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

Statistical evaluation of transcriptomic data generated using the Affymetrix one-cycle, two-cycle and IVT-Express RNA labelling protocols with the Arabidopsis ATH1 microarray

BACKGROUND

Microarrays are a powerful tool used for the determination of global RNA expression. There is an increasing requirement to focus on profiling gene expression in tissues where it is difficult to obtain large quantities of material, for example individual tissues within organs such as the root, or individual isolated cells. From such samples, it is difficult to produce the amount of RNA required for labelling and hybridisation in microarray experiments, thus a process of amplification is usually adopted. Despite the increasing use of two-cycle amplification for transcriptomic analyses on the Affymetrix ATH1 array, there has been no report investigating any potential bias in gene representation that may occur as a result.

RESULTS

Here we compare transcriptomic data generated using Affymetrix one-cycle (standard labelling protocol), two-cycle (small-sample protocol) and IVT-Express protocols with the Affymetrix ATH1 array using Arabidopsis root samples. Results obtained with each protocol are broadly similar. However, we show that there are 35 probe sets (of a total of 22810) that are misrepresented in the two-cycle data sets. Of these, 33 probe sets were classed as mis-amplified when comparisons of two independent publicly available data sets were undertaken.

CONCLUSIONS

Given the unreliable nature of the highlighted probes, we caution against using data associated with the corresponding genes in analyses involving transcriptomic data generated with two-cycle amplification protocols. We have shown that the Affymetrix IVT-E labelling protocol produces data with less associated bias than the two-cycle protocol, and as such, would recommend this kit for new experiments that involve small samples.

Involvement of auxin signaling mediated by IAA14 and ARF7/19 in membrane lipid remodeling during phosphate starvation

In higher plants, phosphate (Pi) deficiency induces the replacement of phospholipids with the nonphosphorous glycolipids digalactosyldiacylglycerol (DGDG) and sulfoquinovosyldiacylglycerol (SQDG). Genes involved in membrane lipid remodeling are coactivated in response to Pi starvation, but the mechanisms that guide this response are largely unknown. Previously, we reported the importance of auxin transport for DGDG accumulation during Pi starvation. To understand the role of auxin signaling in Arabidopsis membrane lipid remodeling, we analyzed slr-1, a gain-of-function mutant of IAA14 (a repressor of auxin signaling), and arf7arf19, a loss-of-function mutant of auxin response factors ARF7 and ARF19. In slr-1 and arf7arf19, Pi stress-induced accumulation of DGDG and SQDG was suppressed. Reduced upregulation of glycolipid synthase and phospholipase genes in these mutants under Pi-deficient conditions indicates that IAA14 and ARF7/19 affect membrane lipid remodeling at the level of transcription. Pi stress-dependent induction of a non-protein-coding gene, IPS1, was also lower in slr-1 and arf7arf19, whereas expression of At4 (another Pi stress-inducible non-protein-coding gene), anthocyanin accumulation, and phosphodiesterase induction were not reduced in the shoot. High free Pi content was observed in slr-1 and arf7arf19 even under Pi-deficient conditions, suggesting that Pi homeostasis during Pi starvation is altered in these mutants. These results demonstrate a requirement of auxin signaling mediated by IAA14 and ARF7/19 for low-Pi adaptation in Arabidopsis.

Bimodular auxin response controls organogenesis in Arabidopsis

Like animals, the mature plant body develops via successive sets of instructions that determine cell fate, patterning, and organogenesis. In the coordination of various developmental programs, several plant hormones play decisive roles, among which auxin is the best-documented hormonal signal. Despite the broad range of processes influenced by auxin, how such a single signaling molecule can be translated into a multitude of distinct responses remains unclear. In Arabidopsis thaliana, lateral root development is a classic example of a developmental process that is controlled by auxin at multiple stages. Therefore, we used lateral root formation as a model system to gain insight into the multifunctionality of auxin. We were able to demonstrate the complementary and sequential action of two discrete auxin response modules, the previously described Solitary Root/indole-3-Acetic Acid (IAA)14-Auxin Response Factor (ARF)7-ARF19-dependent lateral root initiation module and the successive Bodenlos/IAA12-Monopteros/ARF5-dependent module, both of which are required for proper organogenesis. The genetic framework in which two successive auxin response modules control early steps of a developmental process adds an extra dimension to the complexity of auxin's action.

Auxin modulates the transition from the mitotic cycle to the endocycle in Arabidopsis

Amplification of genomic DNA by endoreduplication often marks the initiation of cell differentiation in animals and plants. The transition from mitotic cycles to endocycles should be developmentally programmed but how this process is regulated remains largely unknown. We show that the plant growth regulator auxin modulates the switch from mitotic cycles to endocycles in Arabidopsis; high levels of TIR1-AUX/IAA-ARF-dependent auxin signalling are required to repress endocycles, thus maintaining cells in mitotic cycles. By contrast, lower levels of TIR1-AUX/IAA-ARF-dependent auxin signalling trigger an exit from mitotic cycles and an entry into endocycles. Our data further demonstrate that this auxin-mediated modulation of the mitotic-to-endocycle switch is tightly coupled with the developmental transition from cell proliferation to cell differentiation in the Arabidopsis root meristem. The transient reduction of auxin signalling by an auxin antagonist PEO-IAA rapidly downregulates the expression of several core cell cycle genes, and we show that overexpressing one of the genes, CYCLIN A2;3 (CYCA2;3), partially suppresses an early initiation of cell differentiation induced by PEO-IAA. Taken together, these results suggest that auxin-mediated mitotic-to-endocycle transition might be part of the developmental programmes that balance cell proliferation and cell differentiation in the Arabidopsis root meristem.

