Cytokinin acts through the auxin influx carrier AUX1 to regulate cell elongation in the root

MORF9-dependent specific plastid RNA editing inhibits root growth under sugar starvation in Arabidopsis

Multiple organellar RNA editing factor (MORF) complex was shown to be highly associated with C-to-U RNA editing of vascular plant editosome. However, mechanisms by which MORF9-dependent plastid RNA editing controls plant development and responses to environmental alteration remain obscure. In this study, we found that loss of MORF9 function impaired PSII efficiency, NDH activity, and carbohydrate production, rapidly promoted nuclear gene expression including sucrose transporter and sugar/energy responsive genes, and attenuated root growth under sugar starvation conditions. Sugar repletion increased MORF9 and MORF2 expression in wild-type seedlings and reduced RNA editing of matK-706, accD-794, ndhD-383 and ndhF-290 in the morf9 mutant. RNA editing efficiency of ndhD-383 and ndhF-290 sites was diminished in the gin2/morf9 double mutants, and that of matK-706, accD-794, ndhD-383 and ndhF-290 sites were significantly diminished in the snrk1/morf9 double mutants. In contrast, overexpressing HXK1 or SnRK1 promoted RNA editing rate of matK-706, accD-794, ndhD-383 and ndhF-290 in leaves of morf9 mutants, suggesting that HXK1 partially impacts MORF9 mediated ndhD-383 and ndhF-290 editing, while SnRK1 may only affect MORF9-mediated ndhF-290 site editing. Collectively, these findings suggest that sugar and/or its intermediary metabolites impair MORF9-dependent plastid RNA editing resulting in derangements of plant root development.

Tyrosine-sulfated peptide hormone induces flavonol biosynthesis to control elongation and differentiation in Arabidopsis primary root

In Arabidopsis roots, growth initiation and cessation are organized into distinct zones. How regulatory mechanisms are integrated to coordinate these processes and maintain proper growth progression over time is not well understood. Here, we demonstrate that the peptide hormone PLANT PEPTIDE CONTAINING SULFATED TYROSINE 1 (PSY1) promotes root growth by controlling cell elongation. Higher levels of PSY1 lead to longer differentiated cells with a shootward displacement of characteristics common to mature cells. PSY1 activates genes involved in the biosynthesis of flavonols, a group of plant-specific secondary metabolites. Using genetic and chemical approaches, we show that flavonols are required for PSY1 function. Flavonol accumulation downstream of PSY1 occurs in the differentiation zone, where PSY1 also reduces auxin and reactive oxygen species (ROS) activity. These findings support a model where PSY1 signals the developmental-specific accumulation of secondary metabolites to regulate the extent of cell elongation and the overall progression to maturation.

Cold-upregulated glycosyltransferase gene 1 (OsCUGT1) plays important roles in rice height and spikelet fertility

Glycosyltransferases (GTs) regulate many physiological processes and stress responses in plants. However, little is known about the function of GT in rice development. In this study, molecular analyses revealed that the expression of a rice GT gene (Cold-Upregulated Glycosyltransferase Gene 1, CUGT1) is developmentally controlled and stress-induced. OsCUGT1 was knocked out by using the clustered regularly interspaced short palindromic repeats (CRISPR) system to obtain the mutant oscugt1, which showed a severe dwarf and sterility phenotype. Further cytological analyses indicated that the dwarfism seen in the oscugt1 mutant might be caused by fewer and smaller cells. Histological pollen analysis suggests that the spikelet sterility in oscugt1 mutants may be caused by abnormal microsporogenesis. Moreover, multiple transgenic plants with knockdown of OsCUGT1 expression through RNA interference were obtained, which also showed obvious defects in plant height and fertility. RNA sequencing revealed that multiple biological processes associated with phenylpropanoid biosynthesis, cytokinin metabolism and pollen development are affected in the oscugt1 mutant. Overall, these results suggest that rice OsCUGT1 plays an essential role in rice development.

Arabidopsis TIE1 and TIE2 transcriptional repressors dampen cytokinin response during root development

Cytokinin plays critical roles in root development. Cytokinin signaling depends on activation of key transcription factors known as type B Arabidopsis response regulators (ARRs). However, the mechanisms underlying the finely tuned regulation of type B ARR activity remain unclear. In this study, we demonstrate that the ERF-associated amphiphilic repression (EAR) motif-containing protein TCP interactor containing ear motif protein2 (TIE2) forms a negative feedback loop to finely tune the activity of type B ARRs during root development. Disruption of TIE2 and its close homolog TIE1 causes severely shortened roots. TIE2 interacts with type B ARR1 and represses transcription of ARR1 targets. The cytokinin response is correspondingly enhanced in tie1-1 tie2-1. We further show that ARR1 positively regulates TIE1 and TIE2 by directly binding to their promoters. Our findings demonstrate that TIEs play key roles in controlling plant development and reveal an important negative feedback regulation mechanism for cytokinin signaling.

Crosstalk of Cytokinin with Ethylene and Auxin for Cell Elongation Inhibition and Boron Transport in Arabidopsis Primary Root under Boron Deficiency

Several studies have shown the role of phytohormones in the regulation of root growth of Arabidopsis plants under boron (B) deficiency. Ethylene and auxin play an important role in the control of Arabidopsis primary root cell elongation under short-term B deprivation, whereas cytokinins regulate root growth inhibition under B deficiency by controlling meristem cell proliferation. In this work, we study the possible interaction among cytokinin, ethylene, and auxin in the primary root response to B-deprivation treatment, as well as their possible role in B uptake and transport. Wild type (WT) and two mutants related to auxin and ethylene (aux1 and acs11) Arabidopsis plants were grown in control (10 µM B) or B starvation (0 µM B) treatment, in the absence or presence of trans-zeatin, and their primary root growth was analyzed. The possible interaction between these hormones was also studied by analyzing AUX1 gene expression in the acs11 mutant and ACS11 gene expression in the aux1 mutant. The GUS reporter lines ARR5::GUS, IAA2::GUS, and EBS::GUS were used to observe changes in cytokinin, auxin, and ethylene levels in the root, respectively. The results of this work suggest that cytokinin inhibits root cell elongation under B deficiency through two different mechanisms: (i) an ethylene-dependent mechanism through increased expression of the ACS11 gene, which would lead to increased ethylene in the root, and (ii) an ethylene-independent mechanism through decreased expression of the AUX1 gene, which alters auxin signaling in the meristematic and elongation zones and stele. We also report that changes in the expression of several B transporters occur in response to auxin, ethylene, and cytokinin that may affect the plant B content.

