Evidence for the involvement in nodulation of the two small putative regulatory peptide-encoding genes MtRALFL1 and MtDVL1

Rapid alkalinization factor: function, regulation, and potential applications in agriculture

Rapid alkalinization factor (RALF) is widespread throughout the plant kingdom and controls many aspects of plant life. Current studies on the regulatory mechanism underlying RALF function mainly focus on Arabidopsis, but little is known about the role of RALF in crop plants. Here, we systematically and comprehensively analyzed the relation between RALF family genes from five important crops and those in the model plant Arabidopsis thaliana. Simultaneously, we summarized the functions of RALFs in controlling growth and developmental behavior using conservative motifs as cues and predicted the regulatory role of RALFs in cereal crops. In conclusion, RALF has considerable application potential in improving crop yields and increasing economic benefits. Using gene editing technology or taking advantage of RALF as a hormone additive are effective way to amplify the role of RALF in crop plants.

Genome-Wide Identification and Comparative Analysis of RALF Gene Family in Legume and Non-Legume Species

Rapid alkalinization factor (RALF) are small secreted peptide hormones that can induce rapid alkalinization in a medium. They act as signaling molecules in plants, playing a critical role in plant development and growth, especially in plant immunity. Although the function of RALF peptides has been comprehensively analyzed, the evolutionary mechanism of RALFs in symbiosis has not been studied. In this study, 41, 24, 17 and 12 RALFs were identified in Arabidopsis, soybean, Lotus and Medicago, respectively. A comparative analysis including the molecular characteristics and conserved motifs suggested that the RALF pre-peptides in soybean represented a higher value of isoelectric point and more conservative motifs/residues composition than other species. All 94 RALFs were divided into two clades according to the phylogenetic analysis. Chromosome distribution and synteny analysis suggested that the expansion of the RALF gene family in Arabidopsis mainly depended on tandem duplication, while segment duplication played a dominant role in legume species. The expression levels of most RALFs in soybean were significantly affected by the treatment of rhizobia. Seven GmRALFs are potentially involved in the release of rhizobia in the cortex cells. Overall, our research provides novel insights into the understanding of the role of the RALF gene family in nodule symbiosis.

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.

The Phaseolus vulgaris Receptor-Like Kinase PvFER1 and the Small Peptides PvRALF1 and PvRALF6 Regulate Nodule Number as a Function of Nitrate Availability

Legumes associate with Gram-negative soil bacteria called rhizobia, resulting in the formation of a nitrogen-fixing organ, the nodule. Nodules are an important sink for photosynthates for legumes, so these plants have developed a systemic regulation mechanism that controls their optimal number of nodules, the so-called autoregulation of nodulation (AON) pathway, to balance energy costs with the benefits of nitrogen fixation. In addition, soil nitrate inhibits nodulation in a dose-dependent manner, through systemic and local mechanisms. The CLE family of peptides and their receptors are key to tightly controlling these inhibitory responses. In the present study, a functional analysis revealed that PvFER1, PvRALF1, and PvRALF6 act as positive regulators of the nodule number in growth medium containing 0 mM of nitrate but as negative regulators in medium with 2 and 5 mM of nitrate. Furthermore, the effect on nodule number was found to be consistent with changes in the expression levels of genes associated with the AON pathway and with the nitrate-mediated regulation of nodulation (NRN). Collectively, these data suggest that PvFER1, PvRALF1, and PvRALF6 regulate the optimal number of nodules as a function of nitrate availability.

The rubber tree RALF peptide hormone and its receptor protein kinase FER implicates in rubber production

RAPID ALKALINIZATION FACTORs (RALFs), which are secreted peptides serving as extracellular signals transduced to the inside of the cell, interact with the receptor-like kinase FERONIA (FER) and participates in various biological pathways. Here, we identified 23 RALF and 2 FER genes in Hevea brasiliensis (para rubber tree), and characterized their expression patterns in different tissues, across the process of leaf development, and in response to the rubber yield-stimulating treatments of tapping and ethylene. Four Hevea latex (the cytoplasm of rubber-producing laticifers)-abundant RALF isoforms, HbRALF19, HbRALF3, HbRALF22, and HbRALF16 were listed with descending expression levels. Of the four HbRALFs, expressions of HbRALF3 were markedly regulated in an opposite way by the treatments of tapping (depression) and ethylene (stimulation). All of the four latex-abundant RALFs specifically interacted with the extracellular domain of HbFER1. Transgenic Arabidopsis plants overexpressing these HbRALFs displayed phenotypes similar to those reported for AtRALFs, such as shorter roots, smaller plant architecture, and delayed flowering. The application of HbRALF3 and HbRALF19 recombinant proteins significantly reduced the pH of Hevea latex, an important factor regulating latex metabolism. An in vitro rubber biosynthesis assay in a mixture of latex cytosol (C-serum) revealed a positive role of HbFER1 in rubber biosynthesis. Taken together, these data provide evidence for the participation of the HbRALF-FER module in rubber production.

Cell-specific pathways recruited for symbiotic nodulation in the Medicago truncatula legume

Medicago truncatula is a model legume species that has been studied for decades to understand the symbiotic relationship between legumes and soil bacteria collectively named rhizobia. This symbiosis called nodulation is initiated in roots with the infection of root hair cells by the bacteria, as well as the initiation of nodule primordia from root cortical, endodermal, and pericycle cells, leading to the development of a new root organ, the nodule, where bacteria fix and assimilate the atmospheric dinitrogen for the benefit of the plant. Here, we report the isolation and use of the nuclei from mock and rhizobia-inoculated roots for the single nuclei RNA-seq (sNucRNA-seq) profiling to gain a deeper understanding of early responses to rhizobial infection in Medicago roots. A gene expression map of the Medicago root was generated, comprising 25 clusters, which were annotated as specific cell types using 119 Medicago marker genes and orthologs to Arabidopsis cell-type marker genes. A focus on root hair, cortex, endodermis, and pericycle cell types, showing the strongest differential regulation in response to a short-term (48 h) rhizobium inoculation, revealed not only known genes and functional pathways, validating the sNucRNA-seq approach, but also numerous novel genes and pathways, allowing a comprehensive analysis of early root symbiotic responses at a cell type-specific level.

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.

