GIGANTEA recruits the UBP12 and UBP13 deubiquitylases to regulate accumulation of the ZTL photoreceptor complex

GIGANTEA Is Required for Robust Circadian Rhythms in Wheat

GIGANTEA (GI) is a plant-specific protein that functions in many physiological processes and signalling networks. In Arabidopsis, GI has a central role in circadian oscillators regulating the abundance of ZEITLUPE and TIMING OF CAB EXPRESSION 1 proteins and is essential for photoperiodic regulation of flowering. We have investigated how ortholgues of this component of Arabidopsis circadian oscillators contribute to circadian rhythms and yield traits, including heading (flowering) in wheat. We find that GI is a core component of wheat circadian oscillators that is necessary to maintain robust oscillations in chlorophyll fluorescence and circadian oscillator transcript abundance. The predicted lack of functional GI results in later flowering of wheat in both long days and short days in controlled environment conditions. Our results support and extend previous work, which suggests that the pathways by which photoperiodism regulates flowering are not fully conserved between Arabidopsis and wheat. Understanding the molecular basis for photoperiodism in wheat is important for breeders looking to manipulate flowering time and develop new elite, high-yielding cultivars.

Reversible ubiquitination conferred by domain shuffling controls paired NLR immune receptor complex homeostasis in plant immunity

Plant intracellular NLR immune receptors can function individually or in pairs to detect pathogen effectors and activate immune responses. NLR homeostasis has to be tightly regulated to ensure proper defense without triggering autoimmunity. However, in contrast to singleton NLRs, the mechanisms controlling the paired NLRs complex homeostasis are less understood. The paired Arabidopsis RRS1/RPS4 immune receptor complex confers disease resistance through effector recognition mediated by the integrated WRKY domain of RRS1. Here, through proximity labeling, we reveal a ubiquitination-deubiquitination cycle that controls the homeostasis of the RRS1/RPS4 complex. E3 ligase RARE directly binds and ubiquitinates RRS1's WRKY domain to promote its proteasomal degradation, thereby destabilizing RPS4 indirectly and compromising the stability and function of the RRS1/RPS4 complex. Conversely, the deubiquitinating enzymes UBP12/UBP13 deubiquitinate RRS1's WRKY domain, counteracting RARE's effects. Interestingly, the abundance of WRKY transcription factors WRKY70 and WRKY41 is also regulated by RARE and UBP12/UBP13. Phylogenetic analysis suggests this regulation likely transferred from WRKY70/WRKY41 to RRS1 upon WRKY domain integration. Our findings improve our understanding of homeostatic regulation of paired NLR complex and uncover a paradigm whereby domain integration can co-opt preexisting post-translational modification to regulate novel protein functions.

Transcriptome and Metabolome Analyses Reveal the Regulatory Mechanism of TC1a in the Sucrose and Starch Synthesis Pathways in Arabidopsis thaliana

Tumor necrosis factor receptor-associated factor (TRAF) proteins, originally identified in mammals, have since been found in most plants. TRAF proteins in plants have been shown to be involved in cellular autophagy, immunity, drought resistance, and ABA induction. However, the role in regulating sucrose and starch metabolism has not been reported. In this study, we confirmed that TC1a can regulate sucrose and starch metabolism through gene editing, phenotypic observation, transcriptomics and metabolomics analyses. Initially, 200 and 81 TRAF proteins were identified in rapeseed (Brassica napus L.) and Arabidopsis thaliana, respectively, and divided into five classes. We found that overexpression of TC1a inhibited root length, plant height, flowering, and leaf development in A. thaliana. Additionally, 12 differentially expressed genes (DEGs) related to sucrose and starch metabolism pathways were identified in overexpressing and knockout plants, respectively. Six differentially accumulated metabolites (DAMs)-fructose, sucrose, glucose, trehalose, maltose, and 6-phosphate fructose-were identified using widely targeted metabolomics analysis. The results show that TC1a affects the growth and development of Arabidopsis, and induces the expression of sucrose and starch synthase and hydrolases, providing a foundation for further research into its molecular mechanisms.

Cycling DOF factor mediated seasonal regulation of sexual reproduction and cold response is not conserved in Physcomitrium patens

Many land plants have evolved such that the transition from vegetative to reproductive development is synchronized with environmental cues. Examples of reproduction in response to seasonal cues can be found in both vascular and nonvascular species; however, most of our understanding of the molecular events controlling this timing has been worked out in angiosperm model systems. While the organism-level mechanisms of sexual reproduction vary dramatically between vascular and nonvascular plants, phylogenetic and transcriptomic evidence suggest paralogs in nonvascular plants may have conserved function with their vascular counterparts. Given that Physcomitrium patens undergoes sexual reproductive development in response to photoperiodic and cold temperature cues, it is well-suited for studying evolutionarily conserved mechanisms of seasonal control of reproduction. Thus, we used publicly available microarray data to identify genes differentially expressed in response to temperature cues. We identified two CDF-like (CDL) genes in the P. patens genome that are the most like the angiosperm Arabidopsis thaliana CDFs based on conservation of protein motifs and diurnal expression patterns. In angiosperms, DNA-One Finger Transcription Factors (DOFs) play an important role in regulating photoperiodic flowering, regulating physiological changes in response to seasonal temperature changes, and mediating the cold stress response. We created knockout mutations and tested their impact on sexual reproduction and response to cold stress. Unexpectedly, the timing of sexual reproduction in the ppcdl-double mutants did not differ significantly from wild type, suggesting that the PpCDLs are not necessary for seasonal regulation of this developmental transition. We also found that there was no change in expression of downstream cold-regulated genes in response to cold stress and no change in freezing tolerance in the knockout mutant plants. Finally, we observed no interaction between PpCDLs and the partial homologs of FKF1, an A. thaliana repressor of CDFs. This is different from what is observed in angiosperms, which suggests that the functions of CDF proteins in angiosperms are not conserved in P. patens.

Forward genetic approach identifies a phylogenetically conserved serine residue critical for the catalytic activity of UBIQUITIN-SPECIFIC PROTEASE 12 in Arabidopsis

Circadian clocks rely on transcriptional/translational feedback loops involving clock genes and their corresponding proteins. While the primary oscillations originate from gene expression, the precise control of clock protein stability plays a pivotal role in establishing the 24-hour circadian rhythms. Most clock proteins are degraded through the ubiquitin/26S proteasome pathway, yet the enzymes responsible for ubiquitination and deubiquitination remain poorly characterised. We identified a missense allele (ubp12-3, S327F) of the UBP12 gene/protein in Arabidopsis. Despite ubp12-3 exhibited a short period phenotype similar to that of a loss-of-function allele, molecular analysis indicated elevated protease activity in ubp12-3. We demonstrated that early flowering of ubp12 mutants is a result of the shortened circadian period rather than a direct alteration of UBP12 function. Analysis of protease activity of non-phosphorylatable (S327A, S327F) and phosphomimetic (S327D) derivatives in bacteria suggested that phosphorylation of serine 327 inhibits UBP12 enzymatic activity, which could explain the over-functioning of S327F in vivo. We showed that phosphomimetic mutations of the conserved serine in the Neurospora and human orthologues reduced ubiquitin cleavage activity suggesting that not only the primary structures of UBP12-like enzymes are phylogenetically conserved across a wide range of species, but also the molecular mechanisms governing their enzymatic activity.

