skip to main content


Title: High-Resolution Translatome Analysis Reveals Cortical Cell Programs During Early Soybean Nodulation
Nodule organogenesis in legumes is regulated temporally and spatially through gene networks. Genome-wide transcriptome, proteomic, and metabolomic analyses have been used previously to define the functional role of various plant genes in the nodulation process. However, while significant progress has been made, most of these studies have suffered from tissue dilution since only a few cells/root regions respond to rhizobial infection, with much of the root non-responsive. To partially overcome this issue, we adopted translating ribosome affinity purification (TRAP) to specifically monitor the response of the root cortex to rhizobial inoculation using a cortex-specific promoter. While previous studies have largely focused on the plant response within the root epidermis (e.g., root hairs) or within developing nodules, much less is known about the early responses within the root cortex, such as in relation to the development of the nodule primordium or growth of the infection thread. We focused on identifying genes specifically regulated during early nodule organogenesis using roots inoculated with Bradyrhizobium japonicum . A number of novel nodulation gene candidates were discovered, as well as soybean orthologs of nodulation genes previously reported in other legumes. The differential cortex expression of several genes was confirmed using a promoter-GUS analysis, and RNAi was used to investigate gene function. Notably, a number of differentially regulated genes involved in phytohormone signaling, including auxin, cytokinin, and gibberellic acid (GA), were also discovered, providing deep insight into phytohormone signaling during early nodule development.  more » « less
Award ID(s):
1734145
PAR ID:
10355389
Author(s) / Creator(s):
; ; ; ; ; ;
Date Published:
Journal Name:
Frontiers in Plant Science
Volume:
13
ISSN:
1664-462X
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. Summary

    Despite of important functions of strigolactones (SLs) and karrikins (KARs) in plant development, plant–parasite and plant–fungi interactions, their roles in soybean–rhizobia interaction remain elusive. SL/KAR signaling genesGmMAX2a, GmD14s,andGmKAIsare activated by rhizobia infection. GmMAX2a restoredatmax2root hair defects and soybean root hairs were changed inGmMAX2aoverexpression (GmMAX2aOE) or knockdown (GmMAX2aKD) mutants.GmMAX2aKDgave fewer, whereasGmMAX2aOEproduced more nodules than GUS hairy roots. Mutation ofGmMAX2ain itsKDorOEtransgenic hairy roots affected the rhizobia infection‐induced increases in early nodulation gene expression. Both mutant hairy roots also displayed the altered auxin, jasmonate and abscisic acid levels, as further verified by transcriptomic analyses of their synthetic genes. Overexpression of an auxin synthetic geneGmYUC2aalso affected SL and KAR signaling genes. GmMAX2a physically interacted with SL/KAR receptors GmD14s, GmKAIs, and GmD14Ls with different binding affinities, depending on variations in the critical amino acids, forming active D14/KAI‐SCFMAX2complexes. The knockdown mutant roots of the nodule‐specifically expressingGmKAIs andGmD14Ls gave fewer nodules, with altered expression of several early nodulation genes. The expression levels ofGmKAIs, andGmD14Ls were markedly changed inGmMAX2amutant roots, so did their target repressor genesGmD53s andGmSMAX1s. Thus, SL and KAR signaling were involved in soybean–rhizobia interaction and nodulation partly through interactions with hormones, and this may explain the different effects of MXA2 orthologs on legume determinate and indeterminate nodulation. The study provides fresh insights into the roles of GmMAX2‐mediated SL/KAR signaling in soybean root hair and nodule formation.

