Seven Lotus japonicus genes required for transcriptional reprogramming of the root during fungal and bacterial symbiosis

How membranes shape plant symbioses: signaling and transport in nodulation and arbuscular mycorrhiza

As sessile organisms that cannot evade adverse environmental conditions, plants have evolved various adaptive strategies to cope with environmental stresses. One of the most successful adaptations is the formation of symbiotic associations with beneficial microbes. In these mutualistic interactions the partners exchange essential nutrients and improve their resistance to biotic and abiotic stresses. In arbuscular mycorrhiza (AM) and in root nodule symbiosis (RNS), AM fungi and rhizobia, respectively, penetrate roots and accommodate within the cells of the plant host. In these endosymbiotic associations, both partners keep their plasma membranes intact and use them to control the bidirectional exchange of signaling molecules and nutrients. Intracellular accommodation requires the exchange of symbiotic signals and the reprogramming of both interacting partners. This involves fundamental changes at the level of gene expression and of the cytoskeleton, as well as of organelles such as plastids, endoplasmic reticulum (ER), and the central vacuole. Symbiotic cells are highly compartmentalized and have a complex membrane system specialized for the diverse functions in molecular communication and nutrient exchange. Here, we discuss the roles of the different cellular membrane systems and their symbiosis-related proteins in AM and RNS, and we review recent progress in the analysis of membrane proteins involved in endosymbiosis.

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.

Polymorphic infection and organogenesis patterns induced by a Rhizobium leguminosarum isolate from Lotus root nodules are determined by the host genotype

To sample the natural variation in genes controlling compatibility in the legume-rhizobium symbiosis, we isolated rhizobia from nodules of endemic Lotus species from 21 sites across Europe. The majority of isolates were identified as Mesorhizobium- or Bradyrhizobium-related and formed nitrogen-fixing root nodules on Lotus corniculatus and L. pendunculatus, respectively, thus confirming previously defined cross-inoculation groups. Rhizobium leguminosarum (Rl) strain Norway, isolated from L. corniculatus nodules, displayed an exceptional phenotypic variation on different Lotus genotypes. On L. burttii, Rl Norway formed infected nodules, whereas tumors and elongated infected swellings were induced on L. glaber and L. japonicus ecotype Nepal, respectively. A symbiosis- and Nod-factor-responsive promoter:uidA fusion was strongly and rapidly induced in L. japonicus Gifu, but infection threads or signs of nodule organogenesis were absent. This complex phenotypic pattern was not mimicked by either of three engineered R. leguminosarum bv viciae strains producing different Nod-factor variants. Intriguingly, Rl Norway formed infection threads on Pisum sativum cv Sparkle, but failed to induce organogenesis. Rl Norway thus uncovered variation in symbiotic capabilities among diploid Lotus species and ecotypes that are obscured by optimally adapted M. loti strains. These contrasting infection and organogenesis phenotypes reveal recent diversification of recognition determinants in Lotus.

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

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

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.

The recent evolution of a symbiotic ion channel in the legume family altered ion conductance and improved functionality in calcium signaling

Arbuscular mycorrhiza and the rhizobia-legume symbiosis are two major root endosymbioses that facilitate plant nutrition. In Lotus japonicus, two symbiotic cation channels, CASTOR and POLLUX, are indispensable for the induction of nuclear calcium spiking, one of the earliest plant responses to symbiotic partner recognition. During recent evolution, a single amino acid substitution in DOES NOT MAKE INFECTIONS1 (DMI1), the POLLUX putative ortholog in the closely related Medicago truncatula, rendered the channel solo sufficient for symbiosis; castor, pollux, and castor pollux double mutants of L. japonicus were rescued by DMI1 alone, while both Lj-CASTOR and Lj-POLLUX were required for rescuing a dmi1 mutant of M. truncatula. Experimental replacement of the critical serine by an alanine in the selectivity filter of Lj-POLLUX conferred a symbiotic performance indistinguishable from DMI1. Electrophysiological characterization of DMI1 and Lj-CASTOR (wild-type and mutants) by planar lipid bilayer experiments combined with calcium imaging in Human Embryonic Kidney-293 cells expressing DMI1 (the wild type and mutants) suggest that the serine-to-alanine substitution conferred reduced conductance with a long open state to DMI1 and improved its efficiency in mediating calcium oscillations. We propose that this single amino acid replacement in the selectivity filter made DMI1 solo sufficient for symbiosis, thus explaining the selective advantage of this allele at the mechanistic level.

Subtilases - versatile tools for protein turnover, plant development, and interactions with the environment

Subtilases (SBTs) constitute a large family of serine peptidases. They are commonly found in Archaea, Bacteria and Eukarya, with many more SBTs in plants as compared to other organisms. The expansion of the SBT family in plants was accompanied by functional diversification, and novel, plant-specific physiological roles were acquired in the course of evolution. In addition to their contribution to general protein turnover, plant SBTs are involved in the development of seeds and fruits, the manipulation of the cell wall, the processing of peptide growth factors, epidermal development and pattern formation, plant responses to their biotic and abiotic environment, and in programmed cell death. Plant SBTs share many properties with their bacterial and mammalian homologs, but the adoption of specific roles in plant physiology is also reflected in the acquisition of unique biochemical and structural features that distinguish SBTs in plants from those in other organisms. In this article we provide an overview of the earlier literature on the discovery of the first SBTs in plants, and highlight recent findings with respect to their physiological relevance, structure and function.

Lotus japonicus E3 ligase SEVEN IN ABSENTIA4 destabilizes the symbiosis receptor-like kinase SYMRK and negatively regulates rhizobial infection

The Lotus japonicus SYMBIOSIS RECEPTOR-LIKE KINASE (SYMRK) is required for symbiotic signal transduction upon stimulation of root cells by microbial signaling molecules. Here, we identified members of the SEVEN IN ABSENTIA (SINA) E3 ubiquitin-ligase family as SYMRK interactors and confirmed their predicted ubiquitin-ligase activity. In Nicotiana benthamiana leaves, SYMRK-yellow fluorescent protein was localized at the plasma membrane, and interaction with SINAs, as determined by bimolecular fluorescence complementation, was observed in small punctae at the cytosolic interface of the plasma membrane. Moreover, fluorescence-tagged SINA4 partially colocalized with SYMRK and caused SYMRK relocalization as well as disappearance of SYMRK from the plasma membrane. Neither the localization nor the abundance of Nod-factor receptor1 was altered by the presence of SINA4. SINA4 was transcriptionally upregulated during root symbiosis, and rhizobia inoculated roots ectopically expressing SINA4 showed reduced SYMRK protein levels. In accordance with a negative regulatory role in symbiosis, infection thread development was impaired upon ectopic expression of SINA4. Our results implicate SINA4 E3 ubiquitin ligase in the turnover of SYMRK and provide a conceptual mechanism for its symbiosis-appropriate spatio-temporal containment.

