A novel putative auxin carrier family regulates intracellular auxin homeostasis in plants

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.

Molecular and genetic regulation of petal number variation

Floral forms with an increased number of petals, also known as double-flower phenotypes, have been selected and conserved in many domesticated plants, particularly in ornamentals, because of their great economic value. The molecular and genetic mechanisms that control this trait are therefore of great interest, not only for scientists, but also for breeders. In this review, we summarize current knowledge of the gene regulatory networks of flower initiation and development and known mutations that lead to variation of petal number in many species. In addition to the well-accepted miR172/AP2-like module, for which many questions remain unanswered, we also discuss other pathways in which mutations also lead to the formation of extra petals, such as those involved in meristem maintenance, hormone signalling, epigenetic regulation, and responses to environmental signals. We discuss how the concept of 'natural mutants' and recent advances in genomics and genome editing make it possible to explore the molecular mechanisms underlying double-flower formation, and how such knowledge could contribute to the future breeding and selection of this trait in more crops.

ZmPILS6 is an auxin efflux carrier required for maize root morphogenesis

Plant root systems play a pivotal role in plant physiology and exhibit diverse phenotypic traits. Understanding the genetic mechanisms governing root growth and development in model plants like maize is crucial for enhancing crop resilience to drought and nutrient limitations. This study focused on identifying and characterizing ZmPILS6, an annotated auxin efflux carrier, as a key regulator of various crown root traits in maize. ZmPILS6-modified roots displayed reduced network area and suppressed lateral root formation, which are desirable traits for the "steep, cheap, and deep" ideotype. The research revealed that ZmPILS6 localizes to the endoplasmic reticulum and plays a vital role in controlling the spatial distribution of indole-3-acetic acid (IAA or "auxin") in primary roots. The study also demonstrated that ZmPILS6 can actively efflux IAA when expressed in yeast. Furthermore, the loss of ZmPILS6 resulted in significant proteome remodeling in maize roots, particularly affecting hormone signaling pathways. To identify potential interacting partners of ZmPILS6, a weighted gene coexpression analysis was performed. Altogether, this research contributes to the growing knowledge of essential genetic determinants governing maize root morphogenesis, which is crucial for guiding agricultural improvement strategies.

Auxin efflux carrier PsPIN4 identified through genome-wide analysis as vital factor of petal abscission

PIN-FORMED (PIN) proteins, which function as efflux transporters, play many crucial roles in the polar transportation of auxin within plants. In this study, the exogenous applications of auxin IAA and TIBA were found to significantly prolong and shorten the florescence of tree peony (Paeonia suffruticosa Andr.) flowers. This finding suggests that auxin has some regulatory influence in petal senescence and abscission. Further analysis revealed a total of 8 PsPINs distributed across three chromosomes, which could be categorized into two classes based on phylogenetic and structural analysis. PsPIN1, PsPIN2a-b, and PsPIN4 were separated into the "long" PIN category, while PsPIN5, PsPIN6a-b, and PsPIN8 belonged to the "short" one. Additionally, the cis-regulatory elements of PsPIN promoters were associated with plant development, phytohormones, and environmental stress. These genes displayed tissue-specific expression, and phosphorylation sites were abundant throughout the protein family. Notably, PsPIN4 displayed distinct and elevated expression levels in roots, leaves, and flower organs. Expression patterns among the abscission zone (AZ) and adjacent areas during various flowering stages and IAA treatment indicate that PsPIN4 likely influences the initiation of peony petal abscission. The PsPIN4 protein was observed to be co-localized on both the plasma membrane and the cell nucleus. The ectopic expression of PsPIN4 reversed the premature flower organs abscission in the Atpin4 and significantly protracted florescence when introduced to Col Arabidopsis. Our findings established a strong basis for further investigation of PIN gene biological functions, particularly concerning intrinsic relationship between PIN-mediated auxin polar.

AtIAR1 is a Zn transporter that regulates auxin metabolism in Arabidopsis thaliana

Root growth in Arabidopsis is inhibited by exogenous auxin-amino acid conjugates, and mutants resistant to one such conjugate [indole-3-acetic acid (IAA)-Ala] map to a gene (AtIAR1) that is a member of a metal transporter family. Here, we test the hypothesis that AtIAR1 controls the hydrolysis of stored conjugated auxin to free auxin through zinc transport. AtIAR1 complements a yeast mutant sensitive to zinc, but not manganese- or iron-sensitive mutants, and the transporter is predicted to be localized to the endoplasmic reticulum/Golgi in plants. A previously identified Atiar1 mutant and a non-expressed T-DNA mutant both exhibit altered auxin metabolism, including decreased IAA-glucose conjugate levels in zinc-deficient conditions and insensitivity to the growth effect of exogenous IAA-Ala conjugates. At a high concentration of zinc, wild-type plants show a novel enhanced response to root growth inhibition by exogenous IAA-Ala which is disrupted in both Atiar1 mutants. Furthermore, both Atiar1 mutants show changes in auxin-related phenotypes, including lateral root density and hypocotyl length. The findings therefore suggest a role for AtIAR1 in controlling zinc release from the secretory system, where zinc homeostasis plays a key role in regulation of auxin metabolism and plant growth regulation.

Expression of auxin transporter genes in flax (Linum usitatissimum) fibers during gravity response

Gravitropism is an adaptive reaction of plants associated with the ability of various plant organs to be located and to grow in a certain direction relative to the gravity vector, while usually the asymmetric distribution of the phytohormone auxin is a necessary condition for the gravitropical bending of plant organs. Earlier, we described significant morphological changes in phloem fibers with a thickened cell wall located on different sides of the stem in the area of the gravitropic curvature. The present study is the first work devoted to the identification of genes encoding auxin transporters in cells at different stages of development and during gravity response. In this study, the flax genes encoding the AUX1/LAX, PIN-FORMED, PIN-LIKES, and ABCB auxin transporters were identified. A comparative analysis of the expression of these genes in flax phloem fibers at different stages of development revealed increased expression of some of these genes at the stage of intrusive growth (LusLAX2 (A, B), LuxPIN1-D, LusPILS7 (C, D)), at the early stage of tertiary cell wall formation (LusAUX1 (A, D), LusABCB1 (A, B), LusABCB15-A, LusPIN1 (A, B), LusPIN4-A, and LusPIN5-A), and at the late stage of tertiary cell wall development (LusLAX3 (A, B)). It was shown that in the course of gravitropism, the expression of many genes, including those responsible for the influx of auxin in cells (LusAUX1-D), in the studied families increased. Differential expression of auxin transporter genes was revealed during gravity response in fibers located on different sides of the stem (upper (PUL) and lower (OPP)). The difference was observed due to the expression of genes, the products of which are responsible for auxin intracellular transport (LusPILS3, LusPILS7-A) and its efflux (LusABCB15-B, LusABCB19-B). It was noted that the increased expression of PIN genes and ABCB genes was more typical of fibers on the opposite side. The results obtained allow us to make an assumption about the presence of differential auxin content in the fibers of different sides of gravistimulated flax plants, which may be determined by an uneven outflow of auxin. This study gives an idea of auxin carriers in flax and lays the foundation for further studies of their functions in the development of phloem fiber and in gravity response.

