Lotus japonicus NOOT-BOP-COCH-LIKE1 is essential for nodule, nectary, leaf and flower development

From Inception to Maturation: Recent Insights in Nodule Organogenesis

Root branching and lateral root formation aided successful colonization of land plants in terrestrial ecosystems, eventually resulting in the origin of an adaptive trait called nodulation in specific land plant lineages. Nodule and lateral root formations involve de novo organogenesis, which is induced post-embryonically with coordinated steps of cell division and differentiation. There are substantial resemblances between the initiation of nodule and lateral root, including the types of root cell lineages that acquire mitotic competence to induce new organ formation and the pattern of formative division within the incipient organ primordia, both converging on a localized auxin response. The recruitment of specific genetic modules of lateral root developmental pathways during nodule organogenesis corroborates their evolutionary origin as modified lateral roots. However, such genetic modules are likely to be regulated differentially depending on the acquisition of nodulation-specific adaptations to ensure novelty in nodule organogenesis. Despite commonalities, these two lateral organs have differential morphology, vascular organizations, and functions due to the acquisition of different organ identities, suggesting involvement of distinct differentiation pathways during the maturation of both these organs. The current review provides a consolidated idea of the recent advances in nodule development with its resemblance to lateral root formation, emphasizing the shared and unique genetic regulators involved from their inception to maturation.

A BLADE-ON-PETIOLE orthologue regulates corolla differentiation in the proximal region in Torenia fournieri

The three-dimensional shape of a flower is integrated by morphogenesis along different axes. Differentiation along the petal proximodistal axis is tightly linked to the specification of pollinators; however, it is still unclear how a petal patterns this axis. The corolla of Torenia fournieri exhibits strong differentiation along the proximodistal axis, and we previously found a proximal regulator, TfALOG3, controlling corolla neck differentiation. Here, we report another gene, TfBOP2, which is predominantly expressed in the proximal region of the corolla. TfBOP2 mutants have shorter proximal corolla tubes and longer distal lobe, demonstrating its function as a proximal regulator. Arabidopsis BOPs mutant shows similar defects, favouring a shared role of BOPs homologues. Genetic analysis demonstrates the interaction between TfBOP2 and TfALOG3, and we further found that TfALOG3 physically interacts with TfBOP2 and can recruit TfBOP2 to the nuclear region. Our study favours a hypothetical shared BOP-ALOG complex that is recruited to regulate corolla differentiation in the proximal region axis of T. fournieri.

The transcriptional co-regulators NBCL1 and NBCL2 redundantly coordinate aerial organ development and root nodule identity in legumes

Medicago truncatula NODULE ROOT1 (MtNOOT1) and Pisum sativum COCHLEATA1 (PsCOCH1) are orthologous genes belonging to the NOOT-BOP-COCH-LIKE (NBCL) gene family which encodes key transcriptional co-regulators of plant development. In Mtnoot1 and Pscoch1 mutants, the development of stipules, flowers, and symbiotic nodules is altered. MtNOOT2 and PsCOCH2 represent the single paralogues of MtNOOT1 and PsCOCH1, respectively. In M. truncatula, MtNOOT1 and MtNOOT2 are both required for the establishment and maintenance of symbiotic nodule identity. In legumes, the role of NBCL2 in above-ground development is not known. To better understand the roles of NBCL genes in legumes, we used M. truncatula and P. sativum nbcl mutants, isolated a knockout mutant for the PsCOCH2 locus and generated Pscoch1coch2 double mutants in P. sativum. Our work shows that single Mtnoot2 and Pscoch2 mutants develop wild-type stipules, flowers, and symbiotic nodules. However, the number of flowers was increased and the pods and seeds were smaller compared to the wild type. Furthermore, in comparison to the corresponding nbcl1 single mutants, both the M. truncatula and P. sativum nbcl double mutants show a drastic alteration in stipule, inflorescence, flower, and nodule development. Remarkably, in both M. truncatula and P. sativum nbcl double mutants, stipules are transformed into a range of aberrant leaf-like structures.

