Casein kinase 1 family regulates PRR5 and TOC1 in the Arabidopsis circadian clock

Abundant clock proteins point to missing molecular regulation in the plant circadian clock

Understanding the biochemistry behind whole-organism traits such as flowering time is a longstanding challenge, where mathematical models are critical. Very few models of plant gene circuits use the absolute units required for comparison to biochemical data. We refactor two detailed models of the plant circadian clock from relative to absolute units. Using absolute RNA quantification, a simple model predicted abundant clock protein levels in Arabidopsis thaliana, up to 100,000 proteins per cell. NanoLUC reporter protein fusions validated the predicted levels of clock proteins in vivo. Recalibrating the detailed models to these protein levels estimated their DNA-binding dissociation constants (Kd). We estimate the same Kd from multiple results in vitro, extending the method to any promoter sequence. The detailed models simulated the Kd range estimated from LUX DNA-binding in vitro but departed from the data for CCA1 binding, pointing to further circadian mechanisms. Our analytical and experimental methods should transfer to understand other plant gene regulatory networks, potentially including the natural sequence variation that contributes to evolutionary adaptation.

Circadian gating: concepts, processes, and opportunities

Circadian clocks provide a biological measure of time that coordinates metabolism, physiology and behaviour with 24 h cycles in the environment. Circadian systems have a variety of characteristic properties, such as entrainment to environmental cues, a self-sustaining rhythm of about 24 h and temperature compensation of the circadian rhythm. In this perspective, we discuss the process of circadian gating, which refers to the restriction of a biological event to particular times of day by the circadian clock. We introduce principles and processes associated with circadian gating in a variety of organisms, including some associated mechanisms. We highlight socioeconomic opportunities presented by the investigation of circadian gating, using selected examples from circadian medicine and agricultural crop production to illustrate its importance.This article is part of the Theo Murphy meeting issue 'Circadian rhythms in infection and immunity'.

Small molecules and heat treatments reverse vernalization via epigenetic modification in Arabidopsis

Monocarpic plants flower only once and then produce seeds. Many monocarpic plants require a cold treatment known as vernalization before they flower. This requirement delays flowering until the plant senses warm temperatures in the spring. Exposure to high temperatures following vernalization causes devernalization, which cancels the vernalized state, inhibiting flowering and promoting vegetative growth. In this study, we screened over 16,000 chemical compounds and identified five small molecules (devernalizers; DVRs) that induce devernalization in Arabidopsis thaliana at room temperature without requiring a high-temperature treatment. Treatment with DVRs reactivated the expression of FLOWERING LOCUS C (FLC), a master repressor of flowering, by reducing the deposition of repressive histone modifications, thereby delaying flowering time. Three of the DVRs identified shared two structures: a hydantoin-like region and a spiro-like carbon. Treatment with DVR06, which has a simple chemical structure containing these domains, delayed flowering time and reduced the deposition of repressive histone modifications at FLC. RNA-seq and ChIP-seq analyses revealed both shared and specific transcriptomic and epigenetic effects between DVR06- and heat-induced devernalization. Overall, our extensive chemical screening indicated that hydantoin and spiro are key chemical signatures that reduce repressive histone modifications and promote devernalization in plants.

Cold-induced degradation of core clock proteins implements temperature compensation in the Arabidopsis circadian clock

The period of circadian clocks is maintained at close to 24 hours over a broad range of physiological temperatures due to temperature compensation of period length. Here, we show that the quantitative control of the core clock proteins TIMING OF CAB EXPRESSION 1 [TOC1; also known as PSEUDO-RESPONSE REGULATOR 1 (PRR1)] and PRR5 is crucial for temperature compensation in Arabidopsis thaliana. The prr5 toc1 double mutant has a shortened period at higher temperatures, resulting in weak temperature compensation. Low ambient temperature reduces amounts of PRR5 and TOC1. In low-temperature conditions, PRR5 and TOC1 interact with LOV KELCH PROTEIN 2 (LKP2), a component of the E3 ubiquitin ligase Skp, Cullin, F-box (SCF) complex. The lkp2 mutations attenuate low temperature-induced decrease of PRR5 and TOC1, and the mutants display longer period only at lower temperatures. Our findings reveal that the circadian clock maintains its period length despite ambient temperature fluctuations through temperature- and LKP2-dependent control of PRR5 and TOC1 abundance.

Appropriate induction of TOC1 ensures optimal MYB44 expression in ABA signaling and stress response in Arabidopsis

Plants possess the remarkable ability to integrate the circadian clock with various signalling pathways, enabling them to quickly detect and react to both external and internal stress signals. However, the interplay between the circadian clock and biological processes in orchestrating responses to environmental stresses remains poorly understood. TOC1, a core component of the plant circadian clock, plays a vital role in maintaining circadian rhythmicity and participating in plant defences. Here, our study reveals a direct interaction between TOC1 and the promoter region of MYB44, a key gene involved in plant defence. TOC1 rhythmically represses MYB44 expression, thereby ensuring elevated MYB44 expression at dawn to help the plant in coping with lowest temperatures during diurnal cycles. Additionally, both TOC1 and MYB44 can be induced by cold stress in an Abscisic acid (ABA)-dependent and independent manner. TOC1 demonstrates a rapid induction in response to lower temperatures compared to ABA treatment, suggesting timely flexible regulation of TOC1-MYB44 regulatory module by the circadian clock in ensuring a proper response to diverse stresses and maintaining a balance between normal physiological processes and energy-consuming stress responses. Our study elucidates the role of TOC1 in effectively modulating expression of MYB44, providing insights into the regulatory network connecting the circadian clock, ABA signalling, and stress-responsive genes.

In vitro induction of tetraploids and their phenotypic and transcriptome analysis in Glehnia littoralis

BACKGROUND

Glehnia littoralis is a medicinal and edible plant species having commercial value and has several hundred years of cultivation history. Polyploid breeding is one of the most important and fastest ways to generate novel varieties. To obtain tetraploids of G. littoralis in vitro, colchicine treatment was given to the seeds and then were screened based on morphology, flow cytometry, and root tip pressing assays. Furthermore, transcriptome analysis was performed to identity the differentially expressed genes associated with phenotypic changes in tetraploid G. littoralis.

RESULTS

The results showed that 0.05% (w/v) colchicine treatment for 48 h was effective in inducing tetraploids in G. littoralis. The tetraploid G. littoralis (2n = 4x = 44) was superior in leaf area, leaf thickness, petiole diameter, SPAD value (Chl SPAD), stomatal size, epidermal tissues thickness, palisade tissues thickness, and spongy tissues thickness to the diploid ones, while the stomatal density of tetraploids was significantly lower. Transcriptome sequencing revealed, a total of 1336 differentially expressed genes (DEGs) between tetraploids and diploids. Chromosome doubling may lead to DNA content change and gene dosage effect, which directly affects changes in quantitative traits, with changes such as increased chlorophyll content, larger stomata and thicker tissue of leaves. Several up-regulated DEGs were found related to growth and development in tetraploid G. littoralis such as CKI, PPDK, hisD and MDP1. KEGG pathway enrichment analyses showed that most of DEGs were enriched in metabolic pathways.