All-Year High IAA and ABA Contents in Rhizome Buds May Contribute to Natural Four-Season Shooting in Woody Bamboo Cephalostachyum pingbianense

To explore the regulation mechanism of endogenous phytohormones on rhizome bud germination in Cephalostachyum pingbianense, the contents of IAA, ABA, GA, and CTK in seven above- and under-ground bamboo structure components were determined using enzyme-linked immunosorbent assays (ELISA). The results showed that a higher content of IAA, GA, and CTK all year was found in above-ground components and dormant rhizome buds. Meanwhile, a higher ABA content in young shoots and a lower ABA content in the culm base and dormant rhizome buds were detected during the peak period of shooting. The amounts of emerging shoots and the grown bamboo culms were positively correlated with the content of IAA and the ratio of IAA/ABA and (IAA + CTK + GA)/ABA, while they were negatively correlated with the ratio of CTK/IAA in dormant rhizome buds. The all-year high contents of IAA (19-31 ng/g) and ABA (114-144 ng/g) in rhizome buds, as well as interactions among four hormones, may be the key physiological mechanisms to maintain rhizome bud germination throughout the year in C. pingbianense. As C. pingbianense is a special bamboo species of multi-season shoot sprouting, the above results may supplement scientific data for a comprehensive understanding of physiological mechanisms within the bamboo subfamily.

Organ-Specific Microsomes from Dark-Grown Hypocotyls of Arabidopsis thaliana

In this book chapter, we present a method for microsome isolation from the hypocotyl tissue of dark-grown Arabidopsis thaliana. Microsomes are heterogeneous, vesicle-like membranes, which are, not exclusively, derived but enriched with membranes of the endoplasmic reticulum (ER). Here, we describe the experimental setup, including sample preparation, homogenization, differential centrifugation steps, and quality control measures after microsome isolation.

Epigenetic modifications regulate cultivar-specific root development and metabolic adaptation to nitrogen availability in wheat

The breeding of crops with improved nitrogen use efficiency (NUE) is crucial for sustainable agriculture, but the involvement of epigenetic modifications remains unexplored. Here, we analyze the chromatin landscapes of two wheat cultivars (KN9204 and J411) that differ in NUE under varied nitrogen conditions. The expression of nitrogen metabolism genes is closely linked to variation in histone modification instead of differences in DNA sequence. Epigenetic modifications exhibit clear cultivar-specificity, which likely contributes to distinct agronomic traits. Additionally, low nitrogen (LN) induces H3K27ac and H3K27me3 to significantly enhance root growth in KN9204, while remarkably inducing NRT2 in J411. Evidence from histone deacetylase inhibitor treatment and transgenic plants with loss function of H3K27me3 methyltransferase shows that changes in epigenetic modifications could alter the strategy preference for root development or nitrogen uptake in response to LN. Here, we show the importance of epigenetic regulation in mediating cultivar-specific adaptation to LN in wheat.

Temperature regulation of auxin-related gene expression and its implications for plant growth

Twenty-five years ago, a seminal paper demonstrated that warm temperatures increase auxin levels to promote hypocotyl growth in Arabidopsis thaliana. Here we highlight recent advances in auxin-mediated thermomorphogenesis and identify unanswered questions. In the warmth, PHYTOCHROME INTERACTING FACTOR 4 (PIF4) and PIF7 bind the YUCCA8 gene promoter and, in concert with histone modifications, enhance its expression to increase auxin synthesis in the cotyledons. Once transported to the hypocotyl, auxin promotes cell elongation. The meta-analysis of expression of auxin-related genes in seedlings exposed to temperatures ranging from cold to hot shows complex patterns of response. Changes in auxin only partially account for these responses. The expression of many SMALL AUXIN UP RNA (SAUR) genes reaches a maximum in the warmth, decreasing towards both temperature extremes in correlation with the rate of hypocotyl growth. Warm temperatures enhance primary root growth, the response requires auxin, and the hormone levels increase in the root tip but the impacts on cell division and cell expansion are not clear. A deeper understanding of auxin-mediated temperature control of plant architecture is necessary to face the challenge of global warming.

Auxin transport at the endoplasmic reticulum: roles and structural similarity of PIN-FORMED and PIN-LIKES

Auxin is a crucial plant hormone that controls a multitude of developmental processes. The directional movement of auxin between cells is largely facilitated by canonical PIN-FORMED proteins in the plasma membrane. In contrast, non-canonical PIN-FORMED proteins and PIN-LIKES proteins appear to reside mainly in the endoplasmic reticulum. Despite recent progress in identifying the roles of the endoplasmic reticulum in cellular auxin responses, the transport dynamics of auxin at the endoplasmic reticulum are not well understood. PIN-LIKES are structurally related to PIN-FORMED proteins, and recently published structures of these transporters have provided new insights into PIN-FORMED proteins and PIN-LIKES function. In this review, we summarize current knowledge on PIN-FORMED proteins and PIN-LIKES in intracellular auxin transport. We discuss the physiological properties of the endoplasmic reticulum and the consequences for transport processes across the ER membrane. Finally, we highlight the emerging role of the endoplasmic reticulum in the dynamics of cellular auxin signalling and its impact on plant development.

Transcriptomic and physiological comparison of Shatangju (Citrus reticulata) and its late-maturing mutant provides insights into auxin regulation of citrus fruit maturation

Previous studies have shown that abscisic acid (ABA) and ethylene are involved in pulp maturation and peel coloration in the nonclimacteric citrus fruits. There are also signs indicating that other plant hormones may play some roles in citrus fruit ripening. In this study, we compared profiles of genome-wide gene expression and changes in hormones and peel pigments between fruits of Shatangju mandarin (Citrus reticulata Blanco, designated WT) and its natural mutant, Yuenongwanju (designated MT). The MT fruit matures ~2 months later than the WT fruit. Significant differences in fruit diameter, total soluble solids, titratable acid content, chlorophylls and carotenoids were detected between the fruits of the two genotypes at the sampled time points. Genome-wide transcriptome profiling showed that many genes involved in auxin and ABA metabolism and/or signaling pathways were differentially expressed between the MT and the WT fruits. Importantly, the expression of CrYUCCA8 was significantly lower and the expression of CrNCED5 was significantly higher in WT than in MT fruits at 230 and 250 DPA, respectively. In addition, the indole-3-acetic acid (IAA) level in the MT fruit was significantly higher than that in the WT counterpart, whereas a significantly lower level of ABA was detected in the mutant. Treatment of the WT fruit with exogenous IAA significantly delayed fruit maturation. Our results provide experimental evidence supporting the notion that auxin is a negative regulator of fruit maturation in citrus.

Wheat type one protein phosphatase promotes salt and osmotic stress tolerance in arabidopsis via auxin-mediated remodelling of the root system

The control of optimal root growth and plant stress responses depends largely on a variety of phytohormones among which auxin and brassinosteroids (BRs) are the most influential. We have previously reported that the durum wheat type 1 protein phosphatase TdPP1 participates in the control of root growth by modulating BR signaling. In this study, we pursue our understanding of how TdPP1 fulfills this regulatory function on root growth by evaluating the physiological and molecular responses of Arabidopsis TdPP1 over-expressing lines to abiotic stresses. Our results showed that when exposed to 300 mM Mannitol or 100 mM NaCl, the seedlings of TdPP1 over-expressors exhibit modified root architecture with higher lateral root density, and longer root hairs concomitant with a lower inhibition of the primary root growth. These lines also exhibit faster gravitropic response and a decrease in primary root growth inhibition when exposed to high concentrations of exogenous IAA. On another hand, a cross between TdPP1 overexpressors and DR5:GUS marker line was performed to monitor auxin accumulation in roots. Remarkably, the TdPP1 overexpression resulted in an enhanced auxin gradient under salt stress with a higher accumulation in primary and lateral root tips. Moreover, TdPP1 transgenics exhibit a significant induction of a subset of auxin-responsive genes under salt stress conditions. Therefore, our results reveal a role of PP1 in enhancing auxin signaling to help shape greater root plasticity thus improving plant stress resilience.