The formation of stipule requires the coordinated actions of the legume orthologs of Arabidopsis BLADE-ON-PETIOLE and LEAFY

Stipule morphology is a classical botanical key character used in plant identification. Stipules are considerably diverse in size, function and architecture, such as leaf-like stipules, spines or tendrils. However, the molecular mechanism that regulates stipule identity remains largely unknown. We isolated mutants with abnormal stipules. The mutated gene encodes the NODULE ROOT1 (MtNOOT1), which is the ortholog of BLADE-ON-PETIOLE (BOP) in Medicago truncatula. We also obtained mutants of MtNOOT2, the homolog of MtNOOT1, but they do not show obvious defects in stipules. The mtnoot1 mtnoot2 double mutant shows a higher proportion of transformation from stipules to leaflet-like stipules than the single mutants, suggesting that they redundantly determine stipule identity. Further investigations show that MtNOOTs control stipule initiation together with SINGLE LEAFLET1 (SGL1), which functions in development of lateral leaflets. Increasing SGL1 activity in mtnoot1 mtnoot2 is sufficient for the transformation of stipules to leaves. Moreover, MtNOOTs inhibit SGL1 expression during stipule development, which is probably conserved in legume species. Our study proposes a genetic regulatory model for stipule development, specifically with regard to the MtNOOTs-SGL1 module, which functions in two phases of stipule development, first in the control of stipule initiation and second in stipule patterning.

An LCO-responsive homolog of NODULE INCEPTION positively regulates lateral root formation in Populus sp

The transcription factor NODULE INCEPTION (NIN) has been studied extensively for its multiple roles in root nodule symbiosis within plants of the nitrogen-fixing clade (NFC) that associate with soil bacteria, such as rhizobia and Frankia. However, NIN homologs are present in plants outside the NFC, suggesting a role in other developmental processes. Here, we show that the biofuel crop Populus sp., which is not part of the NFC, contains eight copies of NIN with diversified protein sequence and expression patterns. Lipo-chitooligosaccharides (LCOs) are produced by rhizobia and a wide range of fungi, including mycorrhizal ones, and act as symbiotic signals that promote lateral root formation. RNAseq analysis of Populus sp. treated with purified LCO showed induction of the PtNIN2 subfamily. Moreover, the expression of PtNIN2b correlated with the formation of lateral roots and was suppressed by cytokinin treatment. Constitutive expression of PtNIN2b overcame the inhibition of lateral root development by cytokinin under high nitrate conditions. Lateral root induction in response to LCOs likely represents an ancestral function of NIN retained and repurposed in nodulating plants, as we demonstrate that the role of NIN in LCO-induced root branching is conserved in both Populus sp. and legumes. We further established a visual marker of LCO perception in Populus sp. roots, the putative sulfotransferase PtSS1 that can be used to study symbiotic interactions with the bacterial and fungal symbionts of Populus sp.

Phenotypes of Floral Nectaries in Developmental Mutants of Legumes and What They May Tell about Genetic Control of Nectary Formation

Simple Summary

The third largest angiosperm family, Leguminosae, is remarkable with the outstanding diversity of its flowers, usually monosymmetric and adapted to different pollination strategies. A key attractant of leguminous flowers is nectar. Compared with Arabidopsis (Brassicaceae), very little is known about regulation of floral nectaries development in legumes. This work aimed to investigate details of these nectaries’ morphology in flowers of mutants of different legume species. It was found that the changes in identity of petals and stamens usually do not affect a proper structure and position of nectaries in leguminous flowers, thus suggesting a high stability of attracting structures versus the pronounced plasticity of perianth and stamens. Some of genes involved in regulation of nectary development in Arabidopsis seem to have the same functions in legumes. The principal difference between Arabidopsis and legumes is connected with a flower monosymmetry in most representatives of the latter taxon, which is also reflected in structure of their floral nectaries.