LIP1 Regulates the Plant Circadian Oscillator by Modulating the Function of the Clock Component GIGANTEA

Circadian clocks are biochemical timers regulating many physiological and molecular processes according to the day/night cycles. The function of the oscillator relies on negative transcriptional/translational feedback loops operated by the so-called clock genes and the encoded clock proteins. Previously, we identified the small GTPase LIGHT INSENSITIVE PERIOD 1 (LIP1) as a circadian-clock-associated protein that regulates light input to the clock in the model plant Arabidopsis thaliana. We showed that LIP1 is also required for suppressing red and blue light-mediated photomorphogenesis, pavement cell shape determination and tolerance to salt stress. Here, we demonstrate that LIP1 is present in a complex of clock proteins GIGANTEA (GI), ZEITLUPE (ZTL) and TIMING OF CAB 1 (TOC1). LIP1 participates in this complex via GUANINE EX-CHANGE FACTOR 7. Analysis of genetic interactions proved that LIP1 affects the oscillator via modulating the function of GI. We show that LIP1 and GI independently and additively regulate photomorphogenesis and salt stress responses, whereas controlling cell shape and photoperiodic flowering are not shared functions of LIP1 and GI. Collectively, our results suggest that LIP1 affects a specific function of GI, possibly by altering binding of GI to downstream signalling components.

Erasing marks: Functions of plant deubiquitylating enzymes in modulating the ubiquitin code

Plant cells need to respond to environmental stimuli and developmental signals accurately and promptly. Ubiquitylation is a reversible posttranslational modification that enables the adaptation of cellular proteostasis to internal or external factors. The different topologies of ubiquitin linkages serve as the structural basis for the ubiquitin code, which can be interpreted by ubiquitin-binding proteins or readers in specific processes. The ubiquitylation status of target proteins is regulated by ubiquitylating enzymes or writers, as well as deubiquitylating enzymes (DUBs) or erasers. DUBs can remove ubiquitin molecules from target proteins. Arabidopsis (A. thaliana) DUBs belong to 7 protein families and exhibit a wide range of functions and play an important role in regulating selective protein degradation processes, including proteasomal, endocytic, and autophagic protein degradation. DUBs also shape the epigenetic landscape and modulate DNA damage repair processes. In this review, we summarize the current knowledge on DUBs in plants, their cellular functions, and the molecular mechanisms involved in the regulation of plant DUBs.

A circadian clock output functions independently of phyB to sustain daytime PIF3 degradation

The circadian clock is an endogenous oscillator, and its importance lies in its ability to impart rhythmicity on downstream biological processes, or outputs. Our knowledge of output regulation, however, is often limited to an understanding of transcriptional connections between the clock and outputs. For instance, the clock is linked to plant growth through the gating of photoreceptors via rhythmic transcription of the nodal growth regulators, PHYTOCHROME-INTERACTING FACTORs (PIFs), but the clock's role in PIF protein stability is less clear. Here, we identified a clock-regulated, F-box type E3 ubiquitin ligase, CLOCK-REGULATED F-BOX WITH A LONG HYPOCOTYL 1 (CFH1), that specifically interacts with and degrades PIF3 during the daytime. Additionally, genetic evidence indicates that CFH1 functions primarily in monochromatic red light, yet CFH1 confers PIF3 degradation independent of the prominent red-light photoreceptor phytochrome B (phyB). This work reveals a clock-mediated growth regulation mechanism in which circadian expression of CFH1 promotes sustained, daytime PIF3 degradation in parallel with phyB signaling.

40S Ribosomal protein S6 kinase integrates daylength perception and growth regulation in Arabidopsis thaliana

Plant growth occurs via the interconnection of cell growth and proliferation in each organ following specific developmental and environmental cues. Therefore, different photoperiods result in distinct growth patterns due to the integration of light and circadian perception with specific Carbon (C) partitioning strategies. In addition, the TARGET OF RAPAMYCIN (TOR) kinase pathway is an ancestral signaling pathway that integrates nutrient information with translational control and growth regulation. Recent findings in Arabidopsis (Arabidopsis thaliana) have shown a mutual connection between the TOR pathway and the circadian clock. However, the mechanistical network underlying this interaction is mostly unknown. Here, we show that the conserved TOR target, the 40S ribosomal protein S6 kinase (S6K) is under circadian and photoperiod regulation both at the transcriptional and post-translational level. Total S6K (S6K1 and S6K2) and TOR-dependent phosphorylated-S6K protein levels were higher during the light period and decreased at dusk especially under short day conditions. Using chemical and genetic approaches, we found that the diel pattern of S6K accumulation results from 26S proteasome-dependent degradation and is altered in mutants lacking the circadian F-box protein ZEITLUPE (ZTL), further strengthening our hypothesis that S6K could incorporate metabolic signals via TOR, which are also under circadian regulation. Moreover, under short days when C/energy levels are limiting, changes in S6K1 protein levels affected starch, sucrose and glucose accumulation and consequently impacted root and rosette growth responses. In summary, we propose that S6K1 constitutes a missing molecular link where day-length perception, nutrient availability and TOR pathway activity converge to coordinate growth responses with environmental conditions.

The RING-Type E3 Ubiquitin Ligase Gene GhDIRP1 Negatively Regulates Verticillium dahliae Resistance in Cotton (Gossypium hirsutum)

Cotton is one of the world's most important economic crops. Verticillium wilt is a devastating cotton disease caused by Verticillium dahliae, significantly impacting cotton yield and quality. E3 ubiquitin ligases are essential components of the ubiquitin-mediated 26S proteasome system, responsible for recognizing ubiquitinated target proteins and promoting their degradation, which play a crucial regulatory role in plant immune responses. In this study, on the basis of the confirmation of differential expression of GhDIRP1, a RING-type E3 ubiquitin ligase encoding gene, in two cotton varieties resistant (Zhongzhimian 2) or susceptible (Jimian 11) to V. dahliae, we demonstrated that GhDIRP1 is a negative regulator of V. dahliae resistance because silencing GhDIRP1 in cotton and heterogeneously overexpressing the gene in Arabidopsis enhanced and compromised resistance to V. dahliae, respectively. The GhDIRP1-mediated immune response seemed to be realized through multiple physiological pathways, including hormone signaling, reactive oxygen species, and lignin biosynthesis. Based on the sequences of GhDIRP1 isolated from Zhongzhimian 2 and Jimian 11, we found that GhDIRP1 had identical coding but different promoter sequences in the two varieties, with the promoter of Zhongzhimian 2 being more active than that of Jimian 11 because the former drove a stronger expression of GUS and LUC reporter genes. The results link the ubiquitination pathway to multiple physiological pathways acting in the cotton immune response and provide a candidate gene for breeding cotton varieties resistant to V. dahliae.

An insight into the roles of ubiquitin-specific proteases in plants: development and growth, morphogenesis, and stress response

Ubiquitination is a highly conserved and dynamic post-translational modification in which protein substrates are modified by ubiquitin to influence their activity, localization, or stability. Deubiquitination enzymes (DUBs) counter ubiquitin signaling by removing ubiquitin from the substrates. Ubiquitin-specific proteases (UBPs), the largest subfamily of DUBs, are conserved in plants, serving diverse functions across various cellular processes, although members within the same group often exhibit functional redundancy. Here, we briefly review recent advances in understanding the biological roles of UBPs, particularly the molecular mechanism by which UBPs regulate plant development and growth, morphogenesis, and stress response, which sheds light on the mechanistic roles of deubiquitination in plants.

