The Ubiquitin E3 Ligase PRU1 Regulates WRKY6 Degradation to Modulate Phosphate Homeostasis in Response to Low-Pi Stress in Arabidopsis

AtPHR1 and SlPHL1 positively regulate phosphorus remobilization in response to phosphate starvation by directly facilitating the transcription of genes encoding S-like ribonucleases in Arabidopsis and tomato, respectively

Phosphorus (P) is a crucial element for plant growth and development, with inorganic phosphate (Pi) being the primary form absorbed by plant roots. However, soil often experiences Pi deficiency, leading to early leaf senescence and hastening the P re-mobilization from senescent leaves to young tissues. The PHOSPHATE STARVATION RESPONSE (PHR) proteins are widely acknowledged as pivotal regulatory factors in response to low Pi, and they may be involved in the regulation of leaf senescence and P remobilization triggered by Pi deprivation. Nevertheless, the mechanisms underlying the regulation of these processes require further elucidation. In this study, it was observed that overexpression of AtPHR1 accelerates leaf senescence, facilitates P transfer, and upregulates the expression of S-like RNase-encoding genes such as RNS1, RNS2, and RNS5. Subsequent investigations utilizing yeast one-hybrid (Y1H), electrophoretic mobility shift assay (EMSA), and transient transcription expression assay (TTEA) revealed direct binding of AtPHR1 to the P1BS motifs within the promoters of these genes, thereby activating their transcription. Similarly, the overexpression of tomato PHR protein SlPHL1 also increased the transcript levels of the S-like RNase-encoding genes including LE and LX. Moreover, experiments using Y1H, EMSA, and TTEA confirmed that SlPHL1 directly binds to the promoters of these two genes through P1BS motifs and subsequently activates their transcription. Additionally, introducing SlPHL1 into Arabidopsis led to an enhanced P turnover and RNA degradation, along with an increase in the expression of RNS1 and RNS2. Further investigations revealed that similar to AtPHR1, SlPHL1 is capable of directly activating the transcription of RNS1 and RNS2. Taken together, these findings suggest that AtPHR1 and SlPHL1 play a pivotal role in facilitating P remobilization by directly stimulating the transcription of S-like RNase-encoding genes. This mechanism appears to be conserved across Arabidopsis and tomato, highlighting the importance of PHRs in optimizing plant P utilization.

Phosphorus acquisition, translocation, and redistribution in maize

Phosphorus (P) is an essential nutrient for crop growth, making it important for maintaining food security as the global population continues to increase. Plants acquire P primarily via the uptake of inorganic phosphate (Pi) in soil through their roots. Pi, which is usually sequestered in soils, is not easily absorbed by plants and represses plant growth. Plants have developed a series of mechanisms to cope with P deficiency. Moreover, P fertilizer applications are critical for maximizing crop yield. Maize is a major cereal crop cultivated worldwide. Increasing its P-use efficiency is important for optimizing maize production. Over the past two decades, considerable progresses have been achieved in studies aimed at adapting maize varieties to changes in environmental P supply. Here, we present an overview of the morphological, physiological, and molecular mechanisms involved in P acquisition, translocation, and redistribution in maize and combine the advances in Arabidopsis and rice, to better elucidate the progress of P nutrition. Additionally, we summarize the correlation between P and abiotic stress responses. Clarifying the mechanisms relevant to improving P absorption and use in maize can guide future research on sustainable agriculture.

WRKY transcription factors: Hubs for regulating plant growth and stress responses

As sessile organisms, plants must directly face various stressors. Therefore, plants have evolved a powerful stress resistance system and can adjust their growth and development strategies appropriately in different stressful environments to adapt to complex and ever-changing conditions. Nevertheless, prioritizing defensive responses can hinder growth; this is a crucial factor for plant survival but is detrimental to crop production. As such, comprehending the impact of adverse environments on plant growth is not only a fundamental scientific inquiry but also imperative for the agricultural industry and for food security. The traditional view that plant growth is hindered during defense due to resource allocation trade-offs is challenged by evidence that plants exhibit both robust growth and defensive capabilities through human intervention. These findings suggest that the growth‒defense trade-off is not only dictated by resource limitations but also influenced by intricate transcriptional regulatory mechanisms. Hence, it is imperative to conduct thorough investigations on the central genes that govern plant resistance and growth in unfavorable environments. Recent studies have consistently highlighted the importance of WRKY transcription factors in orchestrating stress responses and plant-specific growth and development, underscoring the pivotal role of WRKYs in modulating plant growth under stressful conditions. Here, we review recent advances in understanding the dual roles of WRKYs in the regulation of plant stress resistance and growth across diverse stress environments. This information will be crucial for elucidating the intricate interplay between plant stress response and growth and may aid in identifying gene loci that could be utilized in future breeding programs to develop crops with enhanced stress resistance and productivity.

COP9 SIGNALOSOME SUBUNIT 5A facilitates POLYAMINE OXIDASE 5 degradation to regulate strawberry plant growth and fruit ripening

Polyamines (PAs), such as putrescine, spermidine, and spermine, are essential for plant growth and development. However, the post-translational regulation of PA metabolism remains unknown. Here, we report the COP9 SIGNALOSOME SUBUNIT 5A (FvCSN5A) mediates the degradation of the POLYAMINE OXIDASE 5 (FvPAO5), which catalyzes the conversion of spermidine/spermine to produce H2O2 in strawberry (Fragaria vesca). FvCSN5A is localized in the cytoplasm and nucleus, is ubiquitously expressed in strawberry plants, and is rapidly induced during fruit ripening. FvCSN5A RNA interference (RNAi) transgenic strawberry lines exhibit pleiotropic effects on plant development, fertility, and fruit ripening due to altered PA and H2O2 homeostasis, similar to FvPAO5 transgenic overexpression lines. Moreover, FvCSN5A interacts with FvPAO5 in vitro and in vivo, and the ubiquitination and degradation of FvPAO5 are impaired in FvCSN5A RNAi lines. Additionally, FvCSN5A interacts with cullin 1 (FvCUL1), a core component of the E3 ubiquitin-protein ligase complex. Transient genetic analysis in cultivated strawberry (Fragaria × ananassa) fruits showed that inhibiting FaPAO5 expression could partially rescue the ripening phenotype of FaCSN5A RNAi fruits. Taken together, our results suggest that the CSN5A-CUL1-PAO5 signaling pathway responsible for PA and H2O2 homeostasis is crucial for strawberry vegetative and reproductive growth in particular fruit ripening. Our findings present a promising strategy for improving crop yield and quality.

MdZFP7 integrates JA and GA signals via interaction with MdJAZ2 and MdRGL3a in regulating anthocyanin biosynthesis and undergoes degradation by the E3 ubiquitin ligase MdBRG3

Jasmonic acid (JA) and gibberellin (GA) coordinate many aspects of plant growth and development, including anthocyanin biosynthesis. However, the crossover points of JA and GA signals and the pathways through which they interact to regulate anthocyanin biosynthesis are poorly understood. Here, we investigated the molecular mechanism by which the zinc finger protein (ZFP) transcription factor Malus domestica ZFP7 (MdZFP7) regulates anthocyanin biosynthesis by integrating JA and GA signals at the transcriptional and post-translational levels. MdZFP7 is a positive regulator of anthocyanin biosynthesis, which fulfills its role by directly activating the expression of MdMYB1 and enhancing the transcriptional activation of MdWRKY6 on the target genes MdDFR and MdUF3GT. MdZFP7 integrates JA and GA signals by interacting with the JA repressor apple JASMONATE ZIM-DOMAIN2 (MdJAZ2) and the GA repressor apple REPRESSOR-of-ga1-3-like 3a (MdRGL3a). MdJAZ2 weakens the transcriptional activation of MdMYB1 by MdZFP7 and disrupts the MdZFP7-MdWRKY6 interaction, thereby reducing the anthocyanin biosynthesis promoted by MdZFP7. MdRGL3a contributes to the stimulation of anthocyanin biosynthesis by MdZFP7 by sequestering MdJAZ2 from the MdJAZ2-MdZFP7 complex. The E3 ubiquitin ligase apple BOI-related E3 ubiquitin-protein ligase 3 (MdBRG3), which is antagonistically regulated by JA and GA, targets the ubiquitination degradation of MdZFP7. The MdBRG3-MdZFP7 module moves the crosstalk of JA and GA signals from the realm of transcriptional regulation and into the protein post-translational modification. In conclusion, this study not only elucidates the node-role of MdZFP7 in the integration of JA and GA signals, but also describes the transcriptional and post-translational regulatory network of anthocyanin biosynthesis with MdZFP7 as the hub.

