A cytokinin perception mutant colonized by Rhizobium in the absence of nodule organogenesis

Host-specific Nod-factors associated with Medicago truncatula nodule infection differentially induce calcium influx and calcium spiking in root hairs

Rhizobial nodulation (Nod) factors activate both nodule morphogenesis and infection thread development during legume nodulation. Nod factors induce two different calcium responses: intra-nuclear calcium oscillations and a calcium influx at the root hair tip. Calcium oscillations activate nodule development; we wanted to test if the calcium influx is associated with infection. Sinorhizobium meliloti nodL and nodF mutations additively reduce infection of Medicago truncatula. Nod-factors made by the nodL mutant lack an acetyl group; mutation of nodF causes the nitrogen (N)-linked C16:2 acyl chain to be replaced by C18:1. We tested whether these Nod-factors differentially induced calcium influx and calcium spiking. The absence of the NodL-determined acetyl group greatly reduced the induction of calcium influx without affecting calcium spiking. The calcium influx was even further reduced if the N-linked C16:2 acyl group was replaced by C18:1. These additive effects on calcium influx correlate with the additive effects of mutations in nodF and nodL on legume infection. Infection thread development is inhibited by ethylene, which also inhibited Nod-factor-induced calcium influx. We conclude that Nod-factor perception differentially activates the two developmental pathways required for nodulation and that activation of the pathway involving the calcium influx is important for efficient infection.

Hijacking of leguminous nodulation signaling by the rhizobial type III secretion system

Root-nodule symbiosis between leguminous plants and nitrogen-fixing bacteria (rhizobia) involves molecular communication between the two partners. Key components for the establishment of symbiosis are rhizobium-derived lipochitooligosaccharides (Nod factors; NFs) and their leguminous receptors (NFRs) that initiate nodule development and bacterial entry. Here we demonstrate that the soybean microsymbiont Bradyrhizobium elkanii uses the type III secretion system (T3SS), which is known for its delivery of virulence factors by pathogenic bacteria, to promote symbiosis. Intriguingly, wild-type B. elkanii, but not the T3SS-deficient mutant, was able to form nitrogen-fixing nodules on soybean nfr mutant En1282. Furthermore, even the NF-deficient B. elkanii mutant induced nodules unless T3SS genes were mutated. Transcriptional analysis revealed that expression of the soybean nodulation-specific genes ENOD40 and NIN was increased in the roots of En1282 inoculated with B. elkanii but not with its T3SS mutant, suggesting that T3SS activates host nodulation signaling by bypassing NF recognition. Root-hair curling and infection threads were not observed in the roots of En1282 inoculated with B. elkanii, indicating that T3SS is involved in crack entry or intercellular infection. These findings suggest that B. elkanii has adopted a pathogenic system for activating host symbiosis signaling to promote its infection.

Rhizobial synthesized cytokinins contribute to but are not essential for the symbiotic interaction between photosynthetic Bradyrhizobia and Aeschynomene legumes

Cytokinins (CK) play an important role in the formation of nitrogen-fixing root nodules. It has been known for years that rhizobia secrete CK in the extracellular medium but whether they play a role in nodule formation is not known. We have examined this question using the photosynthetic Bradyrhizobium sp. strain ORS285 which is able to nodulate Aeschynomene afraspera and A. indica using a Nod-dependent or Nod-independent symbiotic process, respectively. CK profiling showed that the most abundant CK secreted by Bradyrhizobium sp. strain ORS285 are the 2MeS (2-methylthiol) derivatives of trans-zeatin and isopentenyladenine. In their pure form, these CK can activate legume CK receptors in vitro, and their exogenous addition induced nodule-like structures on host plants. Deletion of the miaA gene showed that transfer RNA degradation is the source of CK production in Bradyrhizobium sp. strain ORS285. In nodulation studies performed with A. indica and A. afraspera, the miaA mutant had a 1-day delay in nodulation and nitrogen fixation. Moreover, A. indica plants formed considerably smaller but more abundant nodules when inoculated with the miaA mutant. These data show that CK produced by Bradyrhizobium sp. strain ORS285 are not the key signal triggering nodule formation during the Nod-independent symbiosis but they contribute positively to nodule development in Aeschynomene plants.

Bioactive cytokinins are selectively secreted by Sinorhizobium meliloti nodulating and nonnodulating strains

Bacteria present in the rhizosphere of plants often synthesize phytohormones, and these signals can consequently affect root system development. In legumes, plants adapt to nitrogen starvation by forming lateral roots as well as a new organ, the root nodule, following a symbiotic interaction with bacteria collectively referred to as rhizobia. As cytokinin (CK) phytohormones were shown to be necessary and sufficient to induce root nodule organogenesis, the relevance of CK production by symbiotic rhizobia was questioned. In this study, we analyzed quantitatively, by liquid chromatography-tandem mass spectrometry, the production of 25 forms of CK in nine rhizobia strains belonging to four different species. All bacterial strains were able to synthesize a mix of CK, and bioactive forms of CK, such as iP, were notably found to be secreted in bacterial culture supernatants. Use of a mutant affected in extracellular polysaccharide (EPS) production revealed a negative correlation of EPS production with the ability to secrete CK. In addition, analysis of a nonnodulating Sinorhizobium meliloti strain revealed a similar pattern of CK production and secretion when compared with a related nodulating strain. This indicates that bacterially produced CK are not sufficient to induce symbiotic nodulation.

Nitrogen modulation of legume root architecture signaling pathways involves phytohormones and small regulatory molecules

Nitrogen, particularly nitrate is an important yield determinant for crops. However, current agricultural practice with excessive fertilizer usage has detrimental effects on the environment. Therefore, legumes have been suggested as a sustainable alternative for replenishing soil nitrogen. Legumes can uniquely form nitrogen-fixing nodules through symbiotic interaction with specialized soil bacteria. Legumes possess a highly plastic root system which modulates its architecture according to the nitrogen availability in the soil. Understanding how legumes regulate root development in response to nitrogen availability is an important step to improving root architecture. The nitrogen-mediated root development pathway starts with sensing soil nitrogen level followed by subsequent signal transduction pathways involving phytohormones, microRNAs and regulatory peptides that collectively modulate the growth and shape of the root system. This review focuses on the current understanding of nitrogen-mediated legume root architecture including local and systemic regulations by different N-sources and the modulations by phytohormones and small regulatory molecules.

Predicting gene regulatory networks of soybean nodulation from RNA-Seq transcriptome data

BACKGROUND

High-throughput RNA sequencing (RNA-Seq) is a revolutionary technique to study the transcriptome of a cell under various conditions at a systems level. Despite the wide application of RNA-Seq techniques to generate experimental data in the last few years, few computational methods are available to analyze this huge amount of transcription data. The computational methods for constructing gene regulatory networks from RNA-Seq expression data of hundreds or even thousands of genes are particularly lacking and urgently needed.