Insights into a functional model of key deubiquitinases UBP12/13 in plants

Understanding the complexities of protein ubiquitination is crucial, as it plays a multifaceted role in controlling protein stability, activity, subcellular localization, and interaction, which are central to diverse biological processes. Deubiquitinases (DUBs) serve to reverse ubiquitination, but research progress in plant DUBs is noticeably limited. Among existing studies, UBIQUITIN-SPECIFIC PROTEASE 12 (UBP12) and UBP13 have garnered attention for their extensive role in diverse biological processes in plants. This review systematically summarizes the recent advancements in UBP12/13 studies, emphasizing their function, and their substrate specificity, their relationship with E3 ubiquitin ligases, and the similarities and differences with their mammalian orthologue, USP7. By unraveling the molecular mechanisms of UBP12/13, this review offers in-depth insights into the ubiquitin-proteasome system (UPS) in plants and aims to catalyze further explorations and comprehensive understanding in this field.

A dynamic ubiquitination balance of cell proliferation and endoreduplication regulators determines plant organ size

Ubiquitination plays a crucial role throughout plant growth and development. The E3 ligase DA2 has been reported to activate the peptidase DA1 by ubiquitination, hereby limiting cell proliferation. However, the molecular mechanisms that regulate DA2 remain elusive. Here, we demonstrate that DA2 has a very high turnover and auto-ubiquitinates with K48-linkage polyubiquitin chains, which is counteracted by two deubiquitinating enzymes, UBIQUITIN-SPECIFIC PROTEASE 12 (UBP12) and UBP13. Unexpectedly, we found that auto-ubiquitination of DA2 does not influence its stability but determines its E3 ligase activity. We also demonstrate that impairing the protease activity of DA1 abolishes the growth-reducing effect of DA2. Last, we show that synthetic, constitutively activated DA1-ubiquitin fusion proteins overrule this complex balance of ubiquitination and deubiquitination and strongly restrict growth and promote endoreduplication. Our findings highlight a nonproteolytic function of K48-linked polyubiquitination and reveal a mechanism by which DA2 auto-ubiquitination levels, in concert with UBP12 and UBP13, precisely monitor the activity of DA1 and fine-tune plant organ size.

The Function, Regulation, and Mechanism of Protein Turnover in Circadian Systems in Neurospora and Other Species

Circadian clocks drive a large array of physiological and behavioral activities. At the molecular level, circadian clocks are composed of positive and negative elements that form core oscillators generating the basic circadian rhythms. Over the course of the circadian period, circadian negative proteins undergo progressive hyperphosphorylation and eventually degrade, and their stability is finely controlled by complex post-translational pathways, including protein modifications, genetic codon preference, protein-protein interactions, chaperon-dependent conformation maintenance, degradation, etc. The effects of phosphorylation on the stability of circadian clock proteins are crucial for precisely determining protein function and turnover, and it has been proposed that the phosphorylation of core circadian clock proteins is tightly correlated with the circadian period. Nonetheless, recent studies have challenged this view. In this review, we summarize the research progress regarding the function, regulation, and mechanism of protein stability in the circadian clock systems of multiple model organisms, with an emphasis on Neurospora crassa, in which circadian mechanisms have been extensively investigated. Elucidation of the highly complex and dynamic regulation of protein stability in circadian clock networks would greatly benefit the integrated understanding of the function, regulation, and mechanism of protein stability in a wide spectrum of other biological processes.

Decoding plant adaptation: deubiquitinating enzymes UBP12 and UBP13 in hormone signaling, light response, and developmental processes

Ubiquitination, a vital post-translational modification in plants, plays a significant role in regulating protein activity, localization, and stability. This process occurs through a complex enzyme cascade that involves E1, E2, and E3 enzymes, leading to the covalent attachment of ubiquitin molecules to substrate proteins. Conversely, deubiquitinating enzymes (DUBs) work in opposition to this process by removing ubiquitin moieties. Despite extensive research on ubiquitination in plants, our understanding of the function of DUBs is still emerging. UBP12 and UBP13, two plant DUBs, have received much attention recently and are shown to play pivotal roles in hormone signaling, light perception, photoperiod responses, leaf development, senescence, and epigenetic transcriptional regulation. This review summarizes current knowledge of these two enzymes, highlighting the central role of deubiquitination in regulating the abundance and activity of critical regulators such as receptor kinases and transcription factors during phytohormone and developmental signaling.

GIGANTEA Unveiled: Exploring Its Diverse Roles and Mechanisms

GIGANTEA (GI) is a conserved nuclear protein crucial for orchestrating the clock-associated feedback loop in the circadian system by integrating light input, modulating gating mechanisms, and regulating circadian clock resetting. It serves as a core component which transmits blue light signals for circadian rhythm resetting and overseeing floral initiation. Beyond circadian functions, GI influences various aspects of plant development (chlorophyll accumulation, hypocotyl elongation, stomatal opening, and anthocyanin metabolism). GI has also been implicated to play a pivotal role in response to stresses such as freezing, thermomorphogenic stresses, salinity, drought, and osmotic stresses. Positioned at the hub of complex genetic networks, GI interacts with hormonal signaling pathways like abscisic acid (ABA), gibberellin (GA), salicylic acid (SA), and brassinosteroids (BRs) at multiple regulatory levels. This intricate interplay enables GI to balance stress responses, promoting growth and flowering, and optimize plant productivity. This review delves into the multifaceted roles of GI, supported by genetic and molecular evidence, and recent insights into the dynamic interplay between flowering and stress responses, which enhance plants' adaptability to environmental challenges.

Dual roles of the Arabidopsis PEAT complex in histone H2A deubiquitination and H4K5 acetylation

Histone H2A monoubiquitination is associated with transcriptional repression and needs to be removed by deubiquitinases to facilitate gene transcription in eukaryotes. However, the deubiquitinase responsible for genome-wide H2A deubiquitination in plants has yet to be identified. In this study, we found that the previously identified PWWP-EPCR-ARID-TRB (PEAT) complex components interact with both the ubiquitin-specific protease UBP5 and the redundant histone acetyltransferases HAM1 and HAM2 (HAM1/2) to form a larger version of PEAT complex in Arabidopsis thaliana. UBP5 functions as an H2A deubiquitinase in a nucleosome substrate-dependent manner in vitro and mediates H2A deubiquitination at the whole-genome level in vivo. HAM1/2 are shared subunits of the PEAT complex and the conserved NuA4 histone acetyltransferase complex, and are responsible for histone H4K5 acetylation. Within the PEAT complex, the PWWP components (PWWP1, PWWP2, and PWWP3) directly interact with UBP5 and are necessary for UBP5-mediated H2A deubiquitination, while the EPCR components (EPCR1 and EPCR2) directly interact with HAM1/2 and are required for HAM1/2-mediated H4K5 acetylation. Collectively, our study not only identifies dual roles of the PEAT complex in H2A deubiquitination and H4K5 acetylation but also illustrates how these processes collaborate at the whole-genome level to regulate the transcription and development in plants.

Machine learning classification of plant genotypes grown under different light conditions through the integration of multi-scale time-series data

In order to mitigate the effects of a changing climate, agriculture requires more effective evaluation, selection, and production of crop cultivars in order to accelerate genotype-to-phenotype connections and the selection of beneficial traits. Critically, plant growth and development are highly dependent on sunlight, with light energy providing plants with the energy required to photosynthesize as well as a means to directly intersect with the environment in order to develop. In plant analyses, machine learning and deep learning techniques have a proven ability to learn plant growth patterns, including detection of disease, plant stress, and growth using a variety of image data. To date, however, studies have not assessed machine learning and deep learning algorithms for their ability to differentiate a large cohort of genotypes grown under several growth conditions using time-series data automatically acquired across multiple scales (daily and developmentally). Here, we extensively evaluate a wide range of machine learning and deep learning algorithms for their ability to differentiate 17 well-characterized photoreceptor deficient genotypes differing in their light detection capabilities grown under several different light conditions. Using algorithm performance measurements of precision, recall, F1-Score, and accuracy, we find that Suport Vector Machine (SVM) maintains the greatest classification accuracy, while a combined ConvLSTM2D deep learning model produces the best genotype classification results across the different growth conditions. Our successful integration of time-series growth data across multiple scales, genotypes and growth conditions sets a new foundational baseline from which more complex plant science traits can be assessed for genotype-to-phenotype connections.