Mechanism of auxin-regulated gene expression in plants

Plant hormones control most aspects of the plant life cycle by regulating genome expression. Expression of auxin-responsive genes involves interactions among auxin-responsive DNA sequence elements, transcription factors and trans-acting transcriptional repressors. Transcriptional output from these auxin signaling complexes is regulated by proteasome-mediated degradation that is triggered by interaction with auxin receptor-E3 ubiquitin ligases such SCF(TIR1). Auxin signaling components are conserved throughout land plant evolution and have proliferated and specialized to control specific developmental processes.

The ectomycorrhizal fungus Laccaria bicolor stimulates lateral root formation in poplar and Arabidopsis through auxin transport and signaling

The early phase of the interaction between tree roots and ectomycorrhizal fungi, prior to symbiosis establishment, is accompanied by a stimulation of lateral root (LR) development. We aimed to identify gene networks that regulate LR development during the early signal exchanges between poplar (Populus tremula x Populus alba) and the ectomycorrhizal fungus Laccaria bicolor with a focus on auxin transport and signaling pathways. Our data demonstrated that increased LR development in poplar and Arabidopsis (Arabidopsis thaliana) interacting with L. bicolor is not dependent on the ability of the plant to form ectomycorrhizae. LR stimulation paralleled an increase in auxin accumulation at root apices. Blocking plant polar auxin transport with 1-naphthylphthalamic acid inhibited LR development and auxin accumulation. An oligoarray-based transcript profile of poplar roots exposed to molecules released by L. bicolor revealed the differential expression of 2,945 genes, including several components of polar auxin transport (PtaPIN and PtaAUX genes), auxin conjugation (PtaGH3 genes), and auxin signaling (PtaIAA genes). Transcripts of PtaPIN9, the homolog of Arabidopsis AtPIN2, and several PtaIAAs accumulated specifically during the early interaction phase. Expression of these rapidly induced genes was repressed by 1-naphthylphthalamic acid. Accordingly, LR stimulation upon contact with L. bicolor in Arabidopsis transgenic plants defective in homologs of these genes was decreased or absent. Furthermore, in Arabidopsis pin2, the root apical auxin increase during contact with the fungus was modified. We propose a model in which fungus-induced auxin accumulation at the root apex stimulates LR formation through a mechanism involving PtaPIN9-dependent auxin redistribution together with PtaIAA-based auxin signaling.

Knockdown of CELL DIVISION CYCLE16 reveals an inverse relationship between lateral root and nodule numbers and a link to auxin in Medicago truncatula

The postembryonic development of lateral roots and nodules is a highly regulated process. Recent studies suggest the existence of cross talk and interdependency in the growth of these two organs. Although plant hormones, including auxin and cytokinin, appear to be key players in coordinating this cross talk, very few genes that cross-regulate root and nodule development have been uncovered so far. This study reports that a homolog of CELL DIVISION CYCLE16 (CDC16), a core component of the Anaphase Promoting Complex, is one of the key mediators in controlling the overall number of lateral roots and nodules. A partial suppression of this gene in Medicago truncatula leads to a decrease in number of lateral roots and a 4-fold increase in number of nodules. The roots showing lowered expression of MtCDC16 also show reduced sensitivity to phytohormone auxin, thus providing a potential function of CDC16 in auxin signaling.

Expression of the Arabidopsis jasmonate signalling repressor JAZ1/TIFY10A is stimulated by auxin

Plant hormones have pivotal roles in almost every aspect of plant development. Over the past decades, physiological and genetic studies have revealed that hormone action in plants is determined by complex interactions between hormonal signalling pathways. Evidence is accumulating for the existence of crosstalk between the auxin and jasmonate (JA) signalling pathways. Recently, the JASMONATE ZIM-domain (JAZ) proteins have been identified as the long-sought repressors of JA signalling. Here, we show that expression of JAZ1/TIFY10A is not solely inducible by JA, but that it is also an early auxin-responsive gene. Furthermore, we could show that the auxin-inducible expression of JAZ1/TIFY10A is independent of the JA signalling pathway but is controlled by the auxin/indole-3-acetic acid-auxin response transcription factor signalling pathway. Our results provide evidence for the existence of at least two different input signals regarding JAZ1/TIFY10A expression and thus support the idea of an intimate molecular interplay between auxin and JA signalling.

Arabidopsis lateral root development: an emerging story

Lateral root formation is a major determinant of root systems architecture. The degree of root branching impacts the efficiency of water uptake, acquisition of nutrients and anchorage by plants. Understanding the regulation of lateral root development is therefore of vital agronomic importance. The molecular and cellular basis of lateral root formation has been most extensively studied in the plant model Arabidopsis thaliana (Arabidopsis). Significant progress has recently been made in identifying many new Arabidopsis genes that regulate lateral root initiation, patterning and emergence processes. We review how these studies have revealed that the plant hormone auxin represents a common signal that integrates these distinct yet interconnected developmental processes.