A MAP kinase kinase interacts with SymRK and regulates nodule organogenesis in Lotus japonicus

The symbiosis receptor kinase, SymRK, is required for root nodule development. A SymRK-interacting protein (SIP2) was found to form protein complex with SymRK in vitro and in planta. The interaction between SymRK and SIP2 is conserved in legumes. The SIP2 gene was expressed in all Lotus japonicus tissues examined. SIP2 represents a typical plant mitogen-activated protein kinase kinase (MAPKK) and exhibited autophosphorylation and transphosphorylation activities. Recombinant SIP2 protein could phosphorylate casein and the Arabidopsis thaliana MAP kinase MPK6. SymRK and SIP2 could not use one another as a substrate for phosphorylation. Instead, SymRK acted as an inhibitor of SIP2 kinase when MPK6 was used as a substrate, suggesting that SymRK may serve as a negative regulator of the SIP2 signaling pathway. Knockdown expression of SIP2 via RNA interference (RNAi) resulted in drastic reduction of nodules formed in transgenic hairy roots. A significant portion of SIP2 RNAi hairy roots failed to form a nodule. In these roots, the expression levels of SIP2 and three marker genes for infection thread and nodule primordium formation were downregulated drastically, while the expression of two other MAPKK genes were not altered. These observations demonstrate an essential role of SIP2 in the early symbiosis signaling and nodule organogenesis.

Nuclear-localized and deregulated calcium- and calmodulin-dependent protein kinase activates rhizobial and mycorrhizal responses in Lotus japonicus

The common symbiosis pathway is at the core of symbiosis signaling between plants and soil microbes. In this pathway, calcium- and calmodulin-dependent protein kinase (CCaMK) plays a crucial role in integrating the signals both in arbuscular mycorrhizal symbiosis (AMS) and in root nodule symbiosis (RNS). However, the molecular mechanism by which CCaMK coordinates AMS and RNS is largely unknown. Here, we report that the gain-of-function (GOF) variants of CCaMK without the regulatory domains activate both AMS and RNS signaling pathways in the absence of symbiotic partners. This activation requires nuclear localization of CCaMK. Enforced nuclear localization of the GOF-CCaMK variants by fusion with a canonical nuclear localization signal enhances signaling activity of AMS and RNS. The GOF-CCaMK variant triggers formation of a structure similar to the prepenetration apparatus, which guides infection of arbuscular mycorrhizal fungi to host root cells. In addition, the GOF-CCaMK variants without the regulatory domains partly restore AMS but fail to support rhizobial infection in ccamk mutants. These data indicate that AMS, the more ancient type of symbiosis, can be mainly regulated by the kinase activity of CCaMK, whereas RNS, which evolved more recently, requires complex regulation performed by the regulatory domains of CCaMK.

Functional domain analysis of the Remorin protein LjSYMREM1 in Lotus japonicus

In legumes rhizobial infection during root nodule symbiosis (RNS) is controlled by a conserved set of receptor proteins and downstream components. MtSYMREM1, a protein of the Remorin family in Medicago truncatula, was shown to interact with at least three receptor-like kinases (RLKs) that are essential for RNS. Remorins are comprised of a conserved C-terminal domain and a variable N-terminal region that defines the six different Remorin groups. While both N- and C-terminal regions of Remorins belonging to the same phylogenetic group are similar to each other throughout the plant kingdom, the N-terminal domains of legume-specific group 2 Remorins show exceptional high degrees of sequence divergence suggesting evolutionary specialization of this protein within this clade. We therefore identified and characterized the MtSYMREM1 ortholog from Lotus japonicus (LjSYMREM1), a model legume that forms determinate root nodules. Here, we resolved its spatio-temporal regulation and showed that over-expression of LjSYMREM1 increases nodulation on transgenic roots. Using a structure-function approach we show that protein interactions including Remorin oligomerization are mainly mediated and stabilized by the Remorin C-terminal region with its coiled-coil domain while the RLK kinase domains transiently interact in vivo and phosphorylate a residue in the N-terminal region of the LjSYMREM1 protein in vitro. These data provide novel insights into the mechanism of this putative molecular scaffold protein and underline its importance during rhizobial infection.

Ecological and agronomic importance of the plant genus Lotus. Its application in grassland sustainability and the amelioration of constrained and contaminated soils

The genus Lotus comprises around 100 annual and perennial species with worldwide distribution. The relevance of Lotus japonicus as a model plant has been recently demonstrated in numerous studies. In addition, some of the Lotus species show a great potential for adaptation to a number of abiotic stresses. Therefore, they are relevant components of grassland ecosystems in environmentally constrained areas of several South American countries and Australia, where they are used for livestock production. Also, the fact that the roots of these species form rhizobial and mycorrhizal associations makes the annual L. japonicus a suitable model plant for legumes, particularly in studies directed to recognize the mechanisms intervening in the tolerance to abiotic factors in the field, where these interactions occur. These properties justify the increased utilization of some Lotus species as a strategy for dunes revegetation and reclamation of heavy metal-contaminated or burned soils in Europe.

An Arabidopsis (malectin-like) leucine-rich repeat receptor-like kinase contributes to downy mildew disease

Biotrophic filamentous plant pathogens frequently establish intimate contact with host cells through intracellular feeding structures called haustoria. To form and maintain these structures, pathogens must avoid or suppress defence responses and reprogramme the host cell. We used Arabidopsis whole-genome microarrays to characterize genetic programmes that are deregulated during infection by the biotrophic' oomycete downy mildew pathogen, Hyaloperonospora arabidopsidis. Marked differences were observed between early and late stages of infection, but a gene encoding a putative leucine-rich repeat receptor-like kinase (LRR-RLK) was constantly up-regulated. We investigated the evolutionary history of this gene and noticed it being one of the first to have emerged from a common ancestral gene that gave rise to a cluster of 11 genes through duplications. The encoded LRR-RLKs harbour an extracellular malectin-like (ML) domain in addition to a short stretch of leucine-rich repeats, and are thus similar to proteins from the symbiosis receptor-like kinase family. Detailed expression analysis showed that the pathogen-responsive gene was locally expressed in cells surrounding the oomycete. A knockout mutant showed reduced downy mildew infection, but susceptibility was fully restored through complementation of the mutation, suggesting that the (ML-)LRR-RLK contributes to disease. According to the mutant phenotype, we denominated it Impaired Oomycete Susceptibility 1 (IOS1).

