A predictive model for ethylene-mediated auxin and cytokinin patterning in the Arabidopsis root.

The interaction between auxin and cytokinin is important in many aspects of plant development. Experimental measurements of both auxin and cytokinin concentration and reporter gene expression clearly show the coexistence of auxin and cytokinin concentration patterning in Arabidopsis root development. However, in the context of crosstalk among auxin, cytokinin, and ethylene, little is known about how auxin and cytokinin concentration patterns simultaneously emerge and how they regulate each other in the Arabidopsis root. This work utilizes a wide range of experimental observations to propose a mechanism for simultaneous patterning of auxin and cytokinin concentrations. In addition to revealing the regulatory relationships between auxin and cytokinin, this mechanism shows that ethylene signaling is an important factor in achieving simultaneous auxin and cytokinin patterning, while also predicting other experimental observations. Combining the mechanism with a realistic in silico root model reproduces experimental observations of both auxin and cytokinin patterning. Predictions made by the mechanism can be compared with a variety of experimental observations, including those obtained by our group and other independent experiments reported by other groups. Examples of these predictions include patterning of auxin biosynthesis rate, changes in PIN1 and PIN2 patterns in pin3,4,7 mutants, changes in cytokinin patterning in the pls mutant, PLS patterning, and various trends in different mutants. This research reveals a plausible mechanism for simultaneous patterning of auxin and cytokinin concentrations in Arabidopsis root development and suggests a key role for ethylene pattern integration.

MERISTEM-DEFECTIVE regulates the balance between stemness and differentiation in the root meristem through RNA splicing control.

Plants respond to environmental stresses through controlled stem cell maintenance and meristem activity. One level of gene regulation is RNA alternative splicing. However, the mechanistic link between stress, meristem function and RNA splicing is poorly understood. The MERISTEM-DEFECTIVE (MDF) Arabidopsis gene encodes an SR-related family protein, required for meristem function and leaf vascularization, and is the likely orthologue of the human SART1 and yeast Snu66 splicing factors. MDF is required for the correct splicing and expression of key transcripts associated with root meristem function. We identified RSZ33 and ACC1, both known to regulate cell patterning, as splicing targets required for MDF function in the meristem. MDF expression is modulated by osmotic and cold stress, associated with differential splicing and specific isoform accumulation and shuttling between nucleus and cytosol, and acts in part via a splicing target SR34. We propose a model in which MDF controls splicing in the root meristem to promote stemness and to repress stress response, cell differentiation and cell death pathways.

Gibberellin signaling mediates lateral root inhibition in response to K+-deprivation.

The potassium ion (K+) is vital for plant growth and development, and K+-deprivation leads to reduced crop yields. Here we describe phenotypic, transcriptomic, and mutant analyses to investigate the signaling mechanisms mediating root architectural changes in Arabidopsis (Arabidopsis thaliana) Columbia. We showed effects on root architecture are mediated through a reduction in cell division in the lateral root (LR) meristems, the rate of LR initiation is reduced but LR density is unaffected, and primary root growth is reduced only slightly. This was primarily regulated through gibberellic acid (GA) signaling, which leads to the accumulation of growth-inhibitory DELLA proteins. The short LR phenotype was rescued by exogenous application of GA but not of auxin or by the inhibition of ethylene signaling. RNA-seq analysis showed upregulation by K+-deprivation of the transcription factors JUNGBRUNNEN1 (JUB1) and the C-repeat-binding factor (CBF)/dehydration-responsive element-binding factor 1 regulon, which are known to regulate GA signaling and levels that regulate DELLAs. Transgenic overexpression of JUB1 and CBF1 enhanced responses to K+ stress. Attenuation of the reduced LR growth response occurred in mutants of the CBF1 target gene SFR6, implicating a role for JUB1, CBF1, and SFR6 in the regulation of LR growth in response to K+-deprivation via DELLAs. We propose this represents a mechanism to limit horizontal root growth in conditions where K+ is available deeper in the soil.

Putrescine Depletion Affects Arabidopsis Root Meristem Size by Modulating Auxin and Cytokinin Signaling and ROS Accumulation.

