GNOM/FEWER ROOTS is required for the establishment of an auxin response maximum for arabidopsis lateral root initiation

The translocation of a chloride channel from the Golgi to the plasma membrane helps plants adapt to salt stress

A key mechanism employed by plants to adapt to salinity stress involves maintaining ion homeostasis via the actions of ion transporters. While the function of cation transporters in maintaining ion homeostasis in plants has been extensively studied, little is known about the roles of their anion counterparts in this process. Here, we describe a mechanism of salt adaptation in plants. We characterized the chloride channel (CLC) gene AtCLCf, whose expression is regulated by WRKY transcription factor under salt stress in Arabidopsis thaliana. Loss-of-function atclcf seedlings show increased sensitivity to salt, whereas AtCLCf overexpression confers enhanced resistance to salt stress. Salt stress induces the translocation of GFP-AtCLCf fusion protein to the plasma membrane (PM). Blocking AtCLCf translocation using the exocytosis inhibitor brefeldin-A or mutating the small GTPase gene AtRABA1b/BEX5 (RAS GENES FROM RAT BRAINA1b homolog) increases salt sensitivity in plants. Electrophysiology and liposome-based assays confirm the Cl-/H+ antiport function of AtCLCf. Therefore, we have uncovered a mechanism of plant adaptation to salt stress involving the NaCl-induced translocation of AtCLCf to the PM, thus facilitating Cl- removal at the roots, and increasing the plant's salinity tolerance.

Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery

The GNOM (GN) Guanine nucleotide Exchange Factor for ARF small GTPases (ARF-GEF) is among the best studied trafficking regulators in plants, playing crucial and unique developmental roles in patterning and polarity. The current models place GN at the Golgi apparatus (GA), where it mediates secretion/recycling, and at the plasma membrane (PM) presumably contributing to clathrin-mediated endocytosis (CME). The mechanistic basis of the developmental function of GN, distinct from the other ARF-GEFs including its closest homologue GNOM-LIKE1 (GNL1), remains elusive. Insights from this study largely extend the current notions of GN function. We show that GN, but not GNL1, localizes to the cell periphery at long-lived structures distinct from clathrin-coated pits, while CME and secretion proceed normally in gn knockouts. The functional GN mutant variant GNfewerroots, absent from the GA, suggests that the cell periphery is the major site of GN action responsible for its developmental function. Following inhibition by Brefeldin A, GN, but not GNL1, relocates to the PM likely on exocytic vesicles, suggesting selective molecular associations en route to the cell periphery. A study of GN-GNL1 chimeric ARF-GEFs indicates that all GN domains contribute to the specific GN function in a partially redundant manner. Together, this study offers significant steps toward the elucidation of the mechanism underlying unique cellular and development functions of GNOM.

Genetic Interaction between Arabidopsis SUR2/CYP83B1 and GNOM Indicates the Importance of Stabilizing Local Auxin Accumulation in Lateral Root Initiation

Lateral root (LR) formation is an important developmental event for the establishment of the root system in most vascular plants. In Arabidopsis thaliana, the fewer roots (fwr) mutation in the GNOM gene, encoding a guanine nucleotide exchange factor of ADP ribosylation factor that regulates vesicle trafficking, severely inhibits LR formation. Local accumulation of auxin response for LR initiation is severely affected in fwr. To better understand how local accumulation of auxin response for LR initiation is regulated, we identified a mutation, fewer roots suppressor1 (fsp1), that partially restores LR formation in fwr. The gene responsible for fsp1 was identified as SUPERROOT2 (SUR2), encoding CYP83B1 that positions at the metabolic branch point in the biosynthesis of auxin/indole-3-acetic acid (IAA) and indole glucosinolate. The fsp1 mutation increases both endogenous IAA levels and the number of the sites where auxin response locally accumulates prior to LR formation in fwr. SUR2 is expressed in the pericycle of the differentiation zone and in the apical meristem in roots. Time-lapse imaging of the auxin response revealed that local accumulation of auxin response is more stable in fsp1. These results suggest that SUR2/CYP83B1 affects LR founder cell formation at the xylem pole pericycle cells where auxin accumulates. Analysis of the genetic interaction between SUR2 and GNOM indicates the importance of stabilization of local auxin accumulation sites for LR initiation.

ERF1 inhibits lateral root emergence by promoting local auxin accumulation and repressing ARF7 expression

Lateral roots (LRs) are crucial for plants to sense environmental signals in addition to water and nutrient absorption. Auxin is key for LR formation, but the underlying mechanisms are not fully understood. Here, we report that Arabidopsis ERF1 inhibits LR emergence by promoting local auxin accumulation with altered distribution and regulating auxin signaling. Loss of ERF1 increases LR density compared with the wild type, whereas ERF1 overexpression causes the opposite phenotype. ERF1 enhances auxin transport by upregulating PIN1 and AUX1, resulting in excessive auxin accumulation in the endodermal, cortical, and epidermal cells surrounding LR primordia. Furthermore, ERF1 represses ARF7 transcription, thereby downregulating the expression of cell-wall remodeling genes that facilitate LR emergence. Together, our study reveals that ERF1 integrates environmental signals to promote local auxin accumulation with altered distribution and repress ARF7, consequently inhibiting LR emergence in adaptation to fluctuating environments.