Abstract

The vast majority of angiosperms attracts animal pollinators with the nectar secreted through specialized floral nectaries (FNs). Although there is evidence that principal patterns of regulation of FN development are conserved in large angiosperm clades, these structures are very diverse considering their morphology and position within a flower. Most data on genetic control of FN formation were obtained in surveys of a model plant species, Arabidopsis thaliana (Brassicaceae). There are almost no data on genetic factors affecting FN development in Leguminosae, the plant family of a high agricultural value and possessing outstandingly diverse flowers. In this work, the morphology of FNs was examined in a set of leguminous species, both wild-type and developmental mutants, by the means of a scanning electron microscopy. Unlike Brassicaceae, FNs in legumes are localized between stamens and a carpel instead of being associated with a certain floral organ. FNs were found stable in most cases of mutants when perianth and/or androecium morphology was affected. However, regulation of FN development by BLADE-ON-PETIOLE-like genes seems to be a shared feature between legumes (at least Pisum) and Arabidopsis. In some legumes, the adaxial developmental program (most probably CYCLOIDEA-mediated) suppresses the FN development. The obtained results neither confirm the role of orthologues of UNUSUAL FLORAL ORGANS and LEAFY in FN development in legumes nor reject it, as two studied pea mutants were homozygous at the weakest alleles of the corresponding loci and possessed FNs similar to those of wild-type.

Are legumes different? Origins and consequences of evolving nitrogen fixing symbioses

Nitrogen fixing symbioses between plants and bacteria are ancient and, while not numerous, are formed in diverse lineages of plants ranging from microalgae to angiosperms. One symbiosis stands out as the most widespread one is that between legumes and rhizobia, leading to the formation of nitrogen-fixing nodules. The legume family is one of the largest and most diverse group of plants and legumes have been used by humans since the beginning of agriculture, both as high nitrogen food, as well as pastures and rotation crops. One open question is whether their ability to form a nitrogen-fixing symbiosis has contributed to legumes' success, and whether legumes have any unique characteristics that have made them more diverse and widespread than other groups of plants. This review examines the evolutionary journey that has led to the diversification of legumes, in particular its nitrogen-fixing symbiosis, and asks four questions to investigate which legume traits might have contributed to their success: 1. In what ways do legumes differ from other plant groups that have evolved nitrogen-fixing symbioses? In order to answer this question, the characteristics of the symbioses, and efficiencies of nitrogen fixation are compared between different groups of nitrogen fixing plants. 2. Could certain unique features of legumes be a reason for their success? This section examines the manifestations and possible benefits of a nitrogen-rich 'lifestyle' in legumes. 3. If nitrogen fixation was a reason for such a success, why have some species lost the symbiosis? Formation of symbioses has trade-offs, and while these are less well known for non-legumes, there are known energetic and ecological reasons for loss of symbiotic potential in legumes. 4. What can we learn from the unique traits of legumes for future crop improvements? While exploiting some of the physiological properties of legumes could be used to improve legume breeding, our increasing molecular understanding of the essential regulators of root nodule symbioses raise hope of creating new nitrogen fixing symbioses in other crop species.

Microscopic and Transcriptomic Analyses of Dalbergoid Legume Peanut Reveal a Divergent Evolution Leading to Nod-Factor-Dependent Epidermal Crack-Entry and Terminal Bacteroid Differentiation

Root nodule symbiosis (RNS) is the pillar behind sustainable agriculture and plays a pivotal role in the environmental nitrogen cycle. Most of the genetic, molecular, and cell-biological knowledge on RNS comes from model legumes that exhibit a root-hair mode of bacterial infection, in contrast to the Dalbergoid legumes exhibiting crack-entry of rhizobia. As a step toward understanding this important group of legumes, we have combined microscopic analysis and temporal transcriptome to obtain a dynamic view of plant gene expression during Arachis hypogaea (peanut) nodule development. We generated comprehensive transcriptome data by mapping the reads to A. hypogaea, and two diploid progenitor genomes. Additionally, we performed BLAST searches to identify nodule-induced yet-to-be annotated peanut genes. Comparison between peanut, Medicago truncatula, Lotus japonicus, and Glycine max showed upregulation of 61 peanut orthologs among 111 tested known RNS-related genes, indicating conservation in mechanisms of nodule development among members of the Papilionoid family. Unlike model legumes, recruitment of class 1 phytoglobin-derived symbiotic hemoglobin (SymH) in peanut indicates diversification of oxygen-scavenging mechanisms in the Papilionoid family. Finally, the absence of cysteine-rich motif-1-containing nodule-specific cysteine-rich peptide (NCR) genes but the recruitment of defensin-like NCRs suggest a diverse molecular mechanism of terminal bacteroid differentiation. In summary, our work describes genetic conservation and diversification in legume-rhizobia symbiosis in the Papilionoid family, as well as among members of the Dalbergoid legumes.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Stress-regulated elements in Lotus spp., as a possible starting point to understand signalling networks and stress adaptation in legumes