Nodulin 41, a novel late nodulin of common bean with peptidase activity

BACKGROUND

The legume-rhizobium symbiosis requires the formation of root nodules, specialized organs where the nitrogen fixation process takes place. Nodule development is accompanied by the induction of specific plant genes, referred to as nodulin genes. Important roles in processes such as morphogenesis and metabolism have been assigned to nodulins during the legume-rhizobium symbiosis.

RESULTS

Here we report the purification and biochemical characterization of a novel nodulin from common bean (Phaseolus vulgaris L.) root nodules. This protein, called nodulin 41 (PvNod41) was purified through affinity chromatography and was partially sequenced. A genomic clone was then isolated via PCR amplification. PvNod41 is an atypical aspartyl peptidase of the A1B subfamily with an optimal hydrolytic activity at pH 4.5. We demonstrate that PvNod41 has limited peptidase activity against casein and is partially inhibited by pepstatin A. A PvNod41-specific antiserum was used to assess the expression pattern of this protein in different plant organs and throughout root nodule development, revealing that PvNod41 is found only in bean root nodules and is confined to uninfected cells.

CONCLUSIONS

To date, only a small number of atypical aspartyl peptidases have been characterized in plants. Their particular spatial and temporal expression patterns along with their unique enzymatic properties imply a high degree of functional specialization. Indeed, PvNod41 is closely related to CDR1, an Arabidopsis thaliana extracellular aspartyl protease involved in defense against bacterial pathogens. PvNod41's biochemical properties and specific cell-type localization, in uninfected cells of the common bean root nodule, strongly suggest that this aspartyl peptidase has a key role in plant defense during the symbiotic interaction.

Lotus japonicus symRK-14 uncouples the cortical and epidermal symbiotic program

SYMRK is a leucine-rich-repeat (LRR)-receptor kinase that mediates intracellular symbioses of legumes with rhizobia and arbuscular mycorrhizal fungi. It participates in signalling events that lead to epidermal calcium spiking, an early cellular response that is typically considered as central for intracellular accommodation and nodule organogenesis. Here, we describe the Lotus japonicus symRK-14 mutation that alters a conserved GDPC amino-acid sequence in the SYMRK extracellular domain. Normal infection of the epidermis by fungal or bacterial symbionts was aborted in symRK-14. Likewise, epidermal responses of symRK-14 to bacterial signalling, including calcium spiking, NIN gene expression and infection thread formation, were significantly reduced. In contrast, no major negative effects on the formation of nodule primordia and cortical infection were detected. Cumulatively, our data show that the symRK-14 mutation uncouples the epidermal and cortical symbiotic program, while indicating that the SYMRK extracellular domain participates in transduction of non-equivalent signalling events. The GDPC sequence was found to be highly conserved in LRR-receptor kinases in legumes and non-legumes, including the evolutionarily distant bryophytes. Conservation of the GDPC sequence in nearly one-fourth of LRR-receptor-like kinases in the genome of Arabidopsis thaliana suggests, however, that this sequence might also play an important non-symbiotic function in this plant.

AM fungal exudates activate MAP kinases in plant cells in dependence from cytosolic Ca(2+) increase

The molecular dialogue occurring prior to direct contact between the fungal and plant partners of arbuscular-mycorrhizal (AM) symbioses begins with the release of fungal elicitors, so far only partially identified chemically, which can activate specific signaling pathways in the host plant. We show here that the activation of MAPK is also induced by exudates of germinating spores of Gigaspora margarita in cultured cells of the non-leguminous species tobacco (Nicotiana tabacum), as well as in those of the model legume Lotus japonicus. MAPK activity peaked about 15 min after the exposure of the host cells to the fungal exudates (FE). FE were also responsible for a rapid and transient increase in free cytosolic Ca(2+) in Nicotiana plumbaginifolia and tobacco cells, and pre-treatment with a Ca(2+)-channel blocker (La(3+)) showed that in these cells, MAPK activation was dependent on the cytosolic Ca(2+) increase. A partial dependence of MAPK activity on the common Sym pathway could be demonstrated for a cell line of L. japonicus defective for LjSym4 and hence unable to establish an AM symbiosis. Our results show that MAPK activation is triggered by an FE-induced cytosolic Ca(2+) transient, and that a Sym genetic determinant acts to modulate the intensity and duration of this activity.

Lipo-chitooligosaccharide signaling in endosymbiotic plant-microbe interactions

The arbuscular mycorrhizal (AM) and the rhizobia-legume (RL) root endosymbioses are established as a result of signal exchange in which there is mutual recognition of diffusible signals produced by plant and microbial partners. It was discovered 20 years ago that the key symbiotic signals produced by rhizobial bacteria are lipo-chitooligosaccharides (LCO), called Nod factors. These LCO are perceived via lysin-motif (LysM) receptors and activate a signaling pathway called the common symbiotic pathway (CSP), which controls both the RL and the AM symbioses. Recent work has established that an AM fungus, Glomus intraradices, also produces LCO that activate the CSP, leading to induction of gene expression and root branching in Medicago truncatula. These Myc-LCO also stimulate mycorrhization in diverse plants. In addition, work on the nonlegume Parasponia andersonii has shown that a LysM receptor is required for both successful mycorrhization and nodulation. Together these studies show that structurally related signals and the LysM receptor family are key components of both nodulation and mycorrhization. LysM receptors are also involved in the perception of chitooligosaccharides (CO), which are derived from fungal cell walls and elicit defense responses and resistance to pathogens in diverse plants. The discovery of Myc-LCO and a LysM receptor required for the AM symbiosis, therefore, not only raises questions of how legume plants discriminate fungal and bacterial endosymbionts but also, more generally, of how plants discriminate endosymbionts from pathogenic microorganisms using structurally related LCO and CO signals and of how these perception mechanisms have evolved.

Successful joint ventures of plants: arbuscular mycorrhiza and beyond

Among the oldest symbiotic associations of plants are arbuscular mycorrhiza (AM) with fungi of the phylum Glomeromycota. Although many of the symbiotic signaling components have been identified on the side of the plant, AM fungi have long evaded genetic analysis owing to their strict biotrophy and their exceptional genetics. Recently, the identification of the fungal symbiosis signal (Myc factor) and of a corresponding Myc factor receptor, and new insights into AM fungal genetics, have opened new avenues to address early communication and functional aspects of AM symbiosis. These advances will pave the way for breeding programs towards adapted AM fungi for crop production, and will shed light on the ecology and evolution of this remarkably successful symbiosis.

