Affordable and robust phenotyping framework to analyse root system architecture of soil-grown plants

The phenotypic analysis of root system growth is important to inform efforts to enhance plant resource acquisition from soils; however, root phenotyping remains challenging because of the opacity of soil, requiring systems that facilitate root system visibility and image acquisition. Previously reported systems require costly or bespoke materials not available in most countries, where breeders need tools to select varieties best adapted to local soils and field conditions. Here, we report an affordable soil-based growth (rhizobox) and imaging system to phenotype root development in glasshouses or shelters. All components of the system are made from locally available commodity components, facilitating the adoption of this affordable technology in low-income countries. The rhizobox is large enough (approximately 6000 cm² of visible soil) to avoid restricting vertical root system growth for most if not all of the life cycle, yet light enough (approximately 21 kg when filled with soil) for routine handling. Support structures and an imaging station, with five cameras covering the whole soil surface, complement the rhizoboxes. Images are acquired via the Phenotiki sensor interface, collected, stitched and analysed. Root system architecture (RSA) parameters are quantified without intervention. The RSAs of a dicot species (Cicer arietinum, chickpea) and a monocot species (Hordeum vulgare, barley), exhibiting contrasting root systems, were analysed. Insights into root system dynamics during vegetative and reproductive stages of the chickpea life cycle were obtained. This affordable system is relevant for efforts in Ethiopia and other low- and middle-income countries to enhance crop yields and climate resilience sustainably.

The impact of the rhizobia-legume symbiosis on host root system architecture

Legumes form symbioses with rhizobia to fix N2 in root nodules to supplement their nitrogen (N) requirements. Many studies have shown how symbioses affect the shoot, but far less is understood about how they modify root development and root system architecture (RSA). RSA is the distribution of roots in space and over time. RSA reflects host resource allocation into below-ground organs and patterns of host resource foraging underpinning its resource acquisition capacity. Recent studies have revealed a more comprehensive relationship between hosts and symbionts: the latter can affect host resource acquisition for phosphate and iron, and the symbiont's production of plant growth regulators can enhance host resource flux and abundance. We review the current understanding of the effects of rhizobia-legume symbioses on legume root systems. We focus on resource acquisition and allocation within the host to conceptualize the effect of symbioses on RSA, and highlight opportunities for new directions of research.

Inducible reporter/driver lines for the Arabidopsis root with intrinsic reporting of activity state

Cell-, tissue- or organ-specific inducible expression systems are powerful tools for functional analysis of changes to the pattern, level or timing of gene expression. However, plant researchers lack standardised reagents that promote reproducibility across the community. Here, we report the development and functional testing of a Gateway-based system for quantitatively, spatially and temporally controlling inducible gene expression in Arabidopsis that overcomes several drawbacks of the legacy systems. We used this modular driver/effector system with intrinsic reporting of spatio-temporal promoter activity to generate 18 well-characterised homozygous transformed lines showing the expected expression patterns specific for the major cell types of the Arabidopsis root; seed and plasmid vectors are available through the Arabidopsis stock centre. The system's tight regulation was validated by assessing the effects of diphtheria toxin A chain expression. We assessed the utility of Production of Anthocyanin Pigment 1 (PAP1) as an encoded effector mediating cell-autonomous marks. With this shared resource of characterised reference driver lines, which can be expanded with additional promoters and the use of other fluorescent proteins, we aim to contribute towards enhancing reproducibility of qualitative and quantitative analyses.

Pheno-Deep Counter: a unified and versatile deep learning architecture for leaf counting

Direct observation of morphological plant traits is tedious and a bottleneck for high-throughput phenotyping. Hence, interest in image-based analysis is increasing, with the requirement for software that can reliably extract plant traits, such as leaf count, preferably across a variety of species and growth conditions. However, current leaf counting methods do not work across species or conditions and therefore may lack broad utility. In this paper, we present Pheno-Deep Counter, a single deep network that can predict leaf count in two-dimensional (2D) plant images of different species with a rosette-shaped appearance. We demonstrate that our architecture can count leaves from multi-modal 2D images, such as visible light, fluorescence and near-infrared. Our network design is flexible, allowing for inputs to be added or removed to accommodate new modalities. Furthermore, our architecture can be used as is without requiring dataset-specific customization of the internal structure of the network, opening its use to new scenarios. Pheno-Deep Counter is able to produce accurate predictions in many plant species and, once trained, can count leaves in a few seconds. Through our universal and open source approach to deep counting we aim to broaden utilization of machine learning-based approaches to leaf counting. Our implementation can be downloaded at https://bitbucket.org/tuttoweb/pheno-deep-counter.

