Auxin: at the root of nodule development?

Root nodules are formed as a result of an orchestrated exchange of chemical signals between symbiotic nitrogen fixing bacteria and certain plants. In plants that form nodules in symbiosis with actinorhizal bacteria, nodules are derived from lateral roots. In most legumes, nodules are formed de novo from pericycle and cortical cells that are re-stimulated for division and differentiation by rhizobia. The ability of plants to nodulate has only evolved recently and it has, therefore, been suggested that nodule development is likely to have co-opted existing mechanisms for development and differentiation from lateral root formation. Auxin is an important regulator of cell division and differentiation, and changes in auxin accumulation and transport are essential for lateral root development. There is growing evidence that rhizobia alter the root auxin balance as a prerequisite for nodule formation, and that nodule numbers are regulated by shoot-to-root auxin transport. Whereas auxin requirements appear to be similar for lateral root and nodule primordium activation and organ differentiation, the major difference between the two developmental programs lies in the specification of founder cells. It is suggested that differing ratios of auxin and cytokinin are likely to specify the precursors of the different root organs.

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Prenodule formation and primary nodule development in roots of Comptonia (Myricaceae)

Canadian Journal of Botany ◽

10.1139/b77-262 ◽

1977 ◽

Vol 55 (17) ◽

pp. 2306-2318 ◽

Cited By ~ 49

Author(s):

Dale Callaham ◽

John G. Torrey

Keyword(s):

Root Hair ◽

Lateral Root ◽

Lateral Roots ◽

Cortical Cell ◽

Host Cells ◽

Nodule Development ◽

Nodule Formation ◽

Cortical Cells ◽

Lateral Root Primordium ◽

Root Primordium

Seedlings of the sweet fern, Comptonia peregrina (L.) Coult., grown aeroponically, were inoculated with a nodule suspension to allow infection by the actinomycete-like organism which causes nodule formation. Roots with early stages of infection and nodule initiation were fixed, embedded in resin, sectioned, and examined. Infection is infrequent in Comptonia with only a few nodules per seedling root system. Infection via root hair invasion causes the retention of the curled and deformed root hair in an intensely cytoplasmic state with ramification of multiple filamentous strands of the endophyte. A limited cortical proliferation occurs in response to the infection forming the prenodule; endophyte filaments grow radially inward from the base of the infected epidermal root hair and invade a portion of the prenodular cells resulting in their hypertrophy. Distal and proximal to the prenodule site, a number of primary nodule primordia are initiated, varying from a few up to a dozen or more. These primordia appear to develop more or less simultaneously under the stimulus of the invading endophyte; they are like lateral roots in their site of origin, occurring largely opposite the protoxylem poles and involving pericyclic and endodermal cell proliferation. They differ in that the cortical cells external to each primordium are stimulated to undergo divisions and these cortical cell derivatives are incorporated into the developing primordium. The endophyte enters the cortical tissues of the lateral root on which the prenodule has formed and then invades proximal and distal to the infection site, progressing into the cortical tissues of each of the developing nodule primordia. A cork-like layer develops on the original lateral root in areas not occupied by primordia by initiation of subepidermal cell divisions and wall thickening. Normal lateral root primordium formation occurs in the pericycle opposite the protoxylem poles and involves cellular derivatives of the pericycle and endodermis but no cortical cells, which instead are crushed and displaced by the lateral root primordium as it develops. Nodule formation clearly involves complex chemical interactions, which remain for further study, between the host cells and the invading endophyte.

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A shared gene drives lateral root development and root nodule symbiosis pathways in Lotus

Science ◽

10.1126/science.aax2153 ◽

2019 ◽

Vol 366 (6468) ◽

pp. 1021-1023 ◽

Cited By ~ 20

Author(s):

Takashi Soyano ◽

Yoshikazu Shimoda ◽

Masayoshi Kawaguchi ◽

Makoto Hayashi

Keyword(s):

