Arabidopsis DELLA protein degradation is controlled by a type-one protein phosphatase, TOPP4

C-TERMINAL DOMAIN PHOSPHATASE-LIKE 3 contributes to GA-mediated growth and flowering by interaction with DELLA proteins

Gibberellic acid (GA) plays a central role in many plant developmental processes and is crucial for crop improvement. DELLA proteins, the core suppressors in the GA signaling pathway, are degraded by GA via the 26S proteasomal pathway to release the GA response. However, little is known about the phosphorylation-mediated regulation of DELLA proteins. In this study, we combined GA response assays with protein-protein interaction analysis to infer the connection between Arabidopsis thaliana DELLAs and the C-TERMINAL DOMAIN PHOSPHATASE-LIKE 3 (CPL3), a phosphatase involved in the dephosphorylation of RNA polymerase II. We show that CPL3 directly interacts with DELLA proteins and promotes DELLA protein stability by inhibiting its degradation by the 26S proteasome. Consequently, CPL3 negatively modulates multiple GA-mediated processes of plant development, including hypocotyl elongation, flowering time, and anthocyanin accumulation. Taken together, our findings demonstrate that CPL3 serves as a novel regulator that could improve DELLA stability and thereby participate in GA signaling transduction.

Leaf growth - complex regulation of a seemingly simple process

Understanding the underlying mechanisms of plant development is crucial to successfully steer or manipulate plant growth in a targeted manner. Leaves, the primary sites of photosynthesis, are vital organs for many plant species, and leaf growth is controlled by a tight temporal and spatial regulatory network. In this review, we focus on the genetic networks governing leaf cell proliferation, one major contributor to final leaf size. First, we provide an overview of six regulator families of leaf growth in Arabidopsis: DA1, PEAPODs, KLU, GRFs, the SWI/SNF complexes, and DELLAs, together with their surrounding genetic networks. Next, we discuss their evolutionary conservation to highlight similarities and differences among species, because knowledge transfer between species remains a big challenge. Finally, we focus on the increase in knowledge of the interconnectedness between these genetic pathways, the function of the cell cycle machinery as their central convergence point, and other internal and environmental cues.

GSK3 phosphorylates and regulates the Green Revolution protein Rht-B1b to reduce plant height in wheat

The utilization of stabilized DELLA proteins Rht-B1b and Rht-D1b was crucial for increasing wheat (Triticum aestivum) productivity during the Green Revolution. However, the underlying mechanisms remain to be clarified. Here, we cloned a gain-of-function allele of the GSK3/SHAGGY-like kinase-encoding gene GSK3 by characterizing a dwarf wheat mutant. Furthermore, we determined that GSK3 interacts with and phosphorylates the Green Revolution protein Rht-B1b to promote it to reduce plant height in wheat. Specifically, phosphorylation by GSK3 may enhance the activity and stability of Rht-B1b, allowing it to inhibit the activities of its target transcription factors. Taken together, we reveal a positive regulatory mechanism for the Green Revolution protein Rht-B1b by GSK3, which might have contributed to the Green Revolution in wheat.

The E3 ubiquitin ligases SINA1 and SINA2 integrate with the protein kinase CIPK20 to regulate the stability of RGL2a, a positive regulator of anthocyanin biosynthesis

Although DELLA protein destabilization mediated by post-translational modifications is essential for gibberellin (GA) signal transduction and GA-regulated anthocyanin biosynthesis, the related mechanisms remain largely unknown. In this study, we report the ubiquitination and phosphorylation of an apple DELLA protein MdRGL2a in response to GA signaling and its regulatory role in anthocyanin biosynthesis. MdRGL2a could interact with MdWRKY75 to enhance the MdWRKY75-activated transcription of anthocyanin activator MdMYB1 and interfere with the interaction between anthocyanin repressor MdMYB308 and MdbHLH3 or MdbHLH33, thereby promoting anthocyanin accumulation. A protein kinase MdCIPK20 was found to phosphorylate and protect MdRGL2a from degradation, and it was essential for MdRGL2a-promoting anthocyanin accumulation. However, MdRGL2a and MdCIPK20 were ubiquitinated and degraded by E3 ubiquitin ligases MdSINA1 and MdSINA2, respectively, both of which were activated in the presence of GA. Our results display the integration of SINA1/2 with CIPK20 to dynamically regulate GA signaling and will be helpful toward understanding the mechanism of GA signal transduction and GA-inhibited anthocyanin biosynthesis. The discovery of extensive interactions between DELLA and SINA and CIPK proteins in apple will provide reference for the study of ubiquitination and phosphorylation of DELLA proteins in other species.

The role of forkhead-associated (FHA)-domain proteins in plant biology

The forkhead-associated (FHA) domain, a well-characterized small protein module that mediates protein-protein interactions by targeting motifs containing phosphothreonine, is present in many regulatory molecules like protein kinase, phosphatases, transcription factors, and other functional proteins. FHA-domain containing proteins in yeast and human are involved in a large variety of cellular processes such as DNA repair, cell cycle arrest, or pre-mRNA processing. Since the first FHA-domain protein, kinase-associated protein phosphatase (KAPP) was found in plants, the interest in plant FHA-containing proteins has increased dramatically, mainly due to the important role of FHA domain-containing proteins in plant growth and development. In this review, we provide a comprehensive overview of the fundamental properties of FHA domain-containing proteins in plants, and systematically summarized and analyzed the research progress of proteins containing the FHA domain in plants. We also emphasized that AT5G47790 and its homologs may play an important role as the regulatory subunit of protein phosphatase 1 (PP1) in plants.

Protein phosphatases and their targets: Comprehending the interactions in plant signaling pathways

Protein phosphorylation is a vital reversible post-translational modification. This process is established by two classes of enzymes: protein kinases and protein phosphatases. Protein kinases phosphorylate proteins while protein phosphatases dephosphorylate phosphorylated proteins, thus, functioning as 'critical regulators' in signaling pathways. The eukaryotic protein phosphatases are classified as phosphoprotein phosphatases (PPP), metallo-dependent protein phosphatases (PPM), protein tyrosine (Tyr) phosphatases (PTP), and aspartate (Asp)-dependent phosphatases. The PPP and PPM families are serine (Ser)/threonine (Thr) specific phosphatases (STPs) that dephosphorylate Ser and Thr residues. The PTP family dephosphorylates Tyr residues while dual-specificity phosphatases (DsPTPs/DSPs) dephosphorylate Ser, Thr, and Tyr residues. The composition of these enzymes as well as their substrate specificity are important determinants of their functional significance in a number of cellular processes and stress responses. Their role in animal systems is well-understood and characterized. The functional characterization of protein phosphatases has been extensively covered in plants, although the comprehension of their mechanistic basis is an ongoing pursuit. The nature of their interactions with other key players in the signaling process is vital to our understanding. The substrates or targets determine their potential as well as magnitude of the impact they have on signaling pathways. In this article, we exclusively overview the various substrates of protein phosphatases in plant signaling pathways, which are a critical determinant of the outcome of various developmental and stress stimuli.

Type one protein phosphatase regulates fixed-carbon starvation-induced autophagy in Arabidopsis

Autophagy, a conserved pathway that carries out the bulk degradation of cytoplasmic material in eukaryotic cells, is critical for plant physiology and development. This process is tightly regulated by ATG13, a core component of the ATG1 kinase complex, which initiates autophagy. Although ATG13 is known to be dephosphorylated immediately after nutrient starvation, the phosphatase regulating this process is poorly understood. Here, we determined that the Arabidopsis (Arabidopsis thaliana) septuple mutant (topp-7m) and octuple mutant (topp-8m) of TYPE ONE PROTEIN PHOSPHATASE (TOPP) exhibited significantly reduced tolerance to fixed-carbon (C) starvation due to compromised autophagy activity. Genetic analysis placed TOPP upstream of autophagy. Interestingly, ATG13a was found to be an interactor of TOPP. TOPP directly dephosphorylated ATG13a in vitro and in vivo. We identified 18 phosphorylation sites in ATG13a by LC-MS. Phospho-dead ATG13a at these 18 sites significantly promoted autophagy and increased the tolerance of the atg13ab mutant to fixed-C starvation. The dephosphorylation of ATG13a facilitated ATG1a-ATG13a complex formation. Consistently, the recruitment of ATG13a for ATG1a was markedly inhibited in topp-7m-1. Finally, TOPP-controlled dephosphorylation of ATG13a boosted ATG1a phosphorylation. Taken together, our study reveals the crucial role of TOPP in regulating autophagy by stimulating the formation of the ATG1a-ATG13a complex by dephosphorylating ATG13a in Arabidopsis.

