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

Ectopic expression of the GRAS-type transcriptional regulator NSP2 in Parasponia triggers contrasting effects on symbioses

Introduction

Plants strictly control root endosymbioses with nutrient-scavenging arbuscular endomycorrhizal fungi or nodule inducing diazotrophic bacteria. The GRAS-type transcriptional regulator NODULATION SIGNALING PATHWAY 2 (NSP2) is a conserved hub in this process. The NSP2-regulated transcriptional network is instrumental in balancing nutrient homeostasis with symbiotic interactions. NSP2 activity is modulated post-transcriptionally by a specific microRNA. Overriding this control mechanism by ectopic expression of a miRNA-resistant NSP2 transgene enhances the symbiotic permissiveness to arbuscular endomycorrhizal fungi. Such engineered plants may possess enhanced capacities for nutrient uptake. However, the trade-off of this strategy on plant development or other symbiotic interactions, like nodulation, is yet to be fully understood.

Method

We used the nodulating Cannabaceae species Parasponia andersonii as an experimental system to study the effect of ectopic NSP2 expression. Parasponia and legumes (Fabaceae) diverged 100 million years ago, providing a unique comparative system to dissect the nodulation trait.

Results

Six independent transgenic Parasponia lines were generated that differed in the level of NSP2 expression in the root from 6 to 95-fold higher when compared to the empty vector control plants. Analysis of these plants revealed a positive correlation between mycorrhization and the NSP2 expression level, as well as with the expression of the symbiosis transcription factor CYCLOPS and the rate-limiting enzyme in the carotenoid biosynthetic pathway PHYTOENE SYNTHASE1 (PSY1). Yet ectopic expression of NSP2 affected plant architecture and root nodule organogenesis.

Discussion

This indicates a significant trade-off when leveraging NSP2 over-expression to enhance endomycorrhization.

Overexpression of GmPHR1 Promotes Soybean Yield through Global Regulation of Nutrient Acquisition and Root Development

MYB-CC transcription factors (TFs) are essential for plant growth and development. Members of the MYB-CC subfamily with long N terminal domains, such as phosphate starvation response 1 (PHR1) or PHR1-like TFs, have well documented functions, while those with short N terminal domains remain less understood. In this study, we identified a nodule specific MYB-CC transcription factor 1 (GmPHR1) in soybean that is different from other canonical PHR family genes in that GmPHR1 harbors a short N terminal ahead of its MYB-CC domain and was highly induced by rhizobium infection. The overexpression of GmPHR1 dramatically increased the ratio of deformed root hairs, enhanced subsequent soybean nodulation, and promoted soybean growth in pot experiments. The growth promotion effects of GmPHR1 overexpression were further demonstrated in field trails in which two GmPHR1-OE lines yielded 10.78% and 8.19% more than the wild type line. Transcriptome analysis suggested that GmPHR1 overexpression led to global reprogramming, with 749 genes upregulated and 279 genes downregulated, especially for genes involved in MYB transcription factor activities, root growth, and nutrient acquisition. Taken together, we conclude that GmPHR1 is a key gene involved in the global regulation of nodulation, root growth, and nutrient acquisition in soybeans, and is thus a promising candidate gene to target for soybean yield enhancement.

NSP2, a key symbiotic regulator in the spotlight

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Peng Z, Chen H, Tan L, Shu H, Varshney R.K., Zhou Z, Zhao Z, Luo Z, Chitikineni A, Wang L, Maku J, López Y, Gallo M, Zhou H, Wang J. 2021. Natural polymorphisms in a pair of NSP2 homoeologs can cause loss of nodulation in peanut. Journal of Experimental Botany 72, 1104–1118.

Natural polymorphisms in a pair of NSP2 homoeologs can cause loss of nodulation in peanut

Microbial symbiosis in legumes is achieved through nitrogen-fixing root nodules, and these are important for sustainable agriculture. The molecular mechanisms underlying development of root nodules in polyploid legume crops are largely understudied. Through map-based cloning and QTL-seq approaches, we identified a pair of homoeologous GRAS transcription factor genes, Nodulation Signaling Pathway 2 (AhNSP2-B07 or Nb) and AhNSP2-A08 (Na), controlling nodulation in cultivated peanut (Arachis hypogaea L.), an allotetraploid legume crop, which exhibited non-Mendelian and Mendelian inheritance, respectively. The segregation of nodulation in the progeny of Nananbnb genotypes followed a 3:1 Mendelian ratio, in contrast to the 5:3~1:1 non-Mendelian ratio for nanaNbnb genotypes. Additionally, a much higher frequency of the nb allele (13%) than the na allele (4%) exists in the peanut germplasm collection, suggesting that Nb is less essential than Na in nodule organogenesis. Our findings reveal the genetic basis of naturally occurred non-nodulating peanut plants, which can be potentially used for nitrogen fixation improvement in peanut. Furthermore, the results have implications for and provide insights into the evolution of homoeologous genes in allopolyploid species.

