The PLETHORA genes mediate patterning of the Arabidopsis root stem cell niche

Chromatin remodeling in Arabidopsis root growth

The basic structural unit of chromatin is the nucleosome, which consists of 146 bp of DNA wrapped around the histone octamer constituted by two molecules each of histones H2A, H2B, H3 and H4. Nucleosome assembly/disassembly/reassembly processes occur primarily during DNA replication and also during transcription, DNA repair and recombination. Several chromatin-remodeling factors had been previously shown to have pleiotropic roles in different processes of plant growth and development. We have recently demonstrated that the Arabidopsis NRP1 and NRP2 genes encode H2A/H2B chaperones and are required for the maintenance of post-embryonic root growth. The nrp1-1nrp2-1 double mutant plants specifically showed a short-root phenotype in normal growth conditions. They were also hypersensitive to DNA damage and showed release of transcriptional gene silencing. We propose that NRP1 and NRP2 act as histone H2A/H2B chaperones in nucleosome assembly, playing critical roles for a correct genome transcription in the maintenance of root growth.

Stem-cell niches: nursery rhymes across kingdoms

Despite the large evolutionary distance between the plant and animal kingdoms, stem cells in both reside in specialized cellular contexts called stem-cell niches. Although stem-cell-specification factors have been recruited from plant-specific gene families, maintenance factors that repress stem-cell differentiation are conserved between plants and animals. Recent evidence indicates that stem cells in multicellular organisms can be specified by kingdom-specific patterning mechanisms that connect to a related core of epigenetic stem-cell factors.

Towards the systems biology of auxin-transport-mediated patterning

Polar auxin transport intimately connects plant cell polarity and multicellular patterning. Through the transport of the small molecule indole-3-acetic acid, plant cells integrate their polarities and communicate the degree of their polarization. In this way, they generate an apical-basal axis that serves as a positional reference anchoring subsequent patterning events. Research in recent years has brought the molecular mechanisms underlying auxin perception and auxin transport to light. This knowledge has been used to derive spectacular molecular visualization tools and animated computer simulations, which are now allied in a joint systems biology effort towards a mathematical description of auxin-transport-mediated patterning processes.

Conserved factors regulate signalling in Arabidopsis thaliana shoot and root stem cell organizers

Throughout the lifespan of a plant, which in some cases can last more than one thousand years, the stem cell niches in the root and shoot apical meristems provide cells for the formation of complete root and shoot systems, respectively. Both niches are superficially different and it has remained unclear whether common regulatory mechanisms exist. Here we address whether root and shoot meristems use related factors for stem cell maintenance. In the root niche the quiescent centre cells, surrounded by the stem cells, express the homeobox gene WOX5 (WUSCHEL-RELATED HOMEOBOX 5), a homologue of the WUSCHEL (WUS) gene that non-cell-autonomously maintains stem cells in the shoot meristem. Loss of WOX5 function in the root meristem stem cell niche causes terminal differentiation in distal stem cells and, redundantly with other regulators, also provokes differentiation of the proximal meristem. Conversely, gain of WOX5 function blocks differentiation of distal stem cell descendents that normally differentiate. Importantly, both WOX5 and WUS maintain stem cells in either a root or shoot context. Together, our data indicate that stem cell maintenance signalling in both meristems employs related regulators.

Cytokinins Determine Arabidopsis Root-Meristem Size by Controlling Cell Differentiation

Plant postembryonic development takes place in the meristems, where stem cells self-renew and produce daughter cells that differentiate and give rise to different organ structures. For the maintenance of meristems, the rate of differentiation of daughter cells must equal the generation of new cells: How this is achieved is a central question in plant development. In the Arabidopsis root meristem, stem cells surround a small group of organizing cells, the quiescent center. Together they form a stem cell niche [1, 2], whose position and activity depends on the combinatorial action of two sets of genes - PLETHORA1 (PLT1) and PLETHORA2 (PLT2)[3, 4] and SCARECROW (SCR) and SHORTROOT (SHR)[2] - as well as on polar auxin transport. In contrast, the mechanisms controlling meristematic cell differentiation remain unclear. Here, we report that cytokinins control the rate of meristematic cell differentiation and thus determine root-meristem size via a two-component receptor histidine kinase-transcription factor signaling pathway. Analysis of the root meristems of cytokinin mutants, spatial cytokinin depletion, and exogenous cytokinin application indicates that cytokinins act in a restricted region of the root meristem, where they antagonize a non-cell-autonomous cell-division signal, and we provide evidence that this signal is auxin.

Hormone signalling and root development: an update on the latest Arabidopsis thaliana research

Plants are sessile organisms whose developmental programs depend mainly on environmental cues that are sensed and interpreted through hormonal signalling pathways. Roots are specialised plant organs that are instrumental during water and nutrient uptake, biotic interactions, stress responses and for mechanical support. Our knowledge about the basic molecular events shaping root patterning and growth has advanced significantly in the past few years thanks to the use of Arabidopsis thaliana (L.) Heynh. as a model system. In this review, I will discuss recent findings that indicate crosstalk between growth regulators and hormone signalling pathways during primary root development. Further comparative research using non-model species will shed light on the conserved developmental modules among distant lineages involved in root architecture.