Polyamines (PAs) dramatically affect root architecture and development, mainly by unknown mechanisms; however, accumulating evidence points to hormone signaling and reactive oxygen species (ROS) as candidate mechanisms. To test this hypothesis, PA levels were modified by progressively reducing ADC1/2 activity and Put levels, and then changes in root meristematic zone (MZ) size, ROS, and auxin and cytokinin (CK) signaling were investigated. Decreasing putrescine resulted in an interesting inverted-U-trend in primary root growth and a similar trend in MZ size, and differential changes in putrescine (Put), spermidine (Spd), and combined spermine (Spm) plus thermospermine (Tspm) levels. At low Put concentrations, ROS accumulation increased coincidently with decreasing MZ size, and treatment with ROS scavenger KI partially rescued this phenotype. Analysis of double AtrbohD/F loss-of-function mutants indicated that NADPH oxidases were not involved in H2O2 accumulation and that elevated ROS levels were due to changes in PA back-conversion, terminal catabolism, PA ROS scavenging, or another pathway. Decreasing Put resulted in a non-linear trend in auxin signaling, whereas CK signaling decreased, re-balancing auxin and CK signaling. Different levels of Put modulated the expression of PIN1 and PIN2 auxin transporters, indicating changes to auxin distribution. These data strongly suggest that PAs modulate MZ size through both hormone signaling and ROS accumulation in Arabidopsis.

The Arabidopsis R-SNARE VAMP714 is essential for polarisation of PIN proteins and auxin responses.

The plant hormone auxin and its directional intercellular transport play a major role in diverse aspects of plant growth and development. The establishment of auxin gradients requires the asymmetric distribution of members of the auxin efflux carrier PIN-FORMED (PIN) protein family to the plasma membrane. An endocytic pathway regulates the recycling of PIN proteins between the plasma membrane and endosomes, providing a mechanism for dynamic localisation. N-Ethylmaleimide-sensitive factor adaptor protein receptors (SNAP receptors, SNAREs) mediate fusion between vesicles and target membranes and are classed as Q- or R-SNAREs based on their sequence. We analysed gain- and loss-of-function mutants, dominant-negative transgenics and localisation of the Arabidopsis R-SNARE VAMP714 protein to understand its function. We demonstrate that VAMP714 is essential for the insertion of PINs into the plasma membrane, for polar auxin transport, root gravitropism and morphogenesis. VAMP714 gene expression is upregulated by auxin, and the VAMP714 protein co-localises with endoplasmic reticulum and Golgi vesicles and with PIN proteins at the plasma membrane. It is proposed that VAMP714 mediates the delivery of PIN-carrying vesicles to the plasma membrane, and that this forms part of a positive regulatory loop in which auxin activates a VAMP714-dependent PIN/auxin transport system to control development.

Root growth responses to mechanical impedance are regulated by a network of ROS, ethylene and auxin signalling in Arabidopsis.

The growth and development of root systems is influenced by mechanical properties of the substrate in which the plants grow. Mechanical impedance, such as by compacted soil, can reduce root elongation and limit crop productivity. To understand better the mechanisms involved in plant root responses to mechanical impedance stress, we investigated changes in the root transcriptome and hormone signalling responses of Arabidopsis to artificial root barrier systems in vitro. We demonstrate that upon encountering a barrier, reduced Arabidopsis root growth and a characteristic 'step-like' growth pattern is due to a reduction in cell elongation associated with changes in signalling gene expression. Data from RNA-sequencing combined with reporter line and mutant studies identified essential roles for reactive oxygen species, ethylene and auxin signalling during the barrier response. We propose a model in which early responses to mechanical impedance include reactive oxygen signalling integrated with ethylene and auxin responses to mediate root growth changes. Inhibition of ethylene responses allows improved growth in response to root impedance, an observation that may inform future crop breeding programmes.

Will rising atmospheric CO2 concentration inhibit nitrate assimilation in shoots but enhance it in roots of C3 plants?

Bloom et al. proposed that rising atmospheric CO2 concentrations 'inhibit malate production in chloroplasts and thus impede assimilation of nitrate into protein of C3 plants, a phenomenon that will strongly influence primary productivity and food security under the environmental conditions anticipated during the next few decades'. Previously we argued that the weight of evidence in the literature indicated that elevated atmospheric [CO2 ] does not inhibit NO3 - assimilation in C3 plants. New data for common bean (Phaseolus vulgaris) and wheat (Triticum aestivum) were presented that supported this view and indicated that the effects of elevated atmospheric [CO2 ] on nitrogen (N) assimilation and growth of C3 vascular plants were similar regardless of the form of N assimilated. Bloom et al. strongly criticised the arguments presented in Andrews et al. Here we respond to these criticisms and again conclude that the available data indicate that elevated atmospheric [CO2 ] does not inhibit NO3 - assimilation of C3 plants. Measurement of the partitioning of NO3 - assimilation between root and shoot of C3 species under different NO3 - supply, at ambient and elevated CO2 would determine if their NO3 - assimilation is inhibited in shoots but enhanced in roots at elevated atmospheric CO2 .