Rice protein phosphatase 1 regulatory subunits OsINH2 and OsINH3 participate actively in growth and adaptive responses under abscisic acid

Rice (Oryza sativa L.), a worldwide staple food crop, is affected by various environmental stressors that ultimately reduce yield. However, diversified physiological and molecular responses enable it to cope with adverse factors. It includes the integration of numerous signaling in which protein phosphatase 1 (PP1) plays a pivotal role. Research on PP1 has been mostly limited to the PP1 catalytic subunit in numerous cellular progressions. Therefore, we focused on the role of PP1 regulatory subunits (PP1r), OsINH2 and OsINH3, homologs of AtINH2 and AtINH3 in Arabidopsis, in rice growth and stress adaptations. Our observations revealed that these are ubiquitously expressed regulatory subunits that interacted and colocalized with their counter partners, type 1 protein phosphatase (OsTOPPs) but could not change their subcellular localization. The mutation in OsINH2 and OsINH3 reduced pollen viability, thereby affected rice fertility. They were involved in abscisic acid (ABA)-mediated inhibition of seed germination, perhaps by interacting with osmotic stress/ABA-activated protein kinases (OsSAPKs). Meanwhile, they positively participated in osmotic adjustment by proline biosynthesis, detoxifying reactive oxygen species (ROS) through peroxidases (POD), reducing malondialdehyde formation (MDA), and regulating stress-responsive genes. Moreover, their co-interaction proposed they might mediate cellular processes together or by co-regulation; however, the special behavior of two different PP1r is needed to explore. In a nutshell, this research enlightened the involvement of OsINH2 and OsINH3 in the reproductive growth of rice and adaptive strategies under stress. Hence, their genetic interaction with ABA components and deep mechanisms underlying osmotic regulation and ROS adjustment would explain their role in complex signaling. This research offers the basis for introducing stress-resistant crops.

Wheat genomic study for genetic improvement of traits in China

Bread wheat (Triticum aestivum L.) is a major crop that feeds 40% of the world's population. Over the past several decades, advances in genomics have led to tremendous achievements in understanding the origin and domestication of wheat, and the genetic basis of agronomically important traits, which promote the breeding of elite varieties. In this review, we focus on progress that has been made in genomic research and genetic improvement of traits such as grain yield, end-use traits, flowering regulation, nutrient use efficiency, and biotic and abiotic stress responses, and various breeding strategies that contributed mainly by Chinese scientists. Functional genomic research in wheat is entering a new era with the availability of multiple reference wheat genome assemblies and the development of cutting-edge technologies such as precise genome editing tools, high-throughput phenotyping platforms, sequencing-based cloning strategies, high-efficiency genetic transformation systems, and speed-breeding facilities. These insights will further extend our understanding of the molecular mechanisms and regulatory networks underlying agronomic traits and facilitate the breeding process, ultimately contributing to more sustainable agriculture in China and throughout the world.

Interactions of Gibberellins with Phytohormones and Their Role in Stress Responses

Gibberellins are amongst the main plant growth regulators. Discovered over a century ago, the interest in gibberellins research is growing due to their current and potential applications in crop production and their role in the responses to environmental stresses. In the present review, the current knowledge on gibberellins’ homeostasis and modes of action is outlined. Besides this, the complex interrelations between gibberellins and other plant growth regulators are also described, providing an intricate network of interactions that ultimately drives towards precise and specific gene expression. Thus, genes and proteins identified as being involved in gibberellin responses in model and non-model species are highlighted. Furthermore, the molecular mechanisms governing the gibberellins’ relation to stress responses are also depicted. This review aims to provide a comprehensive picture of the state-of-the-art of the current perceptions of the interactions of gibberellins with other phytohormones, and their responses to plant stresses, thus allowing for the identification of the specific mechanisms involved. This knowledge will help us to improve our understanding of gibberellins’ biology, and might help increase the biotechnological toolbox needed to refine plant resilience, particularly under a climate change scenario.

The GA-DELLA-OsMS188 module controls male reproductive development in rice

Pollen protects male sperm and allows flowering plants to adapt to diverse terrestrial environments, thereby leading to the rapid expansion of plants into new regions. The process of anther/pollen development is coordinately regulated by internal and external factors including hormones. Currently, the molecular mechanisms underlying gibberellin (GA)-mediated male reproductive development in plants remain unknown. We show here that rice DELLA/SLR1, which encodes the central negative regulator of GA signaling, is essential for rice anther development. The slr1-5 mutant exhibits premature programmed cell death of the tapetum, lacks Ubisch bodies, and has no exine and no mature pollen. SLR1 is mainly expressed in tapetal cells and tetrads, and is required for the appropriate expression of genes encoding key factors of pollen development, which are suggested to be OsMS188-targeted genes. OsMS188 is the main component in the essential genetic program of tapetum and pollen development. Further, we demonstrate that SLR1 interacts with OsMS188 to cooperatively activate the expression of the sporopollenin biosynthesis and transport-related genes CYP703A3, DPW, ABCG15 and PKS1 for rapid formation of pollen walls. Overall, the results of this study suggest that the GA hormonal signal is integrated into the anther genetic program and regulates rice anther development through the GA-DELLA-OsMS188 module.

The converging path of protein SUMOylation in phytohormone signalling: highlights and new frontiers

The intersection of phytohormone signalling pathways with SUMOylation, a key post-translational modification, offers an additional layer of control to the phytohormone signalling for sophisticated regulation of plant development. Plants live in a constantly changing environment that are often challenging for the growth and development of plants. Phytohormones play a critical role in modulating molecular-level changes for enabling plants to resist climatic aberrations. The orchestration of such effective molecular responses entails rapid regulation of phytohormone signalling at transcriptional, translational and post-translational levels. Post-translational modifications have emerged as a key player in modulating hormonal pathways. The current review lays emphasis on the role of SUMOylation, a key post-translational modification, in manipulating individual hormone signalling pathways for better plant adaptability. Here, we discuss the recent advancement in the field and highlights how SUMO targets key signalling intermediates including transcription factors to provide a quick response to different biotic or abiotic stresses, sometimes even prior to changes in hormone levels. The understanding of the convergence of SUMOylation and hormonal pathways will offer an additional layer of control to the phytohormone signalling for an intricate and sophisticated regulation of plant development and can be utilised as a tool to generate climate-resilient crops.

Wheat Type One Protein Phosphatase Participates in the Brassinosteroid Control of Root Growth via Activation of BES1

Brassinosteroids (BRs) play key roles in diverse plant growth processes through a complex signaling pathway. Components orchestrating the BR signaling pathway include receptors such as kinases, transcription factors, protein kinases and phosphatases. The proper functioning of the receptor kinase BRI1 and the transcription factors BES1/BZR1 depends on their dephosphorylation by type 2A protein phosphatases (PP2A). In this work, we report that an additional phosphatase family, type one protein phosphatases (PP1), contributes to the regulation of the BR signaling pathway. Co-immunoprecipitation and BiFC experiments performed in Arabidopsis plants overexpressing durum wheat TdPP1 showed that TdPP1 interacts with dephosphorylated BES1, but not with the BRI1 receptor. Higher levels of dephosphorylated, active BES1 were observed in these transgenic lines upon BR treatment, indicating that TdPP1 modifies the BR signaling pathway by activating BES1. Moreover, ectopic expression of durum wheat TdPP1 lead to an enhanced growth of primary roots in comparison to wild-type plants in presence of BR. This phenotype corroborates with a down-regulation of the BR-regulated genes CPD and DWF4. These data suggest a role of PP1 in fine-tuning BR-driven responses, most likely via the control of the phosphorylation status of BES1.

