Role of transcriptional regulation in auxin-mediated response to abiotic stresses.

Global climate change (GCC) is posing a serious threat to organisms, particularly plants, which are sessile. Drought, salinity, and the accumulation of heavy metals alter soil composition and have detrimental effects on crops and wild plants. The hormone auxin plays a pivotal role in the response to stress conditions through the fine regulation of plant growth. Hence, rapid, tight, and coordinated regulation of its concentration is achieved by auxin modulation at multiple levels. Beyond the structural enzymes involved in auxin biosynthesis, transport, and signal transduction, transcription factors (TFs) can finely and rapidly drive auxin response in specific tissues. Auxin Response Factors (ARFs) such as the ARF4, 7, 8, 19 and many other TF families, such as WRKY and MADS, have been identified to play a role in modulating various auxin-mediated responses in recent times. Here, we review the most relevant and recent literature on TFs associated with the regulation of the biosynthetic, transport, and signalling auxin pathways and miRNA-related feedback loops in response to major abiotic stresses. Knowledge of the specific role of TFs may be of utmost importance in counteracting the effects of GCC on future agriculture and may pave the way for increased plant resilience.

microRNA165 and 166 modulate response of the Arabidopsis root apical meristem to salt stress.

In plants, developmental plasticity allows for the modulation of organ growth in response to environmental cues. Being in contact with soil, roots are the first organ that responds to various types of soil abiotic stress such as high salt concentration. In the root, developmental plasticity relies on changes in the activity of the apical meristem, the region at the tip of the root where a set of self-renewing undifferentiated stem cells sustain growth. Here, we show that salt stress promotes differentiation of root meristem cells via reducing the dosage of the microRNAs miR165 and 166. By means of genetic, molecular and computational analysis, we show that the levels of miR165 and 166 respond to high salt concentration, and that miR165 and 166-dependent PHABULOSA (PHB) modulation is central to the response of root growth to this stress. Specifically, we show that salt-dependent reduction of miR165 and 166 causes a rapid increase in PHB expression and, hence, production of the root meristem pro-differentiation hormone cytokinin. Our data provide direct evidence for how the miRNA-dependent modulation of transcription factor dosage mediates plastic development in plants.

The Mutual Inhibition between PLETHORAs and ARABIDOPSIS RESPONSE REGULATORs Controls Root Zonation.

During organogenesis, a key step toward the development of a functional organ is the separation of cells into specific domains with different activities. Mutual inhibition of gene expression has been shown to be sufficient to establish and maintain these domains during organogenesis in several multicellular organisms. Here, we show that the mutual inhibition between the PLETHORA transcription factors (PLTs) and the ARABIDOPSIS RESPONSE REGULATORs (ARRs) transcription factors is sufficient to separate cell division and cell differentiation during root organogenesis. In particular, we show that ARR1 suppresses PLT activities and that PLTs suppress ARR1 and ARR12 by targeting their proteins for degradation via the KISS ME DEADLY 2 F-box protein. These findings reveal new important aspects of the complex process of root zonation and development.

It's Time for a Change: The Role of Gibberellin in Root Meristem Development.

One of the most amazing characteristics of plants is their ability to grow and adapt their development to environmental changes. This fascinating feature is possible thanks to the activity of meristems, tissues that contain lasting self-renewal stem cells. Because of its simple and symmetric structure, the root meristem emerged as a potent system to uncover the developmental mechanisms behind the development of the meristems. The root meristem is formed during embryogenesis and sustains root growth for all the plant's lifetime. In the last decade, gibberellins have emerged as a key regulator for root meristem development. This phytohormone functions as a molecular clock for root development. This mini review discusses the latest advances in understanding the role of gibberellin in root development and highlights the central role of this hormone as developmental timer.

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.

A small cog in a large wheel: crucial role of miRNAs in root apical meristem patterning.

In both animal and plants, establishment of body axes is fundamental for proper organ development. Plant roots show two main developmental axes: the proximo-distal axis, which spans from the hypocotyl-root junction to the root tip; and the radial axis, which traverses from the vascular tissue to the epidermis. Root axes are determined in the root meristem. The root meristem occupies the tip of the root and contains self-renewing stem cells, which continuously produce new root cells. An intricate network of signalling pathways regulates meristem function and patterning to ensure proper root development and growth. In the last decade, miRNAs, 20-21 nucleotide-long molecules with morphogenetic activity, emerged as central regulators of root cell patterning. Their activity intersects with master regulators of meristematic activity, including phytohormones. In this review, we discuss the latest findings about the activity of miRNAs and their interaction with other molecular networks in the formation of root meristem axes. Furthermore, we describe how these small molecules allow root growth to adapt to changes in the environment, while maintaining the correct patterning.