RESULTS

We developed an automated bioinformatics method to predict gene regulatory networks from the quantitative expression values of differentially expressed genes based on RNA-Seq transcriptome data of a cell in different stages and conditions, integrating transcriptional, genomic and gene function data. We applied the method to the RNA-Seq transcriptome data generated for soybean root hair cells in three different development stages of nodulation after rhizobium infection. The method predicted a soybean nodulation-related gene regulatory network consisting of 10 regulatory modules common for all three stages, and 24, 49 and 70 modules separately for the first, second and third stage, each containing both a group of co-expressed genes and several transcription factors collaboratively controlling their expression under different conditions. 8 of 10 common regulatory modules were validated by at least two kinds of validations, such as independent DNA binding motif analysis, gene function enrichment test, and previous experimental data in the literature.

CONCLUSIONS

We developed a computational method to reliably reconstruct gene regulatory networks from RNA-Seq transcriptome data. The method can generate valuable hypotheses for interpreting biological data and designing biological experiments such as ChIP-Seq, RNA interference, and yeast two hybrid experiments.

Comparison of the nodule vs. root transcriptome of the actinorhizal plant Datisca glomerata: actinorhizal nodules contain a specific class of defensins

Actinorhizal root nodule symbioses are very diverse, and the symbiosis of Datisca glomerata has previously been shown to have many unusual aspects. In order to gain molecular information on the infection mechanism, nodule development and nodule metabolism, we compared the transcriptomes of D. glomerata roots and nodules. Root and nodule libraries representing the 3′-ends of cDNAs were subjected to high-throughput parallel 454 sequencing. To identify the corresponding genes and to improve the assembly, Illumina sequencing of the nodule transcriptome was performed as well. The evaluation revealed 406 differentially regulated genes, 295 of which (72.7%) could be assigned a function based on homology. Analysis of the nodule transcriptome showed that genes encoding components of the common symbiosis signaling pathway were present in nodules of D. glomerata, which in combination with the previously established function of SymRK in D. glomerata nodulation suggests that this pathway is also active in actinorhizal Cucurbitales. Furthermore, comparison of the D. glomerata nodule transcriptome with nodule transcriptomes from actinorhizal Fagales revealed a new subgroup of nodule-specific defensins that might play a role specific to actinorhizal symbioses. The D. glomerata members of this defensin subgroup contain an acidic C-terminal domain that was never found in plant defensins before.

Ectopic expression of miR160 results in auxin hypersensitivity, cytokinin hyposensitivity, and inhibition of symbiotic nodule development in soybean

Symbiotic root nodules in leguminous plants result from interaction between the plant and nitrogen-fixing rhizobia bacteria. There are two major types of legume nodules, determinate and indeterminate. Determinate nodules do not have a persistent meristem, while indeterminate nodules have a persistent meristem. Auxin is thought to play a role in the development of both these types of nodules. However, inhibition of rootward auxin transport at the site of nodule initiation is crucial for the development of indeterminate nodules but not determinate nodules. Using the synthetic auxin-responsive DR5 promoter in soybean (Glycine max), we show that there is relatively low auxin activity during determinate nodule initiation and that it is restricted to the nodule periphery subsequently during development. To examine if and what role auxin plays in determinate nodule development, we generated soybean composite plants with altered sensitivity to auxin. We overexpressed microRNA393 to silence the auxin receptor gene family, and these roots were hyposensitive to auxin. These roots nodulated normally, suggesting that only minimal/reduced auxin signaling is required for determinate nodule development. We overexpressed microRNA160 to silence a set of repressor auxin response factor transcription factors, and these roots were hypersensitive to auxin. These roots were not impaired in epidermal responses to rhizobia but had significantly reduced nodule primordium formation, suggesting that auxin hypersensitivity inhibits nodule development. These roots were also hyposensitive to cytokinin and had attenuated expression of key nodulation-associated transcription factors known to be regulated by cytokinin. We propose a regulatory feedback loop involving auxin and cytokinin during nodulation.

The involvement of Medicago truncatula non-specific lipid transfer protein N5 in the control of rhizobial infection

Cysteine-rich proteins seem to play important regulatory roles in Medicago truncatula/Sinorhizobium meliloti symbiosis. In particular, a large family of nodule-specific cysteine-rich (NCR) peptides is crucial for the differentiation of nitrogen-fixing bacteroids. The Medicago truncatula N5 protein (MtN5) is currently the only reported non-specific lipid transfer protein necessary for successful rhizobial symbiosis; in addition, MtN5 shares several characteristics with NCR peptides: a small size, a conserved cysteine-rich motif, an N-terminal signal peptide for secretion and antimicrobial activity. Unlike NCR peptides, MtN5 expression is not restricted to the root nodules and is induced during the early phases of symbiosis in root hairs and nodule primordia. Recently, MtN5 was determined to be involved in the regulation of root tissue invasion; while, it was dispensable for nodule primordia formation. Here, we discuss the hypothesis that MtN5 participates in linking the progression of bacterial invasion with restricting the competence of root hairs for infection.

Spatiotemporal changes in the role of cytokinin during root development

The root is a dynamic system whose structure is regulated by a complex network of interactions between hormones. The primary root meristem is specified in the embryo. After germination, the primary root meristem grows and then reaches a final size that will be maintained during the life of the plant. Subsequently, secondary structures such as lateral roots and root nodules form via the re-specification of differentiated cells. Cytokinin plays key roles in the regulation of root development. Down-regulation of the cytokinin response is required for the specification of a new stem cell niche, during both embryo and lateral root development. In the root meristem, cytokinin signalling regulates the longitudinal zonation of the meristem by controlling cell differentiation. Moreover, cytokinin regulates radial patterning of root vasculature by promoting protophloem cell identity and by spatially inhibiting protoxylem formation. In this review, an effort is made to describe the known details of the role of cytokinin during root development, taking into account also the interactions between cytokinin and other hormones. Attention is given on the dynamicity of cytokinin signalling output during different developmental events. Indeed, there is much evidence that the effects of cytokinin change as organs grow, underlining the importance of the spatiotemporal specificity of cytokinin signalling.

Root colonization and phytostimulation by phytohormones producing entophytic Nostoc sp. AH-12

Nostoc, a nitrogen-fixing cyanobacterium, has great potential to make symbiotic associations with a wide range of plants and benefit its hosts with nitrogen in the form of nitrates. It may also use phytohormones as a tool to promote plant growth. Phytohormones [cytokinin (Ck) and IAA] were determined in the culture of an endophytic Nostoc isolated from rice roots. The strain was able to accumulate as well as release phytohormones to the culture media. Optimum growth conditions for the production of zeatin and IAA were a temperature of 25 °C and a pH of 8.0. Time-dependent increase in the accumulation and release of phytohormones was recorded. To evaluate the impact of cytokinins, an ipt knockout mutant in the background of Nostoc was generated by homologous recombination method. A sharp decline (up to 80 %) in the zeatin content was observed in the culture of mutant strain Nostoc AHM-12. Association of the mutant and wild type strain with rice and wheat roots was studied under axenic conditions. The efficacy of Nostoc to colonize plant root was significantly reduced (P < 0.05) as a result of ipt inactivation as evident by low chlorophyll a concentration in the roots. In contrast to the mutant strain, wild type strain showed good association with the roots and enhanced several growth parameters, such as fresh weight, dry weight, shoot length, and root length of the crop plants. The study clearly demonstrated that Ck is a tool of endophytic Nostoc to colonize plant root and promote its growth.

