Medicago truncatula plants overexpressing the early nodulin gene enod40 exhibit accelerated mycorrhizal colonization and enhanced formation of arbuscules

From environmental responses to adaptation: the roles of plant lncRNAs

As sessile organisms, plants are continuously exposed to heterogeneous and changing environments and constantly need to adapt their growth strategies. They have evolved complex mechanisms to recognize various stress factors, activate appropriate signaling pathways, and respond accordingly by reprogramming the expression of multiple genes at the transcriptional, post-transcriptional, and even epigenome levels to tolerate stressful conditions such as drought, high temperature, nutrient deficiency, and pathogenic interactions. Apart from protein-coding genes, long non-coding RNAs (lncRNAs) have emerged as key players in plant adaptation to environmental stresses. They are transcripts larger than 200 nucleotides without protein-coding potential. Still, they appear to regulate a wide range of processes, including epigenetic modifications and chromatin reorganization, as well as transcriptional and post-transcriptional modulation of gene expression, allowing plant adaptation to various environmental stresses. LncRNAs can positively or negatively modulate stress responses, affecting processes such as hormone signaling, temperature tolerance, and nutrient deficiency adaptation. Moreover, they also seem to play a role in stress memory, wherein prior exposure to mild stress enhances plant ability to adapt to subsequent stressful conditions. In this review, we summarize the contribution of lncRNAs in plant adaptation to biotic and abiotic stresses, as well as stress memory. The complex evolutionary conservation of lncRNAs is also discussed and provides insights into future research directions in this field.

Biological Activity of Artificial Plant Peptides Corresponding to the Translational Products of Small ORFs in Primary miRNAs and Other Long "Non-Coding" RNAs

Generally, lncPEPs (peptides encoded by long non-coding RNAs) have been identified in many plant species of several families and in some animal species. Importantly, molecular mechanisms of the miPEPs (peptides encoded by primary microRNAs, pri-miRNAs) are often poorly understood in different flowering plants. Requirement for the additional studies in these directions is highlighted by alternative findings concerning positive regulation of pri-miRNA/miRNA expression by synthetic miPEPs in plants. Further extensive studies are also needed to understand the full set of their roles in eukaryotic organisms. This review mainly aims to consider the available data on the regulatory functions of the synthetic miPEPs. Studies of chemically synthesized miPEPs and analyzing the fine molecular mechanisms of their functional activities are reviewed. Brief description of the studies to identify lncORFs (open reading frames of long non-coding RNAs) and the encoded protein products is also provided.

Conserved structured domains in plant non-coding RNA enod40, their evolution and recruitment of sequences from transposable elements

Plant long noncoding RNA enod40 is involved in the regulation of symbiotic associations with bacteria, in particular, in nitrogen-fixing root nodules of legumes, and with fungi in phosphate-acquiring arbuscular mycorrhizae formed by various plants. The presence of enod40 genes in plants that do not form such symbioses indicates its other roles in cell physiology. The molecular mechanisms of enod40 RNA function are poorly understood. Enod40 RNAs form several structured domains, conserved to different extents. Due to relatively low sequence similarity, identification of enod40 sequences in plant genomes is not straightforward, and many enod40 genes remain unannotated even in complete genomes. Here, we used comparative structure analysis and sequence similarity searches in order to locate enod40 genes and determine enod40 RNA structures in nitrogen-fixing clade plants and in grasses. The structures combine conserved features with considerable diversity of structural elements, including insertions of structured domain modules originating from transposable elements. Remarkably, these insertions contain sequences similar to tandem repeats and several stem-loops are homologous to microRNA precursors.