Root Development ◽

Lateral Root ◽

Root Nodule ◽

Root Nodules ◽

Lotus Japonicus ◽

Cortical Cell ◽

Cortical Cells ◽

Lateral Root Development ◽

Lateral Organ ◽

Nodule Symbiosis

Legumes develop root nodules in symbiosis with nitrogen-fixing rhizobial bacteria. Rhizobia evoke cell division of differentiated cortical cells into root nodule primordia for accommodating bacterial symbionts. In this study, we show that NODULE INCEPTION (NIN), a transcription factor in Lotus japonicus that is essential for initiating cortical cell divisions during nodulation, regulates the gene ASYMMETRIC LEAVES 2-LIKE18/LATERAL ORGAN BOUNDARIES DOMAIN16a (ASL18/LBD16a). Orthologs of ASL18/LBD16a in nonlegume plants are required for lateral root development. Coexpression of ASL18a and the CCAAT box–binding protein Nuclear Factor-Y (NF-Y) subunits, which are also directly targeted by NIN, partially suppressed the nodulation-defective phenotype of L. japonicusdaphne mutants, in which cortical expression of NIN was attenuated. Our results demonstrate that ASL18a and NF-Y together regulate nodule organogenesis. Thus, a lateral root developmental pathway is incorporated downstream of NIN to drive nodule symbiosis.

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Natural variation identifies a Pxy gene controlling root vascular organization and formation of nodules and lateral roots in Lotus japonicus

10.1101/2020.04.08.031260 ◽

2020 ◽

Author(s):

Yasuyuki Kawaharada ◽

Niels Sandal ◽

Vikas Gupta ◽

Haojie Jin ◽

Maya Kawaharada ◽

...

Keyword(s):

Lateral Root ◽

Reverse Genetics ◽

De Novo ◽

Lateral Roots ◽

Lotus Japonicus ◽

Nodule Formation ◽

Mesorhizobium Loti ◽

Genetic Overlap ◽

Natural Variants ◽

Trait Locus

AbstractForward and reverse genetics using the model legumes Lotus japonicus and Medicago truncatula have been instrumental for identifying the essential genes governing legume-rhizobial symbiosis. However, little is known about the effects of intraspecific variation on symbiotic signaling. The Lotus accessions Gifu and MG20 show differentiated phenotypic responses to the Mesorhizobium loti exoU mutant that produces truncated exopolysaccharides. Using Quantitative Trait Locus sequencing (QTL-seq), we identify the Pxy gene as a component of this differential exoU response. Lotus Pxy encodes a leucine-rich-repeat kinase similar to Arabidopsis PXY, which regulates stem vascular development. We show that Lotus pxy insertion mutants display defects in root vascular organization, as well as lateral root and nodule formation. Our work links Pxy to de novo organogenesis in the root, highlights the genetic overlap between regulation of lateral root and nodule formation, and demonstrates that specific natural variants of Pxy differentially affect nodulation signaling.

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Determinate development of nodule roots in actinomycete-induced root nodules of Myrica gale

Canadian Journal of Botany ◽

10.1139/b78-155 ◽

1978 ◽

Vol 56 (11) ◽

pp. 1357-1364 ◽

Cited By ~ 16

Author(s):

John G. Torrey ◽

Dale Callaham

Keyword(s):

Root Development ◽

Root Nodules ◽

Cortical Cell ◽

Gas Diffusion ◽

Nodule Development ◽

Nodule Formation ◽

Low Oxygen ◽

Cortical Cells ◽

Continuous Growth ◽

Myrica Gale

Young seedlings of Myrica gale L. grown in water culture were inoculated with a nodule suspension containing the effective actinomycete which induced root nodule formation. Nodule development was followed from initiation to nodule lobe formation and nodule root development using living materials and fixed nodules sectioned for light microscopy. After root hair infection and prenodule formation, three stages were observed: nodule lobe formation, a transition or arrested state, and nodule root development. The primary nodule lobe meristem originates endogenously and its formation involves pericycle, endodermis, and cortical cell derivatives. The lobe develops slowly to about 2 mm in length while the cortical cells are invaded by the actinomycete endophyte. After a period of arrest of variable duration, from a few days to several weeks, the nodule lobe meristem begins altered development, forming the elongate nodule root which undergoes slow but continuous growth to about 3- to 4-cm final length. New nodule lobe primordia are initiated endogenously at the base of existing nodules lobes, ultimately forming a cluster of nodule roots. Each nodule root, which elongates at about 0.1–1.0 mm per day, has a terminal apical meristem with reduced root cap formation and produces a modified root structure possessing an elaborate cortical intercellular space system and a reduced central cylinder. Nodule root growth is distinctive in that it shows strong negative geotropism. The endophyte is restricted to cortical cells of the nodule lobe and is totally absent from tissues of the nodule root. A probable role for nodule roots is to facilitate gas diffusion to the nitrogen-fixing endophyte site in the nodule lobe when nodules occur under conditions of low oxygen tension.