The blue light receptor CRY1 interacts with GID1 and DELLA proteins to repress GA signaling during photomorphogenesis in Arabidopsis

Light is a critical environmental cue that regulates a variety of diverse plant developmental processes. Cryptochrome 1 (CRY1) is the major photoreceptor that mediates blue light-dependent photomorphogenic responses such as the inhibition of hypocotyl elongation. Gibberellin (GA) participates in the repression of photomorphogenesis and promotes hypocotyl elongation. However, the antagonistic interaction between blue light and GA is not well understood. Here, we report that blue light represses GA-induced degradation of the DELLA proteins (DELLAs), which are key negative regulators in the GA signaling pathway, via CRY1, thereby inhibiting the GA response during hypocotyl elongation. Both in vitro and in vivo biochemical analyses demonstrated that CRY1 physically interacts with GA receptors-GA-INSENSITIVE DWARF 1 proteins (GID1s)-and DELLAs in a blue light-dependent manner. Furthermore, we showed that CRY1 inhibits the association between GID1s and DELLAs. Genetically, CRY1 antagonizes the function of GID1s to repress the expression of cell elongation-related genes and thus hypocotyl elongation. Taken together, our findings demonstrate that CRY1 coordinates blue light and GA signaling for plant photomorphogenesis by stabilizing DELLAs through the binding and inactivation of GID1s, providing new insights into the mechanism by which blue light antagonizes the function of GA in photomorphogenesis.

Understanding and Exploiting Post-Translational Modifications for Plant Disease Resistance

Plants are constantly threatened by pathogens, so have evolved complex defence signalling networks to overcome pathogen attacks. Post-translational modifications (PTMs) are fundamental to plant immunity, allowing rapid and dynamic responses at the appropriate time. PTM regulation is essential; pathogen effectors often disrupt PTMs in an attempt to evade immune responses. Here, we cover the mechanisms of disease resistance to pathogens, and how growth is balanced with defence, with a focus on the essential roles of PTMs. Alteration of defence-related PTMs has the potential to fine-tune molecular interactions to produce disease-resistant crops, without trade-offs in growth and fitness.

Decoding the molecular mechanism of parthenocarpy in Musa spp. through protein-protein interaction network

Banana, one of the most important staple fruit among global consumers is highly sterile owing to natural parthenocarpy. Identification of genetic factors responsible for parthenocarpy would facilitate the conventional breeders to improve the seeded accessions. We have constructed Protein-protein interaction (PPI) network through mining differentially expressed genes and the genes used for transgenic studies with respect to parthenocarpy. Based on the topological and pathway enrichment analysis of proteins in PPI network, 12 candidate genes were shortlisted. By further validating these candidate genes in seeded and seedless accession of Musa spp. we put forward MaAGL8, MaMADS16, MaGH3.8, MaMADS29, MaRGA1, MaEXPA1, MaGID1C, MaHK2 and MaBAM1 as possible target genes in the study of natural parthenocarpy. In contrary, expression profile of MaACLB-2 and MaZEP is anticipated to highlight the difference in artificially induced and natural parthenocarpy. By exploring the PPI of validated genes from the network, we postulated a putative pathway that bring insights into the significance of cytokinin mediated CLAVATA(CLV)-WUSHEL(WUS) signaling pathway in addition to gibberellin mediated auxin signaling in parthenocarpy. Our analysis is the first attempt to identify candidate genes and to hypothesize a putative mechanism that bridges the gaps in understanding natural parthenocarpy through PPI network.

Diurnal dynamics of the Arabidopsis rosette proteome and phosphoproteome

Plant growth depends on the diurnal regulation of cellular processes, but it is not well understood if and how transcriptional regulation controls diurnal fluctuations at the protein level. Here, we report a high-resolution Arabidopsis thaliana (Arabidopsis) leaf rosette proteome acquired over a 12 hr light:12 hr dark diurnal cycle and the phosphoproteome immediately before and after the light-to-dark and dark-to-light transitions. We quantified nearly 5,000 proteins and 800 phosphoproteins, of which 288 fluctuated in their abundance and 226 fluctuated in their phosphorylation status. Of the phosphoproteins, 60% were quantified for changes in protein abundance. This revealed six proteins involved in nitrogen and hormone metabolism that had concurrent changes in both protein abundance and phosphorylation status. The diurnal proteome and phosphoproteome changes involve proteins in key cellular processes, including protein translation, light perception, photosynthesis, metabolism and transport. The phosphoproteome at the light-dark transitions revealed the dynamics at phosphorylation sites in either anticipation of or response to a change in light regime. Phosphorylation site motif analyses implicate casein kinase II and calcium/calmodulin-dependent kinases among the primary light-dark transition kinases. The comparative analysis of the diurnal proteome and diurnal and circadian transcriptome established how mRNA and protein accumulation intersect in leaves during the diurnal cycle of the plant.

Function of histone H2B monoubiquitination in transcriptional regulation of auxin biosynthesis in Arabidopsis

The auxin IAA is a vital plant hormone in controlling growth and development, but our knowledge about its complicated biosynthetic pathways and molecular regulation are still limited and fragmentary. cytokinin induced root waving 2 (ckrw2) was isolated as one of the auxin-deficient mutants in a large-scale forward genetic screen aiming to find more genes functioning in auxin homeostasis and/or its regulation. Here we show that CKRW2 is identical to Histone Monoubiquitination 1 (HUB1), a gene encoding an E3 ligase required for histone H2B monoubiquitination (H2Bub1) in Arabidopsis. In addition to pleiotropic defects in growth and development, loss of CKRW2/HUB1 function also led to typical auxin-deficient phenotypes in roots, which was associated with significantly lower expression levels of several functional auxin synthetic genes, namely TRP2/TSB1, WEI7/ASB1, YUC7 and AMI1. Corresponding defects in H2Bub1 were detected in the coding regions of these genes by chromatin immunoprecipitation (ChIP) analysis, indicating the involvement of H2Bub1 in regulating auxin biosynthesis. Importantly, application of exogenous cytokinin (CK) could stimulate CKRW2/HUB1 expression, providing an epigenetic avenue for CK to regulate the auxin homeostasis. Our results reveal a previously unknown mechanism for regulating auxin biosynthesis via HUB1/2-mediated H2Bub1 at the chromatin level.

The Rice Abscisic Acid-Responsive RING Finger E3 Ligase OsRF1 Targets OsPP2C09 for Degradation and Confers Drought and Salinity Tolerance in Rice

Drought and salinity are major important factors that restrain growth and productivity of rice. In plants, many really interesting new gene (RING) finger proteins have been reported to enhance drought and salt tolerance. However, their mode of action and interacting substrates are largely unknown. Here, we identified a new small RING-H2 type E3 ligase OsRF1, which is involved in the ABA and stress responses of rice. OsRF1 transcripts were highly induced by ABA, salt, or drought treatment. Upregulation of OsRF1 in transgenic rice conferred drought and salt tolerance and increased endogenous ABA levels. Consistent with this, faster transcriptional activation of key ABA biosynthetic genes, ZEP, NCED3, and ABA4, was observed in OsRF1-OE plants compared with wild type in response to drought stress. Yeast two-hybrid assay, BiFC, and co-immunoprecipitation analysis identified clade A PP2C proteins as direct interacting partners with OsRF1. In vitro ubiquitination assay indicated that OsRF1 exhibited E3 ligase activity, and that it targeted OsPP2C09 protein for ubiquitination and degradation. Cell-free degradation assay further showed that the OsPP2C09 protein is more rapidly degraded by ABA in the OsRF1-OE rice than in the wild type. The combined results suggested that OsRF1 is a positive player of stress responses by modulating protein stability of clade A PP2C proteins, negative regulators of ABA signaling.

Protein Phosphorylation in Plant Cell Signaling

Owing to their sessile nature, plants have evolved sophisticated sensory mechanisms to respond quickly and precisely to the changing environment. The extracellular stimuli are perceived and integrated by diverse receptors, such as receptor-like protein kinases (RLKs) and receptor-like proteins (RLPs), and then transmitted to the nucleus by complex cellular signaling networks, which play vital roles in biological processes including plant growth, development, reproduction, and stress responses. The posttranslational modifications (PTMs) are important regulators for the diversification of protein functions in plant cell signaling. Protein phosphorylation is an important and well-characterized form of the PTMs, which influences the functions of many receptors and key components in cellular signaling. Protein phosphorylation in plants predominantly occurs on serine (Ser) and threonine (Thr) residues, which is dynamically and reversibly catalyzed by protein kinases and protein phosphatases, respectively. In this review, we focus on the function of protein phosphorylation in plant cell signaling, especially plant hormone signaling, and highlight the roles of protein phosphorylation in plant abiotic stress responses.

