A single cell view of the transcriptome during lateral root initiation in Arabidopsis thaliana

AbstractRoot architecture is a major determinant of fitness, and is under constant modification in response to favorable and unfavorable environmental stimuli. Beyond impacts on the primary root, the environment can alter the position, spacing, density and length of secondary or lateral roots. Lateral root development is among the best-studied examples of plant organogenesis, yet there are still many unanswered questions about its earliest steps. Among the challenges faced in capturing these first molecular events is the fact that this process occurs in a small number of cells with unpredictable timing. Single-cell sequencing methods afford the opportunity to isolate the specific transcriptional changes occurring in cells undergoing this fate transition. Using this approach, we successfully captured the transcriptomes of initiating lateral root primordia, and discovered many previously unreported upregulated genes associated with this process. We developed a method to selectively repress target gene transcription in the xylem pole pericycle cells where lateral roots originate, and demonstrated that expression of several of these targets was required for normal root development. We also discovered novel subpopulations of cells in the pericycle and endodermal cell files that respond to lateral root initiation, highlighting the coordination across cell files required for this fate transition.One sentence summarySingle cell RNA sequencing reveals new molecular details about lateral root initiation, including the transcriptional impacts of the primordia on bordering cells.

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B1L regulates lateral root development by exocytic vesicular trafficking-mediated polar auxin transport

10.1101/2021.06.07.447418 ◽

2021 ◽

Author(s):

Yang Gang ◽

Chen Bi-xia ◽

Chen Tao ◽

Chen Jia-hui ◽

Sun Rui ◽

...

Keyword(s):

Root Development ◽

Lateral Root ◽

Auxin Transport ◽

Polar Auxin Transport ◽

Vesicular Trafficking ◽

Root Initiation ◽

Root Primordia ◽

Lateral Root Primordia ◽

Lateral Root Development ◽

Lateral Root Initiation

Auxin and auxin-mediated signaling pathways involved in the regulation of lateral root development are well documented. Although exocytic vesicle trafficking plays an important role in PIN-auxin-efflux carrier recycling, and polar auxin transport during lateral root formation, however, the mechanistic details of these processes are not well understood. Here, we demonstrate an essential regulatory mechanism of B1L that interacts with the exocyst to regulate PIN-mediated polar auxin transport and lateral root initiation. B1L is highly expressed in Arabidopsis roots, and genetic and cellular analyses have revealed that B1L is mainly involved in lateral root primordia initiation. Furthermore, DR5::GUS expression analyses revealed that auxin levels were higher in lateral root primordia of the b1l mutant than in the wild-type. Exogenous auxin treatment confirmed that the lateral root phenotype correlated closely with auxin levels. Additionally, auxin transport-inhibitory treatment indicated that B1L regulates auxin efflux. Consistently, b1l mutants exhibited higher levels of auxin efflux carriers PIN1-GFP and PIN3-GFP in lateral root primordia. Moreover, B1L interacts with the exocyst and functions in recycling PIN2-GFP. Finally, the b1l-1/exo70b1-1 double-mutant exhibited a significant increase in the number of lateral roots compared to the wildtype, b1l-1, and exo70b1-1. Collectively, this study improves our understanding of the highly sophisticated processes involved in exocytic vesicular trafficking-mediated polar auxin transport and lateral root initiation in plants.

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AT-HOOK MOTIF NUCLEAR LOCALISED PROTEIN 18 as a Novel Modulator of Root System Architecture

10.20944/preprints202003.0046.v1 ◽

2020 ◽

Author(s):

Marek Šírl ◽

Tereza Šnajdrová ◽

Dolores Gutiérrez-Alanís ◽

Joseph G. Dubrovsky ◽

Jean Phillipe Vielle-Calzada ◽

...

Keyword(s):

Root System ◽

System Architecture ◽

Lateral Root ◽

Apical Meristem ◽

Lateral Roots ◽

Primary Root ◽

Root System Architecture ◽

Root Apical Meristem ◽

Root Initiation ◽

Lateral Root Initiation

The AT-HOOK MOTIF NUCLEAR LOCALIZED PROTEIN (AHL) gene family encodes embryophyte-specific nuclear proteins with DNA binding activity. They modulate gene expression and affect various developmental processes in plants. We identify AHL18 (At3G60870) as a developmental modulator of root system architecture and growth. AHL18 regulates the length of the proliferation domain and number of dividing cells in the root apical meristem and thereby, cell production. Both primary root growth and lateral root development respond according to AHL18 transcription level. The ahl18 knock-out plants show reduced root systems due to a shorter primary root and a lower number of lateral roots. This change results from a higher number of arrested and non-developing lateral root primordia (LRP) rather than from decreased initiation. Overexpression of AHL18 results in a more extensive root system, longer primary roots, and increased density of lateral root initiation events. Formation of lateral roots is affected during the initiation of LRP and later development. AHL18 regulate root apical meristem activity, lateral root initiation and emergence, which is in accord with localization of its expression.