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Rhizobia Can Induce Nodules in White Clover by “Hijacking” Mature Cortical Cells Activated During Lateral Root Development

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi.2000.13.2.170 ◽

2000 ◽

Vol 13 (2) ◽

pp. 170-182 ◽

Cited By ~ 63

Author(s):

Ulrike Mathesius ◽

Jeremy J. Weinman ◽

Barry G. Rolfe ◽

Michael A. Djordjevic

Keyword(s):

Lateral Root ◽

Chalcone Synthase ◽

Root Hairs ◽

Gus Expression ◽

Flavonoid Compound ◽

Nodule Formation ◽

Cortical Cells ◽

Lateral Root Development ◽

Bacterial Genes ◽

Mature Root

We examined a range of responses of root cortical cells to Rhizobium sp. inoculation to investigate why rhizobia preferentially nodulate legume roots in the zone of emerging root hairs, but generally fail to nodulate the mature root. We tested whether the inability to form nodules in the mature root is due to a lack of plant flavonoids to induce the bacterial genes required for nodulation or a failure of mature cortical cells to respond to Rhizobium spp. When rhizobia were inoculated in the zone of emerging root hairs, changes in β-glucuronidase (GUS) expression from an auxin-responsive promoter (GH3), expression from three chalcone synthase promoters, and the accumulation of specific flavonoid compounds occurred in cortical cells prior to nodule formation. Rhizobia failed to induce these responses when inoculated in the mature root, even when co-inoculated with nod gene-inducing flavonoids. However, mature root hairs remained responsive to rhizobia and could support infection thread formation. This suggests that a deficiency in signal transduction is the reason for nodulation failure in the mature root. However, nodules could be initiated in the mature root at sites of lateral root emergence. A comparison between lateral root and nodule formation showed that similar patterns of GH3:gusA expression, chalcone synthase gene expression, and accumulation of a particular flavonoid compound occurred in the cortical cells involved in both processes. The results suggest that rhizobia can“ hijack” cortical cells next to lateral root emergence sites because some of the early responses required for nodule formation have already been activated by the plant in those cells.

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A plant lipocalin is required for retinal-mediated de novo root organogenesis

10.1101/2020.11.09.375444 ◽

2020 ◽

Author(s):

Alexandra J. Dickinson ◽

Jingyuan Zhang ◽

Michael Luciano ◽

Guy Wachsman ◽

Martin Schnermann ◽

...

Keyword(s):

Lateral Root ◽

Binding Proteins ◽

De Novo ◽

Lateral Roots ◽

Time Lapse ◽

Homology Search ◽

Lateral Root Development ◽

Root Organogenesis ◽

Retinoid Binding Proteins ◽

Β Carotene

AbstractBranching of root systems enables the exploration and colonization of the soil environment. In Arabidopsis roots, de novo organogenesis of lateral roots is patterned by an oscillatory mechanism called the root clock, which is dependent on metabolites derived from the β-carotene pathway1, 2. Retinoids are β-carotene-derived regulators of organogenesis in the animal kingdom. To determine if retinoids function in plant development, we conducted time-lapse imaging of a chemical reporter for retinoid binding proteins. We found that it oscillates with a comparable frequency to the root clock and accurately predicts sites of lateral root organogenesis. Exogenous application of retinal to wild-type plants is sufficient to induce root clock oscillations and lateral root organogenesis. A homology search yielded a potential Arabidopsis homolog, TEMPERATURE INDUCED LIPOCALIN (TIL) to vertebrate retinoid binding proteins. Genetic analysis indicates that TIL is necessary for normal lateral root development and a til mutant has decreased retinal sensitivity. TIL expression in a heterologous system conferred retinal binding activity, suggesting that it may directly interact with this molecule. Together, these results demonstrate an essential role for retinal and for plant retinal binding proteins in lateral root organogenesis.