A legume-specific novel type of phytosulfokine, PSK-δ, promotes nodulation by enhancing nodule organogenesis

Phytosulfokine-α (PSK-α), a tyrosine-sulfated pentapeptide with the sequence YSO3IYSO3TQ, is widely distributed across the plant kingdom and plays multiple roles in plant growth, development, and immune response. Here, we report a novel type of phytosulfokine, PSK-δ, and its precursor proteins (MtPSKδ, LjPSKδ, and GmPSKδ1), specifically from legume species. The sequence YSO3IYSO3TN of sulfated PSK-δ peptide is different from PSK-α at the last amino acid. Expression pattern analysis revealed PSK-δ-encoding precursor genes to be expressed primarily in legume root nodules. Specifically, in Medicago truncatula, MtPSKδ expression was detected in root cortical cells undergoing nodule organogenesis, in nodule primordia and young nodules, and in the apical region of mature nodules. Accumulation of sulfated PSK-δ peptide in M. truncatula nodules was detected by LC/MS. Application of synthetic PSK-δ peptide significantly increased nodule number in legumes. Similarly, overexpression of MtPSKδ in transgenic M. truncatula markedly promoted symbiotic nodulation. This increase in nodule number was attributed to enhanced nodule organogenesis induced by PSK-δ. Additional genetic evidence from the MtPSKδ mutant and RNA interference assays suggested that the PSK-δ and PSK-α peptides function redundantly in regulating nodule organogenesis. These results suggest that PSK-δ, a legume-specific novel type of phytosulfokine, promotes symbiotic nodulation by enhancing nodule organogenesis.

Molecular traits and functional analysis of Rapid Alkalinization Factors (RALFs) in four Gossypium species

Rapid Alkalinization Factors (RALFs) are plant-secreted, cysteine-rich polypeptides which are known to play essential roles in plant developmental processes and in several defense mechanisms. So far, RALF polypeptides have not been investigated in the Gossypium genus. In this study, 42, 38, 104 and 120 RALFs were identified from diploid G. arboreum and G. raimondi and tetraploid G. hirsutum and G. barbadense, respectively. These were further divided into four groups. Protein characteristics, sequence alignment, gene structure, conserved motifs, chromosomal location and cis-element identification were comprehensively analyzed. Whole genome duplication (WGD) /segmental duplication may be the reason why the number of RALF genes doubled in tetraploid Gossypium species. Expression patterns analysis showed that GhRALFs had different transcript accumulation patterns in the tested tissues and were differentially expressed in response to various abiotic stresses. Furthermore, GhRALF41-3 over-expressing (OE) plants showed reduction in root length and developed later with short stems and small rosettes than that of the wild type. The GhRALF14-8 and GhRALF27-8 OE plants, especially the latter, showed increase in seed abortion. Both transgenic Arabidopsis and VIGS cotton demonstrate that three GhRALFs are negative regulators in response to salt stress. Our systematic analyses provided insights into the characterization of RALF genes in Gossypium, which forms genetic basis for further exploration in their potential applications in cotton production.

Granger-causal testing for irregularly sampled time series with application to nitrogen signalling in Arabidopsis

MOTIVATION

Identification of system-wide causal relationships can contribute to our understanding of long-distance, intercellular signalling in biological organisms. Dynamic transcriptome analysis holds great potential to uncover coordinated biological processes between organs. However, many existing dynamic transcriptome studies are characterized by sparse and often unevenly spaced time points that make the identification of causal relationships across organs analytically challenging. Application of existing statistical models, designed for regular time series with abundant time points, to sparse data may fail to reveal biologically significant, causal relationships. With increasing research interest in biological time series data, there is a need for new statistical methods that are able to determine causality within and between time series data sets. Here, a statistical framework was developed to identify (Granger) causal gene-gene relationships of unevenly spaced, multivariate time series data from two different tissues of Arabidopsis thaliana in response to a nitrogen signal.

RESULTS

This work delivers a statistical approach for modelling irregularly sampled bivariate signals which embeds functions from the domain of engineering that allow to adapt the model's dependence structure to the specific sampling time. Using maximum-likelihood to estimate the parameters of this model for each bivariate time series, it is then possible to use bootstrap procedures for small samples (or asymptotics for large samples) in order to test for Granger-Causality. When applied to the A.thaliana data, the proposed approach produced 3078 significant interactions, in which 2012 interactions have root causal genes and 1066 interactions have shoot causal genes. Many of the predicted causal and target genes are known players in local and long-distance nitrogen signalling, including genes encoding transcription factors, hormones and signalling peptides. Of the 1007 total causal genes (either organ), 384 are either known or predicted mobile transcripts, suggesting that the identified causal genes may be directly involved in long-distance nitrogen signalling through intercellular interactions. The model predictions and subsequent network analysis identified nitrogen-responsive genes that can be further tested for their specific roles in long-distance nitrogen signalling.

AVAILABILITY AND IMPLEMENTATION

The method was developed with the R statistical software and is made available through the R package 'irg' hosted on the GitHub repository https://github.com/SMAC-Group/irg where also a running example vignette can be found (https://smac-group.github.io/irg/articles/vignette.html). A few signals from the original data set are made available in the package as an example to apply the method and the complete A.thaliana data can be found at: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE97500.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Granger-Causal Testing for Irregularly Sampled Time Series with Application to Nitrogen Signaling in Arabidopsis

Motivation

Identification of system-wide causal relationships can contribute to our understanding of long-distance, intercellular signalling in biological organisms. Dynamic transcriptome analysis holds great potential to uncover coordinated biological processes between organs. However, many existing dynamic transcriptome studies are characterized by sparse and often unevenly spaced time points that make the identification of causal relationships across organs analytically challenging. Application of existing statistical models, designed for regular time series with abundant time points, to sparse data may fail to reveal biologically significant, causal relationships. With increasing research interest in biological time series data, there is a need for new statistical methods that are able to determine causality within and between time series data sets. Here, a statistical framework was developed to identify (Granger) causal gene-gene relationships of unevenly spaced, multivariate time series data from two different tissues of Arabidopsis thaliana in response to a nitrogen signal.

Results

This work delivers a statistical approach for modelling irregularly sampled bivariate signals which embeds functions from the domain of engineering that allow to adapt the model’s dependence structure to the specific sampling time. Using maximum-likelihood to estimate the parameters of this model for each bivariate time series, it is then possible to use bootstrap procedures for small samples (or asymptotics for large samples) in order to test for Granger-Causality. When applied to the A.thaliana data, the proposed approach produced 3078 significant interactions, in which 2012 interactions have root causal genes and 1066 interactions have shoot causal genes. Many of the predicted causal and target genes are known players in local and long-distance nitrogen signalling, including genes encoding transcription factors, hormones and signalling peptides. Of the 1007 total causal genes (either organ), 384 are either known or predicted mobile transcripts, suggesting that the identified causal genes may be directly involved in long-distance nitrogen signalling through intercellular interactions. The model predictions and subsequent network analysis identified nitrogen-responsive genes that can be further tested for their specific roles in long-distance nitrogen signalling.