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Effects of IAA, Kinetin, and Trifluralin on Cotton Seedlings

Weed Science ◽

10.1017/s0043174500048852 ◽

1971 ◽

Vol 19 (3) ◽

pp. 265-268 ◽

Cited By ~ 7

Author(s):

Ghanem S. Hassawy ◽

K. C. Hamilton

Keyword(s):

Gossypium Hirsutum ◽

Root Development ◽

Lateral Root ◽

Indoleacetic Acid ◽

Lateral Roots ◽

Primary Root ◽

Lateral Root Development

Trifluralin (α,α,α-trifluoro-2,6-dinitro-N,N-dipropyl-p-toluidine), IAA (indoleacetic acid), kinetin (6-furfurylamino purine), and their combinations in culture solutions did not affect cotton (Gossypium hirsutumL., var. Deltapine Smooth Leaf) germination but reduced primary root and shoot lengths of seedlings. Trifluralin alone and in combination with IAA or kinetin inhibited lateral root development. When IAA and kinetin were both applied with 5 ppmw trifluralin, lateral roots developed.

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Systemic signalling through translationally controlled tumour protein controls lateral root formation in Arabidopsis

Journal of Experimental Botany ◽

10.1093/jxb/erz204 ◽

2019 ◽

Vol 70 (15) ◽

pp. 3927-3940 ◽

Cited By ~ 9

Author(s):

Rémi Branco ◽

Josette Masle

Keyword(s):

Lateral Root ◽

Root Elongation ◽

Developmental Plasticity ◽

Lateral Roots ◽

Primary Root ◽

Dual Function ◽

Growth Promoter ◽

Root Initiation ◽

Long Distance ◽

Lateral Root Initiation

Abstract The plant body plan and primary organs are established during embryogenesis. However, in contrast to animals, plants have the ability to generate new organs throughout their whole life. These give them an extraordinary developmental plasticity to modulate their size and architecture according to environmental constraints and opportunities. How this plasticity is regulated at the whole-organism level is elusive. Here we provide evidence for a role for translationally controlled tumour protein (TCTP) in regulating the iterative formation of lateral roots in Arabidopsis. AtTCTP1 modulates root system architecture through a dual function: as a general constitutive growth promoter enhancing root elongation and as a systemic signalling agent via mobility in the vasculature. AtTCTP1 encodes mRNAs with long-distance mobility between the shoot and roots. Mobile shoot-derived TCTP1 gene products act specifically to enhance the frequency of lateral root initiation and emergence sites along the primary root pericycle, while root elongation is controlled by local constitutive TCTP1 expression and scion size. These findings uncover a novel type for an integrative signal in the control of lateral root initiation and the compromise for roots between branching more profusely or elongating further. They also provide the first evidence in plants of an extracellular function of the vital, highly expressed ubiquitous TCTP1.

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Application of Phytohormones to Pea Roots After Removal of the Apex: Effect on Lateral Root Production

Functional Plant Biology ◽

10.1071/pp9790195 ◽

1979 ◽

Vol 6 (2) ◽

pp. 195 ◽

Cited By ~ 9

Author(s):

PB Goodwin ◽

SC Morris

Keyword(s):

Lateral Root ◽

Lateral Roots ◽

Primary Root ◽

Root Production ◽

Root Tip ◽

Naphthaleneacetic Acid ◽

Root Initiation ◽

Lateral Root Initiation ◽

Lateral Bud ◽

Bud Growth

Removal of 2 mm of the primary root tip of Pisum sativum caused a complete halt to primary root elongation, but did not alter the total number of laterals formed. The auxins indole-3-acetic acid and 1-naphthaleneacetic acid, when applied to the stump in a lanolin emulsion, increased the number of lateral roots. High levels of abscisic acid and low levels of the cytokinins N6-benzylaminopurine and N6-(γ, γ-dimethylallylamino)purine, and of the gibberellins GA3 and GA7, resulted in decreased lateral root production. Kinetin was without effect. There appears to be an inverse relationship between auxins and cytokinins in root/shoot growth coordination. Auxins, which are produced in the shoot tip, inhibit lateral bud growth but promote lateral root initiation. Cytokinins, which are produced in the root tip, inhibit lateral root initiation, but promote lateral stem growth.