Decoding Plant-Pathogen Interactions: A Comprehensive Exploration of Effector-Plant Transcription Factor Dynamics

In the coevolutionary process between plant pathogens and hosts, pathogen effectors, primarily proteinaceous, engage in interactions with host proteins, such as plant transcription factors (TFs), during the infection process. This review delves into the intricate interplay between TFs and effectors, a key aspect in the prolonged and complex battle between plants and pathogens. Effectors strategically manipulate TFs using diverse tactics. These include modulating activity of TFs, influencing their incorporation into multimeric complexes, directly changing TF expression levels, promoting their degradation via the ubiquitin-proteasome system, and inducing their subcellular relocalization. The review systematically presents documented interactions, elucidating key mechanisms and their profound impact on host-pathogen dynamics. It emphasises the central role of TFs in plant defence and investigates the convergent evolution of effectors targeting TFs. By providing this overview, we offer valuable insights into this dynamic interaction landscape and suggest potential directions for future research.

Genome-Wide Identification and Expression Analysis of the Alfalfa (Medicago sativa L.) U-Box Gene Family in Response to Abiotic Stresses

E3 ubiquitin ligases known as plant U-box (PUB) proteins regulate a variety of aspects of plant growth, development, and stress response. However, the functions and characteristics of the PUB gene family in alfalfa remain unclear. This work involved a genome-wide examination of the alfalfa U-box E3 ubiquitin ligase gene. In total, 210 members were identified and divided into five categories according to their homology with the members of the U-box gene family in Arabidopsis thaliana. The phylogenetic analysis, conserved motifs, chromosomal localization, promoters, and regulatory networks of this gene were investigated. Chromosomal localization and covariance analyses indicated that the MsPUB genes expanded MsPUB gene family members through gene duplication events during evolution. MsPUB genes may be involved in the light response, phytohormone response, growth, and development of several biological activities, according to cis-acting element analysis of promoters. In addition, transcriptome analysis and expression analysis by qRT-PCR indicated that most MsPUB genes were significantly upregulated under cold stress, drought stress, and salt stress treatments. Among them, MsPUBS106 and MsPUBS185 were significantly and positively correlated with cold resistance in alfalfa. MsPUBS110, MsPUBS067, MsPUBS111 and MsPUB155 were comprehensively involved in drought stress, low temperature, and salt stress resistance. All things considered, these discoveries offer fresh perspectives on the composition, development, and roles of the PUB gene family in alfalfa. They also provide theoretical guidance for further investigations into the mechanisms regulating the development, evolution, and stress tolerance of MsPUB.

Evolutionary Conserved and Divergent Responses to Copper Zinc Superoxide Dismutase Inhibition in Plants

After an initial evolution in a reducing environment, life got successively challenged by reactive oxygen species (ROS), especially during the great oxidation event (GOE) that followed the development of photosynthesis. Therefore, ROS are deeply intertwined into the physiological, morphological and transcriptional responses of most present-day organisms. Copper-zinc superoxide dismutases (CuZnSODs) evolved during the GOE and are present in charophytes and extant land plants, but nearly absent from chlorophytes. The chemical inhibitor of CuZnSOD, lung cancer screen 1 (LCS-1), could greatly facilitate the study of SODs in diverse plants. Here, we determined the impact of chemical inhibition of plant CuZnSOD activity, on plant growth, transcription and metabolism. We followed a comparative approach by using different plant species, including Marchantia Polymorpha and Physcomitrium patens, representing bryophytes, the sister lineage to vascular plants, and Arabidopsis thaliana. We show that LCS-1 causes oxidative stress in plants and that the inhibition of CuZnSODs provoked a similar core response that mainly impacted glutathione homoeostasis in all plant species analysed. That said, Physcomitrium and Arabidopsis, which contain multiple CuZnSOD isoforms showed a more complex and exacerbated response. In addition, an untargeted metabolomics approach revealed a specific metabolic signature for each plant species. Our comparative analysis exposes a conserved core response at the physiological and transcriptional level towards LCS-1, while the metabolic response largely varies. These differences correlate with the number and localization of the CuZnSOD isoforms present in each species.

Early exposure to phosphorus starvation induces genetically determined responses in Sorghum bicolor roots

KEY MESSAGE

We identified novel physiological and genetic responses to phosphorus starvation in sorghum diversity lines that augment current knowledge of breeding for climate-smart crops in Europe. Phosphorus (P) deficiency and finite P reserves for fertilizer production pose a threat to future global crop production. Understanding root system architecture (RSA) plasticity is central to breeding for P-efficient crops. Sorghum is regarded as a P-efficient and climate-smart crop with strong adaptability to different climatic regions of the world. Here we investigated early genetic responses of sorghum RSA to P deficiency in order to identified genotypes with interesting root phenotypes and responses under low P. A diverse set of sorghum lines (n = 285) was genotyped using DarTSeq generating 12,472 quality genome wide single-nucleotide polymorphisms. Root phenotyping was conducted in a paper-based hydroponic rhizotron system under controlled greenhouse conditions with low and optimal P nutrition, using 16 RSA traits to describe genetic and phenotypic variability at two time points. Genotypic and phenotypic P-response variations were observed for multiple root traits at 21 and 42 days after germination with high broad sense heritability (0.38-0.76). The classification of traits revealed four distinct sorghum RSA types, with genotypes clustering separately under both low and optimal P conditions, suggesting genetic control of root responses to P availability. Association studies identified quantitative trait loci in chromosomes Sb02, Sb03, Sb04, Sb06 and Sb09 linked with genes potentially involved in P transport and stress responses. The genetic dissection of key factors underlying RSA responses to P deficiency could enable early identification of P-efficient sorghum genotypes. Genotypes with interesting RSA traits for low P environments will be incorporated into current sorghum breeding programs for later growth stages and field-based evaluations.

Post-Translational Modification of WRKY Transcription Factors

Post-translational modifications (PTMs) of proteins are involved in numerous biological processes, including signal transduction, cell cycle regulation, growth and development, and stress responses. WRKY transcription factors (TFs) play significant roles in plant growth, development, and responses to both biotic and abiotic stresses, making them one of the largest and most vital TF families in plants. Recent studies have increasingly highlighted the importance of PTMs of WRKY TFs in various life processes. This review focuses on the recent advancements in understanding the phosphorylation and ubiquitination of WRKY TFs, particularly their roles in resistance to biotic and abiotic stresses and in plant growth and development. Future research directions and prospects in this field are also discussed.

Comparative Analysis of Hulless Barley Transcriptomes to Regulatory Effects of Phosphorous Deficiency

Hulless barley is a cold-resistant crop widely planted in the northwest plateau of China. It is also the main food crop in this region. Phosphorus (P), as one of the important essential nutrient elements, regulates plant growth and defense. This study aimed to analyze the development and related molecular mechanisms of hulless barley under P deficiency and explore the regulatory genes so as to provide a basis for subsequent molecular breeding research. Transcriptome analysis was performed on the root and leaf samples of hulless barley cultured with different concentrations of KH2PO4 (1 mM and 10 μM) Hoagland solution. A total of 46,439 genes were finally obtained by the combined analysis of leaf and root samples. Among them, 325 and 453 genes had more than twofold differences in expression. These differentially expressed genes (DEGs) mainly participated in the abiotic stress biosynthetic process through Gene Ontology prediction. Moreover, the Kyoto Encyclopedia of Genes and Genomes showed that DEGs were mainly involved in photosynthesis, plant hormone signal transduction, glycolysis, phenylpropanoid biosynthesis, and synthesis of metabolites. These pathways also appeared in other abiotic stresses. Plants initiated multiple hormone synergistic regulatory mechanisms to maintain growth under P-deficient conditions. Transcription factors (TFs) also proved these predictions. The enrichment of ARR-B TFs, which positively regulated the phosphorelay-mediated cytokinin signal transduction, and some other TFs (AP2, GRAS, and ARF) was related to plant hormone regulation. Some DEGs showed different values in their FPKM (fragment per kilobase of transcript per million mapped reads), but the expression trends of genes responding to stress and phosphorylation remained highly consistent. Therefore, in the case of P deficiency, the first response of plants was the expression of stress-related genes. The effects of this stress on plant metabolites need to be further studied to improve the relevant regulatory mechanisms so as to further understand the importance of P in the development and stress resistance of hulless barley.

