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

Abstract

Growing evidence indicates that small, secreted peptides (SSPs) play critical roles in legume growth and development, yet the annotation of SSP-coding genes is far from complete. Systematic reannotation of the Medicago truncatula genome identified 1,970 homologs of established SSP gene families and an additional 2,455 genes that are potentially novel SSPs, previously unreported in the literature. The expression patterns of known and putative SSP genes based on 144 RNA sequencing data sets covering various stages of macronutrient deficiencies and symbiotic interactions with rhizobia and mycorrhiza were investigated. Focusing on those known or suspected to act via receptor-mediated signaling, 240 nutrient-responsive and 365 nodulation-responsive Signaling-SSPs were identified, greatly expanding the number of SSP gene families potentially involved in acclimation to nutrient deficiencies and nodulation. Synthetic peptide applications were shown to alter root growth and nodulation phenotypes, revealing additional regulators of legume nutrient acquisition. Our results constitute a powerful resource enabling further investigations of specific SSP functions via peptide treatment and reverse genetics.

CLE peptide tri‐arabinosylation and peptide domain sequence composition are essential for SUNN‐dependent autoregulation of nodulation in Medicago truncatula

“…S1) and therefore could be involved in early (MtCLE13), intermediate (MtCLE12 and MtCLE13) or potentially late AON‐related‐responses (MtCLE42) (Fig. S1) (de Bang et al ., ). The predicted domains of MtCLE12, MtCLE13 and MtCLE42 share amino acid similarity in key N‐terminal positions (Fig.…”

Arbuscular mycorrhizal fungi possess a CLAVATA3/embryo surrounding region‐related gene that positively regulates symbiosis

“…Moreover, other LRR‐RLKs, besides CLV2, may be involved in RiCLEp‐triggered root phenotypes. RiCLE1 presents strong sequence similarity with the plant CLE peptides AtCLE9/10 that modulate cytokinin signalling (Kondo et al ., ), and AtCLE14 and MtCLE05 that respond to P deficiency (de Bang et al ., ; Gutiérrez‐Alanís et al ., ). In particular, AtCLE14 was characterized in detail for its role in modulating the root apical meristem function and inducing growth arrest in low‐Pi conditions (Gutiérrez‐Alanís et al ., ).…”

Nodule‐specific PLAT domain proteins are expanded in the Medicago lineage and required for nodulation

“…Additionally, we used RNA‐seq transcripts as a starting point for downstream analyses, rather than rely on the accuracy of different gene prediction programs and approaches used in annotating each legume species. Finally, in contrast to other secreted peptidome (de Bang et al ., ) or secreted proteome (Plett et al ., ) studies, our approach was to identify gene families or subfamilies that are unique to specific lineages within the legume family to identify those that have potential nodulation‐related functions.…”