Molecular and cellular aspects of auxin-transport-mediated development

The plant hormone auxin is frequently observed to be asymmetrically distributed across adjacent cells during crucial stages of growth and development. These auxin gradients depend on polar transport and regulate a wide variety of processes, including embryogenesis, organogenesis, vascular tissue differentiation, root meristem maintenance and tropic growth. Auxin can mediate such a perplexing array of developmental processes by acting as a general trigger for the change in developmental program in cells where it accumulates and by providing vectorial information to the tissues by its polar intercellular flow. In recent years, a wealth of molecular data on the mechanism of auxin transport and its regulation has been generated, providing significant insights into the action of this versatile coordinative signal.

Heterologous expression of the BABY BOOM AP2/ERF transcription factor enhances the regeneration capacity of tobacco (Nicotiana tabacum L.)

Gain-of-function studies have shown that ectopic expression of the BABY BOOM (BBM) AP2/ERF domain transcription factor is sufficient to induce spontaneous somatic embryogenesis in Arabidopsis (Arabidopsis thaliana (L.) Heynh) and Brassica napus (B. napus L.) seedlings. Here we examined the effect of ectopic BBM expression on the development and regenerative capacity of tobacco (Nicotiana tabacum L.) through heterologous expression of Arabidopsis and B. napus BBM genes. 35S::BBM tobacco lines exhibited a number of the phenotypes previously observed in 35S::BBM Arabidopsis and B. napus transgenics, including callus formation, leaf rumpling, and sterility, but they did not undergo spontaneous somatic embryogenesis. 35S::BBM plants with severe ectopic expression phenotypes could not be assessed for enhanced regeneration at the seedling stage due to complete male and female sterility of the primary transformants, therefore fertile BBM ectopic expression lines with strong misexpression phenotypes were generated by expressing a steroid-inducible, post-translationally controlled BBM fusion protein (BBM:GR) under the control of a 35S promoter. These lines exhibited spontaneous shoot and root formation, while somatic embryogenesis could be induced from in-vitro germinated seedling hypocotyls cultured on media supplemented with cytokinin. Together these results suggest that ectopic BBM expression in transgenic tobacco also activates cell proliferation pathways, but differences exist between Arabidopsis/B. napus and N. tabacum with respect to their competence to respond to the BBM signalling molecule.

Asymmetric Cell Division in Plant Development

Plant embryogenesis creates a seedling with a basic body plan. Post-embryonically the seedling elaborates with a lifelong ability to develop new tissues and organs. As a result asymmetric cell divisions serve essential roles during embryonic and postembryonic development to generate cell diversity. This review highlights selective cases of asymmetric division in the model plant Arabidopsis thaliana and describes the current knowledge on fate determinants and mechanisms involved. Common themes that emerge are: 1. role of the plant hormone auxin and its polar transport machinery; 2. a MAP kinase signaling cascade and; 3. asymmetric segregating transcription factors that are involved in several asymmetric cell divisions.

Hidden branches: developments in root system architecture

The root system is fundamentally important for plant growth and survival because of its role in water and nutrient uptake. Therefore, plants rely on modulation of root system architecture (RSA) to respond to a changing soil environment. Although RSA is a highly plastic trait and varies both between and among species, the basic root system morphology and its plasticity are controlled by inherent genetic factors. These mediate the modification of RSA, mostly at the level of root branching, in response to a suite of biotic and abiotic factors. Recent progress in the understanding of the molecular basis of these responses suggests that they largely feed through hormone homeostasis and signaling pathways. Novel factors implicated in the regulation of RSA in response to the myriad endogenous and exogenous signals are also increasingly isolated through alternative approaches such as quantitative trait locus analysis.

The rice heterochronic gene SUPERNUMERARY BRACT regulates the transition from spikelet meristem to floral meristem

Regulating the transition of meristem identity is a critical step in reproductive development. After the shoot apical meristem (SAM) acquires inflorescence meristem identity, it goes through a sequential transition to second- and higher-order meristems that can eventually give rise to floral organs. Despite ample information on the molecular mechanisms that control the transition from SAM to inflorescence meristems, little is known about the mechanism for inflorescence development, especially in monocots. Here, we report the identification of the SUPERNUMERARY BRACT (SNB) gene controlling the transition from spikelet meristem to floral meristem and the floral organ development. This gene encodes a putative transcription factor carrying two AP2 domains. The SNB:GFP fusion protein is localized to the nucleus. SNB is expressed in all the examined tissues, but most strongly in the newly emerging spikelet meristems. In SNB knockout plants, the transition from spikelet meristems to floral meristems is delayed, resulting in the production of multiple rudimentary glumes in an alternative phyllotaxy. The development of additional bracts interferes with subsequent floral architecture. In some spikelets, the empty glumes and lodicules are transformed into lemma/palea-like organs. Occasionally, the number of stamens and carpels is altered and an ectopic floret occurs in the axil of the rachilla. These phenotypes suggest that snb is a heterochronic mutant, affecting the phase transition of spikelet meristems, the pattern formation of floral organs and spikelet meristem determinancy.

Auxin‐Mediated Lateral Root Formation in Higher Plants

Lateral root (LR) formation is an important organogenetic process that contributes to the establishment of root architecture in higher plants. In the angiosperms, LRs are initiated from the pericycle, an inner cell layer of the parent roots. Auxin is a key plant hormone that promotes LR formation, but the molecular mechanisms of auxin-mediated LR formation remain unknown. Molecular genetic studies using Arabidopsis mutants have revealed that the auxin transport system with a balance of influx and efflux is important for LR initiation and subsequent LR primordium development. In addition, normal auxin signaling mediated by two families of transcriptional regulators, Aux/IAAs and ARFs, is necessary for LR formation. This article is an update on the mechanisms of auxin-mediated LR formation in higher plants, particularly in Arabidopsis.