Unsupervised assessment of microarray data quality using a Gaussian mixture model

BACKGROUND

Quality assessment of microarray data is an important and often challenging aspect of gene expression analysis. This task frequently involves the examination of a variety of summary statistics and diagnostic plots. The interpretation of these diagnostics is often subjective, and generally requires careful expert scrutiny.

RESULTS

We show how an unsupervised classification technique based on the Expectation-Maximization (EM) algorithm and the naïve Bayes model can be used to automate microarray quality assessment. The method is flexible and can be easily adapted to accommodate alternate quality statistics and platforms. We evaluate our approach using Affymetrix 3' gene expression and exon arrays and compare the performance of this method to a similar supervised approach.

CONCLUSION

This research illustrates the efficacy of an unsupervised classification approach for the purpose of automated microarray data quality assessment. Since our approach requires only unannotated training data, it is easy to customize and to keep up-to-date as technology evolves. In contrast to other "black box" classification systems, this method also allows for intuitive explanations.

Survival of the flexible: hormonal growth control and adaptation in plant development

Plant development is subject to hormonal growth control and adapts to environmental cues such as light or stress. Recently, significant progress has been made in elucidating hormone synthesis, signalling and degradation pathways, and in resolving spatial and temporal aspects of hormone responses. Here we review how hormones control maintenance of stem cell systems, influence developmental transitions of stem cell daughters and define developmental compartments in Arabidopsis thaliana. We also discuss how environmental cues change plant growth by modulating hormone levels and response. Future analysis of hormone crosstalk and of hormone action at both single cell and organ levels will substantially improve our understanding of how plant development adapts to changes in intrinsic and environmental conditions.

Hormone interactions during lateral root formation

Lateral root (LR) formation, the production of new roots from parent roots, is a hormone- and environmentally-regulated developmental process in higher plants. Physiological and genetic studies using Arabidopsis thaliana and other plant species have revealed the roles of several plant hormones in LR formation, particularly the role of auxin in LR initiation and primordium development, resulting in much progress toward understanding the mechanisms of auxin-mediated LR formation. However, hormone interactions during LR formation have been relatively underexamined. Recent studies have shown that the plant hormones, cytokinin and abscisic acid negatively regulate LR formation whereas brassinosteroids positively regulate LR formation. On the other hand, ethylene has positive and negative roles during LR formation. This review summarizes recent findings on hormone-regulated LR formation in higher plants, focusing on auxin as a trigger and on the other hormones in LR formation, and discusses the possible interactions among plant hormones in this developmental process.

Pluripotency of Arabidopsis xylem pericycle underlies shoot regeneration from root and hypocotyl explants grown in vitro

We have established a detailed framework for the process of shoot regeneration from Arabidopsis root and hypocotyl explants grown in vitro. Using transgenic plant lines in which the GUS or GFP genes were fused to promoters of developmental genes (WUS, CLV1, CLV3, STM, CUC1, PLT1, RCH1, QC25), or to promoters of genes encoding indicators of the auxin response (DR5) or transport (PIN1), cytokinin (CK) response (ARR5) or synthesis (IPT5), or mitotic activity (CYCB1), we showed that regenerated shoots originated directly or indirectly from the pericycle cells adjacent to xylem poles. In addition, shoot regeneration appeared to be partly similar to the formation of lateral root meristems (LRMs). During pre-culture on a 2, 4-dichlorophenoxyacetic acid (2, 4-D)-rich callus-inducing medium (CIM), xylem pericycle reactivation established outgrowths that were not true calli but had many characteristics of LRMs. Transfer to a CK-rich shoot-inducing medium (SIM) resulted in early LRM-like primordia changing to shoot meristems. Direct origin of shoots from the xylem pericycle occurred upon direct culture on CK-containing media without prior growth on CIM. Thus, it appeared that the xylem pericycle is more pluripotent than previously thought. This pluripotency was accompanied by the ability of pericycle derivatives to retain diploidy, even after several rounds of cell division. In contrast, the phloem pericycle did not display such developmental plasticity, and responded to CKs with only periclinal divisions. Such observations reinforce the view that the pericycle is an 'extended meristem' that comprises two types of cell populations. They also suggest that the founder cells for LRM initiation are not initially fully specified for this developmental pathway.

BREVIS RADIX is involved in cytokinin-mediated inhibition of lateral root initiation in Arabidopsis

In contrast to auxin, relatively little is known about the molecular mechanism of cytokinin (CTK) inhibition of lateral root initiation. Previous studies demonstrated that BREVIS RADIX (BRX), a protein of unknown biochemical function, maintains a rate-limiting brassinosteroid biosynthesis enzyme expression to keep brassinosteroid biosynthesis above a critical threshold. Here, we show that the brx-2 mutant is insensitive to exogenous CTK-induced inhibition of lateral root initiation and that this can be restored by embryonic brassinosteroid treatment. However post-embryonic brassinosteroid treatment can not rescue brx-2 mutant phenotype in the presence of CTK. Meanwhile the brassinosteroid receptor defective mutant bri1-6 shows normal CTK-mediated inhibition on LR growth. These results suggest the CTK-mediated inhibition of LR initiation is not directly dependent on brassinosteroid level. Furthermore, compared with wild type, brx-2 exhibits altered auxin response in presumptive founder cells, lateral root primodia and primary root tip in the presence of exogenous CTK. We concluded that CTK inhibition on lateral root initiation depend on specific auxin response loss in presumptive founder cell. The aberrant primary root growth caused by the embryonic brassinosteroid shortage can indirectly result in the lateral root phenotype of brx-2 in presence of CTK.