Regulation of DELLA Proteins by Post-translational Modifications

DELLA proteins are the negative regulators of the gibberellin (GA) signaling pathway. GAs have a pervasive effect on plant physiology, influencing processes that span the entire life cycle of the plant. All the information encoded by GAs, either environmental or developmental in origin, is canalized through DELLAs, which modulate the activity of many transcription factors and transcriptional regulators. GAs unlock the signaling pathway by triggering DELLA polyubiquitination and degradation by the 26S proteasome. Recent reports indicate, however, that there are other pathways that trigger DELLA polyubiquitination and degradation independently of GAs. Moreover, results gathered during recent years indicate that other post-translational modifications (PTMs), namely phosphorylation, SUMOylation and glycosylation, modulate DELLA function. The convergence of several PTMs in DELLA therefore highlights the strict regulation to which these proteins are subject. In this review, we summarize these discoveries and discuss DELLA PTMs from an evolutionary perspective and examine the possibilities these and other post-translational regulations offer to improve DELLA-dependent agronomic traits.

Role of Protein Phosphatase1 Regulatory Subunit3 in Mediating the Abscisic Acid Response

Protein phosphatase1 (PP1) plays important roles in eukaryotes, including in plant hormone responses, and functions as a holoenzyme that consists of catalytic and regulatory subunits. Animal genomes encode ∼200 PP1-interacting proteins; by contrast, only a few have been reported in plants. In this study, PP1 Regulatory Subunit3 (PP1R3), a protein that interacts with PP1 in Arabidopsis (Arabidopsis thaliana), was characterized by mass spectrometry. PP1R3 was widely expressed in various plant tissues and PP1R3 colocalized with Type One Protein Phosphatases (TOPPs) in the nucleus and cytoplasm. The pp1r3 mutants were hypersensitive to abscisic acid (ABA), similar to the dominant-negative mutant topp4-1 or the loss-of-function multiple mutants topp1 topp4-3, topp8 topp9, topp6/7/9, topp1/2/4-3/6/7/9, and topp1/4-3/5/6/7/8/9 (topp-7m). About two-thirds of differentially expressed genes in topp-7m showed the same gene expression changes as in pp1r3-2 In response to ABA, the phenotypes of pp1r3 topp1 topp4-3 and pp1r3 topp4-1 were consistent with those of pp1r3, while pp1r3 abi1-1 showed an additive effect of the pp1r3 and abi1-1 (mutation in Abscisic Acid Insensitive1 [ABI1]) single mutants. Moreover, pp1r3 could partially recover the ABA response-related phenotype, gene expression, and plant morphology of topp4-1 PP1R3 inhibited TOPP enzyme activity and facilitated the nuclear localization of TOPP4. By contrast, ABA treatment increased the amounts of TOPP1 and TOPP4 in the cytoplasm. Importantly, nuclear localization of TOPP4 partially restored the ABA-hypersensitive phenotype of topp4-1 Overall, our results suggest that the PP1R3:TOPP holoenzyme functions in parallel with ABI1 in the nucleus to regulate ABA signaling.

FKF1 F-box protein promotes flowering in part by negatively regulating DELLA protein stability under long-day photoperiod in Arabidopsis

FLAVIN-BINDING KELCH REPEAT F-BOX 1 (FKF1) encodes an F-box protein that regulates photoperiod flowering in Arabidopsis under long-day conditions (LDs). Gibberellin (GA) is also important for regulating flowering under LDs. However, how FKF1 and the GA pathway work in concert in regulating flowering is not fully understood. Here, we showed that the mutation of FKF1 could cause accumulation of DELLA proteins, which are crucial repressors in GA signaling pathway, thereby reducing plant sensitivity to GA in flowering. Both in vitro and in vivo biochemical analyses demonstrated that FKF1 directly interacted with DELLA proteins. Furthermore, we showed that FKF1 promoted ubiquitination and degradation of DELLA proteins. Analysis of genetic data revealed that FKF1 acted partially through DELLAs to regulate flowering under LDs. In addition, DELLAs exerted a negative feedback on FKF1 expression. Collectively, these findings demonstrate that FKF1 promotes flowering partially by negatively regulating DELLA protein stability under LDs, and suggesting a potential mechanism linking the FKF1 to the GA signaling DELLA proteins.

Plant protein phosphatases: What do we know about their mechanism of action?

Protein phosphorylation is a major reversible post-translational modification. Protein phosphatases function as 'critical regulators' in signaling networks through dephosphorylation of proteins, which have been phosphorylated by protein kinases. A large understanding of their working has been sourced from animal systems rather than the plant or the prokaryotic systems. The eukaryotic protein phosphatases include phosphoprotein phosphatases (PPP), metallo-dependent protein phosphatases (PPM), protein tyrosine (Tyr) phosphatases (PTP), and aspartate (Asp)-dependent phosphatases. The PPP and PPM families are serine(Ser)/threonine(Thr)-specific phosphatases (STPs), while PTP family is Tyr specific. Dual-specificity phosphatases (DsPTPs/DSPs) dephosphorylate Ser, Thr, and Tyr residues. PTPs lack sequence homology with STPs, indicating a difference in catalytic mechanisms, while the PPP and PPM families share a similar structural fold indicating a common catalytic mechanism. The catalytic cysteine (Cys) residue in the conserved HCX₅ R active site motif of the PTPs acts as a nucleophile during hydrolysis. The PPP members require metal ions, which coordinate the phosphate group of the substrate, followed by a nucleophilic attack by a water molecule and hydrolysis. The variable holoenzyme assembly of protein phosphatase(s) and the overlap with other post-translational modifications like acetylation and ubiquitination add to their complexity. Though their functional characterization is extensively reported in plants, the mechanistic nature of their action is still being explored by researchers. In this review, we exclusively overview the plant protein phosphatases with an emphasis on their mechanistic action as well as structural characteristics.

An Updated Overview on the Regulation of Seed Germination

The ability of a seed to germinate and establish a plant at the right time of year is of vital importance from an ecological and economical point of view. Due to the fragility of these early growth stages, their swiftness and robustness will impact later developmental stages and crop yield. These traits are modulated by a continuous interaction between the genetic makeup of the plant and the environment from seed production to germination stages. In this review, we have summarized the established knowledge on the control of seed germination from a molecular and a genetic perspective. This serves as a “backbone” to integrate the latest developments in the field. These include the link of germination to events occurring in the mother plant influenced by the environment, the impact of changes in the chromatin landscape, the discovery of new players and new insights related to well-known master regulators. Finally, results from recent studies on hormone transport, signaling, and biophysical and mechanical tissue properties are underscoring the relevance of tissue-specific regulation and the interplay of signals in this crucial developmental process.

Origin and evolution of gibberellin signaling and metabolism in plants

Gibberellins modulate multiple aspects of plant behavior. The molecular mechanism by which these hormones are perceived and how this information is translated into transcriptional changes has been elucidated in vascular plants: gibberellins are perceived by the nuclear receptor GID1, which then interacts with the DELLA nuclear proteins and promote their degradation, resulting in the modification of the activity of transcription factors with which DELLAs interact physically. However, several important questions are still pending: how does a single molecule perform such a vast array of functions along plant development? What property do gibberellins add to plant behavior? A closer look at gibberellin action from an evolutionary perspective can help answer these questions. DELLA proteins are conserved in all land plants, and predate the emergence of a full gibberellin metabolic pathway and the GID1 receptor in the ancestor of vascular plants. The origin of gibberellin signaling is linked to the exaptation by GID1 of the N-terminal domain in DELLA, which already acted as a transcriptional coactivator domain in the ancestral DELLA proteins. At least the ability to control plant growth seems to be encoded already in the ancestral DELLA protein too, suggesting that gibberellins' functional diversity is the direct consequence of DELLA protein activity. Finally, comparative network analysis suggests that gibberellin signaling increases the coordination of transcriptional responses, providing a theoretical framework for the role of gibberellins in plant adaptation at the evolutionary scale, which further needs experimental testing.