The cellular and molecular biology of conifer embryogenesis

Gymnosperms and angiosperms are thought to have evolved from a common ancestor c. 300 million yr ago. The manner in which gymnosperms and angiosperms form seeds has diverged and, although broad similarities are evident, the anatomy and cell and molecular biology of embryogenesis in gymnosperms, such as the coniferous trees pine, spruce and fir, differ significantly from those in the most widely studied model angiosperm Arabidopsis thaliana. Molecular analysis of signaling pathways and processes such as programmed cell death and embryo maturation indicates that many developmental pathways are conserved between angiosperms and gymnosperms. Recent genomics research reveals that almost 30% of mRNAs found in developing pine embryos are absent from other conifer expressed sequence tag (EST) collections. These data show that the conifer embryo differs markedly from other gymnosperm tissues studied to date in terms of the range of genes transcribed. Approximately 72% of conifer embryo-expressed genes are found in the Arabidopsis proteome and conifer embryos contain mRNAs of very similar sequence to key genes that regulate seed development in Arabidopsis. However, 1388 loblolly pine (Pinus taeda) embryo ESTs (11.4% of the collection) are novel and, to date, have been found in no other plant. The data imply that, in gymnosperm embryogenesis, differences in structure and development are achieved by subtle molecular interactions, control of spatial and temporal gene expression and the regulating agency of a few unique proteins.

BOLITA, an Arabidopsis AP2/ERF-like transcription factor that affects cell expansion and proliferation/differentiation pathways

The BOLITA (BOL) gene, an AP2/ERF transcription factor, was characterized with the help of an activation tag mutant and overexpression lines in Arabidopsis and tobacco. The leaf size of plants overexpressing BOL was smaller than wild type plants due to a reduction in both cell size and cell number. Moreover, severe overexpressors showed ectopic callus formation in roots. Accordingly, global gene expression analysis using the overexpression mutant reflected the alterations in cell proliferation, differentiation and growth through expression changes in RBR, CYCD, and TCP genes, as well as genes involved in cell expansion (i.e. expansins and the actin remodeling factor ADF5). Furthermore, the expression of hormone signaling (i.e. auxin and cytokinin), biosynthesis (i.e. ethylene and jasmonic acid) and regulatory genes was found to be perturbed in bol-D mutant leaves.

Arabidopsis NRP1 and NRP2 encode histone chaperones and are required for maintaining postembryonic root growth

NUCLEOSOME ASSEMBLY PROTEIN1 (NAP1) is conserved from yeast to human and was proposed to act as a histone chaperone. While budding yeast contains a single NAP1 gene, multicellular organisms, including plants and animals, contain several NAP1 and NAP1-RELATED PROTEIN (NRP) genes. However, the biological role of these genes has been largely unexamined. Here, we show that, in Arabidopsis thaliana, simultaneous knockout of the two NRP genes, NRP1 and NRP2, impaired postembryonic root growth. In the nrp1-1 nrp2-1 double mutant, arrest of cell cycle progression at G2/M and disordered cellular organization occurred in root tips. The mutant seedlings exhibit perturbed expression of approximately 100 genes, including some genes involved in root proliferation and patterning. The mutant plants are highly sensitive to genotoxic stress and show increased levels of DNA damage and the release of transcriptional gene silencing. NRP1 and NRP2 are localized in the nucleus and can form homomeric and heteromeric protein complexes. Both proteins specifically bind histones H2A and H2B and associate with chromatin in vivo. We propose that NRP1 and NRP2 act as H2A/H2B chaperones in the maintenance of dynamic chromatin in epigenetic inheritance.

Time-lapse analysis of stem-cell divisions in the Arabidopsis thaliana root meristem

In the Arabidopsis root, asymmetric stem-cell divisions produce daughters that form the different root cell types. Here we report the establishment of a confocal tracking system that allows the analysis of numbers and orientations of cell divisions in root stem cells. The system provides direct evidence that stem cells have lower division rates than cells in the proximal meristem. It also allows tracking of cell division timing, which we have used to analyse the synchronization of root cap divisions. Finally, it gives new insights into lateral root cap formation: epidermal stem-cell daughters can rotate the orientation of the division plane like the stem cell.

Transcription factors and hormones: new insights into plant cell differentiation

Plant development is a continuous process, mainly due to the presence of stem cell niches within the root and shoot. The interplay between a host of transcription factors determines whether the cells within the meristem maintain their stem cell state, differentiate into leaves or form secondary meristems, which develop into shoots and flowers. Several recent studies provide new insight into how transcription factors and phytohormones interact within meristems to control cell proliferation and differentiation.

A greenprint for growth: signalling the pattern of proliferation

The shoot and root apical meristems (SAM and RAM, respectively) of plants serve both as sites of cell division and as stem cell niches. The SAM is also responsible for the initiation of new leaves, whereas the analogous process of lateral root initiation occurs in the pericycle, a specialized layer of cells that retains organogenic potential within an otherwise non-dividing region of the root. A picture is emerging of how cell division, growth, and differentiation are coordinated in the meristems and lateral organ primordia of plants. This is starting to reveal striking parallels between the control of stem cell maintenance in both shoots and roots, and to provide information on how signalling from developmental processes and the environment impact on cell behaviour within meristems.

Auxin in action: signalling, transport and the control of plant growth and development

Hormones have been at the centre of plant physiology research for more than a century. Research into plant hormones (phytohormones) has at times been considered as a rather vague subject, but the systematic application of genetic and molecular techniques has led to key insights that have revitalized the field. In this review, we will focus on the plant hormone auxin and its action. We will highlight recent mutagenesis and molecular studies, which have delineated the pathways of auxin transport, perception and signal transduction, and which together define the roles of auxin in controlling growth and patterning.

