Expression of the CLE-RS3 gene suppresses root nodulation in Lotus japonicus

Decoding small peptides: Regulators of plant growth and stress resilience

Small peptides (SPs) are pivotal signaling molecules that play essential roles in the precise regulation of plant growth, development, and stress responses. Recent advancements in sequencing technologies, bioinformatics approaches, and biochemical and molecular techniques have significantly enhanced the accuracy of SP identification, unveiling their diverse biological functions in plants. This review provides a comprehensive overview of the characteristics and methodologies for identifying SPs in plants. It highlights recent discoveries regarding the biological roles and signaling pathways of SPs in regulating plant growth, development, and plant-microbial interactions, as well as their contributions to plant resilience under various environmental stresses, including abiotic stress, nutrient deficiencies, and biotic challenges. Additionally, we discuss current insights into the potential applications of SPs and outline future research directions aimed at leveraging these molecules to enhance plant adaptation to environmental challenges. By integrating recent findings, this review lays a foundation for advancing the understanding and utilization of SPs to improve plant resilience and productivity.

The Small Key to the Treasure Chest: Endogenous Plant Peptides Involved in Symbiotic Interactions

Plant growth and development are inextricably connected with rhizosphere organisms. Plants have to balance between strong defenses against pathogens while modulating their immune responses to recruit beneficial organisms such as bacteria and fungi. In recent years, there has been increasing evidence that regulatory peptides are essential in establishing these symbiotic relationships, orchestrating processes that include nutrient acquisition, root architecture modification, and immune modulation. In this review, we provide a comprehensive summary of the peptide families that facilitate beneficial relationships between plants and rhizosphere organisms.

CLE peptide signaling in plant-microbe interactions

Cell-cell communication is essential for both unicellular and multicellular organisms. Secreted peptides that act as diffusive ligands are utilized by eukaryotic organisms to transduce information between cells to coordinate developmental and physiological processes. In plants, The CLAVATA3/EMBRYO SURROUNDING REGION-RELATED (CLE) genes encode a family of secreted small peptides which play pivotal roles in stem cell homeostasis in various types of meristems. Accumulated evidence has revealed that CLE peptides mediate trans-kingdom interactions between plants and microbes, including pathogens and symbionts. This review highlights the emerging roles of CLE peptide signaling in plant-microbe interactions, focusing on their involvement in nodulation, immunity, and symbiosis with arbuscular mycorrhizal fungi. Understanding these interactions provides insights into the sophisticated regulatory networks to balance plant growth and defense, enhancing our knowledge of plant biology and potential agricultural applications.

The LaCLE35 peptide modifies rootlet density and length in cluster roots of white lupin

White lupin (lupinus albus L.) forms special bottlebrush-like root structures called cluster roots (CR) when phosphorus is low, to remobilise sparingly soluble phosphates in the soil. The molecular mechanisms that control the CR formation remain unknown. Root development in other plants is regulated by CLE  (CLAVATA3/ EMBRYO SURROUNDING REGION (ESR)-RELATED) peptides, which provide more precise control mechanisms than common phytohormones. This makes these peptides interesting candidates to be involved in CR formation, where fine tuning to environmental factors is required. In this study we present an analysis of CLE peptides in white lupin. The peptides LaCLE35 (RGVHy PSGANPLHN) and LaCLE55 (RRVHy PSCHy PDPLHN) reduced root growth and altered CR in hydroponically cultured white lupins. We demonstrate that rootlet density and rootlet length were locally, but not systemically, impaired by exogenously applied CLE35. The peptide was identified in the xylem sap. The inhibitory effect of CLE35 on root growth was attributed to arrested cell elongation in root tips. Taken together, CLE peptides affect both rootlet density and rootlet length, which are two critical factors for CR formation, and may be involved in fine tuning this peculiar root structure that is present in a few crops and many Proteaceae species, under low phosphorus availability.

Staying hungry: a roadmap to harnessing central regulators of symbiotic nitrogen fixation under fluctuating nitrogen availability

Legumes have evolved specific inventions to enhance nitrogen (N) acquisition by establishing symbiotic interactions with N-fixing rhizobial bacteria. Because symbiotic N fixation is energetically costly, legumes have developed sophisticated mechanisms to ensure carbon-nitrogen balance, in a variable environment, both locally and at the whole plant level, by monitoring nodule number, nodule development, and nodular nitrogenase activity, as well as controlling nodule senescence. Studies of the autoregulation of nodulation and regulation of nodulation by nodule inception (NIN) and NIN-LIKE PROTEINs (NLPs) have provided great insights into the genetic mechanisms underlying the nitrate-induced regulation of root nodulation for adapting to N availability in the rhizosphere. However, many aspects of N-induced pleiotropic regulation remain to be fully explained, such as N-triggered senescence in mature nodules. Wang et al. determined that this process is governed by a transcriptional network regulated by NAC-type transcription factors. Characterization and dissection of these soybean nitrogen-associated NAPs (SNAPs) transcription factor-mastered networks have yielded a roadmap for exploring how legumes rewire nodule functions across a range of N levels, laying the foundation for enhancing the growth of N-deprived crops in agricultural settings.

CLAVATA signaling in plant-environment interactions

Plants must rapidly and dynamically adapt to changes in their environment. Upon sensing environmental signals, plants convert them into cellular signals, which elicit physiological or developmental changes that allow them to respond to various abiotic and biotic cues. Because plants can be simultaneously exposed to multiple environmental cues, signal integration between plant cells, tissues, and organs is necessary to induce specific responses. Recently, CLAVATA3/EMBRYO SURROUNDING REGION-related (CLE) peptides and their cognate CLAVATA-type receptors received increased attention for their roles in plant-environment interactions. CLE peptides are mobile signaling molecules, many of which are induced by a variety of biotic and abiotic stimuli. Secreted CLE peptides are perceived by receptor complexes on the surface of their target cells, which often include the leucine-rich repeat receptor-like kinase CLAVATA1. Receptor activation then results in cell-type and/or environment-specific responses. This review summarizes our current understanding of the diverse roles of environment-regulated CLE peptides in modulating plant responses to environmental cues. We highlight how CLE signals regulate plant physiology by fine-tuning plant-microbe interactions, nutrient homeostasis, and carbon allocation. Finally, we describe the role of CLAVATA receptors in the perception of environment-induced CLE signals and discuss how diverse CLE-CLAVATA signaling modules may integrate environmental signals with plant physiology and development.

The Role of CLE Peptides in the Suppression of Mycorrhizal Colonization of Tomato

Symbioses with beneficial microbes are widespread in plants, but these relationships must balance the energy invested by the plants with the nutrients acquired. Symbiosis with arbuscular mycorrhizal (AM) fungi occurs throughout land plants, but our understanding of the genes and signals that regulate colonization levels is limited, especially in non-legumes. Here, we demonstrate that in tomato, two CLV3/EMBRYO-SURROUNDING REGION (CLE) peptides, SlCLE10 and SlCLE11, act to suppress AM colonization of roots. Mutant studies and overexpression via hairy transformation indicate that SlCLE11 acts locally in the root to limit AM colonization. Indeed, SlCLE11 expression is strongly induced in AM-colonized roots, but SlCLE11 is not required for phosphate suppression of AM colonization. SlCLE11 requires the FIN gene that encodes an enzyme required for CLE peptide arabinosylation to suppress mycorrhizal colonization. However, SlCLE11 suppression of AM does not require two CLE receptors with roles in regulating AM colonization, SlFAB (CLAVATA1 ortholog) or SlCLV2. Indeed, multiple parallel pathways appear to suppress mycorrhizal colonization in tomato, as double mutant studies indicate that SlCLV2 and FIN have an additive influence on mycorrhizal colonization. SlCLE10 appears to play a more minor or redundant role, as cle10 mutants did not influence intraradical AM colonization. However, the fact that cle10 mutants had an elevated number of hyphopodia and that ectopic overexpression of SlCLE10 did suppress mycorrhizal colonization suggests that SlCLE10 may also play a role in suppressing AM colonization. Our findings show that CLE peptides regulate AM colonization in tomato and at least SlCLE11 likely requires arabinosylation for activity.