Auxin-Cytokinin Cross Talk in Somatic Embryogenesis of Coffea canephora

Cytokinins (CK) are plant growth regulators involved in multiple physiological processes in plants. One less studied aspect is CK homeostasis (HM). The primary genes related to HM are involved in biosynthesis (IPT), degradation (CKX), and signaling (ARR). This paper demonstrates the effect of auxin (Aux) and CK and their cross talk in a Coffea canephora embryogenic system. The transcriptome and RT-qPCR suggest that Aux in pre-treatment represses biosynthesis, degradation, and signal CK genes. However, in the induction, there is an increase of genes implicated in the CK perception/signal, indicating perhaps, as in other species, Aux is repressing CK, and CK are inducing per se genes involved in its HM. This is reflected in the endogenous concentration of CK; pharmacology experiments helped study the effect of each plant growth regulator in our SE system. We conclude that the Aux–CK balance is crucial to directing somatic embryogenesis in C. canephora.

Spatio-temporal transcriptome profiling and subgenome analysis in Brassica napus

Brassica napus is an important oil crop and an allotetraploid species. However, the detailed analysis of gene function and homoeologous gene expression in all tissues at different developmental stages was not explored. In this study, we performed a global transcriptome analysis of 24 vegetative and reproductive tissues at six developmental stages (totally 111 tissues). These samples were clustered into eight groups. The gene functions of silique pericarp were similar to roots, stems and leaves. In particular, glucosinolate metabolic process was associated with root and silique pericarp. Genes involved in protein phosphorylation were often associated with stamen, anther and the early developmental stage of seeds. Transcription factor (TF) genes were more specific than structural genes. A total of 17 100 genes that were preferentially expressed in one tissue (tissue-preferred genes, TPGs), including 889 TFs (5.2%), were identified in the 24 tissues. Some TPGs were identified as hub genes in the co-expression network analysis, and some TPGs in different tissues were involved in different hormone pathways. About 67.0% of the homoeologs showed balanced expression, whereas biased expression of homoeologs was associated with structural divergence. In addition, the spatiotemporal expression of homoeologs was related to the presence of transposable elements (TEs) and regulatory elements (REs); more TEs and fewer REs in the promoters resulted in divergent expression in different tissues. This study provides a valuable transcriptional map for understanding the growth and development of B. napus, for identifying important genes for future crop improvement, and for exploring gene expression patterns in the B. napus.

Developmental Characteristics and Auxin Response of Epiphytic Root in Dendrobium catenatum

Dendrobium catenatum, a traditional precious Chinese herbal medicine, belongs to epiphytic orchids. Its special life mode leads to the specialization of roots, but there is a lack of systematic research. The aerial root in D. catenatum displays diverse unique biological characteristics, and it initially originates from the opposite pole of the shoot meristem within the protocorm. The root development of D. catenatum is not only regulated by internal cues but also adjusts accordingly with the change in growth environments. D. catenatum root is highly tolerant to auxin, which may be closely related to its epiphytic life. Exogenous auxin treatment has dual effects on D. catenatum roots: relatively low concentration promotes root elongation, which is related to the induced expression of cell wall synthesis genes; excessive concentration inhibits the differentiation of velamen and exodermis and promotes the overproliferation of cortical cells, which is related to the significant upregulation of WOX11-WOX5 regeneration pathway genes and cell division regulatory genes. Overexpression of D. catenatum WOX12 (DcWOX12) in Arabidopsis inhibits cell and organ differentiation, but induces cell dedifferentiation and callus production. Therefore, DcWOX12 not only retains the characteristics of ancestors as stem cell regulators, but also obtains stronger cell fate transformation ability than homologous genes of other species. These findings suggest that the aerial root of D. catenatum evolves special structure and developmental characteristics to adapt to epiphytic life, providing insight into ideal root structure breeding of simulated natural cultivation in D. catenatum and a novel target gene for improving the efficiency of monocot plant transformation.

Mining key genes related to root morphogenesis through genome-wide identification and expression analysis of RR gene family in citrus

Morphogenesis of root is a vital factor to determine the root system architecture. Cytokinin response regulators (RRs) are the key transcription factors in cytokinin signaling, which play important roles in regulating the root morphogenesis. In this study, 29 RR proteins, including 21 RRs and 8 pseudo RRs, were identified from the genome of citrus, and termed as CcRR1-21 and CcPRR1-8, respectively. Phylogenetic analysis revealed that the 29 CcRRs could be classified into four types according to their representative domains. Analysis of cis-elements of CcRRs indicated that they were possibly involved in the regulation of growth and abiotic stress resistance in citrus. Within the type A and type B CcRRs, CcRR4, CcRR5, CcRR6 and CcRR16 highly expressed in roots and leaves, and dramatically responded to the treatments of hormones and abiotic stresses. CcRR2, CcRR10, CcRR14 and CcRR19 also highly expressed in roots under different treatments. Characteristic analysis revealed that the above 8 CcRRs significantly and differentially expressed in the three zones of root, suggesting their functional differences in regulating root growth and development. Further investigation of the 3 highly and differentially expressed CcRRs, CcRR5, CcRR10 and CcRR14, in 9 citrus rootstocks showed that the expression of CcRR5, CcRR10 and CcRR14 was significantly correlated to the length of primary root, the number of lateral roots, and both primary root and the number of lateral roots, respectively. Results of this study indicated that CcRRs were involved in regulating the growth and development of the root in citrus with different functions among the members.