CONCLUSIONS

This is the first report of the successful induction of tetraploids in G. littoralis. The information presented in this study facilitate breeding programs and molecular breeding of G. littoralis varieties.

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.

A Small-Molecule Modulator Affecting the Clock-Associated PSEUDO-RESPONSE REGULATOR 7 Amount

Circadian clocks are biological timekeeping systems that coordinate genetic, metabolic and physiological behaviors with the external day-night cycle. The clock in plants relies on the transcriptional-translational feedback loops transcription-translation feedback loop (TTFL), consisting of transcription factors including PSUEDO-RESPONSE REGULATOR (PRR) proteins, plant lineage-specific transcriptional repressors. Here, we report that a novel synthetic small-molecule modulator, 5-(3,4-dichlorophenyl)-1-phenyl-1,7-dihydro-4H-pyrazolo[3,4-d] pyrimidine-4,6(5H)-dione (TU-892), affects the PRR7 protein amount. A clock reporter line of Arabidopsis was screened against the 10,000 small molecules in the Maybridge Hitfinder 10K chemical library. This screening identified TU-892 as a period-lengthening molecule. Gene expression analyses showed that TU-892 treatment upregulates CIRCADIAN CLOCK-ASSOCIATED 1 (CCA1) mRNA expression. TU-892 treatment reduced the amount of PRR7 protein, a transcriptional repressor of CCA1. Other PRR proteins including TIMING OF CAB EXPRESSION 1 were altered less by TU-892 treatment. TU-892-dependent CCA1 upregulation was attenuated in mutants impaired in PRR7. Collectively, TU-892 is a novel type of clock modulator that reduces the levels of PRR7 protein.

Circadian clock does not play an essential role in daylength measurement for growth-phase transition in Marchantia polymorpha

Daylength is perceived as a seasonal cue to induce growth-phase transition at a proper time of a year. The core of the mechanism of daylength measurement in angiosperms lies in the circadian clock-controlled expression of regulators of growth-phase transition. However, the roles of the circadian clock in daylength measurement in basal land plants remain largely unknown. In this study, we investigated the contribution of circadian clock to daylength measurement in a basal land plant, the liverwort Marchantia polymorpha. In M. polymorpha, transition from vegetative to reproductive phase under long-day conditions results in differentiation of sexual branches called gametangiophores which harbor gametangia. First, we showed that a widely used wild-type accession Takaragaike-1 is an obligate long-day plant with a critical daylength of about 10 hours and requires multiple long days. Then, we compared the timing of gametangiophore formation between wild type and circadian clock mutants in long-day and short-day conditions. Mutations in two clock genes, MpTIMING OF CAB EXPRESSION 1 and MpPSEUDO-RESPONSE REGULATOR, had no significant effects on the timing of gametangiophore formation. In addition, when M. polymorpha plants were treated with a chemical which lengthens circadian period, there was no significant effect on the timing of gametangiophore formation, either. We next observed the timing of gametangiophore formation under various non-24-h light/dark cycles to examine the effect of phase alteration in circadian rhythms. The results suggest that daylength measurement in M. polymorpha is based on the relative amount of light and darkness within a cycle rather than the intrinsic rhythms generated by circadian clock. Our findings suggest that M. polymorpha has a daylength measurement system which is different from that of angiosperms centered on the circadian clock function.

Comparative transcriptome analysis reveals candidate genes for cold stress response and early flowering in pineapple

Pineapple originates from tropical regions in South America and is therefore significantly impacted by cold stress. Periodic cold events in the equatorial regions where pineapple is grown may induce early flowering, also known as precocious flowering, resulting in monetary losses due to small fruit size and the need to make multiple passes for harvesting a single field. Currently, pineapple is one of the most important tropical fruits in the world in terms of consumption, and production losses caused by weather can have major impacts on worldwide exportation potential and economics. To further our understanding of and identify mechanisms for low-temperature tolerance in pineapple, and to identify the relationship between low-temperature stress and flowering time, we report here a transcriptomic analysis of two pineapple genotypes in response to low-temperature stress. Using meristem tissue collected from precocious flowering-susceptible MD2 and precocious flowering-tolerant Dole-17, we performed pairwise comparisons and weighted gene co-expression network analysis (WGCNA) to identify cold stress, genotype, and floral organ development-specific modules. Dole-17 had a greater increase in expression of genes that confer cold tolerance. The results suggested that low temperature stress in Dole-17 plants induces transcriptional changes to adapt and maintain homeostasis. Comparative transcriptomic analysis revealed differences in cuticular wax biosynthesis, carbohydrate accumulation, and vernalization-related gene expression between genotypes. Cold stress induced changes in ethylene and abscisic acid-mediated pathways differentially between genotypes, suggesting that MD2 may be more susceptible to hormone-mediated early flowering. The differentially expressed genes and module hub genes identified in this study are potential candidates for engineering cold tolerance in pineapple to develop new varieties capable of maintaining normal reproduction cycles under cold stress. In addition, a total of 461 core genes involved in the development of reproductive tissues in pineapple were also identified in this study. This research provides an important genomic resource for understanding molecular networks underlying cold stress response and how cold stress affects flowering time in pineapple.

Chemical screening approach using single leaves identifies compounds that affect cold signaling in Arabidopsis

The identification of chemical compounds that affect intracellular processes has greatly contributed to our understanding of plant growth and development. In most cases, these compounds have been identified in germinated seedlings. However, chemical screening using mature plants would benefit and advance our understanding of environmental responses. In this study, we developed a high-throughput screening method using single leaves of mature plants to identify small molecules that affect cold-regulated gene expression. A single excised leaf of Arabidopsis (Arabidopsis thaliana) grown in submerged cultures responded to low temperatures in terms of COLD-REGULATED (COR) gene expression. We used transgenic Arabidopsis harboring a COLD-REGULATED 15A (COR15A) promoter::luciferase (COR15Apro::LUC) construct to screen natural compounds that affect the cold induction of COR15Apro::LUC. This approach allowed us to identify derivatives of 1,4-naphthoquinone as specific inhibitors of COR gene expression. Moreover, 1,4-naphthoquinones appeared to inhibit the rapid induction of upstream C-REPEAT BINDING FACTOR (CBF) transcription factors upon exposure to low temperature, suggesting that 1,4-naphthoquinones alter upstream signaling processes. Our study offers a chemical screening scheme for identifying compounds that affect environmental responses in mature plants. This type of analysis is likely to reveal an unprecedented link between certain compounds and plant environmental responses.