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Gene regulatory networks associated with lateral root and nodule development in soybean

10.1101/2019.12.15.876995 ◽

2019 ◽

Author(s):

Shuchi Smita ◽

Jason Kiehne ◽

Sajag Adhikari ◽

Erliang Zeng ◽

Qin Ma ◽

...

Keyword(s):

Gene Regulatory Networks ◽

Lateral Root ◽

Regulatory Networks ◽

Network Inference ◽

Root Nodules ◽

Lateral Roots ◽

Nodule Development ◽

Inference Algorithms ◽

Lateral Organ ◽

Gene Regulatory

AbstractLegume plants such as soybean produce two major types of root lateral organs, lateral roots and root nodules. A robust computational framework was developed to predict potential gene regulatory networks (GRNs) associated with root lateral organ development in soybean. A genome-scale expression dataset was obtained from soybean root nodules and lateral roots and subjected to biclustering using QUBIC. Biclusters (BCs) and transcription factor (TF) genes with enriched expression in lateral root tissues were converged using different network inference algorithms to predict high confident regulatory modules that are repeatedly retrieved in different methods. The ranked combination of results from all different network inference algorithms into one ensemble solution identified 21 GRN modules of 182 co-regulated genes networks potentially involved in root lateral organ development stages in soybean. The pipeline correctly predicted previously known nodule- and LR-associated TFs including the expected hierarchical relationships. The results revealed high scorer AP2, GRF5, and C3H co-regulated GRN modules during early nodule development; and GRAS, LBD41, and ARR18 co-regulated GRN modules late during nodule maturation. Knowledge from this work supported by experimental validation in the future is expected to help determine key gene targets for biotechnological strategies to optimize nodule formation and enhance nitrogen fixation.

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Gene regulatory networks associated with lateral root and nodule development in soybean

in silico Plants ◽

10.1093/insilicoplants/diaa002 ◽

2020 ◽

Vol 2 (1) ◽

Author(s):

Shuchi Smita ◽

Jason Kiehne ◽

Sajag Adhikari ◽

Erliang Zeng ◽

Qin Ma ◽

...

Keyword(s):

Gene Regulatory Networks ◽

Lateral Root ◽

Regulatory Networks ◽

Network Inference ◽

Root Nodules ◽

Lateral Roots ◽

Nodule Development ◽

Inference Algorithms ◽

Lateral Organ ◽

Gene Regulatory

Abstract Legume plants such as soybean produce two major types of root lateral organs, lateral roots and root nodules. A robust computational framework was developed to predict potential gene regulatory networks (GRNs) associated with root lateral organ development in soybean. A genome-scale expression data set was obtained from soybean root nodules and lateral roots and subjected to biclustering using QUBIC (QUalitative BIClustering algorithm). Biclusters and transcription factor (TF) genes with enriched expression in lateral root tissues were converged using different network inference algorithms to predict high-confidence regulatory modules that were repeatedly retrieved in different methods. The ranked combination of results from all different network inference algorithms into one ensemble solution identified 21 GRN modules of 182 co-regulated genes networks, potentially involved in root lateral organ development stages in soybean. The workflow correctly predicted previously known nodule- and lateral root-associated TFs including the expected hierarchical relationships. The results revealed distinct high-confidence GRN modules associated with early nodule development involving AP2, GRF5 and C3H family TFs, and those associated with nodule maturation involving GRAS, LBD41 and ARR18 family TFs. Knowledge from this work supported by experimental validation in the future is expected to help determine key gene targets for biotechnological strategies to optimize nodule formation and enhance nitrogen fixation.

