Plant recognition of symbiotic bacteria requires two LysM receptor-like kinases

Use of nodulation pattern, stress tolerance, nodC gene amplification, RAPD-PCR and RFLP–16S rDNA analysis to discriminate genotypes of Rhizobium leguminosarum biovar viciae

Twenty-seven new Rhizobium isolates were obtained from root nodules of wild and crop legumes belonging to the genera Vicia, Lathyrus and Pisum from different agroecological areas in central and southern Italy. A polyphasic approach including phenotypic and genotypic techniques was used to study their diversity and their relationships with other biovars and species of rhizobia. Analysis of symbiotic properties and stress tolerance tests revealed that wild isolates showed a wide spectrum of nodulation and a marked variation in stress tolerance compared with reference strains tested in this study. All rhizobial isolates (except for the isolate CG4 from Galega officinalis) were presumptively identified as Rhizobium leguminosarum biovar viciae both by their symbiotic properties and the specific amplification of the nodC gene. In particular, we found that the nodC gene could be used as a diagnostic molecular marker for strains belonging to the bv. viciae. RFLP-PCR 16S rDNA analysis confirms these results, with the exception of two strains that showed different RFLP-genotypes from those of the reference strains of R. leguminosarum bv. viciae. Analysis of intraspecies relationship among strains by using the RAPD-PCR technique showed a high level of genetic polymorphism, grouping our isolates and reference strains into six different major clusters with a similarity level of 20%. Data from seven parameters of phenotypic and genotypic analyses were evaluated by using principal component analysis which indicated the differences among strains and allowed them to be divided into seven different groups.

Nod factor signaling genes and their function in the early stages of Rhizobium infection

A lipochitosaccharide-based signal molecule that is secreted by Rhizobium, named Nod factor (NF), induces root nodule formation in legumes. This molecule is also essential for the establishment of bacterial infection. Genetic analyses in the legume species Lotus japonicus and Medicago truncatula have led to the identification of many components of the NF signaling cascade. At least three of these genes do not function exclusively in the Rhizobium symbiosis but are also essential for the formation of mycorrhiza, an endosymbiosis found in many higher plant species. Recent studies have advanced our understanding of the functions of NF signaling genes in the Rhizobium infection process and the extent to which these genes are unique to legumes.

Expression of LjENOD40 genes in response to symbiotic and non-symbiotic signals: LjENOD40-1 and LjENOD40-2 are differentially regulated in Lotus japonicus

Nitrogen fixation in nodules provides leguminous plants with an ability to grow in nitrogen-starved soil. Infection of the host plants by microsymbionts triggers various physiological and morphological changes during nodule formation. In Lotus japonicus, expression of early nodulin (ENOD) genes is triggered by perception of bacterial signal molecules, nodulation factors (Nod factors). We examined the expression patterns of ENOD40 genes during the nodule formation process. Two ENOD40 genes of L. japonicus were specifically expressed in the nodule formation process, but they showed different expression patterns upon infection. Each ENOD40 gene demonstrates an individual specificity and regulation with regard to rhizobial infection.

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

A combined genetic and transcriptome analysis was performed to study the molecular basis of the arbuscular mycorrhiza (AM) symbiosis. By testing the AM phenotype of nodulation-impaired mutants and complementation analysis, we defined seven Lotus japonicus common symbiosis genes (SYMRK, CASTOR, POLLUX, SYM3, SYM6, SYM15, and SYM24) that are required for both fungal and bacterial entry into root epidermal or cortical cells. To describe the phenotype of these mutants at the molecular level, we screened for differentiating transcriptional responses of mutant and wild-type roots by large-scale gene expression profiling using cDNA-amplified fragment length polymorphism. Two percent of root transcripts was found to increase in abundance during AM development, from which a set of AM-regulated marker genes was established. A Ser-protease (SbtS) and a Cys-protease (CysS) were also activated during root nodule development. AM-induced transcriptional activation was abolished in roots carrying mutations in common symbiosis genes, suggesting a central position of these genes in a pathway leading to the transcriptional activation of downstream genes. By contrast, AM fungus-induced gene repression appeared to be unaffected in mutant backgrounds, which indicates the presence of additional independent signaling pathways.

Formation of organelle-like N2-fixing symbiosomes in legume root nodules is controlled by DMI2

In most legume nodules, the N2-fixing rhizobia are present as organelle-like structures inside their host cells. These structures, named symbiosomes, contain one or a few rhizobia surrounded by a plant membrane. Symbiosome formation requires the release of bacteria from cell-wall-bound infection threads. In primitive legumes, rhizobia are hosted in intracellular infection threads that, in contrast to symbiosomes, are bound by a cell wall. The formation of symbiosomes is presumed to represent a major step in the evolution of legume-nodule symbiosis, because symbiosomes facilitate the exchange of metabolites between the two symbionts. Here, we show that the genes, which are essential for initiating nodule formation, are also actively transcribed in mature Medicago truncatula nodules in the region where symbiosome formation occurs. At least one of these genes, encoding the receptor kinase DOES NOT MAKE INFECTIONS 2 (DMI2) is essential for symbiosome formation. The protein locates to the host cell plasma membrane and to the membrane surrounding the infection threads. A partial reduction of DMI2 expression causes a phenotype that resembles the infection structures found in primitive legume nodules, because infected cells are occupied by large intracellular infection threads instead of by organelle-like symbiosomes.