Mutation of BAM2 rescues the sunn hypernodulation phenotype in Medicago truncatula, suggesting that a signaling pathway like CLV1/BAM in Arabidopsis affects nodule number

The unique evolutionary adaptation of legumes for nitrogen-fixing symbiosis leading to nodulation is tightly regulated by the host plant. The autoregulation of nodulation (AON) pathway negatively regulates the number of nodules formed in response to the carbon/nitrogen metabolic status of the shoot and root by long-distance signaling to and from the shoot and root. Central to AON signaling in the shoots of Medicago truncatula is SUNN, a leucine-rich repeat receptor-like kinase with high sequence similarity with CLAVATA1 (CLV1), part of a class of receptors in Arabidopsis involved in regulating stem cell populations in the root and shoot. This class of receptors in Arabidopsis includes the BARELY ANY MERISTEM family, which, like CLV1, binds to CLE peptides and interacts with CLV1 to regulate meristem development. M. truncatula contains five members of the BAM family, but only MtBAM1 and MtBAM2 are highly expressed in the nodules 48 hours after inoculation. Plants carry mutations in individual MtBAMs, and several double BAM mutant combinations all displayed wild-type nodule number phenotypes. However, Mtbam2 suppressed the sunn-5 hypernodulation phenotype and partially rescued the short root length phenotype of sunn-5 when present in a sunn-5 background. Grafting determined that bam2 suppresses supernodulation from the roots, regardless of the SUNN status of the root. Overexpression of MtBAM2 in wild-type plants increases nodule numbers, while overexpression of MtBAM2 in some sunn mutants rescues the hypernodulation phenotype, but not the hypernodulation phenotypes of AON mutant rdn1-2 or crn. Relative expression measurements of the nodule transcription factor MtWOX5 downstream of the putative bam2 sunn-5 complex revealed disruption of meristem signaling; while both bam2 and bam2 sunn-5 influence MtWOX5 expression, the expression changes are in different directions. We propose a genetic model wherein the specific root interactions of BAM2/SUNN are critical for signaling in nodule meristem cell homeostasis in M. truncatula.

Functional Modules in the Meristems: "Tinkering" in Action

BACKGROUND

A feature of higher plants is the modular principle of body organisation. One of these conservative morphological modules that regulate plant growth, histogenesis and organogenesis is meristems-structures that contain pools of stem cells and are generally organised according to a common principle. Basic content: The development of meristems is under the regulation of molecular modules that contain conservative interacting components and modulate the expression of target genes depending on the developmental context. In this review, we focus on two molecular modules that act in different types of meristems. The WOX-CLAVATA module, which includes the peptide ligand, its receptor and the target transcription factor, is responsible for the formation and control of the activity of all meristem types studied, but it has its own peculiarities in different meristems. Another regulatory module is the so-called florigen-activated complex, which is responsible for the phase transition in the shoot vegetative meristem (e.g., from the vegetative shoot apical meristem to the inflorescence meristem).

CONCLUSIONS

The review considers the composition and functions of these two functional modules in different developmental programmes, as well as their appearance, evolution and use in plant breeding.

Peptide signaling through leucine-rich repeat receptor kinases: insight into land plant evolution

Multicellular organisms need mechanisms for communication between cells so that they can fulfill their purpose in the organism as a whole. Over the last two decades, several small post-translationally modified peptides (PTMPs) have been identified as components of cell-to-cell signaling modules in flowering plants. Such peptides most often influence growth and development of organs not universally conserved among land plants. PTMPs have been matched to subfamily XI leucine-rich repeat receptor-like kinases with > 20 repeats. Phylogenetic analyses, facilitated by recently published genomic sequences of non-flowering plants, have identified seven clades of such receptors with a history back to the common ancestor of bryophytes and vascular plants. This raises a number of questions: When did peptide signaling arise during land plant evolution? Have orthologous peptide-receptor pairs preserved their biological functions? Has peptide signaling contributed to major innovations, such as stomata, vasculature, roots, seeds, and flowers? Using genomic, genetic, biochemical, and structural data and non-angiosperm model species, it is now possible to address these questions. The vast number of peptides that have not yet found their partners suggests furthermore that we have far more to learn about peptide signaling in the coming decades.

Control of the rhizobium-legume symbiosis by the plant nitrogen demand is tightly integrated at the whole plant level and requires inter-organ systemic signaling

Symbiotic nodules formed on legume roots with rhizobia fix atmospheric N₂. Bacteria reduce N₂ to NH₄ ⁺ that is assimilated into amino acids by the plant. In return, the plant provides photosynthates to fuel the symbiotic nitrogen fixation. Symbiosis is tightly adjusted to the whole plant nutritional demand and to the plant photosynthetic capacities, but regulatory circuits behind this control remain poorly understood. The use of split-root systems combined with biochemical, physiological, metabolomic, transcriptomic, and genetic approaches revealed that multiple pathways are acting in parallel. Systemic signaling mechanisms of the plant N demand are required for the control of nodule organogenesis, mature nodule functioning, and nodule senescence. N-satiety/N-deficit systemic signaling correlates with rapid variations of the nodules' sugar levels, tuning symbiosis by C resources allocation. These mechanisms are responsible for the adjustment of plant symbiotic capacities to the mineral N resources. On the one hand, if mineral N can satisfy the plant N demand, nodule formation is inhibited, and nodule senescence is activated. On the other hand, local conditions (abiotic stresses) may impair symbiotic activity resulting in plant N limitation. In these conditions, systemic signaling may compensate the N deficit by stimulating symbiotic root N foraging. In the past decade, several molecular components of the systemic signaling pathways controlling nodule formation have been identified, but a major challenge remains, that is, to understand their specificity as compared to the mechanisms of non-symbiotic plants that control root development and how they contribute to the whole plant phenotypes. Less is known about the control of mature nodule development and functioning by N and C nutritional status of the plant, but a hypothetical model involving the sucrose allocation to the nodule as a systemic signaling process, the oxidative pentose phosphate pathway, and the redox status as potential effectors of this signaling is emerging. This work highlights the importance of organism integration in plant biology.

Plants Recruit Peptides and Micro RNAs to Regulate Nutrient Acquisition from Soil and Symbiosis

Plants engage in symbiotic relationships with soil microorganisms to overcome nutrient limitations in their environment. Among the best studied endosymbiotic interactions in plants are those with arbuscular mycorrhizal (AM) fungi and N-fixing bacteria called rhizobia. The mechanisms regulating plant nutrient homeostasis and acquisition involve small mobile molecules such as peptides and micro RNAs (miRNAs). A large number of CLE (CLAVATA3/EMBRYO SURROUNDING REGION-RELATED) and CEP (C-TERMINALLY ENCODED PEPTIDE) peptide hormones as well as certain miRNAs have been reported to differentially respond to the availability of essential nutrients such as nitrogen (N) and phosphorus (P). Interestingly, a partially overlapping pool of these molecules is involved in plant responses to root colonization by rhizobia and AM fungi, as well as mineral nutrition. The crosstalk between root endosymbiosis and nutrient availability has been subject of intense investigations, and new insights in locally or systemically mobile molecules in nutrient- as well as symbiosis-related signaling continue to arise. Focusing on the key roles of peptides and miRNAs, we review the mechanisms that shape plant responses to nutrient limitation and regulate the establishment of symbiotic associations with beneficial soil microorganisms.