Formation and Development of Taproots in Deciduous Tree Species

Trees are generally long-lived and are therefore exposed to numerous episodes of external stimuli and adverse environmental conditions. In certain trees e.g., oaks, taproots evolved to increase the tree's ability to acquire water from deeper soil layers. Despite the significant role of taproots, little is known about the growth regulation through internal factors (genes, phytohormones, and micro-RNAs), regulating taproot formation and growth, or the effect of external factors, e.g., drought. The interaction of internal and external stimuli, involving complex signaling pathways, regulates taproot growth during tip formation and the regulation of cell division in the root apical meristem (RAM). Assuming that the RAM is the primary regulatory center responsible for taproot growth, factors affecting the RAM function provide fundamental information on the mechanisms affecting taproot development.

Auxin and Target of Rapamycin Spatiotemporally Regulate Root Organogenesis

The programs associated with embryonic roots (ERs), primary roots (PRs), lateral roots (LRs), and adventitious roots (ARs) play crucial roles in the growth and development of roots in plants. The root functions are involved in diverse processes such as water and nutrient absorption and their utilization, the storage of photosynthetic products, and stress tolerance. Hormones and signaling pathways play regulatory roles during root development. Among these, auxin is the most important hormone regulating root development. The target of rapamycin (TOR) signaling pathway has also been shown to play a key role in root developmental programs. In this article, the milestones and influential progress of studying crosstalk between auxin and TOR during the development of ERs, PRs, LRs and ARs, as well as their functional implications in root morphogenesis, development, and architecture, are systematically summarized and discussed.

Isopentenyltransferases as master regulators of crop performance: their function, manipulation, and genetic potential for stress adaptation and yield improvement

Isopentenyltransferase (IPT) in plants regulates a rate-limiting step of cytokinin (CTK) biosynthesis. IPTs are recognized as key regulators of CTK homeostasis and phytohormone crosstalk in both biotic and abiotic stress responses. Recent research has revealed the regulatory function of IPTs in gene expression and metabolite profiles including source-sink modifications, energy metabolism, nutrient allocation and storage, stress defence and signalling pathways, protein synthesis and transport, and membrane transport. This suggests that IPTs play a crucial role in plant growth and adaptation. In planta studies of IPT-driven modifications indicate that, at a physiological level, IPTs improve stay-green characteristics, delay senescence, reduce stress-induced oxidative damage and protect photosynthetic machinery. Subsequently, these improvements often manifest as enhanced or stabilized crop yields and this is especially apparent under environmental stress. These mechanisms merit consideration of the IPTs as 'master regulators' of core cellular metabolic pathways, thus adjusting plant homeostasis/adaptive responses to altered environmental stresses, to maximize yield potential. If their expression can be adequately controlled, both spatially and temporally, IPTs can be a key driver for seed yield. In this review, we give a comprehensive overview of recent findings on how IPTs influence plant stress physiology and yield, and we highlight areas for future research.

Phytohormones: plant switchers in developmental and growth stages in potato

BACKGROUND

Potato is one of the most important food crops worldwide, contributing key nutrients to the human diet. Plant hormones act as vital switchers in the regulation of various aspects of developmental and growth stages in potato. Due to the broad impacts of hormones on many developmental processes, their role in potato growth and developmental stages has been investigated. This review presents a description of hormonal basic pathways, various interconnections between hormonal network and reciprocal relationships, and clarification of molecular events underlying potato growth. In the last decade, new findings have emerged regarding their function during sprout development, vegetative growth, tuber initiation, tuber development, and maturation in potato. Hormones can control the regulation of various aspects of growth and development in potato, either individually or in combination with other hormones. The molecular characterization of interplay between cytokinins (CKs), abscisic acid (ABA), and auxin and/or gibberellins (GAs) during tuber formation requires further undertaking. Recently, new evidences regarding the relative functions of hormones during various stages and an intricate network of several hormones controlling potato tuber formation are emerging. Although some aspects of their functions are widely covered, remarkable breaks in our knowledge and insights yet exist in the regulation of hormonal networks and their interactions during different stages of growth and various aspects of tuber formation.

SHORT CONCLUSION

The present review focuses on the relative roles of hormones during various developmental stages with a view to recognize their mechanisms of function in potato tuber development. For better insight, relevant evidences available on hormonal interaction during tuber development in other species are also described. We predict that the present review highlights some of the conceptual developments in the interplay of hormones and their associated downstream events influencing tuber formation.

Understanding the Intricate Web of Phytohormone Signalling in Modulating Root System Architecture

Root system architecture (RSA) is an important developmental and agronomic trait that is regulated by various physical factors such as nutrients, water, microbes, gravity, and soil compaction as well as hormone-mediated pathways. Phytohormones act as internal mediators between soil and RSA to influence various events of root development, starting from organogenesis to the formation of higher order lateral roots (LRs) through diverse mechanisms. Apart from interaction with the external cues, root development also relies on the complex web of interaction among phytohormones to exhibit synergistic or antagonistic effects to improve crop performance. However, there are considerable gaps in understanding the interaction of these hormonal networks during various aspects of root development. In this review, we elucidate the role of different hormones to modulate a common phenotypic output, such as RSA in Arabidopsis and crop plants, and discuss future perspectives to channel vast information on root development to modulate RSA components.