A PHABULOSA-Controlled Genetic Pathway Regulates Ground Tissue Patterning in the Arabidopsis Root.

In both animals and plants, development involves anatomical modifications. In the root of Arabidopsis thaliana, maturation of the ground tissue (GT)-a tissue comprising all cells between epidermal and vascular ones-is a paradigmatic example of these modifications, as it generates an additional tissue layer, the middle cortex (MC).1-4 In early post-embryonic phases, the Arabidopsis root GT is composed of one layer of endodermis and one of cortex. A second cortex layer, the MC, is generated by asymmetric cell divisions in about 80% of Arabidopsis primary roots, in a time window spanning from 7 to 14 days post-germination (dpg). The cell cycle regulator CYCLIN D6;1 (CYCD6;1) plays a central role in this process, as its accumulation in the endodermis triggers the formation of MC.5 The phytohormone gibberellin (GA) is a key regulator of the timing of MC formation, as alterations in its signaling and homeostasis result in precocious endodermal asymmetric cell divisions.3,6,7 However, little is known on how GAs are regulated during GT maturation. Here, we show that the HOMEODOMAIN LEUCINE ZIPPER III (HD-ZIPIII) transcription factor PHABULOSA (PHB) is a master regulator of MC formation, controlling the accumulation of CYCD6;1 in the endodermis in a cell non-autonomous manner. We show that PHB activates the GA catabolic gene GIBBERELLIN 2 OXIDASE 2 (GA2ox2) in the vascular tissue, thus regulating the stability of the DELLA protein GIBBERELLIN INSENSITIVE (GAI)-a GA signaling repressor-in the root and, hence, CYCD6;1 expression in the endodermis.

A Self-Organized PLT/Auxin/ARR-B Network Controls the Dynamics of Root Zonation Development in Arabidopsis thaliana.

During organogenesis, coherent organ growth arises from spatiotemporally coordinated decisions of individual cells. In the root of Arabidopsis thaliana, this coordination results in the establishment of a division and a differentiation zone. Cells continuously move through these zones; thus, a major question is how the boundary between these domains, the transition zone, is formed and maintained. By combining molecular genetics with computational modeling, we reveal how an auxin/PLETHORA/ARR-B network controls these dynamic patterning processes. We show that after germination, cell division causes a drop in distal PLT2 levels that enables transition zone formation and ARR12 activation. The resulting PLT2-ARR12 antagonism controls expansion of the division zone (the meristem). The successive ARR1 activation antagonizes PLT2 through inducing the cell-cycle repressor KRP2, thus setting final meristem size. Our work indicates a key role for the interplay between cell division dynamics and regulatory networks in root zonation and transition zone patterning.

Plant science's next top models.

BACKGROUND: Model organisms are at the core of life science research. Notable examples include the mouse as a model for humans, baker's yeast for eukaryotic unicellular life and simple genetics, or the enterobacteria phage λ in virology. Plant research was an exception to this rule, with researchers relying on a variety of non-model plants until the eventual adoption of Arabidopsis thaliana as primary plant model in the 1980s. This proved to be an unprecedented success, and several secondary plant models have since been established. Currently, we are experiencing another wave of expansion in the set of plant models. SCOPE: Since the 2000s, new model plants have been established to study numerous aspects of plant biology, such as the evolution of land plants, grasses, invasive and parasitic plant life, adaptation to environmental challenges, and the development of morphological diversity. Concurrent with the establishment of new plant models, the advent of the 'omics' era in biology has led to a resurgence of the more complex non-model plants. With this review, we introduce some of the new and fascinating plant models, outline why they are interesting subjects to study, the questions they will help to answer, and the molecular tools that have been established and are available to researchers. CONCLUSIONS: Understanding the molecular mechanisms underlying all aspects of plant biology can only be achieved with the adoption of a comprehensive set of models, each of which allows the assessment of at least one aspect of plant life. The model plants described here represent a step forward towards our goal to explore and comprehend the diversity of plant form and function. Still, several questions remain unanswered, but the constant development of novel technologies in molecular biology and bioinformatics is already paving the way for the next generation of plant models.

Autoregulation of RCO by Low-Affinity Binding Modulates Cytokinin Action and Shapes Leaf Diversity.

