Lateral root initiation or the birth of a new meristem

An auxin transport-based model of root branching in Arabidopsis thaliana

Root architecture is a crucial part of plant adaptation to soil heterogeneity and is mainly controlled by root branching. The process of root system development can be divided into two successive steps: lateral root initiation and lateral root development/emergence which are controlled by different fluxes of the plant hormone auxin. While shoot architecture appears to be highly regular, following rules such as the phyllotactical spiral, root architecture appears more chaotic. We used stochastic modeling to extract hidden rules regulating root branching in Arabidopsis thaliana. These rules were used to build an integrative mechanistic model of root ramification based on auxin. This model was experimentally tested using plants with modified rhythm of lateral root initiation or mutants perturbed in auxin transport. Our analysis revealed that lateral root initiation and lateral root development/emergence are interacting with each other to create a global balance between the respective ratio of initiation and emergence. A mechanistic model based on auxin fluxes successfully predicted this property and the phenotype alteration of auxin transport mutants or plants with modified rhythms of lateral root initiation. This suggests that root branching is controlled by mechanisms of lateral inhibition due to a competition between initiation and development/emergence for auxin.

Auxin: at the root of nodule development?

Root nodules are formed as a result of an orchestrated exchange of chemical signals between symbiotic nitrogen fixing bacteria and certain plants. In plants that form nodules in symbiosis with actinorhizal bacteria, nodules are derived from lateral roots. In most legumes, nodules are formed de novo from pericycle and cortical cells that are re-stimulated for division and differentiation by rhizobia. The ability of plants to nodulate has only evolved recently and it has, therefore, been suggested that nodule development is likely to have co-opted existing mechanisms for development and differentiation from lateral root formation. Auxin is an important regulator of cell division and differentiation, and changes in auxin accumulation and transport are essential for lateral root development. There is growing evidence that rhizobia alter the root auxin balance as a prerequisite for nodule formation, and that nodule numbers are regulated by shoot-to-root auxin transport. Whereas auxin requirements appear to be similar for lateral root and nodule primordium activation and organ differentiation, the major difference between the two developmental programs lies in the specification of founder cells. It is suggested that differing ratios of auxin and cytokinin are likely to specify the precursors of the different root organs.

Auxin acts as a local morphogenetic trigger to specify lateral root founder cells

Plants exhibit an exceptional adaptability to different environmental conditions. To a large extent, this adaptability depends on their ability to initiate and form new organs throughout their entire postembryonic life. Plant shoot and root systems unceasingly branch and form axillary shoots or lateral roots, respectively. The first event in the formation of a new organ is specification of founder cells. Several plant hormones, prominent among them auxin, have been implicated in the acquisition of founder cell identity by differentiated cells, but the mechanisms underlying this process are largely elusive. Here, we show that auxin and its local accumulation in root pericycle cells is a necessary and sufficient signal to respecify these cells into lateral root founder cells. Analysis of the alf4-1 mutant suggests that specification of founder cells and the subsequent activation of cell division leading to primordium formation represent two genetically separable events. Time-lapse experiments show that the activation of an auxin response is the earliest detectable event in founder cell specification. Accordingly, local activation of auxin response correlates absolutely with the acquisition of founder cell identity and precedes the actual formation of a lateral root primordium through patterned cell division. Local production and subsequent accumulation of auxin in single pericycle cells induced by Cre-Lox-based activation of auxin synthesis converts them into founder cells. Thus, auxin is the local instructive signal that is sufficient for acquisition of founder cell identity and can be considered a morphogenetic trigger in postembryonic plant organogenesis.

SKP2A, an F-box protein that regulates cell division, is degraded via the ubiquitin pathway

Coordination between cell division and cell differentiation is crucial for growth and development of eukaryotic organisms. Progression through the different phases of cell division requires the specific degradation of proteins through the ubiquitin/proteasome 26S (Ub/26S) pathway. In plants, this pathway plays a key role in controlling several developmental processes and responses, including cell proliferation. SKP2A, an F-box protein, regulates the stability of the cell division E2FC-DPB transcription factor. Here, we show that the SKP2A forms a Skp, Cullin containing (SCF) complexin vivo that has E3 ubiquitin ligase activity. Interestingly, SKP2A is degraded through the Ub/26S pathway, and auxin regulates such degradation. SKP2A positively regulates cell division, at least in part by degrading the E2FC/DPB transcription repressor. Plants that overexpress SKP2A increase the number of cells in G2/M, reduce the level of ploidy and develop a higher number of lateral root primordia. Taken together, our results indicate that SKP2A is a positive regulator of cell division, and its stability is controlled by auxin-dependent degradation.