Rhizobial infection is associated with the development of peripheral vasculature in nodules of Medicago truncatula

Nodulation in legumes involves the coordination of epidermal infection by rhizobia with cell divisions in the underlying cortex. During nodulation, rhizobia are entrapped within curled root hairs to form an infection pocket. Transcellular tubes called infection threads then develop from the pocket and become colonized by rhizobia. The infection thread grows toward the developing nodule primordia and rhizobia are taken up into the nodule cells, where they eventually fix nitrogen. The epidermal and cortical developmental programs are synchronized by a yet-to-be-identified signal that is transmitted from the outer to the inner cell layers of the root. Using a new allele of the Medicago truncatula mutant Lumpy Infections, lin-4, which forms normal infection pockets but cannot initiate infection threads, we show that infection thread initiation is required for normal nodule development. lin-4 forms nodules with centrally located vascular bundles similar to that found in lateral roots rather than the peripheral vasculature characteristic of legume nodules. The same phenomenon was observed in M. truncatula plants inoculated with the Sinorhizobium meliloti exoY mutant, and the M. truncatula vapyrin-2 mutant, all cases where infections arrest. Nodules on lin-4 have reduced expression of the nodule meristem marker MtCRE1 and do not express root-tip markers. In addition, these mutant nodules have altered patterns of gene expression for the cytokinin and auxin markers CRE1 and DR5. Our work highlights the coordinating role that bacterial infection exerts on the developing nodule and allows us to draw comparisons with primitive actinorhizal nodules and rhizobia-induced nodules on the nonlegume Parasponia andersonii.

Down-regulation of NSP2 expression in developmentally young regions of Lotus japonicus roots in response to rhizobial inoculation

During the early 1980s, Bauer and associates reported that nodulation potential in primary roots of soybean seedlings following inoculation with rhizobia was significantly reduced in developmentally younger regions. They suggested that this phenomenon might be due to a fast-acting regulatory mechanism in the host that prevented excessive nodulation. However, the molecular mechanism of this fast-acting regulatory response remains uncertain. Here, we sought to elucidate components of this regulatory mechanism by investigating the expression of the NSP1 and NSP2 genes that encode a GRAS transcription factor required for nodule initiation. First, we confirmed that younger regions of Lotus japonicus roots also show a reduction in nodule numbers in response to Mesorhizobium loti. Then, we compared the expression levels of NSP1 and NSP2 in developmentally younger regions of primary roots. After inoculation with M. loti, expression of NSP1 was transiently induced whereas that of NSP2 was significantly down-regulated 1 d after inoculation. This result implicates that down-regulation of NSP2 might cause a fast-acting regulatory mechanism to prevent further nodulation. Next we overexpressed NSP2 in wild-type plants. Overexpression resulted in the clustering of nodules in the upper region of the root but strong suppression of nodulation in the lower region. In contrast, overexpression of NSP2 in har1 hypernodulating mutants resulted in an increased number of nodule primordia even in the root tip region. These results indicate that HAR1 negatively regulates NSP2-induced excessive nodule formation in the developmentally younger regions of roots.

Establishment of the Lotus japonicus Gene Expression Atlas (LjGEA) and its use to explore legume seed maturation

Lotus japonicus is a model species for legume genomics. To accelerate legume functional genomics, we developed a Lotus japonicus Gene Expression Atlas (LjGEA), which provides a global view of gene expression in all organ systems of this species, including roots, nodules, stems, petioles, leaves, flowers, pods and seeds. Time-series data covering multiple stages of developing pod and seed are included in the LjGEA. In addition, previously published L. japonicus Affymetrix data are included in the database, making it a 'one-stop shop' for transcriptome analysis of this species. The LjGEA web server (http://ljgea.noble.org/) enables flexible, multi-faceted analyses of the transcriptome. Transcript data may be accessed using the Affymetrix probe identification number, DNA sequence, gene name, functional description in natural language, and GO and KEGG annotation terms. Genes may be discovered through co-expression or differential expression analysis. Users may select a subset of experiments and visualize and compare expression profiles of multiple genes simultaneously. Data may be downloaded in a tabular form compatible with common analytical and visualization software. To illustrate the power of LjGEA, we explored the transcriptome of developing seeds. Genes represented by 36 474 probe sets were expressed at some stage during seed development, and almost half of these genes displayed differential expression during development. Among the latter were 624 transcription factor genes, some of which are orthologs of transcription factor genes that are known to regulate seed development in other species, while most are novel and represent attractive targets for reverse genetics approaches to determine their roles in this important organ.

Photosynthetic Bradyrhizobium sp. strain ORS285 is capable of forming nitrogen-fixing root nodules on soybeans (Glycine max)

The ability of photosynthetic Bradyrhizobium strains ORS285 and ORS278 to nodulate soybeans was investigated. While the nod gene-deficient ORS278 strain induced bumps only on soybean roots, the nod gene-containing ORS285 strain formed nitrogen-fixing nodules. However, symbiotic efficiencies differed drastically depending on both the soybean genotype used and the culture conditions tested.

Nodule inception directly targets NF-Y subunit genes to regulate essential processes of root nodule development in Lotus japonicus

The interactions of legumes with symbiotic nitrogen-fixing bacteria cause the formation of specialized lateral root organs called root nodules. It has been postulated that this root nodule symbiosis system has recruited factors that act in early signaling pathways (common SYM genes) partly from the ancestral mycorrhizal symbiosis. However, the origins of factors needed for root nodule organogenesis are largely unknown. NODULE INCEPTION (NIN) is a nodulation-specific gene that encodes a putative transcription factor and acts downstream of the common SYM genes. Here, we identified two Nuclear Factor-Y (NF-Y) subunit genes, LjNF-YA1 and LjNF-YB1, as transcriptional targets of NIN in Lotus japonicus. These genes are expressed in root nodule primordia and their translational products interact in plant cells, indicating that they form an NF-Y complex in root nodule primordia. The knockdown of LjNF-YA1 inhibited root nodule organogenesis, as did the loss of function of NIN. Furthermore, we found that NIN overexpression induced root nodule primordium-like structures that originated from cortical cells in the absence of bacterial symbionts. Thus, NIN is a crucial factor responsible for initiating nodulation-specific symbiotic processes. In addition, ectopic expression of either NIN or the NF-Y subunit genes caused abnormal cell division during lateral root development. This indicated that the Lotus NF-Y subunits can function to stimulate cell division. Thus, transcriptional regulation by NIN, including the activation of the NF-Y subunit genes, induces cortical cell division, which is an initial step in root nodule organogenesis. Unlike the legume-specific NIN protein, NF-Y is a major CCAAT box binding protein complex that is widespread among eukaryotes. We propose that the evolution of root nodules in legume plants was associated with changes in the function of NIN. NIN has acquired functions that allow it to divert pathways involved in the regulation of cell division to root nodule organogenesis.