Auxin- and pH-induced guttation in Phycomyces sporangiophores: relation between guttation and diminished elongation growth

Guttation, the formation of exudation water, is widespread among plants and fungi, yet the underlying mechanisms remain largely unknown. We describe the conditions for inducing guttation in sporangiophores of the mucoracean fungus, Phycomyces blakesleeanus. Cultivation on peptone-enriched potato dextrose agar elicits vigorous guttation mainly below the apical growing zone, while sporangiophores raised on a glucose-mineral medium manifest only moderate guttation. Mycelia do not guttate irrespective of the employed media. The topology of guttation droplets allows identifying the non-growing part of the sporangiophore as a guttation zone, which responds to humidity and medium composition in ways that become relevant for turgor homeostasis and thus the sensor physiology of the growing zone. Apparently, the entire sporangiophore, rather than exclusively the growing zone, participates in signal reception and integration to generate a common growth output. Exogenous auxin applied to the growing zones elicits two correlated responses: (i) formation of guttation droplets in the growing and transition zones below the sporangium and (ii) a diminution of the growth rate. In sporangiophore populations, guttation-induction by exogenous control buffer occurs at low frequencies; the bias for guttation increases with increasing auxin concentration. Synthetic auxins and the transport inhibitor NPA suppress guttation completely, but leave growth rates largely unaffected. Mutants C2 carA and C148 carA madC display higher sensitivities for auxin-induced guttation compared to wild type. A working model for guttation includes aquaporins and mechanosensitive ion channels that we identified in Phycomyces by sequence domain searches.

Structural and biochemical characterization of the key components of an auxin degradation operon from the rhizosphere bacterium Variovorax

Plant-associated bacteria play important regulatory roles in modulating plant hormone auxin levels, affecting the growth and yields of crops. A conserved auxin degradation (iad) operon was recently identified in the Variovorax genomes, which is responsible for root growth inhibition (RGI) reversion, promoting rhizosphere colonization and root growth. However, the molecular mechanism underlying auxin degradation by Variovorax remains unclear. Here, we systematically screened Variovorax iad operon products and identified 2 proteins, IadK2 and IadD, that directly associate with auxin indole-3-acetic acid (IAA). Further biochemical and structural studies revealed that IadK2 is a highly IAA-specific ATP-binding cassette (ABC) transporter solute-binding protein (SBP), likely involved in IAA uptake. IadD interacts with IadE to form a functional Rieske non-heme dioxygenase, which works in concert with a FMN-type reductase encoded by gene iadC to transform IAA into the biologically inactive 2-oxindole-3-acetic acid (oxIAA), representing a new bacterial pathway for IAA inactivation/degradation. Importantly, incorporation of a minimum set of iadC/D/E genes could enable IAA transformation by Escherichia coli, suggesting a promising strategy for repurposing the iad operon for IAA regulation. Together, our study identifies the key components and underlying mechanisms involved in IAA transformation by Variovorax and brings new insights into the bacterial turnover of plant hormones, which would provide the basis for potential applications in rhizosphere optimization and ecological agriculture.

Integrating stay-green and PIN-FORMED genes: PIN-FORMED genes as potential targets for designing climate-resilient cereal ideotypes

Plant architecture modification (e.g. short-stature crops) is one of the key outcomes of modern crop breeding for high-yielding crop varieties. In cereals, delayed senescence, or stay-green, is an important trait that enables post-anthesis drought stress adaptation. Stay-green crops can prolong photosynthetic capacity during grain-filling period under post-anthesis drought stress, which is essential to ensure grain yield is not impacted under drought stress conditions. Although various stay-green quantitative trait loci have been identified in cereals, the underlying molecular mechanisms regulating stay-green remain elusive. Recent advances in various gene-editing technologies have provided avenues to fast-track crop improvement, such as the breeding of climate-resilient crops in the face of climate change. We present in this viewpoint the focus on using sorghum as the model cereal crop, to study PIN-FORMED (PIN) auxin efflux carriers as means to modulate plant architecture, and the potential to employ it as an adaptive strategy to address the environmental challenges posed by climate uncertainties.

Nitrate, Auxin and Cytokinin-A Trio to Tango

Nitrogen is an important macronutrient required for plant growth and development, thus directly impacting agricultural productivity. In recent years, numerous studies have shown that nitrogen-driven growth depends on pathways that control nitrate/nitrogen homeostasis and hormonal networks that act both locally and systemically to coordinate growth and development of plant organs. In this review, we will focus on recent advances in understanding the role of the plant hormones auxin and cytokinin and their crosstalk in nitrate-regulated growth and discuss the significance of novel findings and possible missing links.

Characterization of the PIN Auxin Efflux Carrier Gene Family and Its Expression during Zygotic Embryogenesis in Persea americana

Auxins are responsible for a large part of the plant development process. To exert their action, they must move throughout the plant and from cell to cell, which is why plants have developed complex transport systems for indole-3-acetic acid (IAA). These transporters involve proteins that transport IAA into cells, transporters that move IAA to or from different organelles, mainly the endoplasmic reticulum, and transporters that move IAA out of the cell. This research determined that Persea americana has 12 PIN transporters in its genome. The twelve transporters are expressed during different stages of development in P. americana zygotic embryos. Using different bioinformatics tools, we determined the type of transporter of each of the P. americana PIN proteins and their structure and possible location in the cell. We also predict the potential phosphorylation sites for each of the twelve-PIN proteins. The data show the presence of highly conserved sites for phosphorylation and those sites involved in the interaction with the IAA.

The NIN-LIKE PROTEIN 7 transcription factor modulates auxin pathways to regulate root cap development in Arabidopsis

The root cap is a small tissue located at the tip of the root with critical functions for root growth. Present in nearly all vascular plants, the root cap protects the root meristem, influences soil penetration, and perceives and transmits environmental signals that are critical for root branching patterns. To perform these functions, the root cap must remain relatively stable in size and must integrate endogenous developmental pathways with environmental signals, yet the mechanism is not clear. We previously showed that low pH conditions altered root cap development, and these changes are mediated by the NIN LIKE PROTEIN 7 (NLP7) transcription factor, a master regulator of nitrate signaling. Here we show that in Arabidopsis NLP7 integrates nitrate signaling with auxin pathways to regulate root cap development. We found that low nitrate conditions promote aberrant release of root cap cells. Nitrate deficiency impacts auxin pathways in the last layer of the root cap, and this is mediated in part by NLP7. Mutations in NLP7 abolish the auxin minimum in the last layer of the root cap and alter root cap expression of the auxin carriers PIN-LIKES 3 (PILS3) and PIN-FORMED 7 (PIN7) as well as transcription factors that regulate PIN expression. Together, our data reveal NLP7 as a link between endogenous auxin pathways and nitrate signaling in the root cap.

The birth of a giant: evolutionary insights into the origin of auxin responses in plants

The plant signaling molecule auxin is present in multiple kingdoms of life. Since its discovery, a century of research has been focused on its action as a phytohormone. In land plants, auxin regulates growth and development through transcriptional and non-transcriptional programs. Some of the molecular mechanisms underlying these responses are well understood, mainly in Arabidopsis. Recently, the availability of genomic and transcriptomic data of green lineages, together with phylogenetic inference, has provided the basis to reconstruct the evolutionary history of some components involved in auxin biology. In this review, we follow the evolutionary trajectory that allowed auxin to become the "giant" of plant biology by focusing on bryophytes and streptophyte algae. We consider auxin biosynthesis, transport, physiological, and molecular responses, as well as evidence supporting the role of auxin as a chemical messenger for communication within ecosystems. Finally, we emphasize that functional validation of predicted orthologs will shed light on the conserved properties of auxin biology among streptophytes.

Cell-specific clock-controlled gene expression program regulates rhythmic fiber cell growth in cotton

BACKGROUND

The epidermis of cotton ovule produces fibers, the most important natural cellulose source for the global textile industry. However, the molecular mechanism of fiber cell growth is still poorly understood.