Receptor-like kinase ACR4 restricts formative cell divisions in the Arabidopsis root

During the development of multicellular organisms, organogenesis and pattern formation depend on formative divisions to specify and maintain pools of stem cells. In higher plants, these activities are essential to shape the final root architecture because the functioning of root apical meristems and the de novo formation of lateral roots entirely rely on it. We used transcript profiling on sorted pericycle cells undergoing lateral root initiation to identify the receptor-like kinase ACR4 of Arabidopsis as a key factor both in promoting formative cell divisions in the pericycle and in constraining the number of these divisions once organogenesis has been started. In the root tip meristem, ACR4 shows a similar action by controlling cell proliferation activity in the columella cell lineage. Thus, ACR4 function reveals a common mechanism of formative cell division control in the main root tip meristem and during lateral root initiation.

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.

New clues to organ size control in plants

A review of the mechanisms that control organ size in plants.

Plant growth has unparalleled importance for human civilization, yet we are only starting to gain an understanding of its mechanisms. The growth rate and final size of plant organs is determined by both genetic constraints and environmental factors. Regulatory inputs act at two control points: on proliferation; and on the transition between proliferation and differentiation. Cell-autonomous and short-range growth signals act within meristematic domains, whereas diffusible signals from differentiated parts to proliferating cells provide measures of geometry and size and channel environmental inputs.

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.

A role for AtWRKY23 in feeding site establishment of plant-parasitic nematodes

During the interaction between sedentary plant-parasitic nematodes and their host, complex morphological and physiological changes occur in the infected plant tissue, finally resulting in the establishment of a nematode feeding site. This cellular transformation is the result of altered plant gene expression most likely induced by proteins injected in the plant cell by the nematode. Here, we report on the identification of a WRKY transcription factor expressed during nematode infection. Using both promoter-reporter gene fusions and in situ reverse transcription-polymerase chain reaction, we could show that AtWRKY23 is expressed during the early stages of feeding site establishment. Knocking down the expression of WRKY23 resulted in lower infection of the cyst nematode Heterodera schachtii. WRKY23 is an auxin-inducible gene and in uninfected plants WRKY23 acts downstream of the Aux/IAA protein SLR/IAA14. Although auxin is known to be involved in feeding site formation, our results suggest that, during early stages, auxin-independent signals might be at play to activate the initial expression of WRKY23.

Loss-of-function mutations in the Arabidopsis heterotrimeric G-protein alpha subunit enhance the developmental defects of brassinosteroid signaling and biosynthesis mutants

Loss-of-function alleles of the sole heterotrimeric G-protein alpha subunit in Arabidopsis, GPA1, display defects in cell proliferation throughout plant development. Previous studies indicated that GPA1 is involved in brassinosteroid (BR) response. Here we provide genetic evidence that loss-of-function mutations in GPA1, gpa1-2 and gpa1-4, enhance the developmental defects of bri1-5, a weak allele of a BR receptor mutant, and det2-1, a BR-deficient mutant in Arabidopsis. gpa1-2 bri1-5 and gpa1-4 det2-1 double mutants had shorter hypocotyls, shorter roots and fewer lateral roots, and displayed more severe dwarfism than bri1-5 and det2-1 single mutants, respectively. By using the Arabidopsis hypocotyl as a model system where the parameters of cell division and cell elongation can be simultaneously measured, we found that gpa1 can specifically enhance the cell division defects of bri1-5 and det2-1 mutants. Similarly, gpa1 specifically enhances cell division defects in the primary roots of bri1-5 and det2-1 mutants. Furthermore, an additive effect on cell division between gpa1 and bri1-5 or det2-1 mutations was observed in the hypocotyls, whereas a synergistic effect was observed in the roots. Taken together, these results provided the first genetic evidence that G-protein- and BR-mediated pathways may be converged to modulate cell proliferation in a cell/tissue-specific manner.

Distinct light-initiated gene expression and cell cycle programs in the shoot apex and cotyledons of Arabidopsis

In darkness, shoot apex growth is repressed, but it becomes rapidly activated by light. We show that phytochromes and cryptochromes play largely redundant roles in this derepression in Arabidopsis thaliana. We examined the light activation of transcriptional changes in a finely resolved time course, comparing the shoot apex (meristem and leaf primordia) and the cotyledon and found >5700 differentially expressed genes. Early events specific to the shoot apices included the repression of genes for Really Interesting New Gene finger proteins and basic domain/leucine zipper and basic helix-loop-helix transcription factors. The downregulation of auxin and ethylene and the upregulation of cytokinin and gibberellin hormonal responses were also characteristic of shoot apices. In the apex, genes involved in ribosome biogenesis and protein translation were rapidly and synchronously induced, simultaneously with cell proliferation genes, preceding visible organ growth. Subsequently, the activation of signaling genes and transcriptional signatures of cell wall expansion, turgor generation, and plastid biogenesis were apparent. Furthermore, light regulates the forms and protein levels of two transcription factors with opposing functions in cell proliferation, E2FB and E2FC, through the Constitutively Photomorphogenic1 (COP1), COP9-Signalosome5, and Deetiolated1 light signaling molecules. These data provide the basis for reconstruction of the regulatory networks for light-regulated meristem, leaf, and cotyledon development.