Legumes produce nodules in roots as the endosymbiotic organs for nitrogen-fixing bacteria, collectively called rhizobia. The symbiotic relationship enables legumes to survive on soil with poor nitrogen sources. The rhizobial infection triggers cell division in the cortex to generate root nodule primordia. The root nodule symbiosis has been thought to be recruited factors for the early signaling pathway from the ancestral mycorrhizal symbiosis, which usually does not accompany the root nodule formation. However, how the root nodule symbiosis-specific pathway inputs nodulation signals to molecular networks, by which cortical cell division is initiated, has not yet been elucidated. We found that NIN, a nodulation specific factor, induced cortical cell division without the rhizobial infection. NIN acted as a transcriptional activator and targeted two genes that encode different subunits of a NF-Y CCAAT box binding protein complex, LjNF-YA1 and LjNF-YB1. Inhibition of the LjNF-YA1 function prevented root nodule formation. Ectopic expression of the NF-Y subunit genes enhanced cell division in lateral root primordia that is not related to root nodule organogenesis. The NF-Y genes are thought to regulate cell division downstream of NIN. NF-Y is a general factor widespread in eukaryotes. We propose that NIN is a mediator between nodulation-specific signals and general regulatory mechanisms associated with cell proliferation.

Induction of localized auxin response during spontaneous nodule development in Lotus japonicus

In leguminous plants, rhizobial infection of the epidermis triggers proliferation of cortical cells to form a nodule primordium. Recent studies have demonstrated that two classic phytohormones, cytokinin and auxin, have important functions in nodulation. The identification of these functions in Lotus japonicus was facilitated by use of the spontaneous nodule formation 2 (snf2) mutation of the putative cytokinin receptor LOTUS HISTIDINE KINASE 1 (LHK1). Analyses using snf2 demonstrated that constitutive activation of cytokinin signaling causes formation of spontaneous nodule-like structures in the absence of rhizobia and that auxin responses are induced in proliferating cortical cells during such spontaneous nodule development. Thus, cytokinin signaling positively regulates the auxin response. In the present study, we further investigated the induction of the auxin response using a gain-of-function mutation of Ca(2+)/calmodulin-dependent protein kinase (CCaMK) that causes spontaneous nodule formation. We demonstrate that CCaMK(T265D)-mediated spontaneous nodule development is accompanied by a localized auxin response. Thus, a localized auxin response at the site of an incipient nodule primordium is essential for nodule organogenesis.

Grafting analysis indicates that malfunction of TRICOT in the root causes a nodulation-deficient phenotype in Lotus japonicus

Leguminous plants develop root nodules in symbiosis with soil rhizobia. Nodule formation occurs following rhizobial infection of the host root that induces dedifferentiation of some cortical cells and the initiation of a new developmental program to form nodule primordia. In a recent study, we identified a novel gene, TRICOT (TCO), that acts as a positive regulator of nodulation in Lotus japonicus. In addition to its role in nodulation, tco mutant plants display pleiotropic defects including abnormal shoot apical meristem formation. Here, we investigated the effect of the tco mutation on nodulation using a grafting approach. The results strongly indicate that the nodulation-deficient phenotype of the mutant results from malfunction of the TCO gene in the root.

TRICOT encodes an AMP1-related carboxypeptidase that regulates root nodule development and shoot apical meristem maintenance in Lotus japonicus

During the course of evolution, mainly leguminous plants have acquired the ability to form de novo structures called root nodules. Recent studies on the autoregulation and hormonal controls of nodulation have identified key mechanisms and also indicated a possible link to other developmental processes, such as the formation of the shoot apical meristem (SAM). However, our understanding of nodulation is still limited by the low number of nodulation-related genes that have been identified. Here, we show that the induced mutation tricot (tco) can suppress the activity of spontaneous nodule formation 2, a gain-of-function mutation of the cytokinin receptor in Lotus japonicus. Our analyses of tco mutant plants demonstrate that TCO positively regulates rhizobial infection and nodule organogenesis. Defects in auxin regulation are also observed during nodule development in tco mutants. In addition to its role in nodulation, TCO is involved in the maintenance of the SAM. The TCO gene was isolated by a map-based cloning approach and found to encode a putative glutamate carboxypeptidase with greatest similarity to Arabidopsis ALTERED MERISTEM PROGRAM 1, which is involved in cell proliferation in the SAM. Taken together, our analyses have not only identified a novel gene for regulation of nodule organogenesis but also provide significant additional evidence for a common genetic regulatory mechanism in nodulation and SAM formation. These new data will contribute further to our understanding of the evolution and genetic basis of nodulation.

Functions of S-nitrosylation in plant hormone networks

In plants, a wide frame of physiological processes are regulated in liaison by both, nitric oxide (NO) and hormones. Such overlapping roles raise the question of how the cross-talk between NO and hormones trigger common physiological responses. In general, NO has been largely accepted as a signaling molecule that works in different processes. Among the most relevant ways NO and the NO-derived reactive species can accomplish their biological functions it is worthy to mention post-translational protein modifications. In the last years, S-nitrosylation has been the most studied NO-dependent regulatory mechanism. Briefly, S-nitrosylation is a redox-based mechanism for cysteine residue modification and is being recognized as a ubiquitous regulatory reaction comparable to phosphorylation. Therefore, it is emerging as a crucial mechanism for the transduction of NO bioactivity in plants and animals. In this mini-review, we provide an overview on S-nitrosylation of target proteins related to hormone networks in plants.

Positive and negative regulation of cortical cell division during root nodule development in Lotus japonicus is accompanied by auxin response

Nodulation is a form of de novo organogenesis that occurs mainly in legumes. During early nodule development, the host plant root is infected by rhizobia that induce dedifferentiation of some cortical cells, which then proliferate to form the symbiotic root nodule primordium. Two classic phytohormones, cytokinin and auxin, play essential roles in diverse aspects of cell proliferation and differentiation. Although recent genetic studies have established how activation of cytokinin signaling is crucial to the control of cortical cell differentiation, the physiological pathways through which auxin might act in nodule development are poorly characterized. Here, we report the detailed patterns of auxin accumulation during nodule development in Lotus japonicus. Our analyses showed that auxin predominantly accumulates in dividing cortical cells and that NODULE INCEPTION, a key transcription factor in nodule development, positively regulates this accumulation. Additionally, we found that auxin accumulation is inhibited by a systemic negative regulatory mechanism termed autoregulation of nodulation (AON). Analysis of the constitutive activation of LjCLE-RS genes, which encode putative root-derived signals that function in AON, in combination with the determination of auxin accumulation patterns in proliferating cortical cells, indicated that activation of LjCLE-RS genes blocks the progress of further cortical cell division, probably through controlling auxin accumulation. Our data provide evidence for the existence of a novel fine-tuning mechanism that controls nodule development in a cortical cell stage-dependent manner.

The non-specific lipid transfer protein N5 of Medicago truncatula is implicated in epidermal stages of rhizobium-host interaction

BACKGROUND

The symbiotic interaction between leguminous plants and rhizobia involves two processes: bacterial infection, resulting in the penetration of bacteria in epidermal and cortical cells, and root nodule organogenesis. Root nodule symbiosis is activated by rhizobial signalling molecules, called Nodulation factors (NFs). NF perception induces the expression of several genes called early nodulins. The early nodulin N5 of Medicago truncatula is a lipid transfer protein that has been shown to positively regulate nodulation although it displays in vitro inhibitory activity against Sinorhizobium meliloti. The purpose of this work was to investigate the role of MtN5 by studying its spatial and temporal pattern of expression during the symbiotic interaction, also in relation to known components of the symbiotic signalling pathway, and by analysing the phenotypic alterations displayed by rhizobia-inoculated MtN5-silenced roots.