Detection of type III effector-induced transcription factors that regulate phytohormone content during symbiosis establishment in soybean

Soybean is a pivotal protein and oil crop that utilizes atmospheric nitrogen via symbiosis with rhizobium soil bacteria. Rhizobial type III effectors (T3Es) are essential regulators during symbiosis establishment. However, how the transcription factors involved in the interaction between phytohormone synthesis and type III effectors are connected is unclear. To detect the responses of phytohormone and transcription factor genes to rhizobial type III effector NopAA and type III secretion system, the candidate genes underlying soybean symbiosis were identified using RNA sequencing (RNA-seq) and phytohormone content analysis of soybean roots infected with wild-type Rhizobium and its derived T3E mutant. Via RNA-seq analysis the WRKY and ERF transcription factor families were identified as the most differentially expressed factors in the T3E mutant compared with the wild-type. Next, qRT-PCR was used to confirm the candidate genes Glyma.09g282900, Glyma.08g018300, Glyma.18g238200, Glyma.03g116300, Glyma.07g246600, Glyma.16g172400 induced by S. fredii HH103, S. fredii HH103ΩNopAA, and S. fredii HH103ΩRhcN. Since the WRKY and ERF families may regulate abscisic acid (ABA) content and underlying nodule formation, we performed phytohormone content analysis at 0.5 and 24 h post-inoculation (hpi). A significant change in ABA content was found between wild Rhizobium and type III effector mutant. Our results support that NopAA can promote the establishment of symbiosis by affecting the ABA signaling pathways by regulating WRKY and ERF which regulate the phytohormone signaling pathway. Specifically, our work provides insights into a signaling interaction of prokaryotic effector-induced phytohormone response involved in host signaling that regulates the establishment of symbiosis and increases nitrogen utilization efficiency in soybean plants.

Genome-wide analyses of the Nodulin-like gene family in bread wheat revealed its potential roles during arbuscular mycorrhizal symbiosis

Nodulin-like (NL) genes are involved in transporting of various substances and may play key roles during the establishment of symbiosis in legumes plants. However, basic biological information of NL genes in the wheat genome is still largely unknown. Here, we identified and characterized NL genes in wheat via integrating genomic information, collinearity analysis, co-expression network analysis (WGCNA) and transcriptome analysis. In addition, we analyzed the polymorphisms and the roles of NL genes during arbuscular mycorrhizal (AM) symbiosis using a large wheat panel consists of 259 wheat genotypes. We identified 181 NL genes in the wheat genome, which were classified into SWEET, Early Nodulin-Like (ENODL), Major Facilitator Superfamily-Nodulin (MFS), Vacuolar Iron Transporter (VIT) and Early nodulin 93 (ENOD93) subfamily. The expansion of NL genes was mainly driven by segmental duplication. The bHLH genes are potential unrecognized transcription factors regulating NL genes. Moreover, two NL genes were more sensitive than other NL genes to AM colonization. The polymorphisms of NL genes are mainly due to random drift, and the natural mutation of NL genes led to significant differences in the mycorrhizal dependence of wheat in phosphorus uptake. The results concluded that NL genes potentially play important roles during AM symbiosis with wheat.

Appressoria and phosphorus fluxes in mycorrhizal plants: connections between soil- and plant-based hyphae

Arbuscular mycorrhizal fungi (AMF) live in symbiosis with plant roots, facilitating mineral nutrient transfer from soil to hosts through large networks of extraradical hyphae. Limited data are available on the fungal structures (appressoria) connecting soil- to root-based mycelium, in relation to plant nutrition. Two in vivo systems were set up using three AMF, Funneliformis mosseae, Funneliformis coronatus and Rhizoglomus irregulare, grown in symbiosis with Cichorium intybus. The assessment of plant P content, number of appressoria, diameter of their subtending hyphae and length of colonized roots allowed calculation of the total cross-section area of appressorium-subtending hyphae, which differed among the three AMF and was correlated with plant P contents and with extraradical mycelium density. A conservative evaluation of P fluxes from soil- to plant-based hyphae occurring through appressoria gave values ranging from 1.7 to 4.2 × 10^-8 mol cm^-2 s^-1 (moles per total cross-section area of the appressorium subtending hyphae per time elapsed), depending on AMF identity. This work suggests that, beyond intraradical colonization and extraradical mycelium extent, connections between extraradical and intraradical fungal mycelium through appressoria are important for mycorrhizal plant nutrition, as appressorium structural traits and density can be related to P transfer mediated by AMF.