Expression of CAP2, an APETALA2-family transcription factor from chickpea, enhances growth and tolerance to dehydration and salt stress in transgenic tobacco

The APETALA2 (AP2) domain defines a large family of DNA-binding proteins that play important roles in plant morphology, development, and stress response. We describe isolation and characterization of a gene (CAP2) from chickpea (Cicer arietinum) encoding a novel AP2-family transcription factor. Recombinant CAP2 protein bound specifically to C-repeat/dehydration-responsive element in gel-shift assay and transactivated reporter genes in yeast (Saccharomyces cerevisiae) one-hybrid assay. CAP2 appeared to be a single/low copy intronless gene, and the protein product localized in the nucleus. Transcript level of CAP2 increased by dehydration and by treatment with sodium chloride, abscisic acid, and auxin, but not by treatment with low temperature, salicylic acid, and jasmonic acid. The 35S promoter-driven expression of CAP2 in tobacco (Nicotiana tabacum) caused drastic increase in the leaf cell size, and, thereby, in leaf surface area and number of lateral roots. Transgenic plants demonstrated more tolerance to dehydration and salt stress than the wild-type plants. Transgenic plants expressed higher steady-state transcript levels of abiotic stress-response genes NtERD10B and NtERD10C and auxin-response genes IAA4.2 and IAA2.5. Taken together, our results indicated a mutual interrelation between plant growth-development and abiotic stress-response pathways and a probable involvement of CAP2 in both the signaling pathways.

Dynamic integration of auxin transport and signalling

Recent years have seen rapid progress in our understanding of the mechanism of action of the plant hormone auxin. A major emerging theme is the central importance of the interplay between auxin signalling and the active transport of auxin through the plant to create dynamic patterns of auxin accumulation. Even in tissues where auxin distribution patterns appear stable, they are the product of standing waves, with auxin flowing through the tissue, maintaining local pockets of high and low concentration. The auxin distribution patterns result in changes in gene expression to trigger diverse, context-dependent growth and differentiation responses. Multi-level feedback loops between the signal transduction network and the auxin transport network provide self-stabilising patterns that remain sensitive to the external environment and to the developmental progression of the plant. The full biological implications of the behaviour of this system are only just beginning to be understood through a combination of experimental manipulation and mathematical modelling.

Non-cell-autonomous rescue of anaphase-promoting complex function revealed by mosaic analysis of HOBBIT, an Arabidopsis CDC27 homolog

The Arabidopsis HOBBIT (HBT) gene encodes a homolog of the CDC27 anaphase-promoting complex/cyclosome subunit and is essential for postembryonic development. We induced loss-of-function clones by Cre/lox-mediated recombination of a single complementing HBT transgene in a background homozygous for the strong mutant allele hbt(2311). Defects in cell division and cell expansion are the primary consequences of ubiquitous postembryonic HBT excision. In roots, both cell division and cell expansion are rapidly affected. In contrast, in leaf primordia, cell division and cell expansion halt after a lag phase, which results in different severities of defects in the proximodistal and mediolateral axes. Surprisingly, small clones reveal non-cell-autonomous rescue of hbt mutant cells, indicating a previously unrecognized compensation mechanism for reduced activity of an anaphase-promoting complex/cyclosome component critical for cell cycle progression.

Differential gene expression of wheat progeny with contrasting levels of transpiration efficiency

High water use efficiency or transpiration efficiency (TE) in wheat is a desirable physiological trait for increasing grain yield under water-limited environments. The identification of genes associated with this trait would facilitate the selection for genotypes with higher TE using molecular markers. We performed an expression profiling (microarray) analysis of approximately 16,000 unique wheat ESTs to identify genes that were differentially expressed between wheat progeny lines with contrasting TE levels from a cross between Quarrion (high TE) and Genaro 81 (low TE). We also conducted a second microarray analysis to identify genes responsive to drought stress in wheat leaves. Ninety-three genes that were differentially expressed between high and low TE progeny lines were identified. One fifth of these genes were markedly responsive to drought stress. Several potential growth-related regulatory genes, which were down-regulated by drought, were expressed at a higher level in the high TE lines than the low TE lines and are potentially associated with a biomass production component of the Quarrion-derived high TE trait. Eighteen of the TE differentially expressed genes were further analysed using quantitative RT-PCR on a separate set of plant samples from those used for microarray analysis. The expression levels of 11 of the 18 genes were positively correlated with the high TE trait, measured as carbon isotope discrimination (Delta(13)C). These data indicate that some of these TE differentially expressed genes are candidates for investigating processes that underlie the high TE trait or for use as expression quantitative trait loci (eQTLs) for TE.

Patterns of auxin transport and gene expression during primordium development revealed by live imaging of the Arabidopsis inflorescence meristem

BACKGROUND

Plants produce leaf and flower primordia from a specialized tissue called the shoot apical meristem (SAM). Genetic studies have identified a large number of genes that affect various aspects of primordium development including positioning, growth, and differentiation. So far, however, a detailed understanding of the spatio-temporal sequence of events leading to primordium development has not been established.