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.

Comprehensive transcriptome analysis of auxin responses in Arabidopsis

In plants, the hormone auxin shapes gene expression to regulate growth and development. Despite the detailed characterization of auxin-inducible genes, a comprehensive overview of the temporal and spatial dynamics of auxin-regulated gene expression is lacking. Here, we analyze transcriptome data from many publicly available Arabidopsis profiling experiments and assess tissue-specific gene expression both in response to auxin concentration and exposure time and in relation to other plant growth regulators. Our analysis shows that the primary response to auxin over a wide range of auxin application conditions and in specific tissues comprises almost exclusively the up-regulation of genes and identifies the most robust auxin marker genes. Tissue-specific auxin responses correlate with differential expression of Aux/IAA genes and the subsequent regulation of context- and sequence-specific patterns of gene expression. Changes in transcript levels were consistent with a distinct sequence of conjugation, increased transport capacity and down-regulation of biosynthesis in the temperance of high cellular auxin concentrations. Our data show that auxin regulates genes associated with the biosynthesis, catabolism and signaling pathways of other phytohormones. We present a transcriptional overview of the auxin response. Specific interactions between auxin and other phytohormones are highlighted, particularly the regulation of their metabolism. Our analysis provides a roadmap for auxin-dependent processes that underpins the concept of an 'auxin code'--a tissue-specific fingerprint of gene expression that initiates specific developmental processes.

An AGAMOUS-related MADS-box gene, XAL1 (AGL12), regulates root meristem cell proliferation and flowering transition in Arabidopsis

MADS-box genes are key components of the networks that control the transition to flowering and flower development, but their role in vegetative development is poorly understood. This article shows that the sister gene of the AGAMOUS (AG) clade, AGL12, has an important role in root development as well as in flowering transition. We isolated three mutant alleles for AGL12, which is renamed here as XAANTAL1 (XAL1): Two alleles, xal1-1 and xal1-2, are in Columbia ecotype and xal1-3 is in Landsberg erecta ecotype. All alleles have a short-root phenotype with a smaller meristem, lower rate of cell production, and abnormal root apical meristem organization. Interestingly, we also encountered a significantly longer cell cycle in the strongest xal1 alleles with respect to wild-type plants. Expression analyses confirmed the presence of XAL1 transcripts in roots, particularly in the phloem. Moreover, XAL1beta-glucuronidase expression was specifically up-regulated by auxins in this tissue. In addition, mRNA in situ hybridization showed that XAL1 transcripts were also found in leaves and floral meristems of wild-type plants. This expression correlates with the late-flowering phenotypes of the xal1 mutants grown under long days. Transcript expression analysis suggests that XAL1 is an upstream regulator of SOC, FLOWERING LOCUS T, and LFY. We propose that XAL1 may have similar roles in both root and aerial meristems that could explain the xal1 late-flowering phenotype.

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.

Cytokinins act directly on lateral root founder cells to inhibit root initiation

In Arabidopsis thaliana, lateral roots are formed from root pericycle cells adjacent to the xylem poles. Lateral root development is regulated antagonistically by the plant hormones auxin and cytokinin. While a great deal is known about how auxin promotes lateral root development, the mechanism of cytokinin repression is still unclear. Elevating cytokinin levels was observed to disrupt lateral root initiation and the regular pattern of divisions that characterizes lateral root development in Arabidopsis. To identify the stage of lateral root development that is sensitive to cytokinins, we targeted the expression of the Agrobacterium tumefaciens cytokinin biosynthesis enzyme isopentenyltransferase to either xylem-pole pericycle cells or young lateral root primordia using GAL4-GFP enhancer trap lines. Transactivation experiments revealed that xylem-pole pericycle cells are sensitive to cytokinins, whereas young lateral root primordia are not. This effect is physiologically significant because transactivation of the Arabidopsis cytokinin degrading enzyme cytokinin oxidase 1 in lateral root founder cells results in increased lateral root formation. We observed that cytokinins perturb the expression of PIN genes in lateral root founder cells and prevent the formation of an auxin gradient that is required to pattern lateral root primordia.

Mitochondrial type-I prohibitins of Arabidopsis thaliana are required for supporting proficient meristem development

The Arabidopsis thaliana genome expresses five evolutionarily conserved prohibitin (PHB) genes that are divided into type-I (AtPHB3 and AtPHB4) and type-II (AtPHB1, AtPHB2 and AtPHB6) classes, based on their phylogenetic relationships with yeast PHB1 and PHB2, respectively. Yeast and animal PHBs are reported to have diverse roles in the cell cycle, mitochondrial electron transport, aging and apoptosis. All transcribed Arabidopsis PHB genes are primarily expressed in both shoot and root proliferative tissues, where they are present in mitochondrial multimeric complexes. Loss of function of the type-I AtPHB4 had no phenotypic effects, while loss of function of the homologous AtPHB3 caused mitochondrial swelling, decreased meristematic cell production, increased cell division time and reduced cell expansion rates, leading to severe growth retardation. Double knockout atphb3 atphb4 plants were not viable, but transgenic lines overexpressing AtPHB3 or AtPHB4 showed leaf shape aberrations and an increased shoot branching phenotype. Genome-wide microarray analysis revealed that both knockout and overexpression perturbations of AtPHB3 and AtPHB4 provoked an altered abundance of mitochondrial and stress-related transcripts. We propose that plant type-I PHBs take part in protein complexes that are necessary for proficient mitochondrial function or biogenesis, thereby supporting cell division and differentiation in apical tissues.