Arbuscular Mycorrhizal Fungi and Associated Microbiota as Plant Biostimulants: Research Strategies for the Selection of the Best Performing Inocula

Arbuscular mycorrhizal fungi (AMF) are beneficial soil microorganisms establishing mutualistic symbioses with the roots of the most important food crops and playing key roles in the maintenance of long-term soil fertility and health. The great inter- and intra-specific AMF diversity can be fully exploited by selecting AMF inocula on the basis of their colonization ability and efficiency, which are affected by fungal and plant genotypes and diverse environmental variables. The multiple services provided by AMF are the result of the synergistic activities of the bacterial communities living in the mycorrhizosphere, encompassing nitrogen fixation, P solubilization, and the production of phytohormones, siderophores, and antibiotics. The tripartite association among host plants, mycorrhizal symbionts, and associated bacteria show beneficial emerging properties which could be efficiently exploited in sustainable agriculture. Further in-depth studies, both in microcosms and in the field, performed on different AMF species and isolates, should evaluate their colonization ability, efficiency, and resilience. Transcriptomic studies can reveal the expression levels of nutrient transporter genes in fungal absorbing hyphae in the presence of selected bacterial strains. Eventually, newly designed multifunctional microbial consortia can be utilized as biofertilizers and biostimulants in sustainable and innovative production systems.

Phytohormone regulation of legume-rhizobia interactions

The symbiosis between legumes and nitrogen fixing bacteria called rhizobia leads to the formation of root nodules. Nodules are highly organized root organs that form in response to Nod factors produced by rhizobia, and they provide rhizobia with a specialized niche to optimize nutrient exchange and nitrogen fixation. Nodule development and invasion by rhizobia is locally controlled by feedback between rhizobia and the plant host. In addition, the total number of nodules on a root system is controlled by a systemic mechanism termed 'autoregulation of nodulation'. Both the local and the systemic control of nodulation are regulated by phytohormones. There are two mechanisms by which phytohormone signalling is altered during nodulation: through direct synthesis by rhizobia and through indirect manipulation of the phytohormone balance in the plant, triggered by bacterial Nod factors. Recent genetic and physiological evidence points to a crucial role of Nod factor-induced changes in the host phytohormone balance as a prerequisite for successful nodule formation. Phytohormones synthesized by rhizobia enhance symbiosis effectiveness but do not appear to be necessary for nodule formation. This review provides an overview of recent advances in our understanding of the roles and interactions of phytohormones and signalling peptides in the regulation of nodule infection, initiation, positioning, development, and autoregulation. Future challenges remain to unify hormone-related findings across different legumes and to test whether hormone perception, response, or transport differences among different legumes could explain the variety of nodules types and the predisposition for nodule formation in this plant family. In addition, the molecular studies carried out under controlled conditions will need to be extended into the field to test whether and how phytohormone contributions by host and rhizobial partners affect the long term fitness of the host and the survival and competition of rhizobia in the soil. It also will be interesting to explore the interaction of hormonal signalling pathways between rhizobia and plant pathogens.

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.

Impact of endochitinase-transformed white spruce on soil fungal biomass and ectendomycorrhizal symbiosis

The impact of transgenic white spruce [Picea glauca (Moench) Voss] containing the endochitinase gene (ech42) on soil fungal biomass and on the ectendomycorrhizal fungi Wilcoxina spp. was tested using a greenhouse trial. The measured level of endochitinase in roots of transgenic white spruce was up to 10 times higher than that in roots of nontransformed white spruce. The level of endochitinase in root exudates of three of four ech42-transformed lines was significantly greater than that in controls. Analysis soil ergosterol showed that the amount of fungal biomass in soil samples from control white spruce was slightly larger than that in soil samples from ech42-transformed white spruce. Nevertheless, the difference was not statistically significant. The rates of mycorrhizal colonization of transformed lines and controls were similar. Sequencing the internal transcribed spacer rRNA region revealed that the root tips were colonized by the ectendomycorrhizal fungi Wilcoxina spp. and the dark septate endophyte Phialocephala fortinii. Colonization of root tips by Wilcoxina spp. was monitored by real-time PCR to quantify the fungus present during the development of ectendomycorrhizal symbiosis in ech42-transformed and control lines. The numbers of Wilcoxina molecules in the transformed lines and the controls were not significantly different (P > 0.05, as determined by analysis of covariance), indicating that in spite of higher levels of endochitinase expression, mycorrhization was not inhibited. Our results indicate that the higher levels of chitinolytic activity in root exudates and root tissues from ech42-transformed lines did not alter the soil fungal biomass or the development of ectendomycorrhizal symbiosis involving Wilcoxina spp.