RESULTS

We use confocal imaging of green fluorescent protein (GFP) reporter genes in living plants to monitor the expression patterns of multiple proteins and genes involved in flower primordial developmental processes. By monitoring the expression and polarity of PINFORMED1 (PIN1), the auxin efflux facilitator, and the expression of the auxin-responsive reporter DR5, we reveal stereotypical PIN1 polarity changes which, together with auxin induction experiments, suggest that cycles of auxin build-up and depletion accompany, and may direct, different stages of primordium development. Imaging of multiple GFP-protein fusions shows that these dynamics also correlate with the specification of primordial boundary domains, organ polarity axes, and the sites of floral meristem initiation.

CONCLUSIONS

These results provide new insight into auxin transport dynamics during primordial positioning and suggest a role for auxin transport in influencing primordial cell type.

Plant meristems: the fiendish SU DOKU of stem-cell maintenance

Three recent studies have uncovered effector mechanisms and novel pathways in the regulation of the dynamic changes to cell behaviour that occur in plant meristems. The results show how exquisite regulation of cell-cycle mechanisms is central to root stem cell homeostasis.

Whole-genome analysis of the SHORT-ROOT developmental pathway in Arabidopsis

Stem cell function during organogenesis is a key issue in developmental biology. The transcription factor SHORT-ROOT (SHR) is a critical component in a developmental pathway regulating both the specification of the root stem cell niche and the differentiation potential of a subset of stem cells in the Arabidopsis root. To obtain a comprehensive view of the SHR pathway, we used a statistical method called meta-analysis to combine the results of several microarray experiments measuring the changes in global expression profiles after modulating SHR activity. Meta-analysis was first used to identify the direct targets of SHR by combining results from an inducible form of SHR driven by its endogenous promoter, ectopic expression, followed by cell sorting and comparisons of mutant to wild-type roots. Eight putative direct targets of SHR were identified, all with expression patterns encompassing subsets of the native SHR expression domain. Further evidence for direct regulation by SHR came from binding of SHR in vivo to the promoter regions of four of the eight putative targets. A new role for SHR in the vascular cylinder was predicted from the expression pattern of several direct targets and confirmed with independent markers. The meta-analysis approach was then used to perform a global survey of the SHR indirect targets. Our analysis suggests that the SHR pathway regulates root development not only through a large transcription regulatory network but also through hormonal pathways and signaling pathways using receptor-like kinases. Taken together, our results not only identify the first nodes in the SHR pathway and a new function for SHR in the development of the vascular tissue but also reveal the global architecture of this developmental pathway.

Meta-analysis to combine the results of several microarray experiments reveals a new function for the transcription factor SHORT-ROOT in the development of vascular tissue.

Plant stem cells carve their own niche

Stem cells are the precursors of differentiated cells and are, thus, indispensable for growth and development in plants and animals. Stem cells from both types of organisms share the fundamental features of a capacity for self-renewal and an ability to generate differentiated cells. The maintenance of stem cells in both systems is dependent upon reciprocal signalling between stem cells and the specialized tissue microenvironment known as the niche, which provides intercellular signals for stem cell regulation. One significantly underexplored facet of plant stem cells is the nature of their intrinsic transcriptional programme. A potentially rich avenue for addressing this deficiency is to combine laser-assisted microdissection and genome-wide transcriptional profiling to unravel the molecular road map controlling plant stem cells and their niches.

A systems approach to understanding root development

Systems theory has been applied to process analysis in a variety of scientific disciplines from engineering to evolutionary biology. In the recent postgenomic era, the accumulation of an enormous amount of data gained from a variety of technologies has led to a revisiting of systems theory concepts. This systems biology approach has been integral in understanding a variety of processes in a number of model organisms. This review gives an overview of systems biology approaches, from component identification to modeling of networks. Various features of the root, including its development and the availability of high resolution gene expression data sets that describe root development, make the root amenable to a systems approach. The current status of systems approaches to understanding root development is reviewed.

Lateral root initiation or the birth of a new meristem

Root branching happens through the formation of new meristems out of a limited number of pericycle cells inside the parent root. As opposed to shoot branching, the study of lateral root formation has been complicated due to its internal nature, and a lot of questions remain unanswered. However, due to the availability of new molecular tools and more complete genomic data in the model species Arabidopsis, the probability to find new and crucial elements in the lateral root formation pathway has increased. Increasingly more data are supporting the idea that lateral root founder cells become specified in young root parts before differentiation is accomplished. Next, pericycle founder cells undergo anticlinal asymmetric, divisions followed by an organized cell division pattern resulting in the formation of a new organ. The whole process of cell cycle progression and stimulation of the molecular pathway towards lateral root initiation is triggered by the plant hormone auxin. In this review, we aim to give an overview on the developmental events taking place from the very early specification of founder cells in the pericycle until the first anticlinal divisions by combining the knowledge originating from classical physiology studies with new insights from genetic-molecular analyses. Based on the current knowledge derived from recent genetic and developmental studies, we propose here a hypothetical model for LRI.

Stem cell signalling networks in plants

The essential nature of meristematic tissues is addressed with reference to conceptual frameworks that have been developed to explain the behaviour of animal stem cells. Comparisons are made between different types of plant meristems with the objective of highlighting common themes that might illuminate underlying mechanisms. A more in depth comparison of the root and shoot apical meristems is made which suggests a common mechanism for maintaining stem cells. The relevance of organogenesis to stem cell maintenance is discussed, along with the nature of underlying mechanisms which help ensure that stem cell production is balanced with the depletion of cells through differentiation. Mechanisms that integrate stem cell behaviour in the whole plant are considered, with a focus on the roles of auxin and cytokinin. The review concludes with a brief discussion of epigenetic mechanisms that act to stabilise and maintain stem cell populations.