The Phosphate Fast-Responsive Genes PECP1 and PPsPase1 Affect Phosphocholine and Phosphoethanolamine Content

Phosphate starvation-mediated induction of the HAD-type phosphatases PPsPase1 (AT1G73010) and PECP1 (AT1G17710) has been reported in Arabidopsis (Arabidopsis thaliana). However, little is known about their in vivo function or impact on plant responses to nutrient deficiency. The preferences of PPsPase1 and PECP1 for different substrates have been studied in vitro but require confirmation in planta. Here, we examined the in vivo function of both enzymes using a reverse genetics approach. We demonstrated that PPsPase1 and PECP1 affect plant phosphocholine and phosphoethanolamine content, but not the pyrophosphate-related phenotypes. These observations suggest that the enzymes play a similar role in planta related to the recycling of polar heads from membrane lipids that is triggered during phosphate starvation. Altering the expression of the genes encoding these enzymes had no effect on lipid composition, possibly due to compensation by other lipid recycling pathways triggered during phosphate starvation. Furthermore, our results indicated that PPsPase1 and PECP1 do not influence phosphate homeostasis, since the inactivation of these genes had no effect on phosphate content or on the induction of molecular markers related to phosphate starvation. A combination of transcriptomics and imaging analyses revealed that PPsPase1 and PECP1 display a highly dynamic expression pattern that closely mirrors the phosphate status. This temporal dynamism, combined with the wide range of induction levels, broad expression, and lack of a direct effect on Pi content and regulation, makes PPsPase1 and PECP1 useful molecular markers of the phosphate starvation response.

Longitudinal zonation pattern in Arabidopsis root tip defined by a multiple structural change algorithm

Background and Aims The Arabidopsis thaliana root is a key experimental system in developmental biology. Despite its importance, we are still lacking an objective and broadly applicable approach for identification of number and position of developmental domains or zones along the longitudinal axis of the root apex or boundaries between them, which is essential for understanding the mechanisms underlying cell proliferation, elongation and differentiation dynamics during root development. Methods We used a statistics approach, the multiple structural change algorithm (MSC), for estimating the number and position of developmental transitions in the growing portion of the root apex. Once the positions of the transitions between domains and zones were determined, linear models were used to estimate the critical size of dividing cells (LcritD) and other parameters. Key Results The MSC approach enabled identification of three discrete regions in the growing parts of the root that correspond to the proliferation domain (PD), the transition domain (TD) and the elongation zone (EZ). Simultaneous application of the MSC approach and G2-to-M transition (CycB1;1DB:GFP) and endoreduplication (pCCS52A1:GUS) molecular markers confirmed the presence and position of the TD. We also found that the MADS-box gene XAANTAL1 (XAL1) is required for the wild-type (wt) PD increase in length during the first 2 weeks of growth. Contrary to wt, in the xal1 loss-of-function mutant the increase and acceleration of root growth were not detected. We also found alterations in LcritD in xal1 compared with wt, which was associated with longer cell cycle duration in the mutant. Conclusions The MSC approach is a useful, objective and versatile tool for identification of the PD, TD and EZ and boundaries between them in the root apices and can be used for the phenotyping of different genetic backgrounds, experimental treatments or developmental changes within a genotype. The tool is publicly available at www.ibiologia.com.mx/MSC_analysis.

The plant-specific CDKB1-CYCB1 complex mediates homologous recombination repair in Arabidopsis

Upon DNA damage, cyclin‐dependent kinases (CDKs) are typically inhibited to block cell division. In many organisms, however, it has been found that CDK activity is required for DNA repair, especially for homology‐dependent repair (HR), resulting in the conundrum how mitotic arrest and repair can be reconciled. Here, we show that Arabidopsis thaliana solves this dilemma by a division of labor strategy. We identify the plant‐specific B1‐type CDKs (CDKB1s) and the class of B1‐type cyclins (CYCB1s) as major regulators of HR in plants. We find that RADIATION SENSITIVE 51 (RAD51), a core mediator of HR, is a substrate of CDKB1‐CYCB1 complexes. Conversely, mutants in CDKB1 and CYCB1 fail to recruit RAD51 to damaged DNA. CYCB1;1 is specifically activated after DNA damage and we show that this activation is directly controlled by SUPPRESSOR OF GAMMA RESPONSE 1 (SOG1), a transcription factor that acts similarly to p53 in animals. Thus, while the major mitotic cell‐cycle activity is blocked after DNA damage, CDKB1‐CYCB1 complexes are specifically activated to mediate HR.

Genetic and molecular basis of nonhost disease resistance: complex, yes; silver bullet, no

Nonhost resistance (NHR), in which a successful pathogen on some plants fails to overcome host barriers on others, has attracted much attention owing to its potential for robust crop improvement. Recent advances reveal that a multitude of underlying mechanisms contribute to NHR, ranging from components shared with recognition-based defenses up to recessive susceptibility factors involved in plant primary metabolism. Most NHR appears multi-factorial and quantitative. This implies that there is no single, 'silver bullet' NHR mechanism that can be used to broadly restrict pathogens in many or all crops.