Although legumes are of primary economic importance for human and livestock consumption, the information regarding signalling networks during plant stress response in this group is very scarce. Lotus japonicus is a major experimental model within the Leguminosae family, whereas L. corniculatus and L. tenuis are frequent components of natural and agricultural ecosystems worldwide. These species display differences in their perception and response to diverse stresses, even at the genotype level, whereby they have been used in many studies aimed at achieving a better understanding of the plant stress-response mechanisms. However, we are far from the identification of key components of their stress-response signalling network, a previous step for implementing transgenic and editing tools to develop legume stress-resilient genotypes, with higher crop yield and quality. In this review we scope a body of literature, highlighting what is currently known on the stress-regulated signalling elements so far reported in Lotus spp. Our work includes a comprehensive review of transcription factors chaperones, redox signals and proteins of unknown function. In addition, we revised strigolactones and genes regulating phytochelatins and hormone metabolism, due to their involvement as intermediates in several physiological signalling networks. This work was intended for a broad readership in the fields of physiology, metabolism, plant nutrition, genetics and signal transduction. Our results suggest that Lotus species provide a valuable information platform for the study of specific protein-protein (PPI) interactions, as a starting point to unravel signalling networks underlying plant acclimatation to bacterial and abiotic stressors in legumes. Furthermore, some Lotus species may be a source of genes whose regulation improves stress tolerance and growth when introduced ectopically in other plant species.

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.

Rhizospheric microbiome: Bio-based emerging strategies for sustainable agriculture development and future perspectives

In the light of intensification of cropping practices and changing climatic conditions, nourishing a growing global population requires optimizing environmental sustainability and reducing ecosystem impacts of food production. The use of microbiological systems to ameliorate the agricultural production in a sustainable and eco-friendly way is widespread accepted as a future key-technology. However, the multitude of interaction possibilities between the numerous beneficial microbes and plants in their habitat calls for systematic analysis and management of the rhizospheric microbiome. This review exploits present and future strategies for rhizospheric microbiome management with the aim to generate a comprehensive understanding of the known tools and techniques. Significant information on the structure and dynamics of rhizospheric microbiota of isolated microbial communities is now available. These microbial communities have beneficial effects including increased plant growth, essential nutrient acquisition, pathogens tolerance, and increased abiotic as well as biotic stress tolerance such as drought, temperature, salinity and antagonistic activities against the phyto-pathogens. A better and comprehensive understanding of the various effects and microbial interactions can be gained by application of molecular approaches as extraction of DNA/RNA and other biochemical markers to analyze microbial soil diversity. Novel techniques like interactome network analysis and split-ubiquitin system framework will enable to gain more insight into communication and interactions between the proteins from microbes and plants. The aim of the analysis tasks leads to the novel approach of Rhizosphere microbiome engineering. The capability of forming the rhizospheric microbiome in a defined way will allow combining several microbes (e.g. bacteria and fungi) for a given environment (soil type and climatic zone) in order to exert beneficial influences on specific plants. This integration will require a large-scale effort among academic researchers, industry researchers and farmers to understand and manage interactions of plant-microbiomes within modern farming systems, and is clearly a multi-domain approach and can be mastered only jointly by microbiology, mathematics and information technology. These innovations will open up a new avenue for designing and implementing intensive farming microbiome management approaches to maximize resource productivity and stress tolerance of agro-ecosystems, which in return will create value to the increasing worldwide population, for both food production and consumption.

