Rhizotaxis Modulation in Arabidopsis Is Induced by Diffusible Compounds Produced during the Cocultivation of Arabidopsis and the Endophytic Fungus Serendipita indica

2020 ◽  
Vol 61 (4) ◽  
pp. 838-850
Author(s):  
Aoi Inaji ◽  
Atsushi Okazawa ◽  
Taiki Taguchi ◽  
Masatoshi Nakamoto ◽  
Nao Katsuyama ◽  
...  
Keyword(s):  
Root System ◽  
Root Development ◽  
Endophytic Fungus ◽  
Molecular Mechanisms ◽  
Primary Root ◽  
Gus Expression ◽  
Chemical Signals ◽  
Auxin Response ◽  
Root Tips

Abstract Rhizotaxis is established under changing environmental conditions via periodic priming of lateral root (LR) initiation at the root tips and adaptive LR formation along the primary root (PR). In contrast to the adaptable LR formation in response to nutrient availability, there is little information on root development during interactions with beneficial microbes. The Arabidopsis root system is characteristically modified upon colonization by the root endophytic fungus Serendipita indica, accompanied by a marked stimulation of LR formation and the inhibition of PR growth. This root system modification has been attributed to endophyte-derived indole-3-acetic acid (IAA). However, it has yet to be clearly explained how fungal IAA affects the intrinsic LR formation process. In this study, we show that diffusible compounds (chemical signals) other than IAA are present in the coculture medium of Arabidopsis and S. indica and induce auxin-responsive DR5::GUS expression in specific sections within the pericycle layer. The DR5::GUS expression was independent of polar auxin transport and the major IAA biosynthetic pathways, implicating unidentified mechanisms responsible for the auxin response and LR formation. Detailed metabolite analysis revealed the presence of multiple compounds that induce local auxin responses and LR formation. We found that benzoic acid (BA) cooperatively acted with exogenous IAA to generate a local auxin response in the pericycle layer, suggesting that BA is one of the chemical signals involved in adaptable LR formation. Identification and characterization of the chemical signals will contribute to a greater understanding of the molecular mechanisms underlying adaptable root development and to unconventional technologies for sustainable agriculture.

Molecular and Environmental Regulation of Root Development

2019 ◽  
Vol 70 (1) ◽  
pp. 465-488 ◽  
Author(s):  
Hans Motte ◽  
Steffen Vanneste ◽  
Tom Beeckman
Keyword(s):  
Root Development ◽  
Molecular Mechanisms ◽  
Current Knowledge ◽  
Primary Root ◽  
Root Apical Meristem ◽  
Control Mechanisms ◽  
Root Branching ◽  
And Control ◽  
The Impact

In order to optimally establish their root systems, plants are endowed with several mechanisms to use at distinct steps during their development. In this review, we zoom in on the major processes involved in root development and detail important new insights that have been generated in recent studies, mainly using the Arabidopsis root as a model. First, we discuss new insights in primary root development with the characterization of tissue-specific transcription factor complexes and the identification of non-cell-autonomous control mechanisms in the root apical meristem. Next, root branching is discussed by focusing on the earliest steps in the development of a new lateral root and control of its postemergence growth. Finally, we discuss the impact of phosphate, nitrogen, and water availability on root development and summarize current knowledge about the major molecular mechanisms involved.

scholarly journals The piperazine compound ASP activates an auxin response in Arabidopsis thaliana

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Fengyang Xu ◽  
Shuqi Xue ◽  
Limeng Deng ◽  
Sufen Zhang ◽  
Yaxuan Li ◽  
...  
Keyword(s):  
Root Growth ◽  
Root Development ◽  
Gene Knockout ◽  
Primary Root ◽  
Inhibitory Effect ◽  
Root Tip ◽  
Ethylene Response Factor ◽  
Auxin Response ◽  
Root Tips ◽  
Chemical Library