Pseudomonas sax genes overcome aliphatic isothiocyanate-mediated non-host resistance in Arabidopsis

Most plant-microbe interactions do not result in disease; natural products restrict non-host pathogens. We found that sulforaphane (4-methylsulfinylbutyl isothiocyanate), a natural product derived from aliphatic glucosinolates, inhibits growth in Arabidopsis of non-host Pseudomonas bacteria in planta. Multiple sax genes (saxCAB/F/D/G) were identified in Pseudomonas species virulent on Arabidopsis. These sax genes are required to overwhelm isothiocyanate-based defenses and facilitate a disease outcome, especially in the young leaves critical for plant survival. Introduction of saxCAB genes into non-host strains enabled them to overcome these Arabidopsis defenses. Our study shows that aliphatic isothiocyanates, previously shown to limit damage by herbivores, are also crucial, robust, and developmentally regulated defenses that underpin non-host resistance in the Arabidopsis-Pseudomonas pathosystem.

Abscisic acid has a key role in modulating diverse plant-pathogen interactions

We isolated an activation-tagged Arabidopsis (Arabidopsis thaliana) line, constitutive disease susceptibility2-1D (cds2-1D), that showed enhanced bacterial growth when challenged with various Pseudomonas syringae strains. Systemic acquired resistance and systemic PATHOGENESIS-RELATED GENE1 induction were also compromised in cds2-1D. The T-DNA insertion adjacent to NINE-CIS-EPOXYCAROTENOID DIOXYGENASE5 (NCED5), one of six genes encoding the abscisic acid (ABA) biosynthetic enzyme NCED, caused a massive increase in transcript level and enhanced ABA levels >2-fold. Overexpression of NCED genes recreated the enhanced disease susceptibility phenotype. NCED2, NCED3, and NCED5 were induced, and ABA accumulated strongly following compatible P. syringae infection. The ABA biosynthetic mutant aba3-1 showed reduced susceptibility to virulent P. syringae, and ABA, whether through exogenous application or endogenous accumulation in response to mild water stress, resulted in increased bacterial growth following challenge with virulent P. syringae, indicating that ABA suppresses resistance to P. syringae. Likewise ABA accumulation also compromised resistance to the biotrophic oomycete Hyaloperonospora arabidopsis, whereas resistance to the fungus Alternaria brassicicola was enhanced in cds2-1D plants and compromised in aba3-1 plants, indicating that ABA promotes resistance to this necrotroph. Comparison of the accumulation of salicylic acid and jasmonic acid in the wild type, cds2-1D, and aba3-1 plants challenged with P. syringae showed that ABA promotes jasmonic acid accumulation and exhibits a complex antagonistic relationship with salicylic acid. Our findings provide genetic evidence that the abiotic stress signal ABA also has profound roles in modulating diverse plant-pathogen interactions mediated at least in part by cross talk with the jasmonic acid and salicylic acid biotic stress signal pathways.

Gibberellin signaling in the endodermis controls Arabidopsis root meristem size

Plant growth is driven by cell proliferation and elongation. The hormone gibberellin (GA) regulates Arabidopsis root growth by controlling cell elongation, but it is currently unknown whether GA also controls root cell proliferation. Here we show that GA biosynthetic mutants are unable to increase their cell production rate and meristem size after germination. GA signals the degradation of the DELLA growth repressor proteins GAI and RGA, promoting root cell production. Targeting the expression of gai (a non-GA-degradable mutant form of GAI) in the root meristem disrupts cell proliferation. Moreover, expressing gai in dividing endodermal cells was sufficient to block root meristem enlargement. We report a novel function for GA regulating cell proliferation where this signal acts by removing DELLA in a subset of, rather than all, meristem cells. We suggest that the GA-regulated rate of expansion of dividing endodermal cells dictates the equivalent rate in other root tissues. Cells must double in size prior to dividing but cannot do so independently, because they are physically restrained by adjacent tissues with which they share cell walls. Our study highlights the importance of probing regulatory mechanisms linking molecular- and cellular-scale processes with tissue and organ growth responses.

Arabidopsis DUO POLLEN3 is a key regulator of male germline development and embryogenesis

Male germline development in angiosperms produces the pair of sperm cells required for double fertilization. A key regulator of this process in Arabidopsis thaliana is the male germline-specific transcription factor DUO POLLEN1 (DUO1) that coordinates germ cell division and gamete specification. Here, we uncover the role of DUO3, a nuclear protein that has a distinct, but overlapping role with DUO1 in male germline development. DUO3 is a conserved protein in land plants and is related to GON-4, a cell lineage regulator of gonadogenesis in Caenorhabditis elegans. Mutant duo3-1 germ cells either fail to divide or show a delay in division, and we show that, unlike DUO1, DUO3 promotes entry into mitosis independent of the G2/M regulator CYCB1;1. We also show that DUO3 is required for the expression of a subset of germline genes under DUO1 control and that like DUO1, DUO3 is essential for sperm cell specification and fertilization. Furthermore, we demonstrate an essential sporophytic role for DUO3 in cell division and embryo patterning. Our findings demonstrate essential developmental roles for DUO3 in cell cycle progression and cell specification in both gametophytic and sporophytic tissues.