Assembly and operation of an imaging system for long-term monitoring of bioluminescent and fluorescent reporters in plants

BACKGROUND

Non-invasive reporter systems are powerful tools to query physiological and transcriptional responses in organisms. For example, fluorescent and bioluminescent reporters have revolutionized cellular and organismal assays and have been used to study plant responses to abiotic and biotic stressors. Integrated, cooled charge-coupled device (CCD) camera systems have been developed to image bioluminescent and fluorescent signals in a variety of organisms; however, these integrated long-term imaging systems are expensive.

RESULTS

We have developed self-assembled systems for both growing and monitoring plant fluorescence and bioluminescence for long-term experiments under controlled environmental conditions. This system combines environmental growth chambers with high-sensitivity CCD cameras, multi-wavelength LEDs, open-source software, and several options for coordinating lights with imaging. This easy-to-assemble system can be used for short and long-term imaging of bioluminescent reporters, acute light-response, circadian rhythms, delayed fluorescence, and fluorescent-protein-based assays in vivo.

CONCLUSIONS

We have developed two self-assembled imaging systems that will be useful to researchers interested in continuously monitoring in vivo reporter systems in various plant species.

Direct attenuation of Arabidopsis ERECTA signalling by a pair of U-box E3 ligases

Plants sense a myriad of signals through cell-surface receptors to coordinate their development and environmental response. The Arabidopsis ERECTA receptor kinase regulates diverse developmental processes via perceiving multiple EPIDERMAL PATTERNING FACTOR (EPF)/EPF-LIKE peptide ligands. How the activated ERECTA protein is turned over is unknown. Here we identify two closely related plant U-box ubiquitin E3 ligases, PUB30 and PUB31, as key attenuators of ERECTA signalling for two developmental processes: inflorescence/pedicel growth and stomatal development. Loss-of-function pub30 pub31 mutant plants exhibit extreme inflorescence/pedicel elongation and reduced stomatal numbers owing to excessive ERECTA protein accumulation. Ligand activation of ERECTA leads to phosphorylation of PUB30/31 via BRI1-ASSOCIATED KINASE1 (BAK1), which acts as a coreceptor kinase and a scaffold to promote PUB30/31 to associate with and ubiquitinate ERECTA for eventual degradation. Our work highlights PUB30 and PUB31 as integral components of the ERECTA regulatory circuit that ensure optimal signalling outputs, thereby defining the role for PUB proteins in developmental signalling.

N6-methyladenosine mRNA methylation is important for the light response in soybean

N6-methyladenosine (m⁶A) modification of messenger RNA (mRNA) is the most prevalent and abundant modification in eukaryotic mRNA and posttranscriptionally modulates the transcriptome at almost all stages of mRNA metabolism. In plants, m⁶A is crucial for embryonic-phase growth, flowering time control, microspore generation and fruit maturation. However, the role of m⁶A in plant responses to light, the most important environmental stimulus, remains unexplored. Here, we profile the m⁶A transcriptome of Williams 82, a soybean cultivar, and reveal that m⁶A is highly conserved and plays an important role in the response to light stimuli in soybean. Similar to the case in Arabidopsis, m⁶A in soybean is enriched not only around the stop codon and within the 3'UTR but also around the start codon. Moreover, genes with methylation occurring in the 3'UTR have higher expression levels and are more prone to alternative splicing. The core genes in the light signaling pathway, GmSPA1a, GmPRR5e and GmBIC2b, undergo changes in methylation modification and transcription levels in response to light. KEGG pathway analysis revealed that differentially expressed genes with differential m⁶A peaks were involved in the "photosynthesis" and "circadian rhythm" pathways. Our results highlight the important role played by epitranscriptomic mRNA methylation in the light response in soybean and provide a solid basis for determining the functional role of light on RNA m⁶A modification in this plant.

Multifunctional chemical inhibitors of the florigen activation complex discovered by structure-based high-throughput screening

Structure-based high-throughput screening of chemical compounds that target protein-protein interactions (PPIs) is a promising technology for gaining insight into how plant development is regulated, leading to many potential agricultural applications. At present, there are no examples of using high-throughput screening to identify chemicals that target plant transcriptional complexes, some of which are responsible for regulating multiple physiological functions. Florigen, a protein encoded by FLOWERING LOCUS T (FT), was initially identified as a molecule that promotes flowering and has since been shown to regulate flowering and other developmental phenomena such as tuber formation in potato (Solanum tuberosum). FT functions as a component of the florigen activation complex (FAC) with a 14-3-3 scaffold protein and FD, a bZIP transcription factor that activates downstream gene expression. Although 14-3-3 is an important component of FAC, little is known about the function of the 14-3-3 protein itself. Here, we report the results of a high-throughput in vitro fluorescence resonance energy transfer (FRET) screening of chemical libraries that enabled us to identify small molecules capable of inhibiting FAC formation. These molecules abrogate the in vitro interaction between the 14-3-3 protein and the OsFD1 peptide, a rice (Oryza sativa) FD, by directly binding to the 14-3-3 protein. Treatment with S4, a specific hit molecule, strongly inhibited FAC activity and flowering in duckweed, tuber formation in potato, and branching in rice in a dose-dependent manner. Our results demonstrate that the high-throughput screening approach based on the three-dimensional structure of PPIs is suitable in plants. In this study, we have proposed good candidate compounds for future modification to obtain inhibitors of florigen-dependent processes through inhibition of FAC formation.

Structure-Function Study of a Novel Inhibitor of Cyclin-Dependent Kinase C in Arabidopsis

The circadian clock, an internal time-keeping system with a period of about 24 h, coordinates many physiological processes with the day-night cycle. We previously demonstrated that BML-259 [N-(5-isopropyl-2-thiazolyl) phenylacetamide], a small molecule with mammal CYCLIN DEPENDENT KINASE 5 (CDK5)/CDK2 inhibition activity, lengthens Arabidopsis thaliana (Arabidopsis) circadian clock periods. BML-259 inhibits Arabidopsis CDKC kinase, which phosphorylates RNA polymerase II in the general transcriptional machinery. To accelerate our understanding of the inhibitory mechanism of BML-259 on CDKC, we performed structure-function studies of BML-259 using circadian period-lengthening activity as an estimation of CDKC inhibitor activity in vivo. The presence of a thiazole ring is essential for period-lengthening activity, whereas acetamide, isopropyl and phenyl groups can be modified without effect. BML-259 analog TT-539, a known mammal CDK5 inhibitor, did not lengthen the period nor did it inhibit Pol II phosphorylation. TT-361, an analog having a thiophenyl ring instead of a phenyl ring, possesses stronger period-lengthening activity and CDKC;2 inhibitory activity than BML-259. In silico ensemble docking calculations using Arabidopsis CDKC;2 obtained by a homology modeling indicated that the different binding conformations between these molecules and CDKC;2 explain the divergent activities of TT539 and TT361.