Quantitative analysis of auxin-regulated proteins from basal part of leaf sheaths in rice by two-dimensional difference gel electrophoresis

To identify the effects of auxin on rice root formation, proteins induced by exogenous addition of auxin to rice seedlings were analyzed by a proteomic approach. Root formation by rice seedlings was promoted by 0.45microM 2,4-dichlorophenoxyacetic acid (2,4-D) and repressed by 60microM p-chlorophenoxyisobutyric acid (PCIB). Proteins extracted from the basal part of leaf sheaths of rice seedlings treated with 2,4-D or PCIB for 48h were labeled with Cy3 and Cy5, and separated by two-dimensional polyacrylamide gel electrophoresis. Out of nine proteins up-regulated by 2,4-D and down-regulated by PCIB, five proteins showing significant difference in abundance were used for expression analysis at the transcript abundance level. Transcript abundance of the mitochondrial complex I subunit slightly increased with 2,4-D treatment and were repressed by PCIB. The transcript abundance of EF-1beta', myosin heavy chain and mitochondrial [Mn]SOD increased with 2,4-D treatment but did not decrease with PCIB. The transcript abundance of aldehyde dehydrogenase was not effected by 2,4-D or PCIB. These results indicate that mitochondrial complex I subunit is part of the downstream signal cascade of PCIB, whereas myosin heavy chain, mitochondrial [Mn]SOD and EF-1beta' are involved in the 2,4-D signal cascade but are probably upstream of PCIB.

Auxin fluxes in the root apex co-regulate gravitropism and lateral root initiation

Root architecture plays an important role in water and nutrient acquisition and in the ability of the plant to adapt to the soil. Lateral root development is the main determinant of the shape of the root system and is controlled by external factors such as nutrient concentration. Here it is shown that lateral root initiation and root gravitropism, two processes that are regulated by auxin, are co-regulated in Arabidopsis. A mathematical model was generated that can predict the effects of gravistimulations on lateral root initiation density and suggests that lateral root initiation is controlled by an inhibitory fields mechanism. Moreover, gene transactivation experiments suggest a mechanism involving a single auxin transport route for both responses. Finally, co-regulation may offer a selective advantage by optimizing soil exploration as supported by a simple quantitative analysis.

Diarch symmetry of the vascular bundle in Arabidopsis root encompasses the pericycle and is reflected in distich lateral root initiation

The outer tissues of dicotyledonous plant roots (i.e. epidermis, cortex, and endodermis) are clearly organized in distinct concentric layers in contrast to the diarch to polyarch vascular tissues of the central stele. Up to now, the outermost layer of the stele, the pericycle, has always been regarded, in accordance with the outer tissue layers, as one uniform concentric layer. However, considering its lateral root-forming competence, the pericycle is composed of two different cell types, with one subset of cells being associated with the xylem, showing strong competence to initiate cell division, whereas another group of cells, associated with the phloem, appears to remain quiescent. Here, we established, using detailed microscopy and specific Arabidopsis thaliana reporter lines, the existence of two distinct pericycle cell types. Analysis of two enhancer trap reporter lines further suggests that the specification between these two subsets takes place early during development, in relation with the determination of the vascular tissues. A genetic screen resulted in the isolation of mutants perturbed in pericycle differentiation. Detailed phenotypical analyses of two of these mutants, combined with observations made in known vascular mutants, revealed an intimate correlation between vascular organization, pericycle fate, and lateral root initiation potency, and illustrated the independence of pericycle differentiation and lateral root initiation from protoxylem differentiation. Taken together, our data show that the pericycle is a heterogeneous cell layer with two groups of cells set up in the root meristem by the same genetic pathway controlling the diarch organization of the vasculature.

Branching out in new directions: the control of root architecture by lateral root formation

Plant roots are required for the acquisition of water and nutrients, for responses to abiotic and biotic signals in the soil, and to anchor the plant in the ground. Controlling plant root architecture is a fundamental part of plant development and evolution, enabling a plant to respond to changing environmental conditions and allowing plants to survive in different ecological niches. Variations in the size, shape and surface area of plant root systems are brought about largely by variations in root branching. Much is known about how root branching is controlled both by intracellular signalling pathays and by environmental signals. Here, we will review this knowledge, with particular emphasis on recent advances in the field that open new and exciting areas of research.

Embryonic patterning in Arabidopsis thaliana

Early embryonic development in the flowering plant Arabidopsis thaliana follows a predictable sequence of cell divisions. Anatomical hallmarks and the expression of marker genes in dynamic patterns indicate that new cell fates are established with virtually every round of mitosis. Although some of the factors regulating these early patterning events have been identified, the overall process remains relatively poorly understood. Starting at the globular stage, when the embryo has approximately 100 cells, the organization of development appears to be taken over by programs that regulate postembryonic patterning throughout the life cycle.