Activation of a Lotus japonicus subtilase gene during arbuscular mycorrhiza is dependent on the common symbiosis genes and two cis-active promoter regions

The subtilisin-like serine protease SbtM1 is strongly and specifically induced during arbuscular mycorrhiza (AM) symbiosis in Lotus japonicus. Another subtilase gene, SbtS, is induced during early stages of nodulation and AM. Transcript profiling in plant symbiosis mutants revealed that the AM-induced expression of SbtM1 and the gene family members SbtM3 and SbtM4 is dependent on the common symbiosis pathway, whereas an independent pathway contributes to the activation of SbtS. We used the specific spatial expression patterns of SbtM1 promoter β-d-glucuronidase (GUS) fusions to isolate cis elements that confer AM responsiveness. A promoter deletion and substitution analysis defined two cis regions (region I and II) in the SbtM1 promoter necessary for AM-induced GUS activity. 35S minimal promoter fusions revealed that either of the two regions is sufficient for AM responsiveness when tested in tandem repeat arrangement. Sequence-related regions were found in the promoters of AM-induced subtilase genes in Medicago truncatula and rice, consistent with an ancient origin of these elements predating the divergence of the angiosperms.

Invasion by invitation: rhizobial infection in legumes

Nodulation of legume roots typically begins with rhizobia attaching to the tip of a growing root-hair cell. The attached rhizobia secrete Nod factors (NF), which are perceived by the plant. This initiates a series of preinfection events that include cytoskeletal rearrangements, curling at the root-hair tip, and formation of radially aligned cytoplasmic bridges called preinfection threads (PIT) in outer cortical cells. Within the root-hair curl, an infection pocket filled with bacteria forms, from which originates a tubular invagination of cell wall and membrane called an infection thread (IT). IT formation is coordinated with nodule development in the underlying root cortex tissues. The IT extends from the infection pocket down through the root hair and into the root cortex, where it passes through PIT and eventually reaches the nascent nodule. As the IT grows, it is colonized by rhizobia that are eventually released into cells within the nodule, where they fix nitrogen. NF can also induce cortical root hairs that appear to originate from PIT and can become infected like normal root hairs. Several genes involved in NF signaling and some of the downstream transcription factors required for infection have been characterized. More recently, several genes with direct roles in infection have been identified, some with roles in actin rearrangement and others with possible roles in protein turnover and secretion. This article provides an overview of the infection process, including the roles of NF signaling, actin, and calcium and the influence of the hormones ethylene and cytokinin.

Germinating spore exudates from arbuscular mycorrhizal fungi: molecular and developmental responses in plants and their regulation by ethylene

Arbuscular mycorrhizal (AM) fungi stimulate root development and induce expression of mycorrhization-specific genes in both eudicots and monocots. Diffusible factors released by AM fungi have been shown to elicit similar responses in Medicago truncatula. Colonization of roots by AM fungi is inhibited by ethylene. We compared the effects of germinating spore exudates (GSE) from Glomus intraradices in monocots and in eudicots, their genetic control, and their regulation by ethylene. GSE modify root architecture and induce symbiotic gene expression in both monocots and eudicots. The genetic regulation of root architecture and gene expression was analyzed using M. truncatula and rice symbiotic mutants. These responses are dependent on the common symbiotic pathway as well as another uncharacterized pathway. Significant differences between monocots and eudicots were observed in the genetic control of plant responses to GSE. However, ethylene inhibits GSE-induced symbiotic gene expression and root development in both groups. Our results indicate that GSE signaling shares similarities and differences in monocots versus eudicots, that only a subset of AM signaling pathways has been co-opted in legumes for the establishment of root nodulation with rhizobia, and that regulation of these pathways by ethylene is a feature conserved across higher land plants.

An outlook on ion signaling and ionome of mycorrhizal symbiosis

The 450-million-year-old interaction between the majority of land plants and mycorrhizal fungi is one of the most ancient, abundant, and ecologically important symbiosis on earth. The early events in the evolution of mycorrhizal symbioses seem to have involved reciprocal genetic changes in ancestral plants and free-living fungi. new data on the mechanism of action of specific signaling molecules and how it influence and is influenced by the membrane ions fluxes and cytoplasm ion oscillations which integrate the symbiotic ionome are improving our understanding of the molecular bases of the mycorrhization process. This mini-review will highlight topics regarding what is known about the ionome and ionic communication in the arbuscular mycorrhizal symbiosis focusing on the signals involved in the development of symbioses. Here we present an overview integrating the available data with the prospects of the research in the field.

From defense to symbiosis: limited alterations in the kinase domain of LysM receptor-like kinases are crucial for evolution of legume-Rhizobium symbiosis

Nitrogen-fixing symbiosis between legumes and rhizobia is initiated by the recognition of rhizobial Nod factors (NFs) by host plants. NFs are diversely modified derivatives of chitin oligosaccharide, a fungal elicitor that induces defense responses in plants. Recent evidence has shown that both NFs and chitin elicitors are recognized by structurally related LysM receptor kinases. Transcriptome analyses of Lotus japonicus roots indicated that NFs not only activate symbiosis genes but also transiently activate defense-related genes through NF receptors. Conversely, chitin oligosaccharides were able to activate symbiosis genes independently of NF receptors. Analyses using chimeric genes consisting of the LysM receptor domain of a Lotus japonicus NF receptor, NFR1, and the kinase domain of an Arabidopsis chitin receptor, CERK1, demonstrated that substitution of a portion of the αEF helix in CERK1 with the amino acid sequence YAQ from the corresponding region of NFR1 enables L. japonicus nfr1 mutants to establish symbiosis with Mesorhizobium loti. We also showed that the kinase domains of two Lotus japonicus LysM receptor kinases, Lys6 and Lys7, which also possess the YAQ sequence, suppress the symbiotic defect of nfr1. These results strongly suggest that, in addition to adaptation of extracellular LysM domains to NFs, limited alterations in the kinase domain of chitin receptors have played a crucial role in shifting the intracellular signaling to symbiosis from defense responses, thus constituting one of the key genetic events in the evolution of root nodule symbiosis in legume plants.

