PIN-dependent auxin transport: action, regulation, and evolution

A Near-Infrared Fluorescent Nanosensor for Direct and Real-Time Measurement of Indole-3-Acetic Acid in Plants

Auxin, particularly indole-3-acetic acid (IAA), is a phytohormone critical for plant growth, development, and response to environmental stresses like shade avoidance syndrome and thermomorphogenesis. Despite its importance, there is no existing method that allows for convenient and direct detection of IAA in various plant species. Here, we introduce a near-infrared fluorescent nanosensor that directly measures IAA in planta using corona phase molecular recognition with high selectivity, specificity, and spatiotemporal resolution. The IAA sensor can be conveniently functionalized to living plants and localized in various tissues, including leaf, cotyledon, and root tip, with the capability to visualize intrinsic IAA distribution. The IAA nanosensor was further tested in Arabidopsis thaliana leaf with tunable levels of endogenous IAA, in which the sensor measured dynamic and spatiotemporal changes of IAA. We also showed that the IAA sensor can be used for qualitative and quantitative mapping of IAA induction and spatial movement in various plant species undergoing environmental or stress response, such as shade avoidance syndrome, high temperature stress, and gravitropism. This highlights the potential application of IAA sensor for monitoring plant health in agriculture.

Super-resolution expansion microscopy in plant roots

Super-resolution methods provide far better spatial resolution than the optical diffraction limit of about half the wavelength of light (∼200-300 nm). Nevertheless, they have yet to attain widespread use in plants, largely due to plants' challenging optical properties. Expansion microscopy (ExM) improves effective resolution by isotropically increasing the physical distances between sample structures while preserving relative spatial arrangements and clearing the sample. However, its application to plants has been hindered by the rigid, mechanically cohesive structure of plant tissues. Here, we report on whole-mount ExM of thale cress (Arabidopsis thaliana) root tissues (PlantEx), achieving a 4-fold resolution increase over conventional microscopy. Our results highlight the microtubule cytoskeleton organization and interaction between molecularly defined cellular constituents. Combining PlantEx with stimulated emission depletion microscopy, we increase nanoscale resolution and visualize the complex organization of subcellular organelles from intact tissues by example of the densely packed COPI-coated vesicles associated with the Golgi apparatus and put these into a cellular structural context. Our results show that ExM can be applied to increase effective imaging resolution in Arabidopsis root specimens.

Auxin Orchestrates Germ Cell Specification in Arabidopsis

The initiation and specification of germline cells are crucial for plant reproduction and the continuity of species. In Arabidopsis thaliana, auxin plays a vital role in guiding the transition of somatic cells into germline fate, orchestrating the specification of both male archesporial cells and female megaspore mother cells. This process is regulated through interaction with the transcription factor Sporocyteless/Nozzle, which forms a feedback mechanism that modulates germ cell specialization. Auxin biosynthesis, polar transport, and signal transduction pathways collectively ensure the accurate determination of germ cell fate. Furthermore, the coordination of auxin signaling with epigenetic regulation and miRNA-mediated control fine-tunes the differentiation between germline and somatic cells. This review discusses the mechanisms underlying auxin-guided germ cell specification. It proposes future research directions, including studies on PIN-FORMED-mediated polar transport, the role of the YUCCA family in auxin biosynthesis, and the involvement of the Transport Inhibitors Response 1/Auxn Signaling F-Box-Auxin Response Factor (TIR1/AFB-ARF) signaling pathway in germ cell fate determination. These insights will enhance our understanding of plant reproductive biology and provide new strategies for crop breeding.

Twisted Sister1: an agravitropic mutant of bread wheat (Triticum aestivum) with altered root and shoot architectures

We identified a mutant of hexaploid wheat (Triticum aestivum) with impaired responses to gravity. The mutant, named Twisted Sister1 (TS1), had agravitropic roots that were often twisted along with altered shoot phenotypes. Roots of TS1 were insensitive to externally applied auxin, with the genetics and physiology suggestive of a mutated AUX/IAA transcription factor gene. Hexaploid wheat possesses over 80 AUX/IAA genes, and sequence information did not identify an obvious candidate. Bulked segregant analysis of an F2 population mapped the mutation to chromosome 5A, and subsequent mapping located the mutation to a 41 Mbp region. RNA-seq identified the TraesCS5A03G0149800 gene encoding a TaAUX/IAA protein to be mutated in the highly conserved domain II motif. We confirmed TraesCS5A03G0149800 as underlying the mutant phenotype by generating transgenic Arabidopsis thaliana. Analysis of RNA-seq data suggested broad similarities between Arabidopsis and wheat for the role of AUX/IAA genes in gravity responses, although there were marked differences. Here we show that the sequenced wheat genome, along with previous knowledge of the physiology of gravity responses from other plant species, gene mapping, RNA-seq, and expression in Arabidopsis have enabled the cloning of a key wheat gene that defines plant architecture.

Plant Signaling Hormones and Transcription Factors: Key Regulators of Plant Responses to Growth, Development, and Stress

Plants constantly encounter a wide range of biotic and abiotic stresses that adversely affect their growth, development, and productivity. Phytohormones such as abscisic acid, jasmonic acid, salicylic acid, and ethylene serve as crucial regulators, integrating internal and external signals to mediate stress responses while also coordinating key developmental processes, including seed germination, root and shoot growth, flowering, and senescence. Transcription factors (TFs) such as WRKY, NAC, MYB, and AP2/ERF play complementary roles by orchestrating complex transcriptional reprogramming, modulating stress-responsive genes, and facilitating physiological adaptations. Recent advances have deepened our understanding of hormonal networks and transcription factor families, revealing their intricate crosstalk in shaping plant resilience and development. Additionally, the synthesis, transport, and signaling of these molecules, along with their interactions with stress-responsive pathways, have emerged as critical areas of study. The integration of cutting-edge biotechnological tools, such as CRISPR-mediated gene editing and omics approaches, provides new opportunities to fine-tune these regulatory networks for enhanced crop resilience. By leveraging insights into transcriptional regulation and hormone signaling, these advancements provide a foundation for developing stress-tolerant, high-yielding crop varieties tailored to the challenges of climate change.

Strigolactone insensitivity affects the hormonal homeostasis in barley

In response to environmental changes, plants continuously make architectural changes in order to optimize their growth and development. The regulation of plant branching, influenced by environmental conditions and affecting hormone balance and gene expression, is crucial for agronomic purposes due to its direct correlation with yield. Strigolactones (SL), the youngest class of phytohormones, function to shape the architecture of plants by inhibiting axillary outgrowth. Barley plants harboring the mutation in the HvDWARF14 (HvD14) gene, which encodes the SL-specific receptor, produce almost twice as many tillers as wild-type (WT) Sebastian plants. Here, through hormone profiling and comparison of transcriptomic and proteomic changes between 2- and 4-week-old plants of WT and hvd14 genotypes, we elucidate a regulatory mechanism that might affect the tillering of SL-insensitive plants. The analysis showed statistically significant increased cytokinin content and decreased auxin and abscisic acid content in 'bushy' hvd14 compared to WT, which aligns with the commonly known actions of these hormones regarding branching regulation. Further, transcriptomic and proteomic analysis revealed a set of differentially expressed genes (DEG) and abundant proteins (DAP), among which 11.6% and 14.6% were associated with phytohormone-related processes, respectively. Bioinformatics analyses then identified a series of potential SL-dependent transcription factors (TF), which may control the differences observed in the hvd14 transcriptome and proteome. Comparison to available Arabidopsis thaliana data implicates a sub-selection of these TF as being involved in the transduction of SL signal in both monocotyledonous and dicotyledonous plants.