A high-resolution root spatiotemporal map reveals dominant expression patterns

Transcriptional programs that regulate development are exquisitely controlled in space and time. Elucidating these programs that underlie development is essential to understanding the acquisition of cell and tissue identity. We present microarray expression profiles of a high-resolution set of developmental time points within a single Arabidopsis root and a comprehensive map of nearly all root cell types. These cell type-specific transcriptional signatures often predict previously unknown cellular functions. A computational pipeline identified dominant expression patterns that demonstrate transcriptional similarity between disparate cell types. Dominant expression patterns along the root's longitudinal axis do not strictly correlate with previously defined developmental zones, and in many cases, we observed expression fluctuation along this axis. Both robust co-regulation of gene expression and potential phasing of gene expression were identified between individual roots. Methods that combine these profiles demonstrate transcriptionally rich and complex programs that define Arabidopsis root development in both space and time.

The ins and outs of the plant cell cycle

Plant growth and development are driven by the continuous generation of new cells. Whereas much has been learned at a molecular level about the mechanisms that orchestrate progression through the different cell-cycle phases, little is known about how the cell-cycle machinery operates in the context of an entire plant and contributes to growth, cell differentiation and the formation of new tissues and organs. Here, we discuss how intrinsic developmental signals and environmental cues affect cell-cycle entry and exit.

Does auxin binding protein 1 control both cell division and cell expansion?

The Auxin-Binding Protein 1 (ABP1) was identified over 30 years ago thanks to it's high affinity for active auxins. ABP1 plays an essential role in plant life yet to this day, its function remains 'enigmatic.' A recent study by our laboratory shows that ABP1 is critical for regulation of the cell cycle, acting both in G(1) and at the G(2)/M transition. We showed that ABP1 is likely to mediate the permissive auxin signal for entry into the cell cycle. These data were obtained by studying a conditional functional knock-out of ABP1 generated by cellular immunization in the model tobacco cell line, Bright Yellow 2.

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.

Mutations in Arabidopsis multidrug resistance-like ABC transporters separate the roles of acropetal and basipetal auxin transport in lateral root development

Auxin affects the shape of root systems by influencing elongation and branching. Because multidrug resistance (MDR)-like ABC transporters participate in auxin transport, they may be expected to contribute to root system development. This reverse genetic study of Arabidopsis thaliana roots shows that MDR4-mediated basipetal auxin transport did not affect root elongation or branching. However, impaired acropetal auxin transport due to mutation of the MDR1 gene caused 21% of nascent lateral roots to arrest their growth and the remainder to elongate 50% more slowly than the wild type. Reporter gene analyses indicated a severe auxin deficit in the apex of mdr1 but not mdr4 lateral roots. The mdr1 deficit was explained by 40% less acropetal auxin transport within the mdr1 lateral roots. The slow elongation of mdr1 lateral roots was rescued by auxin and phenocopied in the wild type by an inhibitor of polar auxin transport. Confocal microscopy analysis of a functional green fluorescent protein-MDR1 translational fusion showed the protein to be auxin inducible and present in the tissues responsible for acropetal transport in the primary root. The protein also accumulated in lateral root primordia and later in the tissues responsible for acropetal transport within the lateral root, fully supporting the conclusion that auxin levels established by MDR1-dependent acropetal transport control lateral root growth rate to influence root system architecture.

The auxin-binding protein 1 is essential for the control of cell cycle

The phytohormone auxin has been known for >50 years to be required for entry into the cell cycle. Despite the critical effects exerted by auxin on the control of cell division, the molecular mechanism by which auxin controls this pathway is poorly understood, and how auxin is perceived upstream of any change in the cell cycle is unknown. Auxin Binding Protein 1 (ABP1) is considered to be a candidate auxin receptor, triggering early modification of ion fluxes across the plasma membrane in response to auxin. ABP1 has also been proposed to mediate auxin-dependent cell expansion, and is essential for early embryonic development. We investigated whether ABP1 has a role in the cell cycle. Functional inactivation of ABP1 in the model plant cell system BY2 was achieved through cellular immunization via the conditional expression of a single-chain fragment variable (scFv). This scFv was derived from a well characterized anti-ABP1 monoclonal antibody previously shown to block the activity of the protein. We demonstrate that functional inactivation of ABP1 results in cell-cycle arrest, and provide evidence that ABP1 plays a critical role in regulation of the cell cycle by acting at both the G1/S and G2/M checkpoints. We conclude that ABP1 is essential for the auxin control of cell division and is likely to constitute the first step of the auxin-signalling pathway mediating auxin effects on the cell cycle.