Cytokinin-Controlled Gradient Distribution of Auxin in Arabidopsis Root Tip

The plant root is a dynamic system, which is able to respond promptly to external environmental stimuli by constantly adjusting its growth and development. A key component regulating this growth and development is the finely tuned cross-talk between the auxin and cytokinin phytohormones. The gradient distribution of auxin is not only important for the growth and development of roots, but also for root growth in various response. Recent studies have shed light on the molecular mechanisms of cytokinin-mediated regulation of local auxin biosynthesis/metabolism and redistribution in establishing active auxin gradients, resulting in cell division and differentiation in primary root tips. In this review, we focus our attention on the molecular mechanisms underlying the cytokinin-controlled auxin gradient in root tips.

SEEDSTICK Controls Arabidopsis Fruit Size by Regulating Cytokinin Levels and FRUITFULL

Upon fertilization, the ovary increases in size and undergoes a complex developmental process to become a fruit. We show that cytokinins (CKs), which are required to determine ovary size before fertilization, have to be degraded to facilitate fruit growth. The expression of CKX7, which encodes a cytosolic CK-degrading enzyme, is directly positively regulated post-fertilization by the MADS-box transcription factor STK. Similar to stk, two ckx7 mutants possess shorter fruits than wild type. Quantification of CKs reveals that stk and ckx7 mutants have high CK levels, which negatively control cell expansion during fruit development, compromising fruit growth. Overexpression of CKX7 partially complements the stk fruit phenotype, confirming a role for CK degradation in fruit development. Finally, we show that STK is required for the expression of FUL, which is essential for valve elongation. Overall, we provide insights into the link between CKs and molecular pathways that control fruit growth.

Auxin and Root Gravitropism: Addressing Basic Cellular Processes by Exploiting a Defined Growth Response

Root architecture and growth are decisive for crop performance and yield, and thus a highly topical research field in plant sciences. The root system of the model plant Arabidopsis thaliana is the ideal system to obtain insights into fundamental key parameters and molecular players involved in underlying regulatory circuits of root growth, particularly in responses to environmental stimuli. Root gravitropism, directional growth along the gravity, in particular represents a highly sensitive readout, suitable to study adjustments in polar auxin transport and to identify molecular determinants involved. This review strives to summarize and give an overview into the function of PIN-FORMED auxin transport proteins, emphasizing on their sorting and polarity control. As there already is an abundance of information, the focus lies in integrating this wealth of information on mechanisms and pathways. This overview of a highly dynamic and complex field highlights recent developments in understanding the role of auxin in higher plants. Specifically, it exemplifies, how analysis of a single, defined growth response contributes to our understanding of basic cellular processes in general.

Highlighting reactive oxygen species as multitaskers in root development

Reactive oxygen species (ROS) are naturally produced by several redox reactions during plant regular metabolism such as photosynthesis and respiration. Due to their chemical properties and high reactivity, ROS were initially described as detrimental for cells during oxidative stress. However, they have been further recognized as key players in numerous developmental and physiological processes throughout the plant life cycle. Recent studies report the important role of ROS as growth regulators during plant root developmental processes such as in meristem maintenance, in root elongation, and in lateral root, root hair, endodermis, and vascular tissue differentiation. All involve multifaceted interplays between steady-state levels of ROS with transcriptional regulators, phytohormones, and nutrients. In this review, we attempt to summarize recent findings about how ROS are involved in multiple stages of plant root development during cell proliferation, elongation, and differentiation.

Integrative Roles of Phytohormones on Cell Proliferation, Elongation and Differentiation in the Arabidopsis thaliana Primary Root

The growth of multicellular organisms relies on cell proliferation, elongation and differentiation that are tightly regulated throughout development by internal and external stimuli. The plasticity of a growth response largely depends on the capacity of the organism to adjust the ratio between cell proliferation and cell differentiation. The primary root of Arabidopsis thaliana offers many advantages toward understanding growth homeostasis as root cells are continuously produced and move from cell proliferation to elongation and differentiation that are processes spatially separated and could be studied along the longitudinal axis. Hormones fine tune plant growth responses and a huge amount of information has been recently generated on the role of these compounds in Arabidopsis primary root development. In this review, we summarized the participation of nine hormones in the regulation of the different zones and domains of the Arabidopsis primary root. In some cases, we found synergism between hormones that function either positively or negatively in proliferation, elongation or differentiation. Intriguingly, there are other cases where the interaction between hormones exhibits unexpected results. Future analysis on the molecular mechanisms underlying crosstalk hormone action in specific zones and domains will unravel their coordination over PR development.

PI4Kγ2 Interacts with E3 Ligase MIEL1 to Regulate Auxin Metabolism and Root Development

Root development is important for normal plant growth and nutrient absorption. Studies have revealed the involvement of various factors in this complex process, improving our understanding of the relevant regulatory mechanisms. Here, we functionally characterize the role of Arabidopsis (Arabidopsis thaliana) phosphatidylinositol 4-kinase γ2 (PI4Kγ2) in root elongation regulation, which functions to modulate stability of the RING-type E3 ligase MYB30-INTERACTING E3 LIGASE1 (MIEL1) and auxin metabolism. Mutant plants deficient in PI4Kγ2 (pi4kγ2) exhibited a shortened root length and elongation zone due to reduced auxin level. PI4Kγ2 was shown to interact with MIEL1, regulating its degradation and furthering the stability of transcription factor MYB30 (which suppresses auxin metabolism by directly binding to promoter regions of GH3 2 and GH3 6). Interestingly, pi4kγ2 plants presented altered hypersensitive response, indicating that PI4Kγ2 regulates synergetic growth and defense of plants through modulating auxin metabolism. These results reveal the importance of protein interaction in regulating ubiquitin-mediated protein degradation in eukaryotic cells, and illustrate a mechanism coordinating plant growth and biotic stress response.