RESULTS

We show here that MtN5 is a NF-responsive gene expressed at a very early phase of symbiosis in epidermal cells and root hairs. MtN5 expression is induced in vitro by rhizobial effector molecules and by auxin and cytokinin, phytohormones involved in nodule organogenesis. Furthermore, lipid signaling is implicated in the response of MtN5 to rhizobia, since the activity of phospholipase D is required for MtN5 induction in S. meliloti-inoculated roots. MtN5-silenced roots inoculated with rhizobia display an increased root hair curling and a reduced number of invaded primordia compared to that in wild type roots, but with no impairment to nodule primordia formation. This phenotype is associated with the stimulation of ENOD11 expression, an early marker of infection, and with the down-regulation of Flotillin 4 (FLOT4), a protein involved in rhizobial entry.

CONCLUSIONS

These data indicate that MtN5 acts downstream of NF perception and upstream of FLOT4 in regulating pre-infection events. The positive effect of MtN5 on nodule primordia invasion is linked to the restriction of bacterial spread at the epidermal level. Furthermore, MtN5 seems to be dispensable for nodule primordia formation. These findings provide new information about the complex mechanism that controls the competence of root epidermal cells for rhizobial invasion.

Negative regulation of CCaMK is essential for symbiotic infection

One of the earliest responses of legumes to symbiotic signalling is oscillation of the calcium concentration in the nucleoplasm of root epidermal cells. Integration and decoding of the calcium-spiking signal involve a calcium- and calmodulin-dependent protein kinase (CCaMK) and its phosphorylation substrates, such as CYCLOPS. Here we describe the Lotus japonicus ccamk-14 mutant that originated from a har1-1 suppressor screen. The ccamk-14 mutation causes a serine to asparagine substitution at position 337 located within the calmodulin binding site, which we determined to be an in vitro phosphorylation site in CCaMK. We show that ccamk-14 exerts cell-specific effects on symbiosis. The mutant is characterized by an increased frequency of epidermal infections and significantly compromised cortical infections by Mesorhizobium loti and also the arbuscular mycorrhiza fungus Rhizophagus irregularis. The S337 residue is conserved across angiosperm CCaMKs, and testing discrete substitutions at this site showed that it participates in a negative regulation of CCaMK activity, which is required for the cell-type-specific integration of symbiotic signalling.

One-step Agrobacterium mediated transformation of eight genes essential for rhizobium symbiotic signaling using the novel binary vector system pHUGE

Advancement in plant research is becoming impaired by the fact that the transfer of multiple genes is difficult to achieve. Here we present a new binary vector for Agrobacterium tumefaciens mediated transformation, pHUGE-Red, in concert with a cloning strategy suited for the transfer of up to nine genes at once. This vector enables modular cloning of large DNA fragments by employing Gateway technology and contains DsRED1 as visual selection marker. Furthermore, an R/Rs inducible recombination system was included allowing subsequent removal of the selection markers in the newly generated transgenic plants. We show the successful use of pHUGE-Red by transferring eight genes essential for Medicago truncatula to establish a symbiosis with rhizobia bacteria as one 74 kb T-DNA into four non-leguminous species; strawberry, poplar, tomato and tobacco. We provide evidence that all transgenes are expressed in the root tissue of the non-legumes. Visual control during the transformation process and subsequent marker gene removal makes the pHUGE-Red vector an excellent tool for the efficient transfer of multiple genes.

The diversity of actinorhizal symbiosis

Filamentous aerobic soil actinobacteria of the genus Frankia can induce the formation of nitrogen-fixing nodules on the roots of a diverse group of plants from eight dicotyledonous families, collectively called actinorhizal plants. Within nodules, Frankia can fix nitrogen while being hosted inside plant cells. Like in legume/rhizobia symbioses, bacteria can enter the plant root either intracellularly through an infection thread formed in a curled root hair, or intercellularly without root hair involvement, and the entry mechanism is determined by the host plant species. Nodule primordium formation is induced in the root pericycle as for lateral root primordia. Mature actinorhizal nodules are coralloid structures consisting of multiple lobes, each of which represents a modified lateral root without a root cap, a superficial periderm and with infected cells in the expanded cortex. In this review, an overview of nodule induction mechanisms and nodule structure is presented including comparisons with the corresponding mechanisms in legume symbioses.

A Phaseolus vulgaris NADPH oxidase gene is required for root infection by Rhizobia

Plant NADPH oxidases [respiratory burst oxidase homologs (RBOHs)] have emerged as key players in the regulation of plant-pathogen interactions. Nonetheless, their role in mutualistic associations, such as the rhizobia-legume symbiosis, is poorly understood. In this work, nine members of the Phaseolus vulgaris Rboh gene family were identified. The transcript of one of these, PvRbohB, accumulated abundantly in shoots, roots and nodules. PvRbohB promoter activity was detected in meristematic regions of P. vulgaris roots, as well as during infection thread (IT) progression and nodule development. RNA interference (RNAi)-mediated PvRbohB down-regulation in transgenic roots reduced reactive oxygen species (ROS) production and lateral root density, and greatly impaired nodulation. Microscopy analysis revealed that progression of the ITs was impeded at the base of root hairs in PvRbohB-RNAi roots. Furthermore, the few nodules that formed in PvRbohB-down-regulated roots displayed abnormally wide ITs and reduced nitrogen fixation. These findings indicate that this common bean NADPH oxidase is crucial for successful rhizobial colonization and probably maintains proper IT growth and shape.

Lotus japonicus ARPC1 is required for rhizobial infection

Remodeling of the plant cell cytoskeleton precedes symbiotic entry of nitrogen-fixing bacteria within the host plant roots. Here we identify a Lotus japonicus gene encoding a predicted ACTIN-RELATED PROTEIN COMPONENT1 (ARPC1) as essential for rhizobial infection but not for arbuscular mycorrhiza symbiosis. In other organisms ARPC1 constitutes a subunit of the ARP2/3 complex, the major nucleator of Y-branched actin filaments. The L. japonicus arpc1 mutant showed a distorted trichome phenotype and was defective in epidermal infection thread formation, producing mostly empty nodules. A few partially colonized nodules that did form in arpc1 contained abnormal infections. Together with previously described L. japonicus Nck-associated protein1 and 121F-specific p53 inducible RNA mutants, which are also impaired in the accommodation of rhizobia, our data indicate that ARPC1 and, by inference a suppressor of cAMP receptor/WASP-family verpolin homologous protein-ARP2/3 pathway, must have been coopted during evolution of nitrogen-fixing symbiosis to specifically mediate bacterial entry.