Cereal mycorrhiza: an ancient symbiosis in modern agriculture

The majority of terrestrial plants live in association with symbiotic fungi that facilitate mineral nutrient uptake. The oldest and most prevalent of these associations are the arbuscular mycorrhizal (AM) symbioses that first evolved approximately 400 million years ago, coinciding with the appearance of the first land plants. Crop domestication, in comparison, is a relatively recent event, beginning approximately 10000 years ago. How has the dramatic change from wild to cultivated ecosystems impacted AM associations, and do these ancient symbioses potentially have a role in modern agriculture? Here, we review recent advances in AM research and the use of breeding approaches to generate new crop varieties that enhance the agronomic potential of AM associations.

Cooperation of plants and microorganisms: getting closer to the genetic construction of sustainable agro-systems

The molecular research into two types of beneficial plant-microbe symbioses is reviewed: nutritional (with N(2)-fixing bacteria or mycorrhizal fungi) and defensive (with endo- and epiphytic microbes suppressing pathogens and phytophagans). These symbioses are based on the signaling interactions that result in the development of novel tissue/cellular structures and of extended metabolic capacities in the partners, which greatly improve the adaptive potential of plants due to a decrease in their sensitivity to biotic and abiotic stresses. The molecular, genetic and ecological knowledge on plant-microbe interactions provides a strategy for the organization of sustainable crop production based on substituting the agrochemicals (mineral fertilizers, pesticides) by microbial inoculants. An improvement of plant-microbe symbioses should involve the coordinated modifications in the partners' genotypes resulting in highly complementary combinations. These modifications should be based on the broad utilization of genetic resources from natural symbiotic systems aimed at: (i) increased competitiveness of the introduced (effective) with respect to local (ineffective) microbial strains, and (ii) overcoming the limiting steps in the metabolic machineries of the symbiotic systems.

Identification of conserved secondary structures and expansion segments in enod40 RNAs reveals new enod40 homologues in plants

enod40 is a plant gene that participates in the regulation of symbiotic interaction between leguminous plants and bacteria or fungi. Furthermore, it has been suggested to play a general role in non-symbiotic plant development. Although enod40 seems to have multiple functions, being present in many land plants, the molecular mechanisms of its activity are unclear; they may be determined though, by short peptides and/or RNA structures encoded in the enod40 genes. We utilized conserved RNA structures in enod40 sequences to search nucleotide sequence databases and identified a number of new enod40 homologues in plant species that belong to known, but also, to yet unknown enod40-containing plant families. RNA secondary structure predictions and comparative sequence analysis of enod40 RNAs allowed us to determine the most conserved structural features, present in all known enod40 genes. Remarkably, the topology and evolution of one of the conserved structural domains are similar to those of the expansion segments found in structural RNAs such as rRNAs, RNase P and SRP RNAs. Surprisingly, the enod40 RNA structural elements are much more stronger conserved than the encoded peptides. This finding suggests that some general functions of enod40 gene could be determined by the encoded RNA structure, whereas short peptides may be responsible for more diverse functions found only in certain plant families.

Signaling in the arbuscular mycorrhizal symbiosis

Many microorganisms form symbioses with plants that range, on a continuous scale, from parasitic to mutualistic. Among these, the most widespread mutualistic symbiosis is the arbuscular mycorrhiza, formed between arbuscular mycorrhizal (AM) fungi and vascular flowering plants. These associations occur in terrestrial ecosystems throughout the world and have a global impact on plant phosphorus nutrition. The arbuscular mycorrhiza is an endosymbiosis in which the fungus inhabits the root cortical cells and obtains carbon provided by the plant while it transfers mineral nutrients from the soil to the cortical cells. Development of the symbiosis involves the differentiation of both symbionts to create novel symbiotic interfaces within the root cells. The aim of this review is to explore the current understanding of the signals and signaling pathways used by the symbionts for the development of the AM symbiosis. Although the signal molecules used for initial communication are not yet known, recent studies point to their existence. Within the plant, there is evidence of arbuscular mycorrhiza-specific signals and of systemic signaling that influences phosphate-starvation responses and root development. The landmark cloning of three plant signaling proteins required for the development of the symbiosis has provided the first insights into a signaling pathway that is used by AM fungi and by rhizobia for their symbiotic associations with legumes.