Evolution and Expression of the Meprin and TRAF Homology Domain-Containing Gene Family in Solanaceae

Meprin and TRAF homology (MATH)-domain-containing proteins are pivotal in modulating plant development and environmental stress responses. To date, members of the MATH gene family have been identified only in a few plant species, including Arabidopsis thaliana, Brassica rapa, maize, and rice, and the functions of this gene family in other economically important crops, especially the Solanaceae family, remain unclear. The present study identified and analyzed 58 MATH genes from three Solanaceae species, including tomato (Solanum lycopersicum), potato (Solanum tuberosum), and pepper (Capsicum annuum). Phylogenetic analysis and domain organization classified these MATH genes into four groups, consistent with those based on motif organization and gene structure. Synteny analysis found that segmental and tandem duplication might have contributed to MATH gene expansion in the tomato and the potato, respectively. Collinearity analysis revealed high conservation among Solanaceae MATH genes. Further cis-regulatory element prediction and gene expression analysis showed that Solanaceae MATH genes play essential roles during development and stress response. These findings provide a theoretical basis for other functional studies on Solanaceae MATH genes.

KNO1‐mediated autophagic degradation of the Bloom syndrome complex component RMI1 promotes homologous recombination

Homologous recombination (HR) is a key DNA damage repair pathway that is tightly adjusted to the state of a cell. A central regulator of homologous recombination is the conserved helicase-containing Bloom syndrome complex, renowned for its crucial role in maintaining genome integrity. Here, we show that in Arabidopsis thaliana, Bloom complex activity is controlled by selective autophagy. We find that the recently identified DNA damage regulator KNO1 facilitates K63-linked ubiquitination of RMI1, a structural component of the complex, thereby triggering RMI1 autophagic degradation and resulting in increased homologous recombination. Conversely, reduced autophagic activity makes plants hypersensitive to DNA damage. KNO1 itself is also controlled at the level of proteolysis, in this case mediated by the ubiquitin-proteasome system, becoming stabilized upon DNA damage via two redundantly acting deubiquitinases, UBP12 and UBP13. These findings uncover a regulatory cascade of selective and interconnected protein degradation steps resulting in a fine-tuned HR response upon DNA damage.

Commentary: Deubiquitination complex platform: a plausible mechanism for regulating the substrate specificity of deubiquitinating enzymes

Deubiquitinating enzymes (DUBs) or deubiquitinases facilitate the escape of multiple proteins from ubiquitin‒proteasome degradation and are critical for regulating protein expression levels in vivo. Therefore, dissecting the underlying mechanism of DUB recognition is needed to advance the development of drugs related to DUB signaling pathways. To data, extensive studies on the ubiquitin chain specificity of DUBs have been reported, but substrate protein recognition is still not clearly understood. As a breakthrough, the scaffolding role may be significant to substrate protein selectivity. From this perspective, we systematically characterized the scaffolding proteins and complexes contributing to DUB substrate selectivity. Furthermore, we proposed a deubiquitination complex platform (DCP) as a potentially generic mechanism for DUB substrate recognition based on known examples, which might fill the gaps in the understanding of DUB substrate specificity.

UBP12/UBP13-mediated deubiquitination of salicylic acid receptor NPR3 suppresses plant immunity

Salicylic acid (SA), a defense hormone produced after pathogen challenge, is critical for plant immunity. Arabidopsis NONEXPRESSER OF PR GENES 1 (NPR1) and its paralogs NPR3 and NPR4 can bind SA and mediate SA signal transduction. NPR1 functions as a transcriptional co-activator to promote defense gene expression, whereas NPR3 and NPR4 have been shown to function as negative regulators in the SA signaling pathway. Although the mechanism about NPR1 regulation has been well studied, how NPR3/NPR4 proteins are regulated in immune responses remains largely unknown. Here, we show that the stability of NPR3/NPR4 is enhanced by SA. In the absence of pathogen challenge, NPR3/NPR4 are unstable and degraded by the 26S proteasome, whereas the increase in cellular SA levels upon pathogen infection suppresses NPR3/NPR4 degradation. We found that UBP12 and UBP13, two homologous deubiquitinases from a ubiquitin-specific protease subfamily, negatively regulate plant immunity by promoting NPR3/NPR4 stability. Our genetic results further showed that UBP12/UBP13-mediated immunity suppression is partially dependent on NPR3/NPR4 functions. By interacting with NPR3 in the nucleus in an SA-dependent manner, UBP12 and UBP13 remove ubiquitin from polyubiquitinated NPR3 to protect it from being degraded. The stabilization of NPR3/NPR4 promoted by UBP12/UBP13 is essential for negative regulation of basal and SA-induced immunity.

Circadian entrainment in Arabidopsis

Circadian clocks coordinate physiology and development as an adaption to the oscillating day/night cycle caused by the rotation of Earth on its axis and the changing length of day and night away from the equator caused by orbiting the sun. Circadian clocks confer advantages by entraining to rhythmic environmental cycles to ensure that internal events within the plant occur at the correct time with respect to the cyclic external environment. Advances in determining the structure of circadian oscillators and the pathways that allow them to respond to light, temperature, and metabolic signals have begun to provide a mechanistic insight to the process of entrainment in Arabidopsis (Arabidopsis thaliana). We describe the concepts of entrainment and how it occurs. It is likely that a thorough mechanistic understanding of the genetic and physiological basis of circadian entrainment will provide opportunities for crop improvement.

Deubiquitination of BES1 by UBP12/UBP13 promotes brassinosteroid signaling and plant growth

As a key transcription factor in the brassinosteroid (BR) signaling pathway, the activity and expression of BES1 (BRI1-EMS-SUPPRESSOR 1) are stringently regulated. BES1 degradation is mediated by ubiquitin-related 26S proteasomal and autophagy pathways, which attenuate and terminate BR signaling; however, the opposing deubiquitinases (DUBs) are still unknown. Here, we showed that the ubp12-2w/13-3 double mutant phenocopies the BR-deficient dwarf mutant, suggesting that the two DUBs UBP12/UBP13 antagonize ubiquitin-mediated degradation to stabilize BES1. These two DUBs can trim tetraubiquitin with K46 and K63 linkages in vitro. UBP12/BES1 and UBP13/BES1 complexes are localized in both cytosol and nuclei. UBP12/13 can deubiquitinate polyubiquitinated BES1 in vitro and in planta, and UBP12 interacts with and deubiquitinates both inactive, phosphorylated BES1 and active, dephosphorylated BES1 in vivo. UBP12 overexpression in BES1^OE plants significantly enhances cell elongation in hypocotyls and petioles and increases the ratio of leaf length to width compared with BES1^OE or UBP12^OE plants. Hypocotyl elongation and etiolation result from elevated BES1 levels because BES1 degradation is retarded by UBP12 in darkness or in light with BR. Protein degradation inhibitor experiments show that the majority of BES1 can be degraded by either the proteasomal or the autophagy pathway, but a minor BES1 fraction remains pathway specific. In conclusion, UBP12/UBP13 deubiquitinate BES1 to stabilize the latter as a positive regulator for BR responses.