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.

Progress in the Self-Regulation System in Legume Nodule Development-AON (Autoregulation of Nodulation)

The formation and development of legumes nodules requires a lot of energy. Legumes must strictly control the number and activity of nodules to ensure efficient energy distribution. The AON system can limit the number of rhizobia infections and nodule numbers through the systemic signal pathway network that the aboveground and belowground parts participate in together. It can also promote the formation of nodules when plants are deficient in nitrogen. The currently known AON pathway includes four parts: soil NO₃⁻ signal and Rhizobium signal recognition and transmission, CLE-SUNN is the negative regulation pathway, CEP-CRA2 is the positive regulation pathway and the miR2111/TML module regulates nodule formation and development. In order to ensure the biological function of this important approach, plants use a variety of plant hormones, polypeptides, receptor kinases, transcription factors and miRNAs for signal transmission and transcriptional regulation. This review summarizes and discusses the research progress of the AON pathway in Legume nodule development.

Innovation and appropriation in mycorrhizal and rhizobial Symbioses

Most land plants benefit from endosymbiotic interactions with mycorrhizal fungi, including legumes and some nonlegumes that also interact with endosymbiotic nitrogen (N)-fixing bacteria to form nodules. In addition to these helpful interactions, plants are continuously exposed to would-be pathogenic microbes: discriminating between friends and foes is a major determinant of plant survival. Recent breakthroughs have revealed how some key signals from pathogens and symbionts are distinguished. Once this checkpoint has been passed and a compatible symbiont is recognized, the plant coordinates the sequential development of two types of specialized structures in the host. The first serves to mediate infection, and the second, which appears later, serves as sophisticated intracellular nutrient exchange interfaces. The overlap in both the signaling pathways and downstream infection components of these symbioses reflects their evolutionary relatedness and the common requirements of these two interactions. However, the different outputs of the symbioses, phosphate uptake versus N fixation, require fundamentally different components and physical environments and necessitated the recruitment of different master regulators, NODULE INCEPTION-LIKE PROTEINS, and PHOSPHATE STARVATION RESPONSES, for nodulation and mycorrhization, respectively.

Nitrate transport via NRT2.1 mediates NIN-LIKE PROTEIN-dependent suppression of root nodulation in Lotus japonicus

Legumes have adaptive mechanisms that regulate nodulation in response to the amount of nitrogen in the soil. In Lotus japonicus, two NODULE INCEPTION (NIN)-LIKE PROTEIN (NLP) transcription factors, LjNLP4 and LjNLP1, play pivotal roles in the negative regulation of nodulation by controlling the expression of symbiotic genes in high nitrate conditions. Despite an improved understanding of the molecular basis for regulating nodulation, how nitrate plays a role in the signaling pathway to negatively regulate this process is largely unknown. Here, we show that nitrate transport via NITRATE TRANSPORTER 2.1 (LjNRT2.1) is a key step in the NLP signaling pathway to control nodulation. A mutation in the LjNRT2.1 gene attenuates the nitrate-induced control of nodulation. LjNLP1 is necessary and sufficient to induce LjNRT2.1 expression, thereby regulating nitrate uptake/transport. Our data suggest that LjNRT2.1-mediated nitrate uptake/transport is required for LjNLP4 nuclear localization and induction/repression of symbiotic genes. We further show that LjNIN, a positive regulator of nodulation, counteracts the LjNLP1-dependent induction of LjNRT2.1 expression, which is linked to a reduction in nitrate uptake. These findings suggest a plant strategy in which nitrogen acquisition switches from obtaining nitrogen from the soil to symbiotic nitrogen fixation.

Lotus japonicus HAR1 regulates root morphology locally and systemically under a moderate nitrate condition in the absence of rhizobia

The local and long-distance signaling pathways mediated by the leucine-rich repeat receptor kinase HAR1 suppress root branching and promote primary root length in response to nitrate supply. The root morphology of higher plants changes plastically to effectively absorb nutrients and water from the soil. In particular, legumes develop root organ nodules, in which symbiotic rhizobia fix atmospheric nitrogen in nitrogen-poor environments. The number of nodules formed in roots is negatively regulated by a long-distance signaling pathway that travels through shoots called autoregulation of nodulation (AON). In the model plant Lotus japonicus, defects in AON genes, such as a leucine-rich repeat receptor kinase HYPERNODULATION ABERRANT ROOT FORMATION 1 (HAR1), an orthologue of CLAVATA1, and the F-box protein TOO MUCH LOVE (TML), induce the formation of an excess number of nodules. The loss-of-function mutant of HAR1 exhibits a short and bushy root phenotype in the absence of rhizobia. We show that the har1 mutant exhibits high nitrate sensitivity during root development. The uninfected har1 mutant significantly increased lateral root number and reduced primary root length in the presence of 3 mM nitrate, compared with the wild-type and tml mutant. Grafting experiments indicated that local and long-distance signaling pathways via root- and shoot-acting HAR1 additively regulated root morphology under the moderate nitrate concentrations. These findings allow us to propose that HAR1-mediated signaling pathways control the root system architecture by suppressing lateral root branching and promoting primary root elongation in response to nitrate availability.

At the Root of Nodule Organogenesis: Conserved Regulatory Pathways Recruited by Rhizobia

The interaction between legume plants and soil bacteria rhizobia results in the formation of new organs on the plant roots, symbiotic nodules, where rhizobia fix atmospheric nitrogen. Symbiotic nodules represent a perfect model to trace how the pre-existing regulatory pathways have been recruited and modified to control the development of evolutionary "new" organs. In particular, genes involved in the early stages of lateral root development have been co-opted to regulate nodule development. Other regulatory pathways, including the players of the KNOX-cytokinin module, the homologues of the miR172-AP2 module, and the players of the systemic response to nutrient availability, have also been recruited to a unique regulatory program effectively governing symbiotic nodule development. The role of the NIN transcription factor in the recruitment of such regulatory modules to nodulation is discussed in more details.

Dynamic transcriptome and co-expression analysis suggest the potential roles of small secreted peptides from Tartary buckwheat (Fagopyrum tataricum) in low nitrogen stress response

Small secreted peptides (SSPs) regulate nitrogen (N) response and signaling in plants. Although much progress has been made in understanding the functions of SSPs in N response, very little information is available regarding non-model plants. Tartary buckwheat (Fagopyrum tataricum), a dicotyledonous crop, has a good adaptability to low N (LN) stress; however, little is known regarding the associated mechanisms underlying this adaptation. In this study, 932 putative SSPs were genome-wide characterized in TB genome. Of these SSPs, 233 SSPs were annotated as established SSPs, such as CLE, RALF, PSK, and CEP peptides. The gene expression of 675 putative SSPs was detected in five tissues and 258 SSPs were tissue-specific expressed genes. To analyze the responses of TB SSPs to LN, the dynamic expression analysis of TB roots under LN stress was conducted by RNA-seq. The expression of 378 putative TB SSP genes was detected with diverse expression patterns under LN stress, and some important LN-responsive SSPs were identified. Co-expression analysis suggested SSPs may regulate the adaptability of TB under LN conditions by modulating the expression of the genes involved in N transport and assimilation and IAA signaling. Furthermore, 53 LN stress-responsive RLKs encoding genes were identified and they were predicted as potential SSP receptors. This study expands the repertoire of SSPs in plants and provides useful information for further investigation of the functions of Tartary buckwheat SSPs in LN stress responses.