Transcriptional regulation of NIN expression by IPN2 is required for root nodule symbiosis in Lotus japonicus

Expression of Nodule Inception (NIN) is essential for initiation of legume-rhizobial symbiosis. An existing model regarding the regulation of NIN expression involves two GRAS transcription factors - NSP1 (Nodulation Signaling Pathway 1) and NSP2. NSP2 forms a complex with NSP1 to directly bind to NIN promoter. However, rhizobial treatment-induced NIN expression could still be detected in the nsp1 mutant plants, suggesting that other proteins must be involved in the regulation of NIN expression. A combination of molecular, biochemical and genetic analyses was used to investigate the molecular basis of IPN2 in regulating root development and NIN expression in Lotus japonicus. In this study, we identified that IPN2 is a close homolog of Arabidopsis APL (ALTERED PHLOEM DEVELOPMENT) with essential function in root development. However, Lotus IPN2 has a different expression pattern compared with the Arabidopsis APL gene. IPN2 binds to the IPN2-responsive cis element (IPN2-RE) of NIN promoter and activates NIN expression. IPN2, NSP1 and NSP2 form a protein complex to directly target NIN promoter and activate NIN expression in the legume-rhizobial symbiosis. Our data refine the regulatory model of NIN expression that NSP2 works together with NSP1 and IPN2 to activate the NIN gene allowing nodulation in L. japonicus.

Characterization of the Spatial and Temporal Expression of Two Soybean miRNAs Identifies SCL6 as a Novel Regulator of Soybean Nodulation

MicroRNAs (miRNAs) control expression of endogenous target genes through transcript cleavage or translational inhibition. Legume plants can form a specialized organ, the nodule, through interaction with nitrogen fixing soil bacteria. To understand the regulatory roles of miRNAs in the nodulation process, we functionally validated gma-miR171o and gma-miR171q and their target genes in soybean. These two miRNA sequences are identical in sequence but their miRNA genes are divergent and show unique, tissue-specific expression patterns. The expression levels of the two miRNAs are negatively correlated with that of their target genes. Ectopic expression of these miRNAs in transgenic hairy roots resulted in a significant reduction in nodule formation. Both gma-miR171o and gma-miR171q target members of the GRAS transcription factor superfamily, namely GmSCL-6 and GmNSP2. Transient interaction of miRNAs and their target genes in tobacco cells further confirmed their cleavage activity. The results suggest that gma-miR171o and gma-miR171q regulate GmSCL-6 and GmNSP2, which in turn, influence expression of the Nodule inception (NIN), Early Nodulin 40 (ENOD40), and Ethylene Response Factor Required for Nodulation (ERN) genes during the Bradyrhizobium japonicum-soybean nodulation process. Collectively, our data suggest a role for two miRNAs, gma-miR171o and gma-miR171q, in regulating the spatial and temporal aspects of soybean nodulation.

The Medicago truncatula GRAS protein RAD1 supports arbuscular mycorrhiza symbiosis and Phytophthora palmivora susceptibility

The roots of most land plants are colonized by symbiotic arbuscular mycorrhiza (AM) fungi. To facilitate this symbiosis, plant genomes encode a set of genes required for microbial perception and accommodation. However, the extent to which infection by filamentous root pathogens also relies on some of these genes remains an open question. Here, we used genome-wide association mapping to identify genes contributing to colonization of Medicago truncatula roots by the pathogenic oomycete Phytophthora palmivora. Single-nucleotide polymorphism (SNP) markers most significantly associated with plant colonization response were identified upstream of RAD1, which encodes a GRAS transcription regulator first negatively implicated in root nodule symbiosis and recently identified as a positive regulator of AM symbiosis. RAD1 transcript levels are up-regulated both in response to AM fungus and, to a lower extent, in infected tissues by P. palmivora where its expression is restricted to root cortex cells proximal to pathogen hyphae. Reverse genetics showed that reduction of RAD1 transcript levels as well as a rad1 mutant are impaired in their full colonization by AM fungi as well as by P. palmivora. Thus, the importance of RAD1 extends beyond symbiotic interactions, suggesting a general involvement in M. truncatula microbe-induced root development and interactions with unrelated beneficial and detrimental filamentous microbes.