Mathematical analysis of long-distance polar auxin transport data of pin mutants questions the role of PIN1 as postulated in the chemi-osmotic theory

The plant hormone auxin (Indole-3-Acetic Acid, IAA) is a key player in nearly every aspect of plant growth and development ranging from cell division and cell elongation to embryogenesis and root formation. The IAA level in specific tissues and cells is regulated by synthesis, conjugation, degradation and transport. Especially long-range polar auxin transport (PAT) has been the subject of numerous studies. The chemi-osmotic theory predicts that intercellular PAT is caused by an asymmetric distribution of auxin efflux transporters in cell membranes of transporting cells, resulting in increased local membrane permeability for IAA. Members of the PIN gene family are generally considered to encode the postulated carriers. The objective of this study was to use the chemi-osmotic theory in an experimental program aimed at describing and interpreting long-range PAT data from mutants of the PIN gene family of Arabidopsis thaliana. Therefore, we put the chemi-osmotic theory in a broader theoretical framework. We find that the observed decrease in both auxin flux and transport velocity in pin1 loss-of-function mutants is not caused by decreased basal membrane permeability, as would be expected according to the chemi-osmotic theory, but is an indirect effect caused by a change in the dynamics of auxin transport due to a decrease in the expression of all four AUX1/LAX1-3 auxin influx carriers in pin1 mutants. On the basis of our findings, we conclude that the exact role of PIN1 in long-distance PAT, as postulated in the chemi-osmotic theory, should be reconsidered.

Regulation of PILS genes by bZIP transcription factor TGA7 in tomato plant growth

Auxin plays a pivotal role in plant growth regulation. The PIN-FORMED (PIN) proteins facilitate long-distance polar auxin transport, whereas the recently identified PIN-LIKES (PILS) proteins regulate intracellular auxin homeostasis. However, the auxin transport mechanisms in horticultural crops remain largely unexplored. Here, we identified and characterized PILS genes in tomato (Solanum lycopersicum). Promoter analysis revealed enrichment in TGA[C/T]G motifs, suggesting transcriptional regulation by TGA factors in the bZIP family. Subcellular localization studies confirmed that all tomato PILS proteins localize in the endoplasmic reticulum. PILS2 exhibited the highest expression across examined tissues, and its close homologue PILS6 showed a similar but less pronounced expression pattern. Silencing PILS2 significantly inhibited shoot and root growth. Phylogenetic and expression analyses identified the homologs of Arabidopsis TGA1, TGA3, TGA4, and TGA7 in tomato genome, with tomato TGA7 showing higher expression in roots. Notably, silencing tomato TGA7, but not TGA1, TGA3, or TGA4, strongly impaired shoot and root growth. Molecular assays demonstrated that TGA7 directly binds to the PILS2 promoter to activate its transcription. These findings uncover a TGA7-PILS2 regulatory module that governs plant growth and offer new insights into the function and regulation of PILS genes in tomato.

BAP regulates lateral bud outgrowth to promote tillering in Paphiopedilum callosum (Orchidaceae)

BACKGROUND

Paphiopedilum orchids have a high ornamental value, and flower abundance is a key horticultural trait. Most Paphiopedilum plants exhibit weak tillering ability, with their tiller buds often entering a dormant state post-formation. Tiller production plays a crucial role in enhancing flower abundance and is potentially regulated by plant hormones. However, the effect of hormones on tillering in Paphiopedilum plants is still unclear.

RESULTS

In this study, we investigated the promotion of tillering in P. callosum through exogenous root irrigation of benzylaminopurine (BAP). We observed a dose-dependent promotion of tiller production by BAP, with the strongest effect observed at a concentration of 400 mg/L. By comparing the expression of key genes in P. 'SCBG Yingchun' (with strong tiller ability) and P callosum (with weak tiller ability), we found that BAP promotes tillering by interacting with abscisic acid (ABA). This interaction involves down-regulation of the ABA degradation gene PcCYP707A, leading to a reduction in ABA content, and the subsequent down-regulation of dormancy-associated genes (PcDRMH1, PcSVP) to release bud dormancy. Additionally, BAP promotes sustained outgrowth of tiller buds by increasing the level of indole-3-acetic acid (IAA) through up-regulation of the IAA synthesis gene PcYUC2 and the transport gene PcPINIC.

CONCLUSIONS

Our results indicated that the application of BAP promotes lateral bud outgrowth and increases tiller production in P. callosum. Through transcriptome analysis, we found that the BAP-promotion of tillering involves not only changes in endogenous IAA, ABA, and CTKs content but is also associated with the regulation of metabolism-related genes and dormancy-associated genes. This study presents the first comprehensive report of BAP-promoted tillering in P. callosum, providing a foundational basis for further mechanistic studies on tiller development in Paphiopedilum species and other non-model plants.

The scaffold protein RACK1 regulates root growth and gravitropic response by recruiting PINOID to phosphorylate the auxin efflux transporter PIN-FORMED2

The scaffolding protein RACK1 is involved in polar auxin transport and signaling. It binds to PINOID and PIN-FORMED2, enhancing their interaction and phosphorylation-dependent auxin efflux. Knocking down RACK1 genes impairs auxin-related processes such as root growth and gravitropic response.

PIN2-mediated self-organizing transient auxin flow contributes to auxin maxima at the tip of Arabidopsis cotyledons

Directional auxin transport and formation of auxin maxima are critical for embryogenesis, organogenesis, pattern formation, and growth coordination in plants, but the mechanisms underpinning the initiation and establishment of these auxin dynamics are not fully understood. Here we show that a self-initiating and -terminating transient auxin flow along the marginal cells (MCs) contributes to the formation of an auxin maximum at the tip of Arabidopsis cotyledon that globally coordinates the interdigitation of puzzle-shaped pavement cells in the cotyledon epidermis. Prior to the interdigitation, indole butyric acid (IBA) is converted to indole acetic acid (IAA) to induce PIN2 accumulation and polarization in the marginal cells, leading to auxin flow toward and accumulation at the cotyledon tip. Once IAA levels at the cotyledon tip reaches a maximum, it activates pavement cell interdigitation as well as the accumulation of the IBA transporter TOB1 in MCs, which sequesters IBA to the vacuole and reduces IBA availability and IAA levels. The reduction of IAA levels results in PIN2 down-regulation and cessation of the auxin flow. Hence, our results elucidate a self-activating and self-terminating transient polar auxin transport system in cotyledons, contributing to the formation of localized auxin maxima that spatiotemporally coordinate pavement cell interdigitation.

Anionic phospholipid-mediated transmembrane transport and intracellular membrane trafficking in plant cells

Cellular membranes primarily consist of proteins and lipids. These proteins perform cellular functions such as metabolic regulation, environmental and hormonal signal sensing, and nutrient transport. There is increasing experimental evidence that certain lipids, particularly anionic phospholipids, can act as signaling molecules. Specific examples of functional regulation by anionic phospholipids in plant cells have been reported for transporters, channels, and even receptors. By regulating the structure and activity of membrane-integral proteins, these phospholipids mediate the transport of phytohormones and ions, and elicit physiological responses to developmental and environmental cues. Phospholipids also control membrane protein abundance and lipid composition and abundance by facilitating vesicular trafficking. In this review, we discuss recent research that elucidates the mechanisms by which membrane-integral transporters and channels are controlled via phospholipid signaling, as well as the regulation of membrane protein accumulation by phospholipids through coordinated removal, recycling, and degradation processes.

The role of signaling systems of plant in responding to key astrophysical factors: increased ionizing radiation, near-null magnetic field and microgravity

Plants will form the basis of artificial ecosystems in space exploration and the creation of bases on other planets. Astrophysical factors, such as ionizing radiation (IR), magnetic fields (MF) and gravity, can significantly affect the growth and development of plants beyond Earth. However, to date, the ways in which these factors influence plants remain largely unexplored. The review shows that, despite the lack of specialized receptors, plants are able to perceive changes in astrophysical factors. Potential mechanisms for perceiving changes in IR, MF and gravity levels are considered. The main pathway for inducing effects in plants is caused by primary physicochemical reactions and change in the levels of secondary messengers, including ROS and Ca2+. The presence of common components, including secondary messengers, in the chain of responses to astrophysical factors determines the complex nature of the response under their combined action. The analysis performed and the proposed hypothesis will help in planning space missions, as well as identifying the most important areas of research in space biology.

