Integrative Proteomics and Metabolomics Analysis Reveals the Role of Small Signaling Peptide Rapid Alkalinization Factor 34 (RALF34) in Cucumber Roots

The main role of RALF small signaling peptides was reported to be the alkalization control of the apoplast for improvement of nutrient absorption; however, the exact function of individual RALF peptides such as RALF34 remains unknown. The Arabidopsis RALF34 (AtRALF34) peptide was proposed to be part of the gene regulatory network of lateral root initiation. Cucumber is an excellent model for studying a special form of lateral root initiation taking place in the meristem of the parental root. We attempted to elucidate the role of the regulatory pathway in which RALF34 is a participant using cucumber transgenic hairy roots overexpressing CsRALF34 for comprehensive, integrated metabolomics and proteomics studies, focusing on the analysis of stress response markers. CsRALF34 overexpression resulted in the inhibition of root growth and regulation of cell proliferation, specifically in blocking the G2/M transition in cucumber roots. Based on these results, we propose that CsRALF34 is not part of the gene regulatory networks involved in the early steps of lateral root initiation. Instead, we suggest that CsRALF34 modulates ROS homeostasis and triggers the controlled production of hydroxyl radicals in root cells, possibly associated with intracellular signal transduction. Altogether, our results support the role of RALF peptides as ROS regulators.

Elucidating the unknown transcriptional responses and PHR1-mediated biotic and abiotic stress tolerance during phosphorus limitation

Phosphorus (P) limitation in the majority of world soils is a major constraint for plant growth and crop productivity. RNA sequencing was used to discover novel P-responsive gene transcripts (PRGTs) in leaves and roots of Arabidopsis. Hisat StringTie and the Cufflinks TopHat transcript assembler were used to analyze reads and identify 1074 PRGTs with a >5-fold altered abundance during P limitation. Interestingly, 60% of these transcripts were not previously reported. Among the novel PRGTs, 106 were from unannotated genes, and some were among the most P-responsive, including At2g36727 which encodes a novel miRNA. Annotated novel PRGTs encode transcription factors, miRNAs, small signaling peptides, long non-coding RNAs, defense-related proteins, and transporters, along with proteins involved in many biological processes. We identified several genes that undergo alternative splicing during P limitation, including a novel miR399-resistant splice variant of PHOSPHATE2 (PHO2.2). Several novel P-responsive genes were regulated by PHOSPHATE STARVATION RESPONSE1 (PHR1), PHR1-LIKE 1 (PHL1), and PHO2. We discovered that P-limited plants show increased resistance to pathogens and drought stress mediated by PHR1-PHL1. Identification of novel P-responsive transcripts and the discovery of the influence of P limitation on biotic and abiotic stress adds a significant component to our understanding of plant P signaling.

A rulebook for peptide control of legume-microbe endosymbioses

Plants engage in mutually beneficial relationships with microbes, such as arbuscular mycorrhizal fungi or nitrogen-fixing rhizobia, for optimized nutrient acquisition. In return, the microbial symbionts receive photosynthetic carbon from the plant. Both symbioses are regulated by the plant nutrient status, indicating the existence of signaling pathways that allow the host to fine-tune its interactions with the beneficial microbes depending on its nutrient requirements. Peptide hormones coordinate a plethora of developmental and physiological processes and, recently, various peptide families have gained special attention as systemic and local regulators of plant-microbe interactions and nutrient homeostasis. In this review, we identify five 'rules' or guiding principles that govern peptide function during symbiotic plant-microbe interactions, and highlight possible points of integration with nutrient acquisition pathways.

Identification of Potential Auxin-Responsive Small Signaling Peptides through a Peptidomics Approach in Arabidopsis thaliana

Small signaling peptides (SSPs) are a class of short peptides playing critical roles in plant growth and development. SSPs are also involved in the phytohormone signaling pathway. However, identification of mature SSPs is still a technical challenge because of their extremely low concentrations in plant tissue and complicated interference by many other metabolites. Here, we report an optimized protocol to extract SSPs based on protoplast extraction and to analyze SSPs based on tandem mass spectrometry peptidomics. Using plant protoplasts as the material, soluble peptides were directly extracted into phosphate buffer. The interference of non-signaling peptides was significantly decreased. Moreover, we applied the protocol to identify potential SSPs in auxin treated wild type and auxin biosynthesis defective mutant yuc2yuc6. Over 100 potential SSPs showed a response to auxin in Arabidopsis thaliana.

Nutrient-Responsive Small Signaling Peptides and Their Influence on the Root System Architecture

The root system architecture (RSA) of plants is highly dependent on the surrounding nutrient environment. The uptake of essential nutrients triggers various signaling cascades and fluctuations in plant hormones to elicit physical changes in RSA. These pathways may involve signaling components known as small signaling peptides (SSPs), which have been implicated in a variety of plant developmental processes. This review discusses known nutrient-responsive SSPs with a focus on several subclasses that have been shown to play roles in root development. Most functionally well-characterized cases of SSP-mediated changes in RSA are found in responses to nitrogen (N) and phosphorus (P) availability, but other nutrients have also been known to affect the expression of SSP-encoding genes. These nutrient-responsive SSPs may interact downstream with leucine-rich repeat receptor kinases (LRR-RKs) to modulate hormone signaling and cellular processes impacting plant root development. SSPs responsive to multiple nutrient cues potentially act as mediators of crosstalk between the signaling pathways. Study of SSP pathways is complicated because of functional redundancy within peptide and receptor families and due to their functionality partly associated with post-translational modifications; however, as genomic research and techniques progress, novel SSP-encoding genes have been identified in many plant species. Understanding and characterizing the roles of SSPs influencing the root phenotypes will help elucidate the processes that plants use to optimize nutrient acquisition in the environment.

Structural Insight into Recognition of Plant Peptide Hormones by Receptors

Secreted signaling peptides or peptide hormones play crucial roles in plant growth and development through coordination of cell-cell communication. Perception of peptide hormones in plants generally relies on membrane-localized receptor kinases (RKs). Progress has recently been made in structural elucidation of interactions between posttranslationally modified peptide hormones and RKs. The structural studies suggest conserved receptor binding and activation mechanisms of this type of peptide hormones involving their conserved C-termini. Here, we review these structural data and discuss how the conserved mechanisms can be used to match peptide-RK pairs.

Regulation of Arabidopsis root development by small signaling peptides

Plant root systems arise de novo from a single embryonic root. Complex and highly coordinated developmental networks are required to ensure the formation of lateral organs maximizes plant fitness. The Arabidopsis root is well-suited to dissection of regulatory and developmental networks due to its highly ordered, predictable structure. A myriad of regulatory signaling networks control the development of plant roots, from the classical hormones such as auxin and cytokinin to short-range positional signaling molecules that relay information between neighboring cells. Small signaling peptides are a growing class of regulatory molecules involved in many aspects of root development including meristem maintenance, the gravitropic response, lateral root development, and vascular formation. Here, recent findings on the roles of regulatory peptides in these aspects of root development are discussed.