Arbuscular mycorrhizal fungi colonize nonfixing root nodules of several legume species

Many legumes form tripartite symbiotic associations with rhizobia and arbuscular mycorrhizal fungi (AMF). Rhizobia are located in root nodules and provide the plant with fixed atmospheric nitrogen, while AMF colonize plant roots and deliver several essential nutrients to the plant. Recent studies showed that AMF are also associated with root nodules. This might point to interactions between AMF and rhizobia inside root nodules. Here, we test whether AMF colonize root nodules in various plant-AMF combinations. We also test whether nodules that are colonized by AMF fix nitrogen. Using microscopy, we observed that AMF colonized the root nodules of three different legume species. The AMF colonization of the nodules ranged from 5% to 74% and depended on plant species, AMF identity and nutrient availability. However, AMF-colonized nodules were not active, that is, they did not fix nitrogen. The results suggest that AMF colonize old senescent nodules after nitrogen fixation has stopped, although it is also possible that AMF colonization of nodules inhibits nitrogen fixation.

Suppression of allene oxide cyclase in hairy roots of Medicago truncatula reduces jasmonate levels and the degree of mycorrhization with Glomus intraradices

During the symbiotic interaction between Medicago truncatula and the arbuscular mycorrhizal (AM) fungus Glomus intraradices, an endogenous increase in jasmonic acid (JA) occurs. Two full-length cDNAs coding for the JA-biosynthetic enzyme allene oxide cyclase (AOC) from M. truncatula, designated as MtAOC1 and MtAOC2, were cloned and characterized. The AOC protein was localized in plastids and found to occur constitutively in all vascular tissues of M. truncatula. In leaves and roots, MtAOCs are expressed upon JA application. Enhanced expression was also observed during mycorrhization with G. intraradices. A partial suppression of MtAOC expression was achieved in roots following transformation with Agrobacterium rhizogenes harboring the MtAOC1 cDNA in the antisense direction under control of the cauliflower mosaic virus 35S promoter. In comparison to samples transformed with 35SuidA, roots with suppressed MtAOC1 expression exhibited lower JA levels and a remarkable delay in the process of colonization with G. intraradices. Both the mycorrhization rate, quantified by fungal rRNA, and the arbuscule formation, analyzed by the expression level of the AM-specific gene MtPT4, were affected. Staining of fungal material in roots with suppressed MtAOC1 revealed a decreased number of arbuscules, but these did not exhibit an altered structure. Our results indicate a crucial role for JA in the establishment of AM symbiosis.

Ectopic expression of the mycorrhiza-specific chitinase gene Mtchit 3-3 in Medicago truncatula root-organ cultures stimulates spore germination of glomalean fungi

Expression of Mtchit 3-3, a class III chitinase gene, is specifically induced by arbuscular mycorrhizal (AM) fungi in roots of the model legume Medicago truncatula and its transcripts accumulate in cells containing arbuscules. Agrobacterium rhizogenes-transformed roots and root-organ cultures of M. truncatula were used to study effects of Mtchit 3-3 on AM fungi. * This work provides evidence for enzymatic activity of the Mtchit 3-3 gene product and shows with promoter:gus fusions that a 2 kb fragment located 5' upstream from the translational start codon of Mtchit 3-3 is sufficient to confer arbuscule-dependent gene expression. By fusing the Mtchit 3-3 coding region to the CaMV 35S promoter the expression pattern was disrupted. Surprisingly, disruption stimulated spore germination of Glomus intraradices and Glomus constrictum, and in the case of G. intraradices resulted in a higher probability of root colonization and spore formation. However, no effect on the abundance of arbuscules within colonized roots became apparent. These observations demonstrate that disruption of the tight arbuscule-dependent expression pattern of Mtchit 3-3 has effects on the early interaction between roots and AM fungi.