Cytokinin receptor-dependent and receptor-independent pathways in the dehydration response of Arabidopsis thaliana

Cytokinin signaling in Arabidopsis thaliana utilizes a multi-step two-component signaling (TCS) system comprised of sensor histidine kinases (AHKs), histidine phosphotransfer proteins (AHPs), and response regulators (ARRs). Recent studies have suggested that the cytokinin TCS system is involved in a variety of other signaling and metabolic pathways. To further explore a potential function of the cytokinin TCS in the Arabidopsis dehydration stress response, we investigated the expression of all type-A ARR genes and a type-C ARR, ARR22, in both wild type and ahk single, double, and triple mutants in response to dehydration compared to cytokinin as well as dehydration tolerance of ahk mutants. We found that drought significantly induced the expression of a subset of ARR genes, ARR5, ARR7, ARR15, and ARR22. The results of expression analyses in ahk single, double, and triple mutants demonstrated that the cytokinin receptors AHK2 and AHK3 are redundantly involved in dehydration-inducible expression of ARR7, but not that of ARR5, ARR15, or ARR22. Dehydration tolerance assays showed that ahk2 and ahk3 single mutants exhibited enhanced dehydration tolerance compared with that of wild-type plants and ahk4 mutants, and that ahk2 ahk3 double mutants exhibited stronger drought tolerance than that of ahk3 ahk4, which exhibited more enhanced drought tolerance than that of wild-type plants and ahk single mutants. Taken together, these results demonstrate that while the cytokinin receptors AHK2 and AHK3 are critically involved in the dehydration tolerance response, both cytokinin receptor-dependent pathway and receptor-independent pathway occur in the dehydration response regulating ARR gene expression. In addition, preincubating ahk2, ahk3, ahk4, and the wild-type plants with cytokinin induced enhanced dehydration stress tolerance in these plants, demonstrating that cytokinins are involved in regulating plant response to dehydration stress.

Effects of engineered Sinorhizobium meliloti on cytokinin synthesis and tolerance of alfalfa to extreme drought stress

Cytokinin is required for the initiation of leguminous nitrogen fixation nodules elicited by rhizobia and the delay of the leaf senescence induced by drought stress. A few free-living rhizobia have been found to produce cytokinin. However, the effects of engineered rhizobia capable of synthesizing cytokinin on host tolerance to abiotic stresses have not yet been described. In this study, two engineered Sinorhizobium strains overproducing cytokinin were constructed. The tolerance of inoculated alfalfa plants to severe drought stress was assessed. The engineered strains, which expressed the Agrobacterium ipt gene under the control of different promoters, synthesized more zeatins than the control strain under free-living conditions, but their own growth was not affected. After a 4-week inoculation period, the effects of engineered strains on alfalfa growth and nitrogen fixation were similar to those of the control strain under nondrought conditions. After being subjected to severe drought stress, most of the alfalfa plants inoculated with engineered strains survived, and the nitrogenase activity in their root nodules showed no apparent change. A small elevation in zeatin concentration was observed in the leaves of these plants. The expression of antioxidant enzymes increased, and the level of reactive oxygen species decreased correspondingly. Although the ipt gene was transcribed in the bacteroids of engineered strains, the level of cytokinin in alfalfa nodules was identical to that of the control. These findings suggest that engineered Sinorhizobium strains synthesizing more cytokinin could improve the tolerance of alfalfa to severe drought stress without affecting alfalfa nodulation or nitrogen fixation.

Two direct targets of cytokinin signaling regulate symbiotic nodulation in Medicago truncatula

Cytokinin regulates many aspects of plant development, and in legume crops, this phytohormone is necessary and sufficient for symbiotic nodule organogenesis, allowing them to fix atmospheric nitrogen. To identify direct links between cytokinins and nodule organogenesis, we determined a consensus sequence bound in vitro by a transcription factor (TF) acting in cytokinin signaling, the nodule-enhanced Medicago truncatula Mt RR1 response regulator (RR). Among genes rapidly regulated by cytokinins and containing this so-called RR binding site (RRBS) in their promoters, we found the nodulation-related Type-A RR Mt RR4 and the Nodulation Signaling Pathway 2 (NSP2) TF. Site-directed mutagenesis revealed that RRBS cis-elements in the RR4 and NSP2 promoters are essential for expression during nodule development and for cytokinin induction. Furthermore, a microRNA targeting NSP2 (miR171 h) is also rapidly induced by cytokinins and then shows an expression pattern anticorrelated with NSP2. Other primary targets regulated by cytokinins depending on the Cytokinin Response1 (CRE1) receptor were a cytokinin oxidase/dehydrogenase (CKX1) and a basic Helix-Loop-Helix TF (bHLH476). RNA interference constructs as well as insertion of a Tnt1 retrotransposon in the bHLH gene led to reduced nodulation. Hence, we identified two TFs, NSP2 and bHLH476, as direct cytokinin targets acting at the convergence of phytohormonal and symbiotic cues.

Molecular characterization of the Lotus japonicus NRT1(PTR) and NRT2 families

Nitrate is an essential element for plant growth, both as a primary nutrient in the nitrogen assimilation pathway and as an important signal for plant development. Low- and high-affinity transport systems are involved in the nitrate uptake from the soil and its distribution between different plant tissues. By an in silico search, we identified putative members of both systems in the model legume Lotus japonicus. We investigated, by a time course analysis, the transcripts abundance in root tissues of nine and four genes encoding putative low-affinity (NRT1) and high-affinity (NRT2) nitrate transporters, respectively. The genes were sub-classified as inducible, repressible and constitutive on the basis of their responses to provision of nitrate, auxin or cytokinin. Furthermore, the analysis of the pattern of expression in root and nodule tissues after Mesorhizobium loti inoculation permitted the identification of sequences significantly regulated during the symbiotic interaction. The interpretation of the global regulative networks obtained allowed to postulate roles for nitrate transporters as possible actors in the cross-talks between different signalling pathways triggered by biotic and abiotic factors.

Epidermal and cortical roles of NFP and DMI3 in coordinating early steps of nodulation in Medicago truncatula

Legumes have evolved the capacity to form a root nodule symbiosis with soil bacteria called rhizobia. The establishment of this symbiosis involves specific developmental events occurring both in the root epidermis (notably bacterial entry) and at a distance in the underlying root cortical cells (notably cell divisions leading to nodule organogenesis). The processes of bacterial entry and nodule organogenesis are tightly linked and both depend on rhizobial production of lipo-chitooligosaccharide molecules called Nod factors. However, how these events are coordinated remains poorly understood. Here, we have addressed the roles of two key symbiotic genes of Medicago truncatula, the lysin motif (LysM) domain-receptor like kinase gene NFP and the calcium- and calmodulin-dependent protein kinase gene DMI3, in the control of both nodule organogenesis and bacterial entry. By complementing mutant plants with corresponding genes expressed either in the epidermis or in the cortex, we have shown that epidermal DMI3, but not NFP, is sufficient for infection thread formation in root hairs. Epidermal NFP is sufficient to induce cortical cell divisions leading to nodule primordia formation, whereas DMI3 is required in both cell layers for these processes. Our results therefore suggest that a signal, produced in the epidermis under the control of NFP and DMI3, is responsible for activating DMI3 in the cortex to trigger nodule organogenesis. We integrate these data to propose a new model for epidermal/cortical crosstalk during early steps of nodulation.

Plant hormonal regulation of nitrogen-fixing nodule organogenesis

Legumes have evolved symbiotic interactions with rhizobial bacteria to efficiently utilize nitrogen. Recent progress in symbiosis has revealed several key components of host plants required for nitrogen-fixing nodule organogenesis, in which complicated metabolic and signaling pathways in the host plant are reprogrammed to generate nodules in the cortex upon perception of the rhizobial Nod factor. Following the recognition of Nod factors, plant hormones are likely to be essential throughout nodule organogenesis for integration of developmental and environmental signaling cues into nodule development. Here, we review the molecular events involved in plant hormonal regulation and signaling cross-talk for nitrogen-fixing nodule development, and discuss how these signaling networks are integrated into Nod factor-mediated signaling during plant-microbe interactions.