Novel impacts of functionalized multi-walled carbon nanotubes in plants: promotion of nodulation and nitrogenase activity in the rhizobium-legume system

The rhizobium-legume symbiosis system is critical for nitrogen-cycle balance in agriculture. However, the potential effects of carbon nanomaterials (CNMs) on this system remain largely unknown. Herein, we studied the effects of four carbon-based materials (activated carbon (AC), single-walled carbon nanotubes (SWCNTs), multi-walled carbon nanotubes (MWCNTs) and graphene oxide (GO)) on the rhizobium-legume symbiosis system consisting of Lotus japonicus and Mesorhizobium loti MAFF303099. Under non-symbiotic conditions, the bacterial growth and root development of plants were both clearly inhibited by SWCNTs and GO, while the elongation of plant stems was enhanced by MWCNTs to a certain degree. More importantly, only MWCNTs could increase the number of nodules and enhance the activity of nitrogenase in the rhizobium-plant interaction. Further analyses showed that the average number of nodules in plants treated with 100 μg mL^-1 MWCNTs was significantly increased by 39% at 14 days post inoculation (dpi) and by 41% at 28 dpi. Meanwhile, the biological nitrogen fixation of the nodules was promoted by more than 10% under 100 μg mL^-1 MWCNT treatment, which enhanced the above- and below-ground fresh biomass by 14% and 25% respectively at 28 dpi. Transmission electron microscopy images further indicated that MWCNTs penetrated the cell wall, and pierced through the cell membrane to be transmitted into the cytoplasm. In addition, gene expression analysis showed that the promotion of nodulation by MWCNTs was correlated with the up-regulation of certain genes involved in this signaling pathway. In particular, the expression of NIN, a crucial gene regulating the development of nodules, was significantly elevated 2-fold by MWCNTs at an early stage of nodulation. These findings are expected to facilitate the understanding and future utilization of MWCNTs in agriculture.

Function and evolution of a Lotus japonicus AP2/ERF family transcription factor that is required for development of infection threads

Legume-rhizobium symbiosis is achieved by two major events evolutionarily acquired: root hair infection and organogenesis. Infection thread (IT) development is a distinct element for rhizobial infection. Through ITs, rhizobia are efficiently transported from infection foci on root hairs to dividing meristematic cortical cells. To unveil this process, we performed genetic screening using Lotus japonicus MG-20 and isolated symbiotic mutant lines affecting nodulation, root hair morphology, and IT development. Map-based cloning identified an AP2/ERF transcription factor gene orthologous to Medicago truncatula ERN1. LjERN1 was activated in response to rhizobial infection and depended on CYCLOPS and NSP2. Legumes conserve an ERN1 homolog, ERN2, that functions redundantly with ERN1 in M. truncatula. Phylogenetic analysis showed that the lineages of ERN1 and ERN2 genes originated from a gene duplication event in the common ancestor of legume plants. However, genomic analysis suggested the lack of ERN2 gene in the L. japonicus genome, consistent with Ljern1 mutants exhibited a root hair phenotype that is observed in ern1/ern2 double mutants in M. truncatula. Molecular evolutionary analysis suggested that the nonsynonymous/synonymous rate ratios of legume ERN1 genes was almost identical to that of non-legume plants, whereas the ERN2 genes experienced a relaxed selective constraint.

Brassinosteroid-related transcription factor BIL1/BZR1 increases plant resistance to insect feeding

The plant steroid hormones brassinosteroids (BRs) play important roles in plant growth and responses to stresses. The up-regulation of pathogen resistance by BR signaling has been analyzed, but the relationship between BR and insect herbivores remains largely unclear. BIL1/BZR1 is a BR master transcription factor known to be involved in the regulation of plant development through work conducted on a gain of function mutation. Here, we analyzed the function of BIL1/BZR1 in response to insect feeding and demonstrated that resistance against thrip feeding was increased in the bil1-1D/bzr1-1D mutant compared to wild-type. We generated Lotus japonicus transgenic plants that over-express the Arabidopsis bil1/bzr1 mutant, Lj-bil1/bzr1-OX. The Lj-bil1/bzr1-OX plants showed increased resistance to thrip feeding. The expression levels of the jasmoninc acid (JA)-inducible VSP genes were increased in both Arabidopsis bil1-1D/bzr1-1D mutants and L. japonicus Lj-bil1/bzr1-OX plants. The resistance to thrip feeding caused by the BIL1/BZR1 gene may involve JA signaling.