Excessive accumulation of auxin inhibits protocorm development during germination of Paphiopedilum spicerianum

KEY MESSAGE

Excessive auxin accumulation inhibits protocorm development during germination of Paphiopedilum spicerianum, delaying shoot meristem formation by downregulating boundary genes (CUC1, CUC2, CLV3) and promoting fungal colonization, essential for seedling establishment. Paphiopedilum, possess high horticultural and conservational value. Asymbiotic germination is a common propagation method, but high rates of protocorm developmental arrest hinder seedling establishment. Our study found that the key difference between normally developing protocorm (NDP) and arrested developmental protocorm (ADP) is their capability for continuous cell differentiation. In ADP, cells divide without differentiating, with indole-3-acetic acid (IAA) levels being 20 times higher than that in NDP. This suggests that auxin level plays a role in protocorm cell fate determination. Exogenous application of NAA demonstrated that elevated auxin level can delay the formation of the shoot apical meristem (SAM) inside the protocorm. Gene expression analysis revealed that elevated auxin can inhibit or even halt the SAM formation through down-regulation of SAM-related genes such as CLV3, CUC1 and CUC2. High auxin levels also led to reduced cell wall rigidity by up-regulation of cell wall expanding protein (EXPB15), thereby creating ideal conditions for fungi entry. Inoculation with a compatible orchid mycorrhizal fungus (OMF) resulted in successful cell differentiation of ADP and eventually triggered the conversion of ADP to NDP. Since the protocorm is a distinct structure that facilitates the establishment of symbiotic associations with compatible OMF, we propose that the excessive auxin accumulation inside Paphiopedilum protocorm can pause the further development of protocorm and soften the cell wall. This strategy likely serves to enhance the attraction and colonization by OMFs in the native habitat of Paphiopedilum, facilitating essential symbiotic relationships necessary for their survival and growth.

Recent Advances in Ubiquitin Signals Regulating Plant Membrane Trafficking

Ubiquitination is a reversible post-translational modification involving the attachment of ubiquitin, a 76-amino acid protein conserved among eukaryotes. The protein 'ubiquitin' was named after it was found to be ubiquitously expressed in cells. Ubiquitination was first identified as a post-translational modification that mediates energy-consuming protein degradation by the proteasome. After half a century, the manifold functions of ubiquitin are widely recognized to play key roles in diverse molecular pathways and physiological processes. Compared to humans, the number of enzymes related to ubiquitination is almost twice as high in plant species, such as Arabidopsis and rice, suggesting that this modification plays a critical role in many aspects of plant physiology including development and environmental stress responses. Here, we summarize and discuss recent knowledge of ubiquitination focusing on the regulation of membrane trafficking in plants. Ubiquitination of plasma membrane-localized proteins often leads to endocytosis and vacuolar targeting. In addition to cargo proteins, ubiquitination of membrane trafficking regulators regulates the morphodynamics of the endomembrane system. Thus, throughout this review, we focus on the physiological responses regulated by ubiquitination and their underlying mechanisms to clarify what is already known and what would be interesting to investigate in the future.

The t-SNARE protein OsSYP132 is required for vesicle fusion and root morphogenesis in rice

Root morphogenesis is crucial for water and nutrient acquisition, but many aspects of root morphogenesis in crops are not well-understood. Here, we cloned and functionally characterized a key gene for root morphogenesis in rice (Oryza sativa) based on mutant analysis. The stop root morphogenesis 1 (srm1) mutant lacks crown roots (CRs) and lateral roots (LRs) and carries a point mutation in the t-SNARE coding gene SYNTAXIN OF PLANTS 132 (OsSYP132), leading to a premature stop codon and ablating the post-transmembrane (PTM) region of OsSYP132. We identified the functional SNARE complex OsSYP132-OsNPSN13-OsSYP71-OsVAMP721/722 and determined that the integrity of the PTM region of OsSYP132 is essential for OsSYP132-based SNARE complex-mediated fusion of OsVAMP721/722 vesicles with the plasma membrane. The loss of this region in srm1 disrupts the intercellular trafficking and plasma membrane localization of OsPIN1b, preventing proper auxin distribution in the primordia of CRs and LRs and inhibiting their outgrowth.

Telomeres: an organized string linking plants and mammals

Telomeres are pivotal determinants of cell stemness, organismal aging, and lifespan. Herein, we examined similarities in telomeres of Arabidopsis thaliana, mice, and humans. We report the common traits, which include their composition in multimers of TTAGGG sequences and their protection by specialized proteins. Moreover, given the link between telomeres, on the one hand, and cell proliferation and stemness on the other, we discuss the counterintuitive convergence between plants and mammals in this regard, focusing on the impact of niches on cell stemness. Finally, we suggest that tackling the study of telomere function and cell stemness by taking into consideration both plants and mammals can aid in the understanding of interconnections and contribute to research focusing on aging and organismal lifespan determinants.

Actin Isovariant ACT2-Mediated Cellular Auxin Homeostasis Regulates Lateral Root Organogenesis in Arabidopsis thaliana

Lateral root (LR) organogenesis is regulated by cellular flux of auxin within pericycle cells, which depends on the membrane distribution and polar localization of auxin carrier proteins. The correct distribution of auxin carrier proteins relies on the intracellular trafficking of these proteins aided by filamentous actin as a track. However, the precise role of actin in lateral root development is still elusive. Here, using vegetative class actin isovariant mutants, we revealed that loss of actin isovariant ACT8 led to increased lateral root formation. The distribution of auxin within pericycle cells was altered in act8 mutant, primarily due to the altered distribution of AUX1 and PIN7. Interestingly, incorporation of act2 mutant in act8 background (act2act8) effectively nullified the LR phenotype observed in act8 mutant, indicating that ACT2 plays an important role in LR development. To explore further, we investigated the possibility that the act8 mutant's LR phenotype and cellular auxin distribution resulted from ACT2 overexpression. Consistent with the idea, enhanced lateral root formation, altered AUX1, PIN7 expression, and auxin distribution in pericycle cells were observed in ACT2 overexpression lines. Collectively, these results suggest that actin isovariant ACT2 but not ACT8 plays a pivotal role in regulating source-to-sink auxin distribution during lateral root organogenesis.

The AP2 transcription factor BARE RECEPTACLE regulates floral organogenesis via auxin pathways in woodland strawberry

During flower development, different floral organs are formed to ensure fertilization and fruit set. Although the genetic networks underlying flower development are increasingly well understood, less is known about the mechanistic basis in different species. Here, we identified a mutant of woodland strawberry (Fragaria vesca), bare receptacle (bre), which produces flowers with greatly reduced carpels and other floral organs. Genetic analysis revealed that BRE encodes an APETALA2 (AP2) transcription factor. BRE was highly expressed in floral meristems and floral organ primordia. BRE could directly bind the GCC-box motif in the YUCCA (YUC) auxin biosynthesis genes FveYUC4 and FveYUC2 and promote their expression. The yuc4 mutant had fewer floral organs, and the bre yuc4 double mutant had similar numbers of petals and carpels to bre. Auxin homeostasis and distribution were severely disrupted in bre. Although auxin application or FveYUC4 overexpression did not rescue the bre phenotypes, bre was hypersensitive to treatment with the polar auxin transport inhibitor N-1-naphthylphthalamic acid (NPA). In addition, BRE was able to directly bind and regulate the expression of five other auxin pathway genes. Overall, these results demonstrate that BRE is required for floral organogenesis, particularly carpel initiation, and acts through the auxin pathway in strawberry.

The auxin efflux carrier PIN1a regulates vascular patterning in cereal roots

Barley (Hordeum vulgare) is an important global cereal crop and a model in genetic studies. Despite advances in characterising barley genomic resources, few mutant studies have identified genes controlling root architecture and anatomy, which plays a critical role in capturing soil resources. Our phenotypic screening of a TILLING mutant collection identified line TM5992 exhibiting a short-root phenotype compared with wild-type (WT) Morex background. Outcrossing TM5992 with barley variety Proctor and subsequent SNP array-based bulk segregant analysis, fine mapped the mutation to a cM scale. Exome sequencing pinpointed a mutation in the candidate gene HvPIN1a, further confirming this by analysing independent mutant alleles. Detailed analysis of root growth and anatomy in Hvpin1a mutant alleles exhibited a slower growth rate, shorter apical meristem and striking vascular patterning defects compared to WT. Expression and mutant analyses of PIN1 members in the closely related cereal brachypodium (Brachypodium distachyon) revealed that BdPIN1a and BdPIN1b were redundantly expressed in root vascular tissues but only Bdpin1a mutant allele displayed root vascular defects similar to Hvpin1a. We conclude that barley PIN1 genes have sub-functionalised in cereals, compared to Arabidopsis (Arabidopsis thaliana), where PIN1a sequences control root vascular patterning.