Elevated CO2 effects on nitrogen assimilation and growth of C3 vascular plants are similar regardless of N-form assimilated.

Atmospheric carbon dioxide concentration ([CO2]) increased from around 280 ppm in 1750 to 400 ppm in 2016 and is likely to continue to increase throughout this century. It has been argued that wheat, Arabidopsis, and C3 plants in general respond more positively to elevated atmospheric [CO2] under ammonium (NH4+) nutrition than under nitrate (NO3-) nutrition because elevated CO2 inhibits their photoreduction of NO3- and hence reduces their total plant nitrogen (N) assimilation and ultimately growth. Here, it is argued that the weight of evidence in the literature indicates that elevated atmospheric [CO2] does not inhibit NO3- assimilation and growth of C3 vascular plants. New data for common bean and wheat support this view and indicate that the effects of elevated atmospheric [CO2] on N assimilation and growth of C3 vascular plants will be similar regardless of the form of N assimilated.

Epidermal expression of a sterol biosynthesis gene regulates root growth by a non-cell-autonomous mechanism in Arabidopsis.

The epidermis is hypothesized to play a signalling role during plant development. One class of mutants showing defects in signal transduction and radial patterning are those in sterol biosynthesis. The expectation is that living cells require sterols, but it is not clear that all cell types express sterol biosynthesis genes. The HYDRA1 (HYD1) gene of Arabidopsis encodes sterol Δ8-Δ7 isomerase, and although hyd1 seedlings are defective in radial patterning across several tissues, we show that the HYD1 gene is expressed most strongly in the root epidermis. Transgenic activation of HYD1 transcription in the epidermis of hyd1 null mutants reveals a major role in root patterning and growth. HYD1 expression in the vascular tissues and root meristem, though not endodermis or pericycle, also leads to some phenotypic rescue. Phenotypic rescue is associated with rescued patterning of the PIN1 and PIN2 auxin efflux carriers. The importance of the epidermis in controlling root growth and development is proposed to be, in part, due to its role as a site for sterol biosynthesis, and auxin is a candidate for the non-cell-autonomous signal.

Abscisic acid regulates root growth under osmotic stress conditions via an interacting hormonal network with cytokinin, ethylene and auxin.

Understanding the mechanisms regulating root development under drought conditions is an important question for plant biology and world agriculture. We examine the effect of osmotic stress on abscisic acid (ABA), cytokinin and ethylene responses and how they mediate auxin transport, distribution and root growth through effects on PIN proteins. We integrate experimental data to construct hormonal crosstalk networks to formulate a systems view of root growth regulation by multiple hormones. Experimental analysis shows: that ABA-dependent and ABA-independent stress responses increase under osmotic stress, but cytokinin responses are only slightly reduced; inhibition of root growth under osmotic stress does not require ethylene signalling, but auxin can rescue root growth and meristem size; osmotic stress modulates auxin transporter levels and localization, reducing root auxin concentrations; PIN1 levels are reduced under stress in an ABA-dependent manner, overriding ethylene effects; and the interplay among ABA, ethylene, cytokinin and auxin is tissue-specific, as evidenced by differential responses of PIN1 and PIN2 to osmotic stress. Combining experimental analysis with network construction reveals that ABA regulates root growth under osmotic stress conditions via an interacting hormonal network with cytokinin, ethylene and auxin.

Spatiotemporal modelling of hormonal crosstalk explains the level and patterning of hormones and gene expression in Arabidopsis thaliana wild-type and mutant roots.

Patterning in Arabidopsis root development is coordinated via a localized auxin concentration maximum in the root tip, requiring the regulated expression of specific genes. However, little is known about how hormone and gene expression patterning is generated. Using a variety of experimental data, we develop a spatiotemporal hormonal crosstalk model that describes the integrated action of auxin, ethylene and cytokinin signalling, the POLARIS protein, and the functions of PIN and AUX1 auxin transporters. We also conduct novel experiments to confirm our modelling predictions. The model reproduces auxin patterning and trends in wild-type and mutants; reveals that coordinated PIN and AUX1 activities are required to generate correct auxin patterning; correctly predicts shoot to root auxin flux, auxin patterning in the aux1 mutant, the amounts of cytokinin, ethylene and PIN protein, and PIN protein patterning in wild-type and mutant roots. Modelling analysis further reveals how PIN protein patterning is related to the POLARIS protein through ethylene signalling. Modelling prediction of the patterning of POLARIS expression is confirmed experimentally. Our combined modelling and experimental analysis reveals that a hormonal crosstalk network regulates the emergence of patterns and levels of hormones and gene expression in wild-type and mutants.