UBP12 and UBP13 deubiquitinases destabilize the CRY2 blue light receptor to regulate Arabidopsis growth

Light is a crucial exogenous signal sensed by cryptochrome (CRY) blue light receptors to modulate growth and the circadian clock in plants and animals. However, how CRYs interpret light quantity to regulate growth in plants remains poorly understood. Furthermore, CRY2 protein levels and activity are tightly regulated in light to fine-tune hypocotyl growth; however, details of the mechanisms that explain precise control of CRY2 levels are not fully understood. We show that in Arabidopsis, UBP12 and UBP13 deubiquitinases physically interact with CRY2 in light. UBP12/13 negatively regulates CRY2 by promoting its ubiquitination and turnover to modulate hypocotyl growth. Growth and development were explicitly affected in blue light when UBP12/13 were disrupted or overexpressed, indicating their role alongside CRY2. UBP12/13 also interacted with and stabilized COP1, which is partially required for CRY2 turnover. Our combined genetic and molecular data support a mechanistic model in which UBP12/13 interact with CRY2 and COP1, leading to the stabilization of COP1. Stabilized COP1 then promotes the ubiquitination and degradation of CRY2 under blue light. Despite decades of studies on deubiquitinases, the knowledge of how their activity is regulated is limited. Our study provides insight into how exogenous signals and ligands, along with their receptors, regulate deubiquitinase activity by protein-protein interaction. Collectively, our results provide a framework of cryptochromes and deubiquitinases to detect and interpret light signals to control plant growth at the most appropriate time.

The emerging roles of deubiquitinases in plant proteostasis

Proper regulation of protein homeostasis (proteostasis) is essential for all organisms to survive. A diverse range of post-translational modifications (PTMs) allow precise control of protein abundance, function and cellular localisation. In eukaryotic cells, ubiquitination is a widespread, essential PTM that regulates most, if not all cellular processes. Ubiquitin is added to target proteins via a well-defined enzymatic cascade involving a range of conjugating enzymes and ligases, while its removal is catalysed by a class of enzymes known as deubiquitinases (DUBs). Many human diseases have now been linked to DUB dysfunction, demonstrating the importance of these enzymes in maintaining cellular function. These findings have led to a recent explosion in studying the structure, molecular mechanisms and physiology of DUBs in mammalian systems. Plant DUBs have however remained relatively understudied, with many DUBs identified but their substrates, binding partners and the cellular pathways they regulate only now beginning to emerge. This review focuses on the most recent findings in plant DUB biology, particularly on newly identified DUB substrates and how these offer clues to the wide-ranging roles that DUBs play in the cell. Furthermore, the future outlook on how new technologies in mammalian systems can accelerate the plant DUB field forward is discussed.

Ubiquitome profiling reveals a regulatory pattern of UPL3 with UBP12 on metabolic-leaf senescence

The HECT-type UPL3 ligase plays critical roles in plant development and stress protection, but understanding of its regulation remains limited. Here, the multi-omics analyses of ubiquitinated proteins in <i>upl3</i> mutants were performed. A landscape of UPL3-dependent ubiquitinated proteins is constructed: Preferential ubiquitination of proteins related to carbon fixation represented the largest set of proteins with increased ubiquitination in the <i>upl3</i> plant, including most of carbohydrate metabolic enzymes, BRM, and variant histone, whereas a small set of proteins with reduced ubiquitination caused by the <i>upl3</i> mutation were linked to cysteine/methionine synthesis, as well as hexokinase 1 (HXK1) and phosphoenolpyruvate carboxylase 2 (PPC2). Notably, ubiquitin hydrolase 12 (UBP12), BRM, HXK1, and PPC2 were identified as the UPL3-interacting partners in vivo and in vitro. Characterization of <i>brm</i>, <i>upl3</i>, <i>ppc2</i>, <i>gin2</i>, and <i>ubp12</i> mutant plants and proteomic and transcriptomic analysis suggested that UPL3 fine-tunes carbohydrate metabolism, mediating cellular senescence by interacting with UBP12, BRM, HXK1, and PPC2. Our results highlight a regulatory pattern of UPL3 with UBP12 as a hub of regulator on proteolysis-independent regulation and proteolysis-dependent degradation.

The deubiquitinases UBP12 and UBP13 integrate with the E3 ubiquitin ligase XBAT35.2 to modulate VPS23A stability in ABA signaling

Ubiquitination-mediated protein degradation in both the 26S proteasome and vacuole is an important process in abscisic acid (ABA) signaling. However, the role of deubiquitination in this process remains elusive. Here, we demonstrate that two deubiquitinating enzymes (DUBs), ubiquitin-specific protease 12 (UBP12) and UBP13, modulate ABA signaling and drought tolerance by deubiquitinating and stabilizing the endosomal sorting complex required for transport-I (ESCRT-I) component vacuolar protein sorting 23A (VPS23A) and thereby affect the stability of ABA receptors in Arabidopsis thaliana. Genetic analysis showed that VPS23A overexpression could rescue the ABA hypersensitive and drought tolerance phenotypes of ubp12-2w or ubp13-1. In addition to the direct regulation of VPS23A, we found that UBP12 and UBP13 also stabilized the E3 ligase XB3 ortholog 5 in A. thaliana (XBAT35.2) in response to ABA treatment. Hence, we demonstrated that UBP12 and UBP13 are previously unidentified rheostatic regulators of ABA signaling and revealed a mechanism by which deubiquitination precisely monitors the XBAT35/VPS23A ubiquitination module in the ABA response.

Deubiquitinating enzymes UBP12 and UBP13 stabilize the brassinosteroid receptor BRI1

Protein ubiquitination is a dynamic and reversible post-translational modification that controls diverse cellular processes in eukaryotes. Ubiquitin-dependent internalization, recycling, and degradation are important mechanisms that regulate the activity and the abundance of plasma membrane (PM)-localized proteins. In plants, although several ubiquitin ligases are implicated in these processes, no deubiquitinating enzymes (DUBs), have been identified that directly remove ubiquitin from membrane proteins and limit their vacuolar degradation. Here, we discover two DUB proteins, UBP12 and UBP13, that directly target the PM-localized brassinosteroid (BR) receptor BR INSENSITIVE1 (BRI1) in Arabidopsis. BRI1 protein abundance is decreased in the ubp12i/ubp13 double mutant that displayed severe growth defects and reduced sensitivity to BRs. UBP13 directly interacts with and effectively removes K63-linked polyubiquitin chains from BRI1, thereby negatively modulating its vacuolar targeting and degradation. Our study reveals that UBP12 and UBP13 play crucial roles in governing BRI1 abundance and BR signaling activity to regulate plant growth.

Circadian clock in plants: Linking timing to fitness

Endogenous circadian clock integrates cyclic signals of environment and daily and seasonal behaviors of organisms to achieve spatiotemporal synchronization, which greatly improves genetic diversity and fitness of species. This review addresses recent studies on the plant circadian system in the field of chronobiology, covering topics on molecular mechanisms, internal and external Zeitgebers, and hierarchical regulation of physiological outputs. The architecture of the circadian clock involves the autoregulatory transcriptional feedback loops, post-translational modifications of core oscillators, and epigenetic modifications of DNA and histones. Here, light, temperature, humidity, and internal elemental nutrients are summarized to illustrate the sensitivity of the circadian clock to timing cues. In addition, the circadian clock runs cell-autonomously, driving independent circadian rhythms in various tissues. The core oscillators responds to each other with biochemical factors including calcium ions, mineral nutrients, photosynthetic products, and hormones. We describe clock components sequentially expressed during a 24-h day that regulate rhythmic growth, aging, immune response, and resistance to biotic and abiotic stresses. Notably, more data have suggested the circadian clock links chrono-culture to key agronomic traits in crops.