Murray J, Wen J, Cosson V, Muni RRD, Wang M, A. Benedito V, Andriankaja A, Cheng X, Jerez IT, Mondy S, Zhang S, Taylor ME, Tadege M, Ratet P, Mysore KS, Chen R, Udvardi MK. A Medicago truncatula tobacco retrotransposon insertion mutant collection with defects in nodule development and symbiotic nitrogen fixation

A Tnt1-insertion mutant population of Medicago truncatula ecotype R108 was screened for defects in nodulation and symbiotic nitrogen fixation. Primary screening of 9,300 mutant lines yielded 317 lines with putative defects in nodule development and/or nitrogen fixation. Of these, 230 lines were rescreened, and 156 lines were confirmed with defective symbiotic nitrogen fixation. Mutants were sorted into six distinct phenotypic categories: 72 nonnodulating mutants (Nod-), 51 mutants with totally ineffective nodules (Nod+ Fix-), 17 mutants with partially ineffective nodules (Nod+ Fix+/-), 27 mutants defective in nodule emergence, elongation, and nitrogen fixation (Nod+/- Fix-), one mutant with delayed and reduced nodulation but effective in nitrogen fixation (dNod+/- Fix+), and 11 supernodulating mutants (Nod++Fix+/-). A total of 2,801 flanking sequence tags were generated from the 156 symbiotic mutant lines. Analysis of flanking sequence tags revealed 14 insertion alleles of the following known symbiotic genes: NODULE INCEPTION (NIN), DOESN'T MAKE INFECTIONS3 (DMI3/CCaMK), ERF REQUIRED FOR NODULATION, and SUPERNUMERARY NODULES (SUNN). In parallel, a polymerase chain reaction-based strategy was used to identify Tnt1 insertions in known symbiotic genes, which revealed 25 additional insertion alleles in the following genes: DMI1, DMI2, DMI3, NIN, NODULATION SIGNALING PATHWAY1 (NSP1), NSP2, SUNN, and SICKLE. Thirty-nine Nod- lines were also screened for arbuscular mycorrhizal symbiosis phenotypes, and 30 mutants exhibited defects in arbuscular mycorrhizal symbiosis. Morphological and developmental features of several new symbiotic mutants are reported. The collection of mutants described here is a source of novel alleles of known symbiotic genes and a resource for cloning novel symbiotic genes via Tnt1 tagging.

Agrobacterium tumefaciens tumor morphology root plastid localization and preferential usage of hydroxylated prenyl donor is important for efficient gall formation

Upon Agrobacterium tumefaciens infection of a host plant, Tumor morphology root (Tmr) a bacterial adenosine phosphate-isopentenyltransferase (IPT), creates a metabolic bypass in the plastid for direct synthesis of trans-zeatin (tZ) with 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate as the prenyl donor. To understand the biological importance of Tmr function for gall formation, we compared Tmr and Trans-zeatin secretion (Tzs) another agrobacterial IPT that functions within the bacterial cell. Although there is no significant difference in their substrate specificities in vitro, ectopic overexpression of Tzs in Arabidopsis (Arabidopsis thaliana) resulted in the accumulation of comparable amounts of tZ- and N⁶-(Δ²-isopentenyl)adenine (iP)-type cytokinins, whereas overexpression of Tmr resulted exclusively in the accumulation of tZ-type cytokinins. Ectopic expression of Tzs in plant cells yields only small amounts of the polypeptide in plastid-enriched fractions. Obligatory localization of Tzs into Arabidopsis plastid stroma by translational fusions with ferredoxin transit peptide (TP-Tzs) increased the accumulation of both tZ- and iP-type cytokinins. Replacement of tmr on the Ti plasmid with tzs, TP-tzs, or an Arabidopsis plastidic IPT induced the formation of smaller galls than wild-type A. tumefaciens, and they were accompanied by the accumulation of iP-type cytokinins. Tmr is thus specialized for plastid localization and preferential usage of 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate in vivo and is important for efficient gall formation.

Modeling a cortical auxin maximum for nodulation: different signatures of potential strategies

Lateral organ formation from plant roots typically requires the de novo creation of a meristem, initiated at the location of a localized auxin maximum. Legume roots can form both root nodules and lateral roots. From the basic principles of auxin transport and metabolism only a few mechanisms can be inferred for increasing the local auxin concentration: increased influx, decreased efflux, and (increased) local production. Using computer simulations we investigate the different spatio-temporal patterns resulting from each of these mechanisms in the context of a root model of a generalized legume. We apply all mechanisms to the same group of preselected cells, dubbed the controlled area. We find that each mechanism leaves its own characteristic signature. Local production by itself can not create a strong auxin maximum. An increase of influx, as is observed in lateral root formation, can result in an auxin maximum that is spatially more confined than the controlled area. A decrease of efflux on the other hand leads to a broad maximum, which is more similar to what is observed for nodule primordia. With our prime interest in nodulation, we further investigate the dynamics following a decrease of efflux. We find that with a homogeneous change in the whole cortex, the first auxin accumulation is observed in the inner cortex. The steady state lateral location of this efflux reduced auxin maximum can be shifted by slight changes in the ratio of central to peripheral efflux carriers. We discuss the implications of this finding in the context of determinate and indeterminate nodules, which originate from different cortical positions. The patterns we have found are robust under disruption of the (artificial) tissue layout. The same patterns are therefore likely to occur in many other contexts.

Nodule numbers are governed by interaction between CLE peptides and cytokinin signaling

CLE peptides are involved in the balance between cell division and differentiation throughout plant development, including nodulation. Previously, two CLE genes of Medicago truncatula, MtCLE12 and MtCLE13, had been identified whose expression correlated with nodule primordium formation and meristem establishment. Gain-of-function analysis indicated that both MtCLE12 and MtCLE13 interact with the SUPER NUMERIC NODULES (SUNN)-dependent auto-regulation of nodulation to control nodule numbers. Here we demonstrate that cytokinin, which is essential for nodule organ formation, regulates MtCLE13 expression. In addition, simultaneous knockdown of MtCLE12 and MtCLE13 resulted in an increase in nodule number, implying that both genes play a role in controlling nodule number. Additionally, a weak link may exist with the ethylene-dependent mechanism that locally controls nodule number.

Down-stream components of cytokinin signaling and the role of cytokinin throughout the plant

Cytokinins constitute a class of plant hormones influencing numerous aspects of growth and development. These processes occur through the downstream components of the cytokinin signaling pathway after its perception and signal transduction. The importance of these downstream signaling components has been revealed through the use of both traditional genetic and advanced molecular approaches studying mutants and transgenic lines involving cytokinin and diverse plant growth and developmental processes. Interestingly, these effects are not always directly via cytokinin, but by interactions with other plants hormones or transcription factor cascades, which can involve regulatory loops that affect transcription as well as hormone concentrations. This review covers recent advancements in understanding the role of cytokinin via its signaling components, specifically the downstream responses regulators in controlling vital plant growth and developmental processes.