Identification of GOLDEN2-like transcription factor genes in soybeans and their role in regulating plant development and metal ion stresses

The Golden 2-Like (G2-like or GLK) transcription factors are essential for plant growth, development, and many stress responses as well as heavy metal stress. However, G2-like regulatory genes have not been studied in soybean. This study identified the genes for 130 G2-Like candidates' in the genome of Glycine max (soybean). These GLK genes were located on all 20 chromosomes, and several of them were segmentally duplicated. Most GLK family proteins are highly conserved in Arabidopsis and soybean and were classified into five major groups based on phylogenetic analysis. These GmGLK gene promoters share cis-acting elements involved in plant responses to abscisic acid, methyl jasmonate, auxin signaling, low temperature, and biotic and abiotic stresses. RNA-seq expression data revealed that the GLK genes were classified into 12 major groups and differentially expressed in different tissues or organs. The co-expression network complex revealed that the GmGLK genes encode proteins involved in the interaction of genes related to chlorophyll biosynthesis, circadian rhythms, and flowering regulation. Real-time quantitative PCR analysis confirmed the expression profiles of eight GLK genes in response to cadmium (Cd) and copper (Cu) stress, with some GLK genes significantly induced by both Cd and Cu stress treatments, implying a functional role in defense responsiveness. Thus, we present a comprehensive perspective of the GLK genes in soybean and emphasize their important role in crop development and metal ion stresses.

Evolution of circadian clocks along the green lineage

Circadian clocks govern temporal programs in the green lineage (Chloroplastida) as they do in other photosynthetic pro- and eukaryotes, bacteria, fungi, animals, and humans. Their physiological properties, including entrainment, phase responses, and temperature compensation, are well conserved. The involvement of transcriptional/translational feedback loops in the oscillatory machinery and reversible phosphorylation events are also maintained. Circadian clocks control a large variety of output rhythms in green algae and terrestrial plants, adjusting their metabolism and behavior to the day-night cycle. The angiosperm Arabidopsis (Arabidopsis thaliana) represents a well-studied circadian clock model. Several molecular components of its oscillatory machinery are conserved in other Chloroplastida, but their functions may differ. Conserved clock components include at least one member of the CIRCADIAN CLOCK ASSOCIATED1/REVEILLE and one of the PSEUDO RESPONSE REGULATOR family. The Arabidopsis evening complex members EARLY FLOWERING3 (ELF3), ELF4, and LUX ARRHYTHMO are found in the moss Physcomitrium patens and in the liverwort Marchantia polymorpha. In the flagellate chlorophyte alga Chlamydomonas reinhardtii, only homologs of ELF4 and LUX (named RHYTHM OF CHLOROPLAST ROC75) are present. Temporal ROC75 expression in C. reinhardtii is opposite to that of the angiosperm LUX, suggesting different clock mechanisms. In the picoalga Ostreococcus tauri, both ELF genes are missing, suggesting that it has a progenitor circadian "green" clock. Clock-relevant photoreceptors and thermosensors vary within the green lineage, except for the CRYPTOCHROMEs, whose variety and functions may differ. More genetically tractable models of Chloroplastida are needed to draw final conclusions about the gradual evolution of circadian clocks within the green lineage.

Plant clock modifications for adapting flowering time to local environments

During and after the domestication of crops from ancestral wild plants, humans selected cultivars that could change their flowering time in response to seasonal daylength. Continuous selection of this trait eventually allowed the introduction of crops into higher or lower latitudes and different climates from the original regions where domestication initiated. In the past two decades, numerous studies have found the causal genes or alleles that change flowering time and have assisted in adapting crop species such as barley (Hordeum vulgare), wheat (Triticum aestivum L.), rice (Oryza sativa L.), pea (Pisum sativum L.), maize (Zea mays spp. mays), and soybean (Glycine max (L.) Merr.) to new environments. This updated review summarizes the genes or alleles that contributed to crop adaptation in different climatic areas. Many of these genes are putative orthologs of Arabidopsis (Arabidopsis thaliana) core clock genes. We also discuss how knowledge of the clock's molecular functioning can facilitate molecular breeding in the future.

Multi-omic analysis shows REVEILLE clock genes are involved in carbohydrate metabolism and proteasome function

Plants are able to sense changes in their light environments, such as the onset of day and night, as well as anticipate these changes in order to adapt and survive. Central to this ability is the plant circadian clock, a molecular circuit that precisely orchestrates plant cell processes over the course of a day. REVEILLE (RVE) proteins are recently discovered members of the plant circadian circuitry that activate the evening complex and PSEUDO-RESPONSE REGULATOR genes to maintain regular circadian oscillation. The RVE8 protein and its two homologs, RVE 4 and 6 in Arabidopsis (Arabidopsis thaliana), have been shown to limit the length of the circadian period, with rve 4 6 8 triple-knockout plants possessing an elongated period along with increased leaf surface area, biomass, cell size, and delayed flowering relative to wild-type Col-0 plants. Here, using a multi-omics approach consisting of phenomics, transcriptomics, proteomics, and metabolomics we draw new connections between RVE8-like proteins and a number of core plant cell processes. In particular, we reveal that loss of RVE8-like proteins results in altered carbohydrate, organic acid, and lipid metabolism, including a starch excess phenotype at dawn. We further demonstrate that rve 4 6 8 plants have lower levels of 20S proteasome subunits and possess significantly reduced proteasome activity, potentially explaining the increase in cell-size observed in RVE8-like mutants. Overall, this robust, multi-omic dataset provides substantial insight into the far-reaching impact RVE8-like proteins have on the diel plant cell environment.

Chemical biology to dissect molecular mechanisms underlying plant circadian clocks

Circadian clocks regulate the diel rhythmic physiological activities of plants, enabling them to anticipate and adapt to day-night and seasonal changes. Genetic and biochemical approaches have suggested that transcription-translation feedback loops (TTFL) are crucial for Arabidopsis clock function. Recently, the study of chemical chronobiology has emerged as a discipline within the circadian clock field, with important and complementary discoveries from both plant and animal research. In this review, we introduce recent advances in chemical biology using small molecules to perturb plant circadian clock function through TTFL components. Studies using small molecule clock modulators have been instrumental for revealing the role of post-translational modification in the clock, or the metabolite-dependent clock input pathway, as well as for controlling clock-dependent flowering time.