Mechanisms through which the evolution of gene regulation causes morphological diversity are largely unclear. The tremendous shape variation among plant leaves offers attractive opportunities to address this question. In cruciferous plants, the REDUCED COMPLEXITY (RCO) homeodomain protein evolved via gene duplication and acquired a novel expression domain that contributed to leaf shape diversity. However, the molecular pathways through which RCO regulates leaf growth are unknown. A key question is to identify genome-wide transcriptional targets of RCO and the DNA sequences to which RCO binds. We investigate this question using Cardamine hirsuta, which has complex leaves, and its relative Arabidopsis thaliana, which evolved simple leaves through loss of RCO. We demonstrate that RCO directly regulates genes controlling homeostasis of the hormone cytokinin to repress growth at the leaf base. Elevating cytokinin signaling in the RCO expression domain is sufficient to both transform A. thaliana simple leaves into complex ones and partially bypass the requirement for RCO in C. hirsuta complex leaf development. We also identify RCO as its own target gene. RCO directly represses its own transcription via an array of low-affinity binding sites, which evolved after RCO duplicated from its progenitor sequence. This autorepression is required to limit RCO expression. Thus, evolution of low-affinity binding sites created a negative autoregulatory loop that facilitated leaf shape evolution by defining RCO expression and fine-tuning cytokinin activity. In summary, we identify a transcriptional mechanism through which conflicts between novelty and pleiotropy are resolved during evolution and lead to morphological differences between species.

Inhibition of Polycomb Repressive Complex 2 activity reduces trimethylation of H3K27 and affects development in Arabidopsis seedlings.

BACKGROUND: Polycomb repressive complex 2 (PRC2) is an epigenetic transcriptional repression system, whose catalytic subunit (ENHANCER OF ZESTE HOMOLOG 2, EZH2 in animals) is responsible for trimethylating histone H3 at lysine 27 (H3K27me3). In mammals, gain-of-function mutations as well as overexpression of EZH2 have been associated with several tumors, therefore making this subunit a suitable target for the development of selective inhibitors. Indeed, highly specific small-molecule inhibitors of EZH2 have been reported. In plants, mutations in some PRC2 components lead to embryonic lethality, but no trial with any inhibitor has ever been reported. RESULTS: We show here that the 1,5-bis (3-bromo-4-methoxyphenyl)penta-1,4-dien-3-one compound (RDS 3434), previously reported as an EZH2 inhibitor in human leukemia cells, is active on the Arabidopsis catalytic subunit of PRC2, since treatment with the drug reduces the total amount of H3K27me3 in a dose-dependent fashion. Consistently, we show that the expression level of two PRC2 targets is significantly increased following treatment with the RDS 3434 compound. Finally, we show that impairment of H3K27 trimethylation in Arabidopsis seeds and seedlings affects both seed germination and root growth. CONCLUSIONS: Our results provide a useful tool for the plant community in investigating how PRC2 affects transcriptional control in plant development.

A Growth-Based Framework for Leaf Shape Development and Diversity.

How do genes modify cellular growth to create morphological diversity? We study this problem in two related plants with differently shaped leaves: Arabidopsis thaliana (simple leaf shape) and Cardamine hirsuta (complex shape with leaflets). We use live imaging, modeling, and genetics to deconstruct these organ-level differences into their cell-level constituents: growth amount, direction, and differentiation. We show that leaf shape depends on the interplay of two growth modes: a conserved organ-wide growth mode that reflects differentiation; and a local, directional mode that involves the patterning of growth foci along the leaf edge. Shape diversity results from the distinct effects of two homeobox genes on these growth modes: SHOOTMERISTEMLESS broadens organ-wide growth relative to edge-patterning, enabling leaflet emergence, while REDUCED COMPLEXITY inhibits growth locally around emerging leaflets, accentuating shape differences created by patterning. We demonstrate the predictivity of our findings by reconstructing key features of C. hirsuta leaf morphology in A. thaliana. VIDEO ABSTRACT.

Cytokinin-Dependent Control of GH3 Group II Family Genes in the Arabidopsis Root.

Abstract: The Arabidopsis root is a dynamic system where the interaction between different plant hormones controls root meristem activity and, thus, organ growth. In the root, a characteristic graded distribution of the hormone auxin provides positional information, coordinating the proliferating and differentiating cell status. The hormone cytokinin shapes this gradient by positioning an auxin minimum in the last meristematic cells. This auxin minimum triggers a cell developmental switch necessary to start the differentiation program, thus, regulating the root meristem size. To position the auxin minimum, cytokinin promotes the expression of the IAA-amido synthase group II gene GH3.17, which conjugates auxin with amino acids, in the most external layer of the root, the lateral root cap tissue. Since additional GH3 genes are expressed in the root, we questioned whether cytokinin to position the auxin minimum also operates via different GH3 genes. Here, we show that cytokinin regulates meristem size by activating the expression of GH3.5 and GH3.6 genes, in addition to GH3.17. Thus, cytokinin activity provides a robust control of auxin activity in the entire organ necessary to regulate root growth.