Vascular transcription factors guide plant epidermal responses to limiting phosphate conditions

Optimal plant growth is hampered by deficiency of the essential macronutrient phosphate in most soils. Plant roots can, however, increase their root hair density to efficiently forage the soil for this immobile nutrient. By generating and exploiting a high-resolution single-cell gene expression atlas of Arabidopsis roots, we show an enrichment of TARGET OF MONOPTEROS 5/LONESOME HIGHWAY (TMO5/LHW) target gene responses in root hair cells. The TMO5/LHW heterodimer triggers biosynthesis of mobile cytokinin in vascular cells and increases root hair density during low-phosphate conditions by modifying both the length and cell fate of epidermal cells. Moreover, root hair responses in phosphate-deprived conditions are TMO5- and cytokinin-dependent. Cytokinin signaling links root hair responses in the epidermis to perception of phosphate depletion in vascular cells.

Overexpression of MsGH3.5 inhibits shoot and root development through the auxin and cytokinin pathways in apple plants

Phytohormonal interactions are crucial for plant development. Auxin and cytokinin (CK) both play critical roles in regulating plant growth and development; however, the interaction between these two phytohormones is complex and not fully understood. Here, we isolated a wild apple (Malus sieversii Roem) GRETCHEN HAGEN3 (GH3) gene, MsGH3.5, encoding an indole-3-acetic acid (IAA)-amido synthetase. Overexpression of MsGH3.5 significantly reduced the free IAA content and increased the content of some IAA-amino acid conjugates, and MsGH3.5-overexpressing lines were dwarfed and produced fewer adventitious roots (ARs) than the control. This phenotype is consistent with the role of GH3 in conjugating excess free active IAA to amino acids in auxin homeostasis. Surprisingly, overexpression of MsGH3.5 significantly increased CK concentrations in the whole plant, and altered the expression of genes involved in CK biosynthesis, metabolism and signaling. Furthermore, exogenous CK application induced MsGH3.5 expression through the activity of the CK type-B response regulator, MsRR1a, which mediates the CK primary response. MsRR1a activated MsGH3.5 expression by directly binding to its promoter, linking auxin and CK signaling. Plants overexpressing MsRR1a also displayed fewer ARs, in agreement with the regulation of MsGH3.5 expression by MsRR1a. Taken together, we reveal that MsGH3.5 affects apple growth and development by modulating auxin and CK levels and signaling pathways. These findings provide insight into the interaction between the auxin and CK pathways, and might have substantial implications for efforts to improve apple architecture.

All Roads Lead to Auxin: Post-translational Regulation of Auxin Transport by Multiple Hormonal Pathways

Auxin is a key hormonal regulator, that governs plant growth and development in concert with other hormonal pathways. The unique feature of auxin is its polar, cell-to-cell transport that leads to the formation of local auxin maxima and gradients, which coordinate initiation and patterning of plant organs. The molecular machinery mediating polar auxin transport is one of the important points of interaction with other hormones. Multiple hormonal pathways converge at the regulation of auxin transport and form a regulatory network that integrates various developmental and environmental inputs to steer plant development. In this review, we discuss recent advances in understanding the mechanisms that underlie regulation of polar auxin transport by multiple hormonal pathways. Specifically, we focus on the post-translational mechanisms that contribute to fine-tuning of the abundance and polarity of auxin transporters at the plasma membrane and thereby enable rapid modification of the auxin flow to coordinate plant growth and development.

Same same, but different: growth responses of primary and lateral roots

The root system architecture describes the shape and spatial arrangement of roots within the soil. Its spatial distribution depends on growth and branching rates as well as directional organ growth. The embryonic primary root gives rise to lateral (secondary) roots, and the ratio of both root types changes over the life span of a plant. Most studies have focused on the growth of primary roots and the development of lateral root primordia. Comparably less is known about the growth regulation of secondary root organs. Here, we review similarities and differences between primary and lateral root organ growth, and emphasize particularly how external stimuli and internal signals differentially integrate root system growth.

Role and Regulation of Cytokinins in Plant Response to Drought Stress

Cytokinins (CKs) are key phytohormones that not only regulate plant growth and development but also mediate plant tolerance to drought stress. Recent advances in genome-wide association studies coupled with in planta characterization have opened new avenues to investigate the drought-responsive expression of CK metabolic and signaling genes, as well as their functions in plant adaptation to drought. Under water deficit, CK signaling has evolved as an inter-cellular communication network which is essential to crosstalk with other types of phytohormones and their regulating pathways in mediating plant stress response. In this review, we revise the current understanding of CK involvement in drought stress tolerance. Particularly, a genetic framework for CK signaling and CK crosstalk with abscisic acid (ABA) in the precise monitoring of drought responses is proposed. In addition, the potential of endogenous CK alteration in crops towards developing drought-tolerant crops is also discussed.

Role of the Cytokinin-Activated Type-B Response Regulators in Hormone Crosstalk

Cytokinin is an important phytohormone that employs a multistep phosphorelay to transduce the signal from receptors to the nucleus, culminating in activation of type-B response regulators which function as transcription factors. Recent chromatin immunoprecipitation-sequencing (ChIP-seq) studies have identified targets of type-B ARABIDOPSIS RESPONSE REGULATORs (ARRs) and integrated these into the cytokinin-activated transcriptional network. Primary targets of the type-B ARRs are enriched for genes involved in hormonal regulation, emphasizing the extensive crosstalk that can occur between cytokinin, auxin, abscisic acid, brassinosteroids, gibberellic acid, ethylene, jasmonic acid, and salicylic acid. Examination of hormone-related targets reveals multiple regulatory points including biosynthesis, degradation/inactivation, transport, and signal transduction. Here, we consider this early response to cytokinin in terms of the hormones involved, points of regulatory crosstalk, and physiological significance.