The BOP-type co-transcriptional regulator NODULE ROOT1 promotes stem secondary growth of the tropical Cannabaceae tree Parasponia andersonii

Tree stems undergo a massive secondary growth in which secondary xylem and phloem tissues arise from the vascular cambium. Vascular cambium activity is driven by endogenous developmental signalling cues and environmental stimuli. Current knowledge regarding the genetic regulation of cambium activity and secondary growth is still far from complete. The tropical Cannabaceae tree Parasponia andersonii is a non-legume research model of nitrogen-fixing root nodulation. Parasponia andersonii can be transformed efficiently, making it amenable for CRISPR-Cas9-mediated reverse genetics. We considered whether P. andersonii also could be used as a complementary research system to investigate tree-related traits, including secondary growth. We established a developmental map of stem secondary growth in P. andersonii plantlets. Subsequently, we showed that the expression of the co-transcriptional regulator PanNODULE ROOT1 (PanNOOT1) is essential for controlling this process. PanNOOT1 is orthologous to Arabidopsis thaliana BLADE-ON-PETIOLE1 (AtBOP1) and AtBOP2, which are involved in the meristem-to-organ-boundary maintenance. Moreover, in species forming nitrogen-fixing root nodules, NOOT1 is known to function as a key nodule identity gene. Parasponia andersonii CRISPR-Cas9 loss-of-function Pannoot1 mutants are altered in the development of the xylem and phloem tissues without apparent disturbance of the cambium organization and size. Transcriptomic analysis showed that the expression of key secondary growth-related genes is significantly down-regulated in Pannoot1 mutants. This allows us to conclude that PanNOOT1 positively contributes to the regulation of stem secondary growth. Our work also demonstrates that P. andersonii can serve as a tree research system.

Circadian Rhythms in Legumes: What Do We Know and What Else Should We Explore?

The natural timing devices of organisms, commonly known as biological clocks, are composed of specific complex folding molecules that interact to regulate the circadian rhythms. Circadian rhythms, the changes or processes that follow a 24-h light–dark cycle, while endogenously programmed, are also influenced by environmental factors, especially in sessile organisms such as plants, which can impact ecosystems and crop productivity. Current knowledge of plant clocks emanates primarily from research on Arabidopsis, which identified the main components of the circadian gene regulation network. Nonetheless, there remain critical knowledge gaps related to the molecular components of circadian rhythms in important crop groups, including the nitrogen-fixing legumes. Additionally, little is known about the synergies and trade-offs between environmental factors and circadian rhythm regulation, especially how these interactions fine-tune the physiological adaptations of the current and future crops in a rapidly changing world. This review highlights what is known so far about the circadian rhythms in legumes, which include major as well as potential future pulse crops that are packed with nutrients, particularly protein. Based on existing literature, this review also identifies the knowledge gaps that should be addressed to build a sustainable food future with the reputed “poor man’s meat”.

Leguminous nodule symbiosis involves recruitment of factors contributing to lateral root development

Legumes and several plant species in the monophyletic nitrogen-fixing clade produce root nodules that function as symbiotic organs and establish mutualistic relationships with nitrogen-fixing bacteria. The modes of nodule organogenesis are distinct from those of lateral root development and also differ among different types of nodules formed in legumes and actinorhizal plants. It is considered that the evolution of new organs occurs through rearrangement of molecular networks interposed by certain neo-functionalized factors. Accumulating evidence has suggested that root nodule organogenesis involves root or lateral root developmental pathways. This review describes the current knowledge about the factors/pathways acquired by the common ancestor of the nitrogen-fixing clade in order to control nodule organogenesis.

Patterning a Leaf by Establishing Polarities

Leaves are the major organ for photosynthesis in most land plants, and leaf structure is optimized for the maximum capture of sunlight and gas exchange. Three polarity axes, the adaxial-abaxial axis, the proximal-distal axis, and the medial-lateral axis are established during leaf development to give rise to a flattened lamina with a large area for photosynthesis and blades that are extended on petioles for maximum sunlight. Adaxial cells are elongated, tightly packed cells with many chloroplasts, and their fate is specified by HD-ZIP III and related factors. Abaxial cells are rounder and loosely packed cells and their fate is established and maintained by YABBY family and KANADI family proteins. The activities of adaxial and abaxial regulators are coordinated by ASYMMETRIC LEAVES2 and auxin. Establishment of the proximodistal axis involves the BTB/POZ domain proteins BLADE-ON-PETIOLE1 and 2, whereas homeobox genes PRESSED FLOWER and WUSCHEL-RELATED HOMEOBOX1 mediate leaf development along the mediolateral axis. This review summarizes recent advances in leaf polarity establishment with a focus on the regulatory networks involved.