Phosphate starvation signaling: a threesome controls systemic P(i) homeostasis

Systemic signaling between roots and shoots is required to maintain mineral nutrient homeostasis for optimal metabolism under varying environmental conditions. Recent work has revealed molecular components of a signaling module that controls systemic phosphate homeostasis, modulates uptake and transport in Arabidopsis. This module comprises PHO2, a protein that controls protein stability, the phloem-mobile microRNA-399 and a ribo-regulator that squelches the activity of miR399 towards PHO2 by a novel mechanism. This advance is a significant step for the design of future rational approaches to improve crop phosphate use efficiency.

Plant roots: recycled auxin energizes patterning and growth

Recent studies show that, in plant roots, mutually dependent regulatory mechanisms operating at cell and tissue levels interact to generate a self-sustaining distribution of the hormone auxin which provides a framework for developmental patterning and growth.

Phenotypic analysis of Arabidopsis mutants: quantitative analysis of root growth

INTRODUCTIONThe growth of plant roots is very easy to measure and is particularly straightforward in Arabidopsis thaliana, because the increase in organ size is essentially restricted to one dimension. The precise measurement of root apical growth can be used to accurately determine growth activity (the rate of growth at a given time) during development in mutants, transgenic backgrounds, or in response to experimental treatments. Root growth is measured in a number of ways, the simplest of which is to grow the seedlings in a Petri dish and record the position of the advancing root tip at appropriate time points. The increase in root length is measured with a ruler and the data are entered into Microsoft Excel for analysis. When dealing with large numbers of seedlings, however, this procedure can be tedious, as well as inaccurate. An alternative approach, described in this protocol, uses "snapshots" of the growing plants, which are taken using gel-documentation equipment (i.e., a video camera with a frame-grabber unit, now commonly used to capture images from ethidium-bromide-stained electrophoresis gels). The images are analyzed using publicly available software (NIH-Image), which allows the user simply to cut and paste data into Microsoft Excel.

Phenotypic analysis of Arabidopsis mutants: quantitative analysis of root growth

INTRODUCTIONThe growth of plant roots is very easy to measure and is particularly straightforward in Arabidopsis thaliana, because the increase in organ size is essentially restricted to one dimension. The precise measurement of root apical growth can be used to accurately determine growth activity (the rate of growth at a given time) during development in mutants, transgenic backgrounds, or in response to experimental treatments. Root growth is measured in a number of ways, the simplest of which is to grow the seedlings in a Petri dish and record the position of the advancing root tip at appropriate time points. The increase in root length is measured with a ruler and the data are entered into Microsoft Excel for analysis. When dealing with large numbers of seedlings, however, this procedure can be tedious, as well as inaccurate. An alternative approach, described in this protocol, uses "snapshots" of the growing plants, which are taken using gel-documentation equipment (i.e., a video camera with a frame-grabber unit, now commonly used to capture images from ethidium-bromide-stained electrophoresis gels). The images are analyzed using publicly available software (NIH-Image), which allows the user simply to cut and paste data into Microsoft Excel.

Plant meristems: cytokinins--the alpha and omega of the meristem

Recent studies have revealed important new details of how cytokinin-dependent mechanisms control plant growth. Intriguingly, cytokinins are involved in both maintaining meristems and promoting differentiation.

Cell division activity determines the magnitude of phosphate starvation responses in Arabidopsis

Phosphate (P(i)) is a major limiting factor for plant growth. Plants respond to limiting P(i) supplies by inducing a suite of adaptive responses comprising altered growth behaviour, enhanced P(i) acquisition and reduced P(i) demand that together define a distinct physiological state. In P(i)-starved plants, continued root growth is required for P(i) acquisition from new sources, yet meristem activity consumes P(i). Therefore, we analysed the relationship between organ growth, phosphate starvation-responsive (PSR) gene expression and P(i) content in Arabidopsis thaliana under growth-promoting or inhibitory conditions. Induction of PSR gene expression after transfer of plants to P(i)-depleted conditions quantitatively reflects prior levels of P(i) acquisition, and hence is sensitive to the balance of P(i) supply and demand. When plants are P(i)-starved, enhanced root or shoot growth exacerbates, whereas growth inhibition suppresses, P(i) starvation responses, suggesting that the magnitude of organ growth activity specifies the level of P(i) demand. Inhibition of cell-cycle activity, but not of cell expansion or cell growth, reduces P(i) starvation-responsive gene expression. Thus, the level of cell-cycle activity specifies the magnitude of P(i) demand in P(i)-starved plants. We propose that cell-cycle activity is the ultimate arbiter for P(i) demand in growing organs, and that other factors that influence levels of PSR gene expression do so by affecting growth through modulation of meristem activity.