The Lateral Root Cap Acts as an Auxin Sink that Controls Meristem Size.

Plant developmental plasticity relies on the activities of meristems, regions where stem cells continuously produce new cells [1]. The lateral root cap (LRC) is the outermost tissue of the root meristem [1], and it is known to play an important role during root development [2-6]. In particular, it has been shown that mechanical or genetic ablation of LRC cells affect meristem size [7, 8]; however, the molecular mechanisms involved are unknown. Root meristem size and, consequently, root growth depend on the position of the transition zone (TZ), a boundary that separates dividing from differentiating cells [9, 10]. The interaction of two phytohormones, cytokinin and auxin, is fundamental in controlling the position of the TZ [9, 10]. Cytokinin via the ARABIDOPSIS RESPONSE REGULATOR 1 (ARR1) control auxin distribution within the meristem, generating an instructive auxin minimum that positions the TZ [10]. We identify a cytokinin-dependent molecular mechanism that acts in the LRC to control the position of the TZ and meristem size. We show that auxin levels within the LRC cells depends on PIN-FORMED 5 (PIN5), a cytokinin-activated intracellular transporter that pumps auxin from the cytoplasm into the endoplasmic reticulum, and on irreversible auxin conjugation mediated by the IAA-amino synthase GRETCHEN HAGEN 3.17 (GH3.17). By titrating auxin in the LRC, the PIN5 and the GH3.17 genes control auxin levels in the entire root meristem. Overall, our results indicate that the LRC serves as an auxin sink that, under the control of cytokinin, regulates meristem size and root growth.

Building the differences: a case for the ground tissue patterning in plants.

A key question in biology is to understand how interspecies morphological diversities originate. Plant roots present a huge interspecific phenotypical variability, mostly because roots largely contribute to adaptation to different kinds of soils. One example is the interspecific cortex layer number variability, spanning from one to several. Here, we review the latest advances in the understanding of the mechanisms expanding and/or restricting cortical layer number in Arabidopsis thaliana and their involvement in cortex pattern variability among multi-cortical layered species such as Cardamine hirsuta or Oryza sativa.

SCARECROW and SHORTROOT control the auxin/cytokinin balance necessary for embryonic stem cell niche specification.

The root apical meristem is established during embryogenesis, when its organizer, the quiescent center, is specified and the stem cell niche is positioned. The SCARECROW-SHORTROOT heterodimer is essential for quiescent center specification and maintenance. As continuous post-embryonic root growth relies upon the SCARECROW-mediated control of the cytokinin/auxin balance, we investigated the role of SCARECROW and SHORTROOT in controlling cytokinin signaling during embryonic quiescent center specification. We found that from embryogenesis onward both SCARECROW and SHORTROOT antagonize cytokinin signaling, thus repressing the expression of the auxin biosynthetic enzyme ANTRANILATHE SYNTHASE BETA 1. This mechanism prevents detrimental and premature high auxin levels in the QC allowing the establishment of a functional embryonic root pole.

Acidic cell elongation drives cell differentiation in the Arabidopsis root.

In multicellular systems, the control of cell size is fundamental in regulating the development and growth of the different organs and of the whole organism. In most systems, major changes in cell size can be observed during differentiation processes where cells change their volume to adapt their shape to their final function. How relevant changes in cell volume are in driving the differentiation program is a long-standing fundamental question in developmental biology. In the Arabidopsis root meristem, characteristic changes in the size of the distal meristematic cells identify cells that initiated the differentiation program. Here, we show that changes in cell size are essential for the initial steps of cell differentiation and that these changes depend on the concomitant activation by the plant hormone cytokinin of the EXPAs proteins and the AHA1 and AHA2 proton pumps. These findings identify a growth module that builds on a synergy between cytokinin-dependent pH modification and wall remodeling to drive differentiation through the mechanical control of cell walls.

Differential spatial distribution of miR165/6 determines variability in plant root anatomy.

A clear example of interspecific variation is the number of root cortical layers in plants. The genetic mechanisms underlying this variability are poorly understood, partly because of the lack of a convenient model. Here, we demonstrate that Cardamine hirsuta, unlike Arabidopsis thaliana, has two cortical layers that are patterned during late embryogenesis. We show that a miR165/6-dependent distribution of the HOMEODOMAIN LEUCINE ZIPPER III (HD-ZIPIII) transcription factor PHABULOSA (PHB) controls this pattern. Our findings reveal that interspecies variation in miRNA distribution can determine differences in anatomy in plants.