In Vivo Bioluminescence Analyses of Circadian Rhythms in Arabidopsis thaliana Using a Microplate Luminometer

Our understanding of the circadian clock function in plants has been markedly assisted by studies with the model species Arabidopsis thaliana. Molecular and genetics approaches have delivered a comprehensive view of the transcriptional regulatory networks underlying the Arabidopsis circadian system. The use of the luciferase as a reporter allowed the precise in vivo determination of circadian periods, phases, and amplitudes of clock promoter activities with unprecedented temporal resolution. An increasing repertoire of fine-tuned luciferases together with additional applications such as translational fusions or bioluminescence molecular complementation assays have considerably expanded our view of circadian protein expression and activity, far beyond transcriptional regulation. Further applications have focused on the in vivo simultaneous examination of rhythms in different parts of the plant. The use of intact versus excised plant organs has also provided a glimpse on both the organ-specific and autonomy of the clocks and the importance of long distance communication for circadian function. This chapter provides a basic protocol for in vivo high-throughput monitoring of circadian rhythms in Arabidopsis seedlings using bioluminescent reporters and a microplate luminometer.

Phosphorylation of RNA Polymerase II by CDKC;2 Maintains the Arabidopsis Circadian Clock Period

The circadian clock is an internal timekeeping system that governs about 24 h biological rhythms of a broad range of developmental and metabolic activities. The clocks in eukaryotes are thought to rely on lineage-specific transcriptional-translational feedback loops. However, the mechanisms underlying the basic transcriptional regulation events for clock function have not yet been fully explored. Here, through a combination of chemical biology and genetic approaches, we demonstrate that phosphorylation of RNA polymerase II by CYCLIN DEPENDENT KINASE C; 2 (CDKC;2) is required for maintaining the circadian period in Arabidopsis. Chemical screening identified BML-259, the inhibitor of mammalian CDK2/CDK5, as a compound lengthening the circadian period of Arabidopsis. Short-term BML-259 treatment resulted in decreased expression of most clock-associated genes. Development of a chemical probe followed by affinity proteomics revealed that BML-259 binds to CDKC;2. Loss-of-function mutations of cdkc;2 caused a long period phenotype. In vitro experiments demonstrated that the CDKC;2 immunocomplex phosphorylates the C-terminal domain of RNA polymerase II, and BML-259 inhibits this phosphorylation. Collectively, this study suggests that transcriptional activity maintained by CDKC;2 is required for proper period length, which is an essential feature of the circadian clock in Arabidopsis.

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.

Regulatory Role of Circadian Clocks on ABA Production and Signaling, Stomatal Responses, and Water-Use Efficiency under Water-Deficit Conditions

Plants deploy molecular, physiological, and anatomical adaptations to cope with long-term water-deficit exposure, and some of these processes are controlled by circadian clocks. Circadian clocks are endogenous timekeepers that autonomously modulate biological systems over the course of the day–night cycle. Plants’ responses to water deficiency vary with the time of the day. Opening and closing of stomata, which control water loss from plants, have diurnal responses based on the humidity level in the rhizosphere and the air surrounding the leaves. Abscisic acid (ABA), the main phytohormone modulating the stomatal response to water availability, is regulated by circadian clocks. The molecular mechanism of the plant’s circadian clock for regulating stress responses is composed not only of transcriptional but also posttranscriptional regulatory networks. Despite the importance of regulatory impact of circadian clock systems on ABA production and signaling, which is reflected in stomatal responses and as a consequence influences the drought tolerance response of the plants, the interrelationship between circadian clock, ABA homeostasis, and signaling and water-deficit responses has to date not been clearly described. In this review, we hypothesized that the circadian clock through ABA directs plants to modulate their responses and feedback mechanisms to ensure survival and to enhance their fitness under drought conditions. Different regulatory pathways and challenges in circadian-based rhythms and the possible adaptive advantage through them are also discussed.

Phosphorylation of Histone H2A at Serine 95 Is Essential for Flowering Time and Development in Arabidopsis

Phosphorylation of H2A at serine 95 (H2AS95ph) mediated by MLK4 promotes flowering and H2A.Z deposition. However, little is known about MLK1, MLK2, and MLK3 during the flowering time. Here, we systemically analyze the functions of MLK family in flowering time and development. Mutation in MLK3, but not MLK1 and MLK2, displayed late-flowering phenotype. Loss of MLK3 function enhanced the late-flowering phenotype of mlk4 mutant, but not reinforced the late-flowering phenotype of mlk1 mlk2 double mutants. MLK3 displayed the kinase activity to histone H2AS95ph in vitro. The global H2AS95ph levels were reduced in mlk3 mlk4, but not in mlk3 and mlk4 single mutant and mlk1 mlk2 double mutant, and the H2AS95ph levels in mlk1 mlk3 mlk4 and mlk2 mlk3 mlk4 were similar to those in mlk3 mlk4 double mutant. MLK3 interacted with CCA1, which binds to the promoter of GI. Correspondingly, the transcription levels and H2AS95ph levels of GI were reduced in mlk3 and mlk4 single mutant, and greatly decreased in mlk3 mlk4 double mutant, but not further attenuated in mlk1 mlk3 mlk4 and mlk2 mlk3 mlk4 triple mutant. Together, our results suggested that H2AS95ph deposition mediated by MLK3 and MLK4 is essential for flowering time in Arabidopsis.

TOC1 clock protein phosphorylation controls complex formation with NF-YB/C to repress hypocotyl growth

Plant photoperiodic growth is coordinated by interactions between circadian clock and light signaling networks. How post-translational modifications of clock proteins affect these interactions to mediate rhythmic growth remains unclear. Here, we identify five phosphorylation sites in the Arabidopsis core clock protein TIMING OF CAB EXPRESSION 1 (TOC1) which when mutated to alanine eliminate detectable phosphorylation. The TOC1 phospho-mutant fails to fully rescue the clock, growth, and flowering phenotypes of the toc1 mutant. Further, the TOC1 phospho-mutant shows advanced phase, a faster degradation rate, reduced interactions with PHYTOCHROME-INTERACTING FACTOR 3 (PIF3) and HISTONE DEACETYLASE 15 (HDA15), and poor binding at pre-dawn hypocotyl growth-related genes (PHGs), leading to a net de-repression of hypocotyl growth. NUCLEAR FACTOR Y subunits B and C (NF-YB/C) stabilize TOC1 at target promoters, and this novel trimeric complex (NF-TOC1) acts as a transcriptional co-repressor with HDA15 to inhibit PIF-mediated hypocotyl elongation. Collectively, we identify a molecular mechanism suggesting how phosphorylation of TOC1 alters its phase, stability, and physical interactions with co-regulators to precisely phase PHG expression to control photoperiodic hypocotyl growth.