Availability and implementation

The method was developed with the R statistical software and is made available through the R package ‘irg’ hosted on the GitHub repository https://github.com/SMAC-Group/irg where also a running example vignette can be found (https://smac-group.github.io/irg/articles/vignette.html). A few signals from the original data set are made available in the package as an example to apply the method and the complete A.thaliana data can be found at: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE97500.

Supplementary information

Supplementary data are available at Bioinformatics online.

Interactions of gene expression, alternative splicing, and DNA methylation in determining nodule identity

Soybean nodulation is a highly controlled process that involves complex gene regulation at both transcriptional and post-transcriptional levels. In the present study, we profiled gene expression changes, alternative splicing events, and DNA methylation patterns during nodule formation, development, and senescence. The transcriptome data uncovered key transcription patterns of nodule development that included 9669 core genes and 7302 stage-specific genes. Alternative splicing analysis uncovered a total of 2323 genes that undergo alternative splicing events in at least one nodule developmental stage, with activation of exon skipping and repression of intron retention being the most common splicing events in nodules compared to roots. Approximately 40% of the differentially spliced genes were also differentially expressed at the same nodule developmental stage, implying a substantial association between gene expression and alternative splicing. Genome-wide-DNA methylation analysis revealed dynamic changes in nodule methylomes that were specific to each nodule stage, occurred in a sequence-specific manner, and impacted the expression of 1864 genes. An attractive hypothesis raised by our data is that increased DNA methylation may contribute to the efficiency of alternative splicing. Together, our results provide intriguing insights into the associations between gene expression, alternative splicing, and DNA methylation that may shape transcriptome complexity and proteome specificity in developing soybean nodules.

Genome-Wide Identification of the CrRLK1L Subfamily and Comparative Analysis of Its Role in the Legume-Rhizobia Symbiosis

The plant receptor-like-kinase subfamily CrRLK1L has been widely studied, and CrRLK1Ls have been described as crucial regulators in many processes in Arabidopsis thaliana (L.), Heynh. Little is known, however, about the functions of these proteins in other plant species, including potential roles in symbiotic nodulation. We performed a phylogenetic analysis of CrRLK1L subfamily receptors of 57 different plant species and identified 1050 CrRLK1L proteins, clustered into 11 clades. This analysis revealed that the CrRLK1L subfamily probably arose in plants during the transition from chlorophytes to embryophytes and has undergone several duplication events during its evolution. Among the CrRLK1Ls of legumes and A. thaliana, protein structure, gene structure, and expression patterns were highly conserved. Some legume CrRLK1L genes were active in nodules. A detailed analysis of eight nodule-expressed genes in Phaseolus vulgaris L. showed that these genes were differentially expressed in roots at different stages of the symbiotic process. These data suggest that CrRLK1Ls are both conserved and underwent diversification in a wide group of plants, and shed light on the roles of these genes in legume–rhizobia symbiosis.

The peptide-encoding MtRGF3 gene negatively regulates nodulation of Medicago truncatula

Leguminous root nodules specifically induced by rhizobium species fix nitrogen gas to gain nitrogen sources, which is important in sustainable agriculture and ecological balance. Several peptide signals are reported to be involved in regulation of legume nodule number and development. There are fifteen genes coding Root Meristem Growth Factor (RGF) peptide in Medicago truncatula, herein we find the expression of MtRGF3 is significantly induced by Sinorhizobium meliloti with production of Nod factors. The gene promoter is active in nodule primordia, young nodules and the meristem region of mature nodules. Knock-down (RNAi) roots of the gene (MtRGF3-RNAi) formed more root nodules than the empty vector control, and the nodule number decreased in MtRGF3-overexpressing (MtRGF3-OX) roots. Exogenous addition of the synthesized peptide significantly promoted primary root growth and inhibited lateral root emergence, in addition, the peptide application reduced the number of infection threads, nodule primordia and root nodules of M. truncatula. We also found that tyrosine sulfation determines the biological activity of MtRGF3 functioning in nodulation process, and MtRGF3 peptide negatively regulates nodulation in a dosage manner. These results demonstrate that the MtRGF3 peptide is a novel regulator during nodulation of Medicago trucatula.

Hormone modulation of legume-rhizobial symbiosis

Leguminous plants can establish symbiotic associations with diazotropic rhizobia to form nitrogen-fixating nodules, which are classified as determinate or indeterminate based on the persistence of nodule meristem. The formation of nitrogen-fixing nodules requires coordinating rhizobial infection and root nodule organogenesis. The formation of an infection thread and the extent of nodule formation are largely under plant control, but vary with environmental conditions and the physiological state of the host plants. Many achievements in these two areas have been made in recent decades. Phytohormone signaling pathways have gradually emerged as important regulators of root nodule symbiosis. Cytokinin, strigolactones (SLs) and local accumulation of auxin can promote nodule development. Ethylene, jasmonic acid (JA), abscisic acid (ABA) and gibberellic acid (GA) all negatively regulate infection thread formation and nodule development. However, salicylic acid (SA) and brassinosteroids (BRs) have different effects on the formation of these two nodule types. Some peptide hormones are also involved in nodulation. This review summarizes recent findings on the roles of these plant hormones in legume-rhizobial symbiosis, and we propose that DELLA proteins may function as a node to integrate plant hormones to regulate nodulation.

