Putting theory to the test: which regulatory mechanisms can drive realistic growth of a root?

Thermomorphogenesis of the Arabidopsis thaliana Root: Flexible Cell Division, Constrained Elongation and the Role of Cryptochrome

Understanding how plants respond to temperature is relevant for agriculture in a warming world. Responses to temperature in the shoot have been characterized more fully than those in the root. Previous work on thermomorphogenesis in roots established that for Arabidopsis thaliana (Columbia) seedlings grown continuously at a given temperature, the root meristem produces cells at the same rate at 15°C as at 25°C and the root's growth zone is the same length. To uncover the pathway(s) underlying this constancy, we screened 34 A. thaliana genotypes for parameters related to growth and division. No line failed to respond to temperature. Behavior was little affected by mutations in phytochrome or other genes that underly thermomorphogenesis in shoots. However, a mutant in cryptochrome 2 was disrupted substantially in both cell division and elongation, specifically at 15°C. Among the 34 lines, cell production rate varied extensively and was associated only weakly with root growth rate; in contrast, parameters relating to elongation were stable. Our data are consistent with models of root growth that invoke cell non-autonomous regulation for establishing boundaries between meristem, elongation zone and mature zone.

Multi-scale mechanisms driving root regeneration: From regeneration competence to tissue repatterning

Plants possess an outstanding capacity to regenerate enabling them to repair damages caused by suboptimal environmental conditions, biotic attacks, or mechanical damages impacting the survival of these sessile organisms. Although the extent of regeneration varies greatly between localized cell damage and whole organ recovery, the process of regeneration can be subdivided into a similar sequence of interlinked regulatory processes. That is, competence to regenerate, cell fate reprogramming, and the repatterning of the tissue. Here, using root tip regeneration as a paradigm system to study plant regeneration, we provide a synthesis of the molecular responses that underlie both regeneration competence and the repatterning of the root stump. Regarding regeneration competence, we discuss the role of wound signaling, hormone responses and synthesis, and rapid changes in gene expression observed in the cells close to the cut. Then, we consider how this rapid response is followed by the tissue repatterning phase, where cells experience cell fate changes in a spatial and temporal order to recreate the lost stem cell niche and columella. Lastly, we argue that a multi-scale modeling approach is fundamental to uncovering the mechanisms underlying root regeneration, as it allows to integrate knowledge of cell-level gene expression, cell-to-cell transport of hormones and transcription factors, and tissue-level growth dynamics to reveal how the bi-directional feedbacks between these processes enable self-organized repatterning of the root apex.

Plant cell size: Links to cell cycle, differentiation and ploidy

Cell size affects many processes, including exchange of nutrients and external signals, cell division and tissue mechanics. Across eukaryotes, cells have evolved mechanisms that assess their own size to inform processes such as cell cycle progression or gene expression. Here, we review recent progress in understanding plant cell size regulation and its implications, relating these findings to work in other eukaryotes. Highlights include use of DNA contents as reference point to control the cell cycle in shoot meristems, a size-dependent cell fate decision during stomatal development and insights into the interconnection between ploidy, cell size and cell wall mechanics.

Modeling reveals posttranscriptional regulation of GA metabolism enzymes in response to drought and cold

The hormone gibberellin (GA) controls plant growth and regulates growth responses to environmental stress. In monocotyledonous leaves, GA controls growth by regulating division-zone size. We used a systems approach to investigate the establishment of the GA distribution in the maize leaf growth zone to understand how drought and cold alter leaf growth. By developing and parameterizing a multiscale computational model that includes cell movement, growth-induced dilution, and metabolic activities, we revealed that the GA distribution is predominantly determined by variations in GA metabolism. Considering wild-type and UBI::GA20-OX-1 leaves, the model predicted the peak in GA concentration, which has been shown to determine division-zone size. Drought and cold modified enzyme transcript levels, although the model revealed that this did not explain the observed GA distributions. Instead, the model predicted that GA distributions are also mediated by posttranscriptional modifications increasing the activity of GA 20-oxidase in drought and of GA 2-oxidase in cold, which we confirmed by enzyme activity measurements. This work provides a mechanistic understanding of the role of GA metabolism in plant growth regulation.