ETR1 Integrates Response to Ethylene and Cytokinins into a Single Multistep Phosphorelay Pathway to Control Root Growth

Cytokinins and ethylene control plant development via sensors from the histidine kinase (HK) family. However, downstream signaling pathways for the key phytohormones are distinct. Here we report that not only cytokinin but also ethylene is able to control root apical meristem (RAM) size through activation of the multistep phosphorelay (MSP) pathway. We found that both cytokinin and ethylene-dependent RAM shortening requires ethylene binding to ETR1 and the HK activity of ETR1. The receiver domain of ETR1 interacts with MSP signaling intermediates acting downstream of cytokinin receptors, further substantiating the role of ETR1 in MSP signaling. We revealed that both cytokinin and ethylene induce the MSP in similar and distinct cell types with ETR1-mediated ethylene signaling controlling MSP output specifically in the root transition zone. We identified members of the MSP pathway specific and common to both hormones and showed that ETR1-regulated ARR3 controls RAM size. ETR1-mediated MSP spatially differs from canonical CTR1/EIN2/EIN3 ethylene signaling and is independent of EIN2, indicating that both pathways can be spatially and functionally separated. Furthermore, we demonstrated that canonical ethylene signaling controls MSP responsiveness to cytokinin specifically in the root transition zone, presumably via regulation of ARR10, one of the positive regulators of MSP signaling in Arabidopsis.

The Systems Biology of Lateral Root Formation: Connecting the Dots

The root system is a major determinant of a plant's access to water and nutrients. The architecture of the root system to a large extent depends on the repeated formation of new lateral roots. In this review, we discuss lateral root development from a systems biology perspective. We focus on studies combining experiments with computational modeling that have advanced our understanding of how the auxin-centered regulatory modules involved in different stages of lateral root development exert their specific functions. Moreover, we discuss how these regulatory networks may enable robust transitions from one developmental stage to the next, a subject that thus far has received limited attention. In addition, we analyze how environmental factors impinge on these modules, and the different manners in which these environmental signals are being integrated to enable coordinated developmental decision making. Finally, we provide some suggestions for extending current models of lateral root development to incorporate multiple processes and stages. Only through more comprehensive models we can fully elucidate the cooperative effects of multiple processes on later root formation, and how one stage drives the transition to the next.

Potassium Stimulation of IAA Transport Mediated by the Arabidopsis Importer AUX1 Investigated in a Heterologous Yeast System

Auxin regulates diverse processes involved in plant growth and development. AUX1 is the first identified and most widely investigated auxin importer, and plays an important role in root gravitropism and the development of lateral root and root hair. However, the regulation of auxin transport by AUX1 is still not well understood. In this study, we examined the effect of metal ions on AUX1 transport function and found that the activity could be specifically stimulated four times by K⁺. Further experiments revealed the preference of KF on the enhancement of transport activity of AUX1 over KCl, KBr, and KI. In addition, the interaction between K⁺ and AUX1 confers AUX1 more resistant to thermal stress but more vulnerable to proteolysis. Conventional chemical modification indicated that the extracellular acidic amino acids of AUX1 play a key role in the K⁺ stimulation. Site-specific mutagenesis showed that the replacement of Asp¹⁶⁶, Asp²⁹³, and Asp³¹² of AUX1 to alanine deteriorated the K⁺-stimulated auxin transport. By contrast, when these residues were mutated to glutamate, lysine, or asparagine, only the D312E variant restored the IAA transport activity to the wild-type level. It is thus convinced that D312 is presumably the most promising residue for the K⁺ stimulation on AUX1.

ARR22 overexpression can suppress plant Two-Component Regulatory Systems

In plants, several developmental processes are co-coordinated by cytokinins via phosphorylation dependent processes of the Two-Component System (TCS). An outstanding challenge is to track phosphorelay flow from cytokinin perception to its molecular outputs, of which gene activation plays a major role. To address this issue, a kinetic-based reporter system was expounded to track TCS phosphorelay activity in vivo that can distinguish between basal and cytokinin dependent effects of overexpressed TCS members. The TCS phosphorelay can be positively activated by cytokinin and inhibited by pharmaceuticals or naturally interfering components. In this case we took advantage of the phosphohistidine-phosphatase Arabidopsis Response Regulator (ARR) 22 and investigated its phosphocompetition with other TCS members in regulating promoters of ARR5 and WUS in Arabidopsis thaliana cell culture protoplasts. In congruency with the proposed function of ARR22, overexpression of ARR22 blocked the activation of all B-type ARRs in this study in a TCS dependent manner. Furthermore, this effect could not be mimicked by A-type response regulator overexpression or compensated by AHP overexpression. Compared to other reporter assays, ours mimicked effects previously observed only in transgenic plants for all of the TCS proteins studied, suggesting that it is possible to expose phosphocompetition. Thus, our approach can be used to investigate gene signaling networks involving the TCS by leveraging ARR22 as a TCS inhibitor along with B-type ARR overexpression.

Developmental Roles of AUX1/LAX Auxin Influx Carriers in Plants

Plant hormone auxin regulates several aspects of plant growth and development. Auxin is predominantly synthesized in the shoot apex and developing leaf primordia and from there it is transported to the target tissues e.g. roots. Auxin transport is polar in nature and is carrier-mediated. AUXIN1/LIKE-AUX1 (AUX1/LAX) family members are the major auxin influx carriers whereas PIN-FORMED (PIN) family and some members of the P-GLYCOPROTEIN/ATP-BINDING CASSETTE B4 (PGP/ABCB) family are major auxin efflux carriers. AUX1/LAX auxin influx carriers are multi-membrane spanning transmembrane proteins sharing similarity to amino acid permeases. Mutations in AUX1/LAX genes result in auxin related developmental defects and have been implicated in regulating key plant processes including root and lateral root development, root gravitropism, root hair development, vascular patterning, seed germination, apical hook formation, leaf morphogenesis, phyllotactic patterning, female gametophyte development and embryo development. Recently AUX1 has also been implicated in regulating plant responses to abiotic stresses. This review summarizes our current understanding of the developmental roles of AUX1/LAX gene family and will also briefly discuss the modelling approaches that are providing new insight into the role of auxin transport in plant development.