Impact of Plant Peptides on Symbiotic Nodule Development and Functioning

Ribosomally synthesized peptides have wide ranges of functions in plants being, for example, signal molecules, transporters, alkaloids, or antimicrobial agents. Legumes are an unprecedented rich source of peptides, which are used to control the symbiosis of these plants with the nitrogen-fixing Rhizobium bacteria. Here, we discuss the function and the evolution of these peptides playing an important role in the formation or functioning of the symbiotic organs, the root nodules. We distinguish peptides that can be either cell-autonomous or secreted short-range or long-range signals, carrying messages in or between plant cells or that can act as effectors interacting with the symbiotic bacteria. Peptides are further classified according to the stage of the symbiotic process where they act. Several peptide classes, including RALF, DLV, ENOD40, and others, control Rhizobium infection and the initiation of cell divisions and the formation of nodule primordia. CLE and CEP peptides are implicated in systemic and local control of nodule initiation during autoregulation of nodulation and in response to the nutritional demands of the plant. Still other peptides act at later stages of the symbiosis. The PSK peptide is thought to be involved in the suppression of immunity in nodules and the nodule-specific cysteine-rich, GRP, and SNARP (LEED..PEED) peptide families are essential in the functioning of the nitrogen fixing root nodules. The NCRs and possibly also the GRP and SNARPs are targeted to the endosymbionts and play essential roles in the terminal differentiation of these bacteria.

Plant Malectin-Like Receptor Kinases: From Cell Wall Integrity to Immunity and Beyond

Plant cells are surrounded by cell walls protecting them from a myriad of environmental challenges. For successful habitat adaptation, extracellular cues are perceived at the cell wall and relayed to downstream signaling constituents to mediate dynamic cell wall remodeling and adapted intracellular responses. Plant malectin-like receptor kinases, also known as Catharanthus roseus receptor-like kinase 1-like proteins (CrRLK1Ls), take part in these perception and relay processes. CrRLK1Ls are involved in many different plant functions. Their ligands, interactors, and downstream signaling partners are being unraveled, and studies about CrRLK1Ls' roles in plant species other than the plant model Arabidopsis thaliana are beginning to flourish. This review focuses on recent CrRLK1L-related advances in cell growth, reproduction, hormone signaling, abiotic stress responses, and, particularly, immunity. We also give an overview of the comparative genomics and evolution of CrRLK1Ls, and present a brief outlook for future research.

LysM Receptor-Like Kinase and LysM Receptor-Like Protein Families: An Update on Phylogeny and Functional Characterization

Members of plant specific families of receptor-like kinases (RLKs) and receptor-like proteins (RLPs), containing 3 extracellular LysMs have been shown to directly bind and/or to be involved in perception of lipo-chitooligosaccharides (LCO), chitooligosaccharides (CO), and peptidoglycan (PGN), three types of GlcNAc-containing molecules produced by microorganisms. These receptors are involved in microorganism perception by plants and can activate different plant responses leading either to symbiosis establishment or to defense responses against pathogens. LysM-RLK/Ps belong to multigenic families. Here, we provide a phylogeny of these families in eight plant species, including dicotyledons and monocotyledons, and we discuss known or putative biological roles of the members in each of the identified phylogenetic groups. We also report and discuss known biochemical properties of the LysM-RLK/Ps.

Small peptide signaling pathways modulating macronutrient utilization in plants

Root system architecture (RSA) and physiological functions define macronutrient uptake efficiency. Small signaling peptides (SSPs), that act in manners similar to hormones, and their cognate receptors transmit signals both locally and systemically. Several SSPs controlling morphological and physiological traits of roots have been identified to be associated with macronutrient uptake. Recent development in plant genome research has provided an avenue toward systems-based identification and prediction of additional SSPs. This review highlights recent studies on SSP pathways important for optimization of macronutrient uptake and provides new insights into the diversity of SSPs regulated in response to changes in macronutrient availabilities.

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

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.

Perigone Lobe Transcriptome Analysis Provides Insights into Rafflesia cantleyi Flower Development

Rafflesia is a biologically enigmatic species that is very rare in occurrence and possesses an extraordinary morphology. This parasitic plant produces a gigantic flower up to one metre in diameter with no leaves, stem or roots. However, little is known about the floral biology of this species especially at the molecular level. In an effort to address this issue, we have generated and characterised the transcriptome of the Rafflesia cantleyi flower, and performed a comparison with the transcriptome of its floral bud to predict genes that are expressed and regulated during flower development. Approximately 40 million sequencing reads were generated and assembled de novo into 18,053 transcripts with an average length of 641 bp. Of these, more than 79% of the transcripts had significant matches to annotated sequences in the public protein database. A total of 11,756 and 7,891 transcripts were assigned to Gene Ontology categories and clusters of orthologous groups respectively. In addition, 6,019 transcripts could be mapped to 129 pathways in Kyoto Encyclopaedia of Genes and Genomes Pathway database. Digital abundance analysis identified 52 transcripts with very high expression in the flower transcriptome of R. cantleyi. Subsequently, analysis of differential expression between developing flower and the floral bud revealed a set of 105 transcripts with potential role in flower development. Our work presents a deep transcriptome resource analysis for the developing flower of R. cantleyi. Genes potentially involved in the growth and development of the R. cantleyi flower were identified and provide insights into biological processes that occur during flower development.

Comprehensive analysis of plant rapid alkalization factor (RALF) genes

Receptor mediated signal carriers play a critical role in the regulation of plant defense and development. Rapid alkalization factor (RALF) proteins potentially comprise important signaling components which may have a key role in plant biology. The RALF gene family contains large number of genes in several plant species, however, only a few RALF genes have been characterized to date. In this study, an extensive database search identified 39, 43, 34 and 18 RALF genes in Arabidopsis, rice, maize and soybean, respectively. These RALF genes were found to be highly conserved across the 4 plant species. A comprehensive analysis including the chromosomal location, gene structure, subcellular location, conserved motifs, protein structure, protein-ligand interaction and promoter analysis was performed. RALF genes from four plant species were divided into 7 groups based on phylogenetic analysis. In silico expression analysis of these genes, using microarray and EST data, revealed that these genes exhibit a variety of expression patterns. Furthermore, RALF genes showed distinct expression patterns of transcript accumulation in vivo following nitrosative and oxidative stresses in Arabidopsis. Predicted interaction between RALF and heme ligand also showed that RALF proteins may contribute towards transporting or scavenging oxygen moieties. This suggests a possible role for RALF genes during changes in cellular redox status. Collectively, our data provides a valuable resource to prime future research in the role of RALF genes in plant growth and development.