Type one protein phosphatases (TOPPs) contribute to the plant defense response in Arabidopsis

Plant immunity must be tightly controlled to avoid activation of defense mechanisms in the absence of pathogen attack. Protein phosphorylation is a common mechanism regulating immune signaling. In Arabidopsis thaliana, nine members of the type one protein phosphatase (TOPP) family (also known as protein phosphatase 1, PP1) have been identified. Here, we characterized the autoimmune phenotype of topp4-1, a previously identified dominant-negative mutant of TOPP4. Epistasis analysis showed that defense activation in topp4-1 depended on NON-RACE-SPECIFIC DISEASE RESISTANCE1, PHYTOALEXIN DEFICIENT4, and the salicylic acid pathway. We generated topp1/4/5/6/7/8/9 septuple mutants to investigate the function of TOPPs in plant immunity. Elevated defense gene expression and enhanced resistance to Pseudomonas syringae pv. tomato (Pst) DC3000 in the septuple mutant indicate that TOPPs function in plant defense responses. Furthermore, TOPPs physically interacted with mitogen-activated protein kinases (MAPKs) and affected the MAPK-mediated downstream defense pathway. Thus, our study reveals that TOPPs are important regulators of plant immunity.

Interplay between REVEILLE1 and RGA-LIKE2 regulates seed dormancy and germination in Arabidopsis

Environmental light signal and GAs synergistically regulate seed dormancy and germination. The phytochrome B (phyB) photoreceptor regulates expression of the REVEILLE1 (RVE1) transcription factor, which directly inhibits GIBBERELLIN 3-OXIDASE2 transcription, suppressing GA biosynthesis. However, whether phyB-RVE1 coordinates with GA signaling in controlling seed dormancy and germination remains unknown. Here, we demonstrate that RVE1 regulation of seed dormancy and germination requires a DELLA repressor, REPRESSOR OF GA-LIKE2 (RGL2), in Arabidopsis thaliana. RVE1 interacts with both RGL2 and its E3 ubiquitin ligase SLEEPY1 (SLY1) and promotes RGL2 stability by restraining the RGL2-SLY1 interaction. Furthermore, RVE1 and RGL2 synergistically regulate global transcriptome changes; RGL2 enhances the DNA-binding capacity and transcriptional activity of RVE1 in regulating downstream gene expression. Moreover, RGL2 expression is repressed by phyB. Our study reveals a novel regulatory mechanism in which the RVE1-RGL2 module coordinately controls seed dormancy and germination by integrating light perception, GA metabolism and GA signaling pathways.

To preserve or to destroy, that is the question: the role of the cell wall integrity pathway in pollen tube growth

In plants, cell-shape is defined by the cell wall, a complex network of polymers located outside the plasma membrane. During cell growth, cell wall properties have to be adjusted, assuring cell expansion without compromising cell integrity. Plasma membrane-located receptors sense cell wall properties, transducing extracellular signals into intracellular cascades through the cell wall integrity (CWI) pathway that, in turn, leads to adjustments in the regulation and composition of the cell wall. Using pollen tube growth as a single celled model system, we describe the importance of RAPID ALKALINIZATION FACTOR (RALF) peptides as sensors of cell wall integrity. RALF peptides can mediate the communication between cell wall components and plasma membrane-localized receptor-like kinases (RLKs) of the CrRLK1L family. The subsequent activation of intracellular pathways regulates H⁺, Ca²⁺, and ROS levels in the cell and apoplast, thereby modulating cell wall integrity. Interestingly, the RALF-CrRLK1L module and some of the components working up- and downstream of the RLK is conserved in many other developmental and physiological signaling processes.

An unreported NB-LRR protein SUT1 is required for the autoimmune response mediated by type one protein phosphatase 4 mutation (topp4-1) in Arabidopsis

Our previous study indicates that protein phosphatase 1 (PP1) is involved in plant immunity. To elucidate the underlying molecular mechanism, a genetic screening assay was carried out to identify suppressors of type one protein phosphatase 4 mutation (topp4-1) (sut). Molecular and genetic approaches were used to investigate the mechanism of activation of autoimmune response in topp4-1. We performed a map-based cloning assay to identify the SUT1 gene, which encodes a coiled-coil nucleotide-binding leucine-rich-repeat (NB-LRR) protein (CNL). SUT1 physically interacts with TYPE ONE PROTEIN PHOSPHATASE 4 (TOPP4) and topp4-1. The mutated topp4-1 protein activates the autoimmune response in the cytoplasm and promotes the accumulation of SUT1 at both the transcription and the protein levels. Furthermore, our genetic and physical interactions confirm that the topp4-1-induced autoimmune responses are probably mediated by HEAT SHOCK PROTEIN 90 (HSP90) and REQUIRED FOR MLA12 RESISTANCE 1 (RAR1). This study reveals that TOPP4 phosphatase is likely guarded by SUT1 in plant immunity.

A single nucleotide mutation in GID1c disrupts its interaction with DELLA1 and causes a GA-insensitive dwarf phenotype in peach

Plant stature is one important factor that affects the productivity of peach orchards. However, little is known about the molecular mechanism(s) underlying the dwarf phenotype of peach tree. Here, we report a dwarfing mechanism in the peach cv. FenHuaShouXingTao (FHSXT). The dwarf phenotype of 'FHSXT' was caused by shorter cell length compared to the standard cv. QiuMiHong (QMH). 'FHSXT' contained higher endogenous GA levels than did 'QMH' and did not response to exogenous GA treatment (internode elongation). These results indicated that 'FHSXT' is a GA-insensitive dwarf mutant. A dwarf phenotype-related single nucleotide mutation in the gibberellic acid receptor GID1 was identified in 'FHSXT' (GID1c^S191F ), which was also cosegregated with dwarf phenotype in 30 tested cultivars. GID1c^S191F was unable to interact with the growth-repressor DELLA1 even in the presence of GA. 'FHSXT' accumulated a higher level of DELLA1, the degradation of which is normally induced by its interaction with GID1. The DELLA1 protein level was almost undetectable in 'QMH', but not reduced in 'FHSXT' after GA₃ treatment. Our results suggested that a nonsynonymous single nucleotide mutation in GID1c disrupts its interaction with DELLA1 resulting in a GA-insensitive dwarf phenotype in peach.

Physiological responses and proteomic changes reveal insights into Stylosanthes response to manganese toxicity

BACKGROUND

Manganese (Mn), an essential element for plants, can be toxic when present in excess. Stylo (Stylosanthes) is a pioneer tropical legume with great potential for Mn tolerance, but its Mn tolerance mechanisms remain poorly understood.

RESULTS

In this study, variations in Mn tolerance were observed among nine stylo genotypes. Stylo genotype 'RY5' exhibited the highest Mn tolerance compared to the other tested genotypes, whereas 'TF2001' was a Mn-sensitive genotype. The mechanisms underlying the response of stylo to Mn toxicity were further investigated using these two genotypes with contrasting Mn tolerance. Results showed that stylo genotype RY5 exhibited Mn tolerance superior to that of genotype TF2001, showing lower reductions in leaf chlorophyll concentration, chlorophyll fluorescence parameters, photosynthetic indexes and plant dry weight under Mn toxicity. A label-free quantitative proteomic analysis was conducted to investigate the protein profiles in the leaves and roots of RY5 in response to Mn toxicity. A total of 356 differentially expressed proteins (DEPs) were identified, including 206 proteins from leaves and 150 proteins from roots, which consisted of 71 upregulated, 62 downregulated, 127 strongly induced and 96 completely suppressed proteins. These DEPs were mainly involved in defense response, photosynthesis, carbon fixation, metabolism, cell wall modulation and signaling. The qRT-PCR analysis verified that 10 out of 12 corresponding gene transcription patterns correlated with their encoding proteins after Mn exposure. Finally, a schematic was constructed to reveal insights into the molecular processes in the leaves and roots of stylo in response to Mn toxicity.

CONCLUSIONS

These findings suggest that stylo plants may cope with Mn toxicity by enhancing their defense response and phenylpropanoid pathways, adjusting photosynthesis and metabolic processes, and modulating protein synthesis and turnover. This study provides a platform for the future study of Mn tolerance mechanisms in stylo and may lead to a better understanding of the potential mechanisms underlying tropical legume adaptation to Mn toxicity.