Parallel genome-wide expression profiling of host and pathogen during soybean cyst nematode infection of soybean

Global analysis of gene expression changes in soybean (Glycine max) and Heterodera glycines (soybean cyst nematode [SCN]) during the course of infection in a compatible interaction was performed using the Affymetrix GeneChip soybean genome array. Among 35,611 soybean transcripts monitored, we identified 429 genes that showed statistically significant differential expression between uninfected and nematode-infected root tissues. These included genes encoding enzymes involved in primary metabolism; biosynthesis of phenolic compounds, lignin, and flavonoids; genes related to stress and defense responses; cell wall modification; cellular signaling; and transcriptional regulation. Among 7,431 SCN transcripts monitored, 1,850 genes showed statistically significant differential expression across different stages of nematode parasitism and development. Differentially expressed SCN genes were grouped into nine different clusters based on their expression profiles during parasitism of soybean roots. The patterns of gene expression we observed in SCN suggest coordinated regulation of genes involved in parasitism. Quantitative real-time reverse-transcription polymerase chain reaction confirmed the results of our microarray analysis. The simultaneous genome-wide analysis of gene expression changes in the host and pathogen during a compatible interaction provides new insights into soybean responses to nematode infection and the first profile of transcript abundance changes occurring in the nematode as it infects and establishes a permanent feeding site within a host plant root.

Auxin-dependent regulation of lateral root positioning in the basal meristem of Arabidopsis

In plants, the developmental mechanisms that regulate the positioning of lateral organs along the primary root are currently unknown. We present evidence on how lateral root initiation is controlled in a spatiotemporal manner in the model plant Arabidopsis thaliana. First, lateral roots are spaced along the main axis in a regular left-right alternating pattern that correlates with gravity-induced waving and depends on AUX1, an auxin influx carrier essential for gravitropic response. Second, we found evidence that the priming of pericycle cells for lateral root initiation might take place in the basal meristem, correlating with elevated auxin sensitivity in this part of the root. This local auxin responsiveness oscillates with peaks of expression at regular intervals of 15 hours. Each peak in the auxin-reporter maximum correlates with the formation of a consecutive lateral root. Third, auxin signaling in the basal meristem triggers pericycle cells for lateral root initiation prior to the action of INDOLE-3-ACETIC ACID14 (SOLITARY ROOT).

ARF7 and ARF19 regulate lateral root formation via direct activation of LBD/ASL genes in Arabidopsis

Lateral root formation in Arabidopsis thaliana is regulated by two related AUXIN RESPONSE FACTORs, ARF7 and ARF19, which are transcriptional activators of early auxin response genes. The arf7 arf19 double knockout mutant is severely impaired in lateral root formation. Target-gene analysis in arf7 arf19 transgenic plants harboring inducible forms of ARF7 and ARF19 revealed that ARF7 and ARF19 directly regulate the auxin-mediated transcription of LATERAL ORGAN BOUNDARIES-DOMAIN16/ASYMMETRIC LEAVES2-LIKE18 (LBD16/ASL18) and/or LBD29/ASL16 in roots. Overexpression of LBD16/ASL18 and LBD29/ASL16 induces lateral root formation in the absence of ARF7 and ARF19. These LBD/ASL proteins are localized in the nucleus, and dominant repression of LBD16/ASL18 activity inhibits lateral root formation and auxin-mediated gene expression, strongly suggesting that these LBD/ASLs function downstream of ARF7- and ARF19-dependent auxin signaling in lateral root formation. Our results reveal that ARFs regulate lateral root formation via direct activation of LBD/ASLs in Arabidopsis.

ARF7 and ARF19 regulate lateral root formation via direct activation of LBD/ASL genes in Arabidopsis

Lateral root formation in Arabidopsis thaliana is regulated by two related AUXIN RESPONSE FACTORs, ARF7 and ARF19, which are transcriptional activators of early auxin response genes. The arf7 arf19 double knockout mutant is severely impaired in lateral root formation. Target-gene analysis in arf7 arf19 transgenic plants harboring inducible forms of ARF7 and ARF19 revealed that ARF7 and ARF19 directly regulate the auxin-mediated transcription of LATERAL ORGAN BOUNDARIES-DOMAIN16/ASYMMETRIC LEAVES2-LIKE18 (LBD16/ASL18) and/or LBD29/ASL16 in roots. Overexpression of LBD16/ASL18 and LBD29/ASL16 induces lateral root formation in the absence of ARF7 and ARF19. These LBD/ASL proteins are localized in the nucleus, and dominant repression of LBD16/ASL18 activity inhibits lateral root formation and auxin-mediated gene expression, strongly suggesting that these LBD/ASLs function downstream of ARF7- and ARF19-dependent auxin signaling in lateral root formation. Our results reveal that ARFs regulate lateral root formation via direct activation of LBD/ASLs in Arabidopsis.

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.

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.