The RETINOBLASTOMA-RELATED gene regulates stem cell maintenance in Arabidopsis roots

The maintenance of stem cells in defined locations is crucial for all multicellular organisms. Although intrinsic factors and signals for stem cell fate have been identified in several species, it has remained unclear how these connect to the ability to reenter the cell cycle that is one of the defining properties of stem cells. We show that local reduction of expression of the RETINOBLASTOMA-RELATED (RBR) gene in Arabidopsis roots increases the amount of stem cells without affecting cell cycle duration in mitotically active cells. Conversely, induced RBR overexpression dissipates stem cells prior to arresting other mitotic cells. Overexpression of D cyclins, KIP-related proteins, and E2F factors also affects root stem cell pool size, and genetic interactions suggest that these factors function in a canonical RBR pathway to regulate somatic stem cells. Expression analysis and genetic interactions position RBR-mediated regulation of the stem cell state downstream of the patterning gene SCARECROW.

Stem cell research goes underground: the RETINOBLASTOMA-RELATED gene in root development

Both cellular differentiation and stem cell maintenance must occur at the root apex in order to ensure the continuous growth of plant roots. In this issue of Cell, it is revealed that a canonical retinoblastoma pathway plays a crucial role in regulating the balance between differentiation and renewal of plant root stem cells.

Characterization of low phosphorus insensitive mutants reveals a crosstalk between low phosphorus-induced determinate root development and the activation of genes involved in the adaptation of Arabidopsis to phosphorus deficiency

Low phosphorus (P) availability is one of the most limiting factors for plant productivity in many natural and agricultural ecosystems. Plants display a wide range of adaptive responses to cope with low P stress, which generally serve to enhance P availability in the soil and to increase its uptake by roots. In Arabidopsis (Arabidopsis thaliana), primary root growth inhibition and increased lateral root formation have been reported to occur in response to P limitation. To gain knowledge of the genetic mechanisms that regulate root architectural responses to P availability, we designed a screen for identifying Arabidopsis mutants that fail to arrest primary root growth when grown under low P conditions. Eleven low phosphorus insensitive (lpi) mutants that define at least four different complementation groups involved in primary root growth responses to P availability were identified. The lpi mutants do not show the typical determinate developmental program induced by P stress in the primary root. Other root developmental aspects of the low P rescue system, including increased root hair elongation and anthocyanin accumulation, remained unaltered in lpi mutants. In addition to the insensitivity of primary root growth inhibition, when subjected to P deprivation, lpi mutants show a reduced induction in the expression of several genes involved in the P starvation rescue system (PHOSPHATE TRANSPORTER 1 and 2, PURPLE ACID PHOSPHATASE 1, ACID PHOSPHATASE 5, and INDUCED BY PHOSPHATE STARVATION 1). Our results provide genetic support for the role of P as an important signal for postembryonic root development and root meristem maintenance and show a crosstalk in developmental and biochemical responses to P deprivation.

Root development--branching into novel spheres

Recent progress in deciphering the genetics of Arabidopsis root development has been driven by the availability of novel molecular tools. For instance, combining enhancer trap lines and microarray analyses enabled the creation of an expression map for over 22000 genes at cellular resolution. Such expression profiles often suggest redundant action of homologous genes, which has indeed been observed for several pivotal factors that are required for the organization and maintenance of root meristems. Additional regulators of root development are also being identified by analysis of natural genetic variation. Moreover, microRNA control of gene expression has recently been implicated in root development, and progress has been made in understanding the interplay between environmental and genetic factors in root branching.

A rice glutamate receptor-like gene is critical for the division and survival of individual cells in the root apical meristem

Glu receptors are known to function as Glu-activated ion channels that mediate mostly excitatory neurotransmission in animals. Glu receptor-like genes have also been reported in higher plants, although their function is largely unknown. We have identified a rice (Oryza sativa) Glu receptor-like gene, designated GLR3.1, in which mutation by T-DNA insertion caused a short-root mutant phenotype. Histology and DNA synthesis analyses revealed that the mutant root meristematic activity is distorted and is accompanied by enhanced programmed cell death. Our results supply genetic evidence that a plant Glu receptor-like gene, rice GLR3.1, is essential for the maintenance of cell division and individual cell survival in the root apical meristem at the early seedling stage.

APETALA2 regulates the stem cell niche in the Arabidopsis shoot meristem

Postembryonic organ formation in higher plants relies on the activity of stem cell niches in shoot and root meristems where differentiation of the resident cells is repressed by signals from surrounding cells. We searched for mutations affecting stem cell maintenance and isolated the semidominant l28 mutant, which displays premature termination of the shoot meristem and differentiation of the stem cells. Allele competition experiments suggest that l28 is a dominant-negative allele of the APETALA2 (AP2) gene, which previously has been implicated in floral patterning and seed development. Expression of both WUSCHEL (WUS) and CLAVATA3 (CLV3) genes, which regulate stem cell maintenance in the wild type, were disrupted in l28 shoot apices from early stages on. Unlike in floral patterning, AP2 mRNA is active in the center of the shoot meristem and acts via a mechanism independent of AGAMOUS, which is a repressor of WUS and stem cell maintenance in the floral meristem. Genetic analysis shows that termination of the primary shoot meristem in l28 mutants requires an active CLV signaling pathway, indicating that AP2 functions in stem cell maintenance by modifying the WUS-CLV3 feedback loop.

Integrating hormone signaling and patterning mechanisms in plant development

Plant growth and development are driven by the bustling integration of a vast number of signals, among which plant hormones dominate. Understanding the role of hormones in particular developmental events requires their integration with developmental regulators known to be specific to those events. Using the increasing number of tools that can be utilized to probe hormone biosynthesis, transport and response, several recent studies have taken such an integrative approach, and in so doing have contributed to a clearer picture of precisely how hormones control plant development.