Auxin-cytokinin interplay shapes root functionality under low-temperature stress

Low-temperature stress alters root system architecture. In particular, changes in the levels and response to auxin and cytokinin determine the fate of root architecture and function under stress because of their vital roles in regulating root cell division, differentiation, and elongation. An intricate nexus of genes encoding components of auxin and cytokinin biosynthesis, signaling, and transport components operate to counteract stress and facilitate optimum development. We review the role of auxin transport and signaling and its regulation by cytokinin during root development and stem cell maintenance under low-temperature stress. We highlight intricate mechanisms operating in root stem cells to minimize DNA damage by altering phytohormone levels, and discuss a working model for cytokinin in low-temperatures stress response.

Hormone released by the microalgae Neochlorisaquatica and alkalinization influence growth of terrestrial and floating aquatic plants

The microalgae Neochloris aquatica were previously evaluated as a potential biological control agent and source of bioactive compounds against immature stages of Culex quinquefasciatus. Larvae reared on microalgae suspension showed mortality or drastic effects with morphological alterations and damage in the midgut. N. aquatica have nutritional and toxic effects, resulting in delayed life cycle and incomplete adult development. Given the possibility of its use as a biological control agent, in this work we evaluate the effect of microalgae on other organisms of the environment, such as plants. Arabidopsis thaliana, a terrestrial plant, and Lemna sp., a floating aquatic plant, were selected as examples. Interaction assays and compound evaluations showed that the microalgae release auxins causing root inhibition, smaller epidermal cells and hairy root development. In Lemna sp., a slight decrease in growth rate was observed, with no deleterious effects on the fronds. On the other hand, we detected a detrimental effect on plants when interactions were performed in a closed environment, in a medium containing soluble carbonate, in which microalgae culture rapidly modifies the pH. The experiments showed that alkalinization of the medium inhibits plant growth, causing bleaching of leaves or fronds. This negative effect in plants was not observed when plants and microalgae were cultured in carbonate-free media. In conclusion, the results showed that N. aquatica can modify plant growth without being harmful, but the rapid alkalinization produced by carbon metabolism of microalgae under CO₂-limiting conditions, could regulate the number of plants.

Arabidopsis Cys2/His2 Zinc Finger Transcription Factor ZAT18 Modulates the Plant Growth-Defense Tradeoff

Plant defense responses under unfavorable conditions are often associated with reduced growth. However, the mechanisms underlying the growth-defense tradeoff remain to be fully elucidated, especially at the transcriptional level. Here, we revealed a Cys2/His2-type zinc finger transcription factor, namely, ZAT18, which played dual roles in plant immunity and growth by oppositely regulating the signaling of defense- and growth-related hormones. ZAT18 was first identified as a salicylic acid (SA)-inducible gene and was required for plant responses to SA in this study. In addition, we observed that ZAT18 enhanced the plant immunity with growth penalties that may have been achieved by activating SA signaling and repressing auxin signaling. Further transcriptome analysis of the zat18 mutant showed that the biological pathways of defense-related hormones, including SA, ethylene and abscisic acid, were repressed and that the biological pathways of auxin and cytokinin, which are growth-related hormones, were activated by abolishing the function of ZAT18. The ZAT18-mediated regulation of hormone signaling was further confirmed using qRT-PCR. Our results explored a mechanism by which plants handle defense and growth at the transcriptional level under stress conditions.

Auxin in Root Development

Root system architecture is an important determinant of below-ground resource capture and hence overall plant fitness. The plant hormone auxin plays a central role in almost every facet of root development from the cellular to the whole-root-system level. Here, using Arabidopsis as a model, we review the multiple gene signaling networks regulated by auxin biosynthesis, conjugation, and transport that underpin primary and lateral root development. We describe the role of auxin in establishing the root apical meristem and discuss how the tight spatiotemporal regulation of auxin distribution controls transitions between cell division, cell growth, and differentiation. This includes the localized reestablishment of mitotic activity required to elaborate the root system via the production of lateral roots. We also summarize recent discoveries on the effects of auxin and auxin signaling and transport on the control of lateral root gravitropic setpoint angle (GSA), a critical determinant of the overall shape of the root system. Finally, we discuss how environmental conditions influence root developmental plasticity by modulation of auxin biosynthesis, transport, and the canonical auxin signaling pathway.

Connected function of PRAF/RLD and GNOM in membrane trafficking controls intrinsic cell polarity in plants

Cell polarity is a fundamental feature underlying cell morphogenesis and organismal development. In the Arabidopsis stomatal lineage, the polarity protein BASL controls stomatal asymmetric cell division. However, the cellular machinery by which this intrinsic polarity site is established remains unknown. Here, we identify the PRAF/RLD proteins as BASL physical partners and mutating four PRAF members leads to defects in BASL polarization. Members of PRAF proteins are polarized in stomatal lineage cells in a BASL-dependent manner. Developmental defects of the praf mutants phenocopy those of the gnom mutants. GNOM is an activator of the conserved Arf GTPases and plays important roles in membrane trafficking. We further find PRAF physically interacts with GNOM in vitro and in vivo. Thus, we propose that the positive feedback of BASL and PRAF at the plasma membrane and the connected function of PRAF and GNOM in endosomal trafficking establish intrinsic cell polarity in the Arabidopsis stomatal lineage.

