The Root Clock as a Signal Integrator System: Ensuring Balance for Survival

Abstract

The root system is essential for the survival of terrestrial plants, plant development, and adaptation to changing environments. The development of the root system relies on post-embryonic organogenesis and more specifically on the formation and growth of lateral roots (LR). The spacing of LR along the main root is underpinned by a precise prepatterning mechanism called the Root Clock. In Arabidopsis, the primary output of this mechanism involves the generation of periodic gene expression oscillations in a zone close to the root tip called the Oscillation Zone (OZ). Because of these oscillations, pre-branch sites (PBS) are established in the positions from which LR will emerge, although the oscillations can also possibly regulate the root wavy pattern and growth. Furthermore, we show that the Root Clock is present in LR. In this review, we describe the recent advances unraveling the inner machinery of Root Clock as well as the new tools to track the Root Clock activity. Moreover, we discuss the basis of how Arabidopsis can balance the creation of a repetitive pattern while integrating both endogenous and exogenous signals to adapt to changing environmental conditions. These signals can work as entrainment signals, but in occasions they also affect the periodicity and amplitude of the oscillatory dynamics in gene expression. Finally, we identify similarities with the Segmentation Clock of vertebrates and postulate the existence of a determination front delimiting the end of the oscillations in gene expression and initiating LR organogenesis through the activation of PBS in an ARF7 dependent-manner.

Keywords: auxin signaling; biological clock; heavy metals; lateral root; oscillating gene expression; retinal; root branching; water deprivation.

Figure 1

The activity of the Root Clock results from an inner oscillator. (A) Left: Schematic representation of the location of Oscillation Zone (OZ) and PreBranch Sites (PBS) in the root system. Right: Location of the OZ and PBS visualized by DR5::Luciferase expression in the primary (PR) and lateral roots (LR). Note that the LR (top right image) show OZ and form PBS the same as the PR (bottom right image). The PR is delimited by a dasshed white line in the top right image. SCN: Stem Cell Niche. (B) Model of the core genetic circuit driving the Root Clock as adapted from (Perianez-Rodriguez et al., 2021). ARF: Auxin Response Factor. IAA: Aux/IAA protein inhibitors. F: predicted factor promoting dimer formation. (C) DR5::Luciferase expression in 6 days post imbibition (dpi) plants treated with 0.25 μm auxin (indol-3-acetic acid, IAA) for 1.5 h. Note that activation of DR5::Luciferase occurs in the OZ of arf7-1, whereas it is impaired in the root region above as delimited by the dashed red line. This switch in behavior of DR5::Luciferase delimits the end of the Root Clock oscillations and marks the initiation of LR organogenesis through PBS activation (PBS activation is followed by LR initiation and patterning).

Figure 2

Light perceived in the root does not affect the Root Clock activity. (A) 7 dpi plants grown in the D-Root system and under standard conditions. L: plate section exposed to light, D: plate section maintained in the dark. (B) DR5::Luciferase imaging of roots grown in the D-Root and under standard conditions. Yellow arrow: PBS. (C) DR5::Luciferase quantification in the OZ of roots in the D-Root and under standard conditions. ADU: Analog-Digital Units (D) Number of PBS formed at 7 dpi in the D-Root and under standard conditions. No statistical significance by Student’s t-test (value of p <0.05) was observed (n = 10).

Figure 3

The Root Clock as a signal integrator system. Schematic representation of the model proposed for the integration of exogenous and endogenous signals by the Root Clock and the resulting outputs.