RESULTS

Here, we develop an optimized protoplasting method, and integrate single-cell RNA sequencing (scRNA-seq) and single-cell ATAC sequencing (scATAC-seq) to systematically characterize the cells of the outer integument of ovules from wild type and fuzzless/lintless (fl) cotton (Gossypium hirsutum). By jointly analyzing the scRNA-seq data from wildtype and fl, we identify five cell populations including the fiber cell type and construct the development trajectory for fiber lineage cells. Interestingly, by time-course diurnal transcriptomic analysis, we demonstrate that the primary growth of fiber cells is a highly regulated circadian rhythmic process. Moreover, we identify a small peptide GhRALF1 that circadian rhythmically controls fiber growth possibly through oscillating auxin signaling and proton pump activity in the plasma membrane. Combining with scATAC-seq, we further identify two cardinal cis-regulatory elements (CREs, TCP motif, and TCP-like motif) which are bound by the trans factors GhTCP14s to modulate the circadian rhythmic metabolism of mitochondria and protein translation through regulating approximately one third of genes that are highly expressed in fiber cells.

CONCLUSIONS

We uncover a fiber-specific circadian clock-controlled gene expression program in regulating fiber growth. This study unprecedentedly reveals a new route to improve fiber traits by engineering the circadian clock of fiber cells.

Auxin regulation on crop: from mechanisms to opportunities in soybean breeding

Breeding crop varieties with high yield and ideal plant architecture is a desirable goal of agricultural science. The success of "Green Revolution" in cereal crops provides opportunities to incorporate phytohormones in crop breeding. Auxin is a critical phytohormone to determine nearly all the aspects of plant development. Despite the current knowledge regarding auxin biosynthesis, auxin transport and auxin signaling have been well characterized in model Arabidopsis (Arabidopsis thaliana) plants, how auxin regulates crop architecture is far from being understood, and the introduction of auxin biology in crop breeding stays in the theoretical stage. Here, we give an overview on molecular mechanisms of auxin biology in Arabidopsis, and mainly summarize auxin contributions for crop plant development. Furthermore, we propose potential opportunities to integrate auxin biology in soybean (Glycine max) breeding.

Genome-wide identification and characterization of PIN-FORMED (PIN) and PIN-LIKES (PILS) gene family reveals their role in adventitious root development in tea nodal cutting (Camellia Sinensis)

Auxin affects all aspects of plant growth and development, including morphogenesis and adaptive responses. Auxin transmembrane transport is promoted by PIN formation (PIN) and a structurally similar PIN-like (PILS) gene family, which jointly controls the directional transport of the auxin between plant cells, and the accumulation of intracellular auxin. At present, there is no study investigating the roles of CslPIN and CslPILS gene family in root development in the tea plant (Camellia sinensis). In this study, 8 CslPIN and 10 CslPILS genes were identified in the tea plant, and their evolutionary relationships, physical and chemical properties, conserved motifs, cis-acting elements, chromosome location, collinearity, and expression characteristics were analyzed. The mechanism of CslPIN and CslPILS in the formation of tea adventitious roots (ARs) was studied by the AR induction system. Through functional verification, the regulation of CslPIN3 gene on root growth and development of tea plant was studied by over-expression of CslPIN3 in Arabidopsis thaliana and in situ hybridization in Camellia sinensis. The results confirmed CslPIN3 was involved in the regulation of root growth and development as well as auxin accumulation. This study provides a better insight into the regulatory mechanism of CslPIN and CslPILS gene family on the formation of AR in tea plant.

Plant Growth Promotion, Phytohormone Production and Genomics of the Rhizosphere-Associated Microalga, Micractinium rhizosphaerae sp. nov

Microalgae are important members of the soil and plant microbiomes, playing key roles in the maintenance of soil and plant health as well as in the promotion of plant growth. However, not much is understood regarding the potential of different microalgae strains in augmenting plant growth, or the mechanisms involved in such activities. In this work, the functional and genomic characterization of strain NFX-FRZ, a eukaryotic microalga belonging to the Micractinium genus that was isolated from the rhizosphere of a plant growing in a natural environment in Portugal, is presented and analyzed. The results obtained demonstrate that strain NFX-FRZ (i) belongs to a novel species, termed Micractinium rhizosphaerae sp. nov.; (ii) can effectively bind to tomato plant tissues and promote its growth; (iii) can synthesize a wide range of plant growth-promoting compounds, including phytohormones such as indole-3-acetic acid, salicylic acid, jasmonic acid and abscisic acid; and (iv) contains multiple genes involved in phytohormone biosynthesis and signaling. This study provides new insights regarding the relevance of eukaryotic microalgae as plant growth-promoting agents and helps to build a foundation for future studies regarding the origin and evolution of phytohormone biosynthesis and signaling, as well as other plant colonization and plant growth-promoting mechanisms in soil/plant-associated Micractinium.

Genome-Wide Identification of PIN and PILS Gene Families in Areca catechu and the Potential Role of AcPIN6 in Lateral Brace Root Formation

PIN-FORMED (PIN) and PIN-LIKES (PILS) are two families of auxin transporters that control the directional cell-to-cell transport and intracellular accumulation of auxin, thereby influencing plant growth and development. Most knowledge of PINs and PILSs was obtained from the dicot model plant Arabidopsis thaliana. Here, we focus on the distribution and expression of the PIN and PILS gene families in areca palm (Areca catechu), a monocot tree. The whole genomic dataset of areca palm was used to identify twelve AcPINs and eight AcPILSs, and a phylogenetic tree was constructed of PINS and PILS together with several other palm species, including the date palm (Phoenix dactylifera), oil palm (Elaeis guineensis), and coconut (Cocos nucifera). We further analyzed the expression patterns of AcPIN and AcPILS in areca palm, and found that AcPIN6 displayed an extremely high transcriptional abundance in the brace roots and was extremely stimulated in the lateral root primordium. This result implies that AcPIN6 plays an important role in the growth and formation of brace roots, especially in lateral root initiation. We also overexpressed AcPIN6 and AcPIN6-eGFP in Arabidopsis, and the results revealed that the PIN6 localized on the plasma membrane and affected auxin-related phenomena. Taken together, we analyzed the evolutionary relationships of PINs and PILSs in palm species, and the roles of PIN6 in areca palm root formation. The results will improve the understanding of root system construction in large palm trees.

Plant-growth promotion by proteobacterial strains depends on the availability of phosphorus and iron in Arabidopsis thaliana plants

Phosphorus (as phosphate, Pi) and iron (Fe) are critical nutrients in plants that are often poorly available in the soil and can be microbially affected. This work aimed to evaluate how plant-rhizobacteria interaction changes due to different Pi or Fe nutritional scenarios and to study the underlying molecular mechanisms of the microbial modulation of these nutrients in plants. Thus, three proteobacteria (Paraburkholderia phytofirmans PsJN, Azospirillum brasilense Sp7, and Pseudomonas putida KT2440) were used to inoculate Arabidopsis seeds. Additionally, the seeds were exposed to a nutritional factor with the following levels for each nutrient: sufficient (control) or low concentrations of a highly soluble source or sufficient concentrations of a low solubility source. Then, the effects of the combinatorial factors were assessed in plant growth, nutrition, and genetic regulation. Interestingly, some bacterial effects in plants depended on the nutrient source (e.g., increased aerial zones induced by the strains), and others (e.g., decreased primary roots induced by Sp7 or KT2440) occurred regardless of the nutritional treatment. In the short-term, PsJN had detrimental effects on plant growth in the presence of the low-solubility Fe compound, but this was not observed in later stages of plant development. A thorough regulation of the phosphorus content was detected in plants independent of the nutritional treatment. Nevertheless, inoculation with KT2440 increased P content by 29% Pi-deficiency exposed plants. Conversely, the inoculation tended to decrease the Fe content in plants, suggesting a competition for this nutrient in the rhizosphere. The P-source also affected the effects of the PsJN strain in a double mutant of the phosphate starvation response (PSR). Furthermore, depending on the nutrient source, PsJN and Sp7 strains differentially regulated PSR and IAA- associated genes, indicating a role of these pathways in the observed differential phenotypical responses. In the case of iron, PsJN and SP7 regulated iron uptake-related genes regardless of the iron source, which may explain the lower Fe content in inoculated plants. Overall, the plant responses to these proteobacteria were not only influenced by the nutrient concentrations but also by their availabilities, the elapsed time of the interaction, and the specific identities of the beneficial bacteria. Graphical AbstractThe effects of the different nutritional and inoculation treatments are indicated for plant growth parameters (A), gene regulation (B) and phosphorus and iron content (C). Figures created with BioRender.com with an academic license.