Nonlegumes, legumes, and root nodules harbor different arbuscular mycorrhizal fungal communities

Legumes are an important plant functional group since they can form a tripartite symbiosis with nitrogen-fixing Rhizobium bacteria and phosphorus-acquiring arbuscular mycorrhizal fungi (AMF). However, not much is known about AMF community composition in legumes and their root nodules. In this study, we analyzed the AMF community composition in the roots of three nonlegumes and in the roots and root nodules of three legumes growing in a natural dune grassland. We amplified a portion of the small-subunit ribosomal DNA and analyzed it by using restriction fragment length polymorphism and direct sequencing. We found differences in AMF communities between legumes and nonlegumes and between legume roots and root nodules. Different plant species also contained different AMF communities, with different AMF diversity. One AMF sequence type was much more abundant in legumes than in nonlegumes (39 and 13%, respectively). Root nodules contained characteristic AMF communities that were different from those in legume roots, even though the communities were similar in nodules from different legume species. One AMF sequence type was found almost exclusively in root nodules. Legumes and root nodules have relatively high nitrogen concentrations and high phosphorus demands. Accordingly, the presence of legume- and nodule-related AMF can be explained by the specific nutritional requirements of legumes or by host-specific interactions among legumes, root nodules, and AMF. In summary, we found that AMF communities vary between plant functional groups (legumes and nonlegumes), between plant species, and between parts of a root system (roots and root nodules).

Regulatory mechanisms during the plant – arbuscular mycorrhizal fungus interaction

Abundant data are available on some aspects of the arbuscular mycorrhizal symbiosis, for example, plant nutrition, but because of difficulties immanent to arbuscular mycorrhizal fungi, such as the inability to culture them axenically, the relatively long time it takes to achieve root colonization, and the simultaneous presence of different morphologic stages of the fungus in the root, less information is accumulated on other aspects such as the regulation of mycorrhization. Regulatory processes in the plant – arbuscular mycorrhizal fungus interaction start before root colonization by the fungus and even before a direct physical contact between the host and the fungal symbiont. Some of the signals exchanged are still a matter of debate and will be discussed further on. After the penetration of the root by the fungus, depending on the developmental stage of the arbuscular mycorrhizal association (e.g., early or mature), a range of plant responses is activated. The possible function of several plant responses in the regulation of mycorrhization is discussed.Key words: arbuscular mycorrhiza, Glomales, autoregulation, flavonoid, recognition, root exudates.

Sinorhizobium meliloti-induced chitinase gene expression in Medicago truncatula ecotype R108-1: a comparison between symbiosis-specific class V and defence-related class IV chitinases

The Medicago truncatula (Gaertn.) ecotypes Jemalong A17 and R108-1 differ in Sinorhizobium meliloti-induced chitinase gene expression. The pathogen-inducible class IV chitinase gene, Mtchit 4, was strongly induced during nodule formation of the ecotype Jemalong A17 with the S. meliloti wild-type strain 1021. In the ecotype R108-1, the S. meliloti wild types Sm1021 and Sm41 did not induce Mtchit 4 expression. On the other hand, expression of the putative class V chitinase gene, Mtchit 5, was found in roots of M. truncatula cv. R108-1 nodulated with either of the rhizobial strains. Mtchit 5 expression was specific for interactions with rhizobia. It was not induced in response to fungal pathogen attack, and not induced in roots colonized with arbuscular mycorrhizal (AM) fungi. Elevated Mtchit 5 gene expression was first detectable in roots forming nodule primordia. In contrast to Mtchit 4, expression of Mtchit 5 was stimulated by purified Nod factors. Conversely, Mtchit 4 expression was strongly elevated in nodules formed with the K-antigen-deficient mutant PP699. Expression levels of Mtchit 5 were similarly increased in nodules formed with PP699 and its parental wild-type strain Sm41. Phylogenetic analysis of the deduced amino acid sequences of Mtchit 5 (calculated molecular weight = 41,810 Da, isoelectric point pH 7.7) and Mtchit 4 (calculated molecular weight 30,527 Da, isoelectric point pH 4.9) revealed that the putative Mtchit 5 chitinase forms a separate clade within class V chitinases of plants, whereas the Mtchit 4 chitinase clusters with pathogen-induced class IV chitinases from other plants. These findings demonstrate that: (i) Rhizobium-induced chitinase gene expression in M. truncatula occurs in a plant ecotype-specific manner, (ii) Mtchit 5 is a putative chitinase gene that is specifically induced by rhizobia, and (iii) rhizobia-specific and defence-related chitinase genes are differentially influenced by rhizobial Nod factors and K antigens.