Nitrate-induced CLE35 signaling peptides inhibit nodulation through the SUNN receptor and miR2111 repression

Legume plants form nitrogen (N)-fixing symbiotic nodules when mineral N is limiting in soils. As N fixation is energetically costly compared to mineral N acquisition, these N sources, and in particular nitrate, inhibit nodule formation and N fixation. Here, in the model legume Medicago truncatula, we characterized a CLAVATA3-like (CLE) signaling peptide, MtCLE35, the expression of which is upregulated locally by high-N environments and relies on the Nodule Inception-Like Protein (NLP) MtNLP1. MtCLE35 inhibits nodule formation by affecting rhizobial infections, depending on the Super Numeric Nodules (MtSUNN) receptor. In addition, high N or the ectopic expression of MtCLE35 represses the expression and accumulation of the miR2111 shoot-to-root systemic effector, thus inhibiting its positive effect on nodulation. Conversely, ectopic expression of miR2111 or downregulation of MtCLE35 by RNA interference increased miR2111 accumulation independently of the N environment, and thus partially bypasses the nodulation inhibitory action of nitrate. Overall, these results demonstrate that the MtNLP1-dependent, N-induced MtCLE35 signaling peptide acts through the MtSUNN receptor and the miR2111 systemic effector to inhibit nodulation.

Nitrogen Systemic Signaling: From Symbiotic Nodulation to Root Acquisition

Plant nutrient acquisition is tightly regulated by resource availability and metabolic needs, implying the existence of communication between roots and shoots to ensure their integration at the whole-plant level. Here, we focus on systemic signaling pathways controlling nitrogen (N) nutrition, achieved both by the root import of mineral N and, in legume plants, through atmospheric N fixation by symbiotic bacteria inside dedicated root nodules. We explore features conserved between systemic pathways repressing or enhancing symbiotic N fixation and the regulation of mineral N acquisition by roots, as well as their integration with other environmental factors, such as phosphate, light, and CO₂ availability.

Plant Protein O-Arabinosylation

A wide range of proteins with diverse functions in development, defense, and stress responses are O-arabinosylated at hydroxyprolines (Hyps) within distinct amino acid motifs of continuous stretches of Hyps, as found in the structural cell wall extensins, or at non-continuous Hyps as, for example, found in small peptide hormones and a variety of plasma membrane proteins involved in signaling. Plant O-glycosylation relies on hydroxylation of Prolines to Hyps in the protein backbone, mediated by prolyl-4-hydroxylase (P4H) which is followed by O-glycosylation of the Hyp C₄-OH group by either galactosyltransferases (GalTs) or arabinofuranosyltranferases (ArafTs) yielding either Hyp-galactosylation or Hyp-arabinosylation. A subset of the P4H enzymes with putative preference to hydroxylation of continuous prolines and presumably all ArafT enzymes needed for synthesis of the substituted arabinose chains of one to four arabinose units, have been identified and functionally characterized. Truncated root-hair phenotype is one common denominator of mutants of Hyp formation and Hyp-arabinosylation glycogenes, which act on diverse groups of O-glycosylated proteins, e.g., the small peptide hormones and cell wall extensins. Dissection of different substrate derived effects may not be regularly feasible and thus complicate translation from genotype to phenotype. Recently, lack of proper arabinosylation on arabinosylated proteins has been shown to influence their transport/fate in the secretory pathway, hinting to an additional layer of functionality of O-arabinosylation. Here, we provide an update on the prevalence and types of O-arabinosylated proteins and the enzymatic machinery responsible for their modifications.

Characterisation of Medicago truncatula CLE34 and CLE35 in nitrate and rhizobia regulation of nodulation

Legumes form a symbiosis with atmospheric nitrogen (N₂ )-fixing soil rhizobia, resulting in new root organs called nodules that enable N₂ -fixation. Nodulation is a costly process that is tightly regulated by the host through autoregulation of nodulation (AON) and nitrate-dependent regulation of nodulation. Both pathways require legume-specific CLAVATA/ESR-related (CLE) peptides. Nitrogen-induced nodulation-suppressing CLE peptides have not previously been investigated in Medicago truncatula, for which only rhizobia-induced MtCLE12 and MtCLE13 have been characterised. Here, we report on novel peptides MtCLE34 and MtCLE35 in nodulation control. The nodulation-suppressing CLE peptides of five legume species were classified into three clades based on sequence homology and phylogeny. This approached identified MtCLE34 and MtCLE35 and four new CLE peptide orthologues of Pisum sativum. Whereas MtCLE12 and MtCLE13 are induced by rhizobia, MtCLE34 and MtCLE35 respond to both rhizobia and nitrate. MtCLE34 was identified as a pseudogene lacking a functional CLE-domain. MtCLE35 was found to inhibit nodulation in a SUNN- and RDN1-dependent manner via overexpression analysis. Together, our findings indicate that MtCLE12 and MtCLE13 have a specific role in AON, while MtCLE35 regulates nodule numbers in response to both rhizobia and nitrate. MtCLE34 likely had a similar role to MtCLE35, but its function was lost due to a premature nonsense mutation.

Systemic Optimization of Legume Nodulation: A Shoot-Derived Regulator, miR2111

Long-distance signaling between the shoot and roots of land plants plays a crucial role in ensuring their growth and development in a fluctuating environment, such as with soil nutrient deficiencies. MicroRNAs (miRNAs) are considered to contribute to such environmental adaptation via long-distance signaling since several miRNAs are transported between the shoot and roots in response to various soil nutrient changes. Leguminous plants adopt a shoot-mediated long-distance signaling system to maintain their mutualism with symbiotic nitrogen-fixing rhizobia by optimizing the number of symbiotic organs and root nodules. Recently, the involvement and importance of shoot-derived miR2111 in regulating nodule numbers have become evident. Shoot-derived miR2111 can systemically enhance rhizobial infection, and its accumulation is quickly suppressed in response to rhizobial inoculation and high-concentration nitrate application. In this mini-review, we briefly summarize the recent progress on the systemic optimization of nodulation in response to external environments, with a focus on systemic regulation via miR2111.

Massive rhizobial genomic variation associated with partner quality in Lotus-Mesorhizobium symbiosis

Variation in partner quality is commonly observed in diverse cooperative relationships, despite the theoretical prediction that selection favoring high-quality partners should eliminate such variation. Here, we investigated how genetic variation in partner quality could be maintained in the nitrogen-fixing mutualism between Lotus japonicus and Mesorhizobium bacteria. We reconstructed de novo assembled full-genome sequences from nine rhizobial symbionts, finding massive variation in the core genome and the similar symbiotic islands, indicating recent horizontal gene transfer (HGT) of the symbiosis islands into diverse Mesorhizobium lineages. A cross-inoculation experiment using 9 sequenced rhizobial symbionts and 15 L. japonicus accessions revealed extensive quality variation represented by plant growth phenotypes, including genotype-by-genotype interactions. Variation in quality was not associated with the presence/absence variation in known symbiosis-related genes in the symbiosis island; rather, it showed significant correlation with the core genome variation. Given the recurrent HGT of the symbiosis islands into diverse Mesorhizobium strains, local Mesorhizobium communities could serve as a major source of variation for core genomes, which might prevent variation in partner quality from fixing, even in the presence of selection favoring high-quality partners. These findings highlight the novel role of HGT of symbiosis islands in maintaining partner quality variation in the legume-rhizobia symbiosis.