Transactivated and chemically inducible gene expression in plants

Several vector systems are available for tissue-specific transactivation or chemical induction of transgene expression in plants. The choice facing researchers is which promoter system to commit to as this determines the range and characteristics of the expression resources available. The decision will not be the same for all species or applications. We present some general discussion on the use of these technologies and review in detail the properties in various (mainly angiosperm) species of the most promising: mGal4:VP16/UAS and pOp/LhG4 for transactivation, and the alc-switch, GVE/VGE, GVG, pOp6/LhGR, and XVE systems for chemical induction.

A Molecular Framework for Plant Regeneration

Plants and some animals have a profound capacity to regenerate organs from adult tissues. Molecular mechanisms for regeneration have, however, been largely unexplored. Here we investigate a local regeneration response in Arabidopsis roots. Laser-induced wounding disrupts the flow of auxin—a cell-fate–instructive plant hormone—in root tips, and we demonstrate that resulting cell-fate changes require the PLETHORA, SHORTROOT, and SCARECROW transcription factors. These transcription factors regulate the expression and polar position of PIN auxin efflux–facilitating membrane proteins to reconstitute auxin transport in renewed root tips.

Thus, a regeneration mechanism using embryonic root stem-cell patterning factors first responds to and subsequently stabilizes a new hormone distribution.

Regulating the regulator: the control of auxin transport

With the discovery of the phytohormone auxin in the late 1920s, it became possible to link the regulation of complex plant growth responses to a single biologically active compound. Among all the plant growth regulators characterised so far, only auxin appears to be actively transported throughout the plant to create complex variations in concentration patterns and flow directions over time. This stimulated interest in the specific mechanisms underlying auxin transport as key factors in plant growth responses. Research in the last decade revealed several genes involved in the controlled transport of auxin and greatly improved our understanding of the basic principles of auxin-mediated responses. We are at this point, however, only starting to understand the complex interplay and control of factors that ultimately underlie the observed spatiotemporal variations in auxin transport and thus mediate plant growth and environmental responses. This review highlights important findings that provide us with a framework of molecular players and potential regulatory mechanisms that should contribute to the formulation of a comprehensive dynamic model of spatiotemporal auxin distribution.

Global studies of cell type-specific gene expression in plants

Technological advances in expression profiling and in the ability to collect minute quantities of tissues have come together to allow a growing number of global transcriptional studies at the cell level in plants. Microarray technology, with a choice of cDNA or oligo-based slides, is now well established, with commercial full-genome platforms for rice and Arabidopsis and extensive expressed sequence tag (EST)-based designs for many other species. Microdissection and cell sorting are two established methodologies that have been used in conjunction with microarrays to provide an early glimpse of the transcriptional landscape at the level of individual cell types. The results indicate that much of the transcriptome is compartmentalized. A minor but consistent percentage of transcripts appear to be unique to specific cell types. Functional analyses of cell-specific patterns of gene expression are providing important clues to cell-specific functions. The spatial dissection of the transcriptome has also yielded insights into the localized mediators of hormone inputs and promises to provide detail on cell-specific effects of microRNAs.

Interactions between the cell cycle and embryonic patterning in Arabidopsis uncovered by a mutation in DNA polymerase epsilon

Pattern formation and morphogenesis require coordination of cell division rates and orientations with developmental signals that specify cell fate. A viable mutation in the TILTED1 locus, which encodes the catalytic subunit of DNA polymerase epsilon of Arabidopsis thaliana, causes a lengthening of the cell cycle by approximately 35% throughout embryo development and alters cell type patterning of the hypophyseal lineage in the root, leading to a displacement of the root pole from its normal position on top of the suspensor. Treatment of preglobular and early globular stages, but not later stage, embryos with the DNA polymerase inhibitor aphidicolin leads to a similar phenotype. The results uncover an interaction between the cell cycle and the processes that determine cell fate during plant embryogenesis.

Tissue-specific expression of stabilized SOLITARY-ROOT/IAA14 alters lateral root development in Arabidopsis

Auxin is important for lateral root (LR) initiation and subsequent LR primordium development. However, the roles of tissue-specific auxin signaling in these processes are poorly understood. We analyzed transgenic Arabidopsis plants expressing the stabilized mutant INDOLE-3 ACETIC ACID 14 (IAA14)/SOLITARY-ROOT (mIAA14) protein as a repressor of the auxin response factors (ARFs), under the control of tissue-specific promoters. We showed that plants expressing the mIAA14-glucocorticoid receptor (GR) fusion protein under the control of the native IAA14 promoter had the solitary-root/iaa14 mutant phenotypes, including the lack of LR formation under dexamethasone (Dex) treatment, indicating that mIAA14-GR is functional in the presence of Dex. We then demonstrated that expression of mIAA14-GR under the control of the stele-specific SHORT-ROOT promoter suppressed LR formation, and showed that mIAA14-GR expression in the protoxylem-adjacent pericycle also blocked LR formation, indicating that the normal auxin response mediated by auxin/indole-3 acetic acid (Aux/IAA) signaling in the protoxylem pericycle is necessary for LR formation. In addition, we demonstrated that expression of mIAA14-GR under either the ARF7 or the ARF19 promoter also suppressed LR formation as in the arf7 arf19 double mutants, and that IAA14 interacted with ARF7 and ARF19 in yeasts. These results strongly suggest that mIAA14-GR directly inactivates ARF7/ARF19 functions, thereby blocking LR formation. Post-embryonic expression of mIAA14-GR under the SCARECROW promoter, which is expressed in the specific cell lineage during LR primordium formation, caused disorganized LR development. This indicates that normal auxin signaling in LR primordia, which involves the unknown ARFs and Aux/IAAs, is necessary for the establishment of LR primordium organization. Thus, our data show that tissue-specific expression of a stabilized Aux/IAA protein allows analysis of tissue-specific auxin responses in LR development by inactivating ARF functions.