SrSymRK, a plant receptor essential for symbiosome formation

The symbiosis between legumes and rhizobia is essential for the nitrogen input into the life cycle on our planet. New root organs, the nodules, are established, which house N2-fixing bacteria internalized into the host cell cytoplasm as horizontally acquired organelles, the symbiosomes. The interaction is initiated by bacterial invasion via epidermal root hair curling and cell division in the cortex, both triggered by bacterial nodulation factors. Of the several genes involved in nodule initiation that have been identified, one encodes the leucine-rich repeat-type receptor kinase SymRK. In SymRK mutants of Lotus japonicus or its orthologs in Medicago sp. and Pisum sativum, nodule initiation is arrested at the level of the root hair interaction. Because of the epidermal block, the role of SymRK at later stages of nodule development remained enigmatic. To analyze the role of SymRK downstream of the epidermis, the water-tolerant legume Sesbania rostrata was used that has developed a nodulation strategy to circumvent root hair responses for bacterial invasion. Evidence is provided that SymRK plays an essential role during endosymbiotic uptake in plant cells.

Improved procedures for in vitro regeneration and for phenotypic analysis in the model legume Lotus japonicus

As a prerequisite for the development of an efficient gene transfer methodology, the possibility of inducing direct somatic embryogenesis in Lotus japonicus (Regel) K. Larsen explants was investigated. Petiole bases, cotyledons, hypocotyls and stem segments were cultivated in the presence of different amounts of benzylaminopurine (BAP) and / or thidiazuron (TDZ). Regeneration was achieved differentially in the different explants and a higher efficiency of shoot formation was obtained with TDZ. By maintaining the same TDZ regime a second cycle of morphogenesis was achieved and the histological analysis of these structures indicated unambiguously their somatic embryogenic nature. Thidiazuron was also tested as an agent to improve the kinetics of shoot formation in a Lotus japonicus transformation-regeneration procedure based on indirect organogenesis. A very significant, highly reproducible, increase in the rate of the shoot formation was observed in independent transformation experiments. We also present an extensive analysis of the feasibility and reproducibility of an in vitro procedure, which can be very useful for the screening of symbiotic phenotypes in transgenic Lotus plants and for the analysis of the cascade of molecular and cytological events occurring soon after Mesorhizobium loti infection.

RESISTANCE TO FUSARIUM OXYSPORUM 1, a dominant Arabidopsis disease-resistance gene, is not race specific

Arabidopsis thaliana ecotypes differ in their susceptibility to Fusarium wilt diseases. Ecotype Taynuilt-0 (Ty-0) is susceptible to Fusarium oxysporum forma specialis (f.) matthioli whereas Columbia-0 (Col-0) is resistant. Segregation analysis of a cross between Ty-0 and Col-0 revealed six dominant RESISTANCE TO FUSARIUM OXYSPORUM (RFO) loci that significantly contribute to f. matthioli resistance in Col-0 relative to Ty-0. We refer to the locus with the strongest effect as RFO1. Ty-0 plants in which only the Col-0 allele of RFO1 (RFO1(Col-0)) was introduced were resistant to f. matthioli. Surprisingly, RFO1(Col-0) also conferred resistance to f. raphani, demonstrating that RFO1-mediated resistance is not race specific. Expression of resistance by RFO2, RFO4, or RFO6 was dependent on RFO1(Col-0). Map-based cloning of RFO1(Col-0) showed that RFO1 is identical to the previously named Arabidopsis gene WAKL22 (WALL-ASSOCIATED KINASE-LIKE KINASE 22), which encodes a receptor-like kinase that does not contain an extracellular leucine-rich repeat domain. Consistent with these results, a Col-0 rfo1 loss-of-function mutant was more susceptible to f. matthioli, f. conglutinans, and f. raphani. Thus, RFO1 encodes a novel type of dominant disease-resistance protein that confers resistance to a broad spectrum of Fusarium races.

NSP1 of the GRAS Protein Family Is Essential for Rhizobial Nod Factor-Induced Transcription

Rhizobial Nod factors induce in their legume hosts the expression of many genes and set in motion developmental processes leading to root nodule formation. Here we report the identification of the Medicago GRAS-type protein Nodulation signaling pathway 1 (NSP1), which is essential for all known Nod factor-induced changes in gene expression. NSP1 is constitutively expressed, and so it acts as a primary transcriptional regulator mediating all known Nod factor-induced transcriptional responses, and therefore, we named it a Nod factor response factor.

A Novel Receptor Kinase Involved in Jasmonate-mediated Wound and Phytochrome Signaling in Maize Coleoptiles

We identified a gene of maize (Zea mays L.) that is transcriptionally activated in decapitated coleoptiles. The amino acid sequence deduced from its full-length cDNA indicated that the identified gene encodes a novel leucine-rich-repeat receptor-like kinase. The gene is named WOUND-RESPONSIVE AND PHYTOCHROME-REGULATED KINASE1 (WPK1) based on the findings of this study. Database searches revealed two and three homologs of WPK1 for Arabidopsis thaliana and rice, respectively. These homologs occurred along with WPK1 on a phylogenetic branch separated from all reported receptor kinases. We uncovered that the level of WPK1 transcripts is up-regulated rapidly and transiently in response to wounding and red light. The response to red light was reversible by far-red light, indicating that it is mediated by phytochrome. Applied jasmonic acid activated the expression of WPK1, while ethylene, salicylic acid and abscisic acid had no such effect. These results strongly suggested that WPK1 is a component of the jasmonate-mediated signaling that participates in both wound-induced defensive and phytochrome-mediated photomorphogenetic responses. Furthermore, it was found that both wounding and red light up-regulate the transcript level of ZmAOS, a gene for the jasmonate biosynthesis enzyme allene oxide synthase, and that auxin inhibits the expression of WPK1 but not of ZmAOS. We present a model of jasmonate-mediated signaling to explain the results obtained.