Actin-bundling protein fimbrin serves as a new auxin biosynthesis orchestrator in Arabidopsis root tips

Plants delicately regulate endogenous auxin levels through the coordination of transport, biosynthesis, and inactivation, which is crucial for growth and development. While it is well-established that the actin cytoskeleton can regulate auxin levels by affecting polar transport, its potential role in auxin biosynthesis has remained largely unexplored. Using LC-MS/MS-based methods combined with fluorescent auxin marker detection, we observed a significant increase in root auxin levels upon deletion of the actin bundling proteins AtFIM4 and AtFIM5. Fluorescent observation, immunoblotting analysis, and biochemical approaches revealed that AtFIM4 and AtFIM5 affect the protein abundance of the key auxin synthesis enzyme YUC8 in roots. AtFIM4 and AtFIM5 regulate the auxin synthesis enzyme YUC8 at the protein level, with its degradation mediated by the 26S proteasome. This regulation modulates auxin synthesis and endogenous auxin levels in roots, consequently impacting root development. Based on these findings, we propose a molecular pathway centered on the 'actin cytoskeleton-26S proteasome-YUC8-auxin' axis that controls auxin levels. Our findings shed light on a new pathway through which plants regulate auxin synthesis. Moreover, this study illuminates a newfound role of the actin cytoskeleton in regulating plant growth and development, particularly through its involvement in maintaining protein homeostasis via the 26S proteasome.

The SCOOP-MIK2 immune pathway modulates Arabidopsis root growth and development by regulating PIN-FORMED abundance and auxin transport

Plants synthesize hundreds of small secretory peptides, which are perceived by the receptor-like kinase (RLK) family at the cell surface. Various signaling peptide-RLK pairs ensure plant adaptation to distinct environmental conditions. Here, we report that SERINE RICH ENDOGENOUS PEPTIDE (SCOOP) immune peptides modulate root growth and development by regulating PIN-FORMED (PIN)-regulated polar auxin transport in Arabidopsis. The SCOOP4 and SCOOP12 treatments impaired root gravitropic growth, auxin redistribution in response to gravistimulation, and PIN abundance in the PM. Furthermore, genetic and cell biological analyses revealed that these physiological and cellular effects of SCOOP4 and SCOOP12 peptides are mediated by the receptor MALE DISCOVERER1-INTERACTING RECEPTOR LIKE KINASE2 (MIK2) and the downstream mitogen-activated kinase MPK6. Biochemical evidence indicates that MPK6 directly phosphorylates the cytosolic loop of PIN proteins. Our work established a link between the immune signaling peptide SCOOPs and root growth pathways, providing insights into the molecular mechanisms underlying plant root adaptive growth in the defense response.

An integrated targeted metabolome of phytohormones and transcriptomics analysis provides insight into the new generation of crops: Polygonatum kingianum var. grandifolium and Polygonatum kingianum

Huangjing is becoming a new generation of crop. Polygonatum kingianum var. grandifolium (XHJ) is a variant of P. kingianum (DHJ), and they are treated as Huangjing. Unlike other Polygonatum species, the rhizome bud of XHJ can germinate both in spring and autumn, which contributes to its high rhizome yield. However, the molecular mechanism of the autumn shooting of XHJ was still unknown. In the present study, cellular observation, comparative targeted metabolome of phytohormones, and transcriptome analysis between XHJ and DHJ in autumn were conducted. Interestingly, 'Diterpenoid biosynthesis' (ko00904) and 'Plant hormone signal transduction' (ko04075) were commonly enriched by differentially accumulated phytohormones (DAPs) and differentially expressed genes (DEGs) in all tissues, which indicated the high auxin content, low cytokinin (CTK) content, and low abscisic acid/gibberellin (ABA/GA) ratio might contribute to the XHJ rhizome buds' differentiation and germination in autumn. Moreover, according to the weighted gene co-expression network analysis (WCGNA), transcript factors (TFs) related to auxin, CTK, GA, and jasmonic acid (JA) metabolism were screened, such as AP2/ERFs, WRKY, and NAC, which deserve further research. In conclusion, we comprehensively illustrated the mechanism of XHJ natural autumn shooting through cytological, metabolic, and transcriptomic analysis, which improves our understanding of the high yield of XHJ rhizomes and the diversity of shooting mechanisms in Polygonatum to lay the foundation for the further development of the Huangjing industry.

Genome-wide gene network uncover temporal and spatial changes of genes in auxin homeostasis during fruit development in strawberry (F. × ananassa)

BACKGROUND

The plant hormone auxin plays a crucial role in regulating important functions in strawberry fruit development. Although a few studies have described the complex auxin biosynthetic and signaling pathway in wild diploid strawberry (Fragaria vesca), the molecular mechanisms underlying auxin biosynthesis and crosstalk in octoploid strawberry fruit development are not fully characterized. To address this knowledge gap, comprehensive transcriptomic analyses were conducted at different stages of fruit development and compared between the achene and receptacle to identify developmentally regulated auxin biosynthetic genes and transcription factors during the fruit ripening process. Similar to wild diploid strawberry, octoploid strawberry accumulates high levels of auxin in achene compared to receptacle.

RESULTS

Genes involved in auxin biosynthesis and conjugation, such as Tryptophan Aminotransferase of Arabidopsis (TAAs), YUCCA (YUCs), and Gretchen Hagen 3 (GH3s), were found to be primarily expressed in the achene, with low expression in the receptacle. Interestingly, several genes involved in auxin transport and signaling like Pin-Formed (PINs), Auxin/Indole-3-Acetic Acid Proteins (Aux/IAAs), Transport Inhibitor Response 1 / Auxin-Signaling F-Box (TIR/AFBs) and Auxin Response Factor (ARFs) were more abundantly expressed in the receptacle. Moreover, by examining DEGs and their transcriptional profiles across all six developmental stages, we identified key auxin-related genes co-clustered with transcription factors from the NAM-ATAF1,2-CUC2/ WRKYGQK motif (NAC/WYKY), Heat Shock Transcription Factor and Heat Shock Proteins (HSF/HSP), APETALA2/Ethylene Responsive Factor (AP2/ERF) and MYB transcription factor groups.

CONCLUSIONS

These results elucidate the complex regulatory network of auxin biosynthesis and its intricate crosstalk within the achene and receptacle, enriching our understanding of fruit development in octoploid strawberries.

Advances in Plant Auxin Biology: Synthesis, Metabolism, Signaling, Interaction with Other Hormones, and Roles under Abiotic Stress

Auxin is a key hormone that regulates plant growth and development, including plant shape and sensitivity to environmental changes. Auxin is biosynthesized and metabolized via many parallel pathways, and it is sensed and transduced by both normal and atypical pathways. The production, catabolism, and signal transduction pathways of auxin primarily govern its role in plant growth and development, and in the response to stress. Recent research has discovered that auxin not only responds to intrinsic developmental signals, but also mediates various environmental signals (e.g., drought, heavy metals, and temperature stresses) and interacts with hormones such as cytokinin, abscisic acid, gibberellin, and ethylene, all of which are involved in the regulation of plant growth and development, as well as the maintenance of homeostatic equilibrium in plant cells. In this review, we discuss the latest research on auxin types, biosynthesis and metabolism, polar transport, signaling pathways, and interactions with other hormones. We also summarize the important role of auxin in plants under abiotic stresses. These discussions provide new perspectives to understand the molecular mechanisms of auxin's functions in plant development.

Polarly localized Bro1 domain proteins regulate PIN-FORMED abundance and root gravitropic growth in Arabidopsis

The developmental plasticity of the root system plays an essential role in the adaptation of plants to the environment. Among many other signals, auxin and its directional, intercellular transport are critical in regulating root growth and development. In particular, the PIN-FORMED2 (PIN2) auxin exporter acts as a key regulator of root gravitropic growth. Multiple regulators have been reported to be involved in PIN2-mediated root growth; however, our information remains incomplete. Here, we identified ROWY Bro1-domain proteins as important regulators of PIN2 sorting control. Genetic analysis revealed that Arabidopsis rowy1 single mutants and higher-order rowy1 rowy2 rowy3 triple mutants presented a wavy root growth phenotype. Cell biological experiments revealed that ROWY1 and PIN2 colocalized to the apical side of the plasma membrane in the root epidermis and that ROWYs are required for correct PM targeting of PIN2. In addition, ROWYs also affected PIN3 protein abundance in the stele, suggesting the potential involvement of additional PIN transporters as well as other proteins. A global transcriptome analysis revealed that ROWY genes are involved in the Fe2+ availability perception pathway. This work establishes ROWYs as important novel regulators of root gravitropic growth by connecting micronutrient availability to the proper subcellular targeting of PIN auxin transporters.