WRKY6 transcription factor modulates root potassium acquisition through promoting expression of AKT1 in Arabidopsis

Potassium (K+), being an essential macronutrient in plants, plays a central role in many aspects. Root growth is highly plastic and is affected by many different abiotic stresses including nutrient deficiency. The Shaker-type K+ channel Arabidopsis (Arabidopsis thaliana) K+ Transporter 1 (AKT1) is responsible for K+ uptake under both low and high external K+ conditions. However, the upstream transcription factor of AKT1 is not clear. Here, we demonstrated that the WRKY6 transcription factor modulates root growth to low potassium (LK) stress in Arabidopsis. WRKY6 showed a quick response to LK stress and also to many other abiotic stress treatments. The two wrky6 T-DNA insertion mutants were highly sensitive to LK treatment, whose primary root lengths were much shorter, less biomass and lower K+ content in roots than those of wild-type plants, while WRKY6-overexpression lines showed opposite phenotypes. A further investigation showed that WRKY6 regulated the expression of the AKT1 gene via directly binding to the W-box elements in its promoter through EMSA and ChIP-qPCR assays. A dual luciferase reporter analysis further demonstrated that WRKY6 enhanced the transcription of AKT1. Genetic analysis further revealed that the overexpression of AKT1 greatly rescued the short root phenotype of the wrky6 mutant under LK stress, suggesting AKT1 is epistatic to WRKY6 in the control of LK response. Further transcriptome profiling suggested that WRKY6 modulates LK response through a complex regulatory network. Thus, this study unveils a transcription factor that modulates root growth under potassium deficiency conditions by affecting the potassium channel gene AKT1 expression.

Recent advances in research on phosphate starvation signaling in plants

Phosphorus is indispensable for plant growth and development, with its status crucial for determining crop productivity. Plants have evolved various biochemical, morphological, and developmental responses to thrive under conditions of low P availability, as inorganic phosphate (Pi), the primary form of P uptake, is often insoluble in soils. Over the past 25 years, extensive research has focused on understanding these responses, collectively forming the Pi starvation response system. This effort has not only expanded our knowledge of strategies to cope with Pi starvation (PS) but also confirmed their adaptive significance. Moreover, it has identified and characterized numerous components of the intricate regulatory network governing P homeostasis. This review emphasizes recent advances in PS signaling, particularly highlighting the physiological importance of local PS signaling in inhibiting primary root growth and uncovering the role of TORC1 signaling in this process. Additionally, advancements in understanding shoot-root Pi allocation and a novel technique for studying Pi distribution in plants are discussed. Furthermore, emerging data on the regulation of plant-microorganism interactions by the PS regulatory system, crosstalk between the signaling pathways of phosphate starvation, phytohormones and immunity, and recent studies on natural variation in Pi homeostasis are addressed.

The transcription factor OsbZIP48 governs rice responses to zinc deficiency

Zinc (Zn) deficiency is the most prevalent micronutrient disorder in rice and leads to delayed development and decreased yield. Nevertheless, despite its primary importance, how rice responds to Zn deficiency remains poorly understood. This study presents genetic evidence supporting the crucial role of OsbZIP48 in regulating rice's response to Zn deficiency, consistent with earlier findings in the model plant Arabidopsis. Genetic inactivation of OsbZIP48 in rice seedlings resulted in heightened sensitivity to Zn deficiency and reduced Zn translocation from roots to shoots. Consistently, OsbZIP48 was constitutively expressed in roots, slightly induced by Zn deficiency in shoots and localized into nuclei induced by Zn deficiency. Comparative transcriptome analysis of the wild-type plants and osbzip48 mutant grown under Zn deficiency enabled the identification of OsbZIP48 target genes, including key Zn transporter genes (OsZIP4 and OsZIP8). We demonstrated that OsbZIP48 controlled the expressions of these genes by directly binding to their promoters, specifically to the Zn deficiency response element motif. This study establishes OsbZIP48 as a critical transcription factor in rice's response to Zn deficiency, offering valuable insights for developing Zn-biofortified rice varieties to combat global Zn limitation.

A cucumber protein, Phloem Phosphate Stress-Repressed 1, rapidly degrades in response to a phosphate stress condition

Under depleted external phosphate (Pi), many plant species adapt to this stress by initiating downstream signaling cascades. In plants, the vascular system delivers nutrients and signaling agents to control physiological and developmental processes. Currently, limited information is available regarding the direct role of phloem-borne long-distance signals in plant growth and development under Pi stress conditions. Here, we report on the identification and characterization of a cucumber protein, Cucumis sativus Phloem Phosphate Stress-Repressed 1 (CsPPSR1), whose level in the phloem translocation stream rapidly responds to imposed Pi-limiting conditions. CsPPSR1 degradation is mediated by the 26S proteasome; under Pi-sufficient conditions, CsPPSR1 is stabilized by its phosphorylation within the sieve tube system through the action of CsPPSR1 kinase. Further, we discovered that CsPPSR1 kinase was susceptible to Pi starvation-induced degradation in the sieve tube system. Our findings offer insight into a molecular mechanism underlying the response of phloem-borne proteins to Pi-limited stress conditions.

Dynamic interactions between SPX proteins, the ubiquitination machinery, and signalling molecules for stress adaptation at a whole-plant level

The plant macronutrient phosphorus is a scarce resource and plant-available phosphate is limiting in most soil types. Generally, a gene regulatory module called the phosphate starvation response (PSR) enables efficient phosphate acquisition by roots and translocation to other organs. Plants growing on moderate to nutrient-rich soils need to co-ordinate availability of different nutrients and repress the highly efficient PSR to adjust phosphate acquisition to the availability of other macro- and micronutrients, and in particular nitrogen. PSR repression is mediated by a small family of single SYG1/Pho81/XPR1 (SPX) domain proteins. The SPX domain binds higher order inositol pyrophosphates that signal cellular phosphorus status and modulate SPX protein interaction with PHOSPHATE STARVATION RESPONSE1 (PHR1), the central transcriptional regulator of PSR. Sequestration by SPX repressors restricts PHR1 access to PSR gene promoters. Here we focus on SPX4 that primarily acts in shoots and sequesters many transcription factors other than PHR1 in the cytosol to control processes beyond the classical PSR, such as nitrate, auxin, and jasmonic acid signalling. Unlike SPX1 and SPX2, SPX4 is subject to proteasomal degradation not only by singular E3 ligases, but also by SCF-CRL complexes. Emerging models for these different layers of control and their consequences for plant acclimation to the environment will be discussed.

Genome-wide identification of U-box gene family and expression analysis in response to saline-alkali stress in foxtail millet (Setaria italica L. Beauv)

E3 ubiquitin ligases are central modifiers of plant signaling pathways that regulate protein function, localization, degradation, and other biological processes by linking ubiquitin to target proteins. E3 ubiquitin ligases include proteins with the U-box domain. However, there has been no report about the foxtail millet (Setaria italica L. Beauv) U-box gene family (SiPUB) to date. To explore the function of SiPUBs, this study performed genome-wide identification of SiPUBs and expression analysis of them in response to saline-alkali stress. A total of 70 SiPUBs were identified, which were unevenly distributed on eight chromosomes. Phylogenetic and conserved motif analysis demonstrated that SiPUBs could be clustered into six subfamilies (I-VI), and most SiPUBs were closely related to the homologues in rice. Twenty-eight types of cis-acting elements were identified in SiPUBs, most of which contained many light-responsive elements and plant hormone-responsive elements. Foxtail millet had 19, 78, 85, 18, and 89 collinear U-box gene pairs with Arabidopsis, rice, sorghum, tomato, and maize, respectively. Tissue specific expression analysis revealed great variations in SiPUB expression among different tissues, and most SiPUBs were relatively highly expressed in roots, indicating that SiPUBs may play important roles in root development or other growth and development processes of foxtail millet. Furthermore, the responses of 15 SiPUBs to saline-alkali stress were detected by qRT-PCR. The results showed that saline-alkali stress led to significantly differential expression of these 15 SiPUBs, and SiPUB20/48/70 may play important roles in the response mechanism against saline-alkali stress. Overall, this study provides important information for further exploration of the biological function of U-box genes.