     
    more » « less
  2. Abstract

    In theMedicago truncatula-Sinorhizobium melilotisymbiosis, chemical signaling initiates rhizobial infection of root nodule tissue, where a large portion of the bacteria are endocytosed into root nodule cells to function in nitrogen-fixing organelles. These intracellular bacteria are subjected to an arsenal of plant-derived nodule-specific cysteine-rich (NCR) peptides, which induce the physiological changes that accompany nitrogen fixation. NCR peptides drive these intracellular bacteria toward terminal differentiation. The bacterial peptidase HrrP was previously shown to degrade host-derived NCR peptides and give the bacterial symbionts greater fitness at the expense of host fitness. ThehrrPgene is found in roughly 10% ofSinorhizobiumisolates, as it is carried on an accessory plasmid. The objective of the present study is to identify peptidase genes in the core genome ofS. melilotithat modulate symbiotic outcome in a manner similar to the accessoryhrrPgene. In an overexpression screen of annotated peptidase genes, we identified one such symbiosis-associated peptidase (sap) gene,sapA(SMc00451). When overexpressed,sapAleads to a significant decrease in plant fitness. Its promoter is active in root nodules, with only weak expression evident under free-living conditions. The SapA enzyme can degrade a broad range of NCR peptides in vitro.

     
    more » « less
  3. Summary

    Symbiotic nitrogen fixation in legumes is mediated by an interplay of signaling processes between plant hosts and rhizobial symbionts. In legumes, several secreted protein families have undergone expansions and play key roles in nodulation. Thus, identifying lineage‐specific expansions (LSEs) of nodulation‐associated genes can be a strategy to discover candidate gene families.

    Using bioinformatic tools, we identified 13LSEs of nodulation‐related secreted protein families, each unique to eitherGlycine,ArachisorMedicagolineages. In theMedicagolineage, nodule‐specific Polycystin‐1, Lipoxygenase, Alpha Toxin (PLAT) domain proteins (NPDs) expanded to five members. We examinedNPDfunction usingCRISPR/Cas9 multiplex genome editing to createMedicago truncatulaNPDknockout lines, targeting one to fiveNPDgenes.

    Mutant lines with differing combinations ofNPDgene inactivations had progressively smaller nodules, earlier onset of nodule senescence, or ineffective nodules compared to the wild‐type control. Double‐ and triple‐knockout lines showed dissimilar nodulation phenotypes but coincided in upregulation of aDHHC‐type zinc finger and an aspartyl protease gene, possible candidates for the observed disturbance of proper nodule function.

    By postulating that gene family expansions can be used to detect candidate genes, we identified a family of nodule‐specificPLATdomain proteins and confirmed that they play a role in successful nodule formation.

     
    more » « less
  4. Abstract

    Legumes, such as peas, beans, and alfalfa, have evolved a remarkable ability to establish root nodule symbioses with nitrogen-fixing soil bacteria to fulfill their nitrogen needs. This partnership is characterized by a high degree of specificity, occurring both within and between host and bacterial species. Consequently, nodulation capacity and nitrogen-fixing efficiency vary significantly among different plant–bacteria pairs. The genetic and molecular mechanisms regulating symbiotic specificity are diverse, involving a wide array of host and bacterial genes and signals with various modes of action. Understanding the genetic basis of symbiotic specificity could enable the development of strategies to enhance nodulation capacity and nitrogen fixation efficiency. This knowledge will also help overcome the host range barrier, which is a critical step toward extending root nodule symbiosis to non-leguminous plants. In this review, we provide an update on our current understanding of the genetics and evolution of recognition specificity in root nodule symbioses, providing more comprehensive insights into the molecular signaling in plant–bacterial interactions.

     
    more » « less
  5. null (Ed.)
    Nitrogen is a major determinant of plant growth and productivity and the ability of legumes to form a symbiotic relationship with nitrogen-fixing rhizobia bacteria allows legumes to exploit nitrogen-poor niches in the biosphere. But hosting nitrogen-fixing bacteria comes with a metabolic cost, and the process requires regulation. The symbiosis is regulated through three signal transduction pathways: in response to available nitrogen, at the initiation of contact between the organisms, and during the development of the nodules that will host the rhizobia. Here we provide an overview of our knowledge of how the three signaling pathways operate in space and time, and what we know about the cross-talk between symbiotic signaling for nodule initiation and organogenesis, nitrate dependent signaling, and autoregulation of nodulation. Identification of common components and points of intersection suggest directions for research on the fine-tuning of the plant’s response to rhizobia. 
    more » « less