Molecular and cell biology of arbuscular mycorrhizal symbiosis

The roots of most extant plants are able to become engaged in an interaction with a small group of fungi of the fungal order Glomales (Glomeromycota). This interaction-arbuscular mycorrhizal (AM) symbiosis-is the evolutionary precursor of most other mutualistic root-microbe associations. The molecular analysis of this interaction can elucidate basic principles regarding such associations. This review summarizes our present knowledge about cellular and molecular aspects of AM. Emphasis is placed on morphological changes in colonized cells, transfer of nutrients between both interacting partners, and plant defence responses. Similarities to and differences from other associations of plant and microorganisms are highlighted regarding defence reactions and signal perception.

Analysis of promoter activity of the early nodulin Enod40 in Lotus japonicus

Our comparative studies on the promoter (pr) activity of Enod40 in the model legume Lotus japonicus in stably transformed GusA reporter lines and in hairy roots of L. japonicus demonstrate a stringent regulation of the Enod40 promoter in the root cortex and root hairs in response to Nod factors. Interestingly, the L. japonicus Enod40-2 promoter fragment also shows symbiotic activity in the reverse orientation. Deletion analyses of the Glycine max (Gm) Enod40 promoter revealed the presence of a minimal region -185 bp upstream of the transcription start. Stable transgenic L. japonicus reporter lines were used in bioassays to test the effect of different compounds on early symbiotic signaling. The responses of prGmEnod40 reporter lines were compared with the responses of L. japonicus (Lj) reporter lines based on the LjNin promoter. Both reporter lines show very early activity postinoculation in root hairs of the responsive zone of the root and later in the dividing cells of nodule primordia. The LjNin promoter was found to be more responsive than the GmEnod40 promoter to Nod factors and related compounds. The use of prGmEnod40 reporter lines to analyze the effect of nodulin genes on the GmEnod40 promoter activity indicates that LJNIN has a positive effect on the regulation of the Enod40 promoter, whereas the latter is not influenced by ectopic overexpression of its own gene product. In addition to pointing to a difference in the regulation of the two nodulin genes Enod40 and Nin during early time points of symbiosis, the bioassays revealed a difference in the response to the synthetic cytokinin 6-benzylaminopurine (BAP) between alfalfa and clover and L. japonicus. In alfalfa and clover, Enod40 expression was induced upon BAP treatment, whereas this seems not to be the case in L. japonicus; these results correlate with effects at the cellular level because BAP can induce pseudonodules in alfalfa and clover but not in L. japonicus. In conclusion, we demonstrate the applicability of the described L. japonicus reporter lines in analyses of the specificity of compounds related to nodulation as well as for the dissection of the interplay between different nodulin genes.

Evolution of NIN-like proteins in Arabidopsis, rice, and Lotus japonicus

Genetic studies in Lotus japonicus and pea have identified Nin as a core symbiotic gene required for establishing symbiosis between legumes and nitrogen fixing bacteria collectively called Rhizobium. Sequencing of additional Lotus cDNAs combined with analysis of genome sequences from Arabidopsis and rice reveals that Nin homologues in all three species constitute small gene families. In total, the Arabidopsis and rice genomes encode nine and three NIN-like proteins (NLPs), respectively. We present here a bioinformatics analysis and prediction of NLP evolution. On a genome scale we show that in Arabidopsis, this family has evolved through segmental duplication rather than through tandem amplification. Alignment of all predicted NLP protein sequences shows a composition with six conserved modules. In addition, Lotus and pea NLPs contain segments that might characterize NIN proteins of legumes and be of importance for their function in symbiosis. The most conserved region in NLPs, the RWP-RK domain, has secondary structure predictions consistent with DNA binding properties. This motif is shared by several other small proteins in both Arabidopsis and rice. In rice, the RWP-RK domain sequences have diversified significantly more than in Arabidopsis. Database searches reveal that, apart from its presence in Arabidopsis and rice, the motif is also found in the algae Chlamydomonas and in the slime mold Dictyostelium discoideum. Thus, the origin of this putative DNA binding region seems to predate the fungus-plant divide.

Characterization of the Lotus japonicus symbiotic mutant lot1 that shows a reduced nodule number and distorted trichomes

We isolated a recessive symbiotic mutant of Lotus japonicus that defines a genetic locus, LOT1 (for low nodulation and trichome distortion). The nodule number per plant of the mutant was about one-fifth of that of the wild type. The lot1 mutant showed a moderate dwarf phenotype and distorted trichomes, but its root hairs showed no apparent differences to those of the wild type. Infection thread formation after inoculation of Mesorhizobium loti was repressed in lot1 compared to that in the wild type. The nodule primordia of lot1 did not result in any aborted nodule-like structure, all nodules becoming mature and exhibiting high nitrogen fixation activity. The mutant was normally colonized by mycorrhizal fungi. lot1 also showed higher sensitivity to nitrate than the wild type. The grown-up seedlings of lot1 were insensitive to any ethylene treatments with regard to nodulation, although the mutant showed normal triple response on germination. It is conceivable that a nodulation-specific ethylene signaling pathway is constitutively activated in the mutant. Grafting experiments with lot1 and wild-type seedlings suggested that the root genotype mainly determines the low nodulation phenotype of the mutant, while the trichome distortion is regulated by the shoot genotype. Grafting of har1-4 shoots to lot1 roots resulted in an intermediate nodule number, i.e. more than that of lot1 and less than that of har1-4. Putative double mutants of lot1 and har1 also showed intermediate nodulation. Thus, it was indicated that LOT1 is involved in a distinct signal transduction pathway independent of HAR1.