Cytokinin promotes growth cessation in the Arabidopsis root

The Arabidopsis root offers good opportunities to investigate how regulated cellular growth shapes different tissues and organs, a key question in developmental biology. Along the root's longitudinal axis, cells sequentially occupy different developmental states. Proliferative meristematic cells give rise to differentiating cells, which rapidly elongate in the elongation zone, then mature and stop growing in the differentiation zone. The phytohormone cytokinin contributes to this zonation by positioning the boundary between the meristem and the elongation zone, called the transition zone. However, the cellular growth profile underlying root zonation is not well understood, and the cellular mechanisms that mediate growth cessation remain unclear. By using time-lapse imaging, genetics, and computational analysis, we analyze the effect of cytokinin on root zonation and cellular growth. We found that cytokinin promotes growth cessation in the distal (shootward) elongation zone in conjunction with accelerating the transition from elongation to differentiation. We estimated cell-wall stiffness by using osmotic treatment experiments and found that cytokinin-mediated growth cessation is associated with cell-wall stiffening and requires the action of an auxin influx carrier, AUX1. Our measurement of growth and cell-wall mechanical properties at a cellular resolution reveal mechanisms via which cytokinin influences cell behavior to shape tissue patterns.

Modeling Auxin Signaling in Roots: Auxin Computations

Auxin signaling and patterning is an inherently complex process, involving polarized auxin transport, metabolism, and signaling, its effect on developmental zones, as well as growth rates, and the feedback between all these different aspects. This complexity has led to an important role for computational modeling in unraveling the multifactorial roles of auxin in plant developmental and adaptive processes. Here we discuss the basic ingredients of auxin signaling and patterning models for root development as well as a series of key modeling studies in this area. These modeling studies have helped elucidate how plants use auxin signaling to compute the size of their root meristem, the direction in which to grow, and when and where to form lateral roots. Importantly, these models highlight how auxin, through patterning of and collaborating with other factors, can fulfill all these roles simultaneously.

The root meristem is shaped by brassinosteroid control of cell geometry

Growth extent and direction determine cell and whole-organ architecture. How they are spatio-temporally modulated to control size and shape is not well known. Here we tackled this question by studying the effect of brassinosteroid (BR) signalling on the structure of the root meristem. Quantification of the three-dimensional geometry of thousands of individual meristematic cells across different tissue types showed that the modulation of BR signalling yields distinct changes in growth rate and anisotropy, which affects the time that cells spend in the meristem and has a strong impact on the final root form. By contrast, the hormone effect on cell volume was minor, establishing cell volume as invariant to the effect of BR. Thus, BR has the highest effect on cell shape and growth anisotropy, regulating the overall longitudinal and radial growth of the meristem, while maintaining a coherent distribution of cell sizes. Moving from single-cell quantification to the whole organ, we developed a computational model of radial growth. The simulation demonstrates how differential BR-regulated growth between the inner and outer tissues shapes the meristem and thus explains the non-intuitive outcomes of tissue-specific perturbation of BR signalling. The combined experimental data and simulation suggest that the inner and outer tissues have distinct but coordinated roles in growth regulation.

A coupled mechano-biochemical model for cell polarity guided anisotropic root growth

Plants develop new organs to adjust their bodies to dynamic changes in the environment. How independent organs achieve anisotropic shapes and polarities is poorly understood. To address this question, we constructed a mechano-biochemical model for Arabidopsis root meristem growth that integrates biologically plausible principles. Computer model simulations demonstrate how differential growth of neighboring tissues results in the initial symmetry-breaking leading to anisotropic root growth. Furthermore, the root growth feeds back on a polar transport network of the growth regulator auxin. Model, predictions are in close agreement with in vivo patterns of anisotropic growth, auxin distribution, and cell polarity, as well as several root phenotypes caused by chemical, mechanical, or genetic perturbations. Our study demonstrates that the combination of tissue mechanics and polar auxin transport organizes anisotropic root growth and cell polarities during organ outgrowth. Therefore, a mobile auxin signal transported through immobile cells drives polarity and growth mechanics to coordinate complex organ development.