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Flavonols modulate lateral root emergence by scavenging reactive oxygen species in Arabidopsis thaliana

Journal of Biological Chemistry ◽

10.1074/jbc.ra120.014543 ◽

2020 ◽

pp. jbc.RA120.014543

Author(s):

Jordan M. Chapman ◽

Gloria K. Muday

Keyword(s):

Arabidopsis Thaliana ◽

Root Development ◽

Lateral Root ◽

Lateral Roots ◽

Negative Regulator ◽

Wild Type ◽

Root Primordia ◽

Lateral Root Primordia ◽

Lateral Root Development ◽

Genes Encoding

Flavonoids are a class of specialized metabolites with subclasses including flavonols and anthocyanins, which have unique properties as antioxidants. Flavonoids modulate plant development, but whether and how they impact lateral root development is unclear. We examined potential roles for flavonols in this process using Arabidopsis thaliana mutants with defects in genes encoding key enzymes in flavonoid biosynthesis. We observed the tt4 and fls1 mutants, which produce no flavonols, have increased lateral root emergence. The tt4 root phenotype was reversed by genetic and chemical complementation. To more specifically define the flavonoids involved, we tested an array of flavonoid biosynthetic mutants, eliminating roles for anthocyanins and the flavonols quercetin and isorhamnetin in modulating root development. Instead, two tt7 mutant alleles, with defects in a branchpoint enzyme blocking quercetin biosynthesis, formed reduced numbers of lateral roots, and tt7-2 had elevated levels of kaempferol. Using a flavonol-specific dye, we observed that in the tt7-2 mutant, kaempferol accumulated within lateral root primordia at higher levels than wild-type. These data are consistent with kaempferol, or downstream derivatives, acting as a negative regulator of lateral root emergence. We examined ROS accumulation using ROS-responsive probes and found reduced fluorescence of a superoxide-selective probe within the primordia of tt7-2 compared to wild type, but not in the tt4 mutant, consistent with opposite effects of these mutants on lateral root emergence. These results support a model in which increased level of kaempferol in the lateral root primordia of tt7-2 reduces superoxide concentration and ROS-stimulated lateral root emergence.

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At-Hook Motif Nuclear Localised Protein 18 as a Novel Modulator of Root System Architecture

International Journal of Molecular Sciences ◽

10.3390/ijms21051886 ◽

2020 ◽

Vol 21 (5) ◽

pp. 1886 ◽

Cited By ~ 3

Author(s):

Marek Širl ◽

Tereza Šnajdrová ◽

Dolores Gutiérrez-Alanís ◽

Joseph G. Dubrovsky ◽

Jean Phillipe Vielle-Calzada ◽

...

Keyword(s):

Root System ◽

System Architecture ◽

Lateral Root ◽

Apical Meristem ◽

Lateral Roots ◽

Primary Root ◽

Root System Architecture ◽

Root Apical Meristem ◽

Root Initiation ◽

Lateral Root Initiation

The At-Hook Motif Nuclear Localized Protein (AHL) gene family encodes embryophyte-specific nuclear proteins with DNA binding activity. They modulate gene expression and affect various developmental processes in plants. We identify AHL18 (At3G60870) as a developmental modulator of root system architecture and growth. AHL18 is involved in regulation of the length of the proliferation domain and number of dividing cells in the root apical meristem and thereby, cell production. Both primary root growth and lateral root development respond according to AHL18 transcription level. The ahl18 knock-out plants show reduced root systems due to a shorter primary root and a lower number of lateral roots. This change results from a higher number of arrested and non-developing lateral root primordia (LRP) rather than from a decreased LRP initiation. The over-expression of AHL18 results in a more extensive root system, longer primary roots, and increased density of lateral root initiation events. AHL18 is thus involved in the formation of lateral roots at both LRP initiation and their later development. We conclude that AHL18 participates in modulation of root system architecture through regulation of root apical meristem activity, lateral root initiation and emergence; these correspond well with expression pattern of AHL18.

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Lateral root formation and nutrients: nitrogen in the spotlight

Plant Physiology ◽

10.1093/plphys/kiab145 ◽

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.

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Formation of lateral root meristems is a two-stage process

Development ◽

10.1242/dev.121.10.3303 ◽

1995 ◽

Vol 121 (10) ◽

pp. 3303-3310 ◽

Cited By ~ 8

Author(s):

M.J. Laskowski ◽

M.E. Williams ◽

H.C. Nusbaum ◽

I.M. Sussex

Keyword(s):

Lateral Root ◽

Lateral Roots ◽

Initial Period ◽

Subsequent Stage ◽

Root Initiation ◽

Root Meristems ◽

Lateral Root Initiation ◽

Cell Layers ◽

Stage Process ◽

Pericycle Cells

In both radish and Arabidopsis, lateral root initiation involves a series of rapid divisions in pericycle cells located on the xylem radius of the root. In Arabidopsis, the number of pericycle cells that divide to form a primordium was estimated to be about 11. To determine the stage at which primordia are able to function as root meristems, primordia of different stages were excised and cultured without added hormones. Under these conditions, primordia that consist of 2 cell layers fail to develop while primordia that consist of at least 3–5 cell layers develop as lateral roots. We hypothesize that meristem formation is a two-step process involving an initial period during which a population of rapidly dividing, approximately isodiametric cells that constitutes the primordium is formed, and a subsequent stage during which meristem organization takes place within the primordium.

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