Diversification of cytokinin phosphotransfer signaling genes in Medicago truncatula and other legume genomes

Sovanna Tan,Frédéric Debellé,Mathias Brault,Pascal Gamas,Florian Frugier

doi:10.1186/s12864-019-5724-z

Abstract

BackgroundLegumes can establish on nitrogen-deprived soils a symbiotic interaction with Rhizobia bacteria, leading to the formation of nitrogen-fixing root nodules. Cytokinin phytohormones are critical for triggering root cortical cell divisions at the onset of nodule initiation. Cytokinin signaling is based on a Two-Component System (TCS) phosphorelay cascade, involving successively Cytokinin-binding Histidine Kinase receptors, phosphorelay proteins shuttling between the cytoplasm and the nucleus, and Type-B Response Regulator (RRB) transcription factors activating the expression of cytokinin primary response genes. Among those, Type-A Response Regulators (RRA) exert a negative feedback on the TCS signaling. To determine whether the legume plant nodulation capacity is linked to specific features of TCS proteins, a genome-wide identification was performed in six legume genomes (Cajanus cajan, pigeonpea; Cicer arietinum, chickpea; Glycine max, soybean; Phaseolus vulgaris, common bean; Lotus japonicus; Medicago truncatula). The diversity of legume TCS proteins was compared to the one found in two non-nodulating species, Arabidopsis thaliana and Vitis vinifera, which are references for functional analyses of TCS components and phylogenetic analyses, respectively.ResultsA striking expansion of non-canonical RRBs was identified, notably leading to the emergence of proteins where the conserved phosphor-accepting aspartate residue is replaced by a glutamate or an asparagine. M. truncatula genome-wide expression datasets additionally revealed that only a limited subset of cytokinin-related TCS genes is highly expressed in different organs, namely MtCHK1/MtCRE1, MtHPT1, and MtRRB3, suggesting that this “core” module potentially acts in most plant organs including nodules.ConclusionsFurther functional analyses are required to determine the relevance of these numerous non-canonical TCS RRBs in symbiotic nodulation, as well as of canonical MtHPT1 and MtRRB3 core signaling elements.

Highlights

Legumes can establish on nitrogen-deprived soils a symbiotic interaction with Rhizobia bacteria, leading to the formation of nitrogen-fixing root nodules
In the four other legume genomes studied, a CHK gene was retrieved in each AtCHK clade and only one additional CHK gene was detected compared to V. vinifera and A. thaliana (Additional file 1)
The independent expression datasets analyzed in this study revealed that in each Two-Component System (TCS) protein family, a few members are more strongly expressed in nodules than others, leading to define a core symbiotic nodule cytokinin signaling module, notably highlighted by a hierarchical clustering focused on transcriptomic datasets from roots and nodules, consisting of the MtCRE1/MtCHK1 receptor, the MtHPT1 phosphotransfer protein, and the MtRRB3 transcription factor, while more variation in expression levels was observed for Response Regulators (RRA)

Summary

Introduction

Legumes can establish on nitrogen-deprived soils a symbiotic interaction with Rhizobia bacteria, leading to the formation of nitrogen-fixing root nodules. Cytokinin signaling is based on a Two-Component System (TCS) phosphorelay cascade, involving successively Cytokinin-binding Histidine Kinase receptors, phosphorelay proteins shuttling between the cytoplasm and the nucleus, and Type-B Response Regulator (RRB) transcription factors activating the expression of cytokinin primary response genes. Cytokinin plant hormones are involved in numerous aspects of plant growth and development in relation to their environment They regulate the balance between cell division and differentiation, and plant growth, and nutrient uptake and shoot/root metabolic relationships, as well as the adaptation toward environmental abiotic or biotic constraints [1,2,3,4]. Features of CHK, HPT and Response Regulator (RR) proteins involved in cytokinin phosphorelay signaling have been well characterized in A. thaliana [3, 12]. A receiver-like domain is found between the kinase domain and the phosphoreceiver domain in all three AHKs

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Conclusion