Transgenic expression of the soybean apyrase in Lotus japonicus enhances nodulation

The soybean apyrase, GS52, was previously characterized as an early nodulin that is expressed in roots and localized to the plasma membrane. Transgenic Lotus japonicus plants were constructed constitutively expressing the GS52 apyrase. Segregation and Southern-blot analysis identified four single-copy sense lines, several double-copy sense lines, and one double-copy antisense line for further analysis. The single- and double-copy sense gs52 L. japonicus lines had enhanced nodulation that correlated with expression of the transgene. The sense transgenic lines were also found to have increased infection thread formation and enhanced infection zone length when infected by Mesorhizobium loti, the natural symbiont of L. japonicus. The data presented show that expression of the GS52 apyrase can enhance nodulation in L. japonicus and points to an important role for this group of enzymes in nodulation.

The evolution of Ca2+ signalling in photosynthetic eukaryotes

It is likely that cytosolic Ca2+ elevations have played a part in eukaryotic signal transduction for about the last 2 Gyr, being mediated by a group of molecules which are collectively known as the [Ca2+]cyt signalling toolkit. Different eukaryotes often display strikingly similar [Ca2+]cyt signalling elevations, which may reflect conservation of toolkit components (homology) or similar constraints acting on different toolkits (homoplasy). Certain toolkit components, which are presumably ancestral, are shared by plants and animals, but some components are unique to photosynthetic organisms. We propose that the structure of modern plant [Ca2+]cyt signalling toolkits may be explained by their modular adaptation from earlier pathways.

Invasion of Lotus japonicus root hairless 1 by Mesorhizobium loti involves the nodulation factor-dependent induction of root hairs

In many legumes, including Lotus japonicus and Medicago truncatula, susceptible root hairs are the primary sites for the initial signal perception and physical contact between the host plant and the compatible nitrogen-fixing bacteria that leads to the initiation of root invasion and nodule organogenesis. However, diverse mechanisms of nodulation have been described in a variety of legume species that do not rely on root hairs. To clarify the significance of root hairs during the L. japonicus-Mesorhizobium loti symbiosis, we have isolated and performed a detailed analysis of four independent L. japonicus root hair developmental mutants. We show that although important for the efficient colonization of roots, the presence of wild-type root hairs is not required for the initiation of nodule primordia (NP) organogenesis and the colonization of the nodule structures. In the genetic background of the L. japonicus root hairless 1 mutant, the nodulation factor-dependent formation of NP provides the structural basis for alternative modes of invasion by M. loti. Surprisingly, one mode of root colonization involves nodulation factor-dependent induction of NP-associated cortical root hairs and epidermal root hairs, which, in turn, support bacterial invasion. In addition, entry of M. loti through cracks at the cortical surface of the NP is described. These novel mechanisms of nodule colonization by M. loti explain the fully functional, albeit significantly delayed, nodulation phenotype of the L. japonicus ROOT HAIRLESS mutant.

Regulation of plant symbiosis receptor kinase through serine and threonine phosphorylation

We studied the biochemical properties of a plant receptor-like kinase to gain insights into the regulatory mechanism of this largest class of plant kinases. SYMRK (symbiosis receptor kinase) is required for early signal transduction leading to plant root symbioses with nitrogen-fixing rhizobia and phosphate-acquiring arbuscular mycorrhizal fungi. Amino acid substitutions in positions critical for activity of other related kinases cause a nonsymbiotic plant phenotype, suggesting that SYMRK kinase activity is required for symbiosis. SYMRK is capable of intermolecular autophosphorylation. Nonphosphorylated SYMRK is less active than the phosphorylated version, suggesting the phosphorylation status of SYMRK determines its activity. Three Ser/Thr residues were identified as residues required for full kinase activation through targeted mutagenesis. Using quadrupole time-of-flight mass spectrometry analysis, two of these were confirmed to be phosphorylated in vitro. These crucial phosphorylation sites are conserved among various plant receptor-like kinases as well as animal Pelle/interleukin-1 receptor associated kinase. Despite the distinct domain architecture of receptor-like kinases versus Pelle/interleukin-1 receptor associated kinase, our results suggest the existence of conserved activation mechanisms.

Root-knot nematodes and bacterial Nod factors elicit common signal transduction events in Lotus japonicus

The symbiosis responsible for nitrogen fixation in legume root nodules is initiated by rhizobial signaling molecules [Nod factors (NF)]. Using transgenically tagged microtubules and actin, we dynamically profiled the spatiotemporal changes in the cytoskeleton of living Lotus japonicus root hairs, which precede root-hair deformation and reflect one of the earliest host responses to NF. Remarkably, plant-parasitic root-knot nematodes (RKN) invoke a cytoskeletal response identical to that seen in response to NF and induce root-hair waviness and branching in legume root hairs via a signal able to function at a distance. Azide-killed nematodes do not produce this signal. A similar response to RKN was seen in tomato. Aspects of the host responses to RKN were altered or abolished by mutations in the NF receptor genes nfr1, nfr5, and symRK, suggesting that RKN produce a molecule with functional equivalence to NF, which we name NemF. Because the ability of RKN to establish feeding sites and reproduce was markedly reduced in the mutant lines, we propose that RKN have adapted at least part of the symbiont-response pathway to enhance their parasitic ability.

The relative orientation of the lipid and carbohydrate moieties of lipochitooligosaccharides related to nodulation factors depends on lipid chain saturation

Lipochitooligosaccharides (LCOs) signal the symbiosis of rhizobia with legumes and the formation of nitrogen-fixing root nodules. LCOs 1 and 2 share identical tetrasaccharide scaffolds but different lipid moieties (1, LCO-IV(C16:1[9Z], SNa) and , LCO-IV(C16:2[2E,9Z], SNa)). The conformational behaviors of both LCOs were studied by molecular modeling and NMR. Modeling predicts that a small lipid modification would result in a different relative orientation of the lipid and tetrasaccharide moieties. Diffusion ordered spectroscopy reports that both LCOs form small aggregates above 1 mM. Nuclear Overhauser spectroscopy (NOESY) data, collected under monomeric conditions, reveals lipid-carbohydrate contacts only for 1, in agreement with the modeling data. The distinct molecular structures of 1 and 2 have the potential to contribute to their selective binding by legume proteins.