Improved imaging of actin filaments in transgenic Arabidopsis plants expressing a green fluorescent protein fusion to the C- and N-termini of the fimbrin actin-binding domain 2

The role of the actin cytoskeleton in plant development is intimately linked to its dynamic behavior. Therefore it is essential to continue refining methods for studying actin organization in living plant cells. The discovery of green fluorescent protein (GFP) has popularized the use of translational fusions of GFP with actin filament (F-actin) side-binding proteins to visualize in vivo actin organization in plants. The most recent of these live cell F-actin reporters are GFP fusions to the actin-binding domain 2 (ABD2) of Arabidopsis fimbrin 1 (ABD2-GFP). To improve ABD2-GFP fluorescence for enhanced in vivo F-actin imaging, transgenic Arabidopsis plants were generated expressing a construct with GFP fused to both the C- and N-termini of ABD2 under the control of the CaMV 35S promoter (35S::GFP-ABD2-GFP). The 35S::GFP-ABD2-GFP lines had significantly increased fluorescence compared with the original 35S::ABD2-GFP lines. The enhanced fluorescence of the 35S::GFP-ABD2-GFP-expressing lines allowed the acquisition of highly resolved images of F-actin in different plant organs and stages of development because of the reduced confocal microscope excitation settings needed for data collection. This simple modification to the ABD2-GFP construct presents an important tool for studying actin function during plant development.

Populus trichocarpa MONOPTEROS/AUXIN RESPONSE FACTOR5(ARF5) genes: comparative structure, sub-functionalization, andPopulus–ArabidopsismicrosyntenyThis article is one of a selection of papers published in the Special Issue on Poplar Research in Canada

The genome of Populus (poplar) has been shaped by a whole genome duplication event specific to the salicoid lineage. The MONOPTEROS (MP)/AUXIN RESPONSE FACTOR5 (ARF5) transcription factor plays a key role in auxin-mediated morphogenesis and vascular development in Arabidopsis , and may play a similar role in secondary xylem development in Populus. We used EST and genome sequence information to identify and characterize two duplicated Populus MP genes, PoptrMP1 and PoptrMP2. PoptrMP1 and PoptrMP2 DNA binding and other domains are highly conserved relative to Arabidopsis MP, while the glutamine-rich middle domains are divergent. The two PoptrMP genes are located on duplicated regions of linkage groups II and V. Comparative analysis of the surrounding genes in both the Populus and Arabidopsis genomes revealed a high degree of conservation of gene content and order extending over 11 genes in the immediate vicinity, but also specific changes to genomic regions surrounding each MP locus, providing insights into genome evolution. Expression studies showed that PoptrMP1 and PoptrMP2 have overlapping but distinct expression patterns, suggesting that subfunctionalization of the duplicated genes has occurred, with PoptrMP1 specialized for expression in developing secondary xylem. Transgenic Populus lines overexpressing PoptrMP1 exhibited a 2–4 fold increase in expression of a Populus AtHB8 homolog, a proposed MP target gene, confirming conservation of this regulatory module.

Patterning the axis in plants – auxin in control

Axis formation and patterning are fundamental processes establishing the body organization of multicellular organisms. In plants, patterning is not confined to embryogenesis but continues to produce new structures--lateral organs--along the growing primary body axis and also initiates secondary body axes. The signalling molecule auxin has been identified as a key player in plant axial patterning. The shoot and root sections of the axis seem to produce lateral organs in different ways. However, very recent findings suggest a general mechanism of branching triggered by local accumulation of auxin in a 'zone of competence' at the margin of stem-cell systems. How the general auxin signal is converted into organ-specific developmental programs remains a major challenge for the future.

The auxin-regulated AP2/EREBP gene PUCHI is required for morphogenesis in the early lateral root primordium of Arabidopsis

Organ primordia develop from founder cells into organs due to coordinated patterns of cell division. How patterned cell division is regulated during organ formation, however, is not well understood. Here, we show that the PUCHI gene, which encodes a putative APETALA2/ethylene-responsive element binding protein transcription factor, is required for the coordinated pattern of cell divisions during lateral root formation in Arabidopsis thaliana. Recessive mutations in PUCHI disturbed cell division patterns in the lateral root primordium, resulting in swelling of the proximal region of lateral roots. PUCHI expression was initially detected in all of the cells in early lateral root primordia, and later it was restricted to the proximal region of the primordia. Stable expression of PUCHI required auxin-responsive elements in its promoter region, and exogenous auxin increased the level of PUCHI mRNA accumulation. These results suggest that PUCHI acts downstream of auxin signaling and that this gene contributes to lateral root morphogenesis through affecting the pattern of cell divisions during the early stages of primordium development.