Roles of BdUNICULME4 and BdLAXATUM-A in the non-domesticated grass Brachypodium distachyon

In cultivated grasses, tillering, spike architecture and seed shattering represent major agronomical traits. In barley, maize and rice, the NOOT-BOP-COCH-LIKE (NBCL) genes play important roles in development, especially in ligule development, tillering and flower identity. However, compared with dicots, the role of grass NBCL genes is underinvestigated. To better understand the role of grass NBCLs and to overcome any effects of domestication that might conceal their original functions, we studied TILLING nbcl mutants in the non-domesticated grass Brachypodium distachyon. In B. distachyon, the NBCL genes BdUNICULME4 (CUL4) and BdLAXATUM-A (LAXA) are orthologous, respectively, to the barley HvUniculme4 and HvLaxatum-a, to the maize Zmtassels replace upper ears1 and Zmtassels replace upper ears2 and to the rice OsBLADE-ON-PETIOLE1 and OsBLADE-ON-PETIOLE2/3. In B. distachyon, our reverse genetics study shows that CUL4 is not essential for the establishment of the blade-sheath boundary but is necessary for the development of the ligule and auricles. We report that CUL4 also exerts a positive role in tillering and a negative role in spikelet meristem activity. On the other hand, we demonstrate that LAXA plays a negative role in tillering, positively participates in spikelet development and contributes to the control of floral organ number and identity. In this work, we functionally characterized two new NBCL genes in a context of non-domesticated grass and highlighted original roles for grass NBCL genes that are related to important agronomical traits.

The Evolutionary Aspects of Legume Nitrogen-Fixing Nodule Symbiosis

Nitrogen-fixing root nodule symbiosis can sustain the development of the host plants under nitrogen-limiting conditions. Such symbiosis occurs only in a clade of angiosperms known as the nitrogen-fixing clade (NFC). It has long been proposed that root nodule symbiosis evolved several times (in parallel) in the NFC. Two recent phylogenomic studies compared the genomes of nodulating and related non-nodulating species across the four orders of the NFC and found that genes essential for nodule formation are lost or pseudogenized in the non-nodulating species. As these symbiosis genes are specifically involved in the symbiotic interaction, it means that the presence of pseudogenes and the loss of symbiosis genes strongly suggest that their ancestor, which still had functional genes, most likely had a symbiosis with nitrogen-fixing bacteria. These findings agree with the hypothesis that nodulation evolved once at the common ancestor of the NFC, and challenge the hypothesis of parallel evolution. In this chapter, we will cover the current understandings on actinorhizal-type and legume nodule development, and discuss the evolution of the legume nodule type.

The Medicago truncatula nodule identity gene MtNOOT1 is required for coordinated apical-basal development of the root

BACKGROUND

Legumes can utilize atmospheric nitrogen by hosting nitrogen-fixing bacteria in special lateral root organs, called nodules. Legume nodules have a unique ontology, despite similarities in the gene networks controlling nodule and lateral root development. It has been shown that Medicago truncatula NODULE ROOT1 (MtNOOT1) is required for the maintenance of nodule identity, preventing the conversion to lateral root development. MtNOOT1 and its orthologs in other plant species -collectively called the NOOT-BOP-COCH-LIKE (NBCL) family- specify boundary formation in various aerial organs. However, MtNOOT1 is not only expressed in nodules and aerial organs, but also in developing roots, where its function remains elusive.

RESULTS

We show that Mtnoot1 mutant seedlings display accelerated root elongation due to an enlarged root apical meristem. Also, Mtnoot1 mutant roots are thinner than wild-type and are delayed in xylem cell differentiation. We provide molecular evidence that the affected spatial development of Mtnoot1 mutant roots correlates with delayed induction of genes involved in xylem cell differentiation. This coincides with a basipetal shift of the root zone that is susceptible to rhizobium-secreted symbiotic signal molecules.

CONCLUSIONS

Our data show that MtNOOT1 regulates the size of the root apical meristem and vascular differentiation. Our data demonstrate that MtNOOT1 not only functions as a homeotic gene in nodule development but also coordinates the spatial development of the root.