Gallic acid regulates primary root elongation via modulating auxin transport and signal transduction

Gallic acid is an important secondary metabolite in plants, with great value in medicine, food, and chemical industry. However, whether and how this widely existing natural polyphenolic compound affects the growth and development of plants themselves remains elusive. In this study, we revealed that exogenous application of gallic acid has a dual effect on the elongation of primary root in Arabidopsis. While lower concentrations of gallic acid slightly stimulate primary root growth, excessive gallic acid profoundly reduces primary root length and root meristem size in a dose-dependent manner, probably via suppressing cell division in root meristem as indicated by CYCB1;1::GUS. Moreover, as suggested by the DR5::GFP line analysis and confirmed by the LC-MS assay, auxin contents in root tips were dramatically decreased upon excessive gallic acid treatment. Additional application of IAA partially rescued the shortened primary root and root meristem upon excessive gallic acid treatment, suggesting that auxin is required for excessive gallic acid-caused root growth inhibition. Then, we further revealed that excessive gallic acid down-regulated the expression of auxin transporters PIN1, PIN2, PIN3, and PIN7, and triple mutant pin1 pin3 pin7 exhibited a reduced sensitivity to gallic acid treatment. Meanwhile, excessive gallic acid decreased the degradation of AXR3/IAA17 protein as revealed by HS::AXR3NT-GUS reporter line. Auxin signaling mutant tir1 afb2 afb3 and axr3-3 were also less sensitive to excessive gallic acid treatment in terms of primary root length and root meristem size. Taken together, these findings suggested that excessive gallic acid inhibits primary root growth by modulating auxin transport and signaling in Arabidopsis.

Transcriptomic and Physiological Analyses for the Role of Hormones and Sugar in Axillary Bud Development of Wild Strawberry Stolon

Strawberries are mainly propagated by stolons, which can be divided into monopodial and sympodial types. Monopodial stolons consistently produce ramets at each node following the initial single dormant bud, whereas sympodial stolons develop a dormant bud before each ramet. Sympodial stolon encompasses both dormant buds and ramet buds, making it suitable for studying the formation mechanism of different stolon types. In this study, we utilized sympodial stolons from Fragaria nilgerrensis as materials and explored the mechanisms underlying sympodial stolon development through transcriptomic and phytohormonal analyses. The transcriptome results unveiled that auxin, cytokinin, and sugars likely act as main regulators. Endogenous hormone analysis revealed that the inactivation of auxin could influence bud dormancy. Exogenous cytokinin application primarily induced dormant buds to develop into secondary stolons, with the proportion of ramet formation being very low, less than 10%. Furthermore, weighted gene co-expression network analysis identified key genes involved in ramet formation, including auxin transport and response genes, the cytokinin activation gene LOG1, and glucose transport genes SWEET1 and SFP2. Consistently, in vitro cultivation experiments confirmed that glucose enhances the transition of dormant buds into ramets within two days. Collectively, cytokinin and glucose act as dormant breakers, with cytokinin mainly driving secondary stolon formation and glucose promoting ramet generation. This study improved our understanding of stolon patterning and bud development in the sympodial stolon of strawberries.

Dual transcriptomic analysis reveals early induced Castanea defense-related genes and Phytophthora cinnamomi effectors

Phytophthora cinnamomi Rands devastates forest species worldwide, causing significant ecological and economic impacts. The European chestnut (Castanea sativa) is susceptible to this hemibiotrophic oomycete, whereas the Asian chestnuts (Castanea crenata and Castanea mollissima) are resistant and have been successfully used as resistance donors in breeding programs. The molecular mechanisms underlying the different disease outcomes among chestnut species are a key foundation for developing science-based control strategies. However, these are still poorly understood. Dual RNA sequencing was performed in C. sativa and C. crenata roots inoculated with P. cinnamomi. The studied time points represent the pathogen's hemibiotrophic lifestyle previously described at the cellular level. Phytophthora cinnamomi expressed several genes related to pathogenicity in both chestnut species, such as cell wall-degrading enzymes, host nutrient uptake transporters, and effectors. However, the expression of effectors related to the modulation of host programmed cell death (elicitins and NLPs) and sporulation-related genes was higher in the susceptible chestnut. After pathogen inoculation, 1,556 and 488 genes were differentially expressed by C. crenata and C. sativa, respectively. The most significant transcriptional changes occur at 2 h after inoculation (hai) in C. sativa and 48 hai in C. crenata. Nevertheless, C. crenata induced more defense-related genes, indicating that the resistant response to P. cinnamomi is controlled by multiple loci, including several pattern recognition receptors, genes involved in the phenylpropanoid, salicylic acid and ethylene/jasmonic acid pathways, and antifungal genes. Importantly, these results validate previously observed cellular responses for C. crenata. Collectively, this study provides a comprehensive time-resolved description of the chestnut-P. cinnamomi dynamic, revealing new insights into susceptible and resistant host responses and important pathogen strategies involved in disease development.

The Defective in Autoregulation (DAR) gene of Medicago truncatula encodes a protein involved in regulating nodulation and arbuscular mycorrhiza

BACKGROUND

Legumes utilize a long-distance signaling feedback pathway, termed Autoregulation of Nodulation (AON), to regulate the establishment and maintenance of their symbiosis with rhizobia. Several proteins key to this pathway have been discovered, but the AON pathway is not completely understood.

RESULTS

We report a new hypernodulating mutant, defective in autoregulation, with disruption of a gene, DAR (Medtr2g450550/MtrunA17_Chr2g0304631), previously unknown to play a role in AON. The dar-1 mutant produces ten-fold more nodules than wild type, similar to AON mutants with disrupted SUNN gene function. As in sunn mutants, suppression of nodulation by CLE peptides MtCLE12 and MtCLE13 is abolished in dar. Furthermore, dar-1 also shows increased root length colonization by an arbuscular mycorrhizal fungus, suggesting a role for DAR in autoregulation of mycorrhizal symbiosis (AOM). However, unlike SUNN which functions in the shoot to control nodulation, DAR functions in the root.

CONCLUSIONS

DAR encodes a membrane protein that is a member of a small protein family in M. truncatula. Our results suggest that DAR could be involved in the subcellular transport of signals involved in symbiosis regulation, but it is not upregulated during symbiosis. DAR gene family members are also present in Arabidopsis, lycophytes, mosses, and microalgae, suggesting the AON and AOM may use pathway components common to other plants, even those that do not undergo either symbiosis.

Genomic analysis of PIN-FORMED genes reveals the roles of SmPIN3 in root architecture development in Salvia miltiorrhiza

Salvia miltiorrhiza is a widely utilized medicinal herb in China. Its roots serve as crucial raw materials for multiple drugs. The root morphology is essential for the quality of this herb, but little is known about the molecular mechanism underlying the root development in S. miltiorrhiza. Previous study reveals that the polar auxin transport is critical for lateral root development in S. miltiorrhiza. Whether the auxin efflux carriers PIN-FORMEDs (PINs) are involved in this process is worthy investigation. In this study, we identified nine SmPIN genes in S. miltiorrhiza, and their chromosome localization, physico-chemical properties, and phylogenetic relationship were analyzed. SmPINs were unevenly distributed across four chromosomes, and a variety of hormone responsive elements were detected in their promoter regions. The SmPIN proteins were divided into three branches according to the phylogenetic relationship. SmPINs with close evolutionary distance showed similar conserved motif features. The nine SmPINs showed distinct tissue-specific expression patterns and most of them were auxin-inducible genes. We generated SmPIN3 overexpression S. miltiorrhiza seedlings to investigate the function of SmPIN3 in the root development in this species. The results demonstrated that SmPIN3 regulated the root morphogenesis of S. miltiorrhiza by simultaneously affecting the lateral root development and the root anatomical structure. The root morphology, patterns of root xylem and phloem as well as the expressions of genes in the auxin signaling pathway all altered in the SmPIN3 overexpression lines. Our findings provide new insights for elucidating the regulatory roles of SmPINs in the auxin-mediated root development in S. miltiorrhiza.