Perspectives on remorin proteins, membrane rafts, and their role during plant-microbe interactions

Invasion of host cells by pathogenic or mutualistic microbes requires complex molecular dialogues that often determine host survival. Although several components of the underlying signaling cascades have recently been identified and characterized, our understanding of proteins that facilitate signal transduction or assemble signaling complexes is rather sparse. Our knowledge of plant-specific remorin proteins, annotated as proteins with unknown function, has recently advanced with respect to their involvement in host-microbe interactions. Current data demonstrating that a remorin protein restricts viral movement in tomato leaves and the importance of a symbiosis-specific remorin for bacterial infection of root nodules suggest that these proteins may serve such regulatory functions. Direct interactions of other remorins with a resistance protein in Arabidopsis thaliana, and differential phosphorylation upon perception of microbial-associated molecular patterns and during expression of bacterial effector proteins, strongly underline their roles in plant defense. Furthermore, the specific subcellular localization of remorins in plasma membrane microdomains now provides the opportunity to visualize membrane rafts in living plants cells. There, remorins may oligomerize and act as scaffold proteins during early signaling events. This review summarizes current knowledge of this protein family and the potential roles of remorins in membrane rafts.

Phosphate systemically inhibits development of arbuscular mycorrhiza in Petunia hybrida and represses genes involved in mycorrhizal functioning

Most terrestrial plants form arbuscular mycorrhiza (AM), mutualistic associations with soil fungi of the order Glomeromycota. The obligate biotrophic fungi trade mineral nutrients, mainly phosphate (P(i) ), for carbohydrates from the plants. Under conditions of high exogenous phosphate supply, when the plant can meet its own P requirements without the fungus, AM are suppressed, an effect which could be interpreted as an active strategy of the plant to limit carbohydrate consumption of the fungus by inhibiting its proliferation in the roots. However, the mechanisms involved in fungal inhibition are poorly understood. Here, we employ a transcriptomic approach to get insight into potential shifts in metabolic activity and symbiotic signalling, and in the defence status of plants exposed to high P(i) levels. We show that in mycorrhizal roots of petunia, a similar set of symbiosis-related genes is expressed as in mycorrhizal roots of Medicago, Lotus and rice. P(i) acts systemically to repress symbiotic gene expression and AM colonization in the root. In established mycorrhizal roots, P(i) repressed symbiotic gene expression rapidly, whereas the inhibition of colonization followed with a lag of more than a week. Taken together, these results suggest that P(i) acts by repressing essential symbiotic genes, in particular genes encoding enzymes of carotenoid and strigolactone biosynthesis, and symbiosis-associated phosphate transporters. The role of these effects in the suppression of symbiosis under high P(i) conditions is discussed.

Common and not so common symbiotic entry

Great advances have been made in our understanding of the host plant's common symbiosis functions, which in legumes mediate intracellular accommodation of both nitrogen-fixing bacteria and arbuscular mycorrhiza (AM) fungi. However, it has become apparent that additional plant genes are required specifically for bacterial entry inside the host root. In this opinion article, we consider Lotus japonicus nap1 and pir1 symbiotic mutants within the context of other deleterious mutations that impair an intracellular accommodation of bacteria but have no impact on the colonization of roots by AM fungi. We highlight a clear delineation of early signaling events during bacterial versus AM symbioses while suggesting a more intricate origin of the plant's ability for intracellular accommodation of bacteria.

Recent progress in plant nutrition research: cross-talk between nutrients, plant physiology and soil microorganisms

Mineral nutrients taken up from the soil become incorporated into a variety of important compounds with structural and physiological roles in plants. We summarize how plant nutrients are linked to many metabolic pathways, plant hormones and other biological processes. We also focus on nutrient uptake, describing plant-microbe interactions, plant exudates, root architecture, transporters and their applications. Plants need to survive in soils with mineral concentrations that vary widely. Describing the relationships between nutrients and biological processes will enable us to understand the molecular basis for signaling, physiological damage and responses to mineral stresses.

A dominant function of CCaMK in intracellular accommodation of bacterial and fungal endosymbionts

In legumes, Ca(2+)/calmodulin-dependent protein kinase (CCaMK) is a component of the common symbiosis genes that are required for both root nodule (RN) and arbuscular mycorrhiza (AM) symbioses and is thought to be a decoder of Ca(2+) spiking, one of the earliest cellular responses to microbial signals. A gain-of-function mutation of CCaMK has been shown to induce spontaneous nodulation without rhizobia, but the significance of CCaMK activation in bacterial and/or fungal infection processes is not fully understood. Here we show that a gain-of-function CCaMK(T265D) suppresses loss-of-function mutations of common symbiosis genes required for the generation of Ca(2+) spiking, not only for nodule organogenesis but also for successful infection of rhizobia and AM fungi, demonstrating that the common symbiosis genes upstream of Ca(2+) spiking are required solely to activate CCaMK. In RN symbiosis, however, CCaMK(T265D) induced nodule organogenesis, but not rhizobial infection, on Nod factor receptor (NFRs) mutants. We propose a model of symbiotic signaling in host legume plants, in which CCaMK plays a key role in the coordinated induction of infection thread formation and nodule organogenesis.

NENA, a Lotus japonicus homolog of Sec13, is required for rhizodermal infection by arbuscular mycorrhiza fungi and rhizobia but dispensable for cortical endosymbiotic development

Legumes form symbioses with arbuscular mycorrhiza (AM) fungi and nitrogen fixing root nodule bacteria. Intracellular root infection by either endosymbiont is controlled by the activation of the calcium and calmodulin-dependent kinase (CCaMK), a central regulatory component of the plant's common symbiosis signaling network. We performed a microscopy screen for Lotus japonicus mutants defective in AM development and isolated a mutant, nena, that aborted fungal infection in the rhizodermis. NENA encodes a WD40 repeat protein related to the nucleoporins Sec13 and Seh1. Localization of NENA to the nuclear rim and yeast two-hybrid experiments indicated a role for NENA in a conserved subcomplex of the nuclear pore scaffold. Although nena mutants were able to form pink nodules in symbiosis with Mesorhizobium loti, root hair infection was not observed. Moreover, Nod factor induction of the symbiotic genes NIN, SbtM4, and SbtS, as well as perinuclear calcium spiking, were impaired. Detailed phenotypic analyses of nena mutants revealed a rhizobial infection mode that overcame the lack of rhizodermal responsiveness and carried the hallmarks of crack entry, including a requirement for ethylene. CCaMK-dependent processes were only abolished in the rhizodermis but not in the cortex of nena mutants. These data support the concept of tissue-specific components for the activation of CCaMK.