Volatile organic compounds from Lysinibacillus macroides regulating the seedling growth of Arabidopsis thaliana

Volatile organic compounds (VOCs) have the characteristics of long distance propagation, low concentration, perception, and indirect contact between organisms. In this experiment, Lysinibacillus macroides Xi9 was isolated from cassava residue, and the VOCs produced by this strain were analyzed by the SPME-GC-MS method, mainly including alcohols, esters, and alkanes. By inoculation of L. macroides Xi9, VOCs can promote the growth and change the root-system architecture of Arabidopsis seedlings. The results showed that the number of lateral roots, root density, and fresh weight of Arabidopsis seedlings were significantly higher (p ≤ 0.01), and the number of roots hair was also increased after exposure to strain Xi9. Compared with the control group, the transcriptome analysis of Arabidopsis seedlings treated with strain Xi9 for 5 days revealed a total of 508 genes differentially expressed (p < 0.05). After Gene Ontology enrichment analysis, it was found that genes encoding nitrate transport and assimilation, and the lateral root-related gene ANR1 were up-regulated. The content of NO3 - and amino acid in Arabidopsis seedlings were significantly higher from control group (p ≤ 0.01). Plant cell wall-related EXPA family genes and pectin lyase gene were up-regulated, resulting cell elongation of leaf. SAUR41 and up-regulation of its subfamily members, as well as the down-regulation of auxin efflux carrier protein PILS5 and auxin response factor 20 (ARF20) led to the accumulation of auxin. These results indicated that VOCs of strain Xi9 promote Arabidopsis seedlings growth and development by promoting nitrogen uptake, regulating auxin synthesis, and improving cell wall modification.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-022-01268-3.

Nodule INception-independent epidermal events lead to bacterial entry during nodule development in peanut (Arachis hypogaea)

Legumes can host nitrogen-fixing rhizobia inside root nodules. In model legumes, rhizobia enter via infection threads (ITs) and develop nodules in which the infection zone contains a mixture of infected and uninfected cells. Peanut (Arachis hypogaea) diversified from model legumes c. 50-55 million years ago. Rhizobia enter through 'cracks' to form nodules in peanut roots where cells of the infection zone are uniformly infected. Phylogenomic studies have indicated symbiosis as a labile trait in peanut. These atypical features prompted us to investigate the molecular mechanism of peanut nodule development. Combining cell biology, genetics and genomic tools, we visualized the status of hormonal signaling in peanut nodule primordia. Moreover, we dissected the signaling modules of Nodule INception (NIN), a master regulator of both epidermal infection and cortical organogenesis. Cytokinin signaling operates in a broad zone, from the epidermis to the pericycle inside nodule primordia, while auxin signaling is narrower and focused. Nodule INception is involved in nodule organogenesis, but not in crack entry. Nodulation Pectate Lyase, which remodels cell walls during IT formation, is not required. By contrast, Nodule enhanced Glycosyl Hydrolases (AhNGHs) are recruited for cell wall modification during crack entry. While hormonal regulation is conserved, the function of the NIN signaling modules is diversified in peanut.

Characterization and expression profiling of PIN auxin efflux transporters reveal their role in developmental and abiotic stress conditions in rice

The auxin efflux transporter proteins called PINs ferry auxin from its source to sinks in particular directions depending on their polar localizations in the plasma membrane, thus facilitating the development of the entire plant architecture. The rice genome has 12 PIN genes distributed over eight chromosomes. To study their roles in plant development, abiotic stress responsiveness, and shaping an auxin-dependent root architecture, a genome-wide analysis was carried out. Based on phylogeny, cellular localization, and hydrophilic loop domain size, the PINs were categorized into canonical and noncanonical PINs. PINs were found expressed in all of the organs of plants that emphasized their indispensable role throughout the plant's life cycle. We discovered that PIN5C and PIN9 were upregulated during salt and drought stress. We also found that regardless of its cellular level, auxin functioned as a molecular switch to turn on auxin biosynthesis genes. On the contrary, although PIN expression was upregulated upon initial treatment with auxin, prolonged auxin treatment not only led to their downregulation but also led to the development of auxin-dependent altered root formation in rice. Our study paves the way for developing stress-tolerant rice and plants with a desirable root architecture by genetic engineering.

Regeneration pattern and genome-wide transcription profile of rhizome axillary buds after perennial rice harvest

Perennial rice is a new type of rice that allows the harvest of rice for multiple years without growing new seedlings annually. This technology represents a green and sustainable agricultural production mode with many advantages for balancing agricultural ecology and food security. However, the differences in regeneration patterns between perennial and annual rice and the gene regulatory pathways of the apical dominance in axillary bud growth after harvest in perennial rice are still unclear. In this study, perennial rice (PR23) and annual rice (Chugeng28) were used to investigate axillary bud growth patterns before and after apical spike removal. After elimination of apical dominance at different development stages, perennial rice rhizome axillary buds at the compression nodes germinated more rapidly than others and developed into new seedlings. The axillary buds at the high-position nodes in annual rice grew faster than those at other nodes. Furthermore, the global gene expression patterns of PR23 rhizome buds at compression nodes grown for 1, 3, 4, and 5 days after apical spike removal were analyzed by transcriptome sequencing. Compared with the control buds without apical removal, 264, 3,484, 2,095, and 3,398 genes were up-regulated, and 674, 3,484, 1,594, and 1,824 genes were down-regulated in the buds grown for 1, 3, 4, and 5 days after apical spike removal, respectively. Trend analysis of the expressed genes at different time points was performed and co-expression network was constructed to identify key genes in rhizome axillary bud regrowth. The results showed that 85 hub genes involved in 12 co-regulatory networks were mainly enriched in the light system, photosynthesis-antenna protein, plant hormone signal transduction, ABC transporter and metabolic pathways, which suggested that hormone and photosynthetic signals might play important roles in the regulation of rhizome axillary bud regeneration in perennial rice. Overall, this study clarified the differences in the regeneration patterns of axillary buds between perennial and annual rice and provided insight into the complex regulatory networks during the regeneration of rhizome axillary buds in perennial rice.

Plant nitrogen availability and crosstalk with phytohormones signallings and their biotechnology breeding application in crops

Nitrogen (N), one of the most important nutrients, limits plant growth and crop yields in sustainable agriculture system, in which phytohormones are known to play essential roles in N availability. Hence, it is not surprising that massive studies about the crosstalk between N and phytohormones have been constantly emerging. In this review, with the intellectual landscape of N and phytohormones crosstalk provided by the bibliometric analysis, we trace the research story of best-known crosstalk between N and various phytohormones over the last 20 years. Then, we discuss how N regulates various phytohormones biosynthesis and transport in plants. In reverse, we also summarize how phytohormones signallings modulate root system architecture (RSA) in response to N availability. Besides, we expand to outline how phytohormones signallings regulate uptake, transport, and assimilation of N in plants. Further, we conclude advanced biotechnology strategies, explain their application, and provide potential phytohormones-regulated N use efficiency (NUE) targets in crops. Collectively, this review provides not only a better understanding on the recent progress of crosstalk between N and phytohormones, but also targeted strategies for improvement of NUE to increase crop yields in future biotechnology breeding of crops.