Cytokinins - recent news and views of evolutionally old molecules

Cytokinins (CKs) are evolutionally old and highly conserved low-mass molecules that have been identified in almost all known organisms. In plants, they evolved into an important group of plant hormones controlling many physiological and developmental processes throughout the whole lifespan of the plant. CKs and their functions are, however, not unique to plants. In this review, the strategies and mechanisms of plants - and phylogenetically distinct plant-interacting organisms such as bacteria, fungi, nematodes and insects employing CKs or regulation of CK status in plants - are described and put into their evolutionary context. The major breakthroughs made in the last decade in the fields of CK biosynthesis, degradation and signalling are also summarised.

Quantitative trait locus analysis of symbiotic nitrogen fixation activity in the model legume Lotus japonicus

Many legumes form nitrogen-fixing root nodules. An elevation of nitrogen fixation in such legumes would have significant implications for plant growth and biomass production in agriculture. To identify the genetic basis for the regulation of nitrogen fixation, quantitative trait locus (QTL) analysis was conducted with recombinant inbred lines derived from the cross Miyakojima MG-20 × Gifu B-129 in the model legume Lotus japonicus. This population was inoculated with Mesorhizobium loti MAFF303099 and grown for 14 days in pods containing vermiculite. Phenotypic data were collected for acetylene reduction activity (ARA) per plant (ARA/P), ARA per nodule weight (ARA/NW), ARA per nodule number (ARA/NN), NN per plant, NW per plant, stem length (SL), SL without inoculation (SLbac-), shoot dry weight without inoculation (SWbac-), root length without inoculation (RLbac-), and root dry weight (RWbac-), and finally 34 QTLs were identified. ARA/P, ARA/NN, NW, and SL showed strong correlations and QTL co-localization, suggesting that several plant characteristics important for symbiotic nitrogen fixation are controlled by the same locus. QTLs for ARA/P, ARA/NN, NW, and SL, co-localized around marker TM0832 on chromosome 4, were also co-localized with previously reported QTLs for seed mass. This is the first report of QTL analysis for symbiotic nitrogen fixation activity traits.

Plant-activated bacterial receptor adenylate cyclases modulate epidermal infection in the Sinorhizobium meliloti-Medicago symbiosis

Legumes and soil bacteria called rhizobia have coevolved a facultative nitrogen-fixing symbiosis. Establishment of the symbiosis requires bacterial entry via root hair infection threads and, in parallel, organogenesis of nodules that subsequently are invaded by bacteria. Tight control of nodulation and infection is required to maintain the mutualistic character of the interaction. Available evidence supports a passive bacterial role in nodulation and infection after the microsymbiont has triggered the symbiotic plant developmental program. Here we identify in Sinorhizobium meliloti, the Medicago symbiont, a cAMP-signaling regulatory cascade consisting of three receptor-like adenylate cyclases, a Crp-like regulator, and a target gene of unknown function. The cascade is activated specifically by a plant signal during nodule organogenesis. Cascade inactivation results in a hyperinfection phenotype consisting of abortive epidermal infection events uncoupled from nodulation. These findings show that, in response to a plant signal, rhizobia play an active role in the control of infection. We suggest that rhizobia may modulate the plant's susceptibility to infection. This regulatory loop likely aims at optimizing legume infection.

Never too many? How legumes control nodule numbers

Restricted availability of nitrogen compounds in soils is often a major limiting factor for plant growth and productivity. Legumes circumvent this problem by establishing a symbiosis with soil-borne bacteria, called rhizobia that fix nitrogen for the plant. Nitrogen fixation and nutrient exchange take place in specialized root organs, the nodules, which are formed by a coordinated and controlled process that combines bacterial infection and organ formation. Because nodule formation and nitrogen fixation are energy-consuming processes, legumes develop the minimal number of nodules required to ensure optimal growth. To this end, several mechanisms have evolved that adapt nodule formation and nitrogen fixation to the plant's needs and environmental conditions, such as nitrate availability in the soil. In this review, we give an updated view on the mechanisms that control nodulation.

Cytokinin signaling networks

Despite long-standing observations on diverse cytokinin actions, the discovery path to cytokinin signaling mechanisms was tortuous. Unyielding to conventional genetic screens, experimental innovations were paramount in unraveling the core cytokinin signaling circuitry, which employs a large repertoire of genes with overlapping and specific functions. The canonical two-component transcription circuitry involves His kinases that perceive cytokinin and initiate signaling, as well as His-to-Asp phosphorelay proteins that transfer phosphoryl groups to response regulators, transcriptional activators, or repressors. Recent advances have revealed the complex physiological functions of cytokinins, including interactions with auxin and other signal transduction pathways. This review begins by outlining the historical path to cytokinin discovery and then elucidates the diverse cytokinin functions and key signaling components. Highlights focus on the integration of cytokinin signaling components into regulatory networks in specific contexts, ranging from molecular, cellular, and developmental regulations in the embryo, root apical meristem, shoot apical meristem, stem and root vasculature, and nodule organogenesis to organismal responses underlying immunity, stress tolerance, and senescence.

Genetic engineering of cytokinin metabolism: prospective way to improve agricultural traits of crop plants

Cytokinins (CKs) are ubiquitous phytohormones that participate in development, morphogenesis and many physiological processes throughout plant kingdom. In higher plants, mutants and transgenic cells and tissues with altered activity of CK metabolic enzymes or perception machinery, have highlighted their crucial involvement in different agriculturally important traits, such as productivity, increased tolerance to various stresses and overall plant morphology. Furthermore, recent precise metabolomic analyses have elucidated the specific occurrence and distinct functions of different CK types in various plant species. Thus, smooth manipulation of active CK levels in a spatial and temporal way could be a very potent tool for plant biotechnology in the future. This review summarises recent advances in cytokinin research ranging from transgenic alteration of CK biosynthetic, degradation and glucosylation activities and CK perception to detailed elucidation of molecular processes, in which CKs work as a trigger in model plants. The first attempts to improve the quality of crop plants, focused on cereals are discussed, together with proposed mechanism of action of the responses involved.

Cytokinin induction of root nodule primordia in Lotus japonicus is regulated by a mechanism operating in the root cortex

Cytokinin plays a central role in the formation of nitrogen-fixing root nodules following inoculation with rhizobia. We show that exogenous cytokinin induces formation of discrete and easily visible nodule primordia in Lotus japonicus roots. The expression of nodulin genes was up-regulated upon cytokinin treatment, suggesting that the genuine nodulation program was indeed activated. This offers a simple approach for dissecting the underlying mechanism. Cytokinin-induced nodule primordia formation was unperturbed in several loss-of-function mutants impaired in epidermal responses to either rhizobial infection, Nod factor application, or both. However, absence of primordia in nsp1, nsp2, and nin mutants showed the requirement for these transcriptional regulators in the cytokinin-mediated activation of the root cortex. Distinguishing the epidermal and cortical responses further, we found that external cytokinin application induced expression of the Nin::GUS reporter gene within the root cortex but not in the root epidermis. Using L. japonicus lhk1-1 and har1 mutants, we demonstrate that discrete activation of root cortical cells by cytokinin depends on the LHK1 cytokinin receptor and is subjected to HAR1-mediated autoregulation.