A Sight on Single-Cell Transcriptomics in Plants Through the Prism of Cell-Based Computational Modeling Approaches: Benefits and Challenges for Data Analysis

Single-cell technology is a relatively new and promising way to obtain high-resolution transcriptomic data mostly used for animals during the last decade. However, several scientific groups developed and applied the protocols for some plant tissues. Together with deeply-developed cell-resolution imaging techniques, this achievement opens up new horizons for studying the complex mechanisms of plant tissue architecture formation. While the opportunities for integrating data from transcriptomic to morphogenetic levels in a unified system still present several difficulties, plant tissues have some additional peculiarities. One of the plants' features is that cell-to-cell communication topology through plasmodesmata forms during tissue growth and morphogenesis and results in mutual regulation of expression between neighboring cells affecting internal processes and cell domain development. Undoubtedly, we must take this fact into account when analyzing single-cell transcriptomic data. Cell-based computational modeling approaches successfully used in plant morphogenesis studies promise to be an efficient way to summarize such novel multiscale data. The inverse problem's solutions for these models computed on the real tissue templates can shed light on the restoration of individual cells' spatial localization in the initial plant organ-one of the most ambiguous and challenging stages in single-cell transcriptomic data analysis. This review summarizes new opportunities for advanced plant morphogenesis models, which become possible thanks to single-cell transcriptome data. Besides, we show the prospects of microscopy and cell-resolution imaging techniques to solve several spatial problems in single-cell transcriptomic data analysis and enhance the hybrid modeling framework opportunities.

Positioning the Root Elongation Zone Is Saltatory and Receives Input from the Shoot

In the root, meristem and elongation zone lengths remain stable, despite growth and division of cells. To gain insight into zone stability, we imaged individual Arabidopsis thaliana roots through a horizontal microscope and used image analysis to obtain velocity profiles. For a root, velocity profiles obtained every 5 min over 3 h coincided closely, implying that zonation is regulated tightly. However, the position of the elongation zone saltated, by on average 17 μm every 5 min. Saltation was apparently driven by material elements growing faster and then slower, while moving through the growth zone. When the shoot was excised, after about 90 min, growth zone dynamics resembled those of intact roots, except that the position of the elongation zone moved, on average, rootward, by several hundred microns in 24 h. We hypothesize that mechanisms determining elongation zone position receive input from the shoot.

Dissecting mechanisms in root growth from the transition zone perspective

The root of the plant Arabidopsis thaliana is a dynamic structure in which cells continuously divide and differentiate to sustain its postembryonic undetermined growth. Cells at different developmental stages are organized in distinguished zones whose position and activities are maintained constant during root growth. In this review, we will discuss the latest discoveries on the regulatory networks involved in root zonation and, in particular, in the mechanisms involved in maintaining the position of the transition zone, a root developmental boundary. Developmental boundaries physically divide cells with different functions and identities. The transition zone separates dividing cells from differentiating cells in two functional domains, preserving their identity during root growth and thus controlling root development.

How grass keeps growing: an integrated analysis of hormonal crosstalk in the maize leaf growth zone

We studied the maize leaf to understand how long-distance signals, auxin and cytokinin, control leaf growth dynamics. We constructed a mathematical model describing the transport of these hormones along the leaf growth zone and their interaction with the local gibberellin (GA) metabolism in the control of cell division. Assuming gradually declining auxin and cytokinin supply at the leaf base, the model generated spatiotemporal hormone distribution and growth patterns that matched experimental data. At the cellular level, the model predicted a basal leaf growth as a result of cell division driven by auxin and cytokinin. Superimposed on this, GA synthesis regulated growth through the control of the size of the region of active cell division. The predicted hormone and cell length distributions closely matched experimental data. To correctly predict the leaf growth profiles and final organ size of lines with reduced or elevated GA production, the model required a signal proportional to the size of the emerged part of the leaf that inhibited the basal leaf growth driven by auxin and cytokinin. Excision and shading of the emerged part of the growing leaf allowed us to demonstrate that this signal exists and depends on the perception of light intensity.