Señales de reconocimiento entre plantas y hongos formadores de micorrizas arbusculares

La asociación entre Hongo formadores de micorrizas arbusculares (HFMA) y las plantas ha permitido la adaptación de éstas a ecosistemas terrestres, presentándose en más del 80% de las plantas. El hospedero suministra carbohidratos al hongo y éste transporta los nutrientes que la planta requiere. El establecimiento de la simbiosis requiere procesos armónicos a nivel espacio-temporal, que dependen de señales específicas, para reconocimiento, colonización e intercambio de nutrientes. Las plantas presentan respuestas de defensa frente a la posible invasión de microorganismos, sin embargo, en la simbiosis éstas son débiles, localizadas y no impiden la colonización del hongo. Estas señales se observan en todas las etapas de la simbiosis, siendo la primera señal enviada por la planta en exudados de la raíz, especialmente en condiciones de bajo fósforo. Posteriormente los HFMA activan la expresión de genes que favorecen cambios a nivel celular para la formación del apresorio, del aparato de pre-penetración y en células de la corteza, del arbúsculo y la membrana periarbuscular, para el intercambio de nutrientes. Un aspecto de interés está relacionado con los mecanismos de atenuación de las respuestas de defensa de la planta. Se han planteado diversas hipótesis para entender este fenómeno y aunque el control de la simbiosis está regulado principalmente por la planta, aún se desconoce si los HFMA generan señales que facilitan el debilitamiento de las respuestas de defensa del hospedero. Este documento está orientado a hacer una revisión de las señales de reconocimiento HFMA - plantas para cada fase de la simbiosis, así como de algunos mecanismos de regulación de las respuestas de defensa de la planta para el establecimiento de la simbiosis.  

Variations in the mycorrhization characteristics in roots of wild-type and ABA-deficient tomato are accompanied by specific transcriptomic alterations

Abscissic acid (ABA) determines mycorrhiza functionality and arbuscule development. In this study, we performed transcriptome analysis in response to different mycorrhization status according to the ABA content in the root to identify genes that may play a role in arbuscule functionality. Affymetrix Tomato GeneChip (approximately 10,000 probes) allowed us to detect and compare the transcriptional root profiling of tomato (Solanum lycopersicum) wild-type and ABA-deficient sitiens plants colonized by Glomus intraradices. A number of identified genes in tomato belong to a category of genes already described as "mycorrhizal core-set" in other host plants. The impairment in arbuscular mycorrhiza (AM) formation in ABA-deficient mutants was associated with upregulation of genes related to defense and cell wall modification, whereas functional mycorrhization in wild-type plants was associated with activation of genes related to isoprenoid metabolism. The oxylipin pathway was activated in tomato mycorrhizal roots at late stages of interaction, and was related to the control of fungal spread in roots, not with the establishment of the symbiosis. Induction of selected genes, representing a range of biological functions and representative of the three sets of genes specifically upregulated in the different plant phenotype, was confirmed by quantitative reverse-transcription polymerase chain reaction, and their response to phythohormone treatment was tested, showing that ethylene and jasmonic acid are key regulators of gene expression during AM development. Comparative analysis of mycorrhiza upregulated functional categories revealed significant changes in gene expression associated with the different mycorrhization status according to the ABA content in the roots.

Medicago truncatula Vapyrin is a novel protein required for arbuscular mycorrhizal symbiosis

Arbuscular mycorrhizal (AM) symbiosis is a widespread mutualism formed between vascular plants and fungi of the Glomeromycota. In this endosymbiosis, fungal hyphae enter the roots, growing through epidermal cells to the cortex where they establish differentiated hyphae called arbuscules in the cortical cells. Reprogramming of the plant epidermal and cortical cells occurs to enable intracellular growth of the fungal symbiont; however, the plant genes underlying this process are largely unknown. Here, through the use of RNAi, we demonstrate that the expression of a Medicago truncatula gene named Vapyrin is essential for arbuscule formation, and also for efficient epidermal penetration by AM fungi. Vapyrin is induced transiently in the epidermis coincident with hyphal penetration, and then in the cortex during arbuscule formation. The Vapyrin protein is cytoplasmic, and in cells containing AM fungal hyphae, the protein accumulates in small puncta that move through the cytoplasm. Vapyrin is a novel protein composed of two domains that mediate protein-protein interactions: an N-terminal VAMP-associated protein (VAP)/major sperm protein (MSP) domain and a C-terminal ankyrin-repeat domain. Putative Vapyrin orthologs exist widely in the plant kingdom, but not in Arabidopsis, or in non-plant species. The data suggest a role for Vapyrin in cellular remodeling to support the intracellular development of fungal hyphae during AM symbiosis.

Complete transcriptome of the soybean root hair cell, a single-cell model, and its alteration in response to Bradyrhizobium japonicum infection

Nodulation is the result of a mutualistic interaction between legumes and symbiotic soil bacteria (e.g. soybean [Glycine max] and Bradyrhizobium japonicum) initiated by the infection of plant root hair cells by the symbiont. Fewer than 20 plant genes involved in the nodulation process have been functionally characterized. Considering the complexity of the symbiosis, significantly more genes are likely involved. To identify genes involved in root hair cell infection, we performed a large-scale transcriptome analysis of B. japonicum-inoculated and mock-inoculated soybean root hairs using three different technologies: microarray hybridization, Illumina sequencing, and quantitative real-time reverse transcription-polymerase chain reaction. Together, a total of 1,973 soybean genes were differentially expressed with high significance during root hair infection, including orthologs of previously characterized root hair infection-related genes such as NFR5 and NIN. The regulation of 60 genes was confirmed by quantitative real-time reverse transcription-polymerase chain reaction. Our analysis also highlighted changes in the expression pattern of some homeologous and tandemly duplicated soybean genes, supporting their rapid specialization.