Ectopic expression of a pea apyrase enhances root system architecture and drought survival in Arabidopsis and soybean

Ectoapyrases (ecto-NTPDases) function to decrease levels of extracellular ATP and ADP in animals and plants. Prior studies showed that ectopic expression of a pea ectoapyrase, psNTP9, enhanced growth in Arabidopsis seedlings and that the overexpression of the two Arabidopsis apyrases most closely related to psNTP9 enhanced auxin transport and growth in Arabidopsis. These results predicted that ectopic expression of psNTP9 could promote a more extensive root system architecture (RSA) in Arabidopsis. We confirmed that transgenic Arabidopsis seedlings had longer primary roots, more lateral roots, and more and longer root hairs than wild-type plants. Because RSA influences water uptake, we tested whether the transgenic plants could tolerate osmotic stress and water deprivation better than wild-type plants, and we confirmed these properties. Transcriptomic analyses revealed gene expression changes in the transgenic plants that helped account for their enhanced RSA and improved drought tolerance. The effects of psNTP9 were not restricted to Arabidopsis, because its expression in soybeans improved the RSA, growth, and seed yield of this crop and supported higher survival in response to drought. Our results indicate that in both Arabidopsis and soybeans, the constitutive expression of psNTP9 results in a more extensive RSA and improved survival in drought stress conditions.

Cytokinin modulates context-dependent chromatin accessibility through the type-B response regulators

The phytohormone cytokinin regulates diverse aspects of plant growth and development, probably through context-dependent transcriptional regulation that relies on a dynamic interplay between regulatory proteins and chromatin. We employed the assay for transposase accessible chromatin with sequencing to profile changes in the chromatin landscape of Arabidopsis roots and shoots in response to cytokinin. Our results reveal differentially accessible chromatin regions indicative of dynamic regulation in response to cytokinin. These changes in chromatin occur preferentially upstream of cytokinin-regulated genes. The changes also largely overlap with binding sites for the type-B ARABIDOPSIS RESPONSE REGULATORS (ARRs), transcription factors that mediate the primary response to cytokinin. Furthermore, the type-B ARRs were found to be necessary for the changes in chromatin state in response to cytokinin. Last, we identified context-dependent responses by comparing root and shoot profiles. This study provides new insight into the dynamics between cytokinin and chromatin with regard to directing transcriptional programmes and how cytokinin mediates its pleiotropic effects.

Modulation of auxin and cytokinin responses by early steps of the phenylpropanoid pathway

BACKGROUND

The phenylpropanoid pathway is responsible for the synthesis of numerous compounds important for plant growth and responses to the environment. In the first committed step of phenylpropanoid biosynthesis, the enzyme phenylalanine ammonia-lyase (PAL) deaminates L-phenylalanine into trans-cinnamic acid that is then converted into p-coumaric acid by cinnamate-4-hydroxylase (C4H). Recent studies showed that the Kelch repeat F-box (KFB) protein family of ubiquitin ligases control phenylpropanoid biosynthesis by promoting the proteolysis of PAL. However, this ubiquitin ligase family, alternatively named Kiss Me Deadly (KMD), was also implicated in cytokinin signaling as it was shown to promote the degradation of type-B ARRs, including the key response activator ARR1. Considering that ubiquitin ligases typically have narrow target specificity, this dual targeting of structurally and functionally unrelated proteins appeared unusual.

RESULTS

Here we show that the KFBs indeed target PAL but not ARR1. Moreover, we show that changes in early phenylpropanoid biosynthesis alter cytokinin sensitivity - as reported earlier - but that the previously documented cytokinin growth response changes are primarily the result of altered auxin signaling. We found that reduced PAL accumulation decreased, whereas the loss of C4H function increased the strength of the auxin response. The combined loss of function of both enzymes led to a decrease in auxin sensitivity, indicating that metabolic events upstream of C4H control auxin sensitivity. This auxin/phenylpropanoid interaction impacts both shoot and root development and revealed an auxin-dependent stimulatory effect of trans-cinnamic acid feeding on leaf expansion and thus biomass accumulation.

CONCLUSIONS

Collectively, our results show that auxin-regulated plant growth is fine-tuned by early steps in phenylpropanoid biosynthesis and suggest that metabolites accumulating upstream of the C4H step impact the auxin response mechanism.

Quantitative 3D imaging of cell level auxin and cytokinin response ratios in soybean roots and nodules

Legume-Rhizobium symbiosis results in root nodules where rhizobia fix atmospheric nitrogen into plant usable forms in exchange for plant-derived carbohydrates. The development of these specialized root organs involves a set of carefully orchestrated plant hormone signalling. In particular, a spatio-temporal balance between auxin and cytokinin appears to be crucial for proper nodule development. We put together a construct that carried nuclear localized fluorescence sensors for auxin and cytokinin and used two photon induced fluorescence microscopy for concurrent quantitative 3-dimensional imaging to determine cellular level auxin and cytokinin outputs and ratios in root and nodule tissues of soybean. The use of nuclear localization signals on the markers and nuclei segmentation during image processing enabled accurate monitoring of outputs in 3D image volumes. The ratiometric method used here largely compensates for variations in individual outputs due to sample turbidity and scattering, an inherent issue when imaging thick root and nodule samples typical of many legumes. Overlays of determined auxin/cytokinin ratios on specific root zones and cell types accurately reflected those predicted based on previously reported outputs for each hormone individually. Importantly, distinct auxin/cytokinin ratios corresponded to distinct nodule cell types indicating a key role for these hormones in nodule cell type identity.