ATR and ATM play both distinct and additive roles in response to ionizing radiation

The ATR and ATM protein kinases are known to be involved in a wide variety of responses to DNA damage. The Arabidopsis thaliana genome includes both ATR and ATM orthologs, and plants with null alleles of these genes are viable. Arabidopsis atr and atm mutants display hypersensitivity to gamma-irradiation. To further characterize the roles of ATM and ATR in response to ionizing radiation, we performed a short-term global transcription analysis in wild-type and mutant lines. We found that hundreds of genes are upregulated in response to gamma-irradiation, and that the induction of virtually all of these genes is dependent on ATM, but not ATR. The transcript of CYCB1;1 is unique among the cyclin transcripts in being rapidly and powerfully upregulated in response to ionizing radiation, while other G(2)-associated transcripts are suppressed. We found that both ATM and ATR contribute to the induction of a CYCB1;1:GUS fusion by IR, but only ATR is required for the persistence of this response. We propose that this upregulation of CYCB1;1 does not reflect the accumulation of cells in G(2), but instead reflects a still unknown role for this cyclin in DNA damage response.

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.

Arabidopsis REGULATOR OF AXILLARY MERISTEMS1 controls a leaf axil stem cell niche and modulates vegetative development

Shoot branching is a major determinant of variation in plant stature. Branches, which form secondary growth axes, originate from stem cells activated in leaf axils. The initial steps by which axillary meristems (AMs) are specified and their stem cells organized are still poorly understood. We identified gain- and loss-of-function alleles at the Arabidopsis thaliana REGULATOR OF AXILLARY MERISTEMS1 (RAX1) locus. RAX1 is encoded by the Myb-like transcription factor MYB37 and is an Arabidopsis homolog of the tomato (Solanum lycopersicum) Blind gene. RAX1 is transiently expressed in a small central domain within the boundary zone separating shoot apical meristem and leaf primordia early in leaf primordium development. RAX1 genetically interacts with CUP-SHAPED COTYLEDON (CUC) genes and is required for the expression of CUC2 in the RAX1 expression domain, suggesting that RAX1 acts through CUC2. We propose that RAX1 functions to positionally specify a stem cell niche for AM formation. RAX1 also affects the timing of developmental phase transitions by negatively regulating gibberellic acid levels in the shoot apex. RAX1 thus defines a novel activity that links the specification of AM formation with the modulation of the rate of progression through developmental phases.

Arabidopsis TCP20 links regulation of growth and cell division control pathways

During postembryonic plant development, cell division is coupled to cell growth. There is a stringent requirement to couple these processes in shoot and root meristems. As cells pass through meristems, they transit through zones with high rates of cell growth and proliferation during organogenesis. This transition implies a need for coordinate regulation of genes underpinning these two fundamental cell functions. Here, we report a mechanism for coregulation of cell division control genes and cell growth effectors. We identified a GCCCR motif necessary and sufficient for high-level cyclin CYCB1;1 expression at G2/M. This motif is overrepresented in many ribosomal protein gene promoters and is required for high-level expression of the S27 and L24 ribosomal subunit genes we examined. p33(TCP20), encoded by the Arabidopsis TCP20 gene, binds to the GCCCR element in the promoters of cyclin CYCB1;1 and ribosomal protein genes in vitro and in vivo. We propose a model in which organ growth rates, and possibly shape in aerial organs, are regulated by the balance of positively and negatively acting teosinte-branched, cycloidea, PCNA factor (TCP) genes in the distal meristem boundary zone where cells become mitotically quiescent before expansion and differentiation.

Plant meristems: a merry-go-round of signals

Recent studies have provided significant new insights into the gene actions that specify and maintain stem cells in plant shoots and roots. New layers of genetic control and potential signalling pathways and effector mechanisms have emerged from these new studies and will be reviewed here. These new findings refine the current model in which stem cells in plant meristems are regulated by negative feedback loops and uncover a fundamental mechanism for stem cell maintenance that might be common to shoots and roots.