Growth models from a brassinosteroid perspective

Plant growth relies on interconnected hormonal pathways, their corresponding transcriptional networks and mechanical signals. This work reviews recent brassinosteroid (BR) studies and integrates them with current growth models derived from research in roots. The relevance of spatiotemporal BR signaling in the longitudinal and radial root axes and its multifaceted interaction with auxin, the impact of BR on final cell size determination and its interplay with microtubules and the cell wall are discussed. Also highlighted are emerging variations of canonical BR signaling that could function in developmental-specific context.

Gibberellin Enhances the Anisotropy of Cell Expansion in the Growth Zone of the Maize Leaf

Although plant organ shapes are defined by spatio-temporal variations of directional tissue expansion, this is a little characterized aspect of organ growth regulation. Although it is well known that the plant hormone gibberellin increases the leaf length/with ratio, its effects on cell expansion in the growing leaf are largely unknown. To understand how variations in rate and anisotropy of growth establish the typical monocotelydonous leaf shape, we studied the leaf growth zone of maize (Zea mays) with a kinematic analysis of cell expansion in the three directions of growth: proximo-distal, medio-lateral, and dorso-ventral. To determine the effect of gibberellin, we compared a gibberellin-deficient dwarf3 mutant and the overproducing UBI::GA20OX-1 line with their wild types. We found that, as expected, longitudinal growth was dominant throughout the growth zone. The highest degree of anisotropy occurred in the division zone, where relative growth rates in width and thickness were almost zero. Growth anisotropy was smaller in the elongation zone, due to higher lateral and dorso-ventral growth rates. Growth in all directions stopped at the same position. Gibberellin increased the size of the growth zone and the degree of growth anisotropy by stimulating longitudinal growth rates. Inversely, the duration of expansion was negatively affected, so that mature cell length was unaffected, while width and height of cells were reduced. Our study provides a detailed insight in the dynamics of growth anisotropy in the maize leaf and demonstrates that gibberellin specifically stimulates longitudinal growth rates throughout the growth zone.

Cellular Dynamics, a Systems Biology Bottleneck

Developing a mechanistic understanding of plant growth regulation requires studying cell division and cell expansion in addition to molecular studies. A recent time-lapse confocal microscopy study (Fox, S. et al. PLoS Biol. 2018:16;e2005952) quantifying these processes in individual cells in growing organs in combination with multiscale modeling provides profound new insights into the regulatory mechanisms involved.

Week-long imaging of cell divisions in the Arabidopsis root meristem

BACKGROUND

Characterizing the behaviors of dynamic systems requires capturing them with high temporal and spatial resolution. Owing to its transparency and genetic tractability, the Arabidopsis thaliana root lends itself well to live imaging when combined with cell and tissue-specific fluorescent reporters. We developed a novel 4D imaging method that utilizes simple confocal microscopy and readily available components to track cell divisions in the root stem cell niche and surrounding region for up to 1 week.

RESULTS

Using this method, we performed a direct measurement of cell division intervals within and around the root stem cell niche. The results reveal a short, steep gradient of cell division rates in proximal stem cells, with progressively more rapid cell division rates from quiescent center (QC), to cells in direct contact with the QC (initials), to their immediate daughters, after which division rates appear to become more homogeneous.

CONCLUSIONS

These results provide a baseline to study how perturbations in signaling could affect cell division patterns in the root meristem. This new setup further allows us to finely analyze meristematic cell division rates that lead to patterning.