Plant casein kinases phosphorylate and destabilize a cyclin-dependent kinase inhibitor to promote cell division

Cell cycle is one of the most fundamentally conserved biological processes of plants and mammals. Casein kinase1s (CK1s) are critical for cell proliferation in mammalian cells; however, how CK1s coordinate cell division in plants remains unknown. Through genetic and biochemical studies, here we demonstrated that plant CK1, Arabidopsis (Arabidopsis thaliana) EL1-like (AELs), regulate cell cycle/division by modulating the stability and inhibitory effects of Kip-related protein6 (KRP6) through phosphorylation. Cytological analysis showed that AELs deficiency results in suppressed cell-cycle progression mainly due to the decreased DNA replication rate at S phase and increased period of G2 phase. AELs interact with and phosphorylate KRP6 at serines 75 and 109 to stimulate KRP6's interaction with E3 ligases, thus facilitating the KRP6 degradation through the proteasome. These results demonstrate the crucial roles of CK1s/AELs in regulating cell division through modulating cell-cycle rates and elucidate how CK1s/AELs regulate cell division by destabilizing the stability of cyclin-dependent kinase inhibitor KRP6 through phosphorylation, providing insights into the plant cell-cycle regulation through CK1s-mediated posttranslational modification.

The Arabidopsis circadian clock protein PRR5 interacts with and stimulates ABI5 to modulate abscisic acid signaling during seed germination

Seed germination and postgerminative growth require the precise coordination of multiple intrinsic and environmental signals. The phytohormone abscisic acid (ABA) suppresses these processes in Arabidopsis thaliana and the circadian clock contributes to the regulation of ABA signaling. However, the molecular mechanism underlying circadian clock-mediated ABA signaling remains largely unknown. Here, we found that the core circadian clock proteins PSEUDO-RESPONSE REGULATOR5 (PRR5) and PRR7 physically associate with ABSCISIC ACID-INSENSITIVE5 (ABI5), a crucial transcription factor of ABA signaling. PRR5 and PRR7 positively modulate ABA signaling redundantly during seed germination. Disrupting PRR5 and PRR7 simultaneously rendered germinating seeds hyposensitive to ABA, whereas the overexpression of PRR5 enhanced ABA signaling to inhibit seed germination. Consistent with this, the expression of several ABA-responsive genes is upregulated by PRR proteins. Genetic analysis demonstrated that PRR5 promotes ABA signaling mainly dependently on ABI5. Further mechanistic investigation revealed that PRR5 stimulates the transcriptional function of ABI5 without affecting its stability. Collectively, our results indicate that these PRR proteins function synergistically with ABI5 to activate ABA responses during seed germination, thus providing a mechanistic understanding of how ABA signaling and the circadian clock are directly integrated through a transcriptional complex involving ABI5 and central circadian clock components.

Unstable Phase Response Curves Shown by Spatiotemporal Patterns in the Plant Root Circadian Clock

Phase response curves (PRCs) play important roles in the entrainment of periodic environmental cycles. Measuring the PRC is necessary to elucidate the relationship between environmental cues and the circadian clock. Conversely, the PRCs of plant circadian clocks are unstable due to multiple factors such as biotic/abiotic noise, individual differences, changes in amplitude, growth stage, and organ/tissue specificity. However, evaluating the effect of each factor is important because PRCs are commonly obtained by determining the response of many individuals, which include different amplitude states and organs. The plant root circadian clock spontaneously generates a spatiotemporal pattern called a stripe pattern, whereby all phases of the circadian rhythm exist within an individual root. Therefore, stimulating a plant root expressing this pattern enables phase responses at all phases to be measured using an individual root. In this study, we measured PRCs for thermal stimuli using this spatiotemporal pattern method and found that the PRC changed asymmetrically with positive and negative temperature stimuli. Individual differences were observed for weak but not for strong temperature stimuli. The root PRC changed depending on the amplitude of the circadian rhythm. The PRC in the young root near the hypocotyl was more sensitive than those in older roots or near the tip. Simulation with a phase oscillator model revealed the effect of measurement and internal noises on the PRC. These results indicate that instability in the entrainment of the plant circadian clock involves multiple factors, each having different characteristics. These results may help us understand how plant circadian clocks adapt to unstable environments and how plant circadian clocks with different characteristics, such as organ, age, and amplitude, are integrated within individuals.

Phosphorylation-mediated signalling in flowering: prospects and retrospects of phosphoproteomics in crops

Protein phosphorylation is a major post-translational modification, regulating protein function, stability, and subcellular localization. To date, annotated phosphorylation data are available mainly for model organisms and humans, despite the economic importance of crop species and their large kinomes. Our understanding of the phospho-regulation of flowering in relation to the biology and interaction between the pollen and pistil is still significantly lagging, limiting our knowledge on kinase signalling and its potential applications to crop production. To address this gap, we bring together relevant literature that were previously disconnected to present an overview of the roles of phosphoproteomic signalling pathways in modulating molecular and cellular regulation within specific tissues at different morphological stages of flowering. This review is intended to stimulate research, with the potential to increase crop productivity by providing a platform for novel molecular tools.

Genome-wide identification, evolutionary estimation and functional characterization of two cotton CKI gene types

BACKGROUND

Casein kinase I (CKI) is a kind of serine/threonine protein kinase highly conserved in plants and animals. Although molecular function of individual member of CKI family has been investigated in Arabidopsis, little is known about their evolution and functions in Gossypium.

RESULTS

In this study, five cotton species were applied to study CKI gene family in cotton, twenty-two species were applied to trace the origin and divergence of CKI genes. Four important insights were gained: (i) the cotton CKI genes were classified into two types based on their structural characteristics; (ii) two types of CKI genes expanded with tetraploid event in cotton; (iii) two types of CKI genes likely diverged about 1.5 billion years ago when red and green algae diverged; (iv) two types of cotton CKI genes which highly expressed in leaves showed stronger response to photoperiod (circadian clock) and light signal, and most two types of CKI genes highly expressed in anther showed identical heat inducible expression during anther development in tetraploid cotton (Gossypium hirsutum).

CONCLUSION

This study provides genome-wide insights into the evolutionary history of cotton CKI genes and lays a foundation for further investigation of the functional differentiation of two types of CKI genes in specific developmental processes and environmental stress conditions.

Layers of crosstalk between circadian regulation and environmental signalling in plants

Circadian regulation has a pervasive influence upon plant development, physiology and metabolism, impacting upon components of fitness and traits of agricultural importance. Circadian regulation is inextricably connected to the responses of plants to their abiotic environments, from the cellular to whole plant scales. Here, we review the crosstalk that occurs between circadian regulation and responses to the abiotic environment from the intracellular scale through to naturally fluctuating environments. We examine the spatial crosstalk that forms part of plant circadian regulation, at the subcellular, tissue, organ and whole-plant scales. This includes a focus on chloroplast and mitochondrial signalling, alternative splicing, long-distance circadian signalling and circadian regulation within natural environments. We also consider mathematical models for plant circadian regulation, to suggest future areas for advancing understanding of roles for circadian regulation in plant responses to environmental cues.