A putative lipid transfer protein involved in systemic resistance signalling in Arabidopsis

Localized attack by a necrotizing pathogen induces systemic acquired resistance (SAR) to subsequent attack by a broad range of normally virulent pathogens. Salicylic acid accumulation is required for activation of local defenses, such as pathogenesis-related protein accumulation, at the initial site of attack, and for subsequent expression of SAR upon secondary, distant challenge. Although salicylic acid moves through the plant, it is apparently not an essential mobile signal. We screened Agrobacterium tumefaciens transfer DNA (tDNA) tagged lines of Arabidopsis thaliana for mutants specifically compromized in SAR. Here we show that Defective in induced resistance 1-1 (dir1-1) exhibits wild-type local resistance to avirulent and virulent Pseudomonas syringae, but that pathogenesis-related gene expression is abolished in uninoculated distant leaves and dir1-1 fails to develop SAR to virulent Pseudomonas or Peronospora parasitica. Petiole exudate experiments indicate that dir1-1 is defective in the production or transmission from the inoculated leaf of an essential mobile signal. DIR1 encodes a putative apoplastic lipid transfer protein and we propose that DIR1 interacts with a lipid-derived molecule to promote long distance signalling.

KAP-2, a protein that binds to the H-box in a bean chalcone synthase promoter, is a novel plant transcription factor with sequence identity to the large subunit of human Ku autoantigen

The KAP-2 protein that binds to the H-box (CCTACC) element in the bean CHS15 chalcone synthase promoter was purified, and internal peptide sequence used to design primers leading to the cloning of KAP-2 from bean (Phaseolus vulgaris) and barrel medic (Medicago truncatula). KAP-2 shares sequence similarity to the large subunit of mammalian Ku autoantigen, a protein proposed to be involved in control of DNA recombination and transcription. KAP-2 sequences were present in genomic DNA from a range of legumes, and a related protein is found in Arabidopsis thaliana. Recombinant KAP-2 expressed in insect cells showed the same binding specificity for the CHS15 H-box as the protein purified from bean cell extracts. In vitro transcription assays confirmed that KAP-2 stimulates transcription from a promoter harboring the H-box cis element.

Cell cycle controls: genome-wide analysis in Arabidopsis

The first decade of molecular analysis of plant cell cycle control genes revealed how well the important regulators are conserved among eukaryotes. The recent completion of the Arabidopsis genome sequence, and the use of increasingly sophisticated biochemical assays and genetic approaches, heralds a period of more detailed functional analysis of cell cycle regulators aimed at resolving their role in plant growth and development.

Early primordium morphogenesis during lateral root initiation in Arabidopsis thaliana

The first morphogenetic events of lateral root primordium (LRP) formation in the Arabidopsis thaliana (L.) Heynh. pericycle occur soon after cells of the primary root complete elongation. Pericycle cells in direct contact with underlying protoxylem cells participate in LRP formation. Two types of LRP initiation were found, longitudinal uni- and bi-cellular. These occur when a single or two pericycle cells within a file, respectively, become founder cells for the entire longitudinal extent of the LRP. Histochemical and cytological analysis suggests that three is the minimum number of cells required to initiate an LRP. In young primordia comprising less than 32 cells, the average cell-doubling time was 3.7 h, indicating a drastic acceleration of cell cycle progression after lateral root initiation. Early in LRP development, cell growth is limited and therefore cytokinesis leads to a reduction of cell volume, similar to cleavage division cycles during animal and plant embryogenesis. The striking coordination of proliferation between pericycle cells in adjacent files in direct contact with the underlying protoxylem implies that intercellular signaling mechanisms act in the root apical meristem or later in development.

Plant meristems: a ménage à trois to end it all

Regulated termination of stem cell maintenance is required to complete reproductive development in plants. Two recent studies have revealed a new relationship for some old suspects; the WUSCHEL gene, which promotes indeterminancy, is involved as well as the floral regulators LEAFY and AGAMOUS.

Evidence for a role in growth and salt resistance of a plasma membrane H+-ATPase in the root endodermis

The plasma membrane of plant cells is energized by an electrochemical gradient produced by P-type H+-ATPases (proton pumps). These pumps are encoded by at least 12 genes in Arabidopsis. Here we provide evidence that isoform AHA4 contributes to solute transport through the root endodermis. AHA4 is expressed most strongly in the root endodermis and flowers, as suggested by promoter-GUS reporter assays. A disruption of this pump (aha4-1) was identified as a T-DNA insertion in the middle of the gene (after VFP(574)). Truncated aha4-1 transcripts accumulate to approximately 50% of the level observed for AHA4 mRNA in wild-type plants. Plants homozygous for aha4-1 (-/-) show a subtle reduction in root and shoot growth compared with wild-type plants when grown under normal conditions. However, a mutant phenotype is very clear in plants grown under salt stress (e.g., 75 or 110 mM NaCl). In leaves of mutant plants subjected to Na stress, the ratio of Na to K increased 4-5-fold. Interestingly, the aha4-1 mutation appears to be semidominant and was only partially complemented by the introduction of additional wild-type copies of AHA4. These results are consistent with the hypothesis that aha4-1 may produce a dominant negative protein or RNA that partially disrupts the activity of other pumps or functions in the root endodermal tissue, thereby compromising the function of this cell layer in controlling ion homeostasis and nutrient transport.