Nitrate-Induced CLE Peptide Systemically Inhibits Nodulation in Medicago truncatula

Legume plants form nitrogen-fixing nodules in symbiosis with soil bacteria rhizobia. The number of symbiotic nodules is controlled at the whole-plant level with autoregulation of nodulation (AON), which includes a shoot-acting CLV1-like receptor kinase and mobile CLE (CLAVATA3/ENDOSPERM SURROUNDING REGION-related) peptides that are produced in the root in response to rhizobia inoculation. In addition to rhizobia-induced CLE peptides, nitrate-induced CLE genes have been identified in Lotus japonicus and Glycine max, which inhibited nodulation when overexpressed. However, nitrate-induced CLE genes that systemically suppress nodulation in AON-dependent manner have not been identified in Medicago truncatula. Here, we found that MtCLE35 expression is activated by both rhizobia inoculation and nitrate treatment in M. truncatula, similarly to L. japonicus CLE genes. Moreover, we found that MtCLE35 systemically suppresses nodulation in AON-dependent manner, suggesting that MtCLE35 may mediate nitrate-induced inhibition of nodulation in M. truncatula.

MIR2111-5 locus and shoot-accumulated mature miR2111 systemically enhance nodulation depending on HAR1 in Lotus japonicus

Legumes utilize a shoot-mediated signaling system to maintain a mutualistic relationship with nitrogen-fixing bacteria in root nodules. In Lotus japonicus, shoot-to-root transfer of microRNA miR2111 that targets TOO MUCH LOVE, a nodulation suppressor in roots, has been proposed to explain the mechanism underlying nodulation control from shoots. However, the role of shoot-accumulating miR2111s for the systemic regulation of nodulation was not clearly shown. Here, we find L. japonicus has seven miR2111 loci, including those mapped through RNA-seq. MIR2111-5 expression in leaves is the highest among miR2111 loci and repressed after rhizobial infection depending on a shoot-acting HYPERNODULATION ABERRANT ROOT FORMATION1 (HAR1) receptor. MIR2111-5 knockout mutants show significantly decreased nodule numbers and miR2111 levels. Furthermore, grafting experiments using transformants demonstrate scions with altered miR2111 levels influence nodule numbers in rootstocks in a dose-dependent manner. Therefore, miR2111 accumulation in leaves through MIR2111-5 expression is required for HAR1-dependent systemic optimization of nodule number.

No Home without Hormones: How Plant Hormones Control Legume Nodule Organogenesis

The establishment of symbiotic nitrogen fixation requires the coordination of both nodule development and infection events. Despite the evolution of a variety of anatomical structures, nodule organs serve a common purpose in establishing a localized area that facilitates efficient nitrogen fixation. As in all plant developmental processes, the establishment of a new nodule organ is regulated by plant hormones. During nodule initiation, regulation of plant hormone signaling is one of the major targets of symbiotic signaling. We review the role of major developmental hormones in the initiation of the nodule organ and argue that the manipulation of plant hormones is a key requirement for engineering nitrogen fixation in non-legumes as the basis for improved food security and sustainability.

The NIN transcription factor coordinates CEP and CLE signaling peptides that regulate nodulation antagonistically

Legumes tightly regulate nodule number to balance the cost of supporting symbiotic rhizobia with the benefits of nitrogen fixation. C-terminally Encoded Peptides (CEPs) and CLAVATA3-like (CLE) peptides positively and negatively regulate nodulation, respectively, through independent systemic pathways, but how these regulations are coordinated remains unknown. Here, we show that rhizobia, Nod Factors, and cytokinins induce a symbiosis-specific CEP gene, MtCEP7, which positively regulates rhizobial infection. Via grafting and split root studies, we reveal that MtCEP7 increases nodule number systemically through the MtCRA2 receptor. MtCEP7 and MtCLE13 expression in rhizobia-inoculated roots rely on the MtCRE1 cytokinin receptor and on the MtNIN transcription factor. MtNIN binds and transactivates MtCEP7 and MtCLE13, and a NIN Binding Site (NBS) identified within the proximal MtCEP7 promoter is required for its symbiotic activation. Overall, these results demonstrate that a cytokinin-MtCRE1-MtNIN regulatory module coordinates the expression of two antagonistic, symbiosis-related, peptide hormones from different families to fine-tune nodule number.

Autoregulation of nodulation pathway is dispensable for nitrate-induced control of rhizobial infection

Legumes possess the autoregulation of nodulation (AON) pathway which is responsible for maintaining optimal root nodule number. In Lotus japonicus, AON comprises the CLE-HAR1-TML module, which plays an essential role in transmitting signals via root-to-shoot-to-root long-distance signaling. In addition to AON's principal role of negatively regulating nodule number, a recent study revealed another in the systemic control of rhizobial infection. Nitrate also negatively regulates the pleiotropic phases of legume-Rhizobium symbioses, including rhizobial infection and nodule number. Nitrate signaling has recently been shown to use AON components such as CLE-RS2 and HAR1 to control nodule number. Here we consider the role of a loss-of-function mutation in CLE-RS1, -RS2 and TML in rhizobial infection in relation to nitrate. Our results agree with previous findings and support the hypothesis that AON is required for the control of rhizobial infection but not for its nitrate-induced control. Furthermore, we confirm that the tml mutants exhibit nitrate sensitivity that differs from that of cle-rs2 and har1. Hence, while the nitrate-induced control mechanism of nodule number uses AON components, an unknown pathway specific to nitrate may exist downstream of HAR1, acting in parallel with the HAR1> TML pathway.

The Non-Legume Parasponia andersonii Mediates the Fitness of Nitrogen-Fixing Rhizobial Symbionts Under High Nitrogen Conditions

Organisms rely on symbiotic associations for metabolism, protection, and energy. However, these intimate partnerships can be vulnerable to exploitation. What prevents microbial mutualists from parasitizing their hosts? In legumes, there is evidence that hosts have evolved sophisticated mechanisms to manage their symbiotic rhizobia, but the generality and evolutionary origins of these control mechanisms are under debate. Here, we focused on the symbiosis between Parasponia hosts and N2-fixing rhizobium bacteria. Parasponia is the only non-legume lineage to have evolved a rhizobial symbiosis and thus provides an evolutionary replicate to test how rhizobial exploitation is controlled. A key question is whether Parasponia hosts can prevent colonization of rhizobia under high nitrogen conditions, when the contribution of the symbiont becomes nonessential. We grew Parasponia andersonii inoculated with Bradyrhizobium elkanii under four ammonium nitrate concentrations in a controlled growth chamber. We measured shoot and root dry weight, nodule number, nodule fresh weight, nodule volume. To quantify viable rhizobial populations in planta, we crushed nodules and determined colony forming units (CFU), as a rhizobia fitness proxy. We show that, like legumes and actinorhizal plants, P. andersonii is able to control nodule symbiosis in response to exogenous nitrogen. While the relative host growth benefits of inoculation decreased with nitrogen fertilization, our highest ammonium nitrate concentration (3.75 mM) was sufficient to prevent nodule formation on inoculated roots. Rhizobial populations were highest in nitrogen free medium. While we do not yet know the mechanism, our results suggest that control mechanisms over rhizobia are not exclusive to the legume clade.