Rambutan genome revealed gene networks for spine formation and aril development

Rambutan is a popular tropical fruit known for its exotic appearance, has long flexible spines on shells, extraordinary aril growth, desirable nutrition, and a favorable taste. The genome of an elite rambutan cultivar Baoyan 7 was assembled into 328 Mb in 16 pseudo-chromosomes. Comparative genomics analysis between rambutan and lychee revealed that rambutan chromosomes 8 and 12 are collinear with lychee chromosome 1, which resulted in a chromosome fission event in rambutan (n = 16) or a fusion event in lychee (n = 15) after their divergence from a common ancestor 15.7 million years ago. Root development genes played a crucial role in spine development, such as endoplasmic reticulum pathway genes, jasmonic acid response genes, vascular bundle development genes, and K⁺ transport genes. Aril development was regulated by D-class genes (STK and SHP1), plant hormone and phenylpropanoid biosynthesis genes, and sugar metabolism genes. The lower rate of male sterility of hermaphroditic flowers appears to be regulated by MYB24. Population genomic analyses revealed genes in selective sweeps during domestication that are related to fruit morphology and environment stress response. These findings enhance our understanding of spine and aril development and provide genomic resources for rambutan improvement.

Microcystin-LR, a cyanobacterial toxin affects root development by changing levels of PIN proteins and auxin response in Arabidopsis roots

Microcystin-LR (MCY-LR) is a heptapeptide toxin produced mainly by freshwater cyanobacteria. It strongly inhibits protein phosphatases PP2A and PP1. Functioning of the PIN family of auxin efflux carriers is crucial for plant ontogenesis and their functions depend on their reversible phosphorylation. We aimed to reveal the adverse effects of MCY-LR on PIN and auxin distribution in Arabidopsis roots and its consequences for root development. Relatively short-term (24 h) MCY-LR treatments decreased the levels of PIN1, PIN2 and PIN7, but not of PIN3 in tips of primary roots. In contrast, levels of PIN1 and PIN2 increased in emergent lateral roots and their levels depended on the type of PIN in lateral root primordia. DR5:GFP reporter activity showed that the cyanotoxin-induced decrease of auxin levels/responses in tips of main roots in parallel to PIN levels. Those alterations did not affect gravitropic response of roots. However, MCY-LR complemented the altered gravitropic response of crk5-1 mutants, defective in a protein kinase with essential role in the correct membrane localization of PIN2. For MCY-LR treated Col-0 plants, the number of lateral root primordia but not of emergent laterals increased and lateral root primordia showed early development. In conclusion, inhibition of protein phosphatase activities changed PIN and auxin levels, thus altered root development. Previous data on aquatic plants naturally co-occurring with the cyanotoxin showed similar alterations of root development. Thus, our results on the model plant Arabidopsis give a mechanistic explanation of MCY-LR phytotoxicity in aquatic ecosystems.

The Protein Phosphatase PP2A Plays Multiple Roles in Plant Development by Regulation of Vesicle Traffic-Facts and Questions

The protein phosphatase PP2A is essential for the control of integrated eukaryotic cell functioning. Several cellular and developmental events, e.g., plant growth regulator (PGR) mediated signaling pathways are regulated by reversible phosphorylation of vesicle traffic proteins. Reviewing present knowledge on the relevant role of PP2A is timely. We discuss three aspects: (1) PP2A regulates microtubule-mediated vesicle delivery during cell plate assembly. PP2A dephosphorylates members of the microtubule associated protein family MAP65, promoting their binding to microtubules. Regulation of phosphatase activity leads to changes in microtubule organization, which affects vesicle traffic towards cell plate and vesicle fusion to build the new cell wall between dividing cells. (2) PP2A-mediated inhibition of target of rapamycin complex (TORC) dependent signaling pathways contributes to autophagy and this has possible connections to the brassinosteroid signaling pathway. (3) Transcytosis of vesicles transporting PIN auxin efflux carriers. PP2A regulates vesicle localization and recycling of PINs related to GNOM (a GTP-GDP exchange factor) mediated pathways. The proper intracellular traffic of PINs is essential for auxin distribution in the plant body, thus in whole plant development. Overall, PP2A has essential roles in membrane interactions of plant cell and it is crucial for plant development and stress responses.

Cell wall remodeling and vesicle trafficking mediate the root clock in Arabidopsis

In Arabidopsis thaliana, lateral roots initiate in a process preceded by periodic gene expression known as the root clock. We identified the vesicle-trafficking regulator GNOM and its suppressor, ADENOSINE PHOSPHATE RIBOSYLATION FACTOR GTPase ACTIVATION PROTEIN DOMAIN3, as root clock regulators. GNOM is required for the proper distribution of pectin, a mediator of intercellular adhesion, whereas the pectin esterification state is essential for a functional root clock. In sites of lateral root primordia emergence, both esterified and de-esterified pectin variants are differentially distributed. Using a reverse-genetics approach, we show that genes controlling pectin esterification regulate the root clock and lateral root initiation. These results indicate that the balance between esterified and de-esterified pectin states is essential for proper root clock function and the subsequent initiation of lateral root primordia.

ABI3 plays a role in de-novo root regeneration from Arabidopsis thaliana callus cells

Developmental plasticity and the ability to regenerate organs during the life cycle are a signature feature of plant system. De novo organogenesis is a common mode of plant regeneration and may occur directly from the explant or indirectly via callus formation. It is now evident that callus formation occurs through the root development pathway. In fact, callus cells behave like a group of root primordium cells that are under the control of exogenous auxin. Presence or absence of auxin decides the subsequent fate of these cells. While in presence of external supplementation of auxin they are maintained as root primordia cells, absence of exogenous auxin induces the callus cells into patterning, differentiation and finally root emergence. Here we show that in absence of functional ABI3, a prominent member of the B3 superfamily of transcription factors, root regeneration is compromised in Arabidopsis callus cells. In culture medium free of any exogenous hormone supplementation, while adventitious root emergence and growth was prominently observed in wild type cells, no such features were observed in abi3-6 cells. Expression of auxin-responsive AUX1 and GH3 genes was significantly reduced in abi3-6 cells, indicating that auxin levels or distribution may be altered in absence of ABI3.