Plastid proteins crucial for symbiotic fungal and bacterial entry into plant roots

The roots of most higher plants form arbuscular mycorrhiza, an ancient, phosphate-acquiring symbiosis with fungi, whereas only four related plant orders are able to engage in the evolutionary younger nitrogen-fixing root-nodule symbiosis with bacteria. Plant symbioses with bacteria and fungi require a set of common signal transduction components that redirect root cell development. Here we present two highly homologous genes from Lotus japonicus, CASTOR and POLLUX, that are indispensable for microbial admission into plant cells and act upstream of intracellular calcium spiking, one of the earliest plant responses to symbiotic stimulation. Surprisingly, both twin proteins are localized in the plastids of root cells, indicating a previously unrecognized role of this ancient endosymbiont in controlling intracellular symbioses that evolved more recently.

The evolution of chronic infection strategies in the alpha-proteobacteria

Many of the alpha-proteobacteria establish long-term, often chronic, interactions with higher eukaryotes. These interactions range from pericellular colonization through facultative intracellular multiplication to obligate intracellular lifestyles. A common feature in this wide range of interactions is modulation of host-cell proliferation, which sometimes leads to the formation of tumour-like structures in which the bacteria can grow. Comparative genome analyses reveal genome reduction by gene loss in the intracellular alpha-proteobacterial lineages, and genome expansion by gene duplication and horizontal gene transfer in the free-living species. In this review, we discuss alpha-proteobacterial genome evolution and highlight strategies and mechanisms used by these bacteria to infect and multiply in eukaryotic cells.

Disabling surveillance: bacterial type III secretion system effectors that suppress innate immunity

Many Gram-negative bacterial pathogens of plants and animals are dependent on a type III protein secretion system (TTSS). TTSSs translocate effector proteins into host cells and are capable of modifying signal transduction pathways. The innate immune system of eukaryotes detects the presence of pathogens using specific pathogen recognition receptors (PRRs). Plant PRRs include the FLS2 receptor kinase and resistance proteins. Animal PRRs include Toll-like receptors and nucleotide-binding oligomerization domain proteins. PRRs initiate signal transduction pathways that include mitogen-activated protein kinase (MAPK) cascades that activate defence-related transcription factors. This results in induction of proinflammatory cytokines in animals, and hallmarks of defence in plants including the hypersensitive response, callose deposition and the production of pathogenesis-related proteins. Several type III effectors from animal and plant pathogens have evolved to counteract innate immunity. For example, the Yersinia YopJ/P cysteine protease and the Pseudomonas syringae HopPtoD2 protein tyrosine phosphatase inhibits defence-related MAPK kinase activity in animals and plants respectively. Thus, type III effectors can suppress signal transduction pathways activated by PRR surveillance systems. Understanding targets and activities of type III effectors will reveal much about bacterial pathogenicity and the innate immune system in plants and animals.

Pharmacological evidence that multiple phospholipid signaling pathways link Rhizobium nodulation factor perception in Medicago truncatula root hairs to intracellular responses, including Ca2+ spiking and specific ENOD gene expression

Rhizobium nodulation (Nod) factors are specific lipochito-oligosaccharide signals essential for initiating in root hairs of the host legume developmental responses that are required for controlled entry of the microsymbiont. In this article, we focus on the Nod factor signal transduction pathway leading to specific and cell autonomous gene activation in Medicago truncatula cv Jemalong in a study making use of the Nod factor-inducible MtENOD11 gene. First, we show that pharmacological antagonists that interfere with intracellular ion channel and Ca2+ pump activities are efficient blockers of Nod factor-elicited pMtENOD11-beta-glucuronidase (GUS) expression in root hairs of transgenic M. truncatula. These results indicate that intracellular Ca2+ release and recycling activities, essential for Ca2+ spiking, are also required for specific gene activation. Second, pharmacological effectors that inhibit phospholipase D and phosphoinositide-dependent phospholipase C activities are also able to block pMtENOD11-GUS activation, thus underlining a central role for multiple phospholipid signaling pathways in Nod factor signal transduction. Finally, pMtENOD11-GUS was introduced into all three Nod-/Myc- dmi M. truncatula mutant backgrounds, and gene expression was evaluated in response to the mastoparan peptide agonist Mas7. We found that Mas7 elicits root hair MtENOD11 expression in dmi1 and dmi2 mutants, but not in the dmi3 mutant, suggesting that the agonist acts downstream of DMI1/DMI2 and upstream of DMI3. In light of these results and the recently discovered identities of the DMI gene products, we propose an integrated cellular model for Nod factor signaling in legume root hairs in which phospholipids play a key role in linking the Nod factor perception apparatus to downstream components such as Ca2+ spiking and ENOD gene expression.

cDNA macroarray analysis of gene expression in ineffective nodules induced on the Lotus japonicus sen1 mutant

The Lotus japonicus sen1 mutant forms ineffective nodules in which development is arrested at the stage of bacterial differentiation into nitrogen-fixing bacteroids. Here, we used cDNA macroarray systems to compare gene expression in ineffective nodules induced on the sen1 mutant with gene expression in wild-type nodules, in order to identify the host plant genes that are involved in nitrogen fixation. Macroarray analysis coupled with Northern blot analysis revealed that the expression of 18 genes was significantly enhanced in ineffective sen1 nodules, whereas the expression of 30 genes was repressed. Many of the enhanced genes encoded hydrolase enzymes, such as cysteine proteinase and asparaginase, that might function in the early senescence of sen1 nodules. By contrast, the repressed genes encoded nodulins, enzymes that are involved in carbon and nitrogen metabolism, membrane transporters, enzymes involved in phytohormone metabolism and secondary metabolism, and regulatory proteins. These proteins might have a role in the establishment of nitrogen fixation. In addition, we discovered two novel genes that encoded glutamate-rich proteins and were localized in the vascular bundles of the nodules. The expression of these genes was repressed in the ineffective nodules, which had lower levels of nitrogenase activity.