Regulation of Symbiotic Nitrogen Fixation in Legume Root Nodules

In most legume nodules, the di-nitrogen (N2)-fixing rhizobia are present as organelle-like structures inside their root host cells. Many processes operate and interact within the symbiotic relationship between plants and nodules, including nitrogen (N)/carbon (C) metabolisms, oxygen flow through nodules, oxidative stress, and phosphorous (P) levels. These processes, which influence the regulation of N2 fixation and are finely tuned on a whole-plant basis, are extensively reviewed in this paper. The carbonic anhydrase (CA)-phosphoenolpyruvate carboxylase (PEPC)-malate dehydrogenase (MDH) is a key pathway inside nodules involved in this regulation, and malate seems to play a crucial role in many aspects of symbiotic N2 fixation control. How legumes specifically sense N-status and how this stimulates all of the regulatory factors are key issues for understanding N2 fixation regulation on a whole-plant basis. This must be thoroughly studied in the future since there is no unifying theory that explains all of the aspects involved in regulating N2 fixation rates to date. Finally, high-throughput functional genomics and molecular tools (i.e., miRNAs) are currently very valuable for the identification of many regulatory elements that are good candidates for accurately dissecting the particular N2 fixation control mechanisms associated with physiological responses to abiotic stresses. In combination with existing information, utilizing these abundant genetic molecular tools will enable us to identify the specific mechanisms underlying the regulation of N2 fixation.

A GmNINa-miR172c-NNC1 Regulatory Network Coordinates the Nodulation and Autoregulation of Nodulation Pathways in Soybean

Symbiotic root nodules are root lateral organs of plants in which nitrogen-fixing bacteria (rhizobia) convert atmospheric nitrogen to ammonia. The formation and number of nodules in legumes are precisely controlled by a rhizobia-induced signal cascade and host-controlled autoregulation of nodulation (AON). However, how these pathways are integrated and their underlying mechanisms are unclear. Here, we report that microRNA172c (miR172c) activates soybean (Glycine max) Rhizobia-Induced CLE1 (GmRIC1) and GmRIC2 by removing the transcriptional repression of these genes by Nodule Number Control 1 (NNC1), leading to the activation of the AON pathway. NNC1 interacts with GmNINa, the soybean ortholog of Lotus NODULE INCEPTION (NIN), and hampers its transcriptional activation of GmRIC1 and GmRIC2. Importantly, GmNINa acts as a transcriptional activator of miR172c. Intriguingly, NNC1 can transcriptionally repress miR172c expression, adding a negative feedback loop into the NNC1 regulatory network. Moreover, GmNINa interacts with NNC1 and can relieve the NNC1-mediated repression of miR172c transcription. Thus, the GmNINa-miR172c-NNC1 network is a master switch that coordinately regulates and optimizes NF and AON signaling, supporting the balance between nodulation and AON in soybean.

Exploring Genetic Diversity and Signatures of Horizontal Gene Transfer in Nodule Bacteria Associated with Lotus japonicus in Natural Environments

To investigate the genetic diversity and understand the process of horizontal gene transfer (HGT) in nodule bacteria associated with Lotus japonicus, we analyzed sequences of three housekeeping and five symbiotic genes using samples from a geographically wide range in Japan. A phylogenetic analysis of the housekeeping genes indicated that L. japonicus in natural environments was associated with diverse lineages of Mesorhizobium spp., whereas the sequences of symbiotic genes were highly similar between strains, resulting in remarkably low nucleotide diversity at both synonymous and nonsynonymous sites. Guanine-cytosine content values were lower in symbiotic genes, and relative frequencies of recombination between symbiotic genes were also lower than those between housekeeping genes. An analysis of molecular variance showed significant genetic differentiation among populations in both symbiotic and housekeeping genes. These results confirm that the Mesorhizobium genes required for symbiosis with L. japonicus behave as a genomic island (i.e., a symbiosis island) and suggest that this island has spread into diverse genomic backgrounds of Mesorhizobium via HGT events in natural environments. Furthermore, our data compilation revealed that the genetic diversity of symbiotic genes in L. japonicus-associated symbionts was among the lowest compared with reports of other species, which may be related to the recent population expansion proposed in Japanese populations of L. japonicus.

Inside out: root cortex-localized LHK1 cytokinin receptor limits epidermal infection of Lotus japonicus roots by Mesorhizobium loti

During Lotus japonicus-Mesorhizobium loti symbiosis, the LOTUS HISTIDINE KINASE1 (LHK1) cytokinin receptor regulates both the initiation of nodule formation and the scope of root infection. However, the exact spatiotemporal mechanism by which this receptor exerts its symbiotic functions has remained elusive. In this study, we performed cell type-specific complementation experiments in the hyperinfected lhk1-1 mutant background, targeting LHK1 to either the root epidermis or the root cortex. We also utilized various genetic backgrounds to characterize expression of several genes regulating symbiotic infection. We show here that expression of LHK1 in the root cortex is required and sufficient to regulate both nodule formation and epidermal infections. The LHK1-dependent signalling that restricts subsequent infection events is triggered before initial cell divisions for nodule primordium formation. We also demonstrate that AHK4, the Arabidopsis orthologue of LHK1, is able to regulate M. loti infection in L. japonicus, suggesting that an endogenous cytokinin receptor could be sufficient for engineering nitrogen-fixing root nodule symbiosis in nonlegumes. Our data provide experimental evidence for the existence of an LHK1-dependent root cortex-to-epidermis feedback mechanism regulating rhizobial infection. This root-localized regulatory module functionally links with the systemic autoregulation of nodulation (AON) to maintain the homeostasis of symbiotic infection.

A member of the ALOG gene family has a novel role in regulating nodulation in Lotus japonicus

Legumes can control the number of symbiotic nodules that form on their roots, thus balancing nitrogen assimilation and energy consumption. Two major pathways participate in nodulation: the Nod factor (NF) signaling pathway which involves recognition of rhizobial bacteria by root cells and promotion of nodulation, and the autoregulation of nodulation (AON) pathway which involves long-distance negative feedback between roots and shoots. Although a handful of genes have a clear role in the maintenance of nodule number, additional unknown factors may also be involved in this process. Here, we identify a novel function for a Lotus japonicus ALOG (Arabidopsis LSH1 and Oryza G1) family member, LjALOG1, involved in positively regulating nodulation. LjALOG1 expression increased substantially after inoculation with rhizobia, with high levels of expression in whole nodule primordia and in the base of developing nodules. The ljalog1 mutants, which have an insertion of the LORE1 retroelement in LjALOG1, had significantly fewer nodules compared with wild type, along with increased expression of LjCLE-RS1 (L. japonicus CLE Root Signal 1), which encodes a nodulation suppressor in the AON pathway. In summary, our findings identified a novel factor that participates in controlling nodulation, possibly by suppressing the AON pathway.

