 30 RALF and RALF‐related genes were identified in Arabidopsis and their function is only beginning to emerge (Murphy & De Smet ; Campbell & Turner ). In contrast to the previously discussed small post‐translationally modified peptides, RALFs are not perceived by LRR‐RLKs, but rather by malectin‐like‐domain‐containing receptor kinases of the Catharanthus roseus RLK1‐like (CrRLK1L) family.…”

“…; Srivastava et al . ; Campbell & Turner ), which is quite misleading. Yes, the motif does contain two basic amino acids and these residues are in fact required for substrate recognition (Matos et al .…”