PHT1;5 Repressed by ANT Mediates Pi Acquisition and Distribution under Low Pi and Salinity in Salt Cress

Salinity and phosphate (Pi) starvation are the most common abiotic stresses that threaten crop productivity. Salt cress (Eutrema salsugineum) displays good tolerance to both salinity and Pi limitation. Previously, we found several Phosphate Transporter (PHT) genes in salt cress upregulated under salinity. Here, EsPHT1;5 induced by both low Pi (LP) and salinity was further characterized. Overexpression of EsPHT1;5 in salt cress enhanced plant tolerance to LP and salinity, while the knock-down lines exhibited growth retardation. The analysis of phosphorus (P) content and shoot/root ratio of total P in EsPHT1;5-overexpressing salt cress seedlings and the knock-down lines as well as arsenate uptake assays suggested the role of EsPHT1;5 in Pi acquisition and root-shoot translocation under Pi limitation. In addition, overexpression of EsPHT1;5 driven by the native promoter in salt cress enhanced Pi mobilization from rosettes to siliques upon a long-term salt treatment. Particularly, the promoter of EsPHT1;5 outperformed that of AtPHT1;5 in driving gene expression under salinity. We further identified a transcription factor EsANT, which negatively regulated EsPHT1;5 expression and plant tolerance to LP and salinity. Taken together, EsPHT1;5 plays an integral role in Pi acquisition and distribution in plant response to LP and salt stress. Further, EsANT may be involved in the cross-talk between Pi starvation and salinity signaling pathways. This work provides further insight into the mechanism underlying high P use efficiency in salt cress in its natural habitat, and evidence for a link between Pi and salt signaling.

Deciphering the protein ubiquitylation system in plants

Protein ubiquitylation is a post-translational modification (PTM) process that covalently modifies a protein substrate with either mono-ubiquitin moieties or poly-ubiquitin chains often at the lysine residues. In Arabidopsis, bioinformatic predictions have suggested that over 5% of its proteome constitutes the protein ubiquitylation system. Despite advancements in functional genomic studies in plants, only a small fraction of this bioinformatically predicted system has been functionally characterized. To expand our understanding about the regulatory function of protein ubiquitylation to that rivalling several other major systems, such as transcription regulation and epigenetics, I describe the status, issues, and new approaches of protein ubiquitylation studies in plant biology. I summarize the methods utilized in defining the ubiquitylation machinery by bioinformatics, identifying ubiquitylation substrates by proteomics, and characterizing the ubiquitin E3 ligase-substrate pathways by functional genomics. Based on the functional and evolutionary analyses of the F-box gene superfamily, I propose a deleterious duplication model for the large expansion of this family in plant genomes. Given this model, I present new perspectives of future functional genomic studies on the plant ubiquitylation system to focus on core and active groups of ubiquitin E3 ligase genes.

WRKY transcription factors in Arachis hypogaea and its donors: From identification to function prediction

WRKY transcription factors (TFs) play important roles in plant growth and development and responses to abiotic and biotic stresses. Since the initial isolation of a WRKY TF in Ipomoea batatas in 1994, WRKY TFs have been identified in plants, protozoa, and fungi. Peanut (Arachis hypogaea) is a key oil and protein crop for humans and a forage source for animal consumption. Several Arachis genomes have been sequenced and genome-wide WRKY TFs have been identified. In this review, we summarized WRKY TFs and their functions in A. hypogaea and its donors. We also standardized the nomenclature for Arachis WRKY TFs to ensure uniformity. We determined the evolutionary relationships between Arachis and Arabidopsis thaliana WRKY (AtWRKY) TFs using a phylogenetic analysis. Biological functions and regulatory networks of Arachis WRKY TFs were predicted using AtWRKY TFs. Thus, this review paves the way for studies of Arachis WRKY TFs.

ClNAC100 Is a NAC Transcription Factor of Chinese Fir in Response to Phosphate Starvation

Phosphate (Pi) deficiency is one of the most limiting factors for Chinese fir growth and production. Moreover, continuous cultivation of Chinese fir for multiple generations led to the reduction of soil nutrients, which hindered the yield of Chinese fir in southern China. Although NAC (NAM, ATAF, and CUC) transcription factors (TFs) play critical roles in plant development and abiotic stress resistance, it is still unclear how they regulate the response of Chinese fir to phosphate (Pi) starvation. Based on Pi-deficient transcriptome data of Chinses fir root, we identified a NAC transcription factor with increased expression under Pi deficiency, which was obtained by PCR and named ClNAC100. RT-qPCR confirmed that the expression of ClNAC100 in the root of Chinese fir was induced by phosphate deficiency and showed a dynamic change with time. It was positively regulated by ABA and negatively regulated by JA, and ClNAC100 was highly expressed in the roots and leaves of Chinese fir. Transcriptional activation assay confirmed that ClNAC100 was a transcriptional activator. The promoter of ClNAC100 was obtained by genome walking, which was predicted to contain a large number of stress, hormone, and growth-related cis-elements. Tobacco infection was used to verify the activity of the promoter, and the core promoter was located between -1519 bp and -589 bp. We identified 18 proteins bound to the ClNAC100 promoter and 5 ClNAC100 interacting proteins by yeast one-hybrid and yeast two-hybrid, respectively. We speculated that AHL and TIFY family transcription factors, calmodulin, and E3 ubiquitin ligase in these proteins might be important phosphorus-related proteins. These results provide a basis for the further study of the regulatory mechanism and pathways of ClNAC100 under Pi starvation.

The good, the bad, and the phosphate: regulation of beneficial and detrimental plant-microbe interactions by the plant phosphate status

Phosphate (P_i ) is indispensable for life on this planet. However, for sessile land plants it is poorly accessible. Therefore, plants have developed a variety of strategies for enhanced acquisition and recycling of P_i . The mechanisms to cope with P_i limitation as well as direct uptake of P_i from the substrate via the root epidermis are regulated by a conserved P_i starvation response (PSR) system based on a family of key transcription factors (TFs) and their inhibitors. Furthermore, plants obtain P_i indirectly through symbiosis with mycorrhiza fungi, which employ their extensive hyphal network to drastically increase the soil volume that can be explored by plants for P_i . Besides mycorrhizal symbiosis, there is also a variety of other interactions with epiphytic, endophytic, and rhizospheric microbes that can indirectly or directly influence plant P_i uptake. It was recently discovered that the PSR pathway is involved in the regulation of genes that promote formation and maintenance of AM symbiosis. Furthermore, the PSR system influences plant immunity and can also be a target of microbial manipulation. It is known for decades that the nutritional status of plants influences the outcome of plant-microbe interactions. The first molecular explanations for these observations are now emerging.

PsRGL1 negatively regulates chilling- and gibberellin-induced dormancy release by PsF-box1-mediated targeting for proteolytic degradation in tree peony

Tree peony bud endodormancy is a common survival strategy similar to many perennial woody plants in winter, and the activation of the GA signaling pathway is the key to breaking endodormancy. GA signal transduction is involved in many physiological processes. Although the GA-GID1-DELLA regulatory module is conserved in many plants, it has a set of specific components that add complexity to the GA response mechanism. DELLA proteins are key switches in GA signaling. Therefore, there is an urgent need to identify the key DELLA proteins involved in tree peony bud dormancy release. In this study, the prolonged chilling increased the content of endogenously active gibberellins. PsRGL1 among three DELLA proteins was significantly downregulated during chilling- and exogenous GA3-induced bud dormancy release by cell-free degradation assay, and a high level of polyubiquitination was detected. Silencing PsRGL1 accelerated bud dormancy release by increasing the expression of the genes associated with dormancy release, including PsCYCD, PsEBB1, PsEBB3, PsBG6, and PsBG9. Three F-box protein family members responded to chilling and GA3 treatments, resulting in PsF-box1 induction. Yeast two-hybrid and BiFC assays indicated that only PsF-box1 could bind to PsRGL1, and the binding site was in the C-terminal domain. PsF-box1 overexpression promoted dormancy release and upregulated the expression of the dormancy-related genes. In addition, yeast two-hybrid and pull-down assays showed that PsF-box1 also interacted with PsSKP1 to form an E3 ubiquitin ligase. These findings enriched the molecular mechanism of the GA signaling pathway during dormancy release, and enhanced the understanding of tree peony bud endodormancy.

Dual functions of PsmiR172b-PsTOE3 module in dormancy release and flowering in tree peony (Paeonia suffruticosa)

MicroRNAs (miRNAs) are non-coding RNAs that interact with target genes and are involved in many physiological processes in plants. miR172-AP2 mainly plays a role in the regulation of flowering time and floral organ differentiation. Bud dormancy release is necessary for forcing culture of tree peony in winter, but the mechanism of dormancy regulation is unclear. In this study, we found that a miR172 family member, PsmiR172b, was downregulated during chilling-induced bud dormancy release in tree peony, exhibiting a trend opposite to that of PsTOE3. RNA ligase-mediated (RLM) 5'-RACE (rapid amplification of cDNA ends) confirmed that miR172b targeted PsTOE3, and the cleavage site was between bases 12 (T) and 13 (C) within the complementary site to miR172b. The functions of miR172b and PsTOE3 were detected by virus-induced gene silencing (VIGS) and their overexpression in tree peony buds. PsmiR172b negatively regulated bud dormancy release, but PsTOE3 promoted bud dormancy release, and the genes associated with bud dormancy release, including PsEBB1, PsEBB3, PsCYCD, and PsBG6, were upregulated. Further analysis indicated that PsTOE3 directly regulated PsEBB1 by binding to its promoter, and the specific binding site was a C-repeat (ACCGAC). Ectopic expression in Arabidopsis revealed that the PsmiR172b-PsTOE3 module displayed conservative function in regulating flowering. In conclusion, our results provided a novel insight into the functions of PsmiR172-PsTOE3 and possible molecular mechanism underlying bud dormancy release in tree peony.