Characterization of the genetic and regulatory networks associated with sugar and acid metabolism in apples via an integrated strategy

Although sugars and acids have a substantial influence on the taste of apple fruits, the genetic and regulatory networks underlying their metabolism in fruit remain insufficiently determined. To fully decipher the genetic basis of the accumulation of sugars and acids in apple fruits, we adopted an integrated strategy that included time-course RNA-seq, QTL mapping, and whole-genome sequencing to examine two typical cultivars ('HanFu' and 'Huahong') characterized by distinctive flavors. Whole-genome sequencing revealed substantial genetic variation between the two cultivars, thereby providing an indication of the genetic basis of the distinct phenotypes. Constructed co-expression networks yielded information regarding the intra-relationships among the accumulation of different types of metabolites, and also revealed key regulatory nodes associated with the accumulation of sugars and acids, including the genes MdEF2, MdPILS5, and MdGUN8. Additionally, on the basis of QTL mapping using a high-density genetic map, we identified a series of QTLs and functional genes underlying vital traits, including sugar and acid contents. Collectively, our methodology and observations will provide an important reference for further studies focusing on the flavor of apples.

Rhizomania: Hide and Seek of Polymyxa betae and the Beet Necrotic Yellow Vein Virus with Beta vulgaris

The molecular interactions between Polymyxa betae, the protist vector of sugar beet viruses, beet necrotic yellow vein virus (BNYVV), the causal agent of rhizomania, and Beta vulgaris have not been extensively studied. Here, the transmission of BNYVV to sugar beet by P. betae zoospores was optimized using genetically characterized organisms. Molecular interactions of aviruliferous and viruliferous protist infection on sugar beet were highlighted by transcriptomic analysis. P. betae alone induced limited gene expression changes in sugar beet, as a biotrophic asymptomatic parasite. Most differentially expressed plant genes were down-regulated and included resistance gene analogs and cell wall peroxidases. Several enzymes involved in stress regulation, such as the glutathione-S-transferases, were significantly induced. With BNYVV, the first stages of the P. betae life cycle on sugar beet were accelerated with a faster increase of relative protist DNA level and an earlier appearance of sporangia and sporosori in plants roots. A clear activation of plant defenses and the modulation of genes involved in plant cell wall metabolism were observed. The P. betae transcriptome in the presence of BNYVV revealed induction of genes possibly involved in the switch to the survival stage. The interactions were different depending on the presence or absence of the virus. P. betae alone alleviates plant defense response, playing hide-and-seek with sugar beet and allowing for their mutual development. Conversely, BNYVV manipulates plant defense and promotes the rapid invasion of plant roots by P. betae. This accelerated colonization is accompanied by the development of thick-walled resting spores, supporting the virus survival. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Identification and functional analysis of PIN family genes in Gossypium barbadense

Background

PIN proteins are an important class of auxin polar transport proteins that play an important regulatory role in plant growth and development. However, their characteristics and functions have not been identified in Gossypium barbadense.

Methods

PIN family genes were identified in the cotton species G. barbadense, Gossypium hirsutum, Gossypium raimondii, and Gossypium arboreum, and detailed bioinformatics analyses were conducted to explore the roles of these genes in G. barbadense using transcriptome data and quantitative reverse-transcription polymerase chain reaction (qRT-PCR) technology. Functional verification of the genes was performed using virus-induced gene silencing (VIGS) technology.

Results

A total of 138 PIN family genes were identified in the four cotton species; the genes were divided into seven subgroups. GbPIN gene family members were widely distributed on 20 different chromosomes, and most had repeated duplication events. Transcriptome analysis showed that some genes had differential expression patterns in different stages of fiber development. According to 'PimaS-7' and '5917' transcript component association analysis, the transcription of five genes was directly related to endogenous auxin content in cotton fibers. qRT-PCR analysis showed that the GbPIN7 gene was routinely expressed during fiber development, and there were significant differences among materials. Transient silencing of the GbPIN7 gene by VIGS led to significantly higher cotton plant growth rates and significantly lower endogenous auxin content in leaves and stems. This study provides comprehensive analyses of the roles of PIN family genes in G. barbadense and their expression during cotton fiber development. Our results will form a basis for further PIN auxin transporter research.

Genetic and molecular pathways controlling rice inflorescence architecture

Rice inflorescence is one of the major organs in determining grain yield. The genetic and molecular regulation on rice inflorescence architecture has been well investigated over the past years. In the present review, we described genes regulating rice inflorescence architecture based on their roles in meristem activity maintenance, meristem identity conversion and branch elongation. We also introduced the emerging regulatory pathways of phytohormones involved in rice inflorescence development. These studies show the intricacies and challenges of manipulating inflorescence architecture for rice yield improvement.

Histidine kinase inhibitors impair shoot regeneration in Arabidopsis thaliana via cytokinin signaling and SAM patterning determinants

Reversible protein phosphorylation is a post-translational modification involved in virtually all plant processes, as it mediates protein activity and signal transduction. Here, we probe dynamic protein phosphorylation during de novo shoot organogenesis in Arabidopsis thaliana. We find that application of three kinase inhibitors in various time intervals has different effects on root explants. Short exposures to the putative histidine (His) kinase inhibitor TCSA during the initial days on shoot induction medium (SIM) are detrimental for regeneration in seven natural accessions. Investigation of cytokinin signaling mutants, as well as reporter lines for hormone responses and shoot markers, suggests that TCSA impedes cytokinin signal transduction via AHK3, AHK4, AHP3, and AHP5. A mass spectrometry-based phosphoproteome analysis further reveals profound deregulation of Ser/Thr/Tyr phosphoproteins regulating protein modification, transcription, vesicle trafficking, organ morphogenesis, and cation transport. Among TCSA-responsive factors are prior candidates with a role in shoot apical meristem patterning, such as AGO1, BAM1, PLL5, FIP37, TOP1ALPHA, and RBR1, as well as proteins involved in polar auxin transport (e.g., PIN1) and brassinosteroid signaling (e.g., BIN2). Putative novel regeneration determinants regulated by TCSA include RD2, AT1G52780, PVA11, and AVT1C, while NAIP2, OPS, ARR1, QKY, and aquaporins exhibit differential phospholevels on control SIM. LC-MS/MS data are available via ProteomeXchange with identifier PXD030754.

Formulating Zwitterionic, Responsive Polymers for Designing Smart Soils

The design of new remediation strategies and materials for treating saline-alkaline soils is of fundamental and practical importantance for many applications. Conventional soil remediation strategies mainly focus on the development of fertilizers or additives for water, nutrient, and heavy metal managements in soils, but they often overlook a soil sensing function for early detection of salinization/alkalization levels toward optimal and timely soil remediation. Here, new smart soils, structurally consisting of the upper signal soil and the bottom hygroscopic bed and chemically including zwitterionic, thermo-responsive poly(NIPAM-co-VPES) and poly(NIPAM-co-SBAA) aerogels in each soil layer are formulated. Upon salinization, the resultant smart soils exhibit multiple superior capacities for reducing the soil salinity and alkalinity through ion exchange, controlling the water cycling, modulating the degradation of pyridine-base ligands into water-soluble, nitrogenous salts-rich ingredients for soil fertility, and real-time monitoring salinized soils via pH-induced allochroic color changes. Further studies of plant growth in smart soils with or without salinization treatments confirm a synergy effect of soil remediation and soil sensing on facilitating the growth of plants and increasing the saline-alkaline tolerance of plants. The esign concept of smart soils can be further expanded for soil remediation and assessment.