Transcriptional analysis through RNA sequencing of giant cells induced by Meloidogyne graminicola in rice roots.

One of the reasons for the progressive yield decline observed in aerobic rice production is the rapid build-up of populations of the rice root knot nematode Meloidogyne graminicola. These nematodes induce specialized feeding cells inside root tissue, called giant cells. By injecting effectors in and sipping metabolites out of these cells, they reprogramme normal cell development and deprive the plant of its nutrients. In this research we have studied the transcriptome of giant cells in rice, after isolation of these cells by laser-capture microdissection. The expression profiles revealed a general induction of primary metabolism inside the giant cells. Although the roots were shielded from light induction, we detected a remarkable induction of genes involved in chloroplast biogenesis and tetrapyrrole synthesis. The presence of chloroplast-like structures inside these dark-grown cells was confirmed by confocal microscopy. On the other hand, genes involved in secondary metabolism and more specifically, the majority of defence-related genes were strongly suppressed in the giant cells. In addition, significant induction of transcripts involved in epigenetic processes was detected inside these cells 7 days after infection.

Components of complex lipid biosynthetic pathways in developing castor (Ricinus communis) seeds identified by MudPIT analysis of enriched endoplasmic reticulum.

Ricinoleic acid is a feedstock for nylon-11 (N11) synthesis which is currently obtained from castor (Ricinus communis) oil. Production of this fatty acid in a temperate oilseed crop is of great commercial interest, but the highest reported level in transgenic plant oils is 30%, below the 90% observed in castor and insufficient for commercial exploitation. To identify castor oil-biosynthetic enzymes and inform strategies to improve ricinoleic acid yields, we performed MudPIT analysis on endoplasmic reticulum (ER) purified from developing castor bean endosperm. Candidate enzymes for all steps of triacylglycerol synthesis were identified among 72 proteins in the data set related to complex-lipid metabolism. Previous reported proteomic data from oilseeds had not included any membrane-bound enzyme that might incorporate ricinoleic acid into oil. Analysis of enriched ER enabled determination of which protein isoforms for these enzymes were in developing castor seed. To complement this data, quantitative RT-PCR experiments with castor seed and leaf RNA were performed for orthologues of Arabidopsis oil-synthetic enzymes, determining which were highly expressed in the seed. These data provide important information for further manipulation of ricinoleic acid content in oilseeds and peptide data for future quantification strategies.

MERISTEM-DEFECTIVE, an RS domain protein, is required for the correct meristem patterning and function in Arabidopsis.

Plant growth and development is dependent on the specification and maintenance of pools of stem cells found in the meristems. Mutations in the Arabidopsis MERISTEM-DEFECTIVE (MDF) gene lead to a loss of stem cell and meristematic activity in the root and vegetative shoot. MDF encodes a putative RS domain protein with a predicted role in transcription or RNA processing control. mdf mutants exhibit decreased levels of PINFORMED2 (PIN2) and PIN4 mRNAs, which is associated with a reduction in PIN:GFP levels, and with a defective auxin maximum in the basal region of the developing mdf embryo and seedling root meristem. Seedling roots also exhibit reduced PLETHORA (PLT), SCARECROW and SHORTROOT gene expression, a loss of stem cell activity, terminal differentiation of the root meristem and defective cell patterning. MDF expression is not defective in the bodenlos, pin1 or eir1/pin2 auxin mutants, and is not modulated by exogenous auxin. plt1 plt2 double mutants have unaffected levels of MDF RNA, indicating that MDF acts upstream of PIN and PLT gene expression. Differentiation of the shoot stem cell pool also occurs in mdf mutants, associated with a reduced WUSCHEL (WUS) expression domain and expanded CLAVATA3 (CLV3) domain. Overexpression of MDF leads to the activation of markers of embryonic identity and ectopic meristem activity in vegetative tissues. These results demonstrate a requirement for the MDF-dependent pathway in regulating PIN/PLT- and WUS/CLV-mediated meristem activity.

Rescue of defective auxin-mediated gene expression and root meristem function by inhibition of ethylene signalling in sterol biosynthesis mutants of Arabidopsis.