Genome-Wide Identification of the U-Box E3 Ubiquitin Ligase Gene Family in Cabbage (Brassica oleracea var. capitata) and Its Expression Analysis in Response to Cold Stress and Pathogen Infection

Plant U-box E3 ubiquitin ligases (PUBs) play an important role in growth, development, and stress responses in many species. However, the characteristics of U-box E3 ubiquitin ligase genes in cabbage (Brassica oleracea var. capitata) are still unclear. Here, we carry out the genome-wide analysis of U-box E3 ubiquitin ligase genes in cabbage and identify 65 Brassica oleracea var. capitata U-box E3 ubiquitin ligase (BoPUB) genes in the cabbage genome. Phylogenetic analysis indicates that all 65 BoPUB genes are grouped into six subfamilies, whose members are relatively conserved in the protein domain and exon-intron structure. Chromosomal localization and synteny analyses show that segmental and tandem duplication events contribute to the expansion of the U-box E3 ubiquitin ligase gene family in cabbage. Protein interaction prediction presents that heterodimerization may occur in BoPUB proteins. In silico promoter analysis and spatio-temporal expression profiling of BoPUB genes reveal their involvement in light response, phytohormone response, and growth and development. Furthermore, we find that BoPUB genes participate in the biosynthesis of cuticular wax and in response to cold stress and pathogenic attack. Our findings provide a deep insight into the U-box E3 ubiquitin ligase gene family in cabbage and lay a foundation for the further functional analysis of BoPUB genes in different biological processes.

RNAseq-Based Working Model for Transcriptional Regulation of Crosstalk between Simultaneous Abiotic UV-B and Biotic Stresses in Plants

Plants adjust their secondary metabolism by altering the expression of corresponding genes to cope with both abiotic and biotic stresses. In the case of UV-B radiation, plants produce protective flavonoids; however, this reaction is impeded during pattern-triggered immunity (PTI) induced by pathogens. Pathogen attack can be mimicked by the application of microbial associated molecular patterns (e.g., flg22) to study crosstalk between PTI and UV-B-induced signaling pathways. Switching from Arabidopsis cell cultures to in planta studies, we analyzed whole transcriptome changes to gain a deeper insight into crosstalk regulation. We performed a comparative transcriptomic analysis by RNAseq with four distinct mRNA libraries and identified 10778, 13620, and 11294 genes, which were differentially expressed after flg22, UV-B, and stress co-treatment, respectively. Focusing on genes being either co-regulated with the UV-B inducible marker gene chalcone synthase CHS or the flg22 inducible marker gene FRK1 identified a large set of transcription factors from diverse families, such as MYB, WRKY, or NAC. These data provide a global view of transcriptomic reprogramming during this crosstalk and constitute a valuable dataset for further deciphering the underlying regulatory mechanism(s), which appear to be much more complex than previously anticipated. The possible involvement of MBW complexes in this context is discussed.

Transcriptional regulation of oil biosynthesis in seed plants: Current understanding, applications, and perspectives

Plants produce and accumulate triacylglycerol (TAG) in their seeds as an energy reservoir to support the processes of seed germination and seedling development. Plant seed oils are vital not only for the human diet but also as renewable feedstocks for industrial use. TAG biosynthesis consists of two major steps: de novo fatty acid biosynthesis in the plastids and TAG assembly in the endoplasmic reticulum. The latest advances in unraveling transcriptional regulation have shed light on the molecular mechanisms of plant oil biosynthesis. We summarize recent progress in understanding the regulatory mechanisms of well-characterized and newly discovered transcription factors and other types of regulators that control plant fatty acid biosynthesis. The emerging picture shows that plant oil biosynthesis responds to developmental and environmental cues that stimulate a network of interacting transcriptional activators and repressors, which in turn fine-tune the spatiotemporal regulation of the pathway genes.

Arsenic perception and signaling: The yet unexplored world

Arsenic is one of the most potent carcinogens in the biosphere, jeopardizing the health of millions of people due to its entrance into the human food chain through arsenic-contaminated waters and staple crops, particularly rice. Although the mechanisms of arsenic sensing are widely known in yeast and bacteria, scientific evidence concerning arsenic sensors or components of early arsenic signaling in plants is still in its infancy. However, in recent years, we have gained understanding of the mechanisms involved in arsenic uptake and detoxification in different plant species and started to get insights into arsenic perception and signaling, which allows us to glimpse the possibility to design effective strategies to prevent arsenic accumulation in edible crops or to increase plant arsenic extraction for phytoremediation purposes. In this context, it has been recently described a mechanism according to which arsenite, the reduced form of arsenic, regulates the arsenate/phosphate transporter, consistent with the idea that arsenite functions as a selective signal that coordinates arsenate uptake with detoxification mechanisms. Additionally, several transcriptional and post-translational regulators, miRNAs and phytohormones involved in arsenic signaling and tolerance have been identified. On the other hand, studies concerning the developmental programs triggered to adapt root architecture in order to cope with arsenic toxicity are just starting to be disclosed. In this review, we compile and analyze the latest advances toward understanding how plants perceive arsenic and coordinate its acquisition with detoxification mechanisms and root developmental programs.

Phosphate (Pi) stress-responsive transcription factors PdeWRKY6 and PdeWRKY65 regulate the expression of PdePHT1;9 to modulate tissue Pi concentration in poplar

Phosphorus (P) is an important nutrient for plants. Here, we identify a WRKY transcription factor (TF) in poplar (Populus deltoides × Populus euramericana) (PdeWRKY65) that modulates tissue phosphate (Pi) concentrations in poplar. PdeWRKY65 overexpression (OE) transgenic lines showed reduced shoot Pi concentrations under both low and normal Pi availabilities, while PdeWRKY65 reduced expression (RE) lines showed the opposite phenotype. A gene encoding a Pi transporter (PHT), PdePHT1;9, was identified as the direct downstream target of PdeWRKY65 by RNA sequencing (RNA-Seq). The negative regulation of PdePHT1;9 expression by PdeWRKY65 was confirmed by DNA-protein interaction assays, including yeast one-hybrid (Y1H), electrophoretic mobility shift assay (EMSA), co-expression of the promoters of PdePHT1;9 and PdeWRKY65 in tobacco (Nicotiana benthamiana) leaves, and chromatin immunoprecipitation-quantitative PCR. A second WRKY TF, PdeWRKY6, was subsequently identified and confirmed to positively regulate the expression of PdePHT1;9 by DNA-protein interaction assays. PdePHT1;9 and PdeWRKY6 OE and RE poplar transgenic lines were used to confirm their positive regulation of shoot Pi concentrations, under both normal and low Pi availabilities. No interaction between PdeWRKY6 and PdeWRKY65 was observed at the DNA or protein levels. Collectively, these data suggest that the low Pi-responsive TFs PdeWRKY6 and PdeWRKY65 independently regulate the expression of PHT1;9 to modulate tissue Pi concentrations in poplar.

SHORT-ROOT stabilizes PHOSPHATE1 to regulate phosphate allocation in Arabidopsis

The coordinated distribution of inorganic phosphate (Pi) between roots and shoots is an important process that plants use to maintain Pi homeostasis. SHORT-ROOT (SHR) is well characterized for its function in root radial patterning. Here we demonstrate a role of SHR in controlling Pi allocation from root to shoot by regulating PHOSPHATE1 in the root differentiation zone. We recovered a weak mutant allele of SHR in Arabidopsis that accumulates much less Pi in the shoot and shows a constitutive Pi starvation response under Pi-sufficient conditions. In addition, Pi starvation suppresses SHR protein accumulation and releases its inhibition on the HD-ZIP III transcription factor PHB. PHB accumulates and directly binds the promoter of PHOSPHATE2 to upregulate its transcription, resulting in PHOSPHATE1 degradation in the xylem-pole pericycle cells. Our findings reveal a previously unrecognized mechanism of how plants regulate Pi translocation from roots to shoots.