PIN and PILS family genes analyses in Chrysanthemum seticuspe reveal their potential functions in flower bud development and drought stress

Auxin affects almost all plant growth and developmental processes. The PIN-FORMED (PIN) and PIN-LIKES (PILS) family genes determine the direction and distribution gradient of auxin flow by polar localization on the cell membrane. However, there are no systematic studies on PIN and PILS family genes in chrysanthemum. Here, 18 PIN and 13 PILS genes were identified in Chrysanthemum seticuspe. The evolutionary relationships, physicochemical properties, conserved motifs, cis-acting elements, chromosome localization, collinearity, and expression characteristics of these genes were analyzed. CsPIN10a, CsPIN10b, and CsPIN10c are unique PIN genes in C. seticuspe. Expression pattern analysis showed that these genes had different tissue specificities, and the expression levels of CsPIN8, CsPINS1, CsPILS6, and CsPILS10 were linearly related to the developmental period of the flower buds. In situ hybridization assay showed that CsPIN1a, CsPIN1b, and CsPILS8 were expressed in floret primordia and petal tips, and CsPIN1a was specifically expressed in the middle of the bract primordia, which might regulate lateral expansion of the bracts. CsPIN and CsPILS family genes are also involved in drought stress responses. This study provides theoretical support for the cultivation of new varieties with attractive flower forms and high drought tolerance.

OsSPL14 acts upstream of OsPIN1b and PILS6b to modulate axillary bud outgrowth by fine-tuning auxin transport in rice

As a multigenic trait, rice tillering can optimize plant architecture for the maximum agronomic yield. SQUAMOSA PROMOTER BINDING PROTEIN-LIKE14 (OsSPL14) has been demonstrated to be necessary and sufficient to inhibit rice branching, but the underlying mechanism remains largely unclear. Here, we demonstrated that OsSPL14, which is cleaved by miR529 and miR156, inhibits tillering by fine-tuning auxin transport in rice. RNA interference of OsSPL14 or miR529 and miR156 overexpression significantly increased the tiller number, whereas OsSPL14 overexpression decreased the tiller number. Histological analysis revealed that the OsSPL14-overexpressing line had normal initiation of axillary buds but inhibited outgrowth of tillers. Moreover, OsSPL14 was found to be responsive to indole-acetic acid and 1-naphthylphthalamic acid, and RNA interference of OsSPL14 reduced polar auxin transport and increased 1-naphthylphthalamic acid sensitivity of rice plants. Further analysis revealed that OsSPL14 directly binds to the promoter of PIN-FORMED 1b (OsPIN1b) and PIN-LIKE6b (PILS6b) to regulate their expression positively. OsPIN1b and PILS6b were highly expressed in axillary buds and proved involved in bud outgrowth. Loss of function of OsPIN1b or PILS6b increased the tiller number of rice. Taken together, our findings suggested that OsSPL14 could control axillary bud outgrowth and tiller number by activating the expression of OsPIN1b and PILS6b to fine-tune auxin transport in rice.

Red and Blue Light Affect the Formation of Adventitious Roots of Tea Cuttings (Camellia sinensis) by Regulating Hormone Synthesis and Signal Transduction Pathways of Mature Leaves

Light is an important environmental factor which affects plant growth, through changes of intensity and quality. In this study, monochromatic white (control), red (660 nm), and blue (430 nm) light-emitting diodes (LEDs) were used to treat tea short cuttings. The results showed the most adventitious roots in blue light treated tea cuttings, but the lowest roots in that treated by red light. In order to explore the molecular mechanism of light quality affecting adventitious root formation, we performed full-length transcriptome and metabolome analyses of mature leaves under three light qualities, and then conducted weighted gene co-expression network analysis (WGCNA). Phytohormone analysis showed that Indole-3-carboxylic acid (ICA), Abscisic acid (ABA), ABA-glucosyl ester (ABA-GE), trans-Zeatin (tZ), and Jasmonic acid (JA) contents in mature leaves under blue light were significantly higher than those under white and red light. A crosstalk regulatory network comprising 23 co-expression modules was successfully constructed. Among them, the "MEblue" module which had a highly positive correlation with ICA (R = 0.92, P = 4e-04). KEGG analysis showed that related genes were significantly enriched in the "Plant hormone signal transduction (ko04075)" pathway. YUC (a flavin-containing monooxygenase), AUX1, AUX/IAA, and ARF were identified as hub genes, and gene expression analysis showed that the expression levels of these hub genes under blue light were higher than those under white and red light. In addition, we also identified 6 auxin transport-related genes, including PIN1, PIN3, PIN4, PILS5, PILS6, and PILS7. Except PILS5, all of these genes showed the highest expression level under blue light. In conclusion, this study elucidated the molecular mechanism of light quality regulating adventitious root formation of tea short cutting through WGCNA analysis, which provided an innovation for "rapid seedling" of tea plants.

PILS proteins provide a homeostatic feedback on auxin signaling output

Multiple internal and external signals modulate the metabolism, intercellular transport and signaling of the phytohormone auxin. Considering this complexity, it remains largely unknown how plant cells monitor and ensure the homeostasis of auxin responses. PIN-LIKES (PILS) intracellular auxin transport facilitators at the endoplasmic reticulum are suitable candidates to buffer cellular auxin responses because they limit nuclear abundance and signaling of auxin. We used forward genetics to identify gloomy and shiny pils (gasp) mutants that define the PILS6 protein abundance in a post-translational manner. Here, we show that GASP1 encodes an uncharacterized RING/U-box superfamily protein that impacts on auxin signaling output. The low auxin signaling in gasp1 mutants correlates with reduced abundance of PILS5 and PILS6 proteins. Mechanistically, we show that high and low auxin conditions increase and reduce PILS6 protein levels, respectively. Accordingly, non-optimum auxin concentrations are buffered by alterations in PILS6 abundance, consequently leading to homeostatic auxin output regulation. We envision that this feedback mechanism provides robustness to auxin-dependent plant development.

Summary: Auxin exerts a posttranslational feedback regulation on the PILS proteins, contributing to cellular auxin homeostasis and providing robustness to plant growth and development.

Fourteen Stations of Auxin

Auxin has always been at the forefront of research in plant physiology and development. Since the earliest contemplations by Julius von Sachs and Charles Darwin, more than a century-long struggle has been waged to understand its function. This largely reflects the failures, successes, and inevitable progress in the entire field of plant signaling and development. Here I present 14 stations on our long and sometimes mystical journey to understand auxin. These highlights were selected to give a flavor of the field and to show the scope and limits of our current knowledge. A special focus is put on features that make auxin unique among phytohormones, such as its dynamic, directional transport network, which integrates external and internal signals, including self-organizing feedback. Accented are persistent mysteries and controversies. The unexpected discoveries related to rapid auxin responses and growth regulation recently disturbed our contentment regarding understanding of the auxin signaling mechanism. These new revelations, along with advances in technology, usher us into a new, exciting era in auxin research.