The histone H3.1 variant regulates TONSOKU-mediated DNA repair during replication

The tail of replication-dependent histone H3.1 varies from that of replication-independent H3.3 at the amino acid located at position 31 in plants and animals, but no function has been assigned to this residue to demonstrate a unique and conserved role for H3.1 during replication. We found that TONSOKU (TSK/TONSL), which rescues broken replication forks, specifically interacts with H3.1 via recognition of alanine 31 by its tetratricopeptide repeat domain. Our results indicate that genomic instability in the absence of ATXR5/ATXR6-catalyzed histone H3 lysine 27 monomethylation in plants depends on H3.1, TSK, and DNA polymerase theta (Pol θ). This work reveals an H3.1-specific function during replication and a common strategy used in multicellular eukaryotes for regulating post-replicative chromatin maturation and TSK, which relies on histone monomethyltransferases and reading of the H3.1 variant.

TRAF proteins as key regulators of plant development and stress responses

Tumor necrosis factor receptor-associated factor (TRAF) proteins are conserved in higher eukaryotes and play key roles in transducing cellular signals across different organelles. They are characterized by their C-terminal region (TRAF-C domain) containing seven to eight anti-parallel β-sheets, also known as the meprin and TRAF-C homology (MATH) domain. Over the past few decades, significant progress has been made toward understanding the diverse roles of TRAF proteins in mammals and plants. Compared to other eukaryotic species, the Arabidopsis thaliana and rice (Oryza sativa) genomes encode many more TRAF/MATH domain-containing proteins; these plant proteins cluster into five classes: TRAF/MATH-only, MATH-BPM, MATH-UBP (ubiquitin protease), Seven in absentia (SINA), and MATH-Filament and MATH-PEARLI-4 proteins, suggesting parallel evolution of TRAF proteins in plants. Increasing evidence now indicates that plant TRAF proteins form central signaling networks essential for multiple biological processes, such as vegetative and reproductive development, autophagosome formation, plant immunity, symbiosis, phytohormone signaling, and abiotic stress responses. Here, we summarize recent advances and highlight future prospects for understanding on the molecular mechanisms by which TRAF proteins act in plant development and stress responses.

OsLMP1, Encoding a Deubiquitinase, Regulates the Immune Response in Rice

Lesion mimic mutants have become an effective material for understanding plant-microbe interactions and the immune mechanism in plants. Although many mechanisms responsible for the lesion mimic phenotype have been clarified in plants, the mechanism by which lesion mimic is regulated by posttranslational modification remained largely elusive, especially in rice. In this study, a mutant with the lesion mimic phenotype was obtained and named lmp1-1. Physiological measurements and quantitative real-time PCR analysis showed that the defense response was activated in the mutants. Transcriptome analysis showed that the phenylalanine ammonia lyase (PAL) pathway was activated in the mutant, causing the accumulation of salicylic acid (SA). The results of mapping based cloning showed that OsLMP1 encodes a deubiquitinase. OsLMP1 can cleave ubiquitination precursors. Furthermore, OsLMP1 epigenetically modifies SA synthetic pathway genes by deubiquitinating H₂B and regulates the immune response in rice. In summary, this study deepens our understanding of the function of OsLMP1 in the plant immune response and provides further insight into the relationship between plants and pathogenic microorganisms.

ZEITLUPE Promotes ABA-Induced Stomatal Closure in Arabidopsis and Populus

Plants balance water availability with gas exchange and photosynthesis by controlling stomatal aperture. This control is regulated in part by the circadian clock, but it remains unclear how signalling pathways of daily rhythms are integrated into stress responses. The serine/threonine protein kinase OPEN STOMATA 1 (OST1) contributes to the regulation of stomatal closure via activation of S-type anion channels. OST1 also mediates gene regulation in response to ABA/drought stress. We show that ZEITLUPE (ZTL), a blue light photoreceptor and clock component, also regulates ABA-induced stomatal closure in Arabidopsis thaliana, establishing a link between clock and ABA-signalling pathways. ZTL sustains expression of OST1 and ABA-signalling genes. Stomatal closure in response to ABA is reduced in ztl mutants, which maintain wider stomatal apertures and show higher rates of gas exchange and water loss than wild-type plants. Detached rosette leaf assays revealed a stronger water loss phenotype in ztl-3, ost1-3 double mutants, indicating that ZTL and OST1 contributed synergistically to the control of stomatal aperture. Experimental studies of Populus sp., revealed that ZTL regulated the circadian clock and stomata, indicating ZTL function was similar in these trees and Arabidopsis. PSEUDO-RESPONSE REGULATOR 5 (PRR5), a known target of ZTL, affects ABA-induced responses, including stomatal regulation. Like ZTL, PRR5 interacted physically with OST1 and contributed to the integration of ABA responses with circadian clock signalling. This suggests a novel mechanism whereby the PRR proteins-which are expressed from dawn to dusk-interact with OST1 to mediate ABA-dependent plant responses to reduce water loss in time of stress.

Tobacco ubiquitin-specific protease 12 (NbUBP12) positively modulates drought resistance

Deubiquitination, a type of post-translational modification, cleaves ubiquitin from target proteins, thereby regulating their stability or activity. Deubiquitination enzymes, ubiquitin-specific proteases (UBP/USP), have been reported to be involved in numerous cellular processes in plants, including meristem development, circadian clock regulation, and immunity. In contrast to model plants, however, the functions of UBP in other higher plants remain poorly understood. Here, we isolated a deubiquitination enzyme, ubiquitin-specific protease 12 (NbUBP12), from Nicotiana benthamiana, which shows high sequence homology with the core enzyme regions of UBP12 from other plants. Quantitative reverse-transcription PCR analysis revealed that NbUBP12 gene expression was significantly induced after drought treatment, and its level was higher in seed than in other tissues. Using a virus-induced gene silencing technique, we generated NbUBP12-silenced tobacco plants to analyze NbUBP12 gene function in response to drought stress and found that compared with control plants, NbUBP12-silenced plants exhibited a lower survival rate after exposure to drought stress. In addition, they were characterized by lower leaf surface temperatures and larger stomatal pore size following abscisic acid (ABA) treatment. On the basis of these observations, we suggest that NbUBP12 is involved in modulating drought resistance in N. benthamiana, which is associated with ABA-mediated stomatal closure.

Ubiquitin-specific proteases UBP12 and UBP13 promote shade avoidance response by enhancing PIF7 stability

For plants grown in a crowded environment, PHYTOCHROME INTERACTING FACTOR 7 (PIF7) plays a critical role by initiating a series of adaptive growth responses. Here, we demonstrate that, in addition to transcription activity and subcellular localization, the PIF7 protein level, which is stringently regulated, is also important for shade avoidance responses. We identified two ubiquitin-specific proteases, UBP12 and UBP13, which positively regulate rapid plant growth in response to shade light. These two ubiquitin proteases directly interact with PIF7 and protect the latter from destruction by 26S proteasomes. The dynamic changes of PIF7 abundance regulated by UBP12 and UBP13 provide insight into the roles of posttranslational modifications of PIF7 in integrating environmental changes with endogenous responses.