Global proteome analyses of phosphorylation and succinylation of barley root proteins in response to phosphate starvation and recovery

Phosphate (Pi) stress is an important environmental factor that limits plant growth and development. Of various posttranslational modifications (PTMs), protein phosphorylation and succinylation are the two most important PTMs that regulate multiple biological processes in response to Pi stress. However, these PTMs have been investigated individually but their interactions with proteins in response to Pi stress remain poorly understood. In this study, to elucidate the underlying mechanisms of protein phosphorylation and succinylation in response to Pi stress, we performed a global analysis of the barley root phosphorylome and succinylome in Pi starvation and recovery stages, respectively. A total of 3,634 and 884 unique phosphorylated and succinylated proteins, respectively, corresponding to 11,538 and 2,840 phospho- and succinyl-sites, were identified; of these, 275 proteins were found to be simultaneously phosphorylated and succinylated. Gene Set Enrichment Analysis was performed with a Kyoto Encyclopedia of Genes and Genomes pathway database revealing pathways that significantly enriched in the phosphorylome and succinylome. Such pathways, were dynamically regulated by Pi starvation and recovery treatments, and could be partitioned into distinct metabolic processes. In particular, phosphorylated proteins related to purine, the mitogen-activated protein kinase (MAPK) signaling pathway, pyrimidine, and ATP-binding cassette (ABC) transporters were upregulated in both Pi deprivation and recovery stages. Succinylated proteins, significantly upregulated by both Pi starvation and recovery, were enriched in nitrogen metabolism and phenylpropanoid biosynthesis. Meanwhile, succinylated proteins that were significantly downregulated by both Pi starvation and recovery were enriched in lysine degradation and tryptophan metabolism. This highlighted the importance of these metabolic pathways in regulating Pi homeostasis. Furthermore, protein-protein interaction network analyses showed that the response of central metabolic pathways to Pi starvation and recovery was significantly modulated by phosphorylation or succinylation, both individually and together. In addition, we discovered relevant proteins involved in MAPK signaling and phenylpropanoid biosynthetic pathways existing in interactions between phosphorylated and succinylated proteins in response to Pi recovery. The current study not only provides a comprehensive analysis of phosphorylated and succinylated proteins in plant responses to Pi starvation and recovery, but also reveals detailed interactions between phosphorylated and succinylated proteins in barley roots.

PHR1 positively regulates phosphate starvation-induced anthocyanin accumulation through direct upregulation of genes F3'H and LDOX in Arabidopsis

Phosphate deficiency promotes anthocyanin accumulation in Arabidopsis through direct binding of PHR1 to the P1BS motifs on the promoters of F3'H and LDOX and thereby upregulating their expression. Phosphorus is one of the essential elements for plants, and plants mainly absorb inorganic phosphate (Pi) from soil. But Pi deficiency is a common factor limiting plant growth and development. Anthocyanin accumulation in green tissues (such as leaves) is one of the characteristics of many plants in response to Pi starvation. However, little is known about the mechanism by which Pi starvation induces anthocyanin accumulation. Here, we found that the mutation of the gene PHOSPHATE STARVATION RESPONSE1 (PHR1), which encodes a key factor involved in Pi starvation signaling in Arabidopsis, significantly attenuates anthocyanin accumulation under Pi-limiting conditions. Moreover, the expression of several Pi deficiency-upregulated genes that are involved in anthocyanin biosyntheses, such as flavanone 3'-hydroxylase (F3'H), dihydroflavonol 4-reductase (DFR), leucoanthocyanidin dioxygenase (LDOX), and production of anthocyanin pigment 1 (PAP1), was significantly lower in the phr1-1 mutant than in the wild type (WT). Both yeast one-hybrid (Y1H) analysis and chromatin immunoprecipitation quantitative PCR (ChIP-qPCR) showed that PHR1 can interact with the promoters of F3'H and LDOX, but not DFR and PAP1. By electrophoretic mobility shift assay (EMSA), it was further confirmed that the PHR1-binding sequence (P1BS) motifs located on the F3'H and LDOX promoters are required for the PHR1 bindings. Also, in Arabidopsis protoplasts, PHR1 enhanced the transcriptional activity of the F3'H and LDOX promoters, but these effects were markedly impaired when the P1BS motifs were mutated. Taken together, these results indicate that PHR1 positively regulates Pi starvation-induced anthocyanin accumulation in Arabidopsis, at least in part, by directly binding the P1BS motifs located on the promoters to upregulate the transcription of anthocyanin biosynthetic genes F3'H and LDOX.

MaMYB4 is a negative regulator and a substrate of RING-type E3 ligases MaBRG2/3 in controlling banana fruit ripening

Fruit ripening is a complex developmental process, which is modulated by both transcriptional and post-translational events. Control of fruit ripening is important in maintaining moderate quality traits and minimizing postharvest deterioration. In this study, we discovered that the transcription factor MaMYB4 acts as a negative regulator of fruit ripening in banana. The protein levels of MaMYB4 decreased gradually with banana fruit ripening, paralleling ethylene production, and decline in firmness. DNA affinity purification sequencing combined with RNA-sequencing analyses showed that MaMYB4 preferentially binds to the promoters of various ripening-associated genes including ethylene biosynthetic and cell wall modifying genes. Furthermore, ectopic expression of MaMYB4 in tomato delayed tomato fruit ripening, which was accompanied by downregulation of ethylene biosynthetic and cell wall modifying genes. Importantly, two RING finger E3 ligases MaBRG2/3, whose protein accumulation increased progressively with fruit ripening, were found to interact with and ubiquitinate MaMYB4, contributing to decreased accumulation of MaMYB4 during fruit ripening. Transient overexpression of MaMYB4 and MaBRG2/3 in banana fruit ripening delayed or promoted fruit ripening by inhibiting or stimulating ethylene biosynthesis, respectively. Taken together, we demonstrate that MaMYB4 negatively modulates banana fruit ripening, and that MaMYB4 abundance could be regulated by protein ubiquitination, thus providing insights into the role of MaMYB4 in controlling fruit ripening at both transcriptional and post-translational levels.

The Ubiquitin Proteasome System and Nutrient Stress Response

Plants utilize different molecular mechanisms, including the Ubiquitin Proteasome System (UPS) that facilitates changes to the proteome, to mitigate the impact of abiotic stresses on growth and development. The UPS encompasses the ubiquitination of selected substrates followed by the proteasomal degradation of the modified proteins. Ubiquitin ligases, or E3s, are central to the UPS as they govern specificity and facilitate the attachment of one or more ubiquitin molecules to the substrate protein. From recent studies, the UPS has emerged as an important regulator of the uptake and translocation of essential macronutrients and micronutrients. In this review, we discuss select E3s that are involved in regulating nutrient uptake and responses to stress conditions, including limited or excess levels of nitrogen, phosphorus, iron, and copper.

The Xanthomonas type-III effector XopS stabilizes CaWRKY40a to regulate defense responses and stomatal immunity in pepper (Capsicum annuum)

As a critical part of plant immunity, cells that are attacked by pathogens undergo rapid transcriptional reprogramming to minimize virulence. Many bacterial phytopathogens use type III effector (T3E) proteins to interfere with plant defense responses, including this transcriptional reprogramming. Here, we show that Xanthomonas outer protein S (XopS), a T3E of Xanthomonas campestris pv. vesicatoria (Xcv), interacts with and inhibits proteasomal degradation of WRKY40, a transcriptional regulator of defense gene expression. Virus-induced gene silencing of WRKY40 in pepper (Capsicum annuum) enhanced plant tolerance to Xcv infection, indicating that WRKY40 represses immunity. Stabilization of WRKY40 by XopS reduces the expression of its targets, which include salicylic acid-responsive genes and the jasmonic acid signaling repressor JAZ8. Xcv bacteria lacking XopS display significantly reduced virulence when surface inoculated onto susceptible pepper leaves. XopS delivery by Xcv, as well as ectopic expression of XopS in Arabidopsis thaliana or Nicotiana benthamiana, prevented stomatal closure in response to bacteria and biotic elicitors. Silencing WRKY40 in pepper or N. benthamiana abolished XopS's ability to prevent stomatal closure. This suggests that XopS interferes with both preinvasion and apoplastic defense by manipulating WRKY40 stability and downstream gene expression, eventually altering phytohormone crosstalk to promote pathogen proliferation.