Combined genetic and transcriptomic analysis reveals three major signalling pathways activated by Myc-LCOs in Medicago truncatula

Myc-LCOs are newly identified symbiotic signals produced by arbuscular mycorrhizal (AM) fungi. Like rhizobial Nod factors, they are lipo-chitooligosaccharides that activate the common symbiotic signalling pathway (CSSP) in plants. To increase our limited understanding of the roles of Myc-LCOs we aimed to analyse Myc-LCO-induced transcriptional changes and their genetic control. Whole genome RNA sequencing (RNA-seq) was performed on roots of Medicago truncatula wild-type plants, and dmi3 and nsp1 symbiotic mutants affected in nodulation and mycorrhizal signalling. Plants were treated separately with the two major types of Myc-LCOs, sulphated and nonsulphated. Generalized linear model analysis identified 2201 differentially expressed genes and classified them according to genotype and/or treatment effects. Three genetic pathways for Myc-LCO-regulation of transcriptomic reprogramming were highlighted: DMI3- and NSP1-dependent; DMI3-dependent and NSP1-independent; and DMI3- and NSP1-independent. Comprehensive analysis revealed overlaps with previous AM studies, and highlighted certain functions, especially signalling components and transcription factors. These data provide new insights into mycorrhizal signalling mechanisms, supporting a role for NSP1, and specialisation for NSP1-dependent and -independent pathways downstream of DMI3. Our data also indicate significant Myc-LCO-activated signalling upstream of DMI3 and/or parallel to the CSSP and some constitutive activity of the CSSP.

Hormonal Control of Lateral Root and Nodule Development in Legumes

Many plants can establish symbioses with nitrogen-fixing bacteria, some of which lead to nodulation, including legumes. Indeed, in the rhizobium/legume symbiosis, new root organs, called nodules, are formed by the plant in order to host the rhizobia in protective conditions, optimized for nitrogen fixation. In this way, these plants can benefit from the reduction of atmospheric dinitrogen into ammonia by the hosted bacteria, and in exchange the plant provides the rhizobia with a carbon source. Since this symbiosis is costly for the plant it is highly regulated. Both legume nodule and lateral root organogenesis involve divisions of the root inner tissues, and both developmental programs are tightly controlled by plant hormones. In fact, most of the major plant hormones, such as auxin, cytokinins, abscisic acid, and strigolactones, control both lateral root formation and nodule organogenesis, but often in an opposite manner. This suggests that the sensitivity of legume plants to some phytohormones could be linked to the antagonism that exists between the processes of nodulation and lateral root formation. Here, we will review the implication of some major phytohormones in lateral root formation in legumes, compare them with their roles in nodulation, and discuss specificities and divergences from non-legume eudicot plants such as Arabidopsis thaliana.

Small-peptide signals that control root nodule number, development, and symbiosis

Many legumes have the capacity to enter into a symbiotic association with soil bacteria generically called 'rhizobia' that results in the formation of new lateral organs on roots called nodules within which the rhizobia fix atmospheric nitrogen (N). Up to 200 million tonnes of N per annum is fixed by this association. Therefore, this symbiosis plays an integral role in the N cycle and is exploited in agriculture to support the sustainable fixation of N for cropping and animal production in developing and developed nations. Root nodulation is an expendable developmental process and competency for nodulation is coupled to low-N conditions. Both nodule initiation and development is suppressed under high-N conditions. Although root nodule formation enables sufficient N to be fixed for legumes to grow under N-deficient conditions, the carbon cost is high and nodule number is tightly regulated by local and systemic mechanisms. How legumes co-ordinate nodule formation with the other main organs of nutrient acquisition, lateral roots, is not fully understood. Independent mechanisms appear to regulate lateral roots and nodules under low- and high-N regimes. Recently, several signalling peptides have been implicated in the local and systemic regulation of nodule and lateral root formation. Other peptide classes control the symbiotic interaction of rhizobia with the host. This review focuses on the roles played by signalling peptides during the early stages of root nodule formation, in the control of nodule number, and in the establishment of symbiosis. Here, we highlight the latest findings and the gaps in our understanding of these processes.

Comparative analysis of the RTFL peptide family on the control of plant organogenesis

Plant peptides play important roles in various aspects of plant growth and development. The RTFL/DVL family includes small peptides that are widely conserved among land plants. Overexpression of six RTFL genes in Arabidopsis was suggestive of their functions as negative regulators of cell proliferation and as positional cues along the longitudinal axis of the plant body . At this time, few reports are available on RTFL paralogs in other species and the evolutionary relationship of RTFL members among land plants remains unclear. In this study, we compared and analyzed whole amino acid sequences of 188 RTFL members from 22 species among land plants and identified 73 motifs. All RTFL members could be grouped into four clades, and each clade exhibited specific motif patterns, indicative of unique evolutionary traits in the RTFL family. In agreement with this hypothesis, we analyzed two RTFL members from Oryza sativa and Arabidopsis by overexpressing them in Arabidopsis, revealing similar phenotypes suggestive of a conserved function of the RTFL family between eudicots and monocots, as well as different phenotypes and unique functions.

Understanding the RALF family: a tale of many species

Small secreted peptides are gaining importance as signalling molecules in plants. Among the 1000 open reading frames (ORFs) in the Arabidopsis (Arabidopsis thaliana) genome potentially encoding small secreted peptides, the members of the RAPID ALKALINIZATION FACTOR (RALF) family of peptides have been linked to several physiological and developmental processes. Here, we provide a comprehensive overview of current knowledge on the RALF family. Discovered in tobacco (Nicotiana tabacum), the role of RALF peptides has been investigated in numerous plant species. Together, these observations suggest that RALF peptides impact on acidification and cell expansion during growth and development. Although few components of the signalling pathway have been revealed, the recent identification of FERONIA (FER) as a RALF receptor and plasma membrane H(+)-ATPase 2 as a downstream target provide a major step forward.

Phytohormone regulation of legume-rhizobia interactions

The symbiosis between legumes and nitrogen fixing bacteria called rhizobia leads to the formation of root nodules. Nodules are highly organized root organs that form in response to Nod factors produced by rhizobia, and they provide rhizobia with a specialized niche to optimize nutrient exchange and nitrogen fixation. Nodule development and invasion by rhizobia is locally controlled by feedback between rhizobia and the plant host. In addition, the total number of nodules on a root system is controlled by a systemic mechanism termed 'autoregulation of nodulation'. Both the local and the systemic control of nodulation are regulated by phytohormones. There are two mechanisms by which phytohormone signalling is altered during nodulation: through direct synthesis by rhizobia and through indirect manipulation of the phytohormone balance in the plant, triggered by bacterial Nod factors. Recent genetic and physiological evidence points to a crucial role of Nod factor-induced changes in the host phytohormone balance as a prerequisite for successful nodule formation. Phytohormones synthesized by rhizobia enhance symbiosis effectiveness but do not appear to be necessary for nodule formation. This review provides an overview of recent advances in our understanding of the roles and interactions of phytohormones and signalling peptides in the regulation of nodule infection, initiation, positioning, development, and autoregulation. Future challenges remain to unify hormone-related findings across different legumes and to test whether hormone perception, response, or transport differences among different legumes could explain the variety of nodules types and the predisposition for nodule formation in this plant family. In addition, the molecular studies carried out under controlled conditions will need to be extended into the field to test whether and how phytohormone contributions by host and rhizobial partners affect the long term fitness of the host and the survival and competition of rhizobia in the soil. It also will be interesting to explore the interaction of hormonal signalling pathways between rhizobia and plant pathogens.