The isoleucic acid triad: distinct impacts on plant defense, root growth, and formation of reactive oxygen species

Isoleucic acid (ILA), a branched-chain amino acid-related 2-hydroxycarboxylic acid, occurs ubiquitously in plants. It enhances pathogen resistance and inhibits root growth of Arabidopsis. The salicylic acid (SA) glucosyltransferase UGT76B1 is able to conjugate ILA. Here, we investigate the role of ILA in planta in Arabidopsis and reveal a triad of distinct responses to this small molecule. ILA synergistically co-operates with SA to activate SA-responsive gene expression and resistance in a UGT76B1-dependent manner in agreement with the observed competitive ILA-dependent repression of SA glucosylation by UGT76B1. However, ILA also shows an SA-independent stress response. Nitroblue tetrazolium staining and pharmacological experiments indicate that ILA induces superoxide formation of the wild type and of an SA-deficient (NahG sid2) line. In contrast, the inhibitory effect of ILA on root growth is independent of both SA and superoxide induction. These effects of ILA are specific and distinct from its isomeric compound leucic acid and from the amino acid isoleucine. Leucic acid and isoleucine do not induce expression of defense marker genes or superoxide production, whereas both compounds inhibit root growth. All three responses to ILA are also observed in Brassica napus.

Non-intrinsic ATP-binding cassette proteins ABCI19, ABCI20 and ABCI21 modulate cytokinin response at the endoplasmic reticulum in Arabidopsis thaliana

The non-intrinsic ABC proteins ABCI20 and ABCI21 are induced by light under HY5 regulation, localize to the ER, and ameliorate cytokinin-driven growth inhibition in young Arabidopsis thaliana seedlings. The plant ATP-binding cassette (ABC) I subfamily (ABCIs) comprises heterogeneous proteins containing any of the domains found in other ABC proteins. Some ABCIs are known to function in basic metabolism and stress responses, but many remain functionally uncharacterized. ABCI19, ABCI20, and ABCI21 of Arabidopsis thaliana cluster together in a phylogenetic tree, and are suggested to be targets of the transcription factor ELONGATED HYPOCOTYL 5 (HY5). Here, we reveal that these three ABCIs are involved in modulating cytokinin responses during early seedling development. The ABCI19, ABCI20 and ABCI21 promoters harbor HY5-binding motifs, and ABCI20 and ABCI21 expression was induced by light in a HY5-dependent manner. abci19 abci20 abci21 triple and abci20 abci21 double knockout mutants were hypersensitive to cytokinin in seedling growth retardation assays, but did not show phenotypic differences from the wild type in either control medium or auxin-, ABA-, GA-, ACC- or BR-containing media. ABCI19, ABCI20, and ABCI21 were expressed in young seedlings and the three proteins interacted with each other, forming a large protein complex at the endoplasmic reticulum (ER) membrane. These results suggest that ABCI19, ABCI20, and ABCI21 fine-tune the cytokinin response at the ER under the control of HY5 at the young seedling stage.

Coordination of tissue cell polarity by auxin transport and signaling

Plants coordinate the polarity of hundreds of cells during vein formation, but how they do so is unclear. The prevailing hypothesis proposes that GNOM, a regulator of membrane trafficking, positions PIN-FORMED auxin transporters to the correct side of the plasma membrane; the resulting cell-to-cell, polar transport of auxin would coordinate tissue cell polarity and induce vein formation. Contrary to predictions of the hypothesis, we find that vein formation occurs in the absence of PIN-FORMED or any other intercellular auxin-transporter; that the residual auxin-transport-independent vein-patterning activity relies on auxin signaling; and that a GNOM-dependent signal acts upstream of both auxin transport and signaling to coordinate tissue cell polarity and induce vein formation. Our results reveal synergism between auxin transport and signaling, and their unsuspected control by GNOM in the coordination of tissue cell polarity during vein patterning, one of the most informative expressions of tissue cell polarization in plants.

Plants, animals and other living things grow and develop over their lifetimes: for example, oak trees come from acorns and chickens begin their lives as eggs. To achieve these transformations, the cells in those living things must grow, divide and change their shape and other features.

Plants and animals specify the directions in which their cells will grow and develop by gathering specific proteins to one side of the cells. This makes one side different from all the other sides, which the cells use as an internal compass that points in one direction. To align their internal compasses, animal cells touch one another and often move around inside the body. Plant cells, on the other hand, are surrounded by a wall that keeps them apart and prevents them from moving around. So how do plant cells align their internal compasses?

Scientists have long thought that a protein called GNOM aligns the internal compasses of plant cells. The hypothesis proposes that GNOM gathers another protein, called PIN1, to one side of a cell. PIN1 would then pump a plant hormone known as auxin out of this first cell and, in doing so, would also drain auxin away from the cell on the opposite side. In this second cell, GNOM would then gather PIN1 to the side facing the first cell, and this process would repeat until all the cells' compasses were aligned.

To test this hypothesis, Verna et al. combined microscopy with genetic approaches to study how cells' compasses are aligned in the leaves of a plant called Arabidopsis thaliana. The experiments revealed that auxin needs to move from cell-to-cell to align the cells’ compasses. However, contrary to the above hypothesis, this movement of auxin was not sufficient: the cells also needed to be able to detect and respond to the auxin that entered them. Along with controlling how auxin moved between the cells, GNOM also regulated how the cells responded to the auxin.