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Auxin Response Factor 2 (ARF2), ARF3, and ARF4 Mediate Both Lateral Root and Nitrogen Fixing Nodule Development in Medicago truncatula

Frontiers in Plant Science ◽

10.3389/fpls.2021.659061 ◽

2021 ◽

Vol 12 ◽

Author(s):

Cristina Kirolinko ◽

Karen Hobecker ◽

Jiangqi Wen ◽

Kirankumar S. Mysore ◽

Andreas Niebel ◽

...

Keyword(s):

Medicago Truncatula ◽

Root Development ◽

Lateral Root ◽

Lateral Roots ◽

Nodule Development ◽

Nodule Formation ◽

Mrna Levels ◽

Nitrogen Fixing ◽

Auxin Response ◽

Small Interference Rna

Auxin Response Factors (ARFs) constitute a large family of transcription factors that mediate auxin-regulated developmental programs in plants. ARF2, ARF3, and ARF4 are post-transcriptionally regulated by the microRNA390 (miR390)/trans-acting small interference RNA 3 (TAS3) module through the action of TAS3-derived trans-acting small interfering RNAs (ta-siRNA). We have previously reported that constitutive activation of the miR390/TAS3 pathway promotes elongation of lateral roots but impairs nodule organogenesis and infection by rhizobia during the nitrogen-fixing symbiosis established between Medicago truncatula and its partner Sinorhizobium meliloti. However, the involvement of the targets of the miR390/TAS3 pathway, i.e., MtARF2, MtARF3, MtARF4a, and MtARF4b, in root development and establishment of the nitrogen-fixing symbiosis remained unexplored. Here, promoter:reporter fusions showed that expression of both MtARF3 and MtARF4a was associated with lateral root development; however, only the MtARF4a promoter was active in developing nodules. In addition, up-regulation of MtARF2, MtARF3, and MtARF4a/b in response to rhizobia depends on Nod Factor perception. We provide evidence that simultaneous knockdown of MtARF2, MtARF3, MtARF4a, and MtARF4b or mutation in MtARF4a impaired nodule formation, and reduced initiation and progression of infection events. Silencing of MtARF2, MtARF3, MtARF4a, and MtARF4b altered mRNA levels of the early nodulation gene nodulation signaling pathway 2 (MtNSP2). In addition, roots with reduced levels of MtARF2, MtARF3, MtARF4a, and MtARF4b, as well as arf4a mutant plants exhibited altered root architecture, causing a reduction in primary and lateral root length, but increasing lateral root density. Taken together, our results suggest that these ARF members are common key players of the morphogenetic programs that control root development and the formation of nitrogen-fixing nodules.

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Host–endophyte interactions in effective and ineffective nodules induced by the endophyte of Myrica gale

Canadian Journal of Botany ◽

10.1139/b83-323 ◽

1983 ◽

Vol 61 (11) ◽

pp. 2898-2909 ◽

Cited By ~ 36

Author(s):

Kathryn A. VandenBosch ◽

John G. Torrey

Keyword(s):

Nitrogenase Activity ◽

Root Nodules ◽

Seedling Development ◽

Nodule Development ◽

Nodule Formation ◽

Cortical Tissue ◽

Intercellular Spaces ◽

Cortical Cells ◽

Myrica Gale ◽

Infected Cells

Suspensions of crushed root nodules of Myrica gale containing the actinomycete Frankia induced nodule formation on roots of seedlings of M. gale and Comptonia peregrina grown in nutrient water culture. Nodules formed on M. gale were normal in structure and exhibited nitrogenase activity (measured as acetylene reduction) and provided the necessary nitrogen for seedling development. These effective nodules showed typical external and internal structure with the endophyte developing both vesicles and sporangia within cortical cells of the host tissue. Small nodules formed on C. peregrina representing the primary nodule stage. They lacked nitrogenase activity and were termed ineffective. Vesicles failed to develop within these ineffective nodules. However, sporangia were formed in infected cells and within intercellular spaces of the nodule cortical tissue. In addition, prominent amyloplasts occurred in infected cells of the ineffective nodules, a feature lacking in effective nodules. Exogenously supplied combined nitrogen increased seedling growth but did not improve nodule development or endophyte morphogenesis in the ineffective nodules.

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