Membrane steroid-binding protein 1 induced by a diffusible fungal signal is critical for mycorrhization in Medicago truncatula

Arbuscular mycorrhiza (AM) is a mutualistic biotrophic association that requires a complex exchange of signals between plant and fungus to allow accommodation of the mycosymbiont in the root cortex. Signal exchange happens even before physical contact, activating the plant symbiotic program. We investigated very early transcriptional responses in Medicago truncatula to inoculation with Glomus intraradices and identified four genes induced by diffusible AM fungal signals before contact. Three of them were previously shown to be mycorrhiza induced at later stages of the symbiosis, while MtMSBP1, encoding a membrane-bound steroid-binding protein, is a novel mycorrhizal marker. Expression analyses in plants defective in the symbiotic receptor kinase DMI2 allowed discrimination of two different signaling cascades involved in the perception of the diffusible signals. Thus, while some of the genes are activated in a DMI2-dependent manner, the induction of one of them encoding a proteinase inhibitor is DMI2-independent. Downregulation of MtMSBP1 by RNAi led to an aberrant mycorrhizal phenotype with thick and septated appressoria, decrease number of arbuscules and distorted arbuscule morphology. This provides genetic evidence that MtMSBP1 is critical for mycorrhiza development. We hypothesize that MtMSBP1 plays a role in sterol homeostasis in the root.

Microarray analysis and functional tests suggest the involvement of expansins in the early stages of symbiosis of the arbuscular mycorrhizal fungus Glomus intraradices on tomato (Solanum lycopersicum)

Arbuscular mycorrhizal (AM) symbiosis occurs between fungi of the phylum Glomeromycota and most terrestrial plants. However, little is known about the molecular symbiotic signalling between AM fungi (AMFs) and non-leguminous plant species. We sought to further elucidate the molecular events occurring in tomato, a non-leguminous host plant, during the early, pre-symbiotic stage of AM symbiosis, i.e. immediately before and after contact between the AMF (Glomus intraradices) and the host. We adopted a semi-synchronized AMF root infection protocol, followed by genomic-scale, microarray-based, gene expression profiling at several defined time points during pre-symbiotic AM stages. The microarray results suggested differences in the number of differentially expressed genes and in the differential regulation of several functional groups of genes at the different time points examined. The microarray results were validated and one of the genes induced during contact between AMF and tomato, the expansin-like EXLB1, was functionally analysed. Expansins, encoded by a large multigene family, facilitate plant cell expansion. However, no biological or biochemical function has yet been established for plant-originated expansin-like proteins. EXLB1 transcripts were localized early during the association to cells that may perceive the fungal signal, and later during the association in close proximity to sites of AMF hypha-root colonization. Moreover, in transgenic roots, we demonstrated that a reduction in the steady-state level of EXLB1 transcript was correlated with a reduced rate of infection, reduced arbuscule expansion and reduced AMF spore formation.

RNA interference highlights the role of CCaMK in dissemination of endosymbionts in the Aeschynomeneae legume Arachis

In legume-rhizobia symbiosis, Ca2+/calmodulin-dependent protein kinase (CCaMK) is essential for rhizobial invasion through infection threads in the epidermis and nodule organogenesis in the cortex. Though CCaMK is actively transcribed in the infected zone of nodules, its role in the later stages of nodule development remain elusive because of the epidermal arrest of "loss-of-function" mutants. In Aeschynomeneae legumes such as Arachis hypogea, rhizobia directly access the cortex, where nodule organogenesis as well as endosymbiont dissemination take place by multiplication of infected cortical cells. We characterized CCaMK (GI:195542474) from A. hypogea and downregulated the kinase through RNA interference (RNAi) to understand its role during organogenesis of its characteristic aeschynomenoid nodules. In CCaMK downregulated plants, the inception of nodules was delayed by approximately 4 weeks and nodulation capacity was decreased (>90%). The infected zones of the RNA interference nodules were scattered with uninfected or binucleated cells as opposed to the homogeneous infection zone in empty-vector-transformed nodules. Symbiosomes in RNAi nodules were pleomorphic with diverse geometrical shapes or arrested during division in the final stages of their fission as opposed to uniform-sized, spherical symbiosomes in empty-vector-transformed nodules. Together, our results reveal CCaMK to be essential for development of functional aeschynomenoid nodules, with a critical role in rhizobial dissemination during nodule organogenesis.

Dissection of symbiosis and organ development by integrated transcriptome analysis of lotus japonicus mutant and wild-type plants

Genetic analyses of plant symbiotic mutants has led to the identification of key genes involved in Rhizobium-legume communication as well as in development and function of nitrogen fixing root nodules. However, the impact of these genes in coordinating the transcriptional programs of nodule development has only been studied in limited and isolated studies. Here, we present an integrated genome-wide analysis of transcriptome landscapes in Lotus japonicus wild-type and symbiotic mutant plants. Encompassing five different organs, five stages of the sequentially developed determinate Lotus root nodules, and eight mutants impaired at different stages of the symbiotic interaction, our data set integrates an unprecedented combination of organ- or tissue-specific profiles with mutant transcript profiles. In total, 38 different conditions sampled under the same well-defined growth regimes were included. This comprehensive analysis unravelled new and unexpected patterns of transcriptional regulation during symbiosis and organ development. Contrary to expectations, none of the previously characterized nodulins were among the 37 genes specifically expressed in nodules. Another surprise was the extensive transcriptional response in whole root compared to the susceptible root zone where the cellular response is most pronounced. A large number of transcripts predicted to encode transcriptional regulators, receptors and proteins involved in signal transduction, as well as many genes with unknown function, were found to be regulated during nodule organogenesis and rhizobial infection. Combining wild type and mutant profiles of these transcripts demonstrates the activation of a complex genetic program that delineates symbiotic nitrogen fixation. The complete data set was organized into an indexed expression directory that is accessible from a resource database, and here we present selected examples of biological questions that can be addressed with this comprehensive and powerful gene expression data set.

Nuclear membrane ion channels mediate root nodule development

Previous work has implicated two predicted ion channels in mediating perinuclear calcium spiking, which is essential for rhizobia-induced root nodule formation in legumes. A new study demonstrates that these ion channels are preferentially permeable to cations, such as potassium, and are located in the nuclear envelope. Here, we consider ways in which the ion channels influence perinuclear calcium spiking and discuss a potentially broader role for nuclear membrane ion channels in signal transduction in plants.