These findings reveal how plants specify which directions their cells grow and develop. In the future, this knowledge may eventually aid efforts to improve crop yields by controlling the growth and development of crop plants.

AtTRAPPC11/ROG2: A Role for TRAPPs in Maintenance of the Plant Trans-Golgi Network/Early Endosome Organization and Function

The dynamic trans-Golgi network/early endosome (TGN/EE) facilitates cargo sorting and trafficking and plays a vital role in plant development and environmental response. Transport protein particles (TRAPPs) are multi-protein complexes acting as guanine nucleotide exchange factors and possibly as tethers, regulating intracellular trafficking. TRAPPs are essential in all eukaryotic cells and are implicated in a number of human diseases. It has been proposed that they also play crucial roles in plants; however, our current knowledge about the structure and function of plant TRAPPs is very limited. Here, we identified and characterized AtTRAPPC11/RESPONSE TO OLIGOGALACTURONIDE2 (AtTRAPPC11/ROG2), a TGN/EE-associated, evolutionarily conserved TRAPP protein in Arabidopsis (Arabidopsis thaliana). AtTRAPPC11/ROG2 regulates TGN integrity, as evidenced by altered TGN/EE association of several residents, including SYNTAXIN OF PLANTS61, and altered vesicle morphology in attrappc11/rog2 mutants. Furthermore, endocytic traffic and brefeldin A body formation are perturbed in attrappc11/rog2, suggesting a role for AtTRAPPC11/ROG2 in regulation of endosomal function. Proteomic analysis showed that AtTRAPPC11/ROG2 defines a hitherto uncharacterized TRAPPIII complex in plants. In addition, attrappc11/rog2 mutants are hypersensitive to salinity, indicating an undescribed role of TRAPPs in stress responses. Overall, our study illustrates the plasticity of the endomembrane system through TRAPP protein functions and opens new avenues to explore this dynamic network.

Cold stress response in Arabidopsis thaliana is mediated by GNOM ARF-GEF

Endosomal trafficking plays an important role in regulating plant growth and development both at optimal and stressed conditions. Cold stress response in Arabidopsis root is directly linked to inhibition of the endosomal trafficking of auxin efflux carriers. However, the cellular components that link cold stress and the endosomal trafficking remain elusive. By screening available endosomal trafficking mutants against root growth recovery response under cold stress, we identified GNOM, a SEC7 containing ARF-GEF, as a major modulator of cold response. Contrasting response of partial loss of function mutant gnom^{B4049/emb30-1} and the engineered Brefeldin A (BFA)-resistant GNOM line, both of which contain mutations within SEC7 domain, to cold stress at the whole-plant level highlights the importance of this domain in modulating the cold response pathway of plants. Cold stress selectively and transiently inhibits GNOM expression. The engineered point mutation at 696 amino acid position (Methionine to Leucine) that makes GNOM resistant to BFA in fact results in overexpression of GNOM both at transcriptional and translational levels, and also alters its subcellular localization. Overexpression and altered cellular localization of GNOM were found to be directly linked to conferring striking cold-resistant phenotype in Arabidopsis. Collectively, these results provide a mechanistic link between GNOM, BFA-sensitive GNOM-regulated trafficking and cold stress.

A Strigolactone Signal Inhibits Secondary Lateral Root Development in Rice

Strigolactones (SLs) and their derivatives are plant hormones that have recently been identified as regulators of primary lateral root (LR) development. However, whether SLs mediate secondary LR production in rice (Oryza sativa L.), and how SLs and auxin interact in this process, remain unclear. In this study, the SL-deficient (dwarf10) and SL-insensitive (dwarf3) rice mutants and lines overexpressing OsPIN2 (OE) were used to investigate secondary LR development. The effects of exogenous GR24 (a synthetic SL analogue), 1-naphthylacetic acid (NAA; an exogenous auxin), 1-naphthylphthalamic acid (NPA; a polar auxin transport inhibitor), and abamine (a synthetic SL inhibitor) on rice secondary LR development were investigated. Rice d mutants with impaired SL biosynthesis and signaling exhibited increased secondary LR production compared with wild-type (WT) plants. Application of GR24 decreased the numbers of secondary LRs in dwarf10 (d10) plants but not in dwarf3 (d3), plants. These results indicate that SLs negatively regulate rice secondary LR production. Higher expression of DR5::GUS and more secondary LR primordia were found in the d mutants than in the WT plants. Exogenous NAA application increased expression of DR5::GUS in the WT, but had no effect on secondary LR formation. No secondary LRs were recorded in the OE lines, although DR5::GUS levels were higher than in the WT plants. However, on application of NPA, the numbers of secondary LRs were reduced in d10 and d3 mutants. Application of NAA increased the number of secondary LRs in the d mutants. GR24 eliminated the effect of NAA on secondary LR development in the d10, but not in the d3, mutants. These results demonstrate the importance of auxin in secondary LR formation, and that this process is inhibited by SLs via the D3 response pathway, but the interaction between auxin and SLs is complex.