In Silico Roots: Room for Growth

Computational models are invaluable tools for understanding the hormonal and genetic control of root development. Thus far, models have focused on the crucial roles that auxin transport and metabolism play in determining the auxin signaling gradient that controls the root meristem. Other hormones such as cytokinins, gibberellins, and ethylene have predominantly been considered as modulators of auxin dynamics, but their underlying patterning mechanisms are currently unresolved. In addition, the effects of cell- and tissue-level growth dynamics, which induce dilution and displacement of signaling molecules, have remained unexplored. Elucidating these additional mechanisms will be essential to unravel how root growth is patterned in a robust and self-organized manner. Models incorporating growth will thus be crucial in unraveling the underlying logic of root developmental decision making.

Quantitative dissection of variations in root growth rate: a matter of cell proliferation or of cell expansion?

Plant organ growth results from cell production and cell expansion. Deciphering the contribution of each of these processes to growth rate is an important issue in developmental biology. Here, we investigated the cellular processes governing root elongation rate, considering two sources of variation: genotype and disturbance by chemicals (NaCl, polyethylene glycol, H2O2, abscisic acid). Exploiting the adventitious rooting capacity of the Populus genus, and using time-lapse imaging under infrared-light, particle image velocimetry, histological analysis, and kinematics, we quantified the cellular processes involved in root growth variation, and analysed the covariation patterns between growth parameters. The rate of cell production by the root apical meristem and the number of dividing cells were estimated in vivo without destructive measurement. We found that the rate of cell division contributed more to the variation in cell production rate than the number of dividing cells. Regardless of the source of variation, the length of the elongation zone was the best proxy for growth rate, summarizing rates of cell production and cell elongation into a single parameter. Our results demonstrate that cell production rate is the main driver of growth rate, whereas elemental elongation rate is a key driver of short-term growth adjustments.

A Sizer model for cell differentiation in Arabidopsis thaliana root growth

Plant roots grow due to cell division in the meristem and subsequent cell elongation and differentiation, a tightly coordinated process that ensures growth and adaptation to the changing environment. How the newly formed cells decide to stop elongating becoming fully differentiated is not yet understood. To address this question, we established a novel approach that combines the quantitative phenotypic variability of wild‐type Arabidopsis roots with computational data from mathematical models. Our analyses reveal that primary root growth is consistent with a Sizer mechanism, in which cells sense their length and stop elongating when reaching a threshold value. The local expression of brassinosteroid receptors only in the meristem is sufficient to set this value. Analysis of roots insensitive to BR signaling and of roots with gibberellin biosynthesis inhibited suggests distinct roles of these hormones on cell expansion termination. Overall, our study underscores the value of using computational modeling together with quantitative data to understand root growth.

What determines organ size differences between species? A meta-analysis of the cellular basis

Little is known about how the characteristic differences in organ size between species are regulated. At the cellular level, the size of an organ is strictly regulated by cell division and expansion during its development. We performed a meta-analysis of the growth parameters of roots, and Graminae and eudicotyledonous leaves, to address the question of how quantitative variation in these two processes contributes to size differences across a range of species. We extracted or derived cellular parameters from published kinematic growth analyses. These data were subjected to linear regression analyses to identify the parameters that determine differences in organ growth. Our results demonstrate that, across all species and organs, similar conclusions can be made: cell number rather than cell size determines the final size of plant organs; cell number is determined by meristem size rather than the rate at which cells divide; cells that are small when leaving the meristem compensate by expanding for longer; mature cell size is primarily determined by the duration of cell expansion. These results identify the regulation of the transition from cell division to expansion as the key cellular mechanism targeted by the evolution of organ size.

Virtual Plant Tissue: Building Blocks for Next-Generation Plant Growth Simulation

Motivation: Computational modeling of plant developmental processes is becoming increasingly important. Cellular resolution plant tissue simulators have been developed, yet they are typically describing physiological processes in an isolated way, strongly delimited in space and time. Results: With plant systems biology moving toward an integrative perspective on development we have built the Virtual Plant Tissue (VPTissue) package to couple functional modules or models in the same framework and across different frameworks. Multiple levels of model integration and coordination enable combining existing and new models from different sources, with diverse options in terms of input/output. Besides the core simulator the toolset also comprises a tissue editor for manipulating tissue geometry and cell, wall, and node attributes in an interactive manner. A parameter exploration tool is available to study parameter dependence of simulation results by distributing calculations over multiple systems. Availability: Virtual Plant Tissue is available as open source (EUPL license) on Bitbucket (https://bitbucket.org/vptissue/vptissue). The project has a website https://vptissue.bitbucket.io.