Using CRISPR/Cas9 genome editing in tomato to create a gibberellin-responsive dominant dwarf DELLA allele

The tomato PROCERA gene encodes a DELLA protein, and loss-of-function mutations derepress growth. We used CRISPR/Cas9 and a single guide RNAs (sgRNA) to target mutations to the PROCERA DELLA domain, and recovered several loss-of-function mutations and a dominant dwarf mutation that carries a deletion of one amino acid in the DELLA domain. This is the first report of a dominant dwarf PROCERA allele. This allele retains partial responsiveness to exogenously applied gibberellin. Heterozygotes show an intermediate phenotype at the seedling stage, but adult heterozygotes are as dwarfed as homozygotes.

Protein Language: Post-Translational Modifications Talking to Each Other

Post-translational modifications (PTMs) are at the heart of many cellular signaling events. Apart from a single regulatory PTM, there are also PTMs that function in orchestrated manners. Such PTM crosstalk usually serves as a fine-tuning mechanism to adjust cellular responses to the slightest changes in the environment. While PTM crosstalk has been studied in depth in various species; in plants, this field is just emerging. In this review, we discuss recent studies on crosstalk between three of the most common protein PTMs in plant cells, being phosphorylation, ubiquitination, and sumoylation, and we highlight the diverse underlying mechanisms as well as signaling outputs of such crosstalk.

The plant pathogen Pseudomonas aeruginosa triggers a DELLA-dependent seed germination arrest in Arabidopsis

To anticipate potential seedling damage, plants block seed germination under unfavorable conditions. Previous studies investigated how seed germination is controlled in response to abiotic stresses through gibberellic and abscisic acid signaling. However, little is known about whether seeds respond to rhizosphere bacterial pathogens. We found that Arabidopsis seed germination is blocked in the vicinity of the plant pathogen Pseudomonas aeruginosa. We identified L-2-amino-4-methoxy-trans-3-butenoic acid (AMB), released by P. aeruginosa, as a biotic compound triggering germination arrest. We provide genetic evidence that in AMB-treated seeds DELLA factors promote the accumulation of the germination repressor ABI5 in a GA-independent manner. AMB production is controlled by the quorum sensing system IQS. In vitro experiments show that the AMB-dependent germination arrest protects seedlings from damage induced by AMB. We discuss the possibility that this could serve as a protective response to avoid severe seedling damage induced by AMB and exposure to a pathogen.

The plant embryo within a seed is well protected. While it cannot stay within the seed forever, the embryo can often wait for the right conditions before it develops into a seedling and continues its life cycle. Indeed, plants have evolved several ways to time this process – which is known as germination – to maximize the chances that their seedlings will survive. For example, if the environment is too hot or too dark, the seed will make a hormone that stops it from germinating.

In addition to environmental factors like light and temperature, a seed in the real word is continuously confronted with soil microbes that may harm or benefit the plant. However, few researchers have asked whether seeds control their germination in response to other living organisms.

The bacterium Pseudomonas aeruginosa lives in a wide spectrum of environments, including the soil, and can cause diseases in both and plants and animals. Chahtane et al. now report that seeds of the model plant Arabidopsis thaliana do indeed repress their germination when this microbe is present. Specifically, the seeds respond to a molecule released from the bacteria called L-2-amino-4-methoxy-trans-3-butenoic acid, or AMB for short. Like the bacteria, AMB is harmful to young seedlings, but Chahtane et al. showed that the embryo within the seed is protected from its toxic effects.

Further experiments revealed that the seed's response to the bacterial molecule requires many of the same signaling components that repress germination when environmental conditions are unfavorable. However, Chahtane et al. note that AMB activates these components in an unusual way that they still do not understand.

The genes that control the production of AMB are known to also control how bacterial populations behave as they accumulate to high densities. It is therefore likely that Pseudomonas aeruginosa would make AMB if it reached a high density in the soil. This raises the possibility that plants have specifically evolved to stop germination if there are enough microbes nearby to pose a risk of disease. This hypothesis, however, is only one of several possible explanations and remains speculative at this stage; further work is now needed to evaluate it. Nevertheless, identifying how AMB interferes with the signaling components that control germination and plant growth may guide the design of new herbicides that could, for example, control weeds in the farming industry.

The Protein Phosphatases ATUNIS1 and ATUNIS2 Regulate Cell Wall Integrity in Tip-Growing Cells

Fast tip-growing plant cells such as pollen tubes (PTs) and root hairs (RHs) require a robust coordination between their internal growth machinery and modifications of their extracellular rigid, yet extensible, cell wall (CW). Part of this essential coordination is governed by members of the Catharanthus roseus receptor-like kinase1-like (CrRLK1L) subfamily of RLKs with FERONIA (FER) and its closest homologs, ANXUR1 (ANX1) and ANX2, controlling CW integrity during RH and PT growth, respectively. Recently, Leucine-Rich Repeat Extensin 8 (LRX8) to LRX11 were also shown to be important for CW integrity in PTs. We previously reported an anx1 anx2 suppressor screen in Arabidopsis thaliana that revealed MARIS (MRI) as a positive regulator of both FER- and ANX1/2-dependent CW integrity pathways. Here, we characterize a suppressor that exhibits a weak rescue of the anx1 anx2 PT bursting phenotype and a short RH phenotype. The corresponding suppressor mutation causes a D94N substitution in a Type One Protein Phosphatase we named ATUNIS1 (AUN1). We show that AUN1 and its closest homolog, AUN2, are nucleocytoplasmic negative regulators of tip growth. Moreover, we demonstrate that AUN1^D94N and AUN1^H127A harboring mutations in key amino acids of the conserved catalytic site of phosphoprotein phosphatases function as dominant amorphic variants that repress PT growth. Finally, genetic interaction studies using the hypermorph MRI^R240C and amorph AUN1^D94N dominant variants indicate that LRX8-11 and ANX1/2 function in distinct but converging pathways to fine-tune CW integrity during tip growth.

Identification and functional analysis of cassava DELLA proteins in plant disease resistance against cassava bacterial blight

Gibberellin (GA) is an essential plant hormone in plant growth and development as well as various stress responses. DELLA proteins are important repressors of GA signal pathway. GA and DELLA have been extensively investigated in several model plants. However, the in vivo roles of GA and DELLA in cassava, one of the most important crops and energy crops in the tropical area, are unknown. In this study, systematic genome-wide analysis identified 4 MeDELLAs in cassava, as evidenced by the evolutionary tree, gene structures and motifs analyses. Gene expression analysis found that 4 MeDELLAs were commonly regulated by flg22 and Xanthomonas axonopodis pv manihotis (Xam). Through overexpression in Nicotiana benthamiana, we found that 4 MeDELLAs conferred improved disease resistance against cassava bacterial blight. Through virus-induced gene silencing (VIGS) in cassava, we found that MeDELLA-silenced plants exhibited decreased disease resistance, with less callose deposition and lower transcript levels of defense-related genes. This is the first study identifying MeDELLAs as positive regulators of disease resistance against cassava bacterial blight.

Genome wide identification of wheat and Brachypodium type one protein phosphatases and functional characterization of durum wheat TdPP1a

Reversible phosphorylation is an essential mechanism regulating signal transduction during development and environmental stress responses. An important number of dephosphorylation events in the cell are catalyzed by type one protein phosphatases (PP1), which catalytic activity is driven by the binding of regulatory proteins that control their substrate specificity or subcellular localization. Plants harbor several PP1 isoforms accounting for large functional redundancies. While animal PP1s were reported to play relevant roles in controlling multiple cellular processes, plant orthologs remain poorly studied. To decipher the role of plant PP1s, we compared PP1 genes from three monocot species, Brachypodium, common wheat and rice at the genomic and transcriptomic levels. To gain more insight into the wheat PP1 proteins, we identified and characterized TdPP1a, the first wheat type one protein phosphatase from a Tunisian durum wheat variety Oum Rabiaa3. TdPP1a is highly conserved in sequence and structure when compared to mammalian, yeast and other plant PP1s. We demonstrate that TdPP1a is an active, metallo-dependent phosphatase in vitro and is able to interact with AtI2, a typical regulator of PP1 functions. Also, TdPP1a is capable to complement the heat stress sensitivity of the yeast mutant indicating that TdPP1a is functional also in vivo. Moreover, transient expression of TdPP1a::GFP in tobacco leaves revealed that it is ubiquitously distributed within the cell, with a strong accumulation in the nucleus. Finally, transcriptional analyses showed similar expression levels in roots and leaves of durum wheat seedlings. Interestingly, the expression in leaves is significantly induced following salinity stress, suggesting a potential role of TdPP1a in wheat salt stress response.

