“…Analyses of DR5 showed that the oscillations appeared before root bending, suggesting that changes in the root growth direction and the wavy pattern could be an output of the Root Clock ( Moreno-Risueno et al, 2010 ). Although it has been proposed that the root growth dynamics could drive LR priming in a non-dependent clock mechanism ( Van Den Berg et al, 2021 ), it was previously shown that roots with reduced or variable growth have similar PBS number ( Moreno-Risueno et al, 2010 ). Furthermore, the Root Clock impacts the root hormonal state ( Perianez-Rodriguez et al, 2021 ) that could indirectly modify root growth.…”
Section: Identification Of New Root Clock Activitiesmentioning
confidence: 99%
“…Thus, variation of auxin levels would modify both PBS formation and the primary root growth, thereby facilitating their coordination and optimizing root system architecture. Morphological factors can influence auxin accumulation ( Van Den Berg et al, 2021 ). An example is gravistimulation, which causes transient accumulation of auxin in the OZ.…”
Section: The First Tier Of Root Clock Regulation: Endogenous Cuesmentioning
confidence: 99%
“…Recently, it has been reported that cadmium interferes with the DR5 oscillations (reducing their frequency) and with PBS formation ( Xie et al, 2019 ). Cadmium treatments repressed cell cycle activity in the meristem, which might affect the load of auxin required for priming ( Van Den Berg et al, 2021 ). Most importantly, cadmium inhibits auxin homeostasis and signaling ( Hu et al, 2013 ; Yuan and Huang, 2016 ) which can impact in the Root Clock oscillatory circuit leading to the observed reduction in the DR5 oscillatory frequency.…”
Section: The Second Tier Of Root Clock Regulation: Exogenous Cuesmentioning
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.
“…Analyses of DR5 showed that the oscillations appeared before root bending, suggesting that changes in the root growth direction and the wavy pattern could be an output of the Root Clock ( Moreno-Risueno et al, 2010 ). Although it has been proposed that the root growth dynamics could drive LR priming in a non-dependent clock mechanism ( Van Den Berg et al, 2021 ), it was previously shown that roots with reduced or variable growth have similar PBS number ( Moreno-Risueno et al, 2010 ). Furthermore, the Root Clock impacts the root hormonal state ( Perianez-Rodriguez et al, 2021 ) that could indirectly modify root growth.…”
Section: Identification Of New Root Clock Activitiesmentioning
confidence: 99%
“…Thus, variation of auxin levels would modify both PBS formation and the primary root growth, thereby facilitating their coordination and optimizing root system architecture. Morphological factors can influence auxin accumulation ( Van Den Berg et al, 2021 ). An example is gravistimulation, which causes transient accumulation of auxin in the OZ.…”
Section: The First Tier Of Root Clock Regulation: Endogenous Cuesmentioning
confidence: 99%
“…Recently, it has been reported that cadmium interferes with the DR5 oscillations (reducing their frequency) and with PBS formation ( Xie et al, 2019 ). Cadmium treatments repressed cell cycle activity in the meristem, which might affect the load of auxin required for priming ( Van Den Berg et al, 2021 ). Most importantly, cadmium inhibits auxin homeostasis and signaling ( Hu et al, 2013 ; Yuan and Huang, 2016 ) which can impact in the Root Clock oscillatory circuit leading to the observed reduction in the DR5 oscillatory frequency.…”
Section: The Second Tier Of Root Clock Regulation: Exogenous Cuesmentioning
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.
“…g . Figure 1 ) can be found in the colony growth and spatial positioning mechanisms of bacteria ( Karig et al., 2018 ; Murray and Sourjik, 2017 ), pigment distribution and structural features in fish ( Almuedo-Castillo et al., 2018 ; Cooper et al., 2018 ; Konow et al., 2021 ; Mahalwar et al., 2014 ; Onimaru et al., 2016 ), seashells ( Cooper, 2012 ; Meinhardt, 2009 ), corals ( Cohen et al., 2004 ; Pratchett et al., 2015 ), octopus ( Ishida, 2021 ), plants ( Vadde and Roeder, 2020 ; van den Berg et al., 2021 ), anatomical traits and hair follicle spacing in mammals ( Cetera et al., 2018 ; Economou et al., 2012 , 2020 ; Raspopovic et al., 2014 ; Sheth et al., 2012 ; Sick et al., 2006 ), feather branching and coloration in birds ( Harris et al., 2005 ; Haupaix et al., 2018 ), the left-right asymmetry and teeth development in vertebrates ( Marcon and Sharpe, 2012 ; Salazar-Ciudad and Jernvall, 2010 ), etc. Figure 1 Turing patterns are ubiquitous in Nature (A) The coral Diploria labyrinthiformis which is usually present in the Atlantic Ocean exhibits superficial 2D waves that meet Turing’s criteria; the specimen in the figure was found by the authors as a brick in a wall of the first house that Hernán Cortés constructed during the XVI century in La Antigua, Veracruz, central east Mexico; scale bar is 10 mm, inset is the full specimen in its current location at the coordinates 19°19′16.2"N, 96°19′15.1"W. (B) Fast Fourier transform (FFT) of the photograph shows a 360° annular spot rendered by the isotropic wavelength in the pattern (λ), where the tolerance in λ is indicated by the rim of the ring’s width limits, i .…”
“…Additionally, by revealing an essential role for priming driven upregulation of auxin signalling capacity in stable PBS formation, the proposed mechanism enables us to unite previously diverging viewpoints on the importance of auxin levels versus auxin signalling in lateral root prepatterning. Recently we uncovered how root tip polar auxin transport produces an auxin loading zone at the start of the elongation zone (EZ), while root growth generates periodic variations in the size with which cells enter this zone, causing periodic variations in auxin loading potential particularly in narrow vasculature cells with high surface to volume ratios (van den Berg et al 2021). Combined this generates the oscillations in vascular auxin levels that underly lateral root priming.…”
Priming is the process through which periodic elevations in auxin signalling prepattern future sites for lateral root formation, called prebranch sites. Thusfar is has remained a matter of debate to what extent elevations in auxin concentration and/or auxin signalling are critical for priming and prebranch site formation. Recently, we discovered a reflux-and-growth mechanism for priming generating periodic elevations in auxin concentration that subsequently dissipate. Here we reverse engineer a mechanism for prebranch site formation that translates these transient elevations into a persistent increase in auxin signalling, resolving the prior debate into a two-step process of auxin concentration mediated initial signal and auxin signalling capacity mediated memorization. A critical aspect of the prebranch site formation mechanism is its activation in response to time integrated rather than instantaneous auxin signalling. The proposed mechanism is demonstrated to be consistent with prebranch site auxin signalling dynamics, lateral inhibition and symmetry breaking mechanisms and perturbations in auxin homeostasis.
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