LIN, a Medicago truncatula gene required for nodule differentiation and persistence of rhizobial infections

Ethyl methanesulfonate mutagenesis of the model legume Medicago truncatula has previously identified several genes required for early steps in nodulation. Here, we describe a new mutant that is defective in intermediate steps of nodule differentiation. The lin (lumpy infections) mutant is characterized by a 4-fold reduction in the number of infections, all of which arrest in the root epidermis, and by nodule primordia that initiate normally but fail to mature. Genetic analyses indicate that the symbiotic phenotype is conferred by a single gene that maps to the lower arm of linkage group 1. Transcriptional markers for early Nod factor responses (RIP1 and ENOD40) are induced in lin, as is another early nodulin, ENOD20, a gene expressed during the differentiation of nodule primordia. By contrast, other markers correlated with primordium differentiation (CCS52A), infection progression (MtN6), or nodule morphogenesis (ENOD2 and ENOD8) show reduced or no induction in homozygous lin individuals. Taken together, these results suggest that LIN functions in maintenance of rhizobial infections and differentiation of nodules from nodule primordia.

Signaling between nematodes and plants

After hatching in the soil, root-knot nematodes must locate and penetrate a root, migrate into the vascular cylinder, and establish a permanent feeding site. Presumably, these events are accompanied by extensive signaling between the nematode parasite and the host. Hence, much emphasis has been placed on identifying proteins that are secreted by the nematode during the migratory phase. Further progress in understanding the signaling events has been made recently by studying the host response. Striking parallels can be drawn between the nematode-plant interaction and plant symbioses with other microorganisms, and evidence is emerging to suggest that nematodes acquired components of their parasitic armory from those microbes.

Genetic and genomic analysis in model legumes bring Nod-factor signaling to center stage

The control of host-specificity in the Rhizobium-legume symbiosis has been a topic of long-standing interest to plant biologists. By the early 1990s, biologists had deciphered the chemical signals that trigger early symbiotic responses. Flavonoids from the plant root trigger bacterial gene expression and the production of lipo-chitooligosaccharide signals (called Nod factors) that are recognized by the plant host. Genetic differences between bacterial strains modify the oligosaccharide backbone, for example by the addition of sulfate, acetate or fucose, and simultaneously alter the host-specificity of the purified Nod factor and the bacterium. Recent studies have begun to reveal the genetic and molecular basis of Nod-factor perception in legumes, a signaling system that also controls plant interactions with mycorrhizal fungi.

Molecular genetics of the arbuscular mycorrhizal symbiosis

During arbuscular mycorrhiza (AM) development, fungal hyphae grow throughout root epidermal, exodermal and cortical cell layers to reach the inner cortex where the symbiosis' functional units, the arbuscles, develop. Three essential components of a plant signalling network, a receptor-like kinase, a predicted ion-channel and a calmodulin-dependent protein kinase have been identified. A detailed morphological study of symbiotic plant mutants revealed that different subsets of plant genes support the progress of fungal infection in successive root cell layers. Moreover, evidence of a diffusible fungal signalling factor that triggers gene activation in the root has recently been obtained.

Structural characterization of extracellular polysaccharides of Azorhizobium caulinodans and importance for nodule initiation on Sesbania rostrata

During lateral root base nodulation, the microsymbiont Azorhizobium caulinodans enters its host plant, Sesbania rostrata, via the formation of outer cortical infection pockets, a process that is characterized by a massive production of H(2)O(2). Infection threads guide bacteria from infection pockets towards nodule primordia. Previously, two mutants were constructed that produce lipopolysaccharides (LPSs) similar to one another but different from the wild-type LPS, and that are affected in extracellular polysaccharide (EPS) production. Mutant ORS571-X15 was blocked at the infection pocket stage and unable to produce EPS. The other mutant, ORS571-oac2, was impaired in the release from infection threads and was surrounded by a thin layer of EPS in comparison to the wild-type strain that produced massive amounts of EPS. Structural characterization revealed that EPS purified from cultured and nodule bacteria was a linear homopolysaccharide of alpha-1,3-linked 4,6-O-(1-carboxyethylidene)-D-galactosyl residues. In situ H(2)O(2) localization demonstrated that increased EPS production during early stages of invasion prevented the incorporation of H(2)O(2) inside the bacteria, suggesting a role for EPS in protecting the microsymbiont against H(2)O(2). In addition, ex planta assays confirmed a positive correlation between increased EPS production and enhanced protection against H(2)O(2).

Infection and invasion of roots by symbiotic, nitrogen-fixing rhizobia during nodulation of temperate legumes

Bacteria belonging to the genera Rhizobium, Mesorhizobium, Sinorhizobium, Bradyrhizobium, and Azorhizobium (collectively referred to as rhizobia) grow in the soil as free-living organisms but can also live as nitrogen-fixing symbionts inside root nodule cells of legume plants. The interactions between several rhizobial species and their host plants have become models for this type of nitrogen-fixing symbiosis. Temperate legumes such as alfalfa, pea, and vetch form indeterminate nodules that arise from root inner and middle cortical cells and grow out from the root via a persistent meristem. During the formation of functional indeterminate nodules, symbiotic bacteria must gain access to the interior of the host root. To get from the outside to the inside, rhizobia grow and divide in tubules called infection threads, which are composite structures derived from the two symbiotic partners. This review focuses on symbiotic infection and invasion during the formation of indeterminate nodules. It summarizes root hair growth, how root hair growth is influenced by rhizobial signaling molecules, infection of root hairs, infection thread extension down root hairs, infection thread growth into root tissue, and the plant and bacterial contributions necessary for infection thread formation and growth. The review also summarizes recent advances concerning the growth dynamics of rhizobial populations in infection threads.