IBR3, a novel peroxisomal acyl-CoA dehydrogenase-like protein required for indole-3-butyric acid response

Indole-3-butyric acid (IBA) is an endogenous auxin that acts in Arabidopsis primarily via its conversion to the principal auxin indole-3-acetic acid (IAA). Genetic and biochemical evidence indicates that this conversion is similar to peroxisomal fatty acid beta-oxidation, but the specific enzymes catalyzing IBA beta-oxidation have not been identified. We identified an IBA-response mutant (ibr3) with decreased responses to the inhibitory effects of IBA on root elongation or the stimulatory effects of IBA on lateral root formation. However, ibr3 mutants respond normally to other forms of auxin, including IAA. The mutant seedlings germinate and develop normally, even in the absence of sucrose, suggesting that fatty acid beta-oxidation is unaffected. Additionally, double mutants between ibr3 and acx3, which is defective in an acyl-CoA oxidase acting in fatty acid beta-oxidation, have enhanced IBA resistance, consistent with a distinct role for IBR3. Positional cloning revealed that IBR3 encodes a putative acyl-CoA dehydrogenase with a consensus peroxisomal targeting signal. Based on the singular defect of this mutant in responding to IBA, we propose that IBR3 may act directly in the oxidation of IBA to IAA.

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.

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.

Comprehensive transcriptional profiling of NaCl-stressed Arabidopsis roots reveals novel classes of responsive genes

BACKGROUND

Roots are an attractive system for genomic and post-genomic studies of NaCl responses, due to their primary importance to agriculture, and because of their relative structural and biochemical simplicity. Excellent genomic resources have been established for the study of Arabidopsis roots, however, a comprehensive microarray analysis of the root transcriptome following NaCl exposure is required to further understand plant responses to abiotic stress and facilitate future, systems-based analyses of the underlying regulatory networks.

RESULTS

We used microarrays of 70-mer oligonucleotide probes representing 23,686 Arabidopsis genes to identify root transcripts that changed in relative abundance following 6 h, 24 h, or 48 h of hydroponic exposure to 150 mM NaCl. Enrichment analysis identified groups of structurally or functionally related genes whose members were statistically over-represented among up- or down-regulated transcripts. Our results are consistent with generally observed stress response themes, and highlight potentially important roles for underappreciated gene families, including: several groups of transporters (e.g. MATE, LeOPT1-like); signalling molecules (e.g. PERK kinases, MLO-like receptors), carbohydrate active enzymes (e.g. XTH18), transcription factors (e.g. members of ZIM, WRKY, NAC), and other proteins (e.g. 4CL-like, COMT-like, LOB-Class 1). We verified the NaCl-inducible expression of selected transcription factors and other genes by qRT-PCR.

CONCLUSION

Microarray profiling of NaCl-treated Arabidopsis roots revealed dynamic changes in transcript abundance for at least 20% of the genome, including hundreds of transcription factors, kinases/phosphatases, hormone-related genes, and effectors of homeostasis, all of which highlight the complexity of this stress response. Our identification of these transcriptional responses, and groups of evolutionarily related genes with either similar or divergent transcriptional responses to stress, will facilitate mapping of regulatory networks and extend our ability to improve salt tolerance in plants.

Auxin regulates lateral meristem activation in developing gametophytes ofCeratopteris richardii

This study investigates the auxin regulation of lateral meristem activation in the gametophytes of the fern Ceratopteris richardii Brongn. Exogenous auxin in the form of α-naphthaleneacetic acid or 2,4,5-trichlorophenoxy-acetic acid repressed the activation of the lateral meristem, and generated a male-like body plan. The auxin antagonist p-chlorophenoxyisobutyric acid reduced activity of both the apical and lateral meristems, and produced a circular-shaped gametophyte. Disrupting auxin transport with 2,3,5-triiodobenzoic acid led to a time lag in lateral meristem activation, while disrupting auxin transport with n-1-naphthylphthalamic acid produced several different body plans generated by the formation of a second lateral meristem. These findings suggest auxin mediates the activation of the lateral meristem and regulates lateral meristem function. In addition, auxin transport may be necessary for communication between the lateral meristem and other regions of the developing gametophyte. Auxin also controls the position of rhizoids produced by the gametophyte, and exogenous auxin interferes with the sexual differentiation of the gametophyte. These results are summarized in a model of how auxin regulates lateral meristem activation and meristem activity during gametophyte development in C. richardii.