The roles of sterols in plant development are not well understood, but evidence is emerging that they are required for cell division, polarity and patterning by mechanisms that are independent of brassinosteroids, of which they are precursors. Previous evidence shows that two sterol-defective mutants of Arabidopsis thaliana (L.) Heynh., hyd1 and fk(hyd2), are defective in root development. Here we show that the HYD1 gene, like the FK gene, is transcriptionally active in both primary and lateral root meristems, though not in the shoot apical meristem. The patterns of cell division during early stages of lateral root initiation in the hyd1 and fk(hyd2) mutants appear normal. Previous evidence also suggests that auxin and ethylene signalling is defective in the mutants. Here we show that the cytokinin- and ethylene-responsive ACS1::GUS reporter in the fk(hyd2) mutant responds to exogenous cytokinins but not to the ethylene precursor 1-aminocyclopropane-1-carboxylic acid, indicative of normal cytokinin signalling but supporting the hypothesis that ethylene signalling is defective. The defective root meristem cell division activity and expression patterns of the auxin-regulated DR5::GUS and IAA2::GUS reporters can be rescued to a significant extent by the pharmacological or genetic inhibition of ethylene signalling, but not by treatment with aminoethoxyvinylglycine, an inhibitor of ethylene synthesis. This supports the emerging view that the hyd1 and fk(hyd2) mutants exhibit an enhanced and unregulated ethylene signalling activity, which accounts for at least part of the observed mutant phenotypes, including disrupted auxin signalling. The possible relationship between ethylene signalling, membrane sterols and meristem function is discussed.

Importance of plant sterols in pattern formation and hormone signalling.

The recent identification of sterol mutants in plants has shown that these molecules play essential roles in development. Although several such mutants are dwarfed, predominantly because of the reduced accumulation of brassinosteroids, others show distinctive phenotypes. We put forward the view that sterols also have roles in mediating brassinosteroid-independent signalling, in the trafficking of membrane vesicles that transport key regulatory proteins and in correct signalling protein conformation and function in membranes.

EXORDIUM--a gene expressed in proliferating cells and with a role in meristem function, identified by promoter trapping in Arabidopsis.

To identify new genes expressed in meristematic cells, a promoter trap insertional mutagenesis strategy was used in Arabidopsis thaliana. Transgenic line AtEM201 exhibits promoter trap GUS activity in embryos and in the regions of active cell division in the seedling, notably the apical meristems and young leaves. The tagged gene was named EXORDIUM (EXO). AtEM201 contains a single copy of the promoter trap T-DNA, located in the EXO gene promoter, resulting in a much reduced level of EXO transcription. Seedlings homozygous for the T-DNA insertion have no obvious mutant phenotype. The EXO gene, which forms part of a small gene family in Arabidopsis, is structurally related to the tobacco PHI-1 gene, which is re-activated in cultured cells following release from phosphate starvation-induced cell cycle arrest. Expression of both the EXO-GUS and the native EXO genes is downregulated by exogenous cytokinin. Expression studies using semisynchronised cells suggest that EXO mRNA is preferentially abundant during M phase of the cell cycle. Double mutant studies revealed that the exo mutation can suppress the defective root meristem phenotype of the hydra2 mutant, suggesting that EXO may be a component of a negative regulatory system for cell division.

The POLARIS gene of Arabidopsis encodes a predicted peptide required for correct root growth and leaf vascular patterning.

The POLARIS (PLS) gene of Arabidopsis was identified as a promoter trap transgenic line, showing beta-glucuronidase fusion gene expression predominantly in the embryonic and seedling root, with low expression in aerial parts. Cloning of the PLS locus revealed that the promoter trap T-DNA had inserted into a short open reading frame (ORF). Rapid amplification of cDNA ends PCR, RNA gel blot analysis, and RNase protection assays showed that the PLS ORF is located within a short ( approximately 500 nucleotides) auxin-inducible transcript and encodes a predicted polypeptide of 36 amino acid residues. pls mutants exhibit a short-root phenotype and reduced vascularization of leaves. pls roots are hyperresponsive to exogenous cytokinins and show increased expression of the cytokinin-inducible gene ARR5/IBC6 compared with the wild type. pls seedlings also are less responsive to the growth-inhibitory effects of exogenous auxin and show reduced expression of the auxin-inducible gene IAA1 compared with the wild type. The PLS peptide-encoding region of the cDNA partially complements the pls mutation and requires the PLS ORF ATG for activity, demonstrating the functionality of the peptide-encoding ORF. Ectopic expression of the PLS ORF reduces root growth inhibition by exogenous cytokinins and increases leaf vascularization. We propose that PLS is required for correct auxin-cytokinin homeostasis to modulate root growth and leaf vascular patterning.