MLK4-mediated phosphorylation of histone H3T3 promotes flowering by transcriptional silencing of FLC/MAF in Arabidopsis thaliana

Casein kinase I (CK1), a ubiquitous Ser/Thr protein kinase in eukaryotes, plays a critical role in higher plant flowering. Arabidopsis CK1 family member MUT9-LIKE KINASEs, such as MLK1 and MLK3, have been shown to phosphorylate histone H3 at threonine 3 (H3T3), an evolutionarily conserved residue, and the modification is associated with the transcriptional repression of euchromatic and heterochromatic loci. This study demonstrates that mlk4-3, a T-DNA insertion mutant of MLK4, flowered late, and that overexpression of MLK4 caused early flowering. The nuclear protein MLK4 phosphorylated histone H3T3 both in vitro and in vivo, and this catalytic activity required the conserved lysine residue K175. mutation of MLK4 at K175 failed to restore the level of phosphorylated H3T3 (H3T3ph) or to complement the phenotypic defects of mlk4-3. The FLC/MAF-clade genes, including FLC, MAF4 and MAF5, were significantly upregulated in mlk4-3. The double mutant mlk4-3 flc-3 flowered earlier than mlk4-3, suggesting that functional FLC is crucial for flowering repression in mlk4-3. Chromatin immunoprecipitation assays showed that MLK4 bound to FLC/MAF chromatin and that H3T3ph occupancy at the promoter of FLC/MAF was negatively associated with its transcriptional level. In accordance, H3T3ph accumulated at FLC/MAF in 35S::MLK4/mlk4-3 but diminished in 35S::MLK4(K175R)/mlk4-3 plants. Moreover, the amount of RNA Pol II deposited at FLC/MAF was clearly enriched in mlk4-3 relative to the wild type. Therefore, MLK4-dependent phosphorylation of H3T3 contributes to accelerating flowering by repressing the transcription of negative flowering regulator FLC/MAF. This study sheds light on the delicate control of flowering by the plant-specific CK1, MLK4, via post-translational modification of histone H3.

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.

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 singularity response reveals entrainment properties of the plant circadian clock

Circadian clocks allow organisms to synchronize their physiological processes to diurnal variations. A phase response curve allows researchers to understand clock entrainment by revealing how signals adjust clock genes differently according to the phase in which they are applied. Comprehensively investigating these curves is difficult, however, because of the cost of measuring them experimentally. Here we demonstrate that fundamental properties of the curve are recoverable from the singularity response, which is easily measured by applying a single stimulus to a cellular network in a desynchronized state (i.e. singularity). We show that the singularity response of Arabidopsis to light/dark and temperature stimuli depends on the properties of the phase response curve for these stimuli. The measured singularity responses not only allow the curves to be precisely reconstructed but also reveal organ-specific properties of the plant circadian clock. The method is not only simple and accurate, but also general and applicable to other coupled oscillator systems as long as the oscillators can be desynchronized. This simplified method may allow the entrainment properties of the circadian clock of both plants and other species in nature.

Phase response curves reveal how biological clocks respond to stimuli applied during different circadian phases but can be costly to produce. Here Masuda et al. show that phase response curves for plants can be reconstructed by monitoring how a desynchronized population responds to a single stimulus.

The phosphorylation switch that regulates ticking of the circadian clock

In our 24/7 well-lit world, it's easy to skip or delay sleep to work, study, and play. However, our circadian rhythms are not easily fooled; the consequences of jet lag and shift work are many and severe, including metabolic, mood, and malignant disorders. The internal clock that keeps track of time has at its heart the reversible phosphorylation of the PERIOD proteins, regulated by isoforms of casein kinase 1 (CK1). In-depth biochemical, genetic, and structural studies of these kinases, their mutants, and their splice variants have combined over the past several years to provide a robust understanding of how the core clock is regulated by a phosphoswitch whereby phosphorylation of a stabilizing site on PER blocks phosphorylation of a distant phosphodegron. The recent structure of a circadian mutant form of CK1 implicates an internal activation loop switch that regulates this phosphoswitch and points to new approaches to regulation of the clock.

Identification of a Devernalization Inducer by Chemical Screening Approaches in Arabidopsis thaliana

Vernalization is the promotion of flowering after prolonged exposure to cold. In Arabidopsis thaliana, vernalization induces epigenetic silencing of the floral repressor gene FLOWERING LOCUS C (FLC). The repressive epigenetic mark trimethylation of lysine 27 on histone H3 proteins (H3K27me3) is a critical contributor to the epigenetic silencing of FLC. Interestingly, the deposited H3K27me3 in the FLC locus can be erased by short-term high-temperature treatment. This is referred to as devernalization. In this study, we identified a novel chemical compound, 4-Isoxazolecarboxylic acid, 3,5-dimethyl-2-(4-fluorophenyl)-4-isoxazole carboxylic acid 1-methyl-2-oxoethyl ester named as DEVERNALIZER01 (DVR01), which induces devernalization in Arabidopsis seedlings, by an FLC-luciferase reporter-based high-throughput screening assay. DVR01 decreased the amount of H3K27me3 in the FLC locus in vernalized plants, resulting in the upregulation of FLC in the whole plant, including the vasculature and meristem, where FLC represses floral induction genes. We also showed that a 2-week treatment with DVR01 reverted plants with a vernalized status back to a fully non-vernalized status. Collectively, this study provides a novel structure of DVR01, which modulates devernalization via demethylation of H3K27me3 in the FLC locus.

Phosphorylation Site Motifs in Plant Protein Kinases and Their Substrates

Protein phosphorylation is an important cellular regulatory mechanism affecting the activity, localization, conformation, and interaction of proteins. Protein phosphorylation is catalyzed by kinases, and thus kinases are the enzymes regulating cellular signaling cascades. In the model plant Arabidopsis, 940 genes encode for kinases. The substrate proteins of kinases are phosphorylated at defined sites, which consist of common patterns around the phosphorylation site, known as phosphorylation motifs. The discovery of kinase specificity with a preference of phosphorylation of certain motifs and application of such motifs in deducing signaling cascades helped to reveal underlying regulation mechanisms, and facilitated the prediction of kinase-target pairs. In this mini-review, we took advantage of retrieved data as examples to present the functions of kinase families along with their commonly found phosphorylation motifs from their substrates.

Recent advances in modulators of circadian rhythms: an update and perspective

Circadian rhythm is a universal life phenomenon that plays an important role in maintaining the multiple physiological functions and regulating the adaptability to internal and external environments of flora and fauna. Circadian alignment in humans has the greatest effect on human health, and circadian misalignment is closely associated with increased risk for metabolic syndrome, cardiovascular diseases, neurological diseases, immune diseases, cancer, sleep disorders, and ophthalmic diseases. The recent description of clock proteins and related post-modification targets was involved in several diseases, and numerous lines of evidence are emerging that small molecule modulators of circadian rhythms can be used to rectify circadian disorder. Herein, we attempt to update the disclosures about the modulators targeting core clock proteins and related post-modification targets, as well as the relationship between circadian rhythm disorders and human health as well as the therapeutic role and prospect of these small molecule modulators in circadian rhythm related disease.