MLK1 and MLK2 Coordinate RGA and CCA1 Activity to Regulate Hypocotyl Elongation in Arabidopsis thaliana

Gibberellins (GAs) modulate diverse developmental processes throughout the plant life cycle. However, the interaction between GAs and the circadian rhythm remains unclear. Here, we report that MUT9p-LIKE KINASE1 (MLK1) and MLK2 mediate the interaction between GAs and the circadian clock to regulate hypocotyl elongation in Arabidopsis thaliana DELLA proteins function as master growth repressors that integrate phytohormone signaling and environmental pathways in plant development. MLK1 and MLK2 interact with the DELLA protein REPRESSOR OF ga1-3 (RGA). Loss of MLK1 and MLK2 function results in plants with short hypocotyls and hyposensitivity to GAs. MLK1/2 and RGA directly interact with CIRCADIAN CLOCK ASSOCIATED1 (CCA1), which targets the promoter of DWARF4 (DWF4) to regulate its roles in cell expansion. MLK1/2 antagonize the ability of RGA to bind CCA1, and these factors coordinately regulate the expression of DWF4 RGA suppressed the ability of CCA1 to activate expression from the DWF4 promoter, but MLK1/2 reversed this suppression. Genetically, MLK1/2 act in the same pathway as RGA and CCA1 in hypocotyl elongation. Together, our results provide insight into the mechanism by which MLK1 and MLK2 antagonize the function of RGA in hypocotyl elongation and suggest that MLK1/2 coordinately mediate the regulation of plant development by GAs and the circadian rhythm in Arabidopsis.

Cold-Induced Male Meiotic Restitution in Arabidopsis thaliana Is Not Mediated by GA-DELLA Signaling

Short periods of cold stress induce male meiotic restitution and diploid pollen formation in Arabidopsis thaliana by specifically interfering with male meiotic cytokinesis. Similar alterations in male meiotic cell division and gametophytic ploidy stability occur when gibberellic acid (GA) signaling is perturbed in developing anthers. In this study, we found that exogenous application of GA primarily induces second division restitution (SDR)-type pollen in Arabidopsis, similar to what cold does. Driven by the close similarity in cellular defects, we tested the hypothesis that cold-induced meiotic restitution is mediated by GA-DELLA signaling. Using a combination of chemical, genetic and cytological approaches, however, we found that both exogenously and endogenously altered GA signaling do not affect the cold sensitivity of male meiotic cytokinesis. Moreover, in vivo localization study using a GFP-tagged version of RGA protein revealed that cold does not affect the expression pattern and abundance of DELLA in Arabidopsis anthers at tetrad stage. Expression study found that transcript of RGA appears enhanced in cold-stressed young flower buds. Since our previous work demonstrated that loss of function of DELLA causes irregular male meiotic cytokinesis, we here conclude that cold-induced meiotic restitution is not mediated by DELLA-dependent GA signaling.

Tyrosine phosphorylation of the GARU E3 ubiquitin ligase promotes gibberellin signalling by preventing GID1 degradation

Gibberellin (GA) is a major hormone for plant growth and development. GA response is derived from the degradation of DELLA repressor proteins after GA-dependent complex formation of the GID1 GA receptor with DELLA. Genistein is a known tyrosine (Tyr) kinase inhibitor and inhibits DELLA degradation. However, the biological role of Tyr phosphorylation on the GA response remains unclear. Here, we demonstrate that GARU (GA receptor RING E3 ubiquitin ligase) mediates ubiquitin-dependent degradation of GID1, and that the TAGK2 plant Tyr-kinase is a target of genistein and inhibits GARU–GID1A interactions by phosphorylation of GARU at Tyr321. Genistein induces degradation of GID1 and accumulation of DELLA. Conversely, Arabidopsis garu mutant and TAGK2-overexpressing plants accelerate GID1 stabilization and DELLA degradation. Under salt stress, GARU suppresses seed germination. We propose that GA response is negatively regulated by GARU-dependent GID1 ubiquitination and positively by Tyr phosphorylation of GARU by TAGK2, and genistein inhibits GA signaling by TAGK2 inhibition.

Plants respond to gibberellins via GID1-dependent degradation of DELLA proteins. Here, Nemoto et al. show that the gibberellin response is positively regulated by tyrosine phosphorylation of GARU, an E3 ubiquitin ligase that mediates degradation of GID1.

Complex genetic architecture underlies maize tassel domestication

Maize (Zea mays) tassels underwent profound morphological changes during maize domestication and improvement. Although a number of genes affecting maize inflorescence development have been identified, the genetic basis of the morphological changes in maize tassels since domestication is not well understood. Here, using a large population of 866 maize-teosinte BC₂ S₃ recombinant inbred lines genotyped using 19 838 single nucleotide polymorphism (SNP) markers, we performed high-resolution quantitative trait locus (QTL) mapping for five tassel morphological traits. We showed that the five tassel traits were associated with different genetic architecture features. Known genes for maize inflorescence development identified by mutagenesis were significantly enriched in the tassel trait QTLs, and many of these genes, including ramosa1 (ra1), barren inflorescence2 (bif2), unbranched2 (ub2), zea floricaula leafy2 (zfl2) and barren stalk fastigiate1 (baf1), showed evidence of selection. An in-depth nucleotide diversity analysis at the bif2 locus identified strong selection signatures in the 5'-regulatory region. We also found that several known flowering time genes co-localized with tassel trait QTLs. A further association analysis indicated that the maize photoperiod gene ZmCCT was significantly associated with tassel size variation. Using near-isogenic lines, we narrowed down a major-effect QTL for tassel length, qTL9-1, to a 513-kb physical region. These results provide important insights into the genetic architecture that controls maize tassel evolution.

Identification of Key Proteins and Networks Related to Grain Development in Wheat (Triticum aestivum L.) by Comparative Transcription and Proteomic Analysis of Allelic Variants in TaGW2-6A

In wheat, coding region allelic variants of TaGW2-6A are closely associated with grain width and weight, but the genetic mechanisms involved remain unclear. Thus, to obtain insights into the key functions regulated by TaGW2-6A during wheat grain development, we performed transcriptional and proteomic analyses of TaGW2-6A allelic variants. The transcription results showed that the TaGW2-6A allelic variants differed significantly by several orders of magnitude. Each allelic variant of TaGW2-6A reached its first transcription peak at 6 days after anthesis (DAA), but the insertion type TaGW2-6A allelic variant reached its second peak earlier than the normal type, i.e., at 12 DAA rather than 20 DAA. In total, we identified 228 differentially accumulated protein spots representing 138 unique proteins by two-dimensional gel electrophoresis and tandem MALDI-TOF/TOF-MS in these three stages. Based on the results, we found some key proteins that are closely related to wheat grain development. The results of this analysis improve our understanding of the genetic mechanisms related to TaGW2-6A during wheat grain development as well as providing insights into the biological processes involved in seed formation.

Melatonin mediates the stabilization of DELLA proteins to repress the floral transition in Arabidopsis

Precise floral transition from vegetative growth phase to reproductive growth phase is very important in plant life cycle. In flowering genetic pathways, DELLA proteins are master transcriptional regulators of gibberelic acid (GA) pathway, and FLOWERING LOCUS C (FLC) is a core repressor of vernalization pathway as well as downstream of DELLAs. As a crucial messenger in plants, the possible involvement of melatonin (N-acetyl-5-methoxytryptamine) in flowering and underlying molecular mechanism are unknown in Arabidopsis. In this study, we found that exogenous melatonin treatment delayed floral transition in Arabidopsis. Exogenous melatonin treatment conferred protein stabilizations of DELLAs [REPRESSOR of ga1-3 (RGA) and RGA-LIKE3 (RGL3)], without regulating the transcripts of DELLAs and endogenous GA level. Notably, exogenous melatonin delayed plant flowering and DELLA-activated transcripts of FLC were alleviated in della mutants, and those were exacerbated in DELLA overexpressing plants. Taken together, this study provides direct link between melatonin and floral transition, and indicates the novel involvement of DELLAs-activated FLC in melatonin-mediated flowering in Arabidopsis.