Cytosolic ABA Receptor Kinases phosphorylate the D6 PROTEIN KINASE leading to its stabilization which promotes Arabidopsis growth

The polar auxin transport is required for proper plant growth and development. D6 PROTEIN KINASE (D6PK) is required for the phosphorylation of PIN-FORMED (PIN) auxin efflux carriers to regulate auxin transport, while the regulation of D6PK stabilization is still poorly understood. Here, we found that Cytosolic ABA Receptor Kinases (CARKs) redundantly interact with D6PK, and the interactions are dependent on CARKs' kinase activities. Similarly, CARK3 also could interact with paralogs of D6PK, including D6PKL1, D6PKL2, and D6PKL3. The genetic analysis shows that D6PK acts the downstream of CARKs to regulate Arabidopsis growth, including hypocotyl, leaf area, vein formation, and the length of silique. Loss-of-function of CARK3 in overexpressing GFP-D6PK plants leads to reduce the level of D6PK protein, thereby rescues plant growth. In addition, the cell-free degradation assays indicate that D6PK is degraded through 26 S proteasome pathway, while the phosphorylation by CARK3 represses this process in cells. In summary, D6PK stabilization by the CARK family is required for auxin-mediated plant growth and development.

The hormone regulatory mechanism underlying parthenocarpic fruit formation in tomato

Parthenocarpic fruits, known for their superior taste and reliable yields in adverse conditions, develop without the need for fertilization or pollination. Exploring the physiological and molecular mechanisms behind parthenocarpic fruit development holds both theoretical and practical significance, making it a crucial area of study. This review examines how plant hormones and MADS-box transcription factors control parthenocarpic fruit formation. It delves into various aspects of plant hormones-including auxin, gibberellic acid, cytokinins, ethylene, and abscisic acid-ranging from external application to biosynthesis, metabolism, signaling pathways, and their interplay in influencing parthenocarpic fruit development. The review also explores the involvement of MADS family gene functions in these processes. Lastly, we highlight existing knowledge gaps and propose directions for future research on parthenocarpy.

Low-oxygen-induced root bending is altered by phytoglobin1 through mediation of ethylene response factors (ERFs) and auxin signaling

MAIN CONCLUSION

phytoglobin1 positively regulates root bending in hypoxic Arabidopsis roots through regulation of ethylene response factors and auxin transport. Hypoxia-induced root bending is known to be mediated by the redundant activity of the group VII ethylene response factors (ERFVII) RAP2.12 and HRE2, causing changes in polar auxin transport (PAT). Here, we show that phytoglobin1 (Pgb1), implicated in hypoxic adaptation through scavenging of nitric oxide (NO), can alter root direction under low oxygen. Hypoxia-induced bending is exaggerated in roots over-expressing Pgb1 and attenuated in those where the gene is suppressed. These effects were attributed to Pgb1 repressing both RAP2.12 and HRE2. Expression, immunological and genetic data place Pgb1 upstream of RAP2.12 and HRE2 in the regulation of root bending in oxygen-limiting environments. The attenuation of slanting in Pgb1-suppressing roots was associated with depletion of auxin activity at the root tip because of depression in PAT, while exaggeration of root bending in Pgb1-over-expressing roots with the retention of auxin activity. Changes in PIN2 distribution patterns, suggestive of redirection of auxin movement during hypoxia, might contribute to the differential root bending responses of the transgenic lines. In the end, Pgb1, by regulating NO levels, controls the expression of 2 ERFVIIs which, in a cascade, modulate PAT and, therefore, root bending.

Structure and Function of Auxin Transporters

Auxins, a group of central hormones in plant growth and development, are transported by a diverse range of transporters with distinct biochemical and structural properties. This review summarizes the current knowledge on all known auxin transporters with respect to their biochemical and biophysical properties and the methods used to characterize them. In particular, we focus on the recent advances that were made concerning the PIN-FORMED family of auxin exporters. Insights derived from solving their structures have improved our understanding of the auxin export process, and we discuss the current state of the art on PIN-mediated auxin transport, including the use of biophysical methods to examine their properties. Understanding the mechanisms of auxin transport is crucial for understanding plant growth and development, as well as for the development of more effective strategies for crop production and plant biotechnology.

Evolutionary assembly of the plant terrestrialization toolkit from protein domains

Land plants (embryophytes) came about in a momentous evolutionary singularity: plant terrestrialization. This event marks not only the conquest of land by plants but also the massive radiation of embryophytes into a diverse array of novel forms and functions. The unique suite of traits present in the earliest land plants is thought to have been ushered in by a burst in genomic novelty. Here, we asked the question of how these bursts were possible. For this, we explored: (i) the initial emergence and (ii) the reshuffling of domains to give rise to hallmark environmental response genes of land plants. We pinpoint that a quarter of the embryophytic genes for stress physiology are specific to the lineage, yet a significant portion of this novelty arises not de novo but from reshuffling and recombining of pre-existing domains. Our data suggest that novel combinations of old genomic substrate shaped the plant terrestrialization toolkit, including hallmark processes in signalling, biotic interactions and specialized metabolism.

PIN2-mediated self-organizing transient auxin flow contributes to auxin maxima at the tip of Arabidopsis cotyledons

Directional auxin transport and formation of auxin maxima are critical for embryogenesis, organogenesis, pattern formation, and growth coordination in plants, but the mechanisms underpinning the initiation and establishment of these auxin dynamics are not fully understood. Here we show that a self-initiating and -terminating transient auxin flow along the marginal cells (MCs) contributes to the formation of an auxin maximum at the tip of Arabidopsis cotyledon that globally coordinates the interdigitation of puzzle-shaped pavement cells in the cotyledon epidermis. Prior to the interdigitation, indole butyric acid (IBA) is converted to indole acetic acid (IAA) to induce PIN2 accumulation and polarization in the marginal cells, leading to auxin flow toward and accumulation at the cotyledon tip. When IAA levels at the cotyledon tip reaches a maximum, it activates pavement cell interdigitation as well as the accumulation of the IBA transporter TOB1 in MCs, which sequesters IBA to the vacuole and reduces IBA availability and IAA levels. The reduction of IAA levels results in PIN2 down-regulation and cessation of the auxin flow. Hence, our results elucidate a self-activating and self-terminating transient polar auxin transport system in cotyledons, contributing to the formation of localized auxin maxima that spatiotemporally coordinate pavement cell interdigitation.

GmHXK2 promotes the salt tolerance of soybean seedlings by mediating AsA synthesis, and auxin synthesis and distribution

BACKGROUND

Salt is an important factor that affects crop productivity. Plant hexokinases (HXKs) are key enzymes in the glycolytic pathway and sugar signaling transduction pathways of plants. In previous studies, we identified and confirmed the roles of GmHXK2 in salt tolerance.

RESULTS

In this study, we analyzed the tissue-specific expression of GmHXK2 at different growth stages throughout the plant's life cycle. The results showed that GmHXK2 was expressed significantly in all tissues at vegetative stages, including germination and seedling. However, no expression was detected in the pods, and there was little expression in flowers during the later mature period. Arabidopsis plants overexpressing the GmHXK2 (OE) had more lateral roots. The OE seedlings also produced higher levels of auxin and ascorbic acid (AsA). Additionally, the expression levels of genes PMM, YUC4/YUC6/YUC8, and PIN/LAX1,LAX3, which are involved respectively in the synthesis of AsA and auxin, as well as polar auxin transport, were upregulated in OE plants. This upregulation occurred specifically under exogenous glucose treatment. AtHKT1, AtSOS1, and AtNHX1 were up-regulated in OE plants under salt stress, suggesting that GmHXK2 may modulate salt tolerance by maintaining ion balance within the cells and alleviating damage caused by salt stress. Additionally, we further confirmed the interaction between GmHXK2 and the protein GmPMM through yeast two-hybridization and bimolecular fluorescence complementation assays, respectively.