The casein kinase 2 β subunit CK2B1 is required for swollen stem formation via cell cycle control in vegetable Brassica juncea

The swollen stem is a determinant of yield for the stem-type vegetable Brassica juncea that is representative of vegetative organ formation. However, the genetic mechanism underlying swollen stem formation and its regulation remains unknown. In this study, we identified a casein kinase 2 β subunit 1 (CK2B1) and revealed its role in swollen stem formation. Genotyping analysis revealed that a homozygous variation in the CK2B1 promoter is responsible for swollen stem formation, and the promoter activity of CK2B1 was significantly associated with the variations between swollen stem and non-swollen stem types. CK2B1 was exclusively located in the nucleus and expressed in the stem nodes of the plant. Swollen stem formation was blocked when CK2B1 expression was silenced, and induced in a backcross population carrying a swollen stem genotype, which indicates that CK2B1 is required for swollen stem formation. Cell numbers were increased during swollen stem formation and decreased in CK2B1-silenced expression plant, indicating that CK2B1 regulates swollen stem formation via cell division. CK2B1 directly interacted with E2Fa, a regulator of G1/S transition in the cell cycle, in which CK2 phosphorylates E2Fa. Our results revealed that CK2B1 affects swollen stem formation via the control of the cell cycle. These findings help to elucidate the signals that control swollen stem formation and provide a promising molecular target to enhance the yield of vegetative organ formation.

Brassinosteroids Regulate Circadian Oscillation via the BES1/TPL-CCA1/LHY Module in Arabidopsisthaliana

Brassinosteroids (BRs) regulate a variety of physiological processes in plants via extensive crosstalk with diverse biological signaling networks. Although BRs are known to reciprocally regulate circadian oscillation, the molecular mechanism underlying BR-mediated regulation of circadian clock remains unknown. Here, we demonstrate that the BR-activated transcription factor bri1-EMS-SUPPRESSOR 1 (BES1) integrates BR signaling into the circadian network in Arabidopsis. BES1 repressed expression of CIRCADIAN CLOCK-ASSOCIATED 1 (CCA1) and LATE ELONGATED HYPOCOTYL (LHY) at night by binding to their promoters, together with TOPLESS (TPL). The repression of CCA1 and LHY by BR treatment, which occurred during the night, was compromised in bes1-ko and tpl-8 mutants. Consistently, long-term treatment with BR shortened the circadian period, and BR-induced rhythmic shortening was impaired in bes1-ko and tpl-8 single mutants and in the cca1-1lhy-21 double mutant. Overall, BR signaling is conveyed to the circadian oscillator via the BES1/TPL-CCA1/LHY module, contributing to gating diurnal BR responses in plants.

Genome-wide analysis of PRR gene family uncovers their roles in circadian rhythmic changes and response to drought stress in Gossypium hirsutum L

BACKGROUND

The circadian clock not only participates in regulating various stages of plant growth, development and metabolism, but confers plant environmental adaptability to stress such as drought. Pseudo-Response Regulators (PRRs) are important component of the central oscillator (the core of circadian clock) and play a significant role in plant photoperiod pathway. However, no systematical study about this gene family has been performed in cotton.

METHODS

PRR genes were identified in diploid and tetraploid cotton using bioinformatics methods to investigate their homology, duplication and evolution relationship. Differential gene expression, KEGG enrichment analysis and qRT-PCR were conducted to analyze PRR gene expression patterns under diurnal changes and their response to drought stress.

RESULTS

A total of 44 PRR family members were identified in four Gossypium species, with 16 in G. hirsutum, 10 in G. raimondii, and nine in G. barbadense as well as in G. arboreum. Phylogenetic analysis indicated that PRR proteins were divided into five subfamilies and whole genome duplication or segmental duplication contributed to the expansion of Gossypium PRR gene family. Gene structure analysis revealed that members in the same clade are similar, and multiple cis-elements related to light and drought stress response were enriched in the promoters of GhPRR genes. qRT-PCR results showed that GhPRR genes transcripts presented four expression peaks (6 h, 9 h, 12 h, 15 h) during 24 h and form obvious rhythmic expression trend. Transcriptome data with PEG treatment, along with qRT-PCR verification suggested that members of clade III (GhPRR5a, b, d) and clade V (GhPRR3a and GhPRR3c) may be involved in drought response. This study provides an insight into understanding the function of PRR genes in circadian rhythm and in response to drought stress in cotton.

Chemical Perturbation of Chloroplast-Related Processes Affects Circadian Rhythms of Gene Expression in Arabidopsis: Salicylic Acid Application Can Entrain the Clock

The plant circadian system reciprocally interacts with metabolic processes. To investigate entrainment features in metabolic–circadian interactions, we used a chemical approach to perturb metabolism and monitored the pace of nuclear-driven circadian oscillations. We found that chemicals that alter chloroplast-related functions modified the circadian rhythms. Both vitamin C and paraquat altered the circadian period in a light-quality-dependent manner, whereas rifampicin lengthened the circadian period under darkness. Salicylic acid (SA) increased oscillatory robustness and shortened the period. The latter was attenuated by sucrose addition and was also gated, taking place during the first 3 h of the subjective day. Furthermore, the effect of SA on period length was dependent on light quality and genotype. Period lengthening or shortening by these chemicals was correlated to their inferred impact on photosynthetic electron transport activity and the redox state of plastoquinone (PQ). Based on these data and on previous publications on circadian effects that alter the redox state of PQ, we propose that the photosynthetic electron transport and the redox state of PQ participate in circadian periodicity. Moreover, coupling between chloroplast-derived signals and nuclear oscillations, as observed in our chemical and genetic assays, produces traits that are predicted by previous models. SA signaling or a related process forms a rhythmic input loop to drive robust nuclear oscillations in the context predicted by the zeitnehmer model, which was previously developed for Neurospora. We further discuss the possibility that electron transport chains (ETCs) are part of this mechanism.

The brown clock: circadian rhythms in stramenopiles

Circadian clocks allow organisms to anticipate environmental changes associated with the diurnal light/dark cycle. Circadian oscillators have been described in plants and green algae, cyanobacteria, animals and fungi, however, little is known about the circadian clocks of photosynthetic eukaryotes outside the green lineage. Stramenopiles are a diverse group of secondary endosymbionts whose plastid originated from a red alga. Photosynthetic stramenopiles, which include diatoms and brown algae, play key roles in biogeochemical cycles and are important components of marine ecosystems. Genome annotation efforts indicated the presence of a novel type of oscillator in these organisms and the first circadian clock component in a stramenopile has been recently discovered. This review summarizes the phenotypic characterization of circadian rhythms in stramenopiles and current efforts to determine the mechanisms of this 'brown clock'. The elucidation of this brown clock will enable a deeper understanding of the role of self-sustained oscillations in the adaptation to life in marine environments.