Plant peptides in defense and signaling

This review focuses on plant peptides involved in defense against pathogen infection and those involved in the regulation of growth and development. Defense peptides, defensins, cyclotides and anti-microbial peptides are compared and contrasted. Signaling peptides are classified according to their major sites of activity. Finally, a network approach to creating an interactomic peptide map is described.

Biological activity of nine recombinant AtRALF peptides: implications for their perception and function in Arabidopsis

RALF is a small (5 kDa) and ubiquitous plant peptide signal. It was first isolated from tobacco leaf protein extracts owing to its capacity to alkalinize the extracellular media of cell suspensions. RALFs inhibit root growth and hypocotyl elongation, and a role for RALFs in cell expansion has also been proposed. Arabidopsis has 37 RALF isoforms (AtRALF), but only a small group of nine has high primary structure identity to the original RALF peptide isolated from tobacco. Herein, we report the heterologous production of these nine peptides in Escherichia coli and the evaluation of their activity in five biological assays. All AtRALF peptides produced showed strong alkalinizing activities, with the exception of the pollen-specific isoform AtRALF4. Although it exhibited no inhibitory activity in the root growth and hypocotyl elongation assays, AtRALF4 is a strong inhibitor of pollen germination. Our data demonstrate that the divergence in the tissue specificity and gene expression patterns of the different AtRALFs does not change the fact that their main role seems to be the regulation of cell expansion. Furthermore, different activities in the alkalinization assays upon the addition of two consecutive and saturating doses of the peptides suggest that the peptides are likely being sensed by specific receptors.

Peptide ligands in plants

Plants have evolved small peptide ligands as intercellular signaling molecules. Previous studies have uncovered pairs of ligands and receptors in cell-cell communications. This review focuses on signaling and function of key plant peptide ligands.

Substantial expression of novel small open reading frames in Oryza sativa

In our previous integrated study combining informatics and molecular biology analyses, we revealed that Arabidopsis small open reading frames (sORFs) predicted by computational analysis have biological functions in morphogenesis. Here, we report that sequences homologous to Arabidopsis sORFs are abundant in intergenic regions of the rice genome. These sequences represent a subset of non-protein-coding DNA, and some are transcribed into mRNA. These results indicate that many sORFs associated with morphogenesis are hidden in the genomes of crop species.

Transcriptional responses toward diffusible signals from symbiotic microbes reveal MtNFP- and MtDMI3-dependent reprogramming of host gene expression by arbuscular mycorrhizal fungal lipochitooligosaccharides

The formation of root nodules and arbuscular mycorrhizal (AM) roots is controlled by a common signaling pathway including the calcium/calmodulin-dependent kinase Doesn't Make Infection3 (DMI3). While nodule initiation by lipochitooligosaccharide (LCO) Nod factors is well characterized, diffusible AM fungal signals were only recently identified as sulfated and nonsulfated LCOs. Irrespective of different outcomes, the perception of symbiotic LCOs in Medicago truncatula is mediated by the LysM receptor kinase M. truncatula Nod factor perception (MtNFP). To shed light on transcriptional responses toward symbiotic LCOs and their dependence on MtNFP and Ca(2+) signaling, we performed genome-wide expression studies of wild-type, Nod-factor-perception mutant1, and dmi3 mutant roots challenged with Myc- and Nod-LCOs. We show that Myc-LCOs lead to transient, quick responses in the wild type, whereas Nod-LCOs require prolonged incubation for maximal expression activation. While Nod-LCOs are most efficient for an induction of persistent transcriptional changes, sulfated Myc-LCOs are less active, and nonsulfated Myc-LCOs display the lowest capacity to activate and sustain expression. Although all symbiotic LCOs up-regulated a common set of genes, discrete subsets were induced by individual LCOs, suggesting common and specific functions for these in presymbiotic signaling. Surprisingly, even sulfated fungal Myc-LCOs and Sinorhizobium meliloti Nod-LCOs, having very similar structures, each elicited discrete subsets of genes, while a mixture of both Myc-LCOs activated responses deviating from those induced by single treatments. Focusing on the precontact phase, we identified signaling-related and transcription factor genes specifically up-regulated by Myc-LCOs. Comparative gene expression studies in symbiotic mutants demonstrated that transcriptional reprogramming by AM fungal LCOs strictly depends on MtNFP and largely requires MtDMI3.

Evolution of the RALF Gene Family in Plants: Gene Duplication and Selection Patterns

Rapid alkalinization factors (RALFs) are plant small peptides that could induce a rapid pH increase in the medium of plant cell suspension culture and play a critical role in plant development. The evolutionary process of the RALF gene family remains unclear. To obtain details of the phylogeny of these genes, this study characterized RALF genes in Arabidopsis, rice, poplar and maize. Phylogenetic trees, evolutionary patterns and molecular evolutionary rates were used to elucidate the evolutionary process of this gene family. In addition, the different signatures of selection, expression patterns, and subcellular localization of RALFs were also analyzed. We found that the RALF gene family had a rapid birth process after the separation of the eudicot and monocot species about 145 million years ago, that tandem duplication played a dominant role in the expansion of Arabidopsis and rice RALF gene family, and that RALFs were under purifying selection according to estimations of the substitution rates of these genes. We also identified a diverse expression pattern of RALF genes and predominant extracellular localization feature of RALF proteins. Our findings shed light on several key differences in RALF gene family evolution among the plant species, which may provide a scaffold for future functional analysis of this family.