Unraveling new molecular players involved in the autoregulation of nodulation in Medicago truncatula

The number of legume root nodules resulting from a symbiosis with rhizobia is tightly controlled by the plant. Certain members of the CLAVATA3/Embryo Surrounding Region (CLE) peptide family, specifically MtCLE12 and MtCLE13 in Medicago truncatula, act in the systemic autoregulation of nodulation (AON) pathway that negatively regulates the number of nodules. Little is known about the molecular pathways that operate downstream of the AON-related CLE peptides. Here, by means of a transcriptome analysis, we show that roots ectopically expressing MtCLE13 deregulate only a limited number of genes, including three down-regulated genes encoding lysin motif receptor-like kinases (LysM-RLKs), among which are the nodulation factor (NF) receptor NF Perception gene (NFP) and two up-regulated genes, MtTML1 and MtTML2, encoding Too Much Love (TML)-related Kelch-repeat containing F-box proteins. The observed deregulation was specific for the ectopic expression of nodulation-related MtCLE genes and depended on the Super Numeric Nodules (SUNN) AON RLK. Moreover, overexpression and silencing of these two MtTML genes demonstrated that they play a role in the negative regulation of nodule numbers. Hence, the identified MtTML genes are the functional counterpart of the Lotus japonicus TML gene shown to be central in the AON pathway. Additionally, we propose that the down-regulation of a subset of LysM-RLK-encoding genes, among which is NFP, might contribute to the restriction of further nodulation once the first nodules have been formed.

PLENTY, a hydroxyproline O-arabinosyltransferase, negatively regulates root nodule symbiosis in Lotus japonicus

Legumes can survive in nitrogen-deficient environments by forming root-nodule symbioses with rhizobial bacteria; however, forming nodules consumes energy, and nodule numbers must thus be strictly controlled. Previous studies identified major negative regulators of nodulation in Lotus japonicus, including the small peptides CLAVATA3/ESR (CLE)-RELATED-ROOT SIGNAL1 (CLE-RS1), CLE-RS2, and CLE-RS3, and their putative major receptor HYPERNODULATION AND ABERRANT ROOT FORMATION1 (HAR1). CLE-RS2 is known to be expressed in rhizobia-inoculated roots, and is predicted to be post-translationally arabinosylated, a modification essential for its activity. Moreover, all three CLE-RSs suppress nodulation in a HAR1-dependent manner. Here, we identified PLENTY as a gene responsible for the previously isolated hypernodulation mutant plenty. PLENTY encoded a hydroxyproline O-arabinosyltransferase orthologous to ROOT DETERMINED NODULATION1 in Medicago truncatula. PLENTY was localized to the Golgi, and an in vitro analysis of the recombinant protein demonstrated its arabinosylation activity, indicating that CLE-RS1/2/3 may be substrates for PLENTY. The constitutive expression experiments showed that CLE-RS3 was the major candidate substrate for PLENTY, suggesting the substrate preference of PLENTY for individual CLE-RS peptides. Furthermore, a genetic analysis of the plenty har1 double mutant indicated the existence of another PLENTY-dependent and HAR1-independent pathway negatively regulating nodulation.

Legume nodulation: The host controls the party

Global demand to increase food production and simultaneously reduce synthetic nitrogen fertilizer inputs in agriculture are underpinning the need to intensify the use of legume crops. The symbiotic relationship that legume plants establish with nitrogen-fixing rhizobia bacteria is central to their advantage. This plant-microbe interaction results in newly developed root organs, called nodules, where the rhizobia convert atmospheric nitrogen gas into forms of nitrogen the plant can use. However, the process of developing and maintaining nodules is resource intensive; hence, the plant tightly controls the number of nodules forming. A variety of molecular mechanisms are used to regulate nodule numbers under both favourable and stressful growing conditions, enabling the plant to conserve resources and optimize development in response to a range of circumstances. Using genetic and genomic approaches, many components acting in the regulation of nodulation have now been identified. Discovering and functionally characterizing these components can provide genetic targets and polymorphic markers that aid in the selection of superior legume cultivars and rhizobia strains that benefit agricultural sustainability and food security. This review addresses recent findings in nodulation control, presents detailed models of the molecular mechanisms driving these processes, and identifies gaps in these processes that are not yet fully explained.

Triarabinosylation is required for nodulation-suppressive CLE peptides to systemically inhibit nodulation in Pisum sativum

Legumes form root nodules to house beneficial nitrogen-fixing rhizobia bacteria. However, nodulation is resource demanding; hence, legumes evolved a systemic signalling mechanism called autoregulation of nodulation (AON) to control nodule numbers. AON begins with the production of CLE peptides in the root, which are predicted to be glycosylated, transported to the shoot, and perceived. We synthesized variants of nodulation-suppressing CLE peptides to test their activity using petiole feeding to introduce CLE peptides into the shoot. Hydroxylated, monoarabinosylated, and triarabinosylated variants of soybean GmRIC1a and GmRIC2a were chemically synthesized and fed into recipient Pisum sativum (pea) plants, which were used due to the availability of key AON pathway mutants unavailable in soybean. Triarabinosylated GmRIC1a and GmRIC2a suppressed nodulation of wild-type pea, whereas no other peptide variant tested had this ability. Suppression also occurred in the supernodulating hydroxyproline O-arabinosyltransferase mutant, Psnod3, but not in the supernodulating receptor mutants, Pssym29, and to some extent, Pssym28. During our study, bioinformatic resources for pea became available and our analyses identified 40 CLE peptide-encoding genes, including orthologues of nodulation-suppressive CLE peptides. Collectively, we demonstrated that soybean nodulation-suppressive CLE peptides can function interspecifically in the AON pathway of pea and require arabinosylation for their activity.

Two Negative Regulatory Systems of Root Nodule Symbiosis: How Are Symbiotic Benefits and Costs Balanced?

Root nodule symbiosis is one of the best characterized mutualistic relationships of plant-microbe symbiosis, where mainly leguminous species can obtain nitrogen sources fixed by nitrogen-fixing rhizobia through the formation of symbiotic organ root nodules. In order to drive this symbiotic process, plants need to provide carbon sources that should be used for their growth. Therefore, a balance between the benefits of obtaining nitrogen sources and the costs of losing carbon sources needs to be maintained during root nodule symbiosis. Plants have developed at least two negative regulatory systems of root nodule symbiosis. One strategy involves the regulation of nodule number in response to rhizobial infection. For this regulation, a systemic long-range signaling between roots and shoots called autoregulation of nodulation has a pivotal role. Another strategy involves the regulation of root nodule symbiosis in response to nitrate, the most abundant form of nitrogen nutrients in the soil. Recent studies indicate that long-distance signaling is shared between the two strategies, where NIN and NRSYM1, two paralogous RWP-RK transcription factors, can activate the production of nodulation-related CLE peptides in response to different inputs. Here, we provide an overview of such progress in our understanding of molecular mechanisms relevant to the control of the symbiotic balance, including their biological significance.

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.

Nitrate-mediated control of root nodule symbiosis

Nitrogen is an indispensable inorganic nutrient that is required by plants throughout their life. Root nodule symbiosis (RNS) is an important strategy mainly adopted by legumes to enhance nitrogen acquisition, where several key processes required for the establishment of the symbiosis, are pleiotropically controlled by nitrate availability in soil. Although the autoregulation of nodulation (AON), a systemic long-range signaling, has been suggested to be implicated in nitrate-induced control of RNS, AON alone is insufficient to fully explain the pleiotropic regulation that is induced by nitrate. A recent elucidation of the function of a NIN-LIKE PROTEIN transcription factor has provided greater insights into the genetic mechanisms underlying nitrate-induced control of RNS in varying nitrate environments.