CONCLUSION

The expression of GmHXK2 gene in plants is organ-specific and developmental stage specific. GmHXK2 not only regulates the synthesis of AsA and the synthesis and distribution of auxin, but also promotes root elongation and induces lateral root formation, potentially enhancing soil water absorption. This study reveals the crosstalk between sugar signaling and hormone signaling in plants, where GmHXK2 acts as a glucose sensor through its interaction with GmPMM, and sheds light on the molecular mechanism by which GmHXK2 gene is involved in salt tolerance in plants.

Genome-wide transcript expression analysis reveals major chickpea and lentil genes associated with plant branching

The search for elite cultivars with better architecture has been a demand by farmers of the chickpea and lentil crops, which aims to systematize their mechanized planting and harvesting on a large scale. Therefore, the identification of genes associated with the regulation of the branching and architecture of these plants has currently gained great importance. Herein, this work aimed to gain insight into transcriptomic changes of two contrasting chickpea and lentil cultivars in terms of branching pattern (little versus highly branched cultivars). In addition, we aimed to identify candidate genes involved in the regulation of shoot branching that could be used as future targets for molecular breeding. The axillary and apical buds of chickpea cultivars Blanco lechoso and FLIP07-318C, and lentil cultivars Castellana and Campisi, considered as little and highly branched, respectively, were harvested. A total of 1,624 and 2,512 transcripts were identified as differentially expressed among different tissues and contrasting cultivars of chickpea and lentil, respectively. Several gene categories were significantly modulated such as cell cycle, DNA transcription, energy metabolism, hormonal biosynthesis and signaling, proteolysis, and vegetative development between apical and axillary tissues and contrasting cultivars of chickpea and lentil. Based on differential expression and branching-associated biological function, ten chickpea genes and seven lentil genes were considered the main players involved in differentially regulating the plant branching between contrasting cultivars. These collective data putatively revealed the general mechanism and high-effect genes associated with the regulation of branching in chickpea and lentil, which are potential targets for manipulation through genome editing and transgenesis aiming to improve plant architecture.

Pin1-catalyzed conformational regulation after phosphorylation: A distinct checkpoint in cell signaling and drug discovery

Protein phosphorylation is one of the most common mechanisms regulating cellular signaling pathways, and many kinases and phosphatases are proven drug targets. Upon phosphorylation, protein functions can be further regulated by the distinct isomerase Pin1 through cis-trans isomerization. Numerous protein targets and many important roles have now been elucidated for Pin1. However, no tools are available to detect or target cis and trans conformation events in cells. The development of Pin1 inhibitors and stereo- and phospho-specific antibodies has revealed that cis and trans conformations have distinct and often opposing cellular functions. Aberrant conformational changes due to the dysregulation of Pin1 can drive pathogenesis but can be effectively targeted in age-related diseases, including cancers and neurodegenerative disorders. Here, we review advances in understanding the roles of Pin1 signaling in health and disease and highlight conformational regulation as a distinct signal transduction checkpoint in disease development and treatment.

Biomass ash as soil fertilizers: Supercharging biomass accumulation by shifting auxin distribution

Growing quantities of biomass ashes (phyto-ashs) are currently produced worldwide due to the increasing biomass consumption in energy applications. Utilization of phyto-ash in agriculture is environmentally friendly solution. However, mechanisms involving the coordination of carbon metabolism and distribution in plants and soil amendment are not well known. In the present study, tobacco plants were chemically-fertilized with or without 2‰ phyto-ash addition. The control had sole chemical fertilizer; for two phyto-ash treatments, the one (T1) received comparable levels of nitrogen, phophorus, and potassium from phyto-ash and fertilizers as the control and another (T2) had 2‰ of phyto-ash and the same rates of fertilizers as the control. Compared with the control, phyto-ash addition improved the soil pH from 5.94 to about 6.35; T2 treatment enhanced soil available potassium by 30% but no difference of other elements was recorded among three treatments. Importantly, bacterial (but not fungal) communities were significantly enriched by phyto-ash addition, with the rank of richness as: T2 > T1 > control. Consistent with amelioration of soil properties, phyto-ash promoted plant growth through enlarged leaf area and photosynthesis and induced outgrowth of lateral roots (LRs). Interestingly, increased auxin content was recorded in 2nd and 3rd leaves and roots under phyto-ash application, also with the rank level as T2 > T1 > control, paralleling with higher transcripts of auxin synthetic genes in the topmost leaf and stronger [3H]IAA activity under phyto-ash addition. Furthermore, exogenous application of analog exogenous auxin (NAA) restored leaf area, photosynthesis and LR outgrowth to the similar level as T2 treatment; conversely, application of auxin transport inhibitor (NPA) under T2 treatment retarded leaf and root development. We demonstrated that phyto-ash addition improved soil properties and thus facilitated carbon balance within plants and biomass accumulation in which shifting auxin distribution plays an important role.

Maternal nitric oxide homeostasis impacts female gametophyte development under optimal and stress conditions

In adverse environments, the number of fertilizable female gametophytes (FGs) in plants is reduced, leading to increased survival of the remaining offspring. How the maternal plant perceives internal growth cues and external stress conditions to alter FG development remains largely unknown. We report that homeostasis of the stress signaling molecule nitric oxide (NO) plays a key role in controlling FG development under both optimal and stress conditions. NO homeostasis is precisely regulated by S-nitrosoglutathione reductase (GSNOR). Prior to fertilization, GSNOR protein is exclusively accumulated in sporophytic tissues and indirectly controls FG development in Arabidopsis (Arabidopsis thaliana). In GSNOR null mutants, NO species accumulated in the degenerating sporophytic nucellus, and auxin efflux into the developing FG was restricted, which inhibited FG development, resulting in reduced fertility. Importantly, restoring GSNOR expression in maternal, but not gametophytic tissues, or increasing auxin efflux substrate significantly increased the proportion of normal FGs and fertility. Furthermore, GSNOR overexpression or added auxin efflux substrate increased fertility under drought and salt stress. These data indicate that NO homeostasis is critical to normal auxin transport and maternal control of FG development, which in turn determine seed yield. Understanding this aspect of fertility control could contribute to mediating yield loss under adverse conditions.

Transcriptome analysis of Citrus sinensis reveals potential responsive events triggered by Candidatus Liberibacter asiaticus

Citrus Huanglongbing (HLB), caused by Candidatus Liberibacter asiaticus (CLas), is a devastating immune-mediated disorder that has a detrimental effect on the citrus industry, with the distinguishing feature being an eruption of reactive oxygen species (ROS). This study explored the alterations in antioxidant enzyme activity, transcriptome, and RNA editing events of organelles in C. sinensis during CLas infection. Results indicated that there were fluctuations in the performance of antioxidant enzymes, such as ascorbate peroxidase (APX), catalase (CAT), glutathione reductase (GR), peroxidase (POD), and superoxide dismutase (SOD), in plants affected by HLB. Transcriptome analysis revealed 3604 genes with altered expression patterns between CLas-infected and healthy samples, including those associated with photosynthesis, biotic interactions, and phytohormones. Samples infected with CLas showed a decrease in the expression of most genes associated with photosynthesis and gibberellin metabolism. It was discovered that RNA editing frequency and the expression level of various genes in the chloroplast and mitochondrion genomes were affected by CLas infection. Our findings provide insights into the inhibition of photosynthesis, gibberellin metabolism, and antioxidant enzymes during CLas infection in C. sinensis.

Ectopic assembly of an auxin efflux control machinery shifts developmental trajectories

Polar auxin transport in the Arabidopsis (Arabidopsis thaliana) root tip maintains high auxin levels around the stem cell niche that gradually decrease in dividing cells but increase again once they transition toward differentiation. Protophloem differentiates earlier than other proximal tissues and employs a unique auxin "canalization" machinery that is thought to balance auxin efflux with retention. It consists of a proposed activator of PIN-FORMED (PIN) auxin efflux carriers, the cAMP-, cGMP- and Calcium-dependent (AGC) kinase PROTEIN KINASE ASSOCIATED WITH BRX (PAX); its inhibitor, BREVIS RADIX (BRX); and PHOSPHATIDYLINOSITOL-4-PHOSPHATE-5-KINASE (PIP5K) enzymes, which promote polar PAX and BRX localization. Because of a dynamic PAX-BRX-PIP5K interplay, the net cellular output of this machinery remains unclear. In this study, we deciphered the dosage-sensitive regulatory interactions among PAX, BRX, and PIP5K by their ectopic expression in developing xylem vessels. The data suggest that the dominant collective output of the PAX-BRX-PIP5K module is a localized reduction in PIN abundance. This requires PAX-stimulated clathrin-mediated PIN endocytosis upon site-specific phosphorylation, which distinguishes PAX from other AGC kinases. An ectopic assembly of the PAX-BRX-PIP5K module is sufficient to cause cellular auxin retention and affects root growth vigor by accelerating the trajectory of xylem vessel development. Our data thus provide direct evidence that local manipulation of auxin efflux alters the timing of cellular differentiation in the root.