Abstract Background Auxins play key roles in the phytohormone network. Early auxin response genes in the AUX/IAA, SAUR, and GH3 families show functional redundancy, which makes it very difficult to study the functions of individual genes based on gene knockout analysis or transgenic technology. As an alternative, chemical genetics provides a powerful approach that can be used to address questions relating to plant hormones. Results By screening a small-molecule chemical library of compounds that can induce abnormal seedling and vein development, we identified and characterized a piperazine compound 1-[(4-bromophenoxy) acetyl]-4-[(4-fluorophenyl) sulfonyl] piperazine (ASP). The Arabidopsis DR5::GFP line was used to assess if the effects mentioned were correlated with the auxin response, and we accordingly verified that ASP altered the auxin-related pathway. Subsequently, we examined the regulatory roles of ASP in hypocotyl and root development, auxin distribution, and changes in gene expression. Following ASP treatment, we detected hypocotyl elongation concomitant with enhanced cell elongation. Furthermore, seedlings showed retarded primary root growth, reduced gravitropism and increased root hair development. These phenotypes were associated with an increased induction of DR5::GUS expression in the root/stem transition zone and root tips. Auxin-related mutants including tir1–1, aux1–7 and axr2–1 showed phenotypes with different root-development pattern from that of the wild type (Col-0), and were insensitive to ASP. Confocal images of propidium iodide (PI)-stained root tip cells showed no detectable damage by ASP. Furthermore, RT-qPCR analyses of two other genes, namely, Ethylene Response Factor (ERF115) and Mediator 18 (MED18), which are related to cell regeneration and damage, indicated that the ASP inhibitory effect on root growth was not attributable to toxicity. RT-qPCR analysis provided further evidence that ASP induced the expression of early auxin-response-related genes. Conclusions ASP altered the auxin response pathway and regulated Arabidopsis growth and development. These results provide a basis for dissecting specific molecular components involved in auxin-regulated developmental processes and offer new opportunities to discover novel molecular players involved in the auxin response.

Lateral root formation and nutrients: nitrogen in the spotlight

2021 ◽  
Author(s):  
Pierre-Mathieu Pélissier ◽  
Hans Motte ◽  
Tom Beeckman
Keyword(s):  
Signaling Pathways ◽  
Root System ◽  
Root Development ◽  
Lateral Root ◽  
Molecular Mechanisms ◽  
Root Formation ◽  
Lateral Roots ◽  
Nutrient Use Efficiency ◽  
Lateral Root Formation ◽  
Lateral Root Development

Abstract Lateral roots are important to forage for nutrients due to their ability to increase the uptake area of a root system. Hence, it comes as no surprise that lateral root formation is affected by nutrients or nutrient starvation, and as such contributes to the root system plasticity. Understanding the molecular mechanisms regulating root adaptation dynamics towards nutrient availability is useful to optimize plant nutrient use efficiency. There is at present a profound, though still evolving, knowledge on lateral root pathways. Here, we aimed to review the intersection with nutrient signaling pathways to give an update on the regulation of lateral root development by nutrients, with a particular focus on nitrogen. Remarkably, it is for most nutrients not clear how lateral root formation is controlled. Only for nitrogen, one of the most dominant nutrients in the control of lateral root formation, the crosstalk with multiple key signals determining lateral root development is clearly shown. In this update, we first present a general overview of the current knowledge of how nutrients affect lateral root formation, followed by a deeper discussion on how nitrogen signaling pathways act on different lateral root-mediating mechanisms for which multiple recent studies yield insights.

scholarly journals Bradyrhizobium japonicum IRAT FA3 alters Arabidopsis thaliana root architecture via regulation of auxin efflux transporters PIN2, PIN3, PIN7 and ABCB19

2021 ◽  
Author(s):  
Mercedes Schroeder ◽  
Melissa Y. Gomez ◽  
Nathan K. McLain ◽  
Emma Gachomo
Keyword(s):  
Arabidopsis Thaliana ◽  
Root System ◽  
Root Development ◽  
Bradyrhizobium Japonicum ◽  
Lateral Root ◽  
Plant Root ◽  
Primary Root ◽  
Efflux Transporters ◽  
Loss Of Function ◽  
Lateral Root Primordia

Beneficial rhizobacteria can stimulate changes in plant root development. While root system growth is mediated by multiple factors, the regulated distribution of the phytohormone auxin within root tissues plays a principal role. Auxin transport facilitators help to generate the auxin gradients and maxima that determine root structure. Here, we show that the plant growth-promoting rhizobacterial strain Bradyrhizobium japonicum IRAT FA3 influences specific auxin efflux transporters to alter Arabidopsis thaliana root morphology. Gene expression profiling of host transcripts in control and B. japonicum-inoculated roots of the wild type A. thaliana accession Col-0 confirmed upregulation of PIN2, PIN3, PIN7 and ABCB19 with B. japonicum and identified genes potentially contributing to a diverse array of auxin-related responses. Co-cultivation of the bacterium with loss-of-function auxin efflux transport mutants revealed that B. japonicum requires PIN3, PIN7 and ABCB19 to increase lateral root development and utilizes PIN2 to reduce primary root length. Accelerated lateral root primordia production due to B. japonicum was not observed in single pin3, pin7 or abcb19 mutants, suggesting independent roles for PIN3, PIN7 and ABCB19 during the plant-microbe interaction. Our work demonstrates B. japonicum’s influence over host transcriptional reprogramming during plant interaction with this beneficial microbe and the subsequent alterations to root system architecture.