Developmental regulation of leaf venation patterns: monocot versus eudicots and the role of auxin

Organisation and patterning of the vascular network in land plants varies in different taxonomic, developmental and environmental contexts. In leaves, the degree of vascular strand connectivity influences both light and CO₂ harvesting capabilities as well as hydraulic capacity. As such, developmental mechanisms that regulate leaf venation patterning have a direct impact on physiological performance. Development of the leaf venation network requires the specification of procambial cells within the ground meristem of the primordium and subsequent proliferation and differentiation of the procambial lineage to form vascular strands. An understanding of how diverse venation patterns are manifest therefore requires mechanistic insight into how procambium is dynamically specified in a growing leaf. A role for auxin in this process was identified many years ago, but questions remain. In this review we first provide an overview of the diverse venation patterns that exist in land plants, providing an evolutionary perspective. We then focus on the developmental regulation of leaf venation patterns in angiosperms, comparing patterning in eudicots and monocots, and the role of auxin in each case. Although common themes emerge, we conclude that the developmental mechanisms elucidated in eudicots are unlikely to fully explain how parallel venation patterns in monocot leaves are elaborated.

Exploring the Contribution of Autophagy to the Excess-Sucrose Response in Arabidopsis thaliana

Autophagy is an essential intracellular eukaryotic recycling mechanism, functioning in, among others, carbon starvation. Surprisingly, although autophagy-deficient plants (atg mutants) are hypersensitive to carbon starvation, metabolic analysis revealed that they accumulate sugars under such conditions. In plants, sugars serve as both an energy source and as signaling molecules, affecting many developmental processes, including root and shoot formation. We thus set out to understand the interplay between autophagy and sucrose excess, comparing wild-type and atg mutant seedlings. The presented work showed that autophagy contributes to primary root elongation arrest under conditions of exogenous sucrose and glucose excess but not during fructose or mannitol treatment. Minor or no alterations in starch and primary metabolites were observed between atg mutants and wild-type plants, indicating that the sucrose response relates to its signaling and not its metabolic role. Extensive proteomic analysis of roots performed to further understand the mechanism found an accumulation of proteins essential for ROS reduction and auxin maintenance, which are necessary for root elongation, in atg plants under sucrose excess. The analysis also suggested mitochondrial and peroxisomal involvement in the autophagy-mediated sucrose response. This research increases our knowledge of the complex interplay between autophagy and sugar signaling in plants.

Identification of Key Gene Networks and Deciphering Transcriptional Regulators Associated With Peanut Embryo Abortion Mediated by Calcium Deficiency

Peanut embryo development is easily affected by a variety of nutrient elements in the soil, especially the calcium level. Peanut produces abortive embryos in calcium-deficient soil, but underlying mechanism remains unclear. Thus, identifying key transcriptional regulators and their associated regulatory networks promises to contribute to a better understanding of this process. In this study, cellular biology and gene expression analyses were performed to investigate peanut embryo development with the aim to discern the global architecture of gene regulatory networks underlying peanut embryo abortion under calcium deficiency conditions. The endomembrane systems tended to disintegrate, impairing cell growth and starch, protein and lipid body accumulation, resulting in aborted seeds. RNA-seq analysis showed that the gene expression profile in peanut embryos was significantly changed under calcium deficiency. Further analysis indicated that multiple signal pathways were involved in the peanut embryo abortion. Differential expressed genes (DEGs) related to cytoplasmic free Ca²⁺ were significantly altered. DEGs in plant hormone signaling pathways tended to be associated with increased IAA and ethylene but with decreased ABA, gibberellin, cytokinin, and brassinosteroid levels. Certain vital genes, including apoptosis-inducing factor, WRKYs and ethylene-responsive transcription factors, were up-regulated, while key regulators of embryo development, such as TCP4, WRI1, FUS3, ABI3, and GLK1 were down-regulated. Weighted gene co-expression network analysis (WGCNA) identified 16 significant modules associated with the plant hormone signaling, MAPK signaling, ubiquitin mediated proteolysis, reserve substance biosynthesis and metabolism pathways to decipher regulatory network. The most significant module was darkolivegreen2 and FUS3 (AH06G23930) had the highest connectivity among this module. Importantly, key transcription factors involved in embryogenesis or ovule development including TCP4, GLK1, ABI3, bHLH115, MYC2, etc., were also present in this module and down regulated under calcium deficiency. This study presents the first global view of the gene regulatory network involved in peanut embryo abortion under calcium deficiency conditions and lays foundation for improving peanut tolerances to calcium deficiency by a targeted manipulation of molecular breeding.

MAG2 and MAL Regulate Vesicle Trafficking and Auxin Homeostasis With Functional Redundancy

Auxin is a central phytohormone and controls almost all aspects of plant development and stress response. Auxin homeostasis is coordinately regulated by biosynthesis, catabolism, transport, conjugation, and deposition. Endoplasmic reticulum (ER)-localized MAIGO2 (MAG2) complex mediates tethering of arriving vesicles to the ER membrane, and it is crucial for ER export trafficking. Despite important regulatory roles of MAG2 in vesicle trafficking, the mag2 mutant had mild developmental abnormalities. MAG2 has one homolog protein, MAG2-Like (MAL), and the mal-1 mutant also had slight developmental phenotypes. In order to investigate MAG2 and MAL regulatory function in plant development, we generated the mag2-1 mal-1 double mutant. As expected, the double mutant exhibited serious developmental defects and more alteration in stress response compared with single mutants and wild type. Proteomic analysis revealed that signaling, metabolism, and stress response in mag2-1 mal-1 were affected, especially membrane trafficking and auxin biosynthesis, signaling, and transport. Biochemical and cell biological analysis indicated that the mag2-1 mal-1 double mutant had more serious defects in vesicle transport than the mag2-1 and mal-1 single mutants. The auxin distribution and abundance of auxin transporters were altered significantly in the mag2-1 and mal-1 single mutants and mag2-1 mal-1 double mutant. Our findings suggest that MAG2 and MAL regulate plant development and auxin homeostasis by controlling membrane trafficking, with functional redundancy.

Bradyrhizobium japonicum IRAT FA3 Alters Arabidopsis thaliana Root Architecture via Regulation of Auxin Efflux Transporters PIN2, PIN3, PIN7, and ABCB19

Beneficial rhizobacteria can stimulate changes in plant root development. Although root system growth is mediated by multiple factors, the regulated distribution of the phytohormone auxin within root tissues plays a principal role. Auxin transport facilitators help to generate the auxin gradients and maxima that determine root structure. Here, we show that the plant-growth-promoting rhizobacterial strain Bradyrhizobium japonicum IRAT FA3 influences specific auxin efflux transporters to alter Arabidopsis thaliana root morphology. Gene expression profiling of host transcripts in control and B. japonicum-inoculated roots of the wild-type A. thaliana accession Col-0 confirmed upregulation of PIN2, PIN3, PIN7, and ABCB19 with B. japonicum and identified genes potentially contributing to a diverse array of auxin-related responses. Cocultivation of the bacterium with loss-of-function auxin efflux transport mutants revealed that B. japonicum requires PIN3, PIN7, and ABCB19 to increase lateral root development and utilizes PIN2 to reduce primary root length. Accelerated lateral root primordia production due to B. japonicum was not observed in single pin3, pin7, or abcb19 mutants, suggesting independent roles for PIN3, PIN7, and ABCB19 during the plant-microbe interaction. Our work demonstrates B. japonicum's influence over host transcriptional reprogramming during plant interaction with this beneficial microbe and the subsequent alterations to root system architecture.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Auxin's origin: do PILS hold the key?

Auxin is a key regulator of many developmental processes in land plants and plays a strikingly similar role in the phylogenetically distant brown seaweeds. Emerging evidence shows that the PIN and PIN-like (PILS) auxin transporter families have preceded the evolution of the canonical auxin response pathway. A wide conservation of PILS-mediated auxin transport, together with reports of auxin function in unicellular algae, would suggest that auxin function preceded the advent of multicellularity. We find that PIN and PILS transporters form two eukaryotic subfamilies within a larger bacterial family. We argue that future functional characterisation of algal PIN and PILS transporters can shed light on a common origin of an auxin function followed by independent co-option in a multicellular context.