The Arabidopsis katamari2 Mutant Exhibits a Hypersensitive Seedling Arrest Response at the Phase Transition from Heterotrophic to Autotrophic Growth

Young seedlings use nutrients stored in the seeds to grow and acquire photosynthetic potential. This process, called seedling establishment, involves a developmental phase transition from heterotrophic to autotrophic growth. Some membrane-trafficking mutants of Arabidopsis (Arabidopsis thaliana), such as the katamari2 (kam2) mutant, exhibit growth arrest during seedling development, with a portion of individuals failing to develop true leaves on sucrose-free solid medium. However, the reason for this seedling arrest is unclear. In this study, we show that seedling arrest is a temporal growth arrest response that occurs not only in kam2 but also in wild-type (WT) Arabidopsis; however, the threshold for this response is lower in kam2 than in the WT. A subset of the arrested kam2 seedlings resumed growth after transfer to fresh sucrose-free medium. Growth arrest in kam2 on sucrose-free medium was restored by increasing the gel concentration of the medium or covering the surface of the medium with a perforated plastic sheet. WT Arabidopsis seedlings were also arrested when the gel concentration of sucrose-free medium was reduced. RNA sequencing revealed that transcriptomic changes associated with the rate of seedling establishment were observed as early as 4 d after sowing. Our results suggest that the growth arrest of both kam2 and WT seedlings is an adaptive stress response and is not simply caused by the lack of a carbon source in the medium. This study provides a new perspective on an environmental stress response under unfavorable conditions during the phase transition from heterotrophic to autotrophic growth in Arabidopsis.

Auxin regulates bulbil initiation by mediating sucrose metabolism in Lilium lancifolium

Lily bulbils, which serve as advantageous axillary organs for vegetative propagation, have not been extensively studied in terms of the mechanism of bulbil initiation. The functions of auxin and sucrose metabolism have been implicated in axillary organ development, but their relationship in regulating bulbil initiation remains unclear. In this study, exogenous indole-3-acetic acid (IAA) treatment increased the endogenous auxin levels at leaf axils and significantly decreased bulbil number, whereas treatment with the auxin polar transport inhibitor N-1-naphthylphthalamic acid (NPA), which resulted in a low auxin concentration at leaf axils, stimulated bulbil initiation and increased bulbil number. A low level of auxin caused by NPA spraying or silencing of auxin biosynthesis genes YUCCA FLAVIN MONOOXYGENASE-LIKE 6 (LlYUC6) and TRYPTOPHAN AMINOTRANSFERASERELATED 1 (LlTAR1) facilitated sucrose metabolism by activating the expression of SUCROSE SYNTHASES 1 (LlSusy1) and CELL WALL INVERTASE 2 (LlCWIN2), resulting in enhanced bulbil initiation. Silencing LlSusy1 or LlCWIN2 hindered bulbil initiation. Moreover, the transcription factor BASIC HELIX-LOOP-HELIX 35 (LlbHLH35) directly bound the promoter of LlSusy1, but not the promoter of LlCWIN2, and activated its transcription in response to the auxin content, bridging the gap between auxin and sucrose metabolism. In conclusion, our results reveal that an LlbHLH35-LlSusy1 module mediates auxin-regulated sucrose metabolism during bulbil initiation.

Transient efflux inhibition improves plant regeneration by natural auxins

Plant genome editing and propagation are important tools in crop breeding and production. Both rely heavily on the development of efficient in vitro plant regeneration systems. Two prominent regeneration systems that are widely employed in crop production are somatic embryogenesis (SE) and de novo shoot regeneration. In many of the protocols for SE or shoot regeneration, explants are treated with the synthetic auxin analog 2,4-dichlorophenoxyacetic acid (2,4-D), since natural auxins, such as indole-3-acetic acid (IAA) or 4-chloroindole-3-acetic acid (4-Cl-IAA), are less effective or even fail to induce regeneration. Based on previous reports that 2,4-D, compared to endogenous auxins, is not effectively exported from plant cells, we investigated whether efflux inhibition of endogenous auxins could convert these auxins into efficient inducers of SE in Arabidopsis immature zygotic embryos (IZEs). We show that natural auxins and synthetic analogs thereof become efficient inducers of SE when their efflux is transiently inhibited by co-application of the auxin transport inhibitor naphthylphthalamic acid (NPA). Moreover, IZEs of auxin efflux mutants pin2 or abcb1 abcb19 show enhanced SE efficiency when treated with IAA or efflux-inhibited IAA, confirming that auxin efflux reduces the efficiency of Arabidopsis SE. Importantly, in contrast to the 2,4-D system, where only 50-60% of the embryos converted to seedlings, all SEs induced by transport-inhibited natural auxins converted to seedlings. Efflux-inhibited IAA, like 2,4-D, also efficiently induced SE from carrot suspension cells, whereas IAA alone could not, and efflux-inhibited 4-Cl-IAA significantly improved de novo shoot regeneration in Brassica napus. Our data provides new insights into the action of 2,4-D as an efficient inducer of plant regeneration but also shows that replacing this synthetic auxin for efflux-inhibited natural auxin significantly improves different types of plant regeneration, leading to a more synchronized and homogenous development of the regenerated plants.

A Streptomyces species from the ginseng rhizosphere exhibits biocontrol potential

Plants and their associated microbes live in complicated, changeable, and unpredictable environments. They usually interact with each other in many ways through multidimensional, multiscale, and multilevel coupling manners, leading to challenges in the coexistence of randomness and determinism or continuity and discreteness. Gaining a deeper understanding of these diverse interaction mechanisms can facilitate the development of data-mining theories and methods for complex systems, coupled modeling for systems with different spatiotemporal scales and functional properties, or even a universal theory of information and information interactions. In this study, we use a "closed-loop" model to present a plant-microbe interaction system and describe the probable functions of microbial natural products. Specifically, we report a rhizosphere species, Streptomyces ginsengnesis G7, which produces polyketide lydicamycins and other active metabolites. Interestingly, these distinct molecules have the potential to function both as antibiotics and as herbicides for crop protection. Detailed laboratory experiments conducted in Arabidopsis (Arabidopsis thaliana), combined with a comprehensive bioinformatics analysis, allow us to rationalize a model for this specific plant-microbe interaction process. Our work reveals the benefits of exploring otherwise neglected resources for the identification of potential functional molecules and provides a reference to better understand the system biology of complex ecosystems.

Hardware Development for Plant Cultivation Allowing In Situ Fluorescence Analysis of Calcium Fluxes in Plant Roots Under Microgravity and Ground-Control Conditions

Maintaining an optimal leaf and stem orientation to yield a maximum photosynthetic output is accomplished by terrestrial plants using sophisticated mechanisms to balance their orientation relative to the Earth's gravity vector and the direction of sunlight. Knowledge of the signal transduction chains of both gravity and light perception and how they influence each other is essential for understanding plant development on Earth and plant cultivation in space environments. However, in situ analyses of cellular signal transduction processes in weightlessness, such as live cell imaging of signaling molecules using confocal fluorescence microscopy, require an adapted experimental setup that meets the special requirements of a microgravity environment. In addition, investigations under prolonged microgravity conditions require extensive resources, are rarely accessible, and do not allow for immediate sample preparation for the actual microscopic analysis. Therefore, supply concepts are needed that ensure both the viability of the contained plants over a longer period of time and an unhindered microscopic analysis in microgravity. Here, we present a customized supply unit specifically designed to study gravity-induced Ca2+ mobilization in roots of Arabidopsis thaliana. The unit can be employed for ground-based experiments, in parabolic flights, on sounding rockets, and probably also aboard the International Space Station.