REGULATION OF ROOT APICAL MERISTEM DEVELOPMENT

The establishment of the Angiosperm root apical meristem is dependent on the specification of a stem cell niche and the subsequent development of the quiescent center at the presumptive root pole. Distribution of auxin and the establishment of auxin maxima are early formative steps in niche specification that depend on the expression and distribution of auxin carriers. Auxin specifies stem cell niche formation by directly and indirectly affecting gene activities. Part of the indirect regulation by auxin may involve changes in redox, favoring local, oxidized microenvironments. Formation of a QC is required for root meristem development and elaboration. Many signals likely pass between the QC and the adjacent root meristem tissues. Disappearance of the QC is associated with roots becoming determinate. Given the many auxin feedback loops, we hypothesize that roots evolved as part of an auxin homeostasis mechanism.

Cell cycle progression in the pericycle is not sufficient for SOLITARY ROOT/IAA14-mediated lateral root initiation in Arabidopsis thaliana

To study the mechanisms behind auxin-induced cell division, lateral root initiation was used as a model system. By means of microarray analysis, genome-wide transcriptional changes were monitored during the early steps of lateral root initiation. Inclusion of the dominant auxin signaling mutant solitary root1 (slr1) identified genes involved in lateral root initiation that act downstream of the auxin/indole-3-acetic acid (AUX/IAA) signaling pathway. Interestingly, key components of the cell cycle machinery were strongly defective in slr1, suggesting a direct link between AUX/IAA signaling and core cell cycle regulation. However, induction of the cell cycle in the mutant background by overexpression of the D-type cyclin (CYCD3;1) was able to trigger complete rounds of cell division in the pericycle that did not result in lateral root formation. Therefore, lateral root initiation can only take place when cell cycle activation is accompanied by cell fate respecification of pericycle cells. The microarray data also yielded evidence for the existence of both negative and positive feedback mechanisms that regulate auxin homeostasis and signal transduction in the pericycle, thereby fine-tuning the process of lateral root initiation.

Surge and destroy: the role of auxin in plant embryogenesis

For nearly a century, the plant hormone auxin has been recognized for its effects on post-embryonic plant growth. Now recent insights into the molecular mechanism of auxin transport and signaling are uncovering fundamental roles for auxin in the earliest stages of plant development, such as in the development of the apical-basal (shoot-root) axis in the embryo, as well as in the formation of the root and shoot apical meristems and the cotyledons. Localized surges in auxin within the embryo occur through a sophisticated transcellular transport pathway causing the proteolytic destruction of key transcriptional repressors. As we discuss here, the resulting downstream gene activation, together with other, less well-understood regulatory pathways, establish much of the basic body plan of the angiosperm embryo.

hca: an Arabidopsis mutant exhibiting unusual cambial activity and altered vascular patterning

By screening a T-DNA population of Arabidopsis mutants for alterations in inflorescence stem vasculature, we have isolated a mutant with a dramatic increase in vascular tissue development, characterized by a continuous ring of xylem/phloem. This phenotype is the consequence of premature and numerous cambial cell divisions in both the fascicular and interfascicular regions that result in the loss of the alternate vascular bundle/fiber organization typically observed in Arabidopsis stems. The mutant was therefore designated high cambial activity (hca). The hca mutation also resulted in pleiotropic effects including stunting and a delay in developmental events such as flowering and senescence. The physiological characterization of hca seedlings in vitro revealed an altered auxin and cytokinin response and, most strikingly, an enhanced sensitivity to cytokinin. These results were substantiated by comparative microarray analysis between hca and wild-type plants. The genetic analysis of hca indicated that the mutant phenotype was not tagged by the T-DNA and that the hca mutation segregated as a single recessive locus, mapping to the long arm of chromosome 4. We propose that hca is involved in mechanisms controlling the arrangement of vascular bundles throughout the plant by regulating the auxin-cytokinin sensitivity of vascular cambial cells. Thus, the hca mutant is a useful model for examining the genetic and hormonal control of cambial growth and differentiation.

Stem cells: a plant biology perspective

A recent meeting at the Juan March Foundation in Madrid, Spain brought together plant biologists to discuss the characteristics of plant stem cells that are unique and those that are shared by stem cells from the animal kingdom.

Transcription switches for protoxylem and metaxylem vessel formation

Land plants evolved xylem vessels to conduct water and nutrients, and to support the plant. Microarray analysis with a newly established Arabidopsis in vitro xylem vessel element formation system and promoter analysis revealed the possible involvement of some plant-specific NAC-domain transcription factors in xylem formation. VASCULAR-RELATED NAC-DOMAIN6 (VND6) and VND7 can induce transdifferentiation of various cells into metaxylem- and protoxylem-like vessel elements, respectively, in Arabidopsis and poplar. A dominant repression of VND6 and VND7 specifically inhibits metaxylem and protoxylem vessel formation in roots, respectively. These findings suggest that these genes are transcription switches for plant metaxylem and protoxylem vessel formation.