PICKLE is required for SOLITARY-ROOT/IAA14-mediated repression of ARF7 and ARF19 activity during Arabidopsis lateral root initiation

Lateral root (LR) formation in Arabidopsis is regulated by auxin signaling through AUXIN RESPONSE FACTOR transcriptional activators, ARF7 and ARF19, and auxin/indole-3-acetic acid (Aux/IAA) repressors, including SOLITARY-ROOT (SLR)/IAA14. Previous studies have strongly suggested that, in the gain-of-function slr-1 mutant, stabilized mutant IAA14 (mIAA14) protein inactivates ARF7/19 functions, thereby completely blocking LR initiation. However, the mechanism of inactivation is still unknown. We have now identified an extragenic suppressor mutation of slr-1, suppressor of slr2 (ssl2), which specifically restores LR formation in the slr-1 mutant, and have found that SSL2 negatively regulates the auxin-induced pericycle cell divisions required for LR initiation. The SSL2 gene encodes PICKLE (PKL), a homologue of the animal chromatin-remodeling factor CHD3/Mi-2, and LR formation restored in pkl/ssl2 slr-1 mutants depends on ARF7/19 functions, suggesting that ARF7/19-dependent transcription takes place if there is a pkl/ssl2 mutation in slr-1. In animals, Mi-2 represses transcription as a subunit of the NuRD/Mi-2 complex containing histone deacetylases (HDACs). Inhibition of HDAC activity by trichostatin A also results in LR formation in the slr-1 mutant, but not in the slr-1 arf7 arf19 triple mutant, suggesting that normal HDAC activity is required for the mIAA14-mediated inactivation of ARF7/19 functions in LR initiation. Taken together, our data suggest that PKL/SSL2-mediated chromatin remodeling negatively regulates auxin-mediated LR formation in Arabidopsis.

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.

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.

Role of cytokinin and auxin in shaping root architecture: regulating vascular differentiation, lateral root initiation, root apical dominance and root gravitropism

BACKGROUND AND AIMS

Development and architecture of plant roots are regulated by phytohormones. Cytokinin (CK), synthesized in the root cap, promotes cytokinesis, vascular cambium sensitivity, vascular differentiation and root apical dominance. Auxin (indole-3-acetic acid, IAA), produced in young shoot organs, promotes root development and induces vascular differentiation. Both IAA and CK regulate root gravitropism. The aims of this study were to analyse the hormonal mechanisms that induce the root's primary vascular system, explain how differentiating-protoxylem vessels promote lateral root initiation, propose the concept of CK-dependent root apical dominance, and visualize the CK and IAA regulation of root gravitropiosm.

KEY ISSUES

The hormonal analysis and proposed mechanisms yield new insights and extend previous concepts: how the radial pattern of the root protoxylem vs. protophloem strands is induced by alternating polar streams of high IAA vs. low IAA concentrations, respectively; how differentiating-protoxylem vessel elements stimulate lateral root initiation by auxin-ethylene-auxin signalling; and how root apical dominance is regulated by the root-cap-synthesized CK, which gives priority to the primary root in competition with its own lateral roots.

CONCLUSIONS

CK and IAA are key hormones that regulate root development, its vascular differentiation and root gravitropism; these two hormones, together with ethylene, regulate lateral root initiation.

Mutations in the Diageotropica (Dgt) gene uncouple patterned cell division during lateral root initiation from proliferative cell division in the pericycle

In angiosperms, root branching requires a continuous re-initiation of new root meristems. Through some unknown mechanism, in most eudicots pericycle cells positioned against the protoxylem change identity and initiate patterned division, leading to formation of lateral root primordia that further develop into lateral roots. This process is auxin-regulated. We have observed that three mutations in the Diageotropica (Dgt) gene in tomato prevent primordium formation. Detailed analysis of one of these mutants, dgt1-1, demonstrated that the mutation does not abolish the proliferative capacity of the xylem-adjacent pericycle in the differentiated root portion. Files of shortened pericycle cells found in dgt1-1 roots were unrelated to primordium formation. Auxin application stimulated this unusual proliferation, leading to formation of a multi-layered xylem-adjacent pericycle, but did not rescue the primordium formation. In contrast to wild type, auxin could not induce any cell divisions in the pericycle of the most distal dgt1-1 root-tip portion. In wild-type roots, the Dgt gene promoter was expressed strongly in lateral root primordia starting from their initiation, and on auxin treatment was induced in the primary root meristem. Auxin level and distribution were altered in dgt1-1 root tissues, as judged by direct auxin measurements, and the tissue-specific expression of an auxin-response reporter was altered in transgenic plants. Together, our data demonstrate that the Dgt gene product, a type-A cyclophilin, is essential for morphogenesis of lateral root primordia, and that the dgt mutations uncouple patterned cell division in lateral root initiation from proliferative cell division in the pericycle.

Functional redundancy of PIN proteins is accompanied by auxin-dependent cross-regulation of PIN expression

Plant development displays an exceptional plasticity and adaptability that involves the dynamic, asymmetric distribution of the phytohormone auxin. Polar auxin flow, which requires polarly localized transport facilitators of the PIN family, largely contributes to the establishment and maintenance of the auxin gradients. Functionally overlapping action of PIN proteins mediates multiple developmental processes, including embryo formation, organ development and tropisms. Here we show that PIN proteins exhibit synergistic interactions, which involve cross-regulation of PIN gene expression in pin mutants or plants with inhibited auxin transport. Auxin itself positively feeds back on PIN gene expression in a tissue-specific manner through an AUX/IAA-dependent signalling pathway. This regulatory switch is indicative of a mechanism by which the loss of a specific PIN protein is compensated for by auxin-dependent ectopic expression of its homologues. The compensatory properties of the PIN-dependent transport network might enable the stabilization of auxin gradients and potentially contribute to the robustness of plant adaptive development.