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

MtCLE12 and MtCLE13 encode CLAVATA3/EMBRYO-SURROUNDING REGION RELATED (CLE) peptides which regulate autoregulation of nodulation (AON) in Medicago through the shoot receptor, SUNN (SUPER NUMERIC NODULES). Genetics suggests RDN1 (ROOT-DETERMINED NODULATION 1) arabinosylates MtCLE12 to enable SUNN perception. The functional structures of MtCLE12 and MtCLE13 peptides, however, remain elusive. We combined genetic and chemical synthesis approaches to determine if glyco-modifications of three nodule-expressed CLE peptides are essential for AON. We also examined how root and shoot applied AON-CLEs inhibit nodulation. MtCLE12, MtCLE13 and MtCLE42 peptides were synthesized with hydroxylation, mono-arabinosylation or tri-arabinosylation (TaP) at proline 7. Only MtCLE12-TaP and MtCLE13-TaP peptides induced AON in wild-type (WT) and rdn1-1, but not in sunn-4. The application of MtCLE13-TaP to cotyledons 1 d before rhizobial inoculation completely inhibited both rhizobial infection and nodulation. By contrast, MtCLE12-TaP induced significant AON without abolishing rhizobial infection. The results indicate that key CLE domain amino acids and TaP modifications to MtCLE12 and MtCLE13 are essential for SUNN-dependent AON. We also show evidence that RDN1 does not tri-arabinosylate MtCLE13. Finally, MtCLE13-TaP can induce a strong AON response in shoots that inhibits the entire symbiotic processes in roots. We present a new model for AON in Medicago.

A NIN-LIKE PROTEIN mediates nitrate-induced control of root nodule symbiosis in Lotus japonicus

Legumes and rhizobia establish symbiosis in root nodules. To balance the gains and costs associated with the symbiosis, plants have developed two strategies for adapting to nitrogen availability in the soil: plants can regulate nodule number and/or stop the development or function of nodules. Although the former is accounted for by autoregulation of nodulation, a form of systemic long-range signaling, the latter strategy remains largely enigmatic. Here, we show that the Lotus japonicus NITRATE UNRESPONSIVE SYMBIOSIS 1 (NRSYM1) gene encoding a NIN-LIKE PROTEIN transcription factor acts as a key regulator in the nitrate-induced pleiotropic control of root nodule symbiosis. NRSYM1 accumulates in the nucleus in response to nitrate and directly regulates the production of CLE-RS2, a root-derived mobile peptide that acts as a negative regulator of nodule number. Our data provide the genetic basis for how plants respond to the nitrogen environment and control symbiosis to achieve proper plant growth.

Agrobacterial tumors interfere with nodulation and demonstrate the expression of nodulation-induced CLE genes in pea

CLAVATA (CLV) system including CLV1-like kinase and CLE-peptides is the part of the AON (autoregulation of nodulation) that controls nodule number in legume plants. Moreover, CLV system plays a key role in meristems, where it regulates the expression of WOX genes in organizing centers. Recently, we found that WOX5 homolog in pea is also expressed in nodules and in tumors induced by Agrobacterium tumefaciens. Based on this, we hypothesized that both nodules and agrobacterial tumors may be regulated by and may trigger the same components of AON, including the same WOX and CLV genes. Here, we found that pea plants with agrobacterial tumors induced prior to rhizobial inoculation had reduced the number of nodules. This effect was absent in pea sym29 mutant defective in CLV1-like kinase, the key component of AON. That suggests that agrobacterial tumors may produce a signal activating CLV1-like kinase and thereby decrease the nodule number. Since CLE peptides are known to act upstream of CLV1-like kinase, expression analysis of CLE genes has been performed both in developing nodules and tumors. Overall, 45 CLE genes were identified, and among them nine nodulation-induced CLEs were found in pea. In agrobacterial tumors, no expression of nodule-specific CLE genes the homologues of which inhibit nodulation in other legumes was observed. However, increased expression of two other nodulation-induced CLE genes was observed in agrobacterial tumors, suggesting that CLE genes are expressed in tumors that may still contribute to autoregulatory processes suppressing nodulation.

Nitrate Supply-Dependent Shifts in Communities of Root-Associated Bacteria in Arabidopsis

Root-associated bacterial communities are necessary for healthy plant growth. Nitrate is a signal molecule as well as a major nitrogen source for plant growth. In this study, nitrate-dependent alterations in root-associated bacterial communities and the relationship between nitrate signaling and root-associated bacteria in Arabidopsis were examined. The bacterial community was analyzed by a ribosomal RNA intergenic spacer analysis (RISA) and 16S rRNA amplicon sequencing. The Arabidopsis root-associated bacterial community shifted depending on the nitrate amount and timing of nitrate application. The relative abundance of operational taxonomic units of 25.8% was significantly changed by the amount of nitrate supplied. Moreover, at the family level, the relative abundance of several major root-associated bacteria including Burkholderiaceae, Paenibacillaceae, Bradyrhizobiaceae, and Rhizobiaceae markedly fluctuated with the application of nitrate. These results suggest that the application of nitrate strongly affects root-associated bacterial ecosystems in Arabidopsis. Bulk soil bacterial communities were also affected by the application of nitrate; however, these changes were markedly different from those in root-associated bacteria. These results also suggest that nitrate-dependent alterations in root-associated bacterial communities are mainly affected by plant-derived factors in Arabidopsis. T-DNA insertion plant lines of the genes for two transcription factors involved in nitrate signaling in Arabidopsis roots, NLP7 and TCP20, showed similar nitrate-dependent shifts in root-associated bacterial communities from the wild-type, whereas minor differences were observed in root-associated bacteria. Thus, these results indicate that NLP7 and TCP20 are not major regulators of nitrate-dependent bacterial communities in Arabidopsis roots.

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.

Cytokinins in Symbiotic Nodulation: When, Where, What For?

Substantial progress has been made in the understanding of early stages of the symbiotic interaction between legume plants and rhizobium bacteria. Those include the specific recognition of symbiotic partners, the initiation of bacterial infection in root hair cells, and the inception of a specific organ in the root cortex, the nodule. Increasingly complex regulatory networks have been uncovered in which cytokinin (CK) phytohormones play essential roles in different aspects of early symbiotic stages. Intriguingly, these roles can be either positive or negative, cell autonomous or non-cell autonomous, and vary, depending on time, root tissues, and possibly legume species. Recent developments on CK symbiotic functions and interconnections with other signaling pathways during nodule initiation are the focus of this review.

CLE peptide-encoding gene families in Medicago truncatula and Lotus japonicus, compared with those of soybean, common bean and Arabidopsis

CLE peptide hormones are critical regulators of many cell proliferation and differentiation mechanisms in plants. These 12-13 amino acid glycosylated peptides play vital roles in a diverse range of plant tissues, including the shoot, root and vasculature. CLE peptides are also involved in controlling legume nodulation. Here, the entire family of CLE peptide-encoding genes was identified in Medicago truncatula (52) and Lotus japonicus (53), including pseudogenes and non-functional sequences that were identified. An array of bioinformatic techniques were used to compare and contrast these complete CLE peptide-encoding gene families with those of fellow legumes, Glycine max and Phaseolus vulgaris, in addition to the model plant Arabidopsis thaliana. This approach provided insight into the evolution of CLE peptide families and enabled us to establish putative M. truncatula and L. japonicus orthologues. This includes orthologues of nodulation-suppressing CLE peptides and AtCLE40 that controls the stem cell population of the root apical meristem. A transcriptional meta-analysis was also conducted to help elucidate the function of the CLE peptide family members. Collectively, our analyses considerably increased the number of annotated CLE peptides in the model legume species, M. truncatula and L. japonicus, and substantially enhanced the knowledgebase of this critical class of peptide hormones.