Temperature-compensated cell production rate and elongation zone length in the root of Arabidopsis thaliana

To understand how root growth responds to temperature, we used kinematic analysis to quantify division and expansion parameters in the root of Arabidopsis thaliana. Plants were grown at temperatures from 15 to 30 °C, given continuously from germination. Over these temperatures, root length varies more than threefold in the wild type but by only twofold in a double mutant for phytochrome-interacting factor 4 and 5. For kinematics, the spatial profile of velocity was obtained with new software, Stripflow. We find that 30 °C truncates the elongation zone and curtails cell production, responses that probably reflect the elicitation of a common pathway for handling severe stresses. Curiously, rates of cell division at all temperatures are closely correlated with rates of radial expansion. Between 15 to 25 °C, root growth rate, maximal elemental elongation rate, and final cell length scale positively with temperature whereas the length of the meristem scales negatively. Non-linear temperature scaling characterizes meristem cell number, time to transit through either meristem or elongation zone, and average cell division rate. Surprisingly, the length of the elongation zone and the total rate of cell production are temperature invariant, constancies that have implications for our understanding of how the underlying cellular processes are integrated.

Computational Modeling of Auxin: A Foundation for Plant Engineering

Since the development of agriculture, humans have relied on the cultivation of plants to satisfy our increasing demand for food, natural products, and other raw materials. As we understand more about plant development, we can better manipulate plants to fulfill our particular needs. Auxins are a class of simple metabolites that coordinate many developmental activities like growth and the appearance of functional structures in plants. Computational modeling of auxin has proven to be an excellent tool in elucidating many mechanisms that underlie these developmental events. Due to the complexity of these mechanisms, current modeling efforts are concerned only with single phenomena focused on narrow spatial and developmental contexts; but a general model of plant development could be assembled by integrating the insights from all of them. In this perspective, we summarize the current collection of auxin-driven computational models, focusing on how they could come together into a single model for plant development. A model of this nature would allow researchers to test hypotheses in silico and yield accurate predictions about the behavior of a plant under a given set of physical and biochemical constraints. It would also provide a solid foundation toward the establishment of plant engineering, a proposed discipline intended to enable the design and production of plants that exhibit an arbitrarily defined set of features.

Mechanical Behavior of Cells within a Cell-Based Model of Wheat Leaf Growth

Understanding the principles and mechanisms of cell growth coordination in plant tissue remains an outstanding challenge for modern developmental biology. Cell-based modeling is a widely used technique for studying the geometric and topological features of plant tissue morphology during growth. We developed a quasi-one-dimensional model of unidirectional growth of a tissue layer in a linear leaf blade that takes cell autonomous growth mode into account. The model allows for fitting of the visible cell length using the experimental cell length distribution along the longitudinal axis of a wheat leaf epidermis. Additionally, it describes changes in turgor and osmotic pressures for each cell in the growing tissue. Our numerical experiments show that the pressures in the cell change over the cell cycle, and in symplastically growing tissue, they vary from cell to cell and strongly depend on the leaf growing zone to which the cells belong. Therefore, we believe that the mechanical signals generated by pressures are important to consider in simulations of tissue growth as possible targets for molecular genetic regulators of individual cell growth.