Regulation of Hormonal Control, Cell Reprogramming, and Patterning during De Novo Root Organogenesis

Body regeneration through formation of new organs is a major question in developmental biology. We investigated de novo root formation using whole leaves of Arabidopsis (Arabidopsis thaliana). Our results show that local cytokinin biosynthesis and auxin biosynthesis in the leaf blade followed by auxin long-distance transport to the petiole leads to proliferation of J0121-marked xylem-associated tissues and others through signaling of INDOLE-3-ACETIC ACID INDUCIBLE28 (IAA28), CRANE (IAA18), WOODEN LEG, and ARABIDOPSIS RESPONSE REGULATORS1 (ARR1), ARR10, and ARR12. Vasculature proliferation also involves the cell cycle regulator KIP-RELATED PROTEIN2 and ABERRANT LATERAL ROOT FORMATION4, resulting in a mass of cells with rooting competence that resembles callus formation. Endogenous callus formation precedes specification of postembryonic root founder cells, from which roots are initiated through the activity of SHORT-ROOT, PLETHORA1 (PLT1), and PLT2. Primordia initiation is blocked in shr plt1 plt2 mutant. Stem cell regulators SCHIZORIZA, JACKDAW, BLUEJAY, and SCARECROW also participate in root initiation and are required to pattern the new organ, as mutants show disorganized and reduced number of layers and tissue initials resulting in reduced rooting. Our work provides an organ regeneration model through de novo root formation, stating key stages and the primary pathways involved.

Lateral root formation and the multiple roles of auxin

Root systems can display variable architectures that contribute to survival strategies of plants. The model plant Arabidopsis thaliana possesses a tap root system, in which the primary root and lateral roots (LRs) are major architectural determinants. The phytohormone auxin fulfils multiple roles throughout LR development. In this review, we summarize recent advances in our understanding of four aspects of LR formation: (i) LR positioning, which determines the spatial distribution of lateral root primordia (LRP) and LRs along primary roots; (ii) LR initiation, encompassing the activation of nuclear migration in specified lateral root founder cells (LRFCs) up to the first asymmetric cell division; (iii) LR outgrowth, the 'primordium-intrinsic' patterning of de novo organ tissues and a meristem; and (iv) LR emergence, an interaction between LRP and overlaying tissues to allow passage through cell layers. We discuss how auxin signaling, embedded in a changing developmental context, plays important roles in all four phases. In addition, we discuss how rapid progress in gene network identification and analysis, modeling, and four-dimensional imaging techniques have led to an increasingly detailed understanding of the dynamic regulatory networks that control LR development.

Chloroplastic ATP synthase builds up a proton motive force preventing production of reactive oxygen species in photosystem I

Over-reduction of the photosynthetic electron transport (PET) chain should be avoided, because the accumulation of reducing electron carriers produces reactive oxygen species (ROS) within photosystem I (PSI) in thylakoid membranes and causes oxidative damage to chloroplasts. To prevent production of ROS in thylakoid membranes the H⁺ gradient (ΔpH) needs to be built up across the thylakoid membranes to suppress the over-reduction state of the PET chain. In this study, we aimed to identify the critical component that stimulates ΔpH formation under illumination in higher plants. To do this, we screened ethyl methane sulfonate (EMS)-treated Arabidopsis thaliana, in which the formation of ΔpH is impaired and the PET chain caused over-reduction under illumination. Subsequently, we isolated an allelic mutant that carries a missense mutation in the γ-subunit of chloroplastic CF₀ CF₁ -ATP synthase, named hope2. We found that hope2 suppressed the formation of ΔpH during photosynthesis because of the high H⁺ efflux activity from the lumenal to stromal side of the thylakoid membranes via CF₀ CF₁ -ATP synthase. Furthermore, PSI was in a more reduced state in hope2 than in wild-type (WT) plants, and hope2 was more vulnerable to PSI photoinhibition than WT under illumination. These results suggested that chloroplastic CF₀ CF₁ -ATP synthase adjusts the redox state of the PET chain, especially for PSI, by modulating H⁺ efflux activity across the thylakoid membranes. Our findings suggest the importance of the buildup of ΔpH depending on CF₀ CF₁ -ATP synthase to adjust the redox state of the reaction center chlorophyll P700 in PSI and to suppress the production of ROS in PSI during photosynthesis.

Local Auxin Biosynthesis Mediated by a YUCCA Flavin Monooxygenase Regulates Haustorium Development in the Parasitic Plant Phtheirospermum japonicum

Parasitic plants in the Orobanchaceae cause serious agricultural problems worldwide. Parasitic plants develop a multicellular infectious organ called a haustorium after recognition of host-released signals. To understand the molecular events associated with host signal perception and haustorium development, we identified differentially regulated genes expressed during early haustorium development in the facultative parasite Phtheirospermum japonicum using a de novo assembled transcriptome and a customized microarray. Among the genes that were upregulated during early haustorium development, we identified YUC3, which encodes a functional YUCCA (YUC) flavin monooxygenase involved in auxin biosynthesis. YUC3 was specifically expressed in the epidermal cells around the host contact site at an early time point in haustorium formation. The spatio-temporal expression patterns of YUC3 coincided with those of the auxin response marker DR5, suggesting generation of auxin response maxima at the haustorium apex. Roots transformed with YUC3 knockdown constructs formed haustoria less frequently than nontransgenic roots. Moreover, ectopic expression of YUC3 at the root epidermal cells induced the formation of haustorium-like structures in transgenic P. japonicum roots. Our results suggest that expression of the auxin biosynthesis gene YUC3 at the epidermal cells near the contact site plays a pivotal role in haustorium formation in the root parasitic plant P. japonicum.