TOPP4 Regulates the Stability of PHYTOCHROME INTERACTING FACTOR5 during Photomorphogenesis in Arabidopsis

In plants, photoreceptors transfer light signals to phytochrome-interacting factors (PIFs), inducing the rapid phosphorylation and degradation of PIFs to promote photomorphogenesis. However, the phosphatase responsible for PIF dephosphorylation remains unknown. In this study, we identified a type 1 protein phosphatase, TOPP4, that is essential for PIF5 protein stability in Arabidopsis (Arabidopsis thaliana). Compared with the wild type, the dominant-negative mutant, topp4-1, displayed reduced hypocotyl length and larger apical hook and cotyledon opening angle under red light. Overexpression of topp4-1 in the wild type led to defects that were similar to those in the topp4-1 mutant. Red light induced phytochrome B (phyB)-dependent TOPP4 expression in hypocotyls. The topp4-1 mutation weakened the closed cotyledon angle of phyB-9 and phyA-211 phyB-9, while overexpression of TOPP4 significantly repressed the short hypocotyls of phyB-green fluorescent protein seedlings, indicating that TOPP4 and phyB function in an antagonistic way during photomorphogenesis. Protein interaction assays and phosphorylation studies demonstrate that TOPP4 interacts directly with PIF5 and dephosphorylates it. Furthermore, TOPP4 inhibits the red light-induced ubiquitination and degradation of PIF5. These findings demonstrate that dephosphorylation of PIF5 by TOPP4 inhibits its ubiquitin-mediated degradation during photomorphogenesis. These data outline a novel phytochrome signaling mechanism by which TOPP4-mediated dephosphorylation of PIF5 attenuates phytochrome-dependent light responses.

Protein turnover in plant biology

The protein content of plant cells is constantly being updated. This process is driven by the opposing actions of protein degradation, which defines the half-life of each polypeptide, and protein synthesis. Our understanding of the processes that regulate protein synthesis and degradation in plants has advanced significantly over the past decade. Post-transcriptional modifications that influence features of the mRNA populations, such as poly(A) tail length and secondary structure, contribute to the regulation of protein synthesis. Post-translational modifications such as phosphorylation, ubiquitination and non-enzymatic processes such as nitrosylation and carbonylation, govern the rate of degradation. Regulators such as the plant TOR kinase, and effectors such as the E3 ligases, allow plants to balance protein synthesis and degradation under developmental and environmental change. Establishing an integrated understanding of the processes that underpin changes in protein abundance under various physiological and developmental scenarios will accelerate our ability to model and rationally engineer plants.

TYPE-ONE PROTEIN PHOSPHATASE4 regulates pavement cell interdigitation by modulating PIN-FORMED1 polarity and trafficking in Arabidopsis

In plants, cell morphogenesis is dependent on intercellular auxin accumulation. The polar subcellular localization of the PIN-FORMED (PIN) protein is crucial for this process. Previous studies have shown that the protein kinase PINOID (PID) and protein phosphatase6-type phosphatase holoenzyme regulate the phosphorylation status of PIN1 in root tips and shoot apices. Here, we show that a type-one protein phosphatase, TOPP4, is essential for the formation of interdigitated pavement cell (PC) pattern in Arabidopsis (Arabidopsis thaliana) leaf. The dominant-negative mutant topp4-1 showed severely inhibited interdigitated PC growth. Expression of topp4-1 gene in wild-type plants recapitulated the PC defects in the mutant. Genetic analyses suggested that TOPP4 and PIN1 likely function in the same pathway to regulate PC morphogenesis. Furthermore, colocalization, in vitro and in vivo protein interaction studies, and dephosphorylation assays revealed that TOPP4 mediated PIN1 polar localization and endocytic trafficking in PCs by acting antagonistically with PID to modulate the phosphorylation status of PIN1. In addition, TOPP4 affects the cytoskeleton pattern through the Rho of Plant GTPase-dependent auxin-signaling pathway. Therefore, we conclude that TOPP4-regulated PIN1 polar targeting through direct dephosphorylation is crucial for PC morphogenesis in the Arabidopsis leaf.

Morphological characteristics, anatomical structure, and gene expression: novel insights into gibberellin biosynthesis and perception during carrot growth and development

Gibberellins (GAs) are considered potentially important regulators of cell elongation and expansion in plants. Carrot undergoes significant alteration in organ size during its growth and development. However, the molecular mechanisms underlying gibberellin accumulation and perception during carrot growth and development remain unclear. In this study, five stages of carrot growth and development were investigated using morphological and anatomical structural techniques. Gibberellin levels in leaf, petiole, and taproot tissues were also investigated for all five stages. Gibberellin levels in the roots initially increased and then decreased, but these levels were lower than those in the petioles and leaves. Genes involved in gibberellin biosynthesis and signaling were identified from the carrotDB, and their expression was analyzed. All of the genes were evidently responsive to carrot growth and development, and some of them showed tissue-specific expression. The results suggested that gibberellin level may play a vital role in carrot elongation and expansion. The relative transcription levels of gibberellin pathway-related genes may be the main cause of the different bioactive GAs levels, thus exerting influences on gibberellin perception and signals. Carrot growth and development may be regulated by modification of the genes involved in gibberellin biosynthesis, catabolism, and perception.

Intrinsically disordered proteins and multicellular organisms

Intrinsically disordered proteins (IDPs) and IDP regions lack stable tertiary structure yet carry out numerous biological functions, especially those associated with signaling, transcription regulation, DNA condensation, cell division, and cellular differentiation. Both post-translational modifications (PTMs) and alternative splicing (AS) expand the functional repertoire of IDPs. Here we propose that an "IDP-based developmental toolkit," which is comprised of IDP regions, PTMs, especially multiple PTMs, within these IDP regions, and AS events within segments of pre-mRNA that code for these same IDP regions, allows functional diversification and environmental responsiveness for molecules that direct the development of complex metazoans.

The six conserved serine/threonine sites of REPRESSOR OF ga1-3 protein are important for its functionality and stability in gibberellin signaling in Arabidopsis

Our results provide further insight into the regulation of DELLA proteins in Arabidopsis . We clarified that phosphorylation modification of the six conserved sites is important for RGA functions and stability. The DELLA proteins, important plant growth and development repressors mediate the gibberellin (GA) signaling pathway. Although these proteins exhibit phosphorylation and de-phosphorylation states at the molecular level, little is known regarding the effects of different modifications of DELLA proteins on the regulation of their bioactivity and stability at the genetic level. In this study, six conserved serine (Ser)/threonine (Thr) sites of REPRESSOR OF ga1-3 (RGA) were substituted with alanine (RGA6A) or aspartic acid (RGA6D) to mimic the states of constitutive de-phosphorylation and phosphorylation, respectively. We found that the overexpression of de-phosphomimic RGA in Col-0 plants caused GA-overdose phenotypes, which were similar to DELLA-deficient mutant. These phenotypes were probably attributed to de-phosphomimic RGA, which retained its transcriptional activation activity that induces GA biosynthetic genes, but lost the transcription repressor function that inhibits GA-responsive genes. Further, de-phosphomimic RGA was unstable and easily degradable unlike the wild-type RGA, suggesting that the de-phosphorylated form is necessary for its degradation. In contrast, phosphomimic RGA overexpression caused GA-deficient phenotypes with non-degradable RGA. These phenotypes were probably due to phosphomimic RGA, which represses GA-responsive gene expression instead of inducing GA biosynthetic genes. In addition, phosphomimic RGA was stable and hardly degradable, which aggravated the RGA-inhibiting function in GA signaling. In conclusion, we show that the six conserved Ser/Thr sites are important for the different bioactivities of the RGA protein that regulate the GA response, and also for RGA stability via the mimicking of phosphorylation/de-phosphorylation.