Apoplastic plant subtilases support arbuscular mycorrhiza development in Lotus japonicus

In the arbuscular mycorrhiza (AM) symbiosis, plant roots accommodate Glomeromycota fungi within an intracellular compartment, the arbuscule. At this symbiotic interface, fungal hyphae are surrounded by a plant membrane, which creates an apoplastic compartment, the periarbuscular space (PAS) between fungal and plant cell. Despite the importance of the PAS for symbiotic signal and metabolite exchange, only few of its components have been identified. Here we show that two apoplastic plant proteases of the subtilase family are required for AM development. SbtM1 is the founder member of a family of arbuscular mycorrhiza-induced subtilase genes that occur in at least two clusters in the genome of the legume Lotus japonicus. A detailed expression analysis by RT-PCR revealed that SbtM1, SbtM3, SbtM4 and the more distantly related SbtS are all rapidly induced during development of arbuscular mycorrhiza, but only SbtS and SbtM4 are also up-regulated during root nodule symbiosis. Promoter-reporter fusions indicated specific activation in cells that are adjacent to intra-radical fungal hyphae or in cells that harbour them. Venus fluorescent protein was observed in the apoplast and the PAS when expressed from a fusion construct with the SbtM1 signal peptide or the full-length subtilase. Suppression of SbtM1 or SbtM3 by RNAi caused a decrease in intra-radical hyphae and arbuscule colonization, but had no effect on nodule formation. Our data indicate a role for these subtilases during the fungal infection process in particular arbuscule development.

Developing microbe-plant interactions for applications in plant-growth promotion and disease control, production of useful compounds, remediation and carbon sequestration

Interactions between plants and microbes are an integral part of our terrestrial ecosystem. Microbe–plant interactions are being applied in many areas. In this review, we present recent reports of applications in the areas of plant‐growth promotion, biocontrol, bioactive compound and biomaterial production, remediation and carbon sequestration. Challenges, limitations and future outlook for each field are discussed.

Gibberellin controls the nodulation signaling pathway in Lotus japonicus

Root nodule formation is regulated by several plant hormones, but the details of the regulation of the nodulation signaling pathway are largely unknown. In this study, the role of gibberellin (GA) in the control of root nodule symbiosis was investigated at the physiological and genetic levels in Lotus japonicus. Exogenous application of biologically active GA, GA(3), inhibited the formation of infection threads and nodules, which was counteracted by the application of a biosynthesis inhibitor of GA, Uniconazole P. Nod factor-induced root hair deformation was severely blocked in the presence of GA, which was phenocopied by nsp2 mutants. The number of spontaneous nodules triggered by the gain-of-function mutation of calcium/calmodulin-dependent kinase (CCaMK) or the lotus histidine kinase 1 (LHK1) was decreased upon the addition of GA; moreover, the overexpression of the gain-of-function mutation of L. japonicus, SLEEPY1, a positive regulator of GA signaling, resulted in a reduced nodule number, without other aspects of root development being affected. These results indicate that higher GA signaling levels specifically inhibit the nodulation signaling pathway. Nod factor-dependent induction of NSP2 and NIN was inhibited by exogenous GA. Furthermore, the cytokinin-dependent induction of NIN was suppressed by GA. From these results, we conclude that GA inhibits the nodulation signaling pathway downstream of cytokinin, possibly at NSP2, which is required for Nod factor-dependent NIN expression. These results clarify the roles of GA in the nodulation signaling pathway, and in relation to the cytokinin signaling pathway for nodulation in L. japonicus.

Symbiosis-related plant genes modulate molecular responses in an arbuscular mycorrhizal fungus during early root interactions

To gain further insight into the role of the plant genome in arbuscular mycorrhiza (AM) establishment, we investigated whether symbiosis-related plant genes affect fungal gene expression in germinating spores and at the appressoria stage of root interactions. Glomus intraradices genes were identified in expressed sequence tag libraries of mycorrhizal Medicago truncatula roots by in silico expression analyses. Transcripts of a subset of genes, with predicted functions in transcription, protein synthesis, primary or secondary metabolism, or of unknown function, were monitored in spores and germinating spores and during interactions with roots of wild-type or mycorrhiza-defective (Myc-) mutants of M. truncatula. Not all the fungal genes were active in quiescent spores but all were expressed when G. intraradices spores germinated in wild-type M. truncatula root exudates or when appressoria or arbuscules were formed in association with wild-type M. truncatula roots. Most of the fungal genes were upregulated or induced at the stage of appressorium development. Inactivation of the M. truncatula genes DMI1, DMI2/MtSYM2, or DMI3/MtSYM13 was associated with altered fungal gene expression (nonactivation or inhibition), modified appressorium structure, and plant cell wall responses, providing first evidence that cell processes modified by symbiosis-related plant genes impact on root interactions by directly modulating AM fungal activity.

Reactions of Lotus japonicus ecotypes and mutants to root parasitic plants

Witchweeds (Striga spp.) and broomrapes (Orobanche spp.) are obligate root parasitic plants on economically important field and horticultural crops. The parasites' seeds are induced to germinate by root-derived chemical signals. The radicular end is transformed into a haustorium which attaches, penetrates the host root and establishes connection with the vascular system of the host. Reactions of Lotus japonicus, a model legume for functional genomics, were studied for furthering the understanding of host-parasite interactions. Lotus japonicus was compatible with Orobanche aegyptiaca, but not with Orobanche minor, Striga hermonthica and Striga gesnerioides. Orobanche minor successfully penetrated Lotus japonicus roots, but failed to establish connections with the vascular system. Haustoria in Striga hermonthica attached to the roots, but penetration and subsequent growth of the endophyte in the cortex were restricted. Striga gesnerioides did not parasitize Lotus japonicus. Among seven mutants of Lotus japonicus (castor-5, har1-5, alb1-1, ccamk-3, nup85-3, nfr1-3 and nsp2-1) with altered characteristics in relation to rhizobial nodulation and mycorrhizal colonization, castor-5 and har1-5 were parasitized by Orobanche aegyptiaca with higher frequency than the wild type. In contrast, Orobanche aegyptiaca tubercle development was delayed on the mutants nup85-3, nfr1-3 and nsp2-1. These results suggest that nodulation, mycorrhizal colonization and infection by root parasitic plants in Lotus japonicus may be modulated by similar mechanisms and that Lotus japonicus is a potential model legume for studying plant-plant parasitism.

Evolution of root endosymbiosis with bacteria: How novel are nodules?

Plants form diverse symbioses with nitrogen-fixing bacteria to gain access to ammonium, a product of the prokaryote-exclusive enzyme nitrogenase. Improving the symbiotic effectiveness of crop plants like maize, wheat or rice is a highly topical challenge and could help reduce the need for energy-intense nitrogen fertilizer in staple food production. Root nodule symbiosis (RNS) constitutes one of the most productive nitrogen-fixing systems, but it is restricted to a small group of related angiosperms. Here, we review the genetic regulation of RNS and its interconnections with other plant symbiosis or plant developmental programs. Since RNS uses genetic programs that are widely conserved in land plants, we evaluate the prospects for a transfer to plants that are currently non-nodulating.