As above, so below: Auxin's role in lateral organ development

Organogenesis requires the coordination of many highly-regulated developmental processes, including cell fate determination, cell division and growth, and cell-cell communication. For tissue- and organ-scale coordination, a network of regulators enables molecular events in individual cells to translate into multicellular changes in structure and functional capacity. One recurrent theme in plant developmental networks is a central role for plant hormones, especially auxin. Here, we focus first on describing recent advances in understanding lateral root development, one of the best-studied examples of auxin-mediated organogenesis. We then use this framework to examine the parallel process of emergence of lateral organs in the shoot-a process called phyllotaxy. This comparison reveals a high degree of conservation, highlighting auxin's pivotal role determining overall plant architecture.

The dynamics of plant plasma membrane proteins: PINs and beyond

Plants are permanently situated in a fixed location and thus are well adapted to sense and respond to environmental stimuli and developmental cues. At the cellular level, several of these responses require delicate adjustments that affect the activity and steady-state levels of plasma membrane proteins. These adjustments involve both vesicular transport to the plasma membrane and protein internalization via endocytic sorting. A substantial part of our current knowledge of plant plasma membrane protein sorting is based on studies of PIN-FORMED (PIN) auxin transport proteins, which are found at distinct plasma membrane domains and have been implicated in directional efflux of the plant hormone auxin. Here, we discuss the mechanisms involved in establishing such polar protein distributions, focusing on PINs and other key plant plasma membrane proteins, and we highlight the pathways that allow for dynamic adjustments in protein distribution and turnover, which together constitute a versatile framework that underlies the remarkable capabilities of plants to adjust growth and development in their ever-changing environment.

Auxin overproduction in shoots cannot rescue auxin deficiencies in Arabidopsis roots

Auxin plays an essential role in root development. It has been a long-held dogma that auxin required for root development is mainly transported from shoots into roots by polarly localized auxin transporters. However, it is known that auxin is also synthesized in roots. Here we demonstrate that a group of YUCCA (YUC) genes, which encode the rate-limiting enzymes for auxin biosynthesis, plays an essential role in Arabidopsis root development. Five YUC genes (YUC3, YUC5, YUC7, YUC8 and YUC9) display distinct expression patterns during root development. Simultaneous inactivation of the five YUC genes (yucQ mutants) leads to the development of very short and agravitropic primary roots. The yucQ phenotypes are rescued by either adding 5 nM of the natural auxin, IAA, in the growth media or by expressing a YUC gene in the roots of yucQ. Interestingly, overexpression of a YUC gene in shoots in yucQ causes the characteristic auxin overproduction phenotypes in shoots; however, the root defects of yucQ are not rescued. Our data demonstrate that localized auxin biosynthesis in roots is required for normal root development and that auxin transported from shoots is not sufficient for supporting root elongation and root gravitropic responses.

Symmetry, asymmetry, and the cell cycle in plants: known knowns and some known unknowns

The body architectures of most multicellular organisms consistently display both symmetry and asymmetry. Here, we discuss some of the available knowledge and open questions on how symmetry and asymmetry appear in several conspicuous plant cells and tissues. We focus, where possible, on the role of genes that participate in the maintenance or the breaking of symmetry and that are directly or indirectly related to the cell cycle, under an organ-centric point of view and with an emphasis on the leaf.

Bergmann D, De Smet I, Sozzani R, Weijers D, Brady SM. Omics and modelling approaches for understanding regulation of asymmetric cell divisions in arabidopsis and other angiosperm plants

BACKGROUND

Asymmetric cell divisions are formative divisions that generate daughter cells of distinct identity. These divisions are coordinated by either extrinsic ('niche-controlled') or intrinsic regulatory mechanisms and are fundamentally important in plant development.

SCOPE

This review describes how asymmetric cell divisions are regulated during development and in different cell types in both the root and the shoot of plants. It further highlights ways in which omics and modelling approaches have been used to elucidate these regulatory mechanisms. For example, the regulation of embryonic asymmetric divisions is described, including the first divisions of the zygote, formative vascular divisions and divisions that give rise to the root stem cell niche. Asymmetric divisions of the root cortex endodermis initial, pericycle cells that give rise to the lateral root primordium, procambium, cambium and stomatal cells are also discussed. Finally, a perspective is provided regarding the role of other hormones or regulatory molecules in asymmetric divisions, the presence of segregated determinants and the usefulness of modelling approaches in understanding network dynamics within these very special cells.

CONCLUSIONS

Asymmetric cell divisions define plant development. High-throughput genomic and modelling approaches can elucidate their regulation, which in turn could enable the engineering of plant traits such as stomatal density, lateral root development and wood formation.

Inducible knock-down of GNOM during root formation reveals tissue-specific response to auxin transport and its modulation of local auxin biosynthesis

In plants, active transport of auxin plays an essential role in root development. Localization of the PIN1 auxin transporters to the basal membrane of cells directs auxin flow and depends on the trafficking mediator GNOM. GNOM-dependent auxin transport is vital for root development and thus offers a useful tool for the investigation of a possible tissue-specific response to dynamic auxin transport. To avoid pleiotropic effects, DEX-inducible expression of GNOM antisense RNA was used to disrupt GNOM expression transiently or persistently during embryonic root development. It was found that the elongation zone and the pericycle layer are the most sensitive to GNOM-dependent auxin transport variations, which is shown by the phenotypes in cell elongation and the initiation of lateral root primordia, respectively. This suggests that auxin dynamics is critical to cell differentiation and cell fate transition, but not to cell division. The results also reveal that GNOM-dependent auxin transport could affect local auxin biosynthesis. This suggests that local auxin biosynthesis may also contribute to the establishment of GNOM-dependent auxin gradients in specific tissues, and that auxin transport and local auxin biosynthesis may function together in the regulatory network for initiation and development of lateral root primordia. Thus, the data reveal a tissue-specific response to auxin transport and modulation of local auxin biosynthesis by auxin transport.