Changes in light quality caused by the presence of neighbor proximity regulate many growth and development processes of plants. PHYTOCHROME INTERACTING FACTOR 7 (PIF7), whose subcellular localization, DNA-binding properties, and protein abundance are regulated in a photoreversible manner, plays a central role in linking shade light perception and growth responses. How PIF7 activity is regulated during shade avoidance responses has been well studied, and many factors involved in this process have been identified. However, the detailed molecular mechanism by which shade light regulates the PIF7 protein level is still largely unknown. Here, we show that the PIF7 protein level regulation is important for shade-induced growth. Two ubiquitin-specific proteases, UBP12 and UBP13, were identified as positive regulators in shade avoidance responses by increasing the PIF7 protein level. The ubp12-2w/13–3 double mutant displayed significantly impaired sensitivity to shade-induced cell elongation and reproduction acceleration. Our genetic and biochemical analysis showed that UBP12 and UBP13 act downstream of phyB and directly interact with PIF7 to maintain PIF7 stability and abundance through deubiquitination.

A clock regulatory module is required for salt tolerance and control of heading date in rice

The circadian clock plays multiple roles in plant stress responses and developmental transition phases. Nevertheless, the underlying molecular mechanisms and individual clock components that coordinately regulate important agronomic traits of rice such as salt tolerance and heading date remain to be elucidated. Here, we identify a rice ternary repressive protein complex composed of OsELF4a, OsELF3-1 and OsLUX, which was designated as OsEC1 in analogy to a similar complex in Arabidopsis. OsELF4a physically interacts with OsELF3-1 and OsELF3-2 in nucleus, whilst OsELF3-1 rather than OsELF3-2 strongly interacts with OsLUX, a Myb-domain containing transcriptional factor. Phenotypic analyses show a role for this complex in heading and salt tolerance. The loss-of-function mutants of OsEC1 exhibit lower survival rate under salt stress and late heading date. Transcriptomic profiling together with biochemical assays identified the GIGANTEA homologue OsGI as a direct transcriptional target of OsEC1. Notably, the osgi-101 mutant, generated by CRISPR/Cas9, is salt tolerant and exhibits early heading date in long day conditions. Together, our findings characterized a transcriptional module in rice composed by the OsEC1 repressing OsGI, which links the circadian clock with salt tolerance and control of heading date.

A metabolic daylength measurement system mediates winter photoperiodism in plants

Plants have served as a preeminent study system for photoperiodism due to their propensity to flower in concordance with the seasons. A nearly singular focus on understanding photoperiodic flowering has prevented the discovery of other photoperiod measuring systems necessary for vegetative health. Here, we use bioinformatics to identify photoperiod-induced genes in Arabidopsis. We show that one, PP2-A13, is expressed exclusively in, and required for, plant fitness in short, winter-like photoperiods. We create a real-time photoperiod reporter, using the PP2-A13 promoter driving luciferase, and show that photoperiodic regulation is independent of the canonical CO/FT mechanism for photoperiodic flowering. We then reveal that photosynthesis combines with circadian-clock-controlled starch production to regulate cellular sucrose levels to control photoperiodic expression of PP2-A13. This work demonstrates the existence of a photoperiod measuring system housed in the metabolic network of plants that functions to control seasonal cellular health.

Closing the protein gap in plant chronobiology

Our modern understanding of diel cell regulation in plants stems from foundational work in the late 1990s that analysed the dynamics of selected genes and mutants in Arabidopsis thaliana. The subsequent rise of transcriptomics technologies such as microarrays and RNA sequencing has substantially increased our understanding of anticipatory (circadian) and reactive (light- or dark-triggered) diel events in plants. However, it is also becoming clear that gene expression data fail to capture critical events in diel regulation that can only be explained by studying protein-level dynamics. Over the past decade, mass spectrometry technologies and quantitative proteomic workflows have significantly advanced, finally allowing scientists to characterise diel protein regulation at high throughput. Initial proteomic investigations suggest that the diel transcriptome and proteome generally lack synchrony and that the timing of daily regulatory events in plants is impacted by multiple levels of protein regulation (e.g., post-translational modifications [PTMs] and protein-protein interactions [PPIs]). Here, we highlight and summarise how the use of quantitative proteomics to elucidate diel plant cell regulation has advanced our understanding of these processes. We argue that this new understanding, coupled with the extraordinary developments in mass spectrometry technologies, demands greater focus on protein-level regulation of, and by, the circadian clock. This includes hitherto unexplored diel dynamics of protein turnover, PTMs, protein subcellular localisation and PPIs that can be masked by simple transcript- and protein-level changes. Finally, we propose new directions for how the latest advancements in quantitative proteomics can be utilised to answer outstanding questions in plant chronobiology.

Coordinative regulation of plants growth and development by light and circadian clock

The circadian clock, known as an endogenous timekeeping system, can integrate various cues to regulate plant physiological functions for adapting to the changing environment and thus ensure optimal plant growth. The synchronization of internal clock with external environmental information needs a process termed entrainment, and light is one of the predominant entraining signals for the plant circadian clock. Photoreceptors can detect and transmit light information to the clock core oscillator through transcriptional or post-transcriptional interactions with core-clock components to sustain circadian rhythms and regulate a myriad of downstream responses, including photomorphogenesis and photoperiodic flowering which are key links in the process of growth and development. Here we summarize the current understanding of the molecular network of the circadian clock and how light information is integrated into the circadian system, especially focus on how the circadian clock and light signals coordinately regulate the common downstream outputs. We discuss the functions of the clock and light signals in regulating photoperiodic flowering among various crop species.

Functional domain studies uncover novel roles for the ZTL Kelch repeat domain in clock function

The small LOV/F-box/Kelch family of E3 ubiquitin ligases plays an essential role in the regulation of plant circadian clocks and flowering time by sensing dusk. The family consists of three members, ZEITLUPE (ZTL), LOV KELCH PROTEIN 2 (LKP2), and FLAVIN-BINDING KELCH REPEAT F-BOX PROTEIN 1 (FKF1), which share a unique protein domain architecture allowing them to act as photoreceptors that transduce light signals via altering stability of target proteins. Despite intensive study of this protein family we still lack important knowledge about the biochemical and functional roles of the protein domains that comprise these unique photoreceptors. Here, we perform comparative analyses of transgenic lines constitutively expressing the photoreceptor LOV domain or the Kelch repeat protein-protein interaction domains of ZTL, FKF1, and LKP2. Expression of each domain alone is sufficient to disrupt circadian rhythms and flowering time, but each domain differs in the magnitude of effect. Immunoprecipitation followed by mass spectrometry with the ZTL Kelch repeat domain identified a suite of potential interacting partners. Furthermore, the ZTL Kelch repeat domain can interact with the ZTL homologs, LKP2 and FKF1, and the LOV domain of ZTL itself. This suggests a hypothesis that the Kelch repeat domain of ZTL may mediate inter- and intra-molecular interactions of the three LOV/F-box/Kelch proteins and provides added insight into the composition of the protein complexes and an additional role for the Kelch repeat domain.

Post-Translational Mechanisms of Plant Circadian Regulation

The molecular components of the circadian system possess the interesting feature of acting together to create a self-sustaining oscillator, while at the same time acting individually, and in complexes, to confer phase-specific circadian control over a wide range of physiological and developmental outputs. This means that many circadian oscillator proteins are simultaneously also part of the circadian output pathway. Most studies have focused on transcriptional control of circadian rhythms, but work in plants and metazoans has shown the importance of post-transcriptional and post-translational processes within the circadian system. Here we highlight recent work describing post-translational mechanisms that impact both the function of the oscillator and the clock-controlled outputs.