DVL genes play a role in the coordination of socket cell recruitment and differentiation

Specialized plant cells arise from undifferentiated cells through a series of developmental steps. The decision to enter into a certain differentiation pathway depends in many cases on signals from neighbouring cells. The ability of cells to engage in short-range intercellular communication permits the coordination of cell actions necessary in many developmental processes. Overexpression of genes from the DEVIL/ROTUNDIFOLIA (DVL/ROT) family results in severe developmental alterations, but very little is known about their mechanism of action. This work presents evidence that suggests a role for these genes in local signalling, specifically in the coordination of socket cell recruitment and differentiation. Overexpression of different DVL genes results in protuberances at the base of the trichomes surrounded by several rows of elongated epidermal cells, morphologically similar to socket cells. Localized overexpression of DVL4 in trichomes and socket cells during early developmental stages activates expression of socket cell markers in additional cells, farther away from the trichome. The same phenomenon is observed in an activation tagged line of DVL1, which also shows an increase in the number of socket cells in contact with the trichome. The roles of individual DVL genes have been difficult to discover since their overexpression phenotypes are quite similar. In gl1 leaves that lack trichomes and socket cells DVL1 expression shows a 69% reduction, suggesting that this gene could be involved in the coordination of socket cell development in wild-type plants.

Dual RNAs in plants

Plants have remarkable developmental plasticity, and the same genotype can result in different phenotypes depending on environmental variation. Indeed, abiotic stresses or biotic interactions affect organogenesis and post-embryonic growth and significantly affect gene regulation. The large diversity of non-protein-coding RNAs (npcRNAs) and genes containing only short open reading frames that are expressed during plant growth and development, contribute to the regulation of gene expression. Certain npcRNAs code for oligopeptides and may possess additional biological activity linked to the RNA moiety. The ENOD40 gene is a dual RNA that is activated during a symbiotic interaction leading to root nodule organogenesis. Both the oligopeptides encoded by ENOD40 and the structured regions of the ENOD40 RNA have been shown to interact with different proteins in the cell to control enzymatic activities or induce the relocalisation of ribonucleoproteins, respectively. Other npcRNAs encode for small signalling peptides or are the precursors of small RNAs involved in post-transcriptional or transcriptional gene silencing. They may have RNA-related activities or encode peptides (or even larger proteins), and therefore act as dual RNAs. In addition, long natural antisense RNAs with a coding function and a regulatory RNA-mediated action that are expressed in response to abiotic stress in plants have been identified. In certain cases, these RNAs lead to the synthesis of nat-siRNAs, that are small RNAs derived from the overlapping double-stranded RNA region of natural antisense RNAs, which facilitates the silencing of complementary mRNAs. Finally, the advent of deep sequencing technologies has identified a large number of non-protein-coding RNAs in plants, which could be a large reservoir for dual RNAs.

Long-distance transport of signals during symbiosis: are nodule formation and mycorrhization autoregulated in a similar way?

Legumes enter nodule symbioses with nitrogen-fixing bacteria (rhizobia), whereas most flowering plants establish symbiotic associations with arbuscular mycorrhizal (AM) fungi. Once first steps of symbiosis are initiated, nodule formation and mycorrhization in legumes is negatively controlled by a shoot-derived inhibitor (SDI), a phenomenon termed autoregulation. According to current views, autoregulation of nodulation and mycorrhization in legumes is regulated in a similar way. CLE peptides induced in response to rhizobial nodulation signals (Nod factors) have been proposed to represent the ascending long-distance signals to the shoot. Although not proven yet, these CLE peptides are likely perceived by leucine-rich repeat (LRR) autoregulation receptor kinases in the shoot. Autoregulation of mycorrhization in non-legumes is reminiscent to the phenomenon of "systemic acquired resistance" in plant-pathogen interactions.

Transcription reprogramming during root nodule development in Medicago truncatula

Many genes which are associated with root nodule development and activity in the model legume Medicago truncatula have been described. However information on precise stages of activation of these genes and their corresponding transcriptional regulators is often lacking. Whether these regulators are shared with other plant developmental programs also remains an open question. Here detailed microarray analyses have been used to study the transcriptome of root nodules induced by either wild type or mutant strains of Sinorhizobium meliloti. In this way we have defined eight major activation patterns in nodules and identified associated potential regulatory genes. We have shown that transcription reprogramming during consecutive stages of nodule differentiation occurs in four major phases, respectively associated with (i) early signalling events and/or bacterial infection; plant cell differentiation that is either (ii) independent or (iii) dependent on bacteroid differentiation; (iv) nitrogen fixation. Differential expression of several genes involved in cytokinin biosynthesis was observed in early symbiotic nodule zones, suggesting that cytokinin levels are actively controlled in this region. Taking advantage of databases recently developed for M. truncatula, we identified a small subset of gene expression regulators that were exclusively or predominantly expressed in nodules, whereas most other regulators were also activated under other conditions, and notably in response to abiotic or biotic stresses. We found evidence suggesting the activation of the jasmonate pathway in both wild type and mutant nodules, thus raising questions about the role of jasmonate during nodule development. Finally, quantitative RT-PCR was used to analyse the expression of a series of nodule regulator and marker genes at early symbiotic stages in roots and allowed us to distinguish several early stages of gene expression activation or repression.

Peptide signalling in the rhizobium-legume symbiosis

For two decades, signalling research in the rhizobium-legume symbiosis field has been dominated by oligosaccharide signals (mainly Nod factors and, to a lesser extent, surface polysaccharides made by the microsymbionts) and phytohormones. Recently, plant peptides have emerged as another major class of signalling molecules in the rhizobium-legume symbioses contributing to the control of nodulation, infection and bacteroid differentiation. Here we focus on three examples of symbiotically relevant peptides, namely Enod40, CLE and NCR peptides. The number of genes encoding these peptides, as well as the recent discovery of additional peptide players in the context of symbiosis, suggests that we might be seeing only the tip of the peptide iceberg in the sea of symbiotic regulations.

ROTUNDIFOLIA4 regulates cell proliferation along the body axis in Arabidopsis shoot

Molecular genetics has been successful in identifying leaf- size regulators such as transcription factors, phytohormones, and signal molecules. Among them, a ROTUNDIFOLIA4-LIKE/DEVIL (RTFL/DVL) family of Arabidopsis, genes encoding peptides with no secretion-signal sequence, is unique in that their overexpressors have a reduced number of leaf cells specifically along the proximodistal axis. However, because the RTFL/DVL lack any obvious homology with functionally identified domains, and because of genetic redundancy among RTFL/DVL, their molecular and developmental roles are unclear. In this study we focused on one member in the family, ROTUNDIFOLIA4 (ROT4), and identified the core functional region within it and we found no proteolytic processing in planta. Developmental analysis of leaf primordia revealed that ROT4 overexpression reduces the meristematic zone size within the leaf blade. Moreover, induced local overexpression demonstrated that ROT4 acts as a regulator of the leaf shape via a change in positional cue along the longitudinal axis. Similarly, ROT4 overexpression results in a protrusion of the main inflorescence stem, again indicating a change in positional cue along the longitudinal axis. These results suggest that ROT4 affects the positional cue and cell proliferation along the body axis.