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.

Identification of mycorrhiza-regulated genes with arbuscule development-related expression profile

Suppressive subtractive hybridisation was applied to the analysis of late stage arbuscular mycorrhizal development in pea. 96 cDNA clones were amplified and 81, which carried fragments more than 200 nt in size, were sequence analysed. Among 67 unique fragments, 10 showed no homology and 10 were similar to sequences with unknown function. RNA accumulation of the corresponding 67 genes was analysed by hybridisation of macro-arrays. The cDNAs used as probes were derived from roots of wild type and late mutant pea genotypes, inoculated or not with the AM fungus Glomus mosseae. After calibration, a more than 2.5-fold mycorrhiza-induced RNA accumulation was detected in two independent experiments in the wild type for 25 genes, 22 of which seemed to be induced specifically during late stage AM development. Differential expression for 7 genes was confirmed by RT-PCR using RNA from mycorrhiza and from controls of a different pea cultivar. In order to confirm arbuscule-related expression, the Medicago truncatula EST data base was screened for homologous sequences with putative mycorrhiza-related expression and among a number of sequences with significant similarities, a family of trypsin inhibitor genes could be identified. Mycorrhiza-induced RNA accumulation was verified for five members by real-time PCR and arbuscule-related activation of the promoter could be shown in transgenic roots for one of the genes, MtTi 1.

Identification and characterization of a Zea mays line carrying a transposon-tagged ENOD40

In Zea mays, two ENOD40 homologous were identified that show only 30% of sequence homology to each other. We identified line e40-mum1 carrying a Mu transposon inserted in ZmENOD40-1, the maize gene that has the highest homology to leguminous ENOD40. The insertion causes a dramatic reduction of the ZmENOD40-1 transcript level. Irrespective of this, homozygous e40-mum1 plants are still able to interact with mycorrhizal fungi. Furthermore, no phenotypic aberrations correlated to the presence of e40-mum1 have been identified and therefore it is suggested that Z. mays ENOD40 genes are functionally redundant despite their strikingly low homology.

Comparison of nodule induction in legume and actinorhizal symbioses: the induction of actinorhizal nodules does not involve ENOD40

Two types of root nodule symbioses are known for higher plants, legume and actinorhizal symbioses. In legume symbioses, bacterial signal factors induce the expression of ENOD40 genes. We isolated an ENOD40 promoter from an actinorhizal plant, Casuarina glauca, and compared its expression pattern in a legume (Lotus japonicus) and an actinorhizal plant (Allocasuarina verticillata) with that of an ENOD40 promoter from the legume soybean (GmENOD40-2). In the actinorhizal Allocasuarina sp., CgENOD40-GUS and GmENOD40-2-GUS showed similar expression patterns in both vegetative and symbiotic development, and neither promoter was active during nodule induction. The nonsymbiotic expression pattern of CgENOD40-GUS in the legume genus Lotus resembled the nonsymbiotic expression patterns of legume ENOD40 genes; however, in contrast to GmENOD40-2-GUS, CgENOD40-GUS was not active during nodule induction. The fact that only legume, not actinorhizal, ENOD40 genes are induced during legume nodule induction can be linked to the phloem unloading mechanisms established in the zones of nodule induction in the roots of both types of host plants.

Structural motifs in the RNA encoded by the early nodulation gene enod40 of soybean

The plant gene enod40 is highly conserved among legumes and also present in various non-legume species. It is presumed to play a central regulatory role in the Rhizobium-legume interaction, being expressed well before the initiation of cortical cell divisions resulting in nodule formation. Two small peptides encoded by enod40 mRNA as well as its secondary structure have been shown to be key elements in the signalling processes underlying nodule organogenesis. Here results concerning the secondary structure of mRNA of enod40 in soybean are presented. This study combined a theoretical approach, involving structure prediction and comparison, as well as structure probing. Our study indicates five conserved domains in enod40 mRNA among numerous leguminous species. Structure comparison suggests that some domains are also conserved in non-leguminous species and that an additional domain exists that was found only in leguminous species developing indeterminate nodules. Enzymatic and chemical probing data support the structure for three of the domains, and partially for the remaining two. The rest of the molecule appears to be less structured. Some of the domains include motifs, such as U-containing internal loops and bulges, which seem to be conserved. Therefore, they might be involved in the regulatory role of enod40 RNA.