BLADE-ON-PETIOLE genes are not involved in the transition from protonema to gametophore in the moss Physcomitrella patens

The timing of the transition between developmental phases is a critical determinant of plant form. In the moss Physcomitrella patens, the transition from protonema to gametophore is a particularly important step as it results in a change from two-dimensional to three-dimensional growth of the plant body. It is well known that this transition is promoted by cytokinin (CK), however, the underlying mechanisms are poorly understood. Previously, it was reported that P. patens orthologs of BLADE-ON-PETIOLE (BOP) genes (PpBOPs) work downstream of CK to promote the transition to gametophore. To further understand the role of PpBOPs in the control of this transition, we performed functional analyses of PpBOP genes. We simultaneously disrupted the function of all three PpBOP genes in P. patens using CRISPR technology, however, no abnormal phenotypes were observed in the triple mutant during either the gametophytic or the sporophytic growth stages. CK treatment did not alter the phase change in the triple mutant. We conclude that PpBOP genes are unnecessary in the control of P. patens development under normal conditions. We propose that BOP genes are not involved in the control of developmental processes in bryophytes and other basal land plants, but may function in physiological processes such as in the defense response.

Cotton plant defence against a fungal pathogen is enhanced by expanding BLADE-ON-PETIOLE1 expression beyond lateral-organ boundaries

In the plant response to pathogen infection, many genes' expression is temporally induced, while few spatially induced expression genes have been reported. Here, we show that GhBOP1 can autonomously expand expression from restrained tissue when Gossypium hirsutum plants are attacked by Verticillium dahliae, which is considered to be spatially induced expression. Loss- and gain-of-function analyses show that GhBOP1 is a positive regulator in the modulation of plant resistance to V. dahliae. Yeast two-hybrid assays, luciferase complementation imaging and GUS reporting show that GhBOP1 interaction with GhTGA3 promotes its activation activity, regulating the expression of down-stream defence-related genes. Moreover, the induced spatial expression of GhBOP1 is accompanied by GhBP1 repression. Both antagonistically regulate the lignin biosynthesis, conferring cotton plants enhanced resistance to V. dahliae. Taken together, these results demonstrate that GhBOP1 is an economic positive regulator participating in plant defence through both the GhBOP1-GhTGA3 module and lignin accumulation.

Systems Biology of Plant-Microbiome Interactions

In natural environments, plants are exposed to diverse microbiota that they interact with in complex ways. While plant-pathogen interactions have been intensely studied to understand defense mechanisms in plants, many microbes and microbial communities can have substantial beneficial effects on their plant host. Such beneficial effects include improved acquisition of nutrients, accelerated growth, resilience against pathogens, and improved resistance against abiotic stress conditions such as heat, drought, and salinity. However, the beneficial effects of bacterial strains or consortia on their host are often cultivar and species specific, posing an obstacle to their general application. Remarkably, many of the signals that trigger plant immune responses are molecularly highly similar and often identical in pathogenic and beneficial microbes. Thus, it is unclear what determines the outcome of a particular microbe-host interaction and which factors enable plants to distinguish beneficials from pathogens. To unravel the complex network of genetic, microbial, and metabolic interactions, including the signaling events mediating microbe-host interactions, comprehensive quantitative systems biology approaches will be needed.

BLADE-ON-PETIOLE genes temporally and developmentally regulate the sheath to blade ratio of rice leaves

Axis formation is a fundamental issue in developmental biology. Axis formation and patterning in plant leaves is crucial for morphology and crop productivity. Here, we reveal the basis of proximal-distal patterning in rice leaves, which consist of a proximal sheath, a distal blade, and boundary organs formed between these two regions. Analysis of the three rice homologs of the Arabidopsis BLADE-ON-PETIOLE1 (BOP1) gene indicates that OsBOPs activate proximal sheath differentiation and suppress distal blade differentiation. Temporal expression changes of OsBOPs are responsible for the developmental changes in the sheath:blade ratio. We further identify that the change in the sheath:blade ratio during the juvenile phase is controlled by the miR156/SPL pathway, which modifies the level and pattern of expression of OsBOPs. OsBOPs are also essential for differentiation of the boundary organs. We propose that OsBOPs, the main regulators of proximal-distal patterning, control temporal changes in the sheath:blade ratio of rice leaves.