GNOM regulates root hydrotropism and phototropism independently of PIN-mediated auxin transport

Plant roots exhibit tropisms in response to gravity, unilateral light and moisture gradients. During gravitropism, an auxin gradient is established by PIN auxin transporters, leading to asymmetric growth. GNOM, a guanine nucleotide exchange factor of ARF GTPase (ARF-GEF), regulates PIN localization by regulating subcellular trafficking of PINs. Therefore, GNOM is important for gravitropism. We previously isolated mizu-kussei2 (miz2), which lacks hydrotropic responses; MIZ2 is allelic to GNOM. Since PIN proteins are not required for root hydrotropism in Arabidopsis, the role of GNOM in root hydrotropism should differ from that in gravitropism. To examine this possibility, we conducted genetic analysis of gnom(miz2) and gnom trans-heterozygotes. The mutant gnom(miz2), which lacks hydrotropic responses, was partially recovered by gnom(emb30-1), which lacks GEF activity, but not by gnom(B4049), which lacks heterotypic domain interactions. Furthermore, the phototropic response of gnom trans-heterozygotes differed from that of the pin2 mutant allele eir1-1. Moreover, defects in the polarities of PIN2 and auxin distribution in a severe gnom mutant were recovered by gnom(miz2). Therefore, an unknown GNOM-mediated vesicle trafficking system may mediate root hydrotropism and phototropism independently of PIN trafficking.

Identification of Arabidopsis BAK1-associating receptor-like kinase 1 (BARK1) and characterization of its gene expression and brassinosteroid-regulated root phenotypes

Brassinosteroids (BRs) activate the BRI1 and BAK1/SERK3 membrane receptor complex, which leads to a wide range of changes in gene expression, plant growth and development. As an initial step to elucidate additional roles of BAK1, we cloned a BAK1-binding protein, BAK1-Associating Receptor-Like Kinase 1 (BARK1), and characterized its gene expression and root phenotypes. BARK1 is a putative membrane LRR-RLK (leucine-rich repeat receptor-like kinase) protein that specifically binds to BAK1 and its homologs. Careful examination of BARK1 expression using transgenic plants expressing a green fluorescent protein (GFP) reporter under the control of the native BARK1 promoter (BARK1p::GFP) revealed that this gene is ubiquitously expressed in most plant tissues, and shows especially strong expression in the xylem vasculature of primary and lateral roots as well as in mature pollen. Interestingly, the expression of the BARK1 gene was increased in the BR biosynthetic loss-of-function mutant, det2, and a loss-of-function mutant of BR signaling, bak1-3. In contrast, this gene was down-regulated in the bzr1-1D plant, which is a BR signal gain-of-function mutant. BARK1-overexpressing transgenic plants clearly enhanced primary root growth in a dose-dependent manner, and their roots were hypersensitive to BR-induced root growth inhibition. In addition, both the number and density of lateral roots were dramatically increased in the BARK1 transgenic plants in a dose-dependent manner. Together with observations that ARF (AUXIN RESPONSE FACTOR) genes are up-regulated in the BARK1 overexpressor, we suggest that the BARK1 overexpressor phenotype with more lateral roots is partly due to the increased expression of ARF genes in this genetic background. In conclusion, BAK1-interacting BARK1 protein may be involved in BR-mediated plant growth and development such as in lateral roots via auxin regulation.

Lateral root initiation is a probabilistic event whose frequency is set by fluctuating levels of auxin response

The locations in which lateral roots arise are determined by local peaks of auxin response driven by whole-plant physiology. The architecture of a plant root system adapts it to the conditions in which it grows: large shoot systems demand large root systems, and growth in soils that have low or patchy nutrient distributions is often best managed by non-uniform patterns of root branching. It is not surprising then that the regulation of lateral root spacing is responsive to a wide array of stimuli. Molecular genetic studies have outlined a mechanism by which multiple modules of auxin response in specific cell types drive lateral root initiation. These peaks of auxin responsiveness are functionally controlled by the growth of the plant and the changing environmental conditions it experiences. Thus, the process of lateral root initiation, which depends on strong local auxin response, is globally mediated.

Phyllotaxis and rhizotaxis in Arabidopsis are modified by three PLETHORA transcription factors

BACKGROUND

The juxtaposition of newly formed primordia in the root and shoot differs greatly, but their formation in both contexts depends on local accumulation of the signaling molecule auxin. Whether the spacing of lateral roots along the main root and the arrangement of leaf primordia at the plant apex are controlled by related underlying mechanisms has remained unclear.

RESULTS

Here, we show that, in Arabidopsis thaliana, three transcriptional regulators implicated in phyllotaxis, PLETHORA3 (PLT3), PLT5, and PLT7, are expressed in incipient lateral root primordia where they are required for primordium development and lateral root emergence. Furthermore, all three PLT proteins prevent the formation of primordia close to one another, because, in their absence, successive lateral root primordia are frequently grouped in close longitudinal or radial clusters. The triple plt mutant phenotype is rescued by PLT-vYFP fusion proteins, which are expressed in the shoot meristem as well as the root, but not by expression of PLT7 in the shoot alone. Expression of all three PLT genes requires auxin response factors ARF7 and ARF19, and the reintroduction of PLT activity suffices to rescue lateral root formation in arf7,arf19.

CONCLUSIONS

Intriguingly PLT 3, PLT5, and PLT7 not only control the positioning of organs at the shoot meristem but also in the root; a striking observation that raises many evolutionary questions.