RALFs: peptide regulators of plant growth

Peptide signaling regulates a variety of developmental processes and environmental responses in plants. For example, the peptide systemin induces the systemic defense response in tomato and defensins are small cysteine-rich proteins that are involved in the innate immune system of plants. The CLAVATA3 peptide regulates meristem size and the SCR peptide is the pollen self-incompatibility recognition factor in the Brassicaceae. LURE peptides produced by synergid cells attract pollen tubes to the embryo sac. RALFs are a recently discovered family of plant peptides that play a role in plant cell growth.

Structure-activity studies of RALF, Rapid Alkalinization Factor, reveal an essential--YISY--motif

Rapid Alkalinization Factor (RALF) is a 49-amino acid peptide initially isolated from tobacco leaves that is capable of arresting both root and pollen tube growth. With suspension cells, addition of RALF causes an elevation of the pH of the extracellular media, caused by the blockage of a proton pump. RALF associates with a putative receptor(s) on the surface of the plant cell, initiating a signal transduction pathway. Although the exact function(s) of RALFs are unknown, its presence throughout the plant kingdom attests to its importance in some type of basic regulatory role. In the present study, deletion and substitution analyses of RALF reveal a specific - YISY - motif located at positions 5 through 8 from the N-terminus, highly conserved within the plant kingdom, which is a requirement for productive binding of RALF to its putative receptor. Replacement of isoleucine with alanine in the - YISY - motif caused a severe reduction in alkalinization of suspension cell media and a loss of root growth inhibition with tomato seedlings.

A remorin protein interacts with symbiotic receptors and regulates bacterial infection

Remorin proteins have been hypothesized to play important roles during cellular signal transduction processes. Induction of some members of this multigene family has been reported during biotic interactions. However, no roles during host-bacteria interactions have been assigned to remorin proteins until now. We used root nodule symbiosis between Medicago truncatula and Sinorhizobium meliloti to study the roles of a remorin that is specifically induced during nodulation. Here we show that this oligomeric remorin protein attaches to the host plasma membrane surrounding the bacteria and controls infection and release of rhizobia into the host cytoplasm. It interacts with the core set of symbiotic receptors that are essential for perception of bacterial signaling molecules, and thus might represent a plant-specific scaffolding protein.

(Homo)glutathione depletion modulates host gene expression during the symbiotic interaction between Medicago truncatula and Sinorhizobium meliloti

Under nitrogen-limiting conditions, legumes interact with symbiotic rhizobia to produce nitrogen-fixing root nodules. We have previously shown that glutathione and homoglutathione [(h)GSH] deficiencies impaired Medicago truncatula symbiosis efficiency, showing the importance of the low M(r) thiols during the nodulation process in the model legume M. truncatula. In this study, the plant transcriptomic response to Sinorhizobium meliloti infection under (h)GSH depletion was investigated using cDNA-amplified fragment length polymorphism analysis. Among 6,149 expression tags monitored, 181 genes displayed significant differential expression between inoculated control and inoculated (h)GSH depleted roots. Quantitative reverse transcription polymerase chain reaction analysis confirmed the changes in mRNA levels. This transcriptomic analysis shows a down-regulation of genes involved in meristem formation and a modulation of the expression of stress-related genes in (h)GSH-depleted plants. Promoter-beta-glucuronidase histochemical analysis showed that the putative MtPIP2 aquaporin might be up-regulated during nodule meristem formation and that this up-regulation is inhibited under (h)GSH depletion. (h)GSH depletion enhances the expression of salicylic acid (SA)-regulated genes after S. meliloti infection and the expression of SA-regulated genes after exogenous SA treatment. Modification of water transport and SA signaling pathway observed under (h)GSH deficiency contribute to explain how (h)GSH depletion alters the proper development of the symbiotic interaction.

Cloning and expression analysis of a pollen preferential rapid alkalinization factor gene, BoRALF1, from broccoli flowers

Rapid alkalinization factors (RALFs) are recently reported active peptide hormones and are considered to play important roles in plant development. We previously identified a differentially expressed cDNA fragment between cabbage flower buds of sterility lines and its maintainer line, which showed significant homology to Arabidopsis RALFL9. The novel RALF cDNA (BoRALF1) was isolated from broccoli flower buds by EST assembly. The open reading frame (ORF) comprises 240 bp, encoding a small putative preprotein of 79 amino acids (molecular weight of 8.72 kDa and a pI of 7.8), which contains the mature polypeptide at its C terminus. BoRALF1 shares 70.3% identity with Arabidopsis RALFL9, but has only moderate similarity with functionally characterized RALFs (ranging from 16.2% to 38.0%). BoRALF1 shows typical features of RALFs, including the 28-aa signal peptide, typical arrangement of four position conserved cysteines, the YIXY motif and a similar secondary structure. RT-PCR studies of different tissues and promoter-GUS fusions confirmed that BoRALF1 is expressed strictly in mature pollen grains and in the anther cells around the loculi. Based on in vivo transient assays, we found that BoRALF1 appears to be largely localized in the plasma membrane. Although the function of BoRALF1 remains to be determined, our experiments confirm the presence of RALF peptide in broccoli, and suggest it could have a role in anther or pollen development.

Long-distance control of nodulation: molecules and models

Legume plants develop root nodules to recruit nitrogen-fixing bacteria called rhizobia. This symbiotic relationship allows the host plants to grow even under nitrogen limiting environment. Since nodule development is an energetically expensive process, the number of nodules should be tightly controlled by the host plants. For this purpose, legume plants utilize a long-distance signaling known as autoregulation of nodulation (AON). AON signaling in legumes has been extensively studied over decades but the underlying molecular mechanism had been largely unclear until recently. With the advent of the model legumes, L. japonicus and M. truncatula, we have been seeing a great progress including isolation of the AON-associated receptor kinase. Here, we summarize recent studies on AON and discuss an updated view of the long-distance control of nodulation.