Molecular cloning and characterization of a cDNA encoding a ryegrass (Lolium perenne) ENOD40 homologue

The ENOD40 gene, found in several leguminous and non-leguminous plant species is expressed in the pericycle of legume roots early in the nodulation process, adjacent to the protoxylem poles, but before the cortical cells divide to form the nodule itself. The ENOD40 transcript contains only short open reading frames which give rise to short peptides with a signaling function. The current work reports the cloning and analysis of ENOD40 genes from perennial ryegrass (Lolium perenne) and barley (Hordeum vulgare). Specific polymerase chain reaction (PCR) techniques lead to the isolation of a 659 bp cDNA encoding an ENOD40 homologue, designated LpE-NOD40, from a Lolium perenne stem cDNA library. In addition, a partial ENOD40 cDNA of 384 bp was isolated from barley (Hordeum vulgare) by RT-PCR cloning. The LpENOD40 transcript encodes a putative dodecapeptide, similar to that identified in ENOD40s from leguminous plants and other dicots, and also to ENOD40s from monocots. The coding sequences of ryegrass and barley ENOD40 are represented by a short open reading frame of 12 amino acids. These show a high degree of similarity to each other and to other ENOD40 sequences from monocots. The corresponding genomic DNA from a genomic ryegrass lambda library revealed that the LpENOD40 gene contains no introns. Southern blot analysis shows that the ryegrass genome contains a single copy, possibly two copies, of the gene. Alignment of the ENOD40 cDNA sequences from ryegrass and barley revealed high (77%) nucleotide homology. The ENOD40 peptides are highly conserved, not only among monocots but also on comparison with the dicot peptides. The amino acid identity of region I from ryegrass with its counterparts in maize, barley and rice is 92, 83 and 75% respectively. Expression analysis by RT-PCR demonstrates that a high level of LpENOD40 gene transcript was found expressed in stem tissue, while a lower level was detected in leaves and only a very low expression in flowers of perennial ryegrass. No LpENOD40 transcript was detected in roots.

Transcriptional changes in response to arbuscular mycorrhiza development in the model plant Medicago truncatula

Significant changes in root morphology and physiology during arbuscular mycorrhiza (AM) development are likely to be controlled by specific gene expression pattern in the host plant. Until now, little was known about transcriptional changes which occur AM-exclusively; that is, they do not occur during other root-microbe associations, nor are they induced by improved phosphate nutrition. In order to identify such AM-exclusive gene inductions of Medicago truncatula, we used a pool of different RNA samples as subtractor population in a suppressive subtractive hybridization (SSH) experiment. This approach resulted in the identification of a number of new AM-regulated genes. None of these genes were expressed in nonmycorrhiza roots or leaves. Electronic data obtained by comparison of the cDNA sequences to expressed sequence tag (EST) sequences from a wide range of cDNA libraries in the M. truncatula EST database (Gene Index, MtGI) support the mycorrhiza specificity of the corresponding genes, because sequences in the MtGI that were found to match the identified SSH-cDNA sequences originated exclusively from AM cDNA libraries. The promoter of one of those genes, MtGst1, showing similarities to plant glutathione-S-transferase (GST) encoding genes, was cloned and used in reporter gene studies. In contrast to studies with the potato GST gene PRP, MtGst 1 promoter activity was detected in all zones of the root cortex colonized by Glomus intraradices, but nowhere else.

Beyond the proteome: non-coding regulatory RNAs

A variety of RNA molecules have been found over the last 20 years to have a remarkable range of functions beyond the well-known roles of messenger, ribosomal and transfer RNAs. Here, we present a general categorization of all non-coding RNAs and briefly discuss the ones that affect transcription, translation and protein function.