Dynamic analyses of the expression of the HISTONE::YFP fusion protein in arabidopsis show that syncytial endosperm is divided in mitotic domains

During early seed development, nuclear divisions in the endosperm are not followed by cell division, leading to the development of a syncytium. The simple organization of the Arabidopsis endosperm provides a model in which to study the regulation of the cell cycle in relation to development. To monitor nuclear divisions, we constructed a HISTONE 2B::YELLOW FLUORESCENT PROTEIN gene fusion (H2B::YFP). To validate its use as a vital marker for chromatin in plants, H2B::YFP was expressed constitutively in Arabidopsis. This enabled the observation of mitoses in living root meristems. H2B::YFP was expressed specifically in Arabidopsis syncytial endosperm by using GAL4 transactivation. Monitoring mitotic activity in living syncytial endosperm showed that the syncytium was organized into three domains in which nuclei divide simultaneously with a specific time course. Each mitotic domain has a distinct spatiotemporal pattern of mitotic CYCLIN B1;1 accumulation. The polar spatial organization of the three mitotic domains suggests interactions between developmental mechanisms and the regulation of the cell cycle.

Dynamic analyses of the expression of the HISTONE::YFP fusion protein in arabidopsis show that syncytial endosperm is divided in mitotic domains

During early seed development, nuclear divisions in the endosperm are not followed by cell division, leading to the development of a syncytium. The simple organization of the Arabidopsis endosperm provides a model in which to study the regulation of the cell cycle in relation to development. To monitor nuclear divisions, we constructed a HISTONE 2B::YELLOW FLUORESCENT PROTEIN gene fusion (H2B::YFP). To validate its use as a vital marker for chromatin in plants, H2B::YFP was expressed constitutively in Arabidopsis. This enabled the observation of mitoses in living root meristems. H2B::YFP was expressed specifically in Arabidopsis syncytial endosperm by using GAL4 transactivation. Monitoring mitotic activity in living syncytial endosperm showed that the syncytium was organized into three domains in which nuclei divide simultaneously with a specific time course. Each mitotic domain has a distinct spatiotemporal pattern of mitotic CYCLIN B1;1 accumulation. The polar spatial organization of the three mitotic domains suggests interactions between developmental mechanisms and the regulation of the cell cycle.

Plant stem cells: the only constant thing is change

Recent studies in Arabidopsis have uncovered a negative feedback loop that couples the antagonistic functions of the WUSCHEL and CLAVATA loci to control stem cell fate in the shoot apical meristem. Abundance of the CLAVATA3 protein limits signaling through this pathway.

Root patterning: does auxin provide positional cues?

Patterning of Arabidopsis roots is mediated by cell-cell interactions, information flowing from differentiated to immature cells. The plant growth regulator auxin has now been shown to be involved in organizing the distal end of the root apex, including the extent and pattern of cell division programs and specification of cell identity.

Technical advance: spatio-temporal analysis of mitotic activity with a labile cyclin-GUS fusion protein

Plant growth responds rapidly to developmental and environmental signals, but the underlying changes in cell division activity are poorly understood. A labile cyclin-GUS reporter was developed to facilitate the spatio-temporal analysis of cell division patterns. The chimeric reporter protein is turned over every cell cycle and hence its histochemical activity accurately reports individual mitotic cells. Using Arabidopsis plants transformed with cyclin-GUS, we visualized patterns of mitotic activity in wounded leaves which suggest a role for cell division in structural reinforcement.

Shoot meristems: Intercellular signals keep the balance

Recent studies have identified a complex intercellular communication network which maintains the balance of indeterminate and determinate cells at the plant apical meristem. The widespread presence of homologous regulatory genes indicates that 'stemness' arose before the evolutionary split between plants and animals.

A plant homolog of the neutrophil NADPH oxidase gp91phox subunit gene encodes a plasma membrane protein with Ca2+ binding motifs

Rapid generation of O2- and H2O2, which is reminiscent of the oxidative burst in neutrophils, is a central component of the resistance response of plants to pathogen challenge. Here, we report that the Arabidopsis rbohA (for respiratory burst oxidase homolog A) gene encodes a putative 108-kD protein, with a C-terminal region that shows pronounced similarity to the 69-kD apoprotein of the gp91phox subunit of the neutrophil respiratory burst NADPH oxidase. The RbohA protein has a large hydrophilic N-terminal domain that is not present in gp91phox. This domain contains two Ca2+ binding EF hand motifs and has extended similarity to the human RanGTPase-activating protein 1. rbohA, which is a member of a divergent gene family, generates transcripts of 3.6 and 4.0 kb that differ only in their polyadenylation sites. rbohA transcripts are most abundant in roots, with weaker expression in aerial organs and seedlings. Antibodies raised against a peptide near the RbohA C terminus detected a 105-kD protein that, unlike gp91phox, does not appear to be highly glycosylated. Cell fractionation, two-phase partitioning, and detergent extraction indicate that RbohA is an intrinsic plasma membrane protein. We propose that plants have a plasma membrane enzyme similar to the neutrophil NADPH oxidase but with novel potential regulatory mechanisms for Ca2+ and G protein stimulation of O2- and H2O2 production at the cell surface.