The Modification of Circadian Clock Components in Soybean During Domestication and Improvement

Agricultural production is greatly dependent on daylength, which is determined by latitude. Living organisms align their physiology to daylength through the circadian clock, which is made up of input sensors, core and peripheral clock components, and output. The light/dark cycle is the major input signal, moderated by temperature fluctuations and metabolic changes. The core clock in plants functions mainly through a number of transcription feedback loops. It is known that the circadian clock is not essential for survival. However, alterations in the clock components can lead to substantial changes in physiology. Thus, these clock components have become the de facto targets of artificial selection for crop improvement during domestication. Soybean was domesticated around 5,000 years ago. Although the circadian clock itself is not of particular interest to soybean breeders, specific alleles of the circadian clock components that affect agronomic traits, such as plant architecture, sensitivity to light/dark cycle, flowering time, maturation time, and yield, are. Consequently, compared to their wild relatives, cultivated soybeans have been bred to be more adaptive and productive at different latitudes and habitats for acreage expansion, even though the selection processes were made without any prior knowledge of the circadian clock. Now with the advances in comparative genomics, known modifications in the circadian clock component genes in cultivated soybean have been found, supporting the hypothesis that modifications of the clock are important for crop improvement. In this review, we will summarize the known modifications in soybean circadian clock components as a result of domestication and improvement. In addition to the well-studied effects on developmental timing, we will also discuss the potential of circadian clock modifications for improving other aspects of soybean productivity.

A Decoy Library Uncovers U-Box E3 Ubiquitin Ligases That Regulate Flowering Time in Arabidopsis

Targeted degradation of proteins is mediated by E3 ubiquitin ligases and is important for the execution of many biological processes. Redundancy has prevented the genetic characterization of many E3 ubiquitin ligases in plants. Here, we performed a reverse genetic screen in Arabidopsis using a library of dominant-negative U-box-type E3 ubiquitin ligases to identify their roles in flowering time and reproductive development. We identified five U-box decoy transgenic populations that have defects in flowering time or the floral development program. We used additional genetic and biochemical studies to validate PLANT U-BOX 14 (PUB14), MOS4-ASSOCIATED COMPLEX 3A (MAC3A), and MAC3B as bona fide regulators of flowering time. This work demonstrates the widespread importance of E3 ubiquitin ligases in floral reproductive development. Furthermore, it reinforces the necessity of dominant-negative strategies for uncovering previously unidentified regulators of developmental transitions in an organism with widespread genetic redundancy, and provides a basis on which to model other similar studies.

UBP12 and UBP13 negatively regulate the activity of the ubiquitin-dependent peptidases DA1, DAR1 and DAR2

Protein ubiquitination is a very diverse post-translational modification leading to protein degradation or delocalization, or altering protein activity. In Arabidopsis thaliana, two E3 ligases, BIG BROTHER (BB) and DA2, activate the latent peptidases DA1, DAR1 and DAR2 by mono-ubiquitination at multiple sites. Subsequently, these activated peptidases destabilize various positive growth regulators. Here, we show that two ubiquitin-specific proteases, UBP12 and UBP13, deubiquitinate DA1, DAR1 and DAR2, hence reducing their peptidase activity. Overexpression of UBP12 or UBP13 strongly decreased leaf size and cell area, and resulted in lower ploidy levels. Mutants in which UBP12 and UBP13 were downregulated produced smaller leaves that contained fewer and smaller cells. Remarkably, neither UBP12 nor UBP13 were found to be cleavage substrates of the activated DA1. Our results therefore suggest that UBP12 and UBP13 work upstream of DA1, DAR1 and DAR2 to restrict their protease activity and hence fine-tune plant growth and development.

Light Perception: A Matter of Time

Optimizing the perception of external cues and regulating physiology accordingly help plants to cope with the constantly changing environmental conditions to which they are exposed. An array of photoreceptors and intricate signaling pathways allow plants to convey the surrounding light information and synchronize an endogenous timekeeping system known as the circadian clock. This biological clock integrates multiple cues to modulate a myriad of downstream responses, timing them to occur at the best moment of the day and the year. Notably, the mechanism underlying entrainment of the light-mediated clock is not clear. This review addresses known interactions between the light-signaling and circadian-clock networks, focusing on the role of light in clock entrainment and known molecular players in this process.

GIGANTEA Shapes the Photoperiodic Rhythms of Thermomorphogenic Growth in Arabidopsis

Plants maintain their internal temperature under environments with fluctuating temperatures by adjusting their morphology and architecture, an adaptive process termed thermomorphogenesis. Notably, the rhythmic patterns of plant thermomorphogenesis are governed by day-length information. However, it remains elusive how thermomorphogenic rhythms are regulated by photoperiod. Here, we show that warm temperatures enhance the accumulation of the chaperone GIGANTEA (GI), which thermostabilizes the DELLA protein, REPRESSOR OF ga1-3 (RGA), under long days, thereby attenuating PHYTOCHROME INTERACTING FACTOR 4 (PIF4)-mediated thermomorphogenesis. In contrast, under short days, when GI accumulation is reduced, RGA is readily degraded through the gibberellic acid-mediated ubiquitination-proteasome pathway, promoting thermomorphogenic growth. These data indicate that the GI-RGA-PIF4 signaling module enables plant thermomorphogenic responses to occur in a day-length-dependent manner. We propose that the GI-mediated integration of photoperiodic and temperature information shapes thermomorphogenic rhythms, which enable plants to adapt to diel fluctuations in day length and temperature during seasonal transitions.

Recent advances in understanding regulation of the Arabidopsis circadian clock by local cellular environment

Circadian clocks have evolved to synchronise an organism’s physiology with the environmental rhythms driven by the Earth’s rotation on its axis. Over the past two decades, many of the genetic components of the Arabidopsis thaliana circadian oscillator have been identified. The interactions between these components have been formulized into mathematical models that describe the transcriptional translational feedback loops of the oscillator. More recently, focus has turned to the regulation and functions of the circadian clock. These studies have shown that the system dynamically responds to environmental signals and small molecules. We describe advances that have been made in discovering the cellular mechanisms by which signals regulate the circadian oscillator of Arabidopsis in the context of tissue-specific regulation.

Novel Crosstalks between Circadian Clock and Jasmonic Acid Pathway Finely Coordinate the Tradeoff among Plant Growth, Senescence and Defense

Circadian clock not only functions as a cellular time-keeping mechanism, but also acts as a master regulator to coordinate the tradeoff between plant growth and defense in higher plants by timing a few kinds of phytohormone biosynthesis and signaling, including jasmonic acid (JA). Notably, circadian clock and JA pathway have recently been shown to intertwine with each other to ensure and optimize the plant fitness in an ever-changing environment. It has clearly demonstrated that there are multiple crosstalk pathways between circadian clock and JA at both transcriptional and post-transcriptional levels. In this scenario, circadian clock temporally modulates JA-mediated plant development events, herbivory resistance and susceptibility to pathogen. By contrast, the JA signaling regulates clock activity in a feedback manner. In this review, we summarized the cross networks between circadian clock and JA pathway at both transcriptional and post-transcriptional levels. We proposed that the novel crosstalks between circadian clock and JA pathway not only benefit for the understanding the JA-associated circadian outputs including leaf senescence, biotic, and abiotic defenses, but also put timing as a new key factor to investigate JA pathway in the future.