Expression islands clustered on the symbiosis island of the Mesorhizobium loti genome

Rhizobia are symbiotic nitrogen-fixing soil bacteria that are associated with host legumes. The establishment of rhizobial symbiosis requires signal exchanges between partners in microaerobic environments that result in mutualism for the two partners. We developed a macroarray for Mesorhizobium loti MAFF303099, a microsymbiont of the model legume Lotus japonicus, and monitored the transcriptional dynamics of the bacterium during symbiosis, microaerobiosis, and starvation. Global transcriptional profiling demonstrated that the clusters of genes within the symbiosis island (611 kb), a transmissible region distinct from other chromosomal regions, are collectively expressed during symbiosis, whereas genes outside the island are downregulated. This finding implies that the huge symbiosis island functions as clustered expression islands to support symbiotic nitrogen fixation. Interestingly, most transposase genes on the symbiosis island were highly upregulated in bacteroids, as were nif, fix, fdx, and rpoN. The genome region containing the fixNOPQ genes outside the symbiosis island was markedly upregulated as another expression island under both microaerobic and symbiotic conditions. The symbiosis profiling data suggested that there was activation of amino acid metabolism, as well as nif-fix gene expression. In contrast, genes for cell wall synthesis, cell division, DNA replication, and flagella were strongly repressed in differentiated bacteroids. A highly upregulated gene in bacteroids, mlr5932 (encoding 1-aminocyclopropane-1-carboxylate deaminase), was disrupted and was confirmed to be involved in nodulation enhancement, indicating that disruption of highly expressed genes is a useful strategy for exploring novel gene functions in symbiosis.

Comparative analysis of the receptor-like kinase family in Arabidopsis and rice

Receptor-like kinases (RLKs) belong to the large RLK/Pelle gene family, and it is known that the Arabidopsis thaliana genome contains >600 such members, which play important roles in plant growth, development, and defense responses. Surprisingly, we found that rice (Oryza sativa) has nearly twice as many RLK/Pelle members as Arabidopsis does, and it is not simply a consequence of a larger predicted gene number in rice. From the inferred phylogeny of all Arabidopsis and rice RLK/Pelle members, we estimated that the common ancestor of Arabidopsis and rice had >440 RLK/Pelles and that large-scale expansions of certain RLK/Pelle members and fusions of novel domains have occurred in both the Arabidopsis and rice lineages since their divergence. In addition, the extracellular domains have higher nonsynonymous substitution rates than the intracellular domains, consistent with the role of extracellular domains in sensing diverse signals. The lineage-specific expansions in Arabidopsis can be attributed to both tandem and large-scale duplications, whereas tandem duplication seems to be the major mechanism for recent expansions in rice. Interestingly, although the RLKs that are involved in development seem to have rarely been duplicated after the Arabidopsis-rice split, those that are involved in defense/disease resistance apparently have undergone many duplication events. These findings led us to hypothesize that most of the recent expansions of the RLK/Pelle family have involved defense/resistance-related genes.

Switch from intracellular to intercellular invasion during water stress-tolerant legume nodulation

Rhizobia colonize their legume hosts by different modes of entry while initiating symbiotic nitrogen fixation. Most legumes are invaded via growing root hairs by the root hair-curl mechanism, which involves epidermal cell responses. However, invasion of a number of tropical legumes happens through fissures at lateral root bases by cortical, intercellular crack entry. In the semiaquatic Sesbania rostrata, the bacteria entered via root hair curls under nonflooding conditions. Upon flooding, root hair growth was prevented, invasion on accessible root hairs was inhibited, and intercellular invasion was recruited. The plant hormone ethylene was involved in these processes. The occurrence of both invasion pathways on the same host plant enabled a comparison to be made of the structural requirements for the perception of nodulation factors, which were more stringent for the epidermal root hair invasion than for the cortical intercellular invasion at lateral root bases.

Radiolabeling of lipo-chitooligosaccharides using the NodH sulfotransferase: a two-step enzymatic procedure

Background

The NodH sulfotransferase from Sinorhizobium meliloti has been used to radiolabel lipochitooligosaccharidic (LCO) Nod factor signals with ³⁵S from inorganic sulfate in a two-step enzymatic procedure. The first step involved the production of 3'-phosphoadenosine 5'-phosphosulfate (PAPS), a sulphate donor, using enzymes contained in a yeast extract, and the second step used the NodH enzyme. However with this established procedure, only a low incorporation of the initial inorganic sulfate into the Nod factors was obtained (about 7% after purification of the labeled compounds). The aim of this work was to optimize the radiolabelling of Nod factors with ³⁵S.

Results

The limiting step has been shown to be the sulfation of ATP and its subsequent conversion into PAPS (first step), the sulfate donor for the NodH sulfotransferase activity (second step). By the addition of GTP to the reaction mixture and by manipulating the [ATP]/[Mg²⁺] ratio the yield of PAPS has been increased from 13% to 80%. Using the radiolabeled PAPS we have shown that the efficiency of sulfate transfer to LCOs, by the recombinant S. meliloti NodH sulfotransferase is strongly influenced by the length of the oligosaccharide chain. Variations in the substitutions on the non-reducing sugar, including the structure of the fatty acyl chain, had little effect and Nod factors from the heterologous bacterium Rhizobium tropici could be sulfated by NodH from S. meliloti.