The build-up of osmotic stress responses within the growing root apex using kinematics and RNA-sequencing

Molecular regulation of growth must include spatial and temporal coupling of cell production and cell expansion. The underlying mechanisms, especially under environmental challenge, remain obscure. Spatial patterns of cell processes make the root apex well suited to deciphering stress signaling pathways, and to investigating both processes. Kinematics and RNA-sequencing were used to analyze the immediate growth response of hydroponically grown Populus nigra cuttings submitted to osmotic stress. About 7400 genes and unannotated transcriptionally active regions were differentially expressed between the division and elongation zones. Following the onset of stress, growth decreased sharply, probably due to mechanical effects, before recovering partially. Stress impaired cell expansion over the apex, progressively shortened the elongation zone, and reduced the cell production rate. Changes in gene expression revealed that growth reduction was mediated by a shift in hormone homeostasis. Osmotic stress rapidly elicited auxin, ethylene, and abscisic acid. When growth restabilized, transcriptome remodeling became complex and zone specific, with the deployment of hormone signaling cascades, transcriptional regulators, and stress-responsive genes. Most transcriptional regulations fit growth reduction, but stress also promoted expression of some growth effectors, including aquaporins and expansins Together, osmotic stress interfered with growth by activating regulatory proteins rather than by repressing the machinery of expansive growth.

Shifting foundations: the mechanical cell wall and development

The cell wall has long been acknowledged as an important physical mediator of growth in plants. Recent experimental and modelling work has brought the importance of cell wall mechanics into the forefront again. These data have challenged existing dogmas that relate cell wall structure to cell/organ growth, that uncouple elasticity from extensibility, and those which treat the cell wall as a passive and non-stressed material. Within this review we describe experiments and models which have changed the ways in which we view the mechanical cell wall, leading to new hypotheses and research avenues. It has become increasingly apparent that while we often wish to simplify our systems, we now require more complex multi-scale experiments and models in order to gain further insight into growth mechanics. We are currently experiencing an exciting and challenging shift in the foundations of our understanding of cell wall mechanics in growth and development.

The Maize Leaf: Another Perspective on Growth Regulation

The Arabidopsis thaliana root tip has been a key experimental system to study organ growth regulation. It has clear advantages for genetic, transcriptomic, and cell biological studies that focus on the control of cell division and expansion along its longitudinal axis. However, the system shows some limitations for methods that currently require too much tissue to perform them at subzonal resolution, including quantification of proteins, enzyme activity, hormone, and metabolite levels and cell wall extensibility. By contrast, the larger size of the maize leaf does allow such analyses. Here we highlight exciting new possibilities to advance mechanistic understanding of plant growth regulation by using the maize leaf as a complimentary system to the Arabidopsis root tip.

Modeling plant development: from signals to gene networks

Mathematical modeling has become a common tool in plant developmental biology. Indeed, it allows for the prediction of complex and often unintuitive dynamics of the molecular networks driving plant development. This has enabled the test of their possible involvement in robust and specific developmental processes. Modeling has also been fruitful in predicting new interactions within gene networks, such as the Arabidopsis circadian clock. A new challenge is to integrate patterning issues with tissue growth and biomechanics. The development of new tools to gain resolution in data collection as well as new frameworks to confront models and data might provide even more robust predictions.

Spatial Regulation of Root Growth: Placing the Plant TOR Pathway in a Developmental Perspective

Plant cells contain specialized structures, such as a cell wall and a large vacuole, which play a major role in cell growth. Roots follow an organized pattern of development, making them the organs of choice for studying the spatio-temporal regulation of cell proliferation and growth in plants. During root growth, cells originate from the initials surrounding the quiescent center, proliferate in the division zone of the meristem, and then increase in length in the elongation zone, reaching their final size and differentiation stage in the mature zone. Phytohormones, especially auxins and cytokinins, control the dynamic balance between cell division and differentiation and therefore organ size. Plant growth is also regulated by metabolites and nutrients, such as the sugars produced by photosynthesis or nitrate assimilated from the soil. Recent literature has shown that the conserved eukaryotic TOR (target of rapamycin) kinase pathway plays an important role in orchestrating plant growth. We will summarize how the regulation of cell proliferation and cell expansion by phytohormones are at the heart of root growth and then discuss recent data indicating that the TOR pathway integrates hormonal and nutritive signals to orchestrate root growth.