A plant homolog of the neutrophil NADPH oxidase gp91phox subunit gene encodes a plasma membrane protein with Ca2+ binding motifs

Rapid generation of O2- and H2O2, which is reminiscent of the oxidative burst in neutrophils, is a central component of the resistance response of plants to pathogen challenge. Here, we report that the Arabidopsis rbohA (for respiratory burst oxidase homolog A) gene encodes a putative 108-kD protein, with a C-terminal region that shows pronounced similarity to the 69-kD apoprotein of the gp91phox subunit of the neutrophil respiratory burst NADPH oxidase. The RbohA protein has a large hydrophilic N-terminal domain that is not present in gp91phox. This domain contains two Ca2+ binding EF hand motifs and has extended similarity to the human RanGTPase-activating protein 1. rbohA, which is a member of a divergent gene family, generates transcripts of 3.6 and 4.0 kb that differ only in their polyadenylation sites. rbohA transcripts are most abundant in roots, with weaker expression in aerial organs and seedlings. Antibodies raised against a peptide near the RbohA C terminus detected a 105-kD protein that, unlike gp91phox, does not appear to be highly glycosylated. Cell fractionation, two-phase partitioning, and detergent extraction indicate that RbohA is an intrinsic plasma membrane protein. We propose that plants have a plasma membrane enzyme similar to the neutrophil NADPH oxidase but with novel potential regulatory mechanisms for Ca2+ and G protein stimulation of O2- and H2O2 production at the cell surface.

Root development: quiescent center not so mute after all

Many functions have been attributed to the quiescent center of a root apical meristem, from stem cell reservoir to pattern-generating center. Limited laser ablation of the quiescent center in Arabidopsis has now revealed that it acts to suppress differentiation and to maintain the surrounding initial cells as stem cells.

Rapid stimulation of a soybean protein-serine kinase that phosphorylates a novel bZIP DNA-binding protein, G/HBF-1, during the induction of early transcription-dependent defenses

The G-box (CACGTG) and H-box (CCTACC) cis elements function in the activation of phenylpropanoid biosynthetic genes involved in the elaboration of lignin precursors, phytoalexins and the secondary signal salicylic acid as early responses to pathogen attack. We have isolated a soybean cDNA encoding a novel bZIP protein, G/HBF-1, which binds to both the G-box and adjacent H-box in the proximal region of the chalcone synthase chs15 promoter. While G/HBF-1 transcript and protein levels do not increase during the induction of phenylpropanoid biosynthetic genes, G/HBF-1 is phosphorylated rapidly in elicited soybean cells, almost exclusively on serine residues. Using recombinant G/HBF-1 as a substrate, we identified a cytosolic protein-serine kinase that is rapidly and transiently stimulated in cells elicited with either glutathione or an avirulent strain of the soybean pathogen Pseudomonas syringae pv. glycinea. Phosphorylation of G/HBF-1 in vitro enhances binding to the chs15 promoter and we conclude that stimulation of G/HBF-1 kinase activity and G/HBF-1 phosphorylation are terminal events in a signal pathway for activation of early transcription-dependent plant defense responses.

Control of root growth and development by cyclin expression

Root development is plastic, with post-embryonic organogenesis being mediated by meristems. Although cell division is intrinsic to meristem initiation, maintenance and proliferative growth, the role of the cell cycle in regulating growth and development is unclear. To address this question, we examined the expression of cdc2 and cye genes, which encode the catalytic and regulatory subunits, respectively, of cyclin-dependent protein kinases that control progression through the cell cycle. Unlike cdc2, which is expressed not only in apical meristems but also before lateral root initiation in quiescent, pericycle cells arrested in the G2 phase of the cell cycle, cyc1At transcripts accumulate specifically in dividing cells immediately before cytokinesis. Ectopic expression of cyc1At under the control of the cdc2aAt promoter in Arabidopsis plants markedly accelerates growth without altering the pattern of lateral root development or inducing neoplasia. Thus cyclin expression is a limiting factor for growth, which in turn drives indeterminate development of the root system.

Cell-cell interactions: taking cues from the neighbors

Three lines of inquiry indicate that inductive interactions play a major role in the acquisition of cell identity during plant development.

Arabidopsis embryogenesis. Radicle development(s)

Genetic and anatomical analyses of the developing Arabidopsis embryogenic root reveal that stereotypic patterns of cell division are not required for pattern formation.