Plant E3 Ligases and Their Role in Abiotic Stress Response

Plants, as sessile organisms, have limited means to cope with environmental changes. Consequently, they have developed complex regulatory systems to ameliorate abiotic stresses im-posed by environmental changes. One such system is the ubiquitin proteasome pathway, which utilizes E3 ligases to target proteins for proteolytic degradation via the 26S proteasome. Plants ex-press a plethora of E3 ligases that are categorized into four major groups depending on their structure. They are involved in many biological and developmental processes in plants, such as DNA repair, photomorphogenesis, phytohormones signaling, and biotic stress. Moreover, many E3 ligase targets are proteins involved in abiotic stress responses, such as salt, drought, heat, and cold. In this review, we will provide a comprehensive overview of E3 ligases and their substrates that have been connected with abiotic stress in order to illustrate the diversity and complexity of how this pathway enables plant survival under stress conditions.

Editing of the starch branching enzyme gene SBE2 generates high-amylose storage roots in cassava

The production of high-amylose cassava through CRISPR/Cas9-mediated mutagenesis of the starch branching enzyme gene SBE2 was firstly achieved. High-amylose cassava (Manihot esculenta Crantz) is desirable for starch industrial applications and production of healthier processed food for human consumption. In this study, we report the production of high-amylose cassava through CRISPR/Cas9-mediated mutagenesis of the starch branching enzyme 2 (SBE2). Mutations in two targeted exons of SBE2 were identified in all regenerated plants; these mutations, which included nucleotide insertions, and short or long deletions in the SBE2 gene, were classified into eight mutant lines. Three mutants, M6, M7 and M8, with long fragment deletions in the second exon of SBE2 showed no accumulation of SBE2 protein. After harvest from the field, significantly higher amylose (up to 56% in apparent amylose content) and resistant starch (up to 35%) was observed in these mutants compared with the wild type, leading to darker blue coloration of starch granules after quick iodine staining and altered starch viscosity with a higher pasting temperature and peak time. Further ¹H-NMR analysis revealed a significant reduction in the degree of starch branching, together with fewer short chains (degree of polymerization [DP] 15-25) and more long chains (DP>25 and especially DP>40) of amylopectin, which indicates that cassava SBE2 catalyzes short chain formation during amylopectin biosynthesis. Transition from A- to B-type crystallinity was also detected in the starches. Our study showed that CRISPR/Cas9-mediated mutagenesis of starch biosynthetic genes in cassava is an effective approach for generating novel varieties with valuable starch properties for food and industrial applications.

The Genetic Basis of Phosphorus Utilization Efficiency in Plants Provide New Insight into Woody Perennial Plants Improvement

Soil nutrient restrictions are the main environmental conditions limiting plant growth, development, yield, and quality. Phosphorus (P), an essential macronutrient, is one of the most significant factors that vastly restrains the growth and development of plants. Although the total P is rich in soil, its bio-available concentration is still unable to meet the requirements of plants. To maintain P homeostasis, plants have developed lots of intricate responsive and acclimatory mechanisms at different levels, which contribute to administering the acquisition of inorganic phosphate (Pi), translocation, remobilization, and recycling of Pi. In recent years, significant advances have been made in the exploration of the utilization of P in annual plants, while the research progress in woody perennial plants is still vague. In the meanwhile, compared to annual plants, relevant reviews about P utilization in woody perennial plants are scarce. Therefore, based on the importance of P in the growth and development of plants, we briefly reviewed the latest advances on the genetic and molecular mechanisms of plants to uphold P homeostasis, P sensing, and signaling, ion transporting and metabolic regulation, and proposed the possible sustainable management strategies to fasten the P cycle in modern agriculture and new directions for future studies.

The Ubiquitin E3 Ligase PRU2 Modulates Phosphate Uptake in Arabidopsis

Phosphorus is an essential macronutrient for plants. The phosphate (Pi) concentration in soil solutions is typically low, and plants always suffer from low-Pi stress. During Pi starvation, a number of adaptive mechanisms in plants have evolved to increase Pi uptake, whereas the mechanisms are not very clear. Here, we report that an ubiquitin E3 ligase, PRU2, modulates Pi acquisition in Arabidopsis response to the low-Pi stress. The mutant pru2 showed arsenate-resistant phenotypes and reduced Pi content and Pi uptake rate. The complementation with PRU2 restored these to wild-type plants. PRU2 functioned as an ubiquitin E3 ligase, and the protein accumulation of PRU2 was elevated during Pi starvation. PRU2 interacted with a kinase CK2α1 and a ribosomal protein RPL10 and degraded CK2α1 and RPL10 under low-Pi stress. The in vitro phosphorylation assay showed that CK2α1 phosphorylated PHT1;1 at Ser-514, and prior reports demonstrated that the phosphorylation of PHT1;1 Ser-514 resulted in PHT1;1 retention in the endoplasmic reticulum. Then, the degradation of CK2α1 by PRU2 under low-Pi stress facilitated PHT1;1 to move to the plasma membrane to increase Arabidopsis Pi uptake. Taken together, this study demonstrated that the ubiquitin E3 ligase—PRU2—was an important positive regulator in modulating Pi acquisition in Arabidopsis response to low-Pi stress.

Plant adaptation to low phosphorus availability: Core signaling, crosstalks, and applied implications

Phosphorus (P) is an essential nutrient for plant growth and reproduction. Plants preferentially absorb P as orthophosphate (Pi), an ion that displays low solubility and that is readily fixed in the soil, making P limitation a condition common to many soils and Pi fertilization an inefficient practice. To cope with Pi limitation, plants have evolved a series of developmental and physiological responses, collectively known as the Pi starvation rescue system (PSR), aimed to improve Pi acquisition and use efficiency (PUE) and protect from Pi-starvation-induced stress. Intensive research has been carried out during the last 20 years to unravel the mechanisms underlying the control of the PSR in plants. Here we review the results of this research effort that have led to the identification and characterization of several core Pi starvation signaling components, including sensors, transcription factors, microRNAs (miRNAs) and miRNA inhibitors, kinases, phosphatases, and components of the proteostasis machinery. We also refer to recent results revealing the existence of intricate signaling interplays between Pi and other nutrients and antagonists, N, Fe, Zn, and As, that have changed the initial single-nutrient-centric view to a more integrated view of nutrient homeostasis. Finally, we discuss advances toward improving PUE and future research priorities.

Verticillium dahliae effector VDAL protects MYB6 from degradation by interacting with PUB25 and PUB26 E3 ligases to enhance Verticillium wilt resistance

Verticillium wilt is a severe plant disease that causes massive losses in multiple crops. Increasing the plant resistance to Verticillium wilt is a critical challenge worldwide. Here, we report that the hemibiotrophic Verticillium dahliae-secreted Asp f2-like protein VDAL causes leaf wilting when applied to cotton leaves in vitro but enhances the resistance to V. dahliae when overexpressed in Arabidopsis or cotton without affecting the plant growth and development. VDAL protein interacts with Arabidopsis E3 ligases plant U-box 25 (PUB25) and PUB26 and is ubiquitinated by PUBs in vitro. However, VDAL is not degraded by PUB25 or PUB26 in planta. Besides, the pub25 pub26 double mutant shows higher resistance to V. dahliae than the wild-type. PUBs interact with the transcription factor MYB6 in a yeast two-hybrid screen. MYB6 promotes plant resistance to Verticillium wilt while PUBs ubiquitinate MYB6 and mediate its degradation. VDAL competes with MYB6 for binding to PUBs, and the role of VDAL in increasing Verticillium wilt resistance depends on MYB6. Taken together, these results suggest that plants evolute a strategy to utilize the invaded effector protein VDAL to resist the V. dahliae infection without causing a hypersensitive response (HR); alternatively, hemibiotrophic pathogens may use some effectors to keep plant cells alive during its infection in order to take nutrients from host cells. This study provides the molecular mechanism for plants increasing disease resistance when overexpressing some effector proteins without inducing HR, and may promote searching for more genes from pathogenic fungi or bacteria to engineer plant disease resistance.

Soybean responds to phosphate starvation through reversible protein phosphorylation

Phosphorus (P) deficiency is considered as a major constraint on crop production. Although a set of adaptative strategies are extensively suggested in soybean (Glycine max) to phosphate (Pi) deprivation, molecular mechanisms underlying reversible protein phosphorylation in soybean responses to P deficiency remains largely unclear. In this study, isobaric tags for relative and absolute quantitation, combined with liquid chromatography and tandem mass spectrometry analysis was performed to identify differential phosphoproteins in soybean roots under Pi sufficient and deficient conditions. A total of 427 phosphoproteins were found to exhibit differential accumulations, with 213 up-regulated and 214 down-regulated. Among them, a nitrate reductase, GmNR4 exhibiting increased phosphorylation levels under low Pi conditions, was further selected to evaluate the effects of phosphorylation on its nitrate reductase activity and subcellular localization. Mutations of GmNR4 phosphorylation levels significantly influenced its activity in vitro, but not for its subcellular localization. Taken together, identification of differential phosphoproteins reveled the complex regulatory pathways for soybean adaptation to Pi starvation through reversible protein phosphorylation.