scholarly journals Use of Transcriptomic Analyses to Elucidate the Mechanism Governing Nodal Root Development in Eremochloa ophiuroides (Munro) Hack.

2021 ◽  
Vol 12 ◽  
Author(s):  
Rui Wang ◽  
Haoyan Zhao ◽  
Hailin Guo ◽  
Junqin Zong ◽  
Jianjian Li ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Transcription Factors ◽  
Root Development ◽  
Molecular Mechanisms ◽  
Homologous Gene ◽  
Root Tips ◽  
Rooting Ability ◽  
Nodal Roots ◽  
Nodal Root ◽  
Eremochloa Ophiuroides

Centipedegrass [Eremochloa ophiuroides (Munro) Hack.] is a perennial warm-season grass that originated in China, and its speed of nodal rooting is important for lawn establishment. In our study, centipedegrass nodal rooting ability was limited by node aging. Transcriptome sequencing of nodal roots after 0, 2, 4, and 8 days of water culture was performed to investigate the molecular mechanisms of root development. GO enrichment and KEGG pathway analyses of DEGs indicated that plant hormone signal transduction and transcription factors might play important roles in centipedegrass nodal root growth. Among them, E3 ubiquitin-protein ligases participated in multiple hormone signal transduction pathways and interacted with transcription factors. Furthermore, an E3 ubiquitin protein ligase EoSINAT5 overexpressed in rice resulted in longer roots and more numerous root tips, while knockout of LOC_Os07g46560 (the homologous gene of EoSINAT5 in rice) resulted in shorter roots and fewer root tips. These results indicated that EoSINAT5 and its homologous gene are able to promote nodal root development. This research presents the transcriptomic analyses of centipedegrass nodal roots, and may contribute to elucidating the mechanism governing the development of nodal roots and facilitates the use of molecular breeding in improving rooting ability.

scholarly journals Nitrate Signaling, Functions, and Regulation of Root System Architecture: Insights from Arabidopsis thaliana

Genes ◽  
2020 ◽  
Vol 11 (6) ◽  
pp. 633 ◽  
Author(s):  
Muhammad Asim ◽  
Zia Ullah ◽  
Fangzheng Xu ◽  
Lulu An ◽  
Oluwaseun Olayemi Aluko ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Root System ◽  
Root Development ◽  
System Architecture ◽  
Lateral Root ◽  
Transcriptional Regulatory Network ◽  
Primary Root ◽  
Root System Architecture ◽  
Nitrate Transporter ◽  
Nitrate Transporters

Root system architecture (RSA) is required for the acquisition of water and mineral nutrients from the soil. One of the essential nutrients, nitrate (NO3−), is sensed and transported by nitrate transporters NRT1.1 and NRT2.1 in the plants. Nitrate transporter 1.1 (NRT1.1) is a dual-affinity nitrate transporter phosphorylated at the T101 residue by calcineurin B-like interacting protein kinase (CIPKs); it also regulates the expression of other key nitrate assimilatory genes. The differential phosphorylation (phosphorylation and dephosphorylation) strategies and underlying Ca2+ signaling mechanism of NRT1.1 stimulate lateral root growth by activating the auxin transport activity and Ca2+-ANR1 signaling at the plasma membrane and the endosomes, respectively. NO3− additionally functions as a signal molecule that forms a signaling system, which consists of a vast array of transcription factors that control root system architecture that either stimulate or inhibit lateral and primary root development in response to localized and high nitrate (NO3−), respectively. This review elucidates the so-far identified nitrate transporters, nitrate sensing, signal transduction, and the key roles of nitrate transporters and its downstream transcriptional regulatory network in the primary and lateral root development in Arabidopsis thaliana under stress conditions.