Boron deficiency inhibits root growth by controlling meristem activity under cytokinin regulation

Significant advances have been made in the last years trying to identify regulatory pathways that control plant responses to boron (B) deficiency. Still, there is a lack of a deep understanding of how they act regulating growth and development under B limiting conditions. Here, we analyzed the impact of B deficit on cell division leading to root apical meristem (RAM) disorganization. Our results reveal that inhibition of cell proliferation under the regulatory control of cytokinins (CKs) is an early event contributing to root growth arrest under B deficiency. An early recovery of QC46:GUS expression after transferring B-deficient seedlings to control conditions revealed a role of B in the maintenance of QC identity whose loss under deficiency occurred at later stages of the stress. Additionally, the D-type cyclin CYCD3 overexpressor and triple mutant cycd3;1-3 were used to evaluate the effect on mitosis inhibition at the G1-S boundary. Overall, this study supports the hypothesis that meristem activity is inhibited by B deficiency at early stages of the stress as it does cell elongation. Likewise, distinct regulatory mechanisms seem to take place depending on the severity of the stress. The results presented here are key to better understand early signaling responses under B deficiency.

Morphological, transcriptomics and biochemical characterization of new dwarf mutant of Brassica napus

Plant height is a key trait of plant architecture, and is responsible for both yield and lodging resistance in Brassica napus. A dwarf mutant line (bnaC.dwf) was obtained by chemical mutagenesis of an inbred line T6. However, the molecular mechanisms and changed biological processes of the dwarf mutant remain to be determined. In this study, a comparative transcriptome analysis between bnaC.dwf and T6 plants was performed to identify genome-wide differentially expressed genes (DEGs) and possible biological processes that may explain the phenotype variations in bnaC.dwf. As a result of this analysis, 60,134,746-60,301,384 clean reads were aligned to 60,074 genes in the B. napus genome, and accounted for 60.03% of the annotated genes. In total, 819 differentially expressed genes were used for GO (Gene Ontology) term and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway enrichment analyses with a FDR (false discovery rate) criterion of <0.001, |log₂Ratio| ≥ 1. We focused on plant hormone signal transduction pathways, plant-pathogen interaction pathway, protein phosphorylation and degradation pathways and sugar metabolism pathways. Taken together, the decrease in local auxin (IAA) levels, the variation in BnTCH4, BnKAN1, BnERF109, COI1-JAZ9-MYC2, auxin response genes (BnGH3.11, BnSAUR78, and AUX/IAA19), and ABA (abscisic acid) signaling genes (BnADP5, BnSnRK2.1, BnABF3.1) partially accounted for variations of cell proliferation in internodes, shoot and root apical meristem maintenance, abiotic and biotic stress resistance, and pre-harvest sprouting. As a comprehensive consequence of the cross-talk between plant hormones, sugar metabolism, plant-pathogen interactions and protein metabolism, bnaC.dwf presents distinct phenotypes from T6. These results will be helpful for shedding light on molecular mechanisms in the dwarf mutant, and give insight into further molecular breeding of semi-dwarf B. napus.

A Sizer model for cell differentiation in Arabidopsis thaliana root growth

Plant roots grow due to cell division in the meristem and subsequent cell elongation and differentiation, a tightly coordinated process that ensures growth and adaptation to the changing environment. How the newly formed cells decide to stop elongating becoming fully differentiated is not yet understood. To address this question, we established a novel approach that combines the quantitative phenotypic variability of wild‐type Arabidopsis roots with computational data from mathematical models. Our analyses reveal that primary root growth is consistent with a Sizer mechanism, in which cells sense their length and stop elongating when reaching a threshold value. The local expression of brassinosteroid receptors only in the meristem is sufficient to set this value. Analysis of roots insensitive to BR signaling and of roots with gibberellin biosynthesis inhibited suggests distinct roles of these hormones on cell expansion termination. Overall, our study underscores the value of using computational modeling together with quantitative data to understand root growth.

Cytokinin induces genome-wide binding of the type-B response regulator ARR10 to regulate growth and development in Arabidopsis

The plant hormone cytokinin affects a diverse array of growth and development processes and responses to the environment. How a signaling molecule mediates such a diverse array of outputs and how these response pathways are integrated with other inputs remain fundamental questions in plant biology. To this end, we characterized the transcriptional network initiated by the type-B ARABIDOPSIS RESPONSE REGULATORs (ARRs) that mediate the cytokinin primary response, making use of chromatin immunoprecipitation sequencing (ChIP-seq), protein-binding microarrays, and transcriptomic approaches. By ectopic overexpression of ARR10, Arabidopsis lines hypersensitive to cytokinin were generated and used to clarify the role of cytokinin in regulation of various physiological responses. ChIP-seq was used to identify the cytokinin-dependent targets for ARR10, thereby defining a crucial link between the cytokinin primary-response pathway and the transcriptional changes that mediate physiological responses to this phytohormone. Binding of ARR10 was induced by cytokinin with binding sites enriched toward the transcriptional start sites for both induced and repressed genes. Three type-B ARR DNA-binding motifs, determined by use of protein-binding microarrays, were enriched at ARR10 binding sites, confirming their physiological relevance. WUSCHEL was identified as a direct target of ARR10, with its cytokinin-enhanced expression resulting in enhanced shooting in tissue culture. Results from our analyses shed light on the physiological role of the type-B ARRs in regulating the cytokinin response, mechanism of type-B ARR activation, and basis by which cytokinin regulates diverse aspects of growth and development as well as responses to biotic and abiotic factors.