Conclusions

By characterizing the two steps we have optimized the procedure to radiolabel biologically-important, lipo-chitooligosaccharide (LCO) Nod factors to a specific radioactivity of about 800 Ci.mmol^-1 with an incorporation of 60% of the initial inorganic sulfate. The two-step sulfation procedure may be used to radiolabel a variety of related LCO molecules.

A Ca2+/calmodulin-dependent protein kinase required for symbiotic nodule development: Gene identification by transcript-based cloning

In the establishment of the legume-rhizobial symbiosis, bacterial lipochitooligosaccharide signaling molecules termed Nod factors activate the formation of a novel root organ, the nodule. Nod factors elicit several responses in plant root hair cells, including oscillations in cytoplasmic calcium levels (termed calcium spiking) and alterations in root hair growth. A number of plant mutants with defects in the Nod factor signaling pathway have been identified. One such Medicago truncatula mutant, dmi3, exhibits calcium spiking and root hair swelling in response to Nod factor, but fails to initiate symbiotic gene expression or cell divisions for nodule formation. On the basis of these data, it is thought that the dmi3 mutant perceives Nod factor but fails to transduce the signal downstream of calcium spiking. Additionally, the dmi3 mutant is defective in the symbiosis with mycorrhizal fungi, indicating the importance of the encoded protein in multiple symbioses. We report the identification of the DMI3 gene, using a gene cloning method based on transcript abundance. We show that transcript-based cloning is a valid approach for cloning genes in barley, indicating the value of this technology in crop plants. DMI3 encodes a calcium/calmodulin-dependent protein kinase. Mutants in pea sym9 have phenotypes similar to dmi3 and have alterations in this gene. The DMI3 class of proteins is well conserved among plants that interact with mycorrhizal fungi, but it is less conserved in Arabidopsis thaliana, which does not participate in the mycorrhizal symbiosis.

Activation of a mitogen-activated protein kinase pathway in Arabidopsis by chitin

SUMMARY Chitin, a polysaccharide composed of beta-1-->4-linked N-acetyl-d-glucosamine, has been shown or implicated as a signal in plant defence and development. However, the key components of chitin perception and downstream signalling in non-leguminous plants are largely unknown. In recent years, mitogen-activated protein kinases (MAPKs) and their cascades were shown to transduce various extracellular stimuli into internal cellular responses. To investigate the possible involvement of MAPKs in chitin signalling in plants, the model plant Arabidopsis thaliana was treated with crab-shell chitin and also with the purified chitin oligomers (degree of polymerization, d.p. = 2-8). Both mRNA levels and kinase activity of two MAPK genes, AtMPK6 and AtMPK3, were monitored after treatment. The mRNA of AtMPK3 was strongly up-regulated by both chitin and its larger oligomers (d.p. = 6-8), but the mRNA of AtMPK6 did not appear to be regulated by these treatments. However, the kinase activity of both MAPKs was induced by chitin and the larger oligomers (d.p. = 6-8), with AtMPK6 much more strongly induced. In addition, WRKY22, WRKY29, WRKY33 and WRKY53, which encode four WRKY transcription factors that recognize TTGAC(C/T) W-box elements in promoters of numerous plant defence-related genes, were up-regulated by these treatments. WRKY33 and WRKY53 expression was induced by the transgenic expression of the tobacco MAPKK NtMEK2 active mutant NtMEK2(DD), suggesting a potential role for these WRKY transcription factors in relaying the signal generated from the MAPK cascade to downstream genes. These data suggest that AtMPK6/AtMPK3 and WRKY transcription factors (such as WRKY33 and WRKY53) may be important components of a pathway involved in chitin signalling in Arabidopsis plants.

A putative Ca2+ and calmodulin-dependent protein kinase required for bacterial and fungal symbioses

Legumes can enter into symbiotic relationships with both nitrogen-fixing bacteria (rhizobia) and mycorrhizal fungi. Nodulation by rhizobia results from a signal transduction pathway induced in legume roots by rhizobial Nod factors. DMI3, a Medicago truncatula gene that acts immediately downstream of calcium spiking in this signaling pathway and is required for both nodulation and mycorrhizal infection, has high sequence similarity to genes encoding calcium and calmodulin-dependent protein kinases (CCaMKs). This indicates that calcium spiking is likely an essential component of the signaling cascade leading to nodule development and mycorrhizal infection, and sheds light on the biological role of plant CCaMKs.

Medicago truncatula DMI1 required for bacterial and fungal symbioses in legumes

Legumes form symbiotic associations with both mycorrhizal fungi and nitrogen-fixing soil bacteria called rhizobia. Several of the plant genes required for transduction of rhizobial signals, the Nod factors, are also necessary for mycorrhizal symbiosis. Here, we describe the cloning and characterization of one such gene from the legume Medicago truncatula. The DMI1 (does not make infections) gene encodes a novel protein with low global similarity to a ligand-gated cation channel domain of archaea. The protein is highly conserved in angiosperms and ancestral to land plants. We suggest that DMI1 represents an ancient plant-specific innovation, potentially enabling mycorrhizal associations.

Receptor kinase signalling in plants

Recent plant genome analyses have revealed a large family of plant receptor kinases with very divergent extracellular domains. While a large proportion of this family remains uncharacterized, emerging functions for several plant receptor kinases reveal roles in a variety of biological processes including growth, development, hormone perception, and plant–microbe interactions. Significant progress has also been made in the understanding of four plant receptor kinase systems including their respective ligands and signalling pathways. Interestingly, a wide range of signalling proteins have been identified as functioning with these receptor kinases. In this review, an overview of plant receptor kinases, their biological functions, and their signalling pathways is presented.Key words: plants, Arabidopsis, receptor kinase, signal transduction.