scholarly journals The Plasticity of Root Systems in Response to External Phosphate

2020 ◽  
Vol 21 (17) ◽  
pp. 5955 ◽  
Author(s):  
Guoqiang Huang ◽  
Dabing Zhang
Keyword(s):  
Root System ◽  
System Architecture ◽  
Molecular Mechanisms ◽  
Primary Root ◽  
Root Systems ◽  
Root System Architecture ◽  
Molecular Signaling ◽  
Post Translational Modification ◽  
Phosphate Availability ◽  
Long Time

Phosphate is an essential macro-element for plant growth accumulated in the topsoil. The improvement of phosphate uptake efficiency via manually manipulating root system architecture is of vital agronomic importance. This review discusses the molecular mechanisms of root patterning in response to external phosphate availability, which could be applied on the alleviation of phosphate-starvation stress. During the long time evolution, plants have formed sophisticated mechanisms to adapt to environmental phosphate conditions. In terms of root systems, plants would adjust their root system architecture via the regulation of the length of primary root, the length/density of lateral root and root hair and crown root growth angle to cope with different phosphate conditions. Finally, plants develop shallow or deep root system in low or high phosphate conditions, respectively. The plasticity of root system architecture responds to the local phosphate concentrations and this response was regulated by actin filaments, post-translational modification and phytohormones such as auxin, ethylene and cytokinin. This review summarizes the recent progress of adaptive response to external phosphate with focus on integrated physiological, cellular and molecular signaling transduction in rice and Arabidopsis.

scholarly journals Cytokinin-Controlled Gradient Distribution of Auxin in Arabidopsis Root Tip

2021 ◽  
Vol 22 (8) ◽  
pp. 3874
Author(s):  
Lei Wu ◽  
Jun-Li Wang ◽  
Xiao-Feng Li ◽  
Guang-Qin Guo
Keyword(s):  
Growth And Development ◽  
Molecular Mechanisms ◽  
Plant Root ◽  
Primary Root ◽  
Root Tip ◽  
Root Tips ◽  
Arabidopsis Root ◽  
Gradient Distribution ◽  
Shed Light ◽  
Auxin Gradient

The plant root is a dynamic system, which is able to respond promptly to external environmental stimuli by constantly adjusting its growth and development. A key component regulating this growth and development is the finely tuned cross-talk between the auxin and cytokinin phytohormones. The gradient distribution of auxin is not only important for the growth and development of roots, but also for root growth in various response. Recent studies have shed light on the molecular mechanisms of cytokinin-mediated regulation of local auxin biosynthesis/metabolism and redistribution in establishing active auxin gradients, resulting in cell division and differentiation in primary root tips. In this review, we focus our attention on the molecular mechanisms underlying the cytokinin-controlled auxin gradient in root tips.

scholarly journals Comprehensive Genome-Wide Association Analysis Reveals the Genetic Basis of Root System Architecture in Soybean

2020 ◽  
Vol 11 ◽  
Author(s):  
Waldiodio Seck ◽  
Davoud Torkamaneh ◽  
François Belzile
Keyword(s):  
Root System ◽  
System Architecture ◽  
Phenotypic Variation ◽  
Genetic Basis ◽  
Genome Wide Association Study ◽  
Primary Root ◽  
Root System Architecture ◽  
Genome Wide Association ◽  
Nucleotide Polymorphisms ◽  
Genome Wide

Increasing the understanding genetic basis of the variability in root system architecture (RSA) is essential to improve resource-use efficiency in agriculture systems and to develop climate-resilient crop cultivars. Roots being underground, their direct observation and detailed characterization are challenging. Here, were characterized twelve RSA-related traits in a panel of 137 early maturing soybean lines (Canadian soybean core collection) using rhizoboxes and two-dimensional imaging. Significant phenotypic variation (P < 0.001) was observed among these lines for different RSA-related traits. This panel was genotyped with 2.18 million genome-wide single-nucleotide polymorphisms (SNPs) using a combination of genotyping-by-sequencing and whole-genome sequencing. A total of 10 quantitative trait locus (QTL) regions were detected for root total length and primary root diameter through a comprehensive genome-wide association study. These QTL regions explained from 15 to 25% of the phenotypic variation and contained two putative candidate genes with homology to genes previously reported to play a role in RSA in other species. These genes can serve to accelerate future efforts aimed to dissect genetic architecture of RSA and breed more resilient varieties.

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