Arsenite provides a selective signal that coordinates arsenate uptake and detoxification through the regulation of PHR1 stability in Arabidopsis

In nature, plants acquire nutrients from soils to sustain growth, and at the same time, they need to avoid the uptake of toxic compounds and/or possess tolerance systems to cope with them. This is particularly challenging when the toxic compound and the nutrient are chemically similar, as in the case of phosphate and arsenate. In this study, we demonstrated that regulatory elements of the phosphate starvation response (PSR) coordinate the arsenate detoxification machinery in the cell. We showed that arsenate repression of the phosphate transporter PHT1;1 is associated with the degradation of the PSR master regulator PHR1. Once arsenic is sequestered into the vacuole, PHR1 stability is restored and PHT1;1 expression is recovered. Furthermore, we identified an arsenite responsive SKP1-like protein and a PHR1 interactor F-box (PHIF1) as constituents of the SCF complex responsible for PHR1 degradation.We found that arsenite, the form to which arsenate is reduced for compartmentalization in vacuoles, represses PHT1;1 expression, providing a highly selective signal versus phosphate to control PHT1;1 expression in response to arsenate. Collectively, our results provide molecular insights into a sensing mechanism that regulates arsenate/phosphate uptake depending on the plant's detoxification capacity.

RNA-seq analysis of laser microdissected Arabidopsis thaliana leaf epidermis, mesophyll and vasculature defines tissue-specific transcriptional responses to multiple stress treatments

Acclimation of plants to adverse conditions requires the coordination of gene expression and signalling pathways between tissues and cell types. As the energy and carbon capturing organs, leaves are significantly affected by abiotic and biotic stresses. However, tissue- or cell type-specific analyses of stress responses have focussed on the Arabidopsis root. Here, we comparatively explore the transcriptomes of three leaf tissues (epidermis, mesophyll, vasculature) after induction of diverse stress pathways by chemical stimuli (antimycin A, 3-amino-1,2,4-triazole, methyl viologen, salicylic acid) and ultraviolet light in Arabidopsis using laser capture microdissection followed by RNA sequencing. Stimulation of stress pathways caused an overall reduction in the number of genes expressed in a tissue-specific manner, though a small subset gained or changed their tissue specificity. We find no evidence of a common stress response, with only a few genes consistently responsive to two or more treatments in the analysed tissues. However, differentially expressed genes overlap between tissues for individual treatments. A focussed analysis provided evidence for an interaction of auxin and ethylene that mediates retrograde signalling during mitochondrial dysfunction specifically in the epidermis, and a gene regulatory network defined the hierarchy of interactions. Taken together, we have generated an extensive reference dataset that will be valuable for future experiments analysing transcriptional responses on a tissue or single-cell level. Our results will enable the tailoring of the tissue-specific engineering of stress-tolerant plants.

Role of ubiquitination enzymes in abiotic environmental interactions with plants

Ubiquitination, a post-translational modification, plays a crucial role in various aspects of plant development and stress responses. Protein degradation by ubiquitination is well established and ubiquitin is the main underlying component directing the turnover of proteins. Recent reports have also revealed the non-proteolytic roles of ubiquitination in plants. In the past decade, ubiquitination has emerged to be one of the most important players in modulating plant's responses to abiotic stresses, which led to identification of specific E3 ligases and their targets involved in the process. Most of the E3 ligases play regulatory roles by modifying the stability and accumulation of stress responsive regulatory proteins, such as transcription factors, thus, modifying the downstream responses, or by degrading the proteins involved in the downstream cascade itself. In this review, we summarize and highlight the recent advances in the field of ubiquitination-mediated regulation of plant's responses to various abiotic stresses including limited nutrient availability and metal toxicity. The non-proteolytic role of ubiquitination in epigenetic regulation of abiotic stress induced response has also been discussed.

RING finger protein RGLG1 and RGLG2 negatively modulate MAPKKK18 mediated drought stress tolerance in Arabidopsis

Mitogen activated protein kinase kinase kinase 18 (MAPKKK18) mediated signaling cascade plays important roles in Arabidopsis drought stress tolerance. However, the post-translational modulation patterns of MAPKKK18 are not characterized. In this study, we found that the protein level of MAPKKK18 was tightly controlled by the 26S proteasome. Ubiquitin ligases RGLG1 and RGLG2 ubiquitinated MAPKKK18 at lysine residue K32 and K154, and promoted its degradation. Deletion of RGLG1 and RGLG2 stabilized MAPKKK18 and further enhanced the drought stress tolerance of MAPKKK18-overexpression plants. Our data demonstrate that RGLG1 and RGLG2 negatively regulate MAPKKK18-mediated drought stress tolerance in Arabidopsis.

OsWRKY21 and OsWRKY108 function redundantly to promote phosphate accumulation through maintaining the constitutive expression of OsPHT1;1 under phosphate-replete conditions

Plant Phosphate Transporter 1 (PHT1) proteins, probably the only influx transporters for phosphate (Pi) uptake, are partially degraded on sufficient Pi levels to prevent excessive Pi accumulation. Therefore, the basal/constitutive expression level of PHT1 genes is vital for maintaining Pi uptake under Pi-replete conditions. Rice (Oryza sativa) OsPHT1;1 is a unique gene as it is highly expressed and not responsive to Pi, however the mechanism for maintaining its basal/constitutive expression remains unknown. Using biochemical and genetic approaches, we identified and functionally characterised the transcription factors maintaining the basal/constitutive expression of OsPHT1;1. OsWRKY21 and OsWRKY108 interact within the nucleus and both bind to the W-box in the OsPHT1;1 promoter. Overexpression of OsWRKY21 or OsWRKY108 led to increased Pi accumulation, resulting from elevated expression of OsPHT1;1. By contrast, oswrky21 oswrky108 double mutants showed decreased Pi accumulation and OsPHT1;1 expression in a Pi-dependent manner. Moreover, similar to ospht1;1 mutants, plants expressing the OsWRKY21-SRDX fusion protein (a chimeric dominant suppressor) were impaired in Pi accumulation in Pi-replete roots, accompanied by downregulation of OsPHT1;1 expression. Our findings demonstrated that rice WRKY transcription factors function redundantly to promote Pi uptake by activating OsPHT1;1 expression under Pi-replete conditions, and represent a novel pathway independent of the central Pi signalling system.

Profiling of MicroRNAs and Their Targets in Roots and Shoots Reveals a Potential MiRNA-Mediated Interaction Network in Response to Phosphate Deficiency in the Forestry Tree Betula luminifera

Inorganic phosphate (Pi) is often lacking in natural and agro-climatic environments, which impedes the growth of economically important woody species. Plants have developed strategies to cope with low Pi (LP) availability. MicroRNAs (miRNAs) play important roles in responses to abiotic stresses, including nutrition stress, by regulating target gene expression. However, the miRNA-mediated regulation of these adaptive responses and their underlying coordinating signals are still poorly understood in forestry trees such as Betula luminifera. Transcriptomic libraries, small RNA (sRNA) libraries, and a mixed degradome cDNA library of B. luminifera roots and shoots treated under LP and normal conditions (CK) were constructed and sequenced using next-generation deep sequencing. A comprehensive B. luminifera transcriptome derived from its roots and shoots was constructed, and a total of 76,899 unigenes were generated. Analysis of the transcriptome identified 8,095 and 5,584 differentially expressed genes in roots and shoots, respectively, under LP conditions. sRNA sequencing analyses indicated that 66 and 60 miRNAs were differentially expressed in roots and shoots, respectively, under LP conditions. A total of 109 and 112 miRNA-target pairs were further validated in the roots and shoots, respectively, using degradome sequencing. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis of differential miRNA targets indicated that the "ascorbate and aldarate metabolism" pathway responded to LP, suggesting miRNA-target pairs might participating in the removing of reactive oxidative species under LP stress. Moreover, a putative network of miRNA-target interactions involved in responses to LP stress in B. luminifera is proposed. Taken together, these findings provide useful information to decipher miRNA functions and establish a framework for exploring P signaling networks regulated by miRNAs in B. luminifera and other woody plants. It may